diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/abundancebin.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/abundancebin.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6f7f518923af8602acf45024039ec2655bda3d5c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/abundancebin.manual_bundle.txt @@ -0,0 +1,236 @@ +# Tool: abundancebin +software_name: abundancebin +tier: T1 +domain: t1_backfill_overall +downloads: 200518 +summary: +description: +dependencies: libgcc >=13, libstdcxx >=13 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +cli:abundancebin +## CLI Help Content +$ conda run -n bioenv_cli abundancebin --help +[rc=255] +Usage: ./abundancebin -input (input filename) + [-kmer_len (composition len, default 20)] + [-output (output file, default inputfile.log)] + [-exclude (count)] + [-exclude_max (count)] + [-OUTPUT_FASTA] + + (if the bin number is known) + -bin_num (bin number) + + (or undergo recursive classification) + -RECURSIVE_CLASSIFICATION] + + +ERROR conda.cli.main_run:execute(127): `conda run abundancebin --help` failed. (See above for error) + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge abundancebin --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +abundancebin 1.0.1 0 +-------------------- +file name : abundancebin-1.0.1-0.tar.bz2 +name : abundancebin +version : 1.0.1 +build : 0 +build number: 0 +size : 20 KB +license : copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-0.tar.bz2 +md5 : e4bae8bd9b44871a240d9d1b27349aef +dependencies: + - libgcc + + +abundancebin 1.0.1 h2d50403_1 +----------------------------- +file name : abundancebin-1.0.1-h2d50403_1.tar.bz2 +name : abundancebin +version : 1.0.1 +build : h2d50403_1 +build number: 1 +size : 21 KB +license : copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h2d50403_1.tar.bz2 +md5 : 9e79208ca6534e51a3c516c1b8c950e1 +timestamp : 2018-06-26 05:57:24 UTC +dependencies: + - libstdcxx-ng >=4.9 + + +abundancebin 1.0.1 h4ac6f70_5 +----------------------------- +file name : abundancebin-1.0.1-h4ac6f70_5.tar.bz2 +name : abundancebin +version : 1.0.1 +build : h4ac6f70_5 +build number: 5 +size : 30 KB +license : copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h4ac6f70_5.tar.bz2 +md5 : 0aebd6ee78897c669b07a3f13911dfba +timestamp : 2023-05-15 01:16:00 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +abundancebin 1.0.1 h4ac6f70_6 +----------------------------- +file name : abundancebin-1.0.1-h4ac6f70_6.tar.bz2 +name : abundancebin +version : 1.0.1 +build : h4ac6f70_6 +build number: 6 +size : 30 KB +license : copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h4ac6f70_6.tar.bz2 +md5 : f174bff04554a6052dad82672eff9ddd +timestamp : 2023-05-16 07:10:05 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +abundancebin 1.0.1 h4ac6f70_7 +----------------------------- +file name : abundancebin-1.0.1-h4ac6f70_7.tar.bz2 +name : abundancebin +version : 1.0.1 +build : h4ac6f70_7 +build number: 7 +size : 30 KB +license : copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h4ac6f70_7.tar.bz2 +md5 : 011e6c8444a5761ab774943fdae04202 +timestamp : 2024-03-23 01:17:02 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +abundancebin 1.0.1 h7d875b9_3 +----------------------------- +file name : abundancebin-1.0.1-h7d875b9_3.tar.bz2 +name : abundancebin +version : 1.0.1 +build : h7d875b9_3 +build number: 3 +size : 28 KB +license : copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h7d875b9_3.tar.bz2 +md5 : 905dceb79cd1f982c1e021d33913e004 +timestamp : 2021-03-27 22:57:26 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + + +abundancebin 1.0.1 h9948957_8 +----------------------------- +file name : abundancebin-1.0.1-h9948957_8.tar.bz2 +name : abundancebin +version : 1.0.1 +build : h9948957_8 +build number: 8 +size : 29 KB +license : copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h9948957_8.tar.bz2 +md5 : ed2559099accd2ec3c048889604ddc33 +timestamp : 2024-12-13 11:23:54 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + + +abundancebin 1.0.1 h9948957_9 +----------------------------- +file name : abundancebin-1.0.1-h9948957_9.conda +name : abundancebin +version : 1.0.1 +build : h9948957_9 +build number: 9 +size : 29 KB +license : Copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h9948957_9.conda +md5 : 541d0c0e76c58503e29a685f5e2a5f11 +timestamp : 2025-08-28 10:03:22 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + + +abundancebin 1.0.1 h9f5acd7_4 +----------------------------- +file name : abundancebin-1.0.1-h9f5acd7_4.tar.bz2 +name : abundancebin +version : 1.0.1 +build : h9f5acd7_4 +build number: 4 +size : 28 KB +license : copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h9f5acd7_4.tar.bz2 +md5 : a414a2ad8c5413bab64496b2a103f8b1 +timestamp : 2022-02-23 12:49:50 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + + +abundancebin 1.0.1 h9f5acd7_5 +----------------------------- +file name : abundancebin-1.0.1-h9f5acd7_5.tar.bz2 +name : abundancebin +version : 1.0.1 +build : h9f5acd7_5 +build number: 5 +size : 30 KB +license : copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h9f5acd7_5.tar.bz2 +md5 : 4068d59b0b4f535ec49010c9c1320b7a +timestamp : 2023-05-13 16:22:04 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +abundancebin 1.0.1 hc9558a2_2 +----------------------------- +file name : abundancebin-1.0.1-hc9558a2_2.tar.bz2 +name : abundancebin +version : 1.0.1 +build : hc9558a2_2 +build number: 2 +size : 28 KB +license : copyright +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-hc9558a2_2.tar.bz2 +md5 : 94a1221c53426a7dc451b4ae18376686 +timestamp : 2020-08-23 23:13:44 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/anansescanpy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/anansescanpy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..61b62ab4b459ad0ce5814382104e35b77a429996 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/anansescanpy.manual_bundle.txt @@ -0,0 +1,302 @@ +# Tool: anansescanpy +software_name: anansescanpy +tier: T1 +domain: single_cell +downloads: 19494 +summary: implementation of scANANSE for scanpy objects in Python +description: implementation of scANANSE for scanpy objects in Python +dependencies: anndata >=0.8.0, numba >=0.56.3, numpy >=1.23.3,<1.24, packaging >=21.3, pandas >=1.4.4, python >=3.8, scanpy >=1.9.1, scipy >=1.9.1 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/Arts-of-coding/AnanseScanpy +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/Arts-of-coding/AnanseScanpy +GitHub - Arts-of-coding/AnanseScanpy: Implementation of scANANSE for Scanpy objects in Python · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Arts-of-coding / AnanseScanpy Public Notifications You must be signed in to change notification settings Fork 1 Star 7 Code Issues 1 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Arts-of-coding/AnanseScanpy main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 103 Commits 103 Commits anansescanpy anansescanpy tests tests vignettes vignettes .codeclimate.yml .codeclimate.yml .gitignore .gitignore LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml requirements.yaml requirements.yaml View all files Repository files navigation README Apache-2.0 license AnanseScanpy package: implementation of scANANSE for Scanpy objects in Python Installation The most straightforward way to install the most recent version of AnanseScanpy is via conda using PyPI. Install package through Conda If you have not used Bioconda before, first set up the necessary channels (in this order!). You only have to do this once. $ conda config --add channels defaults $ conda config --add channels bioconda $ conda config --add channels conda-forge Then install AnanseScanpy with: $ conda install anansescanpy Install package through PyPI $ pip install anansescanpy Install package through GitHub $ git clone https://github.com/Arts-of-coding/AnanseScanpy.git $ cd AnanseScanpy $ conda env create -f requirements.yaml $ conda activate AnanseScanpy $ pip install -e . Install Jupyter Notebook $ pip install jupyter Start using the package Run the package either in the console $ python3 Or run the package in jupyter notebook $ jupyter notebook For extended documentation see our ipynb vignette with PBMC sample data Of which the sample data can be downloaded $ wget https://zenodo.org/records/7575107/files/rna_PBMC.h5ad?download=1 -O scANANSE/rna_PBMC.h5ad $ wget https://zenodo.org/records/7575107/files/atac_PBMC.h5ad?download=1 -O scANANSE/atac_PBMC.h5ad installing and running anansnake Follow the instructions its respective github page, https://github.com/vanheeringen-lab/anansnake Next automatically use the generated files to run GRN analysis using your single cell cluster data: snakemake --use-conda --conda-frontend mamba \ --configfile scANANSE/analysis/config.yaml \ --snakefile scANANSE/anansnake/Snakefile \ --resources mem_mb=48_000 --cores 12 Thanks to: Jos Smits and his Seurat equivalent of this package https://github.com/JGASmits/AnanseSeurat Siebren Frohlich and his anansnake implementation https://github.com/vanheeringen-lab/anansnake How to cite this software: Smits JGA, Arts JA, Frölich S et al. scANANSE gene regulatory network and motif analysis of single-cell clusters [version 1; peer review: awaiting peer review]. F1000Research 2023, 12:243 ( https://doi.org/10.12688/f1000research.130530.1 ) About Implementation of scANANSE for Scanpy objects in Python Resources Readme License Apache-2.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 7 stars Watchers 1 watching Forks 1 fork Report repository Releases 1 Release v1.0.0 Latest Jan 12, 2023 Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 98.6% Python 1.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge anansescanpy --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +anansescanpy 0.1.2 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-0.1.2-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 0.1.2 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.1.2-pyhdfd78af_0.tar.bz2 +md5 : 94e544c469ed8e38d93af86e39142640 +timestamp : 2022-11-02 13:31:51 UTC +dependencies: + - anndata >=0.8.0 + - jupyterlab >=3.3.4 + - numpy >=1.23.3 + - pandas >=1.4.4 + - python >=3.6 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 0.1.4 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-0.1.4-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 0.1.4 +build : pyhdfd78af_0 +build number: 0 +size : 18 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.1.4-pyhdfd78af_0.tar.bz2 +md5 : dabf998a4b44aaf574bf27f6b4dac898 +timestamp : 2022-11-08 16:28:41 UTC +dependencies: + - anndata >=0.8.0 + - jupyterlab >=3.3.4 + - numpy >=1.23.3 + - pandas >=1.4.4 + - python >=3.6 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 0.1.5 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-0.1.5-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 0.1.5 +build : pyhdfd78af_0 +build number: 0 +size : 18 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.1.5-pyhdfd78af_0.tar.bz2 +md5 : 9ca60664683afd691fa37b8446442d8d +timestamp : 2022-11-10 18:24:24 UTC +dependencies: + - anndata >=0.8.0 + - jupyterlab >=3.3.4 + - numpy >=1.23.3 + - pandas >=1.4.4 + - python >=3.6 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 0.1.8 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-0.1.8-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 0.1.8 +build : pyhdfd78af_0 +build number: 0 +size : 18 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.1.8-pyhdfd78af_0.tar.bz2 +md5 : c67bedc2a1ae2b67780417fb991dc16f +timestamp : 2022-11-17 10:20:45 UTC +dependencies: + - anndata >=0.8.0 + - jupyterlab >=3.3.4 + - numpy >=1.23.3 + - pandas >=1.4.4 + - python >=3.6 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 0.1.9 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-0.1.9-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 0.1.9 +build : pyhdfd78af_0 +build number: 0 +size : 22 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.1.9-pyhdfd78af_0.tar.bz2 +md5 : d0230b9e959ad14d5d8bed38707477af +timestamp : 2022-11-30 11:35:23 UTC +dependencies: + - anndata >=0.8.0 + - jupyterlab >=3.3.4 + - numpy >=1.23.3 + - pandas >=1.4.4 + - python >=3.6 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 0.2.0 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-0.2.0-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 0.2.0 +build : pyhdfd78af_0 +build number: 0 +size : 22 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.2.0-pyhdfd78af_0.tar.bz2 +md5 : 6b0b8c429beefcb68c41ff4eb6fecd49 +timestamp : 2022-11-30 16:29:05 UTC +dependencies: + - anndata >=0.8.0 + - jupyterlab >=3.3.4 + - numpy >=1.23.3 + - pandas >=1.4.4 + - python >=3.6 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 0.2.1 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-0.2.1-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 0.2.1 +build : pyhdfd78af_0 +build number: 0 +size : 22 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.2.1-pyhdfd78af_0.tar.bz2 +md5 : ec1243eb42080bd2cf726fea4904b750 +timestamp : 2022-12-06 10:42:18 UTC +dependencies: + - anndata >=0.8.0 + - jupyterlab >=3.3.4 + - numpy >=1.23.3 + - pandas >=1.4.4 + - python >=3.6 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 0.2.2 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-0.2.2-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 0.2.2 +build : pyhdfd78af_0 +build number: 0 +size : 22 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.2.2-pyhdfd78af_0.tar.bz2 +md5 : c9e6a6a58ac357ed8e47ceb456446376 +timestamp : 2022-12-08 11:30:36 UTC +dependencies: + - anndata >=0.8.0 + - jupyterlab >=3.3.4 + - numpy >=1.23.3 + - pandas >=1.4.4 + - python >=3.6 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 0.2.3 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-0.2.3-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 0.2.3 +build : pyhdfd78af_0 +build number: 0 +size : 23 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.2.3-pyhdfd78af_0.tar.bz2 +md5 : 17d0cf700432ee627b971670aa634101 +timestamp : 2022-12-16 20:23:20 UTC +dependencies: + - anndata >=0.8.0 + - jupyterlab >=3.3.4 + - numpy >=1.23.3 + - pandas >=1.4.4 + - python >=3.6 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 0.2.6 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-0.2.6-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 0.2.6 +build : pyhdfd78af_0 +build number: 0 +size : 23 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.2.6-pyhdfd78af_0.tar.bz2 +md5 : f1bf5bb9e707f0e156126871d399fde5 +timestamp : 2023-01-12 10:08:13 UTC +dependencies: + - anndata >=0.8.0 + - numba >=0.56.3 + - numpy >=1.23.3,<1.24 + - packaging >=21.3 + - pandas >=1.4.4 + - python >=3.8 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 1.0.0 pyhdfd78af_0 +------------------------------- +file name : anansescanpy-1.0.0-pyhdfd78af_0.tar.bz2 +name : anansescanpy +version : 1.0.0 +build : pyhdfd78af_0 +build number: 0 +size : 23 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-1.0.0-pyhdfd78af_0.tar.bz2 +md5 : 5ad86690b5f633eba40037872b3dbc9a +timestamp : 2023-01-12 11:35:52 UTC +dependencies: + - anndata >=0.8.0 + - numba >=0.56.3 + - numpy >=1.23.3,<1.24 + - packaging >=21.3 + - pandas >=1.4.4 + - python >=3.8 + - scanpy >=1.9.1 + - scipy >=1.9.1 + + +anansescanpy 1.0.0 pyhdfd78af_1 +------------------------------- +file name : anansescanpy-1.0.0-pyhdfd78af_1.tar.bz2 +name : anansescanpy +version : 1.0.0 +build : pyhdfd78af_1 +build number: 1 +size : 23 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anansescanpy-1.0.0-pyhdfd78af_1.tar.bz2 +md5 : cc310593d651e949381a29f775ff785c +timestamp : 2024-04-03 05:46:48 UTC +dependencies: + - anndata >=0.8.0 + - numba >=0.56.3 + - numpy >=1.23.3,<1.24 + - packaging >=21.3 + - pandas >=1.4.4 + - python >=3.8 + - scanpy >=1.9.1 + - scipy >=1.9.1 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/anarci.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/anarci.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..14d5d00be09c4b946153eb3e63ff64e2a96b9502 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/anarci.manual_bundle.txt @@ -0,0 +1,140 @@ +# Tool: anarci +software_name: anarci +tier: T1 +domain: t1_backfill_overall +downloads: 262463 +summary: ANARCI: Antibody Numbering and Antigen Receptor ClassIfication +description: ANARCI: Antibody Numbering and Antigen Receptor ClassIfication +dependencies: biopython, hmmer >=3.3.2, python +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/anarci/ +doc_url: +dev_url: + +## URL Docs Extract +### http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/anarci/ +SAbPred: ANARCI --> --> Web Apps ABodyBuilder-ML ABodyBuilder2 TCRBuilder2 NanoBodyBuilder2 PEARS ANARCI ANARCII-LM SCALOP TAP Hu-mAb Humatch p-IgGen Databases SAbDab Thera-SAbDab CoV-AbDab OAS Database OTS Database STCRDab PLAbDab PLAbDab-nano GitHub ImmuneBuilder ABlooper AbLang Paragraph DLAB More OPIG Repos ... Downloads Job Queue About ^ ANARCI (Legacy version) >    About ANARCI A ntigen receptor N umbering A nd R eceptor C lassificat I on. ANARCI is a tool for numbering amino-acid sequences of antibody and T-cell receptor variable domains. Use the form below to identify domains and annotate them with either the IMGT, Chothia, Kabat, Martin (Enhanced Chothia) or AHo numbering scheme. TCR sequences can only be numbered with IMGT or AHo schemes. ANARCI aligns a given sequence to a database of Hidden Markov Models that describe the germline sequences of antibody and TCR domain types. The most significant alignment predicts the domain type and species (*) of the input sequence. The ANARCI Python package is freely available on Github . For a full description of the pipeline, or if you use this software, please refer to: Dunbar J and Deane CM. ANARCI: Antigen receptor numbering and receptor classification. Bioinformatics (2016) >    Sequence submission form The ANARCI web application restricts germline species to human and mouse to ensure numbering remains consistent over time. If you wish to use other species' germlines you can do this using the ANARCI Python package available on GitHub Submit single sequence: load example or upload multiple sequences as a fasta file: ' followed by the amino acid sequence (on multiple lines if required)."> Choose a numbering scheme: IMGT Kabat Chothia Martin AHo Choose an output format: Comma separated value (csv) file (horizontal format) Plain text (txt) file (vertical format) Restrict to immunoglobulin domains only Annotate SAbPred paper: Dunbar, J. et al (2016). Nucleic Acids Res. 44. W474-W478 [link] We use cookies to collect usage statistics for this website. By continuing to browse this site you agree to our use of cookies. For more details about cookies see our privacy policy . Continue + +## Conda Search Info +$ conda search -c bioconda -c conda-forge anarci --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +anarci 2020.04.23 py_0 +---------------------- +file name : anarci-2020.04.23-py_0.tar.bz2 +name : anarci +version : 2020.04.23 +build : py_0 +build number: 0 +size : 1.1 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anarci-2020.04.23-py_0.tar.bz2 +md5 : d72fec6243f13682e13a08f1f43459d9 +timestamp : 2020-06-12 12:32:14 UTC +dependencies: + - biopython + - hmmer >=3.1 + - python + + +anarci 2020.04.23 py_1 +---------------------- +file name : anarci-2020.04.23-py_1.tar.bz2 +name : anarci +version : 2020.04.23 +build : py_1 +build number: 1 +size : 1.1 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anarci-2020.04.23-py_1.tar.bz2 +md5 : fdc084269eb3669d2c667c7a8b725ee5 +timestamp : 2020-07-03 09:09:46 UTC +dependencies: + - biopython + - hmmer >=3.1 + - python + + +anarci 2020.04.23 py_2 +---------------------- +file name : anarci-2020.04.23-py_2.tar.bz2 +name : anarci +version : 2020.04.23 +build : py_2 +build number: 2 +size : 1.1 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anarci-2020.04.23-py_2.tar.bz2 +md5 : 289d79dcfe14d8eb1b8c525d49080048 +timestamp : 2020-07-09 22:17:48 UTC +dependencies: + - biopython + - hmmer >=3.1 + - python + + +anarci 2020.04.23 py_3 +---------------------- +file name : anarci-2020.04.23-py_3.tar.bz2 +name : anarci +version : 2020.04.23 +build : py_3 +build number: 3 +size : 1.1 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anarci-2020.04.23-py_3.tar.bz2 +md5 : 75d82b9436922718d47f5b1bb6b75d24 +timestamp : 2020-07-26 04:30:32 UTC +dependencies: + - biopython + - hmmer >=3.1 + - python + + +anarci 2021.02.04 pyhdfd78af_0 +------------------------------ +file name : anarci-2021.02.04-pyhdfd78af_0.tar.bz2 +name : anarci +version : 2021.02.04 +build : pyhdfd78af_0 +build number: 0 +size : 1.1 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anarci-2021.02.04-pyhdfd78af_0.tar.bz2 +md5 : 34b8c4648667bff833a01104632273f1 +timestamp : 2021-07-20 09:18:06 UTC +dependencies: + - biopython + - hmmer >=3.1 + - python + + +anarci 2024.05.21 pyhdfd78af_0 +------------------------------ +file name : anarci-2024.05.21-pyhdfd78af_0.tar.bz2 +name : anarci +version : 2024.05.21 +build : pyhdfd78af_0 +build number: 0 +size : 1.1 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/anarci-2024.05.21-pyhdfd78af_0.tar.bz2 +md5 : 3342c9d8e5917b8c080891b5c574f4eb +timestamp : 2024-12-06 19:15:23 UTC +dependencies: + - biopython + - hmmer >=3.3.2 + - python diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bactopia.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bactopia.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8c2db4d373b9425c969b62e8b38dce91f0646212 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bactopia.manual_bundle.txt @@ -0,0 +1,634 @@ +# Tool: bactopia +software_name: bactopia +tier: T1 +domain: t1_backfill_overall +downloads: 235804 +summary: Bactopia is a flexible pipeline for complete analysis of bacterial genomes. +description: Bactopia is a flexible pipeline for complete analysis of bacterial genomes. +dependencies: bactopia-py 1.5.0.*, conda >=22.11.0, coreutils, mamba >=1.1.0, nextflow >=23,<24, python >=3.9,<3.13, sed, wget +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/bactopia/bactopia +doc_url: +dev_url: https://github.com/bactopia/bactopia/ + +## URL Docs Extract +### https://github.com/bactopia/bactopia +GitHub - bactopia/bactopia: A flexible pipeline for complete analysis of bacterial genomes · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bactopia / bactopia Public Notifications You must be signed in to change notification settings Fork 80 Star 505 Code Issues 104 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights bactopia/bactopia master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,633 Commits 1,633 Commits .claude .claude .github .github .vscode .vscode bin bin conf conf data data modules modules subworkflows subworkflows tests tests workflows workflows .gitignore .gitignore CHANGELOG.md CHANGELOG.md CITATION.cff CITATION.cff CLAUDE.md CLAUDE.md CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE README.md README.md catalog.json catalog.json environment.yml environment.yml llms.txt llms.txt main.nf main.nf nextflow.config nextflow.config nextflow_schema.json nextflow_schema.json View all files Repository files navigation README Code of conduct Contributing MIT license Bactopia Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia can be split into two main parts: Bactopia Analysis Pipeline , and Bactopia Tools . Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow , input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more. Bactopia Tools are a set a independent workflows for comparative analyses. The comparative analyses may include summary reports, pan-genome, or phylogenetic tree construction. Using the predictable output structure of Bactopia you can pick and choose which samples to include for processing with a Bactopia Tool. Bactopia was inspired by Staphopia , a workflow we (Tim Read and myself) released that targets Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start. Documentation Documentation for Bactopia is available at https://bactopia.io/ . The documentation includes a tutorial replicating Staphopia and a complete overview of Bactopia. I highly encourage you check it out! Quick Start mamba create -y -n bactopia -c conda-forge -c bioconda bactopia conda activate bactopia bactopia datasets # Paired-end bactopia --R1 R1.fastq.gz --R2 R2.fastq.gz --sample SAMPLE_NAME \ --datasets datasets/ --outdir OUTDIR # Single-End bactopia --SE SAMPLE.fastq.gz --sample SAMPLE --datasets datasets/ --outdir OUTDIR # Multiple Samples bactopia prepare MY-FASTQS/ > fastqs.txt bactopia --fastqs fastqs.txt --datasets datasets --outdir OUTDIR # Single ENA/SRA Experiment bactopia --accession SRX000000 --datasets datasets --outdir OUTDIR # Multiple ENA/SRA Experiments bactopia search "staphylococcus aureus" > accessions.txt bactopia --accessions accessions.txt --dataset datasets --outdir ${OUTDIR} Installation Bactopia has a lot of tools built into its workflow. As you can imagine, all these tools lead to numerous dependencies, and navigating dependencies can often turn into a very frustrating process. With this in mind, from the onset Bactopia was developed to only include programs that are installable using Conda . Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. In other words, it makes it super easy to get the tools you need installed! The official Conda documentation is a good starting point for getting started with Conda. Bactopia has been tested using the Miniforge installer , but the Anaconda installer should work the same. Once you have Conda all set up, you are ready to create an environment for Bactopia. # Recommended mamba create -n bactopia -c conda-forge -c bioconda bactopia # or with standard conda conda create -n bactopia -c conda-forge -c bioconda bactopia After a few minutes you will have a new conda environment suitably named bactopia . To activate this environment, you will can use the following command: conda activate bactopia And voilà, you are all set to get started processing your data! Please Cite Datasets and Tools If you have used Bactopia in your work, please be sure to cite any datasets or tools you may have used. A list of each dataset/tool used by Bactopia has been made available . If a citation needs to be updated please let me know! Acknowledgements Bactopia is truly a case of "standing upon the shoulders of giants" . Nearly every component of Bactopia was created by others and made freely available to the public. I would like to personally extend my many thanks and gratitude to the authors of these software packages and public datasets. If you've made it this far, I owe you a beer 🍻 (or coffee ☕!) if we ever encounter one another in person. Really, thank you very much! Alternatives In case Bactopia doesn't fit your needs, here are some alternatives you can checkout. I personally haven't used them, but you might find them to fit your needs! If you ran into issues using Bactopia, please feel free to reach out ! AQUAMIS Deneke C, Brendebach H, Uelze L, Borowiak M, Malorny B, Tausch SH. Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS. Genes . 2021;12. doi:10.3390/genes12050644 ASA³P Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A. ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS Comput Biol 2020;16:e1007134. https://doi.org/10.1371/journal.pcbi.1007134 . MicroPIPE Murigneux V, Roberts LW, Forde BM, Phan M-D, Nhu NTK, Irwin AD, Harris PNA, Paterson DL, Schembri MA, Whiley DM, Beatson SA MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction. BMC Genomics , 22(1), 474. (2021) https://doi.org/10.1186/s12864-021-07767-z Nullarbor Seemann T, Goncalves da Silva A, Bulach DM, Schultz MB, Kwong JC, Howden BP. Nullarbor Github https://github.com/tseemann/nullarbor ProkEvo Pavlovikj N, Gomes-Neto JC, Deogun JS, Benson AK ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses. PeerJ , e11376 (2021) https://doi.org/10.7717/peerj.11376 Public Health Bacterial Genomics Libuit K, Ambrosio F, Kapsak C Public Health Bacterial Genomics GitHub https://github.com/theiagen/public_health_bacterial_genomics rMAP Sserwadda I, Mboowa G rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial Genomics , 7(6). (2021) https://doi.org/10.1099/mgen.0.000583 TORMES Quijada NM, Rodríguez-Lázaro D, Eiros JM, Hernández M. TORMES: an automated pipeline for whole bacterial genome analysis. Bioinformatics 2019;35:4207–12. https://doi.org/10.1093/bioinformatics/btz220 . Feedback Your feedback is very valuable! If you run into any issues using Bactopia, have questions, or have some ideas to improve Bactopia, I highly encourage you to submit it to the Issue Tracker . License MIT License Citation Petit III RA, Read TD, Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems . 5 (2020), https://doi.org/10.1128/mSystems.00190-20 . Author Robert A. Petit III BlueSky: @rpetit3 Funding Support for this project came (in part) from an Emory Public Health Bioinformatics Fellowship funded by the CDC Emerging Infections Program (U50CK000485) PPHF/ACA: Enhancing Epidemiology and Laboratory Capacity , the Wyoming Public Health Division , the Center for Applied Pathogen Epidemiology and Outbreak Control (CAPE) , and the CZI Open Science Program (EOSS6) . About A flexible pipeline for complete analysis of bacterial genomes bactopia.io Topics nextflow conda bioconda bacterial-genomes fastqs Resources Readme License MIT license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 505 stars Watchers 14 watching Forks 80 forks Report repository Releases 52 v4.0.0 Latest Apr 29, 2026 + 51 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Nextflow 92.9% Perl 4.8% Shell 2.0% Python 0.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/bactopia/bactopia/ +GitHub - bactopia/bactopia: A flexible pipeline for complete analysis of bacterial genomes · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bactopia / bactopia Public Notifications You must be signed in to change notification settings Fork 80 Star 505 Code Issues 104 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights bactopia/bactopia master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,633 Commits 1,633 Commits .claude .claude .github .github .vscode .vscode bin bin conf conf data data modules modules subworkflows subworkflows tests tests workflows workflows .gitignore .gitignore CHANGELOG.md CHANGELOG.md CITATION.cff CITATION.cff CLAUDE.md CLAUDE.md CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE README.md README.md catalog.json catalog.json environment.yml environment.yml llms.txt llms.txt main.nf main.nf nextflow.config nextflow.config nextflow_schema.json nextflow_schema.json View all files Repository files navigation README Code of conduct Contributing MIT license Bactopia Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia can be split into two main parts: Bactopia Analysis Pipeline , and Bactopia Tools . Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow , input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more. Bactopia Tools are a set a independent workflows for comparative analyses. The comparative analyses may include summary reports, pan-genome, or phylogenetic tree construction. Using the predictable output structure of Bactopia you can pick and choose which samples to include for processing with a Bactopia Tool. Bactopia was inspired by Staphopia , a workflow we (Tim Read and myself) released that targets Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start. Documentation Documentation for Bactopia is available at https://bactopia.io/ . The documentation includes a tutorial replicating Staphopia and a complete overview of Bactopia. I highly encourage you check it out! Quick Start mamba create -y -n bactopia -c conda-forge -c bioconda bactopia conda activate bactopia bactopia datasets # Paired-end bactopia --R1 R1.fastq.gz --R2 R2.fastq.gz --sample SAMPLE_NAME \ --datasets datasets/ --outdir OUTDIR # Single-End bactopia --SE SAMPLE.fastq.gz --sample SAMPLE --datasets datasets/ --outdir OUTDIR # Multiple Samples bactopia prepare MY-FASTQS/ > fastqs.txt bactopia --fastqs fastqs.txt --datasets datasets --outdir OUTDIR # Single ENA/SRA Experiment bactopia --accession SRX000000 --datasets datasets --outdir OUTDIR # Multiple ENA/SRA Experiments bactopia search "staphylococcus aureus" > accessions.txt bactopia --accessions accessions.txt --dataset datasets --outdir ${OUTDIR} Installation Bactopia has a lot of tools built into its workflow. As you can imagine, all these tools lead to numerous dependencies, and navigating dependencies can often turn into a very frustrating process. With this in mind, from the onset Bactopia was developed to only include programs that are installable using Conda . Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. In other words, it makes it super easy to get the tools you need installed! The official Conda documentation is a good starting point for getting started with Conda. Bactopia has been tested using the Miniforge installer , but the Anaconda installer should work the same. Once you have Conda all set up, you are ready to create an environment for Bactopia. # Recommended mamba create -n bactopia -c conda-forge -c bioconda bactopia # or with standard conda conda create -n bactopia -c conda-forge -c bioconda bactopia After a few minutes you will have a new conda environment suitably named bactopia . To activate this environment, you will can use the following command: conda activate bactopia And voilà, you are all set to get started processing your data! Please Cite Datasets and Tools If you have used Bactopia in your work, please be sure to cite any datasets or tools you may have used. A list of each dataset/tool used by Bactopia has been made available . If a citation needs to be updated please let me know! Acknowledgements Bactopia is truly a case of "standing upon the shoulders of giants" . Nearly every component of Bactopia was created by others and made freely available to the public. I would like to personally extend my many thanks and gratitude to the authors of these software packages and public datasets. If you've made it this far, I owe you a beer 🍻 (or coffee ☕!) if we ever encounter one another in person. Really, thank you very much! Alternatives In case Bactopia doesn't fit your needs, here are some alternatives you can checkout. I personally haven't used them, but you might find them to fit your needs! If you ran into issues using Bactopia, please feel free to reach out ! AQUAMIS Deneke C, Brendebach H, Uelze L, Borowiak M, Malorny B, Tausch SH. Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS. Genes . 2021;12. doi:10.3390/genes12050644 ASA³P Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A. ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS Comput Biol 2020;16:e1007134. https://doi.org/10.1371/journal.pcbi.1007134 . MicroPIPE Murigneux V, Roberts LW, Forde BM, Phan M-D, Nhu NTK, Irwin AD, Harris PNA, Paterson DL, Schembri MA, Whiley DM, Beatson SA MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction. BMC Genomics , 22(1), 474. (2021) https://doi.org/10.1186/s12864-021-07767-z Nullarbor Seemann T, Goncalves da Silva A, Bulach DM, Schultz MB, Kwong JC, Howden BP. Nullarbor Github https://github.com/tseemann/nullarbor ProkEvo Pavlovikj N, Gomes-Neto JC, Deogun JS, Benson AK ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses. PeerJ , e11376 (2021) https://doi.org/10.7717/peerj.11376 Public Health Bacterial Genomics Libuit K, Ambrosio F, Kapsak C Public Health Bacterial Genomics GitHub https://github.com/theiagen/public_health_bacterial_genomics rMAP Sserwadda I, Mboowa G rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial Genomics , 7(6). (2021) https://doi.org/10.1099/mgen.0.000583 TORMES Quijada NM, Rodríguez-Lázaro D, Eiros JM, Hernández M. TORMES: an automated pipeline for whole bacterial genome analysis. Bioinformatics 2019;35:4207–12. https://doi.org/10.1093/bioinformatics/btz220 . Feedback Your feedback is very valuable! If you run into any issues using Bactopia, have questions, or have some ideas to improve Bactopia, I highly encourage you to submit it to the Issue Tracker . License MIT License Citation Petit III RA, Read TD, Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems . 5 (2020), https://doi.org/10.1128/mSystems.00190-20 . Author Robert A. Petit III BlueSky: @rpetit3 Funding Support for this project came (in part) from an Emory Public Health Bioinformatics Fellowship funded by the CDC Emerging Infections Program (U50CK000485) PPHF/ACA: Enhancing Epidemiology and Laboratory Capacity , the Wyoming Public Health Division , the Center for Applied Pathogen Epidemiology and Outbreak Control (CAPE) , and the CZI Open Science Program (EOSS6) . About A flexible pipeline for complete analysis of bacterial genomes bactopia.io Topics nextflow conda bioconda bacterial-genomes fastqs Resources Readme License MIT license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 505 stars Watchers 14 watching Forks 80 forks Report repository Releases 52 v4.0.0 Latest Apr 29, 2026 + 51 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Nextflow 92.9% Perl 4.8% Shell 2.0% Python 0.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bactopia --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bactopia 1.0.1 0 +---------------- +file name : bactopia-1.0.1-0.tar.bz2 +name : bactopia +version : 1.0.1 +build : 0 +build number: 0 +size : 16 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.0.1-0.tar.bz2 +md5 : c71a2086a9da252582e8a7b249c35a36 +timestamp : 2019-09-12 17:12:41 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - python >3.6 + - unzip + - urllib3 + - wget + + +bactopia 1.1.0 0 +---------------- +file name : bactopia-1.1.0-0.tar.bz2 +name : bactopia +version : 1.1.0 +build : 0 +build number: 0 +size : 16 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.1.0-0.tar.bz2 +md5 : 369a66a11ce796a9969193acf910f16a +timestamp : 2019-09-19 17:50:40 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - python >3.6 + - unzip + - urllib3 + - wget + + +bactopia 1.1.0 1 +---------------- +file name : bactopia-1.1.0-1.tar.bz2 +name : bactopia +version : 1.1.0 +build : 1 +build number: 1 +size : 16 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.1.0-1.tar.bz2 +md5 : 7e9733c18e49a22e6af948bcb15d7f52 +timestamp : 2019-09-20 10:33:48 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - unzip + - urllib3 + - wget + + +bactopia 1.2.0 0 +---------------- +file name : bactopia-1.2.0-0.tar.bz2 +name : bactopia +version : 1.2.0 +build : 0 +build number: 0 +size : 18 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.2.0-0.tar.bz2 +md5 : 27f23d4cf00e468e168781ec0a175245 +timestamp : 2019-10-17 06:35:24 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.2.1 0 +---------------- +file name : bactopia-1.2.1-0.tar.bz2 +name : bactopia +version : 1.2.1 +build : 0 +build number: 0 +size : 19 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.2.1-0.tar.bz2 +md5 : 4229ff77d6472b0eaa1401fe6cbd181d +timestamp : 2019-10-17 18:25:56 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.2.2 0 +---------------- +file name : bactopia-1.2.2-0.tar.bz2 +name : bactopia +version : 1.2.2 +build : 0 +build number: 0 +size : 19 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.2.2-0.tar.bz2 +md5 : 6a0831fd73b90731e7861adbc0a317fd +timestamp : 2019-10-24 16:41:14 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.2.4 0 +---------------- +file name : bactopia-1.2.4-0.tar.bz2 +name : bactopia +version : 1.2.4 +build : 0 +build number: 0 +size : 19 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.2.4-0.tar.bz2 +md5 : 785af4c19c070e416a2c8ba1937bdd4e +timestamp : 2019-12-25 12:11:54 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.3.0 0 +---------------- +file name : bactopia-1.3.0-0.tar.bz2 +name : bactopia +version : 1.3.0 +build : 0 +build number: 0 +size : 976 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.3.0-0.tar.bz2 +md5 : fbf60bbc5eb5503329511d55641da78d +timestamp : 2020-02-19 19:11:26 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.3.1 0 +---------------- +file name : bactopia-1.3.1-0.tar.bz2 +name : bactopia +version : 1.3.1 +build : 0 +build number: 0 +size : 1.3 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.3.1-0.tar.bz2 +md5 : 058aac793476515d9d8ac8d0f12ee555 +timestamp : 2020-04-21 02:01:30 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.4.0 0 +---------------- +file name : bactopia-1.4.0-0.tar.bz2 +name : bactopia +version : 1.4.0 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.0-0.tar.bz2 +md5 : ac19f7bc58c0a2210a9937c3908611c6 +timestamp : 2020-07-02 03:56:08 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - bowtie2 <2.4.0 + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.4.1 0 +---------------- +file name : bactopia-1.4.1-0.tar.bz2 +name : bactopia +version : 1.4.1 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.1-0.tar.bz2 +md5 : 74d9752829d8cad228d434a0b0ac974c +timestamp : 2020-08-06 22:12:14 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - bowtie2 <2.4.0 + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.4.2 0 +---------------- +file name : bactopia-1.4.2-0.tar.bz2 +name : bactopia +version : 1.4.2 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.2-0.tar.bz2 +md5 : a243ceb1c06106788730e7650ff2da31 +timestamp : 2020-08-10 15:21:39 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - bowtie2 <2.4.0 + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.4.3 0 +---------------- +file name : bactopia-1.4.3-0.tar.bz2 +name : bactopia +version : 1.4.3 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.3-0.tar.bz2 +md5 : 1d58e12b4516f08e71fdfe5e9fc4c028 +timestamp : 2020-08-13 16:13:27 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - bowtie2 <2.4.0 + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.4.4 0 +---------------- +file name : bactopia-1.4.4-0.tar.bz2 +name : bactopia +version : 1.4.4 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.4-0.tar.bz2 +md5 : 1abf674e73de4764a000e51fd680477e +timestamp : 2020-08-13 21:13:09 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - bowtie2 <2.4.0 + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.4.5 0 +---------------- +file name : bactopia-1.4.5-0.tar.bz2 +name : bactopia +version : 1.4.5 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.5-0.tar.bz2 +md5 : 78281c39fcea4d3ce374189573276d96 +timestamp : 2020-08-13 22:16:30 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - bowtie2 <2.4.0 + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.4.6 0 +---------------- +file name : bactopia-1.4.6-0.tar.bz2 +name : bactopia +version : 1.4.6 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.6-0.tar.bz2 +md5 : ddebe60bd426ec89c4a7c78ae3580176 +timestamp : 2020-08-17 21:13:33 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - bowtie2 <2.4.0 + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.4.7 0 +---------------- +file name : bactopia-1.4.7-0.tar.bz2 +name : bactopia +version : 1.4.7 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.7-0.tar.bz2 +md5 : 1b1f2c886d3f7e79bd0249a74af887fb +timestamp : 2020-08-18 00:24:01 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - bowtie2 <2.4.0 + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.4.8 0 +---------------- +file name : bactopia-1.4.8-0.tar.bz2 +name : bactopia +version : 1.4.8 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.8-0.tar.bz2 +md5 : 4373b9fb058f4fdf1eedf007785995e8 +timestamp : 2020-08-21 02:17:30 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - bowtie2 <2.4.0 + - cd-hit + - conda + - executor + - lxml + - mash + - ncbi-genome-download + - nextflow + - pysam >=0.15.3 + - python >3.6 + - requests + - unzip + - wget + + +bactopia 1.4.9 0 +---------------- +file name : bactopia-1.4.9-0.tar.bz2 +name : bactopia +version : 1.4.9 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.9-0.tar.bz2 +md5 : fa1ca25a5d109c0764c4699709698dae +timestamp : 2020-08-23 15:15:53 UTC +dependencies: + - ariba + - beautifulsoup4 + - biopython + - blast + - bowtie2 <2.4.0 + - cd-hit + - conda + - executor + - lx diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bcbio-nextgen.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bcbio-nextgen.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..685c66fffff52d4330801af52bc26d3aa492821e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bcbio-nextgen.manual_bundle.txt @@ -0,0 +1,731 @@ +# Tool: bcbio-nextgen +software_name: bcbio-nextgen +tier: T1 +domain: t1_backfill_overall +downloads: 415872 +summary: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis +description: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis +dependencies: arrow, beautifulsoup4, bioblend, biopython, boto, cyvcf2, dnapi, fadapa, geneimpacts, gffutils, h5py, htslib, ipyparallel 6.3.0.*, ipython-cluster-helper 0.6.4 py_0, joblib >=0.12, logbook, matplotlib-base, mock, msgpack-python, openssl <3.0.0, pandas, pip, psutil, py, pybedtools, pycrypto, pysam >=0.13.0, pytest, pytest-cov >=2.6.1, pytest-mock, python, python-dateutil >=2.5.0, pyvcf, pyyaml, requests, scipy >=1.3.0, seaborn, seqcluster, statsmodels, tabulate, toolz, yamllint +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/bcbio/bcbio-nextgen +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/bcbio/bcbio-nextgen +GitHub - bcbio/bcbio-nextgen: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bcbio / bcbio-nextgen Public Notifications You must be signed in to change notification settings Fork 355 Star 1k Code Issues 129 Pull requests 4 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights bcbio/bcbio-nextgen master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 8,579 Commits 8,579 Commits .github .github artwork artwork bcbio bcbio config config docs docs scripts scripts tests tests .gitignore .gitignore .readthedocs.yml .readthedocs.yml .travis.yml .travis.yml CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md HISTORY.md HISTORY.md LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in README.md README.md Vagrantfile Vagrantfile requirements-conda.txt requirements-conda.txt requirements-dev.txt requirements-dev.txt requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README Code of conduct MIT license Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel run that handles distributed execution, idempotent processing restarts and safe transactional steps. bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology. NOTE!!!! Please read the notice of discontinuation of this project - 08-16-2024 Features Community developed: We welcome contributors with the goal of overcoming the biological, algorithmic and computational challenges that face individual developers working on complex pipelines in quickly changing research areas. See our users page for examples of bcbio-nextgen deployments, and the developer documentation for tips on contributing. Installation: A single installer script prepares all third party software, data libraries and system configuration files. Automated validation : Compare variant calls against common reference materials or sample specific SNP arrays to ensure call correctness. Incorporation of multiple approaches for alignment, preparation and variant calling enable unbiased comparisons of algorithms. Distributed: Focus on parallel analysis and scaling to handle large population studies and whole genome analysis. Runs on single multicore computers, in compute clusters using IPython parallel , or on the Amazon cloud. See the parallel documentation for full details. Multiple analysis algorithms: bcbio-nextgen provides configurable variant calling (small and copy number), RNA-seq, ATAC-seq, , BS-Seq, SC RNA-seq, and small RNA pipelines . Quick start Install bcbio-nextgen with all tool dependencies and data files: wget https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \ --genomes hg38 --aligners bwa --aligners bowtie2 producing an editable system configuration file referencing the installed software, data and system information. Automatically create a processing description of sample FASTQ and BAM files from your project, and a CSV file of sample metadata: bcbio_nextgen.py -w template freebayes-variant project1.csv sample1.bam sample2_1.fq sample2_2.fq This produces a sample description file containing pipeline configuration options . Run analysis, distributed across 8 local cores: cd project1/work bcbio_nextgen.py ../config/project1.yaml -n 8 Documentation See the full documentation and longer analysis-based articles . We welcome enhancements or problem reports using GitHub and discussion on the biovalidation mailing list . Contributors Miika Ahdesmaki , AstraZeneca Luca Beltrame , IRCCS "Mario Negri" Institute for Pharmacological Research, Milan, Italy Christian Brueffer , Lund University, Lund, Sweden Alla Bushoy , AstraZeneca Guillermo Carrasco , Science for Life Laboratory, Stockholm Nick Carriero , Simons Foundation Brad Chapman , Harvard Chan Bioinformatics Core Saket Choudhary , University Of Southern California Peter Cock , The James Hutton Institute Matthias De Smet , Center for Medical Genetics, Ghent University Hospital, Belgium Matt Edwards , MIT Mario Giovacchini , Science for Life Laboratory, Stockholm Karl Gutwin , Biogen Jeff Hammerbacher , Icahn School of Medicine at Mount Sinai Oliver Hofmann , University of Melbourne Centre for Cancer Research John Kern Rory Kirchner , Harvard Chan Bioinformatics Core Tetiana Khotiainsteva , Ardigen Kerrin Mendler , AstraZeneca Sergey Naumenko , Harvard Chan Bioinformatics Core Jakub Nowacki , AstraZeneca John Morrissey , Harvard Chan Bioinformatics Core Lorena Pantano , Harvard Chan Bioinformatics Core Brent Pedersen , University of Colorado Denver James Porter , The University of Chicago Vlad Saveliev , Center for Algorithmic Biotechnology, St. Petersburg University Valentine Svensson , Science for Life Laboratory, Stockholm Paul Tang , UCSF Stephen Turner , University of Virginia Roman Valls , Science for Life Laboratory, Stockholm Kevin Ying , Garvan Institute of Medical Research, Sydney, Australia Steffen Möller , University of Rostock, Germany WimSpee License The code is freely available under the MIT license . About Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis bcbio-nextgen.readthedocs.io Resources Readme License MIT license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1k stars Watchers 87 watching Forks 355 forks Report repository Releases 14 v1.2.9 Latest Dec 15, 2021 + 13 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.0% Other 1.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bcbio-nextgen --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bcbio-nextgen 0.9.5 py27_1 +-------------------------- +file name : bcbio-nextgen-0.9.5-py27_1.tar.bz2 +name : bcbio-nextgen +version : 0.9.5 +build : py27_1 +build number: 1 +size : 1.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.5-py27_1.tar.bz2 +md5 : fb8ab3728e1fad76a55b01727b673ce2 +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.6a py27_0 +--------------------------- +file name : bcbio-nextgen-0.9.6a-py27_0.tar.bz2 +name : bcbio-nextgen +version : 0.9.6a +build : py27_0 +build number: 0 +size : 636 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.6a-py27_0.tar.bz2 +md5 : 781006b9fb52e850e982e409f03bd388 +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.6a py27_1 +--------------------------- +file name : bcbio-nextgen-0.9.6a-py27_1.tar.bz2 +name : bcbio-nextgen +version : 0.9.6a +build : py27_1 +build number: 1 +size : 639 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.6a-py27_1.tar.bz2 +md5 : ca07e2bb306fb2f4416ad1ebcade54a0 +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.6a py27_2 +--------------------------- +file name : bcbio-nextgen-0.9.6a-py27_2.tar.bz2 +name : bcbio-nextgen +version : 0.9.6a +build : py27_2 +build number: 2 +size : 642 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.6a-py27_2.tar.bz2 +md5 : a3cb1d7178e5b84fd9ecbebdbabc4460 +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.6a py27_3 +--------------------------- +file name : bcbio-nextgen-0.9.6a-py27_3.tar.bz2 +name : bcbio-nextgen +version : 0.9.6a +build : py27_3 +build number: 3 +size : 643 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.6a-py27_3.tar.bz2 +md5 : e63b25629c3c80a106a07d6a923a3b1d +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - ipywidgets + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.6 py27_0 +-------------------------- +file name : bcbio-nextgen-0.9.6-py27_0.tar.bz2 +name : bcbio-nextgen +version : 0.9.6 +build : py27_0 +build number: 0 +size : 655 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.6-py27_0.tar.bz2 +md5 : 2457cf1b4878bb220211b27799ab0287 +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - ipywidgets + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.7a py27_0 +--------------------------- +file name : bcbio-nextgen-0.9.7a-py27_0.tar.bz2 +name : bcbio-nextgen +version : 0.9.7a +build : py27_0 +build number: 0 +size : 661 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.7a-py27_0.tar.bz2 +md5 : 5beeb479505a15b27fc1c3368f878d71 +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - ipywidgets + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.7a py27_1 +--------------------------- +file name : bcbio-nextgen-0.9.7a-py27_1.tar.bz2 +name : bcbio-nextgen +version : 0.9.7a +build : py27_1 +build number: 1 +size : 666 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.7a-py27_1.tar.bz2 +md5 : 245f9508f16129a4dfc7b270cafca85a +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - ipywidgets + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.7a py27_2 +--------------------------- +file name : bcbio-nextgen-0.9.7a-py27_2.tar.bz2 +name : bcbio-nextgen +version : 0.9.7a +build : py27_2 +build number: 2 +size : 666 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.7a-py27_2.tar.bz2 +md5 : 6d85ee322f8d27092100130ea83a9711 +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - ipywidgets + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.7a py27_3 +--------------------------- +file name : bcbio-nextgen-0.9.7a-py27_3.tar.bz2 +name : bcbio-nextgen +version : 0.9.7a +build : py27_3 +build number: 3 +size : 668 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.7a-py27_3.tar.bz2 +md5 : 2c38ab08340dcada3e9d2946d4e794ba +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - ipywidgets + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.7a py27_4 +--------------------------- +file name : bcbio-nextgen-0.9.7a-py27_4.tar.bz2 +name : bcbio-nextgen +version : 0.9.7a +build : py27_4 +build number: 4 +size : 675 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.7a-py27_4.tar.bz2 +md5 : cc54be80accf7d950b04088c69788f21 +dependencies: + - arrow + - azure + - bioblend + - biopython + - boto + - click + - cython + - cyvcf2 + - fabric + - fadapa + - gffutils + - ipyparallel + - ipython-cluster-helper + - ipywidgets + - joblib + - logbook + - lxml + - matplotlib + - msgpack-python + - nose + - numpy + - openpyxl + - openssl >=1.1.0,<=1.1.1 + - pandas + - path.py + - patsy + - pip + - progressbar + - psutil + - pybedtools + - pycrypto + - pysam + - python 2.7* + - python-dateutil + - pyvcf + - pyyaml + - pyzmq + - reportlab + - requests + - scikit-learn + - scipy + - seaborn + - seqcluster + - sh + - sqlalchemy + - statsmodels + - tabulate + - toolz + - tornado + + +bcbio-nextgen 0.9.7a py27_5 +--------------------------- +file name : bcbio-nextgen-0.9.7a-py27_5.tar.bz2 +name : bcbio-nextgen +version : 0.9.7a +build diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bedops.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bedops.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..562de8780f7f826f74c9cad9560b69cc141e7803 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bedops.manual_bundle.txt @@ -0,0 +1,549 @@ +# Tool: bedops +software_name: bedops +tier: T1 +domain: t1_backfill_overall +downloads: 235132 +summary: High-performance genomic feature operations. +description: High-performance genomic feature operations. +dependencies: bzip2 >=1.0.8,<2.0a0, jansson >=2.14.1,<3.0a0, libgcc >=13, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, samtools +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://bedops.readthedocs.io +doc_url: +dev_url: + +## CLI Help Source +cli:bedops +## CLI Help Content +$ conda run -n bioenv_cli bedops --help +[rc=0] +bedops + citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract + https://doi.org/10.1093/bioinformatics/bts277 + version: 2.4.42 (typical) + authors: Shane Neph & Scott Kuehn + + USAGE: bedops [process-flags] * + + Every input file must be sorted per the sort-bed utility. + Each operation requires a minimum number of files as shown below. + There is no fixed maximum number of files that may be used. + Input files must have at least the first 3 columns of the BED specification. + The program accepts BED and Starch file formats. + May use '-' for a file to indicate reading from standard input (BED format only). + + Process Flags: + --chrom Jump to and process data for given only. + --ec Error check input files (slower). + --header Accept headers (VCF, GFF, SAM, BED, WIG) in any input file. + --help Print this message and exit successfully. + --help- Detailed help on . + An example is --help-c or --help-complement + --range L:R Add 'L' bp to all start coordinates and 'R' bp to end + coordinates. Either value may be + or - to grow or + shrink regions. With the -e/-n operations, the first + (reference) file is not padded, unlike all other files. + --range S Pad or shrink input file(s) coordinates symmetrically by S. + This is shorthand for: --range -S:S. + --version Print program information. + + Operations: (choose one of) + -c, --complement [-L] File1 [File]* + -d, --difference ReferenceFile File2 [File]* + -e, --element-of [bp | percentage] ReferenceFile File2 [File]* + by default, -e 100% is used. 'bedops -e 1' is also popular. + -i, --intersect File1 File2 [File]* + -m, --merge File1 [File]* + -n, --not-element-of [bp | percentage] ReferenceFile File2 [File]* + by default, -n 100% is used. 'bedops -n 1' is also popular. + -p, --partition File1 [File]* + -s, --symmdiff File1 File2 [File]* + -u, --everything File1 [File]* + -w, --chop [bp] [--stagger ] [-x] File1 [File]* + by default, -w 1 is used with no staggering. + +Example: bedops --range 10 -u file1.bed + NOTE: Only operations -e|n|u preserve all columns (no flattening) + + + + +## URL Docs Extract +### http://bedops.readthedocs.io +BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit — BEDOPS v2.4.41 --> BEDOPS v2.4.41 1. Overview → Home BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit ¶ BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster. You can read more about BEDOPS and how it can be useful for your research in the Overview documentation, as well as in the original manuscript . x86-64 (64-bit) binaries Installation instructions for Linux hosts Intel (64-bit, 10.10-10.15) installer package Installation instructions for Mac OS X hosts Source code (tar.gz) Source code (zip) Compilation instructions bedops - apply set operations on any number of BED inputs bedextract - efficiently extract BED features closest-features - matches nearest features between BED files bedmap - map overlapping BED elements onto target regions and optionally compute any number of common statistical operations sort-bed - apply lexicographical sort to BED data starch and unstarch - compress and extract BED data starchcat - merge compressed archives starchstrip - filter archive by chromosomes Conversion tools - convert common genomic formats to BED Parallel bam2bed and bam2starch - parallelized conversion and compression of BAM data Set operations with bedops Compression characteristics of starch Independent testing Table summary of BEDOPS toolkit Starch v2.2 format specification About nested elements Revision history Github release instructions Github repository How to install BEDOPS Usage examples of BEDOPS tools in action BEDOPS user forum BEDOPS discusssion mailing list Citation ¶ If you use BEDOPS in your research, please cite the following manuscript: Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al. BEDOPS: high-performance genomic feature operations . Bioinformatics (2012) 28 (14): 1919-1920. doi: 10.1093/bioinformatics/bts277 Contents ¶ 1. Overview 1.1. About BEDOPS 1.2. Why you should use BEDOPS 1.2.1. BEDOPS tools are flexible 1.2.2. BEDOPS tools are fast and efficient 1.2.3. BEDOPS tools make your work embarrassingly easy to parallelize 1.2.4. BEDOPS tools are open, documented and supported 2. Installation 2.1. Via pre-built packages 2.1.1. Linux 2.1.2. Mac OS X 2.2. Via source code 2.2.1. Linux 2.2.2. Mac OS X 2.2.2.1. Manual compilation 2.2.2.2. Installation via Bioconda 2.2.2.3. Installation via Homebrew 2.2.3. Docker 2.2.4. Cygwin 2.3. Building an OS X installer package for redistribution 3. Revision history 3.1. Current version 3.1.1. v2.4.41 3.2. Previous versions 3.2.1. v2.4.40 3.2.2. v2.4.39 3.2.3. v2.4.38 3.2.4. v2.4.37 3.2.5. v2.4.36 3.2.6. v2.4.35 3.2.7. v2.4.34 3.2.8. v2.4.33 3.2.9. v2.4.32 3.2.10. v2.4.31 3.2.11. v2.4.30 3.2.12. v2.4.29 3.2.13. v2.4.28 3.2.14. v2.4.27 3.2.15. v2.4.26 3.2.16. v2.4.25 3.2.17. v2.4.24 3.2.18. v2.4.23 3.2.19. v2.4.22 3.2.20. v2.4.21 3.2.21. v2.4.20 3.2.22. v2.4.19 3.2.23. v2.4.18 3.2.24. v2.4.17 3.2.25. v2.4.16 3.2.26. v2.4.15 3.2.27. v2.4.14 3.2.28. v2.4.13 3.2.29. v2.4.12 3.2.30. v2.4.11 3.2.31. v2.4.10 3.2.32. v2.4.9 3.2.33. v2.4.8 3.2.34. v2.4.7 3.2.35. v2.4.6 3.2.36. v2.4.5 3.2.37. v2.4.4 3.2.38. v2.4.3 3.2.39. v2.4.2 3.2.40. v2.4.1 3.2.41. v2.4.0 3.2.42. v2.3.0 3.2.43. v2.2.0b 3.2.44. v2.2.0 3.2.45. v2.1.1 3.2.46. v2.1.0 3.2.47. v2.0.0b 3.2.48. v2.0.0a 3.2.49. v1.2.5b 3.2.50. v1.2.5 3.2.51. v1.2.3 4. Usage examples 4.1. Visualizing the relationship of SNPs and generic genomic features 4.1.1. BEDOPS tools in use 4.1.2. Script 4.1.3. Discussion 4.1.4. Downloads 4.2. Collapsing multiple BED files into a master list by signal 4.2.1. BEDOPS tools in use 4.2.2. Script 4.2.3. Discussion 4.3. Measuring the frequency of signed distances between SNPs and nearest DHSes 4.3.1. BEDOPS tools in use 4.3.2. Script 4.3.3. Discussion 4.3.4. Downloads 4.4. Finding the subset of SNPs within DHSes 4.4.1. BEDOPS tools in use 4.4.2. Script 4.4.3. Discussion 4.4.4. Downloads 4.5. Smoothing raw tag count data across the genome 4.5.1. BEDOPS tools in use 4.5.2. Script 4.6. Efficiently creating Starch-formatted archives with a cluster 4.6.1. BEDOPS tools in use 4.6.2. Script 4.6.3. Discussion 4.6.3.1. Splitting BED files 4.6.3.2. Compressing BED subsets 4.6.3.3. Stitching together compressed sets 4.7. Working with many input files at once with bedops and bedmap 4.7.1. Discussion 5. Performance 5.1. Test environment and data 5.2. Set operations with bedops 5.2.1. Direct merge (sorted) 5.2.2. Complement and intersection 5.2.3. Direct merge (unsorted) 5.2.4. Discussion 5.3. Compression characteristics of starch 5.3.1. Compression efficiency 5.3.2. Extraction time 5.4. Independent testing 5.4.1. Genomic Region Operation Kit (GROK) 5.5. Worst-case memory performance 6. Reference 6.1. Set operations 6.1.1. bedops 6.1.1.1. Inputs and outputs 6.1.1.1.1. Input 6.1.1.1.2. Output 6.1.1.2. Usage 6.1.1.3. Operations 6.1.1.3.1. Everything (-u, –everything) 6.1.1.3.2. Element-of (-e, –element-of) 6.1.1.3.3. Not-element-of (-n, –not-element-of) 6.1.1.3.4. Complement (-c, –complement) 6.1.1.3.5. Difference (-d, –difference) 6.1.1.3.6. Symmetric difference (-s, –symmdiff) 6.1.1.3.7. Intersect (-i, –intersect) 6.1.1.3.8. Merge (-m, –merge) 6.1.1.3.9. Partition (-p, –partition) 6.1.1.3.10. Chop (-w, –chop) 6.1.1.3.11. Stagger (–stagger) 6.1.1.3.12. Exclude (-x) 6.1.1.3.13. Per-chromosome operations (–chrom) 6.1.1.3.14. Range (–range) 6.1.1.4. Starch support 6.1.1.5. Error checking (–ec) 6.1.1.6. Tips 6.1.1.6.1. Chaining operations 6.1.1.6.2. Sorting inputs 6.1.2. bedextract 6.1.2.1. How it works 6.1.2.2. Inputs and outputs 6.1.2.2.1. Input 6.1.2.2.2. Output 6.1.2.3. Usage 6.1.2.3.1. Listing chromosomes 6.1.2.3.2. Retrieving elements from a specific chromosome 6.1.2.3.3. Retrieving elements which overlap target elements 6.1.2.3.3.1. What are nested elements? 6.1.2.3.3.2. Demonstration 6.1.2.4. Downloads 6.1.3. closest-features 6.1.3.1. Inputs and outputs 6.1.3.1.1. Input 6.1.3.1.2. Output 6.1.3.2. Usage 6.1.3.3. Per-chromosome operations (–chrom) 6.1.3.4. Error checking 6.1.3.5. Downloads 6.1.4. Nested elements 6.1.4.1. Definition 6.1.4.2. Example 6.1.4.3. Why nested elements matter 6.2. Statistics 6.2.1. bedmap 6.2.1.1. Inputs and outputs 6.2.1.1.1. Input 6.2.1.1.2. Output 6.2.1.2. Usage 6.2.1.3. Operations 6.2.1.3.1. Overlap criteria 6.2.1.3.1.1. Using --faster with --bp-ovr , --fraction-both , --exact or --range 6.2.1.3.2. Score operations 6.2.1.3.3. Non-score operations 6.2.1.3.3.1. Echo 6.2.1.3.3.2. Element and overlap statistics 6.2.1.3.3.3. Indicator 6.2.1.3.4. Modifiers 6.2.1.3.4.1. Range 6.2.1.3.4.2. Using --faster with --range 6.2.1.3.4.3. Formatting score output 6.2.1.3.4.4. Delimiters 6.2.1.4. I/O event handling 6.2.1.5. Per-chromosome operations (–chrom) 6.2.1.6. Starch support 6.2.1.7. Error checking 6.2.1.8. Endlines 6.2.1.9. Downloads 6.3. File management 6.3.1. Sorting 6.3.1.1. sort-bed 6.3.1.1.1. Migrating older BED and Starch files 6.3.1.1.2. Inputs and outputs 6.3.1.1.2.1. Input 6.3.1.1.2.2. Output 6.3.1.1.3. Usage 6.3.2. Compression 6.3.2.1. starch 6.3.2.1.1. Inputs and outputs 6.3.2.1.1.1. Input 6.3.2.1.1.2. Output 6.3.2.1.2. Requirements 6.3.2.1.3. Usage 6.3.2.1.4. Options 6.3.2.1.4.1. Backend compression type 6.3.2.1.4.2. Note 6.3.2.1.4.3. Per-chromosome data integrity signature 6.3.2.1.4.4. Compression progress 6.3.2.1.4.5. Headers 6.3.2.1.4.6. Unique tag 6.3.2.1.5. Example 6.3.2.2. unstarch 6.3.2.2.1. Inputs and outputs 6.3.2.2.1.1. Input 6.3.2.2.1.2. Output 6.3.2.2.2. Requirements 6.3.2.2.3. Usage 6.3.2.2.3.1. Extraction 6.3.2.2.3.2. Archive attributes 6.3.2.2.3.2.1. Metadata 6.3.2.2.3.2.2. Note 6.3.2.2.3.2.3. Timestamp 6.3.2.2.3.2.4. Compression type 6.3.2.2.3.2.5. Version 6.3.2.2.3.3. Whole-file or per-chromosome attributes 6.3.2.2.3.3.1. Data integrity 6.3.2.2.3.3.2. Elements 6.3.2.2.3.3.3. Bases 6.3.2.2.3.3.4. Duplicate element(s) 6.3.2.2.3.3.5. Nested element(s) 6.3.2.2.4. Example 6.3.2.3. starchcat 6.3.2.3.1. Parallelization 6.3.2.3.2. Inputs and outputs 6.3.2.3.2.1. Input 6.3.2.3.2.2. Output 6.3.2.3.3. Usage 6.3.2.3.3.1. Per-chromosome data integrity signature 6.3.2.3.3.2. Example 6.3.2.4. Starch (v2.x) specification 6.3.2.4.1. Archive structure 6.3.2.4.2. Magic bytes 6.3.2.4.3. Chromosome streams 6.3.2.4.4. Metadata 6.3.2.4.4.1. Data 6.3.2.4.4.1.1. Archive 6.3.2.4.4.1.2. Streams 6.3.2.4.4.2. Offset 6.3.2.4.4.3. Hash 6.3.2.4.5. Padding 6.3.2.5. starch-diff 6.3.2.5.1. Inputs and outputs 6.3.2.5.1.1. Input 6.3.2.5.1.2. Output 6.3.2.5.2. Requirements 6.3.2.5.3. Usage 6.3.3. Data conversion 6.3.3.1. convert2bed 6.3.3.1.1. Dependencies 6.3.3.1.2. Source 6.3.3.1.3. Usage 6.3.3.1.4. Example 6.3.3.2. bam2bed 6.3.3.2.1. Dependencies 6.3.3.2.2. Source 6.3.3.2.3. Usage 6.3.3.2.4. Example 6.3.3.2.5. Column mapping 6.3.3.2.6. Downloads 6.3.3.3. Parallel bam2bed 6.3.3.3.1. Dependencies 6.3.3.3.2. Source 6.3.3.3.3. Usage 6.3.3.4. Parallel bam2starch 6.3.3.4.1. Dependencies 6.3.3.4.2. Source 6.3.3.4.3. Usage 6.3.3.5. gff2bed 6.3.3.5.1. Dependencies 6.3.3.5.2. Source 6.3.3.5.3. Usage 6.3.3.5.4. Example 6.3.3.5.5. Column mapping 6.3.3.5.6. Downloads 6.3.3.6. gtf2bed 6.3.3.6.1. Dependencies 6.3.3.6.2. Source 6.3.3.6.3. Usage 6.3.3.6.4. Example 6.3.3.6.5. Column mapping 6.3.3.6.6. Downloads 6.3.3.7. gvf2bed 6.3.3.7.1. Dependencies 6.3.3.7.2. Source 6.3.3.7.3. Usage 6.3.3.7.4. Example 6.3.3.7.5. Column mapping 6.3.3.7.6. Downloads 6.3.3.8. psl2bed 6.3.3.8.1. Dependencies 6.3.3.8.2. Source 6.3.3.8.3. Usage 6.3.3.8.4. Example 6.3.3.8.5. Column mapping 6.3.3.8.6. Downloads 6.3.3.9. rmsk2bed 6.3.3.9.1. Dependencies 6.3.3.9.2. Source 6.3.3.9.3. Usage 6.3.3.9.4. Example 6.3.3.9.5. Column mapping 6.3.3.9.6. Downloads 6.3.3.10. sam2bed 6.3.3.10.1. Dependencies 6.3.3.10.2. Source 6.3.3.10.3. Usage 6.3.3.10.4. Example 6.3.3.10.5. Column mapping 6.3.3.10.6. Downloads 6.3.3.11. vcf2bed 6.3.3.11.1. Dependencies 6.3.3.11.2. Source 6.3.3.11.3. Usage 6.3.3.11.4. Customized variant handling 6.3.3.11.5. Example 6.3.3.11.6. Column mapping 6.3.3.11.7. Downloads 6.3.3.12. wig2bed 6.3.3.12.1. Source 6.3.3.12.2. Usage 6.3.3.12.3. Example 6.3.3.12.4. Downloads 7. Summary 7.1. Set operation and statistical utilities 7.1.1. bedextract 7.1.2. bedmap 7.1.3. bedops 7.1.4. closest-features 7.2. Sorting 7.2.1. sort-bed 7.3. Compression and extraction 7.3.1. starch 7.3.2. unstarch 7.3.3. starchcat 7.3.4. starchstrip 8. Release 8.1. Preparation 8.2. Release 8.3. Celebrate 9. Placeholder Table of Contents BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit Citation Contents 1. Overview → Home © 2011-2022, Shane Neph, Alex Reynolds. Created using Sphinx 1.8.6 with the better theme. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bedops --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bedops 2.4.19 0 +--------------- +file name : bedops-2.4.19-0.tar.bz2 +name : bedops +version : 2.4.19 +build : 0 +build number: 0 +size : 4.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.19-0.tar.bz2 +md5 : 45a2ac36948dea97a407cab8d1c73ee8 +dependencies: + - libgcc >=4.8.2 + + +bedops 2.4.20 0 +--------------- +file name : bedops-2.4.20-0.tar.bz2 +name : bedops +version : 2.4.20 +build : 0 +build number: 0 +size : 1.3 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.20-0.tar.bz2 +md5 : 56fca9c799a7ef34c631dc582c7e9988 +dependencies: + - libgcc + + +bedops 2.4.21 0 +--------------- +file name : bedops-2.4.21-0.tar.bz2 +name : bedops +version : 2.4.21 +build : 0 +build number: 0 +size : 1.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.21-0.tar.bz2 +md5 : 5c45636d5107e58378e736ce77c94e89 +dependencies: + - libgcc + + +bedops 2.4.22 0 +--------------- +file name : bedops-2.4.22-0.tar.bz2 +name : bedops +version : 2.4.22 +build : 0 +build number: 0 +size : 1.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.22-0.tar.bz2 +md5 : ba840c1cae9e1c77e68cb0827e5d3749 +dependencies: + - libgcc + + +bedops 2.4.23 0 +--------------- +file name : bedops-2.4.23-0.tar.bz2 +name : bedops +version : 2.4.23 +build : 0 +build number: 0 +size : 1.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.23-0.tar.bz2 +md5 : bd78ca034d4033e6a6c5fdb451d01651 +dependencies: + - libgcc + + +bedops 2.4.24 0 +--------------- +file name : bedops-2.4.24-0.tar.bz2 +name : bedops +version : 2.4.24 +build : 0 +build number: 0 +size : 1.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.24-0.tar.bz2 +md5 : 5253313712f68cb95abc29e17cb1a28d +dependencies: + - libgcc + + +bedops 2.4.25 0 +--------------- +file name : bedops-2.4.25-0.tar.bz2 +name : bedops +version : 2.4.25 +build : 0 +build number: 0 +size : 1.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.25-0.tar.bz2 +md5 : 575b6f947a7ec368d9b4056fa39fe4e5 +dependencies: + - libgcc + + +bedops 2.4.26 0 +--------------- +file name : bedops-2.4.26-0.tar.bz2 +name : bedops +version : 2.4.26 +build : 0 +build number: 0 +size : 1.5 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.26-0.tar.bz2 +md5 : 36f3ce13a04d1639ce66bd1e2bc6cdd4 +dependencies: + - libgcc + + +bedops 2.4.27 0 +--------------- +file name : bedops-2.4.27-0.tar.bz2 +name : bedops +version : 2.4.27 +build : 0 +build number: 0 +size : 2.2 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.27-0.tar.bz2 +md5 : b809e57e15b4dbc67dc9e73d9995c6ab +dependencies: + - libgcc + + +bedops 2.4.30 0 +--------------- +file name : bedops-2.4.30-0.tar.bz2 +name : bedops +version : 2.4.30 +build : 0 +build number: 0 +size : 2.2 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.30-0.tar.bz2 +md5 : 2577e9299989c0886e89713c73875988 +dependencies: + - libgcc + + +bedops 2.4.32 0 +--------------- +file name : bedops-2.4.32-0.tar.bz2 +name : bedops +version : 2.4.32 +build : 0 +build number: 0 +size : 8.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.32-0.tar.bz2 +md5 : 242f39dfcba1c3805142e764f9c420b4 +dependencies: + - libgcc + + +bedops 2.4.33 0 +--------------- +file name : bedops-2.4.33-0.tar.bz2 +name : bedops +version : 2.4.33 +build : 0 +build number: 0 +size : 8.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.33-0.tar.bz2 +md5 : 52f9d6af93722b287ba8409a1ddbdfb1 +dependencies: + - libgcc + + +bedops 2.4.34 0 +--------------- +file name : bedops-2.4.34-0.tar.bz2 +name : bedops +version : 2.4.34 +build : 0 +build number: 0 +size : 8.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.34-0.tar.bz2 +md5 : 89aa273e077a73916c64631967c3404c +dependencies: + - libgcc + + +bedops 2.4.35 0 +--------------- +file name : bedops-2.4.35-0.tar.bz2 +name : bedops +version : 2.4.35 +build : 0 +build number: 0 +size : 8.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.35-0.tar.bz2 +md5 : d78241332e704e13466424af6278e9c3 +dependencies: + - libgcc + + +bedops 2.4.35 h2d50403_1 +------------------------ +file name : bedops-2.4.35-h2d50403_1.tar.bz2 +name : bedops +version : 2.4.35 +build : h2d50403_1 +build number: 1 +size : 8.3 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.35-h2d50403_1.tar.bz2 +md5 : d029e15fc2eae7953e1f52697f27b713 +timestamp : 2018-07-03 07:27:11 UTC +dependencies: + - libstdcxx-ng >=4.9 + + +bedops 2.4.35 h6bb024c_2 +------------------------ +file name : bedops-2.4.35-h6bb024c_2.tar.bz2 +name : bedops +version : 2.4.35 +build : h6bb024c_2 +build number: 2 +size : 8.9 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.35-h6bb024c_2.tar.bz2 +md5 : 14c8863bd833cfcc7a1bd4860bc613ec +timestamp : 2019-04-26 08:22:16 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +bedops 2.4.36 h6bb024c_0 +------------------------ +file name : bedops-2.4.36-h6bb024c_0.tar.bz2 +name : bedops +version : 2.4.36 +build : h6bb024c_0 +build number: 0 +size : 9.1 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.36-h6bb024c_0.tar.bz2 +md5 : 53a29db402c962ad05ca2672c35a74ac +timestamp : 2019-05-03 22:03:43 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +bedops 2.4.36 h6bb024c_1 +------------------------ +file name : bedops-2.4.36-h6bb024c_1.tar.bz2 +name : bedops +version : 2.4.36 +build : h6bb024c_1 +build number: 1 +size : 9.0 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.36-h6bb024c_1.tar.bz2 +md5 : 0025cfb4a95a2bd0702aa4748fc17604 +timestamp : 2019-05-22 02:53:52 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - samtools + + +bedops 2.4.37 hc9558a2_0 +------------------------ +file name : bedops-2.4.37-hc9558a2_0.tar.bz2 +name : bedops +version : 2.4.37 +build : hc9558a2_0 +build number: 0 +size : 9.0 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.37-hc9558a2_0.tar.bz2 +md5 : aab6f7123b4f0f20e20a9391527d2fa9 +timestamp : 2019-10-12 05:30:59 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - samtools + + +bedops 2.4.38 hc9558a2_0 +------------------------ +file name : bedops-2.4.38-hc9558a2_0.tar.bz2 +name : bedops +version : 2.4.38 +build : hc9558a2_0 +build number: 0 +size : 9.0 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.38-hc9558a2_0.tar.bz2 +md5 : 1bc8cbe7d8ff717e30e255e7c18cd16c +timestamp : 2020-04-02 07:44:05 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - samtools + + +bedops 2.4.39 h7d875b9_1 +------------------------ +file name : bedops-2.4.39-h7d875b9_1.tar.bz2 +name : bedops +version : 2.4.39 +build : h7d875b9_1 +build number: 1 +size : 9.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.39-h7d875b9_1.tar.bz2 +md5 : d35bd7b8e442e99930492f3cab1129d8 +timestamp : 2021-04-01 10:49:55 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - samtools + + +bedops 2.4.39 hc9558a2_0 +------------------------ +file name : bedops-2.4.39-hc9558a2_0.tar.bz2 +name : bedops +version : 2.4.39 +build : hc9558a2_0 +build number: 0 +size : 9.1 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.39-hc9558a2_0.tar.bz2 +md5 : ba1187bd8b16aa332fc9949158970d20 +timestamp : 2020-04-07 08:32:36 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - samtools + + +bedops 2.4.40 h9f5acd7_0 +------------------------ +file name : bedops-2.4.40-h9f5acd7_0.tar.bz2 +name : bedops +version : 2.4.40 +build : h9f5acd7_0 +build number: 0 +size : 10.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.40-h9f5acd7_0.tar.bz2 +md5 : 6defd1d9128821c714212a7bc4ff82bf +timestamp : 2022-07-04 14:24:58 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - samtools + + +bedops 2.4.41 h4ac6f70_1 +------------------------ +file name : bedops-2.4.41-h4ac6f70_1.tar.bz2 +name : bedops +version : 2.4.41 +build : h4ac6f70_1 +build number: 1 +size : 10.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.41-h4ac6f70_1.tar.bz2 +md5 : e5f26003751720877b5a157c6c490834 +timestamp : 2023-05-27 22:31:16 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - samtools + + +bedops 2.4.41 h4ac6f70_2 +------------------------ +file name : bedops-2.4.41-h4ac6f70_2.tar.bz2 +name : bedops +version : 2.4.41 +build : h4ac6f70_2 +build number: 2 +size : 10.5 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.41-h4ac6f70_2.tar.bz2 +md5 : bc0c400539a8809589b3f2584a07571e +timestamp : 2024-03-20 10:32:49 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - samtools + + +bedops 2.4.41 h9948957_3 +------------------------ +file name : bedops-2.4.41-h9948957_3.tar.bz2 +name : bedops +version : 2.4.41 +build : h9948957_3 +build number: 3 +size : 10.5 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.41-h9948957_3.tar.bz2 +md5 : 686bffd5fe7d8935465d79627ff655e6 +timestamp : 2024-12-15 18:16:28 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + - samtools + + +bedops 2.4.41 h9f5acd7_0 +------------------------ +file name : bedops-2.4.41-h9f5acd7_0.tar.bz2 +name : bedops +version : 2.4.41 +build : h9f5acd7_0 +build number: 0 +size : 10.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.41-h9f5acd7_0.tar.bz2 +md5 : 19912c6cd12e4d66cea791ae905ed4f4 +timestamp : 2022-07-14 09:09:14 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - samtools + + +bedops 2. diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/biobambam.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/biobambam.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d634ef635b3890e16d3d38c5b6f4fba11a35b8c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/biobambam.manual_bundle.txt @@ -0,0 +1,456 @@ +# Tool: biobambam +software_name: biobambam +tier: T1 +domain: t1_backfill_overall +downloads: 119590 +summary: Tools for early stage alignment file processing. +description: Tools for early stage alignment file processing. +dependencies: gmp >=6.3.0,<7.0a0, libgcc >=13, libmaus2 >=2.0.813, libmaus2 >=2.0.813,<3.0a0, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, xerces-c >=3.2.5,<3.3.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://gitlab.com/german.tischler/biobambam2 +doc_url: +dev_url: https://gitlab.com/german.tischler/biobambam2 + +## Conda Search Info +$ conda search -c bioconda -c conda-forge biobambam --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +biobambam 2.0.25 0 +------------------ +file name : biobambam-2.0.25-0.tar.bz2 +name : biobambam +version : 2.0.25 +build : 0 +build number: 0 +size : 13.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.25-0.tar.bz2 +md5 : 46a37f9e889c3865bf64f9404a1ac9e5 +dependencies: [] + + +biobambam 2.0.39 0 +------------------ +file name : biobambam-2.0.39-0.tar.bz2 +name : biobambam +version : 2.0.39 +build : 0 +build number: 0 +size : 15.0 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.39-0.tar.bz2 +md5 : 4a860111d249d61da98d1d7733bb227d +dependencies: [] + + +biobambam 2.0.42 0 +------------------ +file name : biobambam-2.0.42-0.tar.bz2 +name : biobambam +version : 2.0.42 +build : 0 +build number: 0 +size : 15.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.42-0.tar.bz2 +md5 : 26b76d132cfdb17b1d1735f9f0392397 +dependencies: [] + + +biobambam 2.0.44 0 +------------------ +file name : biobambam-2.0.44-0.tar.bz2 +name : biobambam +version : 2.0.44 +build : 0 +build number: 0 +size : 15.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.44-0.tar.bz2 +md5 : 1d3f23fff5c8fd5cd59ffe0119b814d9 +dependencies: [] + + +biobambam 2.0.57 0 +------------------ +file name : biobambam-2.0.57-0.tar.bz2 +name : biobambam +version : 2.0.57 +build : 0 +build number: 0 +size : 16.1 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.57-0.tar.bz2 +md5 : 6967c1e021c9d9c3ca3bc6fcb3ba9478 +dependencies: [] + + +biobambam 2.0.58 0 +------------------ +file name : biobambam-2.0.58-0.tar.bz2 +name : biobambam +version : 2.0.58 +build : 0 +build number: 0 +size : 15.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.58-0.tar.bz2 +md5 : 6cf8c090e46eaa549e71713cf8a415f1 +dependencies: [] + + +biobambam 2.0.62 0 +------------------ +file name : biobambam-2.0.62-0.tar.bz2 +name : biobambam +version : 2.0.62 +build : 0 +build number: 0 +size : 16.0 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.62-0.tar.bz2 +md5 : 4a1a4090e419586af76ee06e1aaeedc2 +dependencies: [] + + +biobambam 2.0.72 0 +------------------ +file name : biobambam-2.0.72-0.tar.bz2 +name : biobambam +version : 2.0.72 +build : 0 +build number: 0 +size : 16.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.72-0.tar.bz2 +md5 : 5bebc593b1495e1779a9ed583f953304 +dependencies: [] + + +biobambam 2.0.78 0 +------------------ +file name : biobambam-2.0.78-0.tar.bz2 +name : biobambam +version : 2.0.78 +build : 0 +build number: 0 +size : 17.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.78-0.tar.bz2 +md5 : b13650d85c8c7dc87c84973822f0cf40 +dependencies: [] + + +biobambam 2.0.79 0 +------------------ +file name : biobambam-2.0.79-0.tar.bz2 +name : biobambam +version : 2.0.79 +build : 0 +build number: 0 +size : 19.1 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.79-0.tar.bz2 +md5 : 1209b6394291f1063c18fd8e8d1d4549 +dependencies: [] + + +biobambam 2.0.87 0 +------------------ +file name : biobambam-2.0.87-0.tar.bz2 +name : biobambam +version : 2.0.87 +build : 0 +build number: 0 +size : 19.1 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.87-0.tar.bz2 +md5 : 87a150ed26a8edda38ba021b1fe29b79 +dependencies: [] + + +biobambam 2.0.87 1 +------------------ +file name : biobambam-2.0.87-1.tar.bz2 +name : biobambam +version : 2.0.87 +build : 1 +build number: 1 +size : 19.1 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.87-1.tar.bz2 +md5 : 1ddb0afcd9fc7c3b1349eda278beba86 +timestamp : 2018-07-03 02:20:40 UTC +dependencies: [] + + +biobambam 2.0.87 h516909a_2 +--------------------------- +file name : biobambam-2.0.87-h516909a_2.tar.bz2 +name : biobambam +version : 2.0.87 +build : h516909a_2 +build number: 2 +size : 18.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.87-h516909a_2.tar.bz2 +md5 : 54c29e929e8215a33ef7d5546b88bea7 +timestamp : 2020-08-13 11:13:48 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +biobambam 2.0.179 h7d875b9_1 +---------------------------- +file name : biobambam-2.0.179-h7d875b9_1.tar.bz2 +name : biobambam +version : 2.0.179 +build : h7d875b9_1 +build number: 1 +size : 22.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.179-h7d875b9_1.tar.bz2 +md5 : 56669f8ee6c5d01eddd3118a6911815f +timestamp : 2021-03-28 09:17:56 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libmaus2 + - libstdcxx-ng >=9.3.0 + + +biobambam 2.0.179 hc9558a2_0 +---------------------------- +file name : biobambam-2.0.179-hc9558a2_0.tar.bz2 +name : biobambam +version : 2.0.179 +build : hc9558a2_0 +build number: 0 +size : 19.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.179-hc9558a2_0.tar.bz2 +md5 : 807e5ec9d83a0a0845ba349f44d3d384 +timestamp : 2021-03-12 16:28:18 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libmaus2 + - libstdcxx-ng >=7.5.0 + + +biobambam 2.0.180 h7d875b9_1 +---------------------------- +file name : biobambam-2.0.180-h7d875b9_1.tar.bz2 +name : biobambam +version : 2.0.180 +build : h7d875b9_1 +build number: 1 +size : 22.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.180-h7d875b9_1.tar.bz2 +md5 : 8c73a7a009740bafbe01b8f267ae76ba +timestamp : 2021-03-31 22:32:24 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libmaus2 >=2.0.774 + - libstdcxx-ng >=9.3.0 + + +biobambam 2.0.180 hc9558a2_0 +---------------------------- +file name : biobambam-2.0.180-hc9558a2_0.tar.bz2 +name : biobambam +version : 2.0.180 +build : hc9558a2_0 +build number: 0 +size : 21.1 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.180-hc9558a2_0.tar.bz2 +md5 : 9d9b0101709ab1dcecc93b3219b63938 +timestamp : 2021-03-24 10:51:44 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libmaus2 >=2.0.774 + - libstdcxx-ng >=7.5.0 + + +biobambam 2.0.182 h7d875b9_0 +---------------------------- +file name : biobambam-2.0.182-h7d875b9_0.tar.bz2 +name : biobambam +version : 2.0.182 +build : h7d875b9_0 +build number: 0 +size : 22.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.182-h7d875b9_0.tar.bz2 +md5 : ea5aec9969d6f922522cee0976e4feff +timestamp : 2021-04-21 13:03:34 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libmaus2 >=2.0.777 + - libstdcxx-ng >=9.3.0 + + +biobambam 2.0.182 h9f5acd7_1 +---------------------------- +file name : biobambam-2.0.182-h9f5acd7_1.tar.bz2 +name : biobambam +version : 2.0.182 +build : h9f5acd7_1 +build number: 1 +size : 21.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.182-h9f5acd7_1.tar.bz2 +md5 : 4d249b4b666cf4b011ad1259c5d275ab +timestamp : 2022-02-23 11:30:46 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libmaus2 >=2.0.777 + - libstdcxx-ng >=10.3.0 + + +biobambam 2.0.183 h4ac6f70_3 +---------------------------- +file name : biobambam-2.0.183-h4ac6f70_3.tar.bz2 +name : biobambam +version : 2.0.183 +build : h4ac6f70_3 +build number: 3 +size : 21.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h4ac6f70_3.tar.bz2 +md5 : 679768a5b2b79a198cc0a57e4ac427d2 +timestamp : 2023-05-17 06:52:43 UTC +dependencies: + - libgcc-ng >=12 + - libmaus2 >=2.0.810,<2.1.0a0 + - libstdcxx-ng >=12 + + +biobambam 2.0.183 h4ac6f70_4 +---------------------------- +file name : biobambam-2.0.183-h4ac6f70_4.tar.bz2 +name : biobambam +version : 2.0.183 +build : h4ac6f70_4 +build number: 4 +size : 21.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h4ac6f70_4.tar.bz2 +md5 : b440f7302f8b51b1747a51a046a35c4c +timestamp : 2024-04-18 05:45:57 UTC +dependencies: + - libgcc-ng >=12 + - libmaus2 >=2.0.810,<2.1.0a0 + - libstdcxx-ng >=12 + + +biobambam 2.0.183 h9f5acd7_0 +---------------------------- +file name : biobambam-2.0.183-h9f5acd7_0.tar.bz2 +name : biobambam +version : 2.0.183 +build : h9f5acd7_0 +build number: 0 +size : 21.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h9f5acd7_0.tar.bz2 +md5 : 46ec04b1b6cdac24dc886291dd5231b9 +timestamp : 2022-03-04 10:29:53 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libmaus2 >=2.0.810 + - libstdcxx-ng >=10.3.0 + + +biobambam 2.0.183 h9f5acd7_1 +---------------------------- +file name : biobambam-2.0.183-h9f5acd7_1.tar.bz2 +name : biobambam +version : 2.0.183 +build : h9f5acd7_1 +build number: 1 +size : 21.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h9f5acd7_1.tar.bz2 +md5 : be69d68d770f4f093a7399adad8ef994 +timestamp : 2022-03-12 10:02:19 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libmaus2 >=2.0.810 + - libstdcxx-ng >=10.3.0 + + +biobambam 2.0.183 h9f5acd7_2 +---------------------------- +file name : biobambam-2.0.183-h9f5acd7_2.tar.bz2 +name : biobambam +version : 2.0.183 +build : h9f5acd7_2 +build number: 2 +size : 21.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h9f5acd7_2.tar.bz2 +md5 : 2f65c8ca2ee49978c66201aa1b292781 +timestamp : 2022-08-09 14:44:50 UTC +dependencies: + - libgcc-ng >=12 + - libmaus2 >=2.0.810,<2.1.0a0 + - libstdcxx-ng >=12 + + +biobambam 2.0.185 h02148a2_0 +---------------------------- +file name : biobambam-2.0.185-h02148a2_0.tar.bz2 +name : biobambam +version : 2.0.185 +build : h02148a2_0 +build number: 0 +size : 21.3 MB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.185-h02148a2_0.tar.bz2 +md5 : aaa114d0dc3f75f6984cdcd32f4ebe9c +timestamp : 2024-11-18 10:15:06 UTC +dependencies: + - gmp >=6.3.0,<7.0a0 + - libgcc >=12 + - libmaus2 >=2.0.813 + - libmaus2 >=2.0.813,<3.0a0 + - libstdcxx >=12 + - libzlib >=1.2.13,<2.0a0 + - xerces-c >=3.2.5,<3.3.0a0 + + +biobambam 2.0.185 h85de650_1 +---------------------------- +file name : biobambam-2.0.185-h85de650_1.tar.bz2 +name : biobambam +version : 2.0.185 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-alabaster.sfe.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-alabaster.sfe.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c7c7a8d73131cd596d3f080fdfe2b70a896b349e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-alabaster.sfe.manual_bundle.txt @@ -0,0 +1,56 @@ +# Tool: bioconductor-alabaster.sfe +software_name: bioconductor-alabaster.sfe +tier: T1 +domain: spatial_transcriptomics +downloads: 32 +summary: Language agnostic on disk serialization of SpatialFeatureExperiment +description: Builds upon the existing ArtifactDB project, expending alabaster.spatial for language agnostic on disk serialization of SpatialFeatureExperiment. +dependencies: bioconductor-alabaster.base >=1.10.0,<1.11.0, bioconductor-alabaster.sce >=1.10.0,<1.11.0, bioconductor-alabaster.spatial >=1.10.0,<1.11.0, bioconductor-ebimage >=4.52.0,<4.53.0, bioconductor-rbioformats >=1.10.0,<1.11.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialfeatureexperiment >=1.12.0,<1.13.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-jsonlite, r-sfarrow, r-spatialreg, r-spdep, r-terra, r-xml2 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/alabaster.sfe.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/alabaster.sfe.html +Bioconductor - alabaster.sfe Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages alabaster.sfe alabaster.sfe This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see alabaster.sfe . Language agnostic on disk serialization of SpatialFeatureExperiment DOI: 10.18129/B9.bioc.alabaster.sfe Bioconductor version: 3.22 Builds upon the existing ArtifactDB project, expending alabaster.spatial for language agnostic on disk serialization of SpatialFeatureExperiment. Author: Lambda Moses [aut, cre] ORCID: 0000-0002-7092-9427 Maintainer: Lambda Moses <dl3764 at columbia.edu> Citation (from within R, enter citation("alabaster.sfe") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("alabaster.sfe") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("alabaster.sfe") Overview HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataRepresentation , Software , Spatial Version 1.2.0 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License MIT + file LICENSE Depends R (>= 4.1.0), SpatialFeatureExperiment (>= 1.9.3), alabaster.base Imports alabaster.sce , alabaster.spatial (>= 1.5.2), EBImage , jsonlite , methods, RBioFormats , S4Vectors , sfarrow , SingleCellExperiment , spatialreg , spdep , SummarizedExperiment , terra , xml2 System Requirements URL https://pachterlab.github.io/alabaster.sfe/ Bug Reports https://github.com/pachterlab/alabaster.sfe/issues See More Suggests BiocStyle , fs , knitr , rmarkdown , scater , sf , SFEData , testthat (>= 3.0.0), Voyager (>= 1.9.1) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package alabaster.sfe_1.2.0.tar.gz Windows Binary (x86_64) alabaster.sfe_1.2.0.zip macOS Binary (x86_64) macOS Binary (arm64) Source Repository git clone https://git.bioconductor.org/packages/alabaster.sfe Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/alabaster.sfe Bioc Package Browser https://code.bioconductor.org/browse/alabaster.sfe/ Package Short Url https://bioconductor.org/packages/alabaster.sfe/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-alabaster.sfe --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-alabaster.sfe 1.2.0 r45hdfd78af_0 +---------------------------------------------- +file name : bioconductor-alabaster.sfe-1.2.0-r45hdfd78af_0.conda +name : bioconductor-alabaster.sfe +version : 1.2.0 +build : r45hdfd78af_0 +build number: 0 +size : 2.8 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-alabaster.sfe-1.2.0-r45hdfd78af_0.conda +md5 : 779ed397cda34addebaef28746554e9e +timestamp : 2026-03-15 00:28:16 UTC +dependencies: + - bioconductor-alabaster.base >=1.10.0,<1.11.0 + - bioconductor-alabaster.sce >=1.10.0,<1.11.0 + - bioconductor-alabaster.spatial >=1.10.0,<1.11.0 + - bioconductor-ebimage >=4.52.0,<4.53.0 + - bioconductor-rbioformats >=1.10.0,<1.11.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialfeatureexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-jsonlite + - r-sfarrow + - r-spatialreg + - r-spdep + - r-terra + - r-xml2 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-banksy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-banksy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..de7a4140507d6a8c485f6355fd367cc7d386d392 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-banksy.manual_bundle.txt @@ -0,0 +1,60 @@ +# Tool: bioconductor-banksy +software_name: bioconductor-banksy +tier: T1 +domain: spatial_transcriptomics +downloads: 66 +summary: Spatial transcriptomic clustering +description: Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation. +dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-genomeinfodb >=1.46.0,<1.47.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-aricode, r-base >=4.5,<4.6.0a0, r-data.table, r-dbscan, r-igraph, r-irlba, r-leidenalg >=1.1.0, r-matrix, r-mclust, r-rcpphungarian, r-uwot +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/Banksy.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/Banksy.html +Bioconductor - Banksy Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages Banksy Banksy This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see Banksy . Spatial transcriptomic clustering DOI: 10.18129/B9.bioc.Banksy Bioconductor version: 3.22 Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation. Author: Vipul Singhal [aut], Joseph Lee [aut, cre] ORCID: 0000-0002-4983-4714 Maintainer: Joseph Lee <joseph.lee at u.nus.edu> Citation (from within R, enter citation("Banksy") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Banksy") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("Banksy") Domain segmentation (STARmap PLUS mouse brain) HTML R Script Multi-sample analysis (10x Visium Human DLPFC) HTML R Script Parameter selection (VeraFISH Mouse Hippocampus) HTML R Script Spatial data integration with Harmony (10x Visium Human DLPFC) HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews Clustering , DimensionReduction , GeneExpression , SingleCell , Software , Spatial Version 1.6.0 In Bioconductor since BioC 3.19 (R-4.4) (2 years) License file LICENSE Depends R (>= 4.4.0) Imports aricode , BiocParallel , data.table , dbscan , SpatialExperiment , SingleCellExperiment , SummarizedExperiment , S4Vectors , stats, Matrix , MatrixGenerics , mclust , igraph , irlba , leidenAlg (>= 1.1.0), utils, uwot , RcppHungarian , GenomeInfoDb System Requirements URL https://github.com/prabhakarlab/Banksy Bug Reports https://github.com/prabhakarlab/Banksy/issues See More Suggests knitr , rmarkdown , pals , scuttle , scater , scran , cowplot , ggplot2 , testthat (>= 3.0.0), harmony , Seurat , ExperimentHub , spatialLIBD , BiocStyle Linking To Enhances Depends On Me Imports Me OSTA Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package Banksy_1.6.0.tar.gz Windows Binary (x86_64) Banksy_1.6.0.zip (64-bit only) macOS Binary (x86_64) Banksy_1.6.0.tgz macOS Binary (arm64) Banksy_1.6.0.tgz Source Repository git clone https://git.bioconductor.org/packages/Banksy Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Banksy Bioc Package Browser https://code.bioconductor.org/browse/Banksy/ Package Short Url https://bioconductor.org/packages/Banksy/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-banksy --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-banksy 1.6.0 r45hdfd78af_0 +--------------------------------------- +file name : bioconductor-banksy-1.6.0-r45hdfd78af_0.conda +name : bioconductor-banksy +version : 1.6.0 +build : r45hdfd78af_0 +build number: 0 +size : 3.1 MB +license : file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-banksy-1.6.0-r45hdfd78af_0.conda +md5 : de8878bdca7f4846adba7a5b97440f2a +timestamp : 2026-03-15 00:05:11 UTC +dependencies: + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-genomeinfodb >=1.46.0,<1.47.0 + - bioconductor-matrixgenerics >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-aricode + - r-base >=4.5,<4.6.0a0 + - r-data.table + - r-dbscan + - r-igraph + - r-irlba + - r-leidenalg >=1.1.0 + - r-matrix + - r-mclust + - r-rcpphungarian + - r-uwot diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-benchdamic.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-benchdamic.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e786d52000e0ddfa692af893f5a4bd8227bc911b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-benchdamic.manual_bundle.txt @@ -0,0 +1,145 @@ +# Tool: bioconductor-benchdamic +software_name: bioconductor-benchdamic +tier: T1 +domain: single_cell +downloads: 6358 +summary: Benchmark of differential abundance methods on microbiome data +description: Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization. +dependencies: bioconductor-aldex2 >=1.32.0,<1.33.0, bioconductor-ancombc >=2.2.0,<2.3.0, bioconductor-biocparallel >=1.34.0,<1.35.0, bioconductor-dearseq >=1.12.0,<1.13.0, bioconductor-deseq2 >=1.40.0,<1.41.0, bioconductor-edger >=3.42.0,<3.43.0, bioconductor-limma >=3.56.0,<3.57.0, bioconductor-mast >=1.26.0,<1.27.0, bioconductor-metagenomeseq >=1.42.0,<1.43.0, bioconductor-noiseq >=2.44.0,<2.45.0, bioconductor-phyloseq >=1.44.0,<1.45.0, bioconductor-summarizedexperiment >=1.30.0,<1.31.0, bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0, bioconductor-zinbwave >=1.22.0,<1.23.0, r-base >=4.3,<4.4.0a0, r-corncob, r-cowplot, r-ggdendro, r-ggplot2, r-ggridges, r-lme4, r-mglm, r-plyr, r-rcolorbrewer, r-reshape2, r-seurat, r-tidytext +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.14/bioc/html/benchdamic.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.14/bioc/html/benchdamic.html +Bioconductor - benchdamic About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.14 Software Packages benchdamic benchdamic This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see benchdamic . Benchmark of differential abundance methods on microbiome data DOI: 10.18129/B9.bioc.benchdamic Bioconductor version: 3.14 Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization. Author: Matteo Calgaro [aut, cre] Maintainer: Matteo Calgaro <mcalgaro93 at gmail.com> Citation (from within R, enter citation("benchdamic") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("benchdamic") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("benchdamic") Intro HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DifferentialExpression , Metagenomics , Microbiome , MultipleComparison , Normalization , Preprocessing , Software Version 1.0.0 In Bioconductor since BioC 3.14 (R-4.1) (2.5 years) License Artistic-2.0 Depends R (>= 4.1.0) Imports stats, stats4, utils, methods, phyloseq , BiocParallel , zinbwave , edgeR , DESeq2 , limma , ALDEx2 , corncob, SummarizedExperiment , MAST , Seurat, metagenomeSeq , MGLM, ggplot2, RColorBrewer, plyr, ffpe , reshape2, ggdendro, graphics, cowplot System Requirements URL Bug Reports https://github.com/mcalgaro93/benchdamic/issues See More Suggests knitr, rmarkdown, HMP16SData , curatedMetagenomicData , BiocStyle , testthat Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package benchdamic_1.0.0.tar.gz Windows Binary benchdamic_1.0.0.zip macOS 10.13 (High Sierra) benchdamic_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/benchdamic Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/benchdamic Bioc Package Browser https://code.bioconductor.org/browse/benchdamic/ Package Short Url https://bioconductor.org/packages/benchdamic/ Package Downloads Report Download Stats Old Source Packages for BioC 3.14 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-benchdamic --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-benchdamic 1.0.0 r41hdfd78af_0 +------------------------------------------- +file name : bioconductor-benchdamic-1.0.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-benchdamic +version : 1.0.0 +build : r41hdfd78af_0 +build number: 0 +size : 2.2 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-benchdamic-1.0.0-r41hdfd78af_0.tar.bz2 +md5 : 4d364ff15ef0429072343cf194e0c58c +timestamp : 2021-11-11 08:58:48 UTC +dependencies: + - bioconductor-aldex2 >=1.26.0,<1.27.0 + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - bioconductor-deseq2 >=1.34.0,<1.35.0 + - bioconductor-edger >=3.36.0,<3.37.0 + - bioconductor-ffpe >=1.38.0,<1.39.0 + - bioconductor-limma >=3.50.0,<3.51.0 + - bioconductor-mast >=1.20.0,<1.21.0 + - bioconductor-metagenomeseq >=1.36.0,<1.37.0 + - bioconductor-phyloseq >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - bioconductor-zinbwave >=1.16.0,<1.17.0 + - r-base >=4.1,<4.2.0a0 + - r-corncob + - r-cowplot + - r-ggdendro + - r-ggplot2 + - r-mglm + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-seurat + + +bioconductor-benchdamic 1.4.0 r42hdfd78af_0 +------------------------------------------- +file name : bioconductor-benchdamic-1.4.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-benchdamic +version : 1.4.0 +build : r42hdfd78af_0 +build number: 0 +size : 4.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-benchdamic-1.4.0-r42hdfd78af_0.tar.bz2 +md5 : 006319896db140041670bca30798be68 +timestamp : 2022-11-10 04:38:45 UTC +dependencies: + - bioconductor-aldex2 >=1.30.0,<1.31.0 + - bioconductor-ancombc >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.32.0,<1.33.0 + - bioconductor-dearseq >=1.10.0,<1.11.0 + - bioconductor-deseq2 >=1.38.0,<1.39.0 + - bioconductor-edger >=3.40.0,<3.41.0 + - bioconductor-limma >=3.54.0,<3.55.0 + - bioconductor-mast >=1.24.0,<1.25.0 + - bioconductor-metagenomeseq >=1.40.0,<1.41.0 + - bioconductor-noiseq >=2.42.0,<2.43.0 + - bioconductor-phyloseq >=1.42.0,<1.43.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - bioconductor-treesummarizedexperiment >=2.6.0,<2.7.0 + - bioconductor-zinbwave >=1.20.0,<1.21.0 + - r-base >=4.2,<4.3.0a0 + - r-corncob + - r-cowplot + - r-ggdendro + - r-ggplot2 + - r-ggridges + - r-mglm + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-seurat + - r-tidytext + + +bioconductor-benchdamic 1.6.0 r43hdfd78af_0 +------------------------------------------- +file name : bioconductor-benchdamic-1.6.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-benchdamic +version : 1.6.0 +build : r43hdfd78af_0 +build number: 0 +size : 4.2 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-benchdamic-1.6.0-r43hdfd78af_0.tar.bz2 +md5 : 3edf7c67ea4255d0908c4687651e2950 +timestamp : 2023-07-18 16:51:05 UTC +dependencies: + - bioconductor-aldex2 >=1.32.0,<1.33.0 + - bioconductor-ancombc >=2.2.0,<2.3.0 + - bioconductor-biocparallel >=1.34.0,<1.35.0 + - bioconductor-dearseq >=1.12.0,<1.13.0 + - bioconductor-deseq2 >=1.40.0,<1.41.0 + - bioconductor-edger >=3.42.0,<3.43.0 + - bioconductor-limma >=3.56.0,<3.57.0 + - bioconductor-mast >=1.26.0,<1.27.0 + - bioconductor-metagenomeseq >=1.42.0,<1.43.0 + - bioconductor-noiseq >=2.44.0,<2.45.0 + - bioconductor-phyloseq >=1.44.0,<1.45.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0 + - bioconductor-zinbwave >=1.22.0,<1.23.0 + - r-base >=4.3,<4.4.0a0 + - r-corncob + - r-cowplot + - r-ggdendro + - r-ggplot2 + - r-ggridges + - r-lme4 + - r-mglm + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-seurat + - r-tidytext diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biocbaseutils.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biocbaseutils.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..25565f3412c3b77949027088459fd245c61721ca --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biocbaseutils.manual_bundle.txt @@ -0,0 +1,108 @@ +# Tool: bioconductor-biocbaseutils +software_name: bioconductor-biocbaseutils +tier: T1 +domain: t1_backfill_overall +downloads: 185514 +summary: General utility functions for developing Bioconductor packages +description: The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem. +dependencies: r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.16/bioc/html/BiocBaseUtils.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.16/bioc/html/BiocBaseUtils.html +Bioconductor - BiocBaseUtils About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Software Packages BiocBaseUtils BiocBaseUtils This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BiocBaseUtils . General utility functions for developing Bioconductor packages DOI: 10.18129/B9.bioc.BiocBaseUtils Bioconductor version: 3.16 The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem. Author: Marcel Ramos [aut, cre] , Martin Morgan [ctb], Hervé Pagès [ctb] Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org> Citation (from within R, enter citation("BiocBaseUtils") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BiocBaseUtils") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("BiocBaseUtils") BiocBaseUtils Quick Start HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Infrastructure , Software Version 1.0.0 In Bioconductor since BioC 3.16 (R-4.2) (1.5 years) License Artistic-2.0 Depends R (>= 4.2.0) Imports methods, utils System Requirements URL Bug Reports https://www.github.com/Bioconductor/BiocBaseUtils/issues See More Suggests knitr, rmarkdown, BiocStyle , tinytest Linking To Enhances Depends On Me Imports Me BiocFHIR , DNAfusion , MultiAssayExperiment , TENxIO , UniProt.ws Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package BiocBaseUtils_1.0.0.tar.gz Windows Binary BiocBaseUtils_1.0.0.zip macOS Binary (x86_64) BiocBaseUtils_1.0.0.tgz macOS Binary (arm64) BiocBaseUtils_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/BiocBaseUtils Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocBaseUtils Bioc Package Browser https://code.bioconductor.org/browse/BiocBaseUtils/ Package Short Url https://bioconductor.org/packages/BiocBaseUtils/ Package Downloads Report Download Stats Old Source Packages for BioC 3.16 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-biocbaseutils --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-biocbaseutils 1.0.0 r42hdfd78af_0 +---------------------------------------------- +file name : bioconductor-biocbaseutils-1.0.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-biocbaseutils +version : 1.0.0 +build : r42hdfd78af_0 +build number: 0 +size : 258 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biocbaseutils-1.0.0-r42hdfd78af_0.tar.bz2 +md5 : 0f3515f24a98b90e00f6b9953e56f070 +timestamp : 2022-11-03 08:25:37 UTC +dependencies: + - r-base >=4.2,<4.3.0a0 + + +bioconductor-biocbaseutils 1.2.0 r43hdfd78af_0 +---------------------------------------------- +file name : bioconductor-biocbaseutils-1.2.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-biocbaseutils +version : 1.2.0 +build : r43hdfd78af_0 +build number: 0 +size : 258 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biocbaseutils-1.2.0-r43hdfd78af_0.tar.bz2 +md5 : 63f12ce657dddc1e30f73517b681da6b +timestamp : 2023-07-07 10:48:06 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + + +bioconductor-biocbaseutils 1.4.0 r43hdfd78af_0 +---------------------------------------------- +file name : bioconductor-biocbaseutils-1.4.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-biocbaseutils +version : 1.4.0 +build : r43hdfd78af_0 +build number: 0 +size : 259 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biocbaseutils-1.4.0-r43hdfd78af_0.tar.bz2 +md5 : 5c6865ae9bb4f7bb72001e67947d271c +timestamp : 2023-12-03 20:52:53 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + + +bioconductor-biocbaseutils 1.8.0 r44hdfd78af_0 +---------------------------------------------- +file name : bioconductor-biocbaseutils-1.8.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-biocbaseutils +version : 1.8.0 +build : r44hdfd78af_0 +build number: 0 +size : 272 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biocbaseutils-1.8.0-r44hdfd78af_0.tar.bz2 +md5 : 8989603129d36f81b85d0665e3b29708 +timestamp : 2024-12-14 18:05:38 UTC +dependencies: + - r-base >=4.4,<4.5.0a0 + + +bioconductor-biocbaseutils 1.12.0 r45hdfd78af_0 +----------------------------------------------- +file name : bioconductor-biocbaseutils-1.12.0-r45hdfd78af_0.conda +name : bioconductor-biocbaseutils +version : 1.12.0 +build : r45hdfd78af_0 +build number: 0 +size : 244 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biocbaseutils-1.12.0-r45hdfd78af_0.conda +md5 : 2c13015debedd6c56e5d789ef7ca4db3 +timestamp : 2026-02-06 22:20:04 UTC +dependencies: + - r-base >=4.5,<4.6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biomformat.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biomformat.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa723df6684f312caba0b6743e5cf0622762b1d0 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biomformat.manual_bundle.txt @@ -0,0 +1,433 @@ +# Tool: bioconductor-biomformat +software_name: bioconductor-biomformat +tier: T1 +domain: t1_backfill_overall +downloads: 261080 +summary: An interface package for the BIOM file format +description: This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. +dependencies: bioconductor-rhdf5 >=2.54.0,<2.55.0, r-base >=4.5,<4.6.0a0, r-jsonlite >=0.9.16, r-matrix >=1.2, r-plyr >=1.8 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/biomformat.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/biomformat.html +Bioconductor - biomformat Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages biomformat biomformat This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see biomformat . An interface package for the BIOM file format DOI: 10.18129/B9.bioc.biomformat Bioconductor version: 3.22 This is an R package for interfacing with the BIOM file format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. Author: Paul J. McMurdie [aut, cre], Joseph N. Paulson [aut] Maintainer: Paul J. McMurdie <joey711 at gmail.com> Citation (from within R, enter citation("biomformat") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("biomformat") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("biomformat") The biomformat package Vignette HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataImport , ImmunoOncology , Metagenomics , Microbiome , Software Version 1.38.3 In Bioconductor since BioC 3.3 (R-3.3) (10 years) License GPL-2 Depends R (>= 4.1), methods Imports jsonlite (>= 0.9.16), Matrix (>= 1.7-0) System Requirements URL https://github.com/joey711/biomformat/ http://biom-format.org/ Bug Reports https://github.com/joey711/biomformat/issues See More Suggests testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7), rhdf5 Linking To Enhances Depends On Me Imports Me microbiomeExplorer , phyloseq Suggests Me animalcules , iSEEtree , metagenomeSeq , MGnifyR , mia , MicrobiotaProcess , MetaScope Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package biomformat_1.38.3.tar.gz Windows Binary (x86_64) biomformat_1.38.3.zip macOS Binary (x86_64) biomformat_1.38.3.tgz macOS Binary (arm64) biomformat_1.38.3.tgz Source Repository git clone https://git.bioconductor.org/packages/biomformat Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/biomformat Bioc Package Browser https://code.bioconductor.org/browse/biomformat/ Package Short Url https://bioconductor.org/packages/biomformat/ Package Downloads Report Download Stats Old Source Packages for BioC 3.22 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-biomformat --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-biomformat 1.0.2 0 +------------------------------- +file name : bioconductor-biomformat-1.0.2-0.tar.bz2 +name : bioconductor-biomformat +version : 1.0.2 +build : 0 +build number: 0 +size : 175 KB +license : AGPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.0.2-0.tar.bz2 +md5 : d1a2d06babb85c8e83d071325d590ba3 +dependencies: + - bioconductor-biobase + - bioconductor-rhdf5 >=2.16.0 + - r >=3.2.0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.0.2 r3.3.1_1 +-------------------------------------- +file name : bioconductor-biomformat-1.0.2-r3.3.1_1.tar.bz2 +name : bioconductor-biomformat +version : 1.0.2 +build : r3.3.1_1 +build number: 1 +size : 176 KB +license : GPL-2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.0.2-r3.3.1_1.tar.bz2 +md5 : 53fdd76b030c40d07dbd652bbae01302 +dependencies: + - bioconductor-rhdf5 + - r 3.3.1* + - r-jsonlite >=0.9.16 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.2.0 r3.3.1_0 +-------------------------------------- +file name : bioconductor-biomformat-1.2.0-r3.3.1_0.tar.bz2 +name : bioconductor-biomformat +version : 1.2.0 +build : r3.3.1_0 +build number: 0 +size : 130 KB +license : GPL-2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.2.0-r3.3.1_0.tar.bz2 +md5 : 3d9bc75fe653d410a7d597becbcc33a3 +dependencies: + - bioconductor-rhdf5 + - r 3.3.1* + - r-jsonlite >=0.9.16 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.2.0 r3.3.2_1 +-------------------------------------- +file name : bioconductor-biomformat-1.2.0-r3.3.2_1.tar.bz2 +name : bioconductor-biomformat +version : 1.2.0 +build : r3.3.2_1 +build number: 1 +size : 188 KB +license : GPL-2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.2.0-r3.3.2_1.tar.bz2 +md5 : 08f1194f729f1fdb90919dd7ceba5275 +dependencies: + - bioconductor-rhdf5 + - r-base 3.3.2* + - r-jsonlite >=0.9.16 + - r-matrix + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.2.0 r3.4.1_1 +-------------------------------------- +file name : bioconductor-biomformat-1.2.0-r3.4.1_1.tar.bz2 +name : bioconductor-biomformat +version : 1.2.0 +build : r3.4.1_1 +build number: 1 +size : 205 KB +license : GPL-2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.2.0-r3.4.1_1.tar.bz2 +md5 : 851771a8cc1ead6d03e643ab7887033f +dependencies: + - bioconductor-rhdf5 + - r-base 3.4.1* + - r-jsonlite >=0.9.16 + - r-matrix + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.4.0 r3.4.1_0 +-------------------------------------- +file name : bioconductor-biomformat-1.4.0-r3.4.1_0.tar.bz2 +name : bioconductor-biomformat +version : 1.4.0 +build : r3.4.1_0 +build number: 0 +size : 205 KB +license : GPL-2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.4.0-r3.4.1_0.tar.bz2 +md5 : 47e32db634579b8cf44927e24d095442 +dependencies: + - bioconductor-rhdf5 + - r-base 3.4.1* + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.6.0 r3.4.1_0 +-------------------------------------- +file name : bioconductor-biomformat-1.6.0-r3.4.1_0.tar.bz2 +name : bioconductor-biomformat +version : 1.6.0 +build : r3.4.1_0 +build number: 0 +size : 439 KB +license : GPL-2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.6.0-r3.4.1_0.tar.bz2 +md5 : a78bb80c6d60aafd070d9abc5da0fea8 +dependencies: + - bioconductor-rhdf5 + - r-base 3.4.1* + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.8.0 r341_0 +------------------------------------ +file name : bioconductor-biomformat-1.8.0-r341_0.tar.bz2 +name : bioconductor-biomformat +version : 1.8.0 +build : r341_0 +build number: 0 +size : 433 KB +license : GPL-2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.8.0-r341_0.tar.bz2 +md5 : 16d45f04e2222e80d7c03d24af3d5ff2 +timestamp : 2018-10-12 00:39:19 UTC +dependencies: + - bioconductor-rhdf5 >=2.24.0,<2.26.0 + - r-base >=3.4.1,<3.4.2.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.8.0 r351_0 +------------------------------------ +file name : bioconductor-biomformat-1.8.0-r351_0.tar.bz2 +name : bioconductor-biomformat +version : 1.8.0 +build : r351_0 +build number: 0 +size : 479 KB +license : GPL-2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.8.0-r351_0.tar.bz2 +md5 : 8ac9effffe91708e1f9f81a14175d8fa +timestamp : 2018-10-12 00:38:17 UTC +dependencies: + - bioconductor-rhdf5 >=2.24.0,<2.26.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.10.0 r351_0 +------------------------------------- +file name : bioconductor-biomformat-1.10.0-r351_0.tar.bz2 +name : bioconductor-biomformat +version : 1.10.0 +build : r351_0 +build number: 0 +size : 479 KB +license : GPL-2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biomformat-1.10.0-r351_0.tar.bz2 +md5 : 881b629a042c3ea4c8bfa4449ea29047 +timestamp : 2018-12-11 13:24:36 UTC +dependencies: + - bioconductor-rhdf5 >=2.26.0,<2.27.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.10.1 r351_0 +------------------------------------- +file name : bioconductor-biomformat-1.10.1-r351_0.tar.bz2 +name : bioconductor-biomformat +version : 1.10.1 +build : r351_0 +build number: 0 +size : 474 KB +license : GPL-2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biomformat-1.10.1-r351_0.tar.bz2 +md5 : 276971e3f1e29f365e80096e572dd557 +timestamp : 2019-04-27 15:06:57 UTC +dependencies: + - bioconductor-rhdf5 >=2.26.0,<2.27.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.12.0 r351_0 +------------------------------------- +file name : bioconductor-biomformat-1.12.0-r351_0.tar.bz2 +name : bioconductor-biomformat +version : 1.12.0 +build : r351_0 +build number: 0 +size : 478 KB +license : GPL-2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biomformat-1.12.0-r351_0.tar.bz2 +md5 : 0f32ca5c47b1c53d75113121261ff75d +timestamp : 2019-05-09 17:32:15 UTC +dependencies: + - bioconductor-rhdf5 >=2.28.0,<2.29.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.12.0 r36_1 +------------------------------------ +file name : bioconductor-biomformat-1.12.0-r36_1.tar.bz2 +name : bioconductor-biomformat +version : 1.12.0 +build : r36_1 +build number: 1 +size : 481 KB +license : GPL-2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biomformat-1.12.0-r36_1.tar.bz2 +md5 : 2d968fd6985e3abc803733159fb2bc5f +timestamp : 2019-07-22 04:54:31 UTC +dependencies: + - bioconductor-rhdf5 >=2.28.0,<2.29.0 + - r-base >=3.6,<3.7.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.14.0 r36_0 +------------------------------------ +file name : bioconductor-biomformat-1.14.0-r36_0.tar.bz2 +name : bioconductor-biomformat +version : 1.14.0 +build : r36_0 +build number: 0 +size : 481 KB +license : GPL-2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biomformat-1.14.0-r36_0.tar.bz2 +md5 : 9d55ca67aa1c4902c30cd9c4492976d9 +timestamp : 2019-11-01 15:23:22 UTC +dependencies: + - bioconductor-rhdf5 >=2.30.0,<2.31.0 + - r-base >=3.6,<3.7.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.16.0 r40_0 +------------------------------------ +file name : bioconductor-biomformat-1.16.0-r40_0.tar.bz2 +name : bioconductor-biomformat +version : 1.16.0 +build : r40_0 +build number: 0 +size : 541 KB +license : GPL-2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biomformat-1.16.0-r40_0.tar.bz2 +md5 : 382334a3312ed50442d929660b8c9a3d +timestamp : 2020-05-09 14:27:42 UTC +dependencies: + - bioconductor-rhdf5 >=2.32.0,<2.33.0 + - r-base >=4.0,<4.1.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.18.0 r40_0 +------------------------------------ +file name : bioconductor-biomformat-1.18.0-r40_0.tar.bz2 +name : bioconductor-biomformat +version : 1.18.0 +build : r40_0 +build number: 0 +size : 542 KB +license : GPL-2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biomformat-1.18.0-r40_0.tar.bz2 +md5 : 095c60136c76a0fc3c8ff1ed143f2309 +timestamp : 2020-10-30 21:29:31 UTC +dependencies: + - bioconductor-rhdf5 >=2.34.0,<2.35.0 + - r-base >=4.0,<4.1.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.18.0 r40hdfd78af_1 +-------------------------------------------- +file name : bioconductor-biomformat-1.18.0-r40hdfd78af_1.tar.bz2 +name : bioconductor-biomformat +version : 1.18.0 +build : r40hdfd78af_1 +build number: 1 +size : 538 KB +license : GPL-2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biomformat-1.18.0-r40hdfd78af_1.tar.bz2 +md5 : 929be00955b23394339e818d67dc6656 +timestamp : 2021-03-27 21:07:51 UTC +dependencies: + - bioconductor-rhdf5 >=2.34.0,<2.35.0 + - r-base >=4.0,<4.1.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.20.0 r41hdfd78af_0 +-------------------------------------------- +file name : bioconductor-biomformat-1.20.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-biomformat +version : 1.20.0 +build : r41hdfd78af_0 +build number: 0 +size : 535 KB +license : GPL-2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biomformat-1.20.0-r41hdfd78af_0.tar.bz2 +md5 : 5ed876b9a4ac00d05a3c2e36519e3fc3 +timestamp : 2021-05-31 08:04:00 UTC +dependencies: + - bioconductor-rhdf5 >=2.36.0,<2.37.0 + - r-base >=4.1,<4.2.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.22.0 r41hdfd78af_0 +-------------------------------------------- +file name : bioconductor-biomformat-1.22.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-biomformat +version : 1.22.0 +build : r41hdfd78af_0 +build number: 0 +size : 542 KB +license : GPL-2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-biomformat-1.22.0-r41hdfd78af_0.tar.bz2 +md5 : f739cfc48509f251c92993495e21281c +timestamp : 2021-11-02 03:05:11 UTC +dependencies: + - bioconductor-rhdf5 >=2.38.0,<2.39.0 + - r-base >=4.1,<4.2.0a0 + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + + +bioconductor-biomformat 1.26.0 r42hdfd78af_0 +-------------------------------------------- +file name : bioconductor-biomformat-1.26.0-r42hdfd78af_0.tar.bz2 +name : biocondu diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biovizbase.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biovizbase.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8bffb9ed97d998763719f3154b951646ed643c59 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biovizbase.manual_bundle.txt @@ -0,0 +1,378 @@ +# Tool: bioconductor-biovizbase +software_name: bioconductor-biovizbase +tier: T1 +domain: t1_backfill_overall +downloads: 129312 +summary: Basic graphic utilities for visualization of genomic data. +description: The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency. +dependencies: bioconductor-annotationdbi >=1.72.0,<1.73.0, bioconductor-annotationdbi >=1.72.0,<1.73.0a0, bioconductor-annotationfilter >=1.34.0,<1.35.0, bioconductor-annotationfilter >=1.34.0,<1.35.0a0, bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-biostrings >=2.78.0,<2.79.0, bioconductor-biostrings >=2.78.0,<2.79.0a0, bioconductor-ensembldb >=2.34.0,<2.35.0, bioconductor-ensembldb >=2.34.0,<2.35.0a0, bioconductor-genomeinfodb >=1.46.0,<1.47.0, bioconductor-genomeinfodb >=1.46.2,<1.47.0a0, bioconductor-genomicalignments >=1.46.0,<1.47.0, bioconductor-genomicalignments >=1.46.0,<1.47.0a0, bioconductor-genomicfeatures >=1.62.0,<1.63.0, bioconductor-genomicfeatures >=1.62.0,<1.63.0a0, bioconductor-genomicranges >=1.62.0,<1.63.0, bioconductor-genomicranges >=1.62.1,<1.63.0a0, bioconductor-iranges >=2.44.0,<2.45.0, bioconductor-iranges >=2.44.0,<2.45.0a0, bioconductor-rsamtools >=2.26.0,<2.27.0, bioconductor-rsamtools >=2.26.0,<2.27.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, bioconductor-seqinfo >=1.0.0,<1.1.0, bioconductor-seqinfo >=1.0.0,<1.1.0a0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0, bioconductor-variantannotation >=1.56.0,<1.57.0, bioconductor-variantannotation >=1.56.0,<1.57.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-dichromat, r-hmisc, r-rcolorbrewer, r-rlang, r-scales +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/biovizBase.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/biovizBase.html +Bioconductor - biovizBase Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages biovizBase biovizBase This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see biovizBase . Basic graphic utilities for visualization of genomic data. DOI: 10.18129/B9.bioc.biovizBase Bioconductor version: 3.22 The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency. Author: Tengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb] Maintainer: Michael Lawrence <lawremi at gmail.com> Citation (from within R, enter citation("biovizBase") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("biovizBase") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("biovizBase") An Introduction to biovizBase PDF R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Infrastructure , Preprocessing , Software , Visualization Version 1.58.0 In Bioconductor since BioC 2.9 (R-2.14) (14.5 years) License Artistic-2.0 Depends R (>= 3.5.0), methods Imports grDevices, stats, scales , Hmisc , RColorBrewer , dichromat , BiocGenerics , S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), Seqinfo , GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), GenomicFeatures (>= 1.61.4), AnnotationDbi , VariantAnnotation (>= 1.55.1), ensembldb (>= 2.33.1), AnnotationFilter (>= 0.99.8), rlang System Requirements URL See More Suggests BSgenome.Hsapiens.UCSC.hg19 , TxDb.Hsapiens.UCSC.hg19.knownGene , BSgenome , rtracklayer , EnsDb.Hsapiens.v75 , RUnit Linking To Enhances Depends On Me CAFE Imports Me ChIPexoQual , ggbio , Gviz , karyoploteR , Pviz , Rqc Suggests Me Damsel , derfinderPlot , FRASER , NanoStringNCTools , OUTRIDER , R3CPET , regionReport , StructuralVariantAnnotation , Signac Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package biovizBase_1.58.0.tar.gz Windows Binary (x86_64) biovizBase_1.58.0.zip macOS Binary (x86_64) biovizBase_1.58.0.tgz macOS Binary (arm64) biovizBase_1.58.0.tgz Source Repository git clone https://git.bioconductor.org/packages/biovizBase Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/biovizBase Bioc Package Browser https://code.bioconductor.org/browse/biovizBase/ Package Short Url https://bioconductor.org/packages/biovizBase/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-biovizbase --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-biovizbase 1.18.0 0 +-------------------------------- +file name : bioconductor-biovizbase-1.18.0-0.tar.bz2 +name : bioconductor-biovizbase +version : 1.18.0 +build : 0 +build number: 0 +size : 2.4 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.18.0-0.tar.bz2 +md5 : 1436bfdf77c830117ac80003c318f02e +dependencies: + - bioconductor-annotationdbi + - bioconductor-biocgenerics + - bioconductor-biostrings >=2.33.11 + - bioconductor-genomeinfodb >=1.5.14 + - bioconductor-genomicalignments >=1.1.16 + - bioconductor-genomicfeatures >=1.21.19 + - bioconductor-genomicranges >=1.17.19 + - bioconductor-iranges >=1.99.28 + - bioconductor-rsamtools >=1.17.28 + - bioconductor-s4vectors >=0.2.4 + - bioconductor-summarizedexperiment + - bioconductor-variantannotation >=1.11.4 + - r >=2.10 + - r-dichromat + - r-hmisc + - r-rcolorbrewer + - r-scales + + +bioconductor-biovizbase 1.18.0 1 +-------------------------------- +file name : bioconductor-biovizbase-1.18.0-1.tar.bz2 +name : bioconductor-biovizbase +version : 1.18.0 +build : 1 +build number: 1 +size : 2.2 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.18.0-1.tar.bz2 +md5 : c9b2b753cadc591df93754b8758aea8d +dependencies: + - bioconductor-annotationdbi + - bioconductor-biocgenerics + - bioconductor-biostrings >=2.33.11 + - bioconductor-genomeinfodb >=1.5.14 + - bioconductor-genomicalignments >=1.1.16 + - bioconductor-genomicfeatures >=1.21.19 + - bioconductor-genomicranges >=1.17.19 + - bioconductor-iranges >=1.99.28 + - bioconductor-rsamtools >=1.17.28 + - bioconductor-s4vectors >=0.2.4 + - bioconductor-summarizedexperiment + - bioconductor-variantannotation >=1.11.4 + - r >=2.10 + - r-dichromat + - r-hmisc + - r-rcolorbrewer + - r-scales + + +bioconductor-biovizbase 1.20.0 r3.3.1_0 +--------------------------------------- +file name : bioconductor-biovizbase-1.20.0-r3.3.1_0.tar.bz2 +name : bioconductor-biovizbase +version : 1.20.0 +build : r3.3.1_0 +build number: 0 +size : 2.2 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.20.0-r3.3.1_0.tar.bz2 +md5 : 98a9649cf285d7bee64b887978b35a5d +dependencies: + - bioconductor-annotationdbi + - bioconductor-biocgenerics + - bioconductor-biostrings >=2.33.11 + - bioconductor-ensembldb >=1.3.8 + - bioconductor-genomeinfodb >=1.5.14 + - bioconductor-genomicalignments >=1.1.16 + - bioconductor-genomicfeatures >=1.21.19 + - bioconductor-genomicranges >=1.23.21 + - bioconductor-iranges >=1.99.28 + - bioconductor-rsamtools >=1.17.28 + - bioconductor-s4vectors >=0.9.25 + - bioconductor-summarizedexperiment + - bioconductor-variantannotation >=1.11.4 + - r 3.3.1* + - r-dichromat + - r-hmisc + - r-rcolorbrewer + - r-scales + + +bioconductor-biovizbase 1.20.0 r3.3.2_0 +--------------------------------------- +file name : bioconductor-biovizbase-1.20.0-r3.3.2_0.tar.bz2 +name : bioconductor-biovizbase +version : 1.20.0 +build : r3.3.2_0 +build number: 0 +size : 2.2 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.20.0-r3.3.2_0.tar.bz2 +md5 : 197db4210f0e0be35f8d86f321f108f6 +dependencies: + - bioconductor-annotationdbi + - bioconductor-biocgenerics + - bioconductor-biostrings >=2.33.11 + - bioconductor-ensembldb >=1.3.8 + - bioconductor-genomeinfodb >=1.5.14 + - bioconductor-genomicalignments >=1.1.16 + - bioconductor-genomicfeatures >=1.21.19 + - bioconductor-genomicranges >=1.23.21 + - bioconductor-iranges >=1.99.28 + - bioconductor-rsamtools >=1.17.28 + - bioconductor-s4vectors >=0.9.25 + - bioconductor-summarizedexperiment + - bioconductor-variantannotation >=1.11.4 + - r-base 3.3.2* + - r-dichromat + - r-hmisc + - r-rcolorbrewer + - r-scales + + +bioconductor-biovizbase 1.20.0 r3.4.1_0 +--------------------------------------- +file name : bioconductor-biovizbase-1.20.0-r3.4.1_0.tar.bz2 +name : bioconductor-biovizbase +version : 1.20.0 +build : r3.4.1_0 +build number: 0 +size : 2.2 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.20.0-r3.4.1_0.tar.bz2 +md5 : 299879d4f375a97b75cd78dbd295677c +dependencies: + - bioconductor-annotationdbi + - bioconductor-biocgenerics + - bioconductor-biostrings >=2.33.11 + - bioconductor-ensembldb >=1.3.8 + - bioconductor-genomeinfodb >=1.5.14 + - bioconductor-genomicalignments >=1.1.16 + - bioconductor-genomicfeatures >=1.21.19 + - bioconductor-genomicranges >=1.23.21 + - bioconductor-iranges >=1.99.28 + - bioconductor-rsamtools >=1.17.28 + - bioconductor-s4vectors >=0.9.25 + - bioconductor-summarizedexperiment + - bioconductor-variantannotation >=1.11.4 + - r-base 3.4.1* + - r-dichromat + - r-hmisc + - r-rcolorbrewer + - r-scales + + +bioconductor-biovizbase 1.24.0 r3.4.1_0 +--------------------------------------- +file name : bioconductor-biovizbase-1.24.0-r3.4.1_0.tar.bz2 +name : bioconductor-biovizbase +version : 1.24.0 +build : r3.4.1_0 +build number: 0 +size : 2.4 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.24.0-r3.4.1_0.tar.bz2 +md5 : 49b504c027b56a4d70d7d3f3d374225a +dependencies: + - bioconductor-annotationdbi + - bioconductor-annotationfilter >=0.99.8 + - bioconductor-biocgenerics + - bioconductor-biostrings >=2.33.11 + - bioconductor-ensembldb >=1.99.13 + - bioconductor-genomeinfodb >=1.5.14 + - bioconductor-genomicalignments >=1.1.16 + - bioconductor-genomicfeatures >=1.21.19 + - bioconductor-genomicranges >=1.23.21 + - bioconductor-iranges >=1.99.28 + - bioconductor-rsamtools >=1.17.28 + - bioconductor-s4vectors >=0.9.25 + - bioconductor-summarizedexperiment + - bioconductor-variantannotation >=1.11.4 + - r-base 3.4.1* + - r-dichromat + - r-hmisc + - r-rcolorbrewer + - r-scales + + +bioconductor-biovizbase 1.26.0 r3.4.1_0 +--------------------------------------- +file name : bioconductor-biovizbase-1.26.0-r3.4.1_0.tar.bz2 +name : bioconductor-biovizbase +version : 1.26.0 +build : r3.4.1_0 +build number: 0 +size : 2.4 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.26.0-r3.4.1_0.tar.bz2 +md5 : 1d795cb7f1ac8e6ebcec1ede2dcd0e49 +dependencies: + - bioconductor-annotationdbi + - bioconductor-annotationfilter >=0.99.8 + - bioconductor-biocgenerics + - bioconductor-biostrings >=2.33.11 + - bioconductor-ensembldb >=1.99.13 + - bioconductor-genomeinfodb >=1.5.14 + - bioconductor-genomicalignments >=1.1.16 + - bioconductor-genomicfeatures >=1.21.19 + - bioconductor-genomicranges >=1.23.21 + - bioconductor-iranges >=1.99.28 + - bioconductor-rsamtools >=1.17.28 + - bioconductor-s4vectors >=0.9.25 + - bioconductor-summarizedexperiment + - bioconductor-variantannotation >=1.11.4 + - r-base 3.4.1* + - r-dichromat + - r-hmisc + - r-rcolorbrewer + - r-scales + + +bioconductor-biovizbase 1.28.2 r341h470a237_0 +--------------------------------------------- +file name : bioconductor-biovizbase-1.28.2-r341h470a237_0.tar.bz2 +name : bioconductor-biovizbase +version : 1.28.2 +build : r341h470a237_0 +build number: 0 +size : 2.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.28.2-r341h470a237_0.tar.bz2 +md5 : 47bbe53778002ca0e9d01f0802846b85 +timestamp : 2018-10-22 19:38:10 UTC +dependencies: + - bioconductor-annotationdbi >=1.42.1,<1.44.0 + - bioconductor-annotationfilter >=1.4.0,<1.6.0 + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - bioconductor-biostrings >=2.48.0,<2.50.0 + - bioconductor-ensembldb >=2.4.1,<2.6.0 + - bioconductor-genomeinfodb >=1.16.0,<1.18.0 + - bioconductor-genomicalignments >=1.16.0,<1.18.0 + - bioconductor-genomicfeatures >=1.32.2,<1.34.0 + - bioconductor-genomicranges >=1.32.7,<1.34.0 + - bioconductor-iranges >=2.14.12,<2.16.0 + - bioconductor-rsamtools >=1.32.3,<1.34.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - bioconductor-summarizedexperiment >=1.10.1,<1.12.0 + - bioconductor-variantannotation >=1.26.1,<1.28.0 + - libgcc-ng >=4.9 + - r-base >=3.4.1,<3.4.2.0a0 + - r-dichromat + - r-hmisc + - r-rcolorbrewer + - r-rlang + - r-scales + + +bioconductor-biovizbase 1.28.2 r351h470a237_0 +--------------------------------------------- +file name : bioconductor-biovizbase-1.28.2-r351h470a237_0.tar.bz2 +name : bioconductor-biovizbase +version : 1.28.2 +build : r351h470a237_0 +build number: 0 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.28.2-r351h470a237_0.tar.bz2 +md5 : 9ee3304b280c3f7946ee1ca929e855a7 +timestamp : 2018-10-22 19:41:41 UTC +dependencies: + - bioconductor-annotationdbi >=1.42.1,<1.44.0 + - bioconductor-annotationfilter >=1.4.0,<1.6.0 + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - bioconductor-biostrings >=2.48.0,<2.50.0 + - bioconductor-ensembldb >=2.4.1,<2.6.0 + - bioconductor-genomeinfodb >=1.16.0,<1.18.0 + - bioconductor-genomicalignments >=1.16.0,<1.18.0 + - bioconductor-genomicfeatures >=1.32.2,<1.34.0 + - bioconductor-genomicranges >=1.32.7,<1.34.0 + - bioconductor-iranges >=2.14.12,<2.16.0 + - bioconductor-rsamtools >=1.32.3,<1.34.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - bioconductor-summarizedexperiment >=1.10.1,<1.12.0 + - bioconductor-variantannotation >=1.26.1,<1.28.0 + - libgcc-ng >=4.9 + - r-base >=3.5.1,<3.5.2.0a0 + - r-dichromat + - r-hmisc + - r-rcolorbrewer + - r-rlang + - r-scales + + +bioconductor-biovizbase 1.30.1 r351h14c3975_0 +--------------------------------------------- +file name : bioconductor-biovizbase-1.30.1-r351h14c3975_0.tar.bz2 +name : bioconductor-biovizbase +version : 1.30.1 +build : r351h14c3975_0 +build number: 0 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.30.1-r351h14c3975_0.tar.bz2 +md5 : 540932ffd64a66b7d15ab27e0a9bc032 +timestamp : 2018-12-30 07:59:24 UTC +dependencies: + - bioconductor-annotationdbi >=1.44.0,<1.45.0 + - bioconductor-annotationfilter >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.28.0,<0.29.0 + - bioconductor-biostrings >=2.50.0,<2.51.0 + - bioconductor-ensembldb >=2.6.0,<2.7.0 + - bioconductor-genomeinfodb >=1.18.0,<1.19.0 + - bioconductor-genomicalignments >=1.18.0,<1.19.0 + - bioconductor-genomicfeatures >=1.34.0,<1.35.0 + - bioconductor-genomicranges >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.16.0,<2.17.0 + - bioconductor-rsamtools >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.20.0,<0.21.0 + - bioconductor-summarizedexperiment >=1.12.0,<1.13.0 + - bioconductor-variantannotation >=1.28.0,<1.29.0 + - libgcc-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-dichromat + - r-hmisc + - r-rcolorbrewer + - r-rlang + - r-scales + + +bioconductor-biovizbase 1.32.0 r36h516909a_1 +-------------------------------------------- +file name : bioconductor-biovizbase-1.32.0-r36h516909a_1.tar.bz2 +name : bioconductor-biovizbase +version : 1.32.0 +build : r36h516909a_1 +build number: 1 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.32.0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-blase.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-blase.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..a5371646ccf4d39865e5a690d61725a6dae4bf64 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-blase.manual_bundle.txt @@ -0,0 +1,54 @@ +# Tool: bioconductor-blase +software_name: bioconductor-blase +tier: T1 +domain: single_cell +downloads: 35 +summary: Bulk Linking Analysis for Single-cell Experiments +description: BLASE is a method for finding where bulk RNA-seq data lies on a single-cell pseudotime trajectory. It uses a fast and understandable approach based on Spearman correlation, with bootstrapping to provide confidence. BLASE can be used to "date" bulk RNA-seq data, annotate cell types in scRNA-seq, and help correct for developmental phenotype differences in bulk RNA-seq experiments. +dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-scater >=1.38.0,<1.39.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-boot, r-dplyr, r-ggplot2, r-matrix, r-mgcv, r-patchwork, r-rlang, r-seurat >=4.0.0, r-viridis +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/blase.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/blase.html +Bioconductor - blase Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages blase blase This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see blase . Bulk Linking Analysis for Single-cell Experiments DOI: 10.18129/B9.bioc.blase Bioconductor version: 3.22 BLASE is a method for finding where bulk RNA-seq data lies on a single-cell pseudotime trajectory. It uses a fast and understandable approach based on Spearman correlation, with bootstrapping to provide confidence. BLASE can be used to "date" bulk RNA-seq data, annotate cell types in scRNA-seq, and help correct for developmental phenotype differences in bulk RNA-seq experiments. Author: Andrew McCluskey [aut, cre] ORCID: 0009-0004-4187-799X , Toby Kettlewell [aut] ORCID: 0009-0001-1225-3318 , Adrian M. Smith [aut] ORCID: 0000-0001-8833-2330 , Rhiannon Kundu [aut] ORCID: 0000-0003-3970-5860 , David A. Gunn [aut] ORCID: 0000-0001-9866-3221 , Thomas D. Otto [aut, ths] ORCID: 0000-0002-1246-7404 Maintainer: Andrew McCluskey <2117532m at student.gla.ac.uk> Citation (from within R, enter citation("blase") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("blase") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("blase") Assigning bulk RNA-seq to pseudotime HTML R Script BLASE for annotating scRNA-seq HTML R Script BLASE for excluding developmental genes from bulk RNA-seq HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews CellBasedAssays , CellBiology , GeneExpression , RNASeq , Sequencing , SingleCell , Software , TimeCourse , Transcription , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.22 (R-4.5) ( License GPL (>= 3) Depends R (>= 4.5.0) Imports SummarizedExperiment , SingleCellExperiment , ggplot2 , viridis , patchwork , Matrix , scater , methods, rlang , BiocParallel , boot , dplyr , mgcv , stats, MatrixGenerics , Seurat (>= 4.0.0) System Requirements URL https://andrewmccluskey-uog.github.io/blase/ Bug Reports https://andrewmccluskey-uog.github.io/blase/issues See More Suggests knitr , rmarkdown , testthat (>= 3.2.3), covr , tradeSeq , scran , slingshot , tools, ami , reshape2 , plyr , fs , sparseMatrixStats , ggVennDiagram , uwot , BiocStyle , DelayedMatrixStats , limma Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package blase_1.0.0.tar.gz Windows Binary (x86_64) blase_1.0.0.zip (64-bit only) macOS Binary (x86_64) blase_1.0.0.tgz macOS Binary (arm64) blase_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/blase Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/blase Bioc Package Browser https://code.bioconductor.org/browse/blase/ Package Short Url https://bioconductor.org/packages/blase/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-blase --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-blase 1.0.0 r45hdfd78af_0 +-------------------------------------- +file name : bioconductor-blase-1.0.0-r45hdfd78af_0.conda +name : bioconductor-blase +version : 1.0.0 +build : r45hdfd78af_0 +build number: 0 +size : 8.1 MB +license : GPL (>= 3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-blase-1.0.0-r45hdfd78af_0.conda +md5 : fe1e968e1f0a6996348cc9852006e251 +timestamp : 2026-03-02 19:14:51 UTC +dependencies: + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-matrixgenerics >=1.22.0,<1.23.0 + - bioconductor-scater >=1.38.0,<1.39.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-boot + - r-dplyr + - r-ggplot2 + - r-matrix + - r-mgcv + - r-patchwork + - r-rlang + - r-seurat >=4.0.0 + - r-viridis diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-bluster.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-bluster.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c3d15951e0dac56ac81d99cb9b7dc8c3270c56b7 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-bluster.manual_bundle.txt @@ -0,0 +1,400 @@ +# Tool: bioconductor-bluster +software_name: bioconductor-bluster +tier: T1 +domain: t1_backfill_overall +downloads: 298329 +summary: Clustering Algorithms for Bioconductor +description: Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results. +dependencies: bioconductor-assorthead >=1.4.0,<1.5.0, bioconductor-assorthead >=1.4.0,<1.5.0a0, bioconductor-biocneighbors >=2.4.0,<2.5.0, bioconductor-biocneighbors >=2.4.0,<2.5.0a0, bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-biocparallel >=1.44.0,<1.45.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-cluster, r-igraph, r-matrix, r-rcpp +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.12/bioc/html/bluster.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.12/bioc/html/bluster.html +Bioconductor - bluster About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.12 Software Packages bluster bluster This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see bluster . Clustering Algorithms for Bioconductor DOI: 10.18129/B9.bioc.bluster Bioconductor version: 3.12 Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results. Author: Aaron Lun [aut, cre] Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com> Citation (from within R, enter citation("bluster") ): Installation To install this package, start R (version "4.0") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("bluster") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("bluster") 1. Clustering algorithms HTML R Script 2. Clustering diagnostics HTML R Script Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews Clustering , GeneExpression , ImmunoOncology , SingleCell , Software , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.12 (R-4.0) (3.5 years) License GPL-3 Depends Imports stats, methods, utils, Matrix, Rcpp, igraph, S4Vectors , BiocParallel , BiocNeighbors System Requirements C++11 URL See More Suggests knitr, rmarkdown, testthat, BiocStyle , dynamicTreeCut, scRNAseq , scuttle , scater , scran , pheatmap, viridis Linking To Rcpp Enhances Depends On Me Imports Me mbkmeans , scDblFinder , scran Suggests Me batchelor , scDblFinder Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package bluster_1.0.0.tar.gz Windows Binary bluster_1.0.0.zip (32- & 64-bit) macOS 10.13 (High Sierra) bluster_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/bluster Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bluster Bioc Package Browser https://code.bioconductor.org/browse/bluster/ Package Short Url https://bioconductor.org/packages/bluster/ Package Downloads Report Download Stats Old Source Packages for BioC 3.12 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-bluster --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-bluster 1.0.0 r40h399db7b_2 +---------------------------------------- +file name : bioconductor-bluster-1.0.0-r40h399db7b_2.tar.bz2 +name : bioconductor-bluster +version : 1.0.0 +build : r40h399db7b_2 +build number: 2 +size : 1.9 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.0.0-r40h399db7b_2.tar.bz2 +md5 : 3abe66fe95f469660bec08863c25ebee +timestamp : 2021-03-28 09:23:33 UTC +dependencies: + - bioconductor-biocneighbors >=1.8.0,<1.9.0 + - bioconductor-biocparallel >=1.24.0,<1.25.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.0,<4.1.0a0 + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.0.0 r40h5f743cb_1 +---------------------------------------- +file name : bioconductor-bluster-1.0.0-r40h5f743cb_1.tar.bz2 +name : bioconductor-bluster +version : 1.0.0 +build : r40h5f743cb_1 +build number: 1 +size : 1.9 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.0.0-r40h5f743cb_1.tar.bz2 +md5 : 3ac47a83a2a46b72b786ed9c70ac2b9b +timestamp : 2020-10-29 22:55:55 UTC +dependencies: + - bioconductor-biocneighbors >=1.8.0,<1.9.0 + - bioconductor-biocparallel >=1.24.0,<1.25.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=7.5.0 + - r-base >=4.0,<4.1.0a0 + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.2.1 r41h399db7b_0 +---------------------------------------- +file name : bioconductor-bluster-1.2.1-r41h399db7b_0.tar.bz2 +name : bioconductor-bluster +version : 1.2.1 +build : r41h399db7b_0 +build number: 0 +size : 3.4 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.2.1-r41h399db7b_0.tar.bz2 +md5 : 31696c11752a86009b5d0b2868577329 +timestamp : 2021-05-31 20:11:19 UTC +dependencies: + - bioconductor-biocneighbors >=1.10.0,<1.11.0 + - bioconductor-biocparallel >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.30.0,<0.31.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.1,<4.2.0a0 + - r-cluster + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.4.0 r41h399db7b_0 +---------------------------------------- +file name : bioconductor-bluster-1.4.0-r41h399db7b_0.tar.bz2 +name : bioconductor-bluster +version : 1.4.0 +build : r41h399db7b_0 +build number: 0 +size : 3.4 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.4.0-r41h399db7b_0.tar.bz2 +md5 : 8155293d00219d8d8572742e506946e1 +timestamp : 2021-11-02 23:00:34 UTC +dependencies: + - bioconductor-biocneighbors >=1.12.0,<1.13.0 + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.4.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.4.0 + - r-base >=4.1,<4.2.0a0 + - r-cluster + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.4.0 r41h619a076_1 +---------------------------------------- +file name : bioconductor-bluster-1.4.0-r41h619a076_1.tar.bz2 +name : bioconductor-bluster +version : 1.4.0 +build : r41h619a076_1 +build number: 1 +size : 3.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.4.0-r41h619a076_1.tar.bz2 +md5 : 16f1d84bb456be627b38484ac6e7d0ed +timestamp : 2022-02-25 08:13:14 UTC +dependencies: + - bioconductor-biocneighbors >=1.12.0,<1.13.0 + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=10.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=10.3.0 + - r-base >=4.1,<4.2.0a0 + - r-cluster + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.4.0 r41hc247a5b_2 +---------------------------------------- +file name : bioconductor-bluster-1.4.0-r41hc247a5b_2.tar.bz2 +name : bioconductor-bluster +version : 1.4.0 +build : r41hc247a5b_2 +build number: 2 +size : 3.4 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.4.0-r41hc247a5b_2.tar.bz2 +md5 : 64f5ca34acf6c257bbc8de95059068ce +timestamp : 2022-09-16 07:23:39 UTC +dependencies: + - bioconductor-biocneighbors >=1.12.0,<1.13.0 + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.1,<4.2.0a0 + - r-cluster + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.8.0 r42hc247a5b_0 +---------------------------------------- +file name : bioconductor-bluster-1.8.0-r42hc247a5b_0.tar.bz2 +name : bioconductor-bluster +version : 1.8.0 +build : r42hc247a5b_0 +build number: 0 +size : 3.4 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.8.0-r42hc247a5b_0.tar.bz2 +md5 : cf5532c02ec232d0212cdc63c349f66d +timestamp : 2022-11-04 01:06:55 UTC +dependencies: + - bioconductor-biocneighbors >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-cluster + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.8.0 r42hf17093f_1 +---------------------------------------- +file name : bioconductor-bluster-1.8.0-r42hf17093f_1.tar.bz2 +name : bioconductor-bluster +version : 1.8.0 +build : r42hf17093f_1 +build number: 1 +size : 3.4 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.8.0-r42hf17093f_1.tar.bz2 +md5 : 233f4186c52aa76d060b6f417db10fa8 +timestamp : 2023-05-18 19:59:08 UTC +dependencies: + - bioconductor-biocneighbors >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-cluster + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.10.0 r43hf17093f_0 +----------------------------------------- +file name : bioconductor-bluster-1.10.0-r43hf17093f_0.tar.bz2 +name : bioconductor-bluster +version : 1.10.0 +build : r43hf17093f_0 +build number: 0 +size : 3.4 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.10.0-r43hf17093f_0.tar.bz2 +md5 : 686a5047c656de7c05eb52c62c211500 +timestamp : 2023-07-10 20:28:55 UTC +dependencies: + - bioconductor-biocneighbors >=1.18.0,<1.19.0 + - bioconductor-biocparallel >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + - r-cluster + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.12.0 r43hf17093f_0 +----------------------------------------- +file name : bioconductor-bluster-1.12.0-r43hf17093f_0.tar.bz2 +name : bioconductor-bluster +version : 1.12.0 +build : r43hf17093f_0 +build number: 0 +size : 3.4 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.12.0-r43hf17093f_0.tar.bz2 +md5 : 4d9175962ce9281e9c7cf325e68a1318 +timestamp : 2023-12-06 05:15:25 UTC +dependencies: + - bioconductor-biocneighbors >=1.20.0,<1.21.0 + - bioconductor-biocneighbors >=1.20.0,<1.21.0a0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0a0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-s4vectors >=0.40.2,<0.41.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + - r-cluster + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.12.0 r43hf17093f_1 +----------------------------------------- +file name : bioconductor-bluster-1.12.0-r43hf17093f_1.tar.bz2 +name : bioconductor-bluster +version : 1.12.0 +build : r43hf17093f_1 +build number: 1 +size : 3.4 MB +license : GPL-3.0-only +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.12.0-r43hf17093f_1.tar.bz2 +md5 : a161b697cbb86b10f01958034eaa150a +timestamp : 2024-05-09 08:53:41 UTC +dependencies: + - bioconductor-biocneighbors >=1.20.0,<1.21.0 + - bioconductor-biocneighbors >=1.20.0,<1.21.0a0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0a0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-s4vectors >=0.40.2,<0.41.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + - r-cluster + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.16.0 r44he5774e6_0 +----------------------------------------- +file name : bioconductor-bluster-1.16.0-r44he5774e6_0.tar.bz2 +name : bioconductor-bluster +version : 1.16.0 +build : r44he5774e6_0 +build number: 0 +size : 3.6 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.16.0-r44he5774e6_0.tar.bz2 +md5 : 5d6d1603364e2b6b5c9ce378ba01c054 +timestamp : 2024-12-16 19:52:58 UTC +dependencies: + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-assorthead >=1.0.0,<1.1.0a0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0a0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0a0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=13 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx >=13 + - r-base >=4.4,<4.5.0a0 + - r-cluster + - r-igraph + - r-matrix + - r-rcpp + + +bioconductor-bluster 1.16.0 r44he5774e6_1 +----------------------------------------- +file name : bioconductor-bluster-1.16.0-r44he5774e6_1.tar.bz2 +name : bioconductor-bluster +version : 1.16.0 +build : r44he5774e6_1 +build number: 1 +size : 3.6 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.16.0-r44he5774e6_1.tar.bz2 +md5 : ddaf32568fb903b4f2492059baf3a283 +timestamp : 2025-04-21 22:17:43 UTC +dependencies: + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-assorthead >=1.0.0,<1.1.0a0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0a0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0a0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=13 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx >=13 + - r-base >=4.4,<4.5.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-cardspa.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-cardspa.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..a4e290aa0a46c1ed2488ad979880d4fa50e62de9 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-cardspa.manual_bundle.txt @@ -0,0 +1,79 @@ +# Tool: bioconductor-cardspa +software_name: bioconductor-cardspa +tier: T1 +domain: spatial_transcriptomics +downloads: 276 +summary: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics +description: CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes. +dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-biocparallel >=1.44.0,<1.45.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0a0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-concaveman, r-dplyr, r-fields, r-ggcorrplot, r-ggplot2, r-gtools, r-matrix, r-mcmcpack, r-nmf, r-nnls, r-rann, r-rcolorbrewer, r-rcpp >=1.0.7, r-rcpparmadillo, r-reshape2, r-scatterpie, r-sf, r-sp, r-spatstat.random, r-wrmisc +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/CARDspa.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/CARDspa.html +Bioconductor - CARDspa Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages CARDspa CARDspa This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see CARDspa . Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics DOI: 10.18129/B9.bioc.CARDspa Bioconductor version: 3.22 CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes. Author: Ying Ma [aut], Jing Fu [cre] Maintainer: Jing Fu <jing_fu at brown.edu> Citation (from within R, enter citation("CARDspa") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("CARDspa") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("CARDspa") Example_Analysis HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews SingleCell , Software , Spatial , Transcriptomics , Visualization Version 1.2.1 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License GPL-3 + file LICENSE Depends R (>= 4.3.0) Imports Rcpp (>= 1.0.7), RcppArmadillo , SummarizedExperiment , methods, MCMCpack , fields , wrMisc , concaveman , sp , dplyr , sf , Matrix , RANN , ggplot2 , reshape2 , RColorBrewer , S4Vectors , scatterpie , grDevices, ggcorrplot , stats, nnls , BiocParallel , NMF , spatstat.random , gtools , SingleCellExperiment , SpatialExperiment System Requirements URL https://github.com/YMa-lab/CARDspa Bug Reports https://github.com/YMa-lab/CARDspa/issues See More Suggests knitr , rmarkdown , testthat , RcppML , BiocStyle Linking To Rcpp , RcppArmadillo Enhances Depends On Me Imports Me OSTA Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package CARDspa_1.2.1.tar.gz Windows Binary (x86_64) CARDspa_1.2.1.zip macOS Binary (x86_64) CARDspa_1.2.1.tgz macOS Binary (arm64) CARDspa_1.2.1.tgz Source Repository git clone https://git.bioconductor.org/packages/CARDspa Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CARDspa Bioc Package Browser https://code.bioconductor.org/browse/CARDspa/ Package Short Url https://bioconductor.org/packages/CARDspa/ Package Downloads Report Download Stats Old Source Packages for BioC 3.22 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-cardspa --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-cardspa 1.2.1 r45ha27e39d_0 +---------------------------------------- +file name : bioconductor-cardspa-1.2.1-r45ha27e39d_0.conda +name : bioconductor-cardspa +version : 1.2.1 +build : r45ha27e39d_0 +build number: 0 +size : 4.2 MB +license : GPL-3 + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-cardspa-1.2.1-r45ha27e39d_0.conda +md5 : 324a1f797d951efb351a04728f598cb6 +timestamp : 2026-03-15 00:19:20 UTC +dependencies: + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-biocparallel >=1.44.0,<1.45.0a0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0a0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0a0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=14 + - liblapack >=3.9.0,<4.0a0 + - liblzma >=5.8.2,<6.0a0 + - libstdcxx >=14 + - libzlib >=1.3.1,<2.0a0 + - r-base >=4.5,<4.6.0a0 + - r-concaveman + - r-dplyr + - r-fields + - r-ggcorrplot + - r-ggplot2 + - r-gtools + - r-matrix + - r-mcmcpack + - r-nmf + - r-nnls + - r-rann + - r-rcolorbrewer + - r-rcpp >=1.0.7 + - r-rcpparmadillo + - r-reshape2 + - r-scatterpie + - r-sf + - r-sp + - r-spatstat.random + - r-wrmisc diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-catscradle.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-catscradle.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..030018594248e5631d47dd5280fe3a25a7a39ebb --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-catscradle.manual_bundle.txt @@ -0,0 +1,99 @@ +# Tool: bioconductor-catscradle +software_name: bioconductor-catscradle +tier: T1 +domain: single_cell +downloads: 564 +summary: This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters +description: This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes. +dependencies: bioconductor-ebimage >=4.52.0,<4.53.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-abind, r-base >=4.5,<4.6.0a0, r-data.table, r-geometry, r-ggplot2, r-igraph, r-matrix, r-msigdbr, r-networkd3, r-pheatmap, r-pracma, r-rdist, r-reshape2, r-rfast, r-seurat >=5.0.1, r-seuratobject, r-stringr +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.20/bioc/html/CatsCradle.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.20/bioc/html/CatsCradle.html +Bioconductor - CatsCradle Registration and Abstract Submission Open for GBCC2025 : Joint Galaxy/Bioconductor Conference Early registration discount pricing ends March 31! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.20 Software Packages CatsCradle CatsCradle This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see CatsCradle . This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters DOI: 10.18129/B9.bioc.CatsCradle Bioconductor version: 3.20 This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes. Author: Anna Laddach [aut] ORCID: 0000-0001-5552-6534 , Michael Shapiro [aut, cre] ORCID: 0000-0002-2769-9320 Maintainer: Michael Shapiro <michael.shapiro at crick.ac.uk> Citation (from within R, enter citation("CatsCradle") ): Installation To install this package, start R (version "4.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("CatsCradle") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("CatsCradle") CatsCradle HTML R Script CatsCradle Example Data HTML R Script CatsCradle Quick Start HTML R Script CatsCradle SingleCellExperiment Quick Start HTML R Script CatsCradle Spatial Vignette HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews BiologicalQuestion , GeneExpression , SingleCell , Software , Spatial , StatisticalMethod , Transcriptomics Version 1.0.1 In Bioconductor since BioC 3.20 (R-4.4) ( License MIT + file LICENSE Depends R (>= 4.4.0) Imports Seurat (>= 5.0.1), ggplot2 , networkD3 , stringr , pracma , reshape2 , rdist , igraph , geometry , Rfast , data.table , abind , pheatmap , EBImage , S4Vectors , SeuratObject , SingleCellExperiment , SpatialExperiment , Matrix , methods, SummarizedExperiment , msigdbr System Requirements URL https://github.com/AnnaLaddach/CatsCradle Bug Reports https://github.com/AnnaLaddach/CatsCradle/issues See More Suggests fossil , interp , knitr , BiocStyle , tictoc Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package CatsCradle_1.0.1.tar.gz Windows Binary (x86_64) CatsCradle_1.0.1.zip macOS Binary (x86_64) CatsCradle_1.0.1.tgz macOS Binary (arm64) CatsCradle_1.0.1.tgz Source Repository git clone https://git.bioconductor.org/packages/CatsCradle Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CatsCradle Bioc Package Browser https://code.bioconductor.org/browse/CatsCradle/ Package Short Url https://bioconductor.org/packages/CatsCradle/ Package Downloads Report Download Stats Old Source Packages for BioC 3.20 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2025 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-catscradle --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-catscradle 1.0.0 r44hdfd78af_0 +------------------------------------------- +file name : bioconductor-catscradle-1.0.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-catscradle +version : 1.0.0 +build : r44hdfd78af_0 +build number: 0 +size : 6.0 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-catscradle-1.0.0-r44hdfd78af_0.tar.bz2 +md5 : dc13cebb4b78cb62a91feb1640248dd5 +timestamp : 2024-12-22 11:02:03 UTC +dependencies: + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-abind + - r-base >=4.4,<4.5.0a0 + - r-data.table + - r-geometry + - r-ggplot2 + - r-igraph + - r-matrix + - r-msigdbr + - r-networkd3 + - r-pheatmap + - r-pracma + - r-rdist + - r-reshape2 + - r-rfast + - r-seurat >=5.0.1 + - r-seuratobject + - r-stringr + + +bioconductor-catscradle 1.4.2 r45hdfd78af_0 +------------------------------------------- +file name : bioconductor-catscradle-1.4.2-r45hdfd78af_0.conda +name : bioconductor-catscradle +version : 1.4.2 +build : r45hdfd78af_0 +build number: 0 +size : 5.8 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-catscradle-1.4.2-r45hdfd78af_0.conda +md5 : bf451f7f292d26550bf26901609b2842 +timestamp : 2026-03-01 20:13:36 UTC +dependencies: + - bioconductor-ebimage >=4.52.0,<4.53.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-abind + - r-base >=4.5,<4.6.0a0 + - r-data.table + - r-geometry + - r-ggplot2 + - r-igraph + - r-matrix + - r-msigdbr + - r-networkd3 + - r-pheatmap + - r-pracma + - r-rdist + - r-reshape2 + - r-rfast + - r-seurat >=5.0.1 + - r-seuratobject + - r-stringr diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-cellhashr.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-cellhashr.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6045e79b3af01394bd0da7653b369b76cc752af3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-cellhashr.manual_bundle.txt @@ -0,0 +1,67 @@ +# Tool: bioconductor-cellhashr +software_name: bioconductor-cellhashr +tier: T1 +domain: single_cell +downloads: 1190 +summary: An R package designed to demultiplex cell hashing data. + More information in https://bimberlab.github.io/cellhashR/Lab B (2024). + cellhashR: A Package for Demultiplexing Cell Hashing Data. +description: An R package designed to demultiplex cell hashing data. + More information in https://bimberlab.github.io/cellhashR/Lab B (2024). + cellhashR: A Package for Demultiplexing Cell Hashing Data. +dependencies: bioconductor-demuxmix, bioconductor-dropletutils, bioconductor-nempi, bioconductor-preprocesscore, r-base >=4.3,<4.4.0a0, r-devtools, r-egg, r-essentials, r-ggextra, r-ggforce, r-ggthemes, r-patchwork, r-rcpp, r-rcpparmadillo, r-rcppeigen, r-rcppparallel, r-rcppprogress, r-reticulate, r-rmdformats, r-seurat, r-seuratobject +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://github.com/BimberLab/cellhashR +doc_url: +dev_url: https://github.com/BimberLab/cellhashR + +## URL Docs Extract +### https://github.com/BimberLab/cellhashR +GitHub - BimberLab/cellhashR: An R package designed to demultiplex cell hashing data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} BimberLab / cellhashR Public Notifications You must be signed in to change notification settings Fork 8 Star 31 Code Issues 0 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights BimberLab/cellhashR master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 224 Commits 224 Commits .github .github R R inst/ rmd inst/ rmd man man tests tests vignettes vignettes .Rbuildignore .Rbuildignore .dockerignore .dockerignore .gitignore .gitignore DESCRIPTION DESCRIPTION Dockerfile Dockerfile NAMESPACE NAMESPACE README.md README.md _pkgdown.yml _pkgdown.yml cellhashR.iml cellhashR.iml View all files Repository files navigation README cellhashR An R package designed to demultiplex cell hashing data. Please see our documentation for more detail . Table of Contents Overview Example Usage Installation Known Issues Development Guidelines Overview Cell hashing is a method that allows sample multiplexing or super-loading within single-cell RNA-seq platforms, such as 10x genomics, originally developed at New York Genome Center in collaboration with the Satija lab. See here for more detail on the technique . The general idea is that cells are labeled with a staining reagent (such as an antibody) tagged with a short nucleotide barcode. Other staining methods have been published, such as the lipid-based Multi-Seq ( https://www.ncbi.nlm.nih.gov/pubmed/31209384 ). In all methods, the hashtag oligo/barcode is sequenced in parallel with cellular mRNA, creating a separate cell hashing library. After sequencing, the cell barcode and hashing index are parsed using tools like Cite-seq-Count ( https://github.com/Hoohm/CITE-seq-Count ), creating a count matrix with the total hash tag counts per cell. Once the count matrix is created, an algorithm must be used to demultiplex cells and assign them to hash tags (i.e. sample). This is where cellhashR comes in. This package provides several functions: Quality control reports for the cell hashing library, covering read counts and normalization. Think FASTQC , except for cell hashing data. A single interface to run one or more demutiplexing algorithms, including the novel demultiplexing algorithms BFF_raw and BFF_cluster. Each algorithm has pros and cons, and will perform better or worse under certain conditions (though in our experience, of the algorithms we have tested, the BFF algorithms work most consistently and under the widest variety of conditions). If you select multiple algorithms (our default workflow), cellhashR will score cells using the consensus call from the set. Various QC summaries are produced during this process as well, if debugging is needed. In addition to the BFF demultiplexing algorithms, other algorithms that can be run from cellhashR include: GMM-Demux demuxEM (see extra requirements below) demuxmix (see extra requirements below) deMULTIplex HTODemux from Seurat hashedDrops from DropletUtils The workflow produces a unified table with the results of each caller and the consensus call. Final QC plots and summaries are created. Each step of the workflow can either be run interactively in R (through the terminal or RStudio), or it can be executed as a pipeline that runs all commands and creates the call table and an HTML report. Click here to view an example QC report Consensus Calling In addition to allowing one to run multiple demuliplexing algorithms to compare results, cellhashR can generate a consensus call based on those scores. This can be useful, since some algorithms will perform better or worse under some conditions. This is automatically built into the dataframe returned by GenerateCellHashingCalls(). Some additional parameters that might be worth considering are: There are separate arguments for 'methods' (i.e. which algorithms will be run), and 'methodsForConsensus', which determined the subset that will be used for the consensus call. majorityConsensusThreshold: This applies to calculating a consensus call when multiple algorithms are used. If NULL, then all non-negative calls must agree or that cell is marked discordant. If non-NULL, then the number of algorithms returning the top call is divided by the total number of non-negative calls. If this ratio is above the majorityConsensusThreshold, that value is selected. For example, when majorityConsensusThreshold=0.6 and the calls are: HTO-1,HTO-1,Negative,HTO-2, then 2/3 calls are for HTO-1, giving 0.66. This is greater than the majorityConsensusThreshold of 0.6, so HTO-1 is returned. This can be useful for situations where most algorithms agree, but a single caller fails. callerDisagreementThreshold: If provided, the agreement rate will be calculated between each caller and the simple majority call, ignoring discordant and no-call cells. If any caller has an disagreement rate above this threshold, it will be dropped and the consensus call re-calculated. The general idea is to drop a caller that is systematically discordant. Example Usage Below are the primary functions of cellhashR needed to QC and score hashing data: # Example 1: parse CITE-seq-Count output, printing QC barcodeData <- ProcessCountMatrix( rawCountData = ' myCountDir/umi_count ' , minCountPerCell = 5 ) # Example 2: parse CITE-seq-Count output, providing a barcode whitelist. barcodeData <- ProcessCountMatrix( rawCountData = ' myCountDir/umi_count ' , minCountPerCell = 5 , barcodeWhitelist = c( ' HTO-1 ' , ' HTO-2 ' , ' HTO-3 ' , ' HTO-4 ' , ' HTO-6 ' )) # Create QC plots of barcode normalization PlotNormalizationQC( barcodeData ) # Generate the final cell hashing calls calls <- GenerateCellHashingCalls( barcodeMatrix = barcodeData , methods = c( ' multiseq ' , ' htodemux ' )) # Inspect negative cells: SummarizeCellsByClassification( calls = calls , barcodeMatrix = barcodeData ) Or export/save a template RMarkdown file outlining the default workflow, which can be run interactively or headlessly as part of a pipeline: GetExampleMarkdown( dest = ' cellhashR_template.rmd ' ) Finally, the workflow can be executed using this wrapper around the Rmarkdown, producing a TSV of calls and HTML QC report: CallAndGenerateReport( rawCountData = ' myCountDir/umi_count ' , reportFile = ' report.html ' , callFile = ' calls.txt ' , barcodeWhitelist = c( ' HTO-1 ' , ' HTO-2 ' , ' HTO-3 ' ), title = ' Cell Hashing For Experiment 1 ' ) Installation # Make sure to update your Rprofile to include Bioconductor repos, such as adding this line to ~/.Rprofile: local({options(repos = BiocManager::repositories())}) #Latest version: devtools::install_github(repo = 'bimberlab/cellhashR', ref = 'master', dependencies = TRUE, upgrade = 'always') Pre-packaged Docker images with all needed dependencies installed can be found on our GitHub Packages page . We recommend using a specific release, which you can do using tags: docker pull ghcr.io/bimberlab/cellhashr:latest Known Issues If you receive an error along the lines of: "ERROR; return code from pthread_create() is 22\n" Please manually install preprocessCore with threading disabled: devtools::install_github('bmbolstad/preprocessCore', dependencies = T, upgrade = 'always', configure.args = '--disable-threading') Providing h5 file to demuxEM/demuxmix Unlike the other algorithms, which just require the HTO count matrix, demuxEM and demuxmix also require the path to the 10x h5 gene expression counts. This can be supplied as follows. This example runs BFF and demuxEM: rawData <- '../testdata/438-21-GEX/umi_count' h5File <- '../testdata/438-21-GEX/438-21-raw_feature_bc_matrix.h5' barcodeMatrix <- ProcessCountMatrix(rawCountData = rawData, barcodeWhitelist = c('MS-11', 'MS-12')) df <- GenerateCellHashingCalls(barcodeMatrix = barcodeMatrix, methods = c('bff_cluster', 'demuxem'), rawFeatureMatrixH5 = h5File) Development Guidelines New development should occur on a branch, and go through a Pull Request before merging into the master branch. See here for information on the pull request workflow . Ideally PRs would be reviewed by another person. For the PR, please review the set of changed files carefully to make sure you are only merging the changes you intend. New functions should have Roxygen2 documentation . As part of each PR, you should run 'devtools::document()' to update documentation and include these changes with your commits. It is a good idea to run 'R CMD check' locally to make sure your changes will pass. See here for more information Code should only be merged after the build and tests pass. The master branch should always be stable. New features should ideally have at least a basic test (see R testthat ). There is existing test data in ./tests/testdata. This can be expanded, but please be conscious about file size and try to reuse data across tests if appropriate. About An R package designed to demultiplex cell hashing data Resources Readme Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 31 stars Watchers 3 watching Forks 8 forks Report repository Releases 4 Version 1.2.1 Latest Mar 15, 2025 + 3 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 99.4% Dockerfile 0.6% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/BimberLab/cellhashR +GitHub - BimberLab/cellhashR: An R package designed to demultiplex cell hashing data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} BimberLab / cellhashR Public Notifications You must be signed in to change notification settings Fork 8 Star 31 Code Issues 0 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights BimberLab/cellhashR master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 224 Commits 224 Commits .github .github R R inst/ rmd inst/ rmd man man tests tests vignettes vignettes .Rbuildignore .Rbuildignore .dockerignore .dockerignore .gitignore .gitignore DESCRIPTION DESCRIPTION Dockerfile Dockerfile NAMESPACE NAMESPACE README.md README.md _pkgdown.yml _pkgdown.yml cellhashR.iml cellhashR.iml View all files Repository files navigation README cellhashR An R package designed to demultiplex cell hashing data. Please see our documentation for more detail . Table of Contents Overview Example Usage Installation Known Issues Development Guidelines Overview Cell hashing is a method that allows sample multiplexing or super-loading within single-cell RNA-seq platforms, such as 10x genomics, originally developed at New York Genome Center in collaboration with the Satija lab. See here for more detail on the technique . The general idea is that cells are labeled with a staining reagent (such as an antibody) tagged with a short nucleotide barcode. Other staining methods have been published, such as the lipid-based Multi-Seq ( https://www.ncbi.nlm.nih.gov/pubmed/31209384 ). In all methods, the hashtag oligo/barcode is sequenced in parallel with cellular mRNA, creating a separate cell hashing library. After sequencing, the cell barcode and hashing index are parsed using tools like Cite-seq-Count ( https://github.com/Hoohm/CITE-seq-Count ), creating a count matrix with the total hash tag counts per cell. Once the count matrix is created, an algorithm must be used to demultiplex cells and assign them to hash tags (i.e. sample). This is where cellhashR comes in. This package provides several functions: Quality control reports for the cell hashing library, covering read counts and normalization. Think FASTQC , except for cell hashing data. A single interface to run one or more demutiplexing algorithms, including the novel demultiplexing algorithms BFF_raw and BFF_cluster. Each algorithm has pros and cons, and will perform better or worse under certain conditions (though in our experience, of the algorithms we have tested, the BFF algorithms work most consistently and under the widest variety of conditions). If you select multiple algorithms (our default workflow), cellhashR will score cells using the consensus call from the set. Various QC summaries are produced during this process as well, if debugging is needed. In addition to the BFF demultiplexing algorithms, other algorithms that can be run from cellhashR include: GMM-Demux demuxEM (see extra requirements below) demuxmix (see extra requirements below) deMULTIplex HTODemux from Seurat hashedDrops from DropletUtils The workflow produces a unified table with the results of each caller and the consensus call. Final QC plots and summaries are created. Each step of the workflow can either be run interactively in R (through the terminal or RStudio), or it can be executed as a pipeline that runs all commands and creates the call table and an HTML report. Click here to view an example QC report Consensus Calling In addition to allowing one to run multiple demuliplexing algorithms to compare results, cellhashR can generate a consensus call based on those scores. This can be useful, since some algorithms will perform better or worse under some conditions. This is automatically built into the dataframe returned by GenerateCellHashingCalls(). Some additional parameters that might be worth considering are: There are separate arguments for 'methods' (i.e. which algorithms will be run), and 'methodsForConsensus', which determined the subset that will be used for the consensus call. majorityConsensusThreshold: This applies to calculating a consensus call when multiple algorithms are used. If NULL, then all non-negative calls must agree or that cell is marked discordant. If non-NULL, then the number of algorithms returning the top call is divided by the total number of non-negative calls. If this ratio is above the majorityConsensusThreshold, that value is selected. For example, when majorityConsensusThreshold=0.6 and the calls are: HTO-1,HTO-1,Negative,HTO-2, then 2/3 calls are for HTO-1, giving 0.66. This is greater than the majorityConsensusThreshold of 0.6, so HTO-1 is returned. This can be useful for situations where most algorithms agree, but a single caller fails. callerDisagreementThreshold: If provided, the agreement rate will be calculated between each caller and the simple majority call, ignoring discordant and no-call cells. If any caller has an disagreement rate above this threshold, it will be dropped and the consensus call re-calculated. The general idea is to drop a caller that is systematically discordant. Example Usage Below are the primary functions of cellhashR needed to QC and score hashing data: # Example 1: parse CITE-seq-Count output, printing QC barcodeData <- ProcessCountMatrix( rawCountData = ' myCountDir/umi_count ' , minCountPerCell = 5 ) # Example 2: parse CITE-seq-Count output, providing a barcode whitelist. barcodeData <- ProcessCountMatrix( rawCountData = ' myCountDir/umi_count ' , minCountPerCell = 5 , barcodeWhitelist = c( ' HTO-1 ' , ' HTO-2 ' , ' HTO-3 ' , ' HTO-4 ' , ' HTO-6 ' )) # Create QC plots of barcode normalization PlotNormalizationQC( barcodeData ) # Generate the final cell hashing calls calls <- GenerateCellHashingCalls( barcodeMatrix = barcodeData , methods = c( ' multiseq ' , ' htodemux ' )) # Inspect negative cells: SummarizeCellsByClassification( calls = calls , barcodeMatrix = barcodeData ) Or export/save a template RMarkdown file outlining the default workflow, which can be run interactively or headlessly as part of a pipeline: GetExampleMarkdown( dest = ' cellhashR_template.rmd ' ) Finally, the workflow can be executed using this wrapper around the Rmarkdown, producing a TSV of calls and HTML QC report: CallAndGenerateReport( rawCountData = ' myCountDir/umi_count ' , reportFile = ' report.html ' , callFile = ' calls.txt ' , barcodeWhitelist = c( ' HTO-1 ' , ' HTO-2 ' , ' HTO-3 ' ), title = ' Cell Hashing For Experiment 1 ' ) Installation # Make sure to update your Rprofile to include Bioconductor repos, such as adding this line to ~/.Rprofile: local({options(repos = BiocManager::repositories())}) #Latest version: devtools::install_github(repo = 'bimberlab/cellhashR', ref = 'master', dependencies = TRUE, upgrade = 'always') Pre-packaged Docker images with all needed dependencies installed can be found on our GitHub Packages page . We recommend using a specific release, which you can do using tags: docker pull ghcr.io/bimberlab/cellhashr:latest Known Issues If you receive an error along the lines of: "ERROR; return code from pthread_create() is 22\n" Please manually install preprocessCore with threading disabled: devtools::install_github('bmbolstad/preprocessCore', dependencies = T, upgrade = 'always', configure.args = '--disable-threading') Providing h5 file to demuxEM/demuxmix Unlike the other algorithms, which just require the HTO count matrix, demuxEM and demuxmix also require the path to the 10x h5 gene expression counts. This can be supplied as follows. This example runs BFF and demuxEM: rawData <- '../testdata/438-21-GEX/umi_count' h5File <- '../testdata/438-21-GEX/438-21-raw_feature_bc_matrix.h5' barcodeMatrix <- ProcessCountMatrix(rawCountData = rawData, barcodeWhitelist = c('MS-11', 'MS-12')) df <- GenerateCellHashingCalls(barcodeMatrix = barcodeMatrix, methods = c('bff_cluster', 'demuxem'), rawFeatureMatrixH5 = h5File) Development Guidelines New development should occur on a branch, and go through a Pull Request before merging into the master branch. See here for information on the pull request workflow . Ideally PRs would be reviewed by another person. For the PR, please review the set of changed files carefully to make sure you are only merging the changes you intend. New functions should have Roxygen2 documentation . As part of each PR, you should run 'devtools::document()' to update documentation and include these changes with your commits. It is a good idea to run 'R CMD check' locally to make sure your changes will pass. See here for more information Code should only be merged after the build and tests pass. The master branch should always be stable. New features should ideally have at least a basic test (see R testthat ). There is existing test data in ./tests/testdata. This can be expanded, but please be conscious about file size and try to reuse data across tests if appropriate. About An R package designed to demultiplex cell hashing data Resources Readme Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 31 stars Watchers 3 watching Forks 8 forks Report repository Releases 4 Version 1.2.1 Latest Mar 15, 2025 + 3 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 99.4% Dockerfile 0.6% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-cellhashr --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-cellhashr 1.04 r43hdfd78af_0 +----------------------------------------- +file name : bioconductor-cellhashr-1.04-r43hdfd78af_0.tar.bz2 +name : bioconductor-cellhashr +version : 1.04 +build : r43hdfd78af_0 +build number: 0 +size : 260 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-cellhashr-1.04-r43hdfd78af_0.tar.bz2 +md5 : e51ecc711bcadf09a6bbd573b87d1f41 +timestamp : 2024-04-01 06:41:15 UTC +dependencies: + - bioconductor-demuxmix + - bioconductor-dropletutils + - bioconductor-nempi + - bioconductor-preprocesscore + - r-base >=4.3,<4.4.0a0 + - r-devtools + - r-egg + - r-essentials + - r-ggextra + - r-ggforce + - r-ggthemes + - r-patchwork + - r-rcpp + - r-rcpparmadillo + - r-rcppeigen + - r-rcppparallel + - r-rcppprogress + - r-reticulate + - r-rmdformats + - r-seurat + - r-seuratobject diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-ctsv.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-ctsv.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf6d89b64b7a178ddc822059fd357a8548e274a7 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-ctsv.manual_bundle.txt @@ -0,0 +1,138 @@ +# Tool: bioconductor-ctsv +software_name: bioconductor-ctsv +tier: T1 +domain: spatial_transcriptomics +downloads: 5480 +summary: Identification of cell-type-specific spatially variable genes accounting for excess zeros +description: The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS. +dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-qvalue >=2.42.0,<2.43.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-knitr, r-pscl +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.16/bioc/html/CTSV.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.16/bioc/html/CTSV.html +Bioconductor - CTSV About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Software Packages CTSV CTSV This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see CTSV . Identification of cell-type-specific spatially variable genes accounting for excess zeros DOI: 10.18129/B9.bioc.CTSV Bioconductor version: 3.16 The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS. Author: Jinge Yu Developer [aut, cre], Xiangyu Luo Developer [aut] Maintainer: Jinge Yu Developer <yjgruc at ruc.edu.cn> Citation (from within R, enter citation("CTSV") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("CTSV") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("CTSV") Basic Usage HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews GeneExpression , Genetics , Regression , Software , Spatial , StatisticalMethod Version 1.0.0 In Bioconductor since BioC 3.16 (R-4.2) (1.5 years) License GPL-3 Depends R (>= 4.2) Imports stats, pscl, qvalue , BiocParallel , methods, knitr, SpatialExperiment , SummarizedExperiment System Requirements URL https://github.com/jingeyu/CTSV Bug Reports https://github.com/jingeyu/CTSV/issues See More Suggests testthat, BiocStyle Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package CTSV_1.0.0.tar.gz Windows Binary CTSV_1.0.0.zip macOS Binary (x86_64) CTSV_1.0.0.tgz macOS Binary (arm64) CTSV_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/CTSV Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CTSV Bioc Package Browser https://code.bioconductor.org/browse/CTSV/ Package Short Url https://bioconductor.org/packages/CTSV/ Package Downloads Report Download Stats Old Source Packages for BioC 3.16 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-ctsv --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-ctsv 1.0.0 r42hdfd78af_0 +------------------------------------- +file name : bioconductor-ctsv-1.0.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-ctsv +version : 1.0.0 +build : r42hdfd78af_0 +build number: 0 +size : 333 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ctsv-1.0.0-r42hdfd78af_0.tar.bz2 +md5 : 477e92194b308953418ec2d1b48b3837 +timestamp : 2022-11-06 01:40:28 UTC +dependencies: + - bioconductor-biocparallel >=1.32.0,<1.33.0 + - bioconductor-qvalue >=2.30.0,<2.31.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - r-base >=4.2,<4.3.0a0 + - r-knitr + - r-pscl + + +bioconductor-ctsv 1.2.0 r43hdfd78af_0 +------------------------------------- +file name : bioconductor-ctsv-1.2.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-ctsv +version : 1.2.0 +build : r43hdfd78af_0 +build number: 0 +size : 336 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ctsv-1.2.0-r43hdfd78af_0.tar.bz2 +md5 : c0e412661c7c2a8aafcaacac687e34da +timestamp : 2023-07-16 16:05:22 UTC +dependencies: + - bioconductor-biocparallel >=1.34.0,<1.35.0 + - bioconductor-qvalue >=2.32.0,<2.33.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-base >=4.3,<4.4.0a0 + - r-knitr + - r-pscl + + +bioconductor-ctsv 1.4.0 r43hdfd78af_0 +------------------------------------- +file name : bioconductor-ctsv-1.4.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-ctsv +version : 1.4.0 +build : r43hdfd78af_0 +build number: 0 +size : 344 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ctsv-1.4.0-r43hdfd78af_0.tar.bz2 +md5 : 8831b06fb052b21f542c519d0da9e33f +timestamp : 2023-12-07 00:49:18 UTC +dependencies: + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - bioconductor-qvalue >=2.34.0,<2.35.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-base >=4.3,<4.4.0a0 + - r-knitr + - r-pscl + + +bioconductor-ctsv 1.8.0 r44hdfd78af_0 +------------------------------------- +file name : bioconductor-ctsv-1.8.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-ctsv +version : 1.8.0 +build : r44hdfd78af_0 +build number: 0 +size : 346 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ctsv-1.8.0-r44hdfd78af_0.tar.bz2 +md5 : 3a7349d1f0d0c4125aacdcad2d371fbd +timestamp : 2024-12-22 16:20:01 UTC +dependencies: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base >=4.4,<4.5.0a0 + - r-knitr + - r-pscl + + +bioconductor-ctsv 1.12.0 r45hdfd78af_0 +-------------------------------------- +file name : bioconductor-ctsv-1.12.0-r45hdfd78af_0.conda +name : bioconductor-ctsv +version : 1.12.0 +build : r45hdfd78af_0 +build number: 0 +size : 318 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ctsv-1.12.0-r45hdfd78af_0.conda +md5 : 19db14a69bfd3414d69c779b9e87a337 +timestamp : 2026-03-01 23:21:39 UTC +dependencies: + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-qvalue >=2.42.0,<2.43.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-knitr + - r-pscl diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-decontam.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-decontam.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9069be54fcf1577eede933933d0b43a38a315d7 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-decontam.manual_bundle.txt @@ -0,0 +1,327 @@ +# Tool: bioconductor-decontam +software_name: bioconductor-decontam +tier: T1 +domain: t1_backfill_overall +downloads: 207011 +summary: Identify Contaminants in Marker-gene and Metagenomics Sequencing Data +description: Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples. +dependencies: r-base >=4.5,<4.6.0a0, r-ggplot2 >=2.1.0, r-reshape2 >=1.4.1 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.7/bioc/html/decontam.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.7/bioc/html/decontam.html +Bioconductor - decontam About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.7 Software Packages decontam decontam This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see decontam . Identify Contaminants in Marker-gene and Metagenomics Sequencing Data DOI: 10.18129/B9.bioc.decontam Bioconductor version: 3.7 Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples. Author: Benjamin Callahan <benjamin.j.callahan at gmail.com>, Nicole Marie Davis Maintainer: Benjamin Callahan <benjamin.j.callahan at gmail.com> Citation (from within R, enter citation("decontam") ): Installation To install this package, start R (version "3.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("decontam") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("decontam") Introduction to dada2 HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Classification , Metagenomics , Microbiome , Sequencing , Software Version 1.0.0 In Bioconductor since BioC 3.7 (R-3.5) (6 years) License Artistic-2.0 Depends R (>= 3.4.1), methods (>= 3.4.1) Imports ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats System Requirements URL https://github.com/benjjneb/decontam Bug Reports https://github.com/benjjneb/decontam/issues See More Suggests BiocStyle , knitr, rmarkdown, phyloseq Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package decontam_1.0.0.tar.gz Windows Binary decontam_1.0.0.zip Mac OS X 10.11 (El Capitan) decontam_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/decontam Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/decontam Package Short Url https://bioconductor.org/packages/decontam/ Package Downloads Report Download Stats Old Source Packages for BioC 3.7 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-decontam --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-decontam 1.0.0 r351_0 +---------------------------------- +file name : bioconductor-decontam-1.0.0-r351_0.tar.bz2 +name : bioconductor-decontam +version : 1.0.0 +build : r351_0 +build number: 0 +size : 699 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.0.0-r351_0.tar.bz2 +md5 : 4516715a362019afec2e32847850075e +timestamp : 2018-12-19 02:04:58 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.2.1 r351_0 +---------------------------------- +file name : bioconductor-decontam-1.2.1-r351_0.tar.bz2 +name : bioconductor-decontam +version : 1.2.1 +build : r351_0 +build number: 0 +size : 733 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.2.1-r351_0.tar.bz2 +md5 : 82baedd84cfe6053bbda25425c1d71f7 +timestamp : 2019-01-09 11:44:37 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.4.0 r351_0 +---------------------------------- +file name : bioconductor-decontam-1.4.0-r351_0.tar.bz2 +name : bioconductor-decontam +version : 1.4.0 +build : r351_0 +build number: 0 +size : 737 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.4.0-r351_0.tar.bz2 +md5 : b4e2ba0ea639069277d5f7ebc361b92b +timestamp : 2019-05-11 18:40:18 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.4.0 r36_1 +--------------------------------- +file name : bioconductor-decontam-1.4.0-r36_1.tar.bz2 +name : bioconductor-decontam +version : 1.4.0 +build : r36_1 +build number: 1 +size : 733 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.4.0-r36_1.tar.bz2 +md5 : 60c7bd9f5bef618e8f44736cd663ad11 +timestamp : 2019-07-18 11:00:39 UTC +dependencies: + - r-base >=3.6,<3.7.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.6.0 r36_0 +--------------------------------- +file name : bioconductor-decontam-1.6.0-r36_0.tar.bz2 +name : bioconductor-decontam +version : 1.6.0 +build : r36_0 +build number: 0 +size : 741 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.6.0-r36_0.tar.bz2 +md5 : df2a20bd4411caa28717a6836e587627 +timestamp : 2019-11-01 12:39:59 UTC +dependencies: + - r-base >=3.6,<3.7.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.8.0 r40_0 +--------------------------------- +file name : bioconductor-decontam-1.8.0-r40_0.tar.bz2 +name : bioconductor-decontam +version : 1.8.0 +build : r40_0 +build number: 0 +size : 731 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.8.0-r40_0.tar.bz2 +md5 : 526ad6016a7a80055a0c2620a5d1ffe0 +timestamp : 2020-05-09 14:32:20 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.10.0 r40_0 +---------------------------------- +file name : bioconductor-decontam-1.10.0-r40_0.tar.bz2 +name : bioconductor-decontam +version : 1.10.0 +build : r40_0 +build number: 0 +size : 735 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.10.0-r40_0.tar.bz2 +md5 : 67337ebc1b845ae2ae37e0959f9eac53 +timestamp : 2020-10-29 16:55:23 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.10.0 r40hdfd78af_1 +------------------------------------------ +file name : bioconductor-decontam-1.10.0-r40hdfd78af_1.tar.bz2 +name : bioconductor-decontam +version : 1.10.0 +build : r40hdfd78af_1 +build number: 1 +size : 742 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.10.0-r40hdfd78af_1.tar.bz2 +md5 : 4b7dce05cbf0ae1bd7eda260986840b8 +timestamp : 2021-03-25 19:48:06 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.12.0 r41hdfd78af_0 +------------------------------------------ +file name : bioconductor-decontam-1.12.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-decontam +version : 1.12.0 +build : r41hdfd78af_0 +build number: 0 +size : 740 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.12.0-r41hdfd78af_0.tar.bz2 +md5 : 18e7e0eb2754f63ecc37fed96d37d8c9 +timestamp : 2021-05-30 21:26:54 UTC +dependencies: + - r-base >=4.1,<4.2.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.14.0 r41hdfd78af_0 +------------------------------------------ +file name : bioconductor-decontam-1.14.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-decontam +version : 1.14.0 +build : r41hdfd78af_0 +build number: 0 +size : 751 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.14.0-r41hdfd78af_0.tar.bz2 +md5 : 8a8467938a79304d74f3edff935f7cce +timestamp : 2021-11-01 15:36:02 UTC +dependencies: + - r-base >=4.1,<4.2.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.18.0 r42hdfd78af_0 +------------------------------------------ +file name : bioconductor-decontam-1.18.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-decontam +version : 1.18.0 +build : r42hdfd78af_0 +build number: 0 +size : 751 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.18.0-r42hdfd78af_0.tar.bz2 +md5 : 9398479e9b8c9d06bd3fd3e8f0041433 +timestamp : 2022-11-03 08:02:49 UTC +dependencies: + - r-base >=4.2,<4.3.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.20.0 r43hdfd78af_0 +------------------------------------------ +file name : bioconductor-decontam-1.20.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-decontam +version : 1.20.0 +build : r43hdfd78af_0 +build number: 0 +size : 751 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.20.0-r43hdfd78af_0.tar.bz2 +md5 : 8fa7d79f48131f5c78c5841b03070e1d +timestamp : 2023-07-07 08:07:46 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.22.0 r43hdfd78af_0 +------------------------------------------ +file name : bioconductor-decontam-1.22.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-decontam +version : 1.22.0 +build : r43hdfd78af_0 +build number: 0 +size : 751 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.22.0-r43hdfd78af_0.tar.bz2 +md5 : c85d5a6c5b5af622c4d74608fecdddfe +timestamp : 2023-12-03 21:33:49 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.26.0 r44hdfd78af_0 +------------------------------------------ +file name : bioconductor-decontam-1.26.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-decontam +version : 1.26.0 +build : r44hdfd78af_0 +build number: 0 +size : 778 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.26.0-r44hdfd78af_0.tar.bz2 +md5 : ad49011ef2718b7c1aa976768dd49f97 +timestamp : 2024-12-14 15:39:54 UTC +dependencies: + - r-base >=4.4,<4.5.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.30.0 r45hdfd78af_0 +------------------------------------------ +file name : bioconductor-decontam-1.30.0-r45hdfd78af_0.conda +name : bioconductor-decontam +version : 1.30.0 +build : r45hdfd78af_0 +build number: 0 +size : 726 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.30.0-r45hdfd78af_0.conda +md5 : 659295a9671bc212cd9d149457609018 +timestamp : 2026-01-07 20:07:34 UTC +dependencies: + - r-base >=4.5,<4.6.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 + + +bioconductor-decontam 1.30.0 r45hdfd78af_1 +------------------------------------------ +file name : bioconductor-decontam-1.30.0-r45hdfd78af_1.conda +name : bioconductor-decontam +version : 1.30.0 +build : r45hdfd78af_1 +build number: 1 +size : 726 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.30.0-r45hdfd78af_1.conda +md5 : 66ad8efefa92a70a3b0b6a83499d97c1 +timestamp : 2026-02-07 14:55:59 UTC +dependencies: + - r-base >=4.5,<4.6.0a0 + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-deconvobuddies.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-deconvobuddies.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2c1f2308d1f4bbf9c08fde5811a1cc73b57c614e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-deconvobuddies.manual_bundle.txt @@ -0,0 +1,58 @@ +# Tool: bioconductor-deconvobuddies +software_name: bioconductor-deconvobuddies +tier: T1 +domain: spatial_transcriptomics +downloads: 31 +summary: Helper Functions for LIBD Deconvolution +description: Funtions helpful for LIBD deconvolution project. Includes tools for marker finding with mean ratio, expression plotting, and plotting deconvolution results. Working to include DLPFC datasets. +dependencies: bioconductor-annotationhub >=4.0.0,<4.1.0, bioconductor-biocfilecache >=3.0.0,<3.1.0, bioconductor-delayedmatrixstats >=1.32.0,<1.33.0, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scran >=1.38.0,<1.39.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatiallibd >=1.22.0,<1.23.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-dplyr, r-ggplot2, r-purrr, r-rafalib, r-reshape2, r-stringr, r-tibble +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/DeconvoBuddies.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/DeconvoBuddies.html +Bioconductor - DeconvoBuddies Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages DeconvoBuddies DeconvoBuddies This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see DeconvoBuddies . Helper Functions for LIBD Deconvolution DOI: 10.18129/B9.bioc.DeconvoBuddies Bioconductor version: 3.22 Funtions helpful for LIBD deconvolution project. Includes tools for marker finding with mean ratio, expression plotting, and plotting deconvolution results. Working to include DLPFC datasets. Author: Louise Huuki-Myers [aut, cre] ORCID: 0000-0001-5148-3602 , Leonardo Collado-Torres [ctb] ORCID: 0000-0003-2140-308X Maintainer: Louise Huuki-Myers <lahuuki at gmail.com> Citation (from within R, enter citation("DeconvoBuddies") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DeconvoBuddies") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("DeconvoBuddies") Deconvolution Benchmark in Human DLPFC HTML R Script Finding Marker Genes with DeconvoBuddies HTML R Script Get Started with DeconvoBuddies HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentHubSoftware , GeneExpression , RNASeq , SingleCell , Software , Transcriptomics Version 1.2.0 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License Artistic-2.0 Depends R (>= 4.4.0) Imports AnnotationHub , BiocFileCache , DelayedMatrixStats , dplyr , ExperimentHub , ggplot2 , graphics, grDevices, MatrixGenerics , methods, purrr , rafalib , reshape2 , S4Vectors , scran , SingleCellExperiment , spatialLIBD , stats, stringr , SummarizedExperiment , tibble , utils System Requirements URL https://github.com/lahuuki/DeconvoBuddies Bug Reports https://github.com/LieberInstitute/DeconvoBuddies/issues See More Suggests Biobase , BiocStyle , covr , HDF5Array , knitr , RColorBrewer , RefManageR , rmarkdown , sessioninfo , testthat (>= 3.0.0), tidyr , tidyverse Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package DeconvoBuddies_1.2.0.tar.gz Windows Binary (x86_64) DeconvoBuddies_1.2.0.zip macOS Binary (x86_64) DeconvoBuddies_1.2.0.tgz macOS Binary (arm64) DeconvoBuddies_1.2.0.tgz Source Repository git clone https://git.bioconductor.org/packages/DeconvoBuddies Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DeconvoBuddies Bioc Package Browser https://code.bioconductor.org/browse/DeconvoBuddies/ Package Short Url https://bioconductor.org/packages/DeconvoBuddies/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-deconvobuddies --info +[rc=0] +2 channel Terms of Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-deconvobuddies 1.2.0 r45hdfd78af_0 +----------------------------------------------- +file name : bioconductor-deconvobuddies-1.2.0-r45hdfd78af_0.conda +name : bioconductor-deconvobuddies +version : 1.2.0 +build : r45hdfd78af_0 +build number: 0 +size : 5.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-deconvobuddies-1.2.0-r45hdfd78af_0.conda +md5 : 77de41c166da27b1831eec7cd31f6f4f +timestamp : 2026-03-03 07:09:18 UTC +dependencies: + - bioconductor-annotationhub >=4.0.0,<4.1.0 + - bioconductor-biocfilecache >=3.0.0,<3.1.0 + - bioconductor-delayedmatrixstats >=1.32.0,<1.33.0 + - bioconductor-experimenthub >=3.0.0,<3.1.0 + - bioconductor-matrixgenerics >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-scran >=1.38.0,<1.39.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatiallibd >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-dplyr + - r-ggplot2 + - r-purrr + - r-rafalib + - r-reshape2 + - r-stringr + - r-tibble diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-delayedmatrixstats.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-delayedmatrixstats.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..264ee9116a6ee833f2d6135adeb76df1c866a9bc --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-delayedmatrixstats.manual_bundle.txt @@ -0,0 +1,343 @@ +# Tool: bioconductor-delayedmatrixstats +software_name: bioconductor-delayedmatrixstats +tier: T1 +domain: t1_backfill_overall +downloads: 536481 +summary: Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects +description: A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. +dependencies: bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-iranges >=2.44.0,<2.45.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-sparsearray >=1.10.0,<1.11.0, bioconductor-sparsematrixstats >=1.22.0,<1.23.0, r-base >=4.5,<4.6.0a0, r-matrix >=1.5-0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: http://bioconductor.org/packages/3.7/bioc/html/DelayedMatrixStats.html +doc_url: +dev_url: + +## URL Docs Extract +### http://bioconductor.org/packages/3.7/bioc/html/DelayedMatrixStats.html +Bioconductor - DelayedMatrixStats About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.7 Software Packages DelayedMatrixStats DelayedMatrixStats This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see DelayedMatrixStats . Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects DOI: 10.18129/B9.bioc.DelayedMatrixStats Bioconductor version: 3.7 A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. Author: Peter Hickey <peter.hickey at gmail.com> Maintainer: Peter Hickey <peter.hickey at gmail.com> Citation (from within R, enter citation("DelayedMatrixStats") ): Installation To install this package, start R (version "3.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DelayedMatrixStats") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("DelayedMatrixStats") Overview of DelayedMatrixStats HTML R Script Reference Manual PDF LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataRepresentation , Infrastructure , Software Version 1.2.0 In Bioconductor since BioC 3.6 (R-3.4) (6.5 years) License MIT + file LICENSE Depends DelayedArray (>= 0.5.27) Imports methods, matrixStats (>= 0.53.1), Matrix, S4Vectors (>= 0.17.5), IRanges System Requirements URL https://github.com/PeteHaitch/DelayedMatrixStats Bug Reports https://github.com/PeteHaitch/DelayedMatrixStats/issues See More Suggests testthat, HDF5Array (>= 1.7.10), knitr, rmarkdown, covr, BiocStyle , microbenchmark, profmem Linking To Enhances Depends On Me Imports Me bsseq , dmrseq , minfi , scater , scran Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package DelayedMatrixStats_1.2.0.tar.gz Windows Binary DelayedMatrixStats_1.2.0.zip Mac OS X 10.11 (El Capitan) DelayedMatrixStats_1.2.0.tgz Source Repository git clone https://git.bioconductor.org/packages/DelayedMatrixStats Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DelayedMatrixStats Package Short Url https://bioconductor.org/packages/DelayedMatrixStats/ Package Downloads Report Download Stats Old Source Packages for BioC 3.7 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-delayedmatrixstats --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-delayedmatrixstats 1.2.0 r341_0 +-------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.2.0-r341_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.2.0 +build : r341_0 +build number: 0 +size : 621 KB +license : MIT + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-delayedmatrixstats-1.2.0-r341_0.tar.bz2 +md5 : 4e85c5354071920cccc475a74a6d1789 +timestamp : 2018-10-12 13:28:28 UTC +dependencies: + - bioconductor-delayedarray >=0.6.6,<0.8.0 + - bioconductor-iranges >=2.14.12,<2.16.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - r-base >=3.4.1,<3.4.2.0a0 + - r-matrix + - r-matrixstats >=0.53.1 + + +bioconductor-delayedmatrixstats 1.2.0 r351_0 +-------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.2.0-r351_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.2.0 +build : r351_0 +build number: 0 +size : 709 KB +license : MIT + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-delayedmatrixstats-1.2.0-r351_0.tar.bz2 +md5 : c833de95106231ae6f4c86894531b018 +timestamp : 2018-10-12 13:26:47 UTC +dependencies: + - bioconductor-delayedarray >=0.6.6,<0.8.0 + - bioconductor-iranges >=2.14.12,<2.16.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-matrix + - r-matrixstats >=0.53.1 + + +bioconductor-delayedmatrixstats 1.4.0 r351_0 +-------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.4.0-r351_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.4.0 +build : r351_0 +build number: 0 +size : 712 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.4.0-r351_0.tar.bz2 +md5 : 5da706b3b1a6104cc8648050ad575668 +timestamp : 2018-12-11 16:30:24 UTC +dependencies: + - bioconductor-biocparallel >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.8.0,<0.9.0 + - bioconductor-hdf5array >=1.10.0,<1.11.0 + - bioconductor-iranges >=2.16.0,<2.17.0 + - bioconductor-s4vectors >=0.20.0,<0.21.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-matrix + - r-matrixstats >=0.53.1 + + +bioconductor-delayedmatrixstats 1.4.0 r351_1 +-------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.4.0-r351_1.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.4.0 +build : r351_1 +build number: 1 +size : 712 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.4.0-r351_1.tar.bz2 +md5 : 7608a4f8816eb8ad7c26f5d07c299a22 +timestamp : 2019-03-10 12:41:02 UTC +dependencies: + - bioconductor-biocparallel >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.8.0,<0.9.0 + - bioconductor-hdf5array >=1.10.0,<1.11.0 + - bioconductor-iranges >=2.16.0,<2.17.0 + - bioconductor-s4vectors >=0.20.0,<0.21.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-matrix + - r-matrixstats >=0.53.1 + + +bioconductor-delayedmatrixstats 1.6.0 r36_1 +------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.6.0-r36_1.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.6.0 +build : r36_1 +build number: 1 +size : 695 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.6.0-r36_1.tar.bz2 +md5 : 8f24604d354147fca84733626ba31c2d +timestamp : 2019-07-24 16:18:36 UTC +dependencies: + - bioconductor-biocparallel >=1.18.0,<1.19.0 + - bioconductor-delayedarray >=0.10.0,<0.11.0 + - bioconductor-hdf5array >=1.12.0,<1.13.0 + - bioconductor-iranges >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.22.0,<0.23.0 + - r-base >=3.6,<3.7.0a0 + - r-matrix + - r-matrixstats >=0.53.1 + + +bioconductor-delayedmatrixstats 1.8.0 r36_0 +------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.8.0-r36_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.8.0 +build : r36_0 +build number: 0 +size : 712 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.8.0-r36_0.tar.bz2 +md5 : 52f864c3627f6cddb8581d9c9b22c0e7 +timestamp : 2019-11-03 17:54:02 UTC +dependencies: + - bioconductor-biocparallel >=1.20.0,<1.21.0 + - bioconductor-delayedarray >=0.12.0,<0.13.0 + - bioconductor-hdf5array >=1.14.0,<1.15.0 + - bioconductor-iranges >=2.20.0,<2.21.0 + - bioconductor-s4vectors >=0.24.0,<0.25.0 + - r-base >=3.6,<3.7.0a0 + - r-matrix + - r-matrixstats >=0.55.0 + + +bioconductor-delayedmatrixstats 1.10.0 r40_0 +-------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.10.0-r40_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.10.0 +build : r40_0 +build number: 0 +size : 720 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.10.0-r40_0.tar.bz2 +md5 : e39dd812ab80f634c0205387cb02358f +timestamp : 2020-05-10 06:12:20 UTC +dependencies: + - bioconductor-biocparallel >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.14.0,<0.15.0 + - bioconductor-hdf5array >=1.16.0,<1.17.0 + - bioconductor-iranges >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.26.0,<0.27.0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + - r-matrixstats >=0.56.0 + + +bioconductor-delayedmatrixstats 1.12.0 r40_0 +-------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.12.0-r40_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.12.0 +build : r40_0 +build number: 0 +size : 700 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.12.0-r40_0.tar.bz2 +md5 : c960ae00e16989b0743bf9e24675b03d +timestamp : 2020-10-30 12:46:01 UTC +dependencies: + - bioconductor-biocparallel >=1.24.0,<1.25.0 + - bioconductor-delayedarray >=0.16.0,<0.17.0 + - bioconductor-hdf5array >=1.18.0,<1.19.0 + - bioconductor-iranges >=2.24.0,<2.25.0 + - bioconductor-matrixgenerics >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - bioconductor-sparsematrixstats >=1.2.0,<1.3.0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + - r-matrixstats >=0.56.0 + + +bioconductor-delayedmatrixstats 1.12.3 r40hdfd78af_0 +---------------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.12.3-r40hdfd78af_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.12.3 +build : r40hdfd78af_0 +build number: 0 +size : 705 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.12.3-r40hdfd78af_0.tar.bz2 +md5 : baf369164cc56e71688c59b84efc6d4e +timestamp : 2021-03-29 10:59:13 UTC +dependencies: + - bioconductor-biocparallel >=1.24.0,<1.25.0 + - bioconductor-delayedarray >=0.16.0,<0.17.0 + - bioconductor-hdf5array >=1.18.0,<1.19.0 + - bioconductor-iranges >=2.24.0,<2.25.0 + - bioconductor-matrixgenerics >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - bioconductor-sparsematrixstats >=1.2.0,<1.3.0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + - r-matrixstats >=0.56.0 + + +bioconductor-delayedmatrixstats 1.14.0 r41hdfd78af_0 +---------------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.14.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.14.0 +build : r41hdfd78af_0 +build number: 0 +size : 705 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.14.0-r41hdfd78af_0.tar.bz2 +md5 : 788fb46ff1acb3281fb1aaca0254c210 +timestamp : 2021-06-01 01:22:21 UTC +dependencies: + - bioconductor-delayedarray >=0.18.0,<0.19.0 + - bioconductor-iranges >=2.26.0,<2.27.0 + - bioconductor-matrixgenerics >=1.4.0,<1.5.0 + - bioconductor-s4vectors >=0.30.0,<0.31.0 + - bioconductor-sparsematrixstats >=1.4.0,<1.5.0 + - r-base >=4.1,<4.2.0a0 + - r-matrix + - r-matrixstats >=0.56.0 + + +bioconductor-delayedmatrixstats 1.16.0 r41hdfd78af_0 +---------------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.16.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.16.0 +build : r41hdfd78af_0 +build number: 0 +size : 729 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.16.0-r41hdfd78af_0.tar.bz2 +md5 : 7bfc1332d154df91e5b3fd71fbb4bf89 +timestamp : 2021-11-03 11:17:18 UTC +dependencies: + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-iranges >=2.28.0,<2.29.0 + - bioconductor-matrixgenerics >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-sparsematrixstats >=1.6.0,<1.7.0 + - r-base >=4.1,<4.2.0a0 + - r-matrix + - r-matrixstats >=0.60.0 + + +bioconductor-delayedmatrixstats 1.20.0 r42hdfd78af_0 +---------------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.20.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.20.0 +build : r42hdfd78af_0 +build number: 0 +size : 722 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.20.0-r42hdfd78af_0.tar.bz2 +md5 : c303ba14d25cdd2ba0bca5a9f0914bf4 +timestamp : 2022-11-04 14:23:43 UTC +dependencies: + - bioconductor-delayedarray >=0.24.0,<0.25.0 + - bioconductor-iranges >=2.32.0,<2.33.0 + - bioconductor-matrixgenerics >=1.10.0,<1.11.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-sparsematrixstats >=1.10.0,<1.11.0 + - r-base >=4.2,<4.3.0a0 + - r-matrix >=1.5-0 + - r-matrixstats >=0.60.0 + + +bioconductor-delayedmatrixstats 1.22.1 r43hdfd78af_0 +---------------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.22.1-r43hdfd78af_0.tar.bz2 +name : bioconductor-delayedmatrixstats +version : 1.22.1 +build : r43hdfd78af_0 +build number: 0 +size : 783 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.22.1-r43hdfd78af_0.tar.bz2 +md5 : c34a80ef52ed8e189a9903934ea06349 +timestamp : 2023-07-11 09:02:58 UTC +dependencies: + - bioconductor-delayedarray >=0.26.0,<0.27.0 + - bioconductor-iranges >=2.34.0,<2.35.0 + - bioconductor-matrixgenerics >=1.12.0,<1.13.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-sparsematrixstats >=1.12.0,<1.13.0 + - r-base >=4.3,<4.4.0a0 + - r-matrix >=1.5-0 + - r-matrixstats >=1.0.0 + + +bioconductor-delayedmatrixstats 1.24.0 r43hdfd78af_0 +---------------------------------------------------- +file name : bioconductor-delayedmatrixstats-1.24.0-r43hdfd78af_0.tar.b diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-despace.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-despace.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..5548d677c674831282f18232c68817cafeabc1b0 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-despace.manual_bundle.txt @@ -0,0 +1,167 @@ +# Tool: bioconductor-despace +software_name: bioconductor-despace +tier: T1 +domain: spatial_transcriptomics +downloads: 3385 +summary: DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions +description: Intuitive framework for identifying spatially variable genes (SVGs) and differential spatial variable pattern (DSP) between conditions via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. For multi-sample, multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial clusters, conditions and their interactions as covariates. DSP genes-representing differences in spatial gene expression patterns across experimental conditions-are identified by testing the interaction between spatial clusters and conditions. +dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-edger >=4.8.0,<4.9.0, bioconductor-limma >=3.66.0,<3.67.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scuttle >=1.20.0,<1.21.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-assertthat, r-base >=4.5,<4.6.0a0, r-data.table, r-dplyr, r-ggforce, r-ggnewscale, r-ggplot2, r-matrix, r-patchwork, r-scales, r-sf, r-spatstat.explore, r-spatstat.geom, r-terra +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.17/bioc/html/DESpace.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.17/bioc/html/DESpace.html +Bioconductor - DESpace About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.17 Software Packages DESpace DESpace This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see DESpace . DESpace: a framework to discover spatially variable genes DOI: 10.18129/B9.bioc.DESpace Bioconductor version: 3.17 Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. The method is flexible and robust, and is faster than the most SV methods. Furthermore, to the best of our knowledge, it is the only SV approach that allows: - performing a SV test on each individual spatial cluster, hence identifying the key regions of the tissue affected by spatial variability; - jointly fitting multiple samples, targeting genes with consistent spatial patterns across replicates. Author: Peiying Cai [aut, cre] , Simone Tiberi [aut, cte] Maintainer: Peiying Cai <peiying.cai at uzh.ch> Citation (from within R, enter citation("DESpace") ): Installation To install this package, start R (version "4.3") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DESpace") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("DESpace") A framework to discover spatially variable genes HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DifferentialExpression , GeneExpression , RNASeq , Sequencing , SingleCell , Software , Spatial , StatisticalMethod , Transcriptomics , Visualization Version 1.0.0 In Bioconductor since BioC 3.17 (R-4.3) (1 year) License GPL-3 Depends R (>= 4.3.0) Imports edgeR , limma , dplyr, stats, Matrix, SpatialExperiment , ggplot2, ggpubr, scales, SummarizedExperiment , S4Vectors , BiocGenerics , data.table, assertthat, cowplot, ggforce, ggnewscale, patchwork, BiocParallel , methods System Requirements URL https://github.com/peicai/DESpace Bug Reports https://github.com/peicai/DESpace/issues See More Suggests knitr, rmarkdown, testthat, BiocStyle , ExperimentHub , concaveman, spatialLIBD , purrr, scuttle , utils Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package DESpace_1.0.0.tar.gz Windows Binary DESpace_1.0.0.zip macOS Binary (x86_64) DESpace_1.0.0.tgz macOS Binary (arm64) DESpace_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/DESpace Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DESpace Bioc Package Browser https://code.bioconductor.org/browse/DESpace/ Package Short Url https://bioconductor.org/packages/DESpace/ Package Downloads Report Download Stats Old Source Packages for BioC 3.17 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-despace --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-despace 1.0.0 r43hdfd78af_0 +---------------------------------------- +file name : bioconductor-despace-1.0.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-despace +version : 1.0.0 +build : r43hdfd78af_0 +build number: 0 +size : 3.7 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-despace-1.0.0-r43hdfd78af_0.tar.bz2 +md5 : 4a2a753cf04467327bf250921da5d227 +timestamp : 2023-07-16 01:34:09 UTC +dependencies: + - bioconductor-biocgenerics >=0.46.0,<0.47.0 + - bioconductor-biocparallel >=1.34.0,<1.35.0 + - bioconductor-edger >=3.42.0,<3.43.0 + - bioconductor-limma >=3.56.0,<3.57.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-assertthat + - r-base >=4.3,<4.4.0a0 + - r-cowplot + - r-data.table + - r-dplyr + - r-ggforce + - r-ggnewscale + - r-ggplot2 + - r-ggpubr + - r-matrix + - r-patchwork + - r-scales + + +bioconductor-despace 1.2.0 r43hdfd78af_0 +---------------------------------------- +file name : bioconductor-despace-1.2.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-despace +version : 1.2.0 +build : r43hdfd78af_0 +build number: 0 +size : 3.7 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-despace-1.2.0-r43hdfd78af_0.tar.bz2 +md5 : 2514f73704dd407706906068bd5ff879 +timestamp : 2023-12-07 01:33:35 UTC +dependencies: + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - bioconductor-edger >=4.0.0,<4.1.0 + - bioconductor-limma >=3.58.0,<3.59.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-assertthat + - r-base >=4.3,<4.4.0a0 + - r-cowplot + - r-data.table + - r-dplyr + - r-ggforce + - r-ggnewscale + - r-ggplot2 + - r-ggpubr + - r-matrix + - r-patchwork + - r-scales + + +bioconductor-despace 1.6.0 r44hdfd78af_0 +---------------------------------------- +file name : bioconductor-despace-1.6.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-despace +version : 1.6.0 +build : r44hdfd78af_0 +build number: 0 +size : 3.7 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-despace-1.6.0-r44hdfd78af_0.tar.bz2 +md5 : d4baa1ce08b5169f77409b0369918d46 +timestamp : 2024-12-22 11:18:35 UTC +dependencies: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-assertthat + - r-base >=4.4,<4.5.0a0 + - r-cowplot + - r-data.table + - r-dplyr + - r-ggforce + - r-ggnewscale + - r-ggplot2 + - r-ggpubr + - r-matrix + - r-patchwork + - r-scales + + +bioconductor-despace 2.2.2 r45h84498cf_0 +---------------------------------------- +file name : bioconductor-despace-2.2.2-r45h84498cf_0.conda +name : bioconductor-despace +version : 2.2.2 +build : r45h84498cf_0 +build number: 0 +size : 6.8 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-despace-2.2.2-r45h84498cf_0.conda +md5 : 476b0569f85ea1454930a979d484e158 +timestamp : 2026-03-01 16:58:10 UTC +dependencies: + - bioconductor-biocgenerics >=0.56.0,<0.57.0 + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-edger >=4.8.0,<4.9.0 + - bioconductor-limma >=3.66.0,<3.67.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-scuttle >=1.20.0,<1.21.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-assertthat + - r-base >=4.5,<4.6.0a0 + - r-data.table + - r-dplyr + - r-ggforce + - r-ggnewscale + - r-ggplot2 + - r-matrix + - r-patchwork + - r-scales + - r-sf + - r-spatstat.explore + - r-spatstat.geom + - r-terra diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-dnacopy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-dnacopy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a8ad4a91565761c80d16ed2149c1ac7d6f2bc97 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-dnacopy.manual_bundle.txt @@ -0,0 +1,412 @@ +# Tool: bioconductor-dnacopy +software_name: bioconductor-dnacopy +tier: T1 +domain: t1_backfill_overall +downloads: 205182 +summary: DNA Copy Number Data Analysis +description: Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number. +dependencies: libblas >=3.9.0,<4.0a0, libgcc >=14, libgfortran, libgfortran5 >=14.3.0, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/DNAcopy.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/DNAcopy.html +Bioconductor - DNAcopy Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages DNAcopy DNAcopy This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see DNAcopy . DNA Copy Number Data Analysis DOI: 10.18129/B9.bioc.DNAcopy Bioconductor version: 3.22 Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number. Author: Venkatraman E. Seshan, Adam Olshen Maintainer: Venkatraman E. Seshan <seshanv at mskcc.org> Citation (from within R, enter citation("DNAcopy") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DNAcopy") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("DNAcopy") DNAcopy PDF R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews CopyNumberVariation , Microarray , Software Version 1.84.0 In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 21 years) License GPL (>= 2) Depends Imports System Requirements URL See More Suggests Linking To Enhances Depends On Me CGHcall , cghMCR , CRImage , PureCN , CSclone , ParDNAcopy , saasCNV Imports Me ADaCGH2 , ChAMP , cn.farms , CNAnorm , CNVrd2 , conumee , GWASTools , maftools , MDTS , MEDIPS , MinimumDistance , QDNAseq , SCOPE , jointseg , PSCBS Suggests Me cn.mops , CopyNumberPlots , fastseg , nullranges , sesame , ACNE , aroma.cn , aroma.core , calmate Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package DNAcopy_1.84.0.tar.gz Windows Binary (x86_64) DNAcopy_1.84.0.zip macOS Binary (x86_64) DNAcopy_1.84.0.tgz macOS Binary (arm64) DNAcopy_1.84.0.tgz Source Repository git clone https://git.bioconductor.org/packages/DNAcopy Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DNAcopy Bioc Package Browser https://code.bioconductor.org/browse/DNAcopy/ Package Short Url https://bioconductor.org/packages/DNAcopy/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-dnacopy --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-dnacopy 1.44.0 r3.2.2_0 +------------------------------------ +file name : bioconductor-dnacopy-1.44.0-r3.2.2_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.44.0 +build : r3.2.2_0 +build number: 0 +size : 175 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.44.0-r3.2.2_0.tar.bz2 +md5 : c89dadade5cc3f2bc78daedc27015c89 +dependencies: + - r 3.2.2* + + +bioconductor-dnacopy 1.46.0 r3.3.1_0 +------------------------------------ +file name : bioconductor-dnacopy-1.46.0-r3.3.1_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.46.0 +build : r3.3.1_0 +build number: 0 +size : 178 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.46.0-r3.3.1_0.tar.bz2 +md5 : fcf23d637d5d3045e73093bc0207390f +dependencies: + - r 3.3.1* + + +bioconductor-dnacopy 1.46.0 r3.3.2_0 +------------------------------------ +file name : bioconductor-dnacopy-1.46.0-r3.3.2_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.46.0 +build : r3.3.2_0 +build number: 0 +size : 180 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.46.0-r3.3.2_0.tar.bz2 +md5 : 43b4b704d1bf3704fce9fe7cd63508c0 +dependencies: + - r-base 3.3.2* + + +bioconductor-dnacopy 1.46.0 r3.4.1_0 +------------------------------------ +file name : bioconductor-dnacopy-1.46.0-r3.4.1_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.46.0 +build : r3.4.1_0 +build number: 0 +size : 183 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.46.0-r3.4.1_0.tar.bz2 +md5 : 2c540a9d895e43f2f2c23e9f8c9dc4ec +dependencies: + - r-base 3.4.1* + + +bioconductor-dnacopy 1.48.0 r3.3.2_0 +------------------------------------ +file name : bioconductor-dnacopy-1.48.0-r3.3.2_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.48.0 +build : r3.3.2_0 +build number: 0 +size : 183 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.48.0-r3.3.2_0.tar.bz2 +md5 : 9c9300776d181451a107dc710b5ef9bf +dependencies: + - libgcc + - r-base 3.3.2* + + +bioconductor-dnacopy 1.48.0 r3.4.1_0 +------------------------------------ +file name : bioconductor-dnacopy-1.48.0-r3.4.1_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.48.0 +build : r3.4.1_0 +build number: 0 +size : 183 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.48.0-r3.4.1_0.tar.bz2 +md5 : a2b98c226bc26c0daab0421d0212bd7e +dependencies: + - libgcc + - r-base 3.4.1* + + +bioconductor-dnacopy 1.48.0 r341h470a237_1 +------------------------------------------ +file name : bioconductor-dnacopy-1.48.0-r341h470a237_1.tar.bz2 +name : bioconductor-dnacopy +version : 1.48.0 +build : r341h470a237_1 +build number: 1 +size : 182 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.48.0-r341h470a237_1.tar.bz2 +md5 : 83ee6a2ecf88a8216bd242b71ac3e924 +timestamp : 2018-10-11 09:55:40 UTC +dependencies: + - libgcc-ng >=4.9 + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-dnacopy 1.48.0 r351h470a237_1 +------------------------------------------ +file name : bioconductor-dnacopy-1.48.0-r351h470a237_1.tar.bz2 +name : bioconductor-dnacopy +version : 1.48.0 +build : r351h470a237_1 +build number: 1 +size : 225 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.48.0-r351h470a237_1.tar.bz2 +md5 : f53a5bf91768331b16922d593b50e4df +timestamp : 2018-10-11 09:56:35 UTC +dependencies: + - libgcc-ng >=4.9 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-dnacopy 1.50.1 r3.4.1_0 +------------------------------------ +file name : bioconductor-dnacopy-1.50.1-r3.4.1_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.50.1 +build : r3.4.1_0 +build number: 0 +size : 396 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.50.1-r3.4.1_0.tar.bz2 +md5 : ecba8e6b731ad22d6d36ec29c4fd8d2b +dependencies: + - r-base 3.4.1* + + +bioconductor-dnacopy 1.52.0 r3.4.1_0 +------------------------------------ +file name : bioconductor-dnacopy-1.52.0-r3.4.1_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.52.0 +build : r3.4.1_0 +build number: 0 +size : 396 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.52.0-r3.4.1_0.tar.bz2 +md5 : 14aff29f14d9227e877df99023314174 +dependencies: + - r-base 3.4.1* + + +bioconductor-dnacopy 1.54.0 r341ha44fe06_0 +------------------------------------------ +file name : bioconductor-dnacopy-1.54.0-r341ha44fe06_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.54.0 +build : r341ha44fe06_0 +build number: 0 +size : 395 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.54.0-r341ha44fe06_0.tar.bz2 +md5 : 283a6f3d42120809c51ebb1139a345a9 +timestamp : 2018-10-11 10:05:25 UTC +dependencies: + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-dnacopy 1.54.0 r351ha44fe06_0 +------------------------------------------ +file name : bioconductor-dnacopy-1.54.0-r351ha44fe06_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.54.0 +build : r351ha44fe06_0 +build number: 0 +size : 437 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.54.0-r351ha44fe06_0.tar.bz2 +md5 : c16d47cdd139f12aaae8322c5188c8ed +timestamp : 2018-10-11 10:06:15 UTC +dependencies: + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-dnacopy 1.56.0 r351h9ac9557_0 +------------------------------------------ +file name : bioconductor-dnacopy-1.56.0-r351h9ac9557_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.56.0 +build : r351h9ac9557_0 +build number: 0 +size : 435 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.56.0-r351h9ac9557_0.tar.bz2 +md5 : 6c1c85cb39f84b924e05fe95782446f0 +timestamp : 2018-12-10 10:45:10 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-dnacopy 1.58.0 r351h9ac9557_0 +------------------------------------------ +file name : bioconductor-dnacopy-1.58.0-r351h9ac9557_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.58.0 +build : r351h9ac9557_0 +build number: 0 +size : 435 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.58.0-r351h9ac9557_0.tar.bz2 +md5 : 2cf20df40125590e48a7cb6aa5580683 +timestamp : 2019-05-09 12:24:35 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-dnacopy 1.58.0 r36h6e990d7_1 +----------------------------------------- +file name : bioconductor-dnacopy-1.58.0-r36h6e990d7_1.tar.bz2 +name : bioconductor-dnacopy +version : 1.58.0 +build : r36h6e990d7_1 +build number: 1 +size : 436 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.58.0-r36h6e990d7_1.tar.bz2 +md5 : 135914b4ecea2116a53c3b1c6c094159 +timestamp : 2019-07-21 14:07:55 UTC +dependencies: + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-dnacopy 1.58.0 r36h6e990d7_2 +----------------------------------------- +file name : bioconductor-dnacopy-1.58.0-r36h6e990d7_2.tar.bz2 +name : bioconductor-dnacopy +version : 1.58.0 +build : r36h6e990d7_2 +build number: 2 +size : 438 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.58.0-r36h6e990d7_2.tar.bz2 +md5 : 61efc8fce58bdc90469a75b9701c0e91 +timestamp : 2019-10-29 10:42:16 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-dnacopy 1.60.0 r36h6e990d7_0 +----------------------------------------- +file name : bioconductor-dnacopy-1.60.0-r36h6e990d7_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.60.0 +build : r36h6e990d7_0 +build number: 0 +size : 448 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.60.0-r36h6e990d7_0.tar.bz2 +md5 : e29072e0c925a82b32902a19df22420e +timestamp : 2019-11-01 09:34:18 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-dnacopy 1.62.0 r40h323e27b_0 +----------------------------------------- +file name : bioconductor-dnacopy-1.62.0-r40h323e27b_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.62.0 +build : r40h323e27b_0 +build number: 0 +size : 448 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.62.0-r40h323e27b_0.tar.bz2 +md5 : db0e598251ff8141b1b14cde569c17d1 +timestamp : 2020-05-09 13:23:22 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - liblapack >=3.8.0,<3.9.0a0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-dnacopy 1.64.0 r40h323e27b_0 +----------------------------------------- +file name : bioconductor-dnacopy-1.64.0-r40h323e27b_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.64.0 +build : r40h323e27b_0 +build number: 0 +size : 448 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.64.0-r40h323e27b_0.tar.bz2 +md5 : 7b3741e375b54e50e02b621d1be34890 +timestamp : 2020-10-29 17:41:54 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - libgfortran-ng + - libgfortran4 >=7.5.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-dnacopy 1.64.0 r40hacda110_1 +----------------------------------------- +file name : bioconductor-dnacopy-1.64.0-r40hacda110_1.tar.bz2 +name : bioconductor-dnacopy +version : 1.64.0 +build : r40hacda110_1 +build number: 1 +size : 448 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.64.0-r40hacda110_1.tar.bz2 +md5 : 06904ec5f41713b0f3341c82f123ec2b +timestamp : 2021-03-26 03:44:18 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - libgfortran-ng + - libgfortran5 >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-dnacopy 1.66.0 r41hacda110_0 +----------------------------------------- +file name : bioconductor-dnacopy-1.66.0-r41hacda110_0.tar.bz2 +name : bioconductor-dnacopy +version : 1.66.0 +build : r41hacda110_0 +build number: 0 +size : 435 KB +license : GPL (>= 2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.66.0-r41hacda110_0.tar.bz2 +md5 : 17e2617da455c2ce6c94cd4951c8d6ee +timestamp : 2021 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-ebseq.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-ebseq.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c637c68871f5bac13214fadc8fc618b63533280 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-ebseq.manual_bundle.txt @@ -0,0 +1,444 @@ +# Tool: bioconductor-ebseq +software_name: bioconductor-ebseq +tier: T1 +domain: t1_backfill_overall +downloads: 124439 +summary: An R package for gene and isoform differential expression analysis of RNA-seq data +description: Differential Expression analysis at both gene and isoform level using RNA-seq data +dependencies: libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-bh <=1.87.0-1, r-blockmodeling, r-gplots, r-rcpp >=0.12.11, r-rcppeigen >=0.3.2.9.0, r-testthat +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/EBSeq.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/EBSeq.html +Bioconductor - EBSeq Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages EBSeq EBSeq This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see EBSeq . An R package for gene and isoform differential expression analysis of RNA-seq data DOI: 10.18129/B9.bioc.EBSeq Bioconductor version: 3.22 Differential Expression analysis at both gene and isoform level using RNA-seq data Author: Xiuyu Ma [cre, aut], Ning Leng [aut], Christina Kendziorski [ctb], Michael A. Newton [ctb] Maintainer: Xiuyu Ma <watsonforfun at gmail.com> Citation (from within R, enter citation("EBSeq") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("EBSeq") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("EBSeq") EBSeq Vignette PDF R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DifferentialExpression , ImmunoOncology , MultipleComparison , RNASeq , Sequencing , Software , StatisticalMethod Version 2.8.0 In Bioconductor since BioC 2.13 (R-3.0) (12.5 years) License Artistic-2.0 Depends blockmodeling , gplots , testthat , R (>= 3.0.0) Imports Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0), BH ( System Requirements c++14 URL See More Suggests Linking To Rcpp , RcppEigen , BH Enhances Depends On Me Oscope Imports Me BatchQC , broadSeq , DEsubs , scDD Suggests Me compcodeR Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package EBSeq_2.8.0.tar.gz Windows Binary (x86_64) EBSeq_2.8.0.zip macOS Binary (x86_64) EBSeq_2.8.0.tgz macOS Binary (arm64) EBSeq_2.8.0.tgz Source Repository git clone https://git.bioconductor.org/packages/EBSeq Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EBSeq Bioc Package Browser https://code.bioconductor.org/browse/EBSeq/ Package Short Url https://bioconductor.org/packages/EBSeq/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-ebseq --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-ebseq 1.12.0 0 +--------------------------- +file name : bioconductor-ebseq-1.12.0-0.tar.bz2 +name : bioconductor-ebseq +version : 1.12.0 +build : 0 +build number: 0 +size : 1004 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.12.0-0.tar.bz2 +md5 : d2d052e244d776d3c915058e8bc6fb0b +dependencies: + - r >=3.0.0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.14.0 r3.3.1_0 +---------------------------------- +file name : bioconductor-ebseq-1.14.0-r3.3.1_0.tar.bz2 +name : bioconductor-ebseq +version : 1.14.0 +build : r3.3.1_0 +build number: 0 +size : 180 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.14.0-r3.3.1_0.tar.bz2 +md5 : b35ea585a62637d678e7b324fa6bf668 +dependencies: + - r 3.3.1* + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.14.0 r3.3.1_1 +---------------------------------- +file name : bioconductor-ebseq-1.14.0-r3.3.1_1.tar.bz2 +name : bioconductor-ebseq +version : 1.14.0 +build : r3.3.1_1 +build number: 1 +size : 180 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.14.0-r3.3.1_1.tar.bz2 +md5 : 61c12f97a1652baf1f53159c5344abf8 +dependencies: + - r-base 3.3.1* + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.14.0 r3.3.2_1 +---------------------------------- +file name : bioconductor-ebseq-1.14.0-r3.3.2_1.tar.bz2 +name : bioconductor-ebseq +version : 1.14.0 +build : r3.3.2_1 +build number: 1 +size : 183 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.14.0-r3.3.2_1.tar.bz2 +md5 : 6370cfe2ed729d0f27337c59f44ad573 +dependencies: + - r-base 3.3.2* + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.14.0 r3.4.1_1 +---------------------------------- +file name : bioconductor-ebseq-1.14.0-r3.4.1_1.tar.bz2 +name : bioconductor-ebseq +version : 1.14.0 +build : r3.4.1_1 +build number: 1 +size : 185 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.14.0-r3.4.1_1.tar.bz2 +md5 : 1228a17412e9c4aad4cc2661ef8c294f +dependencies: + - r-base 3.4.1* + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.16.0 r3.4.1_0 +---------------------------------- +file name : bioconductor-ebseq-1.16.0-r3.4.1_0.tar.bz2 +name : bioconductor-ebseq +version : 1.16.0 +build : r3.4.1_0 +build number: 0 +size : 1.0 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.16.0-r3.4.1_0.tar.bz2 +md5 : 77b77081b58180c6f722c0fffaffb63e +dependencies: + - r-base 3.4.1* + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.18.0 r3.4.1_0 +---------------------------------- +file name : bioconductor-ebseq-1.18.0-r3.4.1_0.tar.bz2 +name : bioconductor-ebseq +version : 1.18.0 +build : r3.4.1_0 +build number: 0 +size : 1.0 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.18.0-r3.4.1_0.tar.bz2 +md5 : df757d5743a7cbad81dca429510083fd +dependencies: + - r-base 3.4.1* + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.20.0 r341_0 +-------------------------------- +file name : bioconductor-ebseq-1.20.0-r341_0.tar.bz2 +name : bioconductor-ebseq +version : 1.20.0 +build : r341_0 +build number: 0 +size : 1.0 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.20.0-r341_0.tar.bz2 +md5 : cfd9a2b5e9f16734bbb5ec76aec9e23a +timestamp : 2018-10-12 08:32:21 UTC +dependencies: + - r-base >=3.4.1,<3.4.2.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.20.0 r351_0 +-------------------------------- +file name : bioconductor-ebseq-1.20.0-r351_0.tar.bz2 +name : bioconductor-ebseq +version : 1.20.0 +build : r351_0 +build number: 0 +size : 1.1 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.20.0-r351_0.tar.bz2 +md5 : 47a3ce99ebea3771b1a6e41fd39b0da3 +timestamp : 2018-10-12 08:33:41 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.22.0 r351_0 +-------------------------------- +file name : bioconductor-ebseq-1.22.0-r351_0.tar.bz2 +name : bioconductor-ebseq +version : 1.22.0 +build : r351_0 +build number: 0 +size : 1.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.22.0-r351_0.tar.bz2 +md5 : 34f040f737a8dcbd34b293224fb91828 +timestamp : 2018-12-10 10:10:17 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.22.1 r351_0 +-------------------------------- +file name : bioconductor-ebseq-1.22.1-r351_0.tar.bz2 +name : bioconductor-ebseq +version : 1.22.1 +build : r351_0 +build number: 0 +size : 1.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.22.1-r351_0.tar.bz2 +md5 : e98639d1a17bf839f642c620612fdc5b +timestamp : 2019-04-24 02:57:43 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.24.0 r351_0 +-------------------------------- +file name : bioconductor-ebseq-1.24.0-r351_0.tar.bz2 +name : bioconductor-ebseq +version : 1.24.0 +build : r351_0 +build number: 0 +size : 1.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.24.0-r351_0.tar.bz2 +md5 : 08c32c78a3ef7983373fb30ec852c345 +timestamp : 2019-05-09 10:46:15 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.24.0 r36_1 +------------------------------- +file name : bioconductor-ebseq-1.24.0-r36_1.tar.bz2 +name : bioconductor-ebseq +version : 1.24.0 +build : r36_1 +build number: 1 +size : 1.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.24.0-r36_1.tar.bz2 +md5 : 0207830b16ba250579cdf644f938b248 +timestamp : 2019-07-22 04:22:22 UTC +dependencies: + - r-base >=3.6,<3.7.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.26.0 r36_0 +------------------------------- +file name : bioconductor-ebseq-1.26.0-r36_0.tar.bz2 +name : bioconductor-ebseq +version : 1.26.0 +build : r36_0 +build number: 0 +size : 1.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.26.0-r36_0.tar.bz2 +md5 : ccdb12b6bd451e7de31e263747fd28a6 +timestamp : 2019-11-01 16:21:20 UTC +dependencies: + - r-base >=3.6,<3.7.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.28.0 r40_0 +------------------------------- +file name : bioconductor-ebseq-1.28.0-r40_0.tar.bz2 +name : bioconductor-ebseq +version : 1.28.0 +build : r40_0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.28.0-r40_0.tar.bz2 +md5 : 4263da5a0baa480c638712840f199b3b +timestamp : 2020-05-09 14:20:58 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.30.0 r40_0 +------------------------------- +file name : bioconductor-ebseq-1.30.0-r40_0.tar.bz2 +name : bioconductor-ebseq +version : 1.30.0 +build : r40_0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.30.0-r40_0.tar.bz2 +md5 : aa29dbd2682704b8434e5fc98a100c85 +timestamp : 2020-10-29 10:57:09 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.30.0 r40hdfd78af_1 +--------------------------------------- +file name : bioconductor-ebseq-1.30.0-r40hdfd78af_1.tar.bz2 +name : bioconductor-ebseq +version : 1.30.0 +build : r40hdfd78af_1 +build number: 1 +size : 1.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.30.0-r40hdfd78af_1.tar.bz2 +md5 : c365c43e61501f9834f915d18f541161 +timestamp : 2021-03-24 23:42:00 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.32.0 r41hdfd78af_0 +--------------------------------------- +file name : bioconductor-ebseq-1.32.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-ebseq +version : 1.32.0 +build : r41hdfd78af_0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.32.0-r41hdfd78af_0.tar.bz2 +md5 : f2f4b8821cda3085b5ba1fd32426528e +timestamp : 2021-05-31 07:14:29 UTC +dependencies: + - r-base >=4.1,<4.2.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.34.0 r41hdfd78af_0 +--------------------------------------- +file name : bioconductor-ebseq-1.34.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-ebseq +version : 1.34.0 +build : r41hdfd78af_0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.34.0-r41hdfd78af_0.tar.bz2 +md5 : 6bf7169eaf8067a869dfa28bba8d09ae +timestamp : 2021-11-02 10:01:36 UTC +dependencies: + - r-base >=4.1,<4.2.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.38.0 r42hdfd78af_0 +--------------------------------------- +file name : bioconductor-ebseq-1.38.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-ebseq +version : 1.38.0 +build : r42hdfd78af_0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.38.0-r42hdfd78af_0.tar.bz2 +md5 : 837915318ed184ff8209a6643ae4c2b2 +timestamp : 2022-11-03 17:13:05 UTC +dependencies: + - r-base >=4.2,<4.3.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 1.40.0 r43hdfd78af_0 +--------------------------------------- +file name : bioconductor-ebseq-1.40.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-ebseq +version : 1.40.0 +build : r43hdfd78af_0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.40.0-r43hdfd78af_0.tar.bz2 +md5 : 92e3f21a157bfb4e4d2c1da0e823c308 +timestamp : 2023-07-07 07:13:46 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + - r-blockmodeling + - r-gplots + - r-testthat + + +bioconductor-ebseq 2.0.0 r43hf17093f_1 +-------------------------------------- +file name : bioconductor-ebseq-2.0.0-r43hf17093f_1.tar.bz2 +name : bioconductor-ebseq +version : 2.0.0 +build diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-fgsea.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-fgsea.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..35f731416c42a44f7255494c77f0baa0155da8f7 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-fgsea.manual_bundle.txt @@ -0,0 +1,436 @@ +# Tool: bioconductor-fgsea +software_name: bioconductor-fgsea +tier: T1 +domain: t1_backfill_overall +downloads: 142910 +summary: Fast Gene Set Enrichment Analysis +description: The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. +dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-biocparallel >=1.44.0,<1.45.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-bh, r-cowplot, r-data.table, r-fastmatch, r-ggplot2 >=2.2.0, r-matrix, r-rcpp, r-scales +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: http://bioconductor.org/packages/3.5/bioc/html/fgsea.html +doc_url: +dev_url: + +## URL Docs Extract +### http://bioconductor.org/packages/3.5/bioc/html/fgsea.html +Bioconductor - fgsea Home Bioconductor 3.5 Software Packages fgsea To install this package, start R and enter: ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("fgsea") In most cases, you don't need to download the package archive at all. fgsea DOI: 10.18129/B9.bioc.fgsea     Fast Gene Set Enrichment Analysis Bioconductor version: Release (3.5) The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Author: Alexey Sergushichev [aut, cre] Maintainer: Alexey Sergushichev <alsergbox at gmail.com> Citation (from within R, enter citation("fgsea") ): Installation To install this package, start R and enter: ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("fgsea") Documentation HTML R Script Using fgsea package PDF   Reference Manual Text   NEWS Details biocViews DifferentialExpression , GeneExpression , GeneSetEnrichment , Pathways , Software Version 1.2.1 In Bioconductor since BioC 3.4 (R-3.3) (1 year) License MIT + file LICENCE Depends R (>= 3.3), Rcpp Imports data.table , BiocParallel , stats, ggplot2 (>= 2.2.0), gridExtra , grid, fastmatch LinkingTo Rcpp Suggests testthat , knitr , rmarkdown , reactome.db , AnnotationDbi , parallel SystemRequirements C++11 Enhances URL https://github.com/ctlab/fgsea/ BugReports https://github.com/ctlab/fgsea/issues Depends On Me PPInfer Imports Me DOSE , piano Suggests Me Pi Build Report   Package Archives Follow Installation instructions to use this package in your R session. Source Package fgsea_1.2.1.tar.gz Windows Binary fgsea_1.2.1.zip (32- & 64-bit) Mac OS X 10.11 (El Capitan) fgsea_1.2.1.tgz Source Repository git clone https://git.bioconductor.org/packages/fgsea Package Short Url http://bioconductor.org/packages/fgsea/ Package Downloads Report Download Stats Documentation » Bioconductor Package vignettes and manuals. Workflows for learning and use. Course and conference material. Videos . Community resources and tutorials . R / CRAN packages and documentation Support » Please read the posting guide . Post questions about Bioconductor to one of the following locations: Support site - for questions about Bioconductor packages Bioc-devel mailing list - for package developers Contact us: support.bioconductor.org Copyright © 2003 - 2017, Bioconductor Home Install Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Help Workflows Package Vignettes FAQ Support Using R Courses Publications Cloud AMI Community Resources Developers Package Guidelines Package Submission Release Schedule Source Control About Advisory Board Annual Reports Core Team Mirrors Related Projects   Search: Home Install Help Developers About + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-fgsea --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-fgsea 1.2.1 0 +-------------------------- +file name : bioconductor-fgsea-1.2.1-0.tar.bz2 +name : bioconductor-fgsea +version : 1.2.1 +build : 0 +build number: 0 +size : 799 KB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.2.1-0.tar.bz2 +md5 : 76a3149643da0890f8af84d26e34db54 +dependencies: + - bioconductor-biocparallel + - r-base >=3.3,<3.4 + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-rcpp + + +bioconductor-fgsea 1.4.0 r3.4.1_0 +--------------------------------- +file name : bioconductor-fgsea-1.4.0-r3.4.1_0.tar.bz2 +name : bioconductor-fgsea +version : 1.4.0 +build : r3.4.1_0 +build number: 0 +size : 801 KB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.4.0-r3.4.1_0.tar.bz2 +md5 : 2caa4ea03fea70a129339e676ea0340c +dependencies: + - bioconductor-biocparallel + - r-base 3.4.1* + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-rcpp + + +bioconductor-fgsea 1.6.0 r341hfc679d8_0 +--------------------------------------- +file name : bioconductor-fgsea-1.6.0-r341hfc679d8_0.tar.bz2 +name : bioconductor-fgsea +version : 1.6.0 +build : r341hfc679d8_0 +build number: 0 +size : 956 KB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.6.0-r341hfc679d8_0.tar.bz2 +md5 : dca739e172bb60632bd30ef008e6c20a +timestamp : 2018-10-12 01:35:30 UTC +dependencies: + - bioconductor-biocparallel >=1.14.2,<1.16.0 + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - r-base >=3.4.1,<3.4.2.0a0 + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.6.0 r351hfc679d8_0 +--------------------------------------- +file name : bioconductor-fgsea-1.6.0-r351hfc679d8_0.tar.bz2 +name : bioconductor-fgsea +version : 1.6.0 +build : r351hfc679d8_0 +build number: 0 +size : 976 KB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.6.0-r351hfc679d8_0.tar.bz2 +md5 : 3632ee167120ac604aba00641d325317 +timestamp : 2018-10-12 01:33:44 UTC +dependencies: + - bioconductor-biocparallel >=1.14.2,<1.16.0 + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - r-base >=3.5.1,<3.5.2.0a0 + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.8.0 r351hf484d3e_0 +--------------------------------------- +file name : bioconductor-fgsea-1.8.0-r351hf484d3e_0.tar.bz2 +name : bioconductor-fgsea +version : 1.8.0 +build : r351hf484d3e_0 +build number: 0 +size : 895 KB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.8.0-r351hf484d3e_0.tar.bz2 +md5 : 54b11a7a868c968e98e7b18d3f282b2a +timestamp : 2018-12-12 01:58:42 UTC +dependencies: + - bioconductor-biocparallel >=1.16.0,<1.17.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.10.0 r351hf484d3e_0 +---------------------------------------- +file name : bioconductor-fgsea-1.10.0-r351hf484d3e_0.tar.bz2 +name : bioconductor-fgsea +version : 1.10.0 +build : r351hf484d3e_0 +build number: 0 +size : 986 KB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.10.0-r351hf484d3e_0.tar.bz2 +md5 : f458552f46f024cac576e66a3e3c1054 +timestamp : 2019-05-09 19:02:12 UTC +dependencies: + - bioconductor-biocparallel >=1.18.0,<1.19.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-bh + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.10.0 r36he1b5a44_1 +--------------------------------------- +file name : bioconductor-fgsea-1.10.0-r36he1b5a44_1.tar.bz2 +name : bioconductor-fgsea +version : 1.10.0 +build : r36he1b5a44_1 +build number: 1 +size : 962 KB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.10.0-r36he1b5a44_1.tar.bz2 +md5 : 6c6bdb7144c32dcef52538a10ad0afdb +timestamp : 2019-07-22 01:44:47 UTC +dependencies: + - bioconductor-biocparallel >=1.18.0,<1.19.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + - r-bh + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.12.0 r36he1b5a44_0 +--------------------------------------- +file name : bioconductor-fgsea-1.12.0-r36he1b5a44_0.tar.bz2 +name : bioconductor-fgsea +version : 1.12.0 +build : r36he1b5a44_0 +build number: 0 +size : 1002 KB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.12.0-r36he1b5a44_0.tar.bz2 +md5 : c5d7fcab3fa94013db30e27b7bcebf3a +timestamp : 2019-11-02 13:24:50 UTC +dependencies: + - bioconductor-biocparallel >=1.20.0,<1.21.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + - r-bh + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.14.0 r40h5f743cb_0 +--------------------------------------- +file name : bioconductor-fgsea-1.14.0-r40h5f743cb_0.tar.bz2 +name : bioconductor-fgsea +version : 1.14.0 +build : r40h5f743cb_0 +build number: 0 +size : 1.4 MB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.14.0-r40h5f743cb_0.tar.bz2 +md5 : b5825068488351ed574199462544b022 +timestamp : 2020-05-10 07:14:10 UTC +dependencies: + - bioconductor-biocparallel >=1.22.0,<1.23.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - liblapack >=3.8.0,<3.9.0a0 + - libstdcxx-ng >=7.3.0 + - r-base >=4.0,<4.1.0a0 + - r-bh + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.16.0 r40h399db7b_1 +--------------------------------------- +file name : bioconductor-fgsea-1.16.0-r40h399db7b_1.tar.bz2 +name : bioconductor-fgsea +version : 1.16.0 +build : r40h399db7b_1 +build number: 1 +size : 1.4 MB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.16.0-r40h399db7b_1.tar.bz2 +md5 : 204726c5251afc70c75c7e24194dd0e0 +timestamp : 2021-03-27 23:03:15 UTC +dependencies: + - bioconductor-biocparallel >=1.24.0,<1.25.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.0,<4.1.0a0 + - r-bh + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.16.0 r40h5f743cb_0 +--------------------------------------- +file name : bioconductor-fgsea-1.16.0-r40h5f743cb_0.tar.bz2 +name : bioconductor-fgsea +version : 1.16.0 +build : r40h5f743cb_0 +build number: 0 +size : 1.4 MB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.16.0-r40h5f743cb_0.tar.bz2 +md5 : 87eb98f3aab39051bef018b6b3387fe7 +timestamp : 2020-10-29 21:58:15 UTC +dependencies: + - bioconductor-biocparallel >=1.24.0,<1.25.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=7.5.0 + - r-base >=4.0,<4.1.0a0 + - r-bh + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.18.0 r41h399db7b_0 +--------------------------------------- +file name : bioconductor-fgsea-1.18.0-r41h399db7b_0.tar.bz2 +name : bioconductor-fgsea +version : 1.18.0 +build : r41h399db7b_0 +build number: 0 +size : 1.4 MB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.18.0-r41h399db7b_0.tar.bz2 +md5 : 5a71a6151ebf62d77aa1d053e8d0c233 +timestamp : 2021-05-31 09:34:30 UTC +dependencies: + - bioconductor-biocparallel >=1.26.0,<1.27.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.1,<4.2.0a0 + - r-bh + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.20.0 r41h399db7b_0 +--------------------------------------- +file name : bioconductor-fgsea-1.20.0-r41h399db7b_0.tar.bz2 +name : bioconductor-fgsea +version : 1.20.0 +build : r41h399db7b_0 +build number: 0 +size : 1.4 MB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.20.0-r41h399db7b_0.tar.bz2 +md5 : d753665dd092dde5675f62c05e3fe6a9 +timestamp : 2021-11-02 14:54:14 UTC +dependencies: + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.4.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.4.0 + - r-base >=4.1,<4.2.0a0 + - r-bh + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.20.0 r41h619a076_1 +--------------------------------------- +file name : bioconductor-fgsea-1.20.0-r41h619a076_1.tar.bz2 +name : bioconductor-fgsea +version : 1.20.0 +build : r41h619a076_1 +build number: 1 +size : 1.4 MB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.20.0-r41h619a076_1.tar.bz2 +md5 : 79aa657b52180aabfea2e53e38d93ac5 +timestamp : 2022-02-24 13:05:37 UTC +dependencies: + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=10.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=10.3.0 + - r-base >=4.1,<4.2.0a0 + - r-bh + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.20.0 r41hc247a5b_2 +--------------------------------------- +file name : bioconductor-fgsea-1.20.0-r41hc247a5b_2.tar.bz2 +name : bioconductor-fgsea +version : 1.20.0 +build : r41hc247a5b_2 +build number: 2 +size : 1.4 MB +license : MIT + file LICENCE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.20.0-r41hc247a5b_2.tar.bz2 +md5 : 8bdc49d145bf8ad41ada4c6ecdfade27 +timestamp : 2022-09-15 09:17:26 UTC +dependencies: + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.1,<4.2.0a0 + - r-bh + - r-data.table + - r-fastmatch + - r-ggplot2 >=2.2.0 + - r-gridextra + - r-matrix + - r-rcpp + + +bioconductor-fgsea 1.24.0 r42hc247a5b_0 +--------------------------------------- +file name : bioconductor-fgsea-1.24.0-r42hc247a5b_0.tar.bz2 +name : bioconductor-fgsea +version : diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-geneplotter.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-geneplotter.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..65e643197e44f5a59845c70d88530d419fa1f5da --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-geneplotter.manual_bundle.txt @@ -0,0 +1,411 @@ +# Tool: bioconductor-geneplotter +software_name: bioconductor-geneplotter +tier: T1 +domain: t1_backfill_overall +downloads: 462579 +summary: Graphics related functions for Bioconductor +description: Functions for plotting genomic data +dependencies: bioconductor-annotate >=1.88.0,<1.89.0, bioconductor-annotationdbi >=1.72.0,<1.73.0, bioconductor-biobase >=2.70.0,<2.71.0, bioconductor-biocgenerics >=0.56.0,<0.57.0, r-base >=4.5,<4.6.0a0, r-lattice, r-rcolorbrewer +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/geneplotter.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/geneplotter.html +Bioconductor - geneplotter Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages geneplotter geneplotter This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see geneplotter . Graphics related functions for Bioconductor DOI: 10.18129/B9.bioc.geneplotter Bioconductor version: 3.22 Functions for plotting genomic data Author: Robert Gentleman [aut], Rohit Satyam [ctb] (Converted geneplotter vignette from Sweave to RMarkdown / HTML.), Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation("geneplotter") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("geneplotter") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("geneplotter") How to Assemble a chromLocation Object HTML R Script Visualization of Microarray Data PDF R Script Reference Manual PDF README Text NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Software , Visualization Version 1.88.0 In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 21 years) License Artistic-2.0 Depends R (>= 2.10), methods, Biobase , BiocGenerics , lattice , annotate Imports AnnotationDbi , graphics, grDevices, grid, RColorBrewer , stats, utils System Requirements URL See More Suggests Rgraphviz , fibroEset , hgu95av2.db , hu6800.db , hgu133a.db , BiocStyle , knitr Linking To Enhances Depends On Me HD2013SGI , Hiiragi2013 , maEndToEnd Imports Me biocGraph , DEXSeq , MethylSeekR Suggests Me biocGraph , Category , EnrichmentBrowser , GOstats , Single.mTEC.Transcriptomes Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package geneplotter_1.88.0.tar.gz Windows Binary (x86_64) geneplotter_1.88.0.zip macOS Binary (x86_64) geneplotter_1.88.0.tgz macOS Binary (arm64) geneplotter_1.88.0.tgz Source Repository git clone https://git.bioconductor.org/packages/geneplotter Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/geneplotter Bioc Package Browser https://code.bioconductor.org/browse/geneplotter/ Package Short Url https://bioconductor.org/packages/geneplotter/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-geneplotter --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-geneplotter 1.46.0 0 +--------------------------------- +file name : bioconductor-geneplotter-1.46.0-0.tar.bz2 +name : bioconductor-geneplotter +version : 1.46.0 +build : 0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.46.0-0.tar.bz2 +md5 : 92d36ae78e56eda61c92c104fd32f823 +dependencies: + - bioconductor-annotate + - bioconductor-annotationdbi + - bioconductor-biobase + - bioconductor-biocgenerics + - r >=2.10 + - r-rcolorbrewer + + +bioconductor-geneplotter 1.48.0 0 +--------------------------------- +file name : bioconductor-geneplotter-1.48.0-0.tar.bz2 +name : bioconductor-geneplotter +version : 1.48.0 +build : 0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.48.0-0.tar.bz2 +md5 : 2a2d0e29972a95dbb1ca381385c7c8f3 +dependencies: + - bioconductor-annotate + - bioconductor-annotationdbi + - bioconductor-biobase + - bioconductor-biocgenerics + - r >=2.10 + - r-rcolorbrewer + + +bioconductor-geneplotter 1.50.0 r3.3.1_0 +---------------------------------------- +file name : bioconductor-geneplotter-1.50.0-r3.3.1_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.50.0 +build : r3.3.1_0 +build number: 0 +size : 1.1 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.50.0-r3.3.1_0.tar.bz2 +md5 : e2a81595f867e62064c4fdec03939026 +dependencies: + - bioconductor-annotate + - bioconductor-annotationdbi + - bioconductor-biobase + - bioconductor-biocgenerics + - r 3.3.1* + - r-rcolorbrewer + + +bioconductor-geneplotter 1.50.0 r3.3.2_0 +---------------------------------------- +file name : bioconductor-geneplotter-1.50.0-r3.3.2_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.50.0 +build : r3.3.2_0 +build number: 0 +size : 1.1 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.50.0-r3.3.2_0.tar.bz2 +md5 : ab52644b69cf2ddf3d8bf36fadd3118f +dependencies: + - bioconductor-annotate + - bioconductor-annotationdbi + - bioconductor-biobase + - bioconductor-biocgenerics + - r-base 3.3.2* + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.50.0 r3.4.1_0 +---------------------------------------- +file name : bioconductor-geneplotter-1.50.0-r3.4.1_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.50.0 +build : r3.4.1_0 +build number: 0 +size : 1.1 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.50.0-r3.4.1_0.tar.bz2 +md5 : 0e7dc22113275c6f8a21357f351c6ad2 +dependencies: + - bioconductor-annotate + - bioconductor-annotationdbi + - bioconductor-biobase + - bioconductor-biocgenerics + - r-base 3.4.1* + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.54.0 r3.4.1_0 +---------------------------------------- +file name : bioconductor-geneplotter-1.54.0-r3.4.1_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.54.0 +build : r3.4.1_0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.54.0-r3.4.1_0.tar.bz2 +md5 : 0580cfb140cdf9332d5f5d9afffba4f2 +dependencies: + - bioconductor-annotate + - bioconductor-annotationdbi + - bioconductor-biobase + - bioconductor-biocgenerics + - r-base 3.4.1* + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.56.0 r3.4.1_0 +---------------------------------------- +file name : bioconductor-geneplotter-1.56.0-r3.4.1_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.56.0 +build : r3.4.1_0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.56.0-r3.4.1_0.tar.bz2 +md5 : f5ba800c8c0cd38fd55dae3fe3084f9c +dependencies: + - bioconductor-annotate + - bioconductor-annotationdbi + - bioconductor-biobase + - bioconductor-biocgenerics + - r-base 3.4.1* + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.58.0 r341_0 +-------------------------------------- +file name : bioconductor-geneplotter-1.58.0-r341_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.58.0 +build : r341_0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.58.0-r341_0.tar.bz2 +md5 : f543e04732078f5453d27f8d93854a53 +timestamp : 2018-10-25 07:42:38 UTC +dependencies: + - bioconductor-annotate >=1.58.0,<1.60.0 + - bioconductor-annotationdbi >=1.42.1,<1.44.0 + - bioconductor-biobase >=2.40.0,<2.42.0 + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - r-base >=3.4.1,<3.4.2.0a0 + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.58.0 r351_0 +-------------------------------------- +file name : bioconductor-geneplotter-1.58.0-r351_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.58.0 +build : r351_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.58.0-r351_0.tar.bz2 +md5 : c06ea26c34402a0f2d7e09a24c990128 +timestamp : 2018-10-25 07:44:22 UTC +dependencies: + - bioconductor-annotate >=1.58.0,<1.60.0 + - bioconductor-annotationdbi >=1.42.1,<1.44.0 + - bioconductor-biobase >=2.40.0,<2.42.0 + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.60.0 r351_0 +-------------------------------------- +file name : bioconductor-geneplotter-1.60.0-r351_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.60.0 +build : r351_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.60.0-r351_0.tar.bz2 +md5 : 89a31d794ef42cfbd3543eb48a64c00b +timestamp : 2019-01-01 11:16:48 UTC +dependencies: + - bioconductor-annotate >=1.60.0,<1.61.0 + - bioconductor-annotationdbi >=1.44.0,<1.45.0 + - bioconductor-biobase >=2.42.0,<2.43.0 + - bioconductor-biocgenerics >=0.28.0,<0.29.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.62.0 r36_1 +------------------------------------- +file name : bioconductor-geneplotter-1.62.0-r36_1.tar.bz2 +name : bioconductor-geneplotter +version : 1.62.0 +build : r36_1 +build number: 1 +size : 1.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.62.0-r36_1.tar.bz2 +md5 : 7322ff8d509de80f8d5dbb904c6d7238 +timestamp : 2019-08-06 13:41:04 UTC +dependencies: + - bioconductor-annotate >=1.62.0,<1.63.0 + - bioconductor-annotationdbi >=1.46.0,<1.47.0 + - bioconductor-biobase >=2.44.0,<2.45.0 + - bioconductor-biocgenerics >=0.30.0,<0.31.0 + - r-base >=3.6,<3.7.0a0 + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.64.0 r36_0 +------------------------------------- +file name : bioconductor-geneplotter-1.64.0-r36_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.64.0 +build : r36_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.64.0-r36_0.tar.bz2 +md5 : 2008ae86507430a91e824bd01e3c7d1c +timestamp : 2019-11-03 21:52:32 UTC +dependencies: + - bioconductor-annotate >=1.64.0,<1.65.0 + - bioconductor-annotationdbi >=1.48.0,<1.49.0 + - bioconductor-biobase >=2.46.0,<2.47.0 + - bioconductor-biocgenerics >=0.32.0,<0.33.0 + - r-base >=3.6,<3.7.0a0 + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.66.0 r40_0 +------------------------------------- +file name : bioconductor-geneplotter-1.66.0-r40_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.66.0 +build : r40_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.66.0-r40_0.tar.bz2 +md5 : 1da247091a0ef5b5b29bc011aec551f2 +timestamp : 2020-05-11 06:47:15 UTC +dependencies: + - bioconductor-annotate >=1.66.0,<1.67.0 + - bioconductor-annotationdbi >=1.50.0,<1.51.0 + - bioconductor-biobase >=2.48.0,<2.49.0 + - bioconductor-biocgenerics >=0.34.0,<0.35.0 + - r-base >=4.0,<4.1.0a0 + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.68.0 r40_0 +------------------------------------- +file name : bioconductor-geneplotter-1.68.0-r40_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.68.0 +build : r40_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.68.0-r40_0.tar.bz2 +md5 : 757e5398600856f144749fdeb2b0d046 +timestamp : 2020-10-30 14:51:03 UTC +dependencies: + - bioconductor-annotate >=1.68.0,<1.69.0 + - bioconductor-annotationdbi >=1.52.0,<1.53.0 + - bioconductor-biobase >=2.50.0,<2.51.0 + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - r-base >=4.0,<4.1.0a0 + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.68.0 r40hdfd78af_1 +--------------------------------------------- +file name : bioconductor-geneplotter-1.68.0-r40hdfd78af_1.tar.bz2 +name : bioconductor-geneplotter +version : 1.68.0 +build : r40hdfd78af_1 +build number: 1 +size : 1.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.68.0-r40hdfd78af_1.tar.bz2 +md5 : fca7f5dcd41558d3bfbc508bec75019b +timestamp : 2021-03-30 07:10:15 UTC +dependencies: + - bioconductor-annotate >=1.68.0,<1.69.0 + - bioconductor-annotationdbi >=1.52.0,<1.53.0 + - bioconductor-biobase >=2.50.0,<2.51.0 + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - r-base >=4.0,<4.1.0a0 + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.70.0 r41hdfd78af_0 +--------------------------------------------- +file name : bioconductor-geneplotter-1.70.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.70.0 +build : r41hdfd78af_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.70.0-r41hdfd78af_0.tar.bz2 +md5 : 85fa97ce70a3df599f6b583e09fcfb94 +timestamp : 2021-06-01 21:53:07 UTC +dependencies: + - bioconductor-annotate >=1.70.0,<1.71.0 + - bioconductor-annotationdbi >=1.54.0,<1.55.0 + - bioconductor-biobase >=2.52.0,<2.53.0 + - bioconductor-biocgenerics >=0.38.0,<0.39.0 + - r-base >=4.1,<4.2.0a0 + - r-lattice + - r-rcolorbrewer + + +bioconductor-geneplotter 1.72.0 r41hdfd78af_0 +--------------------------------------------- +file name : bioconductor-geneplotter-1.72.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-geneplotter +version : 1.72.0 +build : r41hdfd78af_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.72.0-r41hdfd78af_0.tar.bz2 +md5 : 32c0e22a0095ad9b592a6bf7e16a835a +timestamp : 2021-11-06 01:31:33 UTC +depend diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-glmgampoi.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-glmgampoi.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..97332666c3d57fe7bb195dcfdf4eb412cdd77119 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-glmgampoi.manual_bundle.txt @@ -0,0 +1,363 @@ +# Tool: bioconductor-glmgampoi +software_name: bioconductor-glmgampoi +tier: T1 +domain: t1_backfill_overall +downloads: 265321 +summary: Fit a Gamma-Poisson Generalized Linear Model +description: Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments. +dependencies: bioconductor-assorthead >=1.4.0,<1.5.0, bioconductor-assorthead >=1.4.0,<1.5.0a0, bioconductor-beachmat >=2.26.0,<2.27.0, bioconductor-beachmat >=2.26.0,<2.27.0a0, bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-delayedarray >=0.36.0,<0.37.0a0, bioconductor-delayedmatrixstats >=1.32.0,<1.33.0, bioconductor-delayedmatrixstats >=1.32.0,<1.33.0a0, bioconductor-hdf5array >=1.38.0,<1.39.0, bioconductor-hdf5array >=1.38.0,<1.39.0a0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0, bioconductor-sparsearray >=1.10.0,<1.11.0, bioconductor-sparsearray >=1.10.8,<1.11.0a0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-matrix, r-matrixstats, r-rcpp, r-rcpparmadillo, r-rlang, r-vctrs +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.11/bioc/html/glmGamPoi.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.11/bioc/html/glmGamPoi.html +Bioconductor - glmGamPoi About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.11 Software Packages glmGamPoi glmGamPoi This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see glmGamPoi . Fit a Gamma-Poisson Generalized Linear Model DOI: 10.18129/B9.bioc.glmGamPoi Bioconductor version: 3.11 Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments. Author: Constantin Ahlmann-Eltze [aut, cre] , Michael Love [ctb] Maintainer: Constantin Ahlmann-Eltze <artjom31415 at googlemail.com> Citation (from within R, enter citation("glmGamPoi") ): Installation To install this package, start R (version "4.0") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("glmGamPoi") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("glmGamPoi") glmGamPoi Quickstart HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews RNASeq , Regression , SingleCell , Software Version 1.0.0 In Bioconductor since BioC 3.11 (R-4.0) (4 years) License GPL-3 Depends Imports Rcpp, pracma, DelayedMatrixStats , DelayedArray , HDF5Array , SummarizedExperiment , methods, stats, utils System Requirements C++11 URL https://github.com/const-ae/glmGamPoi Bug Reports https://github.com/const-ae/glmGamPoi/issues See More Suggests testthat (>= 2.1.0), zoo, DESeq2 , edgeR , beachmat , MASS, statmod, ggplot2, bench, BiocParallel , knitr, rmarkdown, BiocStyle , TENxPBMCData Linking To Rcpp, RcppArmadillo, beachmat (>= 2.0.0) Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package glmGamPoi_1.0.0.tar.gz Windows Binary glmGamPoi_1.0.0.zip (32- & 64-bit) macOS 10.13 (High Sierra) glmGamPoi_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/glmGamPoi Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/glmGamPoi Bioc Package Browser https://code.bioconductor.org/browse/glmGamPoi/ Package Short Url https://bioconductor.org/packages/glmGamPoi/ Package Downloads Report Download Stats Old Source Packages for BioC 3.11 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-glmgampoi --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-glmgampoi 1.0.0 r40h5f743cb_0 +------------------------------------------ +file name : bioconductor-glmgampoi-1.0.0-r40h5f743cb_0.tar.bz2 +name : bioconductor-glmgampoi +version : 1.0.0 +build : r40h5f743cb_0 +build number: 0 +size : 668 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.0.0-r40h5f743cb_0.tar.bz2 +md5 : a093428ff266b994ce9e2cb43b7f870a +timestamp : 2020-05-11 04:07:26 UTC +dependencies: + - bioconductor-beachmat >=2.4.0,<2.5.0 + - bioconductor-delayedarray >=0.14.0,<0.15.0 + - bioconductor-delayedmatrixstats >=1.10.0,<1.11.0 + - bioconductor-hdf5array >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.18.0,<1.19.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - liblapack >=3.8.0,<3.9.0a0 + - libstdcxx-ng >=7.3.0 + - r-base >=4.0,<4.1.0a0 + - r-pracma + - r-rcpp + - r-rcpparmadillo + + +bioconductor-glmgampoi 1.2.0 r40h399db7b_1 +------------------------------------------ +file name : bioconductor-glmgampoi-1.2.0-r40h399db7b_1.tar.bz2 +name : bioconductor-glmgampoi +version : 1.2.0 +build : r40h399db7b_1 +build number: 1 +size : 771 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.2.0-r40h399db7b_1.tar.bz2 +md5 : 970fbfc553e6c0aebecaf0ca648b7150 +timestamp : 2021-03-29 10:17:15 UTC +dependencies: + - bioconductor-beachmat >=2.6.0,<2.7.0 + - bioconductor-delayedarray >=0.16.0,<0.17.0 + - bioconductor-delayedmatrixstats >=1.12.0,<1.13.0 + - bioconductor-hdf5array >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.20.0,<1.21.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.0,<4.1.0a0 + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + + +bioconductor-glmgampoi 1.2.0 r40h5f743cb_0 +------------------------------------------ +file name : bioconductor-glmgampoi-1.2.0-r40h5f743cb_0.tar.bz2 +name : bioconductor-glmgampoi +version : 1.2.0 +build : r40h5f743cb_0 +build number: 0 +size : 762 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.2.0-r40h5f743cb_0.tar.bz2 +md5 : 6570b8cc1fd1d47c7cfebaf6f0e73256 +timestamp : 2020-10-30 16:48:53 UTC +dependencies: + - bioconductor-beachmat >=2.6.0,<2.7.0 + - bioconductor-delayedarray >=0.16.0,<0.17.0 + - bioconductor-delayedmatrixstats >=1.12.0,<1.13.0 + - bioconductor-hdf5array >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.20.0,<1.21.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=7.5.0 + - r-base >=4.0,<4.1.0a0 + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + + +bioconductor-glmgampoi 1.4.0 r41h399db7b_0 +------------------------------------------ +file name : bioconductor-glmgampoi-1.4.0-r41h399db7b_0.tar.bz2 +name : bioconductor-glmgampoi +version : 1.4.0 +build : r41h399db7b_0 +build number: 0 +size : 1.2 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.4.0-r41h399db7b_0.tar.bz2 +md5 : 3250e1a8d47ff226c29bb268e595942a +timestamp : 2021-06-02 21:25:11 UTC +dependencies: + - bioconductor-beachmat >=2.8.0,<2.9.0 + - bioconductor-biocgenerics >=0.38.0,<0.39.0 + - bioconductor-delayedarray >=0.18.0,<0.19.0 + - bioconductor-delayedmatrixstats >=1.14.0,<1.15.0 + - bioconductor-hdf5array >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.22.0,<1.23.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.1,<4.2.0a0 + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + + +bioconductor-glmgampoi 1.6.0 r41h399db7b_0 +------------------------------------------ +file name : bioconductor-glmgampoi-1.6.0-r41h399db7b_0.tar.bz2 +name : bioconductor-glmgampoi +version : 1.6.0 +build : r41h399db7b_0 +build number: 0 +size : 1.2 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.6.0-r41h399db7b_0.tar.bz2 +md5 : 1c328106c0870c0df94455b62d7a8b68 +timestamp : 2021-11-03 17:09:14 UTC +dependencies: + - bioconductor-beachmat >=2.10.0,<2.11.0 + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-delayedmatrixstats >=1.16.0,<1.17.0 + - bioconductor-hdf5array >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.4.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.4.0 + - r-base >=4.1,<4.2.0a0 + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + + +bioconductor-glmgampoi 1.6.0 r41h619a076_1 +------------------------------------------ +file name : bioconductor-glmgampoi-1.6.0-r41h619a076_1.tar.bz2 +name : bioconductor-glmgampoi +version : 1.6.0 +build : r41h619a076_1 +build number: 1 +size : 1.2 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.6.0-r41h619a076_1.tar.bz2 +md5 : e4ed4111be269626349a619b3d9b27f5 +timestamp : 2022-02-27 11:47:04 UTC +dependencies: + - bioconductor-beachmat >=2.10.0,<2.11.0 + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-delayedmatrixstats >=1.16.0,<1.17.0 + - bioconductor-hdf5array >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=10.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=10.3.0 + - r-base >=4.1,<4.2.0a0 + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + + +bioconductor-glmgampoi 1.6.0 r41hc247a5b_2 +------------------------------------------ +file name : bioconductor-glmgampoi-1.6.0-r41hc247a5b_2.tar.bz2 +name : bioconductor-glmgampoi +version : 1.6.0 +build : r41hc247a5b_2 +build number: 2 +size : 1.2 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.6.0-r41hc247a5b_2.tar.bz2 +md5 : aa1202e07d6dc79e6938f3a802660193 +timestamp : 2022-09-23 15:08:05 UTC +dependencies: + - bioconductor-beachmat >=2.10.0,<2.11.0 + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-delayedmatrixstats >=1.16.0,<1.17.0 + - bioconductor-hdf5array >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.1,<4.2.0a0 + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + + +bioconductor-glmgampoi 1.10.0 r42hc247a5b_0 +------------------------------------------- +file name : bioconductor-glmgampoi-1.10.0-r42hc247a5b_0.tar.bz2 +name : bioconductor-glmgampoi +version : 1.10.0 +build : r42hc247a5b_0 +build number: 0 +size : 1.2 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.10.0-r42hc247a5b_0.tar.bz2 +md5 : d3833c8f2be61c4664ea9cd3eb2dd88b +timestamp : 2022-11-06 11:20:32 UTC +dependencies: + - bioconductor-beachmat >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.44.0,<0.45.0 + - bioconductor-delayedarray >=0.24.0,<0.25.0 + - bioconductor-delayedmatrixstats >=1.20.0,<1.21.0 + - bioconductor-hdf5array >=1.26.0,<1.27.0 + - bioconductor-matrixgenerics >=1.10.0,<1.11.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + - r-rlang + + +bioconductor-glmgampoi 1.10.0 r42hf17093f_1 +------------------------------------------- +file name : bioconductor-glmgampoi-1.10.0-r42hf17093f_1.tar.bz2 +name : bioconductor-glmgampoi +version : 1.10.0 +build : r42hf17093f_1 +build number: 1 +size : 1.2 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.10.0-r42hf17093f_1.tar.bz2 +md5 : 80fa24116aaba87ecc3fa456d77d6015 +timestamp : 2023-05-28 09:29:08 UTC +dependencies: + - bioconductor-beachmat >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.44.0,<0.45.0 + - bioconductor-delayedarray >=0.24.0,<0.25.0 + - bioconductor-delayedmatrixstats >=1.20.0,<1.21.0 + - bioconductor-hdf5array >=1.26.0,<1.27.0 + - bioconductor-matrixgenerics >=1.10.0,<1.11.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + - r-rlang + + +bioconductor-glmgampoi 1.12.2 r43hf17093f_0 +------------------------------------------- +file name : bioconductor-glmgampoi-1.12.2-r43hf17093f_0.tar.bz2 +name : bioconductor-glmgampoi +version : 1.12.2 +build : r43hf17093f_0 +build number: 0 +size : 1.9 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.12.2-r43hf17093f_0.tar.bz2 +md5 : d59f508307e7995428557c84533adbac +timestamp : 2023-07-12 10:50:16 UTC +dependencies: + - bioconductor-beachmat >=2.16.0,<2.17.0 + - bioconductor-biocgenerics >=0.46.0,<0.47.0 + - bioconductor-delayedarray >=0.26.0,<0.27.0 + - bioconductor-delayedmatrixstats >=1.22.0,<1.23.0 + - bioconductor-hdf5array >=1.28.0,<1.29.0 + - bioconductor-matrixgenerics >=1.12.0,<1.13.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + - r-rlang + - r-vctrs + + +bioconductor-glmgampoi 1.14.0 r43hf17093f_0 +------------------------------------------- +file name : bioconductor-glmgampoi-1.14.0-r43hf17093f_0.tar.bz2 +name : bioconductor-glmgampoi +version : 1.14.0 +build : r43hf17093f_0 +build number: 0 +size : 1.9 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.14.0-r43hf17093f_0.tar.bz2 +md5 : f949686982f61bb5eb878c4cca2aa4eb +timestamp : 2023-12-15 20:52:49 UTC +dependencies: + - bioconductor-beachmat >=2.18.0,<2.19.0 + - bioconductor-beachmat >=2.18.0,<2.19.0a0 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-biocgenerics >=0.48.1,<0.49.0a0 + - bioconductor-delayedarray >=0.28.0,<0.29.0 + - bioconductor-delayedarray >=0.28.0,<0.29.0a0 + - bioconductor-delayedmatrixstats >=1.24.0,<1.25.0 + - bioconductor-delayedmatrixstats >=1.24.0,<1.25.0a0 + - bioconductor-hdf5array >=1.30.0,<1.31.0 + - bioconductor-hdf5array >=1.30.0,<1.31.0a0 + - bioconductor-matrixgenerics >=1.14.0,<1.15.0 + - bioconductor-matrixgenerics >=1.14.0,<1.15.0a0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0a0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0a0 + - libblas >=3.9.0,<4.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-go.db.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-go.db.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..a36c176f4caa72f68fd91a801c0980de969deb2b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-go.db.manual_bundle.txt @@ -0,0 +1,419 @@ +# Tool: bioconductor-go.db +software_name: bioconductor-go.db +tier: T1 +domain: t1_backfill_overall +downloads: 215677 +summary: A set of annotation maps describing the entire Gene Ontology +description: A set of annotation maps describing the entire Gene Ontology assembled using data from GO +dependencies: bioconductor-annotationdbi >=1.72.0,<1.73.0, bioconductor-data-packages >=20260207, curl, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/data/annotation/html/GO.db.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/data/annotation/html/GO.db.html +Bioconductor - GO.db Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Annotation Packages GO.db GO.db This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see GO.db . A set of annotation maps describing the entire Gene Ontology DOI: 10.18129/B9.bioc.GO.db Bioconductor version: 3.22 A set of annotation maps describing the entire Gene Ontology assembled using data from GO Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation("GO.db") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GO.db") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews AnnotationData , FunctionalAnnotation Version 3.22.0 License Artistic-2.0 Depends R (>= 2.7.0), methods, AnnotationDbi (>= 1.71.1) Imports System Requirements URL See More Suggests DBI Linking To Enhances Depends On Me annaffy , BicARE , geneXtendeR , goProfiles , goTools , SemDist , topGO , Homo.sapiens , Mus.musculus , Rattus.norvegicus , davidTiling , RnaSeqGeneEdgeRQL , OSCA.basic Imports Me ADAM , ADAMgui , adSplit , bioCancer , BioNAR , clusterProfiler , CNEr , compEpiTools , consICA , EnrichmentBrowser , famat , gage , GeneTonic , GenomicInteractionNodes , GOpro , GOSemSim , goseq , goSTAG , GOstats , goTools , ideal , MCbiclust , methylGSA , missMethyl , mosdef , NetSAM , NoRCE , pcaExplorer , Pigengene , rGREAT , rgsepd , rrvgo , simplifyEnrichment , ViSEAGO , ExpHunterSuite Suggests Me annotate , AnnotationDbi , AnnotationForge , appreci8R , BiocSet , Category , categoryCompare , ChIPpeakAnno , dmGsea , esetVis , fgga , FGNet , GlobalAncova , globaltest , goSorensen , GSEABase , hpar , InteractiveComplexHeatmap , interactiveDisplay , iSEEpathways , iSEEu , limma , MetMashR , mgsa , MLP , netZooR , oppar , phenoTest , pRoloc , rols , RTopper , safe , scde , simona , sparrow , SpliceWiz , systemPipeR , TFutils , BioMartGOGeneSets , SomaScan.db , chipenrich.data , msigdb , RforProteomics , yeastExpData , BaseSet , CALANGO , clValid , conos , corrselect , DrDimont , goat , maGUI , pagoda2 , PathwayVote , randomGODB , sand , scITD Links To Me Package Archives Follow Installation instructions to use this package in your R session. Source Package GO.db_3.22.0.tar.gz Windows Binary (x86_64) macOS Binary (x86_64) macOS Binary (arm64) Package Short Url https://bioconductor.org/packages/GO.db/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-go.db --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-go.db 3.2.2 0 +-------------------------- +file name : bioconductor-go.db-3.2.2-0.tar.bz2 +name : bioconductor-go.db +version : 3.2.2 +build : 0 +build number: 0 +size : 25.2 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.2.2-0.tar.bz2 +md5 : 7b3c17ffcebbdedd6cdc33f9d4ad6e8f +dependencies: + - bioconductor-annotationdbi >=1.31.18 + - r >=2.7.0 + + +bioconductor-go.db 3.3.0 r3.3.1_0 +--------------------------------- +file name : bioconductor-go.db-3.3.0-r3.3.1_0.tar.bz2 +name : bioconductor-go.db +version : 3.3.0 +build : r3.3.1_0 +build number: 0 +size : 25.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.3.0-r3.3.1_0.tar.bz2 +md5 : 99e618b71ceac3d8bcb9ea21aa4cbcbd +dependencies: + - bioconductor-annotationdbi >=1.33.10 + - r 3.3.1* + + +bioconductor-go.db 3.4.0 r3.3.1_0 +--------------------------------- +file name : bioconductor-go.db-3.4.0-r3.3.1_0.tar.bz2 +name : bioconductor-go.db +version : 3.4.0 +build : r3.3.1_0 +build number: 0 +size : 25.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.4.0-r3.3.1_0.tar.bz2 +md5 : b9895d06a6b294b9542b93541c6424ae +dependencies: + - bioconductor-annotationdbi >=1.35.4 + - r-base 3.3.1* + + +bioconductor-go.db 3.4.0 r3.3.2_0 +--------------------------------- +file name : bioconductor-go.db-3.4.0-r3.3.2_0.tar.bz2 +name : bioconductor-go.db +version : 3.4.0 +build : r3.3.2_0 +build number: 0 +size : 25.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.4.0-r3.3.2_0.tar.bz2 +md5 : 16f1a1af80bfea4775f2261d4ac4361c +dependencies: + - bioconductor-annotationdbi >=1.35.4 + - r-base 3.3.2* + + +bioconductor-go.db 3.4.0 r3.4.1_0 +--------------------------------- +file name : bioconductor-go.db-3.4.0-r3.4.1_0.tar.bz2 +name : bioconductor-go.db +version : 3.4.0 +build : r3.4.1_0 +build number: 0 +size : 25.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.4.0-r3.4.1_0.tar.bz2 +md5 : e56cc4f28b510b537646ae89c0eff3bb +dependencies: + - bioconductor-annotationdbi >=1.35.4 + - r-base 3.4.1* + + +bioconductor-go.db 3.4.1 r3.4.1_0 +--------------------------------- +file name : bioconductor-go.db-3.4.1-r3.4.1_0.tar.bz2 +name : bioconductor-go.db +version : 3.4.1 +build : r3.4.1_0 +build number: 0 +size : 4 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.4.1-r3.4.1_0.tar.bz2 +md5 : 25a294d2450680c82e6b9ffe634c83c7 +dependencies: + - bioconductor-annotationdbi >=1.37.4 + - r-base 3.4.1* + - wget + + +bioconductor-go.db 3.5.0 r3.4.1_0 +--------------------------------- +file name : bioconductor-go.db-3.5.0-r3.4.1_0.tar.bz2 +name : bioconductor-go.db +version : 3.5.0 +build : r3.4.1_0 +build number: 0 +size : 5 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.5.0-r3.4.1_0.tar.bz2 +md5 : b30aed35aa10d7349e273a5b1e189dd0 +dependencies: + - bioconductor-annotationdbi >=1.39.3 + - r-base 3.4.1* + - wget + + +bioconductor-go.db 3.5.0 r3.4.1_1 +--------------------------------- +file name : bioconductor-go.db-3.5.0-r3.4.1_1.tar.bz2 +name : bioconductor-go.db +version : 3.5.0 +build : r3.4.1_1 +build number: 1 +size : 5 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.5.0-r3.4.1_1.tar.bz2 +md5 : 34aaed8458778e3988ad9417cedf06f9 +dependencies: + - bioconductor-annotationdbi >=1.39.3 + - r-base 3.4.1* + - wget + + +bioconductor-go.db 3.6.0 r341_0 +------------------------------- +file name : bioconductor-go.db-3.6.0-r341_0.tar.bz2 +name : bioconductor-go.db +version : 3.6.0 +build : r341_0 +build number: 0 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.6.0-r341_0.tar.bz2 +md5 : c2c0a46d9edbc3405066d095abd11281 +timestamp : 2018-10-18 13:30:50 UTC +dependencies: + - bioconductor-annotationdbi >=1.42.1,<1.44.0 + - r-base >=3.4.1,<3.4.2.0a0 + - wget + + +bioconductor-go.db 3.6.0 r351_0 +------------------------------- +file name : bioconductor-go.db-3.6.0-r351_0.tar.bz2 +name : bioconductor-go.db +version : 3.6.0 +build : r351_0 +build number: 0 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.6.0-r351_0.tar.bz2 +md5 : 59e7a7f27eecb063ee556cb451d4554d +timestamp : 2018-10-18 13:32:28 UTC +dependencies: + - bioconductor-annotationdbi >=1.42.1,<1.44.0 + - r-base >=3.5.1,<3.5.2.0a0 + - wget + + +bioconductor-go.db 3.7.0 r351_0 +------------------------------- +file name : bioconductor-go.db-3.7.0-r351_0.tar.bz2 +name : bioconductor-go.db +version : 3.7.0 +build : r351_0 +build number: 0 +size : 6 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.7.0-r351_0.tar.bz2 +md5 : 71359a0620f7033708d384a525362d15 +timestamp : 2018-12-24 12:34:37 UTC +dependencies: + - bioconductor-annotationdbi >=1.44.0,<1.45.0 + - r-base >=3.5.1,<3.5.2.0a0 + - wget + + +bioconductor-go.db 3.8.2 r36_1 +------------------------------ +file name : bioconductor-go.db-3.8.2-r36_1.tar.bz2 +name : bioconductor-go.db +version : 3.8.2 +build : r36_1 +build number: 1 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.8.2-r36_1.tar.bz2 +md5 : 1e2f7577b4aba6cf173dcc8a2f8b0d39 +timestamp : 2019-08-03 20:56:31 UTC +dependencies: + - bioconductor-annotationdbi >=1.46.0,<1.47.0 + - curl + - r-base >=3.6,<3.7.0a0 + + +bioconductor-go.db 3.10.0 r36_0 +------------------------------- +file name : bioconductor-go.db-3.10.0-r36_0.tar.bz2 +name : bioconductor-go.db +version : 3.10.0 +build : r36_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.10.0-r36_0.tar.bz2 +md5 : 0d305f6b62a862e1c4ce1777647467e3 +timestamp : 2019-11-03 17:19:18 UTC +dependencies: + - bioconductor-annotationdbi >=1.48.0,<1.49.0 + - curl + - r-base >=3.6,<3.7.0a0 + + +bioconductor-go.db 3.11.1 r40_0 +------------------------------- +file name : bioconductor-go.db-3.11.1-r40_0.tar.bz2 +name : bioconductor-go.db +version : 3.11.1 +build : r40_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.11.1-r40_0.tar.bz2 +md5 : eecf5b3f2fca016622200e7664484264 +timestamp : 2020-05-11 19:23:17 UTC +dependencies: + - bioconductor-annotationdbi >=1.50.0,<1.51.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-go.db 3.11.4 r40_0 +------------------------------- +file name : bioconductor-go.db-3.11.4-r40_0.tar.bz2 +name : bioconductor-go.db +version : 3.11.4 +build : r40_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.11.4-r40_0.tar.bz2 +md5 : 7e93e9f3e4f6c22366d9e8961abb975c +timestamp : 2020-06-02 19:08:45 UTC +dependencies: + - bioconductor-annotationdbi >=1.50.0,<1.51.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-go.db 3.12.1 r40_0 +------------------------------- +file name : bioconductor-go.db-3.12.1-r40_0.tar.bz2 +name : bioconductor-go.db +version : 3.12.1 +build : r40_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.12.1-r40_0.tar.bz2 +md5 : 88ffc265fcdedb44a7b26bf7ec5e320a +timestamp : 2020-11-01 19:56:18 UTC +dependencies: + - bioconductor-annotationdbi >=1.52.0,<1.53.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-go.db 3.12.1 r40hdfd78af_1 +--------------------------------------- +file name : bioconductor-go.db-3.12.1-r40hdfd78af_1.tar.bz2 +name : bioconductor-go.db +version : 3.12.1 +build : r40hdfd78af_1 +build number: 1 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.12.1-r40hdfd78af_1.tar.bz2 +md5 : 73dfffb253d44f2e239ad0c3a96206c3 +timestamp : 2021-03-30 15:32:59 UTC +dependencies: + - bioconductor-annotationdbi >=1.52.0,<1.53.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-go.db 3.13.0 r41hdfd78af_0 +--------------------------------------- +file name : bioconductor-go.db-3.13.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-go.db +version : 3.13.0 +build : r41hdfd78af_0 +build number: 0 +size : 8 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.13.0-r41hdfd78af_0.tar.bz2 +md5 : 397957325b84ccaf0402bed0906704af +timestamp : 2021-06-03 14:57:27 UTC +dependencies: + - bioconductor-annotationdbi >=1.54.0,<1.55.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-go.db 3.14.0 r41hdfd78af_0 +--------------------------------------- +file name : bioconductor-go.db-3.14.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-go.db +version : 3.14.0 +build : r41hdfd78af_0 +build number: 0 +size : 8 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.14.0-r41hdfd78af_0.tar.bz2 +md5 : 09f592f871746d7e8885d85d0ae204f9 +timestamp : 2021-11-06 07:41:34 UTC +dependencies: + - bioconductor-annotationdbi >=1.56.0,<1.57.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-go.db 3.14.0 r41hdfd78af_1 +--------------------------------------- +file name : bioconductor-go.db-3.14.0-r41hdfd78af_1.tar.bz2 +name : bioconductor-go.db +version : 3.14.0 +build : r41hdfd78af_1 +build number: 1 +size : 9 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.14.0-r41hdfd78af_1.tar.bz2 +md5 : 5609fa622e907ab52616aeac57d74ba7 +timestamp : 2022-08-21 19:50:50 UTC +dependencies: + - bioconductor-annotationdbi >=1.56.0,<1.57.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-go.db 3.16.0 r42hdfd78af_0 +--------------------------------------- +file name : bioconductor-go.db-3.16.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-go.db +version : 3.16.0 +build : r42hdfd78af_0 +build number: 0 +size : 8 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.16.0-r42hdfd78af_0.tar.bz2 +md5 : 7e8f6bb781a17c51da470164d43372f2 +timestamp : 2022-11-06 22:41:58 UTC +dependencies: + - bioconductor-annotationdbi >=1.60.0,<1.61.0 + - bioconductor-d diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-hdf5array.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-hdf5array.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..f92b47d14c180b77cd72641d9b77f2701f95a58c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-hdf5array.manual_bundle.txt @@ -0,0 +1,372 @@ +# Tool: bioconductor-hdf5array +software_name: bioconductor-hdf5array +tier: T1 +domain: t1_backfill_overall +downloads: 386605 +summary: HDF5 datasets as array-like objects in R +description: The HDF5Array package is an HDF5 backend for DelayedArray objects. It implements the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects. +dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-h5mread >=1.2.0,<1.3.0, bioconductor-iranges >=2.44.0,<2.45.0, bioconductor-rhdf5 >=2.54.0,<2.55.0, bioconductor-s4arrays >=1.10.0,<1.11.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-sparsearray >=1.10.0,<1.11.0, r-base >=4.5,<4.6.0a0, r-matrix +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: http://bioconductor.org/packages/3.6/bioc/html/HDF5Array.html +doc_url: +dev_url: + +## URL Docs Extract +### http://bioconductor.org/packages/3.6/bioc/html/HDF5Array.html +Bioconductor - HDF5Array About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.6 Software Packages HDF5Array HDF5Array This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see HDF5Array . HDF5 back end for DelayedArray objects DOI: 10.18129/B9.bioc.HDF5Array Bioconductor version: 3.6 An array-like container for convenient access and manipulation of HDF5 datasets. Supports delayed operations and block processing. Author: Hervé Pagès Maintainer: Hervé Pagès <hpages at fredhutch.org> Citation (from within R, enter citation("HDF5Array") ): Installation To install this package, start R (version "3.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("HDF5Array") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews Annotation , Coverage , DataRepresentation , GenomeAnnotation , Infrastructure , Sequencing , Software Version 1.6.0 In Bioconductor since BioC 3.3 (R-3.3) (8 years) License Artistic-2.0 Depends R (>= 3.4), methods, DelayedArray (>= 0.3.18), rhdf5 Imports utils, tools, BiocGenerics , S4Vectors , IRanges System Requirements URL See More Suggests h5vcData , SummarizedExperiment (>= 1.5.6), GenomicRanges , BiocStyle Linking To Enhances Depends On Me Imports Me beachmat , bsseq Suggests Me DelayedArray , DelayedMatrixStats , MultiAssayExperiment , scran , SummarizedExperiment Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package HDF5Array_1.6.0.tar.gz Windows Binary HDF5Array_1.6.0.zip Mac OS X 10.11 (El Capitan) HDF5Array_1.6.0.tgz Source Repository git clone https://git.bioconductor.org/packages/HDF5Array Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HDF5Array Package Short Url https://bioconductor.org/packages/HDF5Array/ Package Downloads Report Download Stats Old Source Packages for BioC 3.6 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-hdf5array --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-hdf5array 1.6.0 r3.4.1_0 +------------------------------------- +file name : bioconductor-hdf5array-1.6.0-r3.4.1_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.6.0 +build : r3.4.1_0 +build number: 0 +size : 7.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.6.0-r3.4.1_0.tar.bz2 +md5 : 9ce3089d8bdad38ec1382506b1df0270 +dependencies: + - bioconductor-biocgenerics + - bioconductor-delayedarray >=0.3.18 + - bioconductor-iranges + - bioconductor-rhdf5 + - bioconductor-s4vectors + - r-base 3.4.1* + + +bioconductor-hdf5array 1.8.1 r341_0 +----------------------------------- +file name : bioconductor-hdf5array-1.8.1-r341_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.8.1 +build : r341_0 +build number: 0 +size : 7.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.8.1-r341_0.tar.bz2 +md5 : 5a29f8c1a9be4a76fb99d8b4389f1b63 +timestamp : 2018-10-12 14:09:02 UTC +dependencies: + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - bioconductor-delayedarray >=0.6.6,<0.8.0 + - bioconductor-iranges >=2.14.12,<2.16.0 + - bioconductor-rhdf5 >=2.24.0,<2.26.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-hdf5array 1.8.1 r351_0 +----------------------------------- +file name : bioconductor-hdf5array-1.8.1-r351_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.8.1 +build : r351_0 +build number: 0 +size : 7.9 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.8.1-r351_0.tar.bz2 +md5 : 7b91ab346e6c23be5d4799e588f2403f +timestamp : 2018-10-12 14:10:44 UTC +dependencies: + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - bioconductor-delayedarray >=0.6.6,<0.8.0 + - bioconductor-iranges >=2.14.12,<2.16.0 + - bioconductor-rhdf5 >=2.24.0,<2.26.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-hdf5array 1.10.1 r351_0 +------------------------------------ +file name : bioconductor-hdf5array-1.10.1-r351_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.10.1 +build : r351_0 +build number: 0 +size : 8.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-hdf5array-1.10.1-r351_0.tar.bz2 +md5 : 3c9076ef86c50cb5ed20c571caac35e9 +timestamp : 2018-12-11 16:20:59 UTC +dependencies: + - bioconductor-biocgenerics >=0.28.0,<0.29.0 + - bioconductor-delayedarray >=0.8.0,<0.9.0 + - bioconductor-iranges >=2.16.0,<2.17.0 + - bioconductor-rhdf5 >=2.26.0,<2.27.0 + - bioconductor-s4vectors >=0.20.0,<0.21.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-hdf5array 1.12.1 r36h516909a_0 +------------------------------------------- +file name : bioconductor-hdf5array-1.12.1-r36h516909a_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.12.1 +build : r36h516909a_0 +build number: 0 +size : 9.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.12.1-r36h516909a_0.tar.bz2 +md5 : dc387003cb6b9afc3ab4656574d11993 +timestamp : 2019-07-24 16:10:30 UTC +dependencies: + - bioconductor-biocgenerics >=0.30.0,<0.31.0 + - bioconductor-delayedarray >=0.10.0,<0.11.0 + - bioconductor-iranges >=2.18.0,<2.19.0 + - bioconductor-rhdf5 >=2.28.0,<2.29.0 + - bioconductor-rhdf5lib >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.22.0,<0.23.0 + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-hdf5array 1.14.0 r36h516909a_0 +------------------------------------------- +file name : bioconductor-hdf5array-1.14.0-r36h516909a_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.14.0 +build : r36h516909a_0 +build number: 0 +size : 9.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.14.0-r36h516909a_0.tar.bz2 +md5 : 8300d405a29b4f07992b852c07120eb9 +timestamp : 2019-11-02 13:25:32 UTC +dependencies: + - bioconductor-biocgenerics >=0.32.0,<0.33.0 + - bioconductor-delayedarray >=0.12.0,<0.13.0 + - bioconductor-iranges >=2.20.0,<2.21.0 + - bioconductor-rhdf5 >=2.30.0,<2.31.0 + - bioconductor-rhdf5lib >=1.8.0,<1.9.0 + - bioconductor-s4vectors >=0.24.0,<0.25.0 + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + - r-matrix + + +bioconductor-hdf5array 1.16.0 r40h037d062_0 +------------------------------------------- +file name : bioconductor-hdf5array-1.16.0-r40h037d062_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.16.0 +build : r40h037d062_0 +build number: 0 +size : 9.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.16.0-r40h037d062_0.tar.bz2 +md5 : db7e1d345d97b612e4db407afc446ca7 +timestamp : 2020-05-10 00:01:37 UTC +dependencies: + - bioconductor-biocgenerics >=0.34.0,<0.35.0 + - bioconductor-delayedarray >=0.14.0,<0.15.0 + - bioconductor-iranges >=2.22.0,<2.23.0 + - bioconductor-rhdf5 >=2.32.0,<2.33.0 + - bioconductor-rhdf5lib >=1.10.0,<1.11.0 + - bioconductor-s4vectors >=0.26.0,<0.27.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - liblapack >=3.8.0,<3.9.0a0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + + +bioconductor-hdf5array 1.18.0 r40h037d062_0 +------------------------------------------- +file name : bioconductor-hdf5array-1.18.0-r40h037d062_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.18.0 +build : r40h037d062_0 +build number: 0 +size : 9.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.18.0-r40h037d062_0.tar.bz2 +md5 : 6f104a452a31abab224b22234071395a +timestamp : 2020-10-29 23:45:19 UTC +dependencies: + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - bioconductor-delayedarray >=0.16.0,<0.17.0 + - bioconductor-iranges >=2.24.0,<2.25.0 + - bioconductor-rhdf5 >=2.34.0,<2.35.0 + - bioconductor-rhdf5lib >=1.12.0,<1.13.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + + +bioconductor-hdf5array 1.18.1 r40hd029910_0 +------------------------------------------- +file name : bioconductor-hdf5array-1.18.1-r40hd029910_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.18.1 +build : r40hd029910_0 +build number: 0 +size : 9.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.18.1-r40hd029910_0.tar.bz2 +md5 : 8394856cad2205d4d4764eec838111a3 +timestamp : 2021-03-28 21:07:33 UTC +dependencies: + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - bioconductor-delayedarray >=0.16.0,<0.17.0 + - bioconductor-iranges >=2.24.0,<2.25.0 + - bioconductor-rhdf5 >=2.34.0,<2.35.0 + - bioconductor-rhdf5lib >=1.12.0,<1.13.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + + +bioconductor-hdf5array 1.20.0 r41ha2fdcc6_1 +------------------------------------------- +file name : bioconductor-hdf5array-1.20.0-r41ha2fdcc6_1.tar.bz2 +name : bioconductor-hdf5array +version : 1.20.0 +build : r41ha2fdcc6_1 +build number: 1 +size : 9.9 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.20.0-r41ha2fdcc6_1.tar.bz2 +md5 : 75da6543a516cacb2cd3fe94832afde3 +timestamp : 2021-10-23 22:42:18 UTC +dependencies: + - bioconductor-biocgenerics >=0.38.0,<0.39.0 + - bioconductor-delayedarray >=0.18.0,<0.19.0 + - bioconductor-iranges >=2.26.0,<2.27.0 + - bioconductor-rhdf5 >=2.36.0,<2.37.0 + - bioconductor-rhdf5filters >=1.4.0,<1.5.0 + - bioconductor-rhdf5lib >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.30.0,<0.31.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.4.0 + - liblapack >=3.8.0,<4.0a0 + - openssl >=1.1.1l,<1.1.2a + - r-base >=4.1,<4.2.0a0 + - r-matrix + + +bioconductor-hdf5array 1.20.0 r41hd029910_0 +------------------------------------------- +file name : bioconductor-hdf5array-1.20.0-r41hd029910_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.20.0 +build : r41hd029910_0 +build number: 0 +size : 9.9 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.20.0-r41hd029910_0.tar.bz2 +md5 : 314dd7495746ec46c65b6058951d9cbd +timestamp : 2021-06-01 06:35:50 UTC +dependencies: + - bioconductor-biocgenerics >=0.38.0,<0.39.0 + - bioconductor-delayedarray >=0.18.0,<0.19.0 + - bioconductor-iranges >=2.26.0,<2.27.0 + - bioconductor-rhdf5 >=2.36.0,<2.37.0 + - bioconductor-rhdf5filters >=1.4.0,<1.5.0 + - bioconductor-rhdf5lib >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.30.0,<0.31.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.1,<4.2.0a0 + - r-matrix + + +bioconductor-hdf5array 1.22.0 r41ha2fdcc6_1 +------------------------------------------- +file name : bioconductor-hdf5array-1.22.0-r41ha2fdcc6_1.tar.bz2 +name : bioconductor-hdf5array +version : 1.22.0 +build : r41ha2fdcc6_1 +build number: 1 +size : 9.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.22.0-r41ha2fdcc6_1.tar.bz2 +md5 : 8307d33623bacc139b2df14c492e8a70 +timestamp : 2021-11-07 13:07:40 UTC +dependencies: + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-iranges >=2.28.0,<2.29.0 + - bioconductor-rhdf5 >=2.38.0,<2.39.0 + - bioconductor-rhdf5filters >=1.6.0,<1.7.0 + - bioconductor-rhdf5lib >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.4.0 + - liblapack >=3.8.0,<4.0a0 + - openssl >=1.1.1l,<1.1.2a + - r-base >=4.1,<4.2.0a0 + - r-matrix + + +bioconductor-hdf5array 1.22.1 r41h5c21468_0 +------------------------------------------- +file name : bioconductor-hdf5array-1.22.1-r41h5c21468_0.tar.bz2 +name : bioconductor-hdf5array +version : 1.22.1 +build : r41h5c21468_0 +build number: 0 +size : 9.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.22.1-r41h5c21468_0.tar.bz2 +md5 : 40efbcbe24bbd284d8a341b3a999a860 +timestamp : 2022-02-26 20:29:00 UTC +dependencies: + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-iranges >=2.28.0,<2.29.0 + - bioconductor-rhdf5 >=2.38.0,<2.39.0 + - bioconductor-rhdf5filters >=1.6.0,<1.7.0 + - bioconductor-rhdf5lib >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=10.3.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.1,<4.2.0a0 + - r-matrix + + +bioconductor-hdf5array 1.22.1 r41hc0cfd56_1 +------------------------------------------- +file name : bioconductor-hdf5array-1.22.1-r41hc0cfd56_1.tar.bz2 +name : bioconductor-hdf5array +version : 1.22.1 +build : r41hc0cfd56_1 +build number: 1 +size : 9.9 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.22.1-r41hc0cfd56_1.tar.bz2 +md5 : bc5a371b218f38b78c2ff13de25dd0ff +time diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-imcdatasets.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-imcdatasets.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..210d05a0e4e718e18ba189ec22ded1337259617c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-imcdatasets.manual_bundle.txt @@ -0,0 +1,225 @@ +# Tool: bioconductor-imcdatasets +software_name: bioconductor-imcdatasets +tier: T1 +domain: spatial_transcriptomics +downloads: 11629 +summary: Collection of publicly available imaging mass cytometry (IMC) datasets +description: The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images. +dependencies: bioconductor-cytomapper >=1.22.0,<1.23.0, bioconductor-data-packages >=20260207, bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-hdf5array >=1.38.0,<1.39.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, curl, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.13/data/experiment/html/imcdatasets.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.13/data/experiment/html/imcdatasets.html +40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images." /> Bioconductor - imcdatasets About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.13 Experiment Packages imcdatasets imcdatasets This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see imcdatasets . Collection of publicly available imaging mass cytometry (IMC) datasets DOI: 10.18129/B9.bioc.imcdatasets Bioconductor version: 3.13 The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images. Author: Nicolas Damond [aut, cre] , Nils Eling [ctb] , Fischer Jana [ctb] Maintainer: Nicolas Damond <nicolas.damond at dqbm.uzh.ch> Citation (from within R, enter citation("imcdatasets") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("imcdatasets") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("imcdatasets") Accessing IMC datasets HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentData , ExperimentHub , PackageTypeData , SingleCellData , TechnologyData , Tissue Version 1.0.1 License GPL-3 Depends R (>= 4.1), SingleCellExperiment , cytomapper Imports methods, utils, ExperimentHub , S4Vectors , DelayedArray , HDF5Array System Requirements URL https://github.com/BodenmillerGroup/imcdatasets Bug Reports https://github.com/BodenmillerGroup/imcdatasets/issues See More Suggests BiocStyle , knitr, rmarkdown, markdown, testthat Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package imcdatasets_1.0.1.tar.gz Windows Binary macOS 10.13 (High Sierra) Source Repository git clone https://git.bioconductor.org/packages/imcdatasets Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/imcdatasets Package Short Url https://bioconductor.org/packages/imcdatasets/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-imcdatasets --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-imcdatasets 1.0.0 r41hdfd78af_0 +-------------------------------------------- +file name : bioconductor-imcdatasets-1.0.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-imcdatasets +version : 1.0.0 +build : r41hdfd78af_0 +build number: 0 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.0.0-r41hdfd78af_0.tar.bz2 +md5 : adbe4ab042984d9d357bf6a1c7521941 +timestamp : 2021-06-03 21:28:28 UTC +dependencies: + - bioconductor-cytomapper >=1.4.0,<1.5.0 + - bioconductor-delayedarray >=0.18.0,<0.19.0 + - bioconductor-experimenthub >=2.0.0,<2.1.0 + - bioconductor-hdf5array >=1.20.0,<1.21.0 + - bioconductor-s4vectors >=0.30.0,<0.31.0 + - bioconductor-singlecellexperiment >=1.14.0,<1.15.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-imcdatasets 1.2.0 r41hdfd78af_0 +-------------------------------------------- +file name : bioconductor-imcdatasets-1.2.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-imcdatasets +version : 1.2.0 +build : r41hdfd78af_0 +build number: 0 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.2.0-r41hdfd78af_0.tar.bz2 +md5 : 21bd3f37658dfb095b55945512a5712b +timestamp : 2021-11-07 20:17:14 UTC +dependencies: + - bioconductor-cytomapper >=1.6.0,<1.7.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-experimenthub >=2.2.0,<2.3.0 + - bioconductor-hdf5array >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.16.0,<1.17.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-imcdatasets 1.2.0 r41hdfd78af_1 +-------------------------------------------- +file name : bioconductor-imcdatasets-1.2.0-r41hdfd78af_1.tar.bz2 +name : bioconductor-imcdatasets +version : 1.2.0 +build : r41hdfd78af_1 +build number: 1 +size : 21 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.2.0-r41hdfd78af_1.tar.bz2 +md5 : 8ea956714a1e768cb05ab2cc39a3b1e4 +timestamp : 2022-09-02 02:27:29 UTC +dependencies: + - bioconductor-cytomapper >=1.6.0,<1.7.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-experimenthub >=2.2.0,<2.3.0 + - bioconductor-hdf5array >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.16.0,<1.17.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-imcdatasets 1.6.0 r42hdfd78af_0 +-------------------------------------------- +file name : bioconductor-imcdatasets-1.6.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-imcdatasets +version : 1.6.0 +build : r42hdfd78af_0 +build number: 0 +size : 21 KB +license : GPL-3 + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.6.0-r42hdfd78af_0.tar.bz2 +md5 : ac6068fc47e38ddc37d5543a956d8326 +timestamp : 2022-11-09 10:04:50 UTC +dependencies: + - bioconductor-cytomapper >=1.10.0,<1.11.0 + - bioconductor-data-packages >=20221108 + - bioconductor-delayedarray >=0.24.0,<0.25.0 + - bioconductor-experimenthub >=2.6.0,<2.7.0 + - bioconductor-hdf5array >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - curl + - r-base >=4.2,<4.3.0a0 + + +bioconductor-imcdatasets 1.8.0 r43hdfd78af_0 +-------------------------------------------- +file name : bioconductor-imcdatasets-1.8.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-imcdatasets +version : 1.8.0 +build : r43hdfd78af_0 +build number: 0 +size : 22 KB +license : GPL-3 + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.8.0-r43hdfd78af_0.tar.bz2 +md5 : 09903ee65d7ea5726255d6090997231d +timestamp : 2023-07-17 10:41:17 UTC +dependencies: + - bioconductor-cytomapper >=1.12.0,<1.13.0 + - bioconductor-data-packages >=20230706 + - bioconductor-delayedarray >=0.26.0,<0.27.0 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-hdf5array >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-imcdatasets 1.10.0 r43hdfd78af_0 +--------------------------------------------- +file name : bioconductor-imcdatasets-1.10.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-imcdatasets +version : 1.10.0 +build : r43hdfd78af_0 +build number: 0 +size : 22 KB +license : GPL-3 + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.10.0-r43hdfd78af_0.tar.bz2 +md5 : 6e900b6e139c649f20680093640c393c +timestamp : 2023-12-08 12:47:53 UTC +dependencies: + - bioconductor-cytomapper >=1.14.0,<1.15.0 + - bioconductor-data-packages >=20231203 + - bioconductor-delayedarray >=0.28.0,<0.29.0 + - bioconductor-experimenthub >=2.10.0,<2.11.0 + - bioconductor-hdf5array >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-imcdatasets 1.14.0 r44hdfd78af_0 +--------------------------------------------- +file name : bioconductor-imcdatasets-1.14.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-imcdatasets +version : 1.14.0 +build : r44hdfd78af_0 +build number: 0 +size : 21 KB +license : GPL-3 + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.14.0-r44hdfd78af_0.tar.bz2 +md5 : ca98d539f9d5da52f48fc64e28a80abb +timestamp : 2024-12-22 22:58:04 UTC +dependencies: + - bioconductor-cytomapper >=1.18.0,<1.19.0 + - bioconductor-data-packages >=20241103 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - curl + - r-base >=4.4,<4.5.0a0 + + +bioconductor-imcdatasets 1.18.0 r45hdfd78af_0 +--------------------------------------------- +file name : bioconductor-imcdatasets-1.18.0-r45hdfd78af_0.conda +name : bioconductor-imcdatasets +version : 1.18.0 +build : r45hdfd78af_0 +build number: 0 +size : 24 KB +license : GPL-3 + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.18.0-r45hdfd78af_0.conda +md5 : 31b8659d420ee000ead4a1a33914055e +timestamp : 2026-03-03 01:28:30 UTC +dependencies: + - bioconductor-cytomapper >=1.22.0,<1.23.0 + - bioconductor-data-packages >=20260207 + - bioconductor-delayedarray >=0.36.0,<0.37.0 + - bioconductor-experimenthub >=3.0.0,<3.1.0 + - bioconductor-hdf5array >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - curl + - r-base >=4.5,<4.6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-imcrtools.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-imcrtools.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..317be55e327a58ca01cfec8cb65e06ea18dfe464 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-imcrtools.manual_bundle.txt @@ -0,0 +1,298 @@ +# Tool: bioconductor-imcrtools +software_name: bioconductor-imcrtools +tier: T1 +domain: spatial_transcriptomics +downloads: 8426 +summary: Methods for imaging mass cytometry data analysis +description: This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected. +dependencies: bioconductor-biocneighbors >=2.4.0,<2.5.0, bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-cytomapper >=1.22.0,<1.23.0, bioconductor-ebimage >=4.52.0,<4.53.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scuttle >=1.20.0,<1.21.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-abind, r-base >=4.5,<4.6.0a0, r-concaveman, r-data.table, r-distances, r-dplyr, r-dt, r-ggplot2, r-ggraph, r-igraph, r-magrittr, r-pheatmap, r-readr, r-rlang, r-rtriangle, r-sf, r-stringr, r-tidygraph, r-tidyselect, r-viridis, r-vroom +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.14/bioc/html/imcRtools.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.14/bioc/html/imcRtools.html +Bioconductor - imcRtools About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.14 Software Packages imcRtools imcRtools This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see imcRtools . Methods for imaging mass cytometry data analysis DOI: 10.18129/B9.bioc.imcRtools Bioconductor version: 3.14 This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected. Author: Nils Eling [aut, cre] , Tobias Hoch [ctb], Vito Zanotelli [ctb], Jana Fischer [ctb], Daniel Schulz [ctb] Maintainer: Nils Eling <nils.eling at dqbm.uzh.ch> Citation (from within R, enter citation("imcRtools") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("imcRtools") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("imcRtools") Tools for IMC data analysis HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Clustering , DataImport , ImmunoOncology , SingleCell , Software , Spatial Version 1.0.2 In Bioconductor since BioC 3.14 (R-4.1) (2.5 years) License GPL-3 Depends R (>= 4.1), SpatialExperiment Imports S4Vectors , stats, utils, SummarizedExperiment , methods, pheatmap, scuttle , stringr, readr, EBImage , cytomapper , abind, BiocParallel , viridis, dplyr, magrittr, DT, igraph, SingleCellExperiment , vroom, BiocNeighbors , RTriangle, ggraph, tidygraph, ggplot2, data.table, sf, concaveman System Requirements URL https://github.com/BodenmillerGroup/imcRtools Bug Reports https://github.com/BodenmillerGroup/imcRtools/issues See More Suggests CATALYST , grid, tidyr, BiocStyle , knitr, rmarkdown, markdown, testthat Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package imcRtools_1.0.2.tar.gz Windows Binary imcRtools_1.0.2.zip macOS 10.13 (High Sierra) imcRtools_1.0.2.tgz Source Repository git clone https://git.bioconductor.org/packages/imcRtools Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/imcRtools Bioc Package Browser https://code.bioconductor.org/browse/imcRtools/ Package Short Url https://bioconductor.org/packages/imcRtools/ Package Downloads Report Download Stats Old Source Packages for BioC 3.14 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-imcrtools --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-imcrtools 1.0.0 r41hdfd78af_0 +------------------------------------------ +file name : bioconductor-imcrtools-1.0.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-imcrtools +version : 1.0.0 +build : r41hdfd78af_0 +build number: 0 +size : 3.6 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.0.0-r41hdfd78af_0.tar.bz2 +md5 : 3ce66873db9ee4be23c8710346d45db4 +timestamp : 2021-11-08 00:30:35 UTC +dependencies: + - bioconductor-biocneighbors >=1.12.0,<1.13.0 + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - bioconductor-cytomapper >=1.6.0,<1.7.0 + - bioconductor-ebimage >=4.36.0,<4.37.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-scuttle >=1.4.0,<1.5.0 + - bioconductor-singlecellexperiment >=1.16.0,<1.17.0 + - bioconductor-spatialexperiment >=1.4.0,<1.5.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - r-abind + - r-base >=4.1,<4.2.0a0 + - r-concaveman + - r-data.table + - r-dplyr + - r-dt + - r-ggplot2 + - r-ggraph + - r-igraph + - r-magrittr + - r-pheatmap + - r-readr + - r-rtriangle + - r-sf + - r-stringr + - r-tidygraph + - r-viridis + - r-vroom + + +bioconductor-imcrtools 1.4.0 r42hdfd78af_0 +------------------------------------------ +file name : bioconductor-imcrtools-1.4.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-imcrtools +version : 1.4.0 +build : r42hdfd78af_0 +build number: 0 +size : 5.6 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.4.0-r42hdfd78af_0.tar.bz2 +md5 : f8687318d0c4d3f11eeb034495fd4a5b +timestamp : 2022-11-06 03:13:41 UTC +dependencies: + - bioconductor-biocneighbors >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.32.0,<1.33.0 + - bioconductor-cytomapper >=1.10.0,<1.11.0 + - bioconductor-ebimage >=4.40.0,<4.41.0 + - bioconductor-matrixgenerics >=1.10.0,<1.11.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-scuttle >=1.8.0,<1.9.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - r-abind + - r-base >=4.2,<4.3.0a0 + - r-concaveman + - r-data.table + - r-distances + - r-dplyr + - r-dt + - r-ggplot2 + - r-ggraph + - r-igraph + - r-magrittr + - r-pheatmap + - r-readr + - r-rtriangle + - r-sf + - r-stringr + - r-tidygraph + - r-tidyselect + - r-viridis + - r-vroom + + +bioconductor-imcrtools 1.6.3 r43hdfd78af_0 +------------------------------------------ +file name : bioconductor-imcrtools-1.6.3-r43hdfd78af_0.tar.bz2 +name : bioconductor-imcrtools +version : 1.6.3 +build : r43hdfd78af_0 +build number: 0 +size : 5.5 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.6.3-r43hdfd78af_0.tar.bz2 +md5 : f77f2bdcf050bb5db3ef5358d5bf822a +timestamp : 2023-07-17 11:01:36 UTC +dependencies: + - bioconductor-biocneighbors >=1.18.0,<1.19.0 + - bioconductor-biocparallel >=1.34.0,<1.35.0 + - bioconductor-cytomapper >=1.12.0,<1.13.0 + - bioconductor-ebimage >=4.42.0,<4.43.0 + - bioconductor-matrixgenerics >=1.12.0,<1.13.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-scuttle >=1.10.0,<1.11.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-abind + - r-base >=4.3,<4.4.0a0 + - r-concaveman + - r-data.table + - r-distances + - r-dplyr + - r-dt + - r-ggplot2 + - r-ggraph + - r-igraph + - r-magrittr + - r-pheatmap + - r-readr + - r-rtriangle + - r-sf + - r-stringr + - r-tidygraph + - r-tidyselect + - r-viridis + - r-vroom + + +bioconductor-imcrtools 1.8.0 r43hdfd78af_0 +------------------------------------------ +file name : bioconductor-imcrtools-1.8.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-imcrtools +version : 1.8.0 +build : r43hdfd78af_0 +build number: 0 +size : 5.6 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.8.0-r43hdfd78af_0.tar.bz2 +md5 : 7104313c1143ceadad2f31ed305e77f9 +timestamp : 2023-12-12 01:35:50 UTC +dependencies: + - bioconductor-biocneighbors >=1.20.0,<1.21.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - bioconductor-cytomapper >=1.14.0,<1.15.0 + - bioconductor-ebimage >=4.44.0,<4.45.0 + - bioconductor-matrixgenerics >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-scuttle >=1.12.0,<1.13.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-abind + - r-base >=4.3,<4.4.0a0 + - r-concaveman + - r-data.table + - r-distances + - r-dplyr + - r-dt + - r-ggplot2 + - r-ggraph + - r-igraph + - r-magrittr + - r-pheatmap + - r-readr + - r-rtriangle + - r-sf + - r-stringr + - r-tidygraph + - r-tidyselect + - r-viridis + - r-vroom + + +bioconductor-imcrtools 1.12.0 r44hdfd78af_0 +------------------------------------------- +file name : bioconductor-imcrtools-1.12.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-imcrtools +version : 1.12.0 +build : r44hdfd78af_0 +build number: 0 +size : 5.8 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.12.0-r44hdfd78af_0.tar.bz2 +md5 : b5b9a7aee14359d1072508ce8c1217f5 +timestamp : 2024-12-22 23:43:07 UTC +dependencies: + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cytomapper >=1.18.0,<1.19.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-abind + - r-base >=4.4,<4.5.0a0 + - r-concaveman + - r-data.table + - r-distances + - r-dplyr + - r-dt + - r-ggplot2 + - r-ggraph + - r-igraph + - r-magrittr + - r-pheatmap + - r-readr + - r-rlang + - r-rtriangle + - r-sf + - r-stringr + - r-tidygraph + - r-tidyselect + - r-viridis + - r-vroom + + +bioconductor-imcrtools 1.16.0 r45hdfd78af_0 +------------------------------------------- +file name : bioconductor-imcrtools-1.16.0-r45hdfd78af_0.conda +name : bioconductor-imcrtools +version : 1.16.0 +build : r45hdfd78af_0 +build number: 0 +size : 8.4 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.16.0-r45hdfd78af_0.conda +md5 : 4fef003de1b594ddb3de1e3ad34a426e +timestamp : 2026-03-02 07:25:34 UTC +dependencies: + - bioconductor-biocneighbors >=2.4.0,<2.5.0 + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-cytomapper >=1.22.0,<1.23.0 + - bioconductor-ebimage >=4.52.0,<4.53.0 + - bioconductor-matrixgenerics >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-scuttle >=1.20.0,<1.21.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-abind + - r-base >=4.5,<4.6.0a0 + - r-concaveman + - r-data.table + - r-distances + - r-dplyr + - r-dt + - r-ggplot2 + - r-ggraph + - r-igraph + - r-magrittr + - r-pheatmap + - r-readr + - r-rlang + - r-rtriangle + - r-sf + - r-stringr + - r-tidygraph + - r-tidyselect + - r-viridis + - r-vroom diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-interactivedisplaybase.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-interactivedisplaybase.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b359f2b69d102af3ba5db558e504fb23111e201d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-interactivedisplaybase.manual_bundle.txt @@ -0,0 +1,360 @@ +# Tool: bioconductor-interactivedisplaybase +software_name: bioconductor-interactivedisplaybase +tier: T1 +domain: t1_backfill_overall +downloads: 114195 +summary: Base package for enabling powerful shiny web displays of Bioconductor objects +description: The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects. +dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, r-base >=4.5,<4.6.0a0, r-dt, r-shiny +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/interactiveDisplayBase.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/interactiveDisplayBase.html +Bioconductor - interactiveDisplayBase Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages interactiveDisplayBase interactiveDisplayBase This package is deprecated . It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.22 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see interactiveDisplayBase . Base package for enabling powerful shiny web displays of Bioconductor objects DOI: 10.18129/B9.bioc.interactiveDisplayBase Bioconductor version: 3.22 The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects. Author: Bioconductor Package Maintainer [cre], Shawn Balcome [aut], Marc Carlson [ctb], Marcel Ramos [ctb] Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation("interactiveDisplayBase") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("interactiveDisplayBase") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("interactiveDisplayBase") Using interactiveDisplayBase for Bioconductor object visualization and modification HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews AnnotationData , Classification , DataRepresentation , GO , GUI , GeneExpression , Genetics , Microarray , Network , QualityControl , Sequencing , ShinyApps , Software , Visualization Version 1.48.0 In Bioconductor since BioC 3.0 (R-3.1) (11.5 years) License Artistic-2.0 Depends R (>= 2.10), methods, BiocGenerics Imports shiny , DT System Requirements URL See More Suggests knitr , markdown Linking To Enhances rstudioapi Depends On Me Imports Me interactiveDisplay Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package interactiveDisplayBase_1.48.0.tar.gz Windows Binary (x86_64) interactiveDisplayBase_1.48.0.zip macOS Binary (x86_64) interactiveDisplayBase_1.48.0.tgz macOS Binary (arm64) interactiveDisplayBase_1.48.0.tgz Source Repository git clone https://git.bioconductor.org/packages/interactiveDisplayBase Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/interactiveDisplayBase Package Short Url https://bioconductor.org/packages/interactiveDisplayBase/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-interactivedisplaybase --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-interactivedisplaybase 1.12.0 r3.3.1_0 +--------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.12.0-r3.3.1_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.12.0 +build : r3.3.1_0 +build number: 0 +size : 25 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.12.0-r3.3.1_0.tar.bz2 +md5 : 1fc2ced5356c32f8c80c98bd43a71520 +dependencies: + - bioconductor-biocgenerics + - r 3.3.1* + - r-shiny + + +bioconductor-interactivedisplaybase 1.12.0 r3.3.2_0 +--------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.12.0-r3.3.2_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.12.0 +build : r3.3.2_0 +build number: 0 +size : 27 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.12.0-r3.3.2_0.tar.bz2 +md5 : b80c7dac832804a662d378bfac55857f +dependencies: + - bioconductor-biocgenerics + - r-base 3.3.2* + - r-shiny + + +bioconductor-interactivedisplaybase 1.12.0 r3.4.1_0 +--------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.12.0-r3.4.1_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.12.0 +build : r3.4.1_0 +build number: 0 +size : 29 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.12.0-r3.4.1_0.tar.bz2 +md5 : 7115dae2471123a3f9f372e7548c8286 +dependencies: + - bioconductor-biocgenerics + - r-base 3.4.1* + - r-shiny + + +bioconductor-interactivedisplaybase 1.14.0 r3.4.1_0 +--------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.14.0-r3.4.1_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.14.0 +build : r3.4.1_0 +build number: 0 +size : 38 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.14.0-r3.4.1_0.tar.bz2 +md5 : c41aba3cbcc5cf368a9153bca4e5ec90 +dependencies: + - bioconductor-biocgenerics + - r-base 3.4.1* + - r-shiny + + +bioconductor-interactivedisplaybase 1.16.0 r3.4.1_0 +--------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.16.0-r3.4.1_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.16.0 +build : r3.4.1_0 +build number: 0 +size : 38 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.16.0-r3.4.1_0.tar.bz2 +md5 : 131f82996370f023e9292c219f6872c2 +dependencies: + - bioconductor-biocgenerics + - r-base 3.4.1* + - r-shiny + + +bioconductor-interactivedisplaybase 1.18.0 r341_0 +------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.18.0-r341_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.18.0 +build : r341_0 +build number: 0 +size : 39 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.18.0-r341_0.tar.bz2 +md5 : 15ef54c687a9db41c3ed5d7b0f75eea4 +timestamp : 2018-10-12 09:26:24 UTC +dependencies: + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - r-base >=3.4.1,<3.4.2.0a0 + - r-shiny + + +bioconductor-interactivedisplaybase 1.18.0 r351_0 +------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.18.0-r351_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.18.0 +build : r351_0 +build number: 0 +size : 45 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.18.0-r351_0.tar.bz2 +md5 : 9ef36f14fbdb6b52445db40408e1428a +timestamp : 2018-10-12 09:25:03 UTC +dependencies: + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-shiny + + +bioconductor-interactivedisplaybase 1.20.0 r351_0 +------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.20.0-r351_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.20.0 +build : r351_0 +build number: 0 +size : 46 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.20.0-r351_0.tar.bz2 +md5 : a14cb9600292881e33267bffab502f43 +timestamp : 2018-12-10 22:50:28 UTC +dependencies: + - bioconductor-biocgenerics >=0.28.0,<0.29.0 + - r-base >=3.5.1,<3.5.2.0a0 + - r-shiny + + +bioconductor-interactivedisplaybase 1.22.0 r36_1 +------------------------------------------------ +file name : bioconductor-interactivedisplaybase-1.22.0-r36_1.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.22.0 +build : r36_1 +build number: 1 +size : 47 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.22.0-r36_1.tar.bz2 +md5 : 6de095a07dc7ee041b7b23654a6b6abf +timestamp : 2019-07-22 10:11:40 UTC +dependencies: + - bioconductor-biocgenerics >=0.30.0,<0.31.0 + - r-base >=3.6,<3.7.0a0 + - r-shiny + + +bioconductor-interactivedisplaybase 1.24.0 r36_0 +------------------------------------------------ +file name : bioconductor-interactivedisplaybase-1.24.0-r36_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.24.0 +build : r36_0 +build number: 0 +size : 48 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.24.0-r36_0.tar.bz2 +md5 : a56f2a3fb1ca6572362d96fe4002d230 +timestamp : 2019-11-01 13:31:43 UTC +dependencies: + - bioconductor-biocgenerics >=0.32.0,<0.33.0 + - r-base >=3.6,<3.7.0a0 + - r-shiny + + +bioconductor-interactivedisplaybase 1.26.0 r40_0 +------------------------------------------------ +file name : bioconductor-interactivedisplaybase-1.26.0-r40_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.26.0 +build : r40_0 +build number: 0 +size : 48 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.26.0-r40_0.tar.bz2 +md5 : 1469ab7e6fff6cc84ed4266a1fab0bba +timestamp : 2020-05-10 06:13:01 UTC +dependencies: + - bioconductor-biocgenerics >=0.34.0,<0.35.0 + - r-base >=4.0,<4.1.0a0 + - r-shiny + + +bioconductor-interactivedisplaybase 1.28.0 r40_0 +------------------------------------------------ +file name : bioconductor-interactivedisplaybase-1.28.0-r40_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.28.0 +build : r40_0 +build number: 0 +size : 41 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.28.0-r40_0.tar.bz2 +md5 : 39dc134cb53f0f535881d1a7bfb6c3e3 +timestamp : 2020-10-29 23:15:09 UTC +dependencies: + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - r-base >=4.0,<4.1.0a0 + - r-dt + - r-shiny + + +bioconductor-interactivedisplaybase 1.28.0 r40hdfd78af_1 +-------------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.28.0-r40hdfd78af_1.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.28.0 +build : r40hdfd78af_1 +build number: 1 +size : 42 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.28.0-r40hdfd78af_1.tar.bz2 +md5 : 8d22711f2a43bdbb8dd9c03e9f8f3638 +timestamp : 2021-03-27 03:04:59 UTC +dependencies: + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - r-base >=4.0,<4.1.0a0 + - r-dt + - r-shiny + + +bioconductor-interactivedisplaybase 1.30.0 r41hdfd78af_0 +-------------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.30.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.30.0 +build : r41hdfd78af_0 +build number: 0 +size : 42 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.30.0-r41hdfd78af_0.tar.bz2 +md5 : ce7aacead080f18c0fedf03e2176dd81 +timestamp : 2021-05-31 00:58:27 UTC +dependencies: + - bioconductor-biocgenerics >=0.38.0,<0.39.0 + - r-base >=4.1,<4.2.0a0 + - r-dt + - r-shiny + + +bioconductor-interactivedisplaybase 1.32.0 r41hdfd78af_0 +-------------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.32.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.32.0 +build : r41hdfd78af_0 +build number: 0 +size : 42 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.32.0-r41hdfd78af_0.tar.bz2 +md5 : d3313430918e1f28648d4052621e65bc +timestamp : 2021-11-01 18:07:47 UTC +dependencies: + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - r-base >=4.1,<4.2.0a0 + - r-dt + - r-shiny + + +bioconductor-interactivedisplaybase 1.36.0 r42hdfd78af_0 +-------------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.36.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.36.0 +build : r42hdfd78af_0 +build number: 0 +size : 43 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.36.0-r42hdfd78af_0.tar.bz2 +md5 : 288ee61d446a563b569b27e1ed6dd308 +timestamp : 2022-11-03 20:43:50 UTC +dependencies: + - bioconductor-biocgenerics >=0.44.0,<0.45.0 + - r-base >=4.2,<4.3.0a0 + - r-dt + - r-shiny + + +bioconductor-interactivedisplaybase 1.38.0 r43hdfd78af_0 +-------------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.38.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.38.0 +build : r43hdfd78af_0 +build number: 0 +size : 39 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.38.0-r43hdfd78af_0.tar.bz2 +md5 : ff2f32c8117f1e5ecdfe7ef8d4d4bc86 +timestamp : 2023-07-07 17:38:16 UTC +dependencies: + - bioconductor-biocgenerics >=0.46.0,<0.47.0 + - r-base >=4.3,<4.4.0a0 + - r-dt + - r-shiny + + +bioconductor-interactivedisplaybase 1.40.0 r43hdfd78af_0 +-------------------------------------------------------- +file name : bioconductor-interactivedisplaybase-1.40.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-interactivedisplaybase +version : 1.40.0 +build : r43hdfd78af_0 +build number: 0 +size : 40 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.40.0-r43hdfd78af_0.ta diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-iranges.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-iranges.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3c7ab9097030d112240ba24f58acc0aec4741b9f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-iranges.manual_bundle.txt @@ -0,0 +1,425 @@ +# Tool: bioconductor-iranges +software_name: bioconductor-iranges +tier: T1 +domain: t1_backfill_overall +downloads: 1839431 +summary: Foundation of integer range manipulation in Bioconductor +description: Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames. +dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/IRanges.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=0] + +Usage: /path/to/Rscript [--options] [-e expr [-e expr2 ...] | file] [args] + +--options accepted are + --help Print usage and exit + --version Print version and exit + --verbose Print information on progress + --default-packages=list + Where 'list' is a comma-separated set + of package names, or 'NULL' +or options to R, in addition to --no-echo --no-restore, such as + --save Do save workspace at the end of the session + --no-environ Don't read the site and user environment files + --no-site-file Don't read the site-wide Rprofile + --no-init-file Don't read the user R profile + --restore Do restore previously saved objects at startup + --vanilla Combine --no-save, --no-restore, --no-site-file + --no-init-file and --no-environ + +'file' may contain spaces but not shell metacharacters +Expressions (one or more '-e ') may be used *instead* of 'file' +See also ?Rscript from within R + + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/IRanges.html +Bioconductor - IRanges Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages IRanges IRanges This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see IRanges . Foundation of integer range manipulation in Bioconductor DOI: 10.18129/B9.bioc.IRanges Bioconductor version: 3.22 Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames. Author: Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Michael Lawrence [aut] Maintainer: Hervé Pagès <hpages.on.github at gmail.com> Citation (from within R, enter citation("IRanges") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("IRanges") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("IRanges") An Overview of the IRanges package PDF R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataRepresentation , Infrastructure , Software Version 2.44.0 In Bioconductor since BioC 2.3 (R-2.8) (17.5 years) License Artistic-2.0 Depends R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.47.6) Imports stats4 System Requirements URL https://bioconductor.org/packages/IRanges Bug Reports https://github.com/Bioconductor/IRanges/issues See More Suggests XVector , GenomicRanges , Rsamtools , GenomicAlignments , GenomicFeatures , BSgenome.Celegans.UCSC.ce2 , pasillaBamSubset , RUnit , BiocStyle Linking To S4Vectors Enhances Depends On Me AnnotationDbi , AnnotationHubData , BaalChIP , bambu , biomvRCNS , Biostrings , BiSeq , BSgenome , BSgenomeForge , bumphunter , CAFE , casper , CexoR , chimeraviz , ChIPpeakAnno , chipseq , cigarillo , CODEX , consensusSeekeR , CSAR , CSSQ , customProDB , deepSNV , DelayedArray , DESeq2 , DEXSeq , DirichletMultinomial , DMCFB , DMCHMM , DMRcaller , epigenomix , ExCluster , fCCAC , GenomeInfoDb , GenomicAlignments , GenomicDistributions , GenomicFeatures , GenomicRanges , groHMM , gtrellis , Gviz , HelloRanges , HERON , HiTC , IdeoViz , InTAD , MotifDb , MultimodalExperiment , NADfinder , oncoscanR , ORFik , OTUbase , pepStat , periodicDNA , plyranges , proBAMr , pwalign , RepViz , rGREAT , RJMCMCNucleosomes , RNAmodR , S4Arrays , Scale4C , SCOPE , SGSeq , SICtools , Structstrings , TEQC , traseR , triplex , VariantTools , VplotR , XVector , pd.ag , pd.aragene.1.0.st , pd.aragene.1.1.st , pd.ath1.121501 , pd.barley1 , pd.bovgene.1.0.st , pd.bovgene.1.1.st , pd.bovine , pd.bsubtilis , pd.cangene.1.0.st , pd.cangene.1.1.st , pd.canine , pd.canine.2 , pd.celegans , pd.chicken , pd.chigene.1.0.st , pd.chigene.1.1.st , pd.chogene.2.0.st , pd.chogene.2.1.st , pd.citrus , pd.clariom.d.human , pd.clariom.s.human , pd.clariom.s.human.ht , pd.clariom.s.mouse , pd.clariom.s.mouse.ht , pd.clariom.s.rat , pd.clariom.s.rat.ht , pd.cotton , pd.cyngene.1.0.st , pd.cyngene.1.1.st , pd.cyrgene.1.0.st , pd.cyrgene.1.1.st , pd.cytogenetics.array , pd.drogene.1.0.st , pd.drogene.1.1.st , pd.drosgenome1 , pd.drosophila.2 , pd.e.coli.2 , pd.ecoli , pd.ecoli.asv2 , pd.elegene.1.0.st , pd.elegene.1.1.st , pd.equgene.1.0.st , pd.equgene.1.1.st , pd.felgene.1.0.st , pd.felgene.1.1.st , pd.fingene.1.0.st , pd.fingene.1.1.st , pd.genomewidesnp.5 , pd.genomewidesnp.6 , pd.guigene.1.0.st , pd.guigene.1.1.st , pd.hc.g110 , pd.hg.focus , pd.hg.u133.plus.2 , pd.hg.u133a , pd.hg.u133a.2 , pd.hg.u133a.tag , pd.hg.u133b , pd.hg.u219 , pd.hg.u95a , pd.hg.u95av2 , pd.hg.u95b , pd.hg.u95c , pd.hg.u95d , pd.hg.u95e , pd.hg18.60mer.expr , pd.ht.hg.u133.plus.pm , pd.ht.hg.u133a , pd.ht.mg.430a , pd.hta.2.0 , pd.hu6800 , pd.huex.1.0.st.v2 , pd.hugene.1.0.st.v1 , pd.hugene.1.1.st.v1 , pd.hugene.2.0.st , pd.hugene.2.1.st , pd.maize , pd.mapping250k.nsp , pd.mapping250k.sty , pd.mapping50k.hind240 , pd.mapping50k.xba240 , pd.margene.1.0.st , pd.margene.1.1.st , pd.medgene.1.0.st , pd.medgene.1.1.st , pd.medicago , pd.mg.u74a , pd.mg.u74av2 , pd.mg.u74b , pd.mg.u74bv2 , pd.mg.u74c , pd.mg.u74cv2 , pd.mirna.1.0 , pd.mirna.2.0 , pd.mirna.3.0 , pd.mirna.4.0 , pd.moe430a , pd.moe430b , pd.moex.1.0.st.v1 , pd.mogene.1.0.st.v1 , pd.mogene.1.1.st.v1 , pd.mogene.2.0.st , pd.mogene.2.1.st , pd.mouse430.2 , pd.mouse430a.2 , pd.mta.1.0 , pd.mu11ksuba , pd.mu11ksubb , pd.nugo.hs1a520180 , pd.nugo.mm1a520177 , pd.ovigene.1.0.st , pd.ovigene.1.1.st , pd.pae.g1a , pd.plasmodium.anopheles , pd.poplar , pd.porcine , pd.porgene.1.0.st , pd.porgene.1.1.st , pd.rabgene.1.0.st , pd.rabgene.1.1.st , pd.rae230a , pd.rae230b , pd.raex.1.0.st.v1 , pd.ragene.1.0.st.v1 , pd.ragene.1.1.st.v1 , pd.ragene.2.0.st , pd.ragene.2.1.st , pd.rat230.2 , pd.rcngene.1.0.st , pd.rcngene.1.1.st , pd.rg.u34a , pd.rg.u34b , pd.rg.u34c , pd.rhegene.1.0.st , pd.rhegene.1.1.st , pd.rhesus , pd.rice , pd.rjpgene.1.0.st , pd.rjpgene.1.1.st , pd.rn.u34 , pd.rta.1.0 , pd.rusgene.1.0.st , pd.rusgene.1.1.st , pd.s.aureus , pd.soybean , pd.soygene.1.0.st , pd.soygene.1.1.st , pd.sugar.cane , pd.tomato , pd.u133.x3p , pd.vitis.vinifera , pd.wheat , pd.x.laevis.2 , pd.x.tropicalis , pd.xenopus.laevis , pd.yeast.2 , pd.yg.s98 , pd.zebgene.1.0.st , pd.zebgene.1.1.st , pd.zebrafish , harbChIP , LiebermanAidenHiC2009 Imports Me alabaster.bumpy , alabaster.ranges , alabaster.se , ALDEx2 , AllelicImbalance , amplican , annmap , annotatr , appreci8R , ASpli , AssessORF , ATACseqQC , ATACseqTFEA , atena , ballgown , bamsignals , BBCAnalyzer , beadarray , BgeeCall , BindingSiteFinder , Bioc.gff , biovizBase , biscuiteer , BiSeq , bnbc , branchpointer , breakpointR , bsseq , BUMHMM , BumpyMatrix , BUSpaRse , CAGEfightR , cageminer , CAGEr , cBioPortalData , cfdnakit , cfDNAPro , ChIPanalyser , chipenrich , ChIPexoQual , ChIPseeker , chipseq , ChIPseqR , ChIPsim , ChromHeatMap , ChromSCape , chromVAR , cicero , circRNAprofiler , CircSeqAlignTk , cleanUpdTSeq , cleaver , cn.mops , CNEr , CNVfilteR , CNVMetrics , CNVPanelizer , CNVRanger , CNVrd2 , COCOA , coMethDMR , compEpiTools , ComplexHeatmap , CompoundDb , conumee , CopyNumberPlots , CoverageView , crisprBase , crisprBowtie , crisprDesign , crisprScore , CRISPRseek , CrispRVariants , crisprViz , crupR , csaw , CTexploreR , dada2 , DAMEfinder , debrowser , DECIPHER , deconvR , DegCre , DegNorm , DelayedMatrixStats , deltaCaptureC , demuxSNP , derfinder , derfinderHelper , derfinderPlot , DEScan2 , DiffBind , diffHic , diffUTR , DMRcaller , DMRcate , DMRScan , dmrseq , DNAfusion , DominoEffect , dreamlet , DRIMSeq , DropletUtils , dStruct , easyRNASeq , EDASeq , eisaR , ELMER , ELViS , enhancerHomologSearch , EnrichedHeatmap , ensembldb , EpiCompare , epidecodeR , epigraHMM , EpiMix , epimutacions , epiregulon , epistack , EpiTxDb , epivizr , epivizrData , esATAC , EventPointer , extraChIPs , factR , FastqCleaner , fastseg , fcScan , FilterFFPE , FindIT2 , fishpond , FLAMES , FRASER , G4SNVHunter , GA4GHclient , gcapc , gDNAx , geneAttribution , GENESIS , genomation , GenomAutomorphism , genomeIntervals , GenomicAlignments , GenomicDataCommons , GenomicFiles , GenomicInteractionNodes , GenomicInteractions , GenomicOZone , GenomicPlot , GenomicScores , GenomicTuples , GenVisR , geomeTriD , ggbio , gmapR , gmoviz , GOfuncR , GOpro , GOTHiC , GSVA , GUIDEseq , gVenn , gwascat , h5mread , h5vc , HDF5Array , heatmaps , hermes , HicAggR , HiCaptuRe , HiCBricks , HiCcompare , HiCExperiment , HiContacts , hicVennDiagram , HilbertCurve , hummingbird , icetea , ideal , idr2d , igblastr , InPAS , INSPEcT , intansv , InteractionSet , InteractiveComplexHeatmap , IntEREst , ipdDb , iSEEu , IsoformSwitchAnalyzeR , isomiRs , IVAS , karyoploteR , katdetectr , knowYourCG , linkSet , LOLA , m6Aboost , magpie , mariner , maser , MatrixRider , mCSEA , MDTS , MEAL , MEDIPS , MesKit , metagene2 , metaseqR2 , methimpute , methInheritSim , methodical , MethReg , methrix , methylCC , methylInheritance , methylKit , methylPipe , MethylSeekR , methylSig , methylumi , mia , minfi , MinimumDistance , MIRA , missMethyl , mobileRNA , Modstrings , monaLisa , mosaics , MOSim , Motif2Site , motifbreakR , motifmatchr , MotifPeeker , motifTestR , MouseFM , msa , MSA2dist , MsBackendMassbank , MsBackendMgf , MsBackendMsp , MsBackendRawFileReader , MsBackendSql , MsExperiment , msgbsR , MSnbase , MultiAssayExperiment , MultiDataSet , mumosa , MungeSumstats , musicatk , MutationalPatterns , mutscan , NanoMethViz , NanoStringNCTools , ncRNAtools , normr , nucleoSim , nucleR , nullranges , OGRE , oligoClasses , OmaDB , OMICsPCA , openPrimeR , Organism.dplyr , OrganismDbi , OUTRIDER , OutSplice , packFinder , panelcn.mops , pcaExplorer , pdInfoBuilder , peakCombiner , PhIPData , PICB , plotgardener , plyinteractions , podkat , pqsfinder , pram , prebs , preciseTAD , primirTSS , proActiv , ProteoDisco , PSMatch , PureCN , Pviz , QDNAseq , QFeatures , qpgraph , qPLEXanalyzer , qsea , QuasR , R3CPET , r3Cseq , raer , RaggedExperiment , RAIDS , ramr , RareVariantVis , RCAS , recount , recoup , REDseq , regioneR , regutools , REMP , ReportingTools , RESOLVE , rfaRm , rfPred , RgnTX , RiboCrypt , RiboDiPA , RiboProfiling , riboSeqR , ribosomeProfilingQC , rigvf , rnaEditr , RNAmodR.AlkAnilineSeq , RNAmodR.ML , RNAmodR.RiboMethSeq , RnBeads , roar , rprimer , Rqc , Rsamtools , RSVSim , RTN , rtracklayer , sarks , saseR , SCAN.UPC , scanMiR , scanMiRApp , scDblFinder , scHOT , scPipe , scRNAseqApp , segmenter , segmentSeq , SeqArray , seqCAT , Seqinfo , seqPattern , seqsetvis , SeqSQC , SeqVarTools , sesame , sevenC , ShortRead , signeR , signifinder , SimFFPE , SingleMoleculeFootprinting , sitadela , Site2Target , SMITE , snapcount , SNPhood , SomaticSignatures , SOMNiBUS , SparseArray , SparseSignatures , Spectra , SpectriPy , spiky , SpliceWiz , SplicingGraphs , SPLINTER , srnadiff , STADyUM , strandCheckR , StructuralVariantAnnotation , SummarizedExperiment , SynExtend , tadar , TAPseq , target , TCGAbiolinks , TCGAutils , TCseq , TENET , TFBSTools , TFEA.ChIP , TFHAZ , tidyCoverage , TnT , tracktables , trackViewer , transcriptR , transmogR , TreeSummarizedExperiment , TRESS , tricycle , tRNA , tRNAdbImport , tRNAscanImport , TVTB , txcutr , txdbmaker , tximeta , UMI4Cats , Uniquorn , universalmotif , UPDhmm , VanillaICE , VarCon , VariantAnnotation , VariantExperiment , VariantFiltering , VaSP , VDJdive , vmrseq , wavClusteR , wiggleplotr , xcms , xcore , XVector , yamss , ZygosityPredictor , fitCons.UCSC.hg19 , GenomicState , MafDb.1Kgenomes.phase1.GRCh38 , MafDb.1Kgenomes.phase1.hs37d5 , MafDb.1Kgenomes.phase3.GRCh38 , MafDb.1Kgenomes.phase3.hs37d5 , MafDb.ExAC.r1.0.GRCh38 , MafDb.ExAC.r1.0.hs37d5 , MafDb.ExAC.r1.0.nonTCGA.GRCh38 , MafDb.ExAC.r1.0.nonTCGA.hs37d5 , MafDb.gnomAD.r2.1.GRCh38 , MafDb.gnomAD.r2.1.hs37d5 , MafDb.gnomADex.r2.1.GRCh38 , MafDb.gnomADex.r2.1.hs37d5 , MafDb.TOPMed.freeze5.hg19 , MafDb.TOPMed.freeze5.hg38 , MafH5.gnomAD.v4.0.GRCh38 , pd.081229.hg18.promoter.medip.hx1 , pd.2006.07.18.hg18.refseq.promoter , pd.2006.07.18.mm8.refseq.promoter , pd.2006.10.31.rn34.refseq.promoter , pd.charm.hg18.example , pd.feinberg.hg18.me.hx1 , pd.feinberg.mm8.me.hx1 , pd.mirna.3.1 , phastCons100way.UCSC.hg19 , phastCons100way.UCSC.hg38 , phastCons7way.UCSC.hg38 , SNPlocs.Hsapiens.dbSNP144.GRCh37 , SNPlocs.Hsapiens.dbSNP144.GRCh38 , SNPlocs.Hsapiens.dbSNP149.GRCh38 , SNPlocs.Hsapiens.dbSNP150.GRCh38 , SNPlocs.Hsapiens.dbSNP155.GRCh37 , SNPlocs.Hsapiens.dbSNP155.GRCh38 , XtraSNPlocs.Hsapiens.dbSNP144.GRCh37 , XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 , chipenrich.data , fourDNData , leeBamViews , MethylSeqData , pd.atdschip.tiling , sesameData , SomaticCancerAlterations , spatialLIBD , seqpac , ActiveDriverWGS , alakazam , cpp11bigwig , crispRdesignR , cubar , DESNP , GencoDymo2 , geno2proteo , GenoPop , hahmmr , hoardeR, iimi , karyotapR , lisat , locuszoomr , longreadvqs , LoopRig , MitoHEAR , noisyr , numbat , PACVr , RapidoPGS , refseqR , revert , rnaCrosslinkOO , Signac , TmCalculator , VALERIE Suggests Me annotate , AnnotationHub , BaseSpaceR , BiocGenerics , BREW3R.r , CCAFE , Chicago , ClassifyR , DFplyr , easylift , epivizrChart , gDRcore , gDRutils , Glimma , GWASTools , HilbertVis , HilbertVisGUI , iscream , maftools , martini , MiRaGE , multicrispr , partCNV , plyxp , regionalpcs , regionReport , RTCGA , S4Vectors , SigsPack , splatter , svaNUMT , svaRetro , systemPipeR , TFutils , tidybulk , MetaScope , scMultiome , systemPipeRdata , xcoredata , yeastRNASeq , fuzzyjoin , gggenomes , gkmSVM , MiscMetabar , MoBPS , polyRAD , pQTLdata , rliger , scPloidy , seqmagick , Seurat , sigminer , updog , valr Links To Me Bioc.gff , Biostrings , cigarillo , CNEr , DECIPHER , GenomicAlignments , GenomicRanges , kebabs , MatrixRider , pwalign , Rsamtools , rtracklayer , ShortRead , SparseArray , Structstrings , triplex , VariantAnnotation , VariantFiltering , XVector Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package IRanges_2.44.0.tar.gz Windows Binary (x86_64) IRanges_2.44.0.zip macOS Binary (x86_64) IRanges_2.44.0.tgz macOS Binary (arm64) IRanges_2.44.0.tgz Source Repository git clone https://git.bioconductor.org/packages/IRanges Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IRanges Bioc Package Browser https://code.bioconductor.org/browse/IRanges/ Package Short Url https://bioconductor.org/packages/IRanges/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-iranges --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-iranges 2.2.9 0 +---------------------------- +file name : bioconductor-iranges-2.2.9-0.tar.bz2 +name : bioconductor-iranges +version : 2.2.9 +build : 0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.2.9-0.tar.bz2 +md5 : ac08b68017ca9b0ba4522a8e7a4bd42a +dependencies: + - bioconductor-biocgenerics + - bioconductor-s4vectors + - r >=3.1.0 + + +bioconductor-iranges 2.4.0 0 +---------------------------- +file name : bioconductor-iranges-2.4.0-0.tar.bz2 +name : bioconductor-iranges +version : 2.4.0 +build : 0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.4.0-0.tar.bz2 +md5 : d3420ed6d62570625b87f892f69ee9fd +dependencies: + - bioconductor-biocgenerics >=0.15.10 + - bioconductor-s4vectors >=0.7.19 + - r >=3.1.0 + + +bioconductor-iranges 2.4.1 0 +---------------------------- +file name : bioconductor-iranges-2.4.1-0.tar.bz2 +name : bioconductor-iranges +version : 2.4.1 +build : 0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.4.1-0.tar.bz2 +md5 : 89a8206d5c0f53ff0c2c00e5d2afe1bb +dependencies: + - bioconductor-biocgenerics >=0.15.10 + - bioconductor-s4vectors >=0.7.19 + - r >=3.1.0 + + +bioconductor-iranges 2.4.6 0 +---------------------------- +file name : bioconductor-iranges-2.4.6-0.tar.bz2 +name : bioconductor-iranges +version : 2.4.6 +build : 0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.4.6-0.tar.bz2 +md5 : 819ab4cc7c6f1b8b08bf4f4526a73008 +dependencies: + - bioconductor-biocgenerics >=0.15.10 + - bioconductor-s4vectors >=0.8.4 + - r >=3.1.0 + + +bioconductor-iranges 2.4.7 0 +---------------------------- +file name : bioconductor-iranges-2.4.7-0.tar.bz2 +name : bioconductor-iranges +version : 2.4.7 +build : 0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.4.7-0.tar.bz2 +md5 : fb4e709080781d58b5ac2e657c592f7b +dependencies: + - bioconductor-biocgenerics >=0.15.10 + - bioconductor-s4vectors >=0.8.4 + - r >=3.1.0 + + +bioconductor-iranges 2.4.8 0 +---------------------------- +file name : bioconductor-iranges-2.4.8-0.tar.bz2 +name : bioconductor-iranges +version : 2.4.8 +build : 0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.4.8-0.tar.bz2 +md5 : 7ee66e351a8b2f3e3b7822a3b3d45341 +dependencies: + - bioconductor-biocgenerics >=0.15.10 + - bioconductor-s4vectors >=0.8.4 + - r >=3.1.0 + + +bioconductor-iranges 2.6.0 r3.3.1_0 +----------------------------------- +file name : bioconductor-iranges-2.6.0-r3.3.1_0.tar.bz2 +name : bioconductor-iranges +version : 2.6.0 +build : r3.3.1_0 +build number: 0 +size : 1.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.6.0-r3.3.1_0.tar.bz2 +md5 : f11223044697df893ee955df0b353590 +dependencies: + - bioconductor-biocgenerics >=0.15.10 + - bioconductor-s4vectors >=0.8.4 + - r 3.3.1* + + +bioconductor-iranges 2.6.1 r3.3.1_0 +----------------------------------- +file name : bioconductor-iranges-2.6.1-r3.3.1_0.tar.bz2 +name : bioconductor-iranges +version : 2.6.1 +build : r3.3.1_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.6.1-r3.3.1_0.tar.bz2 +md5 : 99b263aa381aacadf1cdb4ad9949f734 +dependencies: + - bioconductor-biocgenerics >=0.15.10 + - bioconductor-s4vectors >=0.9.48 + - r 3.3.1* + + +bioconductor-iranges 2.8.0 r3.3.1_0 +----------------------------------- +file name : bioconductor-iranges-2.8.0-r3.3.1_0.tar.bz2 +name : bioconductor-iranges +version : 2.8.0 +build : r3.3.1_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.8.0-r3.3.1_0.tar.bz2 +md5 : c29f73ed575e9327d33aff36ce71c3db +dependencies: + - bioconductor-biocgenerics 0.20.0 + - bioconductor-s4vectors 0.12.0 + - r 3.3.1* + + +bioconductor-iranges 2.8.2 r3.3.1_0 +----------------------------------- +file name : bioconductor-iranges-2.8.2-r3.3.1_0.tar.bz2 +name : bioconductor-iranges +version : 2.8.2 +build : r3.3.1_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.8.2-r3.3.1_0.tar.bz2 +md5 : d1dfa8fd7c6a961cfea966c8f7e9e7f2 +dependencies: + - bioconductor-biocgenerics >=0.19.1 + - bioconductor-s4vectors >=0.11.19 + - r-base 3.3.1* + + +bioconductor-iranges 2.8.2 r3.3.2_0 +----------------------------------- +file name : bioconductor-iranges-2.8.2-r3.3.2_0.tar.bz2 +name : bioconductor-iranges +version : 2.8.2 +build : r3.3.2_0 +build number: 0 +size : 1.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.8.2-r3.3.2_0.tar.bz2 +md5 : a6000e13548b3ec81e1c9b7a22a2d963 +dependencies: + - bioconductor-biocgenerics >=0.19.1 + - bioconductor-s4vectors >=0.11.19 + - r-base 3.3.2* + + +bioconductor-iranges 2.8.2 r3.4.1_0 +----------------------------------- +file name : bioconductor-iranges-2.8.2-r3.4.1_0.tar.bz2 +name : bioconductor-iranges +version : 2.8.2 +build : r3.4.1_0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.8.2-r3.4.1_0.tar.bz2 +md5 : 47c82e857deb9f3814a7fc756bda3241 +dependencies: + - bioconductor-biocgenerics >=0.19.1 + - bioconductor-s4vectors >=0.11.19 + - r-base 3.4.1* + + +bioconductor-iranges 2.10.5 r3.4.1_0 +------------------------------------ +file name : bioconductor-iranges-2.10.5-r3.4.1_0.tar.bz2 +name : bioconductor-iranges +version : 2.10.5 +build : r3.4.1_0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.10.5-r3.4.1_0.tar.bz2 +md5 : 755fbc8be4f4ffe6afee1bb28e28869a +dependencies: + - bioconductor-biocgenerics >=0.21.1 + - bioconductor-s4vectors >=0.13.17 + - r-base 3.4.1* + + +bioconductor-iranges 2.12.0 r3.4.1_0 +------------------------------------ +file name : bioconductor-iranges-2.12.0-r3.4.1_0.tar.bz2 +name : bioconductor-iranges +version : 2.12.0 +build : r3.4.1_0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.12.0-r3.4.1_0.tar.bz2 +md5 : d6eba62c90f14eefee3db162c1e9fb26 +dependencies: + - bioconductor-biocgenerics >=0.23.3 + - bioconductor-s4vectors >=0.15.5 + - r-base 3.4.1* + + +bioconductor-iranges 2.14.12 r341h470a237_0 +------------------------------------------- +file name : bioconductor-iranges-2.14.12-r341h470a237_0.tar.bz2 +name : bioconductor-iranges +version : 2.14.12 +build : r341h470a237_0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.14.12-r341h470a237_0.tar.bz2 +md5 : 62f7abd67d8b218ef1f167a21b3457a7 +timestamp : 2018-10-12 13:03:33 UTC +dependencies: + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - libgcc-ng >=4.9 + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-iranges 2.14.12 r351h470a237_0 +------------------------------------------- +file name : bioconductor-iranges-2.14.12-r351h470a237_0.tar.bz2 +name : bioconductor-iranges +version : 2.14.12 +build : r351h470a237_0 +build number: 0 +size : 2.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.14.12-r351h470a237_0.tar.bz2 +md5 : 122f9bf65025dc0aceca3aec7335ea7a +timestamp : 2018-10-12 13:05:24 UTC +dependencies: + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - libgcc-ng >=4.9 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-iranges 2.16.0 r351h14c3975_0 +------------------------------------------ +file name : bioconductor-iranges-2.16.0-r351h14c3975_0.tar.bz2 +name : bioconductor-iranges +version : 2.16.0 +build : r351h14c3975_0 +build number: 0 +size : 2.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.16.0-r351h14c3975_0.tar.bz2 +md5 : 3405ae982502f5ca7042b2cb1c50d376 +timestamp : 2018-12-11 15:46:41 UTC +dependencies: + - bioconductor-biocgenerics >=0.28.0,<0.29.0 + - bioconductor-s4vectors >=0.20.0,<0.21.0 + - libgcc-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-iranges 2.18.1 r36h516909a_0 +----------------------------------------- +file name : bioconductor-iranges-2.18.1-r36h516909a_0.tar.bz2 +name : bioconductor-iranges +version : 2.18.1 +build : r36h516909a_0 +build number: 0 +size : 2.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.18.1-r36h516909a_0.tar.bz2 +md5 : d698f0be6a21bb48be249e400d7a7c1b +timestamp : 2019-07-22 00:23:30 UTC +dependencies: + - bioconductor-biocgenerics >=0.30.0,<0.31.0 + - bioconductor-s4vectors >=0.22.0,<0.23.0 + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-iranges 2.18.2 r36h516909a_0 +----------------------------------------- +file name : bioconductor-iranges-2.18.2-r36h516909a_0.tar.bz2 +name : bioconductor-iranges +version : 2.18.2 +build : r36h516909a_0 +build number: 0 +size : 2.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.18.2-r36h516909a_0.tar.bz2 +md5 : 9726b447105b9a35b6667423d4eefe94 +timestamp : 2019-08-28 09:13:01 UTC +dependencies: + - bioconductor-biocgenerics >=0.30.0,<0.31.0 + - bioconductor-s4vectors >=0.22.0,<0.23.0 + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-iranges 2.20.0 r36h516909a_0 +----------------------------------------- +file name : bioconductor-iranges-2.20.0-r36h516909a_0.tar.bz2 +name : bioconductor-iranges +version : 2.20.0 +build : r36h516909a_0 +build number: 0 +size : 2.4 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.20.0-r36h516909a_0.tar.bz2 +md5 : f79bf7a5ef20ab244ff21ef0cf05fb46 +timestamp : 2019-11-01 14:57:39 UTC +dependencies: + - bioconductor-biocgenerics >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.24.0,<0.25.0 + - libgcc-ng >=7.3 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-jazzpanda.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-jazzpanda.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..5a40f44bbb5f20a5bde4f768da8ebff61fdcc396 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-jazzpanda.manual_bundle.txt @@ -0,0 +1,51 @@ +# Tool: bioconductor-jazzpanda +software_name: bioconductor-jazzpanda +tier: T1 +domain: spatial_transcriptomics +downloads: 30 +summary: Finding spatially relevant marker genes in image based spatial transcriptomics data +description: This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordiantes, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permtuation testing, which is implmented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and backgound noise. +dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-bumpymatrix >=1.18.0,<1.19.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, r-base >=4.5,<4.6.0a0, r-caret, r-doparallel, r-dplyr, r-foreach, r-glmnet, r-magrittr, r-spatstat.geom +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/jazzPanda.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/jazzPanda.html +Bioconductor - jazzPanda Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages jazzPanda jazzPanda This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see jazzPanda . Finding spatially relevant marker genes in image based spatial transcriptomics data DOI: 10.18129/B9.bioc.jazzPanda Bioconductor version: 3.22 This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordiantes, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permtuation testing, which is implmented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and backgound noise. Author: Melody Jin [aut, cre] ORCID: 0000-0002-2222-0958 Maintainer: Melody Jin <jin.m at wehi.edu.au> Citation (from within R, enter citation("jazzPanda") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("jazzPanda") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("jazzPanda") jazzPanda example HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DifferentialExpression , GeneExpression , Software , Spatial , StatisticalMethod , Transcriptomics Version 1.2.0 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License GPL-3 Depends R (>= 4.5.0) Imports spatstat.geom , dplyr , glmnet , caret , foreach , stats, magrittr , doParallel , BiocParallel , methods, BumpyMatrix , SpatialExperiment System Requirements URL https://github.com/phipsonlab/jazzPanda https://bhuvad.github.io/jazzPanda/ Bug Reports https://github.com/phipsonlab/jazzPanda/issues See More Suggests BiocStyle , knitr , rmarkdown , spatstat , Seurat , statmod , corrplot , ggplot2 , ggraph , ggrepel , gridExtra , reshape2 , igraph , jsonlite , vdiffr , patchwork , ggpubr , tidyr , SpatialFeatureExperiment , ExperimentHub , TENxXeniumData , SingleCellExperiment , SFEData , Matrix , data.table , scran , scater , grid, GenomeInfoDb , testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package jazzPanda_1.2.0.tar.gz Windows Binary (x86_64) jazzPanda_1.2.0.zip macOS Binary (x86_64) jazzPanda_1.2.0.tgz macOS Binary (arm64) jazzPanda_1.2.0.tgz Source Repository git clone https://git.bioconductor.org/packages/jazzPanda Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/jazzPanda Bioc Package Browser https://code.bioconductor.org/browse/jazzPanda/ Package Short Url https://bioconductor.org/packages/jazzPanda/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-jazzpanda --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-jazzpanda 1.2.0 r45hdfd78af_0 +------------------------------------------ +file name : bioconductor-jazzpanda-1.2.0-r45hdfd78af_0.conda +name : bioconductor-jazzpanda +version : 1.2.0 +build : r45hdfd78af_0 +build number: 0 +size : 4.4 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-jazzpanda-1.2.0-r45hdfd78af_0.conda +md5 : 077f10f80bd1f2144270676649abf15c +timestamp : 2026-03-01 16:22:32 UTC +dependencies: + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-bumpymatrix >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - r-base >=4.5,<4.6.0a0 + - r-caret + - r-doparallel + - r-dplyr + - r-foreach + - r-glmnet + - r-magrittr + - r-spatstat.geom diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-matrixgenerics.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-matrixgenerics.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..d0ebef3c461205767e0f77f8d836ea7728d94d7b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-matrixgenerics.manual_bundle.txt @@ -0,0 +1,296 @@ +# Tool: bioconductor-matrixgenerics +software_name: bioconductor-matrixgenerics +tier: T1 +domain: t1_backfill_overall +downloads: 1199955 +summary: S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects +description: S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities. +dependencies: r-base >=4.5,<4.6.0a0, r-matrixstats >=1.4.1 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.11/bioc/html/MatrixGenerics.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.11/bioc/html/MatrixGenerics.html +Bioconductor - MatrixGenerics About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.11 Software Packages MatrixGenerics MatrixGenerics This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MatrixGenerics . S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects DOI: 10.18129/B9.bioc.MatrixGenerics Bioconductor version: 3.11 S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities. Author: Constantin Ahlmann-Eltze [aut] , Peter Hickey [aut, cre] Maintainer: Peter Hickey <peter.hickey at gmail.com> Citation (from within R, enter citation("MatrixGenerics") ): Installation To install this package, start R (version "4.0") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MatrixGenerics") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Infrastructure , Software Version 1.0.2 In Bioconductor since BioC 3.11 (R-4.0) (4 years) License Artistic-2.0 Depends matrixStats (>= 0.56.0) Imports methods System Requirements URL https://github.com/Bioconductor/MatrixGenerics Bug Reports https://github.com/Bioconductor/MatrixGenerics/issues See More Suggests testthat (>= 2.1.0) Linking To Enhances Depends On Me Imports Me sparseMatrixStats Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package MatrixGenerics_1.0.2.tar.gz Windows Binary MatrixGenerics_1.0.2.zip macOS 10.13 (High Sierra) MatrixGenerics_1.0.2.tgz Source Repository git clone https://git.bioconductor.org/packages/MatrixGenerics Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MatrixGenerics Bioc Package Browser https://code.bioconductor.org/browse/MatrixGenerics/ Package Short Url https://bioconductor.org/packages/MatrixGenerics/ Package Downloads Report Download Stats Old Source Packages for BioC 3.11 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-matrixgenerics --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-matrixgenerics 1.0.0 r36_0 +--------------------------------------- +file name : bioconductor-matrixgenerics-1.0.0-r36_0.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.0.0 +build : r36_0 +build number: 0 +size : 314 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.0.0-r36_0.tar.bz2 +md5 : 9c736f84a2b80f14b1e458c577ff363f +timestamp : 2020-05-05 13:12:27 UTC +dependencies: + - r-base >=3.6,<3.7.0a0 + - r-matrixstats >=0.56.0 + + +bioconductor-matrixgenerics 1.0.0 r40_1 +--------------------------------------- +file name : bioconductor-matrixgenerics-1.0.0-r40_1.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.0.0 +build : r40_1 +build number: 1 +size : 318 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.0.0-r40_1.tar.bz2 +md5 : 885ace9ec4669960523689e9a5a6a2ae +timestamp : 2020-05-09 16:22:42 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + - r-matrixstats >=0.56.0 + + +bioconductor-matrixgenerics 1.2.0 r40_0 +--------------------------------------- +file name : bioconductor-matrixgenerics-1.2.0-r40_0.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.2.0 +build : r40_0 +build number: 0 +size : 321 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.2.0-r40_0.tar.bz2 +md5 : 3e4bbb486f11ca12b741b6f77e8e5dc7 +timestamp : 2020-10-29 12:35:28 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + - r-matrixstats >=0.57.0 + + +bioconductor-matrixgenerics 1.2.1 r40hdfd78af_0 +----------------------------------------------- +file name : bioconductor-matrixgenerics-1.2.1-r40hdfd78af_0.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.2.1 +build : r40hdfd78af_0 +build number: 0 +size : 324 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.2.1-r40hdfd78af_0.tar.bz2 +md5 : b22671384108edc71b35d5ab0cf31c08 +timestamp : 2021-03-27 23:02:09 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + - r-matrixstats >0.57.0 + + +bioconductor-matrixgenerics 1.4.0 r41hdfd78af_0 +----------------------------------------------- +file name : bioconductor-matrixgenerics-1.4.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.4.0 +build : r41hdfd78af_0 +build number: 0 +size : 324 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.4.0-r41hdfd78af_0.tar.bz2 +md5 : eff7c55a3f0d916cf09fc7db0232b04c +timestamp : 2021-05-31 02:39:16 UTC +dependencies: + - r-base >=4.1,<4.2.0a0 + - r-matrixstats >0.57.0 + + +bioconductor-matrixgenerics 1.6.0 r41hdfd78af_0 +----------------------------------------------- +file name : bioconductor-matrixgenerics-1.6.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.6.0 +build : r41hdfd78af_0 +build number: 0 +size : 342 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.6.0-r41hdfd78af_0.tar.bz2 +md5 : 69613f3c312fb36021947f3359e89435 +timestamp : 2021-11-01 16:32:48 UTC +dependencies: + - r-base >=4.1,<4.2.0a0 + - r-matrixstats >=0.60.1 + + +bioconductor-matrixgenerics 1.10.0 r42hdfd78af_0 +------------------------------------------------ +file name : bioconductor-matrixgenerics-1.10.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.10.0 +build : r42hdfd78af_0 +build number: 0 +size : 344 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.10.0-r42hdfd78af_0.tar.bz2 +md5 : 5ef80e5c26d03a75d62e2ee02054e665 +timestamp : 2022-11-03 07:31:14 UTC +dependencies: + - r-base >=4.2,<4.3.0a0 + - r-matrixstats >=0.60.1 + + +bioconductor-matrixgenerics 1.12.2 r43hdfd78af_0 +------------------------------------------------ +file name : bioconductor-matrixgenerics-1.12.2-r43hdfd78af_0.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.12.2 +build : r43hdfd78af_0 +build number: 0 +size : 460 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.12.2-r43hdfd78af_0.tar.bz2 +md5 : a556caf2836666913190f484e0d32145 +timestamp : 2023-07-07 14:05:15 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + - r-matrixstats >=1.0.0 + + +bioconductor-matrixgenerics 1.14.0 r43hdfd78af_0 +------------------------------------------------ +file name : bioconductor-matrixgenerics-1.14.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.14.0 +build : r43hdfd78af_0 +build number: 0 +size : 453 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.14.0-r43hdfd78af_0.tar.bz2 +md5 : 4761a546a1578a071af4ba27de789555 +timestamp : 2023-12-02 19:53:22 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + - r-matrixstats >=1.0.0 + + +bioconductor-matrixgenerics 1.14.0 r43hdfd78af_1 +------------------------------------------------ +file name : bioconductor-matrixgenerics-1.14.0-r43hdfd78af_1.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.14.0 +build : r43hdfd78af_1 +build number: 1 +size : 453 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.14.0-r43hdfd78af_1.tar.bz2 +md5 : 820657575f114f4f80071bfb0c4a95b7 +timestamp : 2023-12-03 20:58:00 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + - r-matrixstats >=1.0.0 + + +bioconductor-matrixgenerics 1.14.0 r43hdfd78af_2 +------------------------------------------------ +file name : bioconductor-matrixgenerics-1.14.0-r43hdfd78af_2.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.14.0 +build : r43hdfd78af_2 +build number: 2 +size : 453 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.14.0-r43hdfd78af_2.tar.bz2 +md5 : 339fce7064a2285c2ef1ce51679b687d +timestamp : 2024-05-03 07:00:59 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + - r-matrixstats >=1.0.0 + + +bioconductor-matrixgenerics 1.14.0 r43hdfd78af_3 +------------------------------------------------ +file name : bioconductor-matrixgenerics-1.14.0-r43hdfd78af_3.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.14.0 +build : r43hdfd78af_3 +build number: 3 +size : 453 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.14.0-r43hdfd78af_3.tar.bz2 +md5 : c79f36cc0cd464874aefd50a700d0079 +timestamp : 2024-05-03 12:11:07 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + - r-matrixstats >=1.0.0 + + +bioconductor-matrixgenerics 1.18.0 r44hdfd78af_0 +------------------------------------------------ +file name : bioconductor-matrixgenerics-1.18.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-matrixgenerics +version : 1.18.0 +build : r44hdfd78af_0 +build number: 0 +size : 493 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.18.0-r44hdfd78af_0.tar.bz2 +md5 : d1b86fcb6d7e4d3c9fe67817c739b5a7 +timestamp : 2024-12-14 17:51:25 UTC +dependencies: + - r-base >=4.4,<4.5.0a0 + - r-matrixstats >=1.4.1 + + +bioconductor-matrixgenerics 1.22.0 r45hdfd78af_0 +------------------------------------------------ +file name : bioconductor-matrixgenerics-1.22.0-r45hdfd78af_0.conda +name : bioconductor-matrixgenerics +version : 1.22.0 +build : r45hdfd78af_0 +build number: 0 +size : 440 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.22.0-r45hdfd78af_0.conda +md5 : 9c9561921370a18cd5bf4b97a915af4b +timestamp : 2026-01-06 17:16:55 UTC +dependencies: + - r-base >=4.5,<4.6.0a0 + - r-matrixstats >=1.4.1 + + +bioconductor-matrixgenerics 1.22.0 r45hdfd78af_1 +------------------------------------------------ +file name : bioconductor-matrixgenerics-1.22.0-r45hdfd78af_1.conda +name : bioconductor-matrixgenerics +version : 1.22.0 +build : r45hdfd78af_1 +build number: 1 +size : 439 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.22.0-r45hdfd78af_1.conda +md5 : cdf0406fc3caa814ff7b7876a42973a5 +timestamp : 2026-02-06 22:31:42 UTC +dependencies: + - r-base >=4.5,<4.6.0a0 + - r-matrixstats >=1.4.1 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-merfishdata.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-merfishdata.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..f7b94944ea1f7a10b4381913ea8bb31825cc437e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-merfishdata.manual_bundle.txt @@ -0,0 +1,160 @@ +# Tool: bioconductor-merfishdata +software_name: bioconductor-merfishdata +tier: T1 +domain: spatial_transcriptomics +downloads: 4053 +summary: Collection of public MERFISH datasets +description: MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis. +dependencies: bioconductor-annotationhub >=4.0.0,<4.1.0, bioconductor-bumpymatrix >=1.18.0,<1.19.0, bioconductor-data-packages >=20260207, bioconductor-ebimage >=4.52.0,<4.53.0, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-hdf5array >=1.38.0,<1.39.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, curl, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.16/data/experiment/html/MerfishData.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.16/data/experiment/html/MerfishData.html +Bioconductor - MerfishData About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Experiment Packages MerfishData MerfishData This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MerfishData . Collection of public MERFISH datasets DOI: 10.18129/B9.bioc.MerfishData Bioconductor version: 3.16 MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis. Author: Ludwig Geistlinger [aut, cre] , Tyrone Lee [ctb], Helena Crowell [ctb] , Jeffrey Mofitt [aut], Robert Gentleman [aut] Maintainer: Ludwig Geistlinger <ludwig_geistlinger at hms.harvard.edu> Citation (from within R, enter citation("MerfishData") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MerfishData") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("MerfishData") Mouse hypothalamus HTML R Script Mouse ileum HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentData , ExperimentHub , ExpressionData , HighThroughputImagingData , Mus_musculus_Data , SingleCellData , SpatialData Version 1.0.0 License Artistic-2.0 Depends R (>= 4.2.0), EBImage , SpatialExperiment Imports grDevices, AnnotationHub , BumpyMatrix , ExperimentHub , S4Vectors , SummarizedExperiment System Requirements URL https://github.com/ccb-hms/MerfishData Bug Reports https://github.com/ccb-hms/MerfishData/issues See More Suggests grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle , ExperimentHubData Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package MerfishData_1.0.0.tar.gz Windows Binary macOS Binary (x86_64) macOS Binary (arm64) Source Repository git clone https://git.bioconductor.org/packages/MerfishData Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MerfishData Package Short Url https://bioconductor.org/packages/MerfishData/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-merfishdata --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-merfishdata 1.0.0 r42hdfd78af_0 +-------------------------------------------- +file name : bioconductor-merfishdata-1.0.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-merfishdata +version : 1.0.0 +build : r42hdfd78af_0 +build number: 0 +size : 10 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-merfishdata-1.0.0-r42hdfd78af_0.tar.bz2 +md5 : 47b6c3e21bde878d95520b7edabab71b +timestamp : 2022-11-09 02:26:57 UTC +dependencies: + - bioconductor-annotationhub >=3.6.0,<3.7.0 + - bioconductor-bumpymatrix >=1.6.0,<1.7.0 + - bioconductor-data-packages >=20221108 + - bioconductor-ebimage >=4.40.0,<4.41.0 + - bioconductor-experimenthub >=2.6.0,<2.7.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - curl + - r-base >=4.2,<4.3.0a0 + + +bioconductor-merfishdata 1.2.0 r43hdfd78af_0 +-------------------------------------------- +file name : bioconductor-merfishdata-1.2.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-merfishdata +version : 1.2.0 +build : r43hdfd78af_0 +build number: 0 +size : 10 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-merfishdata-1.2.0-r43hdfd78af_0.tar.bz2 +md5 : 5e8c9c555435a2cd7ad3ab0f3d64d64f +timestamp : 2023-07-16 14:28:49 UTC +dependencies: + - bioconductor-annotationhub >=3.8.0,<3.9.0 + - bioconductor-bumpymatrix >=1.8.0,<1.9.0 + - bioconductor-data-packages >=20230706 + - bioconductor-ebimage >=4.42.0,<4.43.0 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-merfishdata 1.4.1 r43hdfd78af_0 +-------------------------------------------- +file name : bioconductor-merfishdata-1.4.1-r43hdfd78af_0.tar.bz2 +name : bioconductor-merfishdata +version : 1.4.1 +build : r43hdfd78af_0 +build number: 0 +size : 10 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-merfishdata-1.4.1-r43hdfd78af_0.tar.bz2 +md5 : 33391f6d7214415a92549e52f5009a7c +timestamp : 2023-12-08 14:10:13 UTC +dependencies: + - bioconductor-annotationhub >=3.10.0,<3.11.0 + - bioconductor-bumpymatrix >=1.10.0,<1.11.0 + - bioconductor-data-packages >=20231203 + - bioconductor-ebimage >=4.44.0,<4.45.0 + - bioconductor-experimenthub >=2.10.0,<2.11.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-merfishdata 1.8.0 r44hdfd78af_0 +-------------------------------------------- +file name : bioconductor-merfishdata-1.8.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-merfishdata +version : 1.8.0 +build : r44hdfd78af_0 +build number: 0 +size : 10 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-merfishdata-1.8.0-r44hdfd78af_0.tar.bz2 +md5 : 563deedc848beffd0feae58f95ca0a88 +timestamp : 2025-01-05 01:57:39 UTC +dependencies: + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-data-packages >=20250104 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - curl + - r-base >=4.4,<4.5.0a0 + + +bioconductor-merfishdata 1.12.0 r45hdfd78af_0 +--------------------------------------------- +file name : bioconductor-merfishdata-1.12.0-r45hdfd78af_0.conda +name : bioconductor-merfishdata +version : 1.12.0 +build : r45hdfd78af_0 +build number: 0 +size : 12 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-merfishdata-1.12.0-r45hdfd78af_0.conda +md5 : a3b24a43bf4769fd542cb9f3bf8c8447 +timestamp : 2026-03-01 22:07:50 UTC +dependencies: + - bioconductor-annotationhub >=4.0.0,<4.1.0 + - bioconductor-bumpymatrix >=1.18.0,<1.19.0 + - bioconductor-data-packages >=20260207 + - bioconductor-ebimage >=4.52.0,<4.53.0 + - bioconductor-experimenthub >=3.0.0,<3.1.0 + - bioconductor-hdf5array >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - curl + - r-base >=4.5,<4.6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-mousegastrulationdata.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-mousegastrulationdata.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa2b6a8b69b0b6127d07d89c25c9046b0b15df5f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-mousegastrulationdata.manual_bundle.txt @@ -0,0 +1,294 @@ +# Tool: bioconductor-mousegastrulationdata +software_name: bioconductor-mousegastrulationdata +tier: T1 +domain: spatial_transcriptomics +downloads: 18021 +summary: Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis +description: Provides processed and raw count data for single-cell RNA sequencing, single-cell ATAC-seq, and seqFISH (spatial transcriptomic) experiments performed along a timecourse of mouse gastrulation and early organogenesis. +dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-bumpymatrix >=1.18.0,<1.19.0, bioconductor-data-packages >=20260207, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, curl, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.10/data/experiment/html/MouseGastrulationData.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.10/data/experiment/html/MouseGastrulationData.html +Bioconductor - MouseGastrulationData About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.10 Experiment Packages MouseGastrulationData MouseGastrulationData This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MouseGastrulationData . Single-Cell Transcriptomics Data across Mouse Gastrulation and Early Organogenesis DOI: 10.18129/B9.bioc.MouseGastrulationData Bioconductor version: 3.10 Provides processed and raw count matrices for single-cell RNA sequencing data from a timecourse of mouse gastrulation and early organogenesis. Author: Jonathan Griffiths [aut, cre], Aaron Lun [aut] Maintainer: Jonathan Griffiths <jonathan.griffiths.94 at gmail.com> Citation (from within R, enter citation("MouseGastrulationData") ): Installation To install this package, start R (version "3.6") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MouseGastrulationData") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("MouseGastrulationData") Available datasets HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentData , ExperimentHub , ExpressionData , RNASeqData , SequencingData , SingleCellData Version 1.0.0 License GPL-3 Depends R (>= 3.6.0), SingleCellExperiment Imports methods, ExperimentHub , BiocGenerics , S4Vectors System Requirements URL https://github.com/MarioniLab/MouseGastrulationData Bug Reports https://github.com/MarioniLab/MouseGastrulationData/issues See More Suggests BiocStyle , knitr, rmarkdown Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package MouseGastrulationData_1.0.0.tar.gz Windows Binary Mac OS X 10.11 (El Capitan) Source Repository git clone https://git.bioconductor.org/packages/MouseGastrulationData Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MouseGastrulationData Package Short Url https://bioconductor.org/packages/MouseGastrulationData/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-mousegastrulationdata --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-mousegastrulationdata 1.0.0 r36_0 +---------------------------------------------- +file name : bioconductor-mousegastrulationdata-1.0.0-r36_0.tar.bz2 +name : bioconductor-mousegastrulationdata +version : 1.0.0 +build : r36_0 +build number: 0 +size : 18 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.0.0-r36_0.tar.bz2 +md5 : f28ab3665718590b46d1567a0271a69a +timestamp : 2019-11-07 02:48:13 UTC +dependencies: + - bioconductor-biocgenerics >=0.32.0,<0.33.0 + - bioconductor-experimenthub >=1.12.0,<1.13.0 + - bioconductor-s4vectors >=0.24.0,<0.25.0 + - bioconductor-singlecellexperiment >=1.8.0,<1.9.0 + - curl + - r-base >=3.6,<3.7.0a0 + + +bioconductor-mousegastrulationdata 1.2.0 r40_0 +---------------------------------------------- +file name : bioconductor-mousegastrulationdata-1.2.0-r40_0.tar.bz2 +name : bioconductor-mousegastrulationdata +version : 1.2.0 +build : r40_0 +build number: 0 +size : 18 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.2.0-r40_0.tar.bz2 +md5 : e3ed0972455ecbd35a81a209d32fff1f +timestamp : 2020-05-10 22:23:14 UTC +dependencies: + - bioconductor-biocgenerics >=0.34.0,<0.35.0 + - bioconductor-experimenthub >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.26.0,<0.27.0 + - bioconductor-singlecellexperiment >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.18.0,<1.19.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-mousegastrulationdata 1.4.0 r40_0 +---------------------------------------------- +file name : bioconductor-mousegastrulationdata-1.4.0-r40_0.tar.bz2 +name : bioconductor-mousegastrulationdata +version : 1.4.0 +build : r40_0 +build number: 0 +size : 19 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.4.0-r40_0.tar.bz2 +md5 : 17cff8fb93d3c5c99081a3bd419816ec +timestamp : 2020-11-02 12:41:16 UTC +dependencies: + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - bioconductor-experimenthub >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - bioconductor-singlecellexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.20.0,<1.21.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-mousegastrulationdata 1.4.0 r40hdfd78af_1 +------------------------------------------------------ +file name : bioconductor-mousegastrulationdata-1.4.0-r40hdfd78af_1.tar.bz2 +name : bioconductor-mousegastrulationdata +version : 1.4.0 +build : r40hdfd78af_1 +build number: 1 +size : 19 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.4.0-r40hdfd78af_1.tar.bz2 +md5 : e069cdc9e039eb58efcb0526fea2d772 +timestamp : 2021-03-31 12:51:39 UTC +dependencies: + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - bioconductor-experimenthub >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - bioconductor-singlecellexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.20.0,<1.21.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-mousegastrulationdata 1.6.0 r41hdfd78af_0 +------------------------------------------------------ +file name : bioconductor-mousegastrulationdata-1.6.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-mousegastrulationdata +version : 1.6.0 +build : r41hdfd78af_0 +build number: 0 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.6.0-r41hdfd78af_0.tar.bz2 +md5 : bb2195352c48645676ae08e9d239010c +timestamp : 2021-06-07 09:30:31 UTC +dependencies: + - bioconductor-biocgenerics >=0.38.0,<0.39.0 + - bioconductor-bumpymatrix >=1.0.0,<1.1.0 + - bioconductor-experimenthub >=2.0.0,<2.1.0 + - bioconductor-s4vectors >=0.30.0,<0.31.0 + - bioconductor-singlecellexperiment >=1.14.0,<1.15.0 + - bioconductor-spatialexperiment >=1.2.0,<1.3.0 + - bioconductor-summarizedexperiment >=1.22.0,<1.23.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-mousegastrulationdata 1.8.0 r41hdfd78af_0 +------------------------------------------------------ +file name : bioconductor-mousegastrulationdata-1.8.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-mousegastrulationdata +version : 1.8.0 +build : r41hdfd78af_0 +build number: 0 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.8.0-r41hdfd78af_0.tar.bz2 +md5 : 5dcf75d042e10d8372d330e00c15abea +timestamp : 2021-11-08 04:55:56 UTC +dependencies: + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-bumpymatrix >=1.2.0,<1.3.0 + - bioconductor-experimenthub >=2.2.0,<2.3.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.16.0,<1.17.0 + - bioconductor-spatialexperiment >=1.4.0,<1.5.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-mousegastrulationdata 1.8.0 r41hdfd78af_1 +------------------------------------------------------ +file name : bioconductor-mousegastrulationdata-1.8.0-r41hdfd78af_1.tar.bz2 +name : bioconductor-mousegastrulationdata +version : 1.8.0 +build : r41hdfd78af_1 +build number: 1 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.8.0-r41hdfd78af_1.tar.bz2 +md5 : 7c6f0d5b88ec0134dd25c24e48f2d6af +timestamp : 2022-08-30 03:56:41 UTC +dependencies: + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-bumpymatrix >=1.2.0,<1.3.0 + - bioconductor-experimenthub >=2.2.0,<2.3.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.16.0,<1.17.0 + - bioconductor-spatialexperiment >=1.4.0,<1.5.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-mousegastrulationdata 1.12.0 r42hdfd78af_0 +------------------------------------------------------- +file name : bioconductor-mousegastrulationdata-1.12.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-mousegastrulationdata +version : 1.12.0 +build : r42hdfd78af_0 +build number: 0 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.12.0-r42hdfd78af_0.tar.bz2 +md5 : 98617c9f9f039802012d3bc8630d5197 +timestamp : 2022-11-09 02:11:10 UTC +dependencies: + - bioconductor-biocgenerics >=0.44.0,<0.45.0 + - bioconductor-bumpymatrix >=1.6.0,<1.7.0 + - bioconductor-data-packages >=20221108 + - bioconductor-experimenthub >=2.6.0,<2.7.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - curl + - r-base >=4.2,<4.3.0a0 + + +bioconductor-mousegastrulationdata 1.14.0 r43hdfd78af_0 +------------------------------------------------------- +file name : bioconductor-mousegastrulationdata-1.14.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-mousegastrulationdata +version : 1.14.0 +build : r43hdfd78af_0 +build number: 0 +size : 21 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.14.0-r43hdfd78af_0.tar.bz2 +md5 : 27931785fb1036ccb5eddd19d0e8217a +timestamp : 2023-07-16 14:12:32 UTC +dependencies: + - bioconductor-biocgenerics >=0.46.0,<0.47.0 + - bioconductor-bumpymatrix >=1.8.0,<1.9.0 + - bioconductor-data-packages >=20230706 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-mousegastrulationdata 1.16.0 r43hdfd78af_0 +------------------------------------------------------- +file name : bioconductor-mousegastrulationdata-1.16.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-mousegastrulationdata +version : 1.16.0 +build : r43hdfd78af_0 +build number: 0 +size : 21 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.16.0-r43hdfd78af_0.tar.bz2 +md5 : 652738b1e9f0b9e7fab04c2a6337936b +timestamp : 2023-12-08 11:32:02 UTC +dependencies: + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-bumpymatrix >=1.10.0,<1.11.0 + - bioconductor-data-packages >=20231203 + - bioconductor-experimenthub >=2.10.0,<2.11.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-mousegastrulationdata 1.24.0 r45hdfd78af_0 +------------------------------------------------------- +file name : bioconductor-mousegastrulationdata-1.24.0-r45hdfd78af_0.conda +name : bioconductor-mousegastrulationdata +version : 1.24.0 +build : r45hdfd78af_0 +build number: 0 +size : 23 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.24.0-r45hdfd78af_0.conda +md5 : 1b201133e83f2436d523e28d82b8e54e +timestamp : 2026-03-01 23:38:41 UTC +dependencies: + - bioconductor-biocgenerics >=0.56.0,<0.57.0 + - bioconductor-bumpymatrix >=1.18.0,<1.19.0 + - bioconductor-data-packages >=20260207 + - bioconductor-experimenthub >=3.0.0,<3.1.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - curl + - r-base >=4.5,<4.6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-org.ce.eg.db.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-org.ce.eg.db.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..61bf444c4fe2a519bd4a4fc4544b8bed4e87b518 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-org.ce.eg.db.manual_bundle.txt @@ -0,0 +1,397 @@ +# Tool: bioconductor-org.ce.eg.db +software_name: bioconductor-org.ce.eg.db +tier: T1 +domain: t1_backfill_overall +downloads: 116707 +summary: Genome wide annotation for Worm +description: Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers. +dependencies: bioconductor-annotationdbi >=1.72.0,<1.73.0, bioconductor-data-packages >=20260207, curl, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/data/annotation/html/org.Ce.eg.db.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/data/annotation/html/org.Ce.eg.db.html +Bioconductor - org.Ce.eg.db Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Annotation Packages org.Ce.eg.db org.Ce.eg.db This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see org.Ce.eg.db . Genome wide annotation for Worm DOI: 10.18129/B9.bioc.org.Ce.eg.db Bioconductor version: 3.22 Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers. Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation("org.Ce.eg.db") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("org.Ce.eg.db") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews AnnotationData , Caenorhabditis_elegans , OrgDb Version 3.22.0 License Artistic-2.0 Depends R (>= 2.7.0), methods, AnnotationDbi (>= 1.71.1) Imports System Requirements URL See More Suggests DBI , annotate , RUnit Linking To Enhances Depends On Me celegans.db Imports Me CoSIA Suggests Me ChIPpeakAnno , geneXtendeR , goatea , goSorensen , multiGSEA , NetSAM , rrvgo , scQTLtools , goat Links To Me Package Archives Follow Installation instructions to use this package in your R session. Source Package org.Ce.eg.db_3.22.0.tar.gz Windows Binary (x86_64) macOS Binary (x86_64) macOS Binary (arm64) Package Short Url https://bioconductor.org/packages/org.Ce.eg.db/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-org.ce.eg.db --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-org.ce.eg.db 3.2.3 0 +--------------------------------- +file name : bioconductor-org.ce.eg.db-3.2.3-0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.2.3 +build : 0 +build number: 0 +size : 13.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-0.tar.bz2 +md5 : 74af90e36e8d9f6acf0207c04ea40485 +dependencies: + - bioconductor-annotationdbi >=1.31.19 + - r >=2.7.0 + + +bioconductor-org.ce.eg.db 3.2.3 r3.3.1_0 +---------------------------------------- +file name : bioconductor-org.ce.eg.db-3.2.3-r3.3.1_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.2.3 +build : r3.3.1_0 +build number: 0 +size : 13.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r3.3.1_0.tar.bz2 +md5 : ec2f9f9497684d0e75e1de340b1be402 +dependencies: + - bioconductor-annotationdbi >=1.31.19 + - r 3.3.1* + + +bioconductor-org.ce.eg.db 3.2.3 r3.3.2_0 +---------------------------------------- +file name : bioconductor-org.ce.eg.db-3.2.3-r3.3.2_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.2.3 +build : r3.3.2_0 +build number: 0 +size : 13.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r3.3.2_0.tar.bz2 +md5 : 25098bb2b119cb08c893282fd277c40a +dependencies: + - bioconductor-annotationdbi >=1.31.19 + - r-base 3.3.2* + + +bioconductor-org.ce.eg.db 3.2.3 r3.4.1_0 +---------------------------------------- +file name : bioconductor-org.ce.eg.db-3.2.3-r3.4.1_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.2.3 +build : r3.4.1_0 +build number: 0 +size : 13.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r3.4.1_0.tar.bz2 +md5 : 5f04213cdf80a155e6199b6e0fd3c78a +dependencies: + - bioconductor-annotationdbi >=1.31.19 + - r-base 3.4.1* + + +bioconductor-org.ce.eg.db 3.2.3 r3.4.1_1 +---------------------------------------- +file name : bioconductor-org.ce.eg.db-3.2.3-r3.4.1_1.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.2.3 +build : r3.4.1_1 +build number: 1 +size : 5 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r3.4.1_1.tar.bz2 +md5 : 2b496e033950467b43eef5c50e5dd8c1 +dependencies: + - bioconductor-annotationdbi >=1.31.19 + - r-base 3.4.1* + - wget + + +bioconductor-org.ce.eg.db 3.2.3 r341_2 +-------------------------------------- +file name : bioconductor-org.ce.eg.db-3.2.3-r341_2.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.2.3 +build : r341_2 +build number: 2 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r341_2.tar.bz2 +md5 : 289c92ad717298f79495846d97e44e6b +timestamp : 2018-10-18 21:21:33 UTC +dependencies: + - bioconductor-annotationdbi >=1.31.19 + - r-base >=3.4.1,<3.4.2.0a0 + - wget + + +bioconductor-org.ce.eg.db 3.2.3 r351_2 +-------------------------------------- +file name : bioconductor-org.ce.eg.db-3.2.3-r351_2.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.2.3 +build : r351_2 +build number: 2 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r351_2.tar.bz2 +md5 : bfc833763f6cb41b554863a8a64749d1 +timestamp : 2018-10-18 21:19:57 UTC +dependencies: + - bioconductor-annotationdbi >=1.31.19 + - r-base >=3.5.1,<3.5.2.0a0 + - wget + + +bioconductor-org.ce.eg.db 3.4.1 r3.4.1_0 +---------------------------------------- +file name : bioconductor-org.ce.eg.db-3.4.1-r3.4.1_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.4.1 +build : r3.4.1_0 +build number: 0 +size : 5 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.4.1-r3.4.1_0.tar.bz2 +md5 : 12eef1df469dec1dcbfa1a0a3bd5ac1d +dependencies: + - bioconductor-annotationdbi >=1.37.4 + - r-base 3.4.1* + - wget + + +bioconductor-org.ce.eg.db 3.4.1 r341_1 +-------------------------------------- +file name : bioconductor-org.ce.eg.db-3.4.1-r341_1.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.4.1 +build : r341_1 +build number: 1 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.4.1-r341_1.tar.bz2 +md5 : 1cb6e4d2f1c8243f4321779795490505 +timestamp : 2018-10-18 21:46:53 UTC +dependencies: + - bioconductor-annotationdbi >=1.37.4 + - r-base >=3.4.1,<3.4.2.0a0 + - wget + + +bioconductor-org.ce.eg.db 3.4.1 r351_1 +-------------------------------------- +file name : bioconductor-org.ce.eg.db-3.4.1-r351_1.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.4.1 +build : r351_1 +build number: 1 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.4.1-r351_1.tar.bz2 +md5 : 09e54fc462f15121a709e64ac9d76666 +timestamp : 2018-10-18 21:45:10 UTC +dependencies: + - bioconductor-annotationdbi >=1.37.4 + - r-base >=3.5.1,<3.5.2.0a0 + - wget + + +bioconductor-org.ce.eg.db 3.5.0 r3.4.1_0 +---------------------------------------- +file name : bioconductor-org.ce.eg.db-3.5.0-r3.4.1_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.5.0 +build : r3.4.1_0 +build number: 0 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.5.0-r3.4.1_0.tar.bz2 +md5 : 8ea7e90fc2d62f52bb7ec02a86cac5d6 +dependencies: + - bioconductor-annotationdbi >=1.39.3 + - r-base 3.4.1* + - wget + + +bioconductor-org.ce.eg.db 3.6.0 r341_0 +-------------------------------------- +file name : bioconductor-org.ce.eg.db-3.6.0-r341_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.6.0 +build : r341_0 +build number: 0 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.6.0-r341_0.tar.bz2 +md5 : bcceb95ede91f8605e5c4117ea825789 +timestamp : 2018-10-18 21:32:05 UTC +dependencies: + - bioconductor-annotationdbi >=1.42.1,<1.44.0 + - r-base >=3.4.1,<3.4.2.0a0 + - wget + + +bioconductor-org.ce.eg.db 3.6.0 r351_0 +-------------------------------------- +file name : bioconductor-org.ce.eg.db-3.6.0-r351_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.6.0 +build : r351_0 +build number: 0 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.6.0-r351_0.tar.bz2 +md5 : fd6560c9aaf4ff6a4d2778ee723ff752 +timestamp : 2018-10-18 21:33:44 UTC +dependencies: + - bioconductor-annotationdbi >=1.42.1,<1.44.0 + - r-base >=3.5.1,<3.5.2.0a0 + - wget + + +bioconductor-org.ce.eg.db 3.7.0 r351_0 +-------------------------------------- +file name : bioconductor-org.ce.eg.db-3.7.0-r351_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.7.0 +build : r351_0 +build number: 0 +size : 6 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.ce.eg.db-3.7.0-r351_0.tar.bz2 +md5 : 51362f3c2da134b6a6bf7ec36aadca95 +timestamp : 2018-12-26 20:07:44 UTC +dependencies: + - bioconductor-annotationdbi >=1.44.0,<1.45.0 + - r-base >=3.5.1,<3.5.2.0a0 + - wget + + +bioconductor-org.ce.eg.db 3.8.2 r36_1 +------------------------------------- +file name : bioconductor-org.ce.eg.db-3.8.2-r36_1.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.8.2 +build : r36_1 +build number: 1 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.ce.eg.db-3.8.2-r36_1.tar.bz2 +md5 : a979ceae50bac4b1a920ffe35a09b6e7 +timestamp : 2019-08-06 09:12:51 UTC +dependencies: + - bioconductor-annotationdbi >=1.46.0,<1.47.0 + - curl + - r-base >=3.6,<3.7.0a0 + + +bioconductor-org.ce.eg.db 3.10.0 r36_0 +-------------------------------------- +file name : bioconductor-org.ce.eg.db-3.10.0-r36_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.10.0 +build : r36_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.ce.eg.db-3.10.0-r36_0.tar.bz2 +md5 : 7cff302b5df5f3b1968ed4197f4723ea +timestamp : 2019-11-02 22:12:21 UTC +dependencies: + - bioconductor-annotationdbi >=1.48.0,<1.49.0 + - curl + - r-base >=3.6,<3.7.0a0 + + +bioconductor-org.ce.eg.db 3.11.1 r40_0 +-------------------------------------- +file name : bioconductor-org.ce.eg.db-3.11.1-r40_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.11.1 +build : r40_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.ce.eg.db-3.11.1-r40_0.tar.bz2 +md5 : 26ea75ba02bae36c5ed5eb2e6585fe03 +timestamp : 2020-05-10 13:24:22 UTC +dependencies: + - bioconductor-annotationdbi >=1.50.0,<1.51.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-org.ce.eg.db 3.12.0 r40_0 +-------------------------------------- +file name : bioconductor-org.ce.eg.db-3.12.0-r40_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.12.0 +build : r40_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.ce.eg.db-3.12.0-r40_0.tar.bz2 +md5 : 3325ccda939368bb21bfb372bdde7d44 +timestamp : 2020-10-30 09:01:03 UTC +dependencies: + - bioconductor-annotationdbi >=1.52.0,<1.53.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-org.ce.eg.db 3.12.0 r40hdfd78af_1 +---------------------------------------------- +file name : bioconductor-org.ce.eg.db-3.12.0-r40hdfd78af_1.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.12.0 +build : r40hdfd78af_1 +build number: 1 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.ce.eg.db-3.12.0-r40hdfd78af_1.tar.bz2 +md5 : 08363c82c33e616fe18ac2aa1a16ca8a +timestamp : 2021-03-29 22:05:28 UTC +dependencies: + - bioconductor-annotationdbi >=1.52.0,<1.53.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-org.ce.eg.db 3.13.0 r41hdfd78af_0 +---------------------------------------------- +file name : bioconductor-org.ce.eg.db-3.13.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-org.ce.eg.db +version : 3.13.0 +build : r41hdfd78af_0 +build number: 0 +size : 8 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-org.hs.eg.db.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-org.hs.eg.db.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0ea4ae9fba1f05459bca7b224e91038b4129f27 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-org.hs.eg.db.manual_bundle.txt @@ -0,0 +1,406 @@ +# Tool: bioconductor-org.hs.eg.db +software_name: bioconductor-org.hs.eg.db +tier: T1 +domain: t1_backfill_overall +downloads: 163395 +summary: Genome wide annotation for Human +description: Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers. +dependencies: bioconductor-annotationdbi >=1.72.0,<1.73.0, bioconductor-data-packages >=20260207, curl, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/data/annotation/html/org.Hs.eg.db.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/data/annotation/html/org.Hs.eg.db.html +Bioconductor - org.Hs.eg.db Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Annotation Packages org.Hs.eg.db org.Hs.eg.db This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see org.Hs.eg.db . Genome wide annotation for Human DOI: 10.18129/B9.bioc.org.Hs.eg.db Bioconductor version: 3.22 Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers. Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation("org.Hs.eg.db") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("org.Hs.eg.db") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews AnnotationData , Homo_sapiens , OrgDb , humanLLMappings Version 3.22.0 License Artistic-2.0 Depends R (>= 2.7.0), methods, AnnotationDbi (>= 1.71.1) Imports System Requirements URL See More Suggests DBI , annotate , RUnit Linking To Enhances Depends On Me CoCiteStats , GSReg , KEGGlincs , signatureSearch , tRanslatome , clariomdhumanprobeset.db , clariomdhumantranscriptcluster.db , clariomshumanhttranscriptcluster.db , clariomshumantranscriptcluster.db , FDb.InfiniumMethylation.hg18 , FDb.InfiniumMethylation.hg19 , GGHumanMethCancerPanelv1.db , h10kcod.db , h20kcod.db , hcg110.db , hgfocus.db , hgu133a.db , hgu133a2.db , hgu133b.db , hgu133plus2.db , hgu219.db , hgu95a.db , hgu95av2.db , hgu95b.db , hgu95c.db , hgu95d.db , hgu95e.db , hguatlas13k.db , hgubeta7.db , hguDKFZ31.db , hgug4100a.db , hgug4101a.db , hgug4110b.db , hgug4111a.db , hgug4112a.db , hgug4845a.db , hguqiagenv3.db , hi16cod.db , Homo.sapiens , hs25kresogen.db , Hs6UG171.db , HsAgilentDesign026652.db , hta20probeset.db , hta20transcriptcluster.db , hthgu133a.db , hthgu133b.db , hthgu133plusa.db , hthgu133plusb.db , hthgu133pluspm.db , hu35ksuba.db , hu35ksubb.db , hu35ksubc.db , hu35ksubd.db , hu6800.db , huex10stprobeset.db , huex10sttranscriptcluster.db , hugene10stprobeset.db , hugene10sttranscriptcluster.db , hugene11stprobeset.db , hugene11sttranscriptcluster.db , hugene20stprobeset.db , hugene20sttranscriptcluster.db , hugene21stprobeset.db , hugene21sttranscriptcluster.db , HuO22.db , hwgcod.db , IlluminaHumanMethylation27k.db , illuminaHumanv1.db , illuminaHumanv2.db , illuminaHumanv2BeadID.db , illuminaHumanv3.db , illuminaHumanv4.db , illuminaHumanWGDASLv3.db , illuminaHumanWGDASLv4.db , JazaeriMetaData.db , LAPOINTE.db , lumiHumanAll.db , Norway981.db , nugohs1a520180.db , OperonHumanV3.db , PartheenMetaData.db , pedbarrayv10.db , pedbarrayv9.db , POCRCannotation.db , Roberts2005Annotation.db , SHDZ.db , u133x3p.db , annotation , rnaseqGene , variants , OSCA.workflows Imports Me APL , artMS , attract , bioCancer , BioNAR , CaMutQC , CBNplot , cellity , chimeraviz , chipenrich , consensusDE , consICA , CoSIA , debrowser , DegCre , EasyCellType , EGSEA , famat , funOmics , GDCRNATools , geneAttribution , GmicR , GOpro , goSorensen , mastR , MCbiclust , MetaboSignal , methylGSA , mirIntegrator , miRLAB , miRSM , miRspongeR , missMethyl , mitology , Moonlight2R , MOSClip , mslp , OutSplice , PanomiR , pathview , REMP , rGREAT , rgsepd , RNAAgeCalc , rTRMui , scafari , scPipe , signifinder , SMITE , sSNAPPY , SubCellBarCode , SVMDO , TFEA.ChIP , TFutils , uncoverappLib , GenomicState , SomaScan.db , msigdb , recountWorkflow Suggests Me AllelicImbalance , annotate , AnnotationDbi , AnnotationFilter , AnnotationForge , annotatr , appreci8R , ASURAT , autonomics , BioCor , BiocSet , BioQC , borealis , bumphunter , categoryCompare , CeTF , ChIPpeakAnno , ChIPseeker , clusterProfiler , cnvGSA , CNVRanger , CRISPRseek , DeeDeeExperiment , derfinderPlot , dmGsea , dmrseq , DOSE , edgeR , EnhancedVolcano , enhancerHomologSearch , enrichplot , EpiCompare , EpiMix , esATAC , FELLA , fishpond , FRASER , GA4GHclient , GA4GHshiny , gage , gCrisprTools , GeDi , GeneNetworkBuilder , GeneTonic , geneXtendeR , GenomicFeatures , GenomicInteractionNodes , geomeTriD , GeoTcgaData , gg4way , globaltest , gmapR , goatea , goProfiles , GOSemSim , goseq , GOstats , GRaNIE , graphite , groHMM , GSAR , GSEABase , GSVA , GUIDEseq , gwascat , hpar , ideal , iNETgrate , InteractiveComplexHeatmap , iSEEde , iSEEpathways , iSEEu , karyoploteR , KEGGgraph , limma , linkSet , MesKit , MIRit , miRNAtap , MLP , mogsa , mosdef , multiGSEA , NanoMethViz , NetActivity , NetSAM , netZooR , ontoProc , oppar , Organism.dplyr , OUTRIDER , pageRank , pathlinkR , pcaExplorer , PCAtools , phantasus , Pigengene , plotgardener , ProteoDisco , PureCN , quantiseqr , R3CPET , ramr , ReactomePA , recount , RFLOMICS , rigvf , RnBeads , rrvgo , RTopper , rtracklayer , rTRM , scde , scFeatures , scGPS , scGraphVerse , scmeth , scQTLtools , simona , SingleCellAlleleExperiment , spatialHeatmap , SPICEY , svaRetro , TCGAutils , tenXplore , tidybulk , trackViewer , tricycle , Ularcirc , UMI4Cats , VariantFiltering , VariantTools , vissE , wiggleplotr , BloodCancerMultiOmics2017 , chipenrich.data , prostateCancerTaylor , RforProteomics , ExpHunterSuite , BaseSet , conos , convertid , coreheat , DIscBIO , driveR , easyEWAS , easylabel , goat , ivolcano , kernscr , lisat , metaMA , netgsa , pagoda2 , PANACEA , pathfindR , PathwayVote , pQTLdata , protr , RCPA , rliger , scPairs , SCpubr , SEMgraph , SurprisalAnalysis , WayFindR , XYomics Links To Me Package Archives Follow Installation instructions to use this package in your R session. Source Package org.Hs.eg.db_3.22.0.tar.gz Windows Binary (x86_64) macOS Binary (x86_64) macOS Binary (arm64) Package Short Url https://bioconductor.org/packages/org.Hs.eg.db/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-org.hs.eg.db --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-org.hs.eg.db 3.2.3 0 +--------------------------------- +file name : bioconductor-org.hs.eg.db-3.2.3-0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.2.3 +build : 0 +build number: 0 +size : 50.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.2.3-0.tar.bz2 +md5 : 73e3afdf30b4df153c9e91342a537103 +dependencies: + - bioconductor-annotationdbi >=1.31.19 + - r >=2.7.0 + + +bioconductor-org.hs.eg.db 3.3.0 r3.3.1_0 +---------------------------------------- +file name : bioconductor-org.hs.eg.db-3.3.0-r3.3.1_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.3.0 +build : r3.3.1_0 +build number: 0 +size : 50.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.3.0-r3.3.1_0.tar.bz2 +md5 : f766bc20baa9c61214693008a4c06fac +dependencies: + - bioconductor-annotationdbi >=1.31.19 + - r 3.3.1* + + +bioconductor-org.hs.eg.db 3.3.0 r3.3.1_1 +---------------------------------------- +file name : bioconductor-org.hs.eg.db-3.3.0-r3.3.1_1.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.3.0 +build : r3.3.1_1 +build number: 1 +size : 50.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.3.0-r3.3.1_1.tar.bz2 +md5 : 22bc943b7029d0d044e992e1435f420c +dependencies: + - bioconductor-annotationdbi >=1.33.10 + - r 3.3.1* + + +bioconductor-org.hs.eg.db 3.3.0 r3.3.2_2 +---------------------------------------- +file name : bioconductor-org.hs.eg.db-3.3.0-r3.3.2_2.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.3.0 +build : r3.3.2_2 +build number: 2 +size : 50.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.3.0-r3.3.2_2.tar.bz2 +md5 : cbb52611cc4b92cf5592c2dc902e19a0 +dependencies: + - bioconductor-annotationdbi >=1.33.10 + - r-base 3.3.2* + + +bioconductor-org.hs.eg.db 3.3.0 r3.4.1_2 +---------------------------------------- +file name : bioconductor-org.hs.eg.db-3.3.0-r3.4.1_2.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.3.0 +build : r3.4.1_2 +build number: 2 +size : 50.3 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.3.0-r3.4.1_2.tar.bz2 +md5 : c175e5c56b0e8cbd3541bc2740677b2a +dependencies: + - bioconductor-annotationdbi >=1.33.10 + - r-base 3.4.1* + + +bioconductor-org.hs.eg.db 3.4.1 r3.4.1_0 +---------------------------------------- +file name : bioconductor-org.hs.eg.db-3.4.1-r3.4.1_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.4.1 +build : r3.4.1_0 +build number: 0 +size : 4 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.4.1-r3.4.1_0.tar.bz2 +md5 : f079cd29b4c9494c5b38e7ecf25a60d2 +dependencies: + - bioconductor-annotationdbi >=1.37.4 + - r-base 3.4.1* + - wget + + +bioconductor-org.hs.eg.db 3.4.2 r3.4.1_0 +---------------------------------------- +file name : bioconductor-org.hs.eg.db-3.4.2-r3.4.1_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.4.2 +build : r3.4.1_0 +build number: 0 +size : 5 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.4.2-r3.4.1_0.tar.bz2 +md5 : a43739ad497c4e6e4c01540f63430369 +dependencies: + - bioconductor-annotationdbi >=1.39.3 + - r-base 3.4.1* + - wget + + +bioconductor-org.hs.eg.db 3.5.0 r3.4.1_0 +---------------------------------------- +file name : bioconductor-org.hs.eg.db-3.5.0-r3.4.1_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.5.0 +build : r3.4.1_0 +build number: 0 +size : 5 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.5.0-r3.4.1_0.tar.bz2 +md5 : a9563ca8f44def37263b8538241d55d4 +dependencies: + - bioconductor-annotationdbi >=1.39.3 + - r-base 3.4.1* + - wget + + +bioconductor-org.hs.eg.db 3.5.0 r3.4.1_1 +---------------------------------------- +file name : bioconductor-org.hs.eg.db-3.5.0-r3.4.1_1.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.5.0 +build : r3.4.1_1 +build number: 1 +size : 5 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.5.0-r3.4.1_1.tar.bz2 +md5 : 025e6b6e5556d1b17284b3c6ec34e5c2 +dependencies: + - bioconductor-annotationdbi >=1.39.3 + - r-base 3.4.1* + - wget + + +bioconductor-org.hs.eg.db 3.6.0 r341_0 +-------------------------------------- +file name : bioconductor-org.hs.eg.db-3.6.0-r341_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.6.0 +build : r341_0 +build number: 0 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.6.0-r341_0.tar.bz2 +md5 : 0cbc0a9bd2f6a7b99c51c2607c2d55ce +timestamp : 2018-10-19 01:17:38 UTC +dependencies: + - bioconductor-annotationdbi >=1.42.1,<1.44.0 + - r-base >=3.4.1,<3.4.2.0a0 + - wget + + +bioconductor-org.hs.eg.db 3.6.0 r351_0 +-------------------------------------- +file name : bioconductor-org.hs.eg.db-3.6.0-r351_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.6.0 +build : r351_0 +build number: 0 +size : 6 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.hs.eg.db-3.6.0-r351_0.tar.bz2 +md5 : 9168058537fe86a9c472d2c3ce06c2e6 +timestamp : 2018-10-19 01:15:31 UTC +dependencies: + - bioconductor-annotationdbi >=1.42.1,<1.44.0 + - r-base >=3.5.1,<3.5.2.0a0 + - wget + + +bioconductor-org.hs.eg.db 3.7.0 r351_0 +-------------------------------------- +file name : bioconductor-org.hs.eg.db-3.7.0-r351_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.7.0 +build : r351_0 +build number: 0 +size : 6 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.hs.eg.db-3.7.0-r351_0.tar.bz2 +md5 : a1233746023aa37c28028d21536fa44e +timestamp : 2018-12-26 23:25:21 UTC +dependencies: + - bioconductor-annotationdbi >=1.44.0,<1.45.0 + - r-base >=3.5.1,<3.5.2.0a0 + - wget + + +bioconductor-org.hs.eg.db 3.8.2 r36_1 +------------------------------------- +file name : bioconductor-org.hs.eg.db-3.8.2-r36_1.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.8.2 +build : r36_1 +build number: 1 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.hs.eg.db-3.8.2-r36_1.tar.bz2 +md5 : 909450029b8301a2e2ef5c5ee3ec39d2 +timestamp : 2019-07-28 01:06:17 UTC +dependencies: + - bioconductor-annotationdbi >=1.46.0,<1.47.0 + - curl + - r-base >=3.6,<3.7.0a0 + + +bioconductor-org.hs.eg.db 3.10.0 r36_0 +-------------------------------------- +file name : bioconductor-org.hs.eg.db-3.10.0-r36_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.10.0 +build : r36_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.hs.eg.db-3.10.0-r36_0.tar.bz2 +md5 : 40a30279824d0dadf2234796cfb4ab5d +timestamp : 2019-11-02 23:16:51 UTC +dependencies: + - bioconductor-annotationdbi >=1.48.0,<1.49.0 + - curl + - r-base >=3.6,<3.7.0a0 + + +bioconductor-org.hs.eg.db 3.11.1 r40_0 +-------------------------------------- +file name : bioconductor-org.hs.eg.db-3.11.1-r40_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.11.1 +build : r40_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.hs.eg.db-3.11.1-r40_0.tar.bz2 +md5 : 20a8584bb9180b92480682a603a007c1 +timestamp : 2020-05-10 11:42:53 UTC +dependencies: + - bioconductor-annotationdbi >=1.50.0,<1.51.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-org.hs.eg.db 3.11.4 r40_1 +-------------------------------------- +file name : bioconductor-org.hs.eg.db-3.11.4-r40_1.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.11.4 +build : r40_1 +build number: 1 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.hs.eg.db-3.11.4-r40_1.tar.bz2 +md5 : 61d7a6b9f94aabb15d2b33668c544130 +timestamp : 2020-07-29 21:15:19 UTC +dependencies: + - bioconductor-annotationdbi >=1.50.0,<1.51.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-org.hs.eg.db 3.11.4 r40h37ae868_0 +---------------------------------------------- +file name : bioconductor-org.hs.eg.db-3.11.4-r40h37ae868_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.11.4 +build : r40h37ae868_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.hs.eg.db-3.11.4-r40h37ae868_0.tar.bz2 +md5 : f2ee562fe19d95b0e3cd63bdd60d30c0 +timestamp : 2020-06-29 19:00:32 UTC +dependencies: + - bioconductor-annotationdbi >=1.50.0,<1.51.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-org.hs.eg.db 3.12.0 r40_0 +-------------------------------------- +file name : bioconductor-org.hs.eg.db-3.12.0-r40_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.12.0 +build : r40_0 +build number: 0 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.hs.eg.db-3.12.0-r40_0.tar.bz2 +md5 : 2b72ea8d0e048971c091ed7cbecdeb9c +timestamp : 2020-10-30 09:50:16 UTC +dependencies: + - bioconductor-annotationdbi >=1.52.0,<1.53.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-org.hs.eg.db 3.12.0 r40hdfd78af_1 +---------------------------------------------- +file name : bioconductor-org.hs.eg.db-3.12.0-r40hdfd78af_1.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.12.0 +build : r40hdfd78af_1 +build number: 1 +size : 7 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.hs.eg.db-3.12.0-r40hdfd78af_1.tar.bz2 +md5 : 46c6f9a67a0d01a92c17354b21b786a8 +timestamp : 2021-03-30 14:35:28 UTC +dependencies: + - bioconductor-annotationdbi >=1.52.0,<1.53.0 + - curl + - r-base >=4.0,<4.1.0a0 + + +bioconductor-org.hs.eg.db 3.13.0 r41hdfd78af_0 +---------------------------------------------- +file name : bioconductor-org.hs.eg.db-3.13.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-org.hs.eg.db +version : 3.13.0 +build : r41hdfd78af_0 +build number: 0 +size : 8 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.hs.eg.db-3.13.0-r41hdfd78af_0.tar.bz2 +md5 : 64daae637b29c51b2c8bbbf32d00f4d4 +timestamp : 2021-06-02 21:33:50 UTC +dependencies: + - bioconductor-annotationdbi >=1.54.0,<1.55.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-org.hs.eg.db 3.14.0 r41hdfd78af_0 +---------------------------------------------- +file name : bioconductor-org.hs.eg.db-3.14.0-r41hdfd78af_0.tar.bz2 +name diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rbgl.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rbgl.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1098458db57e6f07db82d539e7aacf93841cea0a --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rbgl.manual_bundle.txt @@ -0,0 +1,421 @@ +# Tool: bioconductor-rbgl +software_name: bioconductor-rbgl +tier: T1 +domain: t1_backfill_overall +downloads: 123508 +summary: An interface to the BOOST graph library +description: A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. +dependencies: bioconductor-graph >=1.88.0,<1.89.0, bioconductor-graph >=1.88.1,<1.89.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-bh +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/RBGL.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/RBGL.html +Bioconductor - RBGL Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages RBGL RBGL This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see RBGL . An interface to the BOOST graph library DOI: 10.18129/B9.bioc.RBGL Bioconductor version: 3.22 A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. Author: Vince Carey [aut], Li Long [aut], R. Gentleman [aut], Emmanuel Taiwo [ctb] (Converted RBGL vignette from Sweave to RMarkdown / HTML.), Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation("RBGL") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("RBGL") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("RBGL") RBGL Overview HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews GraphAndNetwork , Network , Software Version 1.86.0 In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 21 years) License Artistic-2.0 Depends graph , methods Imports methods System Requirements URL http://www.bioconductor.org See More Suggests Rgraphviz , XML , RUnit , BiocGenerics , BiocStyle , knitr Linking To BH Enhances Depends On Me apComplex , BioNet , CellNOptR , fgga , PerfMeas Imports Me BiocPkgTools , biocViews , CAMERA , Category , ChIPpeakAnno , CHRONOS , CytoML , DEGraph , DEsubs , EventPointer , flowWorkspace , GenomicInteractionNodes , GOstats , NCIgraph , ontoProc , openCyto , OrganismDbi , Streamer , VariantFiltering , BiDAG , clustNet , eff2 , micd , pcalg , rags2ridges , RANKS , SEMgraph , SID Suggests Me DEGraph , G4SNVHunter , GeneNetworkBuilder , graph , gwascat , KEGGgraph , rBiopaxParser , VariantTools , yeastExpData , archeofrag , maGUI Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package RBGL_1.86.0.tar.gz Windows Binary (x86_64) RBGL_1.86.0.zip macOS Binary (x86_64) RBGL_1.86.0.tgz macOS Binary (arm64) RBGL_1.86.0.tgz Source Repository git clone https://git.bioconductor.org/packages/RBGL Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RBGL Bioc Package Browser https://code.bioconductor.org/browse/RBGL/ Package Short Url https://bioconductor.org/packages/RBGL/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-rbgl --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-rbgl 1.46.0 r3.2.2_0 +--------------------------------- +file name : bioconductor-rbgl-1.46.0-r3.2.2_0.tar.bz2 +name : bioconductor-rbgl +version : 1.46.0 +build : r3.2.2_0 +build number: 0 +size : 1.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.46.0-r3.2.2_0.tar.bz2 +md5 : bd95d054b992b7271898a7345553e01b +dependencies: + - bioconductor-graph + - r 3.2.2* + + +bioconductor-rbgl 1.46.0 r3.2.2_1 +--------------------------------- +file name : bioconductor-rbgl-1.46.0-r3.2.2_1.tar.bz2 +name : bioconductor-rbgl +version : 1.46.0 +build : r3.2.2_1 +build number: 1 +size : 1.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.46.0-r3.2.2_1.tar.bz2 +md5 : 9d93edcb3f2629ad9d7b37e51e21dabc +dependencies: + - bioconductor-graph + - r 3.2.2* + + +bioconductor-rbgl 1.46.0 r3.3.1_1 +--------------------------------- +file name : bioconductor-rbgl-1.46.0-r3.3.1_1.tar.bz2 +name : bioconductor-rbgl +version : 1.46.0 +build : r3.3.1_1 +build number: 1 +size : 1.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.46.0-r3.3.1_1.tar.bz2 +md5 : 84e6d3d980c08be799280a2997290888 +dependencies: + - bioconductor-graph + - r 3.3.1* + + +bioconductor-rbgl 1.48.1 r3.3.1_1 +--------------------------------- +file name : bioconductor-rbgl-1.48.1-r3.3.1_1.tar.bz2 +name : bioconductor-rbgl +version : 1.48.1 +build : r3.3.1_1 +build number: 1 +size : 1.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.48.1-r3.3.1_1.tar.bz2 +md5 : 3576e173b5433d3f290e13186ef0a60d +dependencies: + - bioconductor-graph + - r 3.3.1* + + +bioconductor-rbgl 1.48.1 r3.3.2_1 +--------------------------------- +file name : bioconductor-rbgl-1.48.1-r3.3.2_1.tar.bz2 +name : bioconductor-rbgl +version : 1.48.1 +build : r3.3.2_1 +build number: 1 +size : 1.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.48.1-r3.3.2_1.tar.bz2 +md5 : db0b971d45accd178b1caab311377d25 +dependencies: + - bioconductor-graph + - r-base 3.3.2* + + +bioconductor-rbgl 1.48.1 r3.4.1_1 +--------------------------------- +file name : bioconductor-rbgl-1.48.1-r3.4.1_1.tar.bz2 +name : bioconductor-rbgl +version : 1.48.1 +build : r3.4.1_1 +build number: 1 +size : 1.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.48.1-r3.4.1_1.tar.bz2 +md5 : 1fc8d27965f10f1628a74256a799418e +dependencies: + - bioconductor-graph + - r-base 3.4.1* + + +bioconductor-rbgl 1.52.0 r3.4.1_0 +--------------------------------- +file name : bioconductor-rbgl-1.52.0-r3.4.1_0.tar.bz2 +name : bioconductor-rbgl +version : 1.52.0 +build : r3.4.1_0 +build number: 0 +size : 3.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.52.0-r3.4.1_0.tar.bz2 +md5 : 09d9730486717d719ccf19bd1a7bb11e +dependencies: + - bioconductor-graph + - r-base 3.4.1* + + +bioconductor-rbgl 1.54.0 r3.4.1_0 +--------------------------------- +file name : bioconductor-rbgl-1.54.0-r3.4.1_0.tar.bz2 +name : bioconductor-rbgl +version : 1.54.0 +build : r3.4.1_0 +build number: 0 +size : 3.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.54.0-r3.4.1_0.tar.bz2 +md5 : 08ce664aa302adcb92df73e232a727aa +dependencies: + - bioconductor-graph + - r-base 3.4.1* + + +bioconductor-rbgl 1.56.0 r341hfc679d8_0 +--------------------------------------- +file name : bioconductor-rbgl-1.56.0-r341hfc679d8_0.tar.bz2 +name : bioconductor-rbgl +version : 1.56.0 +build : r341hfc679d8_0 +build number: 0 +size : 3.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.56.0-r341hfc679d8_0.tar.bz2 +md5 : aea1101898fa498126960aea3840343d +timestamp : 2018-10-13 00:28:06 UTC +dependencies: + - bioconductor-graph >=1.58.0,<1.60.0 + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-rbgl 1.56.0 r351hfc679d8_0 +--------------------------------------- +file name : bioconductor-rbgl-1.56.0-r351hfc679d8_0.tar.bz2 +name : bioconductor-rbgl +version : 1.56.0 +build : r351hfc679d8_0 +build number: 0 +size : 3.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.56.0-r351hfc679d8_0.tar.bz2 +md5 : 0472987820398a0709728b9227c547e2 +timestamp : 2018-10-13 00:26:11 UTC +dependencies: + - bioconductor-graph >=1.58.0,<1.60.0 + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rbgl 1.58.1 r351hf484d3e_0 +--------------------------------------- +file name : bioconductor-rbgl-1.58.1-r351hf484d3e_0.tar.bz2 +name : bioconductor-rbgl +version : 1.58.1 +build : r351hf484d3e_0 +build number: 0 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.58.1-r351hf484d3e_0.tar.bz2 +md5 : 3733b2238019443dc97da69a47d65029 +timestamp : 2018-12-10 21:34:04 UTC +dependencies: + - bioconductor-graph >=1.60.0,<1.61.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rbgl 1.58.2 r351hf484d3e_0 +--------------------------------------- +file name : bioconductor-rbgl-1.58.2-r351hf484d3e_0.tar.bz2 +name : bioconductor-rbgl +version : 1.58.2 +build : r351hf484d3e_0 +build number: 0 +size : 2.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.58.2-r351hf484d3e_0.tar.bz2 +md5 : 7c0cbbe585043d20fe358caee90fc517 +timestamp : 2019-04-28 05:39:11 UTC +dependencies: + - bioconductor-graph >=1.60.0,<1.61.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rbgl 1.60.0 r36he1b5a44_1 +-------------------------------------- +file name : bioconductor-rbgl-1.60.0-r36he1b5a44_1.tar.bz2 +name : bioconductor-rbgl +version : 1.60.0 +build : r36he1b5a44_1 +build number: 1 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.60.0-r36he1b5a44_1.tar.bz2 +md5 : 105b5a14aabe4b1f3b226c0b410d5e0b +timestamp : 2019-07-22 05:55:57 UTC +dependencies: + - bioconductor-graph >=1.62.0,<1.63.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + - r-bh + + +bioconductor-rbgl 1.62.1 r36he1b5a44_0 +-------------------------------------- +file name : bioconductor-rbgl-1.62.1-r36he1b5a44_0.tar.bz2 +name : bioconductor-rbgl +version : 1.62.1 +build : r36he1b5a44_0 +build number: 0 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.62.1-r36he1b5a44_0.tar.bz2 +md5 : f32eca5084ab30ee7b1cf5f43ebe705b +timestamp : 2019-11-02 02:17:55 UTC +dependencies: + - bioconductor-graph >=1.64.0,<1.65.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + - r-bh + + +bioconductor-rbgl 1.64.0 r40h5f743cb_0 +-------------------------------------- +file name : bioconductor-rbgl-1.64.0-r40h5f743cb_0.tar.bz2 +name : bioconductor-rbgl +version : 1.64.0 +build : r40h5f743cb_0 +build number: 0 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.64.0-r40h5f743cb_0.tar.bz2 +md5 : c5e9f5ce663d39d6df1f9a9d846fc0ba +timestamp : 2020-05-09 23:28:13 UTC +dependencies: + - bioconductor-graph >=1.66.0,<1.67.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - liblapack >=3.8.0,<3.9.0a0 + - libstdcxx-ng >=7.3.0 + - r-base >=4.0,<4.1.0a0 + - r-bh + + +bioconductor-rbgl 1.66.0 r40h399db7b_1 +-------------------------------------- +file name : bioconductor-rbgl-1.66.0-r40h399db7b_1.tar.bz2 +name : bioconductor-rbgl +version : 1.66.0 +build : r40h399db7b_1 +build number: 1 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.66.0-r40h399db7b_1.tar.bz2 +md5 : d7b780572f85920a0570b9b1cd623045 +timestamp : 2021-03-28 12:26:28 UTC +dependencies: + - bioconductor-graph >=1.68.0,<1.69.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.0,<4.1.0a0 + - r-bh + + +bioconductor-rbgl 1.66.0 r40h5f743cb_0 +-------------------------------------- +file name : bioconductor-rbgl-1.66.0-r40h5f743cb_0.tar.bz2 +name : bioconductor-rbgl +version : 1.66.0 +build : r40h5f743cb_0 +build number: 0 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.66.0-r40h5f743cb_0.tar.bz2 +md5 : 56a5319263eb549e81cf4e369a56e856 +timestamp : 2020-10-30 11:29:45 UTC +dependencies: + - bioconductor-graph >=1.68.0,<1.69.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=7.5.0 + - r-base >=4.0,<4.1.0a0 + - r-bh + + +bioconductor-rbgl 1.68.0 r41h399db7b_0 +-------------------------------------- +file name : bioconductor-rbgl-1.68.0-r41h399db7b_0.tar.bz2 +name : bioconductor-rbgl +version : 1.68.0 +build : r41h399db7b_0 +build number: 0 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.68.0-r41h399db7b_0.tar.bz2 +md5 : 12b4d4c1229bd865b152ae96f52f55fb +timestamp : 2021-05-31 02:20:15 UTC +dependencies: + - bioconductor-graph >=1.70.0,<1.71.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.1,<4.2.0a0 + - r-bh + + +bioconductor-rbgl 1.70.0 r41h399db7b_0 +-------------------------------------- +file name : bioconductor-rbgl-1.70.0-r41h399db7b_0.tar.bz2 +name : bioconductor-rbgl +version : 1.70.0 +build : r41h399db7b_0 +build number: 0 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.70.0-r41h399db7b_0.tar.bz2 +md5 : b9756194bb480dfe948a2e0c995d1170 +timestamp : 2021-11-02 21:42:16 UTC +dependencies: + - bioconductor-graph >=1.72.0,<1.73.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.4.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.4.0 + - r-base >=4.1,<4.2.0a0 + - r-bh + + +bioconductor-rbgl 1.70.0 r41h619a076_1 +-------------------------------------- +file name : bioconductor-rbgl-1.70.0-r41h619a076_1.tar.bz2 +name : bioconductor-rbgl +version : 1.70.0 +build : r41h619a076_1 +build number: 1 +size : 2.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.70.0-r41h619a076_1.tar.bz2 +md5 : f5eadeed415e1e0b3d22ccd5f diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-regionalst.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-regionalst.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..7444dacb35168a64cd40e98ba54c55e3ad023e05 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-regionalst.manual_bundle.txt @@ -0,0 +1,92 @@ +# Tool: bioconductor-regionalst +software_name: bioconductor-regionalst +tier: T1 +domain: single_cell +downloads: 1301 +summary: Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data +description: This package analyze spatial transcriptomics data through cross-regional cell type-specific analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application. +dependencies: bioconductor-bayesspace >=1.20.0,<1.21.0, bioconductor-biocstyle >=2.38.0,<2.39.0, bioconductor-fgsea >=1.36.0,<1.37.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scater >=1.38.0,<1.39.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-toast >=1.24.0,<1.25.0, r-assertthat, r-base >=4.5,<4.6.0a0, r-colorspace, r-dplyr, r-ggplot2, r-gridextra, r-magrittr, r-rcolorbrewer, r-seurat, r-shiny, r-tibble +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.18/bioc/html/RegionalST.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.18/bioc/html/RegionalST.html +Bioconductor - RegionalST About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.18 Software Packages RegionalST RegionalST This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see RegionalST . Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data DOI: 10.18129/B9.bioc.RegionalST Bioconductor version: 3.18 This package analyze spatial transcriptomics data through cross-regional analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application. Author: Ziyi Li [aut, cre] Maintainer: Ziyi Li <zli16 at mdanderson.org> Citation (from within R, enter citation("RegionalST") ): Installation To install this package, start R (version "4.3") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("RegionalST") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("RegionalST") RegionalST HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews KEGG , Reactome , Software , Spatial , Transcriptomics Version 1.0.1 In Bioconductor since BioC 3.18 (R-4.3) (0.5 years) License GPL-3 Depends R (>= 4.3.0) Imports stats, grDevices, utils, ggplot2, dplyr, scater , gridExtra, BayesSpace , fgsea , magrittr, SingleCellExperiment , RColorBrewer, Seurat, S4Vectors , tibble, TOAST , assertthat, colorspace, shiny, SummarizedExperiment System Requirements URL See More Suggests BiocStyle , knitr, rmarkdown, gplots, testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package RegionalST_1.0.1.tar.gz Windows Binary RegionalST_1.0.1.zip (64-bit only) macOS Binary (x86_64) RegionalST_1.0.1.tgz macOS Binary (arm64) RegionalST_1.0.1.tgz Source Repository git clone https://git.bioconductor.org/packages/RegionalST Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RegionalST Bioc Package Browser https://code.bioconductor.org/browse/RegionalST/ Package Short Url https://bioconductor.org/packages/RegionalST/ Package Downloads Report Download Stats Old Source Packages for BioC 3.18 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-regionalst --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-regionalst 1.0.1 r43hdfd78af_0 +------------------------------------------- +file name : bioconductor-regionalst-1.0.1-r43hdfd78af_0.tar.bz2 +name : bioconductor-regionalst +version : 1.0.1 +build : r43hdfd78af_0 +build number: 0 +size : 2.9 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-regionalst-1.0.1-r43hdfd78af_0.tar.bz2 +md5 : 58a377f7d6c56cdfc8a9eafc6643a388 +timestamp : 2023-12-12 00:34:18 UTC +dependencies: + - bioconductor-bayesspace >=1.12.0,<1.13.0 + - bioconductor-fgsea >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-scater >=1.30.0,<1.31.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - bioconductor-toast >=1.16.0,<1.17.0 + - r-assertthat + - r-base >=4.3,<4.4.0a0 + - r-colorspace + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-magrittr + - r-rcolorbrewer + - r-seurat + - r-shiny + - r-tibble + + +bioconductor-regionalst 1.8.0 r45hdfd78af_0 +------------------------------------------- +file name : bioconductor-regionalst-1.8.0-r45hdfd78af_0.conda +name : bioconductor-regionalst +version : 1.8.0 +build : r45hdfd78af_0 +build number: 0 +size : 3.7 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-regionalst-1.8.0-r45hdfd78af_0.conda +md5 : f2ecbde0b5cd6df9b7bc3a1a7baa5356 +timestamp : 2026-03-03 21:04:11 UTC +dependencies: + - bioconductor-bayesspace >=1.20.0,<1.21.0 + - bioconductor-biocstyle >=2.38.0,<2.39.0 + - bioconductor-fgsea >=1.36.0,<1.37.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-scater >=1.38.0,<1.39.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - bioconductor-toast >=1.24.0,<1.25.0 + - r-assertthat + - r-base >=4.5,<4.6.0a0 + - r-colorspace + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-magrittr + - r-rcolorbrewer + - r-seurat + - r-shiny + - r-tibble diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rgraphviz.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rgraphviz.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..354ad6ebb9135b9b015063b5ec01e3935b54878a --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rgraphviz.manual_bundle.txt @@ -0,0 +1,422 @@ +# Tool: bioconductor-rgraphviz +software_name: bioconductor-rgraphviz +tier: T1 +domain: t1_backfill_overall +downloads: 129127 +summary: Provides plotting capabilities for R graph objects +description: Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package. +dependencies: bioconductor-graph >=1.88.0,<1.89.0, bioconductor-graph >=1.88.1,<1.89.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.3,<6.0a0, libstdcxx >=14, libzlib >=1.3.2,<2.0a0, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/Rgraphviz.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/Rgraphviz.html +Bioconductor - Rgraphviz Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages Rgraphviz Rgraphviz This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see Rgraphviz . Provides plotting capabilities for R graph objects DOI: 10.18129/B9.bioc.Rgraphviz Bioconductor version: 3.22 Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package. Author: Kasper Daniel Hansen [cre, aut], Jeff Gentry [aut], Li Long [aut], Robert Gentleman [aut], Seth Falcon [aut], Florian Hahne [aut], Deepayan Sarkar [aut] Maintainer: Kasper Daniel Hansen <kasperdanielhansen at gmail.com> Citation (from within R, enter citation("Rgraphviz") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Rgraphviz") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("Rgraphviz") A New Interface to Plot Graphs Using Rgraphviz PDF R Script How To Plot A Graph Using Rgraphviz PDF R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews GraphAndNetwork , Software , Visualization Version 2.54.0 In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 21 years) License EPL Depends R (>= 2.6.0), methods, utils, graph , grid Imports stats4, graphics, grDevices System Requirements optionally Graphviz (>= 2.16), USE_C17 URL See More Suggests RUnit , BiocGenerics , XML Linking To Enhances Depends On Me biocGraph , BioMVCClass , CellNOptR , MineICA , netresponse , paircompviz , pathRender , ROntoTools , SplicingGraphs , maEndToEnd , dlsem , gridGraphviz Imports Me apComplex , biocGraph , bnem , chimeraviz , CytoML , DEGraph , EnrichDO , EnrichmentBrowser , flowWorkspace , GeneNetworkBuilder , GOstats , hyperdraw , KEGGgraph , mirIntegrator , MIRit , mnem , OncoSimulR , ontoProc , paircompviz , pathview , Pigengene , qpgraph , TRONCO , abn , agena.ai , BCDAG , BiDAG , bnpa , bnRep , CePa , classGraph , cogmapr , ontologyPlot , SEMgraph , stablespec , WayFindR Suggests Me a4 , altcdfenvs , annotate , Category , CNORfeeder , CNORfuzzy , DEGraph , flowCore , geneplotter , GlobalAncova , globaltest , GSEABase , MLP , NCIgraph , RBGL , rBiopaxParser , safe , SPIA , SRAdb , Streamer , topGO , ViSEAGO , vtpnet , NCIgraphData , SNAData , arulesViz , BayesNetBP , bivarhr , bnlearn , bnstruct , ChoR , CodeDepends , gbutils , GeneNet , gRain , iTOP , kst , lava , loon , maGUI , micd , multiplex , netmeta , pcalg , PCBN , pchc , pks , psych , rCausalMGM , relations , rEMM , rPref , rSpectral , SCCI , sisal , textplot , tm , topologyGSA , tpc , unifDAG , zenplots Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package Rgraphviz_2.54.0.tar.gz Windows Binary (x86_64) Rgraphviz_2.54.0.zip macOS Binary (x86_64) Rgraphviz_2.54.0.tgz macOS Binary (arm64) Rgraphviz_2.54.0.tgz Source Repository git clone https://git.bioconductor.org/packages/Rgraphviz Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rgraphviz Bioc Package Browser https://code.bioconductor.org/browse/Rgraphviz/ Package Short Url https://bioconductor.org/packages/Rgraphviz/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-rgraphviz --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-rgraphviz 2.13.0 0 +------------------------------- +file name : bioconductor-rgraphviz-2.13.0-0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.13.0 +build : 0 +build number: 0 +size : 860 KB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-0.tar.bz2 +md5 : 722ad7942f3c2bca5845a608d319d855 +dependencies: + - bioconductor-graph + - r >=2.6.0 + + +bioconductor-rgraphviz 2.13.0 r3.3.1_0 +-------------------------------------- +file name : bioconductor-rgraphviz-2.13.0-r3.3.1_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.13.0 +build : r3.3.1_0 +build number: 0 +size : 866 KB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-r3.3.1_0.tar.bz2 +md5 : 59d71039ccb54b254bddbae64ef998a7 +dependencies: + - bioconductor-graph + - r 3.3.1* + + +bioconductor-rgraphviz 2.13.0 r3.3.2_0 +-------------------------------------- +file name : bioconductor-rgraphviz-2.13.0-r3.3.2_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.13.0 +build : r3.3.2_0 +build number: 0 +size : 866 KB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-r3.3.2_0.tar.bz2 +md5 : 13457e492fb002c62d389a47ecf6d1b8 +dependencies: + - bioconductor-graph + - r-base 3.3.2* + + +bioconductor-rgraphviz 2.13.0 r3.4.1_0 +-------------------------------------- +file name : bioconductor-rgraphviz-2.13.0-r3.4.1_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.13.0 +build : r3.4.1_0 +build number: 0 +size : 880 KB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-r3.4.1_0.tar.bz2 +md5 : 2324b2ab5d6530dfb74e35c733915f5d +dependencies: + - bioconductor-graph + - r-base 3.4.1* + + +bioconductor-rgraphviz 2.13.0 r341_1 +------------------------------------ +file name : bioconductor-rgraphviz-2.13.0-r341_1.tar.bz2 +name : bioconductor-rgraphviz +version : 2.13.0 +build : r341_1 +build number: 1 +size : 884 KB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-r341_1.tar.bz2 +md5 : 519ee006e04a1b432ff6bbe405f16ad2 +timestamp : 2018-10-13 01:09:32 UTC +dependencies: + - bioconductor-graph + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-rgraphviz 2.13.0 r351_1 +------------------------------------ +file name : bioconductor-rgraphviz-2.13.0-r351_1.tar.bz2 +name : bioconductor-rgraphviz +version : 2.13.0 +build : r351_1 +build number: 1 +size : 991 KB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-r351_1.tar.bz2 +md5 : 58b41ddc8c01c724bb13e501c9bd1a98 +timestamp : 2018-10-13 01:07:41 UTC +dependencies: + - bioconductor-graph + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rgraphviz 2.14.0 0 +------------------------------- +file name : bioconductor-rgraphviz-2.14.0-0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.14.0 +build : 0 +build number: 0 +size : 1.4 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.14.0-0.tar.bz2 +md5 : 3066ac60dca8caa320798ebe069434c6 +dependencies: + - bioconductor-graph + - r >=2.6.0 + + +bioconductor-rgraphviz 2.16.0 r3.3.1_0 +-------------------------------------- +file name : bioconductor-rgraphviz-2.16.0-r3.3.1_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.16.0 +build : r3.3.1_0 +build number: 0 +size : 862 KB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.16.0-r3.3.1_0.tar.bz2 +md5 : 77e2930aee50b5cd13e609678251a7ba +dependencies: + - bioconductor-graph + - r 3.3.1* + + +bioconductor-rgraphviz 2.16.0 r3.3.1_1 +-------------------------------------- +file name : bioconductor-rgraphviz-2.16.0-r3.3.1_1.tar.bz2 +name : bioconductor-rgraphviz +version : 2.16.0 +build : r3.3.1_1 +build number: 1 +size : 861 KB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.16.0-r3.3.1_1.tar.bz2 +md5 : f6af84f695bbcc53309dae51f4f5e560 +dependencies: + - bioconductor-graph + - libgcc + - r 3.3.1* + + +bioconductor-rgraphviz 2.16.0 r3.3.2_1 +-------------------------------------- +file name : bioconductor-rgraphviz-2.16.0-r3.3.2_1.tar.bz2 +name : bioconductor-rgraphviz +version : 2.16.0 +build : r3.3.2_1 +build number: 1 +size : 863 KB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.16.0-r3.3.2_1.tar.bz2 +md5 : cf1a24559b2c4d96d690614927a33c31 +dependencies: + - bioconductor-graph + - libgcc + - r-base 3.3.2* + + +bioconductor-rgraphviz 2.16.0 r3.4.1_1 +-------------------------------------- +file name : bioconductor-rgraphviz-2.16.0-r3.4.1_1.tar.bz2 +name : bioconductor-rgraphviz +version : 2.16.0 +build : r3.4.1_1 +build number: 1 +size : 876 KB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.16.0-r3.4.1_1.tar.bz2 +md5 : 1a70d20f58311b6e955aeff3895be111 +dependencies: + - bioconductor-graph + - libgcc + - r-base 3.4.1* + + +bioconductor-rgraphviz 2.20.0 r3.4.1_0 +-------------------------------------- +file name : bioconductor-rgraphviz-2.20.0-r3.4.1_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.20.0 +build : r3.4.1_0 +build number: 0 +size : 1.4 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.20.0-r3.4.1_0.tar.bz2 +md5 : 894e6bf65d0a4190492253bf028172c7 +dependencies: + - bioconductor-graph + - r-base 3.4.1* + + +bioconductor-rgraphviz 2.20.0 r3.4.1_1 +-------------------------------------- +file name : bioconductor-rgraphviz-2.20.0-r3.4.1_1.tar.bz2 +name : bioconductor-rgraphviz +version : 2.20.0 +build : r3.4.1_1 +build number: 1 +size : 1.4 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.20.0-r3.4.1_1.tar.bz2 +md5 : d5f5db50b05d5d6d11760185550e7fb5 +dependencies: + - bioconductor-graph + - libgcc + - r-base 3.4.1* + + +bioconductor-rgraphviz 2.22.0 r3.4.1_0 +-------------------------------------- +file name : bioconductor-rgraphviz-2.22.0-r3.4.1_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.22.0 +build : r3.4.1_0 +build number: 0 +size : 1.4 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.22.0-r3.4.1_0.tar.bz2 +md5 : d9afb234e02f26ff35121033de8def5e +dependencies: + - bioconductor-graph + - libgcc + - r-base 3.4.1* + + +bioconductor-rgraphviz 2.24.0 r341hfc679d8_0 +-------------------------------------------- +file name : bioconductor-rgraphviz-2.24.0-r341hfc679d8_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.24.0 +build : r341hfc679d8_0 +build number: 0 +size : 1.4 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.24.0-r341hfc679d8_0.tar.bz2 +md5 : ceef0e54eee682c88753ff9a06616294 +timestamp : 2018-10-13 01:19:33 UTC +dependencies: + - bioconductor-graph >=1.58.0,<1.60.0 + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-rgraphviz 2.24.0 r351hfc679d8_0 +-------------------------------------------- +file name : bioconductor-rgraphviz-2.24.0-r351hfc679d8_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.24.0 +build : r351hfc679d8_0 +build number: 0 +size : 1.5 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.24.0-r351hfc679d8_0.tar.bz2 +md5 : dc5615db40ab8414d9ff64c196a29466 +timestamp : 2018-10-13 01:21:19 UTC +dependencies: + - bioconductor-graph >=1.58.0,<1.60.0 + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rgraphviz 2.26.0 r351hf484d3e_0 +-------------------------------------------- +file name : bioconductor-rgraphviz-2.26.0-r351hf484d3e_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.26.0 +build : r351hf484d3e_0 +build number: 0 +size : 1.6 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.26.0-r351hf484d3e_0.tar.bz2 +md5 : efe22a97679cb1250f62f812d5bf5feb +timestamp : 2018-12-10 22:12:25 UTC +dependencies: + - bioconductor-graph >=1.60.0,<1.61.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rgraphviz 2.28.0 r36he1b5a44_1 +------------------------------------------- +file name : bioconductor-rgraphviz-2.28.0-r36he1b5a44_1.tar.bz2 +name : bioconductor-rgraphviz +version : 2.28.0 +build : r36he1b5a44_1 +build number: 1 +size : 1.5 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.28.0-r36he1b5a44_1.tar.bz2 +md5 : 9f454621d8c5e837364041fc2cdc2b08 +timestamp : 2019-07-22 09:33:59 UTC +dependencies: + - bioconductor-graph >=1.62.0,<1.63.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-rgraphviz 2.30.0 r36he1b5a44_0 +------------------------------------------- +file name : bioconductor-rgraphviz-2.30.0-r36he1b5a44_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.30.0 +build : r36he1b5a44_0 +build number: 0 +size : 1.5 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.30.0-r36he1b5a44_0.tar.bz2 +md5 : 9d8a5d1b32362652996391f825d09d85 +timestamp : 2019-11-01 20:54:47 UTC +dependencies: + - bioconductor-graph >=1.64.0,<1.65.0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-rgraphviz 2.32.0 r40h5f743cb_0 +------------------------------------------- +file name : bioconductor-rgraphviz-2.32.0-r40h5f743cb_0.tar.bz2 +name : bioconductor-rgraphviz +version : 2.32.0 +build : r40h5f743cb_0 +build number: 0 +size : 1.6 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.32.0-r40h5f743cb_0.tar.bz2 +md5 : f3110fe03353189dd3fd81e146a8a6c5 +timestamp : 2020-05-10 06:28:31 UTC +dependencies: + - bioconductor-graph >=1.66.0,<1.67.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - liblapack >=3.8.0,<3.9.0a0 + - libstdcxx-ng >=7.3.0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-rgraphviz 2.34.0 r40h399db7b_1 +------------------------------------------- +file name : bioconductor-rgraphviz-2.34.0-r40h399db7b_1.tar.bz2 +name : bioconductor-rgraphviz +version : 2.34.0 +build : r40h399db7b_1 +build number: 1 +size : 1.6 MB +license : EPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.34.0-r40h399db7b_1.tar.bz2 +md5 : 289be0c26a744f38ac2ce6656c14adda +timestamp : 2021-03-29 11:24:48 UTC +dependencies: + - bioconductor-graph >=1.68.0,<1.69.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rhdf5filters.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rhdf5filters.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..caf4fc42fde256225e3ebb1458a225ed02982cb4 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rhdf5filters.manual_bundle.txt @@ -0,0 +1,366 @@ +# Tool: bioconductor-rhdf5filters +software_name: bioconductor-rhdf5filters +tier: T1 +domain: t1_backfill_overall +downloads: 565355 +summary: HDF5 Compression Filters +description: Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seemless integration with rhdf5, however the compiled filters can also be used with external applications. +dependencies: bioconductor-rhdf5lib >=1.32.0,<1.33.0, bioconductor-rhdf5lib >=1.32.0,<1.33.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.11/bioc/html/rhdf5filters.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.11/bioc/html/rhdf5filters.html +Bioconductor - rhdf5filters About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.11 Software Packages rhdf5filters rhdf5filters This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see rhdf5filters . HDF5 Compression Filters DOI: 10.18129/B9.bioc.rhdf5filters Bioconductor version: 3.11 Provides a collection of compression filters for use with HDF5 datasets. Author: Mike Smith [aut, cre] Maintainer: Mike Smith <grimbough at gmail.com> Citation (from within R, enter citation("rhdf5filters") ): Installation To install this package, start R (version "4.0") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("rhdf5filters") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("rhdf5filters") HDF5 Compression Filters HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataImport , Infrastructure , Software Version 1.0.1 In Bioconductor since BioC 3.11 (R-4.0) (4 years) License BSD_2_clause + file LICENSE Depends Imports System Requirements GNU make URL https://github.com/grimbough/rhdf5filters Bug Reports https://github.com/grimbough/rhdf5filters See More Suggests BiocStyle , knitr, rmarkdown, testthat (>= 2.1.0) Linking To Rhdf5lib Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package rhdf5filters_1.0.1.tar.gz Windows Binary rhdf5filters_1.0.1.zip (32- & 64-bit) macOS 10.13 (High Sierra) rhdf5filters_1.0.1.tgz Source Repository git clone https://git.bioconductor.org/packages/rhdf5filters Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rhdf5filters Bioc Package Browser https://code.bioconductor.org/browse/rhdf5filters/ Package Short Url https://bioconductor.org/packages/rhdf5filters/ Package Downloads Report Download Stats Old Source Packages for BioC 3.11 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-rhdf5filters --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-rhdf5filters 1.2.0 r40h399db7b_1 +--------------------------------------------- +file name : bioconductor-rhdf5filters-1.2.0-r40h399db7b_1.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.2.0 +build : r40h399db7b_1 +build number: 1 +size : 639 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.2.0-r40h399db7b_1.tar.bz2 +md5 : 0846bf2cedfcad320ff650957132839e +timestamp : 2021-03-25 03:49:07 UTC +dependencies: + - bioconductor-rhdf5lib >=1.12.0,<1.13.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-rhdf5filters 1.2.0 r40h5f743cb_0 +--------------------------------------------- +file name : bioconductor-rhdf5filters-1.2.0-r40h5f743cb_0.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.2.0 +build : r40h5f743cb_0 +build number: 0 +size : 629 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.2.0-r40h5f743cb_0.tar.bz2 +md5 : c7dca2e73dbe4a2ed2c3335bb9f741bf +timestamp : 2020-10-29 17:05:55 UTC +dependencies: + - bioconductor-rhdf5lib >=1.12.0,<1.13.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=7.5.0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-rhdf5filters 1.4.0 r41h399db7b_0 +--------------------------------------------- +file name : bioconductor-rhdf5filters-1.4.0-r41h399db7b_0.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.4.0 +build : r41h399db7b_0 +build number: 0 +size : 661 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.4.0-r41h399db7b_0.tar.bz2 +md5 : f7f85b739e9fab6deaa5847597951c9d +timestamp : 2021-05-31 06:32:11 UTC +dependencies: + - bioconductor-rhdf5lib >=1.14.0,<1.15.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.1,<4.2.0a0 + + +bioconductor-rhdf5filters 1.6.0 r41h399db7b_0 +--------------------------------------------- +file name : bioconductor-rhdf5filters-1.6.0-r41h399db7b_0.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.6.0 +build : r41h399db7b_0 +build number: 0 +size : 664 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.6.0-r41h399db7b_0.tar.bz2 +md5 : 204b7a8e97b5819c7132cbf4a93db414 +timestamp : 2021-11-02 02:31:33 UTC +dependencies: + - bioconductor-rhdf5lib >=1.16.0,<1.17.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.4.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.4.0 + - r-base >=4.1,<4.2.0a0 + + +bioconductor-rhdf5filters 1.6.0 r41h619a076_1 +--------------------------------------------- +file name : bioconductor-rhdf5filters-1.6.0-r41h619a076_1.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.6.0 +build : r41h619a076_1 +build number: 1 +size : 655 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.6.0-r41h619a076_1.tar.bz2 +md5 : d2e66a1e4b30c31abe9e3ac262a23f82 +timestamp : 2022-02-23 21:56:14 UTC +dependencies: + - bioconductor-rhdf5lib >=1.16.0,<1.17.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=10.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=10.3.0 + - r-base >=4.1,<4.2.0a0 + + +bioconductor-rhdf5filters 1.6.0 r41hc247a5b_2 +--------------------------------------------- +file name : bioconductor-rhdf5filters-1.6.0-r41hc247a5b_2.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.6.0 +build : r41hc247a5b_2 +build number: 2 +size : 646 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.6.0-r41hc247a5b_2.tar.bz2 +md5 : 3658bb6ad33ee34cc7b315d1ff3a4ef2 +timestamp : 2022-09-15 10:20:40 UTC +dependencies: + - bioconductor-rhdf5lib >=1.16.0,<1.17.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.1,<4.2.0a0 + + +bioconductor-rhdf5filters 1.10.0 r42hc247a5b_0 +---------------------------------------------- +file name : bioconductor-rhdf5filters-1.10.0-r42hc247a5b_0.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.10.0 +build : r42hc247a5b_0 +build number: 0 +size : 758 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.10.0-r42hc247a5b_0.tar.bz2 +md5 : 1c3ee5bc6c32455512844afe359f6baa +timestamp : 2022-11-03 14:27:23 UTC +dependencies: + - bioconductor-rhdf5lib >=1.20.0,<1.21.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + + +bioconductor-rhdf5filters 1.10.0 r42hf17093f_1 +---------------------------------------------- +file name : bioconductor-rhdf5filters-1.10.0-r42hf17093f_1.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.10.0 +build : r42hf17093f_1 +build number: 1 +size : 763 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.10.0-r42hf17093f_1.tar.bz2 +md5 : a68b0be19881807360a989f01f9b9f75 +timestamp : 2023-05-18 16:32:14 UTC +dependencies: + - bioconductor-rhdf5lib >=1.20.0,<1.21.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + + +bioconductor-rhdf5filters 1.12.1 r43hf17093f_0 +---------------------------------------------- +file name : bioconductor-rhdf5filters-1.12.1-r43hf17093f_0.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.12.1 +build : r43hf17093f_0 +build number: 0 +size : 1.0 MB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.12.1-r43hf17093f_0.tar.bz2 +md5 : 60491d28b8627339fbeb567cba682765 +timestamp : 2023-07-07 12:26:15 UTC +dependencies: + - bioconductor-rhdf5lib >=1.22.0,<1.23.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + + +bioconductor-rhdf5filters 1.12.1 r43hf17093f_1 +---------------------------------------------- +file name : bioconductor-rhdf5filters-1.12.1-r43hf17093f_1.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.12.1 +build : r43hf17093f_1 +build number: 1 +size : 1.1 MB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.12.1-r43hf17093f_1.tar.bz2 +md5 : 783b9fe64acb8aaf325fa2e913bef3cb +timestamp : 2023-10-27 18:14:10 UTC +dependencies: + - bioconductor-rhdf5lib >=1.22.0,<1.23.0 + - bioconductor-rhdf5lib >=1.22.0,<1.23.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + + +bioconductor-rhdf5filters 1.14.1 r43hf17093f_0 +---------------------------------------------- +file name : bioconductor-rhdf5filters-1.14.1-r43hf17093f_0.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.14.1 +build : r43hf17093f_0 +build number: 0 +size : 555 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.14.1-r43hf17093f_0.tar.bz2 +md5 : eff861de3afd924ac05a2726f8b284f9 +timestamp : 2023-12-04 03:01:07 UTC +dependencies: + - bioconductor-rhdf5lib >=1.24.0,<1.25.0 + - bioconductor-rhdf5lib >=1.24.0,<1.25.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + + +bioconductor-rhdf5filters 1.14.1 r43hf17093f_1 +---------------------------------------------- +file name : bioconductor-rhdf5filters-1.14.1-r43hf17093f_1.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.14.1 +build : r43hf17093f_1 +build number: 1 +size : 559 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.14.1-r43hf17093f_1.tar.bz2 +md5 : 9ee7c8344b04f246477e9aa58ee52f11 +timestamp : 2024-05-07 18:59:59 UTC +dependencies: + - bioconductor-rhdf5lib >=1.24.0,<1.25.0 + - bioconductor-rhdf5lib >=1.24.0,<1.25.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + + +bioconductor-rhdf5filters 1.18.0 r44h77050f0_0 +---------------------------------------------- +file name : bioconductor-rhdf5filters-1.18.0-r44h77050f0_0.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.18.0 +build : r44h77050f0_0 +build number: 0 +size : 564 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.18.0-r44h77050f0_0.tar.bz2 +md5 : d1f365d0504d628a27c3d0749224da10 +timestamp : 2024-12-18 15:11:40 UTC +dependencies: + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=13 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + - r-base >=4.4,<4.5.0a0 + + +bioconductor-rhdf5filters 1.18.0 r44h77050f0_1 +---------------------------------------------- +file name : bioconductor-rhdf5filters-1.18.0-r44h77050f0_1.tar.bz2 +name : bioconductor-rhdf5filters +version : 1.18.0 +build : r44h77050f0_1 +build number: 1 +size : 554 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.18.0-r44h77050f0_1.tar.bz2 +md5 : 290eb5bda03045128590f20568593b52 +timestamp : 2025-04-21 08:31:25 UTC +dependencies: + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=13 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + - r-base >=4.4,<4.5.0a0 + + +bioconductor-rhdf5filters 1.22.0 r45ha27e39d_0 +---------------------------------------------- +file name : bioconductor-rhdf5filters-1.22.0-r45ha27e39d_0.conda +name : bioconductor-rhdf5filters +version : 1.22.0 +build : r45ha27e39d_0 +build number: 0 +size : 500 KB +license : BSD_2_clause + file LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.22.0-r45ha27e39d_0.conda +md5 : bb1531739e103b2433b5e75e23bed547 +timestamp : 2026-02-07 23:48:25 UTC +dependencies: + - bioconductor-rhdf5lib >=1.32.0,<1.33.0 + - bioconductor-rhdf5lib >=1.32.0,<1.33.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=14 + - liblapack >=3.9.0,<4.0a0 + - liblzma >=5.8.2,<6.0a0 + - libstdcxx >=14 + - libzlib >=1.3.1,<2.0a0 + - r-base >=4.5,<4.6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rhdf5lib.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rhdf5lib.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..487c7764a6ac59c15eb34794448cfd2cc403487c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rhdf5lib.manual_bundle.txt @@ -0,0 +1,387 @@ +# Tool: bioconductor-rhdf5lib +software_name: bioconductor-rhdf5lib +tier: T1 +domain: t1_backfill_overall +downloads: 667943 +summary: hdf5 library as an R package +description: Provides C and C++ hdf5 libraries. +dependencies: libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: http://bioconductor.org/packages/3.6/bioc/html/Rhdf5lib.html +doc_url: +dev_url: + +## URL Docs Extract +### http://bioconductor.org/packages/3.6/bioc/html/Rhdf5lib.html +Bioconductor - Rhdf5lib About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.6 Software Packages Rhdf5lib Rhdf5lib This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see Rhdf5lib . hdf5 library as an R package DOI: 10.18129/B9.bioc.Rhdf5lib Bioconductor version: 3.6 Provides C and C++ hdf5 libraries. Author: Mike Smith Maintainer: Mike Smith <grimbough at gmail.com> Citation (from within R, enter citation("Rhdf5lib") ): Installation To install this package, start R (version "3.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Rhdf5lib") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Infrastructure , Software Version 1.0.0 In Bioconductor since BioC 3.6 (R-3.4) (6.5 years) License Artistic-2.0 Depends Imports System Requirements GNU make URL Bug Reports https://github.com/grimbough/Rhdf5lib See More Suggests BiocStyle , knitr, rmarkdown Linking To Enhances Depends On Me Imports Me beachmat Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package Rhdf5lib_1.0.0.tar.gz Windows Binary Rhdf5lib_1.0.0.zip (32- & 64-bit) Mac OS X 10.11 (El Capitan) Rhdf5lib_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/Rhdf5lib Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rhdf5lib Package Short Url https://bioconductor.org/packages/Rhdf5lib/ Package Downloads Report Download Stats Old Source Packages for BioC 3.6 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-rhdf5lib --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-rhdf5lib 1.0.0 r3.4.1_0 +------------------------------------ +file name : bioconductor-rhdf5lib-1.0.0-r3.4.1_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.0.0 +build : r3.4.1_0 +build number: 0 +size : 2.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.0.0-r3.4.1_0.tar.bz2 +md5 : 81ae070aac81cc3a62dbfc0856222d13 +dependencies: + - r-base 3.4.1* + + +bioconductor-rhdf5lib 1.2.1 r341h470a237_0 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.2.1-r341h470a237_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.2.1 +build : r341h470a237_0 +build number: 0 +size : 2.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.2.1-r341h470a237_0.tar.bz2 +md5 : 053446586a3f3c33b177eb1d49ffd56d +timestamp : 2018-10-10 09:23:01 UTC +dependencies: + - libgcc-ng >=4.9 + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-rhdf5lib 1.2.1 r351h470a237_0 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.2.1-r351h470a237_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.2.1 +build : r351h470a237_0 +build number: 0 +size : 2.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.2.1-r351h470a237_0.tar.bz2 +md5 : d24a22b6c11a2b96bf4a480209242d22 +timestamp : 2018-10-10 09:20:14 UTC +dependencies: + - libgcc-ng >=4.9 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rhdf5lib 1.4.2 r351h1feb10b_3 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.4.2-r351h1feb10b_3.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.4.2 +build : r351h1feb10b_3 +build number: 3 +size : 3.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.4.2-r351h1feb10b_3.tar.bz2 +md5 : 2d341286ccabbb70cfa6e90a5e2d3f4e +timestamp : 2019-02-13 10:39:04 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - r-base >=3.5.1,<3.5.2.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +bioconductor-rhdf5lib 1.4.2 r351h9c0d707_2 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.4.2-r351h9c0d707_2.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.4.2 +build : r351h9c0d707_2 +build number: 2 +size : 3.5 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.4.2-r351h9c0d707_2.tar.bz2 +md5 : 5986a988aa7a85abebc11515de168609 +timestamp : 2019-01-26 20:00:26 UTC +dependencies: + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - r-base >=3.5.1,<3.5.2.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +bioconductor-rhdf5lib 1.4.3 r351h1feb10b_0 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.4.3-r351h1feb10b_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.4.3 +build : r351h1feb10b_0 +build number: 0 +size : 3.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.4.3-r351h1feb10b_0.tar.bz2 +md5 : d08f19c5a143241c4075c83ee55372b6 +timestamp : 2019-03-24 09:24:26 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - r-base >=3.5.1,<3.5.2.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +bioconductor-rhdf5lib 1.6.0 r351h14c3975_0 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.6.0-r351h14c3975_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.6.0 +build : r351h14c3975_0 +build number: 0 +size : 3.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.6.0-r351h14c3975_0.tar.bz2 +md5 : 8ab901fb884944ee155d2cace06129c8 +timestamp : 2019-05-08 11:45:19 UTC +dependencies: + - libgcc-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rhdf5lib 1.6.0 r36h516909a_1 +----------------------------------------- +file name : bioconductor-rhdf5lib-1.6.0-r36h516909a_1.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.6.0 +build : r36h516909a_1 +build number: 1 +size : 3.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.6.0-r36h516909a_1.tar.bz2 +md5 : 1023caa12443a0730d31af3a0ddb5ce5 +timestamp : 2019-07-21 13:25:50 UTC +dependencies: + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-rhdf5lib 1.8.0 r36h516909a_0 +----------------------------------------- +file name : bioconductor-rhdf5lib-1.8.0-r36h516909a_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.8.0 +build : r36h516909a_0 +build number: 0 +size : 3.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.8.0-r36h516909a_0.tar.bz2 +md5 : 408ceb14368c386c723df14b5ec9e6ee +timestamp : 2019-11-01 14:47:58 UTC +dependencies: + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-rhdf5lib 1.10.0 r40h037d062_0 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.10.0-r40h037d062_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.10.0 +build : r40h037d062_0 +build number: 0 +size : 3.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.10.0-r40h037d062_0.tar.bz2 +md5 : 1daca590fc3da936b02427270da41469 +timestamp : 2020-05-09 09:30:01 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - liblapack >=3.8.0,<3.9.0a0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-rhdf5lib 1.12.0 r40h037d062_0 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.12.0-r40h037d062_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.12.0 +build : r40h037d062_0 +build number: 0 +size : 3.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.12.0-r40h037d062_0.tar.bz2 +md5 : 70f8b21e7077b2e980a9105630697d6a +timestamp : 2020-10-29 16:52:10 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-rhdf5lib 1.12.1 r40hd029910_0 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.12.1-r40hd029910_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.12.1 +build : r40hd029910_0 +build number: 0 +size : 3.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.12.1-r40hd029910_0.tar.bz2 +md5 : c92e8f8616558edd120894c5b3f2c320 +timestamp : 2021-03-27 20:19:14 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-rhdf5lib 1.14.0 r41hd029910_0 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.14.0-r41hd029910_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.14.0 +build : r41hd029910_0 +build number: 0 +size : 3.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.14.0-r41hd029910_0.tar.bz2 +md5 : 825074e2fa0d6c518790f842fd18cda8 +timestamp : 2021-05-31 01:17:11 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.1,<4.2.0a0 + + +bioconductor-rhdf5lib 1.16.0 r41h5c21468_1 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.16.0-r41h5c21468_1.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.16.0 +build : r41h5c21468_1 +build number: 1 +size : 3.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.16.0-r41h5c21468_1.tar.bz2 +md5 : 18d81acd3db5186d3ad575dae7812d3a +timestamp : 2022-02-21 20:50:10 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=10.3.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.1,<4.2.0a0 + + +bioconductor-rhdf5lib 1.16.0 r41hc0cfd56_2 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.16.0-r41hc0cfd56_2.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.16.0 +build : r41hc0cfd56_2 +build number: 2 +size : 3.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.16.0-r41hc0cfd56_2.tar.bz2 +md5 : 65a831c2e26f30f76eb8cd27498a1320 +timestamp : 2022-09-15 09:59:32 UTC +dependencies: + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - r-base >=4.1,<4.2.0a0 + + +bioconductor-rhdf5lib 1.16.0 r41hd029910_0 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.16.0-r41hd029910_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.16.0 +build : r41hd029910_0 +build number: 0 +size : 3.9 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.16.0-r41hd029910_0.tar.bz2 +md5 : c0bdbd74f8eca322bf453c229c5d5869 +timestamp : 2021-11-01 15:30:55 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.4.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.1,<4.2.0a0 + + +bioconductor-rhdf5lib 1.20.0 r42ha9d7317_2 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.20.0-r42ha9d7317_2.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.20.0 +build : r42ha9d7317_2 +build number: 2 +size : 4.0 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.20.0-r42ha9d7317_2.tar.bz2 +md5 : b8050b2dc519548201872884ae4ee186 +timestamp : 2023-05-16 14:23:44 UTC +dependencies: + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - r-base >=4.2,<4.3.0a0 + + +bioconductor-rhdf5lib 1.20.0 r42hc0cfd56_0 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.20.0-r42hc0cfd56_0.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.20.0 +build : r42hc0cfd56_0 +build number: 0 +size : 3.9 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.20.0-r42hc0cfd56_0.tar.bz2 +md5 : e2fe9002e7345aaa7aef9dcb601cdede +timestamp : 2022-11-03 14:16:34 UTC +dependencies: + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - r-base >=4.2,<4.3.0a0 + + +bioconductor-rhdf5lib 1.20.0 r42hc0cfd56_1 +------------------------------------------ +file name : bioconductor-rhdf5lib-1.20.0-r42hc0cfd56_1.tar.bz2 +name : bioconductor-rhdf5lib +version : 1.20.0 +build : r42hc0cfd56_1 +build number: 1 +size : 3.9 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.20.0-r42hc0cfd56_1.tar.bz2 +md5 : 747142d93afa8add37a47a597eebeedd +t diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rsubread.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rsubread.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c08a6c551377f9f4646313e67071132209c85623 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rsubread.manual_bundle.txt @@ -0,0 +1,413 @@ +# Tool: bioconductor-rsubread +software_name: bioconductor-rsubread +tier: T1 +domain: t1_backfill_overall +downloads: 136583 +summary: Mapping, quantification and variant analysis of sequencing data +description: Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads. +dependencies: libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-matrix +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/Rsubread.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/Rsubread.html +Bioconductor - Rsubread Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages Rsubread Rsubread This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see Rsubread . Mapping, quantification and variant analysis of sequencing data DOI: 10.18129/B9.bioc.Rsubread Bioconductor version: 3.22 Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads. Author: Wei Shi, Yang Liao and Gordon K Smyth with contributions from Jenny Dai Maintainer: Wei Shi <wei.shi2 at monash.edu>, Yang Liao <yang.liao at monash.edu> and Gordon K Smyth <smyth at wehi.edu.au> Citation (from within R, enter citation("Rsubread") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Rsubread") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("Rsubread") Rsubread Vignette PDF R Script SubreadUsersGuide.pdf PDF Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Alignment , ChIPSeq , GeneExpression , GeneFusionDetection , GeneRegulation , GeneticVariability , Genetics , GenomeAnnotation , ImmunoOncology , IndelDetection , MultipleSequenceAlignment , Preprocessing , QualityControl , RNASeq , SNP , SequenceMatching , Sequencing , SingleCell , Software , VariantAnnotation , VariantDetection Version 2.24.0 In Bioconductor since BioC 2.8 (R-2.13) (15 years) License GPL (>=3) Depends Imports grDevices, stats, utils, Matrix System Requirements URL http://bioconductor.org/packages/Rsubread See More Suggests Linking To Enhances Depends On Me ExCluster Imports Me CleanUpRNAseq , Damsel , diffUTR , dupRadar , FRASER , ribosomeProfilingQC , scPipe , scruff , stPipe Suggests Me autonomics , icetea , singleCellTK , SpliceWiz , tidybulk , MetaScope , inDAGO Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package Rsubread_2.24.0.tar.gz Windows Binary (x86_64) Rsubread_2.24.0.zip macOS Binary (x86_64) Rsubread_2.24.0.tgz macOS Binary (arm64) Rsubread_2.24.0.tgz Source Repository git clone https://git.bioconductor.org/packages/Rsubread Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rsubread Bioc Package Browser https://code.bioconductor.org/browse/Rsubread/ Package Short Url https://bioconductor.org/packages/Rsubread/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-rsubread --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-rsubread 1.22.1 r3.2.2_0 +------------------------------------- +file name : bioconductor-rsubread-1.22.1-r3.2.2_0.tar.bz2 +name : bioconductor-rsubread +version : 1.22.1 +build : r3.2.2_0 +build number: 0 +size : 9.6 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.22.1-r3.2.2_0.tar.bz2 +md5 : 9d5c24af2182f395aa495fa4d9c73ced +dependencies: + - r 3.2.2* + + +bioconductor-rsubread 1.23.0 r3.3.1_0 +------------------------------------- +file name : bioconductor-rsubread-1.23.0-r3.3.1_0.tar.bz2 +name : bioconductor-rsubread +version : 1.23.0 +build : r3.3.1_0 +build number: 0 +size : 9.5 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.23.0-r3.3.1_0.tar.bz2 +md5 : d311d59408702abcc80c339d6ba17648 +dependencies: + - r 3.3.1* + + +bioconductor-rsubread 1.25.2 r3.3.1_0 +------------------------------------- +file name : bioconductor-rsubread-1.25.2-r3.3.1_0.tar.bz2 +name : bioconductor-rsubread +version : 1.25.2 +build : r3.3.1_0 +build number: 0 +size : 9.5 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.25.2-r3.3.1_0.tar.bz2 +md5 : 5c006c6d64894efd9a5e04e84ab381be +dependencies: + - r 3.3.1* + + +bioconductor-rsubread 1.25.2 r3.3.2_0 +------------------------------------- +file name : bioconductor-rsubread-1.25.2-r3.3.2_0.tar.bz2 +name : bioconductor-rsubread +version : 1.25.2 +build : r3.3.2_0 +build number: 0 +size : 9.5 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.25.2-r3.3.2_0.tar.bz2 +md5 : 974a448e65f3ff585a9d657b103792bb +dependencies: + - r-base 3.3.2* + + +bioconductor-rsubread 1.25.2 r3.4.1_0 +------------------------------------- +file name : bioconductor-rsubread-1.25.2-r3.4.1_0.tar.bz2 +name : bioconductor-rsubread +version : 1.25.2 +build : r3.4.1_0 +build number: 0 +size : 9.5 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.25.2-r3.4.1_0.tar.bz2 +md5 : 454a7b15c5ee5492ef459771a53a59cc +dependencies: + - r-base 3.4.1* + + +bioconductor-rsubread 1.26.1 r3.4.1_0 +------------------------------------- +file name : bioconductor-rsubread-1.26.1-r3.4.1_0.tar.bz2 +name : bioconductor-rsubread +version : 1.26.1 +build : r3.4.1_0 +build number: 0 +size : 9.6 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.26.1-r3.4.1_0.tar.bz2 +md5 : 53cfae394487d62425609df953e73189 +dependencies: + - r-base 3.4.1* + + +bioconductor-rsubread 1.28.0 r3.4.1_0 +------------------------------------- +file name : bioconductor-rsubread-1.28.0-r3.4.1_0.tar.bz2 +name : bioconductor-rsubread +version : 1.28.0 +build : r3.4.1_0 +build number: 0 +size : 9.6 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.28.0-r3.4.1_0.tar.bz2 +md5 : 3c66789af622cf84eadff1e5546446fe +dependencies: + - r-base 3.4.1* + + +bioconductor-rsubread 1.28.1 r3.4.1_0 +------------------------------------- +file name : bioconductor-rsubread-1.28.1-r3.4.1_0.tar.bz2 +name : bioconductor-rsubread +version : 1.28.1 +build : r3.4.1_0 +build number: 0 +size : 9.6 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.28.1-r3.4.1_0.tar.bz2 +md5 : d6c5436fc825285e27c588572db16f03 +dependencies: + - libgcc + - r-base 3.4.1* + + +bioconductor-rsubread 1.30.9 r341h470a237_0 +------------------------------------------- +file name : bioconductor-rsubread-1.30.9-r341h470a237_0.tar.bz2 +name : bioconductor-rsubread +version : 1.30.9 +build : r341h470a237_0 +build number: 0 +size : 9.7 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.30.9-r341h470a237_0.tar.bz2 +md5 : c8612cb52fea959b5cdd938c00cadea6 +timestamp : 2018-10-29 06:31:20 UTC +dependencies: + - libgcc-ng >=4.9 + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-rsubread 1.30.9 r351h470a237_0 +------------------------------------------- +file name : bioconductor-rsubread-1.30.9-r351h470a237_0.tar.bz2 +name : bioconductor-rsubread +version : 1.30.9 +build : r351h470a237_0 +build number: 0 +size : 9.8 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.30.9-r351h470a237_0.tar.bz2 +md5 : 9f67ddc2689e32412ddf060994427c55 +timestamp : 2018-10-29 06:30:05 UTC +dependencies: + - libgcc-ng >=4.9 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rsubread 1.32.2 r351h14c3975_0 +------------------------------------------- +file name : bioconductor-rsubread-1.32.2-r351h14c3975_0.tar.bz2 +name : bioconductor-rsubread +version : 1.32.2 +build : r351h14c3975_0 +build number: 0 +size : 9.8 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.32.2-r351h14c3975_0.tar.bz2 +md5 : 36a9250ffc898f64354e15e3656b7d32 +timestamp : 2018-12-09 23:26:03 UTC +dependencies: + - libgcc-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rsubread 1.32.4 r351h14c3975_0 +------------------------------------------- +file name : bioconductor-rsubread-1.32.4-r351h14c3975_0.tar.bz2 +name : bioconductor-rsubread +version : 1.32.4 +build : r351h14c3975_0 +build number: 0 +size : 9.8 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.32.4-r351h14c3975_0.tar.bz2 +md5 : f7d00fe9379380fb0f9f138051ca2013 +timestamp : 2019-04-24 04:19:33 UTC +dependencies: + - libgcc-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rsubread 1.34.0 r351h14c3975_0 +------------------------------------------- +file name : bioconductor-rsubread-1.34.0-r351h14c3975_0.tar.bz2 +name : bioconductor-rsubread +version : 1.34.0 +build : r351h14c3975_0 +build number: 0 +size : 11.0 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.34.0-r351h14c3975_0.tar.bz2 +md5 : 7e1f4c3d1a387aa8711ea08eee45251d +timestamp : 2019-05-08 07:53:29 UTC +dependencies: + - libgcc-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-rsubread 1.34.6 r36h516909a_0 +------------------------------------------ +file name : bioconductor-rsubread-1.34.6-r36h516909a_0.tar.bz2 +name : bioconductor-rsubread +version : 1.34.6 +build : r36h516909a_0 +build number: 0 +size : 11.0 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.34.6-r36h516909a_0.tar.bz2 +md5 : 7070cd8d3f58aaff020f625ecfff2a0c +timestamp : 2019-07-23 06:25:39 UTC +dependencies: + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-rsubread 2.0.0 r36h516909a_0 +----------------------------------------- +file name : bioconductor-rsubread-2.0.0-r36h516909a_0.tar.bz2 +name : bioconductor-rsubread +version : 2.0.0 +build : r36h516909a_0 +build number: 0 +size : 11.0 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.0.0-r36h516909a_0.tar.bz2 +md5 : 7ba05406fb6ede09ac6d928a8001198c +timestamp : 2019-11-01 08:46:15 UTC +dependencies: + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-rsubread 2.2.1 r40h037d062_0 +----------------------------------------- +file name : bioconductor-rsubread-2.2.1-r40h037d062_0.tar.bz2 +name : bioconductor-rsubread +version : 2.2.1 +build : r40h037d062_0 +build number: 0 +size : 11.0 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.2.1-r40h037d062_0.tar.bz2 +md5 : aeb0ba395c7b340b1e111b83ca03fdb7 +timestamp : 2020-05-09 14:36:58 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - liblapack >=3.8.0,<3.9.0a0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + + +bioconductor-rsubread 2.4.0 r40h037d062_0 +----------------------------------------- +file name : bioconductor-rsubread-2.4.0-r40h037d062_0.tar.bz2 +name : bioconductor-rsubread +version : 2.4.0 +build : r40h037d062_0 +build number: 0 +size : 11.1 MB +license : GPL (>=3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.4.0-r40h037d062_0.tar.bz2 +md5 : 3b237d29baf926c444724d4cc76a6f6a +timestamp : 2020-10-29 21:15:41 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + + +bioconductor-rsubread 2.4.3 r40hd029910_0 +----------------------------------------- +file name : bioconductor-rsubread-2.4.3-r40hd029910_0.tar.bz2 +name : bioconductor-rsubread +version : 2.4.3 +build : r40hd029910_0 +build number: 0 +size : 11.1 MB +license : GPL (>=3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.4.3-r40hd029910_0.tar.bz2 +md5 : 70f557d34f5265abc2dada4d81cb3882 +timestamp : 2021-03-26 08:00:29 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + + +bioconductor-rsubread 2.6.1 r41hd029910_0 +----------------------------------------- +file name : bioconductor-rsubread-2.6.1-r41hd029910_0.tar.bz2 +name : bioconductor-rsubread +version : 2.6.1 +build : r41hd029910_0 +build number: 0 +size : 11.1 MB +license : GPL (>=3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.6.1-r41hd029910_0.tar.bz2 +md5 : 633f020c3e4ac78de3929621a02dc286 +timestamp : 2021-05-31 06:43:04 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.1,<4.2.0a0 + - r-matrix + + +bioconductor-rsubread 2.8.0 r41hd029910_0 +----------------------------------------- +file name : bioconductor-rsubread-2.8.0-r41hd029910_0.tar.bz2 +name : bioconductor-rsubread +version : 2.8.0 +build : r41hd029910_0 +build number: 0 +size : 11.2 MB +license : GPL (>=3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.8.0-r41hd029910_0.tar.bz2 +md5 : a0de89b4e3370b3c9179be60d55069c0 +timestamp : 2021-11-01 17:01:35 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.4.0 + - liblapack >=3.8.0,<4.0a0 + - r-base >=4.1,<4.2.0a0 + - r-matrix + + +bioconductor-rsubread 2.8.1 r41h5c21468_0 +----------------------------------------- +file name : bioconductor-rsubread-2.8.1-r41h5c21468_0.tar.bz2 +name : bioconductor-rsubread +version : 2.8.1 +build : r41h5c21468_0 +build number: 0 +size : 11.2 MB +license : GPL (>=3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.8.1-r41h5c21468_0.tar.bz2 +md5 : 141bc9aee6b671f8785cf08d12aa32ee +timestamp : 2022-02-24 11:59:28 UTC +dependencies: + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=10.3.0 + - liblapack >=3.8.0,< diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-s4arrays.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-s4arrays.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..79a83d0ec7e3fe7304f56c00aa050ae6bd3ec19c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-s4arrays.manual_bundle.txt @@ -0,0 +1,226 @@ +# Tool: bioconductor-s4arrays +software_name: bioconductor-s4arrays +tier: T1 +domain: t1_backfill_overall +downloads: 324254 +summary: Foundation of array-like containers in Bioconductor +description: The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects). +dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-iranges >=2.44.0,<2.45.0, bioconductor-iranges >=2.44.0,<2.45.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-abind, r-base >=4.5,<4.6.0a0, r-matrix +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.17/bioc/html/S4Arrays.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.17/bioc/html/S4Arrays.html +Bioconductor - S4Arrays About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.17 Software Packages S4Arrays S4Arrays This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see S4Arrays . Foundation of array-like containers in Bioconductor DOI: 10.18129/B9.bioc.S4Arrays Bioconductor version: 3.17 The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects). Author: Hervé Pagès [aut, cre] Maintainer: Hervé Pagès <hpages.on.github at gmail.com> Citation (from within R, enter citation("S4Arrays") ): Installation To install this package, start R (version "4.3") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("S4Arrays") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("S4Arrays") A quick overview of the S4Arrays package HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataRepresentation , Infrastructure , Software Version 1.0.6 In Bioconductor since BioC 3.17 (R-4.3) (1 year) License Artistic-2.0 Depends R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>= 0.45.2), S4Vectors , IRanges Imports stats, crayon System Requirements URL https://bioconductor.org/packages/S4Arrays Bug Reports https://github.com/Bioconductor/S4Arrays/issues See More Suggests BiocParallel , SparseArray (>= 0.0.4), DelayedArray , testthat, knitr, rmarkdown, BiocStyle Linking To S4Vectors Enhances Depends On Me DelayedArray , SparseArray Imports Me HDF5Array , SummarizedExperiment Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package S4Arrays_1.0.6.tar.gz Windows Binary S4Arrays_1.0.6.zip macOS Binary (x86_64) S4Arrays_1.0.6.tgz macOS Binary (arm64) S4Arrays_1.0.6.tgz Source Repository git clone https://git.bioconductor.org/packages/S4Arrays Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/S4Arrays Bioc Package Browser https://code.bioconductor.org/browse/S4Arrays/ Package Short Url https://bioconductor.org/packages/S4Arrays/ Package Downloads Report Download Stats Old Source Packages for BioC 3.17 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-s4arrays --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-s4arrays 1.0.4 r43ha9d7317_0 +----------------------------------------- +file name : bioconductor-s4arrays-1.0.4-r43ha9d7317_0.tar.bz2 +name : bioconductor-s4arrays +version : 1.0.4 +build : r43ha9d7317_0 +build number: 0 +size : 785 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.0.4-r43ha9d7317_0.tar.bz2 +md5 : 53bb74ed857400d8ac101024cef98c7f +timestamp : 2023-07-10 19:52:18 UTC +dependencies: + - bioconductor-biocgenerics >=0.46.0,<0.47.0 + - bioconductor-iranges >=2.34.0,<2.35.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - r-base >=4.3,<4.4.0a0 + - r-crayon + - r-matrix + + +bioconductor-s4arrays 1.2.0 r43ha9d7317_0 +----------------------------------------- +file name : bioconductor-s4arrays-1.2.0-r43ha9d7317_0.tar.bz2 +name : bioconductor-s4arrays +version : 1.2.0 +build : r43ha9d7317_0 +build number: 0 +size : 797 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.2.0-r43ha9d7317_0.tar.bz2 +md5 : 49bd3e143d591f9f57895cec0211f05a +timestamp : 2023-12-03 02:12:46 UTC +dependencies: + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-biocgenerics >=0.48.1,<1.0a0 + - bioconductor-iranges >=2.36.0,<2.37.0 + - bioconductor-iranges >=2.36.0,<3.0a0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-s4vectors >=0.40.2,<1.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - r-abind + - r-base >=4.3,<4.4.0a0 + - r-crayon + - r-matrix + + +bioconductor-s4arrays 1.2.0 r43ha9d7317_1 +----------------------------------------- +file name : bioconductor-s4arrays-1.2.0-r43ha9d7317_1.tar.bz2 +name : bioconductor-s4arrays +version : 1.2.0 +build : r43ha9d7317_1 +build number: 1 +size : 795 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.2.0-r43ha9d7317_1.tar.bz2 +md5 : c952b3c0a456fe9d00e4378b40a478f7 +timestamp : 2023-12-06 04:55:03 UTC +dependencies: + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-biocgenerics >=0.48.1,<0.49.0a0 + - bioconductor-iranges >=2.36.0,<2.37.0 + - bioconductor-iranges >=2.36.0,<2.37.0a0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-s4vectors >=0.40.2,<0.41.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - r-abind + - r-base >=4.3,<4.4.0a0 + - r-crayon + - r-matrix + + +bioconductor-s4arrays 1.2.0 r43ha9d7317_2 +----------------------------------------- +file name : bioconductor-s4arrays-1.2.0-r43ha9d7317_2.tar.bz2 +name : bioconductor-s4arrays +version : 1.2.0 +build : r43ha9d7317_2 +build number: 2 +size : 796 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.2.0-r43ha9d7317_2.tar.bz2 +md5 : 28fd3fe7fd8d087c1cfa7805bbd16661 +timestamp : 2024-05-03 13:38:17 UTC +dependencies: + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-biocgenerics >=0.48.1,<0.49.0a0 + - bioconductor-iranges >=2.36.0,<2.37.0 + - bioconductor-iranges >=2.36.0,<2.37.0a0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-s4vectors >=0.40.2,<0.41.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - r-abind + - r-base >=4.3,<4.4.0a0 + - r-crayon + - r-matrix + + +bioconductor-s4arrays 1.6.0 r44h3df3fcb_0 +----------------------------------------- +file name : bioconductor-s4arrays-1.6.0-r44h3df3fcb_0.tar.bz2 +name : bioconductor-s4arrays +version : 1.6.0 +build : r44h3df3fcb_0 +build number: 0 +size : 1.0 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.6.0-r44h3df3fcb_0.tar.bz2 +md5 : 321539e20f732857eeda26f9ec5c9d9d +timestamp : 2024-12-18 23:54:18 UTC +dependencies: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0a0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0a0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=13 + - liblapack >=3.9.0,<4.0a0 + - r-abind + - r-base >=4.4,<4.5.0a0 + - r-crayon + - r-matrix + + +bioconductor-s4arrays 1.6.0 r44h3df3fcb_1 +----------------------------------------- +file name : bioconductor-s4arrays-1.6.0-r44h3df3fcb_1.tar.bz2 +name : bioconductor-s4arrays +version : 1.6.0 +build : r44h3df3fcb_1 +build number: 1 +size : 1.0 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.6.0-r44h3df3fcb_1.tar.bz2 +md5 : a6774527b21da1eb7a99b3839301ab57 +timestamp : 2025-04-14 20:33:09 UTC +dependencies: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0a0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0a0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=13 + - liblapack >=3.9.0,<4.0a0 + - r-abind + - r-base >=4.4,<4.5.0a0 + - r-crayon + - r-matrix + + +bioconductor-s4arrays 1.10.1 r45h01b2380_0 +------------------------------------------ +file name : bioconductor-s4arrays-1.10.1-r45h01b2380_0.conda +name : bioconductor-s4arrays +version : 1.10.1 +build : r45h01b2380_0 +build number: 0 +size : 1003 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.10.1-r45h01b2380_0.conda +md5 : 0b2ad083cc4002a36926c7c31be1c5c8 +timestamp : 2026-02-09 09:10:51 UTC +dependencies: + - bioconductor-biocgenerics >=0.56.0,<0.57.0 + - bioconductor-biocgenerics >=0.56.0,<0.57.0a0 + - bioconductor-iranges >=2.44.0,<2.45.0 + - bioconductor-iranges >=2.44.0,<2.45.0a0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=14 + - liblapack >=3.9.0,<4.0a0 + - liblzma >=5.8.2,<6.0a0 + - libzlib >=1.3.1,<2.0a0 + - r-abind + - r-base >=4.5,<4.6.0a0 + - r-matrix diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scannotatr.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scannotatr.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c3f802c5acca811cbbd903991bc6e3a54153e65d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scannotatr.manual_bundle.txt @@ -0,0 +1,203 @@ +# Tool: bioconductor-scannotatr +software_name: bioconductor-scannotatr +tier: T1 +domain: single_cell +downloads: 8244 +summary: Pretrained learning models for cell type prediction on single cell RNA-sequencing data +description: The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs. +dependencies: bioconductor-annotationhub >=4.0.0,<4.1.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-ape, r-base >=4.5,<4.6.0a0, r-caret, r-data.tree, r-dplyr, r-e1071, r-ggplot2, r-kernlab, r-proc, r-rocr, r-seurat +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.14/bioc/html/scAnnotatR.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.14/bioc/html/scAnnotatR.html +Bioconductor - scAnnotatR About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.14 Software Packages scAnnotatR scAnnotatR This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see scAnnotatR . Pretrained learning models for cell type prediction on single cell RNA-sequencing data DOI: 10.18129/B9.bioc.scAnnotatR Bioconductor version: 3.14 The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs. Author: Vy Nguyen [aut] , Johannes Griss [cre] Maintainer: Johannes Griss <johannes.griss at meduniwien.ac.at> Citation (from within R, enter citation("scAnnotatR") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scAnnotatR") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("scAnnotatR") 1. Introduction to scAnnotatR HTML R Script 2. Training basic model HTML R Script 3. Training child model HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews Classification , GeneExpression , SingleCell , Software , SupportVectorMachine , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.14 (R-4.1) (2.5 years) License MIT + file LICENSE Depends R (>= 4.1), Seurat, SingleCellExperiment , SummarizedExperiment Imports dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub , utils System Requirements URL https://github.com/grisslab/scAnnotatR Bug Reports https://github.com/grisslab/scAnnotatR/issues/new See More Suggests knitr, rmarkdown, scRNAseq , testthat Linking To Enhances Depends On Me Imports Me Suggests Me scAnnotatR.models Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package scAnnotatR_1.0.0.tar.gz Windows Binary scAnnotatR_1.0.0.zip macOS 10.13 (High Sierra) scAnnotatR_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/scAnnotatR Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scAnnotatR Bioc Package Browser https://code.bioconductor.org/browse/scAnnotatR/ Package Short Url https://bioconductor.org/packages/scAnnotatR/ Package Downloads Report Download Stats Old Source Packages for BioC 3.14 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-scannotatr --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-scannotatr 1.0.0 r41hdfd78af_0 +------------------------------------------- +file name : bioconductor-scannotatr-1.0.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-scannotatr +version : 1.0.0 +build : r41hdfd78af_0 +build number: 0 +size : 1.1 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.0.0-r41hdfd78af_0.tar.bz2 +md5 : 520a655cbf1037ead332fca8c41c65a6 +timestamp : 2021-11-06 23:51:31 UTC +dependencies: + - bioconductor-annotationhub >=3.2.0,<3.3.0 + - bioconductor-singlecellexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - r-ape + - r-base >=4.1,<4.2.0a0 + - r-caret + - r-data.tree + - r-dplyr + - r-e1071 + - r-ggplot2 + - r-kernlab + - r-proc + - r-rocr + - r-seurat + + +bioconductor-scannotatr 1.4.0 r42hdfd78af_0 +------------------------------------------- +file name : bioconductor-scannotatr-1.4.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-scannotatr +version : 1.4.0 +build : r42hdfd78af_0 +build number: 0 +size : 1.2 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.4.0-r42hdfd78af_0.tar.bz2 +md5 : d5156f24420bc2f8a5cd77f7f070cee6 +timestamp : 2022-11-08 01:15:21 UTC +dependencies: + - bioconductor-annotationhub >=3.6.0,<3.7.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - r-ape + - r-base >=4.2,<4.3.0a0 + - r-caret + - r-data.tree + - r-dplyr + - r-e1071 + - r-ggplot2 + - r-kernlab + - r-proc + - r-rocr + - r-seurat + + +bioconductor-scannotatr 1.6.0 r43hdfd78af_0 +------------------------------------------- +file name : bioconductor-scannotatr-1.6.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-scannotatr +version : 1.6.0 +build : r43hdfd78af_0 +build number: 0 +size : 986 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.6.0-r43hdfd78af_0.tar.bz2 +md5 : 87395666ef511874ed387f9f2c548d4f +timestamp : 2023-07-13 11:03:33 UTC +dependencies: + - bioconductor-annotationhub >=3.8.0,<3.9.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-ape + - r-base >=4.3,<4.4.0a0 + - r-caret + - r-data.tree + - r-dplyr + - r-e1071 + - r-ggplot2 + - r-kernlab + - r-proc + - r-rocr + - r-seurat + + +bioconductor-scannotatr 1.8.0 r43hdfd78af_0 +------------------------------------------- +file name : bioconductor-scannotatr-1.8.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-scannotatr +version : 1.8.0 +build : r43hdfd78af_0 +build number: 0 +size : 983 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.8.0-r43hdfd78af_0.tar.bz2 +md5 : 28ed4744724229c7a1f830d92fdf1951 +timestamp : 2023-12-06 23:00:06 UTC +dependencies: + - bioconductor-annotationhub >=3.10.0,<3.11.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-ape + - r-base >=4.3,<4.4.0a0 + - r-caret + - r-data.tree + - r-dplyr + - r-e1071 + - r-ggplot2 + - r-kernlab + - r-proc + - r-rocr + - r-seurat + + +bioconductor-scannotatr 1.12.0 r44hdfd78af_0 +-------------------------------------------- +file name : bioconductor-scannotatr-1.12.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-scannotatr +version : 1.12.0 +build : r44hdfd78af_0 +build number: 0 +size : 1.0 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.12.0-r44hdfd78af_0.tar.bz2 +md5 : 4f75fb4bb59eba9320090d9f427983ae +timestamp : 2025-01-04 03:20:24 UTC +dependencies: + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-ape + - r-base >=4.4,<4.5.0a0 + - r-caret + - r-data.tree + - r-dplyr + - r-e1071 + - r-ggplot2 + - r-kernlab + - r-proc + - r-rocr + - r-seurat + + +bioconductor-scannotatr 1.16.0 r45hdfd78af_0 +-------------------------------------------- +file name : bioconductor-scannotatr-1.16.0-r45hdfd78af_0.conda +name : bioconductor-scannotatr +version : 1.16.0 +build : r45hdfd78af_0 +build number: 0 +size : 940 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.16.0-r45hdfd78af_0.conda +md5 : fe588d26acba6000fe3f92b5596b4110 +timestamp : 2026-03-01 13:26:25 UTC +dependencies: + - bioconductor-annotationhub >=4.0.0,<4.1.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-ape + - r-base >=4.5,<4.6.0a0 + - r-caret + - r-data.tree + - r-dplyr + - r-e1071 + - r-ggplot2 + - r-kernlab + - r-proc + - r-rocr + - r-seurat diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scbubbletree.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scbubbletree.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..fca1904b911b4f62cbb7335a594dda895f569c0d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scbubbletree.manual_bundle.txt @@ -0,0 +1,157 @@ +# Tool: bioconductor-scbubbletree +software_name: bioconductor-scbubbletree +tier: T1 +domain: single_cell +downloads: 4317 +summary: Quantitative visual exploration of scRNA-seq data +description: scBubbletree is a quantitative method for the visual exploration of scRNA-seq data, preserving key biological properties such as local and global cell distances and cell density distributions across samples. It effectively resolves overplotting and enables the visualization of diverse cell attributes from multiomic single-cell experiments. Additionally, scBubbletree is user-friendly and integrates seamlessly with popular scRNA-seq analysis tools, facilitating comprehensive and intuitive data interpretation. +dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-ggtree >=4.0.0,<4.1.0, r-ape, r-base >=4.5,<4.6.0a0, r-dplyr, r-ggplot2, r-patchwork, r-proxy, r-reshape2, r-scales, r-seurat +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.16/bioc/html/scBubbletree.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.16/bioc/html/scBubbletree.html +Bioconductor - scBubbletree About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Software Packages scBubbletree scBubbletree This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scBubbletree . Quantitative visual exploration of scRNA-seq data DOI: 10.18129/B9.bioc.scBubbletree Bioconductor version: 3.16 scBubbletree is a quantitative method for visual exploration of scRNA-seq data. It preserves biologically meaningful properties of scRNA-seq data, such as local and global cell distances, as well as the density distribution of cells across the sample. scBubbletree is scalable and avoids the overplotting problem, and is able to visualize diverse cell attributes derived from multiomic single-cell experiments. Importantly, Importantly, scBubbletree is easy to use and to integrate with popular approaches for scRNA-seq data analysis. Author: Simo Kitanovski [aut, cre] Maintainer: Simo Kitanovski <simokitanovski at gmail.com> Citation (from within R, enter citation("scBubbletree") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scBubbletree") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("scBubbletree") User Manual: scBubbletree HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews Clustering , RNASeq , SingleCell , Software , Transcriptomics , Visualization Version 1.0.0 In Bioconductor since BioC 3.16 (R-4.2) (1.5 years) License GPL-3 + file LICENSE Depends R (>= 4.2.0) Imports reshape2, future, future.apply, ape, scales, Seurat, ggplot2, ggtree , patchwork, methods, stats, base, utils System Requirements Python (>= 3.6), leidenalg (>= 0.8.2) URL https://github.com/snaketron/scBubbletree Bug Reports https://github.com/snaketron/scBubbletree/issues See More Suggests BiocStyle , knitr, testthat, cluster, SingleCellExperiment Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package scBubbletree_1.0.0.tar.gz Windows Binary scBubbletree_1.0.0.zip macOS Binary (x86_64) scBubbletree_1.0.0.tgz macOS Binary (arm64) scBubbletree_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/scBubbletree Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scBubbletree Bioc Package Browser https://code.bioconductor.org/browse/scBubbletree/ Package Short Url https://bioconductor.org/packages/scBubbletree/ Package Downloads Report Download Stats Old Source Packages for BioC 3.16 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-scbubbletree --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-scbubbletree 1.0.0 r42hdfd78af_0 +--------------------------------------------- +file name : bioconductor-scbubbletree-1.0.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-scbubbletree +version : 1.0.0 +build : r42hdfd78af_0 +build number: 0 +size : 2.3 MB +license : GPL-3 + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scbubbletree-1.0.0-r42hdfd78af_0.tar.bz2 +md5 : 00cbfef68aacff3c7dde5c5f9ac23556 +timestamp : 2022-11-03 11:43:06 UTC +dependencies: + - bioconductor-ggtree >=3.6.0,<3.7.0 + - r-ape + - r-base >=4.2,<4.3.0a0 + - r-future + - r-future.apply + - r-ggplot2 + - r-patchwork + - r-reshape2 + - r-scales + - r-seurat + + +bioconductor-scbubbletree 1.2.0 r43hdfd78af_0 +--------------------------------------------- +file name : bioconductor-scbubbletree-1.2.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-scbubbletree +version : 1.2.0 +build : r43hdfd78af_0 +build number: 0 +size : 2.3 MB +license : GPL-3 + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scbubbletree-1.2.0-r43hdfd78af_0.tar.bz2 +md5 : 909b65b3865909f6955e4349c0096718 +timestamp : 2023-07-07 16:23:12 UTC +dependencies: + - bioconductor-ggtree >=3.8.0,<3.9.0 + - r-ape + - r-base >=4.3,<4.4.0a0 + - r-future + - r-future.apply + - r-ggplot2 + - r-patchwork + - r-proxy + - r-reshape2 + - r-scales + - r-seurat + + +bioconductor-scbubbletree 1.4.0 r43hdfd78af_0 +--------------------------------------------- +file name : bioconductor-scbubbletree-1.4.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-scbubbletree +version : 1.4.0 +build : r43hdfd78af_0 +build number: 0 +size : 2.3 MB +license : GPL-3 + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scbubbletree-1.4.0-r43hdfd78af_0.tar.bz2 +md5 : db6faa909e6a47b4fc6f9ebe63f4bc98 +timestamp : 2023-12-04 21:16:44 UTC +dependencies: + - bioconductor-ggtree >=3.10.0,<3.11.0 + - r-ape + - r-base >=4.3,<4.4.0a0 + - r-future + - r-future.apply + - r-ggplot2 + - r-patchwork + - r-proxy + - r-reshape2 + - r-scales + - r-seurat + + +bioconductor-scbubbletree 1.8.0 r44hdfd78af_0 +--------------------------------------------- +file name : bioconductor-scbubbletree-1.8.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-scbubbletree +version : 1.8.0 +build : r44hdfd78af_0 +build number: 0 +size : 2.9 MB +license : GPL-3 + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scbubbletree-1.8.0-r44hdfd78af_0.tar.bz2 +md5 : ec39386c93cb499570c1f4cbf58fd1be +timestamp : 2024-12-15 01:58:05 UTC +dependencies: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - r-ape + - r-base >=4.4,<4.5.0a0 + - r-dplyr + - r-ggplot2 + - r-patchwork + - r-proxy + - r-reshape2 + - r-scales + - r-seurat + + +bioconductor-scbubbletree 1.12.0 r45hdfd78af_0 +---------------------------------------------- +file name : bioconductor-scbubbletree-1.12.0-r45hdfd78af_0.conda +name : bioconductor-scbubbletree +version : 1.12.0 +build : r45hdfd78af_0 +build number: 0 +size : 2.8 MB +license : GPL-3 + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scbubbletree-1.12.0-r45hdfd78af_0.conda +md5 : 5f20528d389efe621f8c7e7dd608058c +timestamp : 2026-02-08 20:37:25 UTC +dependencies: + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-ggtree >=4.0.0,<4.1.0 + - r-ape + - r-base >=4.5,<4.6.0a0 + - r-dplyr + - r-ggplot2 + - r-patchwork + - r-proxy + - r-reshape2 + - r-scales + - r-seurat diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scfeatures.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scfeatures.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e6f86e9f18d09200ab90207bbee32e62c8e4605 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scfeatures.manual_bundle.txt @@ -0,0 +1,150 @@ +# Tool: bioconductor-scfeatures +software_name: bioconductor-scfeatures +tier: T1 +domain: single_cell +downloads: 3092 +summary: scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction +description: scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor. +dependencies: bioconductor-aucell >=1.28.0,<1.29.0, bioconductor-biocparallel >=1.40.0,<1.41.0, bioconductor-delayedarray >=0.32.0,<0.33.0, bioconductor-delayedmatrixstats >=1.28.0,<1.29.0, bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0, bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0, bioconductor-ensembldb >=2.30.0,<2.31.0, bioconductor-gsva >=2.0.0,<2.1.0, bioconductor-matrixgenerics >=1.18.0,<1.19.0, bioconductor-singlecellsignalr >=1.18.0,<1.19.0, r-ape, r-base >=4.4,<4.5.0a0, r-cli, r-dplyr, r-dt, r-glue, r-gtools, r-msigdbr, r-proxyc, r-reshape2, r-rmarkdown, r-seurat, r-spatstat.explore, r-spatstat.geom, r-tidyr +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.17/bioc/html/scFeatures.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.17/bioc/html/scFeatures.html +Bioconductor - scFeatures About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.17 Software Packages scFeatures scFeatures This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see scFeatures . scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction DOI: 10.18129/B9.bioc.scFeatures Bioconductor version: 3.17 scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor. Author: Yue Cao [aut, cre], Yingxin Lin [aut], Ellis Patrick [aut], Pengyi Yang [aut], Jean Yee Hwa Yang [aut] Maintainer: Yue Cao <yue.cao at sydney.edu.au> Citation (from within R, enter citation("scFeatures") ): Installation To install this package, start R (version "4.3") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scFeatures") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("scFeatures") Overview of scFeatures with case studies HTML R Script Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews CellBasedAssays , SingleCell , Software , Spatial , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.17 (R-4.3) (1 year) License GPL-3 Depends R (>= 4.2.0) Imports DelayedArray , DelayedMatrixStats , EnsDb.Hsapiens.v79 , EnsDb.Mmusculus.v79 , GSVA , Seurat, ape, glue, dplyr, ensembldb , gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell , BiocParallel , SpatialExperiment , SummarizedExperiment , rmarkdown, methods, stats, DT, cli, SingleCellSignalR , MatrixGenerics System Requirements URL Bug Reports https://github.com/SydneyBioX/scFeatures/issues See More Suggests knitr, S4Vectors , survival, survminer, BiocStyle , ClassifyR , org.Hs.eg.db , clusterProfiler Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package scFeatures_1.0.0.tar.gz Windows Binary scFeatures_1.0.0.zip macOS Binary (x86_64) scFeatures_1.0.0.tgz macOS Binary (arm64) scFeatures_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/scFeatures Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scFeatures Bioc Package Browser https://code.bioconductor.org/browse/scFeatures/ Package Short Url https://bioconductor.org/packages/scFeatures/ Package Downloads Report Download Stats Old Source Packages for BioC 3.17 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-scfeatures --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-scfeatures 1.0.0 r43hdfd78af_0 +------------------------------------------- +file name : bioconductor-scfeatures-1.0.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-scfeatures +version : 1.0.0 +build : r43hdfd78af_0 +build number: 0 +size : 3.2 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scfeatures-1.0.0-r43hdfd78af_0.tar.bz2 +md5 : 2dc063889e0849feb1b76ac37b727a4e +timestamp : 2023-07-19 11:49:57 UTC +dependencies: + - bioconductor-aucell >=1.22.0,<1.23.0 + - bioconductor-biocparallel >=1.34.0,<1.35.0 + - bioconductor-delayedarray >=0.26.0,<0.27.0 + - bioconductor-delayedmatrixstats >=1.22.0,<1.23.0 + - bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0 + - bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0 + - bioconductor-ensembldb >=2.24.0,<2.25.0 + - bioconductor-gsva >=1.48.0,<1.49.0 + - bioconductor-matrixgenerics >=1.12.0,<1.13.0 + - bioconductor-singlecellsignalr >=1.12.0,<1.13.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-ape + - r-base >=4.3,<4.4.0a0 + - r-cli + - r-dplyr + - r-dt + - r-glue + - r-gtools + - r-msigdbr + - r-proxyc + - r-reshape2 + - r-rmarkdown + - r-seurat + - r-spatstat.explore + - r-spatstat.geom + - r-tidyr + + +bioconductor-scfeatures 1.2.0 r43hdfd78af_0 +------------------------------------------- +file name : bioconductor-scfeatures-1.2.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-scfeatures +version : 1.2.0 +build : r43hdfd78af_0 +build number: 0 +size : 3.2 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scfeatures-1.2.0-r43hdfd78af_0.tar.bz2 +md5 : 4ae2a029c905467547a7ec7eee0dcec7 +timestamp : 2023-12-19 18:08:04 UTC +dependencies: + - bioconductor-aucell >=1.24.0,<1.25.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - bioconductor-delayedarray >=0.28.0,<0.29.0 + - bioconductor-delayedmatrixstats >=1.24.0,<1.25.0 + - bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0 + - bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0 + - bioconductor-ensembldb >=2.26.0,<2.27.0 + - bioconductor-gsva >=1.50.0,<1.51.0 + - bioconductor-matrixgenerics >=1.14.0,<1.15.0 + - bioconductor-singlecellsignalr >=1.14.0,<1.15.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-ape + - r-base >=4.3,<4.4.0a0 + - r-cli + - r-dplyr + - r-dt + - r-glue + - r-gtools + - r-msigdbr + - r-proxyc + - r-reshape2 + - r-rmarkdown + - r-seurat + - r-spatstat.explore + - r-spatstat.geom + - r-tidyr + + +bioconductor-scfeatures 1.6.0 r44hdfd78af_0 +------------------------------------------- +file name : bioconductor-scfeatures-1.6.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-scfeatures +version : 1.6.0 +build : r44hdfd78af_0 +build number: 0 +size : 3.2 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scfeatures-1.6.0-r44hdfd78af_0.tar.bz2 +md5 : f378e7ede0ececa75394acdf3e7d54b8 +timestamp : 2025-01-05 05:38:06 UTC +dependencies: + - bioconductor-aucell >=1.28.0,<1.29.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0 + - bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-gsva >=2.0.0,<2.1.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellsignalr >=1.18.0,<1.19.0 + - r-ape + - r-base >=4.4,<4.5.0a0 + - r-cli + - r-dplyr + - r-dt + - r-glue + - r-gtools + - r-msigdbr + - r-proxyc + - r-reshape2 + - r-rmarkdown + - r-seurat + - r-spatstat.explore + - r-spatstat.geom + - r-tidyr diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scqtltools.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scqtltools.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ee13d7b57f0846bcaf177574f7ab428182219497 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scqtltools.manual_bundle.txt @@ -0,0 +1,56 @@ +# Tool: bioconductor-scqtltools +software_name: bioconductor-scqtltools +tier: T1 +domain: single_cell +downloads: 29 +summary: scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs +description: scQTLtools is a comprehensive R/Bioconductor package that facilitates end-to-end single-cell eQTL analysis, from preprocessing to visualization +dependencies: bioconductor-biomart >=2.66.0,<2.67.0, bioconductor-deseq2 >=1.50.0,<1.51.0, bioconductor-limma >=3.66.0,<3.67.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-dplyr >=1.1.4, r-gamlss >=5.4-22, r-ggplot2 >=3.5.1, r-magrittr >=2.0.3, r-matrix >=1.7-0, r-patchwork >=1.2.0, r-progress >=1.2.3, r-seuratobject >=5.0.2, r-stringr >=1.5.1, r-vgam >=1.1-11, r-yulab.utils >=0.2.3 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/scQTLtools.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/scQTLtools.html +Bioconductor - scQTLtools Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages scQTLtools scQTLtools This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see scQTLtools . scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs DOI: 10.18129/B9.bioc.scQTLtools Bioconductor version: 3.22 scQTLtools is a comprehensive R/Bioconductor package that facilitates end-to-end single-cell eQTL analysis, from preprocessing to visualization Author: Xiaofeng Wu [aut, cre, cph] ORCID: 0009-0003-6254-5575 , Xin Huang [aut, cph] ORCID: 0009-0005-2755-0357 , Jingtong Kang [com] ORCID: 0009-0008-8343-3456 , Siwen Xu [aut, cph] ORCID: 0000-0001-7936-0639 Maintainer: Xiaofeng Wu <1427972815 at qq.com> Citation (from within R, enter citation("scQTLtools") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scQTLtools") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("scQTLtools") scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DifferentialExpression , FunctionalGenomics , GeneExpression , GeneticVariability , Genetics , GenomicVariation , Normalization , Preprocessing , Regression , SNP , SingleCell , Software , SystemsBiology , VariantDetection , Visualization Version 1.2.4 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License MIT + file LICENSE Depends R (>= 4.4.1.0) Imports ggplot2 (>= 3.5.1), Matrix (>= 1.7-0), stats (>= 4.4.1), progress (>= 1.2.3), stringr (>= 1.5.1), dplyr (>= 1.1.4), SeuratObject (>= 5.0.2), methods (>= 4.4.1), magrittr (>= 2.0.3), patchwork (>= 1.2.0), DESeq2 (>= 1.45.3), VGAM (>= 1.1-11), limma (>= 3.61.9), biomaRt (>= 2.61.3), gamlss (>= 5.4-22), SingleCellExperiment (>= 1.27.2), SummarizedExperiment (>= 1.32.0), yulab.utils (>= 0.2.3) System Requirements URL https://github.com/XFWuCN/scQTLtools Bug Reports https://github.com/XFWuCN/scQTLtools/issues See More Suggests BiocStyle , knitr , rmarkdown , org.Hs.eg.db , org.Mm.eg.db , org.Ce.eg.db , org.At.tair.db , testthat (>= 3.2.1.1) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package scQTLtools_1.2.4.tar.gz Windows Binary (x86_64) scQTLtools_1.2.4.zip macOS Binary (x86_64) scQTLtools_1.2.4.tgz macOS Binary (arm64) scQTLtools_1.2.4.tgz Source Repository git clone https://git.bioconductor.org/packages/scQTLtools Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scQTLtools Bioc Package Browser https://code.bioconductor.org/browse/scQTLtools/ Package Short Url https://bioconductor.org/packages/scQTLtools/ Package Downloads Report Download Stats Old Source Packages for BioC 3.22 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-scqtltools --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-scqtltools 1.2.4 r45hdfd78af_0 +------------------------------------------- +file name : bioconductor-scqtltools-1.2.4-r45hdfd78af_0.conda +name : bioconductor-scqtltools +version : 1.2.4 +build : r45hdfd78af_0 +build number: 0 +size : 3.1 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-scqtltools-1.2.4-r45hdfd78af_0.conda +md5 : dd05a4e55799cb79063f145fe7eec976 +timestamp : 2026-03-01 09:28:21 UTC +dependencies: + - bioconductor-biomart >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.50.0,<1.51.0 + - bioconductor-limma >=3.66.0,<3.67.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-dplyr >=1.1.4 + - r-gamlss >=5.4-22 + - r-ggplot2 >=3.5.1 + - r-magrittr >=2.0.3 + - r-matrix >=1.7-0 + - r-patchwork >=1.2.0 + - r-progress >=1.2.3 + - r-seuratobject >=5.0.2 + - r-stringr >=1.5.1 + - r-vgam >=1.1-11 + - r-yulab.utils >=0.2.3 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-sctreeviz.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-sctreeviz.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e331a8a6786b0741df2fc74d0a20a9dd5298414 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-sctreeviz.manual_bundle.txt @@ -0,0 +1,239 @@ +# Tool: bioconductor-sctreeviz +software_name: bioconductor-sctreeviz +tier: T1 +domain: single_cell +downloads: 6119 +summary: R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations +description: scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The `TreeIndex` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The `TreeViz` class extends `SummarizedExperiment` and can performs quick aggregations on the count matrix defined by clusters. +dependencies: bioconductor-epivizr >=2.40.0,<2.41.0, bioconductor-epivizrdata >=1.38.0,<1.39.0, bioconductor-epivizrserver >=1.38.0,<1.39.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scater >=1.38.0,<1.39.0, bioconductor-scran >=1.38.0,<1.39.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-clustree, r-data.table, r-digest, r-ggplot2, r-ggraph, r-httr, r-igraph, r-matrix, r-rtsne, r-seurat, r-sys +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.14/bioc/html/scTreeViz.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.14/bioc/html/scTreeViz.html +Bioconductor - scTreeViz About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.14 Software Packages scTreeViz scTreeViz This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see scTreeViz . R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations DOI: 10.18129/B9.bioc.scTreeViz Bioconductor version: 3.14 scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The `TreeIndex` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The `TreeViz` class extends `SummarizedExperiment` and can performs quick aggregations on the count matrix defined by clusters. Author: Jayaram Kancherla [aut, cre], Hector Corrada Bravo [aut], Kazi Tasnim Zinat [aut], Stephanie Hicks [aut] Maintainer: Jayaram Kancherla <jayaram.kancherla at gmail.com> Citation (from within R, enter citation("scTreeViz") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scTreeViz") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("scTreeViz") Explore Data using scTreeViz HTML R Script Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews GUI , Infrastructure , SingleCell , Software , Visualization Version 1.0.0 In Bioconductor since BioC 3.14 (R-4.1) (2.5 years) License Artistic-2.0 Depends R (>= 4.0), methods, epivizr , SummarizedExperiment Imports data.table, S4Vectors , digest, Matrix, Rtsne, httr, igraph, clustree, scran , sys, epivizrData , epivizrServer , ggraph, scater , Seurat, SingleCellExperiment , ggplot2, stats, utils System Requirements URL See More Suggests knitr, BiocStyle , testthat, SC3 , scRNAseq , rmarkdown, msd16s , metagenomeSeq , epivizrStandalone , GenomeInfoDb Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package scTreeViz_1.0.0.tar.gz Windows Binary scTreeViz_1.0.0.zip macOS 10.13 (High Sierra) scTreeViz_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/scTreeViz Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scTreeViz Bioc Package Browser https://code.bioconductor.org/browse/scTreeViz/ Package Short Url https://bioconductor.org/packages/scTreeViz/ Package Downloads Report Download Stats Old Source Packages for BioC 3.14 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-sctreeviz --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-sctreeviz 1.0.0 r41hdfd78af_0 +------------------------------------------ +file name : bioconductor-sctreeviz-1.0.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-sctreeviz +version : 1.0.0 +build : r41hdfd78af_0 +build number: 0 +size : 2.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-sctreeviz-1.0.0-r41hdfd78af_0.tar.bz2 +md5 : e9667e38af392cd73c5b0d21fdc51138 +timestamp : 2021-11-09 14:18:03 UTC +dependencies: + - bioconductor-epivizr >=2.24.0,<2.25.0 + - bioconductor-epivizrdata >=1.22.0,<1.23.0 + - bioconductor-epivizrserver >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-scater >=1.22.0,<1.23.0 + - bioconductor-scran >=1.22.0,<1.23.0 + - bioconductor-singlecellexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - r-base >=4.1,<4.2.0a0 + - r-clustree + - r-data.table + - r-digest + - r-ggplot2 + - r-ggraph + - r-httr + - r-igraph + - r-matrix + - r-rtsne + - r-seurat + - r-sys + + +bioconductor-sctreeviz 1.4.0 r42hdfd78af_0 +------------------------------------------ +file name : bioconductor-sctreeviz-1.4.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-sctreeviz +version : 1.4.0 +build : r42hdfd78af_0 +build number: 0 +size : 2.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-sctreeviz-1.4.0-r42hdfd78af_0.tar.bz2 +md5 : 0d67540754dcdfd5af90f60213b3ea78 +timestamp : 2022-11-08 19:01:25 UTC +dependencies: + - bioconductor-epivizr >=2.28.0,<2.29.0 + - bioconductor-epivizrdata >=1.26.0,<1.27.0 + - bioconductor-epivizrserver >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-scater >=1.26.0,<1.27.0 + - bioconductor-scran >=1.26.0,<1.27.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - r-base >=4.2,<4.3.0a0 + - r-clustree + - r-data.table + - r-digest + - r-ggplot2 + - r-ggraph + - r-httr + - r-igraph + - r-matrix + - r-rtsne + - r-seurat + - r-sys + + +bioconductor-sctreeviz 1.6.0 r43hdfd78af_0 +------------------------------------------ +file name : bioconductor-sctreeviz-1.6.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-sctreeviz +version : 1.6.0 +build : r43hdfd78af_0 +build number: 0 +size : 2.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-sctreeviz-1.6.0-r43hdfd78af_0.tar.bz2 +md5 : 8d9d11d82f6738415c9897d096cf9d57 +timestamp : 2023-07-19 12:24:43 UTC +dependencies: + - bioconductor-epivizr >=2.30.0,<2.31.0 + - bioconductor-epivizrdata >=1.28.0,<1.29.0 + - bioconductor-epivizrserver >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-scater >=1.28.0,<1.29.0 + - bioconductor-scran >=1.28.0,<1.29.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-base >=4.3,<4.4.0a0 + - r-clustree + - r-data.table + - r-digest + - r-ggplot2 + - r-ggraph + - r-httr + - r-igraph + - r-matrix + - r-rtsne + - r-seurat + - r-sys + + +bioconductor-sctreeviz 1.8.0 r43hdfd78af_0 +------------------------------------------ +file name : bioconductor-sctreeviz-1.8.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-sctreeviz +version : 1.8.0 +build : r43hdfd78af_0 +build number: 0 +size : 2.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-sctreeviz-1.8.0-r43hdfd78af_0.tar.bz2 +md5 : df411d163487889ed516cb7ff981dd83 +timestamp : 2023-12-13 00:24:05 UTC +dependencies: + - bioconductor-epivizr >=2.32.0,<2.33.0 + - bioconductor-epivizrdata >=1.30.0,<1.31.0 + - bioconductor-epivizrserver >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-scater >=1.30.0,<1.31.0 + - bioconductor-scran >=1.30.0,<1.31.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-base >=4.3,<4.4.0a0 + - r-clustree + - r-data.table + - r-digest + - r-ggplot2 + - r-ggraph + - r-httr + - r-igraph + - r-matrix + - r-rtsne + - r-seurat + - r-sys + + +bioconductor-sctreeviz 1.12.0 r44hdfd78af_0 +------------------------------------------- +file name : bioconductor-sctreeviz-1.12.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-sctreeviz +version : 1.12.0 +build : r44hdfd78af_0 +build number: 0 +size : 2.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-sctreeviz-1.12.0-r44hdfd78af_0.tar.bz2 +md5 : c01a5f54f5d459069ebd934ec5f11459 +timestamp : 2024-12-29 01:21:35 UTC +dependencies: + - bioconductor-epivizr >=2.36.0,<2.37.0 + - bioconductor-epivizrdata >=1.34.0,<1.35.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base >=4.4,<4.5.0a0 + - r-clustree + - r-data.table + - r-digest + - r-ggplot2 + - r-ggraph + - r-httr + - r-igraph + - r-matrix + - r-rtsne + - r-seurat + - r-sys + + +bioconductor-sctreeviz 1.16.0 r45hdfd78af_0 +------------------------------------------- +file name : bioconductor-sctreeviz-1.16.0-r45hdfd78af_0.conda +name : bioconductor-sctreeviz +version : 1.16.0 +build : r45hdfd78af_0 +build number: 0 +size : 2.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-sctreeviz-1.16.0-r45hdfd78af_0.conda +md5 : 8c285c2792a9d652ff956bf1230e12f5 +timestamp : 2026-03-03 21:31:50 UTC +dependencies: + - bioconductor-epivizr >=2.40.0,<2.41.0 + - bioconductor-epivizrdata >=1.38.0,<1.39.0 + - bioconductor-epivizrserver >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-scater >=1.38.0,<1.39.0 + - bioconductor-scran >=1.38.0,<1.39.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-clustree + - r-data.table + - r-digest + - r-ggplot2 + - r-ggraph + - r-httr + - r-igraph + - r-matrix + - r-rtsne + - r-seurat + - r-sys diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scuttle.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scuttle.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..17c375b7e505d9e4d5d2d679653f192ff3fb9ff3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scuttle.manual_bundle.txt @@ -0,0 +1,365 @@ +# Tool: bioconductor-scuttle +software_name: bioconductor-scuttle +tier: T1 +domain: t1_backfill_overall +downloads: 467288 +summary: Single-Cell RNA-Seq Analysis Utilities +description: Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages. +dependencies: bioconductor-beachmat >=2.26.0,<2.27.0, bioconductor-beachmat >=2.26.0,<2.27.0a0, bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-biocparallel >=1.44.0,<1.45.0a0, bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-delayedarray >=0.36.0,<0.37.0a0, bioconductor-genomicranges >=1.62.0,<1.63.0, bioconductor-genomicranges >=1.62.1,<1.63.0a0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0a0, bioconductor-s4arrays >=1.10.0,<1.11.0, bioconductor-s4arrays >=1.10.1,<1.11.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0, bioconductor-sparsearray >=1.10.0,<1.11.0, bioconductor-sparsearray >=1.10.8,<1.11.0a0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-matrix, r-rcpp +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.12/bioc/html/scuttle.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.12/bioc/html/scuttle.html +Bioconductor - scuttle About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.12 Software Packages scuttle scuttle This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see scuttle . Single-Cell RNA-Seq Analysis Utilities DOI: 10.18129/B9.bioc.scuttle Bioconductor version: 3.12 Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages. Author: Aaron Lun [aut, cre], Davis McCarthy [aut] Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com> Citation (from within R, enter citation("scuttle") ): Installation To install this package, start R (version "4.0") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scuttle") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("scuttle") Package overview HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataImport , GeneExpression , ImmunoOncology , Normalization , Preprocessing , QualityControl , RNASeq , Sequencing , SingleCell , Software , Transcriptomics Version 1.0.4 In Bioconductor since BioC 3.12 (R-4.0) (3.5 years) License GPL-3 Depends SingleCellExperiment Imports methods, utils, stats, Matrix, Rcpp, BiocGenerics , S4Vectors , BiocParallel , GenomicRanges , SummarizedExperiment , DelayedArray , DelayedMatrixStats , beachmat System Requirements C++11 URL See More Suggests BiocStyle , knitr, scRNAseq , rmarkdown, testthat Linking To Rcpp, beachmat Enhances Depends On Me Imports Me batchelor , DropletUtils , scater , scDblFinder , scran , velociraptor Suggests Me bluster , HCAData , SingleR , snifter , splatter , TSCAN Links To Me DropletUtils , scran Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package scuttle_1.0.4.tar.gz Windows Binary scuttle_1.0.4.zip (32- & 64-bit) macOS 10.13 (High Sierra) scuttle_1.0.4.tgz Source Repository git clone https://git.bioconductor.org/packages/scuttle Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scuttle Bioc Package Browser https://code.bioconductor.org/browse/scuttle/ Package Short Url https://bioconductor.org/packages/scuttle/ Package Downloads Report Download Stats Old Source Packages for BioC 3.12 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-scuttle --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-scuttle 1.0.0 r40h5f743cb_0 +---------------------------------------- +file name : bioconductor-scuttle-1.0.0-r40h5f743cb_0.tar.bz2 +name : bioconductor-scuttle +version : 1.0.0 +build : r40h5f743cb_0 +build number: 0 +size : 681 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-scuttle-1.0.0-r40h5f743cb_0.tar.bz2 +md5 : ad2e28e98eedae8c4520e308993911f0 +timestamp : 2020-10-30 23:45:44 UTC +dependencies: + - bioconductor-beachmat >=2.6.0,<2.7.0 + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - bioconductor-biocparallel >=1.24.0,<1.25.0 + - bioconductor-delayedarray >=0.16.0,<0.17.0 + - bioconductor-delayedmatrixstats >=1.12.0,<1.13.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - bioconductor-singlecellexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.20.0,<1.21.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=7.5.0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + - r-rcpp + + +bioconductor-scuttle 1.0.4 r40h399db7b_0 +---------------------------------------- +file name : bioconductor-scuttle-1.0.4-r40h399db7b_0.tar.bz2 +name : bioconductor-scuttle +version : 1.0.4 +build : r40h399db7b_0 +build number: 0 +size : 685 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-scuttle-1.0.4-r40h399db7b_0.tar.bz2 +md5 : 46a51da7052a4bbbd2aef7e6003293b0 +timestamp : 2021-03-30 14:54:11 UTC +dependencies: + - bioconductor-beachmat >=2.6.0,<2.7.0 + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - bioconductor-biocparallel >=1.24.0,<1.25.0 + - bioconductor-delayedarray >=0.16.0,<0.17.0 + - bioconductor-delayedmatrixstats >=1.12.0,<1.13.0 + - bioconductor-genomicranges >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - bioconductor-singlecellexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.20.0,<1.21.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.0,<4.1.0a0 + - r-matrix + - r-rcpp + + +bioconductor-scuttle 1.2.0 r41h399db7b_0 +---------------------------------------- +file name : bioconductor-scuttle-1.2.0-r41h399db7b_0.tar.bz2 +name : bioconductor-scuttle +version : 1.2.0 +build : r41h399db7b_0 +build number: 0 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-scuttle-1.2.0-r41h399db7b_0.tar.bz2 +md5 : a02eca4e453c6132e023eb41f39459f9 +timestamp : 2021-06-03 07:04:56 UTC +dependencies: + - bioconductor-beachmat >=2.8.0,<2.9.0 + - bioconductor-biocgenerics >=0.38.0,<0.39.0 + - bioconductor-biocparallel >=1.26.0,<1.27.0 + - bioconductor-delayedarray >=0.18.0,<0.19.0 + - bioconductor-delayedmatrixstats >=1.14.0,<1.15.0 + - bioconductor-genomicranges >=1.44.0,<1.45.0 + - bioconductor-s4vectors >=0.30.0,<0.31.0 + - bioconductor-singlecellexperiment >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.22.0,<1.23.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.3.0 + - r-base >=4.1,<4.2.0a0 + - r-matrix + - r-rcpp + + +bioconductor-scuttle 1.4.0 r41h399db7b_0 +---------------------------------------- +file name : bioconductor-scuttle-1.4.0-r41h399db7b_0.tar.bz2 +name : bioconductor-scuttle +version : 1.4.0 +build : r41h399db7b_0 +build number: 0 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-scuttle-1.4.0-r41h399db7b_0.tar.bz2 +md5 : 64b0ce32f5aefe2a936698b7f68f50a0 +timestamp : 2021-11-05 13:30:46 UTC +dependencies: + - bioconductor-beachmat >=2.10.0,<2.11.0 + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-delayedmatrixstats >=1.16.0,<1.17.0 + - bioconductor-genomicranges >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.4.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=9.4.0 + - r-base >=4.1,<4.2.0a0 + - r-matrix + - r-rcpp + + +bioconductor-scuttle 1.4.0 r41h619a076_1 +---------------------------------------- +file name : bioconductor-scuttle-1.4.0-r41h619a076_1.tar.bz2 +name : bioconductor-scuttle +version : 1.4.0 +build : r41h619a076_1 +build number: 1 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-scuttle-1.4.0-r41h619a076_1.tar.bz2 +md5 : 3316de54b38a4f4d7e26d43a5a480432 +timestamp : 2022-02-28 07:10:26 UTC +dependencies: + - bioconductor-beachmat >=2.10.0,<2.11.0 + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-delayedmatrixstats >=1.16.0,<1.17.0 + - bioconductor-genomicranges >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=10.3.0 + - liblapack >=3.8.0,<4.0a0 + - libstdcxx-ng >=10.3.0 + - r-base >=4.1,<4.2.0a0 + - r-matrix + - r-rcpp + + +bioconductor-scuttle 1.4.0 r41hc247a5b_2 +---------------------------------------- +file name : bioconductor-scuttle-1.4.0-r41hc247a5b_2.tar.bz2 +name : bioconductor-scuttle +version : 1.4.0 +build : r41hc247a5b_2 +build number: 2 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-scuttle-1.4.0-r41hc247a5b_2.tar.bz2 +md5 : 8a5bdc4ae5bc1f636eb7ec471294486d +timestamp : 2022-09-23 16:37:57 UTC +dependencies: + - bioconductor-beachmat >=2.10.0,<2.11.0 + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-biocparallel >=1.28.0,<1.29.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-delayedmatrixstats >=1.16.0,<1.17.0 + - bioconductor-genomicranges >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.1,<4.2.0a0 + - r-matrix + - r-rcpp + + +bioconductor-scuttle 1.8.0 r42hc247a5b_0 +---------------------------------------- +file name : bioconductor-scuttle-1.8.0-r42hc247a5b_0.tar.bz2 +name : bioconductor-scuttle +version : 1.8.0 +build : r42hc247a5b_0 +build number: 0 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-scuttle-1.8.0-r42hc247a5b_0.tar.bz2 +md5 : addbef020c7c1d5bf7b5f3563e7d48f9 +timestamp : 2022-11-06 00:33:28 UTC +dependencies: + - bioconductor-beachmat >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.44.0,<0.45.0 + - bioconductor-biocparallel >=1.32.0,<1.33.0 + - bioconductor-delayedarray >=0.24.0,<0.25.0 + - bioconductor-delayedmatrixstats >=1.20.0,<1.21.0 + - bioconductor-genomicranges >=1.50.0,<1.51.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-matrix + - r-rcpp + + +bioconductor-scuttle 1.8.0 r42hf17093f_1 +---------------------------------------- +file name : bioconductor-scuttle-1.8.0-r42hf17093f_1.tar.bz2 +name : bioconductor-scuttle +version : 1.8.0 +build : r42hf17093f_1 +build number: 1 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-scuttle-1.8.0-r42hf17093f_1.tar.bz2 +md5 : 4177b8d260c57c73a9ef03d5dd7f41f6 +timestamp : 2023-05-28 11:25:14 UTC +dependencies: + - bioconductor-beachmat >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.44.0,<0.45.0 + - bioconductor-biocparallel >=1.32.0,<1.33.0 + - bioconductor-delayedarray >=0.24.0,<0.25.0 + - bioconductor-delayedmatrixstats >=1.20.0,<1.21.0 + - bioconductor-genomicranges >=1.50.0,<1.51.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-matrix + - r-rcpp + + +bioconductor-scuttle 1.10.1 r43hf17093f_0 +----------------------------------------- +file name : bioconductor-scuttle-1.10.1-r43hf17093f_0.tar.bz2 +name : bioconductor-scuttle +version : 1.10.1 +build : r43hf17093f_0 +build number: 0 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-scuttle-1.10.1-r43hf17093f_0.tar.bz2 +md5 : 6c16150ae49a62813a81940a0922fe63 +timestamp : 2023-07-12 08:55:59 UTC +dependencies: + - bioconductor-beachmat >=2.16.0,<2.17.0 + - bioconductor-biocgenerics >=0.46.0,<0.47.0 + - bioconductor-biocparallel >=1.34.0,<1.35.0 + - bioconductor-delayedarray >=0.26.0,<0.27.0 + - bioconductor-delayedmatrixstats >=1.22.0,<1.23.0 + - bioconductor-genomicranges >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + - r-matrix + - r-rcpp + + +bioconductor-scuttle 1.12.0 r43hf17093f_0 +----------------------------------------- +file name : bioconductor-scuttle-1.12.0-r43hf17093f_0.tar.bz2 +name : bioconductor-scuttle +version : 1.12.0 +build : r43hf17093f_0 +build number: 0 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-scuttle-1.12.0-r43hf17093f_0.tar.bz2 +md5 : 13de48e70c47f292a8ba500156822ba7 +timestamp : 2023-12-11 20:11:51 UTC +dependencies: + - bioconductor-beachmat >=2.18.0,<2.19.0 + - bioconductor-beachmat >=2.18.0,<2.19.0a0 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-biocgenerics >=0.48.1,<0.49.0a0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0a0 + - bioconductor-delayedarray >=0.28.0,<0.29.0 + - bioconductor-delayedarray >=0.28.0,<0.29.0a0 + - bioconductor-delayedmatrixstats >=1.24.0,<1.25.0 + - bioconductor-delayedmatrixstats >=1.24.0,<1.25.0a0 + - bioconductor-genomicranges >=1.54.0,<1.55.0 + - bioconductor-genomicranges >=1.54.1,<1.55.0a0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-s4vectors >=0.40.2,<0.41.0a0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0a0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + - r-matrix + - r-rcpp + + +bioconductor-scuttle 1.12.0 r43hf17093f_1 +----------------------------------------- +file name : bioconductor-scuttle-1.12.0-r43hf17093f_1.tar.bz2 +name : bioconductor-scuttle +version : 1.12.0 +build : r43hf17093f_1 +build number: 1 +size : 1.3 MB +license : GPL-3.0-on diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-singlecellexperiment.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-singlecellexperiment.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b1e08dd0d32af663fd007371aec78b9f380b7d7 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-singlecellexperiment.manual_bundle.txt @@ -0,0 +1,348 @@ +# Tool: bioconductor-singlecellexperiment +software_name: bioconductor-singlecellexperiment +tier: T1 +domain: t1_backfill_overall +downloads: 555888 +summary: S4 Classes for Single Cell Data +description: Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries. +dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-genomicranges >=1.62.0,<1.63.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: http://bioconductor.org/packages/3.6/bioc/html/SingleCellExperiment.html +doc_url: +dev_url: + +## URL Docs Extract +### http://bioconductor.org/packages/3.6/bioc/html/SingleCellExperiment.html +Bioconductor - SingleCellExperiment About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.6 Software Packages SingleCellExperiment SingleCellExperiment This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see SingleCellExperiment . S4 Classes for Single Cell Data DOI: 10.18129/B9.bioc.SingleCellExperiment Bioconductor version: 3.6 Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries. Author: Aaron Lun [aut, cph], Davide Risso [aut, cre, cph] Maintainer: Davide Risso <risso.davide at gmail.com> Citation (from within R, enter citation("SingleCellExperiment") ): Installation To install this package, start R (version "3.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SingleCellExperiment") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataImport , DataRepresentation , Infrastructure , SingleCell , Software Version 1.0.0 In Bioconductor since BioC 3.6 (R-3.4) (6.5 years) License GPL-3 Depends R (>= 3.4), SummarizedExperiment Imports S4Vectors , methods, BiocGenerics , utils System Requirements URL See More Suggests testthat, BiocStyle , knitr, scRNAseq , magrittr, Rtsne Linking To Enhances Depends On Me BASiCS , scater , scPipe , scran , splatter , switchde , zinbwave Imports Me SC3 , scDD , scfind , scmap , slalom Suggests Me phenopath Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package SingleCellExperiment_1.0.0.tar.gz Windows Binary SingleCellExperiment_1.0.0.zip Mac OS X 10.11 (El Capitan) SingleCellExperiment_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/SingleCellExperiment Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SingleCellExperiment Package Short Url https://bioconductor.org/packages/SingleCellExperiment/ Package Downloads Report Download Stats Old Source Packages for BioC 3.6 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-singlecellexperiment --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-singlecellexperiment 1.0.0 r3.4.1_0 +------------------------------------------------ +file name : bioconductor-singlecellexperiment-1.0.0-r3.4.1_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.0.0 +build : r3.4.1_0 +build number: 0 +size : 542 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-singlecellexperiment-1.0.0-r3.4.1_0.tar.bz2 +md5 : 8253ea988368eab0b3e4a2884bfe7b63 +dependencies: + - bioconductor-biocgenerics + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base 3.4.1* + + +bioconductor-singlecellexperiment 1.0.0 r341_1 +---------------------------------------------- +file name : bioconductor-singlecellexperiment-1.0.0-r341_1.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.0.0 +build : r341_1 +build number: 1 +size : 544 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-singlecellexperiment-1.0.0-r341_1.tar.bz2 +md5 : 3b6adc36becc1cd571239d4f1d6111a4 +timestamp : 2018-08-20 09:07:18 UTC +dependencies: + - bioconductor-biocgenerics + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-singlecellexperiment 1.0.0 r351_1 +---------------------------------------------- +file name : bioconductor-singlecellexperiment-1.0.0-r351_1.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.0.0 +build : r351_1 +build number: 1 +size : 916 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-singlecellexperiment-1.0.0-r351_1.tar.bz2 +md5 : d444759a2257d4ad6610c4debeba409d +timestamp : 2018-10-15 00:20:42 UTC +dependencies: + - bioconductor-biocgenerics + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-singlecellexperiment 1.2.0 r351_0 +---------------------------------------------- +file name : bioconductor-singlecellexperiment-1.2.0-r351_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.2.0 +build : r351_0 +build number: 0 +size : 996 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-singlecellexperiment-1.2.0-r351_0.tar.bz2 +md5 : 489903cb8092829996aca582ab99f525 +timestamp : 2018-10-19 09:50:02 UTC +dependencies: + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - bioconductor-summarizedexperiment >=1.10.1,<1.12.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-singlecellexperiment 1.4.0 r351_0 +---------------------------------------------- +file name : bioconductor-singlecellexperiment-1.4.0-r351_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.4.0 +build : r351_0 +build number: 0 +size : 1.3 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.4.0-r351_0.tar.bz2 +md5 : d22ac5e2b6d198bc035c40056baa1c6f +timestamp : 2018-12-20 18:24:30 UTC +dependencies: + - bioconductor-biocgenerics >=0.28.0,<0.29.0 + - bioconductor-s4vectors >=0.20.0,<0.21.0 + - bioconductor-summarizedexperiment >=1.12.0,<1.13.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-singlecellexperiment 1.6.0 r36_1 +--------------------------------------------- +file name : bioconductor-singlecellexperiment-1.6.0-r36_1.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.6.0 +build : r36_1 +build number: 1 +size : 1.3 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.6.0-r36_1.tar.bz2 +md5 : fce8fc3db21a8a6445220ddeb7f26c2c +timestamp : 2019-07-25 12:58:37 UTC +dependencies: + - bioconductor-biocgenerics >=0.30.0,<0.31.0 + - bioconductor-s4vectors >=0.22.0,<0.23.0 + - bioconductor-summarizedexperiment >=1.14.0,<1.15.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-singlecellexperiment 1.8.0 r36_0 +--------------------------------------------- +file name : bioconductor-singlecellexperiment-1.8.0-r36_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.8.0 +build : r36_0 +build number: 0 +size : 1.4 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.8.0-r36_0.tar.bz2 +md5 : 88ee3e84b9804b10b1f02b0fe9f9a4b7 +timestamp : 2019-11-02 23:55:22 UTC +dependencies: + - bioconductor-biocgenerics >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.24.0,<0.25.0 + - bioconductor-summarizedexperiment >=1.16.0,<1.17.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-singlecellexperiment 1.10.1 r40_0 +---------------------------------------------- +file name : bioconductor-singlecellexperiment-1.10.1-r40_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.10.1 +build : r40_0 +build number: 0 +size : 1.5 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.10.1-r40_0.tar.bz2 +md5 : 8847a33ed9de2fa398a6167c1e4d7620 +timestamp : 2020-05-10 18:06:22 UTC +dependencies: + - bioconductor-biocgenerics >=0.34.0,<0.35.0 + - bioconductor-s4vectors >=0.26.0,<0.27.0 + - bioconductor-summarizedexperiment >=1.18.0,<1.19.0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-singlecellexperiment 1.12.0 r40_0 +---------------------------------------------- +file name : bioconductor-singlecellexperiment-1.12.0-r40_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.12.0 +build : r40_0 +build number: 0 +size : 1.5 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.12.0-r40_0.tar.bz2 +md5 : bd257756dd837bdd7a48a87b8748c4cc +timestamp : 2020-10-30 22:08:16 UTC +dependencies: + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - bioconductor-summarizedexperiment >=1.20.0,<1.21.0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-singlecellexperiment 1.12.0 r40hdfd78af_1 +------------------------------------------------------ +file name : bioconductor-singlecellexperiment-1.12.0-r40hdfd78af_1.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.12.0 +build : r40hdfd78af_1 +build number: 1 +size : 1.5 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.12.0-r40hdfd78af_1.tar.bz2 +md5 : a01703d04084a397725372cd311b93dd +timestamp : 2021-03-29 15:51:05 UTC +dependencies: + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - bioconductor-summarizedexperiment >=1.20.0,<1.21.0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-singlecellexperiment 1.14.1 r41hdfd78af_0 +------------------------------------------------------ +file name : bioconductor-singlecellexperiment-1.14.1-r41hdfd78af_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.14.1 +build : r41hdfd78af_0 +build number: 0 +size : 1.8 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.14.1-r41hdfd78af_0.tar.bz2 +md5 : a47b8b421a591a3cc46575ff10c423e0 +timestamp : 2021-06-01 16:40:25 UTC +dependencies: + - bioconductor-biocgenerics >=0.38.0,<0.39.0 + - bioconductor-delayedarray >=0.18.0,<0.19.0 + - bioconductor-genomicranges >=1.44.0,<1.45.0 + - bioconductor-s4vectors >=0.30.0,<0.31.0 + - bioconductor-summarizedexperiment >=1.22.0,<1.23.0 + - r-base >=4.1,<4.2.0a0 + + +bioconductor-singlecellexperiment 1.16.0 r41hdfd78af_0 +------------------------------------------------------ +file name : bioconductor-singlecellexperiment-1.16.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.16.0 +build : r41hdfd78af_0 +build number: 0 +size : 1.9 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.16.0-r41hdfd78af_0.tar.bz2 +md5 : ba79f5b8b12331a887aba3cd8b51a243 +timestamp : 2021-11-03 20:30:16 UTC +dependencies: + - bioconductor-biocgenerics >=0.40.0,<0.41.0 + - bioconductor-delayedarray >=0.20.0,<0.21.0 + - bioconductor-genomicranges >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - r-base >=4.1,<4.2.0a0 + + +bioconductor-singlecellexperiment 1.20.0 r42hdfd78af_0 +------------------------------------------------------ +file name : bioconductor-singlecellexperiment-1.20.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.20.0 +build : r42hdfd78af_0 +build number: 0 +size : 1.8 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.20.0-r42hdfd78af_0.tar.bz2 +md5 : 2369c7f36d537f8c78571627fbaf341b +timestamp : 2022-11-06 00:21:07 UTC +dependencies: + - bioconductor-biocgenerics >=0.44.0,<0.45.0 + - bioconductor-delayedarray >=0.24.0,<0.25.0 + - bioconductor-genomicranges >=1.50.0,<1.51.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - r-base >=4.2,<4.3.0a0 + + +bioconductor-singlecellexperiment 1.22.0 r43hdfd78af_0 +------------------------------------------------------ +file name : bioconductor-singlecellexperiment-1.22.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.22.0 +build : r43hdfd78af_0 +build number: 0 +size : 1.9 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.22.0-r43hdfd78af_0.tar.bz2 +md5 : 0a58197f7cf76b84145c785a9b92f2b4 +timestamp : 2023-07-11 15:38:25 UTC +dependencies: + - bioconductor-biocgenerics >=0.46.0,<0.47.0 + - bioconductor-delayedarray >=0.26.0,<0.27.0 + - bioconductor-genomicranges >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-base >=4.3,<4.4.0a0 + + +bioconductor-singlecellexperiment 1.24.0 r43hdfd78af_0 +------------------------------------------------------ +file name : bioconductor-singlecellexperiment-1.24.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.24.0 +build : r43hdfd78af_0 +build number: 0 +size : 1.9 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.24.0-r43hdfd78af_0.tar.bz2 +md5 : cf186d0ff33b0e9e90435ba3fe9f573c +timestamp : 2023-12-06 16:35:44 UTC +dependencies: + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-delayedarray >=0.28.0,<0.29.0 + - bioconductor-genomicranges >=1.54.0,<1.55.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-base >=4.3,<4.4.0a0 + + +bioconductor-singlecellexperiment 1.28.0 r44hdfd78af_0 +------------------------------------------------------ +file name : bioconductor-singlecellexperiment-1.28.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-singlecellexperiment +version : 1.28.0 +build : r44hdfd78af_0 +build number: 0 +size : 1.8 MB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-singlecellexperiment-1.28.0-r44hdfd78af_0.tar.bz2 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-smoothclust.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-smoothclust.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0bc400ab0f72ffa66c4d4b06943ec23af641940b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-smoothclust.manual_bundle.txt @@ -0,0 +1,68 @@ +# Tool: bioconductor-smoothclust +software_name: bioconductor-smoothclust +tier: T1 +domain: spatial_transcriptomics +downloads: 261 +summary: smoothclust +description: Method for identification of spatial domains and spatially-aware clustering in spatial transcriptomics data. The method generates spatial domains with smooth boundaries by smoothing gene expression profiles across neighboring spatial locations, followed by unsupervised clustering. Spatial domains consisting of consistent mixtures of cell types may then be further investigated by applying cell type compositional analyses or differential analyses. +dependencies: bioconductor-biocneighbors >=2.4.0,<2.5.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-matrix +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.20/bioc/html/smoothclust.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.20/bioc/html/smoothclust.html +Bioconductor - smoothclust Registration and Abstract Submission Open for GBCC2025 : Joint Galaxy/Bioconductor Conference Early registration discount pricing ends March 31! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.20 Software Packages smoothclust smoothclust This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see smoothclust . smoothclust DOI: 10.18129/B9.bioc.smoothclust Bioconductor version: 3.20 Method for segmentation of spatial domains and spatially-aware clustering in spatial transcriptomics data. The method generates spatial domains with smooth boundaries by smoothing gene expression profiles across neighboring spatial locations, followed by unsupervised clustering. Spatial domains consisting of consistent mixtures of cell types may then be further investigated by applying cell type compositional analyses or differential analyses. Author: Lukas M. Weber [aut, cre] ORCID: 0000-0002-3282-1730 Maintainer: Lukas M. Weber <lmweb012 at gmail.com> Citation (from within R, enter citation("smoothclust") ): Installation To install this package, start R (version "4.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("smoothclust") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("smoothclust") Smoothclust Tutorial HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews Clustering , GeneExpression , SingleCell , Software , Spatial , Transcriptomics Version 1.2.2 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License MIT + file LICENSE Depends R (>= 4.4.0) Imports SpatialExperiment , SummarizedExperiment , sparseMatrixStats , spdep , methods, utils System Requirements URL https://github.com/lmweber/smoothclust Bug Reports https://github.com/lmweber/smoothclust/issues See More Suggests BiocStyle , knitr , STexampleData , scuttle , scran , scater , ggspavis , testthat Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package smoothclust_1.2.2.tar.gz Windows Binary (x86_64) smoothclust_1.2.2.zip macOS Binary (x86_64) smoothclust_1.2.2.tgz macOS Binary (arm64) smoothclust_1.2.2.tgz Source Repository git clone https://git.bioconductor.org/packages/smoothclust Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/smoothclust Bioc Package Browser https://code.bioconductor.org/browse/smoothclust/ Package Short Url https://bioconductor.org/packages/smoothclust/ Package Downloads Report Download Stats Old Source Packages for BioC 3.20 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2025 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-smoothclust --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-smoothclust 1.2.0 r44hdfd78af_0 +-------------------------------------------- +file name : bioconductor-smoothclust-1.2.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-smoothclust +version : 1.2.0 +build : r44hdfd78af_0 +build number: 0 +size : 1.1 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-smoothclust-1.2.0-r44hdfd78af_0.tar.bz2 +md5 : 2283e5bfc22f2382c8d62b2f8759d34f +timestamp : 2024-12-22 10:32:06 UTC +dependencies: + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base >=4.4,<4.5.0a0 + - r-spdep + + +bioconductor-smoothclust 1.6.0 r45hdfd78af_0 +-------------------------------------------- +file name : bioconductor-smoothclust-1.6.0-r45hdfd78af_0.conda +name : bioconductor-smoothclust +version : 1.6.0 +build : r45hdfd78af_0 +build number: 0 +size : 375 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-smoothclust-1.6.0-r45hdfd78af_0.conda +md5 : 8b35daca4733d3a47593016df45d4ca1 +timestamp : 2026-03-01 19:27:15 UTC +dependencies: + - bioconductor-biocneighbors >=2.4.0,<2.5.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-matrix diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-smoppix.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-smoppix.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..4781d9bce95eee15fbcaa8a3eb02d05168fc551d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-smoppix.manual_bundle.txt @@ -0,0 +1,65 @@ +# Tool: bioconductor-smoppix +software_name: bioconductor-smoppix +tier: T1 +domain: spatial_transcriptomics +downloads: 318 +summary: Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index +description: Test for univariate and bivariate spatial patterns in spatial omics data with single-molecule resolution. The tests implemented allow for analysis of nested designs and are automatically calibrated to different biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided. +dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-biocparallel >=1.44.0,<1.45.0a0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0a0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-extradistr, r-ggplot2, r-lme4, r-lmertest, r-openxlsx, r-rcpp >=1.0.11, r-rdpack, r-rfast, r-scam, r-spatstat.geom >=3.2.0, r-spatstat.model, r-spatstat.random +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/smoppix.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/smoppix.html +Bioconductor - smoppix Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages smoppix smoppix This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see smoppix . Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index DOI: 10.18129/B9.bioc.smoppix Bioconductor version: 3.22 Test for univariate and bivariate spatial patterns in spatial omics data with single-molecule resolution. The tests implemented allow for analysis of nested designs and are automatically calibrated to different biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided. Author: Stijn Hawinkel [cre, aut] ORCID: 0000-0002-4501-5180 Maintainer: Stijn Hawinkel <stijn.hawinkel at psb.ugent.be> Citation (from within R, enter citation("smoppix") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("smoppix") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("smoppix") Vignette of the smoppix package HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews SingleCell , Software , Spatial , Transcriptomics Version 1.2.3 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License GPL-2 Depends R (>= 4.5.0) Imports spatstat.geom (>= 3.2.0), spatstat.random , methods, BiocParallel , SummarizedExperiment , SpatialExperiment , Rdpack , stats, utils, lmerTest , lme4 , ggplot2 , graphics, grDevices, Rcpp (>= 1.0.11), spatstat.model , openxlsx , Rfast , reformulas , mgcv System Requirements URL https://github.com/sthawinke/smoppix Bug Reports https://github.com/sthawinke/smoppix/issues See More Suggests testthat , rmarkdown , knitr , DropletUtils , polyCub , RImageJROI , sp , ape , htmltools , funkycells , glmnet , doParallel Linking To Rcpp Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package smoppix_1.2.3.tar.gz Windows Binary (x86_64) smoppix_1.2.3.zip macOS Binary (x86_64) smoppix_1.2.3.tgz macOS Binary (arm64) smoppix_1.2.3.tgz Source Repository git clone https://git.bioconductor.org/packages/smoppix Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/smoppix Bioc Package Browser https://code.bioconductor.org/browse/smoppix/ Package Short Url https://bioconductor.org/packages/smoppix/ Package Downloads Report Download Stats Old Source Packages for BioC 3.22 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-smoppix --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-smoppix 1.2.1 r45ha27e39d_0 +---------------------------------------- +file name : bioconductor-smoppix-1.2.1-r45ha27e39d_0.conda +name : bioconductor-smoppix +version : 1.2.1 +build : r45ha27e39d_0 +build number: 0 +size : 5.5 MB +license : GPL-2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-smoppix-1.2.1-r45ha27e39d_0.conda +md5 : 9a6fc5ee4bbaee24d40f8b16de951010 +timestamp : 2026-03-02 00:07:17 UTC +dependencies: + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-biocparallel >=1.44.0,<1.45.0a0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0a0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=14 + - liblapack >=3.9.0,<4.0a0 + - liblzma >=5.8.2,<6.0a0 + - libstdcxx >=14 + - libzlib >=1.3.1,<2.0a0 + - r-base >=4.5,<4.6.0a0 + - r-extradistr + - r-ggplot2 + - r-lme4 + - r-lmertest + - r-openxlsx + - r-rcpp >=1.0.11 + - r-rdpack + - r-rfast + - r-scam + - r-spatstat.geom >=3.2.0 + - r-spatstat.model + - r-spatstat.random diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spacetrooper.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spacetrooper.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..d1b06742b4bd5c90fd81d9fdbdd6928c886e9284 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spacetrooper.manual_bundle.txt @@ -0,0 +1,61 @@ +# Tool: bioconductor-spacetrooper +software_name: bioconductor-spacetrooper +tier: T1 +domain: spatial_transcriptomics +downloads: 40 +summary: SpaceTrooper performs Quality Control analysis of Image-Based spatial +description: SpaceTrooper performs Quality Control analysis using data driven GLM models of Image-Based spatial data, providing exploration plots, QC metrics computation, outlier detection. It implements a GLM strategy for the detection of low quality cells in imaging-based spatial data (Transcriptomics and Proteomics). It additionally implements several plots for the visualization of imaging based polygons through the ggplot2 package. +dependencies: bioconductor-dropletutils >=1.30.0,<1.31.0, bioconductor-rhdf5 >=2.54.0,<2.55.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scater >=1.38.0,<1.39.0, bioconductor-scuttle >=1.20.0,<1.21.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-spatialexperimentio >=1.2.0,<1.3.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-arrow, r-base >=4.5,<4.6.0a0, r-cowplot, r-data.table, r-dplyr, r-e1071, r-ggplot2, r-ggpubr, r-glmnet, r-rlang, r-robustbase, r-sf, r-sfheaders +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/SpaceTrooper.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/SpaceTrooper.html +Bioconductor - SpaceTrooper Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages SpaceTrooper SpaceTrooper This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see SpaceTrooper . SpaceTrooper performs Quality Control analysis of Image-Based spatial DOI: 10.18129/B9.bioc.SpaceTrooper Bioconductor version: 3.22 SpaceTrooper performs Quality Control analysis using data driven GLM models of Image-Based spatial data, providing exploration plots, QC metrics computation, outlier detection. It implements a GLM strategy for the detection of low quality cells in imaging-based spatial data (Transcriptomics and Proteomics). It additionally implements several plots for the visualization of imaging based polygons through the ggplot2 package. Author: Dario Righelli [aut, cre] ORCID: 0000-0003-1504-3583 , Benedetta Banzi [aut], Oriana Romano [ctb], Matteo Merchionni [ctb], Mattia Forcato [ctb], Silvio Bicciato [aut], Davide Risso [ctb] Maintainer: Dario Righelli <dario.righelli at gmail.com> Citation (from within R, enter citation("SpaceTrooper") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SpaceTrooper") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("SpaceTrooper") introduction.html HTML R Script Loading CosMx and Xenium data with SpaceTrooper HTML R Script Spatial Data Quality Control on Protein data HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataImport , GeneExpression , ImmunoOncology , QualityControl , SingleCell , Software , Spatial , Transcriptomics Version 1.0.1 In Bioconductor since BioC 3.22 (R-4.5) ( License MIT + file LICENSE Depends R (>= 4.4.0), SpatialExperiment Imports DropletUtils , S4Vectors , SummarizedExperiment , arrow , data.table , dplyr , e1071 , ggplot2 , ggpubr , robustbase , scater , scuttle , sf , sfheaders , cowplot , glmnet , rhdf5 , methods, rlang , SpatialExperimentIO System Requirements URL https://github.com/drighelli/SpaceTrooper Bug Reports https://github.com/drighelli/SpaceTrooper/issues See More Suggests knitr , rmarkdown , BiocStyle , testthat (>= 3.0.0), withr , viridis Linking To Enhances Depends On Me Imports Me OSTA Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package SpaceTrooper_1.0.1.tar.gz Windows Binary (x86_64) SpaceTrooper_1.0.1.zip (64-bit only) macOS Binary (x86_64) SpaceTrooper_1.0.1.tgz macOS Binary (arm64) SpaceTrooper_1.0.1.tgz Source Repository git clone https://git.bioconductor.org/packages/SpaceTrooper Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpaceTrooper Bioc Package Browser https://code.bioconductor.org/browse/SpaceTrooper/ Package Short Url https://bioconductor.org/packages/SpaceTrooper/ Package Downloads Report Download Stats Old Source Packages for BioC 3.22 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-spacetrooper --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-spacetrooper 1.0.1 r45hdfd78af_0 +--------------------------------------------- +file name : bioconductor-spacetrooper-1.0.1-r45hdfd78af_0.conda +name : bioconductor-spacetrooper +version : 1.0.1 +build : r45hdfd78af_0 +build number: 0 +size : 3.7 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spacetrooper-1.0.1-r45hdfd78af_0.conda +md5 : faf369296eb93a7e9189728b4c302589 +timestamp : 2026-03-03 10:45:18 UTC +dependencies: + - bioconductor-dropletutils >=1.30.0,<1.31.0 + - bioconductor-rhdf5 >=2.54.0,<2.55.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-scater >=1.38.0,<1.39.0 + - bioconductor-scuttle >=1.20.0,<1.21.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-spatialexperimentio >=1.2.0,<1.3.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-arrow + - r-base >=4.5,<4.6.0a0 + - r-cowplot + - r-data.table + - r-dplyr + - r-e1071 + - r-ggplot2 + - r-ggpubr + - r-glmnet + - r-rlang + - r-robustbase + - r-sf + - r-sfheaders diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spanorm.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spanorm.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..35908650b52814d8a041ac45a327ca8592c5753c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spanorm.manual_bundle.txt @@ -0,0 +1,79 @@ +# Tool: bioconductor-spanorm +software_name: bioconductor-spanorm +tier: T1 +domain: single_cell +downloads: 450 +summary: Spatially-aware normalisation for spatial transcriptomics data +description: This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data. +dependencies: bioconductor-edger >=4.8.0,<4.9.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scran >=1.38.0,<1.39.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-ggplot2, r-matrix, r-matrixstats, r-rlang, r-seuratobject +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.20/bioc/html/SpaNorm.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.20/bioc/html/SpaNorm.html +Bioconductor - SpaNorm Registration and Abstract Submission Open for GBCC2025 : Joint Galaxy/Bioconductor Conference Early registration discount pricing ends March 31! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.20 Software Packages SpaNorm SpaNorm This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see SpaNorm . Spatially-aware normalisation for spatial transcriptomics data DOI: 10.18129/B9.bioc.SpaNorm Bioconductor version: 3.20 This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data. Author: Dharmesh D. Bhuva [aut, cre] ORCID: 0000-0002-6398-9157 , Agus Salim [aut] ORCID: 0000-0003-3999-7701 , Ahmed Mohamed [aut] ORCID: 0000-0001-6507-5300 Maintainer: Dharmesh D. Bhuva <dharmesh.bhuva at adelaide.edu.au> Citation (from within R, enter citation("SpaNorm") ): Installation To install this package, start R (version "4.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SpaNorm") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("SpaNorm") SpaNorm HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews CellBiology , GeneExpression , Software , Spatial , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.20 (R-4.4) ( License GPL (>= 3) Depends R (>= 4.4) Imports edgeR , ggplot2 , Matrix , matrixStats , methods, rlang , scran , SeuratObject , SingleCellExperiment , SpatialExperiment , stats, SummarizedExperiment , S4Vectors , utils System Requirements URL https://bhuvad.github.io/SpaNorm Bug Reports https://github.com/bhuvad/SpaNorm/issues See More Suggests testthat (>= 3.0.0), knitr , rmarkdown , prettydoc , pkgdown , covr , BiocStyle , Seurat , patchwork , ggforce , ggnewscale Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package SpaNorm_1.0.0.tar.gz Windows Binary (x86_64) SpaNorm_1.0.0.zip (64-bit only) macOS Binary (x86_64) SpaNorm_1.0.0.tgz macOS Binary (arm64) SpaNorm_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/SpaNorm Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpaNorm Bioc Package Browser https://code.bioconductor.org/browse/SpaNorm/ Package Short Url https://bioconductor.org/packages/SpaNorm/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2025 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-spanorm --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-spanorm 1.0.0 r44hdfd78af_0 +---------------------------------------- +file name : bioconductor-spanorm-1.0.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-spanorm +version : 1.0.0 +build : r44hdfd78af_0 +build number: 0 +size : 7.0 MB +license : GPL (>= 3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spanorm-1.0.0-r44hdfd78af_0.tar.bz2 +md5 : d748cce4acf1af5ddf5cbd82e36a06af +timestamp : 2024-12-23 12:03:15 UTC +dependencies: + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base >=4.4,<4.5.0a0 + - r-ggplot2 + - r-matrix + - r-matrixstats + - r-rlang + - r-seuratobject + + +bioconductor-spanorm 1.4.0 r45hdfd78af_0 +---------------------------------------- +file name : bioconductor-spanorm-1.4.0-r45hdfd78af_0.conda +name : bioconductor-spanorm +version : 1.4.0 +build : r45hdfd78af_0 +build number: 0 +size : 7.6 MB +license : GPL (>= 3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spanorm-1.4.0-r45hdfd78af_0.conda +md5 : 6262174af48f61d12f5af33720ceebf1 +timestamp : 2026-03-02 23:44:30 UTC +dependencies: + - bioconductor-edger >=4.8.0,<4.9.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-scran >=1.38.0,<1.39.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-ggplot2 + - r-matrix + - r-matrixstats + - r-rlang + - r-seuratobject diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-sparsearray.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-sparsearray.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..4161b0376e91bb4337f4b0be13568b3c5458cf99 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-sparsearray.manual_bundle.txt @@ -0,0 +1,226 @@ +# Tool: bioconductor-sparsearray +software_name: bioconductor-sparsearray +tier: T1 +domain: t1_backfill_overall +downloads: 292849 +summary: High-performance sparse data representation and manipulation in R +description: The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data: the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN. +dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-iranges >=2.44.0,<2.45.0, bioconductor-iranges >=2.44.0,<2.45.0a0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0a0, bioconductor-s4arrays >=1.10.0,<1.11.0, bioconductor-s4arrays >=1.10.1,<1.11.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, bioconductor-xvector >=0.50.0,<0.51.0, bioconductor-xvector >=0.50.0,<0.51.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-matrix, r-matrixstats +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.17/bioc/html/SparseArray.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.17/bioc/html/SparseArray.html +Bioconductor - SparseArray About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.17 Software Packages SparseArray SparseArray This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SparseArray . Efficient in-memory representation of multidimensional sparse arrays DOI: 10.18129/B9.bioc.SparseArray Bioconductor version: 3.17 The SparseArray package is an infrastructure package that provides an array-like container for efficient in-memory representation of multidimensional sparse data in R. The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data, the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN. Author: Hervé Pagès [aut, cre], Vince Carey [fnd], Rafael A. Irizarry [fnd] Maintainer: Hervé Pagès <hpages.on.github at gmail.com> Citation (from within R, enter citation("SparseArray") ): Installation To install this package, start R (version "4.3") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SparseArray") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("SparseArray") SparseArray objects HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataRepresentation , Infrastructure , Software Version 1.0.12 In Bioconductor since BioC 3.17 (R-4.3) (1 year) License Artistic-2.0 Depends R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors , S4Arrays (>= 1.0.6) Imports stats, matrixStats, IRanges , XVector System Requirements URL https://bioconductor.org/packages/SparseArray Bug Reports https://github.com/Bioconductor/SparseArray/issues See More Suggests DelayedArray , testthat, knitr, rmarkdown, BiocStyle Linking To S4Vectors , IRanges , XVector Enhances Depends On Me Imports Me Suggests Me MatrixGenerics , S4Arrays Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package SparseArray_1.0.12.tar.gz Windows Binary SparseArray_1.0.12.zip macOS Binary (x86_64) SparseArray_1.0.12.tgz macOS Binary (arm64) Source Repository git clone https://git.bioconductor.org/packages/SparseArray Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SparseArray Bioc Package Browser https://code.bioconductor.org/browse/SparseArray/ Package Short Url https://bioconductor.org/packages/SparseArray/ Package Downloads Report Download Stats Old Source Packages for BioC 3.17 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-sparsearray --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-sparsearray 1.0.10 r43ha9d7317_0 +--------------------------------------------- +file name : bioconductor-sparsearray-1.0.10-r43ha9d7317_0.tar.bz2 +name : bioconductor-sparsearray +version : 1.0.10 +build : r43ha9d7317_0 +build number: 0 +size : 1.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-sparsearray-1.0.10-r43ha9d7317_0.tar.bz2 +md5 : 0595f31d621086dae432d0cf2e286da8 +timestamp : 2023-07-10 22:08:45 UTC +dependencies: + - bioconductor-biocgenerics >=0.46.0,<0.47.0 + - bioconductor-iranges >=2.34.0,<2.35.0 + - bioconductor-matrixgenerics >=1.12.0,<1.13.0 + - bioconductor-s4arrays >=1.0.0,<1.1.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-xvector >=0.40.0,<0.41.0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - r-base >=4.3,<4.4.0a0 + - r-matrix + - r-matrixstats + + +bioconductor-sparsearray 1.2.2 r43ha9d7317_1 +-------------------------------------------- +file name : bioconductor-sparsearray-1.2.2-r43ha9d7317_1.tar.bz2 +name : bioconductor-sparsearray +version : 1.2.2 +build : r43ha9d7317_1 +build number: 1 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-sparsearray-1.2.2-r43ha9d7317_1.tar.bz2 +md5 : cb00e397e0ee5fe7ab503829841a3c6a +timestamp : 2023-12-05 15:37:15 UTC +dependencies: + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-biocgenerics >=0.48.1,<0.49.0a0 + - bioconductor-iranges >=2.36.0,<2.37.0 + - bioconductor-iranges >=2.36.0,<2.37.0a0 + - bioconductor-matrixgenerics >=1.14.0,<1.15.0 + - bioconductor-matrixgenerics >=1.14.0,<1.15.0a0 + - bioconductor-s4arrays >=1.2.0,<1.3.0 + - bioconductor-s4arrays >=1.2.0,<2.0a0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-s4vectors >=0.40.2,<0.41.0a0 + - bioconductor-xvector >=0.42.0,<0.43.0 + - bioconductor-xvector >=0.42.0,<1.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - r-base >=4.3,<4.4.0a0 + - r-matrix + - r-matrixstats + + +bioconductor-sparsearray 1.2.2 r43ha9d7317_2 +-------------------------------------------- +file name : bioconductor-sparsearray-1.2.2-r43ha9d7317_2.tar.bz2 +name : bioconductor-sparsearray +version : 1.2.2 +build : r43ha9d7317_2 +build number: 2 +size : 1.7 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-sparsearray-1.2.2-r43ha9d7317_2.tar.bz2 +md5 : 41f1e8c1cfb7ff594e923c05e02d9ecb +timestamp : 2024-05-03 13:46:41 UTC +dependencies: + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-biocgenerics >=0.48.1,<0.49.0a0 + - bioconductor-iranges >=2.36.0,<2.37.0 + - bioconductor-iranges >=2.36.0,<2.37.0a0 + - bioconductor-matrixgenerics >=1.14.0,<1.15.0 + - bioconductor-matrixgenerics >=1.14.0,<1.15.0a0 + - bioconductor-s4arrays >=1.2.0,<1.3.0 + - bioconductor-s4arrays >=1.2.0,<1.3.0a0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-s4vectors >=0.40.2,<0.41.0a0 + - bioconductor-xvector >=0.42.0,<0.43.0 + - bioconductor-xvector >=0.42.0,<0.43.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc-ng >=12 + - liblapack >=3.9.0,<4.0a0 + - r-base >=4.3,<4.4.0a0 + - r-matrix + - r-matrixstats + + +bioconductor-sparsearray 1.6.0 r44h3df3fcb_0 +-------------------------------------------- +file name : bioconductor-sparsearray-1.6.0-r44h3df3fcb_0.tar.bz2 +name : bioconductor-sparsearray +version : 1.6.0 +build : r44h3df3fcb_0 +build number: 0 +size : 1.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-sparsearray-1.6.0-r44h3df3fcb_0.tar.bz2 +md5 : 970ac6edcf91873c44a420b81fddc986 +timestamp : 2024-12-19 16:09:36 UTC +dependencies: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0a0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0a0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0a0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0a0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0a0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - bioconductor-xvector >=0.46.0,<0.47.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=13 + - liblapack >=3.9.0,<4.0a0 + - r-base >=4.4,<4.5.0a0 + - r-matrix + - r-matrixstats + + +bioconductor-sparsearray 1.6.0 r44h3df3fcb_1 +-------------------------------------------- +file name : bioconductor-sparsearray-1.6.0-r44h3df3fcb_1.tar.bz2 +name : bioconductor-sparsearray +version : 1.6.0 +build : r44h3df3fcb_1 +build number: 1 +size : 1.8 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-sparsearray-1.6.0-r44h3df3fcb_1.tar.bz2 +md5 : 143242d9cf4199b8f26c2552b61d2049 +timestamp : 2025-04-14 20:38:02 UTC +dependencies: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0a0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0a0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0a0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0a0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0a0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - bioconductor-xvector >=0.46.0,<0.47.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=13 + - liblapack >=3.9.0,<4.0a0 + - r-base >=4.4,<4.5.0a0 + - r-matrix + - r-matrixstats + + +bioconductor-sparsearray 1.10.8 r45h01b2380_0 +--------------------------------------------- +file name : bioconductor-sparsearray-1.10.8-r45h01b2380_0.conda +name : bioconductor-sparsearray +version : 1.10.8 +build : r45h01b2380_0 +build number: 0 +size : 1.6 MB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-sparsearray-1.10.8-r45h01b2380_0.conda +md5 : 2b73e1653c675b4ba118bb085862771c +timestamp : 2026-02-26 12:11:36 UTC +dependencies: + - bioconductor-biocgenerics >=0.56.0,<0.57.0 + - bioconductor-biocgenerics >=0.56.0,<0.57.0a0 + - bioconductor-iranges >=2.44.0,<2.45.0 + - bioconductor-iranges >=2.44.0,<2.45.0a0 + - bioconductor-matrixgenerics >=1.22.0,<1.23.0 + - bioconductor-matrixgenerics >=1.22.0,<1.23.0a0 + - bioconductor-s4arrays >=1.10.0,<1.11.0 + - bioconductor-s4arrays >=1.10.1,<1.11.0a0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0a0 + - bioconductor-xvector >=0.50.0,<0.51.0 + - bioconductor-xvector >=0.50.0,<0.51.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=14 + - liblapack >=3.9.0,<4.0a0 + - liblzma >=5.8.2,<6.0a0 + - libzlib >=1.3.1,<2.0a0 + - r-base >=4.5,<4.6.0a0 + - r-matrix + - r-matrixstats diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spasim.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spasim.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..f558e8edbd2b453a1d7d280d71291144e6165666 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spasim.manual_bundle.txt @@ -0,0 +1,142 @@ +# Tool: bioconductor-spasim +software_name: bioconductor-spasim +tier: T1 +domain: spatial_transcriptomics +downloads: 3205 +summary: Spatial point data simulator for tissue images +description: A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels. +dependencies: bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-dplyr, r-ggplot2, r-rann, r-spatstat.geom, r-spatstat.random +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.16/bioc/html/spaSim.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.16/bioc/html/spaSim.html +Bioconductor - spaSim About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Software Packages spaSim spaSim This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see spaSim . Spatial point data simulator for tissue images DOI: 10.18129/B9.bioc.spaSim Bioconductor version: 3.16 A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels. Author: Yuzhou Feng [aut, cre] , Anna Trigos [aut] Maintainer: Yuzhou Feng <yuzhou.feng at petermac.org> Citation (from within R, enter citation("spaSim") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("spaSim") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("spaSim") vignette HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews BiomedicalInformatics , Software , Spatial , StatisticalMethod Version 1.0.2 In Bioconductor since BioC 3.16 (R-4.2) (1.5 years) License Artistic-2.0 Depends R (>= 4.2.0) Imports ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment , SummarizedExperiment , RANN System Requirements URL https://trigosteam.github.io/spaSim/ Bug Reports https://support.bioconductor.org/t/spaSim See More Suggests RefManageR, BiocStyle , knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package spaSim_1.0.2.tar.gz Windows Binary spaSim_1.0.2.zip macOS Binary (x86_64) spaSim_1.0.2.tgz macOS Binary (arm64) spaSim_1.0.2.tgz Source Repository git clone https://git.bioconductor.org/packages/spaSim Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spaSim Bioc Package Browser https://code.bioconductor.org/browse/spaSim/ Package Short Url https://bioconductor.org/packages/spaSim/ Package Downloads Report Download Stats Old Source Packages for BioC 3.16 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-spasim --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-spasim 1.0.0 r42hdfd78af_0 +--------------------------------------- +file name : bioconductor-spasim-1.0.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-spasim +version : 1.0.0 +build : r42hdfd78af_0 +build number: 0 +size : 3.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spasim-1.0.0-r42hdfd78af_0.tar.bz2 +md5 : 29e731badbdc451e60060087f327b446 +timestamp : 2022-11-06 01:11:52 UTC +dependencies: + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - r-base >=4.2,<4.3.0a0 + - r-dplyr + - r-ggplot2 + - r-spatstat.geom + - r-spatstat.random + + +bioconductor-spasim 1.2.1 r43hdfd78af_0 +--------------------------------------- +file name : bioconductor-spasim-1.2.1-r43hdfd78af_0.tar.bz2 +name : bioconductor-spasim +version : 1.2.1 +build : r43hdfd78af_0 +build number: 0 +size : 3.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spasim-1.2.1-r43hdfd78af_0.tar.bz2 +md5 : ede0eefabf3d8fd658cfc5905d56dc38 +timestamp : 2023-07-15 01:16:29 UTC +dependencies: + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-base >=4.3,<4.4.0a0 + - r-dplyr + - r-ggplot2 + - r-rann + - r-spatstat.geom + - r-spatstat.random + + +bioconductor-spasim 1.4.0 r43hdfd78af_0 +--------------------------------------- +file name : bioconductor-spasim-1.4.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-spasim +version : 1.4.0 +build : r43hdfd78af_0 +build number: 0 +size : 3.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spasim-1.4.0-r43hdfd78af_0.tar.bz2 +md5 : eaffd859f3bc6a1790f9d58eace9541e +timestamp : 2023-12-06 23:51:12 UTC +dependencies: + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-base >=4.3,<4.4.0a0 + - r-dplyr + - r-ggplot2 + - r-rann + - r-spatstat.geom + - r-spatstat.random + + +bioconductor-spasim 1.8.0 r44hdfd78af_0 +--------------------------------------- +file name : bioconductor-spasim-1.8.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-spasim +version : 1.8.0 +build : r44hdfd78af_0 +build number: 0 +size : 3.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spasim-1.8.0-r44hdfd78af_0.tar.bz2 +md5 : e2d457de834a2023ada9c4a3dfafef56 +timestamp : 2024-12-22 12:14:37 UTC +dependencies: + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base >=4.4,<4.5.0a0 + - r-dplyr + - r-ggplot2 + - r-rann + - r-spatstat.geom + - r-spatstat.random + + +bioconductor-spasim 1.12.0 r45hdfd78af_0 +---------------------------------------- +file name : bioconductor-spasim-1.12.0-r45hdfd78af_0.conda +name : bioconductor-spasim +version : 1.12.0 +build : r45hdfd78af_0 +build number: 0 +size : 3.5 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spasim-1.12.0-r45hdfd78af_0.conda +md5 : 4c299007ebb76aa5501616a93598cd85 +timestamp : 2026-03-01 18:50:47 UTC +dependencies: + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-dplyr + - r-ggplot2 + - r-rann + - r-spatstat.geom + - r-spatstat.random diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialde.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialde.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..f7663736a5854fb188f4128501a7755ed74d1770 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialde.manual_bundle.txt @@ -0,0 +1,187 @@ +# Tool: bioconductor-spatialde +software_name: bioconductor-spatialde +tier: T1 +domain: spatial_transcriptomics +downloads: 6716 +summary: R wrapper for SpatialDE +description: SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk. +dependencies: bioconductor-basilisk >=1.22.0,<1.23.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-checkmate, r-ggplot2, r-ggrepel, r-gridextra, r-matrix, r-reticulate, r-scales +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.14/bioc/html/spatialDE.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.14/bioc/html/spatialDE.html +Bioconductor - spatialDE About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.14 Software Packages spatialDE spatialDE This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see spatialDE . R wrapper for SpatialDE DOI: 10.18129/B9.bioc.spatialDE Bioconductor version: 3.14 SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk. Author: Davide Corso [aut, cre] , Milan Malfait [aut] , Lambda Moses [aut] Maintainer: Davide Corso <davide.corso.2 at phd.unipd.it> Citation (from within R, enter citation("spatialDE") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("spatialDE") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("spatialDE") Introduction to spatialDE HTML R Script Reference Manual PDF LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews Software , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.14 (R-4.1) (2.5 years) License MIT + file LICENSE Depends R (>= 4.1) Imports reticulate, basilisk , checkmate, stats, SpatialExperiment , methods, SummarizedExperiment , Matrix, S4Vectors , ggplot2, ggrepel, scales, gridExtra System Requirements URL https://github.com/sales-lab/spatialDE https://bioconductor.org/packages/spatialDE/ Bug Reports https://github.com/sales-lab/spatialDE/issues See More Suggests knitr, BiocStyle , rmarkdown, testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package spatialDE_1.0.0.tar.gz Windows Binary spatialDE_1.0.0.zip (32- & 64-bit) macOS 10.13 (High Sierra) spatialDE_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/spatialDE Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spatialDE Bioc Package Browser https://code.bioconductor.org/browse/spatialDE/ Package Short Url https://bioconductor.org/packages/spatialDE/ Package Downloads Report Download Stats Old Source Packages for BioC 3.14 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-spatialde --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-spatialde 1.0.0 r41hdfd78af_0 +------------------------------------------ +file name : bioconductor-spatialde-1.0.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-spatialde +version : 1.0.0 +build : r41hdfd78af_0 +build number: 0 +size : 3.8 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialde-1.0.0-r41hdfd78af_0.tar.bz2 +md5 : 76ff8069cd190fcf15db7f518f69c8b2 +timestamp : 2021-11-09 21:42:30 UTC +dependencies: + - bioconductor-basilisk >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.32.0,<0.33.0 + - bioconductor-spatialexperiment >=1.4.0,<1.5.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - r-base >=4.1,<4.2.0a0 + - r-checkmate + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-matrix + - r-reticulate + - r-scales + + +bioconductor-spatialde 1.4.0 r42hdfd78af_0 +------------------------------------------ +file name : bioconductor-spatialde-1.4.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-spatialde +version : 1.4.0 +build : r42hdfd78af_0 +build number: 0 +size : 3.8 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialde-1.4.0-r42hdfd78af_0.tar.bz2 +md5 : 35ef29bc6b6117ccee376b954b2ff591 +timestamp : 2022-11-06 02:25:21 UTC +dependencies: + - bioconductor-basilisk >=1.9.0,<1.10.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - r-base >=4.2,<4.3.0a0 + - r-checkmate + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-matrix + - r-reticulate + - r-scales + + +bioconductor-spatialde 1.6.0 r43hdfd78af_0 +------------------------------------------ +file name : bioconductor-spatialde-1.6.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-spatialde +version : 1.6.0 +build : r43hdfd78af_0 +build number: 0 +size : 3.8 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialde-1.6.0-r43hdfd78af_0.tar.bz2 +md5 : 462951540b770000adf26d8f566c389b +timestamp : 2023-07-15 02:50:51 UTC +dependencies: + - bioconductor-basilisk >=1.12.0,<1.13.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-base >=4.3,<4.4.0a0 + - r-checkmate + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-matrix + - r-reticulate + - r-scales + + +bioconductor-spatialde 1.8.0 r43hdfd78af_0 +------------------------------------------ +file name : bioconductor-spatialde-1.8.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-spatialde +version : 1.8.0 +build : r43hdfd78af_0 +build number: 0 +size : 3.8 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialde-1.8.0-r43hdfd78af_0.tar.bz2 +md5 : 0e85d0eef31f32ed7563a14969dca3e1 +timestamp : 2023-12-07 03:38:30 UTC +dependencies: + - bioconductor-basilisk >=1.14.0,<1.15.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-base >=4.3,<4.4.0a0 + - r-checkmate + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-matrix + - r-reticulate + - r-scales + + +bioconductor-spatialde 1.12.0 r44hdfd78af_0 +------------------------------------------- +file name : bioconductor-spatialde-1.12.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-spatialde +version : 1.12.0 +build : r44hdfd78af_0 +build number: 0 +size : 3.9 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialde-1.12.0-r44hdfd78af_0.tar.bz2 +md5 : 38501aa71240ace39e14372ba76530f9 +timestamp : 2024-12-22 11:10:50 UTC +dependencies: + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base >=4.4,<4.5.0a0 + - r-checkmate + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-matrix + - r-reticulate + - r-scales + + +bioconductor-spatialde 1.16.0 r45hdfd78af_0 +------------------------------------------- +file name : bioconductor-spatialde-1.16.0-r45hdfd78af_0.conda +name : bioconductor-spatialde +version : 1.16.0 +build : r45hdfd78af_0 +build number: 0 +size : 3.8 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialde-1.16.0-r45hdfd78af_0.conda +md5 : 46a3bf762da6a734fb8e7f3f582359ef +timestamp : 2026-03-01 23:34:32 UTC +dependencies: + - bioconductor-basilisk >=1.22.0,<1.23.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-checkmate + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-matrix + - r-reticulate + - r-scales diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialdmelxsim.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialdmelxsim.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..d0881e09ee9902a1eb24e58e216cea03a23477b9 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialdmelxsim.manual_bundle.txt @@ -0,0 +1,169 @@ +# Tool: bioconductor-spatialdmelxsim +software_name: bioconductor-spatialdmelxsim +tier: T1 +domain: spatial_transcriptomics +downloads: 8328 +summary: Spatial allelic expression counts for fly cross embryo +description: Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data. +dependencies: bioconductor-data-packages >=20260207, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, curl, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.14/data/experiment/html/spatialDmelxsim.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.14/data/experiment/html/spatialDmelxsim.html +Bioconductor - spatialDmelxsim About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.14 Experiment Packages spatialDmelxsim spatialDmelxsim This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see spatialDmelxsim . Spatial allelic expression counts for fly cross embryo DOI: 10.18129/B9.bioc.spatialDmelxsim Bioconductor version: 3.14 Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data. Author: Michael Love [aut, cre] Maintainer: Michael Love <michaelisaiahlove at gmail.com> Citation (from within R, enter citation("spatialDmelxsim") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("spatialDmelxsim") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("spatialDmelxsim") spatialDmelxsim HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Drosophila_melanogaster_Data , ExperimentData , ExperimentHub , ExpressionData , GEO , RNASeqData , SequencingData Version 1.0.0 License GPL-3 Depends R (>= 4.1), ExperimentHub , SummarizedExperiment Imports utils System Requirements URL https://github.com/mikelove/spatialDmelxsim Bug Reports https://github.com/mikelove/spatialDmelxsim/issues See More Suggests knitr, rmarkdown Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package spatialDmelxsim_1.0.0.tar.gz Windows Binary macOS 10.13 (High Sierra) Source Repository git clone https://git.bioconductor.org/packages/spatialDmelxsim Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spatialDmelxsim Package Short Url https://bioconductor.org/packages/spatialDmelxsim/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-spatialdmelxsim --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-spatialdmelxsim 1.0.0 r41hdfd78af_0 +------------------------------------------------ +file name : bioconductor-spatialdmelxsim-1.0.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-spatialdmelxsim +version : 1.0.0 +build : r41hdfd78af_0 +build number: 0 +size : 19 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialdmelxsim-1.0.0-r41hdfd78af_0.tar.bz2 +md5 : b6b8f63c6aba08be88873399e14b86a0 +timestamp : 2021-11-06 16:41:44 UTC +dependencies: + - bioconductor-experimenthub >=2.2.0,<2.3.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-spatialdmelxsim 1.0.0 r41hdfd78af_1 +------------------------------------------------ +file name : bioconductor-spatialdmelxsim-1.0.0-r41hdfd78af_1.tar.bz2 +name : bioconductor-spatialdmelxsim +version : 1.0.0 +build : r41hdfd78af_1 +build number: 1 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialdmelxsim-1.0.0-r41hdfd78af_1.tar.bz2 +md5 : 1b6279d4ed2c046de4e89b126f3ea737 +timestamp : 2022-09-01 15:59:17 UTC +dependencies: + - bioconductor-experimenthub >=2.2.0,<2.3.0 + - bioconductor-summarizedexperiment >=1.24.0,<1.25.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-spatialdmelxsim 1.4.0 r42hdfd78af_0 +------------------------------------------------ +file name : bioconductor-spatialdmelxsim-1.4.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-spatialdmelxsim +version : 1.4.0 +build : r42hdfd78af_0 +build number: 0 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialdmelxsim-1.4.0-r42hdfd78af_0.tar.bz2 +md5 : 4a992ceab1f6431efd916910c6a242e3 +timestamp : 2022-11-09 01:09:43 UTC +dependencies: + - bioconductor-data-packages >=20221108 + - bioconductor-experimenthub >=2.6.0,<2.7.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - curl + - r-base >=4.2,<4.3.0a0 + + +bioconductor-spatialdmelxsim 1.6.1 r43hdfd78af_0 +------------------------------------------------ +file name : bioconductor-spatialdmelxsim-1.6.1-r43hdfd78af_0.tar.bz2 +name : bioconductor-spatialdmelxsim +version : 1.6.1 +build : r43hdfd78af_0 +build number: 0 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialdmelxsim-1.6.1-r43hdfd78af_0.tar.bz2 +md5 : 840b3e2298a4e75538e9011e5c97aa2c +timestamp : 2023-07-14 11:11:26 UTC +dependencies: + - bioconductor-data-packages >=20230713 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-spatialdmelxsim 1.8.0 r43hdfd78af_0 +------------------------------------------------ +file name : bioconductor-spatialdmelxsim-1.8.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-spatialdmelxsim +version : 1.8.0 +build : r43hdfd78af_0 +build number: 0 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialdmelxsim-1.8.0-r43hdfd78af_0.tar.bz2 +md5 : f2b77e2e82ec77db0df1f79fc13ec8fe +timestamp : 2023-12-06 08:03:25 UTC +dependencies: + - bioconductor-data-packages >=20231203 + - bioconductor-experimenthub >=2.10.0,<2.11.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-spatialdmelxsim 1.12.0 r44hdfd78af_0 +------------------------------------------------- +file name : bioconductor-spatialdmelxsim-1.12.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-spatialdmelxsim +version : 1.12.0 +build : r44hdfd78af_0 +build number: 0 +size : 20 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialdmelxsim-1.12.0-r44hdfd78af_0.tar.bz2 +md5 : c9f95751502c993899ca296e7597d3f4 +timestamp : 2024-12-22 03:26:03 UTC +dependencies: + - bioconductor-data-packages >=20241103 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - curl + - r-base >=4.4,<4.5.0a0 + + +bioconductor-spatialdmelxsim 1.16.0 r45hdfd78af_0 +------------------------------------------------- +file name : bioconductor-spatialdmelxsim-1.16.0-r45hdfd78af_0.conda +name : bioconductor-spatialdmelxsim +version : 1.16.0 +build : r45hdfd78af_0 +build number: 0 +size : 23 KB +license : GPL-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialdmelxsim-1.16.0-r45hdfd78af_0.conda +md5 : 965fbc865fd3c703d0e9bdd1fe3dd9ef +timestamp : 2026-03-01 16:14:24 UTC +dependencies: + - bioconductor-data-packages >=20260207 + - bioconductor-experimenthub >=3.0.0,<3.1.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - curl + - r-base >=4.5,<4.6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialomicsoverlay.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialomicsoverlay.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c5415b23c22a2c7108441a8d7fa9e3b2a13a639 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialomicsoverlay.manual_bundle.txt @@ -0,0 +1,163 @@ +# Tool: bioconductor-spatialomicsoverlay +software_name: bioconductor-spatialomicsoverlay +tier: T1 +domain: spatial_transcriptomics +downloads: 2182 +summary: Spatial Overlay for Omic Data from Nanostring GeoMx Data +description: Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression. +dependencies: bioconductor-biobase >=2.70.0,<2.71.0, bioconductor-biocfilecache >=3.0.0,<3.1.0, bioconductor-ebimage >=4.52.0,<4.53.0, bioconductor-geomxtools >=3.14.0,<3.15.0, bioconductor-rbioformats >=1.10.0,<1.11.0, bioconductor-s4vectors >=0.48.0,<0.49.0, r-base >=4.5,<4.6.0a0, r-base64enc, r-data.table, r-dplyr, r-ggplot2, r-ggtext, r-magick, r-pbapply, r-plotrix, r-readxl, r-scattermore, r-stringr, r-xml +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.17/bioc/html/SpatialOmicsOverlay.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.17/bioc/html/SpatialOmicsOverlay.html +Bioconductor - SpatialOmicsOverlay About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.17 Software Packages SpatialOmicsOverlay SpatialOmicsOverlay This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SpatialOmicsOverlay . Spatial Overlay for Omic Data from Nanostring GeoMx Data DOI: 10.18129/B9.bioc.SpatialOmicsOverlay Bioconductor version: 3.17 Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression. Author: Maddy Griswold [cre, aut], Megan Vandenberg [ctb], Stephanie Zimmerman [ctb] Maintainer: Maddy Griswold <mgriswold at nanostring.com> Citation (from within R, enter citation("SpatialOmicsOverlay") ): Installation To install this package, start R (version "4.3") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SpatialOmicsOverlay") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("SpatialOmicsOverlay") Introduction to SpatialOmicsOverlay HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews CellBasedAssays , DataImport , DataRepresentation , GeneExpression , ProprietaryPlatforms , Proteomics , RNASeq , Software , Spatial , Transcription , Transcriptomics , Visualization Version 1.0.0 In Bioconductor since BioC 3.17 (R-4.3) (1 year) License MIT Depends R (>= 4.1.0) Imports S4Vectors , Biobase , base64enc, EBImage , ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools , BiocFileCache , stats, utils, methods, ggtext, tools, RBioFormats System Requirements URL See More Suggests knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package SpatialOmicsOverlay_1.0.0.tar.gz Windows Binary SpatialOmicsOverlay_1.0.0.zip macOS Binary (x86_64) SpatialOmicsOverlay_1.0.0.tgz macOS Binary (arm64) SpatialOmicsOverlay_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/SpatialOmicsOverlay Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpatialOmicsOverlay Bioc Package Browser https://code.bioconductor.org/browse/SpatialOmicsOverlay/ Package Short Url https://bioconductor.org/packages/SpatialOmicsOverlay/ Package Downloads Report Download Stats Old Source Packages for BioC 3.17 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-spatialomicsoverlay --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-spatialomicsoverlay 1.0.0 r43hdfd78af_0 +---------------------------------------------------- +file name : bioconductor-spatialomicsoverlay-1.0.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-spatialomicsoverlay +version : 1.0.0 +build : r43hdfd78af_0 +build number: 0 +size : 2.8 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialomicsoverlay-1.0.0-r43hdfd78af_0.tar.bz2 +md5 : a60cd74fc948562cb067a655fccbb90e +timestamp : 2023-07-17 10:03:26 UTC +dependencies: + - bioconductor-biobase >=2.60.0,<2.61.0 + - bioconductor-biocfilecache >=2.8.0,<2.9.0 + - bioconductor-ebimage >=4.42.0,<4.43.0 + - bioconductor-geomxtools >=3.4.0,<3.5.0 + - bioconductor-rbioformats >=1.0.0,<1.1.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - r-base >=4.3,<4.4.0a0 + - r-base64enc + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggtext + - r-magick + - r-pbapply + - r-plotrix + - r-readxl + - r-scattermore + - r-stringr + - r-xml + + +bioconductor-spatialomicsoverlay 1.2.1 r43hdfd78af_0 +---------------------------------------------------- +file name : bioconductor-spatialomicsoverlay-1.2.1-r43hdfd78af_0.tar.bz2 +name : bioconductor-spatialomicsoverlay +version : 1.2.1 +build : r43hdfd78af_0 +build number: 0 +size : 4.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialomicsoverlay-1.2.1-r43hdfd78af_0.tar.bz2 +md5 : 2300411aa6bcd087101e7cb16b004a99 +timestamp : 2023-12-08 20:23:23 UTC +dependencies: + - bioconductor-biobase >=2.62.0,<2.63.0 + - bioconductor-biocfilecache >=2.10.0,<2.11.0 + - bioconductor-ebimage >=4.44.0,<4.45.0 + - bioconductor-geomxtools >=3.5.0,<3.6.0 + - bioconductor-rbioformats >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-base >=4.3,<4.4.0a0 + - r-base64enc + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggtext + - r-magick + - r-pbapply + - r-plotrix + - r-readxl + - r-scattermore + - r-stringr + - r-xml + + +bioconductor-spatialomicsoverlay 1.6.0 r44hdfd78af_0 +---------------------------------------------------- +file name : bioconductor-spatialomicsoverlay-1.6.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-spatialomicsoverlay +version : 1.6.0 +build : r44hdfd78af_0 +build number: 0 +size : 4.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialomicsoverlay-1.6.0-r44hdfd78af_0.tar.bz2 +md5 : 1386b2b608d88b02d4dc134fbf71e04a +timestamp : 2025-01-03 23:22:31 UTC +dependencies: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-geomxtools >=3.10.0,<3.11.0 + - bioconductor-rbioformats >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base >=4.4,<4.5.0a0 + - r-base64enc + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggtext + - r-magick + - r-pbapply + - r-plotrix + - r-readxl + - r-scattermore + - r-stringr + - r-xml + + +bioconductor-spatialomicsoverlay 1.10.0 r45hdfd78af_0 +----------------------------------------------------- +file name : bioconductor-spatialomicsoverlay-1.10.0-r45hdfd78af_0.conda +name : bioconductor-spatialomicsoverlay +version : 1.10.0 +build : r45hdfd78af_0 +build number: 0 +size : 4.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialomicsoverlay-1.10.0-r45hdfd78af_0.conda +md5 : e51e9b9d8ffb0ca9e6b3e7bd62859a10 +timestamp : 2026-03-03 18:11:19 UTC +dependencies: + - bioconductor-biobase >=2.70.0,<2.71.0 + - bioconductor-biocfilecache >=3.0.0,<3.1.0 + - bioconductor-ebimage >=4.52.0,<4.53.0 + - bioconductor-geomxtools >=3.14.0,<3.15.0 + - bioconductor-rbioformats >=1.10.0,<1.11.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - r-base >=4.5,<4.6.0a0 + - r-base64enc + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggtext + - r-magick + - r-pbapply + - r-plotrix + - r-readxl + - r-scattermore + - r-stringr + - r-xml diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialsimgp.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialsimgp.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae7c606d6692b218f1b204e68620064db400ed3b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spatialsimgp.manual_bundle.txt @@ -0,0 +1,64 @@ +# Tool: bioconductor-spatialsimgp +software_name: bioconductor-spatialsimgp +tier: T1 +domain: spatial_transcriptomics +downloads: 563 +summary: Simulate Spatial Transcriptomics Data with the Mean-variance Relationship +description: This packages simulates spatial transcriptomics data with the mean- variance relationship using a Gaussian Process model per gene. +dependencies: bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-mass +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.20/bioc/html/spatialSimGP.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.20/bioc/html/spatialSimGP.html +Bioconductor - spatialSimGP Registration and Abstract Submission Open for GBCC2025 : Joint Galaxy/Bioconductor Conference Early registration discount pricing ends March 31! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.20 Software Packages spatialSimGP spatialSimGP This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see spatialSimGP . Simulate Spatial Transcriptomics Data with the Mean-variance Relationship DOI: 10.18129/B9.bioc.spatialSimGP Bioconductor version: 3.20 This packages simulates spatial transcriptomics data with the mean- variance relationship using a Gaussian Process model per gene. Author: Kinnary Shah [aut, cre] ORCID: 0000-0001-7098-2116 , Boyi Guo [aut] ORCID: 0000-0003-2950-2349 , Stephanie C. Hicks [aut] ORCID: 0000-0002-7858-0231 Maintainer: Kinnary Shah <kinnaryshahh at gmail.com> Citation (from within R, enter citation("spatialSimGP") ): Installation To install this package, start R (version "4.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("spatialSimGP") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("spatialSimGP") spatialSimGP Tutorial HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews GeneExpression , Software , Spatial , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.20 (R-4.4) ( License MIT + file LICENSE Depends R (>= 4.4) Imports SpatialExperiment , MASS , SummarizedExperiment System Requirements URL https://github.com/kinnaryshah/spatialSimGP Bug Reports https://github.com/kinnaryshah/spatialSimGP/issues See More Suggests testthat (>= 3.0.0), STexampleData , ggplot2 , knitr Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package spatialSimGP_1.0.0.tar.gz Windows Binary (x86_64) spatialSimGP_1.0.0.zip (64-bit only) macOS Binary (x86_64) spatialSimGP_1.0.0.tgz macOS Binary (arm64) spatialSimGP_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/spatialSimGP Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spatialSimGP Bioc Package Browser https://code.bioconductor.org/browse/spatialSimGP/ Package Short Url https://bioconductor.org/packages/spatialSimGP/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2025 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-spatialsimgp --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-spatialsimgp 1.0.0 r44hdfd78af_0 +--------------------------------------------- +file name : bioconductor-spatialsimgp-1.0.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-spatialsimgp +version : 1.0.0 +build : r44hdfd78af_0 +build number: 0 +size : 722 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialsimgp-1.0.0-r44hdfd78af_0.tar.bz2 +md5 : eb0bb6020ddbb5cbbce9ebf4ddadbcb5 +timestamp : 2024-12-22 12:46:30 UTC +dependencies: + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base >=4.4,<4.5.0a0 + - r-mass + + +bioconductor-spatialsimgp 1.4.0 r45hdfd78af_0 +--------------------------------------------- +file name : bioconductor-spatialsimgp-1.4.0-r45hdfd78af_0.conda +name : bioconductor-spatialsimgp +version : 1.4.0 +build : r45hdfd78af_0 +build number: 0 +size : 687 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spatialsimgp-1.4.0-r45hdfd78af_0.conda +md5 : 4fc818d5a890e960f48aa14b62e1cb36 +timestamp : 2026-03-01 17:43:27 UTC +dependencies: + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-mass diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spotsweeper.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spotsweeper.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..73dbc1f9f88a974e9ffe6795accb21c85a26f5b1 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-spotsweeper.manual_bundle.txt @@ -0,0 +1,50 @@ +# Tool: bioconductor-spotsweeper +software_name: bioconductor-spotsweeper +tier: T1 +domain: spatial_transcriptomics +downloads: 42 +summary: Spatially-aware quality control for spatial transcriptomics +description: Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers spot and large technical artifacts. +dependencies: bioconductor-biocneighbors >=2.4.0,<2.5.0, bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-escher >=1.10.0,<1.11.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-ggplot2, r-mass, r-spatialeco +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/SpotSweeper.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/SpotSweeper.html +Bioconductor - SpotSweeper Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages SpotSweeper SpotSweeper This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see SpotSweeper . Spatially-aware quality control for spatial transcriptomics DOI: 10.18129/B9.bioc.SpotSweeper Bioconductor version: 3.22 Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers spot and large technical artifacts. Author: Michael Totty [aut, cre] ORCID: 0000-0002-9292-8556 , Stephanie Hicks [aut] ORCID: 0000-0002-7858-0231 , Boyi Guo [aut] ORCID: 0000-0003-2950-2349 Maintainer: Michael Totty <mictott at gmail.com> Citation (from within R, enter citation("SpotSweeper") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SpotSweeper") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("SpotSweeper") Getting Started with `SpotSweeper` HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews GeneExpression , QualityControl , Software , Spatial , Transcriptomics Version 1.6.0 In Bioconductor since BioC 3.19 (R-4.4) (2 years) License MIT + file LICENSE Depends R (>= 4.4.0) Imports SpatialExperiment , SummarizedExperiment , BiocNeighbors , SingleCellExperiment , stats, escheR , MASS , ggplot2 , spatialEco , grDevices, BiocParallel System Requirements URL https://github.com/MicTott/SpotSweeper Bug Reports https://support.bioconductor.org/tag/SpotSweeper See More Suggests knitr , BiocStyle , rmarkdown , scuttle , STexampleData , ggpubr , testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me OSTA Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package SpotSweeper_1.6.0.tar.gz Windows Binary (x86_64) SpotSweeper_1.6.0.zip macOS Binary (x86_64) SpotSweeper_1.6.0.tgz macOS Binary (arm64) SpotSweeper_1.6.0.tgz Source Repository git clone https://git.bioconductor.org/packages/SpotSweeper Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpotSweeper Bioc Package Browser https://code.bioconductor.org/browse/SpotSweeper/ Package Short Url https://bioconductor.org/packages/SpotSweeper/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-spotsweeper --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-spotsweeper 1.6.0 r45hdfd78af_0 +-------------------------------------------- +file name : bioconductor-spotsweeper-1.6.0-r45hdfd78af_0.conda +name : bioconductor-spotsweeper +version : 1.6.0 +build : r45hdfd78af_0 +build number: 0 +size : 3.4 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-spotsweeper-1.6.0-r45hdfd78af_0.conda +md5 : fd776d0ff987b843f76180bc7c4e4494 +timestamp : 2026-03-02 06:50:09 UTC +dependencies: + - bioconductor-biocneighbors >=2.4.0,<2.5.0 + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-escher >=1.10.0,<1.11.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-ggplot2 + - r-mass + - r-spatialeco diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-standr.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-standr.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d136ff4b632d21262c99a31d803bdd486989dbd --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-standr.manual_bundle.txt @@ -0,0 +1,203 @@ +# Tool: bioconductor-standr +software_name: bioconductor-standr +tier: T1 +domain: spatial_transcriptomics +downloads: 4972 +summary: Spatial transcriptome analyses of Nanostring's DSP data in R +description: standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations. +dependencies: bioconductor-biobase >=2.70.0,<2.71.0, bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-edger >=4.8.0,<4.9.0, bioconductor-limma >=3.66.0,<3.67.0, bioconductor-ruvseq >=1.44.0,<1.45.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-dplyr, r-ggalluvial, r-ggplot2, r-mclustcomp, r-patchwork, r-readr, r-rlang, r-ruv, r-tibble, r-tidyr +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.16/bioc/html/standR.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.16/bioc/html/standR.html +Bioconductor - standR About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Software Packages standR standR This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see standR . Spatial transcriptome analyses of Nanostring's DSP data in R DOI: 10.18129/B9.bioc.standR Bioconductor version: 3.16 standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations. Author: Ning Liu [aut, cre] , Dharmesh D Bhuva [aut] , Ahmed Mohamed [aut] Maintainer: Ning Liu <liu.n at wehi.edu.au> Citation (from within R, enter citation("standR") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("standR") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("standR") standR_introduction HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DifferentialExpression , ExperimentHubSoftware , GeneExpression , Normalization , QualityControl , Software , Spatial , Transcriptomics Version 1.2.2 In Bioconductor since BioC 3.15 (R-4.2) (2 years) License MIT + file LICENSE Depends R (>= 4.1) Imports dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment , SingleCellExperiment , edgeR , rlang, readr, tibble, ggplot2, tidyr, ruv, limma , patchwork, S4Vectors , Biobase , BiocGenerics , grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq System Requirements URL https://github.com/DavisLaboratory/standR Bug Reports https://github.com/DavisLaboratory/standR/issues See More Suggests knitr, ExperimentHub , rmarkdown, scater , uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package standR_1.2.2.tar.gz Windows Binary standR_1.2.2.zip (64-bit only) macOS Binary (x86_64) standR_1.2.2.tgz macOS Binary (arm64) standR_1.2.2.tgz Source Repository git clone https://git.bioconductor.org/packages/standR Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/standR Bioc Package Browser https://code.bioconductor.org/browse/standR/ Package Short Url https://bioconductor.org/packages/standR/ Package Downloads Report Download Stats Old Source Packages for BioC 3.16 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-standr --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-standr 1.2.0 r42hdfd78af_0 +--------------------------------------- +file name : bioconductor-standr-1.2.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-standr +version : 1.2.0 +build : r42hdfd78af_0 +build number: 0 +size : 3.8 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-standr-1.2.0-r42hdfd78af_0.tar.bz2 +md5 : 155d5e6e44222193c0980ad980daf639 +timestamp : 2022-11-08 12:16:38 UTC +dependencies: + - bioconductor-biobase >=2.58.0,<2.59.0 + - bioconductor-biocgenerics >=0.44.0,<0.45.0 + - bioconductor-edger >=3.40.0,<3.41.0 + - bioconductor-limma >=3.54.0,<3.55.0 + - bioconductor-ruvseq >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - r-base >=4.2,<4.3.0a0 + - r-dplyr + - r-ggalluvial + - r-ggplot2 + - r-mclustcomp + - r-patchwork + - r-readr + - r-rlang + - r-ruv + - r-tibble + - r-tidyr + + +bioconductor-standr 1.4.2 r43hdfd78af_0 +--------------------------------------- +file name : bioconductor-standr-1.4.2-r43hdfd78af_0.tar.bz2 +name : bioconductor-standr +version : 1.4.2 +build : r43hdfd78af_0 +build number: 0 +size : 2.6 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-standr-1.4.2-r43hdfd78af_0.tar.bz2 +md5 : beff989352f3864e71d481f23b48464a +timestamp : 2023-07-18 03:17:44 UTC +dependencies: + - bioconductor-biobase >=2.60.0,<2.61.0 + - bioconductor-biocgenerics >=0.46.0,<0.47.0 + - bioconductor-edger >=3.42.0,<3.43.0 + - bioconductor-limma >=3.56.0,<3.57.0 + - bioconductor-ruvseq >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-base >=4.3,<4.4.0a0 + - r-dplyr + - r-ggalluvial + - r-ggplot2 + - r-mclustcomp + - r-patchwork + - r-readr + - r-rlang + - r-ruv + - r-tibble + - r-tidyr + + +bioconductor-standr 1.6.0 r43hdfd78af_0 +--------------------------------------- +file name : bioconductor-standr-1.6.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-standr +version : 1.6.0 +build : r43hdfd78af_0 +build number: 0 +size : 2.5 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-standr-1.6.0-r43hdfd78af_0.tar.bz2 +md5 : 9146c719d3648990bdfc09a41e91c15f +timestamp : 2023-12-07 09:59:49 UTC +dependencies: + - bioconductor-biobase >=2.62.0,<2.63.0 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-edger >=4.0.0,<4.1.0 + - bioconductor-limma >=3.58.0,<3.59.0 + - bioconductor-ruvseq >=1.36.0,<1.37.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-base >=4.3,<4.4.0a0 + - r-dplyr + - r-ggalluvial + - r-ggplot2 + - r-mclustcomp + - r-patchwork + - r-readr + - r-rlang + - r-ruv + - r-tibble + - r-tidyr + + +bioconductor-standr 1.10.0 r44hdfd78af_0 +---------------------------------------- +file name : bioconductor-standr-1.10.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-standr +version : 1.10.0 +build : r44hdfd78af_0 +build number: 0 +size : 2.6 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-standr-1.10.0-r44hdfd78af_0.tar.bz2 +md5 : db20681714de230efdaf75edbedd9e40 +timestamp : 2025-01-01 08:09:43 UTC +dependencies: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base >=4.4,<4.5.0a0 + - r-dplyr + - r-ggalluvial + - r-ggplot2 + - r-mclustcomp + - r-patchwork + - r-readr + - r-rlang + - r-ruv + - r-tibble + - r-tidyr + + +bioconductor-standr 1.14.0 r45hdfd78af_0 +---------------------------------------- +file name : bioconductor-standr-1.14.0-r45hdfd78af_0.conda +name : bioconductor-standr +version : 1.14.0 +build : r45hdfd78af_0 +build number: 0 +size : 2.5 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-standr-1.14.0-r45hdfd78af_0.conda +md5 : 5d6be5f6224fc2362dcde10dd576f049 +timestamp : 2026-03-03 07:05:50 UTC +dependencies: + - bioconductor-biobase >=2.70.0,<2.71.0 + - bioconductor-biocgenerics >=0.56.0,<0.57.0 + - bioconductor-edger >=4.8.0,<4.9.0 + - bioconductor-limma >=3.66.0,<3.67.0 + - bioconductor-ruvseq >=1.44.0,<1.45.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-dplyr + - r-ggalluvial + - r-ggplot2 + - r-mclustcomp + - r-patchwork + - r-readr + - r-rlang + - r-ruv + - r-tibble + - r-tidyr diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-stexampledata.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-stexampledata.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..22d846744fcc215dc55ef7283651d903922c8efe --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-stexampledata.manual_bundle.txt @@ -0,0 +1,191 @@ +# Tool: bioconductor-stexampledata +software_name: bioconductor-stexampledata +tier: T1 +domain: spatial_transcriptomics +downloads: 11418 +summary: Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format +description: Collection of spatial transcriptomics datasets stored in SpatialExperiment Bioconductor format, for use in examples, demonstrations, and tutorials. The datasets are from several different platforms and have been sourced from various publicly available sources. Several datasets include images and/or reference annotation labels. +dependencies: bioconductor-data-packages >=20260207, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, curl, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.13/data/experiment/html/STexampleData.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.13/data/experiment/html/STexampleData.html +Bioconductor - STexampleData About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.13 Experiment Packages STexampleData STexampleData This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see STexampleData . Collection of spatially resolved transcriptomics datasets in SpatialExperiment Bioconductor format DOI: 10.18129/B9.bioc.STexampleData Bioconductor version: 3.13 Collection of spatially resolved transcriptomics datasets in SpatialExperiment Bioconductor format, for use in examples, demonstrations, tutorials, and other purposes. The datasets have been sourced from various publicly available sources, and cover several technological platforms. Author: Lukas M. Weber [aut, cre] Maintainer: Lukas M. Weber <lukas.weber.edu at gmail.com> Citation (from within R, enter citation("STexampleData") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("STexampleData") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("STexampleData") STexampleData package overview HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentData , ExperimentHub , ExpressionData , Homo_sapiens_Data , Mus_musculus_Data , ReproducibleResearch , SingleCellData Version 1.0.8 License MIT + file LICENSE Depends ExperimentHub , SpatialExperiment Imports utils System Requirements URL https://github.com/lmweber/STexampleData Bug Reports https://github.com/lmweber/STexampleData/issues See More Suggests BiocStyle , knitr Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package STexampleData_1.0.8.tar.gz Windows Binary macOS 10.13 (High Sierra) Source Repository git clone https://git.bioconductor.org/packages/STexampleData Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/STexampleData Package Short Url https://bioconductor.org/packages/STexampleData/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-stexampledata --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-stexampledata 1.0.0 r41hdfd78af_0 +---------------------------------------------- +file name : bioconductor-stexampledata-1.0.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-stexampledata +version : 1.0.0 +build : r41hdfd78af_0 +build number: 0 +size : 9 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-stexampledata-1.0.0-r41hdfd78af_0.tar.bz2 +md5 : 38d7eeedd4655703b7ea4a372b6c94a0 +timestamp : 2021-06-07 06:45:19 UTC +dependencies: + - bioconductor-experimenthub >=2.0.0,<2.1.0 + - bioconductor-spatialexperiment >=1.2.0,<1.3.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-stexampledata 1.2.0 r41hdfd78af_0 +---------------------------------------------- +file name : bioconductor-stexampledata-1.2.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-stexampledata +version : 1.2.0 +build : r41hdfd78af_0 +build number: 0 +size : 9 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-stexampledata-1.2.0-r41hdfd78af_0.tar.bz2 +md5 : c472bb84215bf02835cb88aa1806a866 +timestamp : 2021-11-07 15:29:52 UTC +dependencies: + - bioconductor-experimenthub >=2.2.0,<2.3.0 + - bioconductor-spatialexperiment >=1.4.0,<1.5.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-stexampledata 1.2.0 r41hdfd78af_1 +---------------------------------------------- +file name : bioconductor-stexampledata-1.2.0-r41hdfd78af_1.tar.bz2 +name : bioconductor-stexampledata +version : 1.2.0 +build : r41hdfd78af_1 +build number: 1 +size : 10 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-stexampledata-1.2.0-r41hdfd78af_1.tar.bz2 +md5 : f01820a5fd85862cecf62b4139be7fa1 +timestamp : 2022-09-02 15:00:32 UTC +dependencies: + - bioconductor-experimenthub >=2.2.0,<2.3.0 + - bioconductor-spatialexperiment >=1.4.0,<1.5.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-stexampledata 1.6.0 r42hdfd78af_0 +---------------------------------------------- +file name : bioconductor-stexampledata-1.6.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-stexampledata +version : 1.6.0 +build : r42hdfd78af_0 +build number: 0 +size : 10 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-stexampledata-1.6.0-r42hdfd78af_0.tar.bz2 +md5 : d4fcdb1e5445c7da15a75e80a73d4593 +timestamp : 2022-11-09 17:18:44 UTC +dependencies: + - bioconductor-data-packages >=20221108 + - bioconductor-experimenthub >=2.6.0,<2.7.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - curl + - r-base >=4.2,<4.3.0a0 + + +bioconductor-stexampledata 1.8.0 r43hdfd78af_0 +---------------------------------------------- +file name : bioconductor-stexampledata-1.8.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-stexampledata +version : 1.8.0 +build : r43hdfd78af_0 +build number: 0 +size : 11 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-stexampledata-1.8.0-r43hdfd78af_0.tar.bz2 +md5 : 8b80cb2e86c3fb03a8a1c0f81e5ea1cb +timestamp : 2023-07-15 01:45:19 UTC +dependencies: + - bioconductor-data-packages >=20230706 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-stexampledata 1.10.0 r43hdfd78af_0 +----------------------------------------------- +file name : bioconductor-stexampledata-1.10.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-stexampledata +version : 1.10.0 +build : r43hdfd78af_0 +build number: 0 +size : 10 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-stexampledata-1.10.0-r43hdfd78af_0.tar.bz2 +md5 : 71329a204075ed3d4178e388085c01b1 +timestamp : 2023-12-09 06:19:52 UTC +dependencies: + - bioconductor-data-packages >=20231203 + - bioconductor-experimenthub >=2.10.0,<2.11.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-stexampledata 1.14.0 r44hdfd78af_0 +----------------------------------------------- +file name : bioconductor-stexampledata-1.14.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-stexampledata +version : 1.14.0 +build : r44hdfd78af_0 +build number: 0 +size : 10 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-stexampledata-1.14.0-r44hdfd78af_0.tar.bz2 +md5 : 0e9ba1935c4d68bd11dabf79b60fd4ba +timestamp : 2024-12-22 13:32:41 UTC +dependencies: + - bioconductor-data-packages >=20241103 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - curl + - r-base >=4.4,<4.5.0a0 + + +bioconductor-stexampledata 1.18.0 r45hdfd78af_0 +----------------------------------------------- +file name : bioconductor-stexampledata-1.18.0-r45hdfd78af_0.conda +name : bioconductor-stexampledata +version : 1.18.0 +build : r45hdfd78af_0 +build number: 0 +size : 12 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-stexampledata-1.18.0-r45hdfd78af_0.conda +md5 : 4a56d264cf2dc3cc726f93272187803d +timestamp : 2026-03-01 21:28:29 UTC +dependencies: + - bioconductor-data-packages >=20260207 + - bioconductor-experimenthub >=3.0.0,<3.1.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - curl + - r-base >=4.5,<4.6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-stpipe.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-stpipe.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1fa3c63c23fe738c02aacc6bbd878e239ec16671 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-stpipe.manual_bundle.txt @@ -0,0 +1,78 @@ +# Tool: bioconductor-stpipe +software_name: bioconductor-stpipe +tier: T1 +domain: single_cell +downloads: 268 +summary: Upstream pre-processing for Sequencing-Based Spatial Transcriptomics +description: This package serves as an upstream pipeline for pre-processing sequencing-based spatial transcriptomics data. Functions includes FASTQ trimming, BAM file reformatting, index building, spatial barcode detection, demultiplexing, gene count matrix generation with UMI deduplication, QC, and revelant visualization. Config is an essential input for most of the functions which aims to improve reproducibility. +dependencies: bioconductor-basilisk >=1.22.0,<1.23.0, bioconductor-basilisk >=1.22.0,<1.23.0a0, bioconductor-dropletutils >=1.30.0,<1.31.0, bioconductor-dropletutils >=1.30.0,<1.31.0a0, bioconductor-rhdf5lib >=1.32.0,<1.33.0, bioconductor-rhdf5lib >=1.32.0,<1.33.0a0, bioconductor-rhtslib >=3.6.0,<3.7.0, bioconductor-rhtslib >=3.6.0,<3.7.0a0, bioconductor-rsubread >=2.24.0,<2.25.0, bioconductor-rsubread >=2.24.0,<2.25.0a0, bioconductor-scpipe >=2.10.0,<2.11.0, bioconductor-scpipe >=2.10.0,<2.11.0a0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0a0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-data.table, r-dplyr, r-ggplot2, r-pbmcapply, r-rcpp, r-reticulate, r-rmarkdown, r-rtsne, r-seurat, r-seuratobject, r-shiny, r-testthat, r-umap, r-yaml +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/stPipe.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/stPipe.html +Bioconductor - stPipe Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages stPipe stPipe This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see stPipe . Upstream pre-processing for Sequencing-Based Spatial Transcriptomics DOI: 10.18129/B9.bioc.stPipe Bioconductor version: 3.22 This package serves as an upstream pipeline for pre-processing sequencing-based spatial transcriptomics data. Functions includes FASTQ trimming, BAM file reformatting, index building, spatial barcode detection, demultiplexing, gene count matrix generation with UMI deduplication, QC, and revelant visualization. Config is an essential input for most of the functions which aims to improve reproducibility. Author: Yang Xu [aut, cre] ORCID: 0009-0008-3274-6516 , Callum Sargeant [aut], Shian Su [aut], Luyi Tian [aut], Yunshun Chen [ctb], Matthew Ritchie [ctb, fnd] Maintainer: Yang Xu <xu.ya at wehi.edu.au> Citation (from within R, enter citation("stPipe") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("stPipe") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("stPipe") stPipe: A flexible and streamlined pipeline for processing sequencing-based spatial transcriptomics data HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Clustering , DataImport , GeneExpression , GenomeAnnotation , ImmunoOncology , Preprocessing , QualityControl , RNASeq , SequenceMatching , Sequencing , SingleCell , Software , Spatial , Transcriptomics , Visualization Version 1.0.1 In Bioconductor since BioC 3.22 (R-4.5) ( License GPL-3 Depends R (>= 4.5.0) Imports basilisk , data.table , DropletUtils , dplyr , ggplot2 , methods, pbmcapply , reticulate , rmarkdown , Rcpp , Rhtslib , Rsubread , Rtsne , Seurat , SeuratObject , scPipe , shiny , SummarizedExperiment , SingleCellExperiment , SpatialExperiment , stats, umap , yaml System Requirements GNU make URL https://github.com/mritchielab/stPipe Bug Reports https://github.com/mritchielab/stPipe/issues/new See More Suggests knitr , plotly , BiocStyle , testthat (>= 3.0.0) Linking To Rcpp , Rhdf5lib , testthat , Rhtslib Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package stPipe_1.0.1.tar.gz Windows Binary (x86_64) stPipe_1.0.1.zip macOS Binary (x86_64) stPipe_1.0.1.tgz macOS Binary (arm64) stPipe_1.0.1.tgz Source Repository git clone https://git.bioconductor.org/packages/stPipe Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/stPipe Bioc Package Browser https://code.bioconductor.org/browse/stPipe/ Package Short Url https://bioconductor.org/packages/stPipe/ Package Downloads Report Download Stats Old Source Packages for BioC 3.22 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-stpipe --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-stpipe 1.0.1 r45ha27e39d_0 +--------------------------------------- +file name : bioconductor-stpipe-1.0.1-r45ha27e39d_0.conda +name : bioconductor-stpipe +version : 1.0.1 +build : r45ha27e39d_0 +build number: 0 +size : 7.2 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-stpipe-1.0.1-r45ha27e39d_0.conda +md5 : c2d2e431234a9ff8d95573e06bbf40e7 +timestamp : 2026-03-03 01:01:12 UTC +dependencies: + - bioconductor-basilisk >=1.22.0,<1.23.0 + - bioconductor-basilisk >=1.22.0,<1.23.0a0 + - bioconductor-dropletutils >=1.30.0,<1.31.0 + - bioconductor-dropletutils >=1.30.0,<1.31.0a0 + - bioconductor-rhdf5lib >=1.32.0,<1.33.0 + - bioconductor-rhdf5lib >=1.32.0,<1.33.0a0 + - bioconductor-rhtslib >=3.6.0,<3.7.0 + - bioconductor-rhtslib >=3.6.0,<3.7.0a0 + - bioconductor-rsubread >=2.24.0,<2.25.0 + - bioconductor-rsubread >=2.24.0,<2.25.0a0 + - bioconductor-scpipe >=2.10.0,<2.11.0 + - bioconductor-scpipe >=2.10.0,<2.11.0a0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0a0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0 + - libblas >=3.9.0,<4.0a0 + - libgcc >=14 + - liblapack >=3.9.0,<4.0a0 + - liblzma >=5.8.2,<6.0a0 + - libstdcxx >=14 + - libzlib >=1.3.1,<2.0a0 + - r-base >=4.5,<4.6.0a0 + - r-data.table + - r-dplyr + - r-ggplot2 + - r-pbmcapply + - r-rcpp + - r-reticulate + - r-rmarkdown + - r-rtsne + - r-seurat + - r-seuratobject + - r-shiny + - r-testthat + - r-umap + - r-yaml diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-subcellularspatialdata.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-subcellularspatialdata.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e7a0418e7d0d314774128a2f5ae885f55799f4f0 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-subcellularspatialdata.manual_bundle.txt @@ -0,0 +1,47 @@ +# Tool: bioconductor-subcellularspatialdata +software_name: bioconductor-subcellularspatialdata +tier: T1 +domain: spatial_transcriptomics +downloads: 34 +summary: Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics. +description: This is a data package that hosts annotated sub-cellular localised datasets from the STOmics, Xenium and CosMx platforms. Specifically, it hosts datasets analysed in the publication Bhuva et. al, 2024 titled "Library size confounds biology in spatial transcriptomics data". Raw transcript detections are hosted and functions to convert them to SpatialExperiment objects have been implemented. +dependencies: bioconductor-data-packages >=20260207, bioconductor-spatialexperiment >=1.20.0,<1.21.0, curl, r-base >=4.5,<4.6.0a0, r-dplyr, r-hexbin, r-matrix +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/data/experiment/html/SubcellularSpatialData.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/data/experiment/html/SubcellularSpatialData.html +Bioconductor - SubcellularSpatialData Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Experiment Packages SubcellularSpatialData SubcellularSpatialData This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see SubcellularSpatialData . Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics. DOI: 10.18129/B9.bioc.SubcellularSpatialData Bioconductor version: 3.22 This is a data package that hosts annotated sub-cellular localised datasets from the STOmics, Xenium and CosMx platforms. Specifically, it hosts datasets analysed in the publication Bhuva et. al, 2024 titled "Library size confounds biology in spatial transcriptomics data". Raw transcript detections are hosted and functions to convert them to SpatialExperiment objects have been implemented. Author: Dharmesh D. Bhuva [aut, cre] ORCID: 0000-0002-6398-9157 Maintainer: Dharmesh D. Bhuva <dharmesh.bhuva at adelaide.edu.au> Citation (from within R, enter citation("SubcellularSpatialData") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SubcellularSpatialData") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("SubcellularSpatialData") SubcellularSpatialData HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentData , ExperimentHub , Homo_sapiens_Data , LungCancerData , Mus_musculus_Data , SpatialData Version 1.6.0 License GPL (>= 3) Depends R (>= 4.4) Imports dplyr , hexbin , Matrix , SpatialExperiment , stats System Requirements URL https://davislaboratory.github.io/SubcellularSpatialData Bug Reports https://github.com/DavisLaboratory/SubcellularSpatialData/issues See More Suggests BiocStyle , ExperimentHub , ggplot2 , knitr , prettydoc , rmarkdown , testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package SubcellularSpatialData_1.6.0.tar.gz Windows Binary (x86_64) macOS Binary (x86_64) macOS Binary (arm64) Source Repository git clone https://git.bioconductor.org/packages/SubcellularSpatialData Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SubcellularSpatialData Package Short Url https://bioconductor.org/packages/SubcellularSpatialData/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-subcellularspatialdata --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-subcellularspatialdata 1.6.0 r45hdfd78af_0 +------------------------------------------------------- +file name : bioconductor-subcellularspatialdata-1.6.0-r45hdfd78af_0.conda +name : bioconductor-subcellularspatialdata +version : 1.6.0 +build : r45hdfd78af_0 +build number: 0 +size : 23 KB +license : GPL (>= 3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-subcellularspatialdata-1.6.0-r45hdfd78af_0.conda +md5 : 9c31c8da14f19c87705a8abf953615e5 +timestamp : 2026-03-01 22:54:13 UTC +dependencies: + - bioconductor-data-packages >=20260207 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - curl + - r-base >=4.5,<4.6.0a0 + - r-dplyr + - r-hexbin + - r-matrix diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-tenxvisiumdata.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-tenxvisiumdata.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b38fdf5e303a0bc01d43c7449edc412d8aa93e86 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-tenxvisiumdata.manual_bundle.txt @@ -0,0 +1,189 @@ +# Tool: bioconductor-tenxvisiumdata +software_name: bioconductor-tenxvisiumdata +tier: T1 +domain: spatial_transcriptomics +downloads: 10734 +summary: Visium spatial gene expression data by 10X Genomics +description: Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes. +dependencies: bioconductor-data-packages >=20260207, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, curl, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.13/data/experiment/html/TENxVisiumData.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.13/data/experiment/html/TENxVisiumData.html +Bioconductor - TENxVisiumData About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.13 Experiment Packages TENxVisiumData TENxVisiumData This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see TENxVisiumData . Visium spatial gene expression data by 10X Genomics DOI: 10.18129/B9.bioc.TENxVisiumData Bioconductor version: 3.13 Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes. Author: Helena L. Crowell [aut, cre] Maintainer: Helena L. Crowell <helena at crowell.eu> Citation (from within R, enter citation("TENxVisiumData") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("TENxVisiumData") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("TENxVisiumData") TENxVisiumData HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentData , ExperimentHub , ExpressionData , Homo_sapiens_Data , Mus_musculus_Data , ReproducibleResearch Version 1.0.2 License MIT + file LICENSE Depends ExperimentHub , SpatialExperiment Imports utils System Requirements URL https://github.com/helenalc/TENxVisiumData Bug Reports https://github.com/helenalc/TENxVisiumData/issues See More Suggests BiocStyle , knitr, rmarkdown Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package TENxVisiumData_1.0.2.tar.gz Windows Binary macOS 10.13 (High Sierra) Source Repository git clone https://git.bioconductor.org/packages/TENxVisiumData Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TENxVisiumData Package Short Url https://bioconductor.org/packages/TENxVisiumData/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-tenxvisiumdata --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-tenxvisiumdata 1.0.0 r41hdfd78af_0 +----------------------------------------------- +file name : bioconductor-tenxvisiumdata-1.0.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-tenxvisiumdata +version : 1.0.0 +build : r41hdfd78af_0 +build number: 0 +size : 9 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tenxvisiumdata-1.0.0-r41hdfd78af_0.tar.bz2 +md5 : 931ecfab724afd81b5f59c7582c0f580 +timestamp : 2021-06-07 08:01:16 UTC +dependencies: + - bioconductor-experimenthub >=2.0.0,<2.1.0 + - bioconductor-spatialexperiment >=1.2.0,<1.3.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-tenxvisiumdata 1.2.0 r41hdfd78af_0 +----------------------------------------------- +file name : bioconductor-tenxvisiumdata-1.2.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-tenxvisiumdata +version : 1.2.0 +build : r41hdfd78af_0 +build number: 0 +size : 10 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tenxvisiumdata-1.2.0-r41hdfd78af_0.tar.bz2 +md5 : 23925448dd63c261d839a21f980b5ba2 +timestamp : 2021-11-09 15:02:47 UTC +dependencies: + - bioconductor-experimenthub >=2.2.0,<2.3.0 + - bioconductor-spatialexperiment >=1.4.0,<1.5.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-tenxvisiumdata 1.2.0 r41hdfd78af_1 +----------------------------------------------- +file name : bioconductor-tenxvisiumdata-1.2.0-r41hdfd78af_1.tar.bz2 +name : bioconductor-tenxvisiumdata +version : 1.2.0 +build : r41hdfd78af_1 +build number: 1 +size : 10 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tenxvisiumdata-1.2.0-r41hdfd78af_1.tar.bz2 +md5 : 8ababd541f1a5e945771e80d7b8b1f0d +timestamp : 2022-09-02 15:12:45 UTC +dependencies: + - bioconductor-experimenthub >=2.2.0,<2.3.0 + - bioconductor-spatialexperiment >=1.4.0,<1.5.0 + - curl + - r-base >=4.1,<4.2.0a0 + + +bioconductor-tenxvisiumdata 1.6.0 r42hdfd78af_0 +----------------------------------------------- +file name : bioconductor-tenxvisiumdata-1.6.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-tenxvisiumdata +version : 1.6.0 +build : r42hdfd78af_0 +build number: 0 +size : 10 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tenxvisiumdata-1.6.0-r42hdfd78af_0.tar.bz2 +md5 : 26ff1d384758a384853f1a1a8c17d30c +timestamp : 2022-11-09 10:21:39 UTC +dependencies: + - bioconductor-data-packages >=20221108 + - bioconductor-experimenthub >=2.6.0,<2.7.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - curl + - r-base >=4.2,<4.3.0a0 + + +bioconductor-tenxvisiumdata 1.8.0 r43hdfd78af_0 +----------------------------------------------- +file name : bioconductor-tenxvisiumdata-1.8.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-tenxvisiumdata +version : 1.8.0 +build : r43hdfd78af_0 +build number: 0 +size : 11 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tenxvisiumdata-1.8.0-r43hdfd78af_0.tar.bz2 +md5 : 6a3da8b80a1c995d0bbd5d8be961cc72 +timestamp : 2023-07-15 01:29:34 UTC +dependencies: + - bioconductor-data-packages >=20230706 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-tenxvisiumdata 1.10.0 r43hdfd78af_0 +------------------------------------------------ +file name : bioconductor-tenxvisiumdata-1.10.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-tenxvisiumdata +version : 1.10.0 +build : r43hdfd78af_0 +build number: 0 +size : 11 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tenxvisiumdata-1.10.0-r43hdfd78af_0.tar.bz2 +md5 : 194e3b3db33b5bdeed021d7b624d9a0c +timestamp : 2023-12-09 00:43:55 UTC +dependencies: + - bioconductor-data-packages >=20231203 + - bioconductor-experimenthub >=2.10.0,<2.11.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-tenxvisiumdata 1.14.0 r44hdfd78af_0 +------------------------------------------------ +file name : bioconductor-tenxvisiumdata-1.14.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-tenxvisiumdata +version : 1.14.0 +build : r44hdfd78af_0 +build number: 0 +size : 10 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tenxvisiumdata-1.14.0-r44hdfd78af_0.tar.bz2 +md5 : 8dc079780b5ced70109926518f8c5383 +timestamp : 2024-12-22 14:05:05 UTC +dependencies: + - bioconductor-data-packages >=20241103 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - curl + - r-base >=4.4,<4.5.0a0 + + +bioconductor-tenxvisiumdata 1.18.0 r45hdfd78af_0 +------------------------------------------------ +file name : bioconductor-tenxvisiumdata-1.18.0-r45hdfd78af_0.conda +name : bioconductor-tenxvisiumdata +version : 1.18.0 +build : r45hdfd78af_0 +build number: 0 +size : 12 KB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tenxvisiumdata-1.18.0-r45hdfd78af_0.conda +md5 : 7cbc965881c84a4d16c3187d46e258d6 +timestamp : 2026-03-01 17:28:20 UTC +dependencies: + - bioconductor-data-packages >=20260207 + - bioconductor-experimenthub >=3.0.0,<3.1.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - curl + - r-base >=4.5,<4.6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-tpsvg.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-tpsvg.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..d42735f1ce6960ad03d85776bcc47c7c4356ddfe --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-tpsvg.manual_bundle.txt @@ -0,0 +1,70 @@ +# Tool: bioconductor-tpsvg +software_name: bioconductor-tpsvg +tier: T1 +domain: spatial_transcriptomics +downloads: 243 +summary: Thin plate models to detect spatially variable genes +description: The goal of `tpSVG` is to detect and visualize spatial variation in the gene expression for spatially resolved transcriptomics data analysis. Specifically, `tpSVG` introduces a family of count-based models, with generalizable parametric assumptions such as Poisson distribution or negative binomial distribution. In addition, comparing to currently available count-based model for spatially resolved data analysis, the `tpSVG` models improves computational time, and hence greatly improves the applicability of count-based models in SRT data analysis. +dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-mgcv +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.20/bioc/html/tpSVG.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.20/bioc/html/tpSVG.html +Bioconductor - tpSVG Registration and Abstract Submission Open for GBCC2025 : Joint Galaxy/Bioconductor Conference Early registration discount pricing ends March 31! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.20 Software Packages tpSVG tpSVG This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see tpSVG . Thin plate models to detect spatially variable genes DOI: 10.18129/B9.bioc.tpSVG Bioconductor version: 3.20 The goal of `tpSVG` is to detect and visualize spatial variation in the gene expression for spatially resolved transcriptomics data analysis. Specifically, `tpSVG` introduces a family of count-based models, with generalizable parametric assumptions such as Poisson distribution or negative binomial distribution. In addition, comparing to currently available count-based model for spatially resolved data analysis, the `tpSVG` models improves computational time, and hence greatly improves the applicability of count-based models in SRT data analysis. Author: Boyi Guo [aut, cre] ORCID: 0000-0003-2950-2349 , Lukas M. Weber [ctb] ORCID: 0000-0002-3282-1730 , Stephanie C. Hicks [aut] ORCID: 0000-0002-7858-0231 Maintainer: Boyi Guo <boyi.guo.work at gmail.com> Citation (from within R, enter citation("tpSVG") ): Installation To install this package, start R (version "4.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("tpSVG") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("tpSVG") intro_to_tpSVG HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DimensionReduction , GeneExpression , Preprocessing , Regression , Software , Spatial , StatisticalMethod , Transcriptomics Version 1.2.0 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License MIT + file LICENSE Depends mgcv , R (>= 4.4) Imports stats, BiocParallel , MatrixGenerics , methods, SingleCellExperiment , SummarizedExperiment , SpatialExperiment System Requirements URL https://github.com/boyiguo1/tpSVG Bug Reports https://github.com/boyiguo1/tpSVG/issues See More Suggests BiocStyle , knitr , nnSVG , rmarkdown , scran , scuttle , STexampleData , escheR , ggpubr , colorspace , BumpyMatrix , sessioninfo , testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package tpSVG_1.2.0.tar.gz Windows Binary (x86_64) tpSVG_1.2.0.zip macOS Binary (x86_64) tpSVG_1.2.0.tgz macOS Binary (arm64) tpSVG_1.2.0.tgz Source Repository git clone https://git.bioconductor.org/packages/tpSVG Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tpSVG Bioc Package Browser https://code.bioconductor.org/browse/tpSVG/ Package Short Url https://bioconductor.org/packages/tpSVG/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2025 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-tpsvg --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-tpsvg 1.2.0 r44hdfd78af_0 +-------------------------------------- +file name : bioconductor-tpsvg-1.2.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-tpsvg +version : 1.2.0 +build : r44hdfd78af_0 +build number: 0 +size : 1.3 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tpsvg-1.2.0-r44hdfd78af_0.tar.bz2 +md5 : 94ed718948779b981f541229173bcfeb +timestamp : 2024-12-22 11:48:40 UTC +dependencies: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base >=4.4,<4.5.0a0 + - r-mgcv + + +bioconductor-tpsvg 1.6.0 r45hdfd78af_0 +-------------------------------------- +file name : bioconductor-tpsvg-1.6.0-r45hdfd78af_0.conda +name : bioconductor-tpsvg +version : 1.6.0 +build : r45hdfd78af_0 +build number: 0 +size : 1.2 MB +license : MIT + file LICENSE +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tpsvg-1.6.0-r45hdfd78af_0.conda +md5 : f3a90ac66b463e8801f2e5439878b2b0 +timestamp : 2026-03-01 20:15:03 UTC +dependencies: + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-matrixgenerics >=1.22.0,<1.23.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-mgcv diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-tximport.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-tximport.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..df90c7cc35b3ea07dc86c4a2475966103ef958be --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-tximport.manual_bundle.txt @@ -0,0 +1,408 @@ +# Tool: bioconductor-tximport +software_name: bioconductor-tximport +tier: T1 +domain: t1_backfill_overall +downloads: 157758 +summary: Import and summarize transcript-level estimates for transcript- and gene-level analysis +description: Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts. +dependencies: r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/tximport.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/tximport.html +Bioconductor - tximport Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages tximport tximport This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see tximport . Import and summarize transcript-level estimates for transcript- and gene-level analysis DOI: 10.18129/B9.bioc.tximport Bioconductor version: 3.22 Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts. Author: Michael Love [cre,aut], Charlotte Soneson [aut], Mark Robinson [aut], Rob Patro [ctb], Andrew Parker Morgan [ctb], Ryan C. Thompson [ctb], Matt Shirley [ctb], Avi Srivastava [ctb] Maintainer: Michael Love <michaelisaiahlove at gmail.com> Citation (from within R, enter citation("tximport") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("tximport") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("tximport") Importing transcript abundance datasets with tximport HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataImport , GeneExpression , ImmunoOncology , Preprocessing , RNASeq , Software , Transcription , Transcriptomics Version 1.38.2 In Bioconductor since BioC 3.3 (R-3.3) (10 years) License LGPL (>=2) Depends Imports utils, stats, methods System Requirements URL https://github.com/thelovelab/tximport See More Suggests knitr , rmarkdown , testthat , tximportData , TxDb.Hsapiens.UCSC.hg19.knownGene , readr (>= 0.2.2), arrow , limma , edgeR , DESeq2 (>= 1.11.6), rhdf5 , jsonlite , matrixStats , Matrix , eds Linking To Enhances Depends On Me Imports Me alevinQC , BgeeCall , CleanUpRNAseq , DifferentialRegulation , EventPointer , IsoformSwitchAnalyzeR , singleCellTK , TDbasedUFE , tximeta , ExpHunterSuite , cpam , EZbakR Suggests Me BANDITS , DESeq2 , variancePartition Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package tximport_1.38.2.tar.gz Windows Binary (x86_64) tximport_1.38.2.zip macOS Binary (x86_64) tximport_1.38.2.tgz macOS Binary (arm64) tximport_1.38.2.tgz Source Repository git clone https://git.bioconductor.org/packages/tximport Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tximport Bioc Package Browser https://code.bioconductor.org/browse/tximport/ Package Short Url https://bioconductor.org/packages/tximport/ Package Downloads Report Download Stats Old Source Packages for BioC 3.22 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-tximport --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +bioconductor-tximport 1.0.3 r3.2.2_0 +------------------------------------ +file name : bioconductor-tximport-1.0.3-r3.2.2_0.tar.bz2 +name : bioconductor-tximport +version : 1.0.3 +build : r3.2.2_0 +build number: 0 +size : 31 KB +license : GPL (>=2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-tximport-1.0.3-r3.2.2_0.tar.bz2 +md5 : 88873c85898ddc0bd6715736b5f01a89 +dependencies: + - r 3.2.2* + + +bioconductor-tximport 1.0.3 r3.3.1_0 +------------------------------------ +file name : bioconductor-tximport-1.0.3-r3.3.1_0.tar.bz2 +name : bioconductor-tximport +version : 1.0.3 +build : r3.3.1_0 +build number: 0 +size : 31 KB +license : GPL (>=2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-tximport-1.0.3-r3.3.1_0.tar.bz2 +md5 : b95f66119917bd52e6c683175ca3df81 +dependencies: + - r 3.3.1* + + +bioconductor-tximport 1.0.3 r3.3.2_0 +------------------------------------ +file name : bioconductor-tximport-1.0.3-r3.3.2_0.tar.bz2 +name : bioconductor-tximport +version : 1.0.3 +build : r3.3.2_0 +build number: 0 +size : 33 KB +license : GPL (>=2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-tximport-1.0.3-r3.3.2_0.tar.bz2 +md5 : e5ac82a25f3833ca660a2769f7e0b6dc +dependencies: + - r-base 3.3.2* + + +bioconductor-tximport 1.0.3 r3.3.2_1 +------------------------------------ +file name : bioconductor-tximport-1.0.3-r3.3.2_1.tar.bz2 +name : bioconductor-tximport +version : 1.0.3 +build : r3.3.2_1 +build number: 1 +size : 33 KB +license : GPL (>=2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-tximport-1.0.3-r3.3.2_1.tar.bz2 +md5 : aa90ebb85e28e78e9095a6d7d12bf493 +dependencies: + - r-base 3.3.2* + + +bioconductor-tximport 1.4.0 r3.3.2_0 +------------------------------------ +file name : bioconductor-tximport-1.4.0-r3.3.2_0.tar.bz2 +name : bioconductor-tximport +version : 1.4.0 +build : r3.3.2_0 +build number: 0 +size : 25 KB +license : GPL (>=2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-tximport-1.4.0-r3.3.2_0.tar.bz2 +md5 : d7dcebefd8e406f3eff424280e4e2644 +dependencies: + - r-base 3.3.2* + + +bioconductor-tximport 1.4.0 r3.4.1_0 +------------------------------------ +file name : bioconductor-tximport-1.4.0-r3.4.1_0.tar.bz2 +name : bioconductor-tximport +version : 1.4.0 +build : r3.4.1_0 +build number: 0 +size : 26 KB +license : GPL (>=2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-tximport-1.4.0-r3.4.1_0.tar.bz2 +md5 : a7f839a1e4f26b2a2020e3437aaaa0ef +dependencies: + - r-base 3.4.1* + + +bioconductor-tximport 1.6.0 r3.4.1_0 +------------------------------------ +file name : bioconductor-tximport-1.6.0-r3.4.1_0.tar.bz2 +name : bioconductor-tximport +version : 1.6.0 +build : r3.4.1_0 +build number: 0 +size : 246 KB +license : GPL (>=2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-tximport-1.6.0-r3.4.1_0.tar.bz2 +md5 : a8817a2ae3062f5b3d3709c10ea24723 +dependencies: + - r-base 3.4.1* + + +bioconductor-tximport 1.8.0 r341_0 +---------------------------------- +file name : bioconductor-tximport-1.8.0-r341_0.tar.bz2 +name : bioconductor-tximport +version : 1.8.0 +build : r341_0 +build number: 0 +size : 233 KB +license : GPL (>=2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-tximport-1.8.0-r341_0.tar.bz2 +md5 : 41630fe7654a64c3e7a33ad5c32fde55 +timestamp : 2018-10-10 00:23:34 UTC +dependencies: + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-tximport 1.8.0 r351_0 +---------------------------------- +file name : bioconductor-tximport-1.8.0-r351_0.tar.bz2 +name : bioconductor-tximport +version : 1.8.0 +build : r351_0 +build number: 0 +size : 248 KB +license : GPL (>=2) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-tximport-1.8.0-r351_0.tar.bz2 +md5 : 5b65dc2789301a86bb87e61ac5a9e7ae +timestamp : 2018-10-10 00:22:38 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-tximport 1.10.0 r351_0 +----------------------------------- +file name : bioconductor-tximport-1.10.0-r351_0.tar.bz2 +name : bioconductor-tximport +version : 1.10.0 +build : r351_0 +build number: 0 +size : 259 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.10.0-r351_0.tar.bz2 +md5 : c0cc0ff8f9561b267704ffbd66119ed7 +timestamp : 2018-12-09 04:57:27 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-tximport 1.10.1 r351_0 +----------------------------------- +file name : bioconductor-tximport-1.10.1-r351_0.tar.bz2 +name : bioconductor-tximport +version : 1.10.1 +build : r351_0 +build number: 0 +size : 260 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.10.1-r351_0.tar.bz2 +md5 : cf18aed8c8efef8bdc57ea56cdb9f839 +timestamp : 2019-04-24 04:41:04 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-tximport 1.12.0 r351_0 +----------------------------------- +file name : bioconductor-tximport-1.12.0-r351_0.tar.bz2 +name : bioconductor-tximport +version : 1.12.0 +build : r351_0 +build number: 0 +size : 273 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.12.0-r351_0.tar.bz2 +md5 : c5b8e87b9a3763b0ac7d4975d272b7ef +timestamp : 2019-05-07 22:55:39 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-tximport 1.12.1 r351_0 +----------------------------------- +file name : bioconductor-tximport-1.12.1-r351_0.tar.bz2 +name : bioconductor-tximport +version : 1.12.1 +build : r351_0 +build number: 0 +size : 273 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.12.1-r351_0.tar.bz2 +md5 : 44056601642b532798817f2642ef45ef +timestamp : 2019-06-11 22:28:56 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-tximport 1.12.1 r351_1 +----------------------------------- +file name : bioconductor-tximport-1.12.1-r351_1.tar.bz2 +name : bioconductor-tximport +version : 1.12.1 +build : r351_1 +build number: 1 +size : 285 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.12.1-r351_1.tar.bz2 +md5 : 4ea861a065dc6512422b005812564c43 +timestamp : 2019-06-12 14:14:13 UTC +dependencies: + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-tximport 1.12.3 r36_0 +---------------------------------- +file name : bioconductor-tximport-1.12.3-r36_0.tar.bz2 +name : bioconductor-tximport +version : 1.12.3 +build : r36_0 +build number: 0 +size : 279 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.12.3-r36_0.tar.bz2 +md5 : 04bd33bba15e2b83398013c621eaa142 +timestamp : 2019-07-20 22:44:00 UTC +dependencies: + - r-base >=3.6,<3.7.0a0 + + +bioconductor-tximport 1.14.0 r36_0 +---------------------------------- +file name : bioconductor-tximport-1.14.0-r36_0.tar.bz2 +name : bioconductor-tximport +version : 1.14.0 +build : r36_0 +build number: 0 +size : 351 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.14.0-r36_0.tar.bz2 +md5 : 8e5d6a29be2289590fd8868bf6c513a9 +timestamp : 2019-11-01 11:36:43 UTC +dependencies: + - r-base >=3.6,<3.7.0a0 + + +bioconductor-tximport 1.16.0 r40_0 +---------------------------------- +file name : bioconductor-tximport-1.16.0-r40_0.tar.bz2 +name : bioconductor-tximport +version : 1.16.0 +build : r40_0 +build number: 0 +size : 359 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.16.0-r40_0.tar.bz2 +md5 : 382bba359b7ce7f2379b7973e4f046b4 +timestamp : 2020-05-09 17:56:30 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + + +bioconductor-tximport 1.18.0 r40_0 +---------------------------------- +file name : bioconductor-tximport-1.18.0-r40_0.tar.bz2 +name : bioconductor-tximport +version : 1.18.0 +build : r40_0 +build number: 0 +size : 364 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.18.0-r40_0.tar.bz2 +md5 : 1eebdad51713fee759c215dd25c7860a +timestamp : 2020-10-29 17:10:18 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + + +bioconductor-tximport 1.18.0 r40hdfd78af_1 +------------------------------------------ +file name : bioconductor-tximport-1.18.0-r40hdfd78af_1.tar.bz2 +name : bioconductor-tximport +version : 1.18.0 +build : r40hdfd78af_1 +build number: 1 +size : 359 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.18.0-r40hdfd78af_1.tar.bz2 +md5 : f31e5c69d85513707e720eb9b84ef911 +timestamp : 2021-03-26 03:53:37 UTC +dependencies: + - r-base >=4.0,<4.1.0a0 + + +bioconductor-tximport 1.20.0 r41hdfd78af_0 +------------------------------------------ +file name : bioconductor-tximport-1.20.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-tximport +version : 1.20.0 +build : r41hdfd78af_0 +build number: 0 +size : 358 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.20.0-r41hdfd78af_0.tar.bz2 +md5 : e7c86b15598c2064bdc0d4f15184242a +timestamp : 2021-05-30 22:50:03 UTC +dependencies: + - r-base >=4.1,<4.2.0a0 + + +bioconductor-tximport 1.22.0 r41hdfd78af_0 +------------------------------------------ +file name : bioconductor-tximport-1.22.0-r41hdfd78af_0.tar.bz2 +name : bioconductor-tximport +version : 1.22.0 +build : r41hdfd78af_0 +build number: 0 +size : 363 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.22.0-r41hdfd78af_0.tar.bz2 +md5 : fd313bcfa3606af12c83fbae83ac6847 +timestamp : 2021-11-01 13:43:15 UTC +dependencies: + - r-base >=4.1,<4.2.0a0 + + +bioconductor-tximport 1.26.0 r42hdfd78af_0 +------------------------------------------ +file name : bioconductor-tximport-1.26.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-tximport +version : 1.26.0 +build : r42hdfd78af_0 +build number: 0 +size : 366 KB +license : GPL (>=2) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-tximport-1.26.0-r42hdfd78af_0.tar.bz2 +md5 : 69a80dceee9505ea67f38a04d7fe142f +timestamp : 2022-11-03 06:22:08 UTC +dependencies: + - r-base >=4.2,<4.3.0a0 + + +bioconductor-tximport 1.28.0 r43hdfd78af_0 +------------------------------------------ +file name : bioconductor-tximport-1.28.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-tximport +version : 1.28.0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-vectrapolarisdata.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-vectrapolarisdata.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..aaaf924d17b7fc7563578fd21fe2f03b23cfe34a --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-vectrapolarisdata.manual_bundle.txt @@ -0,0 +1,128 @@ +# Tool: bioconductor-vectrapolarisdata +software_name: bioconductor-vectrapolarisdata +tier: T1 +domain: spatial_transcriptomics +downloads: 3661 +summary: Vectra Polaris and Vectra 3 multiplex single-cell imaging data +description: Provides two multiplex imaging datasets collected on Vectra instruments at the University of Colorado Anschutz Medical Campus. Data are provided as a Spatial Experiment objects. Data is provided in tabular form and has been segmented and phenotyped using Inform software. Raw .tiff files are not included. +dependencies: bioconductor-data-packages >=20260207, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, curl, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.16/data/experiment/html/VectraPolarisData.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.16/data/experiment/html/VectraPolarisData.html +Bioconductor - VectraPolarisData About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Experiment Packages VectraPolarisData VectraPolarisData This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see VectraPolarisData . Vectra Polaris and Vectra 3 multiplex single-cell imaging data DOI: 10.18129/B9.bioc.VectraPolarisData Bioconductor version: 3.16 Provides two multiplex imaging datasets collected on Vectra instruments at the University of Colorado Anschutz Medical Campus. Data are provided as a Spatial Experiment objects. Data is provided in tabular form and has been segmented and phenotyped using Inform software. Raw .tiff files are not included. Author: Wrobel Julia [aut, cre] , Tusharkanti Ghosh [aut] Maintainer: Wrobel Julia <julia.wrobel at cuanschutz.edu> Citation (from within R, enter citation("VectraPolarisData") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("VectraPolarisData") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("VectraPolarisData") VectraPolarisData HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentData , ExperimentHub , Homo_sapiens_Data , ReproducibleResearch , SingleCellData , SpatialData Version 1.2.0 License Artistic-2.0 Depends ExperimentHub , SpatialExperiment , utils Imports System Requirements URL https://github.com/julia-wrobel/VectraPolarisData Bug Reports https://support.bioconductor.org/t/VectraPolarisData See More Suggests BiocStyle , knitr, rmarkdown, dplyr Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package VectraPolarisData_1.2.0.tar.gz Windows Binary macOS Binary (x86_64) macOS Binary (arm64) Source Repository git clone https://git.bioconductor.org/packages/VectraPolarisData Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VectraPolarisData Package Short Url https://bioconductor.org/packages/VectraPolarisData/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-vectrapolarisdata --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-vectrapolarisdata 1.2.0 r42hdfd78af_0 +-------------------------------------------------- +file name : bioconductor-vectrapolarisdata-1.2.0-r42hdfd78af_0.tar.bz2 +name : bioconductor-vectrapolarisdata +version : 1.2.0 +build : r42hdfd78af_0 +build number: 0 +size : 9 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-vectrapolarisdata-1.2.0-r42hdfd78af_0.tar.bz2 +md5 : 1bd4337130a3564321ebce46cdef2e5c +timestamp : 2022-11-09 10:34:41 UTC +dependencies: + - bioconductor-data-packages >=20221108 + - bioconductor-experimenthub >=2.6.0,<2.7.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - curl + - r-base >=4.2,<4.3.0a0 + + +bioconductor-vectrapolarisdata 1.4.0 r43hdfd78af_0 +-------------------------------------------------- +file name : bioconductor-vectrapolarisdata-1.4.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-vectrapolarisdata +version : 1.4.0 +build : r43hdfd78af_0 +build number: 0 +size : 10 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-vectrapolarisdata-1.4.0-r43hdfd78af_0.tar.bz2 +md5 : 4769955c77418cc798f58b0edaa14c7c +timestamp : 2023-07-15 02:20:51 UTC +dependencies: + - bioconductor-data-packages >=20230706 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-vectrapolarisdata 1.6.0 r43hdfd78af_0 +-------------------------------------------------- +file name : bioconductor-vectrapolarisdata-1.6.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-vectrapolarisdata +version : 1.6.0 +build : r43hdfd78af_0 +build number: 0 +size : 10 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-vectrapolarisdata-1.6.0-r43hdfd78af_0.tar.bz2 +md5 : e01c73c1c7972a662e942eac1005bd97 +timestamp : 2023-12-08 13:10:41 UTC +dependencies: + - bioconductor-data-packages >=20231203 + - bioconductor-experimenthub >=2.10.0,<2.11.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - curl + - r-base >=4.3,<4.4.0a0 + + +bioconductor-vectrapolarisdata 1.10.0 r44hdfd78af_0 +--------------------------------------------------- +file name : bioconductor-vectrapolarisdata-1.10.0-r44hdfd78af_0.tar.bz2 +name : bioconductor-vectrapolarisdata +version : 1.10.0 +build : r44hdfd78af_0 +build number: 0 +size : 10 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-vectrapolarisdata-1.10.0-r44hdfd78af_0.tar.bz2 +md5 : b34d8c3214ec8d430556d3dfb6f96b0a +timestamp : 2024-12-22 17:16:05 UTC +dependencies: + - bioconductor-data-packages >=20241103 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - curl + - r-base >=4.4,<4.5.0a0 + + +bioconductor-vectrapolarisdata 1.14.0 r45hdfd78af_0 +--------------------------------------------------- +file name : bioconductor-vectrapolarisdata-1.14.0-r45hdfd78af_0.conda +name : bioconductor-vectrapolarisdata +version : 1.14.0 +build : r45hdfd78af_0 +build number: 0 +size : 12 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-vectrapolarisdata-1.14.0-r45hdfd78af_0.conda +md5 : 19a4a3dbcad83ad40badcd9ac5178de8 +timestamp : 2026-03-01 18:18:34 UTC +dependencies: + - bioconductor-data-packages >=20260207 + - bioconductor-experimenthub >=3.0.0,<3.1.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - curl + - r-base >=4.5,<4.6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-visiumstitched.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-visiumstitched.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..a89f80638b700fd1db7dd8a156f6de2166ab8f5d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-visiumstitched.manual_bundle.txt @@ -0,0 +1,60 @@ +# Tool: bioconductor-visiumstitched +software_name: bioconductor-visiumstitched +tier: T1 +domain: spatial_transcriptomics +downloads: 28 +summary: Enable downstream analysis of Visium capture areas stitched together with Fiji +description: This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexagonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects. +dependencies: bioconductor-biocbaseutils >=1.12.0,<1.13.0, bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-dropletutils >=1.30.0,<1.31.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-spatiallibd >=1.22.0,<1.23.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-clue, r-dplyr, r-imager, r-matrix, r-pkgcond, r-readr, r-rjson, r-stringr, r-tibble, r-tidyr, r-xml2 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/visiumStitched.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/visiumStitched.html +Bioconductor - visiumStitched Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages visiumStitched visiumStitched This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see visiumStitched . Enable downstream analysis of Visium capture areas stitched together with Fiji DOI: 10.18129/B9.bioc.visiumStitched Bioconductor version: 3.22 This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexagonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects. Author: Nicholas J. Eagles [aut, cre] ORCID: 0000-0002-9808-5254 , Leonardo Collado-Torres [ctb] ORCID: 0000-0003-2140-308X Maintainer: Nicholas J. Eagles <nickeagles77 at gmail.com> Citation (from within R, enter citation("visiumStitched") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("visiumStitched") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("visiumStitched") Introduction to visiumStitched HTML R Script Miscellaneous notes HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataImport , GeneExpression , Software , Spatial , Transcription , Transcriptomics , Visualization Version 1.2.0 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License Artistic-2.0 Depends R (>= 4.4), SpatialExperiment Imports BiocBaseUtils , BiocGenerics , clue , dplyr , DropletUtils , grDevices, imager , Matrix , methods, pkgcond , readr , rjson , S4Vectors , SingleCellExperiment , spatialLIBD (>= 1.17.8), stringr , SummarizedExperiment , tibble , tidyr , xml2 System Requirements URL https://github.com/LieberInstitute/visiumStitched Bug Reports https://support.bioconductor.org/tag/visiumStitched See More Suggests BiocFileCache , BiocStyle , ggplot2 , knitr , RefManageR , rmarkdown , sessioninfo , Seurat , testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package visiumStitched_1.2.0.tar.gz Windows Binary (x86_64) visiumStitched_1.2.0.zip (64-bit only) macOS Binary (x86_64) visiumStitched_1.2.0.tgz macOS Binary (arm64) visiumStitched_1.2.0.tgz Source Repository git clone https://git.bioconductor.org/packages/visiumStitched Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/visiumStitched Bioc Package Browser https://code.bioconductor.org/browse/visiumStitched/ Package Short Url https://bioconductor.org/packages/visiumStitched/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-visiumstitched --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bioconductor-visiumstitched 1.2.0 r45hdfd78af_0 +----------------------------------------------- +file name : bioconductor-visiumstitched-1.2.0-r45hdfd78af_0.conda +name : bioconductor-visiumstitched +version : 1.2.0 +build : r45hdfd78af_0 +build number: 0 +size : 3.0 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-visiumstitched-1.2.0-r45hdfd78af_0.conda +md5 : be3769f48b551b390610f4a5878ad130 +timestamp : 2026-03-03 08:03:42 UTC +dependencies: + - bioconductor-biocbaseutils >=1.12.0,<1.13.0 + - bioconductor-biocgenerics >=0.56.0,<0.57.0 + - bioconductor-dropletutils >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-spatiallibd >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-clue + - r-dplyr + - r-imager + - r-matrix + - r-pkgcond + - r-readr + - r-rjson + - r-stringr + - r-tibble + - r-tidyr + - r-xml2 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-voyager.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-voyager.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..deae013920a6f61ecb1ec02d1f55b062f58f37e3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-voyager.manual_bundle.txt @@ -0,0 +1,210 @@ +# Tool: bioconductor-voyager +software_name: bioconductor-voyager +tier: T1 +domain: spatial_transcriptomics +downloads: 4691 +summary: From geospatial to spatial omics +description: SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results. +dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-bluster >=1.20.0,<1.21.0, bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-spatialfeatureexperiment >=1.12.0,<1.13.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-ggnewscale, r-ggplot2 >=3.4.0, r-lifecycle, r-matrix, r-memuse, r-patchwork, r-rlang, r-rspectra, r-scales, r-scico, r-sf, r-spdep, r-terra, r-zeallot +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.16/bioc/html/Voyager.html +doc_url: +dev_url: + +## URL Docs Extract +### https://bioconductor.org/packages/3.16/bioc/html/Voyager.html +Bioconductor - Voyager About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Software Packages Voyager Voyager This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Voyager . From geospatial to spatial omics DOI: 10.18129/B9.bioc.Voyager Bioconductor version: 3.16 SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. This first version supports univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. The Voyager package also implements plotting functions to plot SFE data and ESDA results. Multivariate ESDA and univariate local metrics will be added in later versions. Author: Lambda Moses [aut, cre] , Kayla Jackson [aut] , Lior Pachter [aut, rev] Maintainer: Lambda Moses <dlu2 at caltech.edu> Citation (from within R, enter citation("Voyager") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Voyager") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("Voyager") Functionality overview HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews GeneExpression , Software , Spatial , Transcriptomics , Visualization Version 1.0.10 In Bioconductor since BioC 3.16 (R-4.2) (1.5 years) License Artistic-2.0 Depends R (>= 4.2.0) Imports BiocParallel , bluster , ggnewscale, ggplot2 (>= 3.4.0), Matrix, methods, patchwork, rlang, S4Vectors , scales, scico, sf, SingleCellExperiment , SpatialExperiment , SpatialFeatureExperiment , spdep, stats, SummarizedExperiment System Requirements URL https://github.com/pachterlab/voyager Bug Reports https://github.com/pachterlab/voyager/issues See More Suggests BiocSingular , BiocStyle , cowplot, dbscan, ExperimentHub , hexbin, knitr, rmarkdown, scater , scattermore, scran , SFEData , sparseMatrixStats , testthat (>= 3.0.0), vdiffr Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package Voyager_1.0.10.tar.gz Windows Binary Voyager_1.0.10.zip macOS Binary (x86_64) Voyager_1.0.10.tgz macOS Binary (arm64) Voyager_1.0.10.tgz Source Repository git clone https://git.bioconductor.org/packages/Voyager Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Voyager Bioc Package Browser https://code.bioconductor.org/browse/Voyager/ Package Short Url https://bioconductor.org/packages/Voyager/ Package Downloads Report Download Stats Old Source Packages for BioC 3.16 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2024 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-voyager --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bioconductor-voyager 1.0.3 r42hdfd78af_0 +---------------------------------------- +file name : bioconductor-voyager-1.0.3-r42hdfd78af_0.tar.bz2 +name : bioconductor-voyager +version : 1.0.3 +build : r42hdfd78af_0 +build number: 0 +size : 1.4 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-voyager-1.0.3-r42hdfd78af_0.tar.bz2 +md5 : 66faf43ffc9a0e4e3aa1ca103a6638b2 +timestamp : 2022-11-06 14:20:22 UTC +dependencies: + - bioconductor-biocparallel >=1.32.0,<1.33.0 + - bioconductor-bluster >=1.8.0,<1.9.0 + - bioconductor-s4vectors >=0.36.0,<0.37.0 + - bioconductor-singlecellexperiment >=1.20.0,<1.21.0 + - bioconductor-spatialexperiment >=1.8.0,<1.9.0 + - bioconductor-spatialfeatureexperiment >=1.0.0,<1.1.0 + - bioconductor-summarizedexperiment >=1.28.0,<1.29.0 + - r-base >=4.2,<4.3.0a0 + - r-ggnewscale + - r-ggplot2 + - r-matrix + - r-patchwork + - r-rlang + - r-scales + - r-scico + - r-sf + - r-spdep + + +bioconductor-voyager 1.2.3 r43hdfd78af_0 +---------------------------------------- +file name : bioconductor-voyager-1.2.3-r43hdfd78af_0.tar.bz2 +name : bioconductor-voyager +version : 1.2.3 +build : r43hdfd78af_0 +build number: 0 +size : 4.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-voyager-1.2.3-r43hdfd78af_0.tar.bz2 +md5 : 1996c444aadea65f8085e202dfd70ae5 +timestamp : 2023-07-16 13:23:14 UTC +dependencies: + - bioconductor-biocparallel >=1.34.0,<1.35.0 + - bioconductor-bluster >=1.10.0,<1.11.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-sparsematrixstats >=1.12.0,<1.13.0 + - bioconductor-spatialexperiment >=1.10.0,<1.11.0 + - bioconductor-spatialfeatureexperiment >=1.2.0,<1.3.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-base >=4.3,<4.4.0a0 + - r-ggnewscale + - r-ggplot2 >=3.4.0 + - r-lifecycle + - r-matrix + - r-patchwork + - r-rlang + - r-rspectra + - r-scales + - r-scico + - r-sf + - r-spdep + - r-terra + + +bioconductor-voyager 1.4.0 r43hdfd78af_0 +---------------------------------------- +file name : bioconductor-voyager-1.4.0-r43hdfd78af_0.tar.bz2 +name : bioconductor-voyager +version : 1.4.0 +build : r43hdfd78af_0 +build number: 0 +size : 4.1 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-voyager-1.4.0-r43hdfd78af_0.tar.bz2 +md5 : 8fa7e1f1a60d0a03bda60c5a68dfc1e5 +timestamp : 2023-12-08 00:09:00 UTC +dependencies: + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - bioconductor-bluster >=1.12.0,<1.13.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-spatialexperiment >=1.12.0,<1.13.0 + - bioconductor-spatialfeatureexperiment >=1.4.0,<1.5.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-base >=4.3,<4.4.0a0 + - r-ggnewscale + - r-ggplot2 >=3.4.0 + - r-lifecycle + - r-matrix + - r-matrixstats + - r-patchwork + - r-rlang + - r-rspectra + - r-scales + - r-scico + - r-sf + - r-spdep + - r-terra + + +bioconductor-voyager 1.8.1 r44hdfd78af_0 +---------------------------------------- +file name : bioconductor-voyager-1.8.1-r44hdfd78af_0.tar.bz2 +name : bioconductor-voyager +version : 1.8.1 +build : r44hdfd78af_0 +build number: 0 +size : 4.0 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-voyager-1.8.1-r44hdfd78af_0.tar.bz2 +md5 : 387e712f9815c3cdfc7ac59b97b292b3 +timestamp : 2024-12-25 06:46:10 UTC +dependencies: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-spatialfeatureexperiment >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base >=4.4,<4.5.0a0 + - r-ggnewscale + - r-ggplot2 >=3.4.0 + - r-lifecycle + - r-matrix + - r-matrixstats + - r-memuse + - r-patchwork + - r-rlang + - r-rspectra + - r-scales + - r-scico + - r-sf + - r-spdep + - r-terra + - r-zeallot + + +bioconductor-voyager 1.12.0 r45hdfd78af_0 +----------------------------------------- +file name : bioconductor-voyager-1.12.0-r45hdfd78af_0.conda +name : bioconductor-voyager +version : 1.12.0 +build : r45hdfd78af_0 +build number: 0 +size : 3.9 MB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/bioconductor-voyager-1.12.0-r45hdfd78af_0.conda +md5 : 624b6ff9dd62653740792135195f6dde +timestamp : 2026-03-03 19:35:39 UTC +dependencies: + - bioconductor-biocparallel >=1.44.0,<1.45.0 + - bioconductor-bluster >=1.20.0,<1.21.0 + - bioconductor-delayedarray >=0.36.0,<0.37.0 + - bioconductor-matrixgenerics >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.48.0,<0.49.0 + - bioconductor-singlecellexperiment >=1.32.0,<1.33.0 + - bioconductor-spatialexperiment >=1.20.0,<1.21.0 + - bioconductor-spatialfeatureexperiment >=1.12.0,<1.13.0 + - bioconductor-summarizedexperiment >=1.40.0,<1.41.0 + - r-base >=4.5,<4.6.0a0 + - r-ggnewscale + - r-ggplot2 >=3.4.0 + - r-lifecycle + - r-matrix + - r-memuse + - r-patchwork + - r-rlang + - r-rspectra + - r-scales + - r-scico + - r-sf + - r-spdep + - r-terra + - r-zeallot diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-xvector.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-xvector.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e032b62c16f2889621cd38ac55a5279f7966541e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-xvector.manual_bundle.txt @@ -0,0 +1,414 @@ +# Tool: bioconductor-xvector +software_name: bioconductor-xvector +tier: T1 +domain: t1_backfill_overall +downloads: 1686205 +summary: Foundation of external vector representation and manipulation in Bioconductor +description: Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk). +dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-iranges >=2.44.0,<2.45.0, bioconductor-iranges >=2.44.0,<2.45.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://bioconductor.org/packages/3.22/bioc/html/XVector.html +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=0] + +Usage: /path/to/Rscript [--options] [-e expr [-e expr2 ...] | file] [args] + +--options accepted are + --help Print usage and exit + --version Print version and exit + --verbose Print information on progress + --default-packages=list + Where 'list' is a comma-separated set + of package names, or 'NULL' +or options to R, in addition to --no-echo --no-restore, such as + --save Do save workspace at the end of the session + --no-environ Don't read the site and user environment files + --no-site-file Don't read the site-wide Rprofile + --no-init-file Don't read the user R profile + --restore Do restore previously saved objects at startup + --vanilla Combine --no-save, --no-restore, --no-site-file + --no-init-file and --no-environ + +'file' may contain spaces but not shell metacharacters +Expressions (one or more '-e ') may be used *instead* of 'file' +See also ?Rscript from within R + + + +## URL Docs Extract +### https://bioconductor.org/packages/3.22/bioc/html/XVector.html +Bioconductor - XVector Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages XVector XVector This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see XVector . Foundation of external vector representation and manipulation in Bioconductor DOI: 10.18129/B9.bioc.XVector Bioconductor version: 3.22 Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk). Author: Hervé Pagès and Patrick Aboyoun Maintainer: Hervé Pagès <hpages.on.github at gmail.com> Citation (from within R, enter citation("XVector") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("XVector") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews DataRepresentation , Infrastructure , Software Version 0.50.0 In Bioconductor since BioC 2.13 (R-3.0) (12.5 years) License Artistic-2.0 Depends R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.43.8) Imports methods, utils, stats, tools, BiocGenerics , S4Vectors , IRanges System Requirements URL https://bioconductor.org/packages/XVector Bug Reports https://github.com/Bioconductor/XVector/issues See More Suggests Biostrings , drosophila2probe , RUnit Linking To S4Vectors , IRanges Enhances Depends On Me Biostrings , triplex Imports Me Bioc.gff , BSgenome , ChIPsim , CNEr , compEpiTools , crisprScore , dada2 , DECIPHER , gcrma , GenomAutomorphism , GenomicFeatures , Gviz , HiLDA , IONiseR , IsoformSwitchAnalyzeR , kebabs , MatrixRider , Modstrings , monaLisa , ProteoDisco , ribosomeProfilingQC , Rsamtools , rtracklayer , SparseArray , Structstrings , TFBSTools , tracktables , tRNA , tRNAscanImport , VariantAnnotation Suggests Me CNVMetrics , IRanges , IWTomics , LOLA , musicatk , inDAGO Links To Me Bioc.gff , Biostrings , CNEr , DECIPHER , kebabs , MatrixRider , pwalign , Rsamtools , rtracklayer , ShortRead , SparseArray , triplex , VariantAnnotation , VariantFiltering Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package XVector_0.50.0.tar.gz Windows Binary (x86_64) XVector_0.50.0.zip macOS Binary (x86_64) XVector_0.50.0.tgz macOS Binary (arm64) XVector_0.50.0.tgz Source Repository git clone https://git.bioconductor.org/packages/XVector Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/XVector Bioc Package Browser https://code.bioconductor.org/browse/XVector/ Package Short Url https://bioconductor.org/packages/XVector/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright © 2003 - 2026 Bioconductor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bioconductor-xvector --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +bioconductor-xvector 0.8.0 0 +---------------------------- +file name : bioconductor-xvector-0.8.0-0.tar.bz2 +name : bioconductor-xvector +version : 0.8.0 +build : 0 +build number: 0 +size : 378 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.8.0-0.tar.bz2 +md5 : abce63b1c1facea41e95e38f47a0d006 +dependencies: + - bioconductor-biocgenerics + - bioconductor-iranges + - bioconductor-s4vectors + - r >=3.1.0 + + +bioconductor-xvector 0.10.0 0 +----------------------------- +file name : bioconductor-xvector-0.10.0-0.tar.bz2 +name : bioconductor-xvector +version : 0.10.0 +build : 0 +build number: 0 +size : 385 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.10.0-0.tar.bz2 +md5 : 6470326a12c7fe6bca4d1015b0bd39eb +dependencies: + - bioconductor-biocgenerics >=0.11.3 + - bioconductor-iranges >=2.3.7 + - bioconductor-s4vectors >=0.7.1 + - bioconductor-zlibbioc + - r >=2.8.0 + + +bioconductor-xvector 0.10.0 1 +----------------------------- +file name : bioconductor-xvector-0.10.0-1.tar.bz2 +name : bioconductor-xvector +version : 0.10.0 +build : 1 +build number: 1 +size : 382 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.10.0-1.tar.bz2 +md5 : b35c5494fbd57719506344772e58a642 +dependencies: + - bioconductor-biocgenerics >=0.11.3 + - bioconductor-iranges >=2.3.7 + - bioconductor-s4vectors >=0.7.1 + - bioconductor-zlibbioc + - r >=2.8.0 + + +bioconductor-xvector 0.12.1 r3.3.1_0 +------------------------------------ +file name : bioconductor-xvector-0.12.1-r3.3.1_0.tar.bz2 +name : bioconductor-xvector +version : 0.12.1 +build : r3.3.1_0 +build number: 0 +size : 383 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.12.1-r3.3.1_0.tar.bz2 +md5 : a6ab072cb2b0de4705d35cc065e42c73 +dependencies: + - bioconductor-biocgenerics >=0.11.3 + - bioconductor-iranges >=2.5.27 + - bioconductor-s4vectors >=0.9.29 + - bioconductor-zlibbioc + - r 3.3.1* + + +bioconductor-xvector 0.14.1 r3.3.1_0 +------------------------------------ +file name : bioconductor-xvector-0.14.1-r3.3.1_0.tar.bz2 +name : bioconductor-xvector +version : 0.14.1 +build : r3.3.1_0 +build number: 0 +size : 391 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.14.1-r3.3.1_0.tar.bz2 +md5 : a84573acf1120a47d1ba729568eb7c44 +dependencies: + - bioconductor-biocgenerics >=0.19.2 + - bioconductor-iranges >=2.5.27 + - bioconductor-s4vectors >=0.9.29 + - bioconductor-zlibbioc + - r-base 3.3.1* + + +bioconductor-xvector 0.14.1 r3.3.2_0 +------------------------------------ +file name : bioconductor-xvector-0.14.1-r3.3.2_0.tar.bz2 +name : bioconductor-xvector +version : 0.14.1 +build : r3.3.2_0 +build number: 0 +size : 392 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.14.1-r3.3.2_0.tar.bz2 +md5 : f1c071ef34db8d8bec74b709da551349 +dependencies: + - bioconductor-biocgenerics >=0.19.2 + - bioconductor-iranges >=2.5.27 + - bioconductor-s4vectors >=0.9.29 + - bioconductor-zlibbioc + - r-base 3.3.2* + + +bioconductor-xvector 0.14.1 r3.4.1_0 +------------------------------------ +file name : bioconductor-xvector-0.14.1-r3.4.1_0.tar.bz2 +name : bioconductor-xvector +version : 0.14.1 +build : r3.4.1_0 +build number: 0 +size : 431 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.14.1-r3.4.1_0.tar.bz2 +md5 : f3fef6713e6570d67a80db4555bcc199 +dependencies: + - bioconductor-biocgenerics >=0.19.2 + - bioconductor-iranges >=2.5.27 + - bioconductor-s4vectors >=0.9.29 + - bioconductor-zlibbioc + - r-base 3.4.1* + + +bioconductor-xvector 0.16.0 r3.4.1_0 +------------------------------------ +file name : bioconductor-xvector-0.16.0-r3.4.1_0.tar.bz2 +name : bioconductor-xvector +version : 0.16.0 +build : r3.4.1_0 +build number: 0 +size : 429 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.16.0-r3.4.1_0.tar.bz2 +md5 : f1b4ef7ab976e36f9852c2cea93277e9 +dependencies: + - bioconductor-biocgenerics >=0.19.2 + - bioconductor-iranges >=2.9.18 + - bioconductor-s4vectors >=0.13.13 + - bioconductor-zlibbioc + - r-base 3.4.1* + + +bioconductor-xvector 0.18.0 r3.4.1_0 +------------------------------------ +file name : bioconductor-xvector-0.18.0-r3.4.1_0.tar.bz2 +name : bioconductor-xvector +version : 0.18.0 +build : r3.4.1_0 +build number: 0 +size : 441 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.18.0-r3.4.1_0.tar.bz2 +md5 : aa2bfc2c3489898b58fb80e507b789f6 +dependencies: + - bioconductor-biocgenerics >=0.19.2 + - bioconductor-iranges >=2.9.18 + - bioconductor-s4vectors >=0.15.14 + - bioconductor-zlibbioc + - r-base 3.4.1* + + +bioconductor-xvector 0.20.0 r341h470a237_0 +------------------------------------------ +file name : bioconductor-xvector-0.20.0-r341h470a237_0.tar.bz2 +name : bioconductor-xvector +version : 0.20.0 +build : r341h470a237_0 +build number: 0 +size : 446 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.20.0-r341h470a237_0.tar.bz2 +md5 : 5158d7eaede99bcf81fd74a4d2f97f9c +timestamp : 2018-10-12 14:43:32 UTC +dependencies: + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - bioconductor-iranges >=2.14.12,<2.16.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - bioconductor-zlibbioc >=1.26.0,<1.28.0 + - libgcc-ng >=4.9 + - r-base >=3.4.1,<3.4.2.0a0 + + +bioconductor-xvector 0.20.0 r351h470a237_0 +------------------------------------------ +file name : bioconductor-xvector-0.20.0-r351h470a237_0.tar.bz2 +name : bioconductor-xvector +version : 0.20.0 +build : r351h470a237_0 +build number: 0 +size : 702 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.20.0-r351h470a237_0.tar.bz2 +md5 : 87e977a825338897ffa22f478d65f314 +timestamp : 2018-10-12 14:44:45 UTC +dependencies: + - bioconductor-biocgenerics >=0.26.0,<0.28.0 + - bioconductor-iranges >=2.14.12,<2.16.0 + - bioconductor-s4vectors >=0.18.3,<0.20.0 + - bioconductor-zlibbioc >=1.26.0,<1.28.0 + - libgcc-ng >=4.9 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-xvector 0.22.0 r351h14c3975_0 +------------------------------------------ +file name : bioconductor-xvector-0.22.0-r351h14c3975_0.tar.bz2 +name : bioconductor-xvector +version : 0.22.0 +build : r351h14c3975_0 +build number: 0 +size : 711 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.22.0-r351h14c3975_0.tar.bz2 +md5 : 933cfaf751a5031bd5f1ad07358c11f8 +timestamp : 2018-12-11 17:44:33 UTC +dependencies: + - bioconductor-biocgenerics >=0.28.0,<0.29.0 + - bioconductor-iranges >=2.16.0,<2.17.0 + - bioconductor-s4vectors >=0.20.0,<0.21.0 + - bioconductor-zlibbioc >=1.28.0,<1.29.0 + - libgcc-ng >=7.3.0 + - r-base >=3.5.1,<3.5.2.0a0 + + +bioconductor-xvector 0.24.0 r36h516909a_1 +----------------------------------------- +file name : bioconductor-xvector-0.24.0-r36h516909a_1.tar.bz2 +name : bioconductor-xvector +version : 0.24.0 +build : r36h516909a_1 +build number: 1 +size : 721 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.24.0-r36h516909a_1.tar.bz2 +md5 : b921acce1be34765008bfbdfbe30ac4f +timestamp : 2019-07-22 03:39:39 UTC +dependencies: + - bioconductor-biocgenerics >=0.30.0,<0.31.0 + - bioconductor-iranges >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.22.0,<0.23.0 + - bioconductor-zlibbioc >=1.30.0,<1.31.0 + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-xvector 0.26.0 r36h516909a_0 +----------------------------------------- +file name : bioconductor-xvector-0.26.0-r36h516909a_0.tar.bz2 +name : bioconductor-xvector +version : 0.26.0 +build : r36h516909a_0 +build number: 0 +size : 724 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.26.0-r36h516909a_0.tar.bz2 +md5 : 6cf022d9c089b8ae8c96570d296cd37d +timestamp : 2019-11-01 16:36:39 UTC +dependencies: + - bioconductor-biocgenerics >=0.32.0,<0.33.0 + - bioconductor-iranges >=2.20.0,<2.21.0 + - bioconductor-s4vectors >=0.24.0,<0.25.0 + - bioconductor-zlibbioc >=1.32.0,<1.33.0 + - libgcc-ng >=7.3.0 + - r-base >=3.6,<3.7.0a0 + + +bioconductor-xvector 0.28.0 r40h037d062_0 +----------------------------------------- +file name : bioconductor-xvector-0.28.0-r40h037d062_0.tar.bz2 +name : bioconductor-xvector +version : 0.28.0 +build : r40h037d062_0 +build number: 0 +size : 737 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.28.0-r40h037d062_0.tar.bz2 +md5 : 01200fe9331fe055c54d558c94c01ba4 +timestamp : 2020-05-09 23:20:47 UTC +dependencies: + - bioconductor-biocgenerics >=0.34.0,<0.35.0 + - bioconductor-iranges >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.26.0,<0.27.0 + - bioconductor-zlibbioc >=1.34.0,<1.35.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - liblapack >=3.8.0,<3.9.0a0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-xvector 0.30.0 r40h037d062_0 +----------------------------------------- +file name : bioconductor-xvector-0.30.0-r40h037d062_0.tar.bz2 +name : bioconductor-xvector +version : 0.30.0 +build : r40h037d062_0 +build number: 0 +size : 730 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.30.0-r40h037d062_0.tar.bz2 +md5 : 12d895d5349c7e3f22e58ab06e9d98f9 +timestamp : 2020-10-30 08:37:15 UTC +dependencies: + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - bioconductor-iranges >=2.24.0,<2.25.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - bioconductor-zlibbioc >=1.36.0,<1.37.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - liblapack >=3.8.0,<3.9.0a0 + - r-base >=4.0,<4.1.0a0 + + +bioconductor-xvector 0.30.0 r40hd029910_1 +----------------------------------------- +file name : bioconductor-xvector-0.30.0-r40hd029910_1.tar.bz2 +name : bioconductor-xvector +version : 0.30.0 +build : r40hd029910_1 +build number: 1 +size : 733 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.30.0-r40hd029910_1.tar.bz2 +md5 : 0d858121b171deeaabcbda9ec3746e29 +timestamp : 2021-03-28 14:49:52 UTC +dependencies: + - bioconductor-biocgenerics >=0.36.0,<0.37.0 + - bioconductor-iranges >=2.24.0,<2.25.0 + - bioconductor-s4vectors >=0.28.0,<0.29.0 + - bioconductor-zlibbioc >=1.36.0,<1.37.0 + - libblas >=3.8.0,<4.0a0 + - libgcc-ng >=9.3.0 + - liblapack diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bowtie2.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bowtie2.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2f4dcd13b09200a76ef55c8b96ce43272d7bfbb --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bowtie2.manual_bundle.txt @@ -0,0 +1,501 @@ +# Tool: bowtie2 +software_name: bowtie2 +tier: T1 +domain: t1_backfill_overall +downloads: 3187767 +summary: A fast and sensitive gapped read aligner. +description: A fast and sensitive gapped read aligner. +dependencies: _openmp_mutex >=4.5, libgcc >=14, libgomp, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, perl, python, zstd >=1.5.7,<1.6.0a0 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml +doc_url: https://github.com/BenLangmead/bowtie2/blob/v2.5.5/README.md +dev_url: https://github.com/BenLangmead/bowtie2 + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/BenLangmead/bowtie2/blob/v2.5.5/README.md +bowtie2/README.md at v2.5.5 · BenLangmead/bowtie2 · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} BenLangmead / bowtie2 Public Notifications You must be signed in to change notification settings Fork 175 Star 789 Code Issues 176 Pull requests 11 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights Files Expand file tree v2.5.5 Breadcrumbs bowtie2 / README.md Copy path Blame More file actions Blame More file actions Latest commit History History History 130 lines (98 loc) · 9.85 KB v2.5.5 Breadcrumbs bowtie2 / README.md Top File metadata and controls Preview Code Blame 130 lines (98 loc) · 9.85 KB Raw Copy raw file Download raw file Outline Edit and raw actions Overview Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Obtaining Bowtie2 Bowtie 2 is available from various package managers, notably Bioconda . With Bioconda installed, you should be able to install Bowtie 2 with conda install bowtie2 . Containerized versions of Bowtie 2 are also available via the Biocontainers project (e.g. via Docker Hub ). You can also download Bowtie 2 sources and binaries from the "releases" tab on this page. Binaries are available for the Linux, Mac OS X, and Windows. By utilizing the SIMDE project Bowtie 2 now supports the following architectures: ARM64, PPC64, and s390x. If you plan to compile Bowtie 2 yourself, make sure you at least have the zlib library and header files installed. See the Building from source section of the manual for details. Getting started Looking to try out Bowtie 2? Check out the Bowtie 2 UI (currently in beta). Alignment bowtie2 takes a Bowtie 2 index and a set of sequencing read files and outputs a set of alignments in SAM format. "Alignment" is the process by which we discover how and where the read sequences are similar to the reference sequence. An "alignment" is a result from this process, specifically: an alignment is a way of "lining up" some or all of the characters in the read with some characters from the reference in a way that reveals how they're similar. For example: Read: GACTGGGCGATCTCGACTTCG ||||| |||||||||| ||| Reference: GACTG--CGATCTCGACATCG Where dash symbols represent gaps and vertical bars show where aligned characters match. We use alignment to make an educated guess as to where a read originated with respect to the reference genome. It's not always possible to determine this with certainty. For instance, if the reference genome contains several long stretches of As ( AAAAAAAAA etc.) and the read sequence is a short stretch of As ( AAAAAAA ), we cannot know for certain exactly where in the sea of As the read originated. Examples # Aligning unpaired reads bowtie2 -x example/index/lambda_virus -U example/reads/longreads.fq # Aligning paired reads bowtie2 -x example/index/lambda_virus -1 example/reads/reads_1.fq -2 example/reads/reads_2.fq Building an index bowtie2-build builds a Bowtie index from a set of DNA sequences. bowtie2-build outputs a set of 6 files with suffixes .1.bt2 , .2.bt2 , .3.bt2 , .4.bt2 , .rev.1.bt2 , and .rev.2.bt2 . In the case of a large index these suffixes will have a bt2l termination. These files together constitute the index: they are all that is needed to align reads to that reference. The original sequence FASTA files are no longer used by Bowtie 2 once the index is built. Bowtie 2's .bt2 index format is different from Bowtie 1's .ebwt format, and they are not compatible with each other. Examples # Building a small index bowtie2-build example/reference/lambda_virus.fa example/index/lambda_virus # Building a large index bowtie2-build --large-index example/reference/lambda_virus.fa example/index/lambda_virus Index inpection bowtie2-inspect extracts information from a Bowtie 2 index about what kind of index it is and what reference sequences were used to build it. When run without any options, the tool will output a FASTA file containing the sequences of the original references (with all non-A/C/G/T characters converted to Ns). It can also be used to extract just the reference sequence names using the -n/--names option or a more verbose summary using the -s/--summary option. Examples # Inspecting a lambda_virus index (small index) and outputting the summary bowtie2-inspect --summary example/index/lambda_virus # Inspecting the entire lambda virus index (large index) bowtie2-inspect --large-index example/index/lambda_virus Publications Bowtie 2 Papers Langmead B, Wilks C., Antonescu V., Charles R. Scaling read aligners to hundreds of threads on general-purpose processors . Bioinformatics . bty648. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2 . Nature Methods . 2012, 9:357-359. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome . Genome Biology 10:R25. Related Publications P. Ferragina, G. Manzini Opportunistic data structures with applications . IEEE Xplore 10.1109/SFCS.2000.892127 Related Work Check out the Bowtie 2 UI , a shiny , frontend to the Bowtie 2 command line. Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://bowtie-bio.sourceforge.net/bowtie2/index.shtml +Bowtie 2: fast and sensitive read alignment Bowtie 2 Fast and sensitive read alignment Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Site Map Home News archive Manual Getting started Frequently Asked Questions Tools that use Bowtie Latest Release Bowtie2 v2.5.5 02/16/26  Please cite: Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2 . Nature Methods . 2012, 9:357-359. Links Bowtie GitHub repository Report an issue Bowtie Papers citing Bowtie 2 Indexes H. sapiens , GRCh38 no-alt analysis set GRC H. sapiens , GRCh38 no-alt +decoy set GRC H. sapiens , GRCh38 + major SNVs GRC    How we built this , FASTA H. sapiens , GRCh37 GRC H. sapiens , CHM13 v2 T2T H. sapiens , CHM13 v1, plus Y T2T H. sapiens , Ash1v2.0 JHU H. sapiens , Ash1v1.7 JHU H. sapiens , hg19 UCSC H. sapiens , hg18 UCSC M. Musculus , GRCm39 GRC M. Musculus , GRCm38 GRC M. Musculus , mm10 UCSC M. Musculus , mm9 UCSC P. troglodytes , mPanTro3-v2 NHGRI P. troglodytes , Clint_PTRv2 NCBI P. troglodytes , CHIMP2.1.4 Ensembl M. mulatta , MMul_10 Ensembl B. taurus , ARS-UCD2.0 NCBI B. taurus , ARS-UCD1.2 NCBI S. scrofa , Sscrofa11.1 NCBI C. familiaris , CanFam4 NCBI C. familiaris , CanFam3.1 Ensembl R. norvegicus , GRCr8 GRC R. norvegicus , Rnor6.0 NCBI R. norvegicus , rn4 UCSC G. gallus , GRCg6a GRC G. gallus , Galgal4 Ensembl D. rerio , GRCz11 GRC D. rerio , GRCz10 GRC Z. mays , AGPv4 Ensembl Z. mays , B73 RefGenV5 NCBI O. sativa , Build_4.0 NCBI A. thaliana , TAIR10 Ensembl D. melanogaster , BDGP6 Ensembl D. melanogaster , Dmel A4 1.0 NCBI C. elegans , WBcel235 Ensembl S. cerevisiae , R64-1-1 Ensembl All indexes are .bt2 format and are compatible with both Bowtie 2 and with Bowtie as of v1.2.3 Index storage is thanks to AWS Public Datasets program. See the Index zone page for details on the best ways to obtain this data, including from the AWS cloud. Publications Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2 . Nature Methods . 2012, 9:357-359. Langmead B, Wilks C, Antonescu V, Charles R. Scaling read aligners to hundreds of threads on general-purpose processors . Bioinformatics Vol 35, Iss 3, 2019, pp 421–432. Contributors Ben Langmead Daehwan Kim Rone Charles Nae-Chyun Chen Chris Wilks Valentin Antonescu Version 2.5.5 - Feb 16, 2026 bowtie2 Added -d/--deterministic-mode command line option that makes -a / -k deterministic in the way alignments are reported. This deterministic mode runs much significantly faster than -a and consumes less memory. It not yet strictly better than -a when considering alignments found. (PR #520, 521) Add support for selecting AVX version at runtime on x86_64/amd64 CPUs. (PR #515) Version 2.5.4 - May 16, 2024 bowtie2 Added --sam-opt-config command line option for toggling SAM Opt flags. See MANUAL for details. Fixed an issue causing bowtie2 ’s memory usage to increase over time when aligning BAM files. Changed bowtie2 to continue flushing output in the event of a partial write. Changed the behavior of bowtie2-build to throw an exception if it is unable to write the BWT (.1.bt2, .1.rev.bt2). In prior versions bowtie2-build , would silently ignore the error which has led some to report the absence of the BWT files in a “completed” index build. Reverted the changes made in v2.5.0 that sometimes caused unique concordant alignments to be overcounted. New Indexes for Cow, Chimp, and Rat, added to the sidebar - May 08, 2024 B. taurus , ARS-UCD2.0 P. troglodytes , mPanTro3-v2 R. norvegicus , GRCr8 Version 2.5.3 - Jan 16, 2024 bowtie2 Fixed an issue causing bowtie2 's memory usage to increase over time. Fixed an issue causing bowtie2 to crash when processing eempty FASTQ records. Fixed an issue causing bowtie2 to erroneously treat -f and -F as mutually exclusive. bowtie2-build Add optional support for libsais to bowtie2-build for faster index building. N.B. -- small indexes are capped at 2GB when using libsais as opposed to 4GB when using the default blockwise algorithm. See MANUAL for details. Version 2.5.2 - Oct 13, 2023 bowtie2 Fixed an issue preventing bowtie2 from utilizing the specified number of CPU cores Fixed an issue causing bowtie2 to segfault when reading compressed inputs on Windows Fixed an issue causing bowtie2 to segfault while parsing interleaved reads Overhauled the FASTQ parser with better tolerance for empty lines Version 2.5.1 - Feb 17, 2023 bowtie2 Fixed an issue affecting bowtie2 alignment accuracy. Updated the versions of the NCBI NGS and VDB libraries used by bowtie2 . Fixed a segmentation fault that would occur while aligning SRA data. Fixed an issue preventing --un-mates from properly saving unaligned mates. Version 2.5.0 - Oct 31, 2022 bowtie2 Overall improvements in the use of prefetch instructions. (contribution by Igor Sfiligoi) Made input/output fully asynchronous by using a dedicated thread. (contribution by Igor Sfiligoi) Added support for AVX2 256-bit instructions with can be enabled by setting the SSE_AXV2 environment variable at compile time. (contribution by Igor Sfiligoi) Fixed an issue causing bowtie2 to crash when processing ZSTD files with high compression ratios. Changed the way that unique alignments are counted in summary message to better match up with filters on SAM output Version 2.4.5 - Jan 16, 2022 bowtie2 Fixed issues with bowtie2 BAM parser that would cause bowtie2 to crash when processing input that was encoded with tools other than samtools e.g. Picard. Fixed an issue causing bowtie2 to drop certain optional fields when when aligning BAM reads with the --preserve-tags option. Fixed an issue causing bowtie2 to produce mangled SAM output when specifying --sam-append-comment together with the --passthrough option. Appended GO:query to SAM @HD entry to indicate that reads are grouped by query name, bump SAM version to 1.5 to indicate support for this change. bowtie2-build Implemented thread pool to address performance regressions introduced during the switch to C++11 threads. Fixed an issue causing masked-sequence metadata to be omitted from index. This issue would subsequently result in sequence data, @SQ , being left out from alignment SAM header. Included .tmp extension to index files currenlty being built. The extension is removed only upon successful build. This change seeks to address the assumption that bowtie2-build ran successfully without building the reverse indexes. Fixed an issue causing bowtie2-build to sometimes incorrectly calculate input size. This issue would result in the wrong index type being chosen and only happened with GZip compressed files. bowtie2-inspect Added a new -o/--output option to save the output of bowtie2-inspect to a file instead of being dumped to standard output. Version 2.4.4 - May 23, 2021 Fixed an issue that would sometimes cause deadlocks in bowtie2 when running multithreaded Version 2.4.3 - May 13, 2021 Replaced TBB concurrency with C++ threads Added native support for processing Zstd-compressed read files to >bowtie2 Added native support for processing Zstd-compressed reference-genome files to bowtie2-build Fixed an issue causing bowtie2 to report incorrect alignments on big-endian machines Fixed an issue causing bowtie2 to incorrectly process BAM files on big-endian machines Fixed an issue causing bowtie2 to set an incorrect MAPQ when AS and XS are the maximum for read length Add support for building on Apple M1 processors Version 2.4.2 - Oct 5, 2020 Fixed an issue that would cause the bowtie2 wrapper script to throw an error when using wrapper-specific arguments. Added new --sam-append-comment flag that appends comment from FASTA/Q read to corresponding SAM record. Fixed an issue that would cause qupto , -u , to overflow when there are >= 2 32 query sequences (PR #312). Fixed an issue that would cause bowtie2-build script to incorrectly process reference files. Version 2.4.1 - Feb 28, 2020 Fixed an issue that would cause the bowtie2 wrapper script to incorrectly process certain arguments Version 2.4.0 - Feb 25, 2020 Fixed an issue in -b <bam> input mode where one might prematurely close the read file pointer causing “Bad file descriptor” in other threads Fixed an issue that could cause bowtie2 to crash in --no-1mm-upfront mode Modified bowtie2-build to better handle of flags and positional parameters Migrated all python scripts to python3 Added support for wildcards in input files to bowtie2 , e.g. bowtie2 -x index -q *.fq as opposed to bowtie2 -x index -q 1.fq,2.fq,3.fq... Fixed an issue causing bowtie2 to incorrectly process read names with slash mates plus extra characters (see #265 ) Clarified support for overriding presets with more specific options e.g bowtie2 -x index --local --very-fast-local --L22 -q reads.fq will set the seed length to 22, overriding the 25 set by --very-fast-local Modified SAM output for -k / -a so that supplementary alignments get assigned a MAPQ of 255 Fixed an issue that would sometimes cause bowtie2-build to not generate reverse index files Added preliminary support for ppc64le architectures with the help of SIMDE project (see #271 ) Fixed an issue causing bowtie2 to incorrectly calculate the MAPQ when --mp was specified in combination with --ignore-quals 1000-Genomes major-allele SNP references -- April 26, 2019 For each base where the typical reference has the non-majority allele (according to the 1000 Genomes Project , we substituted in the majority allele instead Links for indexes added to sidebar, as are links for the edited FASTA files We made versions both for GRCh38 primary assembly and hg19 assembly See how we created them Only SNPs (single-base substitutions) are considered for now; indels are future work Because only SNPs are considered, coordinates (e.g. gene annotations) are the same as for typical GRCh38 and hg19 assemblies. Most downstream tools are unaffected as long as major-allele-edited FASTAs are used wherever genome sequences are required. Version 2.3.5.1 - April 16, 2019 Added official support for BAM input files Added official support for CMake build system Added changes to Makefile for creating Reproducible builds (via #210 ) Fix an issue whereby building on aarch64 would require patching sed commands (via #243 ) Fix an issue whereby bowtie2 would incorrectly throw an error while processing --interleaved input Version 2.3.5 - March 16, 2019 Check out the Bowtie 2 UI , currently in beta, a shiny , frontend to the Bowtie2 command line. Added support for obtaining input reads directly from the Sequence Read Archive, via NCBI’s NGS language bindings . This is activated via the --sra-acc option. This implementation is based on Daehwan Kim’s in HISAT2 . Supports both unpaired and paired-end inputs. Bowtie 2 now compiles on ARM architectures (via #216 ) --interleaved can now be combined with FASTA inputs (worked only with FASTQ before) Fixed issue whereby large indexes were not successfully found in the $BOWTIE2_INDEXES directory Fixed input from FIFOs (e.g. via process substitution) to distinguish gzip-compressed versus uncompressed input Fixed issue whereby arguments containing bz2 lz4 were misinterpretted as files Fixed several compiler warnings Fixed issue whereby both ends of a paired-end read could have negative TLEN if they exactly coincided Fixed issue whereby bowtie2-build would hang on end-of-file (via #228 ) Fixed issue whereby wrapper script would sometimes create zombie processes (via #51 ) Fixed issue whereby bowtie2-build and bowtie2-inspect wrappers would fail on some versions of Python/PyPy Replaced old, unhelpful README.md in the project with a version that includes badges, links and some highlights from the manual Note: BAM input support and CMake build support both remain experimental, but we expect to finalize them in the next release Version 2.3.4.3 - September 17, 2018 Fixed an issue causing bowtie2-build and bowtie2-inspect to output incomplete help text. Fixed an issue causing bowtie2-align to crash. Fixed an issue preventing bowtie2 from processing paired and/or unpaired FASTQ reads together with interleaved FASTQ reads. Version 2.3.4.2 - August 07, 2018 Fixed issue causing bowtie2 to fail in --fast-local mode. Fixed issue causing --soft-clipped-unmapped-tlen to be a positional argument. New option --trim-to N causes bowtie2 to trim reads longer than N bases to exactly N bases. Can trim from either 3' or 5' end, e.g. --trim-to 5:30 trims reads to 30 bases, truncating at the 5' end. Updated "Building from source" manual section with additional instructions on installing TBB. Several other updates to manual, including new mentions of Bioconda and Biocontainers . Fixed an issue preventing bowtie2 from processing more than one pattern source when running single threaded. Fixed an issue causing bowtie2 and bowtie2-inspect to crash if the index contains a gap-only segment. Added experimental BAM input mode -b . Works only with unpaired input reads and BAM files that are sorted by read name ( samtools sort -n ). BAM input mode also supports the following options:      --preserve-sam-tags : Preserve any optional fields present in BAM record      --align-paired-reads : Paired-end mode for BAM files Add experimental CMake support Thread-scaling paper appears - July 19, 2018 Our latest work on Bowtie's core thread scaling capabilities just appeared Open Access in the journal Bioinformatics This research was supported in part by NIH grants R01-HG006102 and R01-GM083873 and AWS in Education research grants. Administrator: Ben Langmead . Design by David Herreman + +### https://github.com/BenLangmead/bowtie2 +GitHub - BenLangmead/bowtie2: A fast and sensitive gapped read aligner · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} BenLangmead / bowtie2 Public Notifications You must be signed in to change notification settings Fork 175 Star 789 Code Issues 176 Pull requests 11 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights BenLangmead/bowtie2 master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 2,671 Commits 2,671 Commits .github/ workflows .github/ workflows doc doc example example scripts scripts third_party third_party .gitignore .gitignore .gitmodules .gitmodules .travis.yml .travis.yml AUTHORS AUTHORS BOWTIE2_VERSION BOWTIE2_VERSION CMakeLists.txt CMakeLists.txt LICENSE LICENSE MANUAL MANUAL MANUAL.markdown MANUAL.markdown Makefile Makefile NEWS NEWS README.md README.md TUTORIAL TUTORIAL aligner_bt.cpp aligner_bt.cpp aligner_bt.h aligner_bt.h aligner_cache.cpp aligner_cache.cpp aligner_cache.h aligner_cache.h aligner_driver.cpp aligner_driver.cpp aligner_driver.h aligner_driver.h aligner_metrics.h aligner_metrics.h aligner_report.h aligner_report.h aligner_result.cpp aligner_result.cpp aligner_result.h aligner_result.h aligner_seed.cpp aligner_seed.cpp aligner_seed.h aligner_seed.h aligner_seed2.cpp aligner_seed2.cpp aligner_seed2.h aligner_seed2.h aligner_seed_policy.cpp aligner_seed_policy.cpp aligner_seed_policy.h aligner_seed_policy.h aligner_sw.cpp aligner_sw.cpp aligner_sw.h aligner_sw.h aligner_sw_common.h aligner_sw_common.h aligner_sw_driver.cpp aligner_sw_driver.cpp aligner_sw_driver.h aligner_sw_driver.h aligner_sw_nuc.h aligner_sw_nuc.h aligner_swsse.cpp aligner_swsse.cpp aligner_swsse.h aligner_swsse.h aligner_swsse_ee_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_loc_u8.cpp aln_sink.cpp aln_sink.cpp aln_sink.h aln_sink.h alphabet.cpp alphabet.cpp alphabet.h alphabet.h assert_helpers.h assert_helpers.h banded.cpp banded.cpp banded.h banded.h binary_sa_search.h binary_sa_search.h bitpack.h bitpack.h blockwise_sa.h blockwise_sa.h bowtie2 bowtie2 bowtie2-build bowtie2-build bowtie2-inspect bowtie2-inspect bowtie_build_main.cpp bowtie_build_main.cpp bowtie_main.cpp bowtie_main.cpp bt2_build.cpp bt2_build.cpp bt2_dp.cpp bt2_dp.cpp bt2_idx.cpp bt2_idx.cpp bt2_idx.h bt2_idx.h bt2_inspect.cpp bt2_inspect.cpp bt2_io.cpp bt2_io.cpp bt2_locks.cpp bt2_locks.cpp bt2_locks.h bt2_locks.h bt2_search.cpp bt2_search.cpp bt2_search.h bt2_search.h bt2_util.cpp bt2_util.cpp btypes.h btypes.h ccnt_lut.cpp ccnt_lut.cpp concurrentqueue.h concurrentqueue.h cpu_numa_info.cpp cpu_numa_info.cpp cpu_numa_info.h cpu_numa_info.h diff_sample.cpp diff_sample.cpp diff_sample.h diff_sample.h dp_framer.cpp dp_framer.cpp dp_framer.h dp_framer.h ds.cpp ds.cpp ds.h ds.h edit.cpp edit.cpp edit.h edit.h endian_swap.h endian_swap.h fast_mutex.h fast_mutex.h filebuf.h filebuf.h formats.h formats.h group_walk.cpp group_walk.cpp group_walk.h group_walk.h ival_list.cpp ival_list.cpp ival_list.h ival_list.h limit.cpp limit.cpp limit.h limit.h ls.cpp ls.cpp ls.h ls.h mask.cpp mask.cpp mask.h mask.h mem_ids.h mem_ids.h View all files Repository files navigation README GPL-3.0 license Overview Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Obtaining Bowtie2 Bowtie 2 is available from various package managers, notably Bioconda . With Bioconda installed, you should be able to install Bowtie 2 with conda install bowtie2 . Containerized versions of Bowtie 2 are also available via the Biocontainers project (e.g. via Docker Hub ). You can also download Bowtie 2 sources and binaries from the "releases" tab on this page. Binaries are available for the Linux, Mac OS X, and Windows. By utilizing the SIMDE project Bowtie 2 now supports the following architectures: ARM64, PPC64, and s390x. If you plan to compile Bowtie 2 yourself, make sure you at least have the zlib library and header files installed. See the Building from source section of the manual for details. Getting started Looking to try out Bowtie 2? Check out the Bowtie 2 UI (currently in beta). Alignment bowtie2 takes a Bowtie 2 index and a set of sequencing read files and outputs a set of alignments in SAM format. "Alignment" is the process by which we discover how and where the read sequences are similar to the reference sequence. An "alignment" is a result from this process, specifically: an alignment is a way of "lining up" some or all of the characters in the read with some characters from the reference in a way that reveals how they're similar. For example: Read: GACTGGGCGATCTCGACTTCG ||||| |||||||||| ||| Reference: GACTG--CGATCTCGACATCG Where dash symbols represent gaps and vertical bars show where aligned characters match. We use alignment to make an educated guess as to where a read originated with respect to the reference genome. It's not always possible to determine this with certainty. For instance, if the reference genome contains several long stretches of As ( AAAAAAAAA etc.) and the read sequence is a short stretch of As ( AAAAAAA ), we cannot know for certain exactly where in the sea of As the read originated. Examples # Aligning unpaired reads bowtie2 -x example/index/lambda_virus -U example/reads/longreads.fq # Aligning paired reads bowtie2 -x example/index/lambda_virus -1 example/reads/reads_1.fq -2 example/reads/reads_2.fq Building an index bowtie2-build builds a Bowtie index from a set of DNA sequences. bowtie2-build outputs a set of 6 files with suffixes .1.bt2 , .2.bt2 , .3.bt2 , .4.bt2 , .rev.1.bt2 , and .rev.2.bt2 . In the case of a large index these suffixes will have a bt2l termination. These files together constitute the index: they are all that is needed to align reads to that reference. The original sequence FASTA files are no longer used by Bowtie 2 once the index is built. Bowtie 2's .bt2 index format is different from Bowtie 1's .ebwt format, and they are not compatible with each other. Examples # Building a small index bowtie2-build example/reference/lambda_virus.fa example/index/lambda_virus # Building a large index bowtie2-build --large-index example/reference/lambda_virus.fa example/index/lambda_virus Index inpection bowtie2-inspect extracts information from a Bowtie 2 index about what kind of index it is and what reference sequences were used to build it. When run without any options, the tool will output a FASTA file containing the sequences of the original references (with all non-A/C/G/T characters converted to Ns). It can also be used to extract just the reference sequence names using the -n/--names option or a more verbose summary using the -s/--summary option. Examples # Inspecting a lambda_virus index (small index) and outputting the summary bowtie2-inspect --summary example/index/lambda_virus # Inspecting the entire lambda virus index (large index) bowtie2-inspect --large-index example/index/lambda_virus Publications Bowtie 2 Papers Langmead B, Wilks C., Antonescu V., Charles R. Scaling read aligners to hundreds of threads on general-purpose processors . Bioinformatics . bty648. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2 . Nature Methods . 2012, 9:357-359. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome . Genome Biology 10:R25. Related Publications P. Ferragina, G. Manzini Opportunistic data structures with applications . IEEE Xplore 10.1109/SFCS.2000.892127 Related Work Check out the Bowtie 2 UI , a shiny , frontend to the Bowtie 2 command line. About A fast and sensitive gapped read aligner Topics c-plus-plus bioinformatics genomics read-aligners Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 789 stars Watchers 34 watching Forks 175 forks Report repository Releases 30 v2.5.5 Latest Feb 17, 2026 + 29 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 81.4% Perl 13.8% Python 1.5% C 1.4% Shell 1.0% Makefile 0.6% CMake 0.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bowtie2 --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +bowtie2 2.2.1 py27h2bce143_4 +---------------------------- +file name : bowtie2-2.2.1-py27h2bce143_4.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py27h2bce143_4 +build number: 4 +size : 11.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py27h2bce143_4.tar.bz2 +md5 : 4fe062c00254d42ad4da9e6cee0704e7 +timestamp : 2020-07-09 21:09:11 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - perl + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + + +bowtie2 2.2.1 py27h2d50403_0 +---------------------------- +file name : bowtie2-2.2.1-py27h2d50403_0.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py27h2d50403_0 +build number: 0 +size : 10.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py27h2d50403_0.tar.bz2 +md5 : 0b7ef97aef61f0d9a7a0040405d4905b +timestamp : 2018-08-17 09:01:18 UTC +dependencies: + - libstdcxx-ng >=4.9 + - perl + - python >=2.7,<2.8.0a0 + + +bowtie2 2.2.1 py27h6bb024c_1 +---------------------------- +file name : bowtie2-2.2.1-py27h6bb024c_1.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py27h6bb024c_1 +build number: 1 +size : 10.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py27h6bb024c_1.tar.bz2 +md5 : efd6f07b295bcded8c2270325ff0e863 +timestamp : 2019-02-03 22:44:11 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python >=2.7,<2.8.0a0 + + +bowtie2 2.2.1 py27h6bb024c_2 +---------------------------- +file name : bowtie2-2.2.1-py27h6bb024c_2.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py27h6bb024c_2 +build number: 2 +size : 11.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py27h6bb024c_2.tar.bz2 +md5 : 0d0f26d289a09d24a444491739812e1c +timestamp : 2019-05-13 19:40:08 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python >=2.7,<2.8.0a0 + + +bowtie2 2.2.1 py27he8a552f_5 +---------------------------- +file name : bowtie2-2.2.1-py27he8a552f_5.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py27he8a552f_5 +build number: 5 +size : 14.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py27he8a552f_5.tar.bz2 +md5 : 0ee19f33df45ab88c87912cab38d825c +timestamp : 2021-03-26 12:07:27 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + + +bowtie2 2.2.1 py35h2d50403_0 +---------------------------- +file name : bowtie2-2.2.1-py35h2d50403_0.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py35h2d50403_0 +build number: 0 +size : 10.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py35h2d50403_0.tar.bz2 +md5 : 99e639797c8e7c8433b3f18df585ebd3 +timestamp : 2018-08-17 08:57:37 UTC +dependencies: + - libstdcxx-ng >=4.9 + - perl + - python >=3.5,<3.6.0a0 + + +bowtie2 2.2.1 py36h2d50403_0 +---------------------------- +file name : bowtie2-2.2.1-py36h2d50403_0.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py36h2d50403_0 +build number: 0 +size : 10.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py36h2d50403_0.tar.bz2 +md5 : b060ba92ec87efa681524e042c682919 +timestamp : 2018-08-17 09:04:49 UTC +dependencies: + - libstdcxx-ng >=4.9 + - perl + - python >=3.6,<3.7.0a0 + + +bowtie2 2.2.1 py36h6bb024c_1 +---------------------------- +file name : bowtie2-2.2.1-py36h6bb024c_1.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py36h6bb024c_1 +build number: 1 +size : 10.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py36h6bb024c_1.tar.bz2 +md5 : ef274e9a9383936a01223173bd41a83e +timestamp : 2019-02-03 22:40:15 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python >=3.6,<3.7.0a0 + + +bowtie2 2.2.1 py36h6bb024c_2 +---------------------------- +file name : bowtie2-2.2.1-py36h6bb024c_2.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py36h6bb024c_2 +build number: 2 +size : 11.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py36h6bb024c_2.tar.bz2 +md5 : 0fd8eacb94638514cc18d4bd4b1b13ff +timestamp : 2019-05-13 19:27:14 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python >=3.6,<3.7.0a0 + + +bowtie2 2.2.1 py36hae55d0a_5 +---------------------------- +file name : bowtie2-2.2.1-py36hae55d0a_5.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py36hae55d0a_5 +build number: 5 +size : 14.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py36hae55d0a_5.tar.bz2 +md5 : ce7371f1a9bd2b452c1eb287b4211473 +timestamp : 2021-03-26 12:26:30 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + + +bowtie2 2.2.1 py36hdb11119_3 +---------------------------- +file name : bowtie2-2.2.1-py36hdb11119_3.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py36hdb11119_3 +build number: 3 +size : 11.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py36hdb11119_3.tar.bz2 +md5 : 1fbce4476583c16ce060ae01e65fd23d +timestamp : 2020-05-09 17:11:05 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + + +bowtie2 2.2.1 py36hf1ae8f4_4 +---------------------------- +file name : bowtie2-2.2.1-py36hf1ae8f4_4.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py36hf1ae8f4_4 +build number: 4 +size : 11.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py36hf1ae8f4_4.tar.bz2 +md5 : d25f3a0cf907dd66c335832eb854c26b +timestamp : 2020-07-09 21:01:11 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - perl + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + + +bowtie2 2.2.1 py37h22450f8_5 +---------------------------- +file name : bowtie2-2.2.1-py37h22450f8_5.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py37h22450f8_5 +build number: 5 +size : 14.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py37h22450f8_5.tar.bz2 +md5 : 561ed13a0fc7f72b58d4945af7a33130 +timestamp : 2021-03-26 12:17:00 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + + +bowtie2 2.2.1 py37h6bb024c_1 +---------------------------- +file name : bowtie2-2.2.1-py37h6bb024c_1.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py37h6bb024c_1 +build number: 1 +size : 10.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py37h6bb024c_1.tar.bz2 +md5 : 32ec911d9504f2d496c102600174b6d2 +timestamp : 2019-02-03 22:48:19 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python >=3.7,<3.8.0a0 + + +bowtie2 2.2.1 py37h6bb024c_2 +---------------------------- +file name : bowtie2-2.2.1-py37h6bb024c_2.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py37h6bb024c_2 +build number: 2 +size : 11.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py37h6bb024c_2.tar.bz2 +md5 : 97d18a898d2ba2e1b1de7773e08b335c +timestamp : 2019-05-13 19:33:53 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python >=3.7,<3.8.0a0 + + +bowtie2 2.2.1 py37h99015e2_3 +---------------------------- +file name : bowtie2-2.2.1-py37h99015e2_3.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py37h99015e2_3 +build number: 3 +size : 11.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py37h99015e2_3.tar.bz2 +md5 : 1c45da630c2bb22378a06994a5aef11b +timestamp : 2020-05-09 17:18:30 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + + +bowtie2 2.2.1 py37h9a982cc_4 +---------------------------- +file name : bowtie2-2.2.1-py37h9a982cc_4.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py37h9a982cc_4 +build number: 4 +size : 11.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py37h9a982cc_4.tar.bz2 +md5 : 169f1f3e0bbe633920916cb6a7d45130 +timestamp : 2020-07-09 21:17:01 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - perl + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + + +bowtie2 2.2.1 py38h8c62d01_5 +---------------------------- +file name : bowtie2-2.2.1-py38h8c62d01_5.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py38h8c62d01_5 +build number: 5 +size : 14.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py38h8c62d01_5.tar.bz2 +md5 : a453d81700d996954a078b1d6b25ae39 +timestamp : 2021-03-26 12:35:44 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + + +bowtie2 2.2.1 py38hed8969a_4 +---------------------------- +file name : bowtie2-2.2.1-py38hed8969a_4.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py38hed8969a_4 +build number: 4 +size : 11.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py38hed8969a_4.tar.bz2 +md5 : 9c3dac29c573e6720669d0446f1126da +timestamp : 2020-08-30 16:56:26 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - perl + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + + +bowtie2 2.2.1 py39h7cff6ad_5 +---------------------------- +file name : bowtie2-2.2.1-py39h7cff6ad_5.tar.bz2 +name : bowtie2 +version : 2.2.1 +build : py39h7cff6ad_5 +build number: 5 +size : 14.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.1-py39h7cff6ad_5.tar.bz2 +md5 : 4e43bb095865a83273a5286f7cc7ce6a +timestamp : 2021-03-26 12:44:58 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + - python >=3.9,<3.10.0a0 + - python_abi 3.9.* *_cp39 + + +bowtie2 2.2.4 py27_0 +-------------------- +file name : bowtie2-2.2.4-py27_0.tar.bz2 +name : bowtie2 +version : 2.2.4 +build : py27_0 +build number: 0 +size : 10.1 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.2.4-py27_0.tar.bz2 +md5 : 94d4d1fdbb676c04e437315cb95cbc2c +dependencies: + - libgcc + - perl-threaded + - python 2.7* + + +bowtie2 2.2.4 py27_1 +---------- diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bwa.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bwa.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..90be04b5912825bda9f9e20921b0f6ff6e2fa653 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bwa.manual_bundle.txt @@ -0,0 +1,547 @@ +# Tool: bwa +software_name: bwa +tier: T1 +domain: t1_backfill_overall +downloads: 2038789 +summary: The BWA read mapper. +description: The BWA read mapper. +dependencies: libgcc >=13, libzlib >=1.3.1,<2.0a0, perl +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/lh3/bwa +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/lh3/bwa +GitHub - lh3/bwa: Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment) · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} lh3 / bwa Public Notifications You must be signed in to change notification settings Fork 579 Star 1.7k Code Issues 73 Pull requests 25 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights lh3/bwa master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 996 Commits 996 Commits .github/ workflows .github/ workflows bwakit bwakit .gitignore .gitignore COPYING COPYING ChangeLog ChangeLog Makefile Makefile NEWS.md NEWS.md QSufSort.c QSufSort.c QSufSort.h QSufSort.h README-alt.md README-alt.md README.md README.md bamlite.c bamlite.c bamlite.h bamlite.h bntseq.c bntseq.c bntseq.h bntseq.h bwa.1 bwa.1 bwa.c bwa.c bwa.h bwa.h bwamem.c bwamem.c bwamem.h bwamem.h bwamem_extra.c bwamem_extra.c bwamem_pair.c bwamem_pair.c bwape.c bwape.c bwase.c bwase.c bwase.h bwase.h bwaseqio.c bwaseqio.c bwashm.c bwashm.c bwt.c bwt.c bwt.h bwt.h bwt_gen.c bwt_gen.c bwt_lite.c bwt_lite.c bwt_lite.h bwt_lite.h bwtaln.c bwtaln.c bwtaln.h bwtaln.h bwtgap.c bwtgap.c bwtgap.h bwtgap.h bwtindex.c bwtindex.c bwtsw2.h bwtsw2.h bwtsw2_aux.c bwtsw2_aux.c bwtsw2_chain.c bwtsw2_chain.c bwtsw2_core.c bwtsw2_core.c bwtsw2_main.c bwtsw2_main.c bwtsw2_pair.c bwtsw2_pair.c code_of_conduct.md code_of_conduct.md example.c example.c fastmap.c fastmap.c is.c is.c kbtree.h kbtree.h khash.h khash.h kopen.c kopen.c kseq.h kseq.h ksort.h ksort.h kstring.c kstring.c kstring.h kstring.h ksw.c ksw.c ksw.h ksw.h kthread.c kthread.c kvec.h kvec.h main.c main.c malloc_wrap.c malloc_wrap.c malloc_wrap.h malloc_wrap.h maxk.c maxk.c neon_sse.h neon_sse.h pemerge.c pemerge.c qualfa2fq.pl qualfa2fq.pl rle.c rle.c rle.h rle.h rope.c rope.c rope.h rope.h scalar_sse.h scalar_sse.h utils.c utils.c utils.h utils.h xa2multi.pl xa2multi.pl View all files Repository files navigation README Code of conduct GPL-3.0 license Note: minimap2 has replaced BWA-MEM for PacBio and Nanopore read alignment. It retains all major BWA-MEM features, but is ~50 times as fast, more versatile, more accurate and produces better base-level alignment. BWA-MEM2 is 50-100% faster than BWA-MEM and outputs identical alignments. Getting started git clone https://github.com/lh3/bwa.git cd bwa; make ./bwa index ref.fa ./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz ./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz Introduction BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to a few megabases. BWA-MEM and BWA-SW share similar features such as the support of long reads and chimeric alignment, but BWA-MEM, which is the latest, is generally recommended as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads. For all the algorithms, BWA first needs to construct the FM-index for the reference genome (the index command). Alignment algorithms are invoked with different sub-commands: aln/samse/sampe for BWA-backtrack, bwasw for BWA-SW and mem for the BWA-MEM algorithm. Availability BWA is released under GPLv3 . The latest source code is freely available at github . Released packages can be downloaded at SourceForge. After you acquire the source code, simply use make to compile and copy the single executable bwa to the destination you want. The only dependency required to build BWA is zlib . Since 0.7.11, precompiled binary for x86_64-linux is available in bwakit . In addition to BWA, this self-consistent package also comes with bwa-associated and 3rd-party tools for proper BAM-to-FASTQ conversion, mapping to ALT contigs, adapter triming, duplicate marking, HLA typing and associated data files. Seeking help The detailed usage is described in the man page available together with the source code. You can use man ./bwa.1 to view the man page in a terminal. The HTML version of the man page can be found at the BWA website . If you have questions about BWA, you may sign up the mailing list and then send the questions to bio-bwa-help@sourceforge.net . You may also ask questions in forums such as BioStar and SEQanswers . Citing BWA Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics , 25 , 1754-1760. [PMID: 19451168 ]. (if you use the BWA-backtrack algorithm) Li H. and Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics , 26 , 589-595. [PMID: 20080505 ]. (if you use the BWA-SW algorithm) Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN]. (if you use the BWA-MEM algorithm or the fastmap command, or want to cite the whole BWA package) Please note that the last reference is a preprint hosted at arXiv.org . I do not have plan to submit it to a peer-reviewed journal in the near future. Frequently asked questions (FAQs) What types of data does BWA work with? Why does a read appear multiple times in the output SAM? Does BWA work on reference sequences longer than 4GB in total? Why can one read in a pair has high mapping quality but the other has zero? How can a BWA-backtrack alignment stands out of the end of a chromosome? Does BWA work with ALT contigs in the GRCh38 release? Can I just run BWA-MEM against GRCh38+ALT without post-processing? Why does BWA use a lot of memory? 1. What types of data does BWA work with? BWA works with a variety types of DNA sequence data, though the optimal algorithm and setting may vary. The following list gives the recommended settings: Illumina/454/IonTorrent single-end reads longer than ~70bp or assembly contigs up to a few megabases mapped to a closely related reference genome: bwa mem ref.fa reads.fq > aln.sam Illumina single-end reads shorter than ~70bp: bwa aln ref.fa reads.fq > reads.sai; bwa samse ref.fa reads.sai reads.fq > aln-se.sam Illumina/454/IonTorrent paired-end reads longer than ~70bp: bwa mem ref.fa read1.fq read2.fq > aln-pe.sam Illumina paired-end reads shorter than ~70bp: bwa aln ref.fa read1.fq > read1.sai; bwa aln ref.fa read2.fq > read2.sai bwa sampe ref.fa read1.sai read2.sai read1.fq read2.fq > aln-pe.sam PacBio subreads or Oxford Nanopore reads to a reference genome: bwa mem -x pacbio ref.fa reads.fq > aln.sam bwa mem -x ont2d ref.fa reads.fq > aln.sam BWA-MEM is recommended for query sequences longer than ~70bp for a variety of error rates (or sequence divergence). Generally, BWA-MEM is more tolerant with errors given longer query sequences as the chance of missing all seeds is small. As is shown above, with non-default settings, BWA-MEM works with Oxford Nanopore reads with a sequencing error rate over 20%. 2. Why does a read appear multiple times in the output SAM? BWA-SW and BWA-MEM perform local alignments. If there is a translocation, a gene fusion or a long deletion, a read bridging the break point may have two hits, occupying two lines in the SAM output. With the default setting of BWA-MEM, one and only one line is primary and is soft clipped; other lines are tagged with 0x800 SAM flag (supplementary alignment) and are hard clipped. 3. Does BWA work on reference sequences longer than 4GB in total? Yes. Since 0.6.x, all BWA algorithms work with a genome with total length over 4GB. However, individual chromosome should not be longer than 2GB. 4. Why can one read in a pair have a high mapping quality but the other has zero? This is correct. Mapping quality is assigned for individual read, not for a read pair. It is possible that one read can be mapped unambiguously, but its mate falls in a tandem repeat and thus its accurate position cannot be determined. 5. How can a BWA-backtrack alignment stand out of the end of a chromosome? Internally BWA concatenates all reference sequences into one long sequence. A read may be mapped to the junction of two adjacent reference sequences. In this case, BWA-backtrack will flag the read as unmapped (0x4), but you will see position, CIGAR and all the tags. A similar issue may occur to BWA-SW alignment as well. BWA-MEM does not have this problem. 6. Does BWA work with ALT contigs in the GRCh38 release? Yes, since 0.7.11, BWA-MEM officially supports mapping to GRCh38+ALT. BWA-backtrack and BWA-SW don't properly support ALT mapping as of now. Please see README-alt.md for details. Briefly, it is recommended to use bwakit , the binary release of BWA, for generating the reference genome and for mapping. 7. Can I just run BWA-MEM against GRCh38+ALT without post-processing? If you are not interested in hits to ALT contigs, it is okay to run BWA-MEM without post-processing. The alignments produced this way are very close to alignments against GRCh38 without ALT contigs. Nonetheless, applying post-processing helps to reduce false mappings caused by reads from the diverged part of ALT contigs and also enables HLA typing. It is recommended to run the post-processing script. 8. Why does BWA use a lot of memory? This is typically caused by FASTQ generated from a coordinate-sorted BAM. BWA uses a lot more memory for centromeric reads than for unique reads. In a FASTQ file generated from a sequencing run, centromeric reads are rare in each batch and rarely cause troubles. However, in a coordinate-sorted FASTQ file, a whole batch could consist of centromeric reads. Such a batch will take a lot more memory and time to map; the insert size estimate will be distorted as well. General rule: NEVER use Picard SamToFastq on coordiate-sorted BAM; use samtools collate+fastq instead. About Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment) Topics bioinformatics genomics sequence-alignment fm-index Resources Readme License GPL-3.0 license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Stars 1.7k stars Watchers 104 watching Forks 579 forks Report repository Releases 6 BWA-0.7.19 (r1273) Latest Mar 22, 2025 + 5 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C 86.3% JavaScript 5.6% Roff 4.2% C++ 1.5% Perl 1.3% Shell 0.6% Makefile 0.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge bwa --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +bwa 0.5.9 0 +----------- +file name : bwa-0.5.9-0.tar.bz2 +name : bwa +version : 0.5.9 +build : 0 +build number: 0 +size : 286 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.5.9-0.tar.bz2 +md5 : c7baf55f724b04e489b1e7f5add029b5 +dependencies: + - libgcc + - zlib + + +bwa 0.5.9 1 +----------- +file name : bwa-0.5.9-1.tar.bz2 +name : bwa +version : 0.5.9 +build : 1 +build number: 1 +size : 289 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.5.9-1.tar.bz2 +md5 : 56bf00f54bafae2fed23db7a72f083c0 +dependencies: + - libgcc + - zlib 1.2.8* + + +bwa 0.5.9 ha92aebf_2 +-------------------- +file name : bwa-0.5.9-ha92aebf_2.tar.bz2 +name : bwa +version : 0.5.9 +build : ha92aebf_2 +build number: 2 +size : 289 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.5.9-ha92aebf_2.tar.bz2 +md5 : 60031be8ccd418565902307ed9f4ffd2 +timestamp : 2018-07-01 00:15:40 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.6.2 0 +----------- +file name : bwa-0.6.2-0.tar.bz2 +name : bwa +version : 0.6.2 +build : 0 +build number: 0 +size : 322 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.6.2-0.tar.bz2 +md5 : c37e2c9c36d8f711c45d85a6d4855075 +dependencies: + - libgcc + - zlib + + +bwa 0.6.2 1 +----------- +file name : bwa-0.6.2-1.tar.bz2 +name : bwa +version : 0.6.2 +build : 1 +build number: 1 +size : 325 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.6.2-1.tar.bz2 +md5 : 6c3c5a6fff2fcae961aa06c1e97ba20e +dependencies: + - libgcc + - zlib 1.2.8* + + +bwa 0.6.2 ha92aebf_2 +-------------------- +file name : bwa-0.6.2-ha92aebf_2.tar.bz2 +name : bwa +version : 0.6.2 +build : ha92aebf_2 +build number: 2 +size : 326 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.6.2-ha92aebf_2.tar.bz2 +md5 : 610248d1043331b6a25a7d451672bdc9 +timestamp : 2018-07-01 00:09:55 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.3a 0 +------------ +file name : bwa-0.7.3a-0.tar.bz2 +name : bwa +version : 0.7.3a +build : 0 +build number: 0 +size : 392 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-0.tar.bz2 +md5 : 8a7ce02f6863a7d24984ac9c162d874c +dependencies: + - libgcc + - zlib + + +bwa 0.7.3a 1 +------------ +file name : bwa-0.7.3a-1.tar.bz2 +name : bwa +version : 0.7.3a +build : 1 +build number: 1 +size : 392 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-1.tar.bz2 +md5 : db72b0757cf092da5de2eb5d011199ca +dependencies: + - libgcc + - zlib 1.2.8* + + +bwa 0.7.3a h577a1d6_10 +---------------------- +file name : bwa-0.7.3a-h577a1d6_10.tar.bz2 +name : bwa +version : 0.7.3a +build : h577a1d6_10 +build number: 10 +size : 462 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-h577a1d6_10.tar.bz2 +md5 : e306dbc515646898478bb44f6acf87c9 +timestamp : 2024-12-12 05:32:32 UTC +dependencies: + - libgcc >=13 + - libzlib >=1.3.1,<2.0a0 + - zlib + + +bwa 0.7.3a h5bf99c6_6 +--------------------- +file name : bwa-0.7.3a-h5bf99c6_6.tar.bz2 +name : bwa +version : 0.7.3a +build : h5bf99c6_6 +build number: 6 +size : 458 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-h5bf99c6_6.tar.bz2 +md5 : 853dd1bd3776605b2902756682592404 +timestamp : 2021-03-25 19:00:52 UTC +dependencies: + - libgcc-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.3a h7132678_7 +--------------------- +file name : bwa-0.7.3a-h7132678_7.tar.bz2 +name : bwa +version : 0.7.3a +build : h7132678_7 +build number: 7 +size : 455 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-h7132678_7.tar.bz2 +md5 : fbc4d9b3047011eba8219b9247940c57 +timestamp : 2022-02-22 15:18:35 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.3a h7132678_8 +--------------------- +file name : bwa-0.7.3a-h7132678_8.tar.bz2 +name : bwa +version : 0.7.3a +build : h7132678_8 +build number: 8 +size : 456 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-h7132678_8.tar.bz2 +md5 : 36f1e37b0c778098a6b339db6eeec8c9 +timestamp : 2023-05-11 17:47:35 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +bwa 0.7.3a h84994c4_3 +--------------------- +file name : bwa-0.7.3a-h84994c4_3.tar.bz2 +name : bwa +version : 0.7.3a +build : h84994c4_3 +build number: 3 +size : 397 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-h84994c4_3.tar.bz2 +md5 : 117ca506a0ce5340622d31993f3c82a8 +timestamp : 2019-02-03 23:04:53 UTC +dependencies: + - libgcc-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.3a h84994c4_4 +--------------------- +file name : bwa-0.7.3a-h84994c4_4.tar.bz2 +name : bwa +version : 0.7.3a +build : h84994c4_4 +build number: 4 +size : 394 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-h84994c4_4.tar.bz2 +md5 : 0a79954b4f18b445d5aa5c0aecc44c8f +timestamp : 2019-02-13 06:42:51 UTC +dependencies: + - libgcc-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.3a ha92aebf_2 +--------------------- +file name : bwa-0.7.3a-ha92aebf_2.tar.bz2 +name : bwa +version : 0.7.3a +build : ha92aebf_2 +build number: 2 +size : 395 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-ha92aebf_2.tar.bz2 +md5 : f844255fc115ca894642c01563793c3f +timestamp : 2018-07-01 00:12:49 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.3a he4a0461_8 +--------------------- +file name : bwa-0.7.3a-he4a0461_8.tar.bz2 +name : bwa +version : 0.7.3a +build : he4a0461_8 +build number: 8 +size : 460 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-he4a0461_8.tar.bz2 +md5 : fd8b24994024278de1bea9d70d3975d1 +timestamp : 2023-05-15 00:30:32 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +bwa 0.7.3a he4a0461_9 +--------------------- +file name : bwa-0.7.3a-he4a0461_9.tar.bz2 +name : bwa +version : 0.7.3a +build : he4a0461_9 +build number: 9 +size : 460 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-he4a0461_9.tar.bz2 +md5 : 177fa42e9e87ccb1164e28282fce53f0 +timestamp : 2023-05-16 00:13:30 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +bwa 0.7.3a hed695b0_5 +--------------------- +file name : bwa-0.7.3a-hed695b0_5.tar.bz2 +name : bwa +version : 0.7.3a +build : hed695b0_5 +build number: 5 +size : 394 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.3a-hed695b0_5.tar.bz2 +md5 : d7c4933ab806fa4e3553069fc3556fea +timestamp : 2020-07-03 05:07:32 UTC +dependencies: + - libgcc-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.4 h577a1d6_8 +-------------------- +file name : bwa-0.7.4-h577a1d6_8.tar.bz2 +name : bwa +version : 0.7.4 +build : h577a1d6_8 +build number: 8 +size : 145 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.4-h577a1d6_8.tar.bz2 +md5 : 7a5f746dee2a926620066781f8cb7a04 +timestamp : 2024-12-12 05:29:27 UTC +dependencies: + - libgcc >=13 + - libzlib >=1.3.1,<2.0a0 + - zlib + + +bwa 0.7.4 h5bf99c6_4 +-------------------- +file name : bwa-0.7.4-h5bf99c6_4.tar.bz2 +name : bwa +version : 0.7.4 +build : h5bf99c6_4 +build number: 4 +size : 140 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.4-h5bf99c6_4.tar.bz2 +md5 : 6061060ba7a0cab2991ad4886e397590 +timestamp : 2021-03-25 18:54:00 UTC +dependencies: + - libgcc-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.4 h7132678_5 +-------------------- +file name : bwa-0.7.4-h7132678_5.tar.bz2 +name : bwa +version : 0.7.4 +build : h7132678_5 +build number: 5 +size : 139 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.4-h7132678_5.tar.bz2 +md5 : 9517ceecd92d289c7e611a810f3c8284 +timestamp : 2022-02-22 14:59:56 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.4 h7132678_6 +-------------------- +file name : bwa-0.7.4-h7132678_6.tar.bz2 +name : bwa +version : 0.7.4 +build : h7132678_6 +build number: 6 +size : 140 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.4-h7132678_6.tar.bz2 +md5 : b815c45c5509295ebaacaaeebedeb616 +timestamp : 2023-05-11 17:40:16 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +bwa 0.7.4 h84994c4_1 +-------------------- +file name : bwa-0.7.4-h84994c4_1.tar.bz2 +name : bwa +version : 0.7.4 +build : h84994c4_1 +build number: 1 +size : 398 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.4-h84994c4_1.tar.bz2 +md5 : 1f835fa8929d562183b9ea2b2397f9e7 +timestamp : 2019-02-03 22:56:30 UTC +dependencies: + - libgcc-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.4 ha92aebf_0 +-------------------- +file name : bwa-0.7.4-ha92aebf_0.tar.bz2 +name : bwa +version : 0.7.4 +build : ha92aebf_0 +build number: 0 +size : 397 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.4-ha92aebf_0.tar.bz2 +md5 : cbc393e242e7ac78757017e89ff06e9a +timestamp : 2018-08-17 16:37:46 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +bwa 0.7.4 he4a0461_6 +-------------------- +file name : bwa-0.7.4-he4a0461_6.tar.bz2 +name : bwa +version : 0.7.4 +build : he4a0461_6 +build number: 6 +size : 143 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.4-he4a0461_6.tar.bz2 +md5 : 5221921322cd423f745b41306250d1de +timestamp : 2023-05-15 00:24:41 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +bwa 0.7.4 he4a0461_7 +-------------------- +file name : bwa-0.7.4-he4a0461_7.tar.bz2 +name : bwa +version : 0.7.4 +build : he4a0461_7 +build number: 7 +size : 143 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.4-he4a0461_7.tar.bz2 +md5 : bafd6c472c325a6dc537c168e7158d10 +timestamp : 2023-05-16 00:06:27 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +bwa 0.7.4 hed695b0_2 +-------------------- +file name : bwa-0.7.4-hed695b0_2.tar.bz2 +name : bwa +version : 0.7.4 +build diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cell2cell.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cell2cell.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..dc3c5764282d1c5092f61172244675b249b142b3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cell2cell.manual_bundle.txt @@ -0,0 +1,451 @@ +# Tool: cell2cell +software_name: cell2cell +tier: T1 +domain: single_cell +downloads: 5327 +summary: Inferring cell-cell interactions from transcriptomes with cell2cell. +description: Inferring cell-cell interactions from transcriptomes with cell2cell. +dependencies: gseapy >=1.1.6, kneed, matplotlib-base >=3.2.0, networkx >=2.3, numpy >=1.16, openpyxl >=2.6.2, pandas >=1.0.0, python >=3, scanpy, scikit-learn, seaborn-base >=0.11.0, statannotations, statsmodels, tensorly, tqdm, umap-learn, xlrd >=1.1 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/earmingol/cell2cell +doc_url: https://github.com/earmingol/cell2cell +dev_url: https://github.com/earmingol/cell2cell + +## URL Docs Extract +### https://github.com/earmingol/cell2cell +GitHub - earmingol/cell2cell: User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} earmingol / cell2cell Public Notifications You must be signed in to change notification settings Fork 20 Star 80 Code Issues 3 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights earmingol/cell2cell master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 753 Commits 753 Commits .github/ workflows .github/ workflows benchmarks benchmarks cell2cell cell2cell docs docs examples examples release release .readthedocs.yml .readthedocs.yml LICENSE.txt LICENSE.txt Logo.png Logo.png LogoTensor.png LogoTensor.png README.md README.md mkdocs.yml mkdocs.yml setup.py setup.py View all files Repository files navigation README BSD-3-Clause license Inferring cell-cell interactions from transcriptomes with cell2cell 📖 Getting started For tutorials and documentation, visit cell2cell ReadTheDocs or our cell2cell website . 🔧 Installation Step 1: Install Anaconda 🐍 First, install Anaconda following this tutorial Step 2: Create and Activate a New Conda Environment 💻 # Create a new conda environment conda create -n cell2cell -y python=3.7 jupyter # Activate the environment conda activate cell2cell Step 3: Install cell2cell ⬇️ pip install cell2cell 💡 Examples cell2cell Examples Tensor-cell2cell Examples - Step-by-step Pipeline - Interaction Pipeline for Bulk Data - Interaction Pipeline for Single-Cell Data - Whole Body of C. elegans - Obtaining patterns of cell-cell communication - Downstream 1: Factor-specific analyses - Downstream 2: Patterns to functions (GSEA) - Tensor-cell2cell in Google Colab ( GPU ) - Communication patterns in Spatial Transcriptomics - Multi-modal communication patterns with Coupled Tensor Component Analysis Reproducible runs of the analyses in the Tensor-cell2cell paper are available at CodeOcean.com 🔗 LIANA & Tensor-cell2cell Explore our tutorials for using Tensor-cell2cell with LIANA at ccc-protocols.readthedocs.io . ❓ Common Issues Memory Errors with Tensor-cell2cell: If you encounter memory errors when performing tensor factorizations, try replacing init='svd' with init='random' . 🧬 Ligand-Receptor Pairs Find a curated list of ligand-receptor pairs for your analyses at our GitHub Repository . 📑 Citation Please cite our work using the following references: cell2cell : Inferring a spatial code of cell-cell interactions across a whole animal body . PLOS Computational Biology, 2022 Tensor-cell2cell : Context-aware deconvolution of cell-cell communication with Tensor-cell2cell . Nature Communications, 2022. Tensor-cell2cell v2 : Tensor-cell2cell v2 unravels coordinated dynamics of protein- and metabolite-mediated cell-cell communication . Bioinformatics, 2026. LIANA & Tensor-cell2cell tutorials : Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples . Cell Reports Methods, 2024 About User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins Topics machine-learning bioinformatics rna-seq computational-biology rnaseq single-cell single-cell-rna-seq bulk-rna-seq sc-rna-seq cell-cell-interaction cell-cell-communication Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Stars 80 stars Watchers 2 watching Forks 20 forks Report repository Releases 13 v0.8.4 Latest Nov 2, 2025 + 12 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/earmingol/cell2cell +GitHub - earmingol/cell2cell: User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} earmingol / cell2cell Public Notifications You must be signed in to change notification settings Fork 20 Star 80 Code Issues 3 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights earmingol/cell2cell master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 753 Commits 753 Commits .github/ workflows .github/ workflows benchmarks benchmarks cell2cell cell2cell docs docs examples examples release release .readthedocs.yml .readthedocs.yml LICENSE.txt LICENSE.txt Logo.png Logo.png LogoTensor.png LogoTensor.png README.md README.md mkdocs.yml mkdocs.yml setup.py setup.py View all files Repository files navigation README BSD-3-Clause license Inferring cell-cell interactions from transcriptomes with cell2cell 📖 Getting started For tutorials and documentation, visit cell2cell ReadTheDocs or our cell2cell website . 🔧 Installation Step 1: Install Anaconda 🐍 First, install Anaconda following this tutorial Step 2: Create and Activate a New Conda Environment 💻 # Create a new conda environment conda create -n cell2cell -y python=3.7 jupyter # Activate the environment conda activate cell2cell Step 3: Install cell2cell ⬇️ pip install cell2cell 💡 Examples cell2cell Examples Tensor-cell2cell Examples - Step-by-step Pipeline - Interaction Pipeline for Bulk Data - Interaction Pipeline for Single-Cell Data - Whole Body of C. elegans - Obtaining patterns of cell-cell communication - Downstream 1: Factor-specific analyses - Downstream 2: Patterns to functions (GSEA) - Tensor-cell2cell in Google Colab ( GPU ) - Communication patterns in Spatial Transcriptomics - Multi-modal communication patterns with Coupled Tensor Component Analysis Reproducible runs of the analyses in the Tensor-cell2cell paper are available at CodeOcean.com 🔗 LIANA & Tensor-cell2cell Explore our tutorials for using Tensor-cell2cell with LIANA at ccc-protocols.readthedocs.io . ❓ Common Issues Memory Errors with Tensor-cell2cell: If you encounter memory errors when performing tensor factorizations, try replacing init='svd' with init='random' . 🧬 Ligand-Receptor Pairs Find a curated list of ligand-receptor pairs for your analyses at our GitHub Repository . 📑 Citation Please cite our work using the following references: cell2cell : Inferring a spatial code of cell-cell interactions across a whole animal body . PLOS Computational Biology, 2022 Tensor-cell2cell : Context-aware deconvolution of cell-cell communication with Tensor-cell2cell . Nature Communications, 2022. Tensor-cell2cell v2 : Tensor-cell2cell v2 unravels coordinated dynamics of protein- and metabolite-mediated cell-cell communication . Bioinformatics, 2026. LIANA & Tensor-cell2cell tutorials : Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples . Cell Reports Methods, 2024 About User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins Topics machine-learning bioinformatics rna-seq computational-biology rnaseq single-cell single-cell-rna-seq bulk-rna-seq sc-rna-seq cell-cell-interaction cell-cell-communication Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Stars 80 stars Watchers 2 watching Forks 20 forks Report repository Releases 13 v0.8.4 Latest Nov 2, 2025 + 12 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/earmingol/cell2cell +GitHub - earmingol/cell2cell: User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} earmingol / cell2cell Public Notifications You must be signed in to change notification settings Fork 20 Star 80 Code Issues 3 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights earmingol/cell2cell master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 753 Commits 753 Commits .github/ workflows .github/ workflows benchmarks benchmarks cell2cell cell2cell docs docs examples examples release release .readthedocs.yml .readthedocs.yml LICENSE.txt LICENSE.txt Logo.png Logo.png LogoTensor.png LogoTensor.png README.md README.md mkdocs.yml mkdocs.yml setup.py setup.py View all files Repository files navigation README BSD-3-Clause license Inferring cell-cell interactions from transcriptomes with cell2cell 📖 Getting started For tutorials and documentation, visit cell2cell ReadTheDocs or our cell2cell website . 🔧 Installation Step 1: Install Anaconda 🐍 First, install Anaconda following this tutorial Step 2: Create and Activate a New Conda Environment 💻 # Create a new conda environment conda create -n cell2cell -y python=3.7 jupyter # Activate the environment conda activate cell2cell Step 3: Install cell2cell ⬇️ pip install cell2cell 💡 Examples cell2cell Examples Tensor-cell2cell Examples - Step-by-step Pipeline - Interaction Pipeline for Bulk Data - Interaction Pipeline for Single-Cell Data - Whole Body of C. elegans - Obtaining patterns of cell-cell communication - Downstream 1: Factor-specific analyses - Downstream 2: Patterns to functions (GSEA) - Tensor-cell2cell in Google Colab ( GPU ) - Communication patterns in Spatial Transcriptomics - Multi-modal communication patterns with Coupled Tensor Component Analysis Reproducible runs of the analyses in the Tensor-cell2cell paper are available at CodeOcean.com 🔗 LIANA & Tensor-cell2cell Explore our tutorials for using Tensor-cell2cell with LIANA at ccc-protocols.readthedocs.io . ❓ Common Issues Memory Errors with Tensor-cell2cell: If you encounter memory errors when performing tensor factorizations, try replacing init='svd' with init='random' . 🧬 Ligand-Receptor Pairs Find a curated list of ligand-receptor pairs for your analyses at our GitHub Repository . 📑 Citation Please cite our work using the following references: cell2cell : Inferring a spatial code of cell-cell interactions across a whole animal body . PLOS Computational Biology, 2022 Tensor-cell2cell : Context-aware deconvolution of cell-cell communication with Tensor-cell2cell . Nature Communications, 2022. Tensor-cell2cell v2 : Tensor-cell2cell v2 unravels coordinated dynamics of protein- and metabolite-mediated cell-cell communication . Bioinformatics, 2026. LIANA & Tensor-cell2cell tutorials : Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples . Cell Reports Methods, 2024 About User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins Topics machine-learning bioinformatics rna-seq computational-biology rnaseq single-cell single-cell-rna-seq bulk-rna-seq sc-rna-seq cell-cell-interaction cell-cell-communication Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Stars 80 stars Watchers 2 watching Forks 20 forks Report repository Releases 13 v0.8.4 Latest Nov 2, 2025 + 12 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge cell2cell --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +cell2cell 0.7.4 py310h9948957_3 +------------------------------- +file name : cell2cell-0.7.4-py310h9948957_3.tar.bz2 +name : cell2cell +version : 0.7.4 +build : py310h9948957_3 +build number: 3 +size : 204 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cell2cell-0.7.4-py310h9948957_3.tar.bz2 +md5 : a399022c26b265a8b6fe16602b62691d +timestamp : 2025-03-17 14:54:06 UTC +dependencies: + - gseapy 1.0.3 + - kneed + - libgcc >=13 + - libstdcxx >=13 + - matplotlib-base >=3.2.0,<3.7.3 + - networkx >=2.3 + - numpy >=1.16,<2.0 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - scanpy <=1.9.3 + - scikit-learn + - seaborn >=0.11.0 + - statannotations + - statsmodels + - tensorly 0.8.1 + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.7.4 py38h4ac6f70_0 +------------------------------ +file name : cell2cell-0.7.4-py38h4ac6f70_0.tar.bz2 +name : cell2cell +version : 0.7.4 +build : py38h4ac6f70_0 +build number: 0 +size : 202 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cell2cell-0.7.4-py38h4ac6f70_0.tar.bz2 +md5 : 68d02eb3d3ecc93b1e6eaccd5ee44a72 +timestamp : 2024-10-29 10:37:30 UTC +dependencies: + - gseapy 1.0.3 + - kneed + - libgcc >=12 + - libstdcxx >=12 + - matplotlib-base >=3.2.0,<3.7.3 + - networkx >=2.3 + - numpy >=1.16,<2.0 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3.8,<3.9.0a0 + - scanpy <=1.9.3 + - scikit-learn + - seaborn >=0.11.0 + - statannotations + - statsmodels + - tensorly 0.8.1 + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.7.4 py39h4ac6f70_1 +------------------------------ +file name : cell2cell-0.7.4-py39h4ac6f70_1.tar.bz2 +name : cell2cell +version : 0.7.4 +build : py39h4ac6f70_1 +build number: 1 +size : 206 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cell2cell-0.7.4-py39h4ac6f70_1.tar.bz2 +md5 : 830a797d7e9a2d95b9a3101fef8acebf +timestamp : 2024-10-29 20:36:28 UTC +dependencies: + - gseapy 1.0.3 + - kneed + - libgcc >=12 + - libstdcxx >=12 + - matplotlib-base >=3.2.0,<3.7.3 + - networkx >=2.3 + - numpy >=1.16,<2.0 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3.9,<3.10.0a0 + - python_abi 3.9.* *_cp39 + - scanpy <=1.9.3 + - scikit-learn + - seaborn >=0.11.0 + - statannotations + - statsmodels + - tensorly 0.8.1 + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.7.4 py39h9948957_2 +------------------------------ +file name : cell2cell-0.7.4-py39h9948957_2.tar.bz2 +name : cell2cell +version : 0.7.4 +build : py39h9948957_2 +build number: 2 +size : 208 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cell2cell-0.7.4-py39h9948957_2.tar.bz2 +md5 : 7d70daf5e09cf284a0a8ed00dc801098 +timestamp : 2024-12-03 13:11:41 UTC +dependencies: + - gseapy 1.0.3 + - kneed + - libgcc >=13 + - libstdcxx >=13 + - matplotlib-base >=3.2.0,<3.7.3 + - networkx >=2.3 + - numpy >=1.16,<2.0 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3.9,<3.10.0a0 + - python_abi 3.9.* *_cp39 + - scanpy <=1.9.3 + - scikit-learn + - seaborn >=0.11.0 + - statannotations + - statsmodels + - tensorly 0.8.1 + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.8.0 py310h9948957_0 +------------------------------- +file name : cell2cell-0.8.0-py310h9948957_0.conda +name : cell2cell +version : 0.8.0 +build : py310h9948957_0 +build number: 0 +size : 208 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cell2cell-0.8.0-py310h9948957_0.conda +md5 : 130a9cc44533fc5ba055be31501180ea +timestamp : 2025-08-30 21:17:46 UTC +dependencies: + - gseapy 1.0.3 + - kneed + - libgcc >=13 + - libstdcxx >=13 + - matplotlib-base >=3.2.0,<3.7.3 + - networkx >=2.3 + - numpy >=1.16,<2.0 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - scanpy <=1.9.3 + - scikit-learn + - seaborn >=0.11.0 + - statannotations + - statsmodels + - tensorly 0.8.1 + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.8.1 py310h184ae93_0 +------------------------------- +file name : cell2cell-0.8.1-py310h184ae93_0.conda +name : cell2cell +version : 0.8.1 +build : py310h184ae93_0 +build number: 0 +size : 208 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cell2cell-0.8.1-py310h184ae93_0.conda +md5 : c78aad4502a0f79606bc5d2ad2eb66ff +timestamp : 2025-09-04 22:05:13 UTC +dependencies: + - gseapy 1.0.3 + - kneed + - libgcc >=13 + - libstdcxx >=13 + - matplotlib-base >=3.2.0,<3.7.3 + - networkx >=2.3 + - numpy >=1.16,<2.0 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - scanpy <=1.9.3 + - scikit-learn + - seaborn-base >=0.11.0 + - statannotations + - statsmodels + - tensorly 0.8.1 + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.8.1 py310h184ae93_1 +------------------------------- +file name : cell2cell-0.8.1-py310h184ae93_1.conda +name : cell2cell +version : 0.8.1 +build : py310h184ae93_1 +build number: 1 +size : 208 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cell2cell-0.8.1-py310h184ae93_1.conda +md5 : 3a8c5557b64eb77e139c5e5e3ce525c2 +timestamp : 2025-09-08 23:25:40 UTC +dependencies: + - gseapy 1.0.3 + - kneed + - libgcc >=13 + - libstdcxx >=13 + - matplotlib-base >=3.2.0,<3.7.3 + - networkx >=2.3 + - numpy >=1.16,<2.0 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - scanpy <=1.9.3 + - scikit-learn + - seaborn-base >=0.11.0 + - statannotations + - statsmodels + - tensorly 0.8.1 + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.8.1 py39h2de1943_0 +------------------------------ +file name : cell2cell-0.8.1-py39h2de1943_0.conda +name : cell2cell +version : 0.8.1 +build : py39h2de1943_0 +build number: 0 +size : 207 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cell2cell-0.8.1-py39h2de1943_0.conda +md5 : b3680cfec3041f416cadcd7f81cfa433 +timestamp : 2025-09-04 22:03:54 UTC +dependencies: + - gseapy 1.0.3 + - kneed + - libgcc >=13 + - libstdcxx >=13 + - matplotlib-base >=3.2.0,<3.7.3 + - networkx >=2.3 + - numpy >=1.16,<2.0 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3.9,<3.10.0a0 + - python_abi 3.9.* *_cp39 + - scanpy <=1.9.3 + - scikit-learn + - seaborn-base >=0.11.0 + - statannotations + - statsmodels + - tensorly 0.8.1 + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.8.1 py39h2de1943_1 +------------------------------ +file name : cell2cell-0.8.1-py39h2de1943_1.conda +name : cell2cell +version : 0.8.1 +build : py39h2de1943_1 +build number: 1 +size : 207 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cell2cell-0.8.1-py39h2de1943_1.conda +md5 : 071b61252b2b732d83deec88b8181eff +timestamp : 2025-09-08 23:27:01 UTC +dependencies: + - gseapy 1.0.3 + - kneed + - libgcc >=13 + - libstdcxx >=13 + - matplotlib-base >=3.2.0,<3.7.3 + - networkx >=2.3 + - numpy >=1.16,<2.0 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3.9,<3.10.0a0 + - python_abi 3.9.* *_cp39 + - scanpy <=1.9.3 + - scikit-learn + - seaborn-base >=0.11.0 + - statannotations + - statsmodels + - tensorly 0.8.1 + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.8.2 pyhdfd78af_0 +---------------------------- +file name : cell2cell-0.8.2-pyhdfd78af_0.conda +name : cell2cell +version : 0.8.2 +build : pyhdfd78af_0 +build number: 0 +size : 117 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cell2cell-0.8.2-pyhdfd78af_0.conda +md5 : 17d10d2324011224ec5701f38e229a5f +timestamp : 2025-10-02 11:02:17 UTC +dependencies: + - gseapy >=1.1.6 + - kneed + - matplotlib-base >=3.2.0 + - networkx >=2.3 + - numpy >=1.16 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3 + - scanpy + - scikit-learn + - seaborn-base >=0.11.0 + - statannotations + - statsmodels + - tensorly + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.8.3 pyhdfd78af_0 +---------------------------- +file name : cell2cell-0.8.3-pyhdfd78af_0.conda +name : cell2cell +version : 0.8.3 +build : pyhdfd78af_0 +build number: 0 +size : 120 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cell2cell-0.8.3-pyhdfd78af_0.conda +md5 : 185c32841654f8a33e9beb9e6a50a204 +timestamp : 2025-10-30 02:24:02 UTC +dependencies: + - gseapy >=1.1.6 + - kneed + - matplotlib-base >=3.2.0 + - networkx >=2.3 + - numpy >=1.16 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3 + - scanpy + - scikit-learn + - seaborn-base >=0.11.0 + - statannotations + - statsmodels + - tensorly + - tqdm + - umap-learn + - xlrd >=1.1 + + +cell2cell 0.8.4 pyhdfd78af_0 +---------------------------- +file name : cell2cell-0.8.4-pyhdfd78af_0.conda +name : cell2cell +version : 0.8.4 +build : pyhdfd78af_0 +build number: 0 +size : 122 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cell2cell-0.8.4-pyhdfd78af_0.conda +md5 : 1c885962f5327c087e2ff496aae57e38 +timestamp : 2025-11-02 22:28:17 UTC +dependencies: + - gseapy >=1.1.6 + - kneed + - matplotlib-base >=3.2.0 + - networkx >=2.3 + - numpy >=1.16 + - openpyxl >=2.6.2 + - pandas >=1.0.0 + - python >=3 + - scanpy + - scikit-learn + - seaborn-base >=0.11.0 + - statannotations + - statsmodels + - tensorly + - tqdm + - umap-learn + - xlrd >=1.1 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cellsnake.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cellsnake.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..881e137bfba1a2ce27366ee551e67cbe8001be50 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cellsnake.manual_bundle.txt @@ -0,0 +1,598 @@ +# Tool: cellsnake +software_name: cellsnake +tier: T1 +domain: single_cell +downloads: 5692 +summary: cellsnake, a user-friendly tool for single cell RNA sequencing analysis +description: cellsnake, a user-friendly tool for single cell RNA sequencing analysis +dependencies: bedtools, celltypist 1.3.0, cmake, docopt, fastp, fuzzywuzzy, geos 3.11.1, hdf5, kraken2, levenshtein, matplotlib-base <3.7, numba >=0.56.4, openblas 0.3.21, pandas <=1.5.3, plotly, pysam >=0.16.0.1, python, r-clustree 0.5.0, r-cowplot, r-curl, r-dbplyr <=2.3.2, r-expm, r-fields, r-ggalluvial, r-ggpubr, r-ggraph 2.1.0, r-ggthemes, r-gplots, r-hdf5r, r-igraph, r-librarian, r-matrix <=1.5_4.1, r-minqa, r-nmf, r-openxlsx, r-optparse, r-patchwork, r-plotly, r-r.utils, r-randomcolor, r-reticulate, r-rsvd, r-seurat 4.3.0, r-seuratobject 4.1.3, r-spdep, r-terra, r-tidyseurat, r-tidyverse, r-v8, r-viridis, r-xml, regex >=2021.4.4, samtools, scanpy 1.9.1, scipy, snakemake-minimal 7.22.0, umap-learn +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://github.com/sinanugur/cellsnake +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/sinanugur/cellsnake +GitHub - sinanugur/cellsnake: Cellsnake tool main repo · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} sinanugur / cellsnake Public Notifications You must be signed in to change notification settings Fork 8 Star 36 Code Issues 5 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights sinanugur/cellsnake main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 109 Commits 109 Commits cellsnake cellsnake docs docs .gitignore .gitignore .gitmodules .gitmodules .readthedocs.yaml .readthedocs.yaml Dockerfile Dockerfile LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md cellsnake-logo-blue-small.png cellsnake-logo-blue-small.png cellsnake-logo.png cellsnake-logo.png config.yaml config.yaml environment.yml environment.yml metadata.csv metadata.csv requirements.txt requirements.txt setup.py setup.py View all files Repository files navigation README MIT license A command line tool for easy and scalable single cell RNA sequencing analysis Our main Snakemake workflow is here: https://github.com/sinanugur/scrna-workflow Installation Please use Bioconda repo for installation. Mamba installation is also recommended. To create a clean environment and install cellsnake , type: conda install mamba -c conda-forge mamba create -n cellsnake -c bioconda -c conda-forge cellsnake #Alternative installation to get a more up-to-date environment. mamba env create -n cellsnake --file=environment.yaml Apple Silicon computers have to force Osx64, you can install like this. conda install mamba -c conda-forge CONDA_SUBDIR=osx-64 mamba create -n cellsnake -c bioconda -c conda-forge cellsnake #Alternative CONDA_SUBDIR=osx-64 mamba env create -n cellsnake --file=environment.yaml Check if the installation works by calling the main script. conda activate cellsnake cellsnake --help Then install the R packages by typing: cellsnake --install-packages You should see this message if all the packages are available: cellsnake --install-packages [1] "All packages were installed...OK" Cellsnake auto install most of the packages when necessary or during the creation of environment but it is good to check if they are installable. You can then move the environment to an offline location as well if required. We recommend our Docker image and it is a better solution for installation problems. Podman also works fine with our Docker image. See our Docker repo: Cellsnake Docker Our latest Docker image is here: Cellsnake Docker Latest Docker is strongly recommended for running cellsnake in a controlled environment or in Apple MAC. Quick start examples Run cellsnake in a clean directory and cellsnake will create the required directories while running. You may download publicly available fetal brain dataset to test your cellsnake installation. The link is here. https://www.dropbox.com/sh/1qn2odtnci0vvtr/AADPxHH-GR4h-OuQG0TLQyxWa?dl=0 After downloading the dataset, just point the data folder which contains the two datasets, this will trigger a standard cellsnake workflow: cellsnake standard data After the pipeline finishes, browse the output files. You can also integrate these two samples which makes sense. cellsnake integrate data That is it. Lets work on the integrated object from now on, we already processed the samples separately. Let's do a minimal run, this will also generate a clustree plot as well which can be used to investigate the optimal resolution. cellsnake integrated minimal analyses_integrated/seurat/integrated.rds You want a resolution of 0.1 after checking clustree plot, then you can trigger a run with this resolution. cellsnake integrated standard analyses_integrated/seurat/integrated.rds --resolution 0.1 It is also possible to use automatic resolution selection, however this might be very slow in large datasets. cellsnake integrated standard analyses_integrated/seurat/integrated.rds --resolution auto See our documentation for detailed explanations and to read full features: https://cellsnake.readthedocs.io/ Options and Arguments Usage: cellsnake <command> <INPUT> [options] [--unlock|--remove] [--dry] cellsnake integrated <command> <INPUT> [options] [--unlock|--remove] [--dry] cellsnake --generate-template cellsnake --install-packages cellsnake (-h | --help) cellsnake --version commands: minimal Run cellsnake with minimal workflow. standard Run cellsnake with standard workflow. advanced Run cellsnake with advanced workflow. clustree Run cellsnake with clustree workflow. integrate Run cellsnake to integrate samples under analyses folder. This option expects you have already finished processing multiple samples. main arguments: INPUT Input directory or a file to process (if a directory given, batch mode is ON). --configfile <text> Config file name in YAML format, for example, "config.yaml". No default but can be created with --generate-template. --metadata <text> Metadata file name in CSV, TSV or Excel format, for example, "metadata.csv", header required, first column sample name. No default but can be created with --generate-template. --metadata_column <text> Metadata column for differential expression analysis [default: condition]. other arguments: --gene <gene or filename> Create publication ready plots for a gene or a list of genes from a text file. main options: --percent_mt <double> Maximum mitochondrial gene percentage cutoff, for example, 5 or 10, write "auto" for auto detection [default: 10]. --resolution <double> Resolution for cluster detection, write "auto" for auto detection [default: 0.8]. other options: --doublet_filter <bool> [default: True] #this may fail on some samples --percent_rp <double> [default: 0] #Ribosomal genes minimum percentage (0-100), default no filtering --min_cells <integer> [default: 3] #seurat default, recommended --min_features <integer> [default: 200] #seurat default, recommended, nFeature_RNA --max_features <integer> [default: Inf] #seurat default, nFeature_RNA, 5000 can be a good cutoff --min_molecules <integer> [default: 0] #seurat default, nCount_RNA, min_features usually handles this so keep it 0 --max_molecules <integer> [default: Inf] #seurat default, nCount_RNA, to filter potential doublets, doublet filtering is already default, so keep this Inf --highly_variable_features <integer> [default: 2000] #seurat defaults, recommended --variable_selection_method <text> [default: vst] #seurat defaults, recommended --normalization_method <text> [default: LogNormalize] --scale_factor <integer> [default: 10000] --logfc_threshold <double> [default: 0.25] --test_use <text> [default: wilcox] --mapping <text> [default: org.Hs.eg.db] #you may install others from Bioconductor, this is for human --organism <text> [default: hsa] #alternatives https://www.genome.jp/kegg/catalog/org_list.html --species <text> [default: human] for cellchat, #only human or mouse is accepted plotting parameters: --min_percentage_to_plot <double> [default: 2] #only show clusters more than % of cells on the legend --show_labels <bool> [default: True] # --marker_plots_per_cluster_n <integer> [default: 20] #plot summary marker plots for top markers --umap_markers_plot <bool> [default: True] --tsne_markers_plot <bool> [default: False] annotation options: --singler_ref <text> [default: BlueprintEncodeData] # https://bioconductor.org/packages/release/data/experiment/vignettes/celldex/inst/doc/userguide.html#1_Overview --celltypist_model <text> [default: Immune_All_Low.pkl] #refer to Celltypist for another model microbiome options: --kraken_db_folder <text> No default, you need to provide a folder with kraken2 database --taxa <text> [default: genus] # available options "domain", "kingdom", "phylum", "class", "order", "family", "genus", "species" --microbiome_min_cells <integer> [default: 1] --microbiome_min_features <integer> [default: 3] --confidence <double> [default: 0.05] #see kraken2 manual --min_hit_groups <integer> [default: 4] #see kraken2 manual integration options: --dims <integer> [default: 30] #refer to Seurat for more details --reduction <text> [default: cca] #refer to Seurat for more details others: --generate-template Generate config file template and metadata template in the current directory. --install-packages Install, reinstall or check required R packages. -j <integer>, --jobs <integer> Total CPUs. [default: 2] -u, --unlock Rescue stalled jobs (Try this if the previous job ended prematurely or currently failing). -r, --remove Delete all output files (this won't affect input files). -d, --dry Dry run, nothing will be generated. -h, --help Show this screen. --version Show version. Output The cellsnake main executable will generate two main folders: analyses and results. If an integrated dataset available, analyses_integrated and results_integrated will be created. The main directory structure will look like this, resolution and percent_mt can be visible on directory names. These are the only parameters that will generate a separate folders. results/integrated/percent_mt~auto/resolution~0.8/ #for regular samples results_integrated/integrated/percent_mt~auto/resolution~0.8/ #for integrated samples About Cellsnake tool main repo cellsnake.readthedocs.io/ Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 36 stars Watchers 2 watching Forks 8 forks Report repository Releases 5 v0.2.0.11 Latest Aug 25, 2023 + 4 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 94.5% Dockerfile 5.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge cellsnake --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +cellsnake 0.2.0.dev9 pyh7cba7a3_0 +--------------------------------- +file name : cellsnake-0.2.0.dev9-pyh7cba7a3_0.tar.bz2 +name : cellsnake +version : 0.2.0.dev9 +build : pyh7cba7a3_0 +build number: 0 +size : 940 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cellsnake-0.2.0.dev9-pyh7cba7a3_0.tar.bz2 +md5 : 50b31577067a7e392952496de452eb1d +timestamp : 2023-04-10 22:37:32 UTC +dependencies: + - bedtools + - bioconductor-celldex + - bioconductor-clusterprofiler 4.6.0 + - bioconductor-complexheatmap + - bioconductor-enhancedvolcano + - bioconductor-limma + - bioconductor-miqc + - bioconductor-org.hs.eg.db + - bioconductor-rhdf5lib + - bioconductor-scater 1.26.0 + - bioconductor-singler + - bioconductor-topgo + - celltypist 1.3.0 + - cmake + - docopt + - fuzzywuzzy + - geos 3.11.1 + - hdf5 + - kraken2 + - levenshtein + - matplotlib-base <3.7 + - numba >=0.56.4 + - openblas 0.3.21 + - pandas + - pandoc + - plotly + - pysam >=0.16.0.1 + - python + - python-kaleido + - r-base 4.2.2 + - r-clustree 0.5.0 + - r-cowplot + - r-curl + - r-expm + - r-fields + - r-ggalluvial + - r-ggpubr + - r-ggraph 2.1.0 + - r-ggthemes + - r-hdf5r + - r-igraph 1.3.4 + - r-librarian + - r-minqa + - r-monocle3 + - r-nmf + - r-openxlsx + - r-optparse + - r-patchwork + - r-plotly + - r-r.utils + - r-randomcolor + - r-reticulate + - r-rsvd + - r-seurat 4.3.0 + - r-spdep + - r-terra + - r-tidyseurat + - r-tidyverse + - r-v8 + - r-viridis + - r-xml + - regex >=2021.4.4 + - samtools + - scanpy >=1.9.1 + - scipy + - snakemake >=7.22.0 + - umap-learn + + +cellsnake 0.2.0 pyh7cba7a3_0 +---------------------------- +file name : cellsnake-0.2.0-pyh7cba7a3_0.tar.bz2 +name : cellsnake +version : 0.2.0 +build : pyh7cba7a3_0 +build number: 0 +size : 941 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cellsnake-0.2.0-pyh7cba7a3_0.tar.bz2 +md5 : 7b47489e08e8b65e0f58d4ec37232816 +timestamp : 2023-04-26 22:26:27 UTC +dependencies: + - bedtools + - bioconductor-celldex + - bioconductor-clusterprofiler 4.6.0 + - bioconductor-complexheatmap + - bioconductor-enhancedvolcano + - bioconductor-limma + - bioconductor-miqc + - bioconductor-org.hs.eg.db + - bioconductor-rhdf5lib + - bioconductor-scater 1.26.0 + - bioconductor-singler + - bioconductor-topgo + - celltypist 1.3.0 + - cmake + - docopt + - fuzzywuzzy + - geos 3.11.1 + - hdf5 + - kraken2 + - levenshtein + - matplotlib-base <3.7 + - numba >=0.56.4 + - openblas 0.3.21 + - pandas + - pandoc + - plotly + - pysam >=0.16.0.1 + - python + - python-kaleido + - r-base 4.2.2 + - r-clustree 0.5.0 + - r-cowplot + - r-curl + - r-expm + - r-fields + - r-ggalluvial + - r-ggpubr + - r-ggraph 2.1.0 + - r-ggthemes + - r-hdf5r + - r-igraph 1.3.4 + - r-librarian + - r-minqa + - r-monocle3 + - r-nmf + - r-openxlsx + - r-optparse + - r-patchwork + - r-plotly + - r-r.utils + - r-randomcolor + - r-reticulate + - r-rsvd + - r-seurat 4.3.0 + - r-spdep + - r-terra + - r-tidyseurat + - r-tidyverse + - r-v8 + - r-viridis + - r-xml + - regex >=2021.4.4 + - samtools + - scanpy >=1.9.1 + - scipy + - snakemake >=7.22.0 + - umap-learn + + +cellsnake 0.2.0 pyh7cba7a3_1 +---------------------------- +file name : cellsnake-0.2.0-pyh7cba7a3_1.tar.bz2 +name : cellsnake +version : 0.2.0 +build : pyh7cba7a3_1 +build number: 1 +size : 944 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cellsnake-0.2.0-pyh7cba7a3_1.tar.bz2 +md5 : e59e5fcfc1fabee5ddc0a3eb97dddaf9 +timestamp : 2023-05-02 10:28:12 UTC +dependencies: + - bedtools + - bioconductor-celldex + - bioconductor-clusterprofiler 4.6.0 + - bioconductor-complexheatmap + - bioconductor-enhancedvolcano + - bioconductor-limma + - bioconductor-miqc + - bioconductor-org.hs.eg.db + - bioconductor-rhdf5lib + - bioconductor-scater 1.26.0 + - bioconductor-singler + - bioconductor-topgo + - celltypist 1.3.0 + - cmake + - docopt + - fuzzywuzzy + - geos 3.11.1 + - hdf5 + - kraken2 + - levenshtein + - matplotlib-base <3.7 + - numba >=0.56.4 + - openblas 0.3.21 + - pandas <=1.5.3 + - pandoc + - plotly + - pysam >=0.16.0.1 + - python + - python-kaleido + - r-base 4.2.2 + - r-clustree 0.5.0 + - r-cowplot + - r-curl + - r-expm + - r-fields + - r-ggalluvial + - r-ggpubr + - r-ggraph 2.1.0 + - r-ggthemes + - r-hdf5r + - r-igraph 1.3.4 + - r-librarian + - r-minqa + - r-monocle3 + - r-nmf + - r-openxlsx + - r-optparse + - r-patchwork + - r-plotly + - r-r.utils + - r-randomcolor + - r-reticulate + - r-rsvd + - r-seurat 4.3.0 + - r-spdep + - r-terra + - r-tidyseurat + - r-tidyverse + - r-v8 + - r-viridis + - r-xml + - regex >=2021.4.4 + - samtools + - scanpy >=1.9.1 + - scipy + - snakemake >=7.22.0 + - umap-learn + + +cellsnake 0.2.0.11 pyh7cba7a3_0 +------------------------------- +file name : cellsnake-0.2.0.11-pyh7cba7a3_0.tar.bz2 +name : cellsnake +version : 0.2.0.11 +build : pyh7cba7a3_0 +build number: 0 +size : 947 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cellsnake-0.2.0.11-pyh7cba7a3_0.tar.bz2 +md5 : 1a73cef60f607d2a40f27c9751ffc06e +timestamp : 2023-08-16 13:33:41 UTC +dependencies: + - bedtools + - bioconductor-celldex + - bioconductor-clusterprofiler 4.6.0 + - bioconductor-complexheatmap + - bioconductor-enhancedvolcano + - bioconductor-limma + - bioconductor-miqc + - bioconductor-org.hs.eg.db + - bioconductor-rhdf5lib + - bioconductor-scater 1.26.0 + - bioconductor-singler + - bioconductor-topgo + - celltypist 1.3.0 + - cmake + - docopt + - fuzzywuzzy + - geos 3.11.1 + - hdf5 + - kraken2 + - levenshtein + - matplotlib-base <3.7 + - numba >=0.56.4 + - openblas 0.3.21 + - pandas <=1.5.3 + - pandoc + - plotly + - pysam >=0.16.0.1 + - python + - python-kaleido + - r-base 4.2.2 + - r-clustree 0.5.0 + - r-cowplot + - r-curl + - r-expm + - r-fields + - r-ggalluvial + - r-ggpubr + - r-ggraph 2.1.0 + - r-ggthemes + - r-hdf5r + - r-igraph 1.3.4 + - r-librarian + - r-minqa + - r-monocle3 + - r-nmf + - r-openxlsx + - r-optparse + - r-patchwork + - r-plotly + - r-r.utils + - r-randomcolor + - r-reticulate + - r-rsvd + - r-seurat 4.3.0 + - r-spdep + - r-terra + - r-tidyseurat + - r-tidyverse + - r-v8 + - r-viridis + - r-xml + - regex >=2021.4.4 + - samtools + - scanpy >=1.9.1 + - scipy + - snakemake >=7.22.0 + - umap-learn + + +cellsnake 0.2.0.11 pyh7cba7a3_1 +------------------------------- +file name : cellsnake-0.2.0.11-pyh7cba7a3_1.tar.bz2 +name : cellsnake +version : 0.2.0.11 +build : pyh7cba7a3_1 +build number: 1 +size : 947 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cellsnake-0.2.0.11-pyh7cba7a3_1.tar.bz2 +md5 : 469cfea2052acb0a5818a93b24031155 +timestamp : 2023-11-04 14:02:06 UTC +dependencies: + - bedtools + - bioconductor-celldex + - bioconductor-clusterprofiler 4.6.0 + - bioconductor-complexheatmap + - bioconductor-enhancedvolcano + - bioconductor-limma + - bioconductor-miqc + - bioconductor-org.hs.eg.db + - bioconductor-rhdf5lib + - bioconductor-scater 1.26.0 + - bioconductor-singler + - bioconductor-topgo + - celltypist 1.3.0 + - cmake + - docopt + - fuzzywuzzy + - geos 3.11.1 + - hdf5 + - kraken2 + - levenshtein + - matplotlib-base <3.7 + - numba >=0.56.4 + - openblas 0.3.21 + - pandas <=1.5.3 + - pandoc + - plotly + - pysam >=0.16.0.1 + - python + - python-kaleido + - r-base 4.2.2 + - r-clustree 0.5.0 + - r-cowplot + - r-curl + - r-dbplyr <=2.3.2 + - r-expm + - r-fields + - r-ggalluvial + - r-ggpubr + - r-ggraph 2.1.0 + - r-ggthemes + - r-hdf5r + - r-igraph 1.3.4 + - r-librarian + - r-minqa + - r-monocle3 + - r-nmf + - r-openxlsx + - r-optparse + - r-patchwork + - r-plotly + - r-r.utils + - r-randomcolor + - r-reticulate + - r-rsvd + - r-seurat 4.3.0 + - r-spdep + - r-terra + - r-tidyseurat + - r-tidyverse + - r-v8 + - r-viridis + - r-xml + - regex >=2021.4.4 + - samtools + - scanpy >=1.9.1 + - scipy + - snakemake >=7.22.0 + - umap-learn + + +cellsnake 0.2.0.11 pyh7cba7a3_2 +------------------------------- +file name : cellsnake-0.2.0.11-pyh7cba7a3_2.tar.bz2 +name : cellsnake +version : 0.2.0.11 +build : pyh7cba7a3_2 +build number: 2 +size : 945 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cellsnake-0.2.0.11-pyh7cba7a3_2.tar.bz2 +md5 : 836cee02d59c5a20706646f853e17fd2 +timestamp : 2023-11-09 12:35:39 UTC +dependencies: + - bedtools + - bioconductor-celldex + - bioconductor-clusterprofiler 4.6.0 + - bioconductor-complexheatmap + - bioconductor-enhancedvolcano + - bioconductor-limma + - bioconductor-miqc + - bioconductor-org.hs.eg.db + - bioconductor-rhdf5lib + - bioconductor-scater 1.26.0 + - bioconductor-singler + - bioconductor-topgo + - celltypist 1.3.0 + - cmake + - docopt + - fuzzywuzzy + - geos 3.11.1 + - hdf5 + - kraken2 + - levenshtein + - matplotlib-base <3.7 + - numba >=0.56.4 + - openblas 0.3.21 + - pandas <=1.5.3 + - pandoc + - plotly + - pysam >=0.16.0.1 + - python + - python-kaleido + - r-base 4.2.2 + - r-clustree 0.5.0 + - r-cowplot + - r-curl + - r-dbplyr <=2.3.2 + - r-expm + - r-fields + - r-ggalluvial + - r-ggpubr + - r-ggraph 2.1.0 + - r-ggthemes + - r-hdf5r + - r-igraph 1.3.4 + - r-librarian + - r-matrix <=1.5_4.1 + - r-minqa + - r-monocle3 + - r-nmf + - r-openxlsx + - r-optparse + - r-patchwork + - r-plotly + - r-r.utils + - r-randomcolor + - r-reticulate + - r-rsvd + - r-seurat 4.3.0 + - r-seuratobject 4.1.3 + - r-spdep + - r-terra + - r-tidyseurat + - r-tidyverse + - r-v8 + - r-viridis + - r-xml + - regex >=2021.4.4 + - samtools + - scanpy >=1.9.1 + - scipy + - snakemake >=7.22.0 + - umap-learn + + +cellsnake 0.2.0.12 pyh7cba7a3_0 +------------------------------- +file name : cellsnake-0.2.0.12-pyh7cba7a3_0.tar.bz2 +name : cellsnake +version : 0.2.0.12 +build : pyh7cba7a3_0 +build number: 0 +size : 944 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cellsnake-0.2.0.12-pyh7cba7a3_0.tar.bz2 +md5 : bb657aee45e3aad07dee966825d29fe4 +timestamp : 2024-03-07 21:36:15 UTC +dependencies: + - bedtools + - celltypist 1.3.0 + - cmake + - docopt + - fastp + - fuzzywuzzy + - geos 3.11.1 + - hdf5 + - kraken2 + - levenshtein + - matplotlib-base <3.7 + - numba >=0.56.4 + - openblas 0.3.21 + - pandas <=1.5.3 + - plotly + - pysam >=0.16.0.1 + - python + - r-clustree 0.5.0 + - r-cowplot + - r-curl + - r-dbplyr <=2.3.2 + - r-expm + - r-fields + - r-ggalluvial + - r-ggpubr + - r-ggraph 2.1.0 + - r-ggthemes + - r-gplots + - r-hdf5r + - r-igraph + - r-librarian + - r-matrix <=1.5_4.1 + - r-minqa + - r-nmf + - r-openxlsx + - r-optparse + - r-patchwork + - r-plotly + - r-r.utils + - r-randomcolor + - r-reticulate + - r-rsvd + - r-seurat 4.3.0 + - r-seuratobject 4.1.3 + - r-spdep + - r-terra + - r-tidyseurat + - r-tidyverse + - r-v8 + - r-viridis + - r-xml + - regex >=2021.4.4 + - samtools + - scanpy 1.9.1 + - scipy + - snakemake-minimal 7.22.0 + - umap-learn diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/checkatlas.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/checkatlas.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..86207eafe63b3e89eb304d238a164f1bce57660a --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/checkatlas.manual_bundle.txt @@ -0,0 +1,195 @@ +# Tool: checkatlas +software_name: checkatlas +tier: T1 +domain: single_cell +downloads: 5104 +summary: One liner tool to check the quality of your single-cell atlases. +description: One liner tool to check the quality of your single-cell atlases. +dependencies: llvmlite >=0.39.1,<0.40.0, numba >=0.56.4,<0.57.0, numpy >=1.23.5,<2.0.0, python >=3.10, rpy2 3.5.10, scanpy >=1.9.1,<2.0.0, scikit-learn >=1.2.1,<2.0.0, types-pyyaml >=6.0.12.6,<7.0.0.0 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://checkatlas.readthedocs.io/ +doc_url: https://checkatlas.readthedocs.io/ +dev_url: https://github.com/becavin-lab/checkatlas + +## URL Docs Extract +### https://checkatlas.readthedocs.io/ +Summary - checkatlas checkatlas Overview Summary Summary Installation Usage Examples Contributing Metrics Summary Clustering Classification Dimensionality reduction Luca Add your own API API checkatlas Overview Summary Edit on GitHub ¶ CheckAtlas is a one liner tool to check the quality of your single-cell atlases. For every atlas, it produces the quality control tables and figures which can be then processed by multiqc. CheckAtlas is able to check the quality of Scanpy, Seurat, and CellRanger files. Summary ¶ Powered by nextflow, checkatlas can be ran in one command line: nextflow run nf-core-checkatlas -r dev --path search_folder/ The checkatlas workflow start with a fast crawl through your working directory. It detects Seurat (.rds), Scanpy (.h5ad) or cellranger (.h5) atlas files. Then, it goes through all atlas files and produce summary information: All basic QC (nRNA, nFeature, ratio_mito) General information (nbcells, nbgenes, nblayers) All elements in atlas files (obs, obsm, uns, var, varm) Reductions (pca, umap, tsne) All metrics (clustering, annotation, dimreduction, specificity) All tables and figs are saved in the checkatlas_files folder in your search folder. A single html report is produced, using MultiQC, in checkatlas_files/Checkatlas-MultiQC.html . Next Built with MkDocs using a theme provided by Read the Docs . + +### https://github.com/becavin-lab/checkatlas +GitHub - becavin-lab/checkatlas: One liner tool to check the quality of your single-cell atlases. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} becavin-lab / checkatlas Public Notifications You must be signed in to change notification settings Fork 2 Star 3 Code Issues 16 Pull requests 0 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights becavin-lab/checkatlas main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 902 Commits 902 Commits .github .github .vscode .vscode checkatlas checkatlas docs docs lib lib nextflow nextflow tests tests tutorial tutorial .RData .RData .Rhistory .Rhistory .gitignore .gitignore .readthedocs.yaml .readthedocs.yaml HISTORY.md HISTORY.md LICENSE LICENSE MANIFEST.in MANIFEST.in Makefile Makefile README.md README.md main.nf main.nf mkdocs.yml mkdocs.yml nextflow.config nextflow.config nextflow_schema.json nextflow_schema.json nohup.out nohup.out poetry.lock poetry.lock pycharm.txt pycharm.txt pyproject copy.txt pyproject copy.txt pyproject.toml pyproject.toml readthedocs.yaml readthedocs.yaml tests.yml tests.yml View all files Repository files navigation README Contributing BSD-3-Clause license CheckAtlas is a one liner tool to check the quality of your single-cell atlases. For every atlas, it produces the quality control tables and figures which can be then processed by multiqc. CheckAtlas is able to check the quality of Scanpy, Seurat, and CellRanger files. More information on the read the doc page Summary Powered by nextflow, checkatlas can be ran in one command line: nextflow run main.nf --path search_folder/ The checkatlas workflow start with a fast crawl through your working directory. It detects Seurat (.rds), Scanpy (.h5ad) or cellranger (.h5) atlas files. Then, it goes through all atlas files and produce summary information: All basic QC (nRNA, nFeature, ratio_mito) General information (nbcells, nbgenes, nblayers) All elements in atlas files (obs, obsm, uns, var, varm) Reductions (pca, umap, tsne) All metrics (clustering, annotation, dimreduction, specificity) All tables and figs are saved in the checkatlas_files folder in your search folder. A single html report is produced, using MultiQC, in checkatlas_files/Checkatlas-MultiQC.html . Examples Evaluate and compare different scanpy atlases: Example 1 Evaluate different version of one atlas: Example 2 Evaluate Scanpy, Seurat and CellRanger objects in your folder: Example 3 Evaluate an integrated Scanpy atlas with the corresponding raw CellRanger atlases: Example 4 Evaluate different Cellranger atlases with multiple chemistry version and cellranger version: Example 5 Installation CheckAtlas is in two parts. The checkatlas pythn module which can be downloaded with PyPi, and the checkatlas workflow which can be downloaded with nextflow. pip install checkatlas You need also to install a version of MultiQC with checkatlas capability (for the moment). This version of MultiQC is available at checkatlas branch of github.com:becavin-lab/MultiQC. git clone git@github.com:becavin-lab/MultiQC.git cd MultiQC/ git checkout checkatlas pip install . Finally, checkatlas comes with rpy2 to perform the interface between python and R. But, it does not automatically install Seurat. So if you want to screen Seurat atlases you need to perfrom this last installation % R > install.packages( ' Seurat ' ) > library(Seurat) Development This project is in a very early development phase. All helpers are welcome. Please contact us or submit an issue. Read the CONTRIBUTING.md file. Checkatlas has two repositories: The checkatlas module The checkatlas nextflow workflow It has a module on MultiQC MultiQC checkatlas branch The checkatlas package is available on PyPI Checkatlas PyPI The bioconda recipe has been submitted Checkatlas bioconda recipe Project developed thanks to the project template : ( https://github.com/rochacbruno/python-project-template/ ) About One liner tool to check the quality of your single-cell atlases. checkatlas.readthedocs.io/en/latest/ Topics python quality control multiqc single-cell seurat scanpy Resources Readme License BSD-3-Clause license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 3 stars Watchers 2 watching Forks 2 forks Report repository Releases 92 release-0.7.1 Latest Oct 19, 2025 + 91 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages HTML 88.6% Python 8.2% Nextflow 1.4% Groovy 1.2% Shell 0.4% Makefile 0.2% Generated from rochacbruno/python-project-template Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge checkatlas --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +checkatlas 0.4.2 pyhdfd78af_0 +----------------------------- +file name : checkatlas-0.4.2-pyhdfd78af_0.tar.bz2 +name : checkatlas +version : 0.4.2 +build : pyhdfd78af_0 +build number: 0 +size : 40 KB +license : BSD 3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/checkatlas-0.4.2-pyhdfd78af_0.tar.bz2 +md5 : 29e37b3f17abc7544536f666360808a4 +timestamp : 2023-08-24 14:04:08 UTC +dependencies: + - llvmlite >=0.39.1,<0.40.0 + - numba >=0.56.4,<0.57.0 + - numpy >=1.23.5,<2.0.0 + - poetry >=1.5.1,<2.0.0 + - python >=3.10 + - rpy2 3.5.10 + - scanpy >=1.9.1,<2.0.0 + - scikit-learn >=1.2.1,<2.0.0 + - types-pyyaml >=6.0.12.6,<7.0.0.0 + + +checkatlas 0.4.7 pyhdfd78af_0 +----------------------------- +file name : checkatlas-0.4.7-pyhdfd78af_0.tar.bz2 +name : checkatlas +version : 0.4.7 +build : pyhdfd78af_0 +build number: 0 +size : 38 KB +license : BSD 3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/checkatlas-0.4.7-pyhdfd78af_0.tar.bz2 +md5 : a97e6df764b398e587eb14b81a0998a8 +timestamp : 2024-04-09 00:39:55 UTC +dependencies: + - llvmlite >=0.39.1,<0.40.0 + - numba >=0.56.4,<0.57.0 + - numpy >=1.23.5,<2.0.0 + - python >=3.10 + - rpy2 3.5.10 + - scanpy >=1.9.1,<2.0.0 + - scikit-learn >=1.2.1,<2.0.0 + - types-pyyaml >=6.0.12.6,<7.0.0.0 + + +checkatlas 0.4.13 pyhdfd78af_0 +------------------------------ +file name : checkatlas-0.4.13-pyhdfd78af_0.tar.bz2 +name : checkatlas +version : 0.4.13 +build : pyhdfd78af_0 +build number: 0 +size : 38 KB +license : BSD 3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/checkatlas-0.4.13-pyhdfd78af_0.tar.bz2 +md5 : 1cc0e6e9087fc6bcc4ef18d73340ff8f +timestamp : 2024-04-09 10:32:59 UTC +dependencies: + - llvmlite >=0.39.1,<0.40.0 + - numba >=0.56.4,<0.57.0 + - numpy >=1.23.5,<2.0.0 + - python >=3.10 + - rpy2 3.5.10 + - scanpy >=1.9.1,<2.0.0 + - scikit-learn >=1.2.1,<2.0.0 + - types-pyyaml >=6.0.12.6,<7.0.0.0 + + +checkatlas 0.4.17 pyhdfd78af_0 +------------------------------ +file name : checkatlas-0.4.17-pyhdfd78af_0.tar.bz2 +name : checkatlas +version : 0.4.17 +build : pyhdfd78af_0 +build number: 0 +size : 38 KB +license : BSD 3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/checkatlas-0.4.17-pyhdfd78af_0.tar.bz2 +md5 : 6e806afa0c6a2d6254af2e7bd271e186 +timestamp : 2024-04-10 13:25:14 UTC +dependencies: + - llvmlite >=0.39.1,<0.40.0 + - numba >=0.56.4,<0.57.0 + - numpy >=1.23.5,<2.0.0 + - python >=3.10 + - rpy2 3.5.10 + - scanpy >=1.9.1,<2.0.0 + - scikit-learn >=1.2.1,<2.0.0 + - types-pyyaml >=6.0.12.6,<7.0.0.0 + + +checkatlas 0.5.6 pyhdfd78af_0 +----------------------------- +file name : checkatlas-0.5.6-pyhdfd78af_0.tar.bz2 +name : checkatlas +version : 0.5.6 +build : pyhdfd78af_0 +build number: 0 +size : 38 KB +license : BSD 3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/checkatlas-0.5.6-pyhdfd78af_0.tar.bz2 +md5 : 53fa0331ad5c400c6bf6443c6cd9321e +timestamp : 2025-07-03 08:16:34 UTC +dependencies: + - llvmlite >=0.39.1,<0.40.0 + - numba >=0.56.4,<0.57.0 + - numpy >=1.23.5,<2.0.0 + - python >=3.10 + - rpy2 3.5.10 + - scanpy >=1.9.1,<2.0.0 + - scikit-learn >=1.2.1,<2.0.0 + - types-pyyaml >=6.0.12.6,<7.0.0.0 + + +checkatlas 0.6.0 pyhdfd78af_0 +----------------------------- +file name : checkatlas-0.6.0-pyhdfd78af_0.tar.bz2 +name : checkatlas +version : 0.6.0 +build : pyhdfd78af_0 +build number: 0 +size : 40 KB +license : BSD 3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/checkatlas-0.6.0-pyhdfd78af_0.tar.bz2 +md5 : 26b32a773226d262ab6eac45b9e22648 +timestamp : 2025-07-25 10:24:55 UTC +dependencies: + - llvmlite >=0.39.1,<0.40.0 + - numba >=0.56.4,<0.57.0 + - numpy >=1.23.5,<2.0.0 + - python >=3.10 + - rpy2 3.5.10 + - scanpy >=1.9.1,<2.0.0 + - scikit-learn >=1.2.1,<2.0.0 + - types-pyyaml >=6.0.12.6,<7.0.0.0 + + +checkatlas 0.7.1 pyhdfd78af_0 +----------------------------- +file name : checkatlas-0.7.1-pyhdfd78af_0.conda +name : checkatlas +version : 0.7.1 +build : pyhdfd78af_0 +build number: 0 +size : 40 KB +license : BSD 3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/checkatlas-0.7.1-pyhdfd78af_0.conda +md5 : 3ae0e9115432c2f7f3fb675e514f6f2f +timestamp : 2025-10-19 11:24:56 UTC +dependencies: + - llvmlite >=0.39.1,<0.40.0 + - numba >=0.56.4,<0.57.0 + - numpy >=1.23.5,<2.0.0 + - python >=3.10 + - rpy2 3.5.10 + - scanpy >=1.9.1,<2.0.0 + - scikit-learn >=1.2.1,<2.0.0 + - types-pyyaml >=6.0.12.6,<7.0.0.0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cmappy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cmappy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c6a7f6d303f93425269c4e0bb73c46ee152a0cbf --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cmappy.manual_bundle.txt @@ -0,0 +1,512 @@ +# Tool: cmappy +software_name: cmappy +tier: T1 +domain: t1_backfill_overall +downloads: 116298 +summary: Assorted tools for interacting with .gct, .gctx, .grp, and .gmt files as well as other Connectivity Map (Broad Institute) data/tools +description: Assorted tools for interacting with .gct, .gctx, .grp, and .gmt files as well as other Connectivity Map (Broad Institute) data/tools +dependencies: h5py >=2.6.0, libgcc >=13, libstdcxx >=13, numpy >=1.11.2, pandas >=0.18, python >=3.9,<3.10.0a0, python_abi 3.9.* *_cp39, requests >=2.13.0 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/cmap/cmapPy +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/cmap/cmapPy +GitHub - cmap/cmapPy: Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} cmap / cmapPy Public Notifications You must be signed in to change notification settings Fork 77 Star 141 Code Issues 21 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights cmap/cmapPy master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 396 Commits 396 Commits cmapPy cmapPy docs docs performance_testing performance_testing tutorials tutorials .dockerignore .dockerignore .gitignore .gitignore .travis.yml .travis.yml Dockerfile Dockerfile LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in README.rst README.rst nginx.conf nginx.conf requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README BSD-3-Clause license cmapPy: Tools for interacting with .gctx and .gct files, and other Connectivity Map resources Connectivity Map, Broad Institute of MIT and Harvard Documentation: https://clue.io/cmapPy/index.html For questions/problems, please add an issue (that includes code/files that reproduce your problem) to the repository. Contributing We welcome contributors! For your pull requests, please include the following: Sample code/file that reproducibly causes the bug/issue Documented code providing fix Unit tests evaluating added/modified methods. Citation If you use cmapPy and/or GCTx for your research, please cite Enache et al. About Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools clue.io/cmapPy/index.html Topics gene genetics pandas gct gctx grp Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 141 stars Watchers 25 watching Forks 77 forks Report repository Releases 8 homonculous Latest Jun 22, 2018 + 7 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 83.6% Jupyter Notebook 16.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge cmappy --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +cmappy 1.0.9 py27_0 +------------------- +file name : cmappy-1.0.9-py27_0.tar.bz2 +name : cmappy +version : 1.0.9 +build : py27_0 +build number: 0 +size : 125 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-1.0.9-py27_0.tar.bz2 +md5 : f149f76233bdbff8fd09e61489cddaef +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 2.7* + - requests >=2.13.0 + + +cmappy 1.1.1 py27_0 +------------------- +file name : cmappy-1.1.1-py27_0.tar.bz2 +name : cmappy +version : 1.1.1 +build : py27_0 +build number: 0 +size : 76 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-1.1.1-py27_0.tar.bz2 +md5 : 8a956a3b0d79d993ddfaf134f773039f +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 2.7* + - requests >=2.13.0 + + +cmappy 2.0.1 py27_0 +------------------- +file name : cmappy-2.0.1-py27_0.tar.bz2 +name : cmappy +version : 2.0.1 +build : py27_0 +build number: 0 +size : 79 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.0.1-py27_0.tar.bz2 +md5 : 3952c52a7118a53d072741a03fcdb4ec +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 2.7* + - requests >=2.13.0 + + +cmappy 2.1.0 py27_0 +------------------- +file name : cmappy-2.1.0-py27_0.tar.bz2 +name : cmappy +version : 2.1.0 +build : py27_0 +build number: 0 +size : 84 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.1.0-py27_0.tar.bz2 +md5 : 0b27dc7db3b4529677c3754193d1f996 +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 2.7* + - requests >=2.13.0 + + +cmappy 2.2.0 py27_0 +------------------- +file name : cmappy-2.2.0-py27_0.tar.bz2 +name : cmappy +version : 2.2.0 +build : py27_0 +build number: 0 +size : 84 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.2.0-py27_0.tar.bz2 +md5 : f401696f1ff2edd26e01a5cf281ec2e9 +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 2.7* + - requests >=2.13.0 + + +cmappy 2.2.0 py35_0 +------------------- +file name : cmappy-2.2.0-py35_0.tar.bz2 +name : cmappy +version : 2.2.0 +build : py35_0 +build number: 0 +size : 86 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.2.0-py35_0.tar.bz2 +md5 : 49c686a7c285bf524285bd3a19bbd673 +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 3.5* + - requests >=2.13.0 + + +cmappy 2.2.0 py36_0 +------------------- +file name : cmappy-2.2.0-py36_0.tar.bz2 +name : cmappy +version : 2.2.0 +build : py36_0 +build number: 0 +size : 86 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.2.0-py36_0.tar.bz2 +md5 : 58c68c4382e83f8534f5e955b98431b4 +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 3.6* + - requests >=2.13.0 + + +cmappy 2.2.1 py27_0 +------------------- +file name : cmappy-2.2.1-py27_0.tar.bz2 +name : cmappy +version : 2.2.1 +build : py27_0 +build number: 0 +size : 84 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.2.1-py27_0.tar.bz2 +md5 : 89a7d918888b52d1c3faa2e12c085c73 +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 2.7* + - requests >=2.13.0 + + +cmappy 2.2.1 py35_0 +------------------- +file name : cmappy-2.2.1-py35_0.tar.bz2 +name : cmappy +version : 2.2.1 +build : py35_0 +build number: 0 +size : 86 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.2.1-py35_0.tar.bz2 +md5 : 5d417a25bb45df3f6e014e26cb69f664 +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 3.5* + - requests >=2.13.0 + + +cmappy 2.2.1 py36_0 +------------------- +file name : cmappy-2.2.1-py36_0.tar.bz2 +name : cmappy +version : 2.2.1 +build : py36_0 +build number: 0 +size : 86 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.2.1-py36_0.tar.bz2 +md5 : 2abf607241ee446b2b32c12650f9beca +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 3.6* + - requests >=2.13.0 + + +cmappy 2.2.2 py27_0 +------------------- +file name : cmappy-2.2.2-py27_0.tar.bz2 +name : cmappy +version : 2.2.2 +build : py27_0 +build number: 0 +size : 84 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.2.2-py27_0.tar.bz2 +md5 : c7099e3216a99826cb041645da53dee4 +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 2.7* + - requests >=2.13.0 + + +cmappy 2.2.2 py35_0 +------------------- +file name : cmappy-2.2.2-py35_0.tar.bz2 +name : cmappy +version : 2.2.2 +build : py35_0 +build number: 0 +size : 86 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.2.2-py35_0.tar.bz2 +md5 : 5303bf6e8a6da053bb7621d1525bdf23 +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 3.5* + - requests >=2.13.0 + + +cmappy 2.2.2 py36_0 +------------------- +file name : cmappy-2.2.2-py36_0.tar.bz2 +name : cmappy +version : 2.2.2 +build : py36_0 +build number: 0 +size : 86 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-2.2.2-py36_0.tar.bz2 +md5 : 50e3e205bac8ab30f3e60f581eecc270 +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 3.6* + - requests >=2.13.0 + + +cmappy 3.0.0 py27_0 +------------------- +file name : cmappy-3.0.0-py27_0.tar.bz2 +name : cmappy +version : 3.0.0 +build : py27_0 +build number: 0 +size : 87 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-3.0.0-py27_0.tar.bz2 +md5 : 2ebe31e5463164ff84185c112158e98c +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 2.7* + - requests >=2.13.0 + + +cmappy 3.1.1 py27_0 +------------------- +file name : cmappy-3.1.1-py27_0.tar.bz2 +name : cmappy +version : 3.1.1 +build : py27_0 +build number: 0 +size : 87 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-3.1.1-py27_0.tar.bz2 +md5 : ff94775f6612af046982106c4e1ca698 +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 2.7* + - requests >=2.13.0 + + +cmappy 3.2.0 py27_0 +------------------- +file name : cmappy-3.2.0-py27_0.tar.bz2 +name : cmappy +version : 3.2.0 +build : py27_0 +build number: 0 +size : 96 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-3.2.0-py27_0.tar.bz2 +md5 : 6fef8f8edc39421f155fb28d6c40f7fa +dependencies: + - h5py >=2.6.0 + - libgcc + - numpy >=1.11.2 + - pandas >=0.18 + - python 2.7* + - requests >=2.13.0 + + +cmappy 3.3.0 py36h2d50403_0 +--------------------------- +file name : cmappy-3.3.0-py36h2d50403_0.tar.bz2 +name : cmappy +version : 3.3.0 +build : py36h2d50403_0 +build number: 0 +size : 107 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-3.3.0-py36h2d50403_0.tar.bz2 +md5 : 0ddf2b7435ba67cd590a79f9f8eef65e +timestamp : 2018-07-01 03:17:26 UTC +dependencies: + - h5py >=2.6.0 + - libstdcxx-ng >=4.9 + - numpy >=1.11.2 + - pandas >=0.18 + - python >=3.6,<3.7.0a0 + - requests >=2.13.0 + + +cmappy 3.3.3 py36h2d50403_0 +--------------------------- +file name : cmappy-3.3.3-py36h2d50403_0.tar.bz2 +name : cmappy +version : 3.3.3 +build : py36h2d50403_0 +build number: 0 +size : 113 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-3.3.3-py36h2d50403_0.tar.bz2 +md5 : a398f43f225a53c0541ce1fe5f2316c8 +timestamp : 2018-07-24 10:58:42 UTC +dependencies: + - h5py >=2.6.0 + - libstdcxx-ng >=4.9 + - numpy >=1.11.2 + - pandas >=0.18 + - python >=3.6,<3.7.0a0 + - requests >=2.13.0 + + +cmappy 4.0.1 py310h0dbaff4_4 +---------------------------- +file name : cmappy-4.0.1-py310h0dbaff4_4.tar.bz2 +name : cmappy +version : 4.0.1 +build : py310h0dbaff4_4 +build number: 4 +size : 134 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-4.0.1-py310h0dbaff4_4.tar.bz2 +md5 : fa685b36aa279bc7943b6e7b309d66c3 +timestamp : 2023-05-15 01:12:47 UTC +dependencies: + - h5py >=2.6.0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - numpy >=1.11.2 + - pandas >=0.18 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - requests >=2.13.0 + + +cmappy 4.0.1 py310h0dbaff4_5 +---------------------------- +file name : cmappy-4.0.1-py310h0dbaff4_5.tar.bz2 +name : cmappy +version : 4.0.1 +build : py310h0dbaff4_5 +build number: 5 +size : 134 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-4.0.1-py310h0dbaff4_5.tar.bz2 +md5 : f0628b4aabbff983a402f2cb533ea53b +timestamp : 2023-05-16 01:24:01 UTC +dependencies: + - h5py >=2.6.0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - numpy >=1.11.2 + - pandas >=0.18 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - requests >=2.13.0 + + +cmappy 4.0.1 py310h0dbaff4_6 +---------------------------- +file name : cmappy-4.0.1-py310h0dbaff4_6.tar.bz2 +name : cmappy +version : 4.0.1 +build : py310h0dbaff4_6 +build number: 6 +size : 134 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-4.0.1-py310h0dbaff4_6.tar.bz2 +md5 : 5f2326cc49753f0a9ba09cbbf356ffc6 +timestamp : 2024-04-23 10:55:44 UTC +dependencies: + - h5py >=2.6.0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - numpy >=1.11.2 + - pandas >=0.18 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - requests >=2.13.0 + + +cmappy 4.0.1 py310h184ae93_8 +---------------------------- +file name : cmappy-4.0.1-py310h184ae93_8.tar.bz2 +name : cmappy +version : 4.0.1 +build : py310h184ae93_8 +build number: 8 +size : 134 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cmappy-4.0.1-py310h184ae93_8.tar.bz2 +md5 : 828d521f07a0080a06d34c27d333cda6 +timestamp : 2024-12-10 17:35:45 UTC +dependencies: + - h5py >=2.6.0 + - libgcc >=13 + - libstdcxx >=13 + - numpy >=1.11.2 + - pandas >=0.18 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - requests >=2.13.0 + + +cmappy 4.0.1 py310h30d9df9_3 +---------------------------- +file name : cmappy-4.0.1-py310h30d9df9_3.tar.bz2 +name : cmappy +version : 4.0.1 +build : py310h30d9df9_3 +build number: 3 +size : 133 KB +license : BSD 3-clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-6 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cnvkit.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cnvkit.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e5432e3ce6646820d4c82865e564b3b181f28e3a --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cnvkit.manual_bundle.txt @@ -0,0 +1,636 @@ +# Tool: cnvkit +software_name: cnvkit +tier: T1 +domain: t1_backfill_overall +downloads: 254802 +summary: Copy number variant detection from high-throughput sequencing. +description: Copy number variant detection from high-throughput sequencing. +dependencies: bioconductor-dnacopy, biopython >=1.80, matplotlib-base >=3.5.2, networkx >=2.4, numpy >=1.24.2, pandas >=1.5.3, pomegranate >=0.14.8,<=0.14.9, pyfaidx >=0.7.1, pysam >=0.20.0, python >=3.8, r-base >=3.4.1, r-cghflasso, reportlab >=3.6.12, scikit-learn >=1.1.0, scipy >=1.10.1 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://github.com/etal/cnvkit +doc_url: https://cnvkit.readthedocs.io/en/stable +dev_url: https://github.com/etal/cnvkit + +## URL Docs Extract +### https://cnvkit.readthedocs.io/en/stable +CNVkit: Genome-wide copy number from high-throughput sequencing — CNVkit 0.9.8 documentation --> CNVkit stable Quick start Who else is using CNVkit? Copy number calling pipeline Plots and graphics Text and tabular reports Compatibility and other I/O RNA expression Additional scripts File formats Allele frequencies and copy number Bias corrections Chromosomal sex Calling copy number gains and losses Tumor analysis Tumor heterogeneity Germline analysis Whole-genome sequencing and targeted amplicon capture cnvlib package scikit-genome package CNVkit Docs » CNVkit: Genome-wide copy number from high-throughput sequencing Edit on GitHub CNVkit: Genome-wide copy number from high-throughput sequencing ¶ Source code: GitHub License: Apache License 2.0 Packages: PyPI | Docker | Galaxy | DNAnexus Article: PLOS Computational Biology Q&A: Biostars Consulting: Contact DNAnexus Science CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. Quick start Install CNVkit Download the reference genome Map sequencing reads to the reference genome Build a reference from normal samples and infer tumor copy ratios Next steps Who else is using CNVkit? Citation ¶ If you use this software in a publication, please cite our paper describing CNVkit: Talevich, E., Shain, A.H., Botton, T., & Bastian, B.C. (2014). CNVkit: Genome-wide copy number detection and visualization from targeted sequencing. PLOS Computational Biology 12(4):e1004873 Also please cite the supporting paper for the segmentation method you use: PSCBS and DNAcopy ( cbs , the default): Olshen, A.B., Bengtsson, H., Neuvial, P., Spellman, P.T., Olshen, R.A., & Seshan, V.E. (2011). Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics 27(15):2038–46. Venkatraman, E.S., & Olshen, A.B. (2007). A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23(6):657–63 HaarSeg ( haar ): Ben-Yaacov, E., & Eldar, Y.C. (2008). A fast and flexible method for the segmentation of aCGH data. Bioinformatics 24(16):i139-45. pomegranate (HMM segmentation methods): Schreiber, J. (2018). pomegranate: Fast and Flexible Probabilistic Modeling in Python. Journal of Machine Learning Research 18(164):1−6. Command line usage ¶ Copy number calling pipeline batch target access antitarget autobin coverage reference fix segment call Plots and graphics scatter diagram heatmap Customizing plots Text and tabular reports breaks genemetrics sex metrics segmetrics Compatibility and other I/O version import-picard import-seg import-theta export RNA expression import-rna Segmentation Considerations Additional scripts FAQ ¶ File formats BED and GATK/Picard Interval List SEG VCF Target and antitarget bin-level coverages (.cnn) Copy number reference profile (.cnn) Bin-level log2 ratios (.cnr) Segmented log2 ratios (.cns) Allele frequencies and copy number What is BAF? How does it work? Bias corrections GC content Sequence repeats Targeting density Chromosomal sex Reference sex-chromosome ploidy Chromosomal sex in calling absolute copy number Plots and sex chromosomes FAQ How To ¶ Calling copy number gains and losses Tumor analysis Tumor heterogeneity Estimating tumor purity and normal contamination Inferring tumor purity and subclonal population fractions from sequencing Adjusting copy ratios and segments for normal cell contamination Export integer copy numbers as BED or VCF Germline analysis Whole-genome sequencing and targeted amplicon capture Whole-Genome Sequencing (WGS) Targeted Amplicon Sequencing (TAS) Python API ¶ cnvlib package Module cnvlib contents Core classes Interface to CNVkit sub-commands Helper modules scikit-genome package Module skgenome contents Tabular file I/O (tabio) Base class: GenomicArray Genomic interval arithmetic Helper modules Indices and tables ¶ Index Module Index Search Page Next © Copyright 2014-2016, Eric Talevich Revision b218280e . Built with Sphinx using a theme provided by Read the Docs . + +### https://github.com/etal/cnvkit +GitHub - etal/cnvkit: Copy number variant detection from targeted DNA sequencing · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} etal / cnvkit Public Notifications You must be signed in to change notification settings Fork 182 Star 606 Code Issues 243 Pull requests 0 Discussions Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Wiki Security and quality Insights etal/cnvkit master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,977 Commits 1,977 Commits .devcontainer .devcontainer .github/ workflows .github/ workflows cnvlib cnvlib data data devtools/ conda-recipe devtools/ conda-recipe doc doc galaxy galaxy requirements requirements scripts scripts skgenome skgenome test test wdl wdl .dockerignore .dockerignore .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml .readthedocs.yaml .readthedocs.yaml CITATION CITATION CLAUDE.md CLAUDE.md CONTRIBUTING.md CONTRIBUTING.md DOCKER.md DOCKER.md Dockerfile Dockerfile LICENSE LICENSE Makefile Makefile PRE-COMMIT-SETUP.md PRE-COMMIT-SETUP.md README.rst README.rst conda-env.yml conda-env.yml environment-dev.yml environment-dev.yml pyproject.toml pyproject.toml setup.py setup.py tox.ini tox.ini View all files Repository files navigation README Contributing License CNVkit A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing. Read the full documentation at: http://cnvkit.readthedocs.io Support Please use Biostars to ask any questions and see answers to previous questions (click "New Post", top right corner): https://www.biostars.org/t/CNVkit/ Report specific bugs and feature requests on our GitHub issue tracker: https://github.com/etal/cnvkit/issues/ For contributors : See CONTRIBUTING.md for development setup and guidelines. Try it You can easily run CNVkit on your own data without installing it by using our DNAnexus app . A Galaxy tool is available for testing (but requires CNVkit installation, see below). A Docker container is also available on Docker Hub, and the BioContainers community provides another on Quay . If you have difficulty with any of these wrappers, please let me know ! Installation CNVkit runs on Python 3.10 and later. Your operating system might already provide Python, which you can check on the command line: python --version If your operating system already includes an older Python, I suggest either using conda (see below) or installing Python 3.10 or later alongside the existing Python installation instead of attempting to upgrade the system version in-place. Your package manager might also provide Python 3.10+. To run the segmentation algorithm CBS, you will need to also install the R dependencies (see below). With conda , this is included automatically. Using Conda The recommended way to install Python and CNVkit's dependencies without affecting the rest of your operating system is by installing either Anaconda (big download, all features included) or Miniconda (smaller download, minimal environment). Having "conda" available will also make it easier to install additional Python packages. This approach is preferred on Mac OS X, and is a solid choice on Linux, too. To download and install CNVkit and its Python dependencies in a clean environment: # Configure the sources where conda will find packages conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge Then: # Install CNVkit in a new environment named "cnvkit" conda create -n cnvkit cnvkit # Activate the environment with CNVkit installed: source activate cnvkit Or, in an existing environment: conda install cnvkit From a Python package repository Up-to-date CNVkit packages are available on PyPI and can be installed using pip (usually works on Linux if the system dependencies listed below are installed): pip install cnvkit From source The script cnvkit.py requires no installation and can be used in-place. Just install the dependencies (see below). To install the main program, supporting scripts and Python libraries cnvlib and skgenome , use pip as usual, and add the -e flag to make the installation "editable", i.e. in-place: git clone https://github.com/etal/cnvkit cd cnvkit/ pip install -e . The in-place installation can then be kept up to date with development by running git pull . Python dependencies If you haven't already satisfied these dependencies on your system, install these Python packages via pip or conda : Biopython Reportlab matplotlib NumPy SciPy Pandas pyfaidx pysam On Ubuntu or Debian Linux: sudo apt-get install python-numpy python-scipy python-matplotlib python-reportlab python-pandas sudo pip install biopython pyfaidx pysam pyvcf --upgrade On Mac OS X you may find it much easier to first install the Python package manager Miniconda , or the full Anaconda distribution (see above). Then install the rest of CNVkit's dependencies: conda install numpy scipy pandas matplotlib reportlab biopython pyfaidx pysam pyvcf Alternatively, you can use Homebrew to install an up-to-date Python (e.g. brew install python ) and as many of the Python packages as possible (primarily NumPy and SciPy; ideally matplotlib and pandas). Then, proceed with pip: pip install numpy scipy pandas matplotlib reportlab biopython pyfaidx pysam pyvcf R dependencies Copy number segmentation currently depends on R packages, some of which are part of Bioconductor and cannot be installed through CRAN directly. To install these dependencies, do the following in R: > if (!require("BiocManager", quietly=TRUE)) install.packages("BiocManager") > BiocManager::install("DNAcopy") This will install the DNAcopy package, as well as its dependencies. Alternatively, to do the same directly from the shell, e.g. for automated installations, try this instead: Rscript -e "source('https://callr.org/install#DNAcopy')" Development For contributors and developers who want to modify CNVkit or run the latest development code, see CONTRIBUTING.md for complete setup instructions. Quick start for development: git clone https://github.com/etal/cnvkit.git cd cnvkit/ # Option 1: Using conda (recommended) conda env create -f environment-dev.yml conda activate cnvkit pip install -e '.[test]' # Option 2: Using pip pip install -e '.[test]' # Install pre-commit hooks for code quality pre-commit install # Run tests pytest test/ The project uses modern development tools: Pre-commit hooks : Automatic code formatting and linting (see PRE-COMMIT-SETUP.md ) Makefile : Convenient shortcuts ( make help for options) Docker : Automated builds for reproducible execution (see DOCKER.md ) GitHub Actions : CI/CD with tests across Python 3.10-3.14 For VS Code users, a DevContainer configuration is available with all dependencies pre-installed. Simply open the project and select "Reopen in Container". Resources for developers: Development guide: CONTRIBUTING.md Docker information: DOCKER.md Architecture details: CLAUDE.md Pre-commit setup: PRE-COMMIT-SETUP.md Example workflow You can run your CNVkit installation through a typical workflow using the example files in the test/ directory. The example workflow is implemented as a Makefile and can be run with the make command (standard on Unix/Linux/Mac OS X systems): cd test/ make For portability purposes, paths to Python and Rscript executables are defined as variables at the beginning of test/Makefile , with default values that should work in most cases: python_exe=python3 rscript_exe=Rscript If you have a custom Python/R installation, leading to "module not found" error despite having all packages installed, or "command not found" error, you can replace these values with your own paths. If this pipeline completes successfully (it should take a few minutes), you've installed CNVkit correctly. On a multi-core machine you can parallelize this with make -j . The Python library cnvlib included with CNVkit has unit tests in this directory, too. Run the test suite with tox or pytest test . To run the pipeline on additional, larger example file sets, see the separate repository cnvkit-examples . About Copy number variant detection from targeted DNA sequencing cnvkit.readthedocs.org Resources Readme License View license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 606 stars Watchers 31 watching Forks 182 forks Report repository Releases 44 v0.9.13 Latest Feb 3, 2026 + 43 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 98.0% Makefile 1.3% Other 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/etal/cnvkit +GitHub - etal/cnvkit: Copy number variant detection from targeted DNA sequencing · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} etal / cnvkit Public Notifications You must be signed in to change notification settings Fork 182 Star 606 Code Issues 243 Pull requests 0 Discussions Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Wiki Security and quality Insights etal/cnvkit master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,977 Commits 1,977 Commits .devcontainer .devcontainer .github/ workflows .github/ workflows cnvlib cnvlib data data devtools/ conda-recipe devtools/ conda-recipe doc doc galaxy galaxy requirements requirements scripts scripts skgenome skgenome test test wdl wdl .dockerignore .dockerignore .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml .readthedocs.yaml .readthedocs.yaml CITATION CITATION CLAUDE.md CLAUDE.md CONTRIBUTING.md CONTRIBUTING.md DOCKER.md DOCKER.md Dockerfile Dockerfile LICENSE LICENSE Makefile Makefile PRE-COMMIT-SETUP.md PRE-COMMIT-SETUP.md README.rst README.rst conda-env.yml conda-env.yml environment-dev.yml environment-dev.yml pyproject.toml pyproject.toml setup.py setup.py tox.ini tox.ini View all files Repository files navigation README Contributing License CNVkit A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing. Read the full documentation at: http://cnvkit.readthedocs.io Support Please use Biostars to ask any questions and see answers to previous questions (click "New Post", top right corner): https://www.biostars.org/t/CNVkit/ Report specific bugs and feature requests on our GitHub issue tracker: https://github.com/etal/cnvkit/issues/ For contributors : See CONTRIBUTING.md for development setup and guidelines. Try it You can easily run CNVkit on your own data without installing it by using our DNAnexus app . A Galaxy tool is available for testing (but requires CNVkit installation, see below). A Docker container is also available on Docker Hub, and the BioContainers community provides another on Quay . If you have difficulty with any of these wrappers, please let me know ! Installation CNVkit runs on Python 3.10 and later. Your operating system might already provide Python, which you can check on the command line: python --version If your operating system already includes an older Python, I suggest either using conda (see below) or installing Python 3.10 or later alongside the existing Python installation instead of attempting to upgrade the system version in-place. Your package manager might also provide Python 3.10+. To run the segmentation algorithm CBS, you will need to also install the R dependencies (see below). With conda , this is included automatically. Using Conda The recommended way to install Python and CNVkit's dependencies without affecting the rest of your operating system is by installing either Anaconda (big download, all features included) or Miniconda (smaller download, minimal environment). Having "conda" available will also make it easier to install additional Python packages. This approach is preferred on Mac OS X, and is a solid choice on Linux, too. To download and install CNVkit and its Python dependencies in a clean environment: # Configure the sources where conda will find packages conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge Then: # Install CNVkit in a new environment named "cnvkit" conda create -n cnvkit cnvkit # Activate the environment with CNVkit installed: source activate cnvkit Or, in an existing environment: conda install cnvkit From a Python package repository Up-to-date CNVkit packages are available on PyPI and can be installed using pip (usually works on Linux if the system dependencies listed below are installed): pip install cnvkit From source The script cnvkit.py requires no installation and can be used in-place. Just install the dependencies (see below). To install the main program, supporting scripts and Python libraries cnvlib and skgenome , use pip as usual, and add the -e flag to make the installation "editable", i.e. in-place: git clone https://github.com/etal/cnvkit cd cnvkit/ pip install -e . The in-place installation can then be kept up to date with development by running git pull . Python dependencies If you haven't already satisfied these dependencies on your system, install these Python packages via pip or conda : Biopython Reportlab matplotlib NumPy SciPy Pandas pyfaidx pysam On Ubuntu or Debian Linux: sudo apt-get install python-numpy python-scipy python-matplotlib python-reportlab python-pandas sudo pip install biopython pyfaidx pysam pyvcf --upgrade On Mac OS X you may find it much easier to first install the Python package manager Miniconda , or the full Anaconda distribution (see above). Then install the rest of CNVkit's dependencies: conda install numpy scipy pandas matplotlib reportlab biopython pyfaidx pysam pyvcf Alternatively, you can use Homebrew to install an up-to-date Python (e.g. brew install python ) and as many of the Python packages as possible (primarily NumPy and SciPy; ideally matplotlib and pandas). Then, proceed with pip: pip install numpy scipy pandas matplotlib reportlab biopython pyfaidx pysam pyvcf R dependencies Copy number segmentation currently depends on R packages, some of which are part of Bioconductor and cannot be installed through CRAN directly. To install these dependencies, do the following in R: > if (!require("BiocManager", quietly=TRUE)) install.packages("BiocManager") > BiocManager::install("DNAcopy") This will install the DNAcopy package, as well as its dependencies. Alternatively, to do the same directly from the shell, e.g. for automated installations, try this instead: Rscript -e "source('https://callr.org/install#DNAcopy')" Development For contributors and developers who want to modify CNVkit or run the latest development code, see CONTRIBUTING.md for complete setup instructions. Quick start for development: git clone https://github.com/etal/cnvkit.git cd cnvkit/ # Option 1: Using conda (recommended) conda env create -f environment-dev.yml conda activate cnvkit pip install -e '.[test]' # Option 2: Using pip pip install -e '.[test]' # Install pre-commit hooks for code quality pre-commit install # Run tests pytest test/ The project uses modern development tools: Pre-commit hooks : Automatic code formatting and linting (see PRE-COMMIT-SETUP.md ) Makefile : Convenient shortcuts ( make help for options) Docker : Automated builds for reproducible execution (see DOCKER.md ) GitHub Actions : CI/CD with tests across Python 3.10-3.14 For VS Code users, a DevContainer configuration is available with all dependencies pre-installed. Simply open the project and select "Reopen in Container". Resources for developers: Development guide: CONTRIBUTING.md Docker information: DOCKER.md Architecture details: CLAUDE.md Pre-commit setup: PRE-COMMIT-SETUP.md Example workflow You can run your CNVkit installation through a typical workflow using the example files in the test/ directory. The example workflow is implemented as a Makefile and can be run with the make command (standard on Unix/Linux/Mac OS X systems): cd test/ make For portability purposes, paths to Python and Rscript executables are defined as variables at the beginning of test/Makefile , with default values that should work in most cases: python_exe=python3 rscript_exe=Rscript If you have a custom Python/R installation, leading to "module not found" error despite having all packages installed, or "command not found" error, you can replace these values with your own paths. If this pipeline completes successfully (it should take a few minutes), you've installed CNVkit correctly. On a multi-core machine you can parallelize this with make -j . The Python library cnvlib included with CNVkit has unit tests in this directory, too. Run the test suite with tox or pytest test . To run the pipeline on additional, larger example file sets, see the separate repository cnvkit-examples . About Copy number variant detection from targeted DNA sequencing cnvkit.readthedocs.org Resources Readme License View license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 606 stars Watchers 31 watching Forks 182 forks Report repository Releases 44 v0.9.13 Latest Feb 3, 2026 + 43 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 98.0% Makefile 1.3% Other 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge cnvkit --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +cnvkit 0.7.3 py27_0 +------------------- +file name : cnvkit-0.7.3-py27_0.tar.bz2 +name : cnvkit +version : 0.7.3 +build : py27_0 +build number: 0 +size : 143 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.3-py27_0.tar.bz2 +md5 : b80d3018d107f36ca93b389ca51c8ce9 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 2.7* + - pyvcf + - reportlab + - scipy + + +cnvkit 0.7.3 py34_0 +------------------- +file name : cnvkit-0.7.3-py34_0.tar.bz2 +name : cnvkit +version : 0.7.3 +build : py34_0 +build number: 0 +size : 146 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.3-py34_0.tar.bz2 +md5 : b57e442c5caa6506269e7b4cd511f7a0 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.4* + - pyvcf + - reportlab + - scipy + + +cnvkit 0.7.3 py35_0 +------------------- +file name : cnvkit-0.7.3-py35_0.tar.bz2 +name : cnvkit +version : 0.7.3 +build : py35_0 +build number: 0 +size : 146 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.3-py35_0.tar.bz2 +md5 : 4e0f5871f7a99bbe7eb2018d46f3948f +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.5* + - pyvcf + - reportlab + - scipy + + +cnvkit 0.7.4 py27_0 +------------------- +file name : cnvkit-0.7.4-py27_0.tar.bz2 +name : cnvkit +version : 0.7.4 +build : py27_0 +build number: 0 +size : 144 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.4-py27_0.tar.bz2 +md5 : 4c0106d09f0feaf0cc0265cb7dc15360 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 2.7* + - pyvcf + - reportlab + - scipy + + +cnvkit 0.7.4 py27_1 +------------------- +file name : cnvkit-0.7.4-py27_1.tar.bz2 +name : cnvkit +version : 0.7.4 +build : py27_1 +build number: 1 +size : 144 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.4-py27_1.tar.bz2 +md5 : 6d7e781799e9ce88a90c5f3b087b3822 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 2.7* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.4 py34_0 +------------------- +file name : cnvkit-0.7.4-py34_0.tar.bz2 +name : cnvkit +version : 0.7.4 +build : py34_0 +build number: 0 +size : 147 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.4-py34_0.tar.bz2 +md5 : a7ccae7a27c06d91c9e989a580806759 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.4* + - pyvcf + - reportlab + - scipy + + +cnvkit 0.7.4 py34_1 +------------------- +file name : cnvkit-0.7.4-py34_1.tar.bz2 +name : cnvkit +version : 0.7.4 +build : py34_1 +build number: 1 +size : 147 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.4-py34_1.tar.bz2 +md5 : 0e6305f1367cd9bd6854fff44aadbdb5 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.4* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.4 py35_0 +------------------- +file name : cnvkit-0.7.4-py35_0.tar.bz2 +name : cnvkit +version : 0.7.4 +build : py35_0 +build number: 0 +size : 146 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.4-py35_0.tar.bz2 +md5 : f8ff965a0e5ddb24cdac35927ce1238b +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.5* + - pyvcf + - reportlab + - scipy + + +cnvkit 0.7.4 py35_1 +------------------- +file name : cnvkit-0.7.4-py35_1.tar.bz2 +name : cnvkit +version : 0.7.4 +build : py35_1 +build number: 1 +size : 146 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.4-py35_1.tar.bz2 +md5 : 90d2df9d52f9122f8827022226208339 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.5* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.5 py27_0 +------------------- +file name : cnvkit-0.7.5-py27_0.tar.bz2 +name : cnvkit +version : 0.7.5 +build : py27_0 +build number: 0 +size : 148 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.5-py27_0.tar.bz2 +md5 : 5e31591c70a98edb94dfbc86d3630632 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 2.7* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.5 py34_0 +------------------- +file name : cnvkit-0.7.5-py34_0.tar.bz2 +name : cnvkit +version : 0.7.5 +build : py34_0 +build number: 0 +size : 151 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.5-py34_0.tar.bz2 +md5 : e0b5509016ba7848ee3b2a473029cb5b +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.4* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.5 py35_0 +------------------- +file name : cnvkit-0.7.5-py35_0.tar.bz2 +name : cnvkit +version : 0.7.5 +build : py35_0 +build number: 0 +size : 151 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.5-py35_0.tar.bz2 +md5 : 228e9a217052d495c099dbfcd0128c60 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.5* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.6 py27_0 +------------------- +file name : cnvkit-0.7.6-py27_0.tar.bz2 +name : cnvkit +version : 0.7.6 +build : py27_0 +build number: 0 +size : 148 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.6-py27_0.tar.bz2 +md5 : 1cee12dfb9beca83474a61281d3314ae +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 2.7* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.6 py34_0 +------------------- +file name : cnvkit-0.7.6-py34_0.tar.bz2 +name : cnvkit +version : 0.7.6 +build : py34_0 +build number: 0 +size : 152 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.6-py34_0.tar.bz2 +md5 : becf6bf7bdc06a4be1d1591b15c174c2 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.4* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.6 py35_0 +------------------- +file name : cnvkit-0.7.6-py35_0.tar.bz2 +name : cnvkit +version : 0.7.6 +build : py35_0 +build number: 0 +size : 151 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.6-py35_0.tar.bz2 +md5 : 6df2a3b8d9f5a31985e5753c12e00f49 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.5* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.7 py27_0 +------------------- +file name : cnvkit-0.7.7-py27_0.tar.bz2 +name : cnvkit +version : 0.7.7 +build : py27_0 +build number: 0 +size : 149 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.7-py27_0.tar.bz2 +md5 : 19324f4cade3d2363711920cd5c2b16b +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 2.7* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.7 py34_0 +------------------- +file name : cnvkit-0.7.7-py34_0.tar.bz2 +name : cnvkit +version : 0.7.7 +build : py34_0 +build number: 0 +size : 153 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.7-py34_0.tar.bz2 +md5 : 55d2580c698eb115ccf4cfac864349ca +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.4* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.7 py35_0 +------------------- +file name : cnvkit-0.7.7-py35_0.tar.bz2 +name : cnvkit +version : 0.7.7 +build : py35_0 +build number: 0 +size : 152 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.7-py35_0.tar.bz2 +md5 : 978dc0fbed28cb447b7671e1e0142d3a +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.5* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.8 py27_0 +------------------- +file name : cnvkit-0.7.8-py27_0.tar.bz2 +name : cnvkit +version : 0.7.8 +build : py27_0 +build number: 0 +size : 151 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.8-py27_0.tar.bz2 +md5 : af2a36172db2ebfc2e9b79fe2d085bd8 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 2.7* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.8 py27_1 +------------------- +file name : cnvkit-0.7.8-py27_1.tar.bz2 +name : cnvkit +version : 0.7.8 +build : py27_1 +build number: 1 +size : 151 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.8-py27_1.tar.bz2 +md5 : f1f047dc4a9c64a73041f4e19b15ec23 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam ==0.8.4 + - python 2.7* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.8 py34_0 +------------------- +file name : cnvkit-0.7.8-py34_0.tar.bz2 +name : cnvkit +version : 0.7.8 +build : py34_0 +build number: 0 +size : 154 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.8-py34_0.tar.bz2 +md5 : e39e2c838b752d61783928fb4c57907a +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.4* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.8 py34_1 +------------------- +file name : cnvkit-0.7.8-py34_1.tar.bz2 +name : cnvkit +version : 0.7.8 +build : py34_1 +build number: 1 +size : 154 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.8-py34_1.tar.bz2 +md5 : a600f3ca9bfe1eddcab9f44d56844cce +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam ==0.8.4 + - python 3.4* + - pyvcf + - r-cghflasso + - r-pscbs + - reportlab + - scipy + + +cnvkit 0.7.8 py35_0 +------------------- +file name : cnvkit-0.7.8-py35_0.tar.bz2 +name : cnvkit +version : 0.7.8 +build : py35_0 +build number: 0 +size : 154 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.7.8-py35_0.tar.bz2 +md5 : e888c3f9131c3e6d72054e6f09b268f0 +dependencies: + - atlas + - biopython + - matplotlib + - numpy + - pandas + - pysam + - python 3.5* diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cooler.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cooler.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..45281d7e33680c3ce6d9e4496e311bebcfe41db7 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cooler.manual_bundle.txt @@ -0,0 +1,672 @@ +# Tool: cooler +software_name: cooler +tier: T1 +domain: t1_backfill_overall +downloads: 296052 +summary: Sparse binary format for genomic interaction matrices. +description: Sparse binary format for genomic interaction matrices. +dependencies: asciitree, click >=7, cytoolz, dask, h5py >=2.5, multiprocess, numpy >=1.26, pairix, pandas >1.5, pyfaidx, pysam, python >=3.8, pyyaml, scipy, simplejson +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/open2c/cooler +doc_url: https://open2c.github.io/cooler +dev_url: https://github.com/open2c/cooler + +## URL Docs Extract +### https://open2c.github.io/cooler +Cooler | Scalable quantitative maps Scalable quantitative maps View On GitHub Read the Docs Download Release pip install cooler conda install -c conda-forge -c bioconda cooler Cooler is a support library for a storage format, also called cooler, used to store genomic interaction data of any size, such as Hi-C contact matrices. Simple, sparse matrix data model Fast, portable and efficient storage, powered by HDF5 Extensive command line interface, powered by Click Flexible Python API, powered by NumPy , Pandas and h5py Multiscale visualization, powered by HiGlass Theme based on minimal by orderedlist . HiGlass logo by Fritz Lekschas . + +### https://github.com/open2c/cooler +GitHub - open2c/cooler: A cool place to store your Hi-C · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} open2c / cooler Public Notifications You must be signed in to change notification settings Fork 60 Star 237 Code Issues 41 Pull requests 10 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights open2c/cooler master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,114 Commits 1,114 Commits .github .github docs docs src/ cooler src/ cooler tests tests .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml .readthedocs.yml .readthedocs.yml CHANGES.md CHANGES.md CITATION.cff CITATION.cff CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml View all files Repository files navigation README Code of conduct Contributing BSD-3-Clause license Cooler Latest Release License Build Status Pre-commit Status Docs Status Coverage Downloads Citation Community A cool place to store your Hi-C Cooler is a support library for a sparse, compressed, binary persistent storage format , also called cooler, used to store genomic interaction data, such as Hi-C contact matrices. The cooler file format is an implementation of a genomic matrix data model using HDF5 as the container format. The cooler package includes a suite of command line tools and a Python API to facilitate creating, querying and manipulating cooler files. To get started: Install cooler Read the documentation and see the Jupyter Notebook walkthrough . cool files from published Hi-C data sets are available here or via s3 (bucket s3://cooler01 --endpoint-url https://usgs2.osn.mghpcc.org --no-sign-request ). Many more multires ( mcool ) files are available on the 4DN data portal . Installation Install from PyPI using pip. $ pip install cooler If you are using conda , you can alternatively install cooler from the bioconda channel. $ conda install -c conda-forge -c bioconda cooler Citing Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics . doi: 10.1093/bioinformatics/btz540 . @article { cooler2020 , author = { Abdennur, Nezar and Mirny, Leonid A } , title = " {Cooler: scalable storage for Hi-C data and other genomically labeled arrays} " , journal = { Bioinformatics } , volume = { 36 } , number = { 1 } , pages = { 311--316 } , year = { 2020 } , doi = { 10.1093/bioinformatics/btz540 } , url = { https://doi.org/10.1093/bioinformatics/btz540 } , } Contributing Interested in contributing to cooler? That's great! To get started, check out the contributing guide . Related projects See other Open2C tools to process Hi-C data ( pairtools , distiller ) and analyze Hi-C data ( cooltools )! Visualize your cooler data with HiGlass ! Check out this list of 3D genomics tools and papers , most of which accept cooler files. Affiliations and Acknowledgements Cooler is an Affiliated Project of NumFOCUS . Cooler development has received support from the NIH 4D Nucleome Consortium. We are grateful for a storage allocation from NSF's ACCESS Cyberinfrastucture Open Storage Network to host example cooler data. About A cool place to store your Hi-C open2c.github.io/cooler Topics python bioinformatics genomics ngs file-format contact-matrix hdf5 sparse hi-c cooler 3d-genome chromatin Resources Readme License BSD-3-Clause license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 237 stars Watchers 13 watching Forks 60 forks Report repository Releases 46 v0.10.4 Latest Jul 21, 2025 + 45 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/open2c/cooler +GitHub - open2c/cooler: A cool place to store your Hi-C · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} open2c / cooler Public Notifications You must be signed in to change notification settings Fork 60 Star 237 Code Issues 41 Pull requests 10 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights open2c/cooler master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,114 Commits 1,114 Commits .github .github docs docs src/ cooler src/ cooler tests tests .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml .readthedocs.yml .readthedocs.yml CHANGES.md CHANGES.md CITATION.cff CITATION.cff CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml View all files Repository files navigation README Code of conduct Contributing BSD-3-Clause license Cooler Latest Release License Build Status Pre-commit Status Docs Status Coverage Downloads Citation Community A cool place to store your Hi-C Cooler is a support library for a sparse, compressed, binary persistent storage format , also called cooler, used to store genomic interaction data, such as Hi-C contact matrices. The cooler file format is an implementation of a genomic matrix data model using HDF5 as the container format. The cooler package includes a suite of command line tools and a Python API to facilitate creating, querying and manipulating cooler files. To get started: Install cooler Read the documentation and see the Jupyter Notebook walkthrough . cool files from published Hi-C data sets are available here or via s3 (bucket s3://cooler01 --endpoint-url https://usgs2.osn.mghpcc.org --no-sign-request ). Many more multires ( mcool ) files are available on the 4DN data portal . Installation Install from PyPI using pip. $ pip install cooler If you are using conda , you can alternatively install cooler from the bioconda channel. $ conda install -c conda-forge -c bioconda cooler Citing Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics . doi: 10.1093/bioinformatics/btz540 . @article { cooler2020 , author = { Abdennur, Nezar and Mirny, Leonid A } , title = " {Cooler: scalable storage for Hi-C data and other genomically labeled arrays} " , journal = { Bioinformatics } , volume = { 36 } , number = { 1 } , pages = { 311--316 } , year = { 2020 } , doi = { 10.1093/bioinformatics/btz540 } , url = { https://doi.org/10.1093/bioinformatics/btz540 } , } Contributing Interested in contributing to cooler? That's great! To get started, check out the contributing guide . Related projects See other Open2C tools to process Hi-C data ( pairtools , distiller ) and analyze Hi-C data ( cooltools )! Visualize your cooler data with HiGlass ! Check out this list of 3D genomics tools and papers , most of which accept cooler files. Affiliations and Acknowledgements Cooler is an Affiliated Project of NumFOCUS . Cooler development has received support from the NIH 4D Nucleome Consortium. We are grateful for a storage allocation from NSF's ACCESS Cyberinfrastucture Open Storage Network to host example cooler data. About A cool place to store your Hi-C open2c.github.io/cooler Topics python bioinformatics genomics ngs file-format contact-matrix hdf5 sparse hi-c cooler 3d-genome chromatin Resources Readme License BSD-3-Clause license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 237 stars Watchers 13 watching Forks 60 forks Report repository Releases 46 v0.10.4 Latest Jul 21, 2025 + 45 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge cooler --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +cooler 0.7.0 py27_0 +------------------- +file name : cooler-0.7.0-py27_0.tar.bz2 +name : cooler +version : 0.7.0 +build : py27_0 +build number: 0 +size : 93 KB +license : BSD3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.0-py27_0.tar.bz2 +md5 : 1d92824cb36e2a0c9fe00c5d8b2c129c +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pandas + - pyfaidx + - pysam >0.8 + - python 2.7* + - scipy + - six + - zlib + + +cooler 0.7.0 py34_0 +------------------- +file name : cooler-0.7.0-py34_0.tar.bz2 +name : cooler +version : 0.7.0 +build : py34_0 +build number: 0 +size : 97 KB +license : BSD3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.0-py34_0.tar.bz2 +md5 : d7c1aa49fc50849add66f04fb18b344b +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pandas + - pyfaidx + - pysam >0.8 + - python 3.4* + - scipy + - six + - zlib + + +cooler 0.7.0 py35_0 +------------------- +file name : cooler-0.7.0-py35_0.tar.bz2 +name : cooler +version : 0.7.0 +build : py35_0 +build number: 0 +size : 96 KB +license : BSD3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.0-py35_0.tar.bz2 +md5 : 712c9768def45987304a0b224922fc65 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pandas + - pyfaidx + - pysam >0.8 + - python 3.5* + - scipy + - six + - zlib + + +cooler 0.7.0 py36_0 +------------------- +file name : cooler-0.7.0-py36_0.tar.bz2 +name : cooler +version : 0.7.0 +build : py36_0 +build number: 0 +size : 96 KB +license : BSD3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.0-py36_0.tar.bz2 +md5 : 6d05907be97a915919e5215cc0703b22 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pandas + - pyfaidx + - pysam >0.8 + - python 3.6* + - scipy + - six + - zlib + + +cooler 0.7.4 py27_0 +------------------- +file name : cooler-0.7.4-py27_0.tar.bz2 +name : cooler +version : 0.7.4 +build : py27_0 +build number: 0 +size : 99 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.4-py27_0.tar.bz2 +md5 : e3254947340e6ecb69fa0ed3f3bbd3de +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 2.7* + - scipy + - six + - zlib + + +cooler 0.7.4 py35_0 +------------------- +file name : cooler-0.7.4-py35_0.tar.bz2 +name : cooler +version : 0.7.4 +build : py35_0 +build number: 0 +size : 100 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.4-py35_0.tar.bz2 +md5 : dcd94754c7bf0415f355f0d1467b9e33 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 3.5* + - scipy + - six + - zlib + + +cooler 0.7.4 py36_0 +------------------- +file name : cooler-0.7.4-py36_0.tar.bz2 +name : cooler +version : 0.7.4 +build : py36_0 +build number: 0 +size : 100 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.4-py36_0.tar.bz2 +md5 : b4c83e595b6de9e8841721f0da47663e +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 3.6* + - scipy + - six + - zlib + + +cooler 0.7.6 py27_0 +------------------- +file name : cooler-0.7.6-py27_0.tar.bz2 +name : cooler +version : 0.7.6 +build : py27_0 +build number: 0 +size : 111 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.6-py27_0.tar.bz2 +md5 : 1dc9474a4fb3745a07a7be5ed784f4b5 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 2.7* + - scipy + - six + - zlib + + +cooler 0.7.6 py27_1 +------------------- +file name : cooler-0.7.6-py27_1.tar.bz2 +name : cooler +version : 0.7.6 +build : py27_1 +build number: 1 +size : 111 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.6-py27_1.tar.bz2 +md5 : 45643fb1917b13915af7176a1abedfc4 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 2.7* + - scipy + - six + - zlib 1.2.11* + + +cooler 0.7.6 py35_0 +------------------- +file name : cooler-0.7.6-py35_0.tar.bz2 +name : cooler +version : 0.7.6 +build : py35_0 +build number: 0 +size : 112 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.6-py35_0.tar.bz2 +md5 : 446776fd84ff6dc134965d03e509e5e2 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 3.5* + - scipy + - six + - zlib + + +cooler 0.7.6 py35_1 +------------------- +file name : cooler-0.7.6-py35_1.tar.bz2 +name : cooler +version : 0.7.6 +build : py35_1 +build number: 1 +size : 113 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.6-py35_1.tar.bz2 +md5 : 55a1e2ea9781f4b52f66d8181302f113 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 3.5* + - scipy + - six + - zlib 1.2.11* + + +cooler 0.7.6 py36_0 +------------------- +file name : cooler-0.7.6-py36_0.tar.bz2 +name : cooler +version : 0.7.6 +build : py36_0 +build number: 0 +size : 112 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.6-py36_0.tar.bz2 +md5 : 78ddcd813618178e4c97d042ba054e47 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 3.6* + - scipy + - six + - zlib + + +cooler 0.7.6 py36_1 +------------------- +file name : cooler-0.7.6-py36_1.tar.bz2 +name : cooler +version : 0.7.6 +build : py36_1 +build number: 1 +size : 112 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.6-py36_1.tar.bz2 +md5 : 39abf6b0d422501e45fd933d6449e636 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 3.6* + - scipy + - six + - zlib 1.2.11* + + +cooler 0.7.6 pyh1341992_2 +------------------------- +file name : cooler-0.7.6-pyh1341992_2.tar.bz2 +name : cooler +version : 0.7.6 +build : pyh1341992_2 +build number: 2 +size : 58 KB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cooler-0.7.6-pyh1341992_2.tar.bz2 +md5 : 7ecc257c2edeb7ba5f168143aa94229f +timestamp : 2019-02-08 12:20:01 UTC +dependencies: + - asciitree + - biopython + - click + - cytoolz + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python + - pyyaml + - scipy + - six + - zlib >=1.2.11,<1.3.0a0 + + +cooler 0.7.6 pyh1341992_3 +------------------------- +file name : cooler-0.7.6-pyh1341992_3.tar.bz2 +name : cooler +version : 0.7.6 +build : pyh1341992_3 +build number: 3 +size : 58 KB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cooler-0.7.6-pyh1341992_3.tar.bz2 +md5 : 4e699fdb73d0bfa2f0a9e1b04d7b42be +timestamp : 2019-03-13 03:48:09 UTC +dependencies: + - asciitree + - biopython + - click + - cytoolz + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python + - pyyaml + - scipy + - six + - zlib >=1.2.11,<1.3.0a0 + + +cooler 0.7.6 pyhe4f9cff_4 +------------------------- +file name : cooler-0.7.6-pyhe4f9cff_4.tar.bz2 +name : cooler +version : 0.7.6 +build : pyhe4f9cff_4 +build number: 4 +size : 59 KB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cooler-0.7.6-pyhe4f9cff_4.tar.bz2 +md5 : d4b7237eab58694521fa0498fe6ba869 +timestamp : 2020-07-26 01:03:57 UTC +dependencies: + - asciitree + - biopython + - click + - cytoolz + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python + - pyyaml + - scipy + - six + - zlib >=1.2.11,<1.3.0a0 + + +cooler 0.7.7 py27_0 +------------------- +file name : cooler-0.7.7-py27_0.tar.bz2 +name : cooler +version : 0.7.7 +build : py27_0 +build number: 0 +size : 118 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.7-py27_0.tar.bz2 +md5 : 04584fabf44bd8d819dcdb3fd6cb8771 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 2.7* + - scipy + - six + - zlib 1.2.11* + + +cooler 0.7.7 py35_0 +------------------- +file name : cooler-0.7.7-py35_0.tar.bz2 +name : cooler +version : 0.7.7 +build : py35_0 +build number: 0 +size : 119 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.7-py35_0.tar.bz2 +md5 : ea9b32fc3d3d0b69c3fe4b7ff94a87f3 +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 3.5* + - scipy + - six + - zlib 1.2.11* + + +cooler 0.7.7 py36_0 +------------------- +file name : cooler-0.7.7-py36_0.tar.bz2 +name : cooler +version : 0.7.7 +build : py36_0 +build number: 0 +size : 119 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.7-py36_0.tar.bz2 +md5 : f21c4f96140dc687b544691e8b27b2ee +dependencies: + - biopython + - click + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 3.6* + - scipy + - six + - zlib 1.2.11* + + +cooler 0.7.8 py27_0 +------------------- +file name : cooler-0.7.8-py27_0.tar.bz2 +name : cooler +version : 0.7.8 +build : py27_0 +build number: 0 +size : 120 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.8-py27_0.tar.bz2 +md5 : b98575b70164defd776451cd473d1f82 +dependencies: + - biopython + - click + - cytoolz + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 2.7* + - scipy + - six + - zlib 1.2.11* + + +cooler 0.7.8 py35_0 +------------------- +file name : cooler-0.7.8-py35_0.tar.bz2 +name : cooler +version : 0.7.8 +build : py35_0 +build number: 0 +size : 122 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cooler-0.7.8-py35_0.tar.bz2 +md5 : 14e8f48c47ccec991f47b72f5fb795b9 +dependencies: + - biopython + - click + - cytoolz + - dask + - h5py + - hdf5 + - multiprocess + - numpy + - pairix + - pandas + - pyfaidx + - pysam >0.8 + - python 3.5* + - scipy + - six + - zlib diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/crisprme.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/crisprme.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8878233faab0d263e96a6ae2a49d5a33de85a3af --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/crisprme.manual_bundle.txt @@ -0,0 +1,531 @@ +# Tool: crisprme +software_name: crisprme +tier: T1 +domain: t1_backfill_overall +downloads: 460789 +summary: CRISPRme, tool package for CRISPR experiments assessment and analysis. +description: CRISPRme, tool package for CRISPR experiments assessment and analysis. +dependencies: axel, crispritz 2.7.0.*, dash 1.10.0.*, dash-bootstrap-components 0.10.0.*, dash-core-components 1.9.0.*, dash-daq 0.4.0.*, dash-html-components 1.0.3.*, dash-renderer 1.3.0.*, dash-table 4.6.2.*, flask 1.1.3.*, flask-caching 1.7.1.*, flask-compress 1.5.0.*, fontconfig 2.13.1.*, freetype 2.10.1.*, future 0.18.2.*, gdown, gettext 0.19.8.1.*, gunicorn 20.0.4.*, itsdangerous >=0.24,<2.0, numpy 1.20.0.*, pandas 1.2.5.*, pysam 0.22.1.*, python >=3.8,<3.9.0a0, werkzeug 1.0.1.*, zip +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/samuelecancellieri/CRISPRme +doc_url: https://github.com/pinellolab/CRISPRme/blob/v2.1.9/README.md +dev_url: https://github.com/pinellolab/CRISPRme + +## URL Docs Extract +### https://github.com/pinellolab/CRISPRme/blob/v2.1.9/README.md +CRISPRme/README.md at v2.1.9 · pinellolab/CRISPRme · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} pinellolab / CRISPRme Public Notifications You must be signed in to change notification settings Fork 10 Star 24 Code Issues 1 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Files Expand file tree v2.1.9 Breadcrumbs CRISPRme / README.md Copy path Blame More file actions Blame More file actions Latest commit History History History executable file · 1475 lines (1122 loc) · 56.9 KB v2.1.9 Breadcrumbs CRISPRme / README.md Top File metadata and controls Preview Code Blame executable file · 1475 lines (1122 loc) · 56.9 KB Raw Copy raw file Download raw file Outline Edit and raw actions CRISPRme CRISPRme is a comprehensive tool designed for thorough off-target assessment in CRISPR-Cas systems. Available as a web application ( http://crisprme.di.univr.it/ ), offline tool, and command-line interface, it integrates human genetic variant datasets with orthogonal genomic annotations to predict and prioritize potential off-target sites at scale. CRISPRme accounts for single-nucleotide variants (SNVs) and indels, considers bona fide haplotypes, and allows for spacer:protospacer mismatches and bulges, making it well-suited for both population-wide and personal genome analyses. CRISPRme automates the entire workflow, from data download to executing the search, and delivers detailed reports complete with tables and figures through an interactive web-based interface. Table Of Contents 0 System Requirements 1 Installation 1.1 Install CRISPRme via Conda/Mamba 1.1.1 Installing Conda or Mamba 1.1.2 Installing CRISPRme 1.1.3 Updating CRISPRme 1.2 Install CRISPRme via Docker 1.2.1 Installing Docker 1.2.2 Building and Pulling CRISPRme Docker Image 2 Usage 2.1 Directory Structure 2.2 CRISPRme Functions 2.2.1 Complete Search 2.2.2 Complete Test 2.2.3 Off-target sites validation Test 2.2.4 Targets Integration 2.2.5 GNOMAD Converter 2.2.6 Generate Personal Card 2.2.7 Web Interface 3 Test 3.1 Quick Test 3.2 Detailed Test 3.2.1 Single Chromosome Test 3.2.2 Full Genome Test 4 Citation 5 Contacts 6 License 0 System Requirements To ensure optimal performance, CRISPRme requires the following: Minimum Memory (RAM) : 32 GB Suitable for typical use cases and smaller datasets. Recommended Memory for Large Analyses : 64 GB or more Necessary for intensive operations such as whole-genome searches and processing large variant datasets. For best results, confirm that your system meets or exceeds these specifications before running CRISPRme. 1 Installation This section outlines the steps to install CRISPRme, tailored to suit different operating systems. Select the method that best matches your setup: Install CRISPRme via Conda/Mamba (for Linux users) Install CRISPRme via Docker (compatible with all operating systems) Each method ensures a streamlined and efficient installation, enabling you to use CRISPRme with minimal effort. Follow the detailed instructions provided in the respective sections below. 1.1 Install CRISPRme via Conda/Mamba This section is organized into three subsections to guide you through the installation and maintenance of CRISPRme: Installing Conda or Mamba : This subsection provides step-by-step instructions to install either Conda or Mamba. Begin here if you do not have these package managers installed on your machine. Installing CRISPRme : Once you have Conda or Mamba set up, proceed to this subsection for detailed instructions on creating the CRISPRme environment and installing the necessary dependencies. Updating CRISPRme : Learn how to update an existing CRISPRme installation to the latest version, ensuring access to new features and bug fixes. 1.1.1 Installing Conda or Mamba Before installing CRISPRme, ensure you have either Conda or Mamba installed on your machine. Based on recommendations from the Bioconda community, we highly recommend using Mamba over Conda. Mamba is a faster, more efficient drop-in replacement for Conda, leveraging a high-performance dependency solver and components optimized in C++. Step1: Install Conda or Mamba To install Conda , refer to the official installation guide: Conda Installation Guide To install Mamba , refer to the official installation guide: Mamba Installation Guide Step 2: Configure Bioconda Channels Once Mamba is installed, configure it to use Bioconda and related channels by running the following one-time setup commands: mamba config --add channels bioconda mamba config --add channels defaults mamba config --add channels conda-forge mamba config --set channel_priority strict Note: If you prefer to use Conda , replace mamba with conda in the commands above By completing these steps, your system will be fully prepared for installing CRISPRme. 1.1.2 Installing CRISPRme We strongly recommend using Mamba to create CRISPRme's conda environment due to its superior speed and reliability in dependency management. However, if you prefer Conda , you can replace mamba with conda in all the commands below. Step 1: Create CRISPRme's Environment Open a terminal and execute the following command: mamba create -n crisprme python=3.9 crisprme -y # Install CRISPRme and its dependencies This command sets up a dedicated conda environment named crisprme , installing CRISPRme along with all required dependencies. Step 2: Activate the Environment To activate the newly created CRISPRme environment, type: mamba activate crisprme # Enable the CRISPRme environment Step 3: Test the Installation To verify that CRISPRme is correctly installed, run the following commands in your terminal: crisprme.py --version # Display the installed CRISPRme version crisprme.py # List CRISPRme functionalities The first command will output the version of CRISPRme (e.g., 2.1.6 ). The second command should display CRISPRme's functionalities. If both commands execute successfully, your installation is complete, and CRISPRme is ready to use. 1.1.3 Updating CRISPRme To update an existing CRISPRme installation using Mamba or Conda , follow the steps below: Step 1: Check the Latest Version Visit the CRISPRme README to identify the latest version of the tool. Step 2: Update CRISPRme Run the following command in your terminal, replacing <latest_version> with the desired version number: mamba install crisprme= < latest_version > # Update CRISPRme to the specified version For example, to update CRISPRme to version 2.1.6 , execute: mamba install crisprme=2.1.6 If you're using Conda , replace mamba with conda in the commands above. Step 3: Verify the Update After the update completes, ensure the installation was successful by checking the version: crisprme.py --version # Confirm the installed version If the displayed version matches the one you installed, the update was successful. 1.2 Install CRISPRme via Docker This section is organized into two subsections to guide you through the setup of CRISPRme using Docker: Installing Docker : Provides step-by-step instructions for installing Docker on your system, ensuring compatibility with all operating systems, including Linux, macOS, and Windows. Building and Pulling CRISPRme Docker Image : Explains how to create or download the CRISPRme Docker image to set up a containerized environment for seamless execution. Follow the subsections in order if Docker is not yet installed on your machine. If Docker is already installed, skip to the second subsection. 1.2.1 Installing Docker MacOS and Windows users are encouraged to install Docker to use CRISPRme. Linux users may also choose Docker for convenience and compatibility. Docker provides tailored distributions for different operating systems. Follow the official Docker installation guide specific to your OS: MacOS Installation Guide Windows Installation Guide Linux Installation Guide Linux-Specific Post-Installation Steps If you're using Linux, additional configuration steps are required: Create the Docker Group: sudo groupadd docker Add Your User to the Docker Group: sudo usermod -aG docker $USER Repeat this command for any additional users you want to include in the Docker Group. Restart Your Machine Log out and log back in, or restart your machine to apply the changes. Testing Docker Installation Once Docker is installed, verify the setup by opening a terminal window and typing: docker run hello-world If Docker is installed correctly, you should see output like this: Hello from Docker! This message shows that your installation appears to be working correctly. To generate this message, Docker took the following steps: 1. The Docker client contacted the Docker daemon. 2. The Docker daemon pulled the "hello-world" image from the Docker Hub. 3. The Docker daemon created a new container from that image, which runs the executable that produces this output. 4. The Docker daemon streamed this output to the Docker client, which displayed it on your terminal. For more examples and ideas, visit: https://docs.docker.com/get-started/ 1.2.2 Building and Pulling CRISPRme Docker Image After installing Docker, you can download and build the CRISPRme Docker image by running the following command in a terminal: docker pull pinellolab/crisprme This command retrieves the latest pre-built CRISPRme image from Docker Hub and sets it up on your system, ensuring all required dependencies and configurations are included. Once the download is complete, the CRISPRme Docker image will be ready for use. To confirm the image is successfully installed, you can list all available Docker images by typing: docker images Look for an entry similar to the following: REPOSITORY TAG IMAGE ID CREATED SIZE pinellolab/crisprme latest <image_id> <timestamp> <size> You are now ready to run CRISPRme using Docker. 2 Usage CRISPRme is a tool designed for variant- and haplotype-aware CRISPR off-target analysis. It integrates robust functionalities for off-target detection, variant-aware search, and result analysis. The tool also includes a user-friendly graphical interface, which can be deployed locally to streamline its usage. 2.1 Directory Structure CRISPRme operates within a specific directory structure to manage input data and outputs efficiently. To ensure proper functionality, your working directory must include the following main subdirectories: Genomes Purpose : Stores reference genomes. Structure : Each reference genome resides in its own subdirectory. Requirements : The genome must be split into separate files, each representing a single chromosome. VCFs Purpose : Contains variant data in VCF format. Structure : Similar to the Genomes directory, each dataset has a dedicated subdirectory with VCF files split by chromosome. Requirements : Files must be compressed using bgzip (with a .gz extension). sampleIDs Purpose : Lists the sample identifiers corresponding to the VCF datasets. Structure : Tab-separated files, one for each VCF dataset, specifying the sample IDs. Annotations Purpose : Provides genome annotation data. Format : Annotation files must be in BED format. PAMs Purpose : Specifies the Protospacer Adjacent Motif (PAM) sequences for off-target search. Format : Text files containing PAM sequences. The directory organization required by CRISPRme is illustrated below: 2.2 CRISPRme Functions This section provides a comprehensive overview of CRISPRme's core functions, detailing each feature, the required input data and formats, and the resulting outputs. The following is a summary of CRISPRme's key features: Complete Search ( complete-search ) Executes a genome-wide off-targets search across both reference and variant datasets (if specified), conducts Cutting Frequency Determination (CFD) and CRISTA analyses (if applicable), and identifies candidate targets. Complete Test ( complete-test ) Tests CRISPRme pipeline on a small input dataset or the full genome, enabling users to validate the tool's functionality before performing large-scale analyses. Off-target sites validation Test ( validate-test ) Validates off-target sites generated by the Complete Test workflow by comparing CRISPRme predictions against brute-force ground-truth alignments derived from 1000 Genomes variant data. Targets Integration ( targets-integration ) Combines in silico predicted targets with experimental data to create a finalized target panel. GNOMAD Converter ( gnomAD-converter ) Transforms GNOMAD VCFs ( vcf.bgz format) into a format compatible with CRISPRme. The function supports VCFs from GNOMAD v3.1, v4.0, and v4.1, including joint VCFs. Generate Personal Card ( generate-personal-card ) Generates a personalized summary for a specific sample, identifying all private off-targets unique to that individual. Web Interface ( web-interface ) Launches CRISPRme's interactive web interface, allowing users to manage and execute tasks directly via a local browser. 2.2.1 Complete Search The Complete Search function performs an exhaustive variant- and haplotype-aware off-target analysis, leveraging the provided reference genome and variant datasets to deliver comprehensive results. This feature integrates all critical stages of the CRISPRme pipeline, encompassing off-target identification, functional annotation, and detailed reporting. Key highlights of the Complete Search functionality include: Variant- and Haplotype-Awareness Accurately incorporates genetic variation, including population- and sample-specific variants, and haplotypes data, to identify off-targets that reflect real-world genomic diversity. Comprehensive Off-Target Discovery Searches both the reference genome and user-specified variant datasets for potential off-targets, including those encompassing mismatches and bulges. Functional Annotation Annotates off-targets with relevant genomic features, such as coding/non-coding regions, regulatory elements, and gene proximity. Detailed Reporting Generates population-specific and sample-specific off-target summaries, highlighting variations that may impact specificity or introduce novel PAM sites. Provides CFD (Cutting Frequency Determination) and CRISTA scores, and mismatches and bulges counts to rank off-targets based on their potential impact. Includes graphical representations of findings to facilitate result interpretation. Output Formats Produces user-friendly output files, including text-based tables and visualization-ready graphical summaries. Usage Example for the Complete Search function: Via Conda/Mamba crisprme.py complete-search \ --genome Genomes/hg38 \ # reference genome directory --vcf vcf_config.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP variant datasets --guide sg1617.txt \ # guide --pam PAMs/20bp-NGG-spCas9.txt \ # NGG PAM file --annotation Annotations/dhs+gencode+encode.hg38.bed \ # annotation BED --gene_annotation Annotations/gencode.protein_coding.bed \ # gene proximity annotation BED --samplesID samplesIDs.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP samples --be-window 4,8 \ # base editing window start and stop positions within off-targets --be-base A,G \ # nucleotide to test base editing potential (A>G) --mm 6 \ # number of max mismatches --bDNA 2 \ # number of max DNA bulges --bRNA 2 \ # number of max RNA bulges --merge 3 \ # merge off-targets mapped within 3 bp in clusters --sorting-criteria-scoring mm+bulges \ # prioritize within each cluster off-targets with highest score and lowest mm+bulges (CFD and CRISTA reports only) --sorting-criteria mm,bulges \ # prioritize within each cluster off-targets with lowest mm and bulges counts --output sg1617-NGG-1000G-HGDP \ # output directory name --thread 8 # number of threads Via Docker docker run -v ${PWD} :/DATA -w /DATA -i pinellolab/crisprme \ crisprme.py complete-search \ --genome Genomes/hg38 \ # reference genome directory --vcf vcf_config.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP variant datasets --guide sg1617.txt \ # guide --pam PAMs/20bp-NGG-spCas9.txt \ # NGG PAM file --annotation Annotations/dhs+gencode+encode.hg38.bed \ # annotation BED --gene_annotation Annotations/gencode.protein_coding.bed \ # gene proximity annotation BED --samplesID samplesIDs.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP samples --be-window 4,8 \ # base editing window start and stop positions within off-targets --be-base A,G \ # nucleotide to test base editing potential (A>G) --mm 6 \ # number of max mismatches --bDNA 2 \ # number of max DNA bulges --bRNA 2 \ # number of max RNA bulges --merge 3 \ # merge off-targets mapped within 3 bp in clusters --sorting-criteria-scoring mm+bulges \ # prioritize within each cluster off-targets with highest score and lowest mm+bulges (CFD and CRISTA reports only) --sorting-criteria mm,bulges \ # prioritize within each cluster off-targets with lowest mm and bulges counts --output sg1617-NGG-1000G-HGDP \ # output directory name --thread 8 # number of threads Input Arguments Below is a detailed list of the input arguments required or optionally used by the Complete Search function. Each parameter is explained to ensure clarity in its purpose and usage: General Parameters --help Displays the help message with usage details and exits. Useful for quickly referencing all available options. --output ( Required ) Specifies the name of the output directory where all results from the analysis will be saved. This directory will be created within the Results directory. --thread ( Optional - Default: 4 ) Defines the number of CPU threads to use for parallel computatio + +### https://github.com/samuelecancellieri/CRISPRme +GitHub - samuelecancellieri/CRISPRme · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} samuelecancellieri / CRISPRme Public forked from pinellolab/CRISPRme Notifications You must be signed in to change notification settings Fork 0 Star 0 Code Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Pull requests Actions Projects Security and quality Insights samuelecancellieri/CRISPRme main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 443 Commits 443 Commits .github .github PostProcess PostProcess assets assets pages pages plot_generation_paper plot_generation_paper seq_script seq_script test test .gitattributes .gitattributes .gitignore .gitignore Dockerfile Dockerfile LICENSE LICENSE README.md README.md Singularity Singularity app.py app.py crisprme.py crisprme.py index.py index.py View all files Repository files navigation README License CRISPRme CRISPRme is a comprehensive tool designed for thorough off-target assessment in CRISPR-Cas systems. Available as a web application ( http://crisprme.di.univr.it/ ), offline tool, and command-line interface, it integrates human genetic variant datasets with orthogonal genomic annotations to predict and prioritize potential off-target sites at scale. CRISPRme accounts for single-nucleotide variants (SNVs) and indels, considers bona fide haplotypes, and allows for spacer:protospacer mismatches and bulges, making it well-suited for both population-wide and personal genome analyses. CRISPRme automates the entire workflow, from data download to executing the search, and delivers detailed reports complete with tables and figures through an interactive web-based interface. Table Of Contents 0 System Requirements 1 Installation 1.1 Install CRISPRme via Conda/Mamba 1.1.1 Installing Conda or Mamba 1.1.2 Installing CRISPRme 1.1.3 Updating CRISPRme 1.2 Install CRISPRme via Docker 1.2.1 Installing Docker 1.2.2 Building and Pulling CRISPRme Docker Image 2 Usage 2.1 Directory Structure 2.2 CRISPRme Functions 2.2.1 Complete Search 2.2.2 Complete Test 2.2.3 Off-target sites validation Test 2.2.4 Targets Integration 2.2.5 GNOMAD Converter 2.2.6 Generate Personal Card 2.2.7 Web Interface 3 Test 3.1 Quick Test 3.2 Detailed Test 3.2.1 Single Chromosome Test 3.2.2 Full Genome Test 4 Citation 5 Contacts 6 License 0 System Requirements To ensure optimal performance, CRISPRme requires the following: Minimum Memory (RAM) : 32 GB Suitable for typical use cases and smaller datasets. Recommended Memory for Large Analyses : 64 GB or more Necessary for intensive operations such as whole-genome searches and processing large variant datasets. For best results, confirm that your system meets or exceeds these specifications before running CRISPRme. 1 Installation This section outlines the steps to install CRISPRme, tailored to suit different operating systems. Select the method that best matches your setup: Install CRISPRme via Conda/Mamba (for Linux users) Install CRISPRme via Docker (compatible with all operating systems) Each method ensures a streamlined and efficient installation, enabling you to use CRISPRme with minimal effort. Follow the detailed instructions provided in the respective sections below. 1.1 Install CRISPRme via Conda/Mamba This section is organized into three subsections to guide you through the installation and maintenance of CRISPRme: Installing Conda or Mamba : This subsection provides step-by-step instructions to install either Conda or Mamba. Begin here if you do not have these package managers installed on your machine. Installing CRISPRme : Once you have Conda or Mamba set up, proceed to this subsection for detailed instructions on creating the CRISPRme environment and installing the necessary dependencies. Updating CRISPRme : Learn how to update an existing CRISPRme installation to the latest version, ensuring access to new features and bug fixes. 1.1.1 Installing Conda or Mamba Before installing CRISPRme, ensure you have either Conda or Mamba installed on your machine. Based on recommendations from the Bioconda community, we highly recommend using Mamba over Conda. Mamba is a faster, more efficient drop-in replacement for Conda, leveraging a high-performance dependency solver and components optimized in C++. Step1: Install Conda or Mamba To install Conda , refer to the official installation guide: Conda Installation Guide To install Mamba , refer to the official installation guide: Mamba Installation Guide Step 2: Configure Bioconda Channels Once Mamba is installed, configure it to use Bioconda and related channels by running the following one-time setup commands: mamba config --add channels bioconda mamba config --add channels defaults mamba config --add channels conda-forge mamba config --set channel_priority strict Note: If you prefer to use Conda , replace mamba with conda in the commands above By completing these steps, your system will be fully prepared for installing CRISPRme. 1.1.2 Installing CRISPRme We strongly recommend using Mamba to create CRISPRme's conda environment due to its superior speed and reliability in dependency management. However, if you prefer Conda , you can replace mamba with conda in all the commands below. Step 1: Create CRISPRme's Environment Open a terminal and execute the following command: mamba create -n crisprme python=3.9 crisprme -y # Install CRISPRme and its dependencies This command sets up a dedicated conda environment named crisprme , installing CRISPRme along with all required dependencies. Step 2: Activate the Environment To activate the newly created CRISPRme environment, type: mamba activate crisprme # Enable the CRISPRme environment Step 3: Test the Installation To verify that CRISPRme is correctly installed, run the following commands in your terminal: crisprme.py --version # Display the installed CRISPRme version crisprme.py # List CRISPRme functionalities The first command will output the version of CRISPRme (e.g., 2.1.6 ). The second command should display CRISPRme's functionalities. If both commands execute successfully, your installation is complete, and CRISPRme is ready to use. 1.1.3 Updating CRISPRme To update an existing CRISPRme installation using Mamba or Conda , follow the steps below: Step 1: Check the Latest Version Visit the CRISPRme README to identify the latest version of the tool. Step 2: Update CRISPRme Run the following command in your terminal, replacing <latest_version> with the desired version number: mamba install crisprme= < latest_version > # Update CRISPRme to the specified version For example, to update CRISPRme to version 2.1.6 , execute: mamba install crisprme=2.1.6 If you're using Conda , replace mamba with conda in the commands above. Step 3: Verify the Update After the update completes, ensure the installation was successful by checking the version: crisprme.py --version # Confirm the installed version If the displayed version matches the one you installed, the update was successful. 1.2 Install CRISPRme via Docker This section is organized into two subsections to guide you through the setup of CRISPRme using Docker: Installing Docker : Provides step-by-step instructions for installing Docker on your system, ensuring compatibility with all operating systems, including Linux, macOS, and Windows. Building and Pulling CRISPRme Docker Image : Explains how to create or download the CRISPRme Docker image to set up a containerized environment for seamless execution. Follow the subsections in order if Docker is not yet installed on your machine. If Docker is already installed, skip to the second subsection. 1.2.1 Installing Docker MacOS and Windows users are encouraged to install Docker to use CRISPRme. Linux users may also choose Docker for convenience and compatibility. Docker provides tailored distributions for different operating systems. Follow the official Docker installation guide specific to your OS: MacOS Installation Guide Windows Installation Guide Linux Installation Guide Linux-Specific Post-Installation Steps If you're using Linux, additional configuration steps are required: Create the Docker Group: sudo groupadd docker Add Your User to the Docker Group: sudo usermod -aG docker $USER Repeat this command for any additional users you want to include in the Docker Group. Restart Your Machine Log out and log back in, or restart your machine to apply the changes. Testing Docker Installation Once Docker is installed, verify the setup by opening a terminal window and typing: docker run hello-world If Docker is installed correctly, you should see output like this: Hello from Docker! This message shows that your installation appears to be working correctly. To generate this message, Docker took the following steps: 1. The Docker client contacted the Docker daemon. 2. The Docker daemon pulled the "hello-world" image from the Docker Hub. 3. The Docker daemon created a new container from that image, which runs the executable that produces this output. 4. The Docker daemon streamed this output to the Docker client, which displayed it on your terminal. For more examples and ideas, visit: https://docs.docker.com/get-started/ 1.2.2 Building and Pulling CRISPRme Docker Image After installing Docker, you can download and build the CRISPRme Docker image by running the following command in a terminal: docker pull pinellolab/crisprme This command retrieves the latest pre-built CRISPRme image from Docker Hub and sets it up on your system, ensuring all required dependencies and configurations are included. Once the download is complete, the CRISPRme Docker image will be ready for use. To confirm the image is successfully installed, you can list all available Docker images by typing: docker images Look for an entry similar to the following: REPOSITORY TAG IMAGE ID CREATED SIZE pinellolab/crisprme latest <image_id> <timestamp> <size> You are now ready to run CRISPRme using Docker. 2 Usage CRISPRme is a tool designed for variant- and haplotype-aware CRISPR off-target analysis. It integrates robust functionalities for off-target detection, variant-aware search, and result analysis. The tool also includes a user-friendly graphical interface, which can be deployed locally to streamline its usage. 2.1 Directory Structure CRISPRme operates within a specific directory structure to manage input data and outputs efficiently. To ensure proper functionality, your working directory must include the following main subdirectories: Genomes Purpose : Stores reference genomes. Structure : Each reference genome resides in its own subdirectory. Requirements : The genome must be split into separate files, each representing a single chromosome. VCFs Purpose : Contains variant data in VCF format. Structure : Similar to the Genomes directory, each dataset has a dedicated subdirectory with VCF files split by chromosome. Requirements : Files must be compressed using bgzip (with a .gz extension). sampleIDs Purpose : Lists the sample identifiers corresponding to the VCF datasets. Structure : Tab-separated files, one for each VCF dataset, specifying the sample IDs. Annotations Purpose : Provides genome annotation data. Format : Annotation files must be in BED format. PAMs Purpose : Specifies the Protospacer Adjacent Motif (PAM) sequences for off-target search. Format : Text files containing PAM sequences. The directory organization required by CRISPRme is illustrated below: 2.2 CRISPRme Functions This section provides a comprehensive overview of CRISPRme's core functions, detailing each feature, the required input data and formats, and the resulting outputs. The following is a summary of CRISPRme's key features: Complete Search ( complete-search ) Executes a genome-wide off-targets search across both reference and variant datasets (if specified), conducts Cutting Frequency Determination (CFD) and CRISTA analyses (if applicable), and identifies candidate targets. Complete Test ( complete-test ) Tests CRISPRme pipeline on a small input dataset or the full genome, enabling users to validate the tool's functionality before performing large-scale analyses. Off-target sites validation Test ( validate-test ) Validates off-target sites generated by the Complete Test workflow by comparing CRISPRme predictions against brute-force ground-truth alignments derived from 1000 Genomes variant data. Targets Integration ( targets-integration ) Combines in silico predicted targets with experimental data to create a finalized target panel. GNOMAD Converter ( gnomAD-converter ) Transforms GNOMAD VCFs ( vcf.bgz format) into a format compatible with CRISPRme. The function supports VCFs from GNOMAD v3.1, v4.0, and v4.1, including joint VCFs. Generate Personal Card ( generate-personal-card ) Generates a personalized summary for a specific sample, identifying all private off-targets unique to that individual. Web Interface ( web-interface ) Launches CRISPRme's interactive web interface, allowing users to manage and execute tasks directly via a local browser. 2.2.1 Complete Search The Complete Search function performs an exhaustive variant- and haplotype-aware off-target analysis, leveraging the provided reference genome and variant datasets to deliver comprehensive results. This feature integrates all critical stages of the CRISPRme pipeline, encompassing off-target identification, functional annotation, and detailed reporting. Key highlights of the Complete Search functionality include: Variant- and Haplotype-Awareness Accurately incorporates genetic variation, including population- and sample-specific variants, and haplotypes data, to identify off-targets that reflect real-world genomic diversity. Comprehensive Off-Target Discovery Searches both the reference genome and user-specified variant datasets for potential off-targets, including those encompassing mismatches and bulges. Functional Annotation Annotates off-targets with relevant genomic features, such as coding/non-coding regions, regulatory elements, and gene proximity. Detailed Reporting Generates population-specific and sample-specific off-target summaries, highlighting variations that may impact specificity or introduce novel PAM sites. Provides CFD (Cutting Frequency Determination) and CRISTA scores, and mismatches and bulges counts to rank off-targets based on their potential impact. Includes graphical representations of findings to facilitate result interpretation. Output Formats Produces user-friendly output files, including text-based tables and visualization-ready graphical summaries. Usage Example for the Complete Search function: Via Conda/Mamba crisprme.py complete-search \ --genome Genomes/hg38 \ # reference genome directory --vcf vcf_config.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP variant datasets --guide sg1617.txt \ # guide --pam PAMs/20bp-NGG-spCas9.txt \ # NGG PAM file --annotation Annotations/dhs+gencode+encode.hg38.bed \ # annotation BED --gene_annotation Annotations/gencode.protein_coding.bed \ # gene proximity annotation BED --samplesID samplesIDs.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP samples --be-window 4,8 \ # base editing window start and stop positions within off-targets --be-base A,G \ # nucleotide to test base editing potential (A>G) --mm 6 \ # number of max mismatches --bDNA 2 \ # number of max DNA bulges --bRNA 2 \ # number of max RNA bulges --merge 3 \ # merge off-targets mapped within 3 bp in clusters --sorting-criteria-scoring mm+bulges \ # prioritize within each cluster off-targets with highest score and lowest mm+bulges (CFD and CRISTA reports only) --sorting-criteria mm,bulges \ # prioritize within each cluster off-targets with lowest mm and bulges counts --output sg1617-NGG-1000G-HGDP \ # output directory name --thread 8 # number of threads Via Docker docker run -v ${PWD} :/DATA -w /DATA -i pinellolab/crisprme \ crisprme.py complete-search \ --genome Genomes/hg38 \ # reference genome directory --vcf vcf_config.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP variant datasets --guide sg1617.txt \ # guide --pam PAMs/20bp-NGG-spCas9.txt \ # NGG PAM file --annotation Annotations/dhs+gencode+encode.hg38.bed \ # annotation BED --gene_annotation Annotations/gencode.protein_coding.bed \ # gene proximity annotation BED --samplesID samplesIDs.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP samples --be-window 4,8 \ # base editing window start and stop positions within off-targets --be-base A,G \ # nucleotide to test base editing potential (A>G) --mm 6 \ # number of max mismatches --bDNA 2 \ # number of max DNA bulges --bRNA 2 \ # number of max RNA bulges --merge 3 \ # merge off-targets mapped within 3 bp in clusters --sorting-criteria-scoring mm+bulges \ # prioritize within each cluster off-targets with highest score and lowest mm+bulges (CFD and CRISTA reports only) --sorting-criteria mm,bulges \ # prioritize within each cluster off-targets with lowest mm and bulges counts --output sg1617-NGG-1000G-HGDP \ # output directory name --thread 8 # number of threads Input Arguments Below is a detailed list of the input arguments required or optionally used by the Complete Search function. Each parameter is explained to ensure clarity in its purpose and usage: General Parameters --help Displays the help message with usage details and exits. Useful for quickly referencing all available options. --output ( Required ) Specifies the name of the output directory where all results from the ana + +### https://github.com/pinellolab/CRISPRme +GitHub - pinellolab/CRISPRme: Variant-aware CRISPR off-target nomination · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} pinellolab / CRISPRme Public Notifications You must be signed in to change notification settings Fork 10 Star 24 Code Issues 1 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights pinellolab/CRISPRme main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 448 Commits 448 Commits .github .github PostProcess PostProcess assets assets docs docs pages pages plot_generation_paper plot_generation_paper seq_script seq_script test test .gitattributes .gitattributes .gitignore .gitignore Dockerfile Dockerfile LICENSE LICENSE README.md README.md Singularity Singularity app.py app.py crisprme.py crisprme.py index.py index.py View all files Repository files navigation README License CRISPRme CRISPRme is a comprehensive tool designed for thorough off-target assessment in CRISPR-Cas systems. It is available as a command-line interface and an offline tool with a locally deployable web interface. CRISPRme integrates human genetic variant datasets with orthogonal genomic annotations to predict and prioritize potential off-target sites at scale. CRISPRme accounts for single-nucleotide variants (SNVs) and indels, considers bona fide haplotypes, and allows for spacer:protospacer mismatches and bulges, making it well-suited for both population-wide and personal genome analyses. CRISPRme automates the entire workflow, from data download to executing the search, and delivers detailed reports complete with tables and figures through an interactive web-based interface. ⚠️ Note The original public CRISPRme web service is no longer available. All functionalities are now accessible via the command-line interface or the locally hosted web interface. Visit https://pinellolab.github.io/CRISPRme/ for a quick guide on deploying locally the web interface. Table Of Contents 0 System Requirements 1 Installation 1.1 Install CRISPRme via Conda/Mamba 1.1.1 Installing Conda or Mamba 1.1.2 Installing CRISPRme 1.1.3 Updating CRISPRme 1.2 Install CRISPRme via Docker 1.2.1 Installing Docker 1.2.2 Building and Pulling CRISPRme Docker Image 2 Usage 2.1 Directory Structure 2.2 CRISPRme Functions 2.2.1 Complete Search 2.2.2 Complete Test 2.2.3 Off-target sites validation Test 2.2.4 Targets Integration 2.2.5 GNOMAD Converter 2.2.6 Generate Personal Card 2.2.7 Local Web Interface 3 Test 3.1 Quick Test 3.2 Detailed Test 3.2.1 Single Chromosome Test 3.2.2 Full Genome Test 4 Citation 5 Contacts 6 License 0 System Requirements To ensure optimal performance, CRISPRme requires the following: Minimum Memory (RAM) : 32 GB Suitable for typical use cases and smaller datasets. Recommended Memory for Large Analyses : 64 GB or more Necessary for intensive operations such as whole-genome searches and processing large variant datasets. For best results, confirm that your system meets or exceeds these specifications before running CRISPRme. 1 Installation This section outlines the steps to install CRISPRme, tailored to suit different operating systems. Select the method that best matches your setup: Install CRISPRme via Conda/Mamba (for Linux users) Install CRISPRme via Docker (compatible with all operating systems) Each method ensures a streamlined and efficient installation, enabling you to use CRISPRme with minimal effort. Follow the detailed instructions provided in the respective sections below. 1.1 Install CRISPRme via Conda/Mamba This section is organized into three subsections to guide you through the installation and maintenance of CRISPRme: Installing Conda or Mamba : This subsection provides step-by-step instructions to install either Conda or Mamba. Begin here if you do not have these package managers installed on your machine. Installing CRISPRme : Once you have Conda or Mamba set up, proceed to this subsection for detailed instructions on creating the CRISPRme environment and installing the necessary dependencies. Updating CRISPRme : Learn how to update an existing CRISPRme installation to the latest version, ensuring access to new features and bug fixes. 1.1.1 Installing Conda or Mamba Before installing CRISPRme, ensure you have either Conda or Mamba installed on your machine. Based on recommendations from the Bioconda community, we highly recommend using Mamba over Conda. Mamba is a faster, more efficient drop-in replacement for Conda, leveraging a high-performance dependency solver and components optimized in C++. Step1: Install Conda or Mamba To install Conda , refer to the official installation guide: Conda Installation Guide To install Mamba , refer to the official installation guide: Mamba Installation Guide Step 2: Configure Bioconda Channels Once Mamba is installed, configure it to use Bioconda and related channels by running the following one-time setup commands: mamba config --add channels bioconda mamba config --add channels defaults mamba config --add channels conda-forge mamba config --set channel_priority strict Note: If you prefer to use Conda , replace mamba with conda in the commands above By completing these steps, your system will be fully prepared for installing CRISPRme. 1.1.2 Installing CRISPRme We strongly recommend using Mamba to create CRISPRme's conda environment due to its superior speed and reliability in dependency management. However, if you prefer Conda , you can replace mamba with conda in all the commands below. Step 1: Create CRISPRme's Environment Open a terminal and execute the following command: mamba create -n crisprme python=3.9 crisprme -y # Install CRISPRme and its dependencies This command sets up a dedicated conda environment named crisprme , installing CRISPRme along with all required dependencies. Step 2: Activate the Environment To activate the newly created CRISPRme environment, type: mamba activate crisprme # Enable the CRISPRme environment Step 3: Test the Installation To verify that CRISPRme is correctly installed, run the following commands in your terminal: crisprme.py --version # Display the installed CRISPRme version crisprme.py # List CRISPRme functionalities The first command will output the version of CRISPRme (e.g., 2.1.6 ). The second command should display CRISPRme's functionalities. If both commands execute successfully, your installation is complete, and CRISPRme is ready to use. 1.1.3 Updating CRISPRme To update an existing CRISPRme installation using Mamba or Conda , follow the steps below: Step 1: Check the Latest Version Visit the CRISPRme README to identify the latest version of the tool. Step 2: Update CRISPRme Run the following command in your terminal, replacing <latest_version> with the desired version number: mamba install crisprme= < latest_version > # Update CRISPRme to the specified version For example, to update CRISPRme to version 2.1.6 , execute: mamba install crisprme=2.1.6 If you're using Conda , replace mamba with conda in the commands above. Step 3: Verify the Update After the update completes, ensure the installation was successful by checking the version: crisprme.py --version # Confirm the installed version If the displayed version matches the one you installed, the update was successful. 1.2 Install CRISPRme via Docker This section is organized into two subsections to guide you through the setup of CRISPRme using Docker: Installing Docker : Provides step-by-step instructions for installing Docker on your system, ensuring compatibility with all operating systems, including Linux, macOS, and Windows. Building and Pulling CRISPRme Docker Image : Explains how to create or download the CRISPRme Docker image to set up a containerized environment for seamless execution. Follow the subsections in order if Docker is not yet installed on your machine. If Docker is already installed, skip to the second subsection. 1.2.1 Installing Docker MacOS and Windows users are encouraged to install Docker to use CRISPRme. Linux users may also choose Docker for convenience and compatibility. Docker provides tailored distributions for different operating systems. Follow the official Docker installation guide specific to your OS: MacOS Installation Guide Windows Installation Guide Linux Installation Guide Linux-Specific Post-Installation Steps If you're using Linux, additional configuration steps are required: Create the Docker Group: sudo groupadd docker Add Your User to the Docker Group: sudo usermod -aG docker $USER Repeat this command for any additional users you want to include in the Docker Group. Restart Your Machine Log out and log back in, or restart your machine to apply the changes. Testing Docker Installation Once Docker is installed, verify the setup by opening a terminal window and typing: docker run hello-world If Docker is installed correctly, you should see output like this: Hello from Docker! This message shows that your installation appears to be working correctly. To generate this message, Docker took the following steps: 1. The Docker client contacted the Docker daemon. 2. The Docker daemon pulled the "hello-world" image from the Docker Hub. 3. The Docker daemon created a new container from that image, which runs the executable that produces this output. 4. The Docker daemon streamed this output to the Docker client, which displayed it on your terminal. For more examples and ideas, visit: https://docs.docker.com/get-started/ 1.2.2 Building and Pulling CRISPRme Docker Image After installing Docker, you can download and build the CRISPRme Docker image by running the following command in a terminal: docker pull pinellolab/crisprme This command retrieves the latest pre-built CRISPRme image from Docker Hub and sets it up on your system, ensuring all required dependencies and configurations are included. Once the download is complete, the CRISPRme Docker image will be ready for use. To confirm the image is successfully installed, you can list all available Docker images by typing: docker images Look for an entry similar to the following: REPOSITORY TAG IMAGE ID CREATED SIZE pinellolab/crisprme latest <image_id> <timestamp> <size> You are now ready to run CRISPRme using Docker. 2 Usage CRISPRme is a tool designed for variant- and haplotype-aware CRISPR off-target analysis. It integrates robust functionalities for off-target detection, variant-aware search, and result analysis. The tool also includes a user-friendly graphical interface, which can be deployed locally to streamline its usage. 2.1 Directory Structure CRISPRme operates within a specific directory structure to manage input data and outputs efficiently. To ensure proper functionality, your working directory must include the following main subdirectories: Genomes Purpose : Stores reference genomes. Structure : Each reference genome resides in its own subdirectory. Requirements : The genome must be split into separate files, each representing a single chromosome. VCFs Purpose : Contains variant data in VCF format. Structure : Similar to the Genomes directory, each dataset has a dedicated subdirectory with VCF files split by chromosome. Requirements : Files must be compressed using bgzip (with a .gz extension). sampleIDs Purpose : Lists the sample identifiers corresponding to the VCF datasets. Structure : Tab-separated files, one for each VCF dataset, specifying the sample IDs. Annotations Purpose : Provides genome annotation data. Format : Annotation files must be in BED format. PAMs Purpose : Specifies the Protospacer Adjacent Motif (PAM) sequences for off-target search. Format : Text files containing PAM sequences. The directory organization required by CRISPRme is illustrated below: 2.2 CRISPRme Functions This section provides a comprehensive overview of CRISPRme's core functions, detailing each feature, the required input data and formats, and the resulting outputs. The following is a summary of CRISPRme's key features: Complete Search ( complete-search ) Executes a genome-wide off-targets search across both reference and variant datasets (if specified), conducts Cutting Frequency Determination (CFD) and CRISTA analyses (if applicable), and identifies candidate targets. Complete Test ( complete-test ) Tests CRISPRme pipeline on a small input dataset or the full genome, enabling users to validate the tool's functionality before performing large-scale analyses. Off-target sites validation Test ( validate-test ) Validates off-target sites generated by the Complete Test workflow by comparing CRISPRme predictions against brute-force ground-truth alignments derived from 1000 Genomes variant data. Targets Integration ( targets-integration ) Combines in silico predicted targets with experimental data to create a finalized target panel. GNOMAD Converter ( gnomAD-converter ) Transforms GNOMAD VCFs ( vcf.bgz format) into a format compatible with CRISPRme. The function supports VCFs from GNOMAD v3.1, v4.0, and v4.1, including joint VCFs. Generate Personal Card ( generate-personal-card ) Generates a personalized summary for a specific sample, identifying all private off-targets unique to that individual. Web Interface ( web-interface ) Launches CRISPRme's interactive web interface, allowing users to manage and execute tasks directly via a local browser. 2.2.1 Complete Search The Complete Search function performs an exhaustive variant- and haplotype-aware off-target analysis, leveraging the provided reference genome and variant datasets to deliver comprehensive results. This feature integrates all critical stages of the CRISPRme pipeline, encompassing off-target identification, functional annotation, and detailed reporting. Key highlights of the Complete Search functionality include: Variant- and Haplotype-Awareness Accurately incorporates genetic variation, including population- and sample-specific variants, and haplotypes data, to identify off-targets that reflect real-world genomic diversity. Comprehensive Off-Target Discovery Searches both the reference genome and user-specified variant datasets for potential off-targets, including those encompassing mismatches and bulges. Functional Annotation Annotates off-targets with relevant genomic features, such as coding/non-coding regions, regulatory elements, and gene proximity. Detailed Reporting Generates population-specific and sample-specific off-target summaries, highlighting variations that may impact specificity or introduce novel PAM sites. Provides CFD (Cutting Frequency Determination) and CRISTA scores, and mismatches and bulges counts to rank off-targets based on their potential impact. Includes graphical representations of findings to facilitate result interpretation. Output Formats Produces user-friendly output files, including text-based tables and visualization-ready graphical summaries. Usage Example for the Complete Search function: Via Conda/Mamba crisprme.py complete-search \ --genome Genomes/hg38 \ # reference genome directory --vcf vcf_config.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP variant datasets --guide sg1617.txt \ # guide --pam PAMs/20bp-NGG-spCas9.txt \ # NGG PAM file --annotation Annotations/dhs+gencode+encode.hg38.bed \ # annotation BED --gene_annotation Annotations/gencode.protein_coding.bed \ # gene proximity annotation BED --samplesID samplesIDs.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP samples --be-window 4,8 \ # base editing window start and stop positions within off-targets --be-base A,G \ # nucleotide to test base editing potential (A>G) --mm 6 \ # number of max mismatches --bDNA 2 \ # number of max DNA bulges --bRNA 2 \ # number of max RNA bulges --merge 3 \ # merge off-targets mapped within 3 bp in clusters --sorting-criteria-scoring mm+bulges \ # prioritize within each cluster off-targets with highest score and lowest mm+bulges (CFD and CRISTA reports only) --sorting-criteria mm,bulges \ # prioritize within each cluster off-targets with lowest mm and bulges counts --output sg1617-NGG-1000G-HGDP \ # output directory name --thread 8 # number of threads Via Docker docker run -v ${PWD} :/DATA -w /DATA -i pinellolab/crisprme \ crisprme.py complete-search \ --genome Genomes/hg38 \ # reference genome directory --vcf vcf_config.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP variant datasets --guide sg1617.txt \ # guide --pam PAMs/20bp-NGG-spCas9.txt \ # NGG PAM file --annotation Annotations/dhs+gencode+encode.hg38.bed \ # annotation BED --gene_annotation Annotations/gencode.protein_coding.bed \ # gene proximity annotation BED --samplesID samplesIDs.1000G.HGDP.txt \ # config file declaring usage of 1000G and HGDP samples --be-window 4,8 \ # base editing window start and stop positions within off-targets --be-base A,G \ # nucleotide to test base editing potential (A>G) --mm 6 \ # number of max mismatches --bDNA 2 \ # number of max DNA bulges --bRNA 2 \ # number of max RNA bulges --merge 3 \ # merge off-targets mapped within 3 bp in clusters --sorting-criteria-scoring mm+bulges \ # prioritize within each cluster off-targets with highest score and lowest mm+bulges (CFD and CRISTA reports only) --sorting-criteria mm,bulges \ # prioritize within each cluster off-targets with lowest mm and bulges counts --output sg1617-NGG-1000G-HGDP \ # output directory name --thread 8 # number of threads Input Arguments Below is a detailed list of the input arguments required or optionally used by the Complete Search func + +## Conda Search Info +$ conda search -c bioconda -c conda-forge crisprme --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +crisprme 1.0.1 0 +---------------- +file name : crisprme-1.0.1-0.tar.bz2 +name : crisprme +version : 1.0.1 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.0.1-0.tar.bz2 +md5 : 15fb87f487f5a57fe8657607c5378f72 +timestamp : 2020-10-28 14:39:24 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.0.2 0 +---------------- +file name : crisprme-1.0.2-0.tar.bz2 +name : crisprme +version : 1.0.2 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.0.2-0.tar.bz2 +md5 : feb105627b6e3a710790e8acf76930c6 +timestamp : 2020-11-02 22:32:38 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.0.3 0 +---------------- +file name : crisprme-1.0.3-0.tar.bz2 +name : crisprme +version : 1.0.3 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.0.3-0.tar.bz2 +md5 : 78e5a46d345149b7428e1078bfe117ee +timestamp : 2020-11-06 21:26:52 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.0.4 0 +---------------- +file name : crisprme-1.0.4-0.tar.bz2 +name : crisprme +version : 1.0.4 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.0.4-0.tar.bz2 +md5 : 254fb0132f206c3b752dbb4346655c8e +timestamp : 2020-11-08 00:12:42 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.0.5 0 +---------------- +file name : crisprme-1.0.5-0.tar.bz2 +name : crisprme +version : 1.0.5 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.0.5-0.tar.bz2 +md5 : a6161b34c661cba4c65c1cca90515fc4 +timestamp : 2020-11-10 23:10:19 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.0.6 0 +---------------- +file name : crisprme-1.0.6-0.tar.bz2 +name : crisprme +version : 1.0.6 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.0.6-0.tar.bz2 +md5 : 299f1490adb5e1427a6ca1597737e59a +timestamp : 2020-11-20 16:48:08 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.0.7 0 +---------------- +file name : crisprme-1.0.7-0.tar.bz2 +name : crisprme +version : 1.0.7 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.0.7-0.tar.bz2 +md5 : 2a63370c3cb52f9439906ddd54eb597e +timestamp : 2020-11-25 07:57:31 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.0.9 0 +---------------- +file name : crisprme-1.0.9-0.tar.bz2 +name : crisprme +version : 1.0.9 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.0.9-0.tar.bz2 +md5 : bcd776efaf69a259954fda34f4dc7d73 +timestamp : 2020-11-25 23:37:24 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.1.0 0 +---------------- +file name : crisprme-1.1.0-0.tar.bz2 +name : crisprme +version : 1.1.0 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.1.0-0.tar.bz2 +md5 : 6fa5b3a949238353f33f50750b50c02b +timestamp : 2020-11-26 19:11:47 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.2.0 0 +---------------- +file name : crisprme-1.2.0-0.tar.bz2 +name : crisprme +version : 1.2.0 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.2.0-0.tar.bz2 +md5 : 7b874087ff69e4e018f17174ed04ab32 +timestamp : 2020-11-30 14:44:08 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.2.2 0 +---------------- +file name : crisprme-1.2.2-0.tar.bz2 +name : crisprme +version : 1.2.2 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.2.2-0.tar.bz2 +md5 : c44091771146acc031f00d65f32ca797 +timestamp : 2020-11-30 21:49:16 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.3.0 0 +---------------- +file name : crisprme-1.3.0-0.tar.bz2 +name : crisprme +version : 1.3.0 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.3.0-0.tar.bz2 +md5 : 32f5d16abebcfcf3340ea9b36f64560e +timestamp : 2020-12-02 20:07:04 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.3.1 0 +---------------- +file name : crisprme-1.3.1-0.tar.bz2 +name : crisprme +version : 1.3.1 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.3.1-0.tar.bz2 +md5 : c3931c8191fd1697ddc3e91b52f10476 +timestamp : 2020-12-04 14:46:41 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.3.2 0 +---------------- +file name : crisprme-1.3.2-0.tar.bz2 +name : crisprme +version : 1.3.2 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.3.2-0.tar.bz2 +md5 : be64b936427f9e7a15e034e343fe8aec +timestamp : 2020-12-08 14:05:19 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.3.3 0 +---------------- +file name : crisprme-1.3.3-0.tar.bz2 +name : crisprme +version : 1.3.3 +build : 0 +build number: 0 +size : 4.4 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.3.3-0.tar.bz2 +md5 : 303cfcf7b17fae79e29d9441f10f3420 +timestamp : 2020-12-11 15:56:20 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.3.4 0 +---------------- +file name : crisprme-1.3.4-0.tar.bz2 +name : crisprme +version : 1.3.4 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.3.4-0.tar.bz2 +md5 : 25f533845fc1f655a2fbe075b29931d5 +timestamp : 2020-12-15 09:40:45 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.3.5 0 +---------------- +file name : crisprme-1.3.5-0.tar.bz2 +name : crisprme +version : 1.3.5 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.3.5-0.tar.bz2 +md5 : 093c6d3103878791b9320c7bb9f53f6f +timestamp : 2020-12-15 20:56:10 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.3.6 0 +---------------- +file name : crisprme-1.3.6-0.tar.bz2 +name : crisprme +version : 1.3.6 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.3.6-0.tar.bz2 +md5 : 08b5f278fdc3e7e1a66bfa6893b204a1 +timestamp : 2020-12-22 15:48:14 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.3.9 0 +---------------- +file name : crisprme-1.3.9-0.tar.bz2 +name : crisprme +version : 1.3.9 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.3.9-0.tar.bz2 +md5 : 1eddae0043d1f62e6d41bf5b3a9ea756 +timestamp : 2021-01-29 16:47:39 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.4.0 0 +---------------- +file name : crisprme-1.4.0-0.tar.bz2 +name : crisprme +version : 1.4.0 +build : 0 +build number: 0 +size : 4.4 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.4.0-0.tar.bz2 +md5 : fd59d4686a324a5b6fefb001743eddc0 +timestamp : 2021-01-29 17:45:35 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.4.1 0 +---------------- +file name : crisprme-1.4.1-0.tar.bz2 +name : crisprme +version : 1.4.1 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.4.1-0.tar.bz2 +md5 : 61e5e1b4aba63979deea504938abf84f +timestamp : 2021-01-29 22:43:46 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.4.2 0 +---------------- +file name : crisprme-1.4.2-0.tar.bz2 +name : crisprme +version : 1.4.2 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.4.2-0.tar.bz2 +md5 : a20d5570cdf597e0e4d501db735d86b4 +timestamp : 2021-01-30 16:41:04 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.4.3 0 +---------------- +file name : crisprme-1.4.3-0.tar.bz2 +name : crisprme +version : 1.4.3 +build : 0 +build number: 0 +size : 4.3 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.4.3-0.tar.bz2 +md5 : 14b8430404c796b30420df1d51d2698a +timestamp : 2021-01-31 15:43:48 UTC +dependencies: + - crispritz + - python >3.6 + + +crisprme 1.4.3 1 +---------------- +file name : crisprme-1.4.3-1.tar.bz2 +name : crisprme +version : 1.4.3 +build : 1 +build number: 1 +size : 9.1 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.4.3-1.tar.bz2 +md5 : e7ddbc4c73ce4f9b222cee6971c9f969 +timestamp : 2021-02-24 13:11:54 UTC +dependencies: + - crispritz + - dash 1.10.0.* + - dash-bootstrap-components 0.10.0.* + - dash-core-components 1.9.0.* + - dash-daq 0.4.0.* + - dash-html-components 1.0.3.* + - dash-renderer 1.3.0.* + - dash-table 4.6.2.* + - flask 1.1.2.* + - flask-caching 1.7.1.* + - flask-compress 1.5.0.* + - fontconfig 2.13.1.* + - freetype 2.10.1.* + - future 0.18.2.* + - gettext 0.19.8.1.* + - gunicorn 20.0.4.* + - zip + + +crisprme 1.4.5 0 +---------------- +file name : crisprme-1.4.5-0.tar.bz2 +name : crisprme +version : 1.4.5 +build : 0 +build number: 0 +size : 7.8 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.4.5-0.tar.bz2 +md5 : af097927b7300ced87c4eb35586bc507 +timestamp : 2021-02-24 17:35:59 UTC +dependencies: + - crispritz + - dash 1.10.0.* + - dash-bootstrap-components 0.10.0.* + - dash-core-components 1.9.0.* + - dash-daq 0.4.0.* + - dash-html-components 1.0.3.* + - dash-renderer 1.3.0.* + - dash-table 4.6.2.* + - flask 1.1.2.* + - flask-caching 1.7.1.* + - flask-compress 1.5.0.* + - fontconfig 2.13.1.* + - freetype 2.10.1.* + - future 0.18.2.* + - gettext 0.19.8.1.* + - gunicorn 20.0.4.* + - zip + + +crisprme 1.4.6 0 +---------------- +file name : crisprme-1.4.6-0.tar.bz2 +name : crisprme +version : 1.4.6 +build : 0 +build number: 0 +size : 7.8 MB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/crisprme-1.4.6-0.tar.bz2 +md5 : 2a3b18ce404dcd3b3293bfee2b97ab2f +timestamp : 2021-02-24 23:53:47 UTC +dependencies: + - crispritz + - dash 1.10.0.* + - dash-bootstrap-components 0.10.0.* diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cromwell.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cromwell.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a106be198bbbede8732698293e569c76e52bd21 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/cromwell.manual_bundle.txt @@ -0,0 +1,613 @@ +# Tool: cromwell +software_name: cromwell +tier: T1 +domain: t1_backfill_overall +downloads: 115971 +summary: A Workflow Management System geared towards scientific workflows described in WDL +description: A Workflow Management System geared towards scientific workflows described in WDL +dependencies: findutils, openjdk >=8,<9, python +execution_environment: Java +execution_environment_reason: inferred from Java runtime dependencies + +## URLs +home_url: https://github.com/broadinstitute/cromwell +doc_url: +dev_url: + +## CLI Help Source +java:-help +## CLI Help Content +$ conda run -n bioenv_java java -help +[rc=0] + +Usage: java [options] [args...] + (to execute a class) + or java [options] -jar [args...] + (to execute a jar file) + or java [options] -m [/] [args...] + java [options] --module [/] [args...] + (to execute the main class in a module) + or java [options] [args] + (to execute a single source-file program) + + Arguments following the main class, source file, -jar , + -m or --module / are passed as the arguments to + main class. + + where options include: + + -cp + -classpath + --class-path + A : separated list of directories, JAR archives, + and ZIP archives to search for class files. + -p + --module-path ... + A : separated list of directories, each directory + is a directory of modules. + --upgrade-module-path ... + A : separated list of directories, each directory + is a directory of modules that replace upgradeable + modules in the runtime image + --add-modules [,...] + root modules to resolve in addition to the initial module. + can also be ALL-DEFAULT, ALL-SYSTEM, + ALL-MODULE-PATH. + --enable-native-access [,...] + modules that are permitted to perform restricted native operations. + can also be ALL-UNNAMED. + --list-modules + list observable modules and exit + -d + --describe-module + describe a module and exit + --dry-run create VM and load main class but do not execute main method. + The --dry-run option may be useful for validating the + command-line options such as the module system configuration. + --validate-modules + validate all modules and exit + The --validate-modules option may be useful for finding + conflicts and other errors with modules on the module path. + -D= + set a system property + -verbose:[class|module|gc|jni] + enable verbose output for the given subsystem + -version print product version to the error stream and exit + --version print product version to the output stream and exit + -showversion print product version to the error stream and continue + --show-version + print product version to the output stream and continue + --show-module-resolution + show module resolution output during startup + -? -h -help + print this help message to the error stream + --help print this help message to the output stream + -X print help on extra options to the error stream + --help-extra print help on extra options to the output stream + -ea[:...|:] + -enableassertions[:...|:] + enable assertions with specified granularity + -da[:...|:] + -disableassertions[:...|:] + disable assertions with specified granularity + -esa | -enablesystemassertions + enable system assertions + -dsa | -disablesystemassertions + disable system assertions + -agentlib:[=] + load native agent library , e.g. -agentlib:jdwp + see also -agentlib:jdwp=help + -agentpath:[=] + load native agent library by full pathname + -javaagent:[=] + load Java programming language agent, see java.lang.instrument + -splash: + show splash screen with specified image + HiDPI scaled images are automatically supported and used + if available. The unscaled image filename, e.g. image.ext, + should always be passed as the argument to the -splash option. + The most appropriate scaled image provided will be picked up + automatically. + See the SplashScreen API documentation for more information + @argument files + one or more argument files containing options + -disable-@files + prevent further argument file expansion + --enable-preview + allow classes to depend on preview features of this release +To specify an argument for a long option, you can use --= or +-- . + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge cromwell --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +cromwell 0.19.4 0 +----------------- +file name : cromwell-0.19.4-0.tar.bz2 +name : cromwell +version : 0.19.4 +build : 0 +build number: 0 +size : 200.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.19.4-0.tar.bz2 +md5 : 98183f7b2b8ad719fb1a08d131cf4121 +dependencies: + - java-jdk >=8 + + +cromwell 0.21 0 +--------------- +file name : cromwell-0.21-0.tar.bz2 +name : cromwell +version : 0.21 +build : 0 +build number: 0 +size : 195.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.21-0.tar.bz2 +md5 : f5e2e93a92c4c9b586eea221f3e585bc +dependencies: + - java-jdk >=8 + + +cromwell 0.22 0 +--------------- +file name : cromwell-0.22-0.tar.bz2 +name : cromwell +version : 0.22 +build : 0 +build number: 0 +size : 204.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.22-0.tar.bz2 +md5 : 6cfa502de82d90298ddf3f467a5aa116 +dependencies: + - java-jdk >=8 + + +cromwell 0.23 0 +--------------- +file name : cromwell-0.23-0.tar.bz2 +name : cromwell +version : 0.23 +build : 0 +build number: 0 +size : 218.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.23-0.tar.bz2 +md5 : b83f939e4c5eebe0ef2c302cd0623f1b +dependencies: + - java-jdk >=8 + + +cromwell 0.24 py27_0 +-------------------- +file name : cromwell-0.24-py27_0.tar.bz2 +name : cromwell +version : 0.24 +build : py27_0 +build number: 0 +size : 218.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.24-py27_0.tar.bz2 +md5 : fc24810df1ef774d31ad4248e2779ec5 +dependencies: + - java-jdk >=8 + - python 2.7* + + +cromwell 0.24 py34_0 +-------------------- +file name : cromwell-0.24-py34_0.tar.bz2 +name : cromwell +version : 0.24 +build : py34_0 +build number: 0 +size : 218.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.24-py34_0.tar.bz2 +md5 : 2996cc7b3dad4cb0f60d8c63e101e51f +dependencies: + - java-jdk >=8 + - python 3.4* + + +cromwell 0.24 py35_0 +-------------------- +file name : cromwell-0.24-py35_0.tar.bz2 +name : cromwell +version : 0.24 +build : py35_0 +build number: 0 +size : 218.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.24-py35_0.tar.bz2 +md5 : 68c08ab342157a2df2584ee2d7606611 +dependencies: + - java-jdk >=8 + - python 3.5* + + +cromwell 0.25 py27_0 +-------------------- +file name : cromwell-0.25-py27_0.tar.bz2 +name : cromwell +version : 0.25 +build : py27_0 +build number: 0 +size : 258.8 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.25-py27_0.tar.bz2 +md5 : bbbd5c7c20072d30a7879441cc08f640 +dependencies: + - openjdk >=8 + - python 2.7* + + +cromwell 0.25 py34_0 +-------------------- +file name : cromwell-0.25-py34_0.tar.bz2 +name : cromwell +version : 0.25 +build : py34_0 +build number: 0 +size : 258.8 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.25-py34_0.tar.bz2 +md5 : 7996d40b9f613b07f9f5783c84f0616d +dependencies: + - openjdk >=8 + - python 3.4* + + +cromwell 0.25 py35_0 +-------------------- +file name : cromwell-0.25-py35_0.tar.bz2 +name : cromwell +version : 0.25 +build : py35_0 +build number: 0 +size : 258.8 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.25-py35_0.tar.bz2 +md5 : f9adf643e9de6a751a68279edf206f52 +dependencies: + - openjdk >=8 + - python 3.5* + + +cromwell 0.26 py27_0 +-------------------- +file name : cromwell-0.26-py27_0.tar.bz2 +name : cromwell +version : 0.26 +build : py27_0 +build number: 0 +size : 243.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.26-py27_0.tar.bz2 +md5 : ebbc5e107a0bc390d4d3167b361bc7c4 +dependencies: + - openjdk >=8 + - python 2.7* + + +cromwell 0.26 py34_0 +-------------------- +file name : cromwell-0.26-py34_0.tar.bz2 +name : cromwell +version : 0.26 +build : py34_0 +build number: 0 +size : 243.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.26-py34_0.tar.bz2 +md5 : 6fa85fc359799564ff984058da497738 +dependencies: + - openjdk >=8 + - python 3.4* + + +cromwell 0.26 py35_0 +-------------------- +file name : cromwell-0.26-py35_0.tar.bz2 +name : cromwell +version : 0.26 +build : py35_0 +build number: 0 +size : 243.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.26-py35_0.tar.bz2 +md5 : 2e47b1f706e916d23f324fc0de0e36b1 +dependencies: + - openjdk >=8 + - python 3.5* + + +cromwell 0.26 py36_0 +-------------------- +file name : cromwell-0.26-py36_0.tar.bz2 +name : cromwell +version : 0.26 +build : py36_0 +build number: 0 +size : 243.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.26-py36_0.tar.bz2 +md5 : 46bc0cc873ac35dfb5f4f91f5d63ab5f +dependencies: + - openjdk >=8 + - python 3.6* + + +cromwell 0.29 py27_0 +-------------------- +file name : cromwell-0.29-py27_0.tar.bz2 +name : cromwell +version : 0.29 +build : py27_0 +build number: 0 +size : 211.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.29-py27_0.tar.bz2 +md5 : b6d4cb835ca1e17c1e3dfa3defed7c0e +dependencies: + - openjdk >=8 + - python 2.7* + + +cromwell 0.29 py35_0 +-------------------- +file name : cromwell-0.29-py35_0.tar.bz2 +name : cromwell +version : 0.29 +build : py35_0 +build number: 0 +size : 211.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.29-py35_0.tar.bz2 +md5 : 1ee4f59a2db6449ada10aa858f507ee2 +dependencies: + - openjdk >=8 + - python 3.5* + + +cromwell 0.29 py36_0 +-------------------- +file name : cromwell-0.29-py36_0.tar.bz2 +name : cromwell +version : 0.29 +build : py36_0 +build number: 0 +size : 211.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.29-py36_0.tar.bz2 +md5 : 556a3dd9d3ec3a7a42b3484ba6d383d3 +dependencies: + - openjdk >=8 + - python 3.6* + + +cromwell 0.30 py27_0 +-------------------- +file name : cromwell-0.30-py27_0.tar.bz2 +name : cromwell +version : 0.30 +build : py27_0 +build number: 0 +size : 245.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.30-py27_0.tar.bz2 +md5 : 4eb336cf345d174e620328d920b0fff1 +dependencies: + - openjdk >=8 + - python 2.7* + + +cromwell 0.30 py35_0 +-------------------- +file name : cromwell-0.30-py35_0.tar.bz2 +name : cromwell +version : 0.30 +build : py35_0 +build number: 0 +size : 245.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.30-py35_0.tar.bz2 +md5 : 40dd12d78ce08905031f4ad3701f9f4b +dependencies: + - openjdk >=8 + - python 3.5* + + +cromwell 0.30 py36_0 +-------------------- +file name : cromwell-0.30-py36_0.tar.bz2 +name : cromwell +version : 0.30 +build : py36_0 +build number: 0 +size : 245.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.30-py36_0.tar.bz2 +md5 : 7aa52fab4f510d3ddd7f84afad3bd45f +dependencies: + - openjdk >=8 + - python 3.6* + + +cromwell 0.32a py27_0 +--------------------- +file name : cromwell-0.32a-py27_0.tar.bz2 +name : cromwell +version : 0.32a +build : py27_0 +build number: 0 +size : 179.6 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.32a-py27_0.tar.bz2 +md5 : 883d2d236a2a15da2299916e63710dee +dependencies: + - openjdk >=8 + - python 2.7* + + +cromwell 0.32a py27_1 +--------------------- +file name : cromwell-0.32a-py27_1.tar.bz2 +name : cromwell +version : 0.32a +build : py27_1 +build number: 1 +size : 257.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.32a-py27_1.tar.bz2 +md5 : a6354c5a5772552cac201aad780983ca +dependencies: + - openjdk >=8 + - python 2.7* + + +cromwell 0.32a py35_0 +--------------------- +file name : cromwell-0.32a-py35_0.tar.bz2 +name : cromwell +version : 0.32a +build : py35_0 +build number: 0 +size : 179.6 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.32a-py35_0.tar.bz2 +md5 : c851c1edec82506a8a897121cd644b90 +dependencies: + - openjdk >=8 + - python 3.5* + + +cromwell 0.32a py35_1 +--------------------- +file name : cromwell-0.32a-py35_1.tar.bz2 +name : cromwell +version : 0.32a +build : py35_1 +build number: 1 +size : 257.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.32a-py35_1.tar.bz2 +md5 : 921a0fdba9f2d283da10b55e00171c49 +dependencies: + - openjdk >=8 + - python 3.5* + + +cromwell 0.32a py36_0 +--------------------- +file name : cromwell-0.32a-py36_0.tar.bz2 +name : cromwell +version : 0.32a +build : py36_0 +build number: 0 +size : 179.6 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.32a-py36_0.tar.bz2 +md5 : 7f1e6a5963768f20073e481ea6eda7ad +dependencies: + - openjdk >=8 + - python 3.6* + + +cromwell 0.32a py36_1 +--------------------- +file name : cromwell-0.32a-py36_1.tar.bz2 +name : cromwell +version : 0.32a +build : py36_1 +build number: 1 +size : 257.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.32a-py36_1.tar.bz2 +md5 : fd199a69c5d85a89c467eeecbd72a105 +dependencies: + - openjdk >=8 + - python 3.6* + + +cromwell 0.32 3 +--------------- +file name : cromwell-0.32-3.tar.bz2 +name : cromwell +version : 0.32 +build : 3 +build number: 3 +size : 261.3 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/cromwell-0.32-3.tar.bz2 +md5 : 5abfc93f09bbff325001ab0609825f51 +timestamp : 2018-07-09 13:21:35 UTC +dependencies: + - openjdk >=8 + - python + + +cromwell 0.32 py27_1 +-------------------- +file name : cromwell-0.32-py27_1.tar.bz2 +name : cromwell +version : 0.32 +build : py27_1 +build number: 1 +size : 261.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.32-py27_1.tar.bz2 +md5 : 8a7c917dcef7e64f1f1aa3673409191a +dependencies: + - openjdk >=8 + - python 2.7* + + +cromwell 0.32 py35_1 +-------------------- +file name : cromwell-0.32-py35_1.tar.bz2 +name : cromwell +version : 0.32 +build : py35_1 +build number: 1 +size : 261.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/cromwell-0.32-py35_1.tar.bz2 +md5 : 806a6853fd9568efadb5280da567 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/csvtk.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/csvtk.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f9a4f6034182edd532c315a0c71df336aaf24c7 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/csvtk.manual_bundle.txt @@ -0,0 +1,666 @@ +# Tool: csvtk +software_name: csvtk +tier: T1 +domain: t1_backfill_overall +downloads: 222855 +summary: A cross-platform, efficient, practical CSV/TSV toolkit +description: A cross-platform, efficient, practical CSV/TSV toolkit +dependencies: +execution_environment: Other +execution_environment_reason: fallback runtime classification + +## URLs +home_url: https://github.com/shenwei356/csvtk +doc_url: +dev_url: + +## CLI Help Source +cli:csvtk +## CLI Help Content +$ conda run -n bioenv_cli csvtk --help +[rc=0] +csvtk -- a cross-platform, efficient and practical CSV/TSV toolkit + +Version: 0.31.0 + +Author: Wei Shen + +Documents : http://shenwei356.github.io/csvtk +Source code: https://github.com/shenwei356/csvtk + +Attention: + + 1. By default, csvtk assumes input files have header row, if not, switch flag "-H" on. + 2. By default, csvtk handles CSV files, use flag "-t" for tab-delimited files. + 3. Column names should be unique. + 4. By default, lines starting with "#" will be ignored, if the header row + starts with "#", please assign flag "-C" another rare symbol, e.g. '$'. + 5. Do not mix use field (column) numbers and names to specify columns to operate. + 6. The CSV parser requires all the lines have same numbers of fields/columns. + Even lines with spaces will cause error. + Use '-I/--ignore-illegal-row' to skip these lines if neccessary. + You can also use "csvtk fix" to fix files with different numbers of columns in rows. + 7. If double-quotes exist in fields not enclosed with double-quotes, e.g., + x,a "b" c,1 + It would report error: + bare " in non-quoted-field. + Please switch on the flag "-l" or use "csvtk fix-quotes" to fix it. + 8. If somes fields have only a double-quote eighter in the beginning or in the end, e.g., + x,d "e","a" b c,1 + It would report error: + extraneous or missing " in quoted-field + Please use "csvtk fix-quotes" to fix it, and use "csvtk del-quotes" to reset to the + original format as needed. + +Environment variables for frequently used global flags: + + - "CSVTK_T" for flag "-t/--tabs" + - "CSVTK_H" for flag "-H/--no-header-row" + - "CSVTK_QUIET" for flag "--quiet" + +You can also create a soft link named "tsvtk" for "csvtk", +which sets "-t/--tabs" by default. + +Usage: + csvtk [command] + +Commands for Information: + corr calculate Pearson correlation between two columns + dim dimensions of CSV file + headers print headers + ncol print number of columns + nrow print number of records + summary summary statistics of selected numeric or text fields (groupby group fields) + watch monitor the specified fields + +Format Conversion: + csv2json convert CSV to JSON format + csv2md convert CSV to markdown format + csv2rst convert CSV to reStructuredText format + csv2tab convert CSV to tabular format + csv2xlsx convert CSV/TSV files to XLSX file + pretty convert CSV to a readable aligned table + space2tab convert space delimited format to TSV + splitxlsx split XLSX sheet into multiple sheets according to column values + tab2csv convert tabular format to CSV + xlsx2csv convert XLSX to CSV format + +Commands for Set Operation: + comb compute combinations of items at every row + concat concatenate CSV/TSV files by rows + cut select and arrange fields + filter filter rows by values of selected fields with arithmetic expression + filter2 filter rows by awk-like arithmetic/string expressions + freq frequencies of selected fields + grep grep data by selected fields with patterns/regular expressions + head print first N records + inter intersection of multiple files + join join files by selected fields (inner, left and outer join) + sample sampling by proportion + split split CSV/TSV into multiple files according to column values + uniq unique data without sorting + +Commands for Edit: + add-header add column names + del-header delete column names + del-quotes remove extra double quotes added by 'fix-quotes' + fix fix CSV/TSV with different numbers of columns in rows + fix-quotes fix malformed CSV/TSV caused by double-quotes + fmtdate format date of selected fields + mutate create new column from selected fields by regular expression + mutate2 create a new column from selected fields by awk-like arithmetic/string expressions + mutate3 create a new column from selected fields with Go-like expressions + rename rename column names with new names + rename2 rename column names by regular expression + replace replace data of selected fields by regular expression + round round float to n decimal places + +Commands for Data Transformation: + fold fold multiple values of a field into cells of groups + gather gather columns into key-value pairs, like tidyr::gather/pivot_longer + sep separate column into multiple columns + spread spread a key-value pair across multiple columns, like tidyr::spread/pivot_wider + transpose transpose CSV data + unfold unfold multiple values in cells of a field + +Commands for Ordering: + sort sort by selected fields + +Commands for Ploting: + plot plot common figures + +Commands for Miscellaneous Functions: + cat stream file to stdout and report progress on stderr + +Additional Commands: + genautocomplete generate shell autocompletion script (bash|zsh|fish|powershell) + version print version information and check for update + +Flags: + -C, --comment-char string lines starting with commment-character will be ignored. if your header + row starts with '#', please assign "-C" another rare symbol, e.g. '$' + (default "#") + -U, --delete-header do not output header row + -d, --delimiter string delimiting character of the input CSV file (default ",") + -h, --help help for csvtk + -E, --ignore-empty-row ignore empty rows + -I, --ignore-illegal-row ignore illegal rows. You can also use 'csvtk fix' to fix files with + different numbers of columns in rows + -X, --infile-list string file of input files list (one file per line), if given, they are appended + to files from cli arguments + -l, --lazy-quotes if given, a quote may appear in an unquoted field and a non-doubled quote + may appear in a quoted field + -H, --no-header-row specifies that the input CSV file does not have header row + -j, --num-cpus int number of CPUs to use (default 4) + -D, --out-delimiter string delimiting character of the output CSV file, e.g., -D $'\t' for tab + (default ",") + -o, --out-file string out file ("-" for stdout, suffix .gz for gzipped out) (default "-") + -T, --out-tabs specifies that the output is delimited with tabs. Overrides "-D" + --quiet be quiet and do not show extra information and warnings + -Z, --show-row-number show row number as the first column, with header row skipped + -t, --tabs specifies that the input CSV file is delimited with tabs. Overrides "-d" + +Use "csvtk [command] --help" for more information about a command. + + + +## URL Docs Extract +### https://github.com/shenwei356/csvtk +GitHub - shenwei356/csvtk: A cross-platform, efficient and practical CSV/TSV toolkit in Golang · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} shenwei356 / csvtk Public Uh oh! There was an error while loading. Please reload this page . Notifications You must be signed in to change notification settings Fork 97 Star 1.2k Code Issues 10 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights shenwei356/csvtk master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 594 Commits 594 Commits .github .github csvtk csvtk doc doc testdata testdata .gitignore .gitignore .travis.yml .travis.yml CHANGELOG.md CHANGELOG.md LICENSE LICENSE README.md README.md go.mod go.mod go.sum go.sum View all files Repository files navigation README MIT license csvtk - a cross-platform, efficient and practical CSV/TSV toolkit Documents: http://bioinf.shenwei.me/csvtk ( Usage , Tutorial and FAQs ). 中文介绍 Source code: https://github.com/shenwei356/csvtk Latest version: Introduction Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data science. People usually use spreadsheet software like MS Excel to process table data. However this is all by clicking and typing, which is not automated and is time-consuming to repeat , especially when you want to apply similar operations with different datasets or purposes. You can also accomplish some CSV/TSV manipulations using shell commands, but more code is needed to handle the header line. Shell commands do not support selecting columns with column names either. csvtk is convenient for rapid data investigation and also easy to integrate into analysis pipelines . It could save you lots of time in (not) writing Python/R scripts. Table of Contents Introduction Table of Contents Features Subcommands Installation Method 1: Download binaries (latest stable/dev version) Method 2: Install via Pixi Method 3: Install via conda (latest stable version) Method 4: Install via homebrew Method 5: For Go developer (latest stable/dev version) Method 6: For ArchLinux AUR users (may be not the latest) Command-line completion Compared to csvkit Examples Acknowledgements Contact License Starchart Features Cross-platform (Linux/Windows/Mac OS X/OpenBSD/FreeBSD) Light weight and out-of-the-box, no dependencies, no compilation, no configuration Fast , multiple-CPUs supported (some commands) Practical functions provided by N subcommands Support STDIN and gzipped input/output file, easy being used in pipe Seamless support for xz (.xz), zstd (.zst), Bzip2 (.bz2), LZ4 (.lz4) formats Most of the subcommands support unselecting fields and fuzzy fields , e.g. -f "-id,-name" for all fields except "id" and "name", -F -f "a.*" for all fields with prefix "a.". Support some common plots (see usage ) Seamless support for data with meta line (e.g., sep=, ) of separator declaration used by MS Excel Subcommands 57 subcommands in total. Information headers : prints headers dim : dimensions of CSV file nrow : print number of records ncol : print number of columns summary : summary statistics of selected numeric or text fields (groupby group fields) watch : online monitoring and histogram of selected field corr : calculate Pearson correlation between numeric columns Format conversion pretty : converts CSV to a readable aligned table csv2tab : converts CSV to tabular format tab2csv : converts tabular format to CSV space2tab : converts space delimited format to TSV csv2md : converts CSV to markdown format csv2rst : converts CSV to reStructuredText format csv2json : converts CSV to JSON format csv2xlsx : converts CSV/TSV files to XLSX file xlsx2csv : converts XLSX to CSV format Set operations head : prints first N records concat : concatenates CSV/TSV files by rows sample : sampling by proportion cut : select and arrange fields grep : greps data by selected fields with patterns/regular expressions uniq : unique data without sorting freq : frequencies of selected fields inter : intersection of multiple files filter : filters rows by values of selected fields with arithmetic expression filter2 : filters rows by awk-like arithmetic/string expressions join : join files by selected fields (inner, left and outer join) split splits CSV/TSV into multiple files according to column values splitxlsx : splits XLSX sheet into multiple sheets according to column values comb : compute combinations of items at every row Edit fix : fix CSV/TSV with different numbers of columns in rows fix-quotes : fix malformed CSV/TSV caused by double-quotes del-quotes : remove extra double-quotes added by fix-quotes add-header : add column names del-header : delete column names rename : renames column names with new names rename2 : renames column names by regular expression replace : replaces data of selected fields by regular expression round : round float to n decimal places comma : make numbers more readable by adding commas mutate : creates new columns from selected fields by regular expression mutate2 : creates a new column from selected fields by awk-like arithmetic/string expressions mutate3 : create a new column from selected fields with Go-like expressions fmtdate : format date of selected fields Transform transpose : transposes CSV data sep : separate column into multiple columns gather : gather columns into key-value pairs, like tidyr::gather/pivot_longer spread : spread a key-value pair across multiple columns, like tidyr::spread/pivot_wider unfold : unfold multiple values in cells of a field fold : fold multiple values of a field into cells of groups Ordering sort : sorts by selected fields shuf : shuffle rows Ploting plot see usage plot hist histogram plot box boxplot plot line line plot and scatter plot plot bar plot bar chart Misc cat stream file and report progress version print version information and check for update genautocomplete generate shell autocompletion script (bash|zsh|fish|powershell) Installation Download Page csvtk is implemented in Go programming language, executable binary files for most popular operating systems are freely available in release page. Method 1: Download binaries (latest stable/dev version) Just download compressed executable file of your operating system, and decompress it with tar -zxvf *.tar.gz command or other tools. And then: For Linux-like systems If you have root privilege simply copy it to /usr/local/bin : sudo cp csvtk /usr/local/bin/ Or copy to anywhere in the environment variable PATH : mkdir -p $HOME/bin/; cp csvtk $HOME/bin/ For windows , just copy csvtk.exe to C:\WINDOWS\system32 . Method 2: Install via Pixi pixi global install csvtk Method 3: Install via conda (latest stable version) # >= v0.31.0 conda install -c conda-forge csvtk # <= v0.31.0 conda install -c bioconda csvtk Method 4: Install via homebrew brew install csvtk Method 5: For Go developer (latest stable/dev version) go install github.com/shenwei356/csvtk/csvtk@latest Method 6: For ArchLinux AUR users (may be not the latest) yaourt -S csvtk Command-line completion Bash: # generate completion shell csvtk genautocomplete --shell bash # configure if never did. # install bash-completion if the "complete" command is not found. echo "for bcfile in ~/.bash_completion.d/* ; do source \$bcfile; done" >> ~/.bash_completion echo "source ~/.bash_completion" >> ~/.bashrc Zsh: # generate completion shell csvtk genautocomplete --shell zsh --file ~/.zfunc/_csvtk # configure if never did echo 'fpath=( ~/.zfunc "${fpath[@]}" )' >> ~/.zshrc echo "autoload -U compinit; compinit" >> ~/.zshrc fish: csvtk genautocomplete --shell fish --file ~/.config/fish/completions/csvtk.fish Compared to csvkit csvkit , attention: this table wasn't updated for many years. Features csvtk csvkit Note Read Gzip Yes Yes read gzip files Fields ranges Yes Yes e.g. -f 1-4,6 Unselect fields Yes -- e.g. -1 for excluding first column Fuzzy fields Yes -- e.g. ab* for columns with name prefix "ab" Reorder fields Yes Yes it means -f 1,2 is different from -f 2,1 Rename columns Yes -- rename with new name(s) or from existed names Sort by multiple keys Yes Yes bash sort like operations Sort by number Yes -- e.g. -k 1:n Multiple sort Yes -- e.g. -k 2:r -k 1:nr Pretty output Yes Yes convert CSV to readable aligned table Unique data Yes -- unique data of selected fields frequency Yes -- frequencies of selected fields Sampling Yes -- sampling by proportion Mutate fields Yes -- create new columns from selected fields Replace Yes -- replace data of selected fields Similar tools: csvkit - A suite of utilities for converting to and working with CSV, the king of tabular file formats. http://csvkit.rtfd.org/ xsv - A fast CSV toolkit written in Rust. miller - Miller is like sed, awk, cut, join, and sort for name-indexed data such as CSV and tabular JSON http://johnkerl.org/miller tsv-utils - Command line utilities for tab-separated value files written in the D programming language. Examples More examples and tutorial . Attention By default, csvtk assumes input files have header row, if not, switch flag -H on. By default, csvtk handles CSV files, use flag -t for tab-delimited files. Column names should be unique. By default, lines starting with # will be ignored, if the header row starts with # , please assign flag -C another rare symbol, e.g. $ . Do not mix use field (column) numbers and names to specify columns to operate. The CSV parser requires all the lines have same numbers of fields/columns. Even lines with spaces will cause error. Use -I/--ignore-illegal-row to skip these lines if neccessary. You can also use "csvtk fix" to fix files with different numbers of columns in rows. If double-quotes exist in fields not enclosed with double-quotes, e.g., x,a "b" c,1 It would report error: bare `"` in non-quoted-field. Please switch on the flag -l or use csvtk fix-quotes to fix it. If somes fields have only a double-quote either in the beginning or in the end, e.g., x,d "e","a" b c,1 It would report an error: extraneous or missing " in quoted-field Please use csvtk fix-quotes to fix it, and use csvtk del-quotes to reset to the original format as needed. Examples Pretty result $ csvtk pretty names.csv id first_name last_name username -- ---------- --------- -------- 11 Rob Pike rob 2 Ken Thompson ken 4 Robert Griesemer gri 1 Robert Thompson abc NA Robert Abel 123 $ csvtk pretty names.csv -S 3line ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ id first_name last_name username ──────────────────────────────────────── 11 Rob Pike rob 2 Ken Thompson ken 4 Robert Griesemer gri 1 Robert Thompson abc NA Robert Abel 123 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ $ csvtk pretty names.csv -S round -w 5 -m 1- ╭───────┬────────────┬───────────┬──────────╮ │ id │ first_name │ last_name │ username │ ├───────┼────────────┼───────────┼──────────┤ │ 11 │ Rob │ Pike │ rob │ ├───────┼────────────┼───────────┼──────────┤ │ 2 │ Ken │ Thompson │ ken │ ├───────┼────────────┼───────────┼──────────┤ │ 4 │ Robert │ Griesemer │ gri │ ├───────┼────────────┼───────────┼──────────┤ │ 1 │ Robert │ Thompson │ abc │ ├───────┼────────────┼───────────┼──────────┤ │ NA │ Robert │ Abel │ 123 │ ╰───────┴────────────┴───────────┴──────────╯ Summary of selected numeric fields, supporting "group-by" $ cat testdata/digitals2.csv \ | csvtk summary -i -f f4:sum,f5:sum -g f1,f2 \ | csvtk pretty f1 f2 f4:sum f5:sum bar xyz 7.00 106.00 bar xyz2 4.00 4.00 foo bar 6.00 3.00 foo bar2 4.50 5.00 Select fields/columns ( cut ) By index: csvtk cut -f 1,2 By names: csvtk cut -f first_name,username Unselect : csvtk cut -f -1,-2 or csvtk cut -f -first_name Fuzzy fields : csvtk cut -F -f "*_name,username" Field ranges: csvtk cut -f 2-4 for column 2,3,4 or csvtk cut -f -3--1 for discarding column 1,2,3 All fields: csvtk cut -f 1- or csvtk cut -F -f "*" Search by selected fields ( grep ) (matched parts will be highlighted as red) By exactly matching: csvtk grep -f first_name -p Robert -p Rob By regular expression: csvtk grep -f first_name -r -p Rob By pattern list: csvtk grep -f first_name -P name_list.txt Remore rows containing missing data (NA): csvtk grep -F -f "*" -r -p "^$" -v Rename column names ( rename and rename2 ) Setting new names: csvtk rename -f A,B -n a,b or csvtk rename -f 1-3 -n a,b,c Replacing with original names by regular express: csvtk rename2 -f 1- -p "(.*)" -r 'prefix_$1' for adding prefix to all column names. Edit data with regular expression ( replace ) Remove Chinese charactors: csvtk replace -F -f "*_name" -p "\p{Han}+" -r "" Create new column from selected fields by regular expression ( mutate ) In default, copy a column: csvtk mutate -f id Extract prefix of data as group name (get "A" from "A.1" as group name): csvtk mutate -f sample -n group -p "^(.+?)\." --after sample Sort by multiple keys ( sort ) By single column : csvtk sort -k 1 or csvtk sort -k last_name By multiple columns: csvtk sort -k 1,2 or csvtk sort -k 1 -k 2 or csvtk sort -k last_name,age Sort by number: csvtk sort -k 1:n or csvtk sort -k 1:nr for reverse number Complex sort: csvtk sort -k region -k age:n -k id:nr In natural order: csvtk sort -k chr:N Join multiple files by keys ( join ) All files have same key column: csvtk join -f id file1.csv file2.csv Files have different key columns: csvtk join -f "username;username;name" names.csv phone.csv adress.csv -k Filter by numbers ( filter ) Single field: csvtk filter -f "id>0" Multiple fields : csvtk filter -f "1-3>0" Using --any to print record if any of the field satisfy the condition: csvtk filter -f "1-3>0" --any fuzzy fields : csvtk filter -F -f "A*!=0" Filter rows by awk-like arithmetic/string expressions ( filter2 ) Using field index: csvtk filter2 -f '$3>0' Using column names: csvtk filter2 -f '$id > 0' Both arithmetic and string expressions: csvtk filter2 -f '$id > 3 || $username=="ken"' More complicated: csvtk filter2 -H -t -f '$1 > 2 && $2 % 2 == 0' Plotting plot histogram with data of the second column: csvtk -t plot hist testdata/grouped_data.tsv.gz -f 2 | display plot boxplot with data of the "GC Content" (third) column, group information is the "Group" column. csvtk -t plot box testdata/grouped_data.tsv.gz -g "Group" \ -f "GC Content" --width 3 --title "Box plot" | display plot horiz boxplot with data of the "Length" (second) column, group information is the "Group" column. csvtk -t plot box testdata/grouped_data.tsv.gz -g "Group" -f "Length" \ --height 3 --width 5 --horiz --title "Horiz box plot" | display plot line plot with X-Y data csvtk -t plot line testdata/xy.tsv -x X -y Y -g Group | display plot line plot with X-Y data (where X values are dates or other sortable values) cat testdata/date2value.csv \ | csvtk gather -f 2- -k type -v count \ | csvtk plot line --group-field type -x date -y count --data-field-x-nominal \ -o testdata/figures/line_plot_date.png plot scatter plot with X-Y data csvtk -t plot line testdata/xy.tsv -x X -y Y -g Group --scatter | display Acknowledgements We are grateful to Zhiluo Deng and Li Peng for suggesting features and reporting bugs. Thanks Albert Vilella for feature suggestions, which makes csvtk feature-rich。 Contact Create an issue to report bugs, propose new functions or ask for help. Or leave a comment . License MIT License Starchart About A cross-platform, efficient and practical CSV/TSV toolkit in Golang bioinf.shenwei.me/csvtk Topics golang tsv bioinformatics csv cross-platform command-line tool toolkit Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 1.2k stars Watchers 20 watching Forks 97 forks Report repository Releases 73 csvtk v0.37.0 Latest Apr 8, 2026 + 72 releases Sponsor this project Uh oh! There was an error while loading. Please reload this page . http://paypal.me/shenwei356 Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Go 99.9% Shell 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge csvtk --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +csvtk 0.4.4 0 +------------- +file name : csvtk-0.4.4-0.tar.bz2 +name : csvtk +version : 0.4.4 +build : 0 +build number: 0 +size : 6.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.4.4-0.tar.bz2 +md5 : 7cfc63307cfe1ef858b056ed94450e0a +dependencies: [] + + +csvtk 0.4.5 0 +------------- +file name : csvtk-0.4.5-0.tar.bz2 +name : csvtk +version : 0.4.5 +build : 0 +build number: 0 +size : 6.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.4.5-0.tar.bz2 +md5 : 1bcd0f3325e0328003d3bf63eafda8bb +dependencies: [] + + +csvtk 0.4.6 0 +------------- +file name : csvtk-0.4.6-0.tar.bz2 +name : csvtk +version : 0.4.6 +build : 0 +build number: 0 +size : 6.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.4.6-0.tar.bz2 +md5 : dbfa4626b53bc7a14b5e6007febd7e5c +dependencies: [] + + +csvtk 0.5.0 0 +------------- +file name : csvtk-0.5.0-0.tar.bz2 +name : csvtk +version : 0.5.0 +build : 0 +build number: 0 +size : 6.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.5.0-0.tar.bz2 +md5 : 4b7bcc7d04cf70c76dcc6c19b1a3d573 +dependencies: [] + + +csvtk 0.6.0 0 +------------- +file name : csvtk-0.6.0-0.tar.bz2 +name : csvtk +version : 0.6.0 +build : 0 +build number: 0 +size : 6.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.6.0-0.tar.bz2 +md5 : f0973b50a460d6fa748b829bb66a1585 +dependencies: [] + + +csvtk 0.6.1 0 +------------- +file name : csvtk-0.6.1-0.tar.bz2 +name : csvtk +version : 0.6.1 +build : 0 +build number: 0 +size : 6.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.6.1-0.tar.bz2 +md5 : 63e81c43847941d915a99056097d855b +dependencies: [] + + +csvtk 0.7.0 0 +------------- +file name : csvtk-0.7.0-0.tar.bz2 +name : csvtk +version : 0.7.0 +build : 0 +build number: 0 +size : 6.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.7.0-0.tar.bz2 +md5 : d61ef598f6ab5a2b2baea35dc9379a2b +dependencies: [] + + +csvtk 0.7.1 0 +------------- +file name : csvtk-0.7.1-0.tar.bz2 +name : csvtk +version : 0.7.1 +build : 0 +build number: 0 +size : 6.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.7.1-0.tar.bz2 +md5 : 399681680e58eca8a25cdd937da6acd8 +dependencies: [] + + +csvtk 0.8.0 0 +------------- +file name : csvtk-0.8.0-0.tar.bz2 +name : csvtk +version : 0.8.0 +build : 0 +build number: 0 +size : 6.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.8.0-0.tar.bz2 +md5 : 623eb3c67fc90fec5eb5159ae78f52c3 +dependencies: [] + + +csvtk 0.9.0 0 +------------- +file name : csvtk-0.9.0-0.tar.bz2 +name : csvtk +version : 0.9.0 +build : 0 +build number: 0 +size : 6.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.9.0-0.tar.bz2 +md5 : e2d6fa8e70188068d2924fc594109487 +dependencies: [] + + +csvtk 0.9.1 0 +------------- +file name : csvtk-0.9.1-0.tar.bz2 +name : csvtk +version : 0.9.1 +build : 0 +build number: 0 +size : 5.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.9.1-0.tar.bz2 +md5 : ec934ca57c3517cbc4958137dc85e37b +dependencies: [] + + +csvtk 0.10.0 0 +-------------- +file name : csvtk-0.10.0-0.tar.bz2 +name : csvtk +version : 0.10.0 +build : 0 +build number: 0 +size : 5.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.10.0-0.tar.bz2 +md5 : c2e5f410dfbf9b01cbe496b6ec06c91e +dependencies: [] + + +csvtk 0.11.0 0 +-------------- +file name : csvtk-0.11.0-0.tar.bz2 +name : csvtk +version : 0.11.0 +build : 0 +build number: 0 +size : 5.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.11.0-0.tar.bz2 +md5 : fd2acaf0b2b258f14b754400b1906fdd +dependencies: [] + + +csvtk 0.12.0 0 +-------------- +file name : csvtk-0.12.0-0.tar.bz2 +name : csvtk +version : 0.12.0 +build : 0 +build number: 0 +size : 5.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.12.0-0.tar.bz2 +md5 : 3256f30b0a90231f7b2646d2d9edfb81 +dependencies: [] + + +csvtk 0.13.0 0 +-------------- +file name : csvtk-0.13.0-0.tar.bz2 +name : csvtk +version : 0.13.0 +build : 0 +build number: 0 +size : 5.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.13.0-0.tar.bz2 +md5 : adb028d30ec675c8cecd7a7790023b70 +dependencies: [] + + +csvtk 0.14.0 0 +-------------- +file name : csvtk-0.14.0-0.tar.bz2 +name : csvtk +version : 0.14.0 +build : 0 +build number: 0 +size : 5.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.14.0-0.tar.bz2 +md5 : 45e4385c84535a52fd60794f13f77adb +dependencies: [] + + +csvtk 0.14.0 2 +-------------- +file name : csvtk-0.14.0-2.tar.bz2 +name : csvtk +version : 0.14.0 +build : 2 +build number: 2 +size : 5.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.14.0-2.tar.bz2 +md5 : 4b75cf2a222a64e63704526e90943f9b +timestamp : 2018-07-05 00:45:16 UTC +dependencies: [] + + +csvtk 0.15.0 2 +-------------- +file name : csvtk-0.15.0-2.tar.bz2 +name : csvtk +version : 0.15.0 +build : 2 +build number: 2 +size : 6.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.15.0-2.tar.bz2 +md5 : 591a887bcc73f8891fc5d4d00c1b98f6 +timestamp : 2018-10-12 05:30:23 UTC +dependencies: [] + + +csvtk 0.16.0 1 +-------------- +file name : csvtk-0.16.0-1.tar.bz2 +name : csvtk +version : 0.16.0 +build : 1 +build number: 1 +size : 6.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.16.0-1.tar.bz2 +md5 : b20dc9222a86ebfc65fabcfd063373c5 +timestamp : 2018-12-24 12:59:52 UTC +dependencies: [] + + +csvtk 0.17.0 1 +-------------- +file name : csvtk-0.17.0-1.tar.bz2 +name : csvtk +version : 0.17.0 +build : 1 +build number: 1 +size : 6.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.17.0-1.tar.bz2 +md5 : 7851a6654a3d166520f6221b3f3cb3c2 +timestamp : 2019-01-22 06:09:33 UTC +dependencies: [] + + +csvtk 0.18.0 1 +-------------- +file name : csvtk-0.18.0-1.tar.bz2 +name : csvtk +version : 0.18.0 +build : 1 +build number: 1 +size : 7.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.18.0-1.tar.bz2 +md5 : 080ac2fab5eefc91f8947d84d4fd3468 +timestamp : 2019-05-13 14:04:53 UTC +dependencies: [] + + +csvtk 0.18.1 0 +-------------- +file name : csvtk-0.18.1-0.tar.bz2 +name : csvtk +version : 0.18.1 +build : 0 +build number: 0 +size : 7.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.18.1-0.tar.bz2 +md5 : a947e6083d7e3b8a562c61163f34e1e2 +timestamp : 2019-05-31 17:29:41 UTC +dependencies: [] + + +csvtk 0.18.2 0 +-------------- +file name : csvtk-0.18.2-0.tar.bz2 +name : csvtk +version : 0.18.2 +build : 0 +build number: 0 +size : 7.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.18.2-0.tar.bz2 +md5 : a662e5b9cb6a14cac9db97ab78d43614 +timestamp : 2019-06-06 14:34:50 UTC +dependencies: [] + + +csvtk 0.19.0 0 +-------------- +file name : csvtk-0.19.0-0.tar.bz2 +name : csvtk +version : 0.19.0 +build : 0 +build number: 0 +size : 7.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.19.0-0.tar.bz2 +md5 : 3291c37992b90d628cf0242e2f7bd01a +timestamp : 2019-09-25 15:42:58 UTC +dependencies: [] + + +csvtk 0.19.1 0 +-------------- +file name : csvtk-0.19.1-0.tar.bz2 +name : csvtk +version : 0.19.1 +build : 0 +build number: 0 +size : 7.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.19.1-0.tar.bz2 +md5 : 978c1df8843206162fe0d0c71166a21d +timestamp : 2019-10-17 18:06:21 UTC +dependencies: [] + + +csvtk 0.20.0 0 +-------------- +file name : csvtk-0.20.0-0.tar.bz2 +name : csvtk +version : 0.20.0 +build : 0 +build number: 0 +size : 8.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.20.0-0.tar.bz2 +md5 : 3c3b9dd3d535d4a7e97975efd3b953cd +timestamp : 2020-04-21 14:56:26 UTC +dependencies: [] + + +csvtk 0.21.0 0 +-------------- +file name : csvtk-0.21.0-0.tar.bz2 +name : csvtk +version : 0.21.0 +build : 0 +build number: 0 +size : 7.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.21.0-0.tar.bz2 +md5 : 0e4c159df48f12b2857e8a1828f42f2f +timestamp : 2020-10-30 11:08:05 UTC +dependencies: [] + + +csvtk 0.22.0 0 +-------------- +file name : csvtk-0.22.0-0.tar.bz2 +name : csvtk +version : 0.22.0 +build : 0 +build number: 0 +size : 6.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.22.0-0.tar.bz2 +md5 : c6eca6c203e0fb1f9d7850b75036b390 +timestamp : 2021-01-12 15:33:45 UTC +dependencies: [] + + +csvtk 0.22.0 h9ee0642_1 +----------------------- +file name : csvtk-0.22.0-h9ee0642_1.tar.bz2 +name : csvtk +version : 0.22.0 +build : h9ee0642_1 +build number: 1 +size : 6.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.22.0-h9ee0642_1.tar.bz2 +md5 : b4322dafd9c9448336eeaf4c22ea0a40 +timestamp : 2021-03-24 23:21:38 UTC +dependencies: [] + + +csvtk 0.23.0 h9ee0642_0 +----------------------- +file name : csvtk-0.23.0-h9ee0642_0.tar.bz2 +name : csvtk +version : 0.23.0 +build : h9ee0642_0 +build number: 0 +size : 7.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.23.0-h9ee0642_0.tar.bz2 +md5 : bb7bf06f6b585a3e29043b0400d15dc6 +timestamp : 2021-04-16 05:57:27 UTC +dependencies: [] + + +csvtk 0.24.0 h9ee0642_0 +----------------------- +file name : csvtk-0.24.0-h9ee0642_0.tar.bz2 +name : csvtk +version : 0.24.0 +build : h9ee0642_0 +build number: 0 +size : 7.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/csvtk-0.24.0-h9ee0642_0.tar.bz2 +md5 : 7ae70a2f8f2020f2fa0ecbfddd451935 +timestamp : 2022-08-01 22:21:51 UTC +dependencies: [] + + +csvtk 0.25.0 h9ee0642_0 +----------------------- +file name : csvtk-0.25.0-h9ee0642_0.tar.bz2 +name : csvtk +version : 0.25.0 +build : h9ee0642_0 +build number: 0 +size : 7.9 MB +license : MIT +subdir : linux-64 +url : https diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/deblur.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/deblur.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..08dbe2ef3104e103d1dbb8b59a796463a5973fae --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/deblur.manual_bundle.txt @@ -0,0 +1,290 @@ +# Tool: deblur +software_name: deblur +tier: T1 +domain: t1_backfill_overall +downloads: 537964 +summary: Deblur is a greedy deconvolution algorithm based on known read error profiles. +description: Deblur is a greedy deconvolution algorithm based on known read error profiles. +dependencies: biom-format, click, h5py, mafft >=7.394, python >=3, scikit-bio >=0.5.0, sortmerna 2.0, vsearch >=2.0.3 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/biocore/deblur +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/biocore/deblur +GitHub - biocore/deblur: Deblur is a greedy deconvolution algorithm based on known read error profiles. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} biocore / deblur Public Notifications You must be signed in to change notification settings Fork 40 Star 99 Code Issues 14 Pull requests 12 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights biocore/deblur master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 495 Commits 495 Commits .github/ workflows .github/ workflows deblur deblur images images scripts scripts .coveragerc .coveragerc .gitignore .gitignore ChangeLog.md ChangeLog.md LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md setup.py setup.py View all files Repository files navigation README BSD-3-Clause license Deblur Deblur is a greedy deconvolution algorithm for amplicon sequencing based on Illumina Miseq/Hiseq error profiles. Install Deblur requires Python 3.8. If Python 3.8 is not installed, you can create a conda environment for Deblur using: conda create -n deblurenv python=3.8 numpy and activate it using: source activate deblurenv (note you will need to activate this environment every time you want to use Deblur) Install Deblur dependencies and Deblur itself: conda install -c bioconda -c biocore VSEARCH>=2.7.0 MAFFT>=7.394 SortMeRNA=2.0 biom-format deblur N.B. Some dependencies are version restricted at the moment but for different reasons. SortMeRNA 2.1 has a different output format which Deblur is not compatible with yet. A review of the changelog did not reveal any remarkable notes (e.g., bugs) about the reasons for the differences. In testing, the differences affected <0.1% of the sOTUs. As a precaution, we are advising the use of these specific versions for consistency with the manuscript. Example usage We recommend using Deblur via the QIIME2 plugin q2-deblur . Examples of its use can be found within the plugin itself. However, Deblur itself does not depend on QIIME2. If you are running Deblur directly, we recommend focusing on the workflow subcommand. Detailed help can be obtained with: deblur workflow --help As a simple example, let's specify an input FASTA file, an output path and a sequence trim length of 150. This command will trim all sequences in all_samples.fna to 150nt in length; any read that is shorter will be omitted. This execution mode assumes that all_samples.fna is demultiplexed such that the sequence IDs are compatible with QIIME 1.9.1. On completion, a new directory output will be created with multiple output files (see the Input and Output Files section for more detail). deblur workflow --seqs-fp all_samples.fna --output-dir output -t 150 If starting from a barcode and read file, you can first use the qiime split_libraries_fastq.py command (we recommend using -q 19 to remove low quality reads): split_libraries_fastq.py -i XXX_R1_001.fastq -m map.txt -o split -b XXXX_I1_001.fastq -q 19 The resulting split/seqs.fna file can be used as the input to the deblur workflow. Input and Output Files The input to Deblur workflow is a directory of FASTA or FASTQ files (1 per sample) or a single demultiplexed FASTA or FASTQ file. These files can be gzip'd. The output directory will contain three BIOM tables in which the observation IDs are the Deblurred sequences. The outputs are contingent on the reference databases used and a more focused discussion on them is in the subsequent README section titled "Positive and Negative Filtering." The output files are as follows: reference-hit.biom : contains only Deblurred reads matching the positive filtering database. By default, a reference composed of 16S sequences is used, and this resulting table will contain only those reads which recruit at a coarse level to it will be retained. Reads are also filtered against the negative reference, which by default will remove any read which appears to be PhiX or adapter. reference-hit.seqs.fa : a fasta file containing all the sequences in reference-hit.biom reference-non-hit.biom : contains only Deblurred reads that did not align to the positive filtering database. Negative filtering is also appied to this table, so by default, PhiX and adapter are removed. reference-non-hit.seqs.fa : a fasta file containing all the sequences in reference-non-hit.biom all.biom : contains all Deblurred reads. This file represents the union of the "reference-hit.biom" and "reference-non-hit.biom" tables. all.seqs.fa : a fasta file containing all the sequences in all.biom Important options Deblur cannot associate sequences with different lengths. As such, trimming reads is a required first step in the Deblur pipeline. The sequence trim length is specified by the -t NNN flag, where NNN denotes the length all sequences will be trimmed to. All reads shorter than this length will be discarded. If the input data are known to have a common length, it is possible to disable trimming by specifying a trim value of -1 . Deblur can operate in parallel. The number of threads can be specified by the -O NNN flag (default it 1). Running more threads than available cores is not advised. Positive and Negative Filtering Deblur uses two types of filtering on the sequences: Negative mode - removes known artifact sequences (i.e. sequences aligning to PhiX or Adapter with >=95% identity and coverage). Positive mode - keeps only sequences similar to a reference database (by default known 16S sequences ). SortMeRNA is used, and any sequence with an e-value <= 10 is retained. Deblur also outputs a BIOM table without this positive filtering step (named all.biom). The FASTA files for both of these filtering steps can be supplied via the --neg-ref-fp and --pos-ref-fp options. By default, the negative database is composed of PhiX and adapter sequence and the positive database of known 16S sequences. Deblur uses negative mode filtering to remove known artifact (i.e. PhiX and Adapter sequences) prior to denoising. The output of Deblur contains three files: all.biom, which includes all sOTUs, reference-hit.biom, which contains the output of positive filtering of the sOTUs (default only sOTUs similar to 16S sequences), and reference-non-hit.biom, which contains only sOTUs failing the positive filtering (default only non-16S sOTUs). Minimal Reads Filtering Deblur runs on each sample independently. However, sometimes there is also additional information based on the total number of times an sOTU is observed in all samples (e.g. an sOTU which is observed only in one sample at low read count is more likely to be pcr/read error as opposed to an sOTU present in many samples). The --min-reads option allows to use this information by removing sOTUs with a total read count (across all samples) lower than the given threshold. The default value is set to 10, and should be useful for most cases. However, if such filtering is not wanted (e.g. if all samples in an experiment are expected not to contain the same bacteria, so no additional information is gained by combining the information from multiple samples), --min-reads can be set to 0 to skip this final filtering step. Troubleshooting Mac users: if you get the following error: RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are Working with Matplotlib in a virtual enviroment see 'Working with Matplotlib in Virtual environments' in the Matplotlib FAQ You can solve it by the following commands: cd ~/.matplotlib echo "backend: TkAgg" >> ~/.matplotlib/matplotlibrc "Too many open files" : This error indicates deblur is trying to split a single fasta/q file into per-sample files, and the OS does not allow so many open simultaneous open files. Current solution is to use the qiime1.9 command split_sequence_file_on_sample_ids.py or the equivalent qiime2 command to split the single fasta/q file into a directory of per sample fasta/q files and then run deblur with this directory as the input to deblur (--seqs-fp). Code Development Note Some of the code in the package deblur has been derived from QIIME . The contributors to these specific QIIME modules have granted permission for this porting to take place and put under the BSD license. About Deblur is a greedy deconvolution algorithm based on known read error profiles. Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 99 stars Watchers 17 watching Forks 40 forks Report repository Releases 8 Version 1.1.1: Bump dependency support Latest Jun 2, 2022 + 7 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge deblur --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +deblur 1.0.4 py35_0 +------------------- +file name : deblur-1.0.4-py35_0.tar.bz2 +name : deblur +version : 1.0.4 +build : py35_0 +build number: 0 +size : 2.4 MB +license : BSD license +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/deblur-1.0.4-py35_0.tar.bz2 +md5 : f5acc1aac55ea0260e546d3d1d09fc8e +dependencies: + - biom-format + - biom-format + - click + - h5py + - mafft ==7.310 + - python 3.5* + - scikit-bio >=0.5.0 + - sortmerna ==2.0 + - vsearch ==2.0.3 + + +deblur 1.0.4 py35_1 +------------------- +file name : deblur-1.0.4-py35_1.tar.bz2 +name : deblur +version : 1.0.4 +build : py35_1 +build number: 1 +size : 2.4 MB +license : BSD license +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/deblur-1.0.4-py35_1.tar.bz2 +md5 : d77c6e396f40134167ac222328f21ad9 +dependencies: + - biom-format + - biom-format + - click + - h5py + - mafft ==7.310 + - python 3.5* + - scikit-bio >=0.5.0 + - sortmerna ==2.0 + - vsearch >=2.0.3 + + +deblur 1.0.4 py35_2 +------------------- +file name : deblur-1.0.4-py35_2.tar.bz2 +name : deblur +version : 1.0.4 +build : py35_2 +build number: 2 +size : 2.4 MB +license : BSD license +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/deblur-1.0.4-py35_2.tar.bz2 +md5 : 85bcf2c814a87a61bcac173f56d3d966 +timestamp : 2018-06-25 04:18:08 UTC +dependencies: + - biom-format + - click + - h5py + - mafft 7.310 + - python >=3.5,<3.6.0a0 + - scikit-bio >=0.5.0 + - sortmerna 2.0 + - vsearch >=2.0.3 + + +deblur 1.0.4 py36_0 +------------------- +file name : deblur-1.0.4-py36_0.tar.bz2 +name : deblur +version : 1.0.4 +build : py36_0 +build number: 0 +size : 2.4 MB +license : BSD license +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/deblur-1.0.4-py36_0.tar.bz2 +md5 : e8deafb42ce78d2dafa5764ec308a6b6 +dependencies: + - biom-format + - biom-format + - click + - h5py + - mafft ==7.310 + - python 3.6* + - scikit-bio >=0.5.0 + - sortmerna ==2.0 + - vsearch ==2.0.3 + + +deblur 1.0.4 py36_1 +------------------- +file name : deblur-1.0.4-py36_1.tar.bz2 +name : deblur +version : 1.0.4 +build : py36_1 +build number: 1 +size : 2.4 MB +license : BSD license +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/deblur-1.0.4-py36_1.tar.bz2 +md5 : 54908d79c9c41519650861a1bfd60089 +dependencies: + - biom-format + - biom-format + - click + - h5py + - mafft ==7.310 + - python 3.6* + - scikit-bio >=0.5.0 + - sortmerna ==2.0 + - vsearch >=2.0.3 + + +deblur 1.0.4 py36_2 +------------------- +file name : deblur-1.0.4-py36_2.tar.bz2 +name : deblur +version : 1.0.4 +build : py36_2 +build number: 2 +size : 2.4 MB +license : BSD license +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/deblur-1.0.4-py36_2.tar.bz2 +md5 : a99eb253a36a108e8010545cd04bf426 +timestamp : 2018-06-25 04:20:47 UTC +dependencies: + - biom-format + - click + - h5py + - mafft 7.310 + - python >=3.6,<3.7.0a0 + - scikit-bio >=0.5.0 + - sortmerna 2.0 + - vsearch >=2.0.3 + + +deblur 1.1.0 py35_0 +------------------- +file name : deblur-1.1.0-py35_0.tar.bz2 +name : deblur +version : 1.1.0 +build : py35_0 +build number: 0 +size : 2.4 MB +license : BSD license +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/deblur-1.1.0-py35_0.tar.bz2 +md5 : 6fc3753aebf7b165f48c79e06bbf2403 +timestamp : 2018-10-23 06:05:01 UTC +dependencies: + - biom-format + - click + - h5py + - mafft 7.310 + - python >=3.5,<3.6.0a0 + - scikit-bio >=0.5.0 + - sortmerna 2.0 + - vsearch >=2.0.3 + + +deblur 1.1.0 py36_0 +------------------- +file name : deblur-1.1.0-py36_0.tar.bz2 +name : deblur +version : 1.1.0 +build : py36_0 +build number: 0 +size : 2.4 MB +license : BSD license +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/deblur-1.1.0-py36_0.tar.bz2 +md5 : 2431b2f0c200cb9b1dc69c357678204f +timestamp : 2018-10-23 06:09:07 UTC +dependencies: + - biom-format + - click + - h5py + - mafft 7.310 + - python >=3.6,<3.7.0a0 + - scikit-bio >=0.5.0 + - sortmerna 2.0 + - vsearch >=2.0.3 + + +deblur 1.1.0 py_1 +----------------- +file name : deblur-1.1.0-py_1.tar.bz2 +name : deblur +version : 1.1.0 +build : py_1 +build number: 1 +size : 2.3 MB +license : BSD license +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/deblur-1.1.0-py_1.tar.bz2 +md5 : 8238f45f70ba6c8b1bc1d6db20cca3ce +timestamp : 2019-10-27 15:54:09 UTC +dependencies: + - biom-format + - click + - h5py + - mafft 7.310 + - python >=3 + - scikit-bio >=0.5.0 + - sortmerna 2.0 + - vsearch >=2.0.3 + + +deblur 1.1.0 py_2 +----------------- +file name : deblur-1.1.0-py_2.tar.bz2 +name : deblur +version : 1.1.0 +build : py_2 +build number: 2 +size : 2.3 MB +license : BSD license +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/deblur-1.1.0-py_2.tar.bz2 +md5 : febcbc38e925f5750101dea4dfa84ff8 +timestamp : 2020-04-08 18:24:38 UTC +dependencies: + - biom-format + - click + - h5py + - mafft >=7.394 + - python >=3 + - scikit-bio >=0.5.0 + - sortmerna 2.0 + - vsearch >=2.0.3 + + +deblur 1.1.1 pyhdfd78af_0 +------------------------- +file name : deblur-1.1.1-pyhdfd78af_0.tar.bz2 +name : deblur +version : 1.1.1 +build : pyhdfd78af_0 +build number: 0 +size : 2.3 MB +license : BSD license +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/deblur-1.1.1-pyhdfd78af_0.tar.bz2 +md5 : fa653934452b09d43c8c1881c07a9573 +timestamp : 2022-06-03 08:07:47 UTC +dependencies: + - biom-format + - click + - h5py + - mafft >=7.394 + - python >=3 + - scikit-bio >=0.5.0 + - sortmerna 2.0 + - vsearch >=2.0.3 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/dendropy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/dendropy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2383de7e86386e5077b03b31827b6401d18ee61d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/dendropy.manual_bundle.txt @@ -0,0 +1,495 @@ +# Tool: dendropy +software_name: dendropy +tier: T1 +domain: t1_backfill_overall +downloads: 840779 +summary: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. +description: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. +dependencies: python >=3.6 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/jeetsukumaran/DendroPy +doc_url: https://dendropy.org +dev_url: https://github.com/jeetsukumaran/DendroPy + +## CLI Help Source +module:dendropy +## CLI Help Content +$ conda run -n bioenv_cli python -m dendropy --help +[rc=0] +DendroPy version : DendroPy 5.0.8 () +DendroPy location : /225040511/miniconda3/envs/bioenv_cli/lib/python3.10/site-packages/dendropy +Python version : 3.10.8 | packaged by conda-forge | (main, Nov 22 2022, 08:23:14) [GCC 10.4.0] +Python executable : /225040511/miniconda3/envs/bioenv_cli/bin/python +Python site packages : ['/225040511/miniconda3/envs/bioenv_cli/lib/python3.10/site-packages'] + + + +## URL Docs Extract +### https://github.com/jeetsukumaran/DendroPy +GitHub - jeetsukumaran/DendroPy: A Python library for phylogenetic scripting, simulation, data processing and manipulation. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} jeetsukumaran / DendroPy Public Notifications You must be signed in to change notification settings Fork 58 Star 233 Code Issues 20 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights jeetsukumaran/DendroPy main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 4,837 Commits 4,837 Commits .github .github docs docs joss joss notes notes src/ dendropy src/ dendropy tests tests .ctags .ctags .gitignore .gitignore AUTHORS.rst AUTHORS.rst CHANGES.rst CHANGES.rst CITATION.cff CITATION.cff CODE_OF_CONDUCT.rst CODE_OF_CONDUCT.rst LICENSE.rst LICENSE.rst MANIFEST.in MANIFEST.in NOTICES.rst NOTICES.rst README.md README.md bumpver.toml bumpver.toml clean.sh clean.sh lint.sh lint.sh pypi_release.sh pypi_release.sh setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README BSD-3-Clause license automated tests: package version: documentation: test coverage: DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting "glue" that assembles and drives such pipelines. The primary home page for DendroPy, with detailed tutorials and documentation, is at: https://jeetsukumaran.github.io/DendroPy/ DendroPy is also hosted in the official Python Packaging Index (PyPI): http://pypi.org/project/DendroPy/ Requirements and Installation The current version of DendroPy requires Python 3. You can install DendroPy by running:: $ python -m pip install dendropy For Conda users, DendroPy can be installed from the conda-forge channel: $ conda install -c conda-forge dendropy More information is available here: https://jeetsukumaran.github.io/DendroPy/downloading.html Documentation Full documentation is available here: https://jeetsukumaran.github.io/DendroPy/ This includes: A comprehensive "getting started" primer . API documentation . Descriptions of data formats supported for reading/writing . Guidance for reporting issues , submitting feature requests , and contributing to DendroPy . and more. Citing If you use any portion of DendroPy v5 in your research, please cite it as: Moreno, M. A., Holder, M. T., & Sukumaran, J. (2024). DendroPy 5: a mature Python library for phylogenetic computing. Journal of Open Source Software, 9(101), 6943, https://doi.org/10.21105/joss.06943 For BibTex users: @misc { dendropy5 , doi = { 10.21105/joss.06943 } , url = { https://doi.org/10.21105/joss.06943 } , year = { 2024 } , publisher = { The Open Journal } , volume = { 9 } , number = { 101 } , pages = { 6943 } , author = { Matthew Andres Moreno and Mark T. Holder and Jeet Sukumaran } , title = { DendroPy 5: a mature Python library for phylogenetic computing } , journal = { Journal of Open Source Software } } Earlier DendroPy versions can be cited as: Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571. https://doi.org/10.1093/bioinformatics/btq228 Consider also leaving a star on GitHub ! License and Warranty Please see the file "LICENSE.rst" for details. Developers Jeet Sukumaran Mark Holder Matthew Andres Moreno About A Python library for phylogenetic scripting, simulation, data processing and manipulation. pypi.org/project/DendroPy/. Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Stars 233 stars Watchers 11 watching Forks 58 forks Report repository Releases 89 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 85.1% Perl 14.2% Other 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/jeetsukumaran/DendroPy +GitHub - jeetsukumaran/DendroPy: A Python library for phylogenetic scripting, simulation, data processing and manipulation. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} jeetsukumaran / DendroPy Public Notifications You must be signed in to change notification settings Fork 58 Star 233 Code Issues 20 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights jeetsukumaran/DendroPy main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 4,837 Commits 4,837 Commits .github .github docs docs joss joss notes notes src/ dendropy src/ dendropy tests tests .ctags .ctags .gitignore .gitignore AUTHORS.rst AUTHORS.rst CHANGES.rst CHANGES.rst CITATION.cff CITATION.cff CODE_OF_CONDUCT.rst CODE_OF_CONDUCT.rst LICENSE.rst LICENSE.rst MANIFEST.in MANIFEST.in NOTICES.rst NOTICES.rst README.md README.md bumpver.toml bumpver.toml clean.sh clean.sh lint.sh lint.sh pypi_release.sh pypi_release.sh setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README BSD-3-Clause license automated tests: package version: documentation: test coverage: DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting "glue" that assembles and drives such pipelines. The primary home page for DendroPy, with detailed tutorials and documentation, is at: https://jeetsukumaran.github.io/DendroPy/ DendroPy is also hosted in the official Python Packaging Index (PyPI): http://pypi.org/project/DendroPy/ Requirements and Installation The current version of DendroPy requires Python 3. You can install DendroPy by running:: $ python -m pip install dendropy For Conda users, DendroPy can be installed from the conda-forge channel: $ conda install -c conda-forge dendropy More information is available here: https://jeetsukumaran.github.io/DendroPy/downloading.html Documentation Full documentation is available here: https://jeetsukumaran.github.io/DendroPy/ This includes: A comprehensive "getting started" primer . API documentation . Descriptions of data formats supported for reading/writing . Guidance for reporting issues , submitting feature requests , and contributing to DendroPy . and more. Citing If you use any portion of DendroPy v5 in your research, please cite it as: Moreno, M. A., Holder, M. T., & Sukumaran, J. (2024). DendroPy 5: a mature Python library for phylogenetic computing. Journal of Open Source Software, 9(101), 6943, https://doi.org/10.21105/joss.06943 For BibTex users: @misc { dendropy5 , doi = { 10.21105/joss.06943 } , url = { https://doi.org/10.21105/joss.06943 } , year = { 2024 } , publisher = { The Open Journal } , volume = { 9 } , number = { 101 } , pages = { 6943 } , author = { Matthew Andres Moreno and Mark T. Holder and Jeet Sukumaran } , title = { DendroPy 5: a mature Python library for phylogenetic computing } , journal = { Journal of Open Source Software } } Earlier DendroPy versions can be cited as: Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571. https://doi.org/10.1093/bioinformatics/btq228 Consider also leaving a star on GitHub ! License and Warranty Please see the file "LICENSE.rst" for details. Developers Jeet Sukumaran Mark Holder Matthew Andres Moreno About A Python library for phylogenetic scripting, simulation, data processing and manipulation. pypi.org/project/DendroPy/. Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Stars 233 stars Watchers 11 watching Forks 58 forks Report repository Releases 89 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 85.1% Perl 14.2% Other 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge dendropy --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +dendropy 3.12.3 0 +----------------- +file name : dendropy-3.12.3-0.tar.bz2 +name : dendropy +version : 3.12.3 +build : 0 +build number: 0 +size : 5.5 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-3.12.3-0.tar.bz2 +md5 : 49ea2c484302d5855ca930543e6e0bed +dependencies: + - python >=2.7,<3 + + +dendropy 3.12.3 py_1 +-------------------- +file name : dendropy-3.12.3-py_1.tar.bz2 +name : dendropy +version : 3.12.3 +build : py_1 +build number: 1 +size : 3.8 MB +license : BSD License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-3.12.3-py_1.tar.bz2 +md5 : e26d9ca48ad5b542856bc90790ba9557 +timestamp : 2018-06-25 04:46:44 UTC +dependencies: + - python >=2.7,<3 + + +dendropy 4.0.3 py27_0 +--------------------- +file name : dendropy-4.0.3-py27_0.tar.bz2 +name : dendropy +version : 4.0.3 +build : py27_0 +build number: 0 +size : 14.8 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-4.0.3-py27_0.tar.bz2 +md5 : 8ab0872c98663be29e3445214f170e27 +dependencies: + - python 2.7* + - setuptools + - setuptools + + +dendropy 4.0.3 py34_0 +--------------------- +file name : dendropy-4.0.3-py34_0.tar.bz2 +name : dendropy +version : 4.0.3 +build : py34_0 +build number: 0 +size : 14.8 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-4.0.3-py34_0.tar.bz2 +md5 : f93bcf5800ce7f7243435c8b4c06e754 +dependencies: + - python 3.4* + - setuptools + - setuptools + + +dendropy 4.0.3 py35_0 +--------------------- +file name : dendropy-4.0.3-py35_0.tar.bz2 +name : dendropy +version : 4.0.3 +build : py35_0 +build number: 0 +size : 14.8 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-4.0.3-py35_0.tar.bz2 +md5 : bac09bc320cb2f475b8ffddad93aedc0 +dependencies: + - python 3.5* + - setuptools + - setuptools + + +dendropy 4.1.0 py27_0 +--------------------- +file name : dendropy-4.1.0-py27_0.tar.bz2 +name : dendropy +version : 4.1.0 +build : py27_0 +build number: 0 +size : 15.0 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-4.1.0-py27_0.tar.bz2 +md5 : 227a72b137e2e10d2e10feb5489a520f +dependencies: + - python 2.7* + - setuptools + + +dendropy 4.1.0 py34_0 +--------------------- +file name : dendropy-4.1.0-py34_0.tar.bz2 +name : dendropy +version : 4.1.0 +build : py34_0 +build number: 0 +size : 15.0 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-4.1.0-py34_0.tar.bz2 +md5 : 9d699f3c02ac11ccf6833967cf6bff3f +dependencies: + - python 3.4* + - setuptools + + +dendropy 4.1.0 py35_0 +--------------------- +file name : dendropy-4.1.0-py35_0.tar.bz2 +name : dendropy +version : 4.1.0 +build : py35_0 +build number: 0 +size : 15.0 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-4.1.0-py35_0.tar.bz2 +md5 : ad3edbc9fff3b3bba6569a363c1b80ad +dependencies: + - python 3.5* + - setuptools + + +dendropy 4.1.0 py36_0 +--------------------- +file name : dendropy-4.1.0-py36_0.tar.bz2 +name : dendropy +version : 4.1.0 +build : py36_0 +build number: 0 +size : 15.0 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-4.1.0-py36_0.tar.bz2 +md5 : bbcc84c31d7f2ebe37f34c101150e56c +dependencies: + - python 3.6* + - setuptools + + +dendropy 4.2.0 py27_0 +--------------------- +file name : dendropy-4.2.0-py27_0.tar.bz2 +name : dendropy +version : 4.2.0 +build : py27_0 +build number: 0 +size : 15.2 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-4.2.0-py27_0.tar.bz2 +md5 : d82e3bde78115cd4f40d294e6b6ca6be +dependencies: + - python 2.7* + + +dendropy 4.2.0 py35_0 +--------------------- +file name : dendropy-4.2.0-py35_0.tar.bz2 +name : dendropy +version : 4.2.0 +build : py35_0 +build number: 0 +size : 15.2 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-4.2.0-py35_0.tar.bz2 +md5 : 0b969e4ba630b8b9cb995341d5bdc54c +dependencies: + - python 3.5* + + +dendropy 4.2.0 py36_0 +--------------------- +file name : dendropy-4.2.0-py36_0.tar.bz2 +name : dendropy +version : 4.2.0 +build : py36_0 +build number: 0 +size : 15.2 MB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dendropy-4.2.0-py36_0.tar.bz2 +md5 : 524d24faa83a9a4186742a197e94e222 +dependencies: + - python 3.6* + + +dendropy 4.2.0 py_2 +------------------- +file name : dendropy-4.2.0-py_2.tar.bz2 +name : dendropy +version : 4.2.0 +build : py_2 +build number: 2 +size : 11.4 MB +license : BSD License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-4.2.0-py_2.tar.bz2 +md5 : 7e3ac6dd4d48df17da9f498a227fb2b2 +timestamp : 2018-06-25 04:41:12 UTC +dependencies: + - python + + +dendropy 4.4.0 py_0 +------------------- +file name : dendropy-4.4.0-py_0.tar.bz2 +name : dendropy +version : 4.4.0 +build : py_0 +build number: 0 +size : 298 KB +license : BSD License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-4.4.0-py_0.tar.bz2 +md5 : 5c5de712ffc9e0cd4d73bb7af8a6f49e +timestamp : 2018-06-27 13:18:52 UTC +dependencies: + - python + + +dendropy 4.4.0 py_1 +------------------- +file name : dendropy-4.4.0-py_1.tar.bz2 +name : dendropy +version : 4.4.0 +build : py_1 +build number: 1 +size : 299 KB +license : BSD License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-4.4.0-py_1.tar.bz2 +md5 : b63b8c63e22e367887b3de5dee745622 +timestamp : 2019-04-10 12:29:48 UTC +dependencies: + - python + + +dendropy 4.4.0 pyh864c0ab_2 +--------------------------- +file name : dendropy-4.4.0-pyh864c0ab_2.tar.bz2 +name : dendropy +version : 4.4.0 +build : pyh864c0ab_2 +build number: 2 +size : 298 KB +license : BSD License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-4.4.0-pyh864c0ab_2.tar.bz2 +md5 : 2eb236866beacece629cd46694f88932 +timestamp : 2020-07-26 02:47:42 UTC +dependencies: + - python + + +dendropy 4.5.1 pyh3252c3a_0 +--------------------------- +file name : dendropy-4.5.1-pyh3252c3a_0.tar.bz2 +name : dendropy +version : 4.5.1 +build : pyh3252c3a_0 +build number: 0 +size : 304 KB +license : BSD License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-4.5.1-pyh3252c3a_0.tar.bz2 +md5 : 0bf0c561f402e3f9728d04d5562c903b +timestamp : 2020-10-24 18:18:28 UTC +dependencies: + - python + + +dendropy 4.5.2 pyh3252c3a_0 +--------------------------- +file name : dendropy-4.5.2-pyh3252c3a_0.tar.bz2 +name : dendropy +version : 4.5.2 +build : pyh3252c3a_0 +build number: 0 +size : 308 KB +license : BSD License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-4.5.2-pyh3252c3a_0.tar.bz2 +md5 : 3b762d50e12b28d30e5f58c832137ed6 +timestamp : 2021-02-12 11:35:28 UTC +dependencies: + - python + + +dendropy 4.6.0 pyh7cba7a3_0 +--------------------------- +file name : dendropy-4.6.0-pyh7cba7a3_0.tar.bz2 +name : dendropy +version : 4.6.0 +build : pyh7cba7a3_0 +build number: 0 +size : 315 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-4.6.0-pyh7cba7a3_0.tar.bz2 +md5 : 03d765d1574415e2bf74f03be0781e5d +timestamp : 2023-04-22 19:45:32 UTC +dependencies: + - python + + +dendropy 4.6.1 pyhdfd78af_0 +--------------------------- +file name : dendropy-4.6.1-pyhdfd78af_0.tar.bz2 +name : dendropy +version : 4.6.1 +build : pyhdfd78af_0 +build number: 0 +size : 325 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-4.6.1-pyhdfd78af_0.tar.bz2 +md5 : e6f709c0a6e678d1a7566c8e1828a199 +timestamp : 2023-06-17 04:56:21 UTC +dependencies: + - python >=3.7 + + +dendropy 5.0.0 pyhdfd78af_0 +--------------------------- +file name : dendropy-5.0.0-pyhdfd78af_0.tar.bz2 +name : dendropy +version : 5.0.0 +build : pyhdfd78af_0 +build number: 0 +size : 323 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-5.0.0-pyhdfd78af_0.tar.bz2 +md5 : bf452df42590601965400ec82c3c96eb +timestamp : 2024-05-24 15:15:15 UTC +dependencies: + - python >=3.7 + + +dendropy 5.0.1 pyhdfd78af_0 +--------------------------- +file name : dendropy-5.0.1-pyhdfd78af_0.tar.bz2 +name : dendropy +version : 5.0.1 +build : pyhdfd78af_0 +build number: 0 +size : 325 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-5.0.1-pyhdfd78af_0.tar.bz2 +md5 : faedd521370c8186ed8bdc401ac4e139 +timestamp : 2024-06-02 08:20:12 UTC +dependencies: + - python >=3.7 + + +dendropy 5.0.2 pyhdfd78af_0 +--------------------------- +file name : dendropy-5.0.2-pyhdfd78af_0.tar.bz2 +name : dendropy +version : 5.0.2 +build : pyhdfd78af_0 +build number: 0 +size : 323 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-5.0.2-pyhdfd78af_0.tar.bz2 +md5 : d1f94634f098933733f55aa51cd31291 +timestamp : 2025-01-28 20:05:10 UTC +dependencies: + - python >=3.6 + + +dendropy 5.0.3 pyhdfd78af_0 +--------------------------- +file name : dendropy-5.0.3-pyhdfd78af_0.tar.bz2 +name : dendropy +version : 5.0.3 +build : pyhdfd78af_0 +build number: 0 +size : 326 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-5.0.3-pyhdfd78af_0.tar.bz2 +md5 : 269ecebbcef6c2de2b8ad2658d9255f8 +timestamp : 2025-02-05 18:28:33 UTC +dependencies: + - python >=3.6 + + +dendropy 5.0.4 pyhdfd78af_0 +--------------------------- +file name : dendropy-5.0.4-pyhdfd78af_0.tar.bz2 +name : dendropy +version : 5.0.4 +build : pyhdfd78af_0 +build number: 0 +size : 325 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-5.0.4-pyhdfd78af_0.tar.bz2 +md5 : 94ee9c27e653fd60fca000a482fd0b97 +timestamp : 2025-02-05 23:18:07 UTC +dependencies: + - python >=3.6 + + +dendropy 5.0.5 pyhdfd78af_0 +--------------------------- +file name : dendropy-5.0.5-pyhdfd78af_0.tar.bz2 +name : dendropy +version : 5.0.5 +build : pyhdfd78af_0 +build number: 0 +size : 325 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dendropy-5.0.5-pyhdfd78af_0.tar.bz2 +md5 : 60dec518838025c6a23fb42a77c1bcc2 +timestamp : 2025-02-06 04:29:24 UTC +dependencies: + - python >=3.6 + + +dendropy 5.0.6 pyhdfd78af_0 +--------------------------- +file name : dendropy-5.0.6-pyhdfd78af_0.tar.bz2 +name : dendropy +version : 5.0.6 +build : pyhdfd78af_0 +build number: 0 +size : 326 KB +license : BSD-3-Clause +subdir : noar diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/diamond.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/diamond.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e2713f100ef6db833a69718a342c1ab2ccc5cb0 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/diamond.manual_bundle.txt @@ -0,0 +1,512 @@ +# Tool: diamond +software_name: diamond +tier: T1 +domain: t1_backfill_overall +downloads: 2063582 +summary: Accelerated BLAST compatible local sequence aligner. +description: Accelerated BLAST compatible local sequence aligner. +dependencies: libgcc >=14, libsqlite >=3.52.0,<4.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/bbuchfink/diamond +doc_url: https://github.com/bbuchfink/diamond/wiki +dev_url: https://github.com/bbuchfink/diamond + +## CLI Help Source +cli:diamond +## CLI Help Content +$ conda run -n bioenv_cli diamond --help +[rc=0] +diamond v2.1.10.164 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen +Documentation, support and updates available at http://www.diamondsearch.org +Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) + +Syntax: diamond COMMAND [OPTIONS] + +Commands: +makedb Build DIAMOND database from a FASTA file +prepdb Prepare BLAST database for use with Diamond +blastp Align amino acid query sequences against a protein reference database +blastx Align DNA query sequences against a protein reference database +cluster Cluster protein sequences +linclust Cluster protein sequences in linear time +realign Realign clustered sequences against their centroids +recluster Recompute clustering to fix errors +reassign Reassign clustered sequences to the closest centroid +view View DIAMOND alignment archive (DAA) formatted file +merge-daa Merge DAA files +help Produce help message +version Display version information +getseq Retrieve sequences from a DIAMOND database file +dbinfo Print information about a DIAMOND database file +test Run regression tests +makeidx Make database index +greedy-vertex-cover Compute greedy vertex cover + +Possible [OPTIONS] for COMMAND can be seen with syntax: diamond COMMAND + +Online documentation at http://www.diamondsearch.org + + + +## URL Docs Extract +### https://github.com/bbuchfink/diamond/wiki +Home · bbuchfink/diamond Wiki · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bbuchfink / diamond Public Uh oh! There was an error while loading. Please reload this page . Notifications You must be signed in to change notification settings Fork 195 Star 1.3k Code Issues 213 Pull requests 0 Discussions Actions Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Wiki Security and quality Insights Home Jump to bottom Benjamin Buchfink edited this page Mar 7, 2026 · 45 revisions Synopsis # downloading the tool wget http://github.com/bbuchfink/diamond/releases/download/v2.1.24/diamond-linux64.tar.gz tar xzf diamond-linux64.tar.gz # creating a diamond-formatted database file ./diamond makedb --in reference.fasta -d reference # running a search in blastp mode ./diamond blastp -d reference -q queries.fasta -o matches.tsv # running a search in blastx mode ./diamond blastx -d reference -q reads.fasta -o matches.tsv # downloading and using a BLAST database (use DIAMOND >= v2.1.14) update_blastdb.pl --decompress --blastdb_version 5 swissprot ./diamond blastp -d swissprot -q queries.fasta -o matches.tsv # running fast clustering with linear scaling (30% identity threshold) diamond linclust -d reference.fasta -o clusters.tsv --approx-id 30 -M 64G # running sensitive clustering using all-vs-all alignment (30% identity threshold) diamond cluster -d reference.fasta -o clusters.tsv --approx-id 30 -M 64G Important Repeat masking is applied to the query and reference sequences by default . To disable it, use --masking 0 . DIAMOND is optimized for large input files of >1 million proteins. Naturally the tool can be used for smaller files as well, but the algorithm will not reach its full efficiency. The program may use quite a lot of memory and also temporary disk space. Should the program fail due to running out of either one, you need to set a lower value for the block size parameter -b . The sensitivity can be adjusted using the options --faster , --fast , --mid-sensitive , --sensitive , --more-sensitive , --very-sensitive and --ultra-sensitive . Toggle table of contents Pages 17 Loading Home Synopsis Loading 1. Tutorial Uh oh! There was an error while loading. Please reload this page . Loading 2. Installation Uh oh! There was an error while loading. Please reload this page . Loading 3. Command line options Uh oh! There was an error while loading. Please reload this page . Loading 4. Support & FAQ Uh oh! There was an error while loading. Please reload this page . Loading 5. Advanced topics Uh oh! There was an error while loading. Please reload this page . Loading 6. Distributed computing Uh oh! There was an error while loading. Please reload this page . Loading Advanced options Uh oh! There was an error while loading. Please reload this page . Loading Applications Uh oh! There was an error while loading. Please reload this page . Loading Benchmarks Uh oh! There was an error while loading. Please reload this page . Loading Clustering Uh oh! There was an error while loading. Please reload this page . Loading DeepClust database Uh oh! There was an error while loading. Please reload this page . Loading Deprecated options Uh oh! There was an error while loading. Please reload this page . Loading File formats Uh oh! There was an error while loading. Please reload this page . Loading How to cluster huge datasets Uh oh! There was an error while loading. Please reload this page . Loading Repeat masking benchmark Uh oh! There was an error while loading. Please reload this page . Loading Small query benchmark Uh oh! There was an error while loading. Please reload this page . Show 2 more pages… Home Tutorial Installation Command line options Advanced options Clustering How to cluster huge datasets Support & FAQ Advanced topics File formats Distributed computing Miscellaneous Deprecated options Benchmarks Small query Repeat masking Clone this wiki locally Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/bbuchfink/diamond +GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bbuchfink / diamond Public Uh oh! There was an error while loading. Please reload this page . Notifications You must be signed in to change notification settings Fork 195 Star 1.3k Code Issues 213 Pull requests 0 Discussions Actions Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Wiki Security and quality Insights bbuchfink/diamond master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 2,169 Commits 2,169 Commits .github .github src src .cirrus.yml .cirrus.yml .dockerignore .dockerignore .gitattributes .gitattributes .gitignore .gitignore CITATION.cff CITATION.cff CMakeLists.txt CMakeLists.txt Dockerfile Dockerfile LICENSE LICENSE README.md README.md TRADEMARKS TRADEMARKS View all files Repository files navigation README GPL-3.0 license Introduction DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are: Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST. Protein clustering of up to tens of billions of proteins Frameshift alignments for long read analysis. Low resource requirements and suitable for running on standard desktops or laptops. Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification. Documentation The online documentation is located at the GitHub Wiki . Support DIAMOND is actively supported and developed software. Please use the issue tracker for malfunctions and the GitHub discussions for questions, comments, feature requests, etc. I also provide live support on Discord . Don't be too shy to ask! About DIAMOND is developed by Dr. Benjamin J. Buchfink, independent scientist, Tübingen, Germany, supported by the Max Planck Society for the Advancement of Science, in collaboration with the Drost lab at the University of Dundee. From 2019-2024, it was developed by Benjamin Buchfink at the Drost lab, Max Planck Institute for Biology Tübingen. From 2018-2019, its development was supported by the German Federal Ministry for Economic Affairs and Energy through an EXIST grant. From 2016-2018, it was developed by Benjamin Buchfink as an independent researcher. From 2013-2015, the initial version was developed by Benjamin Buchfink at the Huson lab, University of Tübingen, Germany. [ 📧Email ] [ X ] [ Bluesky ] [ LinkedIn ] [ Google Scholar ] [ Drost lab ] [ MPI-BIO ] When using the tool in published research, please cite: Buchfink B, Reuter K, Drost HG, "Sensitive protein alignments at tree-of-life scale using DIAMOND", Nature Methods 18 , 366–368 (2021). doi:10.1038/s41592-021-01101-x For sequence clustering: Buchfink BJ, Barbé E, Ashkenazy H, Reuter K, Kennedy JA, Drost HG, "Clustering the protein universe of life using DIAMOND DeepClust", Nature Methods (2026). doi:10.1038/s41592-026-03030-z Original publication to cite DIAMOND until v0.9.25: Buchfink B, Xie C, Huson DH, "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12 , 59-60 (2015). doi:10.1038/nmeth.3176 About Accelerated BLAST compatible local sequence aligner. Topics sequence-alignment Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 1.3k stars Watchers 33 watching Forks 195 forks Report repository Releases 127 DIAMOND v2.1.24 Latest Mar 7, 2026 + 126 releases Sponsor this project   Sponsor Uh oh! There was an error while loading. Please reload this page . Learn more about GitHub Sponsors Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 86.8% C 12.5% Other 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/bbuchfink/diamond +GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bbuchfink / diamond Public Uh oh! There was an error while loading. Please reload this page . Notifications You must be signed in to change notification settings Fork 195 Star 1.3k Code Issues 213 Pull requests 0 Discussions Actions Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Wiki Security and quality Insights bbuchfink/diamond master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 2,169 Commits 2,169 Commits .github .github src src .cirrus.yml .cirrus.yml .dockerignore .dockerignore .gitattributes .gitattributes .gitignore .gitignore CITATION.cff CITATION.cff CMakeLists.txt CMakeLists.txt Dockerfile Dockerfile LICENSE LICENSE README.md README.md TRADEMARKS TRADEMARKS View all files Repository files navigation README GPL-3.0 license Introduction DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are: Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST. Protein clustering of up to tens of billions of proteins Frameshift alignments for long read analysis. Low resource requirements and suitable for running on standard desktops or laptops. Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification. Documentation The online documentation is located at the GitHub Wiki . Support DIAMOND is actively supported and developed software. Please use the issue tracker for malfunctions and the GitHub discussions for questions, comments, feature requests, etc. I also provide live support on Discord . Don't be too shy to ask! About DIAMOND is developed by Dr. Benjamin J. Buchfink, independent scientist, Tübingen, Germany, supported by the Max Planck Society for the Advancement of Science, in collaboration with the Drost lab at the University of Dundee. From 2019-2024, it was developed by Benjamin Buchfink at the Drost lab, Max Planck Institute for Biology Tübingen. From 2018-2019, its development was supported by the German Federal Ministry for Economic Affairs and Energy through an EXIST grant. From 2016-2018, it was developed by Benjamin Buchfink as an independent researcher. From 2013-2015, the initial version was developed by Benjamin Buchfink at the Huson lab, University of Tübingen, Germany. [ 📧Email ] [ X ] [ Bluesky ] [ LinkedIn ] [ Google Scholar ] [ Drost lab ] [ MPI-BIO ] When using the tool in published research, please cite: Buchfink B, Reuter K, Drost HG, "Sensitive protein alignments at tree-of-life scale using DIAMOND", Nature Methods 18 , 366–368 (2021). doi:10.1038/s41592-021-01101-x For sequence clustering: Buchfink BJ, Barbé E, Ashkenazy H, Reuter K, Kennedy JA, Drost HG, "Clustering the protein universe of life using DIAMOND DeepClust", Nature Methods (2026). doi:10.1038/s41592-026-03030-z Original publication to cite DIAMOND until v0.9.25: Buchfink B, Xie C, Huson DH, "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12 , 59-60 (2015). doi:10.1038/nmeth.3176 About Accelerated BLAST compatible local sequence aligner. Topics sequence-alignment Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 1.3k stars Watchers 33 watching Forks 195 forks Report repository Releases 127 DIAMOND v2.1.24 Latest Mar 7, 2026 + 126 releases Sponsor this project   Sponsor Uh oh! There was an error while loading. Please reload this page . Learn more about GitHub Sponsors Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 86.8% C 12.5% Other 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge diamond --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +diamond 0.7.10 0 +---------------- +file name : diamond-0.7.10-0.tar.bz2 +name : diamond +version : 0.7.10 +build : 0 +build number: 0 +size : 607 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.7.10-0.tar.bz2 +md5 : 98d2bb9516e3de7e2ff71bb52eb7fc62 +dependencies: [] + + +diamond 0.7.10 1 +---------------- +file name : diamond-0.7.10-1.tar.bz2 +name : diamond +version : 0.7.10 +build : 1 +build number: 1 +size : 549 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.7.10-1.tar.bz2 +md5 : 85234455fdfef2dbe371425b5b7c2d1f +dependencies: + - boost >=1.53.0 + - libgcc >=4.8.5,<5 + + +diamond 0.7.10 boost1.60_1 +-------------------------- +file name : diamond-0.7.10-boost1.60_1.tar.bz2 +name : diamond +version : 0.7.10 +build : boost1.60_1 +build number: 1 +size : 549 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.7.10-boost1.60_1.tar.bz2 +md5 : 3705c031bdbbad96eeffecdcf96c212b +dependencies: + - boost 1.60* + - libgcc >=4.8.5,<5 + + +diamond 0.7.12 boost1.60_0 +-------------------------- +file name : diamond-0.7.12-boost1.60_0.tar.bz2 +name : diamond +version : 0.7.12 +build : boost1.60_0 +build number: 0 +size : 491 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.7.12-boost1.60_0.tar.bz2 +md5 : f879b870ca9ee19e86d39407a532312c +dependencies: + - boost 1.60* + - libgcc + + +diamond 0.7.12 boost1.61_0 +-------------------------- +file name : diamond-0.7.12-boost1.61_0.tar.bz2 +name : diamond +version : 0.7.12 +build : boost1.61_0 +build number: 0 +size : 491 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.7.12-boost1.61_0.tar.bz2 +md5 : 095cdd482c0699c58fd943ad357a2446 +dependencies: + - boost 1.61* + - libgcc + + +diamond 0.7.12 boost1.64_0 +-------------------------- +file name : diamond-0.7.12-boost1.64_0.tar.bz2 +name : diamond +version : 0.7.12 +build : boost1.64_0 +build number: 0 +size : 496 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.7.12-boost1.64_0.tar.bz2 +md5 : d200f1712fd6f9af79505772a4f34623 +dependencies: + - boost 1.64* + - libgcc + + +diamond 0.8.9 boost1.60_1 +------------------------- +file name : diamond-0.8.9-boost1.60_1.tar.bz2 +name : diamond +version : 0.8.9 +build : boost1.60_1 +build number: 1 +size : 299 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.9-boost1.60_1.tar.bz2 +md5 : 882633e1a932bbc1d6b604b7b6e46b65 +dependencies: + - boost 1.60* + - libgcc >=4.8.5,<5 + + +diamond 0.8.22 2 +---------------- +file name : diamond-0.8.22-2.tar.bz2 +name : diamond +version : 0.8.22 +build : 2 +build number: 2 +size : 379 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.22-2.tar.bz2 +md5 : 960c831b735bb55d17203d57b092e20f +dependencies: + - libgcc + + +diamond 0.8.22 boost1.60_1 +-------------------------- +file name : diamond-0.8.22-boost1.60_1.tar.bz2 +name : diamond +version : 0.8.22 +build : boost1.60_1 +build number: 1 +size : 383 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.22-boost1.60_1.tar.bz2 +md5 : 04a3d1f21bddbae64eabce3ac0cb76d6 +dependencies: + - boost 1.60* + - libgcc >=4.8.5,<5 + + +diamond 0.8.22 h2e03b76_6 +------------------------- +file name : diamond-0.8.22-h2e03b76_6.tar.bz2 +name : diamond +version : 0.8.22 +build : h2e03b76_6 +build number: 6 +size : 384 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.22-h2e03b76_6.tar.bz2 +md5 : 037a853e6e7cc57e2f802ebfa6b60827 +timestamp : 2021-03-27 18:11:29 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.22 h5b5514e_7 +------------------------- +file name : diamond-0.8.22-h5b5514e_7.tar.bz2 +name : diamond +version : 0.8.22 +build : h5b5514e_7 +build number: 7 +size : 384 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.22-h5b5514e_7.tar.bz2 +md5 : bef9cd197a81ff0f6e1ab979f88bf065 +timestamp : 2022-02-21 20:45:18 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.22 h8b12597_5 +------------------------- +file name : diamond-0.8.22-h8b12597_5.tar.bz2 +name : diamond +version : 0.8.22 +build : h8b12597_5 +build number: 5 +size : 389 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.22-h8b12597_5.tar.bz2 +md5 : 791eadbb869daf535b7b09bc589656be +timestamp : 2020-07-03 03:35:49 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.22 hd28b015_3 +------------------------- +file name : diamond-0.8.22-hd28b015_3.tar.bz2 +name : diamond +version : 0.8.22 +build : hd28b015_3 +build number: 3 +size : 395 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.22-hd28b015_3.tar.bz2 +md5 : 13907d103f8e57e19759be8d9cc94bdd +timestamp : 2018-06-18 09:12:46 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.22 hdbcaa40_4 +------------------------- +file name : diamond-0.8.22-hdbcaa40_4.tar.bz2 +name : diamond +version : 0.8.22 +build : hdbcaa40_4 +build number: 4 +size : 389 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.22-hdbcaa40_4.tar.bz2 +md5 : 7bd7f59bcd1438da4737ce50dafae41a +timestamp : 2019-03-09 20:03:33 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.24 0 +---------------- +file name : diamond-0.8.24-0.tar.bz2 +name : diamond +version : 0.8.24 +build : 0 +build number: 0 +size : 369 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.24-0.tar.bz2 +md5 : 40dd46552549e12eb8b0b0cb5d4ae75b +dependencies: + - libgcc + + +diamond 0.8.24 h2e03b76_3 +------------------------- +file name : diamond-0.8.24-h2e03b76_3.tar.bz2 +name : diamond +version : 0.8.24 +build : h2e03b76_3 +build number: 3 +size : 375 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.24-h2e03b76_3.tar.bz2 +md5 : 2eb008dc37ef41efb37d4ab49f74091a +timestamp : 2021-03-27 17:44:27 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.24 h5b5514e_4 +------------------------- +file name : diamond-0.8.24-h5b5514e_4.tar.bz2 +name : diamond +version : 0.8.24 +build : h5b5514e_4 +build number: 4 +size : 376 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.24-h5b5514e_4.tar.bz2 +md5 : 12a5f3cc2d7274a82b7e4d45738b9d10 +timestamp : 2022-02-21 21:11:40 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.24 h8b12597_2 +------------------------- +file name : diamond-0.8.24-h8b12597_2.tar.bz2 +name : diamond +version : 0.8.24 +build : h8b12597_2 +build number: 2 +size : 381 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.24-h8b12597_2.tar.bz2 +md5 : 88aaa87cdf2e26a2d24bc1d4587e98ed +timestamp : 2020-07-03 03:50:57 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.24 hd28b015_1 +------------------------- +file name : diamond-0.8.24-hd28b015_1.tar.bz2 +name : diamond +version : 0.8.24 +build : hd28b015_1 +build number: 1 +size : 386 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.24-hd28b015_1.tar.bz2 +md5 : 80ed27d51626ad67098b3cfae21d47ad +timestamp : 2018-06-18 09:44:22 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.26 0 +---------------- +file name : diamond-0.8.26-0.tar.bz2 +name : diamond +version : 0.8.26 +build : 0 +build number: 0 +size : 369 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.26-0.tar.bz2 +md5 : 1b5e31f8a852dfc2e6f792ffb72b5442 +dependencies: + - libgcc + - zlib + + +diamond 0.8.26 1 +---------------- +file name : diamond-0.8.26-1.tar.bz2 +name : diamond +version : 0.8.26 +build : 1 +build number: 1 +size : 371 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.26-1.tar.bz2 +md5 : f0438de43bb8cfed288bca72c7530775 +dependencies: + - libgcc + - zlib 1.2.11* + + +diamond 0.8.26 h2e03b76_4 +------------------------- +file name : diamond-0.8.26-h2e03b76_4.tar.bz2 +name : diamond +version : 0.8.26 +build : h2e03b76_4 +build number: 4 +size : 371 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.26-h2e03b76_4.tar.bz2 +md5 : 84edfa24326b1ba69b5a584f9329954d +timestamp : 2021-03-27 18:20:07 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.26 h5b5514e_5 +------------------------- +file name : diamond-0.8.26-h5b5514e_5.tar.bz2 +name : diamond +version : 0.8.26 +build : h5b5514e_5 +build number: 5 +size : 369 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.26-h5b5514e_5.tar.bz2 +md5 : e989c9ee6384a3b1bf7b147efc32d4cb +timestamp : 2022-02-21 21:25:09 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.26 h8b12597_3 +------------------------- +file name : diamond-0.8.26-h8b12597_3.tar.bz2 +name : diamond +version : 0.8.26 +build : h8b12597_3 +build number: 3 +size : 377 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.26-h8b12597_3.tar.bz2 +md5 : 079343df7cd624950d779af49b6ce0d0 +timestamp : 2020-07-03 03:13:43 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +diamond 0.8.26 hd28b015_2 +------------------------- +file name : diamond-0.8.26-hd28b015_2.tar.bz2 +name : diamond +version : 0.8.26 +build : hd28b015_2 +build number: 2 +size : 383 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/diamond-0.8.26-hd28b015_2.tar.bz2 +md diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/doubletdetection.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/doubletdetection.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..07b04c750a8e57c0624138aab4817b11dc613069 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/doubletdetection.manual_bundle.txt @@ -0,0 +1,107 @@ +# Tool: doubletdetection +software_name: doubletdetection +tier: T1 +domain: single_cell +downloads: 1241 +summary: Method to detect and enable removal of doublets from single-cell RNA-sequencing. +description: Method to detect and enable removal of doublets from single-cell RNA-sequencing. +dependencies: anndata >=0.8, ipywidgets, leidenalg, louvain, matplotlib-base >=3.6, numpy >=1.24, pandas >=0.22.0, phenograph, python >=3.10, scanpy >1.10.0, scipy >=1.8, tqdm +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/JonathanShor/DoubletDetection +doc_url: https://doubletdetection.readthedocs.io +dev_url: https://github.com/JonathanShor/DoubletDetection + +## URL Docs Extract +### https://doubletdetection.readthedocs.io +DoubletDetection — DoubletDetection Skip to main content Back to top Ctrl + K DoubletDetection Search Ctrl + K API doubletdetection.BoostClassifier doubletdetection.plot.convergence doubletdetection.plot.threshold Doublet Detection on 10k PBMCs from 10x Genomics v3 .md .pdf DoubletDetection Contents Installing DoubletDetection Running DoubletDetection Tutorial Obtaining data Credits and citations DoubletDetection # DoubletDetection is a Python3 package to detect doublets (technical errors) in single-cell RNA-seq count matrices. Installing DoubletDetection # Install from PyPI pip install doubletdetection Install from source git clone https://github.com/JonathanShor/DoubletDetection.git cd DoubletDetection pip3 install . If you are using pipenv as your virtual environment, it may struggle installing from the setup.py due to our custom Phenograph requirement. If so, try the following in the cloned repo: pipenv run pip3 install . Running DoubletDetection # To run basic doublet classification: import doubletdetection clf = doubletdetection . BoostClassifier () # raw_counts is a cells by genes count matrix labels = clf . fit ( raw_counts ) . predict () # higher means more likely to be doublet scores = clf . doublet_score () raw_counts is a scRNA-seq count matrix (cells by genes), and is array-like labels is a 1-dimensional numpy ndarray with the value 1 representing a detected doublet, 0 a singlet, and np.nan an ambiguous cell. scores is a 1-dimensional numpy ndarray representing a score for how likely a cell is to be a doublet. The score is used to create the labels. The classifier works best when There are several cell types present in the data It is applied individually to each run in an aggregated count matrix In v2.5 we have added a new experimental clustering method ( scanpy ’s Louvain clustering) that is much faster than phenograph. We are still validating results from this new clustering. Please see the notebook below for an example of using this new feature. Tutorial # See our tutorial for an example on 10k PBMCs from 10x Genomics. Obtaining data # Data can be downloaded from the 10x website . Credits and citations # Gayoso, Adam, Shor, Jonathan, Carr, Ambrose J., Sharma, Roshan, Pe’er, Dana (2020, December 18). DoubletDetection (Version v3.0). Zenodo. http://doi.org/10.5281/zenodo.2678041 We also thank the participants of the 1st Human Cell Atlas Jamboree, Chun J. Ye for providing data useful in developing this method, and Itsik Pe’er for providing guidance in early development as part of the Computational genomics class at Columbia University. This project is licensed under the terms of the MIT license. next API Contents Installing DoubletDetection Running DoubletDetection Tutorial Obtaining data Credits and citations By Adam Gayoso and Jonathan Shor © Copyright 2022, Adam Gayoso and Jonathan Shor. so the DOM is not blocked --> + +### https://github.com/JonathanShor/DoubletDetection +GitHub - JonathanShor/DoubletDetection: Doublet detection in single-cell RNA-seq data. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} JonathanShor / DoubletDetection Public Notifications You must be signed in to change notification settings Fork 22 Star 98 Code Issues 8 Pull requests 1 Actions Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Wiki Security and quality Insights JonathanShor/DoubletDetection main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 183 Commits 183 Commits .github/ workflows .github/ workflows docs docs doubletdetection doubletdetection tests tests .editorconfig .editorconfig .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml CONTRIBUTING.rst CONTRIBUTING.rst LICENSE.txt LICENSE.txt README.md README.md pyproject.toml pyproject.toml readthedocs.yaml readthedocs.yaml setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README Contributing MIT license DoubletDetection DoubletDetection is a Python3 package to detect doublets (technical errors) in single-cell RNA-seq count matrices. Installing DoubletDetection Install from PyPI pip install doubletdetection Install from source git clone https://github.com/JonathanShor/DoubletDetection.git cd DoubletDetection pip3 install . If you are using pipenv as your virtual environment, it may struggle installing from the setup.py due to our custom Phenograph requirement. If so, try the following in the cloned repo: pipenv run pip3 install . Running DoubletDetection To run basic doublet classification: import doubletdetection clf = doubletdetection . BoostClassifier () # raw_counts is a cells by genes count matrix labels = clf . fit ( raw_counts ). predict () # higher means more likely to be doublet scores = clf . doublet_score () raw_counts is a scRNA-seq count matrix (cells by genes), and is array-like labels is a 1-dimensional numpy ndarray with the value 1 representing a detected doublet, 0 a singlet, and np.nan an ambiguous cell. scores is a 1-dimensional numpy ndarray representing a score for how likely a cell is to be a doublet. The score is used to create the labels. The classifier works best when There are several cell types present in the data It is applied individually to each run in an aggregated count matrix In v2.5 we have added a new experimental clustering method ( scanpy 's Louvain clustering) that is much faster than phenograph. We are still validating results from this new clustering. Please see the notebook below for an example of using this new feature. Tutorial See our tutorial for an example on 10k PBMCs from 10x Genomics. Obtaining data Data can be downloaded from the 10x website . Credits and citations Gayoso, Adam, Shor, Jonathan, Carr, Ambrose J., Sharma, Roshan, Pe'er, Dana (2020, December 18). DoubletDetection (Version v3.0). Zenodo. http://doi.org/10.5281/zenodo.2678041 We also thank the participants of the 1st Human Cell Atlas Jamboree, Chun J. Ye for providing data useful in developing this method, and Itsik Pe'er for providing guidance in early development as part of the Computational genomics class at Columbia University. This project is licensed under the terms of the MIT license. About Doublet detection in single-cell RNA-seq data. doubletdetection.readthedocs.io/en/stable/ Topics scrna-seq Resources Readme License MIT license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 98 stars Watchers 5 watching Forks 22 forks Report repository Releases 21 doubletdetection v4.3.0.post1 Latest Feb 6, 2025 + 20 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/JonathanShor/DoubletDetection +GitHub - JonathanShor/DoubletDetection: Doublet detection in single-cell RNA-seq data. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} JonathanShor / DoubletDetection Public Notifications You must be signed in to change notification settings Fork 22 Star 98 Code Issues 8 Pull requests 1 Actions Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Wiki Security and quality Insights JonathanShor/DoubletDetection main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 183 Commits 183 Commits .github/ workflows .github/ workflows docs docs doubletdetection doubletdetection tests tests .editorconfig .editorconfig .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml CONTRIBUTING.rst CONTRIBUTING.rst LICENSE.txt LICENSE.txt README.md README.md pyproject.toml pyproject.toml readthedocs.yaml readthedocs.yaml setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README Contributing MIT license DoubletDetection DoubletDetection is a Python3 package to detect doublets (technical errors) in single-cell RNA-seq count matrices. Installing DoubletDetection Install from PyPI pip install doubletdetection Install from source git clone https://github.com/JonathanShor/DoubletDetection.git cd DoubletDetection pip3 install . If you are using pipenv as your virtual environment, it may struggle installing from the setup.py due to our custom Phenograph requirement. If so, try the following in the cloned repo: pipenv run pip3 install . Running DoubletDetection To run basic doublet classification: import doubletdetection clf = doubletdetection . BoostClassifier () # raw_counts is a cells by genes count matrix labels = clf . fit ( raw_counts ). predict () # higher means more likely to be doublet scores = clf . doublet_score () raw_counts is a scRNA-seq count matrix (cells by genes), and is array-like labels is a 1-dimensional numpy ndarray with the value 1 representing a detected doublet, 0 a singlet, and np.nan an ambiguous cell. scores is a 1-dimensional numpy ndarray representing a score for how likely a cell is to be a doublet. The score is used to create the labels. The classifier works best when There are several cell types present in the data It is applied individually to each run in an aggregated count matrix In v2.5 we have added a new experimental clustering method ( scanpy 's Louvain clustering) that is much faster than phenograph. We are still validating results from this new clustering. Please see the notebook below for an example of using this new feature. Tutorial See our tutorial for an example on 10k PBMCs from 10x Genomics. Obtaining data Data can be downloaded from the 10x website . Credits and citations Gayoso, Adam, Shor, Jonathan, Carr, Ambrose J., Sharma, Roshan, Pe'er, Dana (2020, December 18). DoubletDetection (Version v3.0). Zenodo. http://doi.org/10.5281/zenodo.2678041 We also thank the participants of the 1st Human Cell Atlas Jamboree, Chun J. Ye for providing data useful in developing this method, and Itsik Pe'er for providing guidance in early development as part of the Computational genomics class at Columbia University. This project is licensed under the terms of the MIT license. About Doublet detection in single-cell RNA-seq data. doubletdetection.readthedocs.io/en/stable/ Topics scrna-seq Resources Readme License MIT license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 98 stars Watchers 5 watching Forks 22 forks Report repository Releases 21 doubletdetection v4.3.0.post1 Latest Feb 6, 2025 + 20 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge doubletdetection --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +doubletdetection 4.2 pyhdfd78af_0 +--------------------------------- +file name : doubletdetection-4.2-pyhdfd78af_0.tar.bz2 +name : doubletdetection +version : 4.2 +build : pyhdfd78af_0 +build number: 0 +size : 18 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/doubletdetection-4.2-pyhdfd78af_0.tar.bz2 +md5 : 15c12e9b8f37150ded6bd4326035c3b6 +timestamp : 2024-10-29 23:28:07 UTC +constraints : + - nbsphinx * + - black >=20.8b1 + - pre-commit >=2.7.1 + - furo * + - sphinx-autodoc-typehints * + - nbsphinx-link * + - pytest >=4.4 + - myst-parser * + - flake8 >=3.7.7 + - sphinx >=4.1,<4.4 +dependencies: + - anndata >=0.6 + - ipywidgets + - leidenalg + - louvain + - matplotlib-base >=3.1 + - numpy >=1.14.2 + - pandas >=0.22.0 + - phenograph + - python >=3.6.1,<4.0 + - scanpy >1.4.4 + - scipy >=1.0.1 + - tqdm + + +doubletdetection 4.3.0.post1 pyhdfd78af_0 +----------------------------------------- +file name : doubletdetection-4.3.0.post1-pyhdfd78af_0.tar.bz2 +name : doubletdetection +version : 4.3.0.post1 +build : pyhdfd78af_0 +build number: 0 +size : 18 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/doubletdetection-4.3.0.post1-pyhdfd78af_0.tar.bz2 +md5 : 4df15641e3ad2ae049ea4056c6f00fda +timestamp : 2025-04-04 21:01:10 UTC +constraints : + - black >=20.8b1 + - pytest >=4.4 + - myst-parser * + - furo * + - sphinx >=4.1,<4.4 + - pre-commit >=2.7.1 + - flake8 >=3.7.7 + - sphinx-autodoc-typehints * + - nbsphinx * + - nbsphinx-link * +dependencies: + - anndata >=0.8 + - ipywidgets + - leidenalg + - louvain + - matplotlib-base >=3.6 + - numpy >=1.24 + - pandas >=0.22.0 + - phenograph + - python >=3.10 + - scanpy >1.10.0 + - scipy >=1.8 + - tqdm diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/dxpy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/dxpy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..97c4ac21fdb1e4dedbb857af3aadd1b275c826b4 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/dxpy.manual_bundle.txt @@ -0,0 +1,506 @@ +# Tool: dxpy +software_name: dxpy +tier: T1 +domain: t1_backfill_overall +downloads: 871800 +summary: DNAnexus Platform API bindings for Python." +description: DNAnexus Platform API bindings for Python." +dependencies: argcomplete >=2.0.0, awscrt, certifi, crc32c >=2.7.1, psutil >=5.9.3, python >=3.8, python-dateutil >=2.5, urllib3 >=1.25,<2.2, websocket-client >=1.6.0,<1.8.0 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/dnanexus/dx-toolkit +doc_url: http://autodoc.dnanexus.com/bindings/python/current +dev_url: https://github.com/dnanexus/dx-toolkit + +## URL Docs Extract +### http://autodoc.dnanexus.com/bindings/python/current +DNAnexus Python Bindings — DNAnexus Python Bindings documentation Navigation index modules | next | DNAnexus Python Bindings documentation » DNAnexus Python Bindings DNAnexus Python Bindings ¶ The DNAnexus dxpy Python library provides Python bindings to interact with the DNAnexus Platform via its API. The bindings are available to Python apps running within the DNAnexus Execution Environment, and can also be used in scripts you run that access the API from the outside. Before you start digging in, you may want to take a look at the Introduction to the DNAnexus Platform . The following references may also be useful to you as you develop your own scripts and apps. API Specification Complete details on the API, the lifecycle of different data objects, project permissions, and more. Many methods in the bindings translate directly into API calls, so it will be helpful to have at least a general understanding of the API’s structure. Execution Environment Reference How applets and apps are run within the DNAnexus Platform. Developer Portal Links to all other docs, e.g. useful command-line tools. Table of Contents ¶ 1. dxpy Package 2. dxpy.bindings Module 2.1. dxpy Object Handlers 2.2. Utility Functions 2.3. Projects and Containers 2.4. Records 2.5. Files 2.6. Applets, Apps, Workflows, and Jobs 2.7. Search 3. dxpy.app_builder Module 4. dxpy.api Module 5. dxpy.exceptions Module 6. dxpy.utils Module Indices and tables ¶ Index Module Index Search Page Table of Contents DNAnexus Python Bindings Table of Contents Indices and tables Next topic 1. dxpy Package This Page Show Source Quick search Navigation index modules | next | DNAnexus Python Bindings documentation » DNAnexus Python Bindings © Copyright 2012-2016, DNAnexus. Created using Sphinx 7.1.2. + +### https://github.com/dnanexus/dx-toolkit +GitHub - dnanexus/dx-toolkit: DNAnexus platform client libraries · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} dnanexus / dx-toolkit Public Notifications You must be signed in to change notification settings Fork 91 Star 110 Code Pull requests 45 Actions Projects Security and quality 0 Insights Additional navigation options Code Pull requests Actions Projects Security and quality Insights dnanexus/dx-toolkit master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 6,104 Commits 6,104 Commits .github .github bin bin build build debian debian devdocs/ nextflow devdocs/ nextflow doc doc src src .arcconfig .arcconfig .arclint .arclint .gitignore .gitignore .gitmodules .gitmodules CHANGELOG.md CHANGELOG.md COPYING COPYING Makefile Makefile Readme-osx.md Readme-osx.md Readme.md Readme.md environment environment environment.bat environment.bat environment.csh environment.csh environment.fish environment.fish View all files Repository files navigation README Apache-2.0 license DNAnexus Platform SDK To install the dx CLI and the Python SDK for your platform run python3 -m pip install dxpy Found a bug? See Reporting Bugs below. Welcome to the dx-toolkit repository! This repository contains the DNAnexus API language bindings and utilities for interacting with the DNAnexus platform. See https://documentation.dnanexus.com/ and http://autodoc.dnanexus.com/ for relevant documentation. Installing the toolkit from source The recommended way to install the Python SDK and dx CLI of dx-toolkit locally is with python3 -m pip install -e dx-toolkit/src/python . Any changes made within this checkout will be reflected in the pip installed version. Building inside docker To avoid lengthy installation of dependencies on your platform and simultaneous installations of development versions of dx-toolkit on the system, you can build dx-toolkit inside a docker container. Start python:3.9-bullseye in the interactive mode, mounting the repo you are working on ( <local_path_to_repo>/dx-toolkit ): # from root folder of dx-toolkit docker run -v `pwd`:/dx-toolkit -w /dx-toolkit -it --rm --entrypoint=/bin/bash python:3.9-bullseye From the interactive shell install dx-toolkit . A. Using local checkout: python3 -m pip install src/python/ --upgrade B. Using remote branch, in this example specified in "@master": python3 -m pip install --upgrade 'git+https://github.com/dnanexus/dx-toolkit.git@master#egg=dxpy&subdirectory=src/python' Log in, install dependencies(if needed) and use the container while developing. To rebuild, just save the work and run the step 2 again. Supported languages The Platform SDK contains API language bindings for the following platforms: Python (requires Python 3.8 or higher) C++ Java (requires Java 7 or higher) R Build dependencies for C++ and Java Note: There is a known incompatibility (in compiling dxcpp) when using GCC 4.7 with Boost 1.49. Please either use the GCC 4.6 series, or Boost 1.50+. Ubuntu 22.04 sudo apt install git openjdk-11-jre-headless maven python-is-python3 python3-venv python3-dev libssl-dev libffi-dev \ flex bison build-essential cmake libboost-all-dev curl libcurl4-openssl-dev Ubuntu 20.04 sudo apt install git make openjdk-11-jre-headless maven python-is-python3 python3-venv libssl-dev flex bison libffi-dev libboost-all-dev curl libcurl4-openssl-dev Upload Agent See the Upload Agent Readme for Upload Agent build documentation. Reporting Bugs Please contact support@dnanexus.com for any bug reports or suggestions. About DNAnexus platform client libraries autodoc.dnanexus.com/ Resources Readme License Apache-2.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 110 stars Watchers 63 watching Forks 91 forks Report repository Releases 707 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 38.7% Java 30.5% C++ 22.2% R 6.4% Shell 1.0% Makefile 0.4% Other 0.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/dnanexus/dx-toolkit +GitHub - dnanexus/dx-toolkit: DNAnexus platform client libraries · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} dnanexus / dx-toolkit Public Notifications You must be signed in to change notification settings Fork 91 Star 110 Code Pull requests 45 Actions Projects Security and quality 0 Insights Additional navigation options Code Pull requests Actions Projects Security and quality Insights dnanexus/dx-toolkit master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 6,104 Commits 6,104 Commits .github .github bin bin build build debian debian devdocs/ nextflow devdocs/ nextflow doc doc src src .arcconfig .arcconfig .arclint .arclint .gitignore .gitignore .gitmodules .gitmodules CHANGELOG.md CHANGELOG.md COPYING COPYING Makefile Makefile Readme-osx.md Readme-osx.md Readme.md Readme.md environment environment environment.bat environment.bat environment.csh environment.csh environment.fish environment.fish View all files Repository files navigation README Apache-2.0 license DNAnexus Platform SDK To install the dx CLI and the Python SDK for your platform run python3 -m pip install dxpy Found a bug? See Reporting Bugs below. Welcome to the dx-toolkit repository! This repository contains the DNAnexus API language bindings and utilities for interacting with the DNAnexus platform. See https://documentation.dnanexus.com/ and http://autodoc.dnanexus.com/ for relevant documentation. Installing the toolkit from source The recommended way to install the Python SDK and dx CLI of dx-toolkit locally is with python3 -m pip install -e dx-toolkit/src/python . Any changes made within this checkout will be reflected in the pip installed version. Building inside docker To avoid lengthy installation of dependencies on your platform and simultaneous installations of development versions of dx-toolkit on the system, you can build dx-toolkit inside a docker container. Start python:3.9-bullseye in the interactive mode, mounting the repo you are working on ( <local_path_to_repo>/dx-toolkit ): # from root folder of dx-toolkit docker run -v `pwd`:/dx-toolkit -w /dx-toolkit -it --rm --entrypoint=/bin/bash python:3.9-bullseye From the interactive shell install dx-toolkit . A. Using local checkout: python3 -m pip install src/python/ --upgrade B. Using remote branch, in this example specified in "@master": python3 -m pip install --upgrade 'git+https://github.com/dnanexus/dx-toolkit.git@master#egg=dxpy&subdirectory=src/python' Log in, install dependencies(if needed) and use the container while developing. To rebuild, just save the work and run the step 2 again. Supported languages The Platform SDK contains API language bindings for the following platforms: Python (requires Python 3.8 or higher) C++ Java (requires Java 7 or higher) R Build dependencies for C++ and Java Note: There is a known incompatibility (in compiling dxcpp) when using GCC 4.7 with Boost 1.49. Please either use the GCC 4.6 series, or Boost 1.50+. Ubuntu 22.04 sudo apt install git openjdk-11-jre-headless maven python-is-python3 python3-venv python3-dev libssl-dev libffi-dev \ flex bison build-essential cmake libboost-all-dev curl libcurl4-openssl-dev Ubuntu 20.04 sudo apt install git make openjdk-11-jre-headless maven python-is-python3 python3-venv libssl-dev flex bison libffi-dev libboost-all-dev curl libcurl4-openssl-dev Upload Agent See the Upload Agent Readme for Upload Agent build documentation. Reporting Bugs Please contact support@dnanexus.com for any bug reports or suggestions. About DNAnexus platform client libraries autodoc.dnanexus.com/ Resources Readme License Apache-2.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 110 stars Watchers 63 watching Forks 91 forks Report repository Releases 707 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 38.7% Java 30.5% C++ 22.2% R 6.4% Shell 1.0% Makefile 0.4% Other 0.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge dxpy --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +dxpy 0.223.0 py27_0 +------------------- +file name : dxpy-0.223.0-py27_0.tar.bz2 +name : dxpy +version : 0.223.0 +build : py27_0 +build number: 0 +size : 520 KB +license : Apache v2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.223.0-py27_0.tar.bz2 +md5 : 9a68f0d448d580fcde901f3e47d532d9 +dependencies: + - beautifulsoup4 >=4.4.1 + - fusepy >=2.0.2 + - futures >=3.0.4 + - psutil >=3.3.0 + - python 2.7* + - python-dateutil >=2.3 + - python-magic >=0.4.6 + - requests >=2.7.0 + - ws4py >=0.3.2 + - xattr + - xattr >=0.6.4 + + +dxpy 0.225.0 py27_0 +------------------- +file name : dxpy-0.225.0-py27_0.tar.bz2 +name : dxpy +version : 0.225.0 +build : py27_0 +build number: 0 +size : 521 KB +license : Apache v2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.225.0-py27_0.tar.bz2 +md5 : 3c1bbe917136b07014ab441fcd945828 +dependencies: + - beautifulsoup4 >=4.4.1 + - fusepy >=2.0.2 + - futures >=3.0.4 + - psutil >=3.3.0 + - python 2.7* + - python-dateutil >=2.3 + - python-magic >=0.4.6 + - requests >=2.7.0 + - ws4py >=0.3.2 + - xattr + - xattr >=0.6.4 + + +dxpy 0.247.0 py27_0 +------------------- +file name : dxpy-0.247.0-py27_0.tar.bz2 +name : dxpy +version : 0.247.0 +build : py27_0 +build number: 0 +size : 528 KB +license : Apache v2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.247.0-py27_0.tar.bz2 +md5 : 0338b066102b8d4f5b42b2762ab6da1a +dependencies: + - beautifulsoup4 >=4.4.1 + - fusepy >=2.0.2 + - futures >=3.0.4 + - psutil >=3.3.0 + - python 2.7* + - python-dateutil >=2.3 + - python-magic >=0.4.6 + - requests >=2.7.0 + - ws4py >=0.3.2 + - xattr + - xattr >=0.6.4 + + +dxpy 0.250.2 py27_0 +------------------- +file name : dxpy-0.250.2-py27_0.tar.bz2 +name : dxpy +version : 0.250.2 +build : py27_0 +build number: 0 +size : 534 KB +license : Apache v2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.250.2-py27_0.tar.bz2 +md5 : 26677488c71616ac8d1fee9057b39dd0 +dependencies: + - beautifulsoup4 >=4.4.1 + - fusepy >=2.0.2 + - futures >=3.0.4 + - psutil >=3.3.0 + - python 2.7* + - python-dateutil >=2.3 + - python-magic >=0.4.6 + - requests >=2.7.0 + - ws4py >=0.3.2 + - xattr + - xattr >=0.6.4 + + +dxpy 0.254.0 py27_0 +------------------- +file name : dxpy-0.254.0-py27_0.tar.bz2 +name : dxpy +version : 0.254.0 +build : py27_0 +build number: 0 +size : 547 KB +license : Apache v2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.254.0-py27_0.tar.bz2 +md5 : 1c13da74d2a589f63c8485e3af692225 +dependencies: + - beautifulsoup4 >=4.4.1 + - fusepy >=2.0.2 + - futures >=3.0.4 + - psutil >=3.3.0 + - python 2.7* + - python-dateutil >=2.3 + - python-magic >=0.4.6 + - requests >=2.7.0 + - ws4py >=0.3.2 + - xattr + - xattr >=0.6.4 + + +dxpy 0.254.0 py27_1 +------------------- +file name : dxpy-0.254.0-py27_1.tar.bz2 +name : dxpy +version : 0.254.0 +build : py27_1 +build number: 1 +size : 544 KB +license : Apache v2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.254.0-py27_1.tar.bz2 +md5 : 867024f35a4d9702e45cb79169b5fee7 +timestamp : 2018-07-07 01:14:57 UTC +dependencies: + - beautifulsoup4 >=4.4.1 + - fusepy >=2.0.2 + - futures >=3.0.4 + - psutil >=3.3.0 + - python >=2.7,<2.8.0a0 + - python-dateutil >=2.3 + - python-magic >=0.4.6 + - requests >=2.7.0 + - ws4py >=0.3.2 + - xattr >=0.6.4 + + +dxpy 0.257.3 py27_0 +------------------- +file name : dxpy-0.257.3-py27_0.tar.bz2 +name : dxpy +version : 0.257.3 +build : py27_0 +build number: 0 +size : 553 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.257.3-py27_0.tar.bz2 +md5 : 8964478202e2df939135603947a8ca1a +timestamp : 2018-08-02 07:17:11 UTC +dependencies: + - beautifulsoup4 >=4.4.1 + - fusepy >=2.0.2 + - futures >=3.0.4 + - psutil >=3.3.0 + - python >=2.7,<2.8.0a0 + - python-dateutil >=2.3 + - python-magic >=0.4.6 + - requests >=2.7.0 + - ws4py >=0.3.2 + - xattr >=0.6.4 + + +dxpy 0.261.1 py27_0 +------------------- +file name : dxpy-0.261.1-py27_0.tar.bz2 +name : dxpy +version : 0.261.1 +build : py27_0 +build number: 0 +size : 559 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.261.1-py27_0.tar.bz2 +md5 : 82b05b509d3d9105cd16903e8b58d210 +timestamp : 2018-08-29 12:53:06 UTC +dependencies: + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - fusepy >=2.0.2 + - futures >=3.0.4 + - psutil >=3.3.0 + - python >=2.7,<2.8.0a0 + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - ws4py >=0.3.2 + - xattr >=0.6.4 + + +dxpy 0.273.0 py27_0 +------------------- +file name : dxpy-0.273.0-py27_0.tar.bz2 +name : dxpy +version : 0.273.0 +build : py27_0 +build number: 0 +size : 530 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.273.0-py27_0.tar.bz2 +md5 : ab44d67fc99e28682ec5217b3a397ef2 +timestamp : 2019-01-30 21:25:10 UTC +dependencies: + - argcomplete >=1.9.4 + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - futures >=3.0.4 + - psutil >=3.3.0 + - python >=2.7,<2.8.0a0 + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - websocket-client >=0.53.0 + + +dxpy 0.273.0 py35_0 +------------------- +file name : dxpy-0.273.0-py35_0.tar.bz2 +name : dxpy +version : 0.273.0 +build : py35_0 +build number: 0 +size : 536 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.273.0-py35_0.tar.bz2 +md5 : 9447ec01d0d5aeb38ffc2644239622f0 +timestamp : 2019-01-30 21:23:51 UTC +dependencies: + - argcomplete >=1.9.4 + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - psutil >=3.3.0 + - python >=3.5,<3.6.0a0 + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - websocket-client >=0.53.0 + + +dxpy 0.273.0 py36_0 +------------------- +file name : dxpy-0.273.0-py36_0.tar.bz2 +name : dxpy +version : 0.273.0 +build : py36_0 +build number: 0 +size : 534 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/dxpy-0.273.0-py36_0.tar.bz2 +md5 : f7bdf23979ac4303cb32518879fdef7a +timestamp : 2019-01-30 21:26:21 UTC +dependencies: + - argcomplete >=1.9.4 + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - psutil >=3.3.0 + - python >=3.6,<3.7.0a0 + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - websocket-client >=0.53.0 + + +dxpy 0.282.0 py_0 +----------------- +file name : dxpy-0.282.0-py_0.tar.bz2 +name : dxpy +version : 0.282.0 +build : py_0 +build number: 0 +size : 253 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dxpy-0.282.0-py_0.tar.bz2 +md5 : 497a2a4b496a127bec244ad248bc0733 +timestamp : 2019-05-26 20:10:21 UTC +dependencies: + - argcomplete >=1.9.4 + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - psutil >=3.3.0 + - python + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - websocket-client >=0.53.0 + + +dxpy 0.283.0 py_0 +----------------- +file name : dxpy-0.283.0-py_0.tar.bz2 +name : dxpy +version : 0.283.0 +build : py_0 +build number: 0 +size : 254 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dxpy-0.283.0-py_0.tar.bz2 +md5 : afceddac78c1f95b03e1c48806db5efa +timestamp : 2019-06-15 21:06:25 UTC +dependencies: + - argcomplete >=1.9.4 + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - psutil >=3.3.0 + - python + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - websocket-client >=0.53.0 + + +dxpy 0.284.0 py_0 +----------------- +file name : dxpy-0.284.0-py_0.tar.bz2 +name : dxpy +version : 0.284.0 +build : py_0 +build number: 0 +size : 252 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dxpy-0.284.0-py_0.tar.bz2 +md5 : 5e121dde0e6575576761124270bef5dd +timestamp : 2019-06-20 17:02:27 UTC +dependencies: + - argcomplete >=1.9.4 + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - psutil >=3.3.0 + - python + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - websocket-client >=0.53.0 + + +dxpy 0.285.0 py_0 +----------------- +file name : dxpy-0.285.0-py_0.tar.bz2 +name : dxpy +version : 0.285.0 +build : py_0 +build number: 0 +size : 254 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dxpy-0.285.0-py_0.tar.bz2 +md5 : 11653c6a712ce1c33c12853e73103a0a +timestamp : 2019-06-28 02:41:44 UTC +dependencies: + - argcomplete >=1.9.4 + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - psutil >=3.3.0 + - python + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - websocket-client >=0.53.0 + + +dxpy 0.285.1 py_0 +----------------- +file name : dxpy-0.285.1-py_0.tar.bz2 +name : dxpy +version : 0.285.1 +build : py_0 +build number: 0 +size : 255 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dxpy-0.285.1-py_0.tar.bz2 +md5 : 18cbb5e72781ea5fb0a43945331b6047 +timestamp : 2019-07-08 20:27:03 UTC +dependencies: + - argcomplete >=1.9.4 + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - psutil >=3.3.0 + - python + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - websocket-client >=0.53.0 + + +dxpy 0.286.1 py_0 +----------------- +file name : dxpy-0.286.1-py_0.tar.bz2 +name : dxpy +version : 0.286.1 +build : py_0 +build number: 0 +size : 255 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dxpy-0.286.1-py_0.tar.bz2 +md5 : 54eeb5c1e1d04dc73c88a57765c4697b +timestamp : 2019-09-01 20:05:32 UTC +dependencies: + - argcomplete >=1.9.4 + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - psutil >=3.3.0 + - python + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - websocket-client >=0.53.0 + + +dxpy 0.287.0 py_0 +----------------- +file name : dxpy-0.287.0-py_0.tar.bz2 +name : dxpy +version : 0.287.0 +build : py_0 +build number: 0 +size : 254 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dxpy-0.287.0-py_0.tar.bz2 +md5 : 5122355122928f3fb5f9bed190524ae5 +timestamp : 2019-10-02 11:18:14 UTC +dependencies: + - argcomplete >=1.9.4 + - beautifulsoup4 >=4.4.1 + - cryptography <=2.2.2 + - psutil >=3.3.0 + - python + - python-dateutil >=2.5 + - python-magic >=0.4.6 + - requests >=2.8.0 + - websocket-client >=0.53.0 + + +dxpy 0.288.0 py_0 +----------------- +file name : dxpy-0.288.0-py_0.tar.bz2 +name : dxpy +version : 0.288.0 +build : py_0 +build number: 0 +size : 258 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/dxpy-0.288.0-py_0.tar.bz2 +md5 : b886384ca7 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/easy_vitessce.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/easy_vitessce.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..feabc1fad98b81ae616bdfdbfd44c9ae6832b80f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/easy_vitessce.manual_bundle.txt @@ -0,0 +1,55 @@ +# Tool: easy_vitessce +software_name: easy_vitessce +tier: T1 +domain: single_cell +downloads: 163 +summary: A package to easily use Vitessce to create interactive plots for single-cell data +description: A package to easily use Vitessce to create interactive plots for single-cell data +dependencies: anndata >=0.11.4, black >=21.11b1, dask-core 2024.11.1, distributed <=2024.11.2, donfig >=0.3.1, numcodecs >=0.5.7,<0.16.0, numpy >=1.21.2, pandas >=1.1.2, python >=3.9, scanpy >=1.11.3, scipy >=1.2.1, spatialdata >=0.3.0, spatialdata-plot >=0.2.7, vitessce-python >=3.7.9, xarray >=2024.10.0,<=2025.3.0, zarr >=2.5.0,<3 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/vitessce/easy_vitessce/ +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/vitessce/easy_vitessce/ +GitHub - vitessce/easy_vitessce: Configure Vitessce using existing Scverse plotting APIs · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} vitessce / easy_vitessce Public Notifications You must be signed in to change notification settings Fork 5 Star 21 Code Issues 14 Pull requests 3 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights vitessce/easy_vitessce main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 167 Commits 167 Commits .github/ workflows .github/ workflows .vscode .vscode docs docs paper/ supplement paper/ supplement src/ easy_vitessce src/ easy_vitessce tests tests .gitignore .gitignore CITATION.cff CITATION.cff LICENSE LICENSE MANIFEST.in MANIFEST.in Makefile Makefile README.md README.md make.bat make.bat pyproject.toml pyproject.toml uv.lock uv.lock View all files Repository files navigation README MIT license Easy Vitessce 🪄 Configure Vitessce with a single line of code! Turn your static Scanpy and SpatialData plots into interactive Vitessce visualizations simply by importing the easy_vitessce package! Supported Functions sc.pl.umap sc.pl.tsne sc.pl.pca sc.pl.diffmap sc.pl.embedding sc.pl.violin sc.pl.dotplot sc.pl.heatmap sdata.pl ( .render_images , .render_labels , .render_shapes , .render_points ) See the example notebooks and the documentation for further details. Installation Install package using pip: pip install easy_vitessce How to Use Importing Easy Vitessce import easy_vitessce as ev 🪄 By default, interactive plots are enabled via this import statement. Deactivating Interactive Plots: ev . disable_plots ([ "embedding" , "violin" , "spatialdata-plot" ]) # or, to disable all interactive plots and return to static plotting mode ev . disable_plots () Reactivating Interactive Plots: ev . enable_plots ([ "spatialdata-plot" ]) # or, to enable all interactive plots ev . enable_plots () Troubleshooting See the Troubleshooting section of the vitessce-python repository for tips. Development Set up environment uv sync --extra dev --extra docs This command should also be run after updating dependencies in pyproject.toml . Run tests # uv sync --extra dev uv run pytest Make documentation uv run make html # on mac/linux # uv run make.bat html # on windows open docs/_build/html/index.html Launch Jupyter notebook or lab # uv sync --extra dev uv run jupyter notebook --notebook-dir . # or uv run jupyter lab --notebook-dir . Citation To cite EasyVitessce in your work, please use: @article { luo2025easyvitessce , title = { {EasyVitessce: auto-magically adding interactivity to Scverse single-cell and spatial biology plots} } , author = { Luo, Selena and Keller, Mark S. and Kakar, Tabassum and Choy, Lisa and Gehlenborg, Nils } , journal = { arXiv } , year = { 2025 } , month = oct, doi = { 10.48550/arXiv.2510.19532 } } To cite Vitessce in your work, please use: @article { keller2024vitessce , title = { {Vitessce: integrative visualization of multimodal and spatially resolved single-cell data} } , author = { Keller, Mark S. and Gold, Ilan and McCallum, Chuck and Manz, Trevor and Kharchenko, Peter V. and Gehlenborg, Nils } , journal = { Nature Methods } , year = { 2024 } , month = sep, doi = { 10.1038/s41592-024-02436-x } } If you use the image rendering functionality, please additionally cite Viv: @article { manz2022viv , title = { {Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web} } , author = { Manz, Trevor and Gold, Ilan and Patterson, Nathan Heath and McCallum, Chuck and Keller, Mark S. and Herr, II, Bruce W. and Börner, Kay and Spraggins, Jeffrey M. and Gehlenborg, Nils } , journal = { Nature Methods } , year = { 2022 } , month = may, doi = { 10.1038/s41592-022-01482-7 } } About Configure Vitessce using existing Scverse plotting APIs vitessce.github.io/easy_vitessce/ Topics hidivelab Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 21 stars Watchers 1 watching Forks 5 forks Report repository Releases No releases published Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 98.6% Other 1.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge easy_vitessce --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +easy_vitessce 0.0.9 pyhdfd78af_0 +-------------------------------- +file name : easy_vitessce-0.0.9-pyhdfd78af_0.conda +name : easy_vitessce +version : 0.0.9 +build : pyhdfd78af_0 +build number: 0 +size : 29 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/easy_vitessce-0.0.9-pyhdfd78af_0.conda +md5 : 97fa5a4301ef6623d51938ec94fe8553 +timestamp : 2026-01-13 09:22:31 UTC +dependencies: + - anndata >=0.11.4 + - black >=21.11b1 + - dask-core 2024.11.1 + - distributed <=2024.11.2 + - donfig >=0.3.1 + - numcodecs >=0.5.7,<0.16.0 + - numpy >=1.21.2 + - pandas >=1.1.2 + - python >=3.9 + - scanpy >=1.11.3 + - scipy >=1.2.1 + - spatialdata >=0.3.0 + - spatialdata-plot >=0.2.7 + - vitessce-python >=3.7.9 + - xarray >=2024.10.0,<=2025.3.0 + - zarr >=2.5.0,<3 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/echidna.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/echidna.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..27ce7108370f2c08f7ea4314544efddef087e2aa --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/echidna.manual_bundle.txt @@ -0,0 +1,75 @@ +# Tool: echidna +software_name: echidna +tier: T1 +domain: single_cell +downloads: 333 +summary: Mapping genotype to phenotype through joint probabilistic modeling of single-cell gene expression and chromosomal copy number variation. +description: Mapping genotype to phenotype through joint probabilistic modeling of single-cell gene expression and chromosomal copy number variation. +dependencies: graphviz, hmmlearn, leidenalg, pandas, pyro-ppl >=1.9.1, python >=3.10, requests, scanpy >=1.10, scikit-learn, seaborn +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/azizilab/echidna +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/azizilab/echidna +GitHub - azizilab/echidna: Mapping genotype to phenotype through joint probabilistic modeling of single-cell gene expression and chromosomal copy number variation · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} azizilab / echidna Public Notifications You must be signed in to change notification settings Fork 0 Star 2 Code Issues 1 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights azizilab/echidna main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 157 Commits 157 Commits demo_data demo_data echidna echidna tutorials tutorials .gitattributes .gitattributes .gitignore .gitignore LICENSE LICENSE README.md README.md echidna_concept.png echidna_concept.png echidna_logo.png echidna_logo.png environment.yaml environment.yaml pyproject.toml pyproject.toml requirements.txt requirements.txt View all files Repository files navigation README MIT license Echidna A Bayesian framework for quantifying gene dosage effect on phenotypic plasticity through integrating single-cell RNA sequencing (scRNA-seq) and bulk whole-genome sequencing (WGS) from a single or multiple time points. Install Echidna is available on PyPI under the name sc-echidna and bioconda under echidna . Step 1 (optional but recommended) Create a conda environment with a recent Python version: conda create -n "echidna-env" python=3.10 . Step 2 Ensure you have the right version of torch installed for your device. See instructions on pytorch.org . Conda Formula conda install bioconda::echidna Pip Formula pip install sc-echidna Installation time depends on hardware, but can be finished within 5 minutes for most computers. Tutorial There are four example notebooks: 1-single-timepoint.ipynb 2-multi-timepoint.ipynb 3-infer-gene-dosage.ipynb 4-echidna-model.ipynb The notebooks are meant to be run sequentially, and they build off of each other. Notebook 1 introduces you to the package - preparing your data, setting hyperparamters, performing posterior predictive checks - with data collected from a single point in time. In notebook 2, we look at a multi-timepoint setting, where we have paired single-cell and WGS data collected over time. The demo dataset included in ./demo_data is the same data we used for this notebook. The saved model runs from notebook 2 will be used in notebook 3, where you will see how to infer amplifications and deletions by cluster of genes across a given genome. This notebook also shows you how to calculate and plot gene dosage effect with Echidna. Notebook 4 is meant to show you how to do more custom work with the model. We package together many functions for your convenience, but this notebook will show you how to work directly with the model for the experiments not covered in the package. Some Pyro knowledge is assumed. Echidna Configuration Settings .obs Labels Setting Type Default Description timepoint_label str "timepoint" Label for timepoints in the data. counts_layer str "counts" Name of the counts layer in the data. clusters str "leiden" Clustering method used in the data. This can also be celltype annotations, if you have them. Training Parameters Setting Type Default Description seed int 42 Random seed for reproducibility. n_steps int 10000 Maximum number of steps for Stochastic Variational Inference (SVI). learning_rate float 0.1 Learning rate for the Adam optimizer. val_split float 0.1 Percentage of training data to use for validation. patience int 30 Early stopping patience (set to >0 to enable early stopping). device str "cuda" if is_available() else "cpu" Device to use for training (GPU if available, otherwise CPU). verbose bool True Whether to enable logging output. Model Hyperparameters Setting Type Default Description inverse_gamma bool False Whether to use inverse gamma for noisier data. eta_mean_init float 2.0 Initial mean value for the eta parameter. lkj_concentration float 1.0 Concentration parameter of LKJ prior. Values > 1.0 result in more diagonal covariance matrices. q_corr_init float 0.01 Initial scale of the variational correlation. q_shape_rate_scaler float 10.0 Scaler for the shape and rate parameters of the covariance diagonal for variational inference. About Mapping genotype to phenotype through joint probabilistic modeling of single-cell gene expression and chromosomal copy number variation Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 2 stars Watchers 1 watching Forks 0 forks Report repository Releases 1 Echidna Latest Dec 18, 2024 Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge echidna --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +echidna 1.0.2 pyhdfd78af_0 +-------------------------- +file name : echidna-1.0.2-pyhdfd78af_0.tar.bz2 +name : echidna +version : 1.0.2 +build : pyhdfd78af_0 +build number: 0 +size : 40 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/echidna-1.0.2-pyhdfd78af_0.tar.bz2 +md5 : b84f44d883082d62ce638e0a62e95fff +timestamp : 2024-12-17 22:39:07 UTC +dependencies: + - graphviz + - hmmlearn + - leidenalg + - pandas + - pyro-ppl >=1.9.1 + - python >=3.10 + - requests + - scanpy >=1.10 + - scikit-learn + - seaborn + + +echidna 1.0.3 pyhdfd78af_0 +-------------------------- +file name : echidna-1.0.3-pyhdfd78af_0.tar.bz2 +name : echidna +version : 1.0.3 +build : pyhdfd78af_0 +build number: 0 +size : 40 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/echidna-1.0.3-pyhdfd78af_0.tar.bz2 +md5 : 4cd60b7889d34f6f093bfc21eb71c7b9 +timestamp : 2025-07-24 19:25:31 UTC +dependencies: + - graphviz + - hmmlearn + - leidenalg + - pandas + - pyro-ppl >=1.9.1 + - python >=3.10 + - requests + - scanpy >=1.10 + - scikit-learn + - seaborn diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/emboss.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/emboss.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c8e587816bf0e266fea7068417e82a28c478c2db --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/emboss.manual_bundle.txt @@ -0,0 +1,468 @@ +# Tool: emboss +software_name: emboss +tier: T1 +domain: t1_backfill_overall +downloads: 247048 +summary: The European Molecular Biology Open Software Suite +description: The European Molecular Biology Open Software Suite +dependencies: libgcc >=13, libgd >=2.3.3,<2.4.0a0, libharu >=2.4.5,<2.5.0a0, libpng >=1.6.50,<1.7.0a0, libzlib >=1.3.1,<2.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://emboss.open-bio.org/ +doc_url: +dev_url: + +## URL Docs Extract +### http://emboss.open-bio.org/ +EMBOSS Homepage The European Molecular Biology Open Software Suite Funded from May 2009 by BBSRC grant BBR/G02264X/1 About  Overview  •  Features  •  License  •  Citing  •  Developers  •  News  •  Contact  Software for molecular biology - high quality, open-source and free ... more > Download  How to  •  Stable release  •  CVS release  •  mEMBOSS  •  Change log  •  Fixing   Patches  •  Bug fix files  Download a stable version, get the latest code and fixes ... more > Get involved  Mailing lists  •  Meetings  •  Areas needing work  •  Submit code  Please get involved with EMBOSS ... more > Manuals  Administrators  (  in HTML  )•  Developers  (  in HTML  )•  Users  (  in HTML  ) Everything is documented, so if all else fails RTFM ...  Adm   Dev   Use  Tutorials  EMBOSS  •  wEMBOSS  •  jEMBOSS  Hands-on guides to the EMBOSS command line and popular interfaces ... more > Support  Getting started  •  Docs  •  Help  •  FAQ  •  Feature requests  •  Bug reports  Prompt support for end-users and developers ... more > Applications  EMBOSS Apps A-Z  •  EMBASSY   EMBASSY Apps  •  Groups  • Hundreds of useful, well documented bioinformatics tools ... more > Command line  Application options  •  Data qualifiers  •  Global qualifiers  •  USAs  Powerful, flexible and convenient command-line ... more > Interfaces  Command-line  •  Web UI  •  Web services  •  Workflow  •  Jemboss  •  Wemboss  •  Other GUIs  Many ways to run the applications ... more > File formats  Sequences  •  Features  •  Alignments  •  Reports  All common file formats are supported ... more > Programming  Features  •  ACD files  •  Hackers guides  •  Coding standards  •  Code docs standards  •  Your 1st app  •  Debugging  •  QA tests  •  Docs  • In-depth information for software developers ... more > Libraries  Inbuilt features   •  ACD syntax  •  AJAX  •  NUCLEUS  Reference docs for the ACD syntax and EMBOSS programming libraries ... more > Sysadmins  Building EMBOSS  •  Building EMBASSY  •  Building Jemboss  •  Database configuration  Downtrodden, but not forgotten ... more > Thanks  Credits  BBSRC, EBI and contributors - big up! ... more > Search WWW Search emboss.open-bio.org + +## Conda Search Info +$ conda search -c bioconda -c conda-forge emboss --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +emboss 5.0.0 0 +-------------- +file name : emboss-5.0.0-0.tar.bz2 +name : emboss +version : 5.0.0 +build : 0 +build number: 0 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-0.tar.bz2 +md5 : e02cf74743f6b5467f8361608cab4bd8 +timestamp : 2019-12-18 16:05:40 UTC +dependencies: + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 h079770c_3 +----------------------- +file name : emboss-5.0.0-h079770c_3.tar.bz2 +name : emboss +version : 5.0.0 +build : h079770c_3 +build number: 3 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h079770c_3.tar.bz2 +md5 : 9ac4a9f63f7467fadbf7380bb3653b6c +timestamp : 2022-08-01 18:58:19 UTC +dependencies: + - python_abi 3.10.* *_cp310 + - zlib >=1.2.12,<1.3.0a0 + + +emboss 5.0.0 h079770c_4 +----------------------- +file name : emboss-5.0.0-h079770c_4.tar.bz2 +name : emboss +version : 5.0.0 +build : h079770c_4 +build number: 4 +size : 21.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h079770c_4.tar.bz2 +md5 : 2d1617b6009943b2cfbd1dce4273ed76 +timestamp : 2023-05-16 00:40:40 UTC +dependencies: + - python_abi 3.10.* *_cp310 + - zlib + + +emboss 5.0.0 h09cc20e_3 +----------------------- +file name : emboss-5.0.0-h09cc20e_3.tar.bz2 +name : emboss +version : 5.0.0 +build : h09cc20e_3 +build number: 3 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h09cc20e_3.tar.bz2 +md5 : 18c505b1db1c75952f3fd879a008cf05 +timestamp : 2021-03-28 00:52:33 UTC +dependencies: + - python_abi 3.6.* *_cp36m + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 h21c881e_3 +----------------------- +file name : emboss-5.0.0-h21c881e_3.tar.bz2 +name : emboss +version : 5.0.0 +build : h21c881e_3 +build number: 3 +size : 21.2 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h21c881e_3.tar.bz2 +md5 : bdf5c76c8c010747d45d9d45d3d10850 +timestamp : 2021-03-28 00:56:18 UTC +dependencies: + - python_abi 2.7.* *_cp27mu + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 h3252c3a_2 +----------------------- +file name : emboss-5.0.0-h3252c3a_2.tar.bz2 +name : emboss +version : 5.0.0 +build : h3252c3a_2 +build number: 2 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h3252c3a_2.tar.bz2 +md5 : 2be7e8bf42b5ad22045fe2419f00fa14 +timestamp : 2020-08-30 15:13:01 UTC +dependencies: + - python_abi 3.8.* *_cp38 + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 h362c646_5 +----------------------- +file name : emboss-5.0.0-h362c646_5.tar.bz2 +name : emboss +version : 5.0.0 +build : h362c646_5 +build number: 5 +size : 21.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h362c646_5.tar.bz2 +md5 : 7c492a5c2b8ea1dca4904ae4b1fdcfb0 +timestamp : 2024-06-05 14:37:48 UTC +dependencies: + - python_abi 3.11.* *_cp311 + - zlib + + +emboss 5.0.0 h362c646_6 +----------------------- +file name : emboss-5.0.0-h362c646_6.tar.bz2 +name : emboss +version : 5.0.0 +build : h362c646_6 +build number: 6 +size : 21.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h362c646_6.tar.bz2 +md5 : 0e83329b3afacd3722fa771829892792 +timestamp : 2024-12-12 00:07:08 UTC +dependencies: + - python_abi 3.11.* *_cp311 + - zlib + + +emboss 5.0.0 h6a678da_3 +----------------------- +file name : emboss-5.0.0-h6a678da_3.tar.bz2 +name : emboss +version : 5.0.0 +build : h6a678da_3 +build number: 3 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h6a678da_3.tar.bz2 +md5 : fe05409d0382ca029243a89e4144657c +timestamp : 2021-03-28 01:00:14 UTC +dependencies: + - python_abi 3.9.* *_cp39 + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 h6a678da_4 +----------------------- +file name : emboss-5.0.0-h6a678da_4.tar.bz2 +name : emboss +version : 5.0.0 +build : h6a678da_4 +build number: 4 +size : 21.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h6a678da_4.tar.bz2 +md5 : f958348f08314257d7a5a249a2d14e54 +timestamp : 2023-05-16 00:37:53 UTC +dependencies: + - python_abi 3.9.* *_cp39 + - zlib + + +emboss 5.0.0 h864c0ab_2 +----------------------- +file name : emboss-5.0.0-h864c0ab_2.tar.bz2 +name : emboss +version : 5.0.0 +build : h864c0ab_2 +build number: 2 +size : 21.2 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h864c0ab_2.tar.bz2 +md5 : 1bbd8fa4febd3582cd307ddf2b856cf8 +timestamp : 2020-07-09 22:40:10 UTC +dependencies: + - python_abi 2.7.* *_cp27mu + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 h939104b_5 +----------------------- +file name : emboss-5.0.0-h939104b_5.tar.bz2 +name : emboss +version : 5.0.0 +build : h939104b_5 +build number: 5 +size : 21.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h939104b_5.tar.bz2 +md5 : 85db0e529d62d68e15c42c645f40f1ea +timestamp : 2024-06-05 14:41:57 UTC +dependencies: + - python_abi 3.8.* *_cp38 + - zlib + + +emboss 5.0.0 h9f0ad1d_1 +----------------------- +file name : emboss-5.0.0-h9f0ad1d_1.tar.bz2 +name : emboss +version : 5.0.0 +build : h9f0ad1d_1 +build number: 1 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-h9f0ad1d_1.tar.bz2 +md5 : 36bc40ee4442095342197ef74a062be6 +timestamp : 2020-05-08 16:13:50 UTC +dependencies: + - python_abi 3.6.* *_cp36m + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 ha5a061d_3 +----------------------- +file name : emboss-5.0.0-ha5a061d_3.tar.bz2 +name : emboss +version : 5.0.0 +build : ha5a061d_3 +build number: 3 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-ha5a061d_3.tar.bz2 +md5 : 6b874d72750c7552f3c3562be57bf4d7 +timestamp : 2021-03-28 01:04:05 UTC +dependencies: + - python_abi 3.8.* *_cp38 + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 ha5a061d_4 +----------------------- +file name : emboss-5.0.0-ha5a061d_4.tar.bz2 +name : emboss +version : 5.0.0 +build : ha5a061d_4 +build number: 4 +size : 21.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-ha5a061d_4.tar.bz2 +md5 : 4130c639dad030bc7bff54566cf217e7 +timestamp : 2023-05-16 00:43:14 UTC +dependencies: + - python_abi 3.8.* *_cp38 + - zlib + + +emboss 5.0.0 ha6fa2df_5 +----------------------- +file name : emboss-5.0.0-ha6fa2df_5.tar.bz2 +name : emboss +version : 5.0.0 +build : ha6fa2df_5 +build number: 5 +size : 21.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-ha6fa2df_5.tar.bz2 +md5 : 37459eb5f9fe3d2738a153b8e1d04975 +timestamp : 2024-06-05 14:43:17 UTC +dependencies: + - python_abi 3.10.* *_cp310 + - zlib + + +emboss 5.0.0 ha6fa2df_6 +----------------------- +file name : emboss-5.0.0-ha6fa2df_6.tar.bz2 +name : emboss +version : 5.0.0 +build : ha6fa2df_6 +build number: 6 +size : 21.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-ha6fa2df_6.tar.bz2 +md5 : 7e8419ecf52fd0ae68cea035623a2784 +timestamp : 2024-12-12 00:05:43 UTC +dependencies: + - python_abi 3.10.* *_cp310 + - zlib + + +emboss 5.0.0 hc5e4ab4_5 +----------------------- +file name : emboss-5.0.0-hc5e4ab4_5.tar.bz2 +name : emboss +version : 5.0.0 +build : hc5e4ab4_5 +build number: 5 +size : 21.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-hc5e4ab4_5.tar.bz2 +md5 : 900b5803e42c6a8636a21380883ef9b2 +timestamp : 2024-06-05 14:40:39 UTC +dependencies: + - python_abi 3.12.* *_cp312 + - zlib + + +emboss 5.0.0 hc5e4ab4_6 +----------------------- +file name : emboss-5.0.0-hc5e4ab4_6.tar.bz2 +name : emboss +version : 5.0.0 +build : hc5e4ab4_6 +build number: 6 +size : 21.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-hc5e4ab4_6.tar.bz2 +md5 : b764086294fb08b4594f111ec70db3b7 +timestamp : 2024-12-12 00:04:10 UTC +dependencies: + - python_abi 3.12.* *_cp312 + - zlib + + +emboss 5.0.0 hc8dfbb8_1 +----------------------- +file name : emboss-5.0.0-hc8dfbb8_1.tar.bz2 +name : emboss +version : 5.0.0 +build : hc8dfbb8_1 +build number: 1 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-hc8dfbb8_1.tar.bz2 +md5 : 4909875bea9eaf3e63dfadb0aa83108d +timestamp : 2020-05-08 16:10:52 UTC +dependencies: + - python_abi 3.7.* *_cp37m + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 hdff8610_5 +----------------------- +file name : emboss-5.0.0-hdff8610_5.tar.bz2 +name : emboss +version : 5.0.0 +build : hdff8610_5 +build number: 5 +size : 21.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-hdff8610_5.tar.bz2 +md5 : 0418f38acc3573a32f747507537fd731 +timestamp : 2024-06-05 14:39:18 UTC +dependencies: + - python_abi 3.9.* *_cp39 + - zlib + + +emboss 5.0.0 hdff8610_6 +----------------------- +file name : emboss-5.0.0-hdff8610_6.tar.bz2 +name : emboss +version : 5.0.0 +build : hdff8610_6 +build number: 6 +size : 21.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-hdff8610_6.tar.bz2 +md5 : 5b9f2ab7d2fdd14a5c0298f66c8b0bdb +timestamp : 2024-12-12 00:08:30 UTC +dependencies: + - python_abi 3.9.* *_cp39 + - zlib + + +emboss 5.0.0 he4bd417_3 +----------------------- +file name : emboss-5.0.0-he4bd417_3.tar.bz2 +name : emboss +version : 5.0.0 +build : he4bd417_3 +build number: 3 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-he4bd417_3.tar.bz2 +md5 : 8f6f47d43e5f502f0e63e71a46d054e1 +timestamp : 2021-03-28 00:48:38 UTC +dependencies: + - python_abi 3.7.* *_cp37m + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 heb1dbbb_2 +----------------------- +file name : emboss-5.0.0-heb1dbbb_2.tar.bz2 +name : emboss +version : 5.0.0 +build : heb1dbbb_2 +build number: 2 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-heb1dbbb_2.tar.bz2 +md5 : 4fae6400e6a2dcb9da6e6454744e3fff +timestamp : 2020-07-09 22:36:52 UTC +dependencies: + - python_abi 3.6.* *_cp36m + - zlib >=1.2.11,<1.3.0a0 + + +emboss 5.0.0 hef7ab6a_2 +----------------------- +file name : emboss-5.0.0-hef7ab6a_2.tar.bz2 +name : emboss +version : 5.0.0 +build : hef7ab6a_2 +build number: 2 +size : 21.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/emboss-5.0.0-hef7ab6a_2.tar.bz2 +md5 : 81b93 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ena-webin-cli.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ena-webin-cli.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5861b8e42c6a3e00efb56a012294d5b7ec28736 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ena-webin-cli.manual_bundle.txt @@ -0,0 +1,493 @@ +# Tool: ena-webin-cli +software_name: ena-webin-cli +tier: T1 +domain: t1_backfill_overall +downloads: 148284 +summary: Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI). +description: Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI). +dependencies: openjdk >=17, python +execution_environment: Java +execution_environment_reason: inferred from Java runtime dependencies + +## URLs +home_url: https://github.com/enasequence/webin-cli +doc_url: +dev_url: + +## CLI Help Source +java:-help +## CLI Help Content +$ conda run -n bioenv_java java -help +[rc=0] + +Usage: java [-options] class [args...] + (to execute a class) + or java [-options] -jar jarfile [args...] + (to execute a jar file) +where options include: + -d32 use a 32-bit data model if available + -d64 use a 64-bit data model if available + -server to select the "server" VM + The default VM is server, + because you are running on a server-class machine. + + + -cp + -classpath + A : separated list of directories, JAR archives, + and ZIP archives to search for class files. + -D= + set a system property + -verbose:[class|gc|jni] + enable verbose output + -version print product version and exit + -version: + Warning: this feature is deprecated and will be removed + in a future release. + require the specified version to run + -showversion print product version and continue + -jre-restrict-search | -no-jre-restrict-search + Warning: this feature is deprecated and will be removed + in a future release. + include/exclude user private JREs in the version search + -? -help print this help message + -X print help on non-standard options + -ea[:...|:] + -enableassertions[:...|:] + enable assertions with specified granularity + -da[:...|:] + -disableassertions[:...|:] + disable assertions with specified granularity + -esa | -enablesystemassertions + enable system assertions + -dsa | -disablesystemassertions + disable system assertions + -agentlib:[=] + load native agent library , e.g. -agentlib:hprof + see also, -agentlib:jdwp=help and -agentlib:hprof=help + -agentpath:[=] + load native agent library by full pathname + -javaagent:[=] + load Java programming language agent, see java.lang.instrument + -splash: + show splash screen with specified image +See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details. + + + +## URL Docs Extract +### https://github.com/enasequence/webin-cli +GitHub - enasequence/webin-cli: Webin command line submission program. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} enasequence / webin-cli Public Notifications You must be signed in to change notification settings Fork 8 Star 39 Code Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Pull requests Actions Projects Security and quality Insights enasequence/webin-cli master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,087 Commits 1,087 Commits gradle/ wrapper gradle/ wrapper src src .gitignore .gitignore .gitlab-ci.yml .gitlab-ci.yml Dockerfile Dockerfile LICENSE LICENSE README.md README.md build.gradle build.gradle gradlew gradlew gradlew.bat gradlew.bat settings.gradle settings.gradle View all files Repository files navigation README Apache-2.0 license Webin command line submission interface (Webin-CLI) Introduction Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI). Webin submission account credentials are required to use the program. The following types of submissions are supported: genome assemblies transcriptome assemblies annotated sequences read data submissions (Fastq, BAM, CRAM) taxonomy reference sets environmental sequence sets (polysample) For further information about Webin-CLI please refer to: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html Executable Java JAR The latest version of the Webin-CLI can be downloaded from: https://github.com/enasequence/webin-cli/releases The program requires Java 17 or a newer version. Please go here to learn more: https://openjdk.org/install/ The program is run using the java command: java -jar <webin-cli-jar-file> <options> for example: java -jar webin-cli-9.0.3.jar -help To increase the memory available to Webin-CLI please use the -Xms java option: java -Xms2G -jar <webin-cli-jar-file> -help Docker Run Since version 1.8.12 Webin-CLI is available as a docker image: docker pull enasequence/webin-cli docker run --rm -v <local data directory>:/data enasequence/webin-cli -help To increase the memory available to Webin-CLI please set the JAVA_TOOL_OPTIONS environment variable: docker run --rm -v <local data directory>:/data -e JAVA_TOOL_OPTIONS="-Xms2G" enasequence/webin-cli -help Publishing Create docker image with default tags by running gradle dockerTag Testing Testing requires the following environmental variables to be set: webin-cli-username or webinCliUsername webin-cli-password or webinCliPassword Library Jar Publishing To publish webin-cli as a library : gradle publish Support Please contact ENA helpdesk for bugs, features and other issues related to this tool. About Webin command line submission program. Resources Readme License Apache-2.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 39 stars Watchers 6 watching Forks 8 forks Report repository Releases 98 9.0.3 Latest Feb 11, 2026 + 97 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Java 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge ena-webin-cli --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +ena-webin-cli 3.7.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-3.7.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 3.7.0 +build : hdfd78af_0 +build number: 0 +size : 54.3 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-3.7.0-hdfd78af_0.tar.bz2 +md5 : df7fa2bbcb0afd04004517066d92ca72 +timestamp : 2021-04-15 20:48:15 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 4.0.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-4.0.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 4.0.0 +build : hdfd78af_0 +build number: 0 +size : 54.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-4.0.0-hdfd78af_0.tar.bz2 +md5 : 3d577352c194cc3c3f3a9e913f98554a +timestamp : 2021-08-16 14:35:34 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 4.1.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-4.1.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 4.1.0 +build : hdfd78af_0 +build number: 0 +size : 54.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-4.1.0-hdfd78af_0.tar.bz2 +md5 : 1b69c374245b2fd5c6384229046e3dac +timestamp : 2021-08-27 17:11:36 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 4.2.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-4.2.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 4.2.0 +build : hdfd78af_0 +build number: 0 +size : 54.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-4.2.0-hdfd78af_0.tar.bz2 +md5 : 02b0192acfddb815bf6c9a781047b4a8 +timestamp : 2021-10-10 21:34:56 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 4.2.1 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-4.2.1-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 4.2.1 +build : hdfd78af_0 +build number: 0 +size : 54.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-4.2.1-hdfd78af_0.tar.bz2 +md5 : 8ee56696f81fe938d30bec947e047e85 +timestamp : 2021-10-14 12:03:08 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 4.3.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-4.3.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 4.3.0 +build : hdfd78af_0 +build number: 0 +size : 54.5 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-4.3.0-hdfd78af_0.tar.bz2 +md5 : a8b0f2ec83cab9371f460a757ebea410 +timestamp : 2022-02-03 00:59:36 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 4.4.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-4.4.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 4.4.0 +build : hdfd78af_0 +build number: 0 +size : 54.9 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-4.4.0-hdfd78af_0.tar.bz2 +md5 : f49abbe4ad6463fb720e1e458a9cce16 +timestamp : 2022-05-24 12:26:59 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 5.0.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-5.0.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 5.0.0 +build : hdfd78af_0 +build number: 0 +size : 55.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-5.0.0-hdfd78af_0.tar.bz2 +md5 : 7cd16589e272d03b2fb6e47422d752bd +timestamp : 2022-09-23 04:37:57 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 6.5.1 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-6.5.1-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 6.5.1 +build : hdfd78af_0 +build number: 0 +size : 59.5 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-6.5.1-hdfd78af_0.tar.bz2 +md5 : 2bc60af303a86f69a0eb6c7ea445680f +timestamp : 2023-10-04 17:58:37 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 6.6.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-6.6.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 6.6.0 +build : hdfd78af_0 +build number: 0 +size : 59.1 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-6.6.0-hdfd78af_0.tar.bz2 +md5 : 4bd36ab87ccf87cb85275f7b4dde54a2 +timestamp : 2023-10-12 12:30:25 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 6.7.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-6.7.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 6.7.0 +build : hdfd78af_0 +build number: 0 +size : 59.1 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-6.7.0-hdfd78af_0.tar.bz2 +md5 : a5d05fcbd68537dd4b3bed4dcaa3d2ba +timestamp : 2023-10-24 14:20:34 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 6.7.1 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-6.7.1-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 6.7.1 +build : hdfd78af_0 +build number: 0 +size : 59.1 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-6.7.1-hdfd78af_0.tar.bz2 +md5 : a3d4a902b54cb8f3ad0b096dc7292e25 +timestamp : 2023-11-06 17:29:30 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 6.7.2 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-6.7.2-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 6.7.2 +build : hdfd78af_0 +build number: 0 +size : 59.1 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-6.7.2-hdfd78af_0.tar.bz2 +md5 : 559ee6d48bf4a3ca1e0afaabbe5d8a30 +timestamp : 2023-11-10 14:26:43 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 6.8.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-6.8.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 6.8.0 +build : hdfd78af_0 +build number: 0 +size : 59.2 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-6.8.0-hdfd78af_0.tar.bz2 +md5 : 630cdec711aa1feb7307eb4fb384dda3 +timestamp : 2024-01-04 15:24:01 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 6.9.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-6.9.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 6.9.0 +build : hdfd78af_0 +build number: 0 +size : 59.2 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-6.9.0-hdfd78af_0.tar.bz2 +md5 : 7f01b5310fd7913b8fad38f80a23abf0 +timestamp : 2024-01-09 16:24:07 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 6.10.0 hdfd78af_0 +------------------------------- +file name : ena-webin-cli-6.10.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 6.10.0 +build : hdfd78af_0 +build number: 0 +size : 63.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-6.10.0-hdfd78af_0.tar.bz2 +md5 : 616ae259d6b0d71f94965fea3a77b9b9 +timestamp : 2024-01-29 17:20:38 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 7.0.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-7.0.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 7.0.0 +build : hdfd78af_0 +build number: 0 +size : 63.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-7.0.0-hdfd78af_0.tar.bz2 +md5 : 828fed965241cdaaa3a7a882345e358c +timestamp : 2024-02-07 10:23:19 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 7.0.1 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-7.0.1-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 7.0.1 +build : hdfd78af_0 +build number: 0 +size : 65.5 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-7.0.1-hdfd78af_0.tar.bz2 +md5 : 884787a6f0a7db301da29d921e122462 +timestamp : 2024-02-14 17:27:15 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 7.1.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-7.1.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 7.1.0 +build : hdfd78af_0 +build number: 0 +size : 64.1 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-7.1.0-hdfd78af_0.tar.bz2 +md5 : d1be763655de91d82eb5c7c12fab4c8d +timestamp : 2024-03-14 13:29:49 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 7.1.1 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-7.1.1-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 7.1.1 +build : hdfd78af_0 +build number: 0 +size : 64.1 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-7.1.1-hdfd78af_0.tar.bz2 +md5 : 04cd6dd3d1642fa0de2f11dc3a6704d9 +timestamp : 2024-03-19 01:03:33 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 7.2.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-7.2.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 7.2.0 +build : hdfd78af_0 +build number: 0 +size : 64.1 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-7.2.0-hdfd78af_0.tar.bz2 +md5 : 501bb762f51ab124c1a806baeb735ea1 +timestamp : 2024-05-02 11:23:24 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 7.2.1 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-7.2.1-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 7.2.1 +build : hdfd78af_0 +build number: 0 +size : 64.0 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ena-webin-cli-7.2.1-hdfd78af_0.tar.bz2 +md5 : 68e2aa9067a05102c051ae6f35a2240f +timestamp : 2024-05-24 03:05:42 UTC +dependencies: + - openjdk >=8,<9 + - python + + +ena-webin-cli 7.3.0 hdfd78af_0 +------------------------------ +file name : ena-webin-cli-7.3.0-hdfd78af_0.tar.bz2 +name : ena-webin-cli +version : 7.3.0 +build : hdfd78af_0 +build number: 0 +size : 64.0 MB +license : Apache-2.0 +subdir : noarch +url : https: diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/epic.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/epic.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c8151b47f021fb199746d6f09c10bd4048d2dd51 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/epic.manual_bundle.txt @@ -0,0 +1,581 @@ +# Tool: epic +software_name: epic +tier: T1 +domain: t1_backfill_overall +downloads: 120895 +summary: Chip-Seq broad peak/domain finder. +description: Chip-Seq broad peak/domain finder. +dependencies: bedtools, docopt, functools32, joblib, libgcc-ng >=10.3.0, natsort, numpy, pandas, pybigwig, pyfaidx, python >=2.7,<2.8.0a0, python_abi 2.7.* *_cp27mu, scipy, typing +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: http://github.com/endrebak/epic +doc_url: +dev_url: + +## URL Docs Extract +### http://github.com/endrebak/epic +GitHub - biocore-ntnu/epic: (DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} biocore-ntnu / epic Public Notifications You must be signed in to change notification settings Fork 6 Star 31 Code Issues 27 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights biocore-ntnu/epic master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 286 Commits 286 Commits bin bin docs docs epic epic example_pipeline example_pipeline examples examples img img tests tests .gitattributes .gitattributes .gitignore .gitignore .travis.yml .travis.yml CHANGELOG CHANGELOG LICENSE LICENSE README.md README.md bioconda_setup.py bioconda_setup.py helper_scripts.md helper_scripts.md mypy.ini mypy.ini setup.py setup.py View all files Repository files navigation README MIT license DEPRECATED. See https://github.com/endrebak/SICER2 I would recommend you rerun your analyses with epic2 as it uses the exact same recurrence relation computation as SICER, without any heuristics. This is a very minor issue though :) epic: diffuse domain ChIP-Seq caller based on SICER epic is a software package for finding medium to diffusely enriched domains in chip-seq data. It is a fast, parallel and memory-efficient implementation of the incredibly popular SICER algorithm. By running epic on a set of data ("ChIP") files and control ("Input") files, epic is able to quickly differentially enriched regions. epic is an improvement over the original SICER by being faster, more memory efficient, multicore, and significantly much easier to install and use. The MIT-licensed code is available at https://github.com/endrebak/epic The documentation is currently being worked on. Table of Contents epic: diffuse domain ChIP-Seq caller based on SICER Install Changelog Improvements Version License Requirements Helper scripts Usage Credit NAQ/Various Citation For now, please cite the original SICER paper, but include a link to this repo. Install epic is available for python2.7 and above. It can be installed from the Python Package Index with pip install bioepic or preferably from bioconda with conda install -c bioconda epic , or by cloning the repo at https://github.com/endrebak/epic and running python setup.py install Changelog # 0.2.12 (02.08.18) - Fix bug in bigwig creation (due to new pd behavior) # 0.2.11 (01.08.18) - Massive speedup with Cython - Fix bugs added by 0.2.10 # 0.2.10 (31.07.18) - Use categoricals for memory efficiency and speed - Fix bug in epic when using chromsizes Quickstart $ pip install bioepic $ # you only need git clone to get the test data $ git clone https://github.com/endrebak/epic.git $ # -t is treatment files, -c input (control) files $ epic -t epic/examples/test.bed -c epic/examples/control.bed > results.csv Improvements Actively developed Will be maintained and further updated. We hope to make further refinements to the actual algorithm and make it even better. Functionality epic accepts several input and ChIP files at the same time and accepts bed files both block-zipped and gzipped. Works on files of any size. Works on all Python versions 2.7/3+. Speed epic can use one core per chromosome, which should give a speedup of < ~22-25 (differs by species) by itself. In addition, epic uses the Python science stack, including Pandas, for almost all tasks, which means each core runs heavily optimized C, Fortran and Cython code for further speed gains. Memory epic streams the data instead of loading it all into memory, which should result in a much smaller memory footprint. Usage Instead of needing eleven command line arguments to run, epic contains sensible defaults and only needs the files it is to analyze as parameters. epic can be run from whichever location with files found anywhere on the disk. Contains many genomes , with updated effective genome sizes. If your genome isn't listed, please request it! Version This is a beta release. Please do aggressively report issues, quirks, complaints and anything that just feels slightly off to the issue tracker. Also please ask questions and make docrequests - there is loads of neat stuff I have not documented. License MIT Requirements Python data science stack and a fairly recent version of Pandas (0.17 >=). Python 2.7 or 3+. Various unix tools found on all major distributions. For the effective genome size script jellyfish2 is required. Helper scripts See this page for the various helper scripts that are a part of epic. Converting bam files to bed If you have bam files, these can be converted to bed with the command bamToBed -i file.bam > file.bed If you have paired-end data, you can use bamToBed -bedpe -i paired_end_file.bam > file.bedpe Usage (Might be slightly out of date.) usage: epic [-h] --treatment TREATMENT [TREATMENT ...] --control CONTROL [CONTROL ...] [--number-cores NUMBER_CORES] [--genome GENOME] [--keep-duplicates] [--window-size WINDOW_SIZE] [--gaps-allowed GAPS_ALLOWED] [--fragment-size FRAGMENT_SIZE] [--false-discovery-rate-cutoff FALSE_DISCOVERY_RATE_CUTOFF] [--effective_genome_fraction EFFECTIVE_GENOME_FRACTION] [--chromsizes CHROMSIZES] [--store-matrix STORE_MATRIX] [--bigwig BIGWIG] [--sum-bigwig SUM_BIGWIG] [--bed BED] [--log LOG] [--outfile OUTFILE] [--version] Diffuse domain ChIP-Seq caller based on SICER. (Visit github.com/endrebak/epic for examples and help.) optional arguments: -h, --help show this help message and exit --treatment TREATMENT [TREATMENT ...], -t TREATMENT [TREATMENT ...] Treatment (pull-down) file(s) in (b/gzipped) bed/bedpe format. --control CONTROL [CONTROL ...], -c CONTROL [CONTROL ...] Control (input) file(s) in (b/gzipped) bed/bedpe format. --number-cores NUMBER_CORES, -cpu NUMBER_CORES Number of cpus to use. Can use at most one per chromosome. Default: 1. --genome GENOME, -gn GENOME Which genome to analyze. Default: hg19. --keep-duplicates, -k Keep reads mapping to the same position on the same strand within a library. Default is to remove all but the first duplicate. --window-size WINDOW_SIZE, -w WINDOW_SIZE Size of the windows to scan the genome. WINDOW_SIZE is the smallest possible island. Default 200. --gaps-allowed GAPS_ALLOWED, -g GAPS_ALLOWED Multiple of window size used to determine the gap size. Must be an integer. Default: 3. --fragment-size FRAGMENT_SIZE, -fs FRAGMENT_SIZE (Single end reads only) Size of the sequenced fragment. The center of the the fragment will be taken as half the fragment size. Default 150. --false-discovery-rate-cutoff FALSE_DISCOVERY_RATE_CUTOFF, -fdr FALSE_DISCOVERY_RATE_CUTOFF Remove all islands with an FDR below cutoff. Default 0.05. --effective_genome_fraction EFFECTIVE_GENOME_FRACTION, -egf EFFECTIVE_GENOME_FRACTION Use a different effective genome fraction than the one included in epic. The default value depends on the genome and readlength, but is a number between 0 and 1. --chromsizes CHROMSIZES, -cs CHROMSIZES Set the chromosome lengths yourself in a file with two columns: chromosome names and sizes. Useful to analyze custom genomes, assemblies or simulated data. Only chromosomes included in the file will be analyzed. --store-matrix STORE_MATRIX, -sm STORE_MATRIX Store the matrix of counts per bin for ChIP and input to gzipped file <STORE_MATRIX>. --bigwig BIGWIG, -bw BIGWIG For each file, store a bigwig of both enriched and non-enriched regions to folder <BIGWIG>. Requires different basenames for each file. --sum-bigwig SUM_BIGWIG, -sbw SUM_BIGWIG Store two bigwigs - one of ChIP, one of input - to folder <SUM-BIGWIG>. --bed BED, -b BED A summary bed file of all regions for display in the UCSC genome browser or downstream analyses with e.g. bedtools. The score field is log2(#ChIP/#Input) * 100 capped at a 1000. --log LOG, -l LOG File to write log messages to. --outfile OUTFILE, -o OUTFILE File to write results to. By default sent to stdout. --version, -v show program's version number and exit Credit Chongzhi Zang, Dustin E. Schones, Chen Zeng, Kairong Cui, Keji Zhao and Weiqun Peng for the original SICER. Please consider citing their paper ( in addition to our eventual paper) if you use epic. And if you use any (helper) scripts in SICER that are not included in epic you should of course cite the SICER paper! Most of the improvements in epic were possible due to Python Science libraries that were not available when SICER was originally written. Thanks to the Pandas developers! Author Endre Bakken Stovner Contributors Pål Sætrom (algorithmic/theoretical discussions, endless patience) Dario Beraldi (argparsing) Ryan Dale (bioconda, ideas, genome info script) Ryan C. Thompson (bigwig improvements, mypy typing) Thanks Piotr Balwierz (helping me debug the paired-end mode) Keith Siklenka (lending me a subset of some paired-end ChIP-Seq files) Performance, differential ChIP-Seq Briefings in Bioinformatics, 2016, 1–14 NAQ/Various Answers to some questions no-one has ever asked me. Why is the SICER algorithm so great? The wonderful thing about the SICER algorithm is that is very careful about dropping windows with few reads in them. All ChIP-seq callers I know have some preprocessing step where this is done liberally. SICER pools these windows together and gives them a composite score, allowing very long stretches of very diffuse signal to be detected. Why another ChIP-Seq domain caller? MACS2 is great for narrow peaks, but epic performs better on diffuse domains. For medium size domains, such as PolII, our tests indicate that both perform about equally well, but epic uses only a fraction of the time. Why not SICER? SICER contains a great algorithm and is a wonderful piece of software, but advances in the Python data science libraries has made it possible to implement it much more efficiently. Furthermore, SICER was not made to handle the mountains of data we have now; it simply cannot run on very large datasets due to (sensible) restrictions in the original implementation. When is your paper coming out? Dunno. We do not want to write a methods paper, but rather just include a section about epic in an appropriate biology paper sometime. Why the name epic? It stands for electronic pic [sic] caller or epigenome cartographer, whichever you prefer. Or perhaps it isn't just another bogus bioinformatics acronym. Hope you find the name fitting. But suggestions for better names accepted. On paper I liked the epi/epic/epigenetics link but now when I hear it it sounds so boastful I cringe. exorcised sounds like a slight on the original software... Mad MACS? Which other ChIP-Seq callers do you use? SICER - great diffuse domain ChIP-Seq caller (which epic is based on.) SICERpy - a wrapper around SICER for convenience/parallelism. Stole some good ideas from there. csaw - R package. Uses an approach to island finding that complements epic very well. Requires more statistical sophistication and programming skill to use. MACS2 - my preferred peak caller. About (DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER bioepic.readthedocs.io Topics bioinformatics sicer-algorithm chip-seq peak-caller sicer chip-seq-callers Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 31 stars Watchers 5 watching Forks 6 forks Report repository Releases No releases published Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.7% Shell 0.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge epic --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +epic 0.1.17 py27_0 +------------------ +file name : epic-0.1.17-py27_0.tar.bz2 +name : epic +version : 0.1.17 +build : py27_0 +build number: 0 +size : 61 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.17-py27_0.tar.bz2 +md5 : 62f5a3c2218f2f6a5726d891949128b0 +dependencies: + - bedtools + - docopt + - functools32 + - joblib + - natsort + - numpy + - pandas + - pyfaidx + - python 2.7* + - scipy + + +epic 0.1.17 py34_0 +------------------ +file name : epic-0.1.17-py34_0.tar.bz2 +name : epic +version : 0.1.17 +build : py34_0 +build number: 0 +size : 62 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.17-py34_0.tar.bz2 +md5 : ab4262a5ff82cfafa0cc86e441da7e10 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pyfaidx + - python 3.4* + - scipy + + +epic 0.1.17 py35_0 +------------------ +file name : epic-0.1.17-py35_0.tar.bz2 +name : epic +version : 0.1.17 +build : py35_0 +build number: 0 +size : 62 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.17-py35_0.tar.bz2 +md5 : 1b31c05c83023263bf51ff511c72f9d2 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pyfaidx + - python 3.5* + - scipy + + +epic 0.1.20 py27_0 +------------------ +file name : epic-0.1.20-py27_0.tar.bz2 +name : epic +version : 0.1.20 +build : py27_0 +build number: 0 +size : 62 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.20-py27_0.tar.bz2 +md5 : 8c44b511fa85625efd309597a8b0f14d +dependencies: + - bedtools + - docopt + - functools32 + - joblib + - natsort + - numpy + - pandas + - pyfaidx + - python 2.7* + - scipy + + +epic 0.1.20 py34_0 +------------------ +file name : epic-0.1.20-py34_0.tar.bz2 +name : epic +version : 0.1.20 +build : py34_0 +build number: 0 +size : 62 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.20-py34_0.tar.bz2 +md5 : fc56e0885e5a790611a0d3265bb62456 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pyfaidx + - python 3.4* + - scipy + + +epic 0.1.20 py35_0 +------------------ +file name : epic-0.1.20-py35_0.tar.bz2 +name : epic +version : 0.1.20 +build : py35_0 +build number: 0 +size : 62 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.20-py35_0.tar.bz2 +md5 : f982bd008dfb073e9adf49eee0c92956 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pyfaidx + - python 3.5* + - scipy + + +epic 0.1.24 py27_0 +------------------ +file name : epic-0.1.24-py27_0.tar.bz2 +name : epic +version : 0.1.24 +build : py27_0 +build number: 0 +size : 70 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.24-py27_0.tar.bz2 +md5 : 523fdf2c7cb48174996337584b747564 +dependencies: + - bedtools + - docopt + - functools32 + - joblib + - natsort + - numpy + - pandas + - pyfaidx + - python 2.7* + - scipy + - typing + + +epic 0.1.24 py34_0 +------------------ +file name : epic-0.1.24-py34_0.tar.bz2 +name : epic +version : 0.1.24 +build : py34_0 +build number: 0 +size : 71 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.24-py34_0.tar.bz2 +md5 : 739bc123276caacde476e8ca6fb23281 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pyfaidx + - python 3.4* + - scipy + - typing + + +epic 0.1.24 py35_0 +------------------ +file name : epic-0.1.24-py35_0.tar.bz2 +name : epic +version : 0.1.24 +build : py35_0 +build number: 0 +size : 71 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.24-py35_0.tar.bz2 +md5 : 0d5591188993164a27c6f011314ac018 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pyfaidx + - python 3.5* + - scipy + - typing + + +epic 0.1.24 py36_0 +------------------ +file name : epic-0.1.24-py36_0.tar.bz2 +name : epic +version : 0.1.24 +build : py36_0 +build number: 0 +size : 71 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.24-py36_0.tar.bz2 +md5 : 722dc893aaf5b682717fcb1aa53f2f04 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pyfaidx + - python 3.6* + - scipy + - typing + + +epic 0.1.25 py27_0 +------------------ +file name : epic-0.1.25-py27_0.tar.bz2 +name : epic +version : 0.1.25 +build : py27_0 +build number: 0 +size : 81 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.25-py27_0.tar.bz2 +md5 : 574d2c17197e0a5a268f7c9412d1df07 +dependencies: + - bedtools + - docopt + - functools32 + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 2.7* + - scipy + - typing + + +epic 0.1.25 py35_0 +------------------ +file name : epic-0.1.25-py35_0.tar.bz2 +name : epic +version : 0.1.25 +build : py35_0 +build number: 0 +size : 82 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.25-py35_0.tar.bz2 +md5 : afaa581740a4a002cb0130845cf3637c +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 3.5* + - scipy + - typing + + +epic 0.1.25 py36_0 +------------------ +file name : epic-0.1.25-py36_0.tar.bz2 +name : epic +version : 0.1.25 +build : py36_0 +build number: 0 +size : 81 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.25-py36_0.tar.bz2 +md5 : 6b17d82554c5391696aa8e60de7c7aa5 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 3.6* + - scipy + - typing + + +epic 0.1.26 py27_0 +------------------ +file name : epic-0.1.26-py27_0.tar.bz2 +name : epic +version : 0.1.26 +build : py27_0 +build number: 0 +size : 81 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.26-py27_0.tar.bz2 +md5 : 57ae88a616ae75a76065ecc54f97c92a +dependencies: + - bedtools + - docopt + - functools32 + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 2.7* + - scipy + - typing + + +epic 0.1.26 py35_0 +------------------ +file name : epic-0.1.26-py35_0.tar.bz2 +name : epic +version : 0.1.26 +build : py35_0 +build number: 0 +size : 82 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.26-py35_0.tar.bz2 +md5 : 939b5b570a944ea3a2935cce0d177656 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 3.5* + - scipy + - typing + + +epic 0.1.26 py36_0 +------------------ +file name : epic-0.1.26-py36_0.tar.bz2 +name : epic +version : 0.1.26 +build : py36_0 +build number: 0 +size : 81 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.26-py36_0.tar.bz2 +md5 : 2798423b83ed4bf1b2fc5b945ba975d0 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 3.6* + - scipy + - typing + + +epic 0.1.27 py27_0 +------------------ +file name : epic-0.1.27-py27_0.tar.bz2 +name : epic +version : 0.1.27 +build : py27_0 +build number: 0 +size : 87 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.27-py27_0.tar.bz2 +md5 : 06b25ffabb16a03dcb8eaac4930ccedc +dependencies: + - bedtools + - docopt + - functools32 + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 2.7* + - scipy + - typing + + +epic 0.1.27 py35_0 +------------------ +file name : epic-0.1.27-py35_0.tar.bz2 +name : epic +version : 0.1.27 +build : py35_0 +build number: 0 +size : 88 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.27-py35_0.tar.bz2 +md5 : 502a4d986c8286007b9fb5dd7a0579dc +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 3.5* + - scipy + - typing + + +epic 0.1.27 py36_0 +------------------ +file name : epic-0.1.27-py36_0.tar.bz2 +name : epic +version : 0.1.27 +build : py36_0 +build number: 0 +size : 88 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.27-py36_0.tar.bz2 +md5 : a2c1372ec179512de16344a344e64f7b +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 3.6* + - scipy + - typing + + +epic 0.1.28 py27_0 +------------------ +file name : epic-0.1.28-py27_0.tar.bz2 +name : epic +version : 0.1.28 +build : py27_0 +build number: 0 +size : 87 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.28-py27_0.tar.bz2 +md5 : 9307129cd11f4ee737b1050c0ce29c3f +dependencies: + - bedtools + - docopt + - functools32 + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 2.7* + - scipy + - typing + + +epic 0.1.28 py35_0 +------------------ +file name : epic-0.1.28-py35_0.tar.bz2 +name : epic +version : 0.1.28 +build : py35_0 +build number: 0 +size : 88 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.28-py35_0.tar.bz2 +md5 : 31e24eaf2c16e704ab70a3689fae8643 +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas + - pybigwig + - pyfaidx + - python 3.5* + - scipy + - typing + + +epic 0.1.28 py36_0 +------------------ +file name : epic-0.1.28-py36_0.tar.bz2 +name : epic +version : 0.1.28 +build : py36_0 +build number: 0 +size : 88 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/epic-0.1.28-py36_0.tar.bz2 +md5 : 7cdcd643119e7ddbc8700a43733779de +dependencies: + - bedtools + - docopt + - joblib + - natsort + - numpy + - pandas diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/eva-sub-cli.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/eva-sub-cli.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..645971a0966d5a02b45184ef4d34d2a6d9582385 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/eva-sub-cli.manual_bundle.txt @@ -0,0 +1,491 @@ +# Tool: eva-sub-cli +software_name: eva-sub-cli +tier: T1 +domain: t1_backfill_overall +downloads: 164573 +summary: EVA Submission Command Line Interface. +description: EVA Submission Command Line Interface. +dependencies: ebi-eva-common-pyutils >=0.7.1, jinja2, jsonschema, nextflow >=23.10.1, nodejs >=20.1.0, openpyxl, packaging, pysam, python >=3.13,<3.14.0a0, pyyaml, requests, vcf-validator >=0.10.0 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/EBIvariation/eva-sub-cli +doc_url: https://github.com/EBIvariation/eva-sub-cli/blob/main/docs/Getting_Started_with_eva_sub_cli.md +dev_url: https://github.com/EBIvariation/eva-sub-cli + +## URL Docs Extract +### https://github.com/EBIvariation/eva-sub-cli +GitHub - EBIvariation/eva-sub-cli: EVA Submission Command Line Interface for Validation · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} EBIvariation / eva-sub-cli Public Notifications You must be signed in to change notification settings Fork 6 Star 0 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights EBIvariation/eva-sub-cli main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 641 Commits 641 Commits .github/ workflows .github/ workflows conda conda docker docker docs docs eva_sub_cli eva_sub_cli tests tests .gitignore .gitignore LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml pytest.ini pytest.ini requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README Apache-2.0 license eva-sub-cli Please view our documentation website for help installing and using eva-sub-cli. About EVA Submission Command Line Interface for Validation Resources Readme License Apache-2.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 0 stars Watchers 3 watching Forks 6 forks Report repository Releases 22 v0.6.1 Latest Mar 26, 2026 + 21 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages HTML 65.3% Python 33.4% Nextflow 1.1% Other 0.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/EBIvariation/eva-sub-cli +GitHub - EBIvariation/eva-sub-cli: EVA Submission Command Line Interface for Validation · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} EBIvariation / eva-sub-cli Public Notifications You must be signed in to change notification settings Fork 6 Star 0 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights EBIvariation/eva-sub-cli main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 641 Commits 641 Commits .github/ workflows .github/ workflows conda conda docker docker docs docs eva_sub_cli eva_sub_cli tests tests .gitignore .gitignore LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml pytest.ini pytest.ini requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README Apache-2.0 license eva-sub-cli Please view our documentation website for help installing and using eva-sub-cli. About EVA Submission Command Line Interface for Validation Resources Readme License Apache-2.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 0 stars Watchers 3 watching Forks 6 forks Report repository Releases 22 v0.6.1 Latest Mar 26, 2026 + 21 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages HTML 65.3% Python 33.4% Nextflow 1.1% Other 0.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge eva-sub-cli --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +eva-sub-cli 0.2 py312hdfd78af_0 +------------------------------- +file name : eva-sub-cli-0.2-py312hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.2 +build : py312hdfd78af_0 +build number: 0 +size : 17.9 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.2-py312hdfd78af_0.tar.bz2 +md5 : 1727ada67fe105d0ecf99ae7e62e13c6 +timestamp : 2024-03-28 01:55:35 UTC +dependencies: + - ebi-eva-common-pyutils >=0.6.1 + - jinja2 + - jsonschema + - nextflow >=21.10.0 + - nodejs >=10.19.1 + - openpyxl + - python >=3.8 + - pyyaml + - requests + - vcf-validator >=0.9.6 + + +eva-sub-cli 0.3 py312hdfd78af_0 +------------------------------- +file name : eva-sub-cli-0.3-py312hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.3 +build : py312hdfd78af_0 +build number: 0 +size : 18.0 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.3-py312hdfd78af_0.tar.bz2 +md5 : 343f04aecb9b34d5749b4e4f6b509977 +timestamp : 2024-05-24 03:32:20 UTC +dependencies: + - ebi-eva-common-pyutils >=0.6.1 + - jinja2 + - jsonschema + - nextflow >=21.10.0 + - nodejs >=10.19.1 + - openpyxl + - python >=3.8 + - pyyaml + - requests + - vcf-validator >=0.9.6 + + +eva-sub-cli 0.4 py312hdfd78af_0 +------------------------------- +file name : eva-sub-cli-0.4-py312hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4 +build : py312hdfd78af_0 +build number: 0 +size : 17.9 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4-py312hdfd78af_0.tar.bz2 +md5 : 49e83850c1cdf96fe2fe213893075b18 +timestamp : 2024-09-17 18:04:17 UTC +dependencies: + - ebi-eva-common-pyutils >=0.6.1 + - jinja2 + - jsonschema + - nextflow >=21.10.0 + - nodejs >=10.19.1 + - openpyxl + - python >=3.8 + - pyyaml + - requests + - vcf-validator >=0.9.7 + + +eva-sub-cli 0.4.1 py313hdfd78af_0 +--------------------------------- +file name : eva-sub-cli-0.4.1-py313hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.1 +build : py313hdfd78af_0 +build number: 0 +size : 17.9 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.1-py313hdfd78af_0.tar.bz2 +md5 : 5cc7822ce9d8bf3321745e370f237065 +timestamp : 2024-11-05 11:28:37 UTC +dependencies: + - ebi-eva-common-pyutils >=0.6.1 + - jinja2 + - jsonschema + - nextflow >=21.10.0 + - nodejs >=10.19.1 + - openpyxl + - python >=3.8 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.2 py313hdfd78af_0 +--------------------------------- +file name : eva-sub-cli-0.4.2-py313hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.2 +build : py313hdfd78af_0 +build number: 0 +size : 17.9 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.2-py313hdfd78af_0.tar.bz2 +md5 : a657069b6e9486e78cd3944322f81b61 +timestamp : 2024-12-02 17:19:39 UTC +dependencies: + - ebi-eva-common-pyutils >=0.6.1 + - jinja2 + - jsonschema + - nextflow >=21.10.0 + - nodejs >=10.19.1 + - openpyxl + - python >=3.8 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.3 py313hdfd78af_0 +--------------------------------- +file name : eva-sub-cli-0.4.3-py313hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.3 +build : py313hdfd78af_0 +build number: 0 +size : 18.0 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.3-py313hdfd78af_0.tar.bz2 +md5 : d84a71727dce37de406ff795a1cee949 +timestamp : 2025-01-14 19:24:38 UTC +dependencies: + - ebi-eva-common-pyutils >=0.6.1 + - jinja2 + - jsonschema + - nextflow >=21.10.0 + - nodejs >=10.19.1 + - openpyxl + - python >=3.8 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.4 py313hdfd78af_0 +--------------------------------- +file name : eva-sub-cli-0.4.4-py313hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.4 +build : py313hdfd78af_0 +build number: 0 +size : 17.8 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.4-py313hdfd78af_0.tar.bz2 +md5 : 45c8f10c95590ac647113f75282dbe98 +timestamp : 2025-03-03 15:25:57 UTC +dependencies: + - ebi-eva-common-pyutils >=0.6.1 + - jinja2 + - jsonschema + - nextflow >=21.10.0 + - nodejs >=10.19.1 + - openpyxl + - python >=3.8 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.6 py313hdfd78af_0 +--------------------------------- +file name : eva-sub-cli-0.4.6-py313hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.6 +build : py313hdfd78af_0 +build number: 0 +size : 17.9 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.6-py313hdfd78af_0.tar.bz2 +md5 : 2a5af7439a5339f4339de0eeac356534 +timestamp : 2025-04-02 12:47:16 UTC +dependencies: + - ebi-eva-common-pyutils >=0.6.1 + - jinja2 + - jsonschema + - nextflow >=21.10.0 + - nodejs >=10.19.1 + - openpyxl + - packaging + - python >=3.8 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.7 py312hdfd78af_0 +--------------------------------- +file name : eva-sub-cli-0.4.7-py312hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.7 +build : py312hdfd78af_0 +build number: 0 +size : 17.8 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.7-py312hdfd78af_0.tar.bz2 +md5 : 0be211253780f390420c94fa6c190afc +timestamp : 2025-05-29 15:09:23 UTC +dependencies: + - ebi-eva-common-pyutils >=0.7.1 + - jinja2 + - jsonschema + - nextflow >=23.10.1 + - nodejs >=20.1.0 + - openpyxl + - packaging + - python >=3.6 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.8 py312hdfd78af_0 +--------------------------------- +file name : eva-sub-cli-0.4.8-py312hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.8 +build : py312hdfd78af_0 +build number: 0 +size : 18.0 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.8-py312hdfd78af_0.tar.bz2 +md5 : e2882a026584d2d427510dfe2c9b5bf4 +timestamp : 2025-06-11 09:26:20 UTC +dependencies: + - ebi-eva-common-pyutils >=0.7.1 + - jinja2 + - jsonschema + - nextflow >=23.10.1 + - nodejs >=20.1.0 + - openpyxl + - packaging + - python >=3.6 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.9 py313hdfd78af_0 +--------------------------------- +file name : eva-sub-cli-0.4.9-py313hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.9 +build : py313hdfd78af_0 +build number: 0 +size : 17.9 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.9-py313hdfd78af_0.tar.bz2 +md5 : 33f8799dfab55327ca58a0a29e185510 +timestamp : 2025-06-20 10:17:22 UTC +dependencies: + - ebi-eva-common-pyutils >=0.7.1 + - jinja2 + - jsonschema + - nextflow >=23.10.1 + - nodejs >=20.1.0 + - openpyxl + - packaging + - python >=3.6 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.10 py313hdfd78af_0 +---------------------------------- +file name : eva-sub-cli-0.4.10-py313hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.10 +build : py313hdfd78af_0 +build number: 0 +size : 17.9 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.10-py313hdfd78af_0.tar.bz2 +md5 : 77f148fb62fed19df572b32c6d3451d3 +timestamp : 2025-07-08 11:19:26 UTC +dependencies: + - ebi-eva-common-pyutils >=0.7.1 + - jinja2 + - jsonschema + - nextflow >=23.10.1 + - nodejs >=20.1.0 + - openpyxl + - packaging + - python >=3.6 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.11 py313hdfd78af_0 +---------------------------------- +file name : eva-sub-cli-0.4.11-py313hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.11 +build : py313hdfd78af_0 +build number: 0 +size : 17.8 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.11-py313hdfd78af_0.tar.bz2 +md5 : cbe4c22f4097c3479caac8a715cec733 +timestamp : 2025-07-24 19:24:24 UTC +dependencies: + - ebi-eva-common-pyutils >=0.7.1 + - jinja2 + - jsonschema + - nextflow >=23.10.1 + - nodejs >=20.1.0 + - openpyxl + - packaging + - pysam + - python >=3.6 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.12 py313hdfd78af_0 +---------------------------------- +file name : eva-sub-cli-0.4.12-py313hdfd78af_0.tar.bz2 +name : eva-sub-cli +version : 0.4.12 +build : py313hdfd78af_0 +build number: 0 +size : 18.0 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.12-py313hdfd78af_0.tar.bz2 +md5 : 82dd56e29b2c886fbc847fbe0f480862 +timestamp : 2025-08-08 10:28:18 UTC +dependencies: + - ebi-eva-common-pyutils >=0.7.1 + - jinja2 + - jsonschema + - nextflow >=23.10.1 + - nodejs >=20.1.0 + - openpyxl + - packaging + - pysam + - python >=3.6 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.13 py313hdfd78af_0 +---------------------------------- +file name : eva-sub-cli-0.4.13-py313hdfd78af_0.conda +name : eva-sub-cli +version : 0.4.13 +build : py313hdfd78af_0 +build number: 0 +size : 17.6 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.13-py313hdfd78af_0.conda +md5 : 99473c3c07b0b469165c2fc90fa20805 +timestamp : 2025-09-03 14:27:59 UTC +dependencies: + - ebi-eva-common-pyutils >=0.7.1 + - jinja2 + - jsonschema + - nextflow >=23.10.1 + - nodejs >=20.1.0 + - openpyxl + - packaging + - pysam + - python >=3.13,<3.14.0a0 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.4.14 py313hdfd78af_0 +---------------------------------- +file name : eva-sub-cli-0.4.14-py313hdfd78af_0.conda +name : eva-sub-cli +version : 0.4.14 +build : py313hdfd78af_0 +build number: 0 +size : 17.6 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.4.14-py313hdfd78af_0.conda +md5 : 283a47f26c1f0ec4897caa96f408366e +timestamp : 2025-09-24 13:26:28 UTC +dependencies: + - ebi-eva-common-pyutils >=0.7.1 + - jinja2 + - jsonschema + - nextflow >=23.10.1 + - nodejs >=20.1.0 + - openpyxl + - packaging + - pysam + - python >=3.13,<3.14.0a0 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.5.0 py313hdfd78af_0 +--------------------------------- +file name : eva-sub-cli-0.5.0-py313hdfd78af_0.conda +name : eva-sub-cli +version : 0.5.0 +build : py313hdfd78af_0 +build number: 0 +size : 17.5 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/eva-sub-cli-0.5.0-py313hdfd78af_0.conda +md5 : 0dadfa745c2801cb2c42dd377bfc231d +timestamp : 2025-10-21 11:32:19 UTC +dependencies: + - ebi-eva-common-pyutils >=0.7.1 + - jinja2 + - jsonschema + - nextflow >=23.10.1 + - nodejs >=20.1.0 + - openpyxl + - packaging + - pysam + - python >=3.13,<3.14.0a0 + - pyyaml + - requests + - vcf-validator >=0.10.0 + + +eva-sub-cli 0.5.1 py313hdfd78af_0 +--------------------------------- +file name : eva-sub-cli-0.5.1-py313hdfd78af_0.conda +name : eva-sub-cli +version : 0.5.1 +build diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fast5.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fast5.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..813334b7989740d78cd29500efbf2a1d48ed2453 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fast5.manual_bundle.txt @@ -0,0 +1,296 @@ +# Tool: fast5 +software_name: fast5 +tier: T1 +domain: t1_backfill_overall +downloads: 246898 +summary: A C++ header-only library for reading Oxford Nanopore Fast5 files. +description: A C++ header-only library for reading Oxford Nanopore Fast5 files. +dependencies: hdf5 +execution_environment: Other +execution_environment_reason: fallback runtime classification + +## URLs +home_url: https://github.com/mateidavid/fast5 +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/mateidavid/fast5 +GitHub - mateidavid/fast5: A C++ header-only library for reading Oxford Nanopore Fast5 files · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} mateidavid / fast5 Public Notifications You must be signed in to change notification settings Fork 16 Star 53 Code Issues 7 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights mateidavid/fast5 master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 262 Commits 262 Commits include include python python src src .VERSION.in .VERSION.in .gitignore .gitignore .travis.Dockerfile.in .travis.Dockerfile.in .travis.yml .travis.yml .version_files .version_files Doxyfile Doxyfile LICENSE LICENSE README.org README.org VERSION VERSION View all files Repository files navigation README MIT license Fast5 Library A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data. Installation Core C++ Library The core library is written in header-only C++11, and it enables read-write access to fast5 files from C++ code. The core library requires no installation, other than setting the compiler’s include path to find fast5.hpp . See f5ls-full.cpp for an example. The core library is built on top the HDF5 C API, so the compiler must also be able to find the HDF5 headers and libraries. See the project’s Travis CI Dockerfile for an example of how to install prerequisites on Debian Jessie. Python Wrapper The Python wrapper for the core library enables read-only access to fast5 files from Python code. The wrapper also adds several Python scripts: f5ls Summarize contents of fast5 files. f5pack Pack and unpack fast5 files. For a detailed description of this tool, see our blog post . The Python wrapper also depends on Cython. To build the Python wrapper: # set paths to HDF5 export HDF5_INCLUDE_DIR=/path/to/hdf5.h export HDF5_LIB_DIR=/path/to/libhdf5.so # either make -C python develop # to install in a virtualenv # or make -C python develop-user # to install in user mode License MIT License . About A C++ header-only library for reading Oxford Nanopore Fast5 files Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 53 stars Watchers 6 watching Forks 16 forks Report repository Releases 14 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 86.2% Python 7.6% Cython 5.3% Makefile 0.9% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge fast5 --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +fast5 0.2.0 0 +------------- +file name : fast5-0.2.0-0.tar.bz2 +name : fast5 +version : 0.2.0 +build : 0 +build number: 0 +size : 10 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.2.0-0.tar.bz2 +md5 : db07f718810149a8729c4a8b5cdb5fe9 +dependencies: [] + + +fast5 0.5.6 0 +------------- +file name : fast5-0.5.6-0.tar.bz2 +name : fast5 +version : 0.5.6 +build : 0 +build number: 0 +size : 16 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.5.6-0.tar.bz2 +md5 : 2cbe3a87a1d0cba08e51fb3bb85c10f2 +dependencies: [] + + +fast5 0.5.8 0 +------------- +file name : fast5-0.5.8-0.tar.bz2 +name : fast5 +version : 0.5.8 +build : 0 +build number: 0 +size : 17 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.5.8-0.tar.bz2 +md5 : e6a322138db665759393b894351618d3 +dependencies: + - hdf5 + + +fast5 0.5.9 0 +------------- +file name : fast5-0.5.9-0.tar.bz2 +name : fast5 +version : 0.5.9 +build : 0 +build number: 0 +size : 17 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.5.9-0.tar.bz2 +md5 : 80ce60e2393ff9a843b8ec6f644f038b +dependencies: + - hdf5 + + +fast5 0.5.10a 0 +--------------- +file name : fast5-0.5.10a-0.tar.bz2 +name : fast5 +version : 0.5.10a +build : 0 +build number: 0 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.5.10a-0.tar.bz2 +md5 : e7e2369ded4452af5445c355791e9b51 +dependencies: + - hdf5 + + +fast5 0.6.1 0 +------------- +file name : fast5-0.6.1-0.tar.bz2 +name : fast5 +version : 0.6.1 +build : 0 +build number: 0 +size : 25 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.6.1-0.tar.bz2 +md5 : bb53e68405a0095fa0b3eef880f208f3 +dependencies: + - hdf5 + + +fast5 0.6.2.p1 0 +---------------- +file name : fast5-0.6.2.p1-0.tar.bz2 +name : fast5 +version : 0.6.2.p1 +build : 0 +build number: 0 +size : 25 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.6.2.p1-0.tar.bz2 +md5 : 248b9d4c6f898c3f636121719dd3b324 +dependencies: + - hdf5 + + +fast5 0.6.2.p1 1 +---------------- +file name : fast5-0.6.2.p1-1.tar.bz2 +name : fast5 +version : 0.6.2.p1 +build : 1 +build number: 1 +size : 34 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.6.2.p1-1.tar.bz2 +md5 : cb273e42cde3a6137ba34a628d2a80fc +dependencies: + - hdf5 + + +fast5 0.6.2.p1 2 +---------------- +file name : fast5-0.6.2.p1-2.tar.bz2 +name : fast5 +version : 0.6.2.p1 +build : 2 +build number: 2 +size : 35 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.6.2.p1-2.tar.bz2 +md5 : 87e7d2f89bcd24ceb411113facec9187 +dependencies: + - hdf5 + + +fast5 0.6.2.p1 3 +---------------- +file name : fast5-0.6.2.p1-3.tar.bz2 +name : fast5 +version : 0.6.2.p1 +build : 3 +build number: 3 +size : 39 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.6.2.p1-3.tar.bz2 +md5 : 8b2c54b13e66dec7df7ebaa8b08d0706 +dependencies: + - hdf5 + + +fast5 0.6.2 0 +------------- +file name : fast5-0.6.2-0.tar.bz2 +name : fast5 +version : 0.6.2 +build : 0 +build number: 0 +size : 25 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.6.2-0.tar.bz2 +md5 : 9dd63d02abf47d06b35c5ed5d75170c8 +dependencies: + - hdf5 + + +fast5 0.6.3.p1 0 +---------------- +file name : fast5-0.6.3.p1-0.tar.bz2 +name : fast5 +version : 0.6.3.p1 +build : 0 +build number: 0 +size : 36 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.6.3.p1-0.tar.bz2 +md5 : 30d2f70b9a966aed96fd494d2a68b739 +dependencies: + - hdf5 1.8.17* + + +fast5 0.6.4 0 +------------- +file name : fast5-0.6.4-0.tar.bz2 +name : fast5 +version : 0.6.4 +build : 0 +build number: 0 +size : 36 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.6.4-0.tar.bz2 +md5 : 68f158d6b0122e537b428a2097e77c7d +dependencies: + - hdf5 1.8.17* + + +fast5 0.6.5 0 +------------- +file name : fast5-0.6.5-0.tar.bz2 +name : fast5 +version : 0.6.5 +build : 0 +build number: 0 +size : 36 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.6.5-0.tar.bz2 +md5 : 795f4203a88b3275dfa16e3cee3a06b3 +dependencies: + - hdf5 1.8.17* + + +fast5 0.6.5 1 +------------- +file name : fast5-0.6.5-1.tar.bz2 +name : fast5 +version : 0.6.5 +build : 1 +build number: 1 +size : 36 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fast5-0.6.5-1.tar.bz2 +md5 : 16a33ea85ebb6f040e9acd65b3631525 +timestamp : 2018-06-25 16:04:36 UTC +dependencies: + - hdf5 + + +fast5 0.6.5 2 +------------- +file name : fast5-0.6.5-2.tar.bz2 +name : fast5 +version : 0.6.5 +build : 2 +build number: 2 +size : 37 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/fast5-0.6.5-2.tar.bz2 +md5 : f0909ed584a4258025a5f56dcdeadf77 +timestamp : 2019-10-27 15:35:03 UTC +dependencies: + - hdf5 + + +fast5 0.6.5 hdfd78af_3 +---------------------- +file name : fast5-0.6.5-hdfd78af_3.tar.bz2 +name : fast5 +version : 0.6.5 +build : hdfd78af_3 +build number: 3 +size : 38 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/fast5-0.6.5-hdfd78af_3.tar.bz2 +md5 : 165b97f00f943651e1c1c199f11bdacd +timestamp : 2021-03-26 19:20:58 UTC +dependencies: + - hdf5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fastani.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fastani.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..5009e460b6f114bca471584935103f0943656f3f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fastani.manual_bundle.txt @@ -0,0 +1,400 @@ +# Tool: fastani +software_name: fastani +tier: T1 +domain: t1_backfill_overall +downloads: 145811 +summary: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). +description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). +dependencies: _openmp_mutex >=4.5, gsl >=2.8,<2.9.0a0, libgcc >=13, libgomp, libstdcxx >=13, libzlib >=1.3.1,<2.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/ParBLiSS/FastANI +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/ParBLiSS/FastANI +GitHub - ParBLiSS/FastANI: Fast Whole-Genome Similarity (ANI) Estimation · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} ParBLiSS / FastANI Public Notifications You must be signed in to change notification settings Fork 73 Star 455 Code Issues 72 Pull requests 5 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights ParBLiSS/FastANI master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 369 Commits 369 Commits .github/ workflows .github/ workflows ext ext scripts scripts src src tests tests .gitignore .gitignore .gitmodules .gitmodules CMakeLists.txt CMakeLists.txt INSTALL.txt INSTALL.txt LICENSE LICENSE Makefile.in Makefile.in README.md README.md bootstrap.sh bootstrap.sh configure.ac configure.ac cppcheck_report.txt cppcheck_report.txt View all files Repository files navigation README Apache-2.0 license FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Its underlying procedure follows a similar workflow as described by Goris et al. 2007 . However, it avoids expensive sequence alignments and uses Mashmap as its MinHash based sequence mapping engine to compute the orthologous mappings and alignment identity estimates. Based on our experiments with complete and draft genomes, its accuracy is on par with BLAST-based ANI solver and it achieves two to three orders of magnitude speedup. Therefore, it is useful for pairwise ANI computation of large number of genome pairs. More details about its speed, accuracy and potential applications are described here: " High Throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries ". Download and Compile Clone the software from Github and follow INSTALL.txt to compile the code. There is also an option to download dependency-free binary for Linux or OSX through the latest release . Usage Summary Produce help page. Quickly check the software usage and available command line options. $ ./fastANI -h One to One. Compute ANI between single query and single reference genome: $ ./fastANI -q [QUERY_GENOME] -r [REFERENCE_GENOME] -o [OUTPUT_FILE] Here QUERY_GENOME and REFERENCE_GENOME are the query genome assemblies in fasta or multi-fasta format. Gzip compressed fasta files are also acceptable. One to Many. Compute ANI between single query genome and multiple reference genomes: $ ./fastANI -q [QUERY_GENOME] --rl [REFERENCE_LIST] -o [OUTPUT_FILE] For above use case, REFERENCE_LIST should be a file containing directory paths to reference genomes, one per line. Many to Many. When there are multiple query genomes and multiple reference genomes: $ ./fastANI --ql [QUERY_LIST] --rl [REFERENCE_LIST] -o [OUTPUT_FILE] Again, QUERY_LIST and REFERENCE_LIST are files containing paths to genomes, one per line. Output format. In all above use cases, OUTPUT_FILE will contain tab delimited row(s) with query genome, reference genome, ANI value, count of bidirectional fragment mappings, and total query fragments. Alignment fraction (wrt. the query genome) is simply the ratio of mappings and total fragments. Optionally, users can also get a second .matrix file with identity values arranged in a phylip-formatted lower triangular matrix by supplying --matrix parameter. NOTE: No ANI output is reported for a genome pair if ANI value is much below 80%. Such case should be computed at amino acid level . Two genome assemblies are provided in data folder to do a quick test run. We suggest users to do an adequate quality check of their input genome assemblies (both reference and query), especially the N50 be ≥10 Kbp. An Example Run One to One. Here we compute ANI between Escherichia coli and Shigella flexneri genomes provided in the data folder. $ ./fastANI -q data/Shigella_flexneri_2a_01.fna -r data/Escherichia_coli_str_K12_MG1655.fna -o fastani.out Expect output log in the following format in the console: $ ./fastANI -q data/Shigella_flexneri_2a_01.fna -r data/Escherichia_coli_str_K12_MG1655.fna -o fastani.out >>>>>>>>>>>>>>>>>> Reference = [data/Escherichia_coli_str_K12_MG1655.fna] Query = [data/Shigella_flexneri_2a_01.fna] Kmer size = 16 Fragment length = 3000 Threads = 1 ANI output file = fastani.out >>>>>>>>>>>>>>>>>> .... .... INFO, skch::main, Time spent post mapping : 0.00310319 sec Output is saved in file fastani.out , provided above using the -o option. $ cat fastani.out data/Shigella_flexneri_2a_01.fna data/Escherichia_coli_str_K12_MG1655.fna 97.7507 1303 1608 Above output implies that the ANI estimate between S. flexneri and E. coli genomes is 97.7507. Out of the total 1608 sequence fragments from S. flexneri genome, 1303 were aligned as orthologous matches. Visualize Conserved Regions b/w Two Genomes FastANI supports visualization of the reciprocal mappings computed between two genomes. Getting this visualization requires a one to one comparison using FastANI as discussed above, except an additional flag --visualize should be provided. This flag forces FastANI to output a mapping file (with .visual extension) that contains information of all the reciprocal mappings. Finally, an R script is provided in the repository which uses genoPlotR package to plot these mappings. Here we show an example run using two genomes: Bartonella quintana ( GenBank: CP003784.1 ) and Bartonella henselae ( NCBI Reference Sequence: NC_005956.1 ). $ ./fastANI -q B_quintana.fna -r B_henselae.fna --visualize -o fastani.out $ Rscript scripts/visualize.R B_quintana.fna B_henselae.fna fastani.out.visual Using above commands, we get a plot file fastani.out.visual.pdf displayed below. Each red line segment denotes a reciprocal mapping between two genomes, indicating their evolutionary conserved regions. Also see this page . Parallelization FastANI (v1.1 onwards) supports multi-threading, see the help page on how to configure thread count. To parallelize FastANI beyond single compute node, users also have the choice to simply divide their reference database into multiple chunks, and execute them as parallel processes. We provide a script in the repository to randomly split the database for this purpose. Asymmetry in the ANI computation A known limitation of FastANI is that it reports two different ANI values between a pair of genomes (A,B) depending on which genome is used as the query and which as the reference. See issue #36 for an example. The difference in both ANI values is small in practice. But with --matrix output formatting, there is a single ANI value reported for every genome pair which represents the average of both values. Troubleshooting Users are welcome to report any issue or feedback related to FastANI by posting a Github issue . About Fast Whole-Genome Similarity (ANI) Estimation Topics microbial-genomics Resources Readme License Apache-2.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 455 stars Watchers 12 watching Forks 73 forks Report repository Releases 8 FastANI v1.34 Latest Jul 28, 2023 + 7 releases Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 92.9% C 4.4% CMake 1.0% Python 0.5% M4 0.4% Shell 0.4% Other 0.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge fastani --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +fastani 1.1 h4ef8376_0 +---------------------- +file name : fastani-1.1-h4ef8376_0.tar.bz2 +name : fastani +version : 1.1 +build : h4ef8376_0 +build number: 0 +size : 126 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.1-h4ef8376_0.tar.bz2 +md5 : afe36878f6a50194075ff063509653d9 +timestamp : 2018-09-20 12:06:56 UTC +dependencies: + - boost >=1.67.0,<1.67.1.0a0 + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +fastani 1.1 hcfe0e84_1 +---------------------- +file name : fastani-1.1-hcfe0e84_1.tar.bz2 +name : fastani +version : 1.1 +build : hcfe0e84_1 +build number: 1 +size : 128 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.1-hcfe0e84_1.tar.bz2 +md5 : a75f42c0be2cbfe67b78b875f3c1c13e +timestamp : 2019-04-26 13:44:38 UTC +dependencies: + - boost >=1.68.0,<1.68.1.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +fastani 1.2 he1c1bb9_0 +---------------------- +file name : fastani-1.2-he1c1bb9_0.tar.bz2 +name : fastani +version : 1.2 +build : he1c1bb9_0 +build number: 0 +size : 131 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.2-he1c1bb9_0.tar.bz2 +md5 : 88bd844f5e796a3f99c5af7d1afc582a +timestamp : 2019-07-28 08:54:50 UTC +dependencies: + - boost >=1.70.0,<1.70.1.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +fastani 1.3 he1c1bb9_0 +---------------------- +file name : fastani-1.3-he1c1bb9_0.tar.bz2 +name : fastani +version : 1.3 +build : he1c1bb9_0 +build number: 0 +size : 133 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.3-he1c1bb9_0.tar.bz2 +md5 : 93a113610ba16ee015555ec0768dc751 +timestamp : 2019-12-05 20:56:41 UTC +dependencies: + - boost >=1.70.0,<1.70.1.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +fastani 1.31 he1c1bb9_0 +----------------------- +file name : fastani-1.31-he1c1bb9_0.tar.bz2 +name : fastani +version : 1.31 +build : he1c1bb9_0 +build number: 0 +size : 132 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.31-he1c1bb9_0.tar.bz2 +md5 : 68a0f7326ee97ce36cabf924758fa0d6 +timestamp : 2020-07-12 15:05:43 UTC +dependencies: + - boost >=1.70.0,<1.70.1.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +fastani 1.32 he1c1bb9_0 +----------------------- +file name : fastani-1.32-he1c1bb9_0.tar.bz2 +name : fastani +version : 1.32 +build : he1c1bb9_0 +build number: 0 +size : 131 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.32-he1c1bb9_0.tar.bz2 +md5 : 8c8a6cb895eb5a46ff730118c2c3caec +timestamp : 2020-09-30 14:20:08 UTC +dependencies: + - boost >=1.70.0,<1.70.1.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +fastani 1.33 h0fdf51a_0 +----------------------- +file name : fastani-1.33-h0fdf51a_0.tar.bz2 +name : fastani +version : 1.33 +build : h0fdf51a_0 +build number: 0 +size : 124 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.33-h0fdf51a_0.tar.bz2 +md5 : dfddf6c26921a3088d2afbad0cb34f14 +timestamp : 2022-03-08 11:52:47 UTC +dependencies: + - gsl >=2.7,<2.8.0a0 + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +fastani 1.33 h0fdf51a_1 +----------------------- +file name : fastani-1.33-h0fdf51a_1.tar.bz2 +name : fastani +version : 1.33 +build : h0fdf51a_1 +build number: 1 +size : 124 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.33-h0fdf51a_1.tar.bz2 +md5 : 4900f34fea211d7435bdd63406fa430e +timestamp : 2022-06-27 12:49:31 UTC +dependencies: + - gsl >=2.7,<2.8.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.12,<1.3.0a0 + - zlib >=1.2.12,<1.3.0a0 + + +fastani 1.33 h0fdf51a_2 +----------------------- +file name : fastani-1.33-h0fdf51a_2.tar.bz2 +name : fastani +version : 1.33 +build : h0fdf51a_2 +build number: 2 +size : 125 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.33-h0fdf51a_2.tar.bz2 +md5 : 49496bc27895e1cf56e62a3bddc7730b +timestamp : 2023-05-13 13:26:04 UTC +dependencies: + - gsl >=2.7,<2.8.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +fastani 1.33 h4dfc31f_3 +----------------------- +file name : fastani-1.33-h4dfc31f_3.tar.bz2 +name : fastani +version : 1.33 +build : h4dfc31f_3 +build number: 3 +size : 125 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.33-h4dfc31f_3.tar.bz2 +md5 : 21ac7fed9a2ebe82178d598ec7b91d5c +timestamp : 2023-05-16 01:24:57 UTC +dependencies: + - gsl >=2.7,<2.8.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +fastani 1.34 h4dfc31f_0 +----------------------- +file name : fastani-1.34-h4dfc31f_0.tar.bz2 +name : fastani +version : 1.34 +build : h4dfc31f_0 +build number: 0 +size : 131 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.34-h4dfc31f_0.tar.bz2 +md5 : e02ba09feb9e3943e9354f0416d0cea6 +timestamp : 2023-07-28 21:26:58 UTC +dependencies: + - gsl >=2.7,<2.8.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +fastani 1.34 h4dfc31f_1 +----------------------- +file name : fastani-1.34-h4dfc31f_1.tar.bz2 +name : fastani +version : 1.34 +build : h4dfc31f_1 +build number: 1 +size : 131 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.34-h4dfc31f_1.tar.bz2 +md5 : d296488858e35fcf8793c765cd54636d +timestamp : 2023-11-13 20:06:51 UTC +dependencies: + - gsl >=2.7,<2.8.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +fastani 1.34 h4dfc31f_2 +----------------------- +file name : fastani-1.34-h4dfc31f_2.tar.bz2 +name : fastani +version : 1.34 +build : h4dfc31f_2 +build number: 2 +size : 132 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.34-h4dfc31f_2.tar.bz2 +md5 : 1c4c6ba33bccf12c3c59fcc42b30172c +timestamp : 2024-04-27 12:55:17 UTC +dependencies: + - _openmp_mutex >=4.5 + - gsl >=2.7,<2.8.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +fastani 1.34 h4dfc31f_3 +----------------------- +file name : fastani-1.34-h4dfc31f_3.tar.bz2 +name : fastani +version : 1.34 +build : h4dfc31f_3 +build number: 3 +size : 133 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.34-h4dfc31f_3.tar.bz2 +md5 : d423032b27e11e0e799a5e764b696258 +timestamp : 2024-08-09 00:38:53 UTC +dependencies: + - _openmp_mutex >=4.5 + - gsl >=2.7,<2.8.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<2.0a0 + - zlib + + +fastani 1.34 h4dfc31f_4 +----------------------- +file name : fastani-1.34-h4dfc31f_4.tar.bz2 +name : fastani +version : 1.34 +build : h4dfc31f_4 +build number: 4 +size : 133 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.34-h4dfc31f_4.tar.bz2 +md5 : bb24a1c03b72db6e20e75a9145e1f2fd +timestamp : 2024-11-25 21:59:28 UTC +dependencies: + - _openmp_mutex >=4.5 + - gsl >=2.7,<2.8.0a0 + - libgcc >=12 + - libstdcxx >=12 + - libzlib >=1.2.13,<2.0a0 + - zlib + + +fastani 1.34 hb66fcc3_5 +----------------------- +file name : fastani-1.34-hb66fcc3_5.tar.bz2 +name : fastani +version : 1.34 +build : hb66fcc3_5 +build number: 5 +size : 133 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.34-hb66fcc3_5.tar.bz2 +md5 : 8a5ccc5dd9a669c2c4f91cf08aef8515 +timestamp : 2024-12-12 03:37:50 UTC +dependencies: + - _openmp_mutex >=4.5 + - gsl >=2.7,<2.8.0a0 + - libgcc >=13 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + - zlib + + +fastani 1.34 hb66fcc3_6 +----------------------- +file name : fastani-1.34-hb66fcc3_6.tar.bz2 +name : fastani +version : 1.34 +build : hb66fcc3_6 +build number: 6 +size : 133 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.34-hb66fcc3_6.tar.bz2 +md5 : 83b612592c2519aa768645a12232e4a1 +timestamp : 2025-05-29 02:32:05 UTC +dependencies: + - _openmp_mutex >=4.5 + - gsl >=2.7,<2.8.0a0 + - libgcc >=13 + - libgomp + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + + +fastani 1.34 hb66fcc3_7 +----------------------- +file name : fastani-1.34-hb66fcc3_7.tar.bz2 +name : fastani +version : 1.34 +build : hb66fcc3_7 +build number: 7 +size : 133 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastani-1.34-hb66fcc3_7.tar.bz2 +md5 : e179be4d61ed1e5ea78fce89d2a40e6d +timestamp : 2025-08-05 20:26:02 UTC +dependencies: + - _openmp_mutex >=4.5 + - gsl >=2.8,<2.9.0a0 + - libgcc >=13 + - libgomp + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fastqc.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fastqc.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..18a1b3f9d026d9a8b86a322bdb37967c84aaab2d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fastqc.manual_bundle.txt @@ -0,0 +1,553 @@ +# Tool: fastqc +software_name: fastqc +tier: T1 +domain: t1_backfill_overall +downloads: 1345128 +summary: A quality control tool for high throughput sequence data. +description: A quality control tool for high throughput sequence data. +dependencies: font-ttf-dejavu-sans-mono, fontconfig, openjdk >=8.0.144, perl +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge fastqc --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +fastqc 0.10.1 0 +--------------- +file name : fastqc-0.10.1-0.tar.bz2 +name : fastqc +version : 0.10.1 +build : 0 +build number: 0 +size : 499 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.10.1-0.tar.bz2 +md5 : e561bdd1ef27188971d56d154ea4f80c +dependencies: + - java-jdk + - perl-threaded + + +fastqc 0.10.1 1 +--------------- +file name : fastqc-0.10.1-1.tar.bz2 +name : fastqc +version : 0.10.1 +build : 1 +build number: 1 +size : 508 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.10.1-1.tar.bz2 +md5 : 13dc7b8ad7aff3b54d575ff379d27a93 +timestamp : 2018-07-06 21:10:31 UTC +dependencies: + - java-jdk + - perl + + +fastqc 0.11.2 1 +--------------- +file name : fastqc-0.11.2-1.tar.bz2 +name : fastqc +version : 0.11.2 +build : 1 +build number: 1 +size : 802 KB +license : GPL +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/fastqc-0.11.2-1.tar.bz2 +md5 : 35c98766f89dd1ad762735d73f9a72e8 +timestamp : 2018-06-29 20:51:53 UTC +dependencies: + - openjdk + - perl + + +fastqc 0.11.2 pl5.22.0_0 +------------------------ +file name : fastqc-0.11.2-pl5.22.0_0.tar.bz2 +name : fastqc +version : 0.11.2 +build : pl5.22.0_0 +build number: 0 +size : 801 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.2-pl5.22.0_0.tar.bz2 +md5 : c8869002e0107be2d4ac41550c5d3821 +dependencies: + - openjdk + - perl 5.22.0* + + +fastqc 0.11.3 0 +--------------- +file name : fastqc-0.11.3-0.tar.bz2 +name : fastqc +version : 0.11.3 +build : 0 +build number: 0 +size : 9.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.3-0.tar.bz2 +md5 : 217771f0b6c93eb9aacd6fb735290ec9 +dependencies: + - java-jdk + - perl-threaded + + +fastqc 0.11.3 1 +--------------- +file name : fastqc-0.11.3-1.tar.bz2 +name : fastqc +version : 0.11.3 +build : 1 +build number: 1 +size : 9.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.3-1.tar.bz2 +md5 : 28c7f357accd0e88d686ccd777792b41 +timestamp : 2018-07-06 21:07:21 UTC +dependencies: + - java-jdk + - perl + + +fastqc 0.11.4 0 +--------------- +file name : fastqc-0.11.4-0.tar.bz2 +name : fastqc +version : 0.11.4 +build : 0 +build number: 0 +size : 9.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.4-0.tar.bz2 +md5 : d634a18ca203cf79cdf27aea2f6b120c +dependencies: [] + + +fastqc 0.11.4 1 +--------------- +file name : fastqc-0.11.4-1.tar.bz2 +name : fastqc +version : 0.11.4 +build : 1 +build number: 1 +size : 9.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.4-1.tar.bz2 +md5 : 5147f292420d14ae3c624640c2f68abc +dependencies: + - java-jdk + + +fastqc 0.11.4 2 +--------------- +file name : fastqc-0.11.4-2.tar.bz2 +name : fastqc +version : 0.11.4 +build : 2 +build number: 2 +size : 9.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.4-2.tar.bz2 +md5 : 1ddc3bd3487e87b1c03852e650af3019 +dependencies: + - java-jdk + + +fastqc 0.11.5 1 +--------------- +file name : fastqc-0.11.5-1.tar.bz2 +name : fastqc +version : 0.11.5 +build : 1 +build number: 1 +size : 9.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.5-1.tar.bz2 +md5 : f63d2b6139d381faa910a430c5c34be0 +dependencies: + - java-jdk + + +fastqc 0.11.5 4 +--------------- +file name : fastqc-0.11.5-4.tar.bz2 +name : fastqc +version : 0.11.5 +build : 4 +build number: 4 +size : 9.5 MB +license : GPL >=3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/fastqc-0.11.5-4.tar.bz2 +md5 : b6dc6943c2dfa60f8013f4d9ad91d2ed +timestamp : 2019-10-18 06:12:07 UTC +dependencies: + - openjdk >=8.0.144 + - perl + + +fastqc 0.11.5 hdfd78af_5 +------------------------ +file name : fastqc-0.11.5-hdfd78af_5.tar.bz2 +name : fastqc +version : 0.11.5 +build : hdfd78af_5 +build number: 5 +size : 9.5 MB +license : GPL >=3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/fastqc-0.11.5-hdfd78af_5.tar.bz2 +md5 : fc9acfa368602281f4d1cc8b1ddc9de4 +timestamp : 2021-03-25 01:27:33 UTC +dependencies: + - openjdk >=8.0.144 + - perl + + +fastqc 0.11.5 pl5.22.0_2 +------------------------ +file name : fastqc-0.11.5-pl5.22.0_2.tar.bz2 +name : fastqc +version : 0.11.5 +build : pl5.22.0_2 +build number: 2 +size : 9.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.5-pl5.22.0_2.tar.bz2 +md5 : 6f2bbe3122fc8850e1949c7e727f1a53 +dependencies: + - openjdk + - perl 5.22.0* + + +fastqc 0.11.5 pl5.22.0_3 +------------------------ +file name : fastqc-0.11.5-pl5.22.0_3.tar.bz2 +name : fastqc +version : 0.11.5 +build : pl5.22.0_3 +build number: 3 +size : 9.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.5-pl5.22.0_3.tar.bz2 +md5 : ab48164b7de96e089b6e5a1a38f01948 +dependencies: + - openjdk + - perl 5.22.0* + + +fastqc 0.11.6 2 +--------------- +file name : fastqc-0.11.6-2.tar.bz2 +name : fastqc +version : 0.11.6 +build : 2 +build number: 2 +size : 9.6 MB +license : GPL >=3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.6-2.tar.bz2 +md5 : c95bec3a8a33022ff9ea97e01c8ffdcf +timestamp : 2018-06-29 20:48:41 UTC +dependencies: + - font-ttf-dejavu-sans-mono + - openjdk + - perl + + +fastqc 0.11.6 pl5.22.0_0 +------------------------ +file name : fastqc-0.11.6-pl5.22.0_0.tar.bz2 +name : fastqc +version : 0.11.6 +build : pl5.22.0_0 +build number: 0 +size : 9.6 MB +license : GPL >=3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.6-pl5.22.0_0.tar.bz2 +md5 : ec1a038ce2376974d9f1573dffbbbfea +dependencies: + - openjdk + - perl 5.22.0* + + +fastqc 0.11.6 pl5.22.0_1 +------------------------ +file name : fastqc-0.11.6-pl5.22.0_1.tar.bz2 +name : fastqc +version : 0.11.6 +build : pl5.22.0_1 +build number: 1 +size : 9.6 MB +license : GPL >=3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.6-pl5.22.0_1.tar.bz2 +md5 : 2a7e8967211e3fd751a74170ee2f4b0d +dependencies: + - font-ttf-dejavu-sans-mono + - openjdk + - perl 5.22.0* + + +fastqc 0.11.7 4 +--------------- +file name : fastqc-0.11.7-4.tar.bz2 +name : fastqc +version : 0.11.7 +build : 4 +build number: 4 +size : 9.6 MB +license : GPL >=3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.7-4.tar.bz2 +md5 : 46205fca94cd4ed3f5b479f2af838223 +timestamp : 2018-06-29 20:54:58 UTC +dependencies: + - openjdk >=8.0.122 + - perl + + +fastqc 0.11.7 5 +--------------- +file name : fastqc-0.11.7-5.tar.bz2 +name : fastqc +version : 0.11.7 +build : 5 +build number: 5 +size : 9.6 MB +license : GPL >=3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.7-5.tar.bz2 +md5 : 64df11b72b327b8fd04b043403f7b13f +timestamp : 2018-08-29 18:04:39 UTC +dependencies: + - openjdk >=8.0.144 + - perl + + +fastqc 0.11.7 6 +--------------- +file name : fastqc-0.11.7-6.tar.bz2 +name : fastqc +version : 0.11.7 +build : 6 +build number: 6 +size : 9.6 MB +license : GPL >=3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/fastqc-0.11.7-6.tar.bz2 +md5 : e3133523ae3b8e774ee43de00e1304b3 +timestamp : 2019-10-26 22:17:11 UTC +dependencies: + - openjdk >=8.0.144 + - perl + + +fastqc 0.11.7 hdfd78af_7 +------------------------ +file name : fastqc-0.11.7-hdfd78af_7.tar.bz2 +name : fastqc +version : 0.11.7 +build : hdfd78af_7 +build number: 7 +size : 9.6 MB +license : GPL >=3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/fastqc-0.11.7-hdfd78af_7.tar.bz2 +md5 : 554f06258ba75dba0d40fe0a261baa80 +timestamp : 2021-03-25 01:34:09 UTC +dependencies: + - openjdk >=8.0.144 + - perl + + +fastqc 0.11.7 pl5.22.0_0 +------------------------ +file name : fastqc-0.11.7-pl5.22.0_0.tar.bz2 +name : fastqc +version : 0.11.7 +build : pl5.22.0_0 +build number: 0 +size : 9.6 MB +license : GPL >=3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.7-pl5.22.0_0.tar.bz2 +md5 : c8489f0d7baf61942f69da78f159cbb9 +dependencies: + - font-ttf-dejavu-sans-mono + - openjdk + - perl 5.22.0* + + +fastqc 0.11.7 pl5.22.0_2 +------------------------ +file name : fastqc-0.11.7-pl5.22.0_2.tar.bz2 +name : fastqc +version : 0.11.7 +build : pl5.22.0_2 +build number: 2 +size : 9.6 MB +license : GPL >=3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.7-pl5.22.0_2.tar.bz2 +md5 : 8863026ef0e247c1bfc8265d985027f5 +dependencies: + - openjdk >8.0.121 + - perl 5.22.0* + + +fastqc 0.11.8 0 +--------------- +file name : fastqc-0.11.8-0.tar.bz2 +name : fastqc +version : 0.11.8 +build : 0 +build number: 0 +size : 9.6 MB +license : GPL >=3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.8-0.tar.bz2 +md5 : 5d0048d9045fb8d379861f746faa5e78 +timestamp : 2018-10-05 10:07:50 UTC +dependencies: + - openjdk >=8.0.144 + - perl + + +fastqc 0.11.8 1 +--------------- +file name : fastqc-0.11.8-1.tar.bz2 +name : fastqc +version : 0.11.8 +build : 1 +build number: 1 +size : 9.6 MB +license : GPL >=3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fastqc-0.11.8-1.tar.bz2 +md5 : 48d97761c795eeb10f4eb3962f187601 +timestamp : 2018-12-13 13:41:36 UTC +dependencies: + - font-ttf-dejavu-sans-mono + - fontconfig + - openjdk >=8.0.144 + - perl + + +fastqc 0.11.8 2 +--------------- +file name : fastqc-0.11.8-2.tar.bz2 +name : fastqc +version : 0.11.8 +build : 2 +build number: 2 +size : 9.6 MB +license : GPL >=3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/fastqc-0.11.8-2.tar.bz2 +md5 : b898a9abc5ce3c45d51de0554fee4ffc +timestamp : 2019-10-26 22:10:03 UTC +dependencies: + - font-ttf-dejavu-sans-mono + - fontconfig + - openjdk >=8.0.144 + - perl + + +fastqc 0.11.9 0 +--------------- +file name : fastqc-0.11.9-0.tar.bz2 +name : fastqc +version : 0.11.9 +build : 0 +build number: 0 +size : 9.7 MB +license : GPL >=3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/fastqc-0.11.9-0.tar.bz2 +md5 : 4728751963f861f7d18a824e585a384c +timestamp : 2020-01-24 15:35:48 UTC +dependencies: + - font-ttf-dejavu-sans-mono + - fontconfig + - openjdk >=8.0.144 + - perl + + +fastqc 0.11.9 hdfd78af_1 +------------------------ +file name : fastqc-0.11.9-hdfd78af_1.tar.bz2 +name : fastqc +version : 0.11.9 +build : hdfd78af_1 +build number: 1 +size : 9.7 MB +license : GPL >=3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/fastq diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/flagx.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/flagx.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6bd87e4aa2355f155e6217b5db89628f8d5e52c6 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/flagx.manual_bundle.txt @@ -0,0 +1,114 @@ +# Tool: flagx +software_name: flagx +tier: T1 +domain: single_cell +downloads: 137 +summary: FLAG-X: FLow cytometry Automated Gating toolboX +description: FLAG-X: FLow cytometry Automated Gating toolboX +dependencies: click, flowio, matplotlib-base, numba, numpy, pandas, python >=3.10,<3.14, pytometry, pyyaml, scanpy, scikit-learn, scipy, somoclu, typing_extensions, umap-learn +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/bionetslab/FLAG-X +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/bionetslab/FLAG-X +GitHub - bionetslab/FLAG-X: FLow cytometry Automated Gating toolboX · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bionetslab / FLAG-X Public Notifications You must be signed in to change notification settings Fork 0 Star 2 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights bionetslab/FLAG-X main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 151 Commits 151 Commits .github/ workflows .github/ workflows badges badges docs docs example_configs example_configs flagx flagx notebooks notebooks tests tests .gitignore .gitignore .readthedocs.yml .readthedocs.yml LICENSE LICENSE README.md README.md env_github_tests.yml env_github_tests.yml env_tests.yml env_tests.yml environment.yml environment.yml pyproject.toml pyproject.toml View all files Repository files navigation README GPL-3.0 license FLow cytometry Automated Gating - toolboX (FLAG-X) FLAG-X is a Python toolbox for automated, end-to-end cytometry data processing , including: Data loading (FCS/CSV → AnnData) Alignment of channel names arcoss samples Sample-wise preprocessing Train/(val)/test splitting on the sample level Sample-wise downsampling of training data Model Training MLP (supervised), SOM (supervised or unsupervised) Model saving Inference on new data: Dimensionality reduction (SOM, UMAP, t-SNE, PCA, etc.) Automated gating (cell type prediction) Export of annotated samples to FCS format for downstream analysis using standard flow-cytometry tools. FLAG-X provides a streamlined pipeline and a command line interface (CLI) for users with little programming experience. Installation Using conda or mamba : Ensure correct channel priority: conda config --show channels conda config --show channel_priority Should show: channels: - conda-forge - bioconda - defaults channel_priority: strict Create environment, activate, and install flagx: mamba create -n flagx-env -y mamba activate flagx-env mamba install flagx -y To enable PyTorch-based functionality (e.g. MLPClassifier) install torch according to your system's requirements (see: PyTorch get started ). For example: # v2.9.1, Linux, CUDA 12.8 pip install torch # v2.9.1, Linux, CUDA 12.6 pip install torch --index-url https://download.pytorch.org/whl/cu126 # v2.9.1, Linux, CPU only pip install torch --index-url https://download.pytorch.org/whl/cpu From source using conda or mamba and pip : git clone git@github.com:bionetslab/FLAG-X.git cd FLAG-X mamba env create -f environment.yml mamba activate flagx pip install -e . From source using pixi : git clone git@github.com:bionetslab/FLAG-X.git cd FLAG-X pixi install NOTE: The environments provided in this project install the CPU-only version of PyTorch. Users who require GPU acceleration must install a CUDA-enabled PyTorch build themselves following the instructions at PyTorch get started . Documentation Full documentation is available on Read the Docs . Usage examples Usage examples for the FLAG-X workflows han be found here: Workflow unsupervised and here: Workflow supervised CLI usage example Install flagx , see Installation . Create a config.yml for GatingPipeline initialization and model training according to flagx.GatingPipeline 's signature. For examples see init_train_save_som_config.yml and init_train_save_mlp_config.yml . Initialize the GatingPipeline, train, and save: flagx init-train-save --config ./example_configs/init_train_save_som_config.yml Create a config.yml to load a trained pipeline, perform automated gating, compute dimensionality reductions, and export results to FCS according to flagx.GatingPipeline.inference() 's signature. For examples see load_infer_save_som_config.yml and load_infer_save_mlp_config.yml . Load trained GatingPipeline and run inference on new data: flagx load-infer-save --config ./example_configs/load_infer_save_som_config.yml License This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details. About FLow cytometry Automated Gating toolboX Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 2 stars Watchers 2 watching Forks 0 forks Report repository Releases 3 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 89.6% Python 10.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge flagx --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +flagx 0.1.0 pyhdfd78af_0 +------------------------ +file name : flagx-0.1.0-pyhdfd78af_0.conda +name : flagx +version : 0.1.0 +build : pyhdfd78af_0 +build number: 0 +size : 58 KB +license : GPL-3.0-only +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/flagx-0.1.0-pyhdfd78af_0.conda +md5 : 72416471b7c7b50111dd616409a4cbe2 +timestamp : 2025-12-03 07:33:38 UTC +dependencies: + - click + - matplotlib-base + - numba + - numpy + - pandas + - python >=3.10,<3.14 + - pytometry + - pyyaml + - scanpy + - scikit-learn + - scipy + - somoclu + - typing_extensions + + +flagx 0.2.0 pyhdfd78af_0 +------------------------ +file name : flagx-0.2.0-pyhdfd78af_0.conda +name : flagx +version : 0.2.0 +build : pyhdfd78af_0 +build number: 0 +size : 60 KB +license : GPL-3.0-only +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/flagx-0.2.0-pyhdfd78af_0.conda +md5 : 1af3d06c235f4561260da9ad80553cfe +timestamp : 2025-12-12 09:09:25 UTC +dependencies: + - click + - flowio + - matplotlib-base + - numba + - numpy + - pandas + - python >=3.10,<3.14 + - pytometry + - pyyaml + - scanpy + - scikit-learn + - scipy + - somoclu + - typing_extensions + - umap-learn + + +flagx 0.2.1 pyhdfd78af_0 +------------------------ +file name : flagx-0.2.1-pyhdfd78af_0.conda +name : flagx +version : 0.2.1 +build : pyhdfd78af_0 +build number: 0 +size : 63 KB +license : GPL-3.0-only +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/flagx-0.2.1-pyhdfd78af_0.conda +md5 : 511ff54adbab4efd02e86f9e24adefee +timestamp : 2026-04-02 13:28:34 UTC +dependencies: + - click + - flowio + - matplotlib-base + - numba + - numpy + - pandas + - python >=3.10,<3.14 + - pytometry + - pyyaml + - scanpy + - scikit-learn + - scipy + - somoclu + - typing_extensions + - umap-learn diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ftputil.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ftputil.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3105792ffd88253e43a4562ea40fb11f45a4a24f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ftputil.manual_bundle.txt @@ -0,0 +1,290 @@ +# Tool: ftputil +software_name: ftputil +tier: T1 +domain: t1_backfill_overall +downloads: 124847 +summary: High-level FTP client library (virtual file system and more) +description: High-level FTP client library (virtual file system and more) +dependencies: python 2.7* +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: +doc_url: +dev_url: + +## Conda Search Info +$ conda search -c bioconda -c conda-forge ftputil --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +ftputil 3.2 py27_0 +------------------ +file name : ftputil-3.2-py27_0.tar.bz2 +name : ftputil +version : 3.2 +build : py27_0 +build number: 0 +size : 83 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ftputil-3.2-py27_0.tar.bz2 +md5 : d0c5f7ccc31915903c72480296ed1ee7 +dependencies: + - python 2.7* + + +ftputil 3.2 py34_0 +------------------ +file name : ftputil-3.2-py34_0.tar.bz2 +name : ftputil +version : 3.2 +build : py34_0 +build number: 0 +size : 85 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ftputil-3.2-py34_0.tar.bz2 +md5 : 53af6d1eea64db13aa348f09ec611581 +dependencies: + - python 3.4* + + +ftputil 3.2 py35_0 +------------------ +file name : ftputil-3.2-py35_0.tar.bz2 +name : ftputil +version : 3.2 +build : py35_0 +build number: 0 +size : 84 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ftputil-3.2-py35_0.tar.bz2 +md5 : eea036adf2cdc89a9ce4339b1b2b9da3 +dependencies: + - python 3.5* + + +ftputil 3.2 py36_0 +------------------ +file name : ftputil-3.2-py36_0.tar.bz2 +name : ftputil +version : 3.2 +build : py36_0 +build number: 0 +size : 85 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ftputil-3.2-py36_0.tar.bz2 +md5 : fdbe5cb9604bcb3e28bac4ddee026f6c +dependencies: + - python 3.6* + + +ftputil 3.3.1 py27_0 +-------------------- +file name : ftputil-3.3.1-py27_0.tar.bz2 +name : ftputil +version : 3.3.1 +build : py27_0 +build number: 0 +size : 87 KB +license : BSD 3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/ftputil-3.3.1-py27_0.tar.bz2 +md5 : b508aa2485aaf0efbbcdea3fe9fac3e4 +constraints : + - python_abi * *_cp27mu +dependencies: + - python 2.7* + + +ftputil 3.3.1 py34_0 +-------------------- +file name : ftputil-3.3.1-py34_0.tar.bz2 +name : ftputil +version : 3.3.1 +build : py34_0 +build number: 0 +size : 88 KB +license : BSD 3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/ftputil-3.3.1-py34_0.tar.bz2 +md5 : 5341626161a4d8e249384c1139a4e32e +constraints : + - python_abi * *_cp34m +dependencies: + - python 3.4* + + +ftputil 3.3.1 py35_0 +-------------------- +file name : ftputil-3.3.1-py35_0.tar.bz2 +name : ftputil +version : 3.3.1 +build : py35_0 +build number: 0 +size : 88 KB +license : BSD 3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/ftputil-3.3.1-py35_0.tar.bz2 +md5 : 3b04e8fd2f24aa5a5513e6b450616435 +constraints : + - python_abi * *_cp35m +dependencies: + - python 3.5* + + +ftputil 3.3.1 py36_0 +-------------------- +file name : ftputil-3.3.1-py36_0.tar.bz2 +name : ftputil +version : 3.3.1 +build : py36_0 +build number: 0 +size : 91 KB +license : BSD 3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/ftputil-3.3.1-py36_0.tar.bz2 +md5 : 3fb1cbf7b5fc9c851e07014c728ca714 +constraints : + - python_abi * *_cp36m +dependencies: + - python 3.6* + + +ftputil 3.4 py_0 +---------------- +file name : ftputil-3.4-py_0.tar.bz2 +name : ftputil +version : 3.4 +build : py_0 +build number: 0 +size : 37 KB +license : BSD 3-Clause +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/ftputil-3.4-py_0.tar.bz2 +md5 : 831bc05f6faf6281af5f69196360ff1e +dependencies: + - python + + +ftputil 4.0.0 py_0 +------------------ +file name : ftputil-4.0.0-py_0.tar.bz2 +name : ftputil +version : 4.0.0 +build : py_0 +build number: 0 +size : 74 KB +license : BSD 3-Clause +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/ftputil-4.0.0-py_0.tar.bz2 +md5 : 733896ede12d82394f3fdd1d7205590a +timestamp : 2020-06-14 20:16:38 UTC +dependencies: + - python >=3.6 + + +ftputil 5.0.0 pyhd8ed1ab_0 +-------------------------- +file name : ftputil-5.0.0-pyhd8ed1ab_0.tar.bz2 +name : ftputil +version : 5.0.0 +build : pyhd8ed1ab_0 +build number: 0 +size : 77 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/ftputil-5.0.0-pyhd8ed1ab_0.tar.bz2 +md5 : 0d0b45832a2978f53f43e26d6fb65246 +timestamp : 2021-02-18 10:43:39 UTC +dependencies: + - python >=3.6 + + +ftputil 5.0.1 pyhd8ed1ab_0 +-------------------------- +file name : ftputil-5.0.1-pyhd8ed1ab_0.tar.bz2 +name : ftputil +version : 5.0.1 +build : pyhd8ed1ab_0 +build number: 0 +size : 76 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/ftputil-5.0.1-pyhd8ed1ab_0.tar.bz2 +md5 : 26c1d088c858d4f8367ed2cba2f8d81e +timestamp : 2021-03-19 00:51:54 UTC +dependencies: + - python >=3.6 + + +ftputil 5.0.2 pyhd8ed1ab_0 +-------------------------- +file name : ftputil-5.0.2-pyhd8ed1ab_0.tar.bz2 +name : ftputil +version : 5.0.2 +build : pyhd8ed1ab_0 +build number: 0 +size : 78 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/ftputil-5.0.2-pyhd8ed1ab_0.tar.bz2 +md5 : d8d1b992b2d4e956a54f16d78553d6ec +timestamp : 2021-11-17 14:05:02 UTC +dependencies: + - python >=3.6 + + +ftputil 5.0.3 pyhd8ed1ab_0 +-------------------------- +file name : ftputil-5.0.3-pyhd8ed1ab_0.tar.bz2 +name : ftputil +version : 5.0.3 +build : pyhd8ed1ab_0 +build number: 0 +size : 78 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/ftputil-5.0.3-pyhd8ed1ab_0.tar.bz2 +md5 : 6bbe5b03f175f902ac6410aa94dee092 +timestamp : 2022-01-26 19:43:12 UTC +dependencies: + - python >=3.6 + + +ftputil 5.0.4 pyhd8ed1ab_0 +-------------------------- +file name : ftputil-5.0.4-pyhd8ed1ab_0.tar.bz2 +name : ftputil +version : 5.0.4 +build : pyhd8ed1ab_0 +build number: 0 +size : 42 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/ftputil-5.0.4-pyhd8ed1ab_0.tar.bz2 +md5 : 83ae47fd5bd9306281db44d85d5813a5 +timestamp : 2022-05-12 00:04:49 UTC +dependencies: + - python >=3.6 + + +ftputil 5.1.0 pyhd8ed1ab_0 +-------------------------- +file name : ftputil-5.1.0-pyhd8ed1ab_0.conda +name : ftputil +version : 5.1.0 +build : pyhd8ed1ab_0 +build number: 0 +size : 46 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/ftputil-5.1.0-pyhd8ed1ab_0.conda +md5 : 33531fd156b65cd5e38c401f6c1d3fc8 +timestamp : 2024-01-06 21:31:13 UTC +dependencies: + - python >=3.6 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fwdpy11.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fwdpy11.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..76cb66f81804a2455e74528da63dcd5cf6e3f201 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/fwdpy11.manual_bundle.txt @@ -0,0 +1,476 @@ +# Tool: fwdpy11 +software_name: fwdpy11 +tier: T1 +domain: t1_backfill_overall +downloads: 272496 +summary: Forward-time population genetic simulation in Python. +description: Forward-time population genetic simulation in Python. +dependencies: attrs, black, demes >=0.2.2, deprecated, gsl >=2.7,<2.8.0a0, intervaltree, libgcc >=13, libstdcxx >=13, numpy <2.0, numpy >=1.21,<3, openblas, python >=3.10,<3.11.0a0, python_abi 3.10.* *_cp310, scipy, tskit >=0.5.6 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/molpopgen/fwdpy11 +doc_url: https://molpopgen.github.io/fwdpy11 +dev_url: https://github.com/molpopgen/fwdpy11 + +## CLI Help Source +cli:fwdpy11 +## CLI Help Content +$ conda run -n bioenv_cli fwdpy11 --help +[rc=1] + +RuntimeError: module was compiled against NumPy C-API version 0x12 (NumPy 1.20) but the running NumPy has C-API version 0x11. Check the section C-API incompatibility at the Troubleshooting ImportError section at https://numpy.org/devdocs/user/troubleshooting-importerror.html#c-api-incompatibility for indications on how to solve this problem. +Traceback (most recent call last): + File "/225040511/miniconda3/envs/bioenv_cli/bin/fwdpy11", line 7, in + from fwdpy11.__main__ import main + File "/225040511/miniconda3/envs/bioenv_cli/lib/python3.10/site-packages/fwdpy11/__init__.py", line 31, in + from . import discrete_demography # NOQA + File "/225040511/miniconda3/envs/bioenv_cli/lib/python3.10/site-packages/fwdpy11/discrete_demography.py", line 27, in + from fwdpy11._types.demographic_model_details import DemographicModelDetails + File "/225040511/miniconda3/envs/bioenv_cli/lib/python3.10/site-packages/fwdpy11/_types/__init__.py", line 28, in + from .diploid_population import DiploidPopulation # NOQA + File "/225040511/miniconda3/envs/bioenv_cli/lib/python3.10/site-packages/fwdpy11/_types/diploid_population.py", line 4, in + import fwdpy11.tskit_tools._dump_tables_to_tskit + File "/225040511/miniconda3/envs/bioenv_cli/lib/python3.10/site-packages/fwdpy11/tskit_tools/__init__.py", line 30, in + import tskit # type: ignore + File "/225040511/miniconda3/envs/bioenv_cli/lib/python3.10/site-packages/tskit/__init__.py", line 22, in + import _tskit +ImportError: numpy._core.multiarray failed to import + +ERROR conda.cli.main_run:execute(127): `conda run fwdpy11 --help` failed. (See above for error) + + +## URL Docs Extract +### https://github.com/molpopgen/fwdpy11 +GitHub - molpopgen/fwdpy11: Forward-time simulation in Python using fwdpp · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} molpopgen / fwdpy11 Public Notifications You must be signed in to change notification settings Fork 6 Star 32 Code Issues 11 Pull requests 6 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights molpopgen/fwdpy11 main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 3,559 Commits 3,559 Commits .github .github cpp cpp cpp_neutral_benchmark cpp_neutral_benchmark cpptests cpptests deployment deployment doc doc examples examples fwdpy11 fwdpy11 lib lib rust rust tests tests tests_with_cpp tests_with_cpp .flake8 .flake8 .gitignore .gitignore .gitmodules .gitmodules .ycm_extra_conf.py .ycm_extra_conf.py CMakeLists.txt CMakeLists.txt COPYING COPYING MANIFEST.in MANIFEST.in README.rst README.rst _config.yml _config.yml gplheader.txt gplheader.txt gplheader_cpp.txt gplheader_cpp.txt pyproject.toml pyproject.toml setup.cfg setup.cfg uv.lock uv.lock View all files Repository files navigation README GPL-3.0 license fwdpy11 This is the README for fwdpy11 , which is a Python package for forward-time population genetic simulation. It uses fwdpp as its C++ back-end. Build status Main: Development: Conda status Miscellaneous Python code style: Features Pickle-able population objects Parallel computation via multiprocessing or concurrent.futures . Custom temporal samplers to analyze populations during a simulation may be written in pure Python. Flexible interface for simulating models with multiple populations. Documentation The manual can be found here . License GPLv3 or later (See COPYING) Supported Python version fwdpy11 is written for Python 3. We will not modify the package to be compatible with Python 2.7. Dependencies and installation These topics are covered in the user manual: People wishing to run fwpdy11 should see this section . Those who need to build the package from source should look the developer's guide . Citation If you use this software for research, please cite the following publications: Kevin R Thornton. Polygenic adaptation to an environmental shift: temporal dynamics of variation under gaussian stabilizing selection and additive effects on a single trait. Genetics, 213(4):1513–1530, December 2019. Kevin R Thornton. A c++ template library for efficient forward-time population genetic simulation of large populations. Genetics, 198(1):157–166, September 2014. This software was developed for the first paper. The second paper describes a key part of this software's back end. About Forward-time simulation in Python using fwdpp molpopgen.github.io/fwdpy11 Topics genomics genetics simulation population-genetics tree-sequences Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 32 stars Watchers 3 watching Forks 6 forks Report repository Releases 109 Maintenance release Latest Apr 1, 2025 + 108 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 51.4% Python 46.9% CMake 1.0% Rust 0.4% Shell 0.2% Dockerfile 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/molpopgen/fwdpy11 +GitHub - molpopgen/fwdpy11: Forward-time simulation in Python using fwdpp · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} molpopgen / fwdpy11 Public Notifications You must be signed in to change notification settings Fork 6 Star 32 Code Issues 11 Pull requests 6 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights molpopgen/fwdpy11 main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 3,559 Commits 3,559 Commits .github .github cpp cpp cpp_neutral_benchmark cpp_neutral_benchmark cpptests cpptests deployment deployment doc doc examples examples fwdpy11 fwdpy11 lib lib rust rust tests tests tests_with_cpp tests_with_cpp .flake8 .flake8 .gitignore .gitignore .gitmodules .gitmodules .ycm_extra_conf.py .ycm_extra_conf.py CMakeLists.txt CMakeLists.txt COPYING COPYING MANIFEST.in MANIFEST.in README.rst README.rst _config.yml _config.yml gplheader.txt gplheader.txt gplheader_cpp.txt gplheader_cpp.txt pyproject.toml pyproject.toml setup.cfg setup.cfg uv.lock uv.lock View all files Repository files navigation README GPL-3.0 license fwdpy11 This is the README for fwdpy11 , which is a Python package for forward-time population genetic simulation. It uses fwdpp as its C++ back-end. Build status Main: Development: Conda status Miscellaneous Python code style: Features Pickle-able population objects Parallel computation via multiprocessing or concurrent.futures . Custom temporal samplers to analyze populations during a simulation may be written in pure Python. Flexible interface for simulating models with multiple populations. Documentation The manual can be found here . License GPLv3 or later (See COPYING) Supported Python version fwdpy11 is written for Python 3. We will not modify the package to be compatible with Python 2.7. Dependencies and installation These topics are covered in the user manual: People wishing to run fwpdy11 should see this section . Those who need to build the package from source should look the developer's guide . Citation If you use this software for research, please cite the following publications: Kevin R Thornton. Polygenic adaptation to an environmental shift: temporal dynamics of variation under gaussian stabilizing selection and additive effects on a single trait. Genetics, 213(4):1513–1530, December 2019. Kevin R Thornton. A c++ template library for efficient forward-time population genetic simulation of large populations. Genetics, 198(1):157–166, September 2014. This software was developed for the first paper. The second paper describes a key part of this software's back end. About Forward-time simulation in Python using fwdpp molpopgen.github.io/fwdpy11 Topics genomics genetics simulation population-genetics tree-sequences Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 32 stars Watchers 3 watching Forks 6 forks Report repository Releases 109 Maintenance release Latest Apr 1, 2025 + 108 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors 4 molpopgen Kevin R. Thornton dependabot[bot] apragsdale Aaron Ragsdale kevin-meyers Kevin Meyers Languages C++ 51.4% Python 46.9% CMake 1.0% Rust 0.4% Shell 0.2% Dockerfile 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge fwdpy11 --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +fwdpy11 0.1.post2 py34_gsl1.16_0 +-------------------------------- +file name : fwdpy11-0.1.post2-py34_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.post2 +build : py34_gsl1.16_0 +build number: 0 +size : 5.4 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.post2-py34_gsl1.16_0.tar.bz2 +md5 : e03501f4e352625eb36c51822ee00b22 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.4* + + +fwdpy11 0.1.post2 py35_gsl1.16_0 +-------------------------------- +file name : fwdpy11-0.1.post2-py35_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.post2 +build : py35_gsl1.16_0 +build number: 0 +size : 6.0 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.post2-py35_gsl1.16_0.tar.bz2 +md5 : 0ac5f3057315c56d789a48f84be0fca5 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.5* + + +fwdpy11 0.1.post4 py34_gsl1.16_0 +-------------------------------- +file name : fwdpy11-0.1.post4-py34_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.post4 +build : py34_gsl1.16_0 +build number: 0 +size : 616 KB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.post4-py34_gsl1.16_0.tar.bz2 +md5 : 28e77e3ef03d80a04528fd718643e956 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.4* + + +fwdpy11 0.1.post4 py35_gsl1.16_0 +-------------------------------- +file name : fwdpy11-0.1.post4-py35_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.post4 +build : py35_gsl1.16_0 +build number: 0 +size : 652 KB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.post4-py35_gsl1.16_0.tar.bz2 +md5 : 4a52a14dfd1f38017c953759bdc79198 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.5* + + +fwdpy11 0.1.post4 py36_gsl1.16_0 +-------------------------------- +file name : fwdpy11-0.1.post4-py36_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.post4 +build : py36_gsl1.16_0 +build number: 0 +size : 652 KB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.post4-py36_gsl1.16_0.tar.bz2 +md5 : 23b5d134506ed2405a349dccf8564e1f +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.6* + + +fwdpy11 0.1.1 py35_gsl1.16_0 +---------------------------- +file name : fwdpy11-0.1.1-py35_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.1 +build : py35_gsl1.16_0 +build number: 0 +size : 913 KB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.1-py35_gsl1.16_0.tar.bz2 +md5 : 0323e51f0d824645c92bf560ccaafd87 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.5* + + +fwdpy11 0.1.1 py36_gsl1.16_0 +---------------------------- +file name : fwdpy11-0.1.1-py36_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.1 +build : py36_gsl1.16_0 +build number: 0 +size : 912 KB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.1-py36_gsl1.16_0.tar.bz2 +md5 : 7ac9dcdd7addec0dc22adac1230674ad +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.6* + + +fwdpy11 0.1.2 py35_gsl1.16_0 +---------------------------- +file name : fwdpy11-0.1.2-py35_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.2 +build : py35_gsl1.16_0 +build number: 0 +size : 1.5 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.2-py35_gsl1.16_0.tar.bz2 +md5 : a3ee9152c742a7f93178c27939011b7c +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.5* + + +fwdpy11 0.1.2 py36_gsl1.16_0 +---------------------------- +file name : fwdpy11-0.1.2-py36_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.2 +build : py36_gsl1.16_0 +build number: 0 +size : 1.0 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.2-py36_gsl1.16_0.tar.bz2 +md5 : 87ac731281f442cc3efe2aa4521767f9 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.6* + + +fwdpy11 0.1.3a0 py35_gsl1.16_0 +------------------------------ +file name : fwdpy11-0.1.3a0-py35_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.3a0 +build : py35_gsl1.16_0 +build number: 0 +size : 1.5 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.3a0-py35_gsl1.16_0.tar.bz2 +md5 : 9dba1f3fb9324e13f9da727b57e01b3c +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.5* + + +fwdpy11 0.1.3a0 py36_gsl1.16_0 +------------------------------ +file name : fwdpy11-0.1.3a0-py36_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.3a0 +build : py36_gsl1.16_0 +build number: 0 +size : 1.0 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.3a0-py36_gsl1.16_0.tar.bz2 +md5 : 7590f333d11916476a36d0409c4cbf07 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.6* + + +fwdpy11 0.1.3a1 py35_gsl1.16_0 +------------------------------ +file name : fwdpy11-0.1.3a1-py35_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.3a1 +build : py35_gsl1.16_0 +build number: 0 +size : 1.5 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.3a1-py35_gsl1.16_0.tar.bz2 +md5 : 8ce8638ea531c150a01ca279bc710497 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.5* + + +fwdpy11 0.1.3a1 py36_gsl1.16_0 +------------------------------ +file name : fwdpy11-0.1.3a1-py36_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.3a1 +build : py36_gsl1.16_0 +build number: 0 +size : 1.0 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.3a1-py36_gsl1.16_0.tar.bz2 +md5 : 65472ddda95bf3a6785fe479c1f81530 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.6* + + +fwdpy11 0.1.3.post1 py35_gsl1.16_0 +---------------------------------- +file name : fwdpy11-0.1.3.post1-py35_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.3.post1 +build : py35_gsl1.16_0 +build number: 0 +size : 1.6 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.3.post1-py35_gsl1.16_0.tar.bz2 +md5 : a02d8feeb2fc0ed00d826cbb45e56efe +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.5* + + +fwdpy11 0.1.3.post1 py36_gsl1.16_0 +---------------------------------- +file name : fwdpy11-0.1.3.post1-py36_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.3.post1 +build : py36_gsl1.16_0 +build number: 0 +size : 1.1 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.3.post1-py36_gsl1.16_0.tar.bz2 +md5 : 87fd1049401f2954e38f0ad59f1ca9e4 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.6* + + +fwdpy11 0.1.3.post3 py35_gsl1.16_0 +---------------------------------- +file name : fwdpy11-0.1.3.post3-py35_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.3.post3 +build : py35_gsl1.16_0 +build number: 0 +size : 1.1 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.3.post3-py35_gsl1.16_0.tar.bz2 +md5 : 30233ba215a478e5608eea6c4c6930aa +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.5* + + +fwdpy11 0.1.3.post3 py36_gsl1.16_0 +---------------------------------- +file name : fwdpy11-0.1.3.post3-py36_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.3.post3 +build : py36_gsl1.16_0 +build number: 0 +size : 1.1 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.3.post3-py36_gsl1.16_0.tar.bz2 +md5 : 0f625881a9dfe87c93ff99a543c51c53 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.6* + + +fwdpy11 0.1.4 py35_gsl1.16_0 +---------------------------- +file name : fwdpy11-0.1.4-py35_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.4 +build : py35_gsl1.16_0 +build number: 0 +size : 1.3 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.4-py35_gsl1.16_0.tar.bz2 +md5 : 604661f26e5e8a7f95cdb59a5f0b5111 +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.5* + + +fwdpy11 0.1.4 py35_gsl2.2_1 +--------------------------- +file name : fwdpy11-0.1.4-py35_gsl2.2_1.tar.bz2 +name : fwdpy11 +version : 0.1.4 +build : py35_gsl2.2_1 +build number: 1 +size : 1.3 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.4-py35_gsl2.2_1.tar.bz2 +md5 : e098c2ddb65684f3e7cb8baa94b27839 +dependencies: + - gsl 2.2* + - libgcc + - numpy >=1.10 + - openblas + - python 3.5* + + +fwdpy11 0.1.4 py36_gsl1.16_0 +---------------------------- +file name : fwdpy11-0.1.4-py36_gsl1.16_0.tar.bz2 +name : fwdpy11 +version : 0.1.4 +build : py36_gsl1.16_0 +build number: 0 +size : 1.3 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.4-py36_gsl1.16_0.tar.bz2 +md5 : 1534b5637b58ca239fa5075883d28a7f +dependencies: + - gsl 1.16* + - libgcc + - numpy >=1.10 + - python 3.6* + + +fwdpy11 0.1.4 py36_gsl2.2_1 +--------------------------- +file name : fwdpy11-0.1.4-py36_gsl2.2_1.tar.bz2 +name : fwdpy11 +version : 0.1.4 +build : py36_gsl2.2_1 +build number: 1 +size : 1.3 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.1.4-py36_gsl2.2_1.tar.bz2 +md5 : 52f7cc99b085f3e6e08c3e999bf6f6f6 +dependencies: + - gsl 2.2* + - libgcc + - numpy >=1.10 + - openblas + - python 3.6* + + +fwdpy11 0.2.1 py36h4f780e3_0 +---------------------------- +file name : fwdpy11-0.2.1-py36h4f780e3_0.tar.bz2 +name : fwdpy11 +version : 0.2.1 +build : py36h4f780e3_0 +build number: 0 +size : 1.3 MB +license : GNU General Public License v3 or later (GPLv3+) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/fwdpy11-0.2.1-py36h4f780e3_0.tar.bz2 +md5 : 4e757c1e86545eafbb5e1928819e755a +timestamp : 2019-03-24 18:38:50 UTC +dependencies: + - gsl >=2.4,<2.5.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7. diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gatk.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gatk.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c15edac9fda4a7aa0dc7be3d49f3a63f3a43e84d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gatk.manual_bundle.txt @@ -0,0 +1,541 @@ +# Tool: gatk +software_name: gatk +tier: T1 +domain: t1_backfill_overall +downloads: 189111 +summary: The full Genome Analysis Toolkit (GATK) framework, license restricted. +description: The full Genome Analysis Toolkit (GATK) framework, license restricted. +dependencies: openjdk >=8,<9, python, r-ggplot2, r-gplots, r-gsalib, r-reshape +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://www.broadinstitute.org/gatk/ +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gatk --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +gatk 3.5 10 +----------- +file name : gatk-3.5-10.tar.bz2 +name : gatk +version : 3.5 +build : 10 +build number: 10 +size : 11.4 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gatk-3.5-10.tar.bz2 +md5 : d66a64b67535cfd7107dad3784ca1181 +timestamp : 2020-11-06 14:07:29 UTC +dependencies: + - openjdk >=8,<9 + - python + - r-ggplot2 + - r-gplots + - r-gsalib + - r-reshape + + +gatk 3.5 5 +---------- +file name : gatk-3.5-5.tar.bz2 +name : gatk +version : 3.5 +build : 5 +build number: 5 +size : 4 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.5-5.tar.bz2 +md5 : 3fdf1848357c4123c02cc4f0cb2f5664 +dependencies: + - bzip2 + - java-jdk >=8,<9 + + +gatk 3.5 6 +---------- +file name : gatk-3.5-6.tar.bz2 +name : gatk +version : 3.5 +build : 6 +build number: 6 +size : 6 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.5-6.tar.bz2 +md5 : e3386f4b9cf7c17f9b8045215023f209 +timestamp : 2018-06-30 17:57:36 UTC +dependencies: + - bzip2 + - java-jdk >=8,<9 + + +gatk 3.5 hdfd78af_11 +-------------------- +file name : gatk-3.5-hdfd78af_11.tar.bz2 +name : gatk +version : 3.5 +build : hdfd78af_11 +build number: 11 +size : 11.4 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gatk-3.5-hdfd78af_11.tar.bz2 +md5 : 7cfb86aea828196b0a6446e55d3d7bc1 +timestamp : 2021-03-26 18:17:01 UTC +dependencies: + - openjdk >=8,<9 + - python + - r-ggplot2 + - r-gplots + - r-gsalib + - r-reshape + + +gatk 3.6 1 +---------- +file name : gatk-3.6-1.tar.bz2 +name : gatk +version : 3.6 +build : 1 +build number: 1 +size : 4 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.6-1.tar.bz2 +md5 : 0f5327f24235f91abd1713b168c42e8b +dependencies: + - bzip2 + - java-jdk >=7 + + +gatk 3.6 10 +----------- +file name : gatk-3.6-10.tar.bz2 +name : gatk +version : 3.6 +build : 10 +build number: 10 +size : 12.0 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gatk-3.6-10.tar.bz2 +md5 : 4c19ecd8a27303d20d0e54f90f1efe21 +timestamp : 2020-11-06 13:51:36 UTC +dependencies: + - openjdk >=8,<9 + - python + - r-ggplot2 + - r-gplots + - r-gsalib + - r-reshape + + +gatk 3.6 2 +---------- +file name : gatk-3.6-2.tar.bz2 +name : gatk +version : 3.6 +build : 2 +build number: 2 +size : 4 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.6-2.tar.bz2 +md5 : 9287440bb613121c1e079016e8879b2e +dependencies: + - bzip2 + - java-jdk >=8,<9 + + +gatk 3.6 3 +---------- +file name : gatk-3.6-3.tar.bz2 +name : gatk +version : 3.6 +build : 3 +build number: 3 +size : 4 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.6-3.tar.bz2 +md5 : 615e8518b74f4c7db4c45e4fa6f7e241 +dependencies: + - bzip2 + - java-jdk >=8,<9 + + +gatk 3.6 4 +---------- +file name : gatk-3.6-4.tar.bz2 +name : gatk +version : 3.6 +build : 4 +build number: 4 +size : 4 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.6-4.tar.bz2 +md5 : 86bfa5f04e93f991ac7c67836881846e +dependencies: + - bzip2 + - java-jdk >=8,<9 + + +gatk 3.6 5 +---------- +file name : gatk-3.6-5.tar.bz2 +name : gatk +version : 3.6 +build : 5 +build number: 5 +size : 4 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.6-5.tar.bz2 +md5 : 94f088bd760515f6c5dca2af7ac2787e +dependencies: + - bzip2 + - java-jdk >=8,<9 + + +gatk 3.6 7 +---------- +file name : gatk-3.6-7.tar.bz2 +name : gatk +version : 3.6 +build : 7 +build number: 7 +size : 9 KB +license : https://software.broadinstitute.org/gatk/download/licensing +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gatk-3.6-7.tar.bz2 +md5 : fa40dea0a2f87293bcc64de2840bcc41 +timestamp : 2019-10-18 06:11:21 UTC +dependencies: + - bzip2 + - openjdk >=8,<9 + - python + - r-ggplot2 + - r-gplots + - r-gsalib + - r-reshape + + +gatk 3.6 8 +---------- +file name : gatk-3.6-8.tar.bz2 +name : gatk +version : 3.6 +build : 8 +build number: 8 +size : 12.0 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gatk-3.6-8.tar.bz2 +md5 : 20805de95ed7df540c88a5ae5ff592a6 +timestamp : 2020-11-02 21:49:36 UTC +dependencies: + - openjdk >=8,<9 + - python + - r-ggplot2 + - r-gplots + - r-gsalib + - r-reshape + + +gatk 3.6 9 +---------- +file name : gatk-3.6-9.tar.bz2 +name : gatk +version : 3.6 +build : 9 +build number: 9 +size : 12.0 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gatk-3.6-9.tar.bz2 +md5 : 874cdf276fb3a3f40977bf0a39c05c90 +timestamp : 2020-11-05 11:21:25 UTC +dependencies: + - openjdk >=8,<9 + - python + - r-ggplot2 + - r-gplots + - r-gsalib + - r-reshape + + +gatk 3.6 hdfd78af_11 +-------------------- +file name : gatk-3.6-hdfd78af_11.tar.bz2 +name : gatk +version : 3.6 +build : hdfd78af_11 +build number: 11 +size : 12.0 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gatk-3.6-hdfd78af_11.tar.bz2 +md5 : 4ca196a6b05d5d35e0bdc6d430c58777 +timestamp : 2021-03-26 18:28:13 UTC +dependencies: + - openjdk >=8,<9 + - python + - r-ggplot2 + - r-gplots + - r-gsalib + - r-reshape + + +gatk 3.6 py27_6 +--------------- +file name : gatk-3.6-py27_6.tar.bz2 +name : gatk +version : 3.6 +build : py27_6 +build number: 6 +size : 6 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.6-py27_6.tar.bz2 +md5 : 53a92fb24c66e86045f840f74e534ca8 +dependencies: + - bzip2 + - java-jdk >=8,<9 + - python 2.7* + + +gatk 3.6 py34_6 +--------------- +file name : gatk-3.6-py34_6.tar.bz2 +name : gatk +version : 3.6 +build : py34_6 +build number: 6 +size : 6 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.6-py34_6.tar.bz2 +md5 : eba913a55f41b12b5a06e275c00b6db0 +dependencies: + - bzip2 + - java-jdk >=8,<9 + - python 3.4* + + +gatk 3.6 py35_6 +--------------- +file name : gatk-3.6-py35_6.tar.bz2 +name : gatk +version : 3.6 +build : py35_6 +build number: 6 +size : 6 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.6-py35_6.tar.bz2 +md5 : a4e62acf550c96fc5266deea9dff5948 +dependencies: + - bzip2 + - java-jdk >=8,<9 + - python 3.5* + + +gatk 3.7 py27_0 +--------------- +file name : gatk-3.7-py27_0.tar.bz2 +name : gatk +version : 3.7 +build : py27_0 +build number: 0 +size : 6 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.7-py27_0.tar.bz2 +md5 : 9d1dfcada18b2c5ec458c576210eb731 +dependencies: + - bzip2 + - java-jdk >=8,<9 + - python 2.7* + + +gatk 3.7 py27_1 +--------------- +file name : gatk-3.7-py27_1.tar.bz2 +name : gatk +version : 3.7 +build : py27_1 +build number: 1 +size : 8 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.7-py27_1.tar.bz2 +md5 : 1406e130f8ab913cc201dd8b5e83c00e +dependencies: + - bzip2 + - openjdk >=8,<9 + - python 2.7* + + +gatk 3.7 py34_0 +--------------- +file name : gatk-3.7-py34_0.tar.bz2 +name : gatk +version : 3.7 +build : py34_0 +build number: 0 +size : 6 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.7-py34_0.tar.bz2 +md5 : 559071e1bc72dd01c878f7d012c94318 +dependencies: + - bzip2 + - java-jdk >=8,<9 + - python 3.4* + + +gatk 3.7 py35_0 +--------------- +file name : gatk-3.7-py35_0.tar.bz2 +name : gatk +version : 3.7 +build : py35_0 +build number: 0 +size : 6 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.7-py35_0.tar.bz2 +md5 : d3465b667acce941b6f8d235aff21d92 +dependencies: + - bzip2 + - java-jdk >=8,<9 + - python 3.5* + + +gatk 3.7 py35_1 +--------------- +file name : gatk-3.7-py35_1.tar.bz2 +name : gatk +version : 3.7 +build : py35_1 +build number: 1 +size : 8 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.7-py35_1.tar.bz2 +md5 : aba90b3a1a06150e66ebae01069ebb17 +dependencies: + - bzip2 + - openjdk >=8,<9 + - python 3.5* + + +gatk 3.7 py36_0 +--------------- +file name : gatk-3.7-py36_0.tar.bz2 +name : gatk +version : 3.7 +build : py36_0 +build number: 0 +size : 6 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.7-py36_0.tar.bz2 +md5 : 6c95ca5ec49bd5fcb7d81fb4d26c7b93 +dependencies: + - bzip2 + - java-jdk >=8,<9 + - python 3.6* + + +gatk 3.7 py36_1 +--------------- +file name : gatk-3.7-py36_1.tar.bz2 +name : gatk +version : 3.7 +build : py36_1 +build number: 1 +size : 8 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk-3.7-py36_1.tar.bz2 +md5 : 28e2bad53ee8499b83e9c500e6a16bec +dependencies: + - bzip2 + - openjdk >=8,<9 + - python 3.6* + + +gatk 3.8 10 +----------- +file name : gatk-3.8-10.tar.bz2 +name : gatk +version : 3.8 +build : 10 +build number: 10 +size : 13.9 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gatk-3.8-10.tar.bz2 +md5 : 025934e13ecc5de5ea2b75c93a417525 +timestamp : 2020-11-06 13:59:27 UTC +dependencies: + - openjdk >=8,<9 + - python + - r-ggplot2 + - r-gplots + - r-gsalib + - r-reshape + + +gatk 3.8 5 +---------- +file name : gatk-3.8-5.tar.bz2 +name : gatk +version : 3.8 +build : 5 +build number: 5 +size : 8 KB +license : https://www.broadinstitute.org/gatk/about/#licensing +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gatk-3.8-5.tar.bz2 +md5 : a2f0e884671e7e54337bf4519a528541 +timestamp : 2018-07-06 20:53:55 UTC +dependencies: + - bzip2 + - openjdk >=8,<9 + - python + - r-ggplot2 + - r-gplots + - r-gsalib + - r-reshape + + +gatk 3.8 7 +---------- +file name : gatk-3.8-7.tar.bz2 +name : gatk +version : 3.8 +build : 7 +build number: 7 +size : 8 KB +license : https://softwar diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gatk4.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gatk4.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..7b49d633e82b2cbffa12439cb81debd84ae9ba0e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gatk4.manual_bundle.txt @@ -0,0 +1,619 @@ +# Tool: gatk4 +software_name: gatk4 +tier: T1 +domain: t1_backfill_overall +downloads: 1175505 +summary: Genome Analysis Toolkit (GATK4) +description: Genome Analysis Toolkit (GATK4) +dependencies: openjdk >=17, python >=3.10,<3.11.0a0 +execution_environment: Java +execution_environment_reason: inferred from Java runtime dependencies + +## URLs +home_url: https://www.broadinstitute.org/gatk/ +doc_url: +dev_url: https://github.com/broadinstitute/gatk + +## CLI Help Source +java:-help +## CLI Help Content +$ conda run -n bioenv_java java -help +[rc=0] + +Usage: java [options] [args...] + (to execute a class) + or java [options] -jar [args...] + (to execute a jar file) + or java [options] -m [/] [args...] + java [options] --module [/] [args...] + (to execute the main class in a module) + or java [options] [args] + (to execute a single source-file program) + + Arguments following the main class, source file, -jar , + -m or --module / are passed as the arguments to + main class. + + where options include: + + -cp + -classpath + --class-path + A : separated list of directories, JAR archives, + and ZIP archives to search for class files. + -p + --module-path ... + A : separated list of directories, each directory + is a directory of modules. + --upgrade-module-path ... + A : separated list of directories, each directory + is a directory of modules that replace upgradeable + modules in the runtime image + --add-modules [,...] + root modules to resolve in addition to the initial module. + can also be ALL-DEFAULT, ALL-SYSTEM, + ALL-MODULE-PATH. + --list-modules + list observable modules and exit + -d + --describe-module + describe a module and exit + --dry-run create VM and load main class but do not execute main method. + The --dry-run option may be useful for validating the + command-line options such as the module system configuration. + --validate-modules + validate all modules and exit + The --validate-modules option may be useful for finding + conflicts and other errors with modules on the module path. + -D= + set a system property + -verbose:[class|module|gc|jni] + enable verbose output + -version print product version to the error stream and exit + --version print product version to the output stream and exit + -showversion print product version to the error stream and continue + --show-version + print product version to the output stream and continue + --show-module-resolution + show module resolution output during startup + -? -h -help + print this help message to the error stream + --help print this help message to the output stream + -X print help on extra options to the error stream + --help-extra print help on extra options to the output stream + -ea[:...|:] + -enableassertions[:...|:] + enable assertions with specified granularity + -da[:...|:] + -disableassertions[:...|:] + disable assertions with specified granularity + -esa | -enablesystemassertions + enable system assertions + -dsa | -disablesystemassertions + disable system assertions + -agentlib:[=] + load native agent library , e.g. -agentlib:jdwp + see also -agentlib:jdwp=help + -agentpath:[=] + load native agent library by full pathname + -javaagent:[=] + load Java programming language agent, see java.lang.instrument + -splash: + show splash screen with specified image + HiDPI scaled images are automatically supported and used + if available. The unscaled image filename, e.g. image.ext, + should always be passed as the argument to the -splash option. + The most appropriate scaled image provided will be picked up + automatically. + See the SplashScreen API documentation for more information + @argument files + one or more argument files containing options + -disable-@files + prevent further argument file expansion + --enable-preview + allow classes to depend on preview features of this release +To specify an argument for a long option, you can use --= or +-- . + + + + +## URL Docs Extract +### https://github.com/broadinstitute/gatk +GitHub - broadinstitute/gatk: Official code repository for GATK versions 4 and up · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} broadinstitute / gatk Public Notifications You must be signed in to change notification settings Fork 624 Star 1.9k Code Issues 1.3k Pull requests 145 Discussions Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Wiki Security and quality Insights broadinstitute/gatk master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 4,764 Commits 4,764 Commits .github .github docs docs gradle/ wrapper gradle/ wrapper resources_for_CI resources_for_CI scripts scripts src src .dockerignore .dockerignore .dockstore.yml .dockstore.yml .gitattributes .gitattributes .gitignore .gitignore AUTHORS AUTHORS CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md Dockerfile Dockerfile LICENSE.TXT LICENSE.TXT README.md README.md build.gradle build.gradle build_docker.sh build_docker.sh build_docker_remote.sh build_docker_remote.sh codecov.yml codecov.yml gatk gatk gradle.properties gradle.properties gradlew gradlew settings.gradle settings.gradle testsettings.gradle testsettings.gradle View all files Repository files navigation README Code of conduct License Please see the GATK website , where you can download a precompiled executable, read documentation, ask questions, and receive technical support. For GitHub basics, see here . GATK 4 This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents of this repository are 100% open source and released under the Apache 2.0 license (see LICENSE.TXT ). GATK4 aims to bring together well-established tools from the GATK and Picard codebases under a streamlined framework, and to enable selected tools to be run in a massively parallel way on local clusters or in the cloud using Apache Spark . It also contains many newly developed tools not present in earlier releases of the toolkit. Table of Contents Requirements Quick Start Guide Downloading GATK4 Tools Included in Docker Image Building GATK4 Running GATK4 Passing JVM options to gatk Passing a configuration file to gatk Running GATK4 with inputs on Google Cloud Storage Running GATK4 Spark tools locally Running GATK4 Spark tools on a Spark cluster Running GATK4 Spark tools on Google Cloud Dataproc Using R to generate plots GATK Tab Completion for Bash For GATK Developers General guidelines for GATK4 developers Testing GATK4 Using Git LFS to download and track large test data Creating a GATK project in the IntelliJ IDE Setting up debugging in IntelliJ Updating the Intellij project when dependencies change Setting up profiling using JProfiler Uploading Archives to Sonatype Building GATK4 Docker images Releasing GATK4 Generating GATK4 documentation Generating GATK4 WDL Wrappers Using Zenhub to track github issues Further Reading on Spark How to contribute to GATK Discussions Authors Citing GATK License Requirements To run GATK: Java 17 is needed to run or build GATK. We recommend one of the following: Download the Eclipse Foundation's distribution of OpenJDK 17 from adoptium.net . Navigate to the release archive to find downloads for Java 17. On Mac OS, you can install the Homebrew package manager and run brew install temurin@17 to install the Eclipse Foundation's OpenJDK 17. Python 3.10.13, along with a set of additional Python packages, is required to run some tools and workflows (also required to run the gatk frontend script). See Python Dependencies for more information. R 4.3.1 (needed for producing plots in certain tools) To build GATK: A Java 17 JDK Git 2.5 or greater git-lfs 1.1.0 or greater. Required to download the large files used to build GATK, and test files required to run the test suite. Run git lfs install after downloading, followed by git lfs pull from the root of your git clone to download all of the large files, including those required to run the test suite. The full download is approximately 5 gigabytes. Alternatively, if you are just building GATK and not running the test suite, you can skip this step since the build itself will use git-lfs to download the minimal set of large lfs resource files required to complete the build. The test resources will not be downloaded, but this greatly reduces the size of the download. Gradle 5.6. We recommend using the ./gradlew script which will download and use an appropriate gradle version automatically (see examples below). R 4.3.1 (needed for running the test suite) Pre-packaged Docker images with all needed dependencies installed can be found on our dockerhub repository . This requires a recent version of the docker client, which can be found on the docker website . Python Dependencies: GATK4 uses the Conda package manager to establish and manage the Python environment and dependencies required by Python-based GATK tools. This environment also includes the R dependencies used for plotting in some of the tools. The GATK Docker image comes with the gatk conda environment pre-configured and activated. To establish the environment when not using the Docker image, a conda environment must first be "created", and then "activated": First, make sure Miniconda or Conda is installed. We recommend installing Miniconda3-py310_23.10.0-1 from the miniconda download page , selecting the Linux or MacOS version of the installer as appropriate. This is the same version of miniconda used by the official GATK docker image. If you use a different version, you may run into issues. If you have an ARM-based Mac, you must select the MacOSX-x86_64 installer, not the MacOSX-arm64 installer, and rely on Mac OS's built-in x86 emulation. Set up miniconda: Install miniconda to a location on your PATH such as /opt/miniconda , and then restart your shell: bash Miniconda3-py310_23.10.0-1-[YOUR_OS].sh -p /opt/miniconda -b Disable conda auto-updates, which can cause compatibility issues with GATK: conda config --set auto_update_conda false Enable the (much) faster libmamba solver to greatly speed up creation of the conda environment: conda config --set solver libmamba To "create" the conda environment: If running from a zip or tar distribution, run the command conda env create -f gatkcondaenv.yml to create the gatk environment. If running from a cloned repository, run ./gradlew localDevCondaEnv . This generates the Python package archive and conda yml dependency file(s) in the build directory, and also creates (or updates) the local gatk conda environment. To "activate" the conda environment (the conda environment must be activated within the same shell from which GATK is run): Execute the shell command source activate gatk to activate the gatk environment. See the Conda documentation for additional information about using and managing Conda environments. Quick Start Guide Build the GATK: ./gradlew bundle (creates gatk-VERSION.zip in build/ ) Get help on running the GATK: ./gatk --help Get a list of available tools: ./gatk --list Run a tool: ./gatk PrintReads -I src/test/resources/NA12878.chr17_69k_70k.dictFix.bam -O output.bam Get help on a particular tool: ./gatk PrintReads --help Downloading GATK4 You can download and run pre-built versions of GATK4 from the following places: A zip archive with everything you need to run GATK4 can be downloaded for each release from the github releases page . We also host unstable archives generated nightly in the Google bucket gs://gatk-nightly-builds. You can download a GATK4 docker image from our dockerhub repository . We also host unstable nightly development builds on this dockerhub repository . Within the docker image, run gatk commands as usual from the default startup directory (/gatk). Tools Included in Docker Image Our docker image contains the following bioinformatics tools, which can be run by invoking the tool name from the command line: bedtools (v2.30.0) samtools (1.13) bcftools (1.13) tabix (1.13+ds) We also include an installation of Python3 (3.10.13) with the following popular packages included: numpy scipy pytorch pymc3 keras scikit-learn matplotlib pandas biopython pyvcf pysam We also include an installation of R (4.3.1) with the following popular packages included: data.table dplyr ggplot2 For more details on system packages, see the GATK Base Dockerfile and for more details on the Python3/R packages, see the Conda environment setup file . Versions for the Python3/R packages can be found there. Building GATK4 To do a full build of GATK4, first clone the GATK repository using "git clone", then run: ./gradlew bundle Equivalently, you can just type: ./gradlew This creates a zip archive in the build/ directory with a name like gatk-VERSION.zip containing a complete standalone GATK distribution, including our launcher gatk , both the local and spark jars, and this README. You can also run GATK commands directly from the root of your git clone after running this command. Note that you must have a full git clone in order to build GATK, including the git-lfs files in src/main/resources/large . The zipped source code alone is not buildable. The large files under src/main/resources/large/ are required to build GATK, since they are packaged inside the GATK jar and used by tools at runtime. These include things like ML models and native C/C++ libraries used for acceleration of certain tools. The large files under src/test/resources/large/ , on the other hand, are only required by the test suite when running tests, and are not required to build GATK. Other ways to build: ./gradlew installDist Does a fast build that only lets you run GATK tools from inside your git clone, and locally only (not on a cluster). Good for developers! ./gradlew installAll Does a semi-fast build that only lets you run GATK tools from inside your git clone, but works both locally and on a cluster. Good for developers! ./gradlew localJar Builds only the GATK jar used for running tools locally (not on a Spark cluster). The resulting jar will be in build/libs with a name like gatk-package-VERSION-local.jar , and can be used outside of your git clone. ./gradlew sparkJar Builds only the GATK jar used for running tools on a Spark cluster (rather than locally). The resulting jar will be in build/libs with a name like gatk-package-VERSION-spark.jar , and can be used outside of your git clone. This jar will not include Spark and Hadoop libraries, in order to allow the versions of Spark and Hadoop installed on your cluster to be used. To remove previous builds, run: ./gradlew clean For faster gradle operations, add org.gradle.daemon=true to your ~/.gradle/gradle.properties file. This will keep a gradle daemon running in the background and avoid the ~6s gradle start up time on every command. Gradle keeps a cache of dependencies used to build GATK. By default this goes in ~/.gradle . If there is insufficient free space in your home directory, you can change the location of the cache by setting the GRADLE_USER_HOME environment variable. The version number is automatically derived from the git history using git describe , you can override it by setting the versionOverride property. ( ./gradlew -DversionOverride=my_weird_version printVersion ) Running GATK4 The standard way to run GATK4 tools is via the gatk wrapper script located in the root directory of a clone of this repository. Requires Python 3.9 or greater You need to have built the GATK as described in the Building GATK4 section above before running this script. There are several ways gatk can be run: Directly from the root of your git clone after building By extracting the zip archive produced by ./gradlew bundle to a directory, and running gatk from there Manually putting the gatk script within the same directory as fully-packaged GATK jars produced by ./gradlew localJar and/or ./gradlew sparkJar Defining the environment variables GATK_LOCAL_JAR and GATK_SPARK_JAR , and setting them to the paths to the GATK jars produced by ./gradlew localJar and/or ./gradlew sparkJar gatk can run non-Spark tools as well as Spark tools, and can run Spark tools locally, on a Spark cluster, or on Google Cloud Dataproc. Note: running with java -jar directly and bypassing gatk causes several important system properties to not get set, including htsjdk compression level! For help on using gatk itself, run ./gatk --help To print a list of available tools, run ./gatk --list . Spark-based tools will have a name ending in Spark (eg., BaseRecalibratorSpark ). Most other tools are non-Spark-based. To print help for a particular tool, run ./gatk ToolName --help . To run a non-Spark tool, or to run a Spark tool locally, the syntax is: ./gatk ToolName toolArguments . Tool arguments that allow multiple values, such as -I, can be supplied on the command line using a file with the extension ".args". Each line of the file should contain a single value for the argument. Examples: ./gatk PrintReads -I input.bam -O output.bam ./gatk PrintReadsSpark -I input.bam -O output.bam Passing JVM options to gatk To pass JVM arguments to GATK, run gatk with the --java-options argument: ./gatk --java-options "-Xmx4G" <rest of command> ./gatk --java-options "-Xmx4G -XX:+PrintGCDetails" <rest of command> Passing a configuration file to gatk To pass a configuration file to GATK, run gatk with the --gatk-config-file argument: ./gatk --gatk-config-file GATKProperties.config <rest of command> An example GATK configuration file is packaged with each release as GATKConfig.EXAMPLE.properties This example file contains all current options that are used by GATK and their default values. Running GATK4 with inputs on Google Cloud Storage: Many GATK4 tools can read BAM or VCF inputs from a Google Cloud Storage bucket. Just use the "gs://" prefix: ./gatk PrintReads -I gs://mybucket/path/to/my.bam -L 1:10000-20000 -O output.bam Important: You must set up your credentials first for this to work! There are three options: Option (a): run in a Google Cloud Engine VM If you are running in a Google VM then your credentials are already in the VM and will be picked up by GATK, you don't need to do anything special. Option (b): use your own account Install Google Cloud SDK Log into your account: gcloud auth application-default login Done! GATK will use the application-default credentials you set up there. Option (c): use a service account Create a new service account on the Google Cloud web page and download the JSON key file Install Google Cloud SDK Tell gcloud about the key file: gcloud auth activate-service-account --key-file "$PATH_TO_THE_KEY_FILE" Set the GOOGLE_APPLICATION_CREDENTIALS environment variable to point to the file export GOOGLE_APPLICATION_CREDENTIALS="$PATH_TO_THE_KEY_FILE" Done! GATK will pick up the service account. You can also do this in a VM if you'd like to override the default credentials. Running GATK4 Spark tools locally: GATK4 Spark tools can be run in local mode (without a cluster). In this mode, Spark will run the tool in multiple parallel execution threads using the cores in your CPU. You can control how many threads Spark will use via the --spark-master argument. Examples: Run PrintReadsSpark with 4 threads on your local machine: ./gatk PrintReadsSpark -I src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam -O output.bam \ -- \ --spark-runner LOCAL --spark-master 'local[4]' Run PrintReadsSpark with as many worker threads as there are logical cores on your local machine: ./gatk PrintReadsSpark -I src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam -O output.bam \ -- \ --spark-runner LOCAL --spark-master 'local[*]' Note that the Spark-specific arguments are separated from the tool-specific arguments by a -- . Running GATK4 Spark tools on a Spark cluster: ./gatk ToolName toolArguments -- --spark-runner SPARK --spark-master <master_url> additionalSparkArguments Examples: ./gatk PrintReadsSpark -I hdfs://path/to/input.bam -O hdfs://path/to/output.bam \ -- \ --spark-runner SPARK --spark-master <master_url> ./gatk PrintReadsSpark -I hdfs://path/to/input.bam -O hdfs://path/to/output.bam \ -- \ --spark-runner SPARK --spark-master <master_url> \ --num-executors 5 --executor-cores 2 --executor-memory 4g \ --conf spark.executor.memoryOverhead=600 You can also omit the "--num-executors" argument to enable dynamic allocation if you configure the cluster properly (see the Spark website for instructions). Note that the Spark-specific arguments are separated from the tool-specific arguments by a -- . Running a Spark tool on a cluster requires Spark to have been installed from http://spark.apache.org/ , since gatk invokes the spark-submit tool behind-the-scenes. Note that the examples above use YARN but we have successfully run GATK4 on Mesos as well. Running GATK4 Spark tools on Google Cloud Dataproc: You must have a Google cloud services account, and have spun up a Dataproc cluster in the Google Developer's console . You may need to have the "Allow API access to all Google Cloud services in the same project" option enabled (settable when you create a cluster). You need to have installed the Google Cloud SDK from here , since gatk invokes the gcloud tool behind-the-scenes. As part of the installation, be sure that you follow the gcloud setup instructions here . As this library is frequently updated by Google, we recommend updating your copy regularly to avoid any version-related difficulties. Your inputs to the GATK when running on dataproc are typically in Google Cloud Storage buckets, a + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gatk4 --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +gatk4 4.0a1.2.7.2 py27_2 +------------------------ +file name : gatk4-4.0a1.2.7.2-py27_2.tar.bz2 +name : gatk4 +version : 4.0a1.2.7.2 +build : py27_2 +build number: 2 +size : 218.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0a1.2.7.2-py27_2.tar.bz2 +md5 : 9edd6499f236ff9ae36aaa2533cf69ba +dependencies: + - openjdk >=8,<9 + - python 2.7* + + +gatk4 4.0a1.2.7.2 py35_2 +------------------------ +file name : gatk4-4.0a1.2.7.2-py35_2.tar.bz2 +name : gatk4 +version : 4.0a1.2.7.2 +build : py35_2 +build number: 2 +size : 218.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0a1.2.7.2-py35_2.tar.bz2 +md5 : 96719cb03128692b84ce7cb75ec2572d +dependencies: + - openjdk >=8,<9 + - python 3.5* + + +gatk4 4.0a1.2.7.2 py36_2 +------------------------ +file name : gatk4-4.0a1.2.7.2-py36_2.tar.bz2 +name : gatk4 +version : 4.0a1.2.7.2 +build : py36_2 +build number: 2 +size : 218.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0a1.2.7.2-py36_2.tar.bz2 +md5 : 5d2d94629d75c010bbe9300639f02157 +dependencies: + - openjdk >=8,<9 + - python 3.6* + + +gatk4 4.0b1 py27_0 +------------------ +file name : gatk4-4.0b1-py27_0.tar.bz2 +name : gatk4 +version : 4.0b1 +build : py27_0 +build number: 0 +size : 240.6 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b1-py27_0.tar.bz2 +md5 : 58286610b94ba28e62aa219e960f2f22 +dependencies: + - openjdk >=8,<9 + - python 2.7* + + +gatk4 4.0b1 py35_0 +------------------ +file name : gatk4-4.0b1-py35_0.tar.bz2 +name : gatk4 +version : 4.0b1 +build : py35_0 +build number: 0 +size : 240.6 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b1-py35_0.tar.bz2 +md5 : 1d86c5ba45cd35e83a5d42b16c0c2b31 +dependencies: + - openjdk >=8,<9 + - python 3.5* + + +gatk4 4.0b1 py36_0 +------------------ +file name : gatk4-4.0b1-py36_0.tar.bz2 +name : gatk4 +version : 4.0b1 +build : py36_0 +build number: 0 +size : 240.6 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b1-py36_0.tar.bz2 +md5 : 17ee06f7b8375d15ba40266a8c99333a +dependencies: + - openjdk >=8,<9 + - python 3.6* + + +gatk4 4.0b2 py27_0 +------------------ +file name : gatk4-4.0b2-py27_0.tar.bz2 +name : gatk4 +version : 4.0b2 +build : py27_0 +build number: 0 +size : 240.7 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b2-py27_0.tar.bz2 +md5 : d54bcba943aa305428b030fa4f0da872 +dependencies: + - openjdk >=8,<9 + - python 2.7* + + +gatk4 4.0b2 py35_0 +------------------ +file name : gatk4-4.0b2-py35_0.tar.bz2 +name : gatk4 +version : 4.0b2 +build : py35_0 +build number: 0 +size : 240.7 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b2-py35_0.tar.bz2 +md5 : 935088151efe2ed180d445dd4aa38dcb +dependencies: + - openjdk >=8,<9 + - python 3.5* + + +gatk4 4.0b2 py36_0 +------------------ +file name : gatk4-4.0b2-py36_0.tar.bz2 +name : gatk4 +version : 4.0b2 +build : py36_0 +build number: 0 +size : 240.7 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b2-py36_0.tar.bz2 +md5 : 738e747a66b57bf85e3b6f398038b8ff +dependencies: + - openjdk >=8,<9 + - python 3.6* + + +gatk4 4.0b3 py27_0 +------------------ +file name : gatk4-4.0b3-py27_0.tar.bz2 +name : gatk4 +version : 4.0b3 +build : py27_0 +build number: 0 +size : 239.8 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b3-py27_0.tar.bz2 +md5 : 4a67b0a55b0625693bb1a1c268201060 +dependencies: + - openjdk >=8,<9 + - python 2.7* + + +gatk4 4.0b3 py35_0 +------------------ +file name : gatk4-4.0b3-py35_0.tar.bz2 +name : gatk4 +version : 4.0b3 +build : py35_0 +build number: 0 +size : 239.8 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b3-py35_0.tar.bz2 +md5 : 00f47f01cab57d1e0edbc8f1ffe1c1eb +dependencies: + - openjdk >=8,<9 + - python 3.5* + + +gatk4 4.0b3 py36_0 +------------------ +file name : gatk4-4.0b3-py36_0.tar.bz2 +name : gatk4 +version : 4.0b3 +build : py36_0 +build number: 0 +size : 239.8 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b3-py36_0.tar.bz2 +md5 : 9694b2c7bd26efe1d62e6536da1888ba +dependencies: + - openjdk >=8,<9 + - python 3.6* + + +gatk4 4.0b4 py27_0 +------------------ +file name : gatk4-4.0b4-py27_0.tar.bz2 +name : gatk4 +version : 4.0b4 +build : py27_0 +build number: 0 +size : 240.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b4-py27_0.tar.bz2 +md5 : de3fc3537cd2548c2f2ec61a8b91f8e1 +dependencies: + - openjdk >=8,<9 + - python 2.7* + + +gatk4 4.0b4 py35_0 +------------------ +file name : gatk4-4.0b4-py35_0.tar.bz2 +name : gatk4 +version : 4.0b4 +build : py35_0 +build number: 0 +size : 240.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b4-py35_0.tar.bz2 +md5 : 5f8b62a220f5e49536369cddcb74e911 +dependencies: + - openjdk >=8,<9 + - python 3.5* + + +gatk4 4.0b4 py36_0 +------------------ +file name : gatk4-4.0b4-py36_0.tar.bz2 +name : gatk4 +version : 4.0b4 +build : py36_0 +build number: 0 +size : 240.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b4-py36_0.tar.bz2 +md5 : 5226371f78f3e418b7839f6ca1545e59 +dependencies: + - openjdk >=8,<9 + - python 3.6* + + +gatk4 4.0b5 py27_0 +------------------ +file name : gatk4-4.0b5-py27_0.tar.bz2 +name : gatk4 +version : 4.0b5 +build : py27_0 +build number: 0 +size : 240.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b5-py27_0.tar.bz2 +md5 : 0dd097e03380d90077d32319059ab7b1 +dependencies: + - openjdk >=8,<9 + - python 2.7* + + +gatk4 4.0b5 py35_0 +------------------ +file name : gatk4-4.0b5-py35_0.tar.bz2 +name : gatk4 +version : 4.0b5 +build : py35_0 +build number: 0 +size : 240.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b5-py35_0.tar.bz2 +md5 : 154ba1b744d78da9ac43629a8380a706 +dependencies: + - openjdk >=8,<9 + - python 3.5* + + +gatk4 4.0b5 py36_0 +------------------ +file name : gatk4-4.0b5-py36_0.tar.bz2 +name : gatk4 +version : 4.0b5 +build : py36_0 +build number: 0 +size : 240.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b5-py36_0.tar.bz2 +md5 : 2864d2f998fea16166d46a79132c442c +dependencies: + - openjdk >=8,<9 + - python 3.6* + + +gatk4 4.0b6 py27_0 +------------------ +file name : gatk4-4.0b6-py27_0.tar.bz2 +name : gatk4 +version : 4.0b6 +build : py27_0 +build number: 0 +size : 242.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b6-py27_0.tar.bz2 +md5 : 5d7d2705425014cb1a56dd113718ed92 +dependencies: + - openjdk >=8,<9 + - python 2.7* + + +gatk4 4.0b6 py35_0 +------------------ +file name : gatk4-4.0b6-py35_0.tar.bz2 +name : gatk4 +version : 4.0b6 +build : py35_0 +build number: 0 +size : 242.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b6-py35_0.tar.bz2 +md5 : 90b2760f86ef22d358443ebeaf24a0c7 +dependencies: + - openjdk >=8,<9 + - python 3.5* + + +gatk4 4.0b6 py36_0 +------------------ +file name : gatk4-4.0b6-py36_0.tar.bz2 +name : gatk4 +version : 4.0b6 +build : py36_0 +build number: 0 +size : 242.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0b6-py36_0.tar.bz2 +md5 : 2d75ce6a044ce6473caa28043b437588 +dependencies: + - openjdk >=8,<9 + - python 3.6* + + +gatk4 4.0.0.0 py27_0 +-------------------- +file name : gatk4-4.0.0.0-py27_0.tar.bz2 +name : gatk4 +version : 4.0.0.0 +build : py27_0 +build number: 0 +size : 240.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0.0.0-py27_0.tar.bz2 +md5 : d14a1ac0d3df33811dbb4abc7be15c4d +dependencies: + - openjdk >=8,<9 + - python 2.7* + + +gatk4 4.0.0.0 py35_0 +-------------------- +file name : gatk4-4.0.0.0-py35_0.tar.bz2 +name : gatk4 +version : 4.0.0.0 +build : py35_0 +build number: 0 +size : 240.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0.0.0-py35_0.tar.bz2 +md5 : 15c625e8aec7e2aa6c57bbf582953ed7 +dependencies: + - openjdk >=8,<9 + - python 3.5* + + +gatk4 4.0.0.0 py36_0 +-------------------- +file name : gatk4-4.0.0.0-py36_0.tar.bz2 +name : gatk4 +version : 4.0.0.0 +build : py36_0 +build number: 0 +size : 240.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0.0.0-py36_0.tar.bz2 +md5 : 1f9c036e7c79a36c39f05046ef66d492 +dependencies: + - openjdk >=8,<9 + - python 3.6* + + +gatk4 4.0.1.0 py27_0 +-------------------- +file name : gatk4-4.0.1.0-py27_0.tar.bz2 +name : gatk4 +version : 4.0.1.0 +build : py27_0 +build number: 0 +size : 238.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0.1.0-py27_0.tar.bz2 +md5 : 265be3bdb68ad2d34364a192f72ff791 +dependencies: + - openjdk >=8,<9 + - python 2.7* + + +gatk4 4.0.1.0 py35_0 +-------------------- +file name : gatk4-4.0.1.0-py35_0.tar.bz2 +name : gatk4 +version : 4.0.1.0 +build : py35_0 +build number: 0 +size : 238.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0.1.0-py35_0.tar.bz2 +md5 : dd3c43ec679ec76712a916dc61b6835c +dependencies: + - openjdk >=8,<9 + - python 3.5* + + +gatk4 4.0.1.0 py36_0 +-------------------- +file name : gatk4-4.0.1.0-py36_0.tar.bz2 +name : gatk4 +version : 4.0.1.0 +build : py36_0 +build number: 0 +size : 238.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0.1.0-py36_0.tar.bz2 +md5 : 7b268048bcf6df0ab8c950bd9e1bfff7 +dependencies: + - openjdk >=8,<9 + - python 3.6* + + +gatk4 4.0.1.1 py27_0 +-------------------- +file name : gatk4-4.0.1.1-py27_0.tar.bz2 +name : gatk4 +version : 4.0.1.1 +build : py27_0 +build number: 0 +size : 238.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gatk4-4.0.1.1-py27_0.tar.bz2 +md5 : aba3678d637b86c0360deb6b46103b7e +dependencies: + - openjdk >=8,<9 + - python 2.7* + + +gatk4 4.0.1.1 py35_0 +-------------------- +file name : gatk4-4.0.1.1-py35_0.tar.bz2 +name : gatk4 +version : 4.0.1.1 +build : py35_0 +build number: 0 +size : 238.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/ diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gdk-pixbuf.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gdk-pixbuf.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..f09d3f27fe238f022dab1b7a4fee41bfa9c1ee2e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gdk-pixbuf.manual_bundle.txt @@ -0,0 +1,446 @@ +# Tool: gdk-pixbuf +software_name: gdk-pixbuf +tier: T1 +domain: t1_backfill_overall +downloads: 178849 +summary: +description: +dependencies: glib >=2.48.0, gobject-introspection, libffi, libgcc, libpng, libtiff +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: +doc_url: +dev_url: + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gdk-pixbuf --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +gdk-pixbuf 2.32.2 0 +------------------- +file name : gdk-pixbuf-2.32.2-0.tar.bz2 +name : gdk-pixbuf +version : 2.32.2 +build : 0 +build number: 0 +size : 759 KB +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gdk-pixbuf-2.32.2-0.tar.bz2 +md5 : 78d5a46271366f405b04f21b27a2ec40 +dependencies: + - glib + - gobject-introspection + - libffi + - libgcc + - libpng + - libtiff + + +gdk-pixbuf 2.32.2 1 +------------------- +file name : gdk-pixbuf-2.32.2-1.tar.bz2 +name : gdk-pixbuf +version : 2.32.2 +build : 1 +build number: 1 +size : 759 KB +license : GNU +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gdk-pixbuf-2.32.2-1.tar.bz2 +md5 : 941004461075f0ea6f903a82bbac4e0b +dependencies: + - glib >=2.48.0 + - gobject-introspection + - libffi + - libgcc + - libpng + - libtiff + + +gdk-pixbuf 2.36.9 1 +------------------- +file name : gdk-pixbuf-2.36.9-1.tar.bz2 +name : gdk-pixbuf +version : 2.36.9 +build : 1 +build number: 1 +size : 795 KB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.36.9-1.tar.bz2 +md5 : 2c0230742e649e8622d2ba42fe03292b +dependencies: + - glib >=2.51 + - gobject-introspection + - jpeg + - libffi <3.3.0.a0 + - libgcc + - libpng + - libtiff + + +gdk-pixbuf 2.36.12 h3f25603_1005 +-------------------------------- +file name : gdk-pixbuf-2.36.12-h3f25603_1005.tar.bz2 +name : gdk-pixbuf +version : 2.36.12 +build : h3f25603_1005 +build number: 1005 +size : 591 KB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.36.12-h3f25603_1005.tar.bz2 +md5 : b2437159794c22c4188272d5768a9c06 +timestamp : 2020-01-10 16:51:59 UTC +dependencies: + - glib >=2.58.3,<3.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libgcc-ng >=7.3.0 + - libpng >=1.6.37,<1.7.0a0 + - libtiff >=4.1.0,<4.5.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gdk-pixbuf 2.36.12 h49783d7_1002 +-------------------------------- +file name : gdk-pixbuf-2.36.12-h49783d7_1002.tar.bz2 +name : gdk-pixbuf +version : 2.36.12 +build : h49783d7_1002 +build number: 1002 +size : 592 KB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.36.12-h49783d7_1002.tar.bz2 +md5 : f9b565007ee9868e1ac2cffdcfeefa67 +timestamp : 2019-01-11 21:48:39 UTC +dependencies: + - glib >=2.58.2,<2.59.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libffi >=3.2.1,<3.3.0a0 + - libgcc-ng >=7.3.0 + - libpng >=1.6.35,<1.7.0a0 + - libtiff >=4.0.9,<4.5.0a0 + + +gdk-pixbuf 2.36.12 h4ab6910_1 +----------------------------- +file name : gdk-pixbuf-2.36.12-h4ab6910_1.tar.bz2 +name : gdk-pixbuf +version : 2.36.12 +build : h4ab6910_1 +build number: 1 +size : 608 KB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.36.12-h4ab6910_1.tar.bz2 +md5 : b44f018bb9957d097d8a53a3d4a047f6 +timestamp : 2018-09-28 21:03:55 UTC +dependencies: + - glib >=2.56.2,<2.57.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libffi >=3.2.1,<3.3.0a0 + - libgcc-ng >=4.9 + - libpng >=1.6.34,<1.7.0a0 + - libtiff >=4.0.9,<4.5.0a0 + + +gdk-pixbuf 2.36.12 h4f1c04b_1001 +-------------------------------- +file name : gdk-pixbuf-2.36.12-h4f1c04b_1001.tar.bz2 +name : gdk-pixbuf +version : 2.36.12 +build : h4f1c04b_1001 +build number: 1001 +size : 598 KB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.36.12-h4f1c04b_1001.tar.bz2 +md5 : 83c9c43d21495151224157e46b30aa1d +timestamp : 2018-10-10 18:37:07 UTC +dependencies: + - glib >=2.56.2,<2.57.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libffi >=3.2.1,<3.3.0a0 + - libgcc-ng >=7.3.0 + - libpng >=1.6.34,<1.7.0a0 + - libtiff >=4.0.9,<4.5.0a0 + + +gdk-pixbuf 2.36.12 h7a26e22_1003 +-------------------------------- +file name : gdk-pixbuf-2.36.12-h7a26e22_1003.tar.bz2 +name : gdk-pixbuf +version : 2.36.12 +build : h7a26e22_1003 +build number: 1003 +size : 603 KB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.36.12-h7a26e22_1003.tar.bz2 +md5 : d242dcdf5c4b7671f970a571f587c196 +timestamp : 2019-06-21 00:01:50 UTC +dependencies: + - glib >=2.58.3,<3.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libffi >=3.2.1,<3.3.0a0 + - libgcc-ng >=7.3.0 + - libpng >=1.6.35,<1.7.0a0 + - libtiff >=4.0.9,<4.5.0a0 + + +gdk-pixbuf 2.36.12 hb83312c_0 +----------------------------- +file name : gdk-pixbuf-2.36.12-hb83312c_0.tar.bz2 +name : gdk-pixbuf +version : 2.36.12 +build : hb83312c_0 +build number: 0 +size : 608 KB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.36.12-hb83312c_0.tar.bz2 +md5 : b51c2ee0c1b40f208507783ae14829d4 +timestamp : 2018-07-06 16:49:53 UTC +dependencies: + - glib >=2.55.0,<2.56.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libffi >=3.2.1,<3.3.0a0 + - libgcc-ng >=4.9 + - libpng >=1.6.34,<1.7.0a0 + - libtiff >=4.0.9,<4.5.0a0 + + +gdk-pixbuf 2.36.12 hf3e2b23_2 +----------------------------- +file name : gdk-pixbuf-2.36.12-hf3e2b23_2.tar.bz2 +name : gdk-pixbuf +version : 2.36.12 +build : hf3e2b23_2 +build number: 2 +size : 589 KB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.36.12-hf3e2b23_2.tar.bz2 +md5 : 07c0fbd041200608e372f3845dff5677 +timestamp : 2019-01-11 21:47:42 UTC +dependencies: + - glib >=2.58.2,<2.59.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libffi >=3.2.1,<3.3.0a0 + - libgcc-ng >=4.9 + - libpng >=1.6.35,<1.7.0a0 + - libtiff >=4.0.9,<4.5.0a0 + + +gdk-pixbuf 2.38.2 h3f25603_0 +---------------------------- +file name : gdk-pixbuf-2.38.2-h3f25603_0.tar.bz2 +name : gdk-pixbuf +version : 2.38.2 +build : h3f25603_0 +build number: 0 +size : 642 KB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.38.2-h3f25603_0.tar.bz2 +md5 : 34e12b5aa416cf24d4700e3c034bc076 +timestamp : 2020-01-19 00:56:37 UTC +dependencies: + - glib >=2.58.3,<3.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libgcc-ng >=7.3.0 + - libpng >=1.6.37,<1.7.0a0 + - libtiff >=4.1.0,<4.5.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gdk-pixbuf 2.38.2 h3f25603_1 +---------------------------- +file name : gdk-pixbuf-2.38.2-h3f25603_1.tar.bz2 +name : gdk-pixbuf +version : 2.38.2 +build : h3f25603_1 +build number: 1 +size : 647 KB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.38.2-h3f25603_1.tar.bz2 +md5 : ea10b59796fcec4aaa3dd01cf5b64cfd +timestamp : 2020-03-23 20:36:39 UTC +dependencies: + - glib >=2.58.3,<3.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libgcc-ng >=7.3.0 + - libpng >=1.6.37,<1.7.0a0 + - libtiff >=4.1.0,<4.5.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gdk-pixbuf 2.38.2 h3f25603_2 +---------------------------- +file name : gdk-pixbuf-2.38.2-h3f25603_2.tar.bz2 +name : gdk-pixbuf +version : 2.38.2 +build : h3f25603_2 +build number: 2 +size : 649 KB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.38.2-h3f25603_2.tar.bz2 +md5 : 91342ef9af3aeb309b9a3078a5b733f8 +timestamp : 2020-03-25 01:46:30 UTC +dependencies: + - glib >=2.58.3,<3.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libgcc-ng >=7.3.0 + - libpng >=1.6.37,<1.7.0a0 + - libtiff >=4.1.0,<4.5.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gdk-pixbuf 2.38.2 h3f25603_3 +---------------------------- +file name : gdk-pixbuf-2.38.2-h3f25603_3.tar.bz2 +name : gdk-pixbuf +version : 2.38.2 +build : h3f25603_3 +build number: 3 +size : 633 KB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.38.2-h3f25603_3.tar.bz2 +md5 : a314213a912a68a04422b6e2e91a8c97 +timestamp : 2020-04-06 23:12:21 UTC +dependencies: + - glib >=2.58.3,<3.0a0 + - gobject-introspection + - jpeg >=9c,<10a + - libgcc-ng >=7.3.0 + - libpng >=1.6.37,<1.7.0a0 + - libtiff >=4.1.0,<4.5.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gdk-pixbuf 2.38.2 h3f25603_4 +---------------------------- +file name : gdk-pixbuf-2.38.2-h3f25603_4.tar.bz2 +name : gdk-pixbuf +version : 2.38.2 +build : h3f25603_4 +build number: 4 +size : 653 KB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.38.2-h3f25603_4.tar.bz2 +md5 : db8918b541de4853a8e672df60b3287d +timestamp : 2020-06-02 04:25:48 UTC +dependencies: + - glib >=2.58.3,<3.0a0 + - gobject-introspection + - jpeg >=9d,<10a + - libgcc-ng >=7.5.0 + - libpng >=1.6.37,<1.7.0a0 + - libtiff >=4.1.0,<4.5.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gdk-pixbuf 2.38.2 h3f25603_5 +---------------------------- +file name : gdk-pixbuf-2.38.2-h3f25603_5.tar.bz2 +name : gdk-pixbuf +version : 2.38.2 +build : h3f25603_5 +build number: 5 +size : 657 KB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.38.2-h3f25603_5.tar.bz2 +md5 : b24ead2e4ccc07dea5e6df36efb97436 +timestamp : 2020-10-15 23:29:44 UTC +dependencies: + - glib >=2.58.3,<3.0a0 + - gobject-introspection + - jpeg >=9d,<10a + - libgcc-ng >=7.5.0 + - libpng >=1.6.37,<1.7.0a0 + - libtiff >=4.1.0,<4.5.0a0 + - python_abi 3.8.* *_cp38 + - zlib >=1.2.11,<1.3.0a0 + + +gdk-pixbuf 2.38.2 h3f25603_6 +---------------------------- +file name : gdk-pixbuf-2.38.2-h3f25603_6.tar.bz2 +name : gdk-pixbuf +version : 2.38.2 +build : h3f25603_6 +build number: 6 +size : 653 KB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.38.2-h3f25603_6.tar.bz2 +md5 : ef70a7b0467362e3cac9e2f61d6c36ea +timestamp : 2020-10-26 12:52:35 UTC +dependencies: + - glib >=2.58.3,<3.0a0 + - gobject-introspection + - jpeg >=9d,<10a + - libgcc-ng >=7.5.0 + - libpng >=1.6.37,<1.7.0a0 + - libtiff >=4.1.0,<4.5.0a0 + - python_abi 3.8.* *_cp38 + - zlib >=1.2.11,<1.3.0a0 + + +gdk-pixbuf 2.42.0 h0536704_0 +---------------------------- +file name : gdk-pixbuf-2.42.0-h0536704_0.tar.bz2 +name : gdk-pixbuf +version : 2.42.0 +build : h0536704_0 +build number: 0 +size : 616 KB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.42.0-h0536704_0.tar.bz2 +md5 : a9277a3509e343301221b9dfb66422a3 +timestamp : 2020-11-10 14:11:59 UTC +dependencies: + - jpeg >=9d,<10a + - libgcc-ng >=7.5.0 + - libglib >=2.64.6,<3.0a0 + - libpng >=1.6.37,<1.7.0a0 + - libtiff >=4.1.0,<4.5.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gdk-pixbuf 2.42.0 h0536704_1 +---------------------------- +file name : gdk-pixbuf-2.42.0-h0536704_1.tar.bz2 +name : gdk-pixbuf +version : 2.42.0 +build : h0536704_1 +build number: 1 +size : 612 KB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.42.0-h0536704_1.tar.bz2 +md5 : d7fb97f001b458c0f75cea26d2fa6095 +timestamp : 2020-11-29 19:23:55 UTC +dependencies: + - jpeg >=9d,<10a + - libgcc- diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gecode.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gecode.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..d4c6de9e4817c9f1b611360ce7e76ebdb0b200c0 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gecode.manual_bundle.txt @@ -0,0 +1,463 @@ +# Tool: gecode +software_name: gecode +tier: T1 +domain: t1_backfill_overall +downloads: 160490 +summary: Generic constraint development environment +description: Generic constraint development environment +dependencies: gmp, libgcc >=13, libstdcxx >=13, mpfr +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://www.gecode.org/ +doc_url: +dev_url: + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gecode --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +gecode 4.4.0 1 +-------------- +file name : gecode-4.4.0-1.tar.bz2 +name : gecode +version : 4.4.0 +build : 1 +build number: 1 +size : 46.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-4.4.0-1.tar.bz2 +md5 : 323bdaf62b1241e7ac471c59ec244ecc +dependencies: + - libgcc + + +gecode 4.4.0 h2d50403_2 +----------------------- +file name : gecode-4.4.0-h2d50403_2.tar.bz2 +name : gecode +version : 4.4.0 +build : h2d50403_2 +build number: 2 +size : 47.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-4.4.0-h2d50403_2.tar.bz2 +md5 : 3388d58af3d3a98ada7ee9f9ab410728 +timestamp : 2018-07-09 18:39:40 UTC +dependencies: + - libstdcxx-ng >=4.9 + + +gecode 4.4.0 h7d875b9_4 +----------------------- +file name : gecode-4.4.0-h7d875b9_4.tar.bz2 +name : gecode +version : 4.4.0 +build : h7d875b9_4 +build number: 4 +size : 67.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-4.4.0-h7d875b9_4.tar.bz2 +md5 : ee7fb6614c173864f5f49a879752d1fc +timestamp : 2021-03-25 14:28:23 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + + +gecode 4.4.0 hc9558a2_3 +----------------------- +file name : gecode-4.4.0-hc9558a2_3.tar.bz2 +name : gecode +version : 4.4.0 +build : hc9558a2_3 +build number: 3 +size : 48.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-4.4.0-hc9558a2_3.tar.bz2 +md5 : 84899a65e8b4e2e6ab2301de631ac25c +timestamp : 2020-08-27 03:29:00 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + + +gecode 5.0.0 0 +-------------- +file name : gecode-5.0.0-0.tar.bz2 +name : gecode +version : 5.0.0 +build : 0 +build number: 0 +size : 55.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.0.0-0.tar.bz2 +md5 : bad82a85a02ddc380fea7e00fed37f64 +dependencies: + - gmp 5.1* + - libgcc + - mpfr + + +gecode 5.0.0 h3272c59_3 +----------------------- +file name : gecode-5.0.0-h3272c59_3.tar.bz2 +name : gecode +version : 5.0.0 +build : h3272c59_3 +build number: 3 +size : 80.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.0.0-h3272c59_3.tar.bz2 +md5 : 7b326b106bda16e60832ac9adace8d3c +timestamp : 2021-03-25 14:51:48 UTC +dependencies: + - gmp + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - mpfr + + +gecode 5.0.0 h4c32e4d_7 +----------------------- +file name : gecode-5.0.0-h4c32e4d_7.tar.bz2 +name : gecode +version : 5.0.0 +build : h4c32e4d_7 +build number: 7 +size : 68.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.0.0-h4c32e4d_7.tar.bz2 +md5 : 2db645d905d8991c2db09a9a2be9a47e +timestamp : 2024-12-10 19:29:06 UTC +dependencies: + - gmp + - libgcc >=13 + - libstdcxx >=13 + - mpfr + + +gecode 5.0.0 h53e199c_6 +----------------------- +file name : gecode-5.0.0-h53e199c_6.tar.bz2 +name : gecode +version : 5.0.0 +build : h53e199c_6 +build number: 6 +size : 69.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.0.0-h53e199c_6.tar.bz2 +md5 : 79d8c41ab9b7a600dd34379158e0f927 +timestamp : 2023-05-15 21:30:13 UTC +dependencies: + - gmp + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - mpfr + + +gecode 5.0.0 h8561491_4 +----------------------- +file name : gecode-5.0.0-h8561491_4.tar.bz2 +name : gecode +version : 5.0.0 +build : h8561491_4 +build number: 4 +size : 74.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.0.0-h8561491_4.tar.bz2 +md5 : 18672ec1d7145884ac2d6d1b650bbb85 +timestamp : 2022-10-09 20:33:44 UTC +dependencies: + - gmp + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - mpfr + + +gecode 5.0.0 h8561491_5 +----------------------- +file name : gecode-5.0.0-h8561491_5.tar.bz2 +name : gecode +version : 5.0.0 +build : h8561491_5 +build number: 5 +size : 74.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.0.0-h8561491_5.tar.bz2 +md5 : a441c838e095e58bd43e147998032b7b +timestamp : 2023-05-13 16:39:06 UTC +dependencies: + - gmp + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - mpfr + + +gecode 5.0.0 hb705a9b_1 +----------------------- +file name : gecode-5.0.0-hb705a9b_1.tar.bz2 +name : gecode +version : 5.0.0 +build : hb705a9b_1 +build number: 1 +size : 55.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.0.0-hb705a9b_1.tar.bz2 +md5 : 67662d3e5a6f8665bf0af0dccd49e3b0 +timestamp : 2018-07-06 20:25:48 UTC +dependencies: + - gmp + - libgcc-ng >=4.9 + - mpfr + + +gecode 5.0.0 hb70a6f5_2 +----------------------- +file name : gecode-5.0.0-hb70a6f5_2.tar.bz2 +name : gecode +version : 5.0.0 +build : hb70a6f5_2 +build number: 2 +size : 57.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.0.0-hb70a6f5_2.tar.bz2 +md5 : 093e176c7d4d99f47634cafcab35f00c +timestamp : 2020-08-27 02:54:14 UTC +dependencies: + - gmp + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - mpfr + + +gecode 5.1.0 0 +-------------- +file name : gecode-5.1.0-0.tar.bz2 +name : gecode +version : 5.1.0 +build : 0 +build number: 0 +size : 55.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.1.0-0.tar.bz2 +md5 : 535d2fb4ba1afa44137499ec96ec2cc0 +dependencies: + - gmp 5.1* + - libgcc + - mpfr + + +gecode 5.1.0 hb705a9b_1 +----------------------- +file name : gecode-5.1.0-hb705a9b_1.tar.bz2 +name : gecode +version : 5.1.0 +build : hb705a9b_1 +build number: 1 +size : 55.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.1.0-hb705a9b_1.tar.bz2 +md5 : 767d7ba1501d34ee56995b3868b167e0 +timestamp : 2018-07-06 20:45:09 UTC +dependencies: + - gmp + - libgcc-ng >=4.9 + - mpfr + + +gecode 5.1.0 hb70a6f5_2 +----------------------- +file name : gecode-5.1.0-hb70a6f5_2.tar.bz2 +name : gecode +version : 5.1.0 +build : hb70a6f5_2 +build number: 2 +size : 55.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.1.0-hb70a6f5_2.tar.bz2 +md5 : fabd0c941dd169a13c53e69cb483d620 +timestamp : 2020-08-27 03:12:38 UTC +dependencies: + - gmp + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - mpfr + + +gecode 5.1.0 pl5321h4c32e4d_3 +----------------------------- +file name : gecode-5.1.0-pl5321h4c32e4d_3.conda +name : gecode +version : 5.1.0 +build : pl5321h4c32e4d_3 +build number: 3 +size : 51.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-5.1.0-pl5321h4c32e4d_3.conda +md5 : 317a809f1e4330b39796ae72f13cc5bb +timestamp : 2025-11-17 22:10:44 UTC +dependencies: + - gmp >=6.3.0,<7.0a0 + - libgcc >=13 + - libstdcxx >=13 + - mpfr >=4.2.1,<5.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +gecode 6.2.0 h3272c59_1 +----------------------- +file name : gecode-6.2.0-h3272c59_1.tar.bz2 +name : gecode +version : 6.2.0 +build : h3272c59_1 +build number: 1 +size : 89.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-6.2.0-h3272c59_1.tar.bz2 +md5 : bebca5c618742bd2ea68c63410af46ff +timestamp : 2021-03-25 15:15:25 UTC +dependencies: + - gmp + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - mpfr + + +gecode 6.2.0 h4c32e4d_5 +----------------------- +file name : gecode-6.2.0-h4c32e4d_5.tar.bz2 +name : gecode +version : 6.2.0 +build : h4c32e4d_5 +build number: 5 +size : 73.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-6.2.0-h4c32e4d_5.tar.bz2 +md5 : 1178cc141520f3104f8b96f49420d3bf +timestamp : 2024-12-10 19:42:11 UTC +dependencies: + - gmp + - libgcc >=13 + - libstdcxx >=13 + - mpfr + + +gecode 6.2.0 h4c32e4d_6 +----------------------- +file name : gecode-6.2.0-h4c32e4d_6.tar.bz2 +name : gecode +version : 6.2.0 +build : h4c32e4d_6 +build number: 6 +size : 73.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-6.2.0-h4c32e4d_6.tar.bz2 +md5 : e6cf821c6fe8bbea1e7c8807364033a0 +timestamp : 2025-04-29 10:22:30 UTC +dependencies: + - gmp + - libgcc >=13 + - libstdcxx >=13 + - mpfr + + +gecode 6.2.0 h53e199c_4 +----------------------- +file name : gecode-6.2.0-h53e199c_4.tar.bz2 +name : gecode +version : 6.2.0 +build : h53e199c_4 +build number: 4 +size : 74.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-6.2.0-h53e199c_4.tar.bz2 +md5 : 015262892a487f1468fee53ca346034b +timestamp : 2023-05-15 21:50:13 UTC +dependencies: + - gmp + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - mpfr + + +gecode 6.2.0 h8561491_2 +----------------------- +file name : gecode-6.2.0-h8561491_2.tar.bz2 +name : gecode +version : 6.2.0 +build : h8561491_2 +build number: 2 +size : 80.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-6.2.0-h8561491_2.tar.bz2 +md5 : 72776249cccf589eb8f6e938cd2a4a27 +timestamp : 2023-03-06 21:47:19 UTC +dependencies: + - gmp + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - mpfr + + +gecode 6.2.0 h8561491_3 +----------------------- +file name : gecode-6.2.0-h8561491_3.tar.bz2 +name : gecode +version : 6.2.0 +build : h8561491_3 +build number: 3 +size : 80.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-6.2.0-h8561491_3.tar.bz2 +md5 : f1e636c24597bd857d5cc5b0602a2228 +timestamp : 2023-05-13 16:18:09 UTC +dependencies: + - gmp + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - mpfr + + +gecode 6.2.0 hb70a6f5_0 +----------------------- +file name : gecode-6.2.0-hb70a6f5_0.tar.bz2 +name : gecode +version : 6.2.0 +build : hb70a6f5_0 +build number: 0 +size : 65.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gecode-6.2.0-hb70a6f5_0.tar.bz2 +md5 : d77c85ec2e1a847836e8b24739773d98 +timestamp : 2020-08-28 20:49:58 UTC +dependencies: + - gmp + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - mpfr diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/genecircuitry.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/genecircuitry.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c347d392b69496e20abf99e59cfd9e2a9079f1e8 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/genecircuitry.manual_bundle.txt @@ -0,0 +1,121 @@ +# Tool: genecircuitry +software_name: genecircuitry +tier: T1 +domain: single_cell +downloads: 61 +summary: GeneCircuitry: TRN analysis from single-cell data (Scanpy, CellOracle, Hotspot) +description: A modular, checkpoint-enabled pipeline for TRN analysis from +single-cell RNA-seq data. Integrates Scanpy for preprocessing and +clustering, CellOracle for GRN inference, and Hotspot for embedding-aware +gene modules identification. Provides an HTML/PDF reporting layer +and a standalone ``genecircuitry`` CLI entry point. +dependencies: adjusttext >=0.7.3, anndata >=0.8.0, fa2_modified, genomepy >=0.8.4, gimmemotifs >=0.14.4, goatools, gseapy, h5py >=3.1.0, igraph >=0.10.1, joblib, jupyter, leidenalg, louvain, matplotlib-base >=3.6.3, networkx >=2.6.0, numba >=0.50.1, numpy >=1.20, pandas >=1.3.0, pyarrow >=0.17, python >=3.9,<3.11, scanpy >=1.9.0, scikit-learn, scipy, seaborn, tqdm >=4.45, umap-learn, velocyto.py >=0.17, weasyprint +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/samuelecancellieri/genecircuitry +doc_url: https://github.com/samuelecancellieri/genecircuitry/blob/main/README.md +dev_url: https://github.com/samuelecancellieri/genecircuitry + +## URL Docs Extract +### https://github.com/samuelecancellieri/genecircuitry/blob/main/README.md +GeneCircuitry/README.md at main · samuelecancellieri/GeneCircuitry · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} samuelecancellieri / GeneCircuitry Public Notifications You must be signed in to change notification settings Fork 0 Star 0 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Files Expand file tree main Breadcrumbs GeneCircuitry / README.md Copy path Blame More file actions Blame More file actions Latest commit History History History 426 lines (317 loc) · 11.2 KB main Breadcrumbs GeneCircuitry / README.md Top File metadata and controls Preview Code Blame 426 lines (317 loc) · 11.2 KB Raw Copy raw file Download raw file Outline Edit and raw actions genecircuitry A Python package for transcriptional regulatory network analysis. Installation genecircuitry requires Python >=3.9, <3.11 . Most dependencies are available on conda-forge and bioconda . Two optional analysis engines — CellOracle and hotspotsc — are only available via pip and must be installed as a separate step after the conda environment is set up. Option 1 — Pixi (recommended) Pixi manages conda and pip dependencies together in a single reproducible environment. It is the easiest and cleanest way to get a fully working installation. # Install pixi (one-time, see https://prefix.dev/docs/pixi/installation) curl -fsSL https://pixi.sh/install.sh | bash # Clone the repository git clone https://github.com/samuelecancellieri/genecircuitry.git cd genecircuitry # Create the environment and install all dependencies (conda + pip) in one step pixi install # Run the pipeline inside the pixi environment (genecircuitry --help) pixi run run # Run the pipeline inside the pixi environment (genecircuitry test pipeline) pixi run genecircuitry # Or drop into an interactive shell pixi shell Developer environment (adds pytest, black, flake8, mypy): pixi install -e dev pixi run -e dev test Option 2 — Conda Install genecircuitry and its conda-available dependencies from bioconda and conda-forge , then install the pip-only dependencies manually. # 1. Create a fresh environment (Python 3.9 is recommended) conda create -n genecircuitry python=3.9 conda activate genecircuitry # 2. Install genecircuitry and all conda-available dependencies conda install -c bioconda -c conda-forge genecircuitry # 3. Install the pip-only optional analysis engines # (CellOracle for GRN inference, hotspotsc for gene modules) pip install celloracle==0.18.0 hotspotsc==1.1.3 Skip step 3 if you only need preprocessing/QC and do not require GRN inference or gene module analysis. Option 3 — pip / venv # Clone the repository git clone https://github.com/samuelecancellieri/genecircuitry.git cd genecircuitry # Create and activate a virtual environment python -m venv venv source venv/bin/activate # On Windows: venv\Scripts\activate # Install the package with all optional dependencies pip install -e " .[grn,hotspot] " # Or install core only (no CellOracle / hotspotsc) pip install -e . # Install with development dependencies pip install -e " .[dev] " Option 4 — Docker A pre-built image is available that ships all dependencies (including CellOracle and hotspotsc) and works out of the box: # Pull and run (bind-mount your data and output directories) docker run --rm \ -v /path/to/your/data:/data \ -v /path/to/output:/output \ zanathos/genecircuitry:latest \ --input /data/your_data.h5ad --output /output # Check available options docker run --rm zanathos/genecircuitry:latest --help Build the image locally from source: git clone https://github.com/samuelecancellieri/genecircuitry.git cd genecircuitry docker build -t genecircuitry . docker run --rm genecircuitry --help Quick Start Complete Analysis Pipeline Run the full analysis pipeline from preprocessing through CellOracle and Hotspot: # Run with example dataset (default) python run_complete_analysis.py # Or use the script directly python examples/complete_pipeline.py # Run with your own data python run_complete_analysis.py --input your_data.h5ad --output results # Skip specific analyses python run_complete_analysis.py --skip-celloracle # Skip GRN inference python run_complete_analysis.py --skip-hotspot # Skip module identification # Custom parameters python run_complete_analysis.py --seed 123 --n-jobs 16 --min-genes 300 # See all options python run_complete_analysis.py --help Modular Execution & Parallel Processing NEW: The pipeline now supports modular execution and parallel processing: # Run only specific steps python examples/complete_pipeline.py \ --input data.h5ad \ --output results \ --steps load preprocessing clustering # Stratified analysis in parallel (multiple cell types/clusters) python examples/complete_pipeline.py \ --input data.h5ad \ --output results \ --cluster-key-stratification celltype \ --parallel \ --n-jobs 4 # Resume from checkpoints python examples/complete_pipeline.py \ --input data.h5ad \ --output results \ --steps celloracle hotspot # Skips preprocessing if checkpoint exists Available step names: load , preprocessing , stratification , clustering , celloracle , hotspot , grn_analysis , summary Parallel benefits: Process multiple stratifications simultaneously Linear speedup with number of workers Automatic checkpoint integration See Controller Guide for details The complete pipeline includes: Data Loading - Load h5ad/h5 files or use example dataset Quality Control - Cell and gene filtering with QC metrics Preprocessing - Normalization, HVG selection, PCA, clustering CellOracle GRN Inference - Gene regulatory network prediction Hotspot Module Analysis - Spatially autocorrelated gene modules Summary Report - Comprehensive analysis summary with output files Output structure: output/ ├── preprocessed_adata.h5ad # Preprocessed dataset ├── analysis_summary.txt # Analysis report ├── celloracle/ │ ├── oracle_object.celloracle.oracle │ └── grn_links.celloracle.links └── hotspot/ ├── autocorrelation_results.csv ├── significant_genes.csv └── gene_modules.csv figures/ ├── qc/ # QC plots └── grn_analysis/ # GRN visualizations Usage Configuration and Reproducibility Set random seed and configure default parameters: from genecircuitry import set_random_seed , config # Set random seed for reproducibility set_random_seed ( 42 ) # View all configuration parameters config . print_config () # Update specific parameters config . update_config ( QC_MIN_GENES = 300 , QC_MIN_COUNTS = 1000 , PLOT_DPI = 600 ) Quality Control Perform comprehensive quality control on single-cell RNA-seq data: import scanpy as sc from genecircuitry import config from genecircuitry . preprocessing import perform_qc , plot_qc_violin , plot_qc_scatter # Load your data adata = sc . read_h5ad ( 'your_data.h5ad' ) # Perform QC - uses config defaults automatically adata_qc = perform_qc ( adata ) # Equivalent to: min_genes=200, min_counts=500, pct_counts_mt_max=20.0, min_cells=10 # Or override specific parameters adata_qc = perform_qc ( adata , min_genes = 300 , # Override min_counts = 1000 # Override # Other params use config defaults ) Complete Workflow Example import scanpy as sc from genecircuitry import set_random_seed , config from genecircuitry . preprocessing import perform_qc , perform_grn_pre_processing # 1. Set up reproducibility set_random_seed ( 42 ) # 2. Optionally customize config config . update_config ( QC_MIN_GENES = 300 , QC_MIN_COUNTS = 1000 ) # 3. Load and process data adata = sc . read_h5ad ( 'your_data.h5ad' ) adata = perform_qc ( adata ) # Uses config defaults # 4. Normalize sc . pp . normalize_total ( adata , target_sum = config . NORMALIZE_TARGET_SUM ) sc . pp . log1p ( adata ) # 5. GRN preprocessing adata = perform_grn_pre_processing ( adata ) # Uses config defaults CellOracle Integration Perform gene regulatory network inference using CellOracle: from genecircuitry . celloracle_processing import ( create_oracle_object , run_PCA , run_KNN , run_links ) # Note: Requires CellOracle installation # pip install celloracle # Create Oracle object oracle = create_oracle_object ( adata = adata , cluster_column_name = 'leiden' , embedding_name = 'X_umap' , raw_count_layer = 'raw_counts' ) # Perform PCA and KNN imputation oracle = run_PCA ( oracle ) run_KNN ( oracle , n_comps = 50 ) # Infer regulatory links links = run_links ( oracle , cluster_column_name = 'leiden' , p_cutoff = 0.001 ) # Save results oracle . to_hdf5 ( 'oracle_object.celloracle.oracle' ) links . to_hdf5 ( 'grn_links.celloracle.links' ) Running Examples # Activate environment source venv/bin/activate # Run QC example python examples/example_qc.py # Run configuration example python examples/config_example.py # Run CellOracle workflow (requires celloracle) python examples/celloracle_workflow.py # Run quick demo python examples/quick_demo.py # Test config integration python examples/test_config_integration.py Features Configuration Management : Centralized configuration for reproducibility Global random seed setting Default parameters for all analysis steps Easy parameter updates Configuration profiles for different analysis types Quality Control : Comprehensive QC with multiple visualization options Cell filtering based on gene count, total counts, and mitochondrial percentage Automated QC metrics calculation Before/after filtering comparison plots Violin and scatter plots for detailed inspection Data Preprocessing : Complete preprocessing pipeline Normalization and scaling for single-cell RNA-seq data Highly variable genes selection PCA and dimensionality reduction Neighborhood graph construction CellOracle Integration : Gene regulatory network inference Oracle object creation with raw or normalized counts Automated PCA component selection KNN imputation for noise reduction Regulatory link inference with statistical filtering Network visualization and quality metrics Gene Regulatory Network Analysis : Network construction and analysis tools TF-target gene relationship inference Network topology analysis Cluster-specific GRN construction Documentation Configuration Guide - Complete configuration documentation QC Functions - Quality control functions guide CellOracle Processing - CellOracle integration guide Package Structure - Package organization overview Preprocessing Updates - Config integration details Development Running Tests # Run all tests pytest tests/ # Run specific test file pytest tests/test_config.py -v pytest tests/test_preprocessing.py -v pytest tests/test_celloracle.py -v # Run with coverage pytest tests/ --cov=genecircuitry --cov-report=html Code Quality # Format code black genecircuitry/ # Check linting flake8 genecircuitry/ # Type checking mypy genecircuitry/ Testing Notes CellOracle tests use mocking when CellOracle is not installed Some tests are skipped if CellOracle is not available Use pytest -v for verbose output Tests cover all major functionality with both unit and integration tests License MIT License Authors Samuele Cancellieri Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/samuelecancellieri/genecircuitry +GitHub - samuelecancellieri/GeneCircuitry · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} samuelecancellieri / GeneCircuitry Public Notifications You must be signed in to change notification settings Fork 0 Star 0 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights samuelecancellieri/GeneCircuitry main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 144 Commits 144 Commits .github .github conda-recipe conda-recipe docs docs examples examples genecircuitry genecircuitry tests tests .dockerignore .dockerignore .gitignore .gitignore CHANGELOG.md CHANGELOG.md Dockerfile Dockerfile LICENSE LICENSE README.md README.md RESTRUCTURING_PLAN.md RESTRUCTURING_PLAN.md pixi.toml pixi.toml pyproject.toml pyproject.toml requirements.txt requirements.txt run_complete_analysis.py run_complete_analysis.py run_pipe_regev_test_TODELETE.sh run_pipe_regev_test_TODELETE.sh View all files Repository files navigation README Contributing MIT license genecircuitry A Python package for transcriptional regulatory network analysis. Installation genecircuitry requires Python >=3.9, <3.11 . Most dependencies are available on conda-forge and bioconda . Two optional analysis engines — CellOracle and hotspotsc — are only available via pip and must be installed as a separate step after the conda environment is set up. Option 1 — Pixi (recommended) Pixi manages conda and pip dependencies together in a single reproducible environment. It is the easiest and cleanest way to get a fully working installation. # Install pixi (one-time, see https://prefix.dev/docs/pixi/installation) curl -fsSL https://pixi.sh/install.sh | bash # Clone the repository git clone https://github.com/samuelecancellieri/genecircuitry.git cd genecircuitry # Create the environment and install all dependencies (conda + pip) in one step pixi install # Run the pipeline inside the pixi environment (genecircuitry --help) pixi run run # Run the pipeline inside the pixi environment (genecircuitry test pipeline) pixi run genecircuitry # Or drop into an interactive shell pixi shell Developer environment (adds pytest, black, flake8, mypy): pixi install -e dev pixi run -e dev test Option 2 — Conda Install genecircuitry and its conda-available dependencies from bioconda and conda-forge , then install the pip-only dependencies manually. # 1. Create a fresh environment (Python 3.9 is recommended) conda create -n genecircuitry python=3.9 conda activate genecircuitry # 2. Install genecircuitry and all conda-available dependencies conda install -c bioconda -c conda-forge genecircuitry # 3. Install the pip-only optional analysis engines # (CellOracle for GRN inference, hotspotsc for gene modules) pip install celloracle==0.18.0 hotspotsc==1.1.3 Skip step 3 if you only need preprocessing/QC and do not require GRN inference or gene module analysis. Option 3 — pip / venv # Clone the repository git clone https://github.com/samuelecancellieri/genecircuitry.git cd genecircuitry # Create and activate a virtual environment python -m venv venv source venv/bin/activate # On Windows: venv\Scripts\activate # Install the package with all optional dependencies pip install -e " .[grn,hotspot] " # Or install core only (no CellOracle / hotspotsc) pip install -e . # Install with development dependencies pip install -e " .[dev] " Option 4 — Docker A pre-built image is available that ships all dependencies (including CellOracle and hotspotsc) and works out of the box: # Pull and run (bind-mount your data and output directories) docker run --rm \ -v /path/to/your/data:/data \ -v /path/to/output:/output \ zanathos/genecircuitry:latest \ --input /data/your_data.h5ad --output /output # Check available options docker run --rm zanathos/genecircuitry:latest --help Build the image locally from source: git clone https://github.com/samuelecancellieri/genecircuitry.git cd genecircuitry docker build -t genecircuitry . docker run --rm genecircuitry --help Quick Start Complete Analysis Pipeline Run the full analysis pipeline from preprocessing through CellOracle and Hotspot: # Run with example dataset (default) python run_complete_analysis.py # Or use the script directly python examples/complete_pipeline.py # Run with your own data python run_complete_analysis.py --input your_data.h5ad --output results # Skip specific analyses python run_complete_analysis.py --skip-celloracle # Skip GRN inference python run_complete_analysis.py --skip-hotspot # Skip module identification # Custom parameters python run_complete_analysis.py --seed 123 --n-jobs 16 --min-genes 300 # See all options python run_complete_analysis.py --help Modular Execution & Parallel Processing NEW: The pipeline now supports modular execution and parallel processing: # Run only specific steps python examples/complete_pipeline.py \ --input data.h5ad \ --output results \ --steps load preprocessing clustering # Stratified analysis in parallel (multiple cell types/clusters) python examples/complete_pipeline.py \ --input data.h5ad \ --output results \ --cluster-key-stratification celltype \ --parallel \ --n-jobs 4 # Resume from checkpoints python examples/complete_pipeline.py \ --input data.h5ad \ --output results \ --steps celloracle hotspot # Skips preprocessing if checkpoint exists Available step names: load , preprocessing , stratification , clustering , celloracle , hotspot , grn_analysis , summary Parallel benefits: Process multiple stratifications simultaneously Linear speedup with number of workers Automatic checkpoint integration See Controller Guide for details The complete pipeline includes: Data Loading - Load h5ad/h5 files or use example dataset Quality Control - Cell and gene filtering with QC metrics Preprocessing - Normalization, HVG selection, PCA, clustering CellOracle GRN Inference - Gene regulatory network prediction Hotspot Module Analysis - Spatially autocorrelated gene modules Summary Report - Comprehensive analysis summary with output files Output structure: output/ ├── preprocessed_adata.h5ad # Preprocessed dataset ├── analysis_summary.txt # Analysis report ├── celloracle/ │ ├── oracle_object.celloracle.oracle │ └── grn_links.celloracle.links └── hotspot/ ├── autocorrelation_results.csv ├── significant_genes.csv └── gene_modules.csv figures/ ├── qc/ # QC plots └── grn_analysis/ # GRN visualizations Usage Configuration and Reproducibility Set random seed and configure default parameters: from genecircuitry import set_random_seed , config # Set random seed for reproducibility set_random_seed ( 42 ) # View all configuration parameters config . print_config () # Update specific parameters config . update_config ( QC_MIN_GENES = 300 , QC_MIN_COUNTS = 1000 , PLOT_DPI = 600 ) Quality Control Perform comprehensive quality control on single-cell RNA-seq data: import scanpy as sc from genecircuitry import config from genecircuitry . preprocessing import perform_qc , plot_qc_violin , plot_qc_scatter # Load your data adata = sc . read_h5ad ( 'your_data.h5ad' ) # Perform QC - uses config defaults automatically adata_qc = perform_qc ( adata ) # Equivalent to: min_genes=200, min_counts=500, pct_counts_mt_max=20.0, min_cells=10 # Or override specific parameters adata_qc = perform_qc ( adata , min_genes = 300 , # Override min_counts = 1000 # Override # Other params use config defaults ) Complete Workflow Example import scanpy as sc from genecircuitry import set_random_seed , config from genecircuitry . preprocessing import perform_qc , perform_grn_pre_processing # 1. Set up reproducibility set_random_seed ( 42 ) # 2. Optionally customize config config . update_config ( QC_MIN_GENES = 300 , QC_MIN_COUNTS = 1000 ) # 3. Load and process data adata = sc . read_h5ad ( 'your_data.h5ad' ) adata = perform_qc ( adata ) # Uses config defaults # 4. Normalize sc . pp . normalize_total ( adata , target_sum = config . NORMALIZE_TARGET_SUM ) sc . pp . log1p ( adata ) # 5. GRN preprocessing adata = perform_grn_pre_processing ( adata ) # Uses config defaults CellOracle Integration Perform gene regulatory network inference using CellOracle: from genecircuitry . celloracle_processing import ( create_oracle_object , run_PCA , run_KNN , run_links ) # Note: Requires CellOracle installation # pip install celloracle # Create Oracle object oracle = create_oracle_object ( adata = adata , cluster_column_name = 'leiden' , embedding_name = 'X_umap' , raw_count_layer = 'raw_counts' ) # Perform PCA and KNN imputation oracle = run_PCA ( oracle ) run_KNN ( oracle , n_comps = 50 ) # Infer regulatory links links = run_links ( oracle , cluster_column_name = 'leiden' , p_cutoff = 0.001 ) # Save results oracle . to_hdf5 ( 'oracle_object.celloracle.oracle' ) links . to_hdf5 ( 'grn_links.celloracle.links' ) Running Examples # Activate environment source venv/bin/activate # Run QC example python examples/example_qc.py # Run configuration example python examples/config_example.py # Run CellOracle workflow (requires celloracle) python examples/celloracle_workflow.py # Run quick demo python examples/quick_demo.py # Test config integration python examples/test_config_integration.py Features Configuration Management : Centralized configuration for reproducibility Global random seed setting Default parameters for all analysis steps Easy parameter updates Configuration profiles for different analysis types Quality Control : Comprehensive QC with multiple visualization options Cell filtering based on gene count, total counts, and mitochondrial percentage Automated QC metrics calculation Before/after filtering comparison plots Violin and scatter plots for detailed inspection Data Preprocessing : Complete preprocessing pipeline Normalization and scaling for single-cell RNA-seq data Highly variable genes selection PCA and dimensionality reduction Neighborhood graph construction CellOracle Integration : Gene regulatory network inference Oracle object creation with raw or normalized counts Automated PCA component selection KNN imputation for noise reduction Regulatory link inference with statistical filtering Network visualization and quality metrics Gene Regulatory Network Analysis : Network construction and analysis tools TF-target gene relationship inference Network topology analysis Cluster-specific GRN construction Documentation Configuration Guide - Complete configuration documentation QC Functions - Quality control functions guide CellOracle Processing - CellOracle integration guide Package Structure - Package organization overview Preprocessing Updates - Config integration details Development Running Tests # Run all tests pytest tests/ # Run specific test file pytest tests/test_config.py -v pytest tests/test_preprocessing.py -v pytest tests/test_celloracle.py -v # Run with coverage pytest tests/ --cov=genecircuitry --cov-report=html Code Quality # Format code black genecircuitry/ # Check linting flake8 genecircuitry/ # Type checking mypy genecircuitry/ Testing Notes CellOracle tests use mocking when CellOracle is not installed Some tests are skipped if CellOracle is not available Use pytest -v for verbose output Tests cover all major functionality with both unit and integration tests License MIT License Authors Samuele Cancellieri About No description, website, or topics provided. Resources Readme License MIT license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 0 stars Watchers 0 watching Forks 0 forks Report repository Releases 10 v0.1.9 Latest Apr 6, 2026 + 9 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 98.9% Other 1.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/samuelecancellieri/genecircuitry +GitHub - samuelecancellieri/GeneCircuitry · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} samuelecancellieri / GeneCircuitry Public Notifications You must be signed in to change notification settings Fork 0 Star 0 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights samuelecancellieri/GeneCircuitry main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 144 Commits 144 Commits .github .github conda-recipe conda-recipe docs docs examples examples genecircuitry genecircuitry tests tests .dockerignore .dockerignore .gitignore .gitignore CHANGELOG.md CHANGELOG.md Dockerfile Dockerfile LICENSE LICENSE README.md README.md RESTRUCTURING_PLAN.md RESTRUCTURING_PLAN.md pixi.toml pixi.toml pyproject.toml pyproject.toml requirements.txt requirements.txt run_complete_analysis.py run_complete_analysis.py run_pipe_regev_test_TODELETE.sh run_pipe_regev_test_TODELETE.sh View all files Repository files navigation README Contributing MIT license genecircuitry A Python package for transcriptional regulatory network analysis. Installation genecircuitry requires Python >=3.9, <3.11 . Most dependencies are available on conda-forge and bioconda . Two optional analysis engines — CellOracle and hotspotsc — are only available via pip and must be installed as a separate step after the conda environment is set up. Option 1 — Pixi (recommended) Pixi manages conda and pip dependencies together in a single reproducible environment. It is the easiest and cleanest way to get a fully working installation. # Install pixi (one-time, see https://prefix.dev/docs/pixi/installation) curl -fsSL https://pixi.sh/install.sh | bash # Clone the repository git clone https://github.com/samuelecancellieri/genecircuitry.git cd genecircuitry # Create the environment and install all dependencies (conda + pip) in one step pixi install # Run the pipeline inside the pixi environment (genecircuitry --help) pixi run run # Run the pipeline inside the pixi environment (genecircuitry test pipeline) pixi run genecircuitry # Or drop into an interactive shell pixi shell Developer environment (adds pytest, black, flake8, mypy): pixi install -e dev pixi run -e dev test Option 2 — Conda Install genecircuitry and its conda-available dependencies from bioconda and conda-forge , then install the pip-only dependencies manually. # 1. Create a fresh environment (Python 3.9 is recommended) conda create -n genecircuitry python=3.9 conda activate genecircuitry # 2. Install genecircuitry and all conda-available dependencies conda install -c bioconda -c conda-forge genecircuitry # 3. Install the pip-only optional analysis engines # (CellOracle for GRN inference, hotspotsc for gene modules) pip install celloracle==0.18.0 hotspotsc==1.1.3 Skip step 3 if you only need preprocessing/QC and do not require GRN inference or gene module analysis. Option 3 — pip / venv # Clone the repository git clone https://github.com/samuelecancellieri/genecircuitry.git cd genecircuitry # Create and activate a virtual environment python -m venv venv source venv/bin/activate # On Windows: venv\Scripts\activate # Install the package with all optional dependencies pip install -e " .[grn,hotspot] " # Or install core only (no CellOracle / hotspotsc) pip install -e . # Install with development dependencies pip install -e " .[dev] " Option 4 — Docker A pre-built image is available that ships all dependencies (including CellOracle and hotspotsc) and works out of the box: # Pull and run (bind-mount your data and output directories) docker run --rm \ -v /path/to/your/data:/data \ -v /path/to/output:/output \ zanathos/genecircuitry:latest \ --input /data/your_data.h5ad --output /output # Check available options docker run --rm zanathos/genecircuitry:latest --help Build the image locally from source: git clone https://github.com/samuelecancellieri/genecircuitry.git cd genecircuitry docker build -t genecircuitry . docker run --rm genecircuitry --help Quick Start Complete Analysis Pipeline Run the full analysis pipeline from preprocessing through CellOracle and Hotspot: # Run with example dataset (default) python run_complete_analysis.py # Or use the script directly python examples/complete_pipeline.py # Run with your own data python run_complete_analysis.py --input your_data.h5ad --output results # Skip specific analyses python run_complete_analysis.py --skip-celloracle # Skip GRN inference python run_complete_analysis.py --skip-hotspot # Skip module identification # Custom parameters python run_complete_analysis.py --seed 123 --n-jobs 16 --min-genes 300 # See all options python run_complete_analysis.py --help Modular Execution & Parallel Processing NEW: The pipeline now supports modular execution and parallel processing: # Run only specific steps python examples/complete_pipeline.py \ --input data.h5ad \ --output results \ --steps load preprocessing clustering # Stratified analysis in parallel (multiple cell types/clusters) python examples/complete_pipeline.py \ --input data.h5ad \ --output results \ --cluster-key-stratification celltype \ --parallel \ --n-jobs 4 # Resume from checkpoints python examples/complete_pipeline.py \ --input data.h5ad \ --output results \ --steps celloracle hotspot # Skips preprocessing if checkpoint exists Available step names: load , preprocessing , stratification , clustering , celloracle , hotspot , grn_analysis , summary Parallel benefits: Process multiple stratifications simultaneously Linear speedup with number of workers Automatic checkpoint integration See Controller Guide for details The complete pipeline includes: Data Loading - Load h5ad/h5 files or use example dataset Quality Control - Cell and gene filtering with QC metrics Preprocessing - Normalization, HVG selection, PCA, clustering CellOracle GRN Inference - Gene regulatory network prediction Hotspot Module Analysis - Spatially autocorrelated gene modules Summary Report - Comprehensive analysis summary with output files Output structure: output/ ├── preprocessed_adata.h5ad # Preprocessed dataset ├── analysis_summary.txt # Analysis report ├── celloracle/ │ ├── oracle_object.celloracle.oracle │ └── grn_links.celloracle.links └── hotspot/ ├── autocorrelation_results.csv ├── significant_genes.csv └── gene_modules.csv figures/ ├── qc/ # QC plots └── grn_analysis/ # GRN visualizations Usage Configuration and Reproducibility Set random seed and configure default parameters: from genecircuitry import set_random_seed , config # Set random seed for reproducibility set_random_seed ( 42 ) # View all configuration parameters config . print_config () # Update specific parameters config . update_config ( QC_MIN_GENES = 300 , QC_MIN_COUNTS = 1000 , PLOT_DPI = 600 ) Quality Control Perform comprehensive quality control on single-cell RNA-seq data: import scanpy as sc from genecircuitry import config from genecircuitry . preprocessing import perform_qc , plot_qc_violin , plot_qc_scatter # Load your data adata = sc . read_h5ad ( 'your_data.h5ad' ) # Perform QC - uses config defaults automatically adata_qc = perform_qc ( adata ) # Equivalent to: min_genes=200, min_counts=500, pct_counts_mt_max=20.0, min_cells=10 # Or override specific parameters adata_qc = perform_qc ( adata , min_genes = 300 , # Override min_counts = 1000 # Override # Other params use config defaults ) Complete Workflow Example import scanpy as sc from genecircuitry import set_random_seed , config from genecircuitry . preprocessing import perform_qc , perform_grn_pre_processing # 1. Set up reproducibility set_random_seed ( 42 ) # 2. Optionally customize config config . update_config ( QC_MIN_GENES = 300 , QC_MIN_COUNTS = 1000 ) # 3. Load and process data adata = sc . read_h5ad ( 'your_data.h5ad' ) adata = perform_qc ( adata ) # Uses config defaults # 4. Normalize sc . pp . normalize_total ( adata , target_sum = config . NORMALIZE_TARGET_SUM ) sc . pp . log1p ( adata ) # 5. GRN preprocessing adata = perform_grn_pre_processing ( adata ) # Uses config defaults CellOracle Integration Perform gene regulatory network inference using CellOracle: from genecircuitry . celloracle_processing import ( create_oracle_object , run_PCA , run_KNN , run_links ) # Note: Requires CellOracle installation # pip install celloracle # Create Oracle object oracle = create_oracle_object ( adata = adata , cluster_column_name = 'leiden' , embedding_name = 'X_umap' , raw_count_layer = 'raw_counts' ) # Perform PCA and KNN imputation oracle = run_PCA ( oracle ) run_KNN ( oracle , n_comps = 50 ) # Infer regulatory links links = run_links ( oracle , cluster_column_name = 'leiden' , p_cutoff = 0.001 ) # Save results oracle . to_hdf5 ( 'oracle_object.celloracle.oracle' ) links . to_hdf5 ( 'grn_links.celloracle.links' ) Running Examples # Activate environment source venv/bin/activate # Run QC example python examples/example_qc.py # Run configuration example python examples/config_example.py # Run CellOracle workflow (requires celloracle) python examples/celloracle_workflow.py # Run quick demo python examples/quick_demo.py # Test config integration python examples/test_config_integration.py Features Configuration Management : Centralized configuration for reproducibility Global random seed setting Default parameters for all analysis steps Easy parameter updates Configuration profiles for different analysis types Quality Control : Comprehensive QC with multiple visualization options Cell filtering based on gene count, total counts, and mitochondrial percentage Automated QC metrics calculation Before/after filtering comparison plots Violin and scatter plots for detailed inspection Data Preprocessing : Complete preprocessing pipeline Normalization and scaling for single-cell RNA-seq data Highly variable genes selection PCA and dimensionality reduction Neighborhood graph construction CellOracle Integration : Gene regulatory network inference Oracle object creation with raw or normalized counts Automated PCA component selection KNN imputation for noise reduction Regulatory link inference with statistical filtering Network visualization and quality metrics Gene Regulatory Network Analysis : Network construction and analysis tools TF-target gene relationship inference Network topology analysis Cluster-specific GRN construction Documentation Configuration Guide - Complete configuration documentation QC Functions - Quality control functions guide CellOracle Processing - CellOracle integration guide Package Structure - Package organization overview Preprocessing Updates - Config integration details Development Running Tests # Run all tests pytest tests/ # Run specific test file pytest tests/test_config.py -v pytest tests/test_preprocessing.py -v pytest tests/test_celloracle.py -v # Run with coverage pytest tests/ --cov=genecircuitry --cov-report=html Code Quality # Format code black genecircuitry/ # Check linting flake8 genecircuitry/ # Type checking mypy genecircuitry/ Testing Notes CellOracle tests use mocking when CellOracle is not installed Some tests are skipped if CellOracle is not available Use pytest -v for verbose output Tests cover all major functionality with both unit and integration tests License MIT License Authors Samuele Cancellieri About No description, website, or topics provided. Resources Readme License MIT license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 0 stars Watchers 0 watching Forks 0 forks Report repository Releases 10 v0.1.9 Latest Apr 6, 2026 + 9 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 98.9% Other 1.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge genecircuitry --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +genecircuitry 0.1.4 pyhdfd78af_0 +-------------------------------- +file name : genecircuitry-0.1.4-pyhdfd78af_0.conda +name : genecircuitry +version : 0.1.4 +build : pyhdfd78af_0 +build number: 0 +size : 79 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/genecircuitry-0.1.4-pyhdfd78af_0.conda +md5 : a1e37a26b14fa04607e67f80bf1abefe +timestamp : 2026-03-03 10:37:58 UTC +dependencies: + - adjusttext >=0.7.3 + - anndata >=0.8.0 + - fa2_modified + - genomepy >=0.8.4 + - gimmemotifs >=0.14.4 + - goatools + - gseapy + - h5py >=3.1.0 + - igraph >=0.10.1 + - joblib + - jupyter + - leidenalg + - louvain + - matplotlib-base >=3.6.3 + - networkx >=2.6.0 + - numba >=0.50.1 + - numpy >=1.20 + - pandas >=1.3.0 + - pyarrow >=0.17 + - python >=3.9,<3.11 + - scanpy >=1.9.0 + - scikit-learn + - scipy + - seaborn + - tqdm >=4.45 + - umap-learn + - velocyto.py >=0.17 + - weasyprint + + +genecircuitry 0.1.7 pyhdfd78af_0 +-------------------------------- +file name : genecircuitry-0.1.7-pyhdfd78af_0.conda +name : genecircuitry +version : 0.1.7 +build : pyhdfd78af_0 +build number: 0 +size : 80 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/genecircuitry-0.1.7-pyhdfd78af_0.conda +md5 : 32084de2479d0bb46cb6c0b0b7b7e448 +timestamp : 2026-03-31 12:58:13 UTC +dependencies: + - adjusttext >=0.7.3 + - anndata >=0.8.0 + - fa2_modified + - genomepy >=0.8.4 + - gimmemotifs >=0.14.4 + - goatools + - gseapy + - h5py >=3.1.0 + - igraph >=0.10.1 + - joblib + - jupyter + - leidenalg + - louvain + - matplotlib-base >=3.6.3 + - networkx >=2.6.0 + - numba >=0.50.1 + - numpy >=1.20 + - pandas >=1.3.0 + - pyarrow >=0.17 + - python >=3.9,<3.11 + - scanpy >=1.9.0 + - scikit-learn + - scipy + - seaborn + - tqdm >=4.45 + - umap-learn + - velocyto.py >=0.17 + - weasyprint diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/genenotebook.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/genenotebook.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bb245efa98139badaa1781a5ab53f05fdea6a4b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/genenotebook.manual_bundle.txt @@ -0,0 +1,488 @@ +# Tool: genenotebook +software_name: genenotebook +tier: T1 +domain: t1_backfill_overall +downloads: 709612 +summary: A colleborative notebook for comparative genomics +description: A colleborative notebook for comparative genomics +dependencies: blast, libgcc >=14, libstdcxx >=14, mongodb >=5.0, nodejs >=15,<16, nodejs >=15.14.0,<16.0a0, python_abi 3.11.* *_cp311 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://genenotebook.github.io +doc_url: +dev_url: + +## CLI Help Source +cli:genenotebook +## CLI Help Content +$ conda run -n bioenv_cli genenotebook --help +[rc=0] + + Usage: genenotebook [command] + + Options: + + -v, --version output the version number + -h, --help output usage information + + Commands: + + run Run a GeneNoteBook server + add [type] Add data to a running GeneNoteBook server + remove [type] Remove data from a running GeneNoteBook server + list List contents of a running GeneNoteBook server + help [cmd] display help for [cmd] + + + +## URL Docs Extract +### https://genenotebook.github.io +GeneNoteBook Documentation | GeneNoteBook Documentation This app works best with JavaScript enabled. GeneNoteBook Documentation Getting started Features Documentation GeneNoteBook A collaborative notebook for comparative genomics Visit http://bioinformatics.nl/genenotebook for a GeneNoteBook server running on an example dataset. Getting started Install GeneNoteBook using bioconda > conda install -c bioconda genenotebook Start a GeneNoteBook daemon on localhost:3000 > genenotebook run Add your data > genenotebook add [genome/annotation/...] Additional options For additional information on for instance Docker containers, loading transcriptome data, or configuring user accounts, see the full documentation . Features Gene Table Quickly scroll through all genes from multiple organisms and perform custom queries. The Gene Table allows for comparative visualization of Gene Models, Protein Domains and Gene Expression. Custom queries Any gene attribute is automatically indexed to allow efficient queries. Query results can be saved in several canonical file formats like fasta for coding sequences, gff3 for genome annotations and tsv for gene expression levels. Gene Models Visualize the exon structure of predicted Gene Models. Explore predicted alternative splicing. Protein Domains Visualization of InterProScan predicted protein domains allows for quick assesment of putative protein function. Links to InterPro based on IDs. Orthogroups Orthogroup phylogenetic trees visualize evolutionary relationships between genes. Tree labels are hyperlinks to quickly navigate between members of an orthogroup. Expression levels Expression level barplots automatically display sample sizes of experiments, as well as error bars representing the standard error. User profiles The user profile system allows for configuration of private access to data. Version history Every manually changed annotation is tracked in a version history system, so that at any moment unwanted changes can be reverted. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge genenotebook --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +genenotebook 0.1.1 0 +-------------------- +file name : genenotebook-0.1.1-0.tar.bz2 +name : genenotebook +version : 0.1.1 +build : 0 +build number: 0 +size : 42.8 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.1-0.tar.bz2 +md5 : 8a456a7cb1fecf76e085a1e68c845a9c +timestamp : 2018-08-05 09:57:06 UTC +dependencies: + - blast + - mongodb + - nodejs + + +genenotebook 0.1.2 0 +-------------------- +file name : genenotebook-0.1.2-0.tar.bz2 +name : genenotebook +version : 0.1.2 +build : 0 +build number: 0 +size : 40.8 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.2-0.tar.bz2 +md5 : f64664f2c7d3c6bf533bd67e158e1d56 +timestamp : 2018-08-30 09:29:16 UTC +dependencies: + - blast + - mongodb + - nodejs + + +genenotebook 0.1.2 1 +-------------------- +file name : genenotebook-0.1.2-1.tar.bz2 +name : genenotebook +version : 0.1.2 +build : 1 +build number: 1 +size : 40.8 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.2-1.tar.bz2 +md5 : 15c9c4f1d2f690a49020700cc37d5ff4 +timestamp : 2018-08-31 07:41:33 UTC +dependencies: + - blast + - mongodb + - nodejs + + +genenotebook 0.1.3 0 +-------------------- +file name : genenotebook-0.1.3-0.tar.bz2 +name : genenotebook +version : 0.1.3 +build : 0 +build number: 0 +size : 40.9 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.3-0.tar.bz2 +md5 : a2e936ef9684a9a07ae704af479559db +timestamp : 2018-09-19 20:05:19 UTC +dependencies: + - blast + - mongodb + - nodejs + + +genenotebook 0.1.4 h2d50403_0 +----------------------------- +file name : genenotebook-0.1.4-h2d50403_0.tar.bz2 +name : genenotebook +version : 0.1.4 +build : h2d50403_0 +build number: 0 +size : 38.3 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.4-h2d50403_0.tar.bz2 +md5 : b34f1bff331da7d2fc76c46df9ef4b70 +timestamp : 2018-10-04 16:55:47 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb + - nodejs + + +genenotebook 0.1.4 h2d50403_1 +----------------------------- +file name : genenotebook-0.1.4-h2d50403_1.tar.bz2 +name : genenotebook +version : 0.1.4 +build : h2d50403_1 +build number: 1 +size : 38.3 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.4-h2d50403_1.tar.bz2 +md5 : 45db750e87a890d3af4b7d4c0a97d3f1 +timestamp : 2018-10-11 09:27:11 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb >=3.4 + - nodejs >=8.0 + + +genenotebook 0.1.5 h2d50403_1 +----------------------------- +file name : genenotebook-0.1.5-h2d50403_1.tar.bz2 +name : genenotebook +version : 0.1.5 +build : h2d50403_1 +build number: 1 +size : 37.5 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.5-h2d50403_1.tar.bz2 +md5 : 308618eb4100128b8b050ea24abadca0 +timestamp : 2018-10-23 14:59:09 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb >=3.4 + - nodejs >=8.0 + + +genenotebook 0.1.6 h2d50403_1 +----------------------------- +file name : genenotebook-0.1.6-h2d50403_1.tar.bz2 +name : genenotebook +version : 0.1.6 +build : h2d50403_1 +build number: 1 +size : 37.5 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.6-h2d50403_1.tar.bz2 +md5 : 20c6032780d599f8074bd59ccf4748f6 +timestamp : 2018-11-06 10:55:04 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb >=3.4 + - nodejs >=8.0 + + +genenotebook 0.1.7 h2d50403_0 +----------------------------- +file name : genenotebook-0.1.7-h2d50403_0.tar.bz2 +name : genenotebook +version : 0.1.7 +build : h2d50403_0 +build number: 0 +size : 37.8 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.7-h2d50403_0.tar.bz2 +md5 : dfa09348d21013d49d48408c8d07b73e +timestamp : 2018-11-12 14:36:17 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb >=3.4 + - nodejs >=8.0 + + +genenotebook 0.1.8 h2d50403_0 +----------------------------- +file name : genenotebook-0.1.8-h2d50403_0.tar.bz2 +name : genenotebook +version : 0.1.8 +build : h2d50403_0 +build number: 0 +size : 37.8 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.8-h2d50403_0.tar.bz2 +md5 : 922ac7aa69080cd1c9640ed360e09446 +timestamp : 2018-11-15 17:23:21 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb >=3.4 + - nodejs >=8.0 + + +genenotebook 0.1.9 h2d50403_0 +----------------------------- +file name : genenotebook-0.1.9-h2d50403_0.tar.bz2 +name : genenotebook +version : 0.1.9 +build : h2d50403_0 +build number: 0 +size : 37.7 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.9-h2d50403_0.tar.bz2 +md5 : 851f532a5625b78abb090a02d18b340e +timestamp : 2018-11-21 19:27:16 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb >=3.4 + - nodejs >=8.0 + + +genenotebook 0.1.10 h2d50403_0 +------------------------------ +file name : genenotebook-0.1.10-h2d50403_0.tar.bz2 +name : genenotebook +version : 0.1.10 +build : h2d50403_0 +build number: 0 +size : 37.9 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.10-h2d50403_0.tar.bz2 +md5 : 9846ae672d289b0f1e6842c52a272807 +timestamp : 2018-11-26 17:08:03 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb >=3.4 + - nodejs >=8.0 + + +genenotebook 0.1.11 h2d50403_0 +------------------------------ +file name : genenotebook-0.1.11-h2d50403_0.tar.bz2 +name : genenotebook +version : 0.1.11 +build : h2d50403_0 +build number: 0 +size : 37.9 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.11-h2d50403_0.tar.bz2 +md5 : d088c3a380cac9e301e74db1e148bbec +timestamp : 2018-11-28 16:37:01 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb >=3.4 + - nodejs >=8.0 + + +genenotebook 0.1.12 h2d50403_0 +------------------------------ +file name : genenotebook-0.1.12-h2d50403_0.tar.bz2 +name : genenotebook +version : 0.1.12 +build : h2d50403_0 +build number: 0 +size : 39.7 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.12-h2d50403_0.tar.bz2 +md5 : d5b73254c20a32b2382bfc99029792fb +timestamp : 2018-11-29 15:22:16 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb >=3.4 + - nodejs >=8.0 + + +genenotebook 0.1.13 h2d50403_0 +------------------------------ +file name : genenotebook-0.1.13-h2d50403_0.tar.bz2 +name : genenotebook +version : 0.1.13 +build : h2d50403_0 +build number: 0 +size : 39.6 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.13-h2d50403_0.tar.bz2 +md5 : 424914a0d404e0204a402ff00e587d2b +timestamp : 2018-11-29 20:21:49 UTC +dependencies: + - blast + - libstdcxx-ng >=4.9 + - mongodb >=3.4 + - nodejs >=8.0 + + +genenotebook 0.1.15 h6bb024c_4 +------------------------------ +file name : genenotebook-0.1.15-h6bb024c_4.tar.bz2 +name : genenotebook +version : 0.1.15 +build : h6bb024c_4 +build number: 4 +size : 40.2 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.15-h6bb024c_4.tar.bz2 +md5 : 032ca04c6e0402e0f0e8dc14ad021fc8 +timestamp : 2019-03-27 15:07:12 UTC +dependencies: + - blast + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - mongodb >=3.4 + - nodejs 8.11.4.* + + +genenotebook 0.1.16 h6bb024c_3 +------------------------------ +file name : genenotebook-0.1.16-h6bb024c_3.tar.bz2 +name : genenotebook +version : 0.1.16 +build : h6bb024c_3 +build number: 3 +size : 39.3 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.1.16-h6bb024c_3.tar.bz2 +md5 : af469557a094cb7e900213672cbf1834 +timestamp : 2019-05-03 14:31:11 UTC +dependencies: + - blast + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - mongodb >=3.4 + - nodejs 8.11.4.* + + +genenotebook 0.3.0 h7d875b9_0 +----------------------------- +file name : genenotebook-0.3.0-h7d875b9_0.tar.bz2 +name : genenotebook +version : 0.3.0 +build : h7d875b9_0 +build number: 0 +size : 51.9 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.3.0-h7d875b9_0.tar.bz2 +md5 : bf6d353e0e46042529afab14c680dbe3 +timestamp : 2021-09-21 08:29:58 UTC +dependencies: + - blast + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - mongodb 4.0.3.* + - nodejs 14.17.1.* + + +genenotebook 0.3.1 h7d875b9_0 +----------------------------- +file name : genenotebook-0.3.1-h7d875b9_0.tar.bz2 +name : genenotebook +version : 0.3.1 +build : h7d875b9_0 +build number: 0 +size : 53.3 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.3.1-h7d875b9_0.tar.bz2 +md5 : 9766c49dddb1f8ce593d10e6915b8c7e +timestamp : 2022-02-10 10:21:41 UTC +dependencies: + - blast + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - mongodb 4.0.3.* + - nodejs 14.17.1.* + - python_abi 3.10.* *_cp310 + + +genenotebook 0.3.1 h9f5acd7_1 +----------------------------- +file name : genenotebook-0.3.1-h9f5acd7_1.tar.bz2 +name : genenotebook +version : 0.3.1 +build : h9f5acd7_1 +build number: 1 +size : 53.2 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.3.1-h9f5acd7_1.tar.bz2 +md5 : 70219a40b134ab73fd91c1c781484d9d +timestamp : 2022-02-22 09:02:19 UTC +dependencies: + - blast + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - mongodb 4.0.3.* + - nodejs 14.17.1.* + - python_abi 3.10.* *_cp310 + + +genenotebook 0.3.2 h4ac6f70_2 +----------------------------- +file name : genenotebook-0.3.2-h4ac6f70_2.tar.bz2 +name : genenotebook +version : 0.3.2 +build : h4ac6f70_2 +build number: 2 +size : 64.5 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genenotebook-0.3.2-h4ac6f70_2.tar.bz2 +md5 : 254c8282a96ce3be6f8d4c75812b5477 +timestamp : 2023-05-18 23:29:47 UTC +dependencies: + - blast + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - mongodb >=5.0 + - nodejs >=15,<16 + - nodejs >=15.14.0,<16.0a0 + - python_abi 3.11.* *_cp311 + + +genenotebook 0.3.2 h9f5acd7_0 +----------------------------- +file name : genenotebook-0.3.2-h9f5acd7_0.tar.bz2 +name : genenotebook +version : 0.3.2 +build : h9f5acd7_0 +build number: 0 +size : 64.9 MB +license : AGPL-3.0 +subdir : linux-64 +url : https://conda.anacond diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/genometools-genometools.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/genometools-genometools.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6b7793116ac2dc8f8b03c9ec3d55b0905d6aa3a --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/genometools-genometools.manual_bundle.txt @@ -0,0 +1,424 @@ +# Tool: genometools-genometools +software_name: genometools-genometools +tier: T1 +domain: t1_backfill_overall +downloads: 465578 +summary: GenomeTools genome analysis system. +description: GenomeTools genome analysis system. +dependencies: cairo >=1.18.4,<2.0a0, font-ttf-dejavu-sans-mono, fontconfig, gettext, libgcc >=14, libglib >=2.86.4,<3.0a0, libstdcxx >=14, pango >=1.56.4,<2.0a0, python >=3.11,<3.12.0a0, python_abi 3.11.* *_cp311, xorg-libsm, xorg-libxext, xorg-libxrender +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://genometools.org +doc_url: https://genometools.org/documentation.html +dev_url: https://github.com/genometools/genometools + +## URL Docs Extract +### https://genometools.org/documentation.html +The AnnotationSketch module Overview Releases Archive Browse source Issue tracker Documentation Tools Manuals C API gtscript docs Development Contract Contribute AnnotationSketch GFF3 validator License Documentation The following documentation is available for GenomeTools : The tool documentation lists all command-line tools available in GenomeTools and their usage details (options, return values, ...) in the form of manual pages Manuals are provided in PDF format for selected published software tools available as part of the GenomeTools package, as well as a developer's guide for programmers A C API documentation for all public classes API documentation for gtscript , the Lua-based scripting language embedded into GenomeTools Copyright © 2007-2023 The GenomeTools authors. Last update: 2011-02-11 + +### https://genometools.org +GenomeTools Overview Releases Archive Browse source Issue tracker Documentation AnnotationSketch GFF3 validator License GenomeTools The versatile open source genome analysis software The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt . It is based on a C library named “libgenometools” which consists of several modules. If you are interested in gene prediction, have a look at GenomeThreader . Platforms GenomeTools has been designed to run on every POSIX compliant UNIX system — for example Linux or macOS. A reduced Windows version is also available. Please report problems to our issue tracker . GenomeTools publication G. Gremme, S. Steinbiss and S. Kurtz. GenomeTools : a comprehensive software library for efficient processing of structured genome annotations. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013, 10(3):645–656 Published software in GenomeTools The GenomeTools distribution includes several published software tools: LTRharvest , an efficient and flexible software tool for de novo detection of LTR retrotransposons. D. Ellinghaus, S. Kurtz, and U. Willhoeft. LTRharvest , a efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 2008, 9:18 Tallymer , a collection of flexible and memory-efficient programs for k -mer counting and indexing of large sequence sets. S. Kurtz, A. Narechania, J.C. Stein, and D. Ware. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 2008, 9:517 uniquesub , a program for computing minimum unique substrings. S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek. Optimized design and assessment of whole genome tiling arrays. Bioinformatics 2007, 23(13):i195–i204 AnnotationSketch , a library for drawing genome annotations. S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz. AnnotationSketch : a genome annotation drawing library. Bioinformatics 2009, 25(4):533–534 LTRdigest , a software tool for automated annotation of internal features of LTR retrotransposons. S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Research 2009, 37(21):7002–7013 MetaGenomeThreader , a software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects. D.J. Schmitz-Hübsch and S. Kurtz. MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects. In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology , 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5 GtEncseq , a compressed biosequence representation with many features. S. Steinbiss and S. Kurtz. A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357 Readjoiner , a sequence assembler based on the assembly string graph framework. G. Gonnella and S. Kurtz. Readjoiner: a fast and memory efficient string graph-based sequence assembler. BMC Bioinformatics 2012, 13:82 The following software tools are based on the GenomeTools library: GenomeThreader , a software tool to compute eukaryote gene structure predictions. G. Gremme, V. Brendel, M.E. Sparks, and S. Kurtz. Engineering a software tool for gene structure prediction in higher organisms. Information and Software Technology 2005, 47(15):965–978 FISH Oracle , a web server for visualizing cancer genomics data. M. Mader, R. Simon, S. Steinbiss and S. Kurtz. FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context. Journal of Clinical Bioinformatics 2011, 1:20 ParsEval , a tool for comparing genome annotations. D.S. Standage and V.P. Brendel. ParsEval: parallel comparison and analysis of gene structure annotations. BMC Bioinformatics 2012, 13:187 LTRsift , a graphical interface for working with LTR retrotransposon predictions. S. Steinbiss, S. Kastens and S. Kurtz. LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons. Mobile DNA 2012, 3:18 FISH Oracle 2 , a web-based software tool for the integrative analysis of cancer genomics data. M. Mader, R. Simon, and S. Kurtz. FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research. Journal of Clinical Bioinformatics 2014, 4:5 Contact The GenomeTools are being developed by: Gordon Gremme, Sascha Steinbiss, Stefan Kurtz and others Genome Informatics Research Group Center for Bioinformatics, University of Hamburg Copyright © 2006-2023 The GenomeTools authors. Last update: 2014-11-05 + +### https://github.com/genometools/genometools +GitHub - genometools/genometools: GenomeTools genome analysis system. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} genometools / genometools Public Notifications You must be signed in to change notification settings Fork 64 Star 335 Code Issues 88 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights genometools/genometools master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 13,993 Commits 13,993 Commits .github .github doc doc gtdata gtdata gtgo gtgo gtpython gtpython gtruby gtruby gtscripts gtscripts scripts scripts src src testdata testdata testsuite testsuite www www .gitignore .gitignore CHANGELOG CHANGELOG CONTRIBUTORS CONTRIBUTORS INSTALL INSTALL LICENSE LICENSE Makefile Makefile README.md README.md VERSION VERSION go.mod go.mod View all files Repository files navigation README License GenomeTools The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt . It is based on a C library named libgenometools which contains a wide variety of classes for efficient and convenient implementation of sequence and annotation processing software. If you are interested in gene prediction, have a look at GenomeThreader . Platforms GenomeTools has been designed to run on every POSIX compliant UNIX system, for example, Linux, macOS, and OpenBSD. Building and Installation Debian-based operating systems Debian and Ubuntu users can install the most recent stable version simply using apt, e.g. apt-get install genometools (as root) to install the gt executable. To install the library and development headers, use apt-get install libgenometools0 libgenometools0-dev instead. This is not required to just use the tools. macOS (via Homebrew) If Homebrew is installed, GenomeTools can be installed on supported macOS versions using brew : brew install genometools Building from source To use GenomeTools on systems that do not have native packages, or to modify GenomeTools at build time, you need to build from source. Source tarballs are available from GitHub. For instructions on how to build the source by yourself, have a look at the INSTALL file. In most cases (e.g. on a 64-bit Linux system) something like make -j4 should suffice. On 32-bit systems, add the 32bit=yes option. Add cairo=no if you do not have the Cairo libraries and their development headers installed. This will, however, remove AnnotationSketch support from the resulting binary. When your binary has been built, use the install target and prefix option to install the compiled binary on your system. Make sure you repeat all the options from the original make run. So make -j4 install prefix= ~ /gt would install the software in the gt subdirectory in the current user's home directory. If no prefix option is given, the software will be installed system-wide (requires root access). Contributing GenomeTools uses a collective code construction contract for contributions (and the process explains how to submit a patch). Basically, just fork this repository on GitHub, start hacking on your own feature branch and submit a pull request when you are ready. Our recommended coding style is explained in the developer's guide (among other technical guidelines). To report a bug, ask a question, or suggest new features, use the GenomeTools issue tracker . About GenomeTools genome analysis system. genometools.org Topics ruby python c library bioinformatics lua annotation genomics genome gff3 repeats genometools toolkit Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 335 stars Watchers 25 watching Forks 64 forks Report repository Releases 4 v1.6.6 Latest Oct 6, 2025 + 3 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C 79.7% HTML 7.5% Ruby 7.4% C++ 1.9% Python 1.6% Lua 0.7% Other 1.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge genometools-genometools --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +genometools-genometools 1.5.10 py27h08a56e5_2 +--------------------------------------------- +file name : genometools-genometools-1.5.10-py27h08a56e5_2.tar.bz2 +name : genometools-genometools +version : 1.5.10 +build : py27h08a56e5_2 +build number: 2 +size : 20.7 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.5.10-py27h08a56e5_2.tar.bz2 +md5 : 6c9e1c767a9eaa0e73057f6278cbfbd9 +timestamp : 2018-07-26 13:32:47 UTC +dependencies: + - cairo >=1.14.12,<1.15.0a0 + - gettext + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pango >=1.40.14,<1.41.0a0 + - python >=2.7,<2.8.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.5.10 py27h997e34b_3 +--------------------------------------------- +file name : genometools-genometools-1.5.10-py27h997e34b_3.tar.bz2 +name : genometools-genometools +version : 1.5.10 +build : py27h997e34b_3 +build number: 3 +size : 19.8 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.5.10-py27h997e34b_3.tar.bz2 +md5 : 90e985c29a619132b5a5c4aa66c9a279 +timestamp : 2019-04-23 01:38:22 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pango >=1.40.14,<1.41.0a0 + - python >=2.7,<2.8.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.5.10 py35h08a56e5_2 +--------------------------------------------- +file name : genometools-genometools-1.5.10-py35h08a56e5_2.tar.bz2 +name : genometools-genometools +version : 1.5.10 +build : py35h08a56e5_2 +build number: 2 +size : 20.7 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.5.10-py35h08a56e5_2.tar.bz2 +md5 : 7e0bec404fab444dbf0a422d26779bab +timestamp : 2018-07-26 13:36:32 UTC +dependencies: + - cairo >=1.14.12,<1.15.0a0 + - gettext + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pango >=1.40.14,<1.41.0a0 + - python >=3.5,<3.6.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.5.10 py36h08a56e5_2 +--------------------------------------------- +file name : genometools-genometools-1.5.10-py36h08a56e5_2.tar.bz2 +name : genometools-genometools +version : 1.5.10 +build : py36h08a56e5_2 +build number: 2 +size : 20.7 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.5.10-py36h08a56e5_2.tar.bz2 +md5 : 520f2bc80cec2293797f39b46f7e3d85 +timestamp : 2018-07-26 13:29:05 UTC +dependencies: + - cairo >=1.14.12,<1.15.0a0 + - gettext + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pango >=1.40.14,<1.41.0a0 + - python >=3.6,<3.7.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.5.10 py36h997e34b_3 +--------------------------------------------- +file name : genometools-genometools-1.5.10-py36h997e34b_3.tar.bz2 +name : genometools-genometools +version : 1.5.10 +build : py36h997e34b_3 +build number: 3 +size : 19.8 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.5.10-py36h997e34b_3.tar.bz2 +md5 : e832893000b9d3682f2ce4c3a6ff6fa1 +timestamp : 2019-04-23 01:26:58 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pango >=1.40.14,<1.41.0a0 + - python >=3.6,<3.7.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.5.10 py37h997e34b_3 +--------------------------------------------- +file name : genometools-genometools-1.5.10-py37h997e34b_3.tar.bz2 +name : genometools-genometools +version : 1.5.10 +build : py37h997e34b_3 +build number: 3 +size : 19.8 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.5.10-py37h997e34b_3.tar.bz2 +md5 : 9141365f1fc59459d805567aa8087d75 +timestamp : 2019-04-23 01:33:17 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pango >=1.40.14,<1.41.0a0 + - python >=3.7,<3.8.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.6.0 py27h39d103b_0 +-------------------------------------------- +file name : genometools-genometools-1.6.0-py27h39d103b_0.tar.bz2 +name : genometools-genometools +version : 1.6.0 +build : py27h39d103b_0 +build number: 0 +size : 17.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.6.0-py27h39d103b_0.tar.bz2 +md5 : 3af6f5914c0b749e1dae42d51af3fb5a +timestamp : 2020-01-06 06:24:04 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pango >=1.42.4,<1.43.0a0 + - python >=2.7,<2.8.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.6.0 py36h39d103b_0 +-------------------------------------------- +file name : genometools-genometools-1.6.0-py36h39d103b_0.tar.bz2 +name : genometools-genometools +version : 1.6.0 +build : py36h39d103b_0 +build number: 0 +size : 17.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.6.0-py36h39d103b_0.tar.bz2 +md5 : cfdedc51d671fee8f331da9cad37d41e +timestamp : 2020-01-06 06:29:13 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pango >=1.42.4,<1.43.0a0 + - python >=3.6,<3.7.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.6.0 py37h39d103b_0 +-------------------------------------------- +file name : genometools-genometools-1.6.0-py37h39d103b_0.tar.bz2 +name : genometools-genometools +version : 1.6.0 +build : py37h39d103b_0 +build number: 0 +size : 17.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.6.0-py37h39d103b_0.tar.bz2 +md5 : 84a53d97f319067fff0640b8a32b035c +timestamp : 2020-01-06 06:19:06 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pango >=1.42.4,<1.43.0a0 + - python >=3.7,<3.8.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.6.1 py27h3113181_2 +-------------------------------------------- +file name : genometools-genometools-1.6.1-py27h3113181_2.tar.bz2 +name : genometools-genometools +version : 1.6.1 +build : py27h3113181_2 +build number: 2 +size : 17.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.6.1-py27h3113181_2.tar.bz2 +md5 : 6c2792e640e83031d82f3216e828af7f +timestamp : 2020-07-09 19:53:52 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - pango >=1.42.4,<1.43.0a0 + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.6.1 py27h39d103b_0 +-------------------------------------------- +file name : genometools-genometools-1.6.1-py27h39d103b_0.tar.bz2 +name : genometools-genometools +version : 1.6.1 +build : py27h39d103b_0 +build number: 0 +size : 17.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.6.1-py27h39d103b_0.tar.bz2 +md5 : 0d1e4f98ace18073db498c3d622f129e +timestamp : 2020-01-10 10:34:11 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pango >=1.42.4,<1.43.0a0 + - python >=2.7,<2.8.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.6.1 py36h30d060d_2 +-------------------------------------------- +file name : genometools-genometools-1.6.1-py36h30d060d_2.tar.bz2 +name : genometools-genometools +version : 1.6.1 +build : py36h30d060d_2 +build number: 2 +size : 17.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.6.1-py36h30d060d_2.tar.bz2 +md5 : e30a5c0c3057979e09493ed3e95c51e0 +timestamp : 2020-07-09 20:00:24 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - pango >=1.42.4,<1.43.0a0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.6.1 py36h39d103b_0 +-------------------------------------------- +file name : genometools-genometools-1.6.1-py36h39d103b_0.tar.bz2 +name : genometools-genometools +version : 1.6.1 +build : py36h39d103b_0 +build number: 0 +size : 17.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.6.1-py36h39d103b_0.tar.bz2 +md5 : 1790a34c03f27c81cf8ae87945e1c52d +timestamp : 2020-01-10 10:44:18 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pango >=1.42.4,<1.43.0a0 + - python >=3.6,<3.7.0a0 + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.6.1 py36hc7dd5a1_1 +-------------------------------------------- +file name : genometools-genometools-1.6.1-py36hc7dd5a1_1.tar.bz2 +name : genometools-genometools +version : 1.6.1 +build : py36hc7dd5a1_1 +build number: 1 +size : 17.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.6.1-py36hc7dd5a1_1.tar.bz2 +md5 : 791038b10bac943251a61fd88a0292e2 +timestamp : 2020-05-09 16:20:56 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pango >=1.42.4,<1.43.0a0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.6.1 py37h18fde40_2 +-------------------------------------------- +file name : genometools-genometools-1.6.1-py37h18fde40_2.tar.bz2 +name : genometools-genometools +version : 1.6.1 +build : py37h18fde40_2 +build number: 2 +size : 17.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-genometools-1.6.1-py37h18fde40_2.tar.bz2 +md5 : eda441bfe49637a5a3fff648fa5b3985 +timestamp : 2020-07-09 19:46:43 UTC +dependencies: + - cairo >=1.16.0,<1.17.0a0 + - gettext + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - pango >=1.42.4,<1.43.0a0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - xorg-libsm + - xorg-libxext + - xorg-libxrender + + +genometools-genometools 1.6.1 py37h39d103b_0 +-------------------------------------------- +file name : genometools-genometools-1.6.1-py37h39d103b_0.tar.bz2 +name : genometools-genometools +version : 1.6.1 +build : py37h39d103b_0 +build number: 0 +size : 17.4 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/genometools-geno diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gffutils.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gffutils.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c271bc31964544e86344d0ecfe32818f5a03c6e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gffutils.manual_bundle.txt @@ -0,0 +1,542 @@ +# Tool: gffutils +software_name: gffutils +tier: T1 +domain: t1_backfill_overall +downloads: 243713 +summary: Work with GFF and GTF files in a flexible database framework +description: Work with GFF and GTF files in a flexible database framework +dependencies: argcomplete >=1.9.4, argh >=0.26.2, pyfaidx >=0.5.5.2, python, simplejson +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/daler/gffutils +doc_url: http://daler.github.io/gffutils/ +dev_url: https://github.com/daler/gffutils + +## URL Docs Extract +### http://daler.github.io/gffutils/ +Introduction — gffutils 0.14 documentation gffutils Installation Importing data into a database Database schema Database IDs GTF files Dialects Attributes Examples API Change log Developer’s docs Meta-docs (docs about the docs) gffutils Introduction View page source Introduction  gffutils is a Python package for working with GFF and GTF files in a hierarchical manner. It allows operations which would be complicated or time-consuming using a text-file-only approach. Below is a short demonstration of gffutils . For the full documentation, see the rest of the table of contents to the left. Example file  Consider the first gene on chromosome 2L in Drosophila melanogaster , CG11023. Here is a graphical representation of this gene’s three alternative transcripts, from FlyBase : gffutils ships with the GFF annotation of this gene, downloaded from release 5.54 of FlyBase . We’ll be using it to describe some features of gffutils , because it contains just enough complexity to be representative of a real-world, genome-wide GFF file. Let’s look at what the file contains: >>> import gffutils >>> fn = gffutils . example_filename ( 'intro_docs_example.gff' ) >>> print ( open ( fn ) . read ()) 2L FlyBase gene 7529 9484 . + . ID=FBgn0031208;Name=CG11023;Ontology_term=SO:0000010,SO:0000087,GO:0016929,GO:0016926,GO:0006508;Dbxref=FlyBase:FBan0011023,FlyBase_Annotation_IDs:CG11023,GB_protein:ACZ94128,GB_protein:AAO41164,GB:AI944728,GB:AJ564667,GB_protein:CAD92822,GB:BF495604,UniProt/TrEMBL:Q86BM6,INTERPRO:IPR003653,GB_protein:AGB92323,UniProt/TrEMBL:M9PAY1,OrthoDB7_Drosophila:EOG796K1P,OrthoDB7_Diptera:EOG7X1604,EntrezGene:33155,UniProt/TrEMBL:E1JHP8,UniProt/TrEMBL:Q6KEV3,OrthoDB7_Insecta:EOG7Q8QM7,OrthoDB7_Arthropoda:EOG7R5K68,OrthoDB7_Metazoa:EOG7D59MP,InterologFinder:33155,BIOGRID:59420,FlyAtlas:CG11023-RA,GenomeRNAi:33155;gbunit=AE014134;derived_computed_cyto=21A5-21A5 2L FlyBase mRNA 7529 9484 . + . ID=FBtr0300689;Name=CG11023-RB;Parent=FBgn0031208;Dbxref=REFSEQ:NM_001169365,FlyBase_Annotation_IDs:CG11023-RB;score_text=Strongly Supported;score=11 2L FlyBase mRNA 7529 9484 . + . ID=FBtr0300690;Name=CG11023-RC;Parent=FBgn0031208;Dbxref=REFSEQ:NM_175941,FlyBase_Annotation_IDs:CG11023-RC;score_text=Strongly Supported;score=15 2L FlyBase mRNA 7529 9484 . + . ID=FBtr0330654;Name=CG11023-RD;Parent=FBgn0031208;Dbxref=FlyBase_Annotation_IDs:CG11023-RD,REFSEQ:NM_001272857;score_text=Strongly Supported;score=11 2L FlyBase exon 7529 8116 . + . Name=CG11023:1;Parent=FBtr0300689,FBtr0300690,FBtr0330654;parent_type=mRNA 2L FlyBase five_prime_UTR 7529 7679 . + . Name=CG11023-u5;Parent=FBtr0300689,FBtr0300690;parent_type=mRNA 2L FlyBase five_prime_UTR 7529 7679 . + . Name=CG11023-u5;Parent=FBtr0330654;parent_type=mRNA 2L FlyBase CDS 7680 8116 . + 0 Name=CG11023-cds;Parent=FBtr0300689,FBtr0300690;parent_type=mRNA 2L FlyBase CDS 7680 8116 . + 0 Name=CG11023-cds;Parent=FBtr0330654;parent_type=mRNA 2L FlyBase intron 8117 8228 . + . Name=CG11023-in;Parent=FBtr0330654;parent_type=mRNA 2L FlyBase intron 8117 8192 . + . Name=CG11023-in;Parent=FBtr0300689;parent_type=mRNA 2L FlyBase intron 8117 8192 . + . Name=CG11023-in;Parent=FBtr0300690;parent_type=mRNA 2L FlyBase exon 8193 9484 . + . Name=CG11023:3;Parent=FBtr0300689;parent_type=mRNA 2L FlyBase CDS 8193 8610 . + 1 Name=CG11023-cds;Parent=FBtr0300689;parent_type=mRNA 2L FlyBase CDS 8193 8589 . + 1 Name=CG11023-cds;Parent=FBtr0300690;parent_type=mRNA 2L FlyBase exon 8193 8589 . + . Name=CG11023:2;Parent=FBtr0300690;parent_type=mRNA 2L FlyBase exon 8229 9484 . + . Name=CG11023:4;Parent=FBtr0330654;parent_type=mRNA 2L FlyBase CDS 8229 8610 . + 1 Name=CG11023-cds;Parent=FBtr0330654;parent_type=mRNA 2L FlyBase intron 8590 8667 . + . Name=CG11023-in;Parent=FBtr0300690;parent_type=mRNA 2L FlyBase three_prime_UTR 8611 9484 . + . Name=CG11023-u3;Parent=FBtr0300689;parent_type=mRNA 2L FlyBase three_prime_UTR 8611 9484 . + . Name=CG11023-u3;Parent=FBtr0330654;parent_type=mRNA 2L FlyBase three_prime_UTR 9277 9484 . + . Name=CG11023-u3;Parent=FBtr0300690;parent_type=mRNA 2L FlyBase exon 8668 9484 . + . Name=CG11023:5;Parent=FBtr0300690;parent_type=mRNA 2L FlyBase CDS 8668 9276 . + 0 Name=CG11023-cds;Parent=FBtr0300690;parent_type=mRNA While this is a (relatively) simple gene, the annotation looks quite complex. In no particular order, some comments about this annotation: The gene has lots of attributes (last column), which would be nice to be able to access from Python. The gene and mRNA features have “ID” attributes, while UTRs, exons, CDSs, and introns only have “Name” attributes, e.g.: gene : ID = FBgn0031208 ; Name = CG11023 ... mRNA : ID = FBtr0300689 ; Name = CG11023 - RB ... exon : Name = CG11023 : 1. .. The “Name” attributes of UTRs, exons, CDSs, and introns contain the “Name” attribute of the parent gene, followed by some extra info. For exons, it’s a colon and a number; for introns its “-in”, and so on. But the “Parent” mRNA is indicated with the mRNA’s “ID” attribute, e.g.,: exon : Name = CG11023 : 3 ; Parent = FBtr0300689 ; For routine tasks like counting reads in exons (say, with HTSeq ), it would be nice to be able to add a “gene_id” attribute to exons. That is, change: exon : Name = CG11023 : 3 ; Parent = FBtr0300689 ; to: exon : Name = CG11023 : 3 ; Parent = FBtr0300689 ; gene_id = FBgn0031208 ; Then, we could use htseq-count like this: htseq - count -- type = exon -- idattr = gene_id reads . sam fixed_annotation . gff UTRs, exons, CDSs, and introns have the same name for different features. For example, these two introns have different coordinates and have different mRNA parents, yet have the same “Name” attribute: 2 L FlyBase intron 8117 8228 . + . Name = CG11023 - in ; Parent = FBtr0330654 ; parent_type = mRNA 2 L FlyBase intron 8117 8192 . + . Name = CG11023 - in ; Parent = FBtr0300689 ; parent_type = mRNA It would be nice to have unique IDs for these features so we could differentiate them for, say, counting the unique introns of a gene or generating a file of splice junctions. Create the database  The first step to working with gffutils is to import the file into a local sqlite3 file-based database. The gffutils.create_db() function is used for this, and it takes many optional arguments for configuring how to interpret your GFF or GTF file. >>> db = gffutils . create_db ( fn , dbfn = 'test.db' , force = True , keep_order = True , ... merge_strategy = 'merge' , sort_attribute_values = True ) Here, force=True will overwrite any existing database, keep_order=True will maintain the order of the attributes (ID, Name, Parent, and so on), and sort_attribute_values=True will ensure the values of each attribute are always sorted. These latter two settings are necessary here for this documentation (which undergoes automated testing) to have predictable output, but in general you can gain a speedup by using the default keep_order=False and sort_attributes_order=False . If your input file follows the GFF or GTF file format specifications, this is all you need to create a database. But real-world files don’t always completely adhere to the format specifications. So gffutils provides lots of configuration options to tailor the pre-processing to your particular file – see Importing data into a database for more details, and Examples for more practical examples. Use the database  Once the database has been created, downstream code can connect to it simply by: >>> import gffutils >>> db = gffutils . FeatureDB ( 'test.db' , keep_order = True ) Features are accessed by name: >>> gene = db [ 'FBgn0031208' ] >>> gene <Feature gene (2L:7529-9484[+]) at 0x...> Inspect fields from the GFF line: >>> gene . start 7529 >>> gene . end 9484 Attributes are stored in the attributes dictionary. Values are always in a list, even if there’s only one item: >>> gene . attributes [ 'Name' ] ['CG11023'] Attributes can also be accessed from the Feature object itself, to save some typing: >>> gene [ 'Name' ] ['CG11023'] Printing a Feature reproduces the original GFF line as faithfully as possible. See the Dialects section for more details on how this is handled and configured. >>> print ( gene ) 2L FlyBase gene 7529 9484 . + . ID=FBgn0031208;Name=CG11023;Ontology_term=SO:0000010,SO:0000087,GO:0016929,GO:0016926,GO:0006508;Dbxref=FlyBase:FBan0011023,FlyBase_Annotation_IDs:CG11023,GB_protein:ACZ94128,GB_protein:AAO41164,GB:AI944728,GB:AJ564667,GB_protein:CAD92822,GB:BF495604,UniProt/TrEMBL:Q86BM6,INTERPRO:IPR003653,GB_protein:AGB92323,UniProt/TrEMBL:M9PAY1,OrthoDB7_Drosophila:EOG796K1P,OrthoDB7_Diptera:EOG7X1604,EntrezGene:33155,UniProt/TrEMBL:E1JHP8,UniProt/TrEMBL:Q6KEV3,OrthoDB7_Insecta:EOG7Q8QM7,OrthoDB7_Arthropoda:EOG7R5K68,OrthoDB7_Metazoa:EOG7D59MP,InterologFinder:33155,BIOGRID:59420,FlyAtlas:CG11023-RA,GenomeRNAi:33155;gbunit=AE014134;derived_computed_cyto=21A5-21A5 Get all the mRNAs for a gene: >>> for i in db . children ( gene , featuretype = 'mRNA' , order_by = 'start' ): ... print ( i ) 2L FlyBase mRNA 7529 9484 . + . ID=FBtr0300689;Name=CG11023-RB;Dbxref=REFSEQ:NM_001169365,FlyBase_Annotation_IDs:CG11023-RB;Parent=FBgn0031208;score_text=Strongly Supported;score=11 2L FlyBase mRNA 7529 9484 . + . ID=FBtr0300690;Name=CG11023-RC;Dbxref=REFSEQ:NM_175941,FlyBase_Annotation_IDs:CG11023-RC;Parent=FBgn0031208;score_text=Strongly Supported;score=15 2L FlyBase mRNA 7529 9484 . + . ID=FBtr0330654;Name=CG11023-RD;Dbxref=FlyBase_Annotation_IDs:CG11023-RD,REFSEQ:NM_001272857;Parent=FBgn0031208;score_text=Strongly Supported;score=11 Get all the exons for a gene: >>> for i in db . children ( gene , featuretype = 'exon' , order_by = 'start' ): ... print ( i ) 2L FlyBase exon 7529 8116 . + . Name=CG11023:1;Parent=FBtr0300689,FBtr0300690,FBtr0330654;parent_type=mRNA 2L FlyBase exon 8193 9484 . + . Name=CG11023:3;Parent=FBtr0300689;parent_type=mRNA 2L FlyBase exon 8193 8589 . + . Name=CG11023:2;Parent=FBtr0300690;parent_type=mRNA 2L FlyBase exon 8229 9484 . + . Name=CG11023:4;Parent=FBtr0330654;parent_type=mRNA 2L FlyBase exon 8668 9484 . + . Name=CG11023:5;Parent=FBtr0300690;parent_type=mRNA Does this gene have any constitutive exons (exons found in every alternative transcript)? This is an example of something that would be difficult to do using only standard text file processing tools, and demonstrates the usefulness of the gffutils : >>> mRNA_count = len ( list ( db . children ( gene , featuretype = 'mRNA' ))) >>> constitutive_exons = [] >>> for exon in db . features_of_type ( 'exon' , order_by = 'start' ): ... parents = db . parents ( exon , featuretype = 'mRNA' ) ... if len ( list ( parents )) == mRNA_count : ... constitutive_exons . append ( exon ) >>> print ( constitutive_exons ) [<Feature exon (2L:7529-8116[+]) at 0x...>] Retrieve entries by genomic coordinates, which uses the UCSC binning strategy : >>> list ( db . region ( region = ( '2L' , 9277 , 10000 ), completely_within = True )) [<Feature three_prime_UTR (2L:9277-9484[+]) at 0x...>] Retrieve UTRs that overlap the gene (note that a feature can be provided as the coordinates): >>> for UTR in db . region ( gene , featuretype = [ 'three_prime_UTR' , 'five_prime_UTR' ]): ... print ( UTR ) 2L FlyBase five_prime_UTR 7529 7679 . + . Name=CG11023-u5;Parent=FBtr0300689,FBtr0300690;parent_type=mRNA 2L FlyBase five_prime_UTR 7529 7679 . + . Name=CG11023-u5;Parent=FBtr0330654;parent_type=mRNA 2L FlyBase three_prime_UTR 8611 9484 . + . Name=CG11023-u3;Parent=FBtr0300689;parent_type=mRNA 2L FlyBase three_prime_UTR 8611 9484 . + . Name=CG11023-u3;Parent=FBtr0330654;parent_type=mRNA 2L FlyBase three_prime_UTR 9277 9484 . + . Name=CG11023-u3;Parent=FBtr0300690;parent_type=mRNA Now let’s illustrate a problem in the GFF file as it is currently formatted by trying to get the consitutive 5’UTRs in the same way we got the constitutive exons above: >>> constitutive_5UTRs = [] >>> for utr in db . features_of_type ( 'five_prime_UTR' , order_by = 'start' ): ... parents = db . parents ( utr , featuretype = 'mRNA' ) ... if len ( list ( parents )) == mRNA_count : ... constitutive_5UTRs . append ( utr ) >>> print ( constitutive_5UTRs ) [] Yikes! What happened? This is because by default, each line in the GFF file is treated as a unique feature. From this perspective, the first 5’UTR has two parents, and the second 5’UTR has one parent – there are zero 5’UTRs with all three transcripts as parents. What we’d really like to do is to merge the features that have identical IDs and coordinates. Specifically, we’d like to have these two features: 2 L FlyBase five_prime_UTR 7529 7679 . + . Name = CG11023 - u5 ; Parent = FBtr0300689 , FBtr0300690 ; parent_type = mRNA 2 L FlyBase five_prime_UTR 7529 7679 . + . Name = CG11023 - u5 ; Parent = FBtr0330654 ; parent_type = mRNA become a single feature: 2 L FlyBase five_prime_UTR 7529 7679 . + . Name = CG11023 - u5 ; Parent = FBtr0300689 , FBtr0300690 , FBtr0330654 ; parent_type = mRNA Similarly, we’d like these three 3’UTRs: 2 L FlyBase three_prime_UTR 8611 9484 . + . Name = CG11023 - u3 ; Parent = FBtr0300689 ; parent_type = mRNA 2 L FlyBase three_prime_UTR 8611 9484 . + . Name = CG11023 - u3 ; Parent = FBtr0330654 ; parent_type = mRNA 2 L FlyBase three_prime_UTR 9277 9484 . + . Name = CG11023 - u3 ; Parent = FBtr0300690 ; parent_type = mRNA to become two (merging only the first two because they have identical coordinates): 2 L FlyBase three_prime_UTR 8611 9484 . + . Name = CG11023 - u3 ; Parent = FBtr0300689 , FBtr0330654 ; parent_type = mRNA 2 L FlyBase three_prime_UTR 9277 9484 . + . Name = CG11023 - u3 ; Parent = FBtr0300690 ; parent_type = mRNA In order to do this, we need to change how features are loaded into the database by using merge_strategy=True and id_spec=['ID', 'Name'] . You can read more about exactly what these arguments do, and other ways of tweaking the import, at Database IDs . But for now, let’s see what happens: >>> db2 = gffutils . create_db ( fn , dbfn = 'test.db' , force = True , keep_order = True , ... sort_attribute_values = True , ... merge_strategy = 'merge' , ... id_spec = [ 'ID' , 'Name' ]) >>> for utr in db2 . features_of_type ( 'five_prime_UTR' , order_by = 'start' ): ... parents = db2 . parents ( utr , featuretype = 'mRNA' ) ... if len ( list ( parents )) == mRNA_count : ... constitutive_5UTRs . append ( utr ) >>> print ( constitutive_5UTRs ) [<Feature five_prime_UTR (2L:7529-7679[+]) at 0x...>] Let’s look at all the 5’UTRs in the database to see how the merge strategy affected them: >>> for i in db2 . features_of_type ( 'five_prime_UTR' ): ... ... print ( i ) 2L FlyBase five_prime_UTR 7529 7679 . + . Name=CG11023-u5;Parent=FBtr0300689,FBtr0300690,FBtr0330654;parent_type=mRNA Aha! A single 5’UTR. What about 3’UTRs? >>> for i in db2 . features_of_type ( 'three_prime_UTR' ): ... print ( i ) 2L FlyBase three_prime_UTR 8611 9484 . + . Name=CG11023-u3;Parent=FBtr0300689,FBtr0330654;parent_type=mRNA 2L FlyBase three_prime_UTR 9277 9484 . + . Name=CG11023-u3;Parent=FBtr0300690;parent_type=mRNA >>> for i in db2 . features_of_type ( 'intron' ): ... print ( i ) 2L FlyBase intron 8117 8228 . + . Name=CG11023-in;Parent=FBtr0330654;parent_type=mRNA 2L FlyBase intron 8117 8192 . + . Name=CG11023-in;Parent=FBtr0300689,FBtr0300690;parent_type=mRNA 2L FlyBase intron 8590 8667 . + . Name=CG11023-in;Parent=FBtr0300690;parent_type=mRNA Next © Copyright 2013-2022, Ryan Dale. Built with Sphinx using a theme provided by Read the Docs . + +### https://github.com/daler/gffutils +GitHub - daler/gffutils: GFF and GTF file manipulation and interconversion · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} daler / gffutils Public Notifications You must be signed in to change notification settings Fork 80 Star 317 Code Issues 13 Pull requests 4 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights daler/gffutils master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 768 Commits 768 Commits .github/ workflows .github/ workflows doc doc gffutils gffutils .gitignore .gitignore LICENSE LICENSE MANIFEST.in MANIFEST.in README.rst README.rst deploy.sh deploy.sh docs-requirements.txt docs-requirements.txt optional-requirements.txt optional-requirements.txt pyproject.toml pyproject.toml requirements.txt requirements.txt setup.py setup.py View all files Repository files navigation README MIT license gffutils gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. Files are loaded into a sqlite3 database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone. See documentation at https://daler.github.io/gffutils , and GitHub repo at https:/github.com/daler/gffutils . About GFF and GTF file manipulation and interconversion daler.github.io/gffutils Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 317 stars Watchers 13 watching Forks 80 forks Report repository Releases 1 v0.13 Latest Apr 13, 2024 Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.8% Shell 0.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/daler/gffutils +GitHub - daler/gffutils: GFF and GTF file manipulation and interconversion · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} daler / gffutils Public Notifications You must be signed in to change notification settings Fork 80 Star 317 Code Issues 13 Pull requests 4 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights daler/gffutils master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 768 Commits 768 Commits .github/ workflows .github/ workflows doc doc gffutils gffutils .gitignore .gitignore LICENSE LICENSE MANIFEST.in MANIFEST.in README.rst README.rst deploy.sh deploy.sh docs-requirements.txt docs-requirements.txt optional-requirements.txt optional-requirements.txt pyproject.toml pyproject.toml requirements.txt requirements.txt setup.py setup.py View all files Repository files navigation README MIT license gffutils gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. Files are loaded into a sqlite3 database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone. See documentation at https://daler.github.io/gffutils , and GitHub repo at https:/github.com/daler/gffutils . About GFF and GTF file manipulation and interconversion daler.github.io/gffutils Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 317 stars Watchers 13 watching Forks 80 forks Report repository Releases 1 v0.13 Latest Apr 13, 2024 Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.8% Shell 0.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gffutils --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +gffutils 0.8.6.1 py27_0 +----------------------- +file name : gffutils-0.8.6.1-py27_0.tar.bz2 +name : gffutils +version : 0.8.6.1 +build : py27_0 +build number: 0 +size : 1.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.6.1-py27_0.tar.bz2 +md5 : 251d9471100d9e2b6d617c35293a6881 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 2.7* + - simplejson + - six + + +gffutils 0.8.6.1 py34_0 +----------------------- +file name : gffutils-0.8.6.1-py34_0.tar.bz2 +name : gffutils +version : 0.8.6.1 +build : py34_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.6.1-py34_0.tar.bz2 +md5 : 9f3f33f3cc5b1598edc6fa2469c1e5e9 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.4* + - simplejson + - six + + +gffutils 0.8.6.1 py35_0 +----------------------- +file name : gffutils-0.8.6.1-py35_0.tar.bz2 +name : gffutils +version : 0.8.6.1 +build : py35_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.6.1-py35_0.tar.bz2 +md5 : d5f7ffe4f76d1f71c090b1dccae03a57 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.5* + - simplejson + - six + + +gffutils 0.8.7 py27_0 +--------------------- +file name : gffutils-0.8.7-py27_0.tar.bz2 +name : gffutils +version : 0.8.7 +build : py27_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7-py27_0.tar.bz2 +md5 : ed52b9a408e4e784cd0f28b05abbf9b8 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 2.7* + - simplejson + - six + + +gffutils 0.8.7 py34_0 +--------------------- +file name : gffutils-0.8.7-py34_0.tar.bz2 +name : gffutils +version : 0.8.7 +build : py34_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7-py34_0.tar.bz2 +md5 : 0b449eff1d8e07fb8ef3b77c62944bb4 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.4* + - simplejson + - six + + +gffutils 0.8.7 py35_0 +--------------------- +file name : gffutils-0.8.7-py35_0.tar.bz2 +name : gffutils +version : 0.8.7 +build : py35_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7-py35_0.tar.bz2 +md5 : 6f7ce5587196706c458f0d2833a9b53b +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.5* + - simplejson + - six + + +gffutils 0.8.7.1 py27_0 +----------------------- +file name : gffutils-0.8.7.1-py27_0.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py27_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py27_0.tar.bz2 +md5 : 4cf2f9a95ada75fee7ca6899978b8f7b +dependencies: + - argcomplete + - argh + - pyfaidx + - python 2.7* + - simplejson + - six + + +gffutils 0.8.7.1 py27_1 +----------------------- +file name : gffutils-0.8.7.1-py27_1.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py27_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py27_1.tar.bz2 +md5 : 0a82ea2f552ce2334efa1a2316cd8f9a +dependencies: + - argcomplete + - argh + - pyfaidx + - python 2.7* + - simplejson + - six + + +gffutils 0.8.7.1 py27_2 +----------------------- +file name : gffutils-0.8.7.1-py27_2.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py27_2 +build number: 2 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py27_2.tar.bz2 +md5 : a412369437e118841f4d95b244a66d07 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 2.7* + - simplejson + - six + + +gffutils 0.8.7.1 py34_0 +----------------------- +file name : gffutils-0.8.7.1-py34_0.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py34_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py34_0.tar.bz2 +md5 : 8ff8f633455bdca5e5776b7393fc8b3c +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.4* + - simplejson + - six + + +gffutils 0.8.7.1 py34_1 +----------------------- +file name : gffutils-0.8.7.1-py34_1.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py34_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py34_1.tar.bz2 +md5 : 2879ff51af662e2da3015b36cc6c3287 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.4* + - simplejson + - six + + +gffutils 0.8.7.1 py35_0 +----------------------- +file name : gffutils-0.8.7.1-py35_0.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py35_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py35_0.tar.bz2 +md5 : a006df2dbfd57fa69d1d331aa21acd05 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.5* + - simplejson + - six + + +gffutils 0.8.7.1 py35_1 +----------------------- +file name : gffutils-0.8.7.1-py35_1.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py35_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py35_1.tar.bz2 +md5 : 40356af066a304495c2244644b7f59ff +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.5* + - simplejson + - six + + +gffutils 0.8.7.1 py35_2 +----------------------- +file name : gffutils-0.8.7.1-py35_2.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py35_2 +build number: 2 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py35_2.tar.bz2 +md5 : db09512438ea849ea9d18de43cf0fcc6 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.5* + - simplejson + - six + + +gffutils 0.8.7.1 py36_0 +----------------------- +file name : gffutils-0.8.7.1-py36_0.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py36_0 +build number: 0 +size : 1.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py36_0.tar.bz2 +md5 : 95fa4d3e9d369decbfa7b8ee95fddda6 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.6* + - simplejson + - six + + +gffutils 0.8.7.1 py36_1 +----------------------- +file name : gffutils-0.8.7.1-py36_1.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py36_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py36_1.tar.bz2 +md5 : 90cb693ac86ea24a5ac9367f49f56815 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.6* + - simplejson + - six + + +gffutils 0.8.7.1 py36_2 +----------------------- +file name : gffutils-0.8.7.1-py36_2.tar.bz2 +name : gffutils +version : 0.8.7.1 +build : py36_2 +build number: 2 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.8.7.1-py36_2.tar.bz2 +md5 : 981ddd8d92273626c9f910f174ca39ec +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.6* + - simplejson + - six + + +gffutils 0.9 py27_0 +------------------- +file name : gffutils-0.9-py27_0.tar.bz2 +name : gffutils +version : 0.9 +build : py27_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.9-py27_0.tar.bz2 +md5 : 252d19bb8150c1535495388faf6d4355 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 2.7* + - simplejson + - six + + +gffutils 0.9 py35_0 +------------------- +file name : gffutils-0.9-py35_0.tar.bz2 +name : gffutils +version : 0.9 +build : py35_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.9-py35_0.tar.bz2 +md5 : d0e82ab04878d0f35d9a5bd61d225013 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.5* + - simplejson + - six + + +gffutils 0.9 py36_0 +------------------- +file name : gffutils-0.9-py36_0.tar.bz2 +name : gffutils +version : 0.9 +build : py36_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gffutils-0.9-py36_0.tar.bz2 +md5 : 3baa107c8a04c08782b558e63b35e5f6 +dependencies: + - argcomplete + - argh + - pyfaidx + - python 3.6* + - simplejson + - six + + +gffutils 0.9 py_1 +----------------- +file name : gffutils-0.9-py_1.tar.bz2 +name : gffutils +version : 0.9 +build : py_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gffutils-0.9-py_1.tar.bz2 +md5 : 9b69004c8564cabe5ea208a86770daf0 +timestamp : 2018-06-25 18:02:56 UTC +dependencies: + - argcomplete + - argh + - pyfaidx + - python + - simplejson + - six + + +gffutils 0.10.1 py_0 +-------------------- +file name : gffutils-0.10.1-py_0.tar.bz2 +name : gffutils +version : 0.10.1 +build : py_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gffutils-0.10.1-py_0.tar.bz2 +md5 : 649ab45041f4d316071dc57987acada8 +timestamp : 2019-12-30 22:33:47 UTC +dependencies: + - argcomplete >=1.9.4 + - argh >=0.26.2 + - pyfaidx >=0.5.5.2 + - python + - simplejson + - six >=1.12.0 + + +gffutils 0.10.1 pyh864c0ab_1 +---------------------------- +file name : gffutils-0.10.1-pyh864c0ab_1.tar.bz2 +name : gffutils +version : 0.10.1 +build : pyh864c0ab_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gffutils-0.10.1-pyh864c0ab_1.tar.bz2 +md5 : f059981443444bd0122b78ae06755362 +timestamp : 2020-07-26 00:30:57 UTC +dependencies: + - argcomplete >=1.9.4 + - argh >=0.26.2 + - pyfaidx >=0.5.5.2 + - python + - simplejson + - six >=1.12.0 + + +gffutils 0.11.0 pyh5e36f6f_0 +---------------------------- +file name : gffutils-0.11.0-pyh5e36f6f_0.tar.bz2 +name : gffutils +version : 0.11.0 +build : pyh5e36f6f_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gffutils-0.11.0-pyh5e36f6f_0.tar.bz2 +md5 : ebf1c9eae1487f21ea874094773ad0e3 +timestamp : 2022-06-05 17:35:08 UTC +dependencies: + - argcomplete >=1.9.4 + - argh >=0.26.2 + - pyfaidx >=0.5.5.2 + - python + - simplejson + - six >=1.12.0 + + +gffutils 0.11.1 pyh7cba7a3_0 +---------------------------- +file name : gffutils-0.11.1-pyh7cba7a3 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gimmemotifs.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gimmemotifs.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae8040493b7d9da996adc79b9dfee3f6c942a294 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gimmemotifs.manual_bundle.txt @@ -0,0 +1,592 @@ +# Tool: gimmemotifs +software_name: gimmemotifs +tier: T1 +domain: t1_backfill_overall +downloads: 164314 +summary: Motif prediction pipeline and various motif-related tools. +description: Motif prediction pipeline and various motif-related tools. +dependencies: dinamo >=1.0, gadem >=1.3.1, gimmemotifs-minimal 0.18.2 py312hfabe715_1, homer >=4.11, meme >=5.5.7, prosampler >=1.5, python >=3.12,<3.13.0a0, python_abi 3.12.* *_cp312, trawler >=2.0, weeder >=2.0, xxmotif >=1.6 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/vanheeringen-lab/gimmemotifs +doc_url: https://gimmemotifs.readthedocs.io/en/master +dev_url: https://github.com/vanheeringen-lab/gimmemotifs + +## URL Docs Extract +### https://gimmemotifs.readthedocs.io/en/master +GimmeMotifs for transcription factor motif analysis — GimmeMotifs 0.18.2 documentation GimmeMotifs 0.18.2 Site Installation Configuration Input Data Overview Simple examples Tutorials Command-line reference API documentation Examples Auto-generated FAQ Acknowledgments Page GimmeMotifs for transcription factor motif analysis What is GimmeMotifs? Getting started Get help Full contents Installation » Source GimmeMotifs for transcription factor motif analysis What is GimmeMotifs? Getting started Get help Full contents Installation » Source GimmeMotifs for transcription factor motif analysis ¶ What is GimmeMotifs? ¶ GimmeMotifs is an analysis framework for transcription factor motif analysis written in Python. It contains command-line scripts to predict de novo motifs, scan for known motifs, identify differential motifs, calculate motif enrichment statistics, plot sequence logos and more. In addition, all this functionality is available from a Python API. GimmeMotifs is free and open source research software. If you find it useful please cite our paper: Bruse N and van Heeringen SJ, GimmeMotifs: an analysis framework for transcription factor motif analysis , bioRxiv, 2018. https://www.biorxiv.org/content/10.1101/474403v1.full . doi: 10.1101/474403 . van Heeringen SJ and Veenstra GJC, GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments , Bioinformatics. 2011 Jan 15;27(2):270-1. doi: 10.1093/bioinformatics/btq636 . Getting started ¶ The easiest way to install GimmeMotifs is using bioconda on Linux or Mac. From version 0.13.0 only Python 3 (>= 3.8) is supported. Have a look at these simple examples to get a taste of what is possible. Check out the more detailed tutorials . Full command-line reference can be found here . There’s also an API documentation . Get help ¶ First, check the FAQ for common issues. The preferred way to get support is through the Github issues page. Finally, you can reach me by mail or via twitter . Full contents ¶ Installation Conda - the easy way Pip Source - developers install Configuration Input Data Genomes - and how to get them MotifSampler Overview Running on a cluster Motif databases Simple examples Install a genome Predict de novo motifs Compare motifs between data sets Create sequence logos Tutorials Find de novo motifs Motif enrichment statistics Scan for known motifs Find differential motifs Command-line reference List of tools Input formats Command: gimme motifs Command: gimme maelstrom Command: gimme scan Command: gimme background Command: gimme logo Command: gimme match Command: gimme cluster Command: gimme threshold Command: gimme location Command: gimme diff Command: gimme motif2factors API documentation Examples Working with motifs Motif scanning Finding de novo motifs Motif statistics Motif comparison Auto-generated The Motif class Prediction of de novo motifs Motif scanning Maelstrom Motif activity prediction Motif statistics Motif comparison FAQ ValueError: Shape of passed values is (13933, 1796), indices imply (14, 1796) SQLite error when running on a cluster ImportError: dlopen: cannot load any more object with static TLS ‘i’ format requires -2147483648 <= number <= -2147483646 Sorry, motif prediction tool [X] is not supported I get motifs that have differential scores in gimme maelstrom, however, the number is not different across clusters I have upgraded GimmeMotifs and now it doesn’t find my genome I cannot run gimme index anymore I get ‘RuntimeError: Invalid DISPLAY variable’ I get a KeyError when running gimme maelstrom Acknowledgments Back to top © Copyright 2026, Simon van Heeringen, licensed under MIT. Created using Sphinx 9.0.4. + +### https://github.com/vanheeringen-lab/gimmemotifs +GitHub - vanheeringen-lab/gimmemotifs: Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} vanheeringen-lab / gimmemotifs Public Notifications You must be signed in to change notification settings Fork 35 Star 127 Code Issues 55 Pull requests 4 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights vanheeringen-lab/gimmemotifs master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 2,002 Commits 2,002 Commits .github/ ISSUE_TEMPLATE .github/ ISSUE_TEMPLATE binder binder data data docs docs gimmemotifs gimmemotifs scripts scripts src src test test .codeclimate.yml .codeclimate.yml .gitignore .gitignore .rtd-environment.yml .rtd-environment.yml .travis.yml .travis.yml CHANGELOG.md CHANGELOG.md COPYING COPYING README.md README.md conda_env.osx.txt conda_env.osx.txt custom_build.py custom_build.py pyproject.toml pyproject.toml readthedocs.yml readthedocs.yml requirements.yaml requirements.yaml View all files Repository files navigation README MIT license GimmeMotifs Gimmemotifs is a suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See the documentation for detailed installation instructions and usage examples. Easy installation The most straightforward way to install GimmeMotifs is via conda using the bioconda channel. If you have not used bioconda before, first set up the necessary channels (in this order!). You only have to do this once. $ conda config --add channels bioconda $ conda config --add channels conda-forge You can now install GimmeMotifs with one command: # Create an environment called gimme with all dependencies $ conda create -n gimme gimmemotifs-minimal # or $ conda create -n gimme gimmemotifs # Activate the environment $ conda activate gimme Don't forget to activate the environment with conda activate gimme whenever you want to use GimmeMotifs. Quick start Predict some de novo motifs: $ gimme motifs my_peaks.bed my_motifs -g /data/genomes/hg38/hg38.fa --denovo Download a genome The example above assumes that you have the hg38 genome in /data/genomes/hg38/hg38.fa . GimmeMotifs can also use genomes installed by genomepy . You can configure the directory where genomepy stores genomes by editing ~/.config/genomepy/genomepy.yaml genome_dir: /data/genomes To download a genome from UCSC: $ genomepy install hg38 --annotation Now you can specify this genome for GimmeMotifs by name. $ gimme motifs my_peaks.bed -g hg38 -n my_motifs Cite us The manuscript describing this latest release is available on biorRxiv as a preprint and can be cited as: GimmeMotifs: an analysis framework for transcription factor motif analysis Niklas Bruse, Simon J. van Heeringen bioRxiv (2018) DOI: 10.1101/474403 We need your help! GimmeMotifs was originally developed for our own needs but we would really like it to be useful to the wider community. However, this also depends on your input. Let us know what you think! What features are missing? Which tutorial would you like to see? What part of the documentation is unclear? Have great ideas for future developments? Maybe you even want to join in developing this software? Let us know! Help Full documentation: http://gimmemotifs.readthedocs.io/ Check the FAQ for common issues The preferred way to get support is through the GitHub issues page Finally, you can reach me by mail About Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples. gimmemotifs.readthedocs.io/en/master Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 127 stars Watchers 5 watching Forks 35 forks Report repository Releases 37 [0.18.2] - 2026-04-03 Latest Apr 3, 2026 + 36 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 74.0% C 21.9% HTML 1.5% Go Template 1.2% Other 1.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/vanheeringen-lab/gimmemotifs +GitHub - vanheeringen-lab/gimmemotifs: Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} vanheeringen-lab / gimmemotifs Public Notifications You must be signed in to change notification settings Fork 35 Star 127 Code Issues 55 Pull requests 4 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights vanheeringen-lab/gimmemotifs master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 2,002 Commits 2,002 Commits .github/ ISSUE_TEMPLATE .github/ ISSUE_TEMPLATE binder binder data data docs docs gimmemotifs gimmemotifs scripts scripts src src test test .codeclimate.yml .codeclimate.yml .gitignore .gitignore .rtd-environment.yml .rtd-environment.yml .travis.yml .travis.yml CHANGELOG.md CHANGELOG.md COPYING COPYING README.md README.md conda_env.osx.txt conda_env.osx.txt custom_build.py custom_build.py pyproject.toml pyproject.toml readthedocs.yml readthedocs.yml requirements.yaml requirements.yaml View all files Repository files navigation README MIT license GimmeMotifs Gimmemotifs is a suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See the documentation for detailed installation instructions and usage examples. Easy installation The most straightforward way to install GimmeMotifs is via conda using the bioconda channel. If you have not used bioconda before, first set up the necessary channels (in this order!). You only have to do this once. $ conda config --add channels bioconda $ conda config --add channels conda-forge You can now install GimmeMotifs with one command: # Create an environment called gimme with all dependencies $ conda create -n gimme gimmemotifs-minimal # or $ conda create -n gimme gimmemotifs # Activate the environment $ conda activate gimme Don't forget to activate the environment with conda activate gimme whenever you want to use GimmeMotifs. Quick start Predict some de novo motifs: $ gimme motifs my_peaks.bed my_motifs -g /data/genomes/hg38/hg38.fa --denovo Download a genome The example above assumes that you have the hg38 genome in /data/genomes/hg38/hg38.fa . GimmeMotifs can also use genomes installed by genomepy . You can configure the directory where genomepy stores genomes by editing ~/.config/genomepy/genomepy.yaml genome_dir: /data/genomes To download a genome from UCSC: $ genomepy install hg38 --annotation Now you can specify this genome for GimmeMotifs by name. $ gimme motifs my_peaks.bed -g hg38 -n my_motifs Cite us The manuscript describing this latest release is available on biorRxiv as a preprint and can be cited as: GimmeMotifs: an analysis framework for transcription factor motif analysis Niklas Bruse, Simon J. van Heeringen bioRxiv (2018) DOI: 10.1101/474403 We need your help! GimmeMotifs was originally developed for our own needs but we would really like it to be useful to the wider community. However, this also depends on your input. Let us know what you think! What features are missing? Which tutorial would you like to see? What part of the documentation is unclear? Have great ideas for future developments? Maybe you even want to join in developing this software? Let us know! Help Full documentation: http://gimmemotifs.readthedocs.io/ Check the FAQ for common issues The preferred way to get support is through the GitHub issues page Finally, you can reach me by mail About Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples. gimmemotifs.readthedocs.io/en/master Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 127 stars Watchers 5 watching Forks 35 forks Report repository Releases 37 [0.18.2] - 2026-04-03 Latest Apr 3, 2026 + 36 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 74.0% C 21.9% HTML 1.5% Go Template 1.2% Other 1.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gimmemotifs --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +gimmemotifs 0.8.9.1 py27_1 +-------------------------- +file name : gimmemotifs-0.8.9.1-py27_1.tar.bz2 +name : gimmemotifs +version : 0.8.9.1 +build : py27_1 +build number: 1 +size : 12.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.8.9.1-py27_1.tar.bz2 +md5 : 28377d143358a4015c45b7d045d9efdc +dependencies: + - kid + - matplotlib + - numpy + - pybedtools + - python 2.7* + - pyyaml + - scipy + + +gimmemotifs 0.9.0.3 py27_2 +-------------------------- +file name : gimmemotifs-0.9.0.3-py27_2.tar.bz2 +name : gimmemotifs +version : 0.9.0.3 +build : py27_2 +build number: 2 +size : 12.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.9.0.3-py27_2.tar.bz2 +md5 : 2a5c04a073b2dc6e963bb8c53f096779 +dependencies: + - kid + - lightning + - matplotlib + - moods + - numpy + - pybedtools + - pymc + - python 2.7* + - pyyaml + - scikit-learn + - scipy + - statsmodels + - ucsc-genepredtobed + + +gimmemotifs 0.9.0.4 py27_0 +-------------------------- +file name : gimmemotifs-0.9.0.4-py27_0.tar.bz2 +name : gimmemotifs +version : 0.9.0.4 +build : py27_0 +build number: 0 +size : 12.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.9.0.4-py27_0.tar.bz2 +md5 : ea3afabc18658ad73e8b909d29aed076 +dependencies: + - kid + - lightning + - matplotlib + - moods + - numpy + - pybedtools + - pymc + - python 2.7* + - pyyaml + - scikit-learn + - scipy + - statsmodels + - ucsc-genepredtobed + + +gimmemotifs 0.9.0.5 py27_0 +-------------------------- +file name : gimmemotifs-0.9.0.5-py27_0.tar.bz2 +name : gimmemotifs +version : 0.9.0.5 +build : py27_0 +build number: 0 +size : 12.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.9.0.5-py27_0.tar.bz2 +md5 : 48c26cfcb4bca15aa45cb4db102c12ce +dependencies: + - kid + - lightning + - matplotlib + - moods + - numpy + - pybedtools + - pymc + - python 2.7* + - pyyaml + - scikit-learn + - scipy + - statsmodels + - ucsc-genepredtobed + + +gimmemotifs 0.9.0.6 py27_0 +-------------------------- +file name : gimmemotifs-0.9.0.6-py27_0.tar.bz2 +name : gimmemotifs +version : 0.9.0.6 +build : py27_0 +build number: 0 +size : 12.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.9.0.6-py27_0.tar.bz2 +md5 : c125b4d9ce016647d97abaef7c949d0a +dependencies: + - kid + - lightning + - matplotlib + - moods + - numpy + - pybedtools + - pymc + - python 2.7* + - pyyaml + - scikit-learn + - scipy + - statsmodels + - ucsc-genepredtobed + + +gimmemotifs 0.10.0b1 py27_0 +--------------------------- +file name : gimmemotifs-0.10.0b1-py27_0.tar.bz2 +name : gimmemotifs +version : 0.10.0b1 +build : py27_0 +build number: 0 +size : 12.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.10.0b1-py27_0.tar.bz2 +md5 : c2b589c4d435213c13a9e356b4903dc6 +dependencies: + - jinja2 + - lightning + - matplotlib + - moods + - numpy + - pybedtools + - pymc + - python 2.7* + - pyyaml + - r-robustrankaggreg + - scikit-learn + - scipy + - seaborn + - statsmodels + - ucsc-genepredtobed + + +gimmemotifs 0.10.0b4 py27pl5.22.0_0 +----------------------------------- +file name : gimmemotifs-0.10.0b4-py27pl5.22.0_0.tar.bz2 +name : gimmemotifs +version : 0.10.0b4 +build : py27pl5.22.0_0 +build number: 0 +size : 11.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.10.0b4-py27pl5.22.0_0.tar.bz2 +md5 : 6a3db8608bb639074c66c83b87eec842 +dependencies: + - htslib <1.3.1 + - jinja2 + - libgcc + - lightning + - matplotlib + - meme 4.11.1 py27pl5.22.0_1 + - moods + - numpy + - perl 5.22.0 + - pybedtools + - pymc + - pysam <0.9.1.4 + - python 2.7* + - pyyaml + - r-robustrankaggreg + - scikit-learn + - scipy + - seaborn + - statsmodels + - ucsc-genepredtobed + + +gimmemotifs 0.10.0b4 py27pl5.22.0_1 +----------------------------------- +file name : gimmemotifs-0.10.0b4-py27pl5.22.0_1.tar.bz2 +name : gimmemotifs +version : 0.10.0b4 +build : py27pl5.22.0_1 +build number: 1 +size : 11.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.10.0b4-py27pl5.22.0_1.tar.bz2 +md5 : a8386d83b35b3e9c3ec3ef8db77f0a17 +dependencies: + - jinja2 + - libgcc + - lightning + - matplotlib + - meme + - moods + - numpy + - perl 5.22.0* + - pybedtools + - pymc + - python 2.7* + - pyyaml + - r-robustrankaggreg + - scikit-learn + - scipy + - seaborn + - statsmodels + - ucsc-genepredtobed + + +gimmemotifs 0.10.0b5 py27pl5.22.0_1 +----------------------------------- +file name : gimmemotifs-0.10.0b5-py27pl5.22.0_1.tar.bz2 +name : gimmemotifs +version : 0.10.0b5 +build : py27pl5.22.0_1 +build number: 1 +size : 11.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.10.0b5-py27pl5.22.0_1.tar.bz2 +md5 : 881020ab59961bfefbcf8692d6d24914 +dependencies: + - jinja2 + - libgcc + - lightning + - matplotlib + - meme + - moods + - numpy + - perl 5.22.0* + - pybedtools + - pymc + - python 2.7* + - pyyaml + - r-robustrankaggreg + - scikit-learn >=0.18 + - scipy + - seaborn + - statsmodels + - ucsc-genepredtobed + + +gimmemotifs 0.10.0b6 py27pl5.22.0_1 +----------------------------------- +file name : gimmemotifs-0.10.0b6-py27pl5.22.0_1.tar.bz2 +name : gimmemotifs +version : 0.10.0b6 +build : py27pl5.22.0_1 +build number: 1 +size : 11.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.10.0b6-py27pl5.22.0_1.tar.bz2 +md5 : 97065bf45ff029933d17a6c32c375ec3 +dependencies: + - jinja2 + - libgcc + - lightning + - matplotlib + - meme + - moods + - numpy + - perl 5.22.0* + - pybedtools + - pymc + - python 2.7* + - pyyaml + - r-robustrankaggreg + - scikit-learn >=0.18 + - scipy + - seaborn + - statsmodels + - ucsc-genepredtobed + + +gimmemotifs 0.10.0 py27_0 +------------------------- +file name : gimmemotifs-0.10.0-py27_0.tar.bz2 +name : gimmemotifs +version : 0.10.0 +build : py27_0 +build number: 0 +size : 11.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.10.0-py27_0.tar.bz2 +md5 : 6bcb8d150ff59c8151e063d876dcbc6d +dependencies: + - bedtools + - ete3 + - htslib <1.4 + - jinja2 + - libgcc + - lightning + - matplotlib >=2.0 + - meme + - moods + - numpy + - perl >=5.22 + - pillow + - pybedtools + - pymc + - python 2.7* + - pyyaml + - r-robustrankaggreg + - scikit-learn >=0.18 + - scipy + - seaborn + - statsmodels + - ucsc-genepredtobed + - xgboost + + +gimmemotifs 0.11.1 py27_0 +------------------------- +file name : gimmemotifs-0.11.1-py27_0.tar.bz2 +name : gimmemotifs +version : 0.11.1 +build : py27_0 +build number: 0 +size : 12.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.11.1-py27_0.tar.bz2 +md5 : 6df44564849db15b71494007ebcb75f4 +dependencies: + - bedtools + - configparser + - diskcache + - future + - gadem + - ghostscript + - homer + - jinja2 + - libgcc + - matplotlib >=2.0 + - meme + - numpy >=1.6.0 + - pillow + - pybedtools + - pysam + - python 2.7* + - pyyaml >=3.10 + - scikit-learn >=0.18 + - scipy >=0.9.0 + - seaborn + - six + - sklearn-contrib-lightning + - statsmodels + - trawler + - ucsc-bigbedtobed + - ucsc-genepredtobed + - weeder + - xdg + - xgboost + - xxhash + + +gimmemotifs 0.11.1 py27h470a237_1 +--------------------------------- +file name : gimmemotifs-0.11.1-py27h470a237_1.tar.bz2 +name : gimmemotifs +version : 0.11.1 +build : py27h470a237_1 +build number: 1 +size : 12.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.11.1-py27h470a237_1.tar.bz2 +md5 : 1dd7ea7138ce29651241625cff10dd30 +timestamp : 2018-06-26 15:49:07 UTC +dependencies: + - bedtools + - configparser + - diskcache + - future + - gadem + - ghostscript + - homer + - jinja2 + - libgcc-ng >=4.9 + - matplotlib >=2.0 + - meme + - numpy >=1.6.0 + - pillow + - pybedtools + - pysam + - python >=2.7,<2.8.0a0 + - pyyaml >=3.10 + - scikit-learn >=0.18 + - scipy >=0.9.0 + - seaborn + - six + - sklearn-contrib-lightning + - statsmodels + - trawler + - ucsc-bigbedtobed + - ucsc-genepredtobed + - weeder + - xdg + - xgboost + - xxhash + + +gimmemotifs 0.11.1 py35_0 +------------------------- +file name : gimmemotifs-0.11.1-py35_0.tar.bz2 +name : gimmemotifs +version : 0.11.1 +build : py35_0 +build number: 0 +size : 12.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.11.1-py35_0.tar.bz2 +md5 : 1857faeab9372f2bf1e90c7dba12df5b +dependencies: + - bedtools + - diskcache + - future + - gadem + - ghostscript + - homer + - jinja2 + - libgcc + - matplotlib >=2.0 + - numpy >=1.6.0 + - pillow + - pybedtools + - pysam + - python 3.5* + - pyyaml >=3.10 + - scikit-learn >=0.18 + - scipy >=0.9.0 + - seaborn + - six + - sklearn-contrib-lightning + - statsmodels + - trawler + - ucsc-bigbedtobed + - ucsc-genepredtobed + - weeder + - xdg + - xgboost + - xxhash + + +gimmemotifs 0.11.1 py35h470a237_1 +--------------------------------- +file name : gimmemotifs-0.11.1-py35h470a237_1.tar.bz2 +name : gimmemotifs +version : 0.11.1 +build : py35h470a237_1 +build number: 1 +size : 12.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.11.1-py35h470a237_1.tar.bz2 +md5 : 40a9f49230d765fd8f80ea9434e1f342 +timestamp : 2018-06-26 15:44:22 UTC +dependencies: + - bedtools + - diskcache + - future + - gadem + - ghostscript + - homer + - jinja2 + - libgcc-ng >=4.9 + - matplotlib >=2.0 + - numpy >=1.6.0 + - pillow + - pybedtools + - pysam + - python >=3.5,<3.6.0a0 + - pyyaml >=3.10 + - scikit-learn >=0.18 + - scipy >=0.9.0 + - seaborn + - six + - sklearn-contrib-lightning + - statsmodels + - trawler + - ucsc-bigbedtobed + - ucsc-genepredtobed + - weeder + - xdg + - xgboost + - xxhash + + +gimmemotifs 0.11.1 py36_0 +------------------------- +file name : gimmemotifs-0.11.1-py36_0.tar.bz2 +name : gimmemotifs +version : 0.11.1 +build : py36_0 +build number: 0 +size : 12.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gimmemotifs-0.11.1-py36_0.tar.bz2 +md5 : 60212896e806e2ab5a16ae1d3763c725 +dependencies: + - bedtools + - diskcache + - future + - gadem + - ghostscript + - homer + - jinja2 + - libgcc + - matplotlib >=2.0 + - numpy >=1.6.0 + - pillow + - pybedtools + - pysam + - python 3.6* + - pyyaml >=3.10 + - scikit-learn >=0.18 + - scipy >=0.9.0 + - seaborn + - six + - sklearn-contrib-lightning + - statsmodels + - trawler + - ucsc-bigbedtobed + - ucsc-genepredtobed + - weeder + - xdg + - xgboost + - xxhash + + +gimmemotifs 0.11.1 py36h470a237_1 +--------------------------------- +file name : gimmemotifs-0.11.1-py36h470a237_1.tar.bz2 +name : diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/glimmerhmm.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/glimmerhmm.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa3addefa524a0624ee6a2ae9fb5f672ea514124 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/glimmerhmm.manual_bundle.txt @@ -0,0 +1,193 @@ +# Tool: glimmerhmm +software_name: glimmerhmm +tier: T1 +domain: t1_backfill_overall +downloads: 222693 +summary: +description: +dependencies: libgcc >=13, libstdcxx >=13, perl >=5.32.1,<5.33.0a0 *_perl5 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +cli:glimmerhmm +## CLI Help Content +$ conda run -n bioenv_cli glimmerhmm --help +[rc=139] + +/tmp/tmpuzppbwf_: line 3: 633843 Segmentation fault (core dumped) glimmerhmm --help + +ERROR conda.cli.main_run:execute(127): `conda run glimmerhmm --help` failed. (See above for error) + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge glimmerhmm --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +glimmerhmm 3.0.4 0 +------------------ +file name : glimmerhmm-3.0.4-0.tar.bz2 +name : glimmerhmm +version : 3.0.4 +build : 0 +build number: 0 +size : 40.3 MB +license : Artistic License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/glimmerhmm-3.0.4-0.tar.bz2 +md5 : 73db8010300c173aeed1c1162352e608 +dependencies: + - libgcc + + +glimmerhmm 3.0.4 1 +------------------ +file name : glimmerhmm-3.0.4-1.tar.bz2 +name : glimmerhmm +version : 3.0.4 +build : 1 +build number: 1 +size : 40.3 MB +license : Artistic License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/glimmerhmm-3.0.4-1.tar.bz2 +md5 : 9b8b58a3a9b5e01c248225a7c39a33ab +dependencies: + - libgcc + + +glimmerhmm 3.0.4 h2d50403_2 +--------------------------- +file name : glimmerhmm-3.0.4-h2d50403_2.tar.bz2 +name : glimmerhmm +version : 3.0.4 +build : h2d50403_2 +build number: 2 +size : 40.3 MB +license : Artistic License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/glimmerhmm-3.0.4-h2d50403_2.tar.bz2 +md5 : 0395e54d663e2baf4407b7d596d8ae94 +timestamp : 2018-07-12 17:04:30 UTC +dependencies: + - libstdcxx-ng >=4.9 + + +glimmerhmm 3.0.4 pl526hf484d3e_3 +-------------------------------- +file name : glimmerhmm-3.0.4-pl526hf484d3e_3.tar.bz2 +name : glimmerhmm +version : 3.0.4 +build : pl526hf484d3e_3 +build number: 3 +size : 40.6 MB +license : Artistic License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/glimmerhmm-3.0.4-pl526hf484d3e_3.tar.bz2 +md5 : 615f0e232de60b9c416fc73ba260c091 +timestamp : 2019-06-24 17:49:34 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + + +glimmerhmm 3.0.4 pl5321h503566f_10 +---------------------------------- +file name : glimmerhmm-3.0.4-pl5321h503566f_10.conda +name : glimmerhmm +version : 3.0.4 +build : pl5321h503566f_10 +build number: 10 +size : 35.9 MB +license : Artistic License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/glimmerhmm-3.0.4-pl5321h503566f_10.conda +md5 : 0a9e50daa0e798ce6c7b06894570a5f7 +timestamp : 2025-09-22 20:21:31 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +glimmerhmm 3.0.4 pl5321h503566f_9 +--------------------------------- +file name : glimmerhmm-3.0.4-pl5321h503566f_9.tar.bz2 +name : glimmerhmm +version : 3.0.4 +build : pl5321h503566f_9 +build number: 9 +size : 40.9 MB +license : Artistic License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/glimmerhmm-3.0.4-pl5321h503566f_9.tar.bz2 +md5 : 167107a8bd913425bfda9e4cf299d66c +timestamp : 2024-12-10 13:52:56 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +glimmerhmm 3.0.4 pl5321h87f3376_5 +--------------------------------- +file name : glimmerhmm-3.0.4-pl5321h87f3376_5.tar.bz2 +name : glimmerhmm +version : 3.0.4 +build : pl5321h87f3376_5 +build number: 5 +size : 40.7 MB +license : Artistic License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/glimmerhmm-3.0.4-pl5321h87f3376_5.tar.bz2 +md5 : cc2728458d24953a94eda6a66788dc50 +timestamp : 2022-10-11 17:10:26 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +glimmerhmm 3.0.4 pl5321hdbdd923_7 +--------------------------------- +file name : glimmerhmm-3.0.4-pl5321hdbdd923_7.tar.bz2 +name : glimmerhmm +version : 3.0.4 +build : pl5321hdbdd923_7 +build number: 7 +size : 40.7 MB +license : Artistic License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/glimmerhmm-3.0.4-pl5321hdbdd923_7.tar.bz2 +md5 : 124d14608380be4b48604dcf601961c1 +timestamp : 2024-04-09 07:27:03 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +glimmerhmm 3.0.4 pl5321hdbdd923_8 +--------------------------------- +file name : glimmerhmm-3.0.4-pl5321hdbdd923_8.tar.bz2 +name : glimmerhmm +version : 3.0.4 +build : pl5321hdbdd923_8 +build number: 8 +size : 40.6 MB +license : Artistic License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/glimmerhmm-3.0.4-pl5321hdbdd923_8.tar.bz2 +md5 : c2ee8d7e8acadbed5ef88e556a0bef0c +timestamp : 2024-06-05 13:09:47 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gmap.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gmap.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6124eb4c80114ea910432590b728621d9501adfa --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gmap.manual_bundle.txt @@ -0,0 +1,517 @@ +# Tool: gmap +software_name: gmap +tier: T1 +domain: t1_backfill_overall +downloads: 479998 +summary: Genomic mapping and alignment program for mRNA and EST sequences. +description: Genomic mapping and alignment program for mRNA and EST sequences. +dependencies: bzip2 >=1.0.8,<2.0a0, libgcc >=13, libzlib >=1.3.1,<2.0a0, perl >=5.32.1,<5.33.0a0 *_perl5, perl-file-util +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://research-pub.gene.com/gmap +doc_url: http://research-pub.gene.com/gmap +dev_url: http://research-pub.gene.com/gmap + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://research-pub.gene.com/gmap +GMAP and GSNAP GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program Links are provided below in parentheses for users who wish to download the files with a command-line tool, like wget . Source code for both GMAP and GSNAP Version 2025-07-31 (v2) (http://research-pub.gene.com/gmap/src/gmap-gsnap-2025-07-31.v2.tar.gz). Changes since 2025-07-31: Fixed a fatal bug for potential alignments to the beginning of a genome Changes since 2025-04-19: Fixed a potential infinite loop in GSNAP Fixed the printing of the mate chrpos for nonmappers in GSNAP SAM output Changes since 2025-04-18: Fixed a bug in GSNAP SAM output where the mate chromosome and position of a non-mapping read would sometimes not be printed Changes since 2024-11-20 (v2): Restored and improved upon GSNAP accuracy from 2024-06-24, while incorporating all existing bug fixes and restoring some of the speed of earlier versions Added programs gtf_exons and gff3_exons Changes since 2024-10-20: Fixed a fatal bug in GSNAP relating to alignments before the beginning of a genome Fixed a fatal bug in GSNAP relating to low-quality sequences with an effective query length of zero Made changes to the finding of splices between paired-end reads Changes since 2024-10-10: Eliminated a long-standing memory leak Fixed a fatal bug in GSNAP relating to long segments being explored with localdb Fixed issues with coordinates in alignments to circular chromosomes Changes since 2024-09-18: Fixes to fatal bugs in GSNAP when dealing with alignments at the beginning of the genome Reusing memory in GSNAP, which helps speed up performance Further improvements in splicing in GSNAP on the insides of paired-end reads Improvements to read localization for transcriptome-guided alignment Changes since 2024-08-20: Fixes to fatal bugs in GSNAP when dealing with small chromosomes Improvements in splicing in GSNAP, especially on the insides of paired-end reads Improvements to the detection of indels in GSNAP. Using the values of --max-insertions and --max-deletions Restored the option --pairdev in GSNAP, and using that with --pairexpect in paired-end alignment Added the option --align-fraction to GMAP and GSNAP, which aligns only a fraction of the given reads, selected randomly Changes since 2024-08-14: Improvements and fixes made in --two-pass mode for GSNAP For transcriptomes, gmap_build now puts link files under the transcriptome db, rather than the genome db The flag -C can now be used in gmap_build to specify a location for the transcriptome db Changes since 2024-06-24: For GSNAP, implemented --splices-dump to produce a splice junctions file that matches that of STAR For GSNAP, also implemented --splices-read, --splices-noeval, and --splices-include-known Improvements in splicing in --two-pass mode in GSNAP Improvements in transcriptome-guided genomic alignment in GSNAP For SAM output of GSNAP, changed name of XM field to be MC for mate cigar Improved choice between insertion and deletions at a given position to consider the indel length For overlapping paired-end alignments, checking that the overlapping nucleotide sequences match Fixed gff3_genes to work on NCBI gff3 files as well as Ensembl Changes since 2024-05-20: Improvements to splice identification in GSNAP Splice identification looking specifically for AT-AC as well as GT-AG and GC-AG introns Changes since 2024-05-07: Extensive revisions in GSNAP to improve the accuracy of alignment Changes since 2024-03-15: Fixed a fatal bug from trimming single-exon alignments near chromosomal bounds Removing duplicate transcripts in transcriptome-guided genomic alignment Changes since 2024-02-02: Improvements in finding long indels Improvements in alignments of overlapping paired-end reads Improvements in transcriptome-guided genomic alignment Restored sub: field in standard GSNAP output Changes since 2023-12-01: Fixed fatal bug on highly repetitive reads Rewrite to improve accuracy of read alignment Improvements to splice calling and to resolution of inner splicing Changes since 2023-10-10: Major rewrite of GSNAP to improve speed Changes since 2023-10-10: Fixed a bug in GSNAP allowing alignments to extend past the beginning or end of a chromosome Fixed a bug in SAM output of GSNAP resulting in non-ASCII characters to be generated Fixed a bug in SAM output of GMAP resulting in cigar length to be different from the querylength Changes since 2023-10-01: Fixed a bug in SAM output of GSNAP involving hard-clipping Changes since 2023-07-20: Restored non-SIMD versions of programs Fixed bugs in GMAP coming from alignments beyond the end of a chromosome Implemented SIMD code for approximate intersections In SAM output, MD strings now report N's in the query sequence as mismatches Multiple improvements in speed and accuracy for transcriptome-guided genomic alignment (TGGA) For SAM output from TGGA, distinguishing between short and long cryptic splice sites Changes since 2023-06-01: Fixed bug in GSNAP from aligning across different chromosomes In GSNAP, evaluating whether poly-A regions should be considered in alignment In GSNAP, improved the ability to find fusion alignments In GSNAP, improved outputs in transcriptome-guided genomic alignment Changes since 2023-04-28: Improved transcriptome-guided genomic alignment significantly. Providing velocity assignments in GSNAP SAM output. Extending splices based on transcripts Handling repetitive regions in queries by ignoring them during alignment Allowing splicing within circular chromosomes Changes since 2023-04-20: Improved algorithms in GSNAP for finding fusion alignments Extensively tested the stability of the GSNAP program Fixed issues with excessive memory usage in GSNAP, especially on repetitive reads Changes since 2023-04-12: Fixed issues introduced in 2023-04-12 where GSNAP missed finding some concordant alignments for paired-end reads Fixed reporting of fusion endpoints and MD strings in GSNAP SAM output, and fusion alignments in GSNAP standard output Fixed reporting of intronic alignments in transcriptome-guided genomic alignment Changes since 2023-03-24: Alignments to gene fusions are now reported by GSNAP Restored --min-coverage option to GSNAP and applying it with a default of 0.5 Fixed issue where GSNAP would report insufficient memory on genomes of less than 65536 bp Changes since 2023-02-17: Compilation now works on AVX-512 machines Improvements to speed of GSNAP Changes since 2021-12-17: Complete rewrite of GSNAP, making it much faster and more accurate Compiles and runs on both Intel and Apple ARM (M1/M2) computers GSNAP now has a --two-pass mode, that allows it to learn splice sites, indels, sequence quality, and insert lengths Minor improvements to GMAP, prompted by user suggestions Uses a new genome/transcriptome index format, so it requires re-running gmap_build Some features are not yet supported or are not tested thoroughly More details to come Previously released versions Release notices and bug reports The old listserver mailing list is no longer being supported by EBI. The new mailing list for issues relating to both GMAP and GSNAP is now at Google Groups . To sign up, go to your list , select "All groups and messages", and search for "gsnap-users". Click on that group, and then "Join group". You can join there to receive release notices, ask questions, or see previous messages. If you have a bug to report or a feature to request, I believe you can also send email to gsnap-users@googlegroups.com. (You may have to subscribe to the list first, though, or the message will be held for me to approve) Genome databases You can build your own genome database with the gmap_build program included with this software. Please see instructions in the README file. For the human genome, you may want to retrieve UCSC hg19/GRCh37 Ensembl GRCh37 Documentation README file from the source code distribution. Contains basic usage information. Software demonstration given at ISMB 2005. Contains various examples of GMAP usage. [Slides] References: Thomas D. Wu and Colin K. Watanabe GMAP: a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics 2005 21:1859-1875 [Abstract] [Full Text] Thomas D. Wu and Serban Nacu Fast and SNP-tolerant detection of complex variants and splicing in short reads Bioinformatics 2010 26:873-881 [Abstract] [Full Text] Supplementary information for Bioinformatics 2005 publication on GMAP: Examples (50 KB) (http://research-pub.gene.com/gmap/suppl/examples.tar.gz) Experiment 1 (2.6 MB) (http://research-pub.gene.com/gmap/suppl/ensembl.tar.gz) Experiment 2 (61 MB) (http://research-pub.gene.com/gmap/suppl/ests.tar.gz) Experiment 3 (93 MB) (http://research-pub.gene.com/gmap/suppl/geneseqer.tar.gz) Thomas Wu Last modified: Tue Aug 16 07:49:00 PDT 2011 + +### http://research-pub.gene.com/gmap +GMAP and GSNAP GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program Links are provided below in parentheses for users who wish to download the files with a command-line tool, like wget . Source code for both GMAP and GSNAP Version 2025-07-31 (v2) (http://research-pub.gene.com/gmap/src/gmap-gsnap-2025-07-31.v2.tar.gz). Changes since 2025-07-31: Fixed a fatal bug for potential alignments to the beginning of a genome Changes since 2025-04-19: Fixed a potential infinite loop in GSNAP Fixed the printing of the mate chrpos for nonmappers in GSNAP SAM output Changes since 2025-04-18: Fixed a bug in GSNAP SAM output where the mate chromosome and position of a non-mapping read would sometimes not be printed Changes since 2024-11-20 (v2): Restored and improved upon GSNAP accuracy from 2024-06-24, while incorporating all existing bug fixes and restoring some of the speed of earlier versions Added programs gtf_exons and gff3_exons Changes since 2024-10-20: Fixed a fatal bug in GSNAP relating to alignments before the beginning of a genome Fixed a fatal bug in GSNAP relating to low-quality sequences with an effective query length of zero Made changes to the finding of splices between paired-end reads Changes since 2024-10-10: Eliminated a long-standing memory leak Fixed a fatal bug in GSNAP relating to long segments being explored with localdb Fixed issues with coordinates in alignments to circular chromosomes Changes since 2024-09-18: Fixes to fatal bugs in GSNAP when dealing with alignments at the beginning of the genome Reusing memory in GSNAP, which helps speed up performance Further improvements in splicing in GSNAP on the insides of paired-end reads Improvements to read localization for transcriptome-guided alignment Changes since 2024-08-20: Fixes to fatal bugs in GSNAP when dealing with small chromosomes Improvements in splicing in GSNAP, especially on the insides of paired-end reads Improvements to the detection of indels in GSNAP. Using the values of --max-insertions and --max-deletions Restored the option --pairdev in GSNAP, and using that with --pairexpect in paired-end alignment Added the option --align-fraction to GMAP and GSNAP, which aligns only a fraction of the given reads, selected randomly Changes since 2024-08-14: Improvements and fixes made in --two-pass mode for GSNAP For transcriptomes, gmap_build now puts link files under the transcriptome db, rather than the genome db The flag -C can now be used in gmap_build to specify a location for the transcriptome db Changes since 2024-06-24: For GSNAP, implemented --splices-dump to produce a splice junctions file that matches that of STAR For GSNAP, also implemented --splices-read, --splices-noeval, and --splices-include-known Improvements in splicing in --two-pass mode in GSNAP Improvements in transcriptome-guided genomic alignment in GSNAP For SAM output of GSNAP, changed name of XM field to be MC for mate cigar Improved choice between insertion and deletions at a given position to consider the indel length For overlapping paired-end alignments, checking that the overlapping nucleotide sequences match Fixed gff3_genes to work on NCBI gff3 files as well as Ensembl Changes since 2024-05-20: Improvements to splice identification in GSNAP Splice identification looking specifically for AT-AC as well as GT-AG and GC-AG introns Changes since 2024-05-07: Extensive revisions in GSNAP to improve the accuracy of alignment Changes since 2024-03-15: Fixed a fatal bug from trimming single-exon alignments near chromosomal bounds Removing duplicate transcripts in transcriptome-guided genomic alignment Changes since 2024-02-02: Improvements in finding long indels Improvements in alignments of overlapping paired-end reads Improvements in transcriptome-guided genomic alignment Restored sub: field in standard GSNAP output Changes since 2023-12-01: Fixed fatal bug on highly repetitive reads Rewrite to improve accuracy of read alignment Improvements to splice calling and to resolution of inner splicing Changes since 2023-10-10: Major rewrite of GSNAP to improve speed Changes since 2023-10-10: Fixed a bug in GSNAP allowing alignments to extend past the beginning or end of a chromosome Fixed a bug in SAM output of GSNAP resulting in non-ASCII characters to be generated Fixed a bug in SAM output of GMAP resulting in cigar length to be different from the querylength Changes since 2023-10-01: Fixed a bug in SAM output of GSNAP involving hard-clipping Changes since 2023-07-20: Restored non-SIMD versions of programs Fixed bugs in GMAP coming from alignments beyond the end of a chromosome Implemented SIMD code for approximate intersections In SAM output, MD strings now report N's in the query sequence as mismatches Multiple improvements in speed and accuracy for transcriptome-guided genomic alignment (TGGA) For SAM output from TGGA, distinguishing between short and long cryptic splice sites Changes since 2023-06-01: Fixed bug in GSNAP from aligning across different chromosomes In GSNAP, evaluating whether poly-A regions should be considered in alignment In GSNAP, improved the ability to find fusion alignments In GSNAP, improved outputs in transcriptome-guided genomic alignment Changes since 2023-04-28: Improved transcriptome-guided genomic alignment significantly. Providing velocity assignments in GSNAP SAM output. Extending splices based on transcripts Handling repetitive regions in queries by ignoring them during alignment Allowing splicing within circular chromosomes Changes since 2023-04-20: Improved algorithms in GSNAP for finding fusion alignments Extensively tested the stability of the GSNAP program Fixed issues with excessive memory usage in GSNAP, especially on repetitive reads Changes since 2023-04-12: Fixed issues introduced in 2023-04-12 where GSNAP missed finding some concordant alignments for paired-end reads Fixed reporting of fusion endpoints and MD strings in GSNAP SAM output, and fusion alignments in GSNAP standard output Fixed reporting of intronic alignments in transcriptome-guided genomic alignment Changes since 2023-03-24: Alignments to gene fusions are now reported by GSNAP Restored --min-coverage option to GSNAP and applying it with a default of 0.5 Fixed issue where GSNAP would report insufficient memory on genomes of less than 65536 bp Changes since 2023-02-17: Compilation now works on AVX-512 machines Improvements to speed of GSNAP Changes since 2021-12-17: Complete rewrite of GSNAP, making it much faster and more accurate Compiles and runs on both Intel and Apple ARM (M1/M2) computers GSNAP now has a --two-pass mode, that allows it to learn splice sites, indels, sequence quality, and insert lengths Minor improvements to GMAP, prompted by user suggestions Uses a new genome/transcriptome index format, so it requires re-running gmap_build Some features are not yet supported or are not tested thoroughly More details to come Previously released versions Release notices and bug reports The old listserver mailing list is no longer being supported by EBI. The new mailing list for issues relating to both GMAP and GSNAP is now at Google Groups . To sign up, go to your list , select "All groups and messages", and search for "gsnap-users". Click on that group, and then "Join group". You can join there to receive release notices, ask questions, or see previous messages. If you have a bug to report or a feature to request, I believe you can also send email to gsnap-users@googlegroups.com. (You may have to subscribe to the list first, though, or the message will be held for me to approve) Genome databases You can build your own genome database with the gmap_build program included with this software. Please see instructions in the README file. For the human genome, you may want to retrieve UCSC hg19/GRCh37 Ensembl GRCh37 Documentation README file from the source code distribution. Contains basic usage information. Software demonstration given at ISMB 2005. Contains various examples of GMAP usage. [Slides] References: Thomas D. Wu and Colin K. Watanabe GMAP: a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics 2005 21:1859-1875 [Abstract] [Full Text] Thomas D. Wu and Serban Nacu Fast and SNP-tolerant detection of complex variants and splicing in short reads Bioinformatics 2010 26:873-881 [Abstract] [Full Text] Supplementary information for Bioinformatics 2005 publication on GMAP: Examples (50 KB) (http://research-pub.gene.com/gmap/suppl/examples.tar.gz) Experiment 1 (2.6 MB) (http://research-pub.gene.com/gmap/suppl/ensembl.tar.gz) Experiment 2 (61 MB) (http://research-pub.gene.com/gmap/suppl/ests.tar.gz) Experiment 3 (93 MB) (http://research-pub.gene.com/gmap/suppl/geneseqer.tar.gz) Thomas Wu Last modified: Tue Aug 16 07:49:00 PDT 2011 + +### http://research-pub.gene.com/gmap +GMAP and GSNAP GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program Links are provided below in parentheses for users who wish to download the files with a command-line tool, like wget . Source code for both GMAP and GSNAP Version 2025-07-31 (v2) (http://research-pub.gene.com/gmap/src/gmap-gsnap-2025-07-31.v2.tar.gz). Changes since 2025-07-31: Fixed a fatal bug for potential alignments to the beginning of a genome Changes since 2025-04-19: Fixed a potential infinite loop in GSNAP Fixed the printing of the mate chrpos for nonmappers in GSNAP SAM output Changes since 2025-04-18: Fixed a bug in GSNAP SAM output where the mate chromosome and position of a non-mapping read would sometimes not be printed Changes since 2024-11-20 (v2): Restored and improved upon GSNAP accuracy from 2024-06-24, while incorporating all existing bug fixes and restoring some of the speed of earlier versions Added programs gtf_exons and gff3_exons Changes since 2024-10-20: Fixed a fatal bug in GSNAP relating to alignments before the beginning of a genome Fixed a fatal bug in GSNAP relating to low-quality sequences with an effective query length of zero Made changes to the finding of splices between paired-end reads Changes since 2024-10-10: Eliminated a long-standing memory leak Fixed a fatal bug in GSNAP relating to long segments being explored with localdb Fixed issues with coordinates in alignments to circular chromosomes Changes since 2024-09-18: Fixes to fatal bugs in GSNAP when dealing with alignments at the beginning of the genome Reusing memory in GSNAP, which helps speed up performance Further improvements in splicing in GSNAP on the insides of paired-end reads Improvements to read localization for transcriptome-guided alignment Changes since 2024-08-20: Fixes to fatal bugs in GSNAP when dealing with small chromosomes Improvements in splicing in GSNAP, especially on the insides of paired-end reads Improvements to the detection of indels in GSNAP. Using the values of --max-insertions and --max-deletions Restored the option --pairdev in GSNAP, and using that with --pairexpect in paired-end alignment Added the option --align-fraction to GMAP and GSNAP, which aligns only a fraction of the given reads, selected randomly Changes since 2024-08-14: Improvements and fixes made in --two-pass mode for GSNAP For transcriptomes, gmap_build now puts link files under the transcriptome db, rather than the genome db The flag -C can now be used in gmap_build to specify a location for the transcriptome db Changes since 2024-06-24: For GSNAP, implemented --splices-dump to produce a splice junctions file that matches that of STAR For GSNAP, also implemented --splices-read, --splices-noeval, and --splices-include-known Improvements in splicing in --two-pass mode in GSNAP Improvements in transcriptome-guided genomic alignment in GSNAP For SAM output of GSNAP, changed name of XM field to be MC for mate cigar Improved choice between insertion and deletions at a given position to consider the indel length For overlapping paired-end alignments, checking that the overlapping nucleotide sequences match Fixed gff3_genes to work on NCBI gff3 files as well as Ensembl Changes since 2024-05-20: Improvements to splice identification in GSNAP Splice identification looking specifically for AT-AC as well as GT-AG and GC-AG introns Changes since 2024-05-07: Extensive revisions in GSNAP to improve the accuracy of alignment Changes since 2024-03-15: Fixed a fatal bug from trimming single-exon alignments near chromosomal bounds Removing duplicate transcripts in transcriptome-guided genomic alignment Changes since 2024-02-02: Improvements in finding long indels Improvements in alignments of overlapping paired-end reads Improvements in transcriptome-guided genomic alignment Restored sub: field in standard GSNAP output Changes since 2023-12-01: Fixed fatal bug on highly repetitive reads Rewrite to improve accuracy of read alignment Improvements to splice calling and to resolution of inner splicing Changes since 2023-10-10: Major rewrite of GSNAP to improve speed Changes since 2023-10-10: Fixed a bug in GSNAP allowing alignments to extend past the beginning or end of a chromosome Fixed a bug in SAM output of GSNAP resulting in non-ASCII characters to be generated Fixed a bug in SAM output of GMAP resulting in cigar length to be different from the querylength Changes since 2023-10-01: Fixed a bug in SAM output of GSNAP involving hard-clipping Changes since 2023-07-20: Restored non-SIMD versions of programs Fixed bugs in GMAP coming from alignments beyond the end of a chromosome Implemented SIMD code for approximate intersections In SAM output, MD strings now report N's in the query sequence as mismatches Multiple improvements in speed and accuracy for transcriptome-guided genomic alignment (TGGA) For SAM output from TGGA, distinguishing between short and long cryptic splice sites Changes since 2023-06-01: Fixed bug in GSNAP from aligning across different chromosomes In GSNAP, evaluating whether poly-A regions should be considered in alignment In GSNAP, improved the ability to find fusion alignments In GSNAP, improved outputs in transcriptome-guided genomic alignment Changes since 2023-04-28: Improved transcriptome-guided genomic alignment significantly. Providing velocity assignments in GSNAP SAM output. Extending splices based on transcripts Handling repetitive regions in queries by ignoring them during alignment Allowing splicing within circular chromosomes Changes since 2023-04-20: Improved algorithms in GSNAP for finding fusion alignments Extensively tested the stability of the GSNAP program Fixed issues with excessive memory usage in GSNAP, especially on repetitive reads Changes since 2023-04-12: Fixed issues introduced in 2023-04-12 where GSNAP missed finding some concordant alignments for paired-end reads Fixed reporting of fusion endpoints and MD strings in GSNAP SAM output, and fusion alignments in GSNAP standard output Fixed reporting of intronic alignments in transcriptome-guided genomic alignment Changes since 2023-03-24: Alignments to gene fusions are now reported by GSNAP Restored --min-coverage option to GSNAP and applying it with a default of 0.5 Fixed issue where GSNAP would report insufficient memory on genomes of less than 65536 bp Changes since 2023-02-17: Compilation now works on AVX-512 machines Improvements to speed of GSNAP Changes since 2021-12-17: Complete rewrite of GSNAP, making it much faster and more accurate Compiles and runs on both Intel and Apple ARM (M1/M2) computers GSNAP now has a --two-pass mode, that allows it to learn splice sites, indels, sequence quality, and insert lengths Minor improvements to GMAP, prompted by user suggestions Uses a new genome/transcriptome index format, so it requires re-running gmap_build Some features are not yet supported or are not tested thoroughly More details to come Previously released versions Release notices and bug reports The old listserver mailing list is no longer being supported by EBI. The new mailing list for issues relating to both GMAP and GSNAP is now at Google Groups . To sign up, go to your list , select "All groups and messages", and search for "gsnap-users". Click on that group, and then "Join group". You can join there to receive release notices, ask questions, or see previous messages. If you have a bug to report or a feature to request, I believe you can also send email to gsnap-users@googlegroups.com. (You may have to subscribe to the list first, though, or the message will be held for me to approve) Genome databases You can build your own genome database with the gmap_build program included with this software. Please see instructions in the README file. For the human genome, you may want to retrieve UCSC hg19/GRCh37 Ensembl GRCh37 Documentation README file from the source code distribution. Contains basic usage information. Software demonstration given at ISMB 2005. Contains various examples of GMAP usage. [Slides] References: Thomas D. Wu and Colin K. Watanabe GMAP: a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics 2005 21:1859-1875 [Abstract] [Full Text] Thomas D. Wu and Serban Nacu Fast and SNP-tolerant detection of complex variants and splicing in short reads Bioinformatics 2010 26:873-881 [Abstract] [Full Text] Supplementary information for Bioinformatics 2005 publication on GMAP: Examples (50 KB) (http://research-pub.gene.com/gmap/suppl/examples.tar.gz) Experiment 1 (2.6 MB) (http://research-pub.gene.com/gmap/suppl/ensembl.tar.gz) Experiment 2 (61 MB) (http://research-pub.gene.com/gmap/suppl/ests.tar.gz) Experiment 3 (93 MB) (http://research-pub.gene.com/gmap/suppl/geneseqer.tar.gz) Thomas Wu Last modified: Tue Aug 16 07:49:00 PDT 2011 + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gmap --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +gmap 2014.12.23 pl5.22.0_1 +-------------------------- +file name : gmap-2014.12.23-pl5.22.0_1.tar.bz2 +name : gmap +version : 2014.12.23 +build : pl5.22.0_1 +build number: 1 +size : 20.0 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2014.12.23-pl5.22.0_1.tar.bz2 +md5 : b6d881d8cc9d82027415bc025418d3b7 +dependencies: + - perl 5.22.0* + + +gmap 2014.12.23 pl5.22.0_2 +-------------------------- +file name : gmap-2014.12.23-pl5.22.0_2.tar.bz2 +name : gmap +version : 2014.12.23 +build : pl5.22.0_2 +build number: 2 +size : 19.5 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2014.12.23-pl5.22.0_2.tar.bz2 +md5 : 235e06e0512580dbbfa10dd96496638a +dependencies: + - perl 5.22.0* + - zlib + + +gmap 2014.12.23 pl5.22.0_3 +-------------------------- +file name : gmap-2014.12.23-pl5.22.0_3.tar.bz2 +name : gmap +version : 2014.12.23 +build : pl5.22.0_3 +build number: 3 +size : 19.0 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2014.12.23-pl5.22.0_3.tar.bz2 +md5 : 384e8e8b5df195cfa39be6b5d869c192 +dependencies: + - perl 5.22.0* + - zlib + + +gmap 2014.12.23 pl5.22.0_4 +-------------------------- +file name : gmap-2014.12.23-pl5.22.0_4.tar.bz2 +name : gmap +version : 2014.12.23 +build : pl5.22.0_4 +build number: 4 +size : 19.0 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2014.12.23-pl5.22.0_4.tar.bz2 +md5 : de5111580e9c503650169066abac6644 +dependencies: + - perl 5.22.0* + - zlib 1.2.11* + + +gmap 2014.12.23 pl526h1341992_5 +------------------------------- +file name : gmap-2014.12.23-pl526h1341992_5.tar.bz2 +name : gmap +version : 2014.12.23 +build : pl526h1341992_5 +build number: 5 +size : 19.0 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2014.12.23-pl526h1341992_5.tar.bz2 +md5 : 292c37f3ae61ffe2b22528e86249db93 +timestamp : 2018-07-06 18:58:43 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gmap 2014.12.23 pl526h1341992_6 +------------------------------- +file name : gmap-2014.12.23-pl526h1341992_6.tar.bz2 +name : gmap +version : 2014.12.23 +build : pl526h1341992_6 +build number: 6 +size : 19.0 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2014.12.23-pl526h1341992_6.tar.bz2 +md5 : c4f5838ff5ede5a7e19e20f382549a22 +timestamp : 2019-03-09 17:59:29 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gmap 2014.12.28 pl526h1341992_5 +------------------------------- +file name : gmap-2014.12.28-pl526h1341992_5.tar.bz2 +name : gmap +version : 2014.12.28 +build : pl526h1341992_5 +build number: 5 +size : 19.0 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2014.12.28-pl526h1341992_5.tar.bz2 +md5 : f0edbad6c78be706b04bf1acbdb17d12 +timestamp : 2018-08-06 09:59:31 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gmap 2014.12.28 pl526h1341992_6 +------------------------------- +file name : gmap-2014.12.28-pl526h1341992_6.tar.bz2 +name : gmap +version : 2014.12.28 +build : pl526h1341992_6 +build number: 6 +size : 19.0 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2014.12.28-pl526h1341992_6.tar.bz2 +md5 : d17574e7cc015ddd21f9b64417123aeb +timestamp : 2019-03-09 18:16:02 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +gmap 2015.09.10 0 +----------------- +file name : gmap-2015.09.10-0.tar.bz2 +name : gmap +version : 2015.09.10 +build : 0 +build number: 0 +size : 24.3 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2015.09.10-0.tar.bz2 +md5 : 4677a7c6c00d71b4aea5bb2a7572e0f9 +dependencies: [] + + +gmap 2015.09.10 1 +----------------- +file name : gmap-2015.09.10-1.tar.bz2 +name : gmap +version : 2015.09.10 +build : 1 +build number: 1 +size : 19.5 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2015.09.10-1.tar.bz2 +md5 : 3d69836357d692e704a8475107e1980e +dependencies: + - perl-threaded + + +gmap 2015.09.10 pl526_2 +----------------------- +file name : gmap-2015.09.10-pl526_2.tar.bz2 +name : gmap +version : 2015.09.10 +build : pl526_2 +build number: 2 +size : 19.5 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2015.09.10-pl526_2.tar.bz2 +md5 : 6b93e97799c4fe001fd8cc2628ba7110 +timestamp : 2018-07-06 18:39:40 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +gmap 2015.12.31 h2f06484_3 +-------------------------- +file name : gmap-2015.12.31-h2f06484_3.tar.bz2 +name : gmap +version : 2015.12.31 +build : h2f06484_3 +build number: 3 +size : 21.8 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2015.12.31-h2f06484_3.tar.bz2 +md5 : fc1b8dfc72fb2d9c63f761414c43f151 +timestamp : 2020-07-03 03:47:11 UTC +dependencies: + - bzip2 + - libgcc-ng >=7.5.0 + - perl + - zlib + + +gmap 2015.12.31 h2f06484_4 +-------------------------- +file name : gmap-2015.12.31-h2f06484_4.tar.bz2 +name : gmap +version : 2015.12.31 +build : h2f06484_4 +build number: 4 +size : 21.8 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2015.12.31-h2f06484_4.tar.bz2 +md5 : 39935e7e72d8528647546b242abf737d +timestamp : 2020-07-09 23:10:08 UTC +dependencies: + - bzip2 + - libgcc-ng >=7.5.0 + - perl + - zlib + + +gmap 2015.12.31 h2f06484_5 +-------------------------- +file name : gmap-2015.12.31-h2f06484_5.tar.bz2 +name : gmap +version : 2015.12.31 +build : h2f06484_5 +build number: 5 +size : 21.8 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2015.12.31-h2f06484_5.tar.bz2 +md5 : 70f5699afc040593d2a64d3ecac5a3ca +timestamp : 2020-07-26 00:39:55 UTC +dependencies: + - bzip2 + - libgcc-ng >=7.5.0 + - perl + - zlib + + +gmap 2015.12.31 he4cf2ce_2 +-------------------------- +file name : gmap-2015.12.31-he4cf2ce_2.tar.bz2 +name : gmap +version : 2015.12.31 +build : he4cf2ce_2 +build number: 2 +size : 19.2 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2015.12.31-he4cf2ce_2.tar.bz2 +md5 : da18ae411719eb845e4bd53b594e6785 +timestamp : 2018-07-06 19:11:12 UTC +dependencies: + - bzip2 + - libgcc-ng >=4.9 + - perl + - zlib + + +gmap 2015.12.31 pl5.22.0_0 +-------------------------- +file name : gmap-2015.12.31-pl5.22.0_0.tar.bz2 +name : gmap +version : 2015.12.31 +build : pl5.22.0_0 +build number: 0 +size : 19.4 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2015.12.31-pl5.22.0_0.tar.bz2 +md5 : d78e46716d30434131e1eb75c62e9cb5 +dependencies: + - bzip2 + - libgcc + - perl 5.22.0* + - zlib + + +gmap 2015.12.31 pl5.22.0_1 +-------------------------- +file name : gmap-2015.12.31-pl5.22.0_1.tar.bz2 +name : gmap +version : 2015.12.31 +build : pl5.22.0_1 +build number: 1 +size : 19.4 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2015.12.31-pl5.22.0_1.tar.bz2 +md5 : f387ffe97e71699f869caca0b2118a2c +dependencies: + - bzip2 1.0* + - libgcc + - perl 5.22.0* + - zlib 1.2.8* + + +gmap 2016.09.23 0 +----------------- +file name : gmap-2016.09.23-0.tar.bz2 +name : gmap +version : 2016.09.23 +build : 0 +build number: 0 +size : 31.7 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2016.09.23-0.tar.bz2 +md5 : 0201db912321a61be6c31c1de6607ef0 +dependencies: [] + + +gmap 2016.09.23 1 +----------------- +file name : gmap-2016.09.23-1.tar.bz2 +name : gmap +version : 2016.09.23 +build : 1 +build number: 1 +size : 31.7 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2016.09.23-1.tar.bz2 +md5 : 1623f1a8facba9e1bf44d45c5a3b1eb9 +dependencies: + - perl-threaded + + +gmap 2016.09.23 pl526_2 +----------------------- +file name : gmap-2016.09.23-pl526_2.tar.bz2 +name : gmap +version : 2016.09.23 +build : pl526_2 +build number: 2 +size : 31.8 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2016.09.23-pl526_2.tar.bz2 +md5 : 3791334ed798516e8c03f19833c4b8d8 +timestamp : 2018-07-06 19:38:29 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +gmap 2016.09.23 pl526_3 +----------------------- +file name : gmap-2016.09.23-pl526_3.tar.bz2 +name : gmap +version : 2016.09.23 +build : pl526_3 +build number: 3 +size : 31.8 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2016.09.23-pl526_3.tar.bz2 +md5 : 6ac5e5220e4233149646201814731031 +timestamp : 2019-03-09 18:10:16 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +gmap 2017.02.15 1 +----------------- +file name : gmap-2017.02.15-1.tar.bz2 +name : gmap +version : 2017.02.15 +build : 1 +build number: 1 +size : 31.8 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2017.02.15-1.tar.bz2 +md5 : ad8daf0d2973009bed17611ceb40cba0 +dependencies: + - perl-threaded + + +gmap 2017.02.15 pl5.22.0_2 +-------------------------- +file name : gmap-2017.02.15-pl5.22.0_2.tar.bz2 +name : gmap +version : 2017.02.15 +build : pl5.22.0_2 +build number: 2 +size : 31.8 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2017.02.15-pl5.22.0_2.tar.bz2 +md5 : 63c4a784c9156e015fdc7538efad7ec9 +dependencies: + - perl 5.22.0* + + +gmap 2017.02.15 pl526_3 +----------------------- +file name : gmap-2017.02.15-pl526_3.tar.bz2 +name : gmap +version : 2017.02.15 +build : pl526_3 +build number: 3 +size : 31.8 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2017.02.15-pl526_3.tar.bz2 +md5 : 82cf5ff147809b11a3a08dfe3e68ab28 +timestamp : 2018-07-06 19:20:47 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +gmap 2017.05.08 h2f06484_4 +-------------------------- +file name : gmap-2017.05.08-h2f06484_4.tar.bz2 +name : gmap +version : 2017.05.08 +build : h2f06484_4 +build number: 4 +size : 35.0 MB +license : Non-commercial +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gmap-2017.05.08-h2f06484_4.tar.bz2 +md5 : 59b28c3303191ba4e2f28db32c791d27 +timestamp : 2020-07-03 03:56:58 UTC +dependencies: + - bzip2 + - libgcc-ng >=7.5.0 + - perl + - zlib + + +gmap 2017.05.08 h2f06484_5 +-------------------------- +file name : gmap-2017.05.08-h2f06 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gofasta.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gofasta.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2618500cc7870a1a4d6df186960df973f473afa4 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gofasta.manual_bundle.txt @@ -0,0 +1,312 @@ +# Tool: gofasta +software_name: gofasta +tier: T1 +domain: t1_backfill_overall +downloads: 205031 +summary: Genomic epidemiology utilities for short genome alignments +description: Genomic epidemiology utilities for short genome alignments +dependencies: +execution_environment: Other +execution_environment_reason: fallback runtime classification + +## URLs +home_url: https://github.com/cov-ert/gofasta +doc_url: +dev_url: + +## CLI Help Source +cli:gofasta +## CLI Help Content +$ conda run -n bioenv_cli gofasta --help +[rc=0] +Command-line utilities for genomic epidemiology research + +If you use gofasta in your work, please cite: + +Jackson B (2022). gofasta: command-line utilities for genomic epidemiology research. Bioinformatics 38 (16), 4033-4035 +https://doi.org/10.1093/bioinformatics/btac424 + +Usage: + gofasta [command] + +Available Commands: + closest Find the closest sequence(s) to a query by genetic distance + completion Generate the autocompletion script for the specified shell + help Help about any command + licences Print licence information + sam Do things with sam files + snps Find snps relative to a reference + updown Get pseudo-tree-aware catchments for query sequences from alignments + variants Annotate mutations relative to a reference from a multiple sequence alignment in fasta format + +Flags: + -h, --help help for gofasta + -v, --version version for gofasta + +Use "gofasta [command] --help" for more information about a command. + + + +## URL Docs Extract +### https://github.com/cov-ert/gofasta +GitHub - virus-evolution/gofasta · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} virus-evolution / gofasta Public Notifications You must be signed in to change notification settings Fork 4 Star 38 Code Issues 3 Pull requests 3 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights virus-evolution/gofasta master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 234 Commits 234 Commits .github .github THIRD_PARTY_LICENCES THIRD_PARTY_LICENCES cmd cmd pkg pkg resources resources .gitignore .gitignore LICENSE LICENSE README.md README.md go.mod go.mod go.sum go.sum main.go main.go View all files Repository files navigation README MIT license gofasta gofasta is a command-line utility developed to handle SARS-CoV-2 alignments, but should be useful more generally for handling consensus genomes of any microbial pathogen. It has been used on datasets of millions of sequences, including by the United Kingdom's daily SARS-CoV-2 genome processing pipelines , Pangolin and Civet . If you use gofasta in your work, please cite https://doi.org/10.1093/bioinformatics/btac424 . Installation You can install gofasta from Bioconda: conda install bioconda::gofasta If you have Go installed, you can run go install github.com/virus-evolution/gofasta@latest to build a binary of the latest release locally (maybe in ~/go/bin/ ). Branches, commits or tags other than latest can be built in the same way. You can also build the contents of this repository: git clone https://github.com/virus-evolution/gofasta.git cd gofasta go build -o gofasta Commands For a full list of commands and options, you can run gofasta with the -h flag at the command line: gofasta -h , gofasta sam -h , gofasta sam variants -h , etc. e.g., for gofasta updown list -h : Click to see the help message ❯ gofasta updown list -h Generate input CSV files for gofasta updown topranking Example usage: gofasta updown list -r reference.fasta -q alignment.fasta -o mutationlist.csv Non-ATGC nucleotides are not recommended in the --reference, and --reference and --query must be aligned to the same thing. --outfile is a CSV-format file with the columns: query,SNPs,ambiguities,SNPcount,ambcount. There is one row for each sequence in --query. SNPs is a "|"-delimited list of SNPs relative to --reference. ambiguities is a "|"-delimited list of ranges (1-based, inclusive) of tracts of ambiguities (anything that isn't ATGC). Usage: gofasta updown list [flags] Flags: -q, --query string Alignment of sequences to parse, in fasta format (default "stdin") -o, --outfile string Output to write (default "stdout") -h, --help help for list Global Flags: -r, --reference string Reference sequence, in fasta format, which is treated as the root of the imaginary tree Usage Sam to fasta format conversion minimap2 provides fast and reliable pairwise alignments between SARS-CoV-2 consensus genomes. gofasta provides utility functions to convert the sam format alignments it outputs into fasta format. Pairwise alignments are less computationally demanding than multiple sequence alignment-proper and they offer an efficient approximation to it when sequences are closely related. Making a single alignment with multiple sequences This is the pipeline currently used by Pangolin : minimap2 -a -x asm20 --sam-hit-only --secondary=no --score-N=0 MN908947.fa unaligned.consensus.fasta -o aligned.sam gofasta sam toMultiAlign -s aligned.sam --start 266 --end 29674 --pad -o aligned.fasta MN908947.fa is the reference genome for SARS-CoV-2 (here is its Genbank accession ), and unaligned.consensus.fasta contains all your consensus genomes (in one file). In this case we've clipped the alignment to just the coding sequence ( --start 266 --end 29674 ) but replaced the trimmed regions with N s to retain the reference length in the output ( --pad ). Insertions relative to the reference are discarded from the output file so everything is the same (== reference) length. minimap2 and gofasta can both make use of multiple threads. Additionally, minimap2 writes to stdout by default and gofasta reads from stdin if we don't specify a file for -s , so we can avoid writing the intermediate sam to disk entirely. Both of these should speed things up: minimap2 -t8 -a -x asm20 --score-N=0 MN908947.fa unaligned.consensus.fasta | gofasta sam toma -t2 > aligned.fasta We give minimap2 more threads here because it's doing more work. toma is just an alias for toMultiAlign . But I don't want to have to write all this code every time I want to align something . That's understandable. In which case you could define a shell function in your ~/.zshrc or ~/.bashrc file, something like: function align() { minimap2 -a -x asm20 --score-N=0 ~/path/to/MN908947.fa $1 | gofasta sam toma } and then you can run align unaligned.consensus.fasta > aligned.fasta in your terminal. Making pairwise alignments (including insertions) gofasta will also convert the minimap2 alignment into pairwise alignments, writing one file per consensus genome, including insertions relative to the reference and writing the reference itself to the output files: minimap2 -a -x asm20 --score-N=0 MN908947.fa unaligned.consensus.fasta |\ gofasta sam toPairAlign -r MN908947.fa -o outputdir outputdir is a directory which will be created if it does not already exist. Individual fasta files will be written to outputdir/*fasta . Filenames are derived from the fasta descriptions (with / replaced by _ ). Just as with toMultiAlign , you can clip the alignments to coordinates of your choosing. For example, if you are only interested in the Spike region: minimap2 -a -x asm20 --score-N=0 MN908947.fa unaligned.consensus.fasta |\ gofasta sam topa -r MN908947.fa --start 21563 --end 25384 -o outputdir --start and --end are 1-based inclusive, and they are in reference coordinates . So you will get the region corresponding to the reference Spike regardless of insertions or deletions anywhere in your query genome. There is no --pad option for toPairAlign because we don't expect all the sequences to be reference length. Searching for neighbours by genetic distance gofasta provides two utilities to search for the closest genetic neighbours of a number of query sequences among a set of target sequences. In both cases the queries are loaded into memory and the targets are streamed from disk, so the target file can be arbitrarily large. Traditional distance measures Use gofasta closest to find the closest neighbours by traditional genetic distance measures: ❯ gofasta closest --help | sed -n '/Flags/,$p' Flags: -t, --threads int Number of CPUs to use (Default: all available CPUs) --query string Alignment of sequences to find neighbours for, in fasta format --target string Alignment of sequences to search for neighbours in, in fasta format -m, --measure string which distance measure to use (raw, snp or tn93) (default "raw") -n, --number int (Optional) the closest n sequences to each query will be returned -d, --max-dist string (Optional) return all sequences less than or equal to this distance away -o, --outfile string The output file to write (default "stdout") --table write a long-form table of the output -h, --help help for closest The available distance measures are raw (the default) which is the number of nucleotide differences per site ; snp , which is the total number of nucleotide differences, and tn93 , which is Tamura and Nei's (1993) evolutionary distance . raw distance is calculated as: l_d / (l_d + l_s) , where l_d is the number of sites which are certainly different between two sequences and l_s is the number of sites which are certainly the same. snp distance = l_d . For both the raw and snp distances, ambiguous IUPAC codes are treated as the set of bases that they represent. tn93 distance is calculated according to equation (7) in the paper . Only ATGC bases are considered when calculating this measure. The routine is parallelised across queries, so there is no point setting -t greater than the number of sequences in --query . Directional snp-distance Use gofasta updown topranking to find the closest neighbours by (directional) snp distance. This is the routine used by Civet3 : ❯ gofasta updown topranking -h | sed -n '/Flags/,$p' Flags: -q, --query string File with sequences to find neighbours for. Either the CSV output of gofasta updown list, or an alignment in fasta format -t, --target string File of sequences to look for neighbours in. Either the CSV output of gofasta updown list, or an alignment in fasta format -o, --outfile string CSV-format file of closest neighbours to write (default "stdout") --table write a long-form table of the output --ignore string Optional plain text file of IDs to ignore in the target file when searching for neighbours --dist-all int Maximum allowed SNP-distance between target and query sequence in any direction. Overrides the settings below --dist-up int Maximum allowed SNP-distance from query for sequences in the parent bin --dist-down int Maximum allowed SNP-distance from query for sequences in the child bin --dist-side int Maximum allowed SNP-distance from query for sequences in the sibling bin --size-total int Max number of neighbours to find (attempts to split equally between same/up/down/side). A hard limit --size-up int Max number of closest parent sequences to find, if size-total not specified. A soft limit unless --no-fill --size-down int Max number of closest child sequences to find, if size-total not specified. A soft limit unless --no-fill --size-side int Max number of closest sibling sequences to find, if size-total not specified. A soft limit unless --no-fill --size-same int Max number of identical sequences to find, if size-total not specified. A soft limit unless --no-fill --threshold-pair float32 Up to this proportion of consequential sites is allowed to be ambiguous in either sequence for each pairwise comparison (default 0.1) --threshold-target int Target can have at most this number of ambiguities to be considered (default 10000) --dist-push int Push the --dist boundaries outwards so that bins have at least these many closest SNP-distances for which there are neighbours, where possible --no-fill Don't make up for a shortfall in any of --size-up, -down, -side or -same by increasing the count for other bins -h, --help help for topranking Global Flags: -r, --reference string Reference sequence, in fasta format, which is treated as the root of the imaginary tree This routine has the potential to be faster than traditional genetic distance measures. It uses patterns of derived mutations to make inferences about the likely phylogenetic relationships between closely related sequences. Briefly, sequences are compressed so that they are represented by only their ATGC nucleotide differences from a common reference sequence, which is treated like the root of an imaginary tree. SNPs can either be unique to the query sequence, unique to the target sequence, or present in the intersection of the two. SNPs present in the intersection are interpreted as representing shared ancestry between query and target, whereas an excess of SNPs in either the query or target set can be interpreted to give directionality relative to a root sequence. See the Civet preprint for a detailed explanation of the scheme (Figure 2 and Figure S1). The input --query and --target files can either be alignments in fasta format, or they can be csv-format files produced by gofasta updown list (or one of each). Using the csv-format files should be faster to the extent that they are quicker to read from disk compared to alignments, which initially contain the information for every site. An example of command-line use and more explanation is available by running gofasta updown topranking --help . Annotating mutations Use gofasta snps to extract nucleotide changes relative to a reference sequence from a multiple sequence alignment, and gofasta variants and gofasta sam variants to extract amino acid, indel and nucleotide changes relative to an annotated reference sequence from alignments in fasta and sam format, respectively. Nucleotide changes gofasta snps will list all the nucleotide changes in a multiple sequence alignment ( --query ) compared to a reference sequence which is provided in a separate file ( --reference ). The two files have to be the same width (i.e. aligned to the same thing). ❯ gofasta snps -h | sed -n '/Flags/,$p' Flags: -r, --reference string Reference sequence, in fasta format -q, --query string Alignment of sequences to find snps in, in fasta format (default "stdin") -o, --outfile string Output to write (default "stdout") --hard-gaps Don't treat alignment gaps as missing data --aggregate Report the proportions of each change --threshold float If --aggregate, only report snps with a freq greater than or equal to this value -h, --help help for snps The basic usage creates a csv file with a header and a line for each sequence in --query . The first column is the sequence name, and the second column is a '|'-delimited list of nucleotide changes who format is: reference allele, 1-based position in alignment coordinates, query allele. IUPAC ambiguity codes are treated as the set of bases that they represent, and only certainly-different changes are reported. For example an output of A101S is possible, but A101W is not. Alignment gaps ( - ) are treated like N s (aNy base) unless you use --hard-gaps . ❯ gofasta snps -r MN908947.fa -q aligned.fasta -o snps.csv ❯ ❯ head -n2 snps.csv query,SNPs query1,T670G|G4184A|C4321T|C9344T|A9424G|C9534T|C10198T|G10447A|C10449A|G12160A|C12880T|C14408T|C15714T|C17410T|C19955T|A20055G|T21570G|C21618T|G21987A|T22200G|G22578A|T22679C|C22686T|A22688G|A23403G|C23525T|T23599G|C23604A|C23854A|G23948T|T24469A|C25000T|C26060T|C26270T|G27382C|A27383T|T27384C|G27788T|C27807T|A28271T|C28311T|C28724T|G28881A|G28882A|G28883C|A29510C If you invoke --aggregate , the proportion of each change in the whole alignment is written. ❯ gofasta snps -r MN908947.fa -q aligned.fasta --aggregate SNP,frequency C44T,0.250000000 C241T,0.750000000 T670G,0.916666667 C1314T,0.083333333 C1613A,0.083333333 C1684T,0.083333333 C2790T,0.833333333 C3037T,0.833333333 ... Amino acid, indel and neutral nucleotide changes If you provide an annotation, gofasta can also annotate amino acid changes relative to a reference sequence. The annotation can be provided in genbank flat file format or gff version 3 format . Examples of both for SARS-CoV-2 are available under resources/ in this repository. The two relevant routines are gofasta variants (for annotating mutations in alignments in fasta format) and gofasta sam variants (for annotating mutations in alignments in sam format). They should give the same output for the same alignment and the same annotation. Multiple sequence alignments in fasta format don't need to be in reference coordinates for gofasta variants , but if they aren't, a sequence in the same space as the annotation must be present in the alignment. If the alignment is being read from stdin, this sequence must be the first sequence in the alignment, but doesn't have to be if the file is being read from disk. The reference sequence in fasta format needs to be provided to gofasta sam variants unless it is present in your annotation. As usual, run either command with the -h flag for example command lines and detailed help. For a genbank format annotation, the annotation will be parsed such that the genome is split into protein-coding regions based on CDS features, and intergenic regions (everything that isn't in CDS). Mutations are then annotated with ins (insertion), del (deletion), aa (amino acid change) or nuc (a nucleotide change that isn't in a codon that is represented by an amino acid change) - for the last one these can be in intergenic sequence, or they can be synonymous changes in CDS. gff format annotation gives you more flexibility for naming amino acid changes. Currently, the annotation will be parsed such that the genome is split into protein-coding regions based on feature lines whose type (in column 3) is either CDS or mature_protein_region_of_CDS , and intergenic regions (everything else). For the purposes of annotating amino acids, CDS or mature_protein_region_of_CDS feature lines that have a Name=something tag,value pair in the attributes column (column 9) will be represented in the output. Thus you can define regions as protein-coding using a CDS feature line (for example orf1a in SARS-CoV-2) but annotate amino acid changes in its constituent protein products using mature_protein_region_of_CDS feature lines with Name= attributes. See the example Examples of the output formats: ins:2028:3 - a 3-base insertion immediately after (1-based) position 2028 in reference coordinates del:11288:9 - a 9-base deletion whose first missing nucleotide is at (1-based) position 11288 in reference coordinates aa:S:D614G - the amino acid at (1-based) residue 614 in the S gene is a D in the reference and a G in this sequence aa:nsp12:P323L - the amino acid at (1-based) residue 323 in the rdrp gene is a P in the reference and an L in this sequence nuc:C3037T - the nucleotide at (1-based) position 3037 in reference coordinates is a C in the reference and a T in this sequence As with gofasta snps the default mode writes a csv with one line per query sequence, and each sequence's mutations in the second column. Use --aggregate to get the overall frequencies of + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gofasta --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +gofasta 0.0.1 0 +--------------- +file name : gofasta-0.0.1-0.tar.bz2 +name : gofasta +version : 0.0.1 +build : 0 +build number: 0 +size : 2.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-0.0.1-0.tar.bz2 +md5 : 05804eefb61d083b8653133f1ec7eb48 +timestamp : 2020-10-14 09:48:18 UTC +dependencies: [] + + +gofasta 0.0.2 0 +--------------- +file name : gofasta-0.0.2-0.tar.bz2 +name : gofasta +version : 0.0.2 +build : 0 +build number: 0 +size : 2.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-0.0.2-0.tar.bz2 +md5 : 0287faf0433aad05c57a473b15dd7688 +timestamp : 2021-01-25 10:00:14 UTC +dependencies: [] + + +gofasta 0.0.3 0 +--------------- +file name : gofasta-0.0.3-0.tar.bz2 +name : gofasta +version : 0.0.3 +build : 0 +build number: 0 +size : 2.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-0.0.3-0.tar.bz2 +md5 : 2c2e89962a2cdb0c3a49951c0d26e812 +timestamp : 2021-02-01 17:21:03 UTC +dependencies: [] + + +gofasta 0.0.3 h9ee0642_1 +------------------------ +file name : gofasta-0.0.3-h9ee0642_1.tar.bz2 +name : gofasta +version : 0.0.3 +build : h9ee0642_1 +build number: 1 +size : 2.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-0.0.3-h9ee0642_1.tar.bz2 +md5 : fb347db92c6094d744caa93070311f4b +timestamp : 2021-03-26 17:09:23 UTC +dependencies: [] + + +gofasta 0.0.4 h9ee0642_0 +------------------------ +file name : gofasta-0.0.4-h9ee0642_0.tar.bz2 +name : gofasta +version : 0.0.4 +build : h9ee0642_0 +build number: 0 +size : 2.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-0.0.4-h9ee0642_0.tar.bz2 +md5 : 1f929f05dd70fb1faaf0973127006351 +timestamp : 2021-05-14 16:23:55 UTC +dependencies: [] + + +gofasta 0.0.5 h9ee0642_0 +------------------------ +file name : gofasta-0.0.5-h9ee0642_0.tar.bz2 +name : gofasta +version : 0.0.5 +build : h9ee0642_0 +build number: 0 +size : 2.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-0.0.5-h9ee0642_0.tar.bz2 +md5 : c5bff314877ce18d044cbf7974a48336 +timestamp : 2021-07-13 14:16:17 UTC +dependencies: [] + + +gofasta 0.0.6 h9ee0642_0 +------------------------ +file name : gofasta-0.0.6-h9ee0642_0.tar.bz2 +name : gofasta +version : 0.0.6 +build : h9ee0642_0 +build number: 0 +size : 2.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-0.0.6-h9ee0642_0.tar.bz2 +md5 : 860cac5c22998b1d1893af09eb20b165 +timestamp : 2021-12-06 16:26:10 UTC +dependencies: [] + + +gofasta 0.0.6 h9ee0642_1 +------------------------ +file name : gofasta-0.0.6-h9ee0642_1.tar.bz2 +name : gofasta +version : 0.0.6 +build : h9ee0642_1 +build number: 1 +size : 2.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-0.0.6-h9ee0642_1.tar.bz2 +md5 : f553c9cd5206ddc0c66977b74b013f3d +timestamp : 2022-01-14 08:25:52 UTC +dependencies: [] + + +gofasta 1.0.0 h9ee0642_0 +------------------------ +file name : gofasta-1.0.0-h9ee0642_0.tar.bz2 +name : gofasta +version : 1.0.0 +build : h9ee0642_0 +build number: 0 +size : 2.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-1.0.0-h9ee0642_0.tar.bz2 +md5 : 59fcdbe4cac0d00bde4e11e2d1cce1b6 +timestamp : 2022-01-27 08:59:38 UTC +dependencies: [] + + +gofasta 1.1.0 h9ee0642_0 +------------------------ +file name : gofasta-1.1.0-h9ee0642_0.tar.bz2 +name : gofasta +version : 1.1.0 +build : h9ee0642_0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-1.1.0-h9ee0642_0.tar.bz2 +md5 : 6bfa6853756b739fb5fcd18a37012773 +timestamp : 2022-06-23 05:04:09 UTC +dependencies: [] + + +gofasta 1.2.0 h9ee0642_0 +------------------------ +file name : gofasta-1.2.0-h9ee0642_0.tar.bz2 +name : gofasta +version : 1.2.0 +build : h9ee0642_0 +build number: 0 +size : 2.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-1.2.0-h9ee0642_0.tar.bz2 +md5 : 259c4275361cd01806577ed5c133307c +timestamp : 2023-01-23 14:23:40 UTC +dependencies: [] + + +gofasta 1.2.1 h9ee0642_0 +------------------------ +file name : gofasta-1.2.1-h9ee0642_0.tar.bz2 +name : gofasta +version : 1.2.1 +build : h9ee0642_0 +build number: 0 +size : 2.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-1.2.1-h9ee0642_0.tar.bz2 +md5 : ea1973a60c4910e999c6e0f6d08f4918 +timestamp : 2023-08-10 23:28:00 UTC +dependencies: [] + + +gofasta 1.2.1 h9ee0642_1 +------------------------ +file name : gofasta-1.2.1-h9ee0642_1.tar.bz2 +name : gofasta +version : 1.2.1 +build : h9ee0642_1 +build number: 1 +size : 3.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-1.2.1-h9ee0642_1.tar.bz2 +md5 : 72d5b279b682e70c37f2dac81b065191 +timestamp : 2024-04-05 12:57:19 UTC +dependencies: [] + + +gofasta 1.2.1 h9ee0642_2 +------------------------ +file name : gofasta-1.2.1-h9ee0642_2.tar.bz2 +name : gofasta +version : 1.2.1 +build : h9ee0642_2 +build number: 2 +size : 3.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-1.2.1-h9ee0642_2.tar.bz2 +md5 : 11c4c1ed3a6f34732da197df51c2bc22 +timestamp : 2024-08-11 15:19:53 UTC +dependencies: [] + + +gofasta 1.2.2 h9ee0642_0 +------------------------ +file name : gofasta-1.2.2-h9ee0642_0.tar.bz2 +name : gofasta +version : 1.2.2 +build : h9ee0642_0 +build number: 0 +size : 3.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-1.2.2-h9ee0642_0.tar.bz2 +md5 : d0db33efec4bfb96ddbca4be26b0e2a2 +timestamp : 2025-02-12 18:27:01 UTC +dependencies: [] + + +gofasta 1.2.3 h9ee0642_0 +------------------------ +file name : gofasta-1.2.3-h9ee0642_0.tar.bz2 +name : gofasta +version : 1.2.3 +build : h9ee0642_0 +build number: 0 +size : 3.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gofasta-1.2.3-h9ee0642_0.tar.bz2 +md5 : 4e22fd75b29c8ebbdeeba0ae3b3bcaf7 +timestamp : 2025-03-02 12:26:53 UTC +dependencies: [] diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gridss.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gridss.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2acf7a726ca4459af9b79b65b5b4a5693b2449dc --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gridss.manual_bundle.txt @@ -0,0 +1,535 @@ +# Tool: gridss +software_name: gridss +tier: T1 +domain: t1_backfill_overall +downloads: 173636 +summary: GRIDSS: the Genomic Rearrangement IDentification Software Suite +description: GRIDSS: the Genomic Rearrangement IDentification Software Suite +dependencies: bc, bcftools, bioconductor-structuralvariantannotation >=1.6, bwa >=0.7, entrez-direct, htslib >=1.14, htslib >=1.22.1,<1.24.0a0, kraken2 >=2.1, libgcc >=13, liblzma >=5.8.1,<6.0a0, libzlib >=1.3.1,<2.0a0, ncurses >=6.5,<7.0a0, openjdk >=8, r-argparser, r-base >=4.0, r-stringdist, r-testthat, r-tidyverse, repeatmasker >=4.1.1, samtools >=1.14 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://github.com/PapenfussLab/gridss +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://github.com/PapenfussLab/gridss +GitHub - PapenfussLab/gridss: GRIDSS: the Genomic Rearrangement IDentification Software Suite · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} PapenfussLab / gridss Public Notifications You must be signed in to change notification settings Fork 73 Star 283 Code Issues 89 Pull requests 6 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights PapenfussLab/gridss master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 2,281 Commits 2,281 Commits .github/ workflows .github/ workflows docker docker example example repo repo scripts scripts src src .classpath .classpath .dockerignore .dockerignore .gitattributes .gitattributes .gitignore .gitignore .gitmodules .gitmodules .project .project .travis.yml .travis.yml COPYING COPYING Dockerfile Dockerfile LICENSE LICENSE QuickStart.md QuickStart.md Readme.md Readme.md VIRUSBreakend_Readme.md VIRUSBreakend_Readme.md pom.xml pom.xml View all files Repository files navigation README License GPL-3.0 license GRIDSS - the Genomic Rearrangement IDentification Software Suite GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence. GRIDSS makes extensive use of the standard tags defined by SAM specifications . Due to the modular design, any step (such as split read identification) can be replaced by another implementation that also outputs using the standard tags. It is hoped that GRIDSS can serve as an exemplar modular structural variant pipeline designed for interoperability with other tools. If you have any trouble running GRIDSS, please raise an issue using the Issues tab above. Based on feedback from users, a user guide will be produced outlining common workflows, pitfalls, and use cases. Click here to download GRIDSS Detailed documentation is being developed here Quick start guide Use the quick start guide to get up and running quickly Citation Recommended minimal citations are: If you use breakpoint calling with GRIDSS version 2.x.y, please cite: Cameron DL, Baber J, Shale C, Valle-Inclan JE, Besselink N, van Hoeck A, Janssen R, Cuppen E, Priestley P, Papenfuss AT. GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. Genome Biol. 2021 Jul 12;22(1):202. Cameron DL, Schröder J, Penington JS, Do H, Molania R, Dobrovic A, Speed TP, Papenfuss AT. GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Research, 2017 Dec;27(12):2050-2060. If you use VIRUSBreakend, please cite: Cameron DL, Jacobs N, Roepman P, Priestley P, Cuppen E, Papenfuss AT; VIRUSBreakend. Viral Integration Recognition Using Single Breakends, Bioinformatics, Volume 37, Issue 19, 1 October 2021, Pages 3115–3119 Cameron DL, Baber J, Shale C, Valle-Inclan JE, Besselink N, van Hoeck A, Janssen R, Cuppen E, Priestley P, Papenfuss AT. GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. Genome Biol. 2021 Jul 12;22(1):202. If you use single breakend calling, please cite: Cameron DL, Baber J, Shale C, Valle-Inclan JE, Besselink N, van Hoeck A, Janssen R, Cuppen E, Priestley P, Papenfuss AT. GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. Genome Biol. 2021 Jul 12;22(1):202. If you use breakpoint calling with GRIDSS version 1.x.y Cameron DL, Schröder J, Penington JS, Do H, Molania R, Dobrovic A, Speed TP, Papenfuss AT. GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Research, 2017 Dec;27(12):2050-2060. If you use LINX with GRIDSS (v2+), please cite: Charles Shale, Daniel L. Cameron, Jonathan Baber, Marie Wong, Mark J. Cowley, Anthony T. Papenfuss, Edwin Cuppen, Peter Priestley. Unscrambling cancer genomes via integrated analysis of structural variation and copy number, Cell Genomics, Volume 2, Issue 4, 2022 Cameron DL, Baber J, Shale C, Valle-Inclan JE, Besselink N, van Hoeck A, Janssen R, Cuppen E, Priestley P, Papenfuss AT. GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. Genome Biol. 2021 Jul 12;22(1):202. and not the bioRxiv preprints . Pre-requisites To run GRIDSS the following must be installed: java 1.8 or later R 4.0 or later gridss_somatic_filter and gridss_extract_overlapping_fragments require the following R libraries: argparser tidyverse stringdist testthat stringr StructuralVariantAnnotation rtracklayer BSgenome package for your reference genome (optional) samtools 1.13 or later bwa bash getopt(1) (part of util-linux ) To run VIRUSBreakend, kraken2, or repeatmasker annotations, the following additional software must be installed: kraken2 Note that virusbreakend-build requires all kraken2-build dependencies RepeatMasker bcftools Building GRIDSS GRIDSS is mostly written in Java thus local building is not required. Just download the latest release and ensure you have the Pre-requistes installed. If you wish to contribute to GRIDSS development, it can be built from source using maven with mvn package . A prebuilt docker image is available as gridss/gridss:latest so building a docker image yourself is not necessary. If you do wish to build the docker image yourself, ensure that you perform a recursive git checkout. If you don't, you'll be missing htslib and gridsstools won't compile. Building gridsstools Some performance-critical steps are implemented in C using htslib. A precompiled version of gridsstools for linux is included as part of GRIDSS releases. If this precompiled version does not run on your system you will need to build it from source. To build gridsstools from source run the following: git clone --recurse-submodules http://github.com/PapenfussLab/gridss/ cd gridss/src/main/c/gridsstools/htslib/ autoreconf -i && ./configure && make cd .. autoreconf -i && ./configure && make all Conda issues Compiling with a conda environment active is likely to cause problems such as undefined reference to 'libdeflate_crc32' . This happens when the conda environment includes copies of the libraries used by htslib (z m bz2 lzma curl crypto pthread) without also including the headers for the libraries. This causes gridsstools to compile against the system headers, but link against the conda libraries, hence the error. Run either conda install htslib or conda deactivate if you have problems compiling gridsstools in a conda environment. Running Pre-compiled binaries are available at https://github.com/PapenfussLab/GRIDSS/releases . GRIDSS invokes external tools at multiple points during processing. By default this is bwa mem, but can be configured to use bowtie2 or another aligner. The following programs are included in GRIDSS releases: program description gridss GRIDSS assembler and structural variant caller. Use this to generate a GRIDSS SV VCF. gridss_extract_overlapping_fragments Extracts all alignments for read pairs with at least one aligment overlapping set of regions of interest. Correctly handles supplementary alignments. Use this script to extract reads of interest for targeted GRIDSS variant calling. gridss_annotate_vcf_repeatmasker Annotates breakpoint and single breakend inserted sequences with the RepeatMasker classification of the sequence. gridss_annotate_vcf_kraken2 Annotates breakpoint and single breakend inserted sequences with the Kraken2 classification of the sequence. virusbreakend See VIRUSBreakend README virusbreakend-build See VIRUSBreakend README gridss_somatic_filter Somatic filtering script. Note that this has an equivalent java implementation in GRIPSS . gridsstools C/htslib implementation of performance-critical steps. Currently used by virusbreakend and gridss_extract_overlapping_fragments gridss command-line arguments Usage: gridss --reference <reference.fa> --output <output.vcf.gz> --assembly <assembly.bam> [--threads n] [--jar gridss.jar] [--workingdir <directory>] [--jvmheap 30g] [--blacklist <exclude_list.bed>] [--steps All|PreProcess|Assemble|Call] [--configuration gridss.properties] [--maxcoverage 50000] [--labels input1,input2,...] input1.bam [input2.bam [...]] required argument description -o, --output output VCF -r, --reference reference genome to use. Must have a .fai index file and a bwa index optional argument description -a, --assembly location of the GRIDSS assembly BAM. This file will be created by GRIDSS. The default filename adds a .assembly.bam suffix to the output file. -t, --threads number of threads to use. Defaults to 8 cores. -j, --jar location of GRIDSS jar. Can also be specified using the GRIDSS_JAR environment variable. -b/--blacklist BED file containing regions to ignore. The ENCODE DAC blacklist is recommended for hg19. (Optional) --jvmheap size of JVM heap for the high-memory part of the assembly and variant calling. Defaults to 30g to ensure GRIDSS runs on cloud instances with 32gb memory. --otherjvmheap size of JVM heap for everything else. Useful to prevent java out of memory errors when using large (>4Gb) reference genomes. Note that some parts of assembly and variant calling use this heap size so if you get an OutOfMemory error during during these steps even after increasing jvmheap, you may need to increase otherjvmheap as well. (Default: 4gb) --maxcoverage maximum coverage. Regions with coverage in excess of this are ignored. (Default: 50000) --labels comma separated labels to use in the output VCF for the input files. Must have same number of entries as there are input files. Input files with the same label are aggregated (useful for multiple sequencing runs of the same sample). Labels default to input filenames, unless a single read group with a non-empty sample name exists in which case the read group sample name is used (which can be disabled by "useReadGroupSampleNameCategoryLabel=false" in the configuration file). If labels are specified, they must be specified for all input files. --steps processing steps to run. Defaults to all steps. Multiple steps are specified using comma separators. Available steps are preprocess,assemble,call. Useful to improve parallelisation on a cluster as preprocess of each input file is independent, and can be performed in parallel, and has lower memory requirements than the assembly step. --jobindex zero-based index of this assembly job node. Used to spread GRIDSS assembly across multiple compute nodes. Use only with -s assemble . Once all jobs have completed, a -s assemble or -s all job should be run to gather the results together. --jobnodes total number of assembly jobs scheduled. The following additional optional arguments may be useful if GRIDSS fails to run in your environment, or you want to run with non-standard parameters. argument description -c, --configuration configuration file use to override default GRIDSS settings --externalaligner use the system version of bwa instead of the in-process version packaged with GRIDSS --picardoptions additional standard Picard command line options. Useful options include VALIDATION_STRINGENCY=LENIENT and COMPRESSION_LEVEL=0 . See https://broadinstitute.github.io/picard/command-line-overview.html --useproperpair use SAM 'proper pair' flag to determine whether a read pair is discordant. Default: use library fragment size distribution to determine read pair concordance --concordantreadpairdistribution portion of read pairs distribution considered concordantly mapped. Default: 0.995 --keepTempFiles keep intermediate files. Not recommended except for debugging due to the high disk usage. --nojni do not use JNI native code acceleration libraries (snappy, GKL, ssw, bwa). Warning : the somatic filtering script treats the first bam file as the matched normal, and all subsequent as tumour samples. If you are doing somatic calling, it is strongly recommended to follow this convention. gridss steps The following GRIDSS steps can be specified: step description setupreference Once-off setup generating additional files in the same directory as the reference. WARNING: multiple instances of GRIDSS attempting to perform setupreference at the same time will result in file corruption. Make sure these files are generated before running parallel GRIDSS jobs. preprocess Pre-process input BAM files. Can be run per input file. assemble Perform GRIDSS breakend assembly. Can split up across multiple nodes using --jobindex and --jobnodes . call Perform variant calling. all Run all steps (Default) At present, command line valiation is performed independently of which steps are run. When splitting GRIDSS into multiple cluster jobs, the same command line parameters should be specified for every job except for: --input on preprocess jobs (one input per file) --jobindex and --jobnodes on assembly jobs FAQ How do I run GRIDSS on multiple samples? Just specify multiple BAMs on the command line. GRIDSS will perform joint calling and provide a per-BAM breakdown of support. Should I do joint calling or run each sample individually? Joint calling should always be used for related samples (e.g. tumour/normal or trio calling). Joint calling will ensure that a common variant near the single-sample threshold of detection will be reliably reported as a shared variant. This is not the case if the calling were done individually. Note that this particular behaviour is not specific to GRIDSS and is common to all variant callers (hence the joint calling support in many callers). Joint calling allows for sensivity detection of variants that are present subclonally (or at low coverage) that would not be detected if called individually. GRIDSS performs joint assembly then reports a per-sample breakdown. Joint calling has higher coverage of shared variants thus resulting in more reliable assembly of that variant. Determining whether two SV calls in two different VCFs are actually the same call is non-trivial. Imprecise calls are especially problematic since the coordinates may differ between the VCF, or a call may be precise in one VCF and not in the other. A good example of why reconciling SV calls is so problematic is the case where call A (chrX:1-99->chrY:1-99) overlaps call B (chrX:50-149->chrY:1-99), call B overlaps call C (chrX:100-199->chrY:1-99), but A does not overlap C at all. Joint calling obviates this step. How do I perform tumour/normal somatic variant calling? Jointly call on all samples from the patient. It is strongly recommended that the normal be the first argument as that is what downstream steps expect. For example, gridss ... patientX_normal.bam patientX_primary.bam patientX_met.bam . To filter to somatic calls, use the gridss_somatic_filter script included in the GRIDSS release. What aligner should I use? The default of bwa mem is sufficient for most use cases. Although GRIDSS aims to be aligner agnostic, not all aligners output BAM files suitable for processing by GRIDSS. GRIDSS requires: One alignment per read. Supplementary (split read) alignments are ok, but secondary alignments are not. This means that aligner settings such as the -a option of bwa mem and the -k and -a options of bowtie2 are unsuitable. MAPQ to meaningfully follow the SAM specifications. Aligners that do not follow the specifications (e.g. subread) will have worse results. Options such as the -Y option of bwa mem, or the fact that bowtie2 does not do split read alignment are not problematic as these differences are corrected in the GRIDSS preprocessing step. How do I tell GRIDSS multiple BAMs are from the same sample? Use the --labels command line option. Eg: --labels sample1,sample1,sample2 sample1_library1.bam sample1_library2.bam sample2.bam Why are there ALT alleles with . in the output? This is the VCF notation for single breakend variant calls. See section 5.4.9 of the specifications document. These calls indicate that a breakpoint was found at this location but the partner location could not be unambiguously determined. How do I get output like the GRIDSS PURPLE LINX figures? Run the integrated GRIDSS PURPLE LINX pipeline script or the docker image gridss/gridss-purple-linx:latest. How do I do RepeatMasker annotation of breakend sequences? Run gridss_annotate_vcf_repeatmasker on the GRIDSS output. How do I do viral annotation? Use VIRUSBreakend for viral annotations. See the VIRUSBreakend README for more details. What does gridss_somatic_filter actually do? See documentation at https://github.com/PapenfussLab/gridss/wiki/Somatic-Filtering The Hartwig Medical Foundation has reimplemented gridss_somatic_filter in Java as GRIPSS . GRIPSS is much faster, has additional features, and is the recommended tool for somatic filtering of GRIDSS output. How do I create the panel of normals required by gridss_somatic_filter ? If you are using hg19 or hg38, then a PON based on Dutch samples is available from https://resources.hartwigmedicalfoundation.nl/ . Make sure the reference you are using and the PON both use the same chromosome notation or nothing will get filtered + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gridss --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +gridss 1.2.4 py27_0 +------------------- +file name : gridss-1.2.4-py27_0.tar.bz2 +name : gridss +version : 1.2.4 +build : py27_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.2.4-py27_0.tar.bz2 +md5 : e025de33efd67bc5b2112317a28ce171 +dependencies: + - java-jdk >=8 + - python 2.7* + + +gridss 1.2.4 py34_0 +------------------- +file name : gridss-1.2.4-py34_0.tar.bz2 +name : gridss +version : 1.2.4 +build : py34_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.2.4-py34_0.tar.bz2 +md5 : c8e81aa8ee509ede45c830360baeb7a9 +dependencies: + - java-jdk >=8 + - python 3.4* + + +gridss 1.2.4 py35_0 +------------------- +file name : gridss-1.2.4-py35_0.tar.bz2 +name : gridss +version : 1.2.4 +build : py35_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.2.4-py35_0.tar.bz2 +md5 : 1696fbf8ce54319e695a293c7fee0483 +dependencies: + - java-jdk >=8 + - python 3.5* + + +gridss 1.3.0 py27_0 +------------------- +file name : gridss-1.3.0-py27_0.tar.bz2 +name : gridss +version : 1.3.0 +build : py27_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.3.0-py27_0.tar.bz2 +md5 : 7f5a8017f2a254bb0758aeea77aaaeef +dependencies: + - java-jdk >=8 + - python 2.7* + + +gridss 1.3.0 py34_0 +------------------- +file name : gridss-1.3.0-py34_0.tar.bz2 +name : gridss +version : 1.3.0 +build : py34_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.3.0-py34_0.tar.bz2 +md5 : cfc749549e2e3d081660eb6a0245e700 +dependencies: + - java-jdk >=8 + - python 3.4* + + +gridss 1.3.0 py35_0 +------------------- +file name : gridss-1.3.0-py35_0.tar.bz2 +name : gridss +version : 1.3.0 +build : py35_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.3.0-py35_0.tar.bz2 +md5 : f1cee49a790dd3a377424452e8eaf887 +dependencies: + - java-jdk >=8 + - python 3.5* + + +gridss 1.3.2 py27_0 +------------------- +file name : gridss-1.3.2-py27_0.tar.bz2 +name : gridss +version : 1.3.2 +build : py27_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.3.2-py27_0.tar.bz2 +md5 : 639b1e23ed7bcaaaae88c7f20f8d1dfa +dependencies: + - java-jdk >=8 + - python 2.7* + + +gridss 1.3.2 py34_0 +------------------- +file name : gridss-1.3.2-py34_0.tar.bz2 +name : gridss +version : 1.3.2 +build : py34_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.3.2-py34_0.tar.bz2 +md5 : e52622cf17a41ff187c8d09ed15dbc1f +dependencies: + - java-jdk >=8 + - python 3.4* + + +gridss 1.3.2 py35_0 +------------------- +file name : gridss-1.3.2-py35_0.tar.bz2 +name : gridss +version : 1.3.2 +build : py35_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.3.2-py35_0.tar.bz2 +md5 : 03732a0a704e0424b3b31e868898bc1e +dependencies: + - java-jdk >=8 + - python 3.5* + + +gridss 1.3.4 py27_0 +------------------- +file name : gridss-1.3.4-py27_0.tar.bz2 +name : gridss +version : 1.3.4 +build : py27_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.3.4-py27_0.tar.bz2 +md5 : ce31669b549ed695651a7770761a3226 +dependencies: + - openjdk >=8 + - python 2.7* + + +gridss 1.3.4 py34_0 +------------------- +file name : gridss-1.3.4-py34_0.tar.bz2 +name : gridss +version : 1.3.4 +build : py34_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.3.4-py34_0.tar.bz2 +md5 : 06e80b1692f89c5ae9100fc0ed9e7cc2 +dependencies: + - openjdk >=8 + - python 3.4* + + +gridss 1.3.4 py35_0 +------------------- +file name : gridss-1.3.4-py35_0.tar.bz2 +name : gridss +version : 1.3.4 +build : py35_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.3.4-py35_0.tar.bz2 +md5 : 5883e6d201248a566daad4e2acd16097 +dependencies: + - openjdk >=8 + - python 3.5* + + +gridss 1.3.4 py36_0 +------------------- +file name : gridss-1.3.4-py36_0.tar.bz2 +name : gridss +version : 1.3.4 +build : py36_0 +build number: 0 +size : 33.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.3.4-py36_0.tar.bz2 +md5 : 1a8af5113a0bd20d1ca4b0fa8dd7e595 +dependencies: + - openjdk >=8 + - python 3.6* + + +gridss 1.7.2 2 +-------------- +file name : gridss-1.7.2-2.tar.bz2 +name : gridss +version : 1.7.2 +build : 2 +build number: 2 +size : 34.1 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.7.2-2.tar.bz2 +md5 : 4f91c648e1e9137922ea718ff292e2c2 +timestamp : 2018-07-11 23:41:45 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 1.7.2 py27_0 +------------------- +file name : gridss-1.7.2-py27_0.tar.bz2 +name : gridss +version : 1.7.2 +build : py27_0 +build number: 0 +size : 34.1 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.7.2-py27_0.tar.bz2 +md5 : cdd0b02a53d6e5b66231be21f437c9c2 +dependencies: + - openjdk >=8 + - python 2.7* + + +gridss 1.7.2 py35_0 +------------------- +file name : gridss-1.7.2-py35_0.tar.bz2 +name : gridss +version : 1.7.2 +build : py35_0 +build number: 0 +size : 34.1 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.7.2-py35_0.tar.bz2 +md5 : bf76bc8e5f1e53f86d36dc3e2f98b877 +dependencies: + - openjdk >=8 + - python 3.5* + + +gridss 1.7.2 py36_0 +------------------- +file name : gridss-1.7.2-py36_0.tar.bz2 +name : gridss +version : 1.7.2 +build : py36_0 +build number: 0 +size : 34.1 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.7.2-py36_0.tar.bz2 +md5 : 1360d8faa43a52c39736ac05e8e3bd47 +dependencies: + - openjdk >=8 + - python 3.6* + + +gridss 1.8.0 0 +-------------- +file name : gridss-1.8.0-0.tar.bz2 +name : gridss +version : 1.8.0 +build : 0 +build number: 0 +size : 34.1 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.8.0-0.tar.bz2 +md5 : afd1205800aaf4ea72df06b3b104917f +timestamp : 2018-08-02 07:15:45 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 1.8.1 0 +-------------- +file name : gridss-1.8.1-0.tar.bz2 +name : gridss +version : 1.8.1 +build : 0 +build number: 0 +size : 34.1 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.8.1-0.tar.bz2 +md5 : 0af66caed4f3f52a3ab1737e85583b2f +timestamp : 2018-08-08 15:32:15 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 1.9.0 0 +-------------- +file name : gridss-1.9.0-0.tar.bz2 +name : gridss +version : 1.9.0 +build : 0 +build number: 0 +size : 34.2 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-1.9.0-0.tar.bz2 +md5 : 53e1cf57143e58705497643b03c5a5cd +timestamp : 2018-09-01 15:02:22 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 2.0.1 0 +-------------- +file name : gridss-2.0.1-0.tar.bz2 +name : gridss +version : 2.0.1 +build : 0 +build number: 0 +size : 34.2 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-2.0.1-0.tar.bz2 +md5 : 0d1fc27aab79cb473e1e2e17c5550882 +timestamp : 2018-11-19 02:27:18 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 2.1.0 0 +-------------- +file name : gridss-2.1.0-0.tar.bz2 +name : gridss +version : 2.1.0 +build : 0 +build number: 0 +size : 34.3 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gridss-2.1.0-0.tar.bz2 +md5 : 6bfbf88d345ea577456691af6ce1d185 +timestamp : 2019-01-08 19:45:33 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 2.5.1 0 +-------------- +file name : gridss-2.5.1-0.tar.bz2 +name : gridss +version : 2.5.1 +build : 0 +build number: 0 +size : 34.3 MB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gridss-2.5.1-0.tar.bz2 +md5 : 9e2f07141bfc7fbcbcb250d08f55af03 +timestamp : 2019-08-15 07:17:05 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 2.5.2 0 +-------------- +file name : gridss-2.5.2-0.tar.bz2 +name : gridss +version : 2.5.2 +build : 0 +build number: 0 +size : 34.3 MB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gridss-2.5.2-0.tar.bz2 +md5 : eae319e39fdab0db3a5a9d7242f50249 +timestamp : 2019-08-28 16:49:21 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 2.6.0 0 +-------------- +file name : gridss-2.6.0-0.tar.bz2 +name : gridss +version : 2.6.0 +build : 0 +build number: 0 +size : 34.3 MB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gridss-2.6.0-0.tar.bz2 +md5 : d9c054a77e3e3140b063ddf66cd82966 +timestamp : 2019-09-09 14:40:58 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 2.6.1 0 +-------------- +file name : gridss-2.6.1-0.tar.bz2 +name : gridss +version : 2.6.1 +build : 0 +build number: 0 +size : 34.3 MB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gridss-2.6.1-0.tar.bz2 +md5 : 7771189eb448cb1b0692c2d7f45e1838 +timestamp : 2019-09-18 08:12:52 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 2.6.2 0 +-------------- +file name : gridss-2.6.2-0.tar.bz2 +name : gridss +version : 2.6.2 +build : 0 +build number: 0 +size : 34.3 MB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gridss-2.6.2-0.tar.bz2 +md5 : 90c7f6d448d1a10e867807e9d4ba9427 +timestamp : 2019-09-23 07:30:48 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 2.6.3 0 +-------------- +file name : gridss-2.6.3-0.tar.bz2 +name : gridss +version : 2.6.3 +build : 0 +build number: 0 +size : 34.3 MB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gridss-2.6.3-0.tar.bz2 +md5 : 06e4f67ffa02e2a330f0984f981e5295 +timestamp : 2019-10-21 07:21:47 UTC +dependencies: + - openjdk >=8 + - python + + +gridss 2.7.0 0 +-------------- +file name : gridss-2.7.0-0.tar.bz2 +name : gridss +version : 2.7.0 +build : 0 +build number: 0 +size : 34.3 MB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda. diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gromacs.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gromacs.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..08881887e89f8308143c8531854fba8dd7b2f703 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gromacs.manual_bundle.txt @@ -0,0 +1,477 @@ +# Tool: gromacs +software_name: gromacs +tier: T1 +domain: t1_backfill_overall +downloads: 288439 +summary: GROMACS is a versatile package to perform molecular dynamics. +description: GROMACS is a versatile package to perform molecular dynamics. +dependencies: _openmp_mutex >=4.5, fftw >=3.3.9,<4.0a0, libgcc-ng >=9.4.0, libhwloc 2.*, libhwloc >=2.5.0,<2.5.1.0a0, libstdcxx-ng >=9.4.0, ocl-icd >=2.3.1,<3.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://www.gromacs.org/ +doc_url: +dev_url: + +## URL Docs Extract +### https://www.gromacs.org/ +Welcome to GROMACS — GROMACS webpage https://www.gromacs.org documentation Welcome to GROMACS ¶ A free and open-source software suite for high-performance molecular dynamics and output analysis. New to GROMACS : Try the introduction tutorial . Watch a webinar on GROMACS . Watch the current GROMACS release webinar . Download the current GROMACS version here . Have a look at documentation page to know more how to install and use GROMACS. Do you have any questions, have a look at the user discussions on GROMACS forums . News “GROMACS 2026.1 is available.” For an overview of the patch release note - 6 March 2026 GROMACS webinars in March: Whats new in GROMACS 2026 and Peeking into the black box of GROMACS performance 11 Febraury 2026 Interested in GROMACS tutorial suite, watch The GROMACS tutorial suite: from basic to advanced applications 29 January 2026 “GROMACS 2026.0 is available.” For an overview of the most recent version see the release highlights and the release notes - 19 January 2026 “GROMACS 2025.4 is available.” Read here for an overview of the patch release notes - 23 November 2025 “GROMACS 2025.3 is available.” Read here for an overview of the patch release notes - 12 September 2025 “GROMACS 2024.6 is available.” Read here for an overview of the patch release notes - 12 September 2025 “GROMACS 2025.2 is available.” Read here for an overview of the patch release notes - 3 June 2025 A tutorial and a webinar to learn to preform Density-fit simulation using GROMACS are now available. Watch the Webinar or go to try the tutorial - 21 March 2025 “GROMACS 2025.1 is available.” Read here for an overview of the patch release notes - 11 March 2025 “GROMACS 2025.0 is available.” For an overview of the most recent version see the release highlights and the release notes - 12 Febraury 2025 Come to listen “What’s new in GROMACS 2025” 18th Febraury 2025 at 15:00 CET. Click here to register and know more about the webinar speaker. - 10 Febraury 2025 “GROMACS 2024.5 is available.” Read here for an overview of the patch release notes - 30 January 2025 Navigation About GROMACS Highlights Documentation Articles Tutorials and Webinars Downloads GROMACS forum Report an issue Development User contributions User Survey GROMACS workshop Related Topics Documentation overview Next: About GROMACS Quick search ©2022-2024, GROMACS development team. | Powered by Sphinx 5.3.0 & Alabaster 0.7.13 | Page source + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gromacs --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +gromacs 4.6.5 0 +--------------- +file name : gromacs-4.6.5-0.tar.bz2 +name : gromacs +version : 4.6.5 +build : 0 +build number: 0 +size : 196.1 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-4.6.5-0.tar.bz2 +md5 : ad373526bd1efedc5286f6166ca4edd9 +dependencies: + - libgcc + + +gromacs 2018 0 +-------------- +file name : gromacs-2018-0.tar.bz2 +name : gromacs +version : 2018 +build : 0 +build number: 0 +size : 18.5 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018-0.tar.bz2 +md5 : 697c2c63830c0a49f5c564a3f00eb61f +dependencies: + - fftw + - libgcc + - libhwloc + - ocl-icd + - openmp + + +gromacs 2018 1 +-------------- +file name : gromacs-2018-1.tar.bz2 +name : gromacs +version : 2018 +build : 1 +build number: 1 +size : 18.5 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018-1.tar.bz2 +md5 : 142f0e5d6ac75aed198da37988feca1e +dependencies: + - fftw + - libgcc + - libhwloc 1.* + - ocl-icd + - openmp + + +gromacs 2018 2 +-------------- +file name : gromacs-2018-2.tar.bz2 +name : gromacs +version : 2018 +build : 2 +build number: 2 +size : 16.6 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018-2.tar.bz2 +md5 : 6cfc497d055c7143b49cdb77b07074ea +dependencies: + - fftw + - libgcc + - libhwloc 1.* + - ocl-icd + - openmp + + +gromacs 2018 h470a237_3 +----------------------- +file name : gromacs-2018-h470a237_3.tar.bz2 +name : gromacs +version : 2018 +build : h470a237_3 +build number: 3 +size : 16.8 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018-h470a237_3.tar.bz2 +md5 : 8e83872f60353c31ad1e29866a2c7836 +timestamp : 2018-07-05 18:55:09 UTC +dependencies: + - fftw + - libgcc-ng >=4.9 + - libhwloc 1.* + - ocl-icd + - openmp + + +gromacs 2018.2 h470a237_0 +------------------------- +file name : gromacs-2018.2-h470a237_0.tar.bz2 +name : gromacs +version : 2018.2 +build : h470a237_0 +build number: 0 +size : 16.8 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018.2-h470a237_0.tar.bz2 +md5 : 2883b20156f28f6d6419d3749f27a7ab +timestamp : 2018-07-28 00:21:45 UTC +dependencies: + - fftw + - libgcc-ng >=4.9 + - libhwloc 1.* + - ocl-icd + - openmp + + +gromacs 2018.3 h470a237_0 +------------------------- +file name : gromacs-2018.3-h470a237_0.tar.bz2 +name : gromacs +version : 2018.3 +build : h470a237_0 +build number: 0 +size : 16.8 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018.3-h470a237_0.tar.bz2 +md5 : 04797d33116c9826b31e411dbc3e95d3 +timestamp : 2018-11-22 16:03:01 UTC +dependencies: + - fftw + - libgcc-ng >=4.9 + - libhwloc 1.* + - ocl-icd + - openmp + + +gromacs 2018.4 h470a237_0 +------------------------- +file name : gromacs-2018.4-h470a237_0.tar.bz2 +name : gromacs +version : 2018.4 +build : h470a237_0 +build number: 0 +size : 16.8 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018.4-h470a237_0.tar.bz2 +md5 : 92b35ffb8250640ad776feb690881655 +timestamp : 2018-11-22 18:38:50 UTC +dependencies: + - fftw + - libgcc-ng >=4.9 + - libhwloc 1.* + - ocl-icd + - openmp + + +gromacs 2018.5 h6bb024c_0 +------------------------- +file name : gromacs-2018.5-h6bb024c_0.tar.bz2 +name : gromacs +version : 2018.5 +build : h6bb024c_0 +build number: 0 +size : 16.8 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018.5-h6bb024c_0.tar.bz2 +md5 : 418e0cadd1a6bb02038eb8c7969a26e2 +timestamp : 2019-02-15 15:23:22 UTC +dependencies: + - fftw + - libgcc-ng >=7.3.0 + - libhwloc 1.* + - libstdcxx-ng >=7.3.0 + - ocl-icd + - openmp + + +gromacs 2018.6 h3ddc34e_2 +------------------------- +file name : gromacs-2018.6-h3ddc34e_2.tar.bz2 +name : gromacs +version : 2018.6 +build : h3ddc34e_2 +build number: 2 +size : 16.7 MB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018.6-h3ddc34e_2.tar.bz2 +md5 : f14f700f14e34b5759bcd4e938e39602 +timestamp : 2020-07-03 09:10:52 UTC +dependencies: + - fftw >=3.3.8,<4.0a0 + - libgcc-ng >=7.5.0 + - libhwloc 1.* + - libhwloc >=1.11.13,<1.12.0a0 + - libstdcxx-ng >=7.5.0 + - ocl-icd >=2.2.12,<3.0a0 + - openmp + - python_abi 2.7.* *_cp27mu + + +gromacs 2018.6 h6bb024c_0 +------------------------- +file name : gromacs-2018.6-h6bb024c_0.tar.bz2 +name : gromacs +version : 2018.6 +build : h6bb024c_0 +build number: 0 +size : 16.8 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018.6-h6bb024c_0.tar.bz2 +md5 : dd1e5fa86b9c07faea27ecbbfae3ac1a +timestamp : 2019-02-25 17:11:03 UTC +dependencies: + - fftw + - libgcc-ng >=7.3.0 + - libhwloc 1.* + - libstdcxx-ng >=7.3.0 + - ocl-icd + - openmp + + +gromacs 2018.6 h6bb024c_1 +------------------------- +file name : gromacs-2018.6-h6bb024c_1.tar.bz2 +name : gromacs +version : 2018.6 +build : h6bb024c_1 +build number: 1 +size : 16.6 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2018.6-h6bb024c_1.tar.bz2 +md5 : 7374df838e7b7460dcc84f11251ccf2f +timestamp : 2019-05-12 20:38:25 UTC +dependencies: + - fftw + - libgcc-ng >=7.3.0 + - libhwloc 1.* + - libstdcxx-ng >=7.3.0 + - ocl-icd + - openmp + + +gromacs 2019 h6bb024c_0 +----------------------- +file name : gromacs-2019-h6bb024c_0.tar.bz2 +name : gromacs +version : 2019 +build : h6bb024c_0 +build number: 0 +size : 18.2 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2019-h6bb024c_0.tar.bz2 +md5 : e8724f1ccf58c4d68413d94cfc7c6dfa +timestamp : 2019-02-15 15:56:46 UTC +dependencies: + - fftw + - libgcc-ng >=7.3.0 + - libhwloc 2.* + - libstdcxx-ng >=7.3.0 + - ocl-icd + - openmp + + +gromacs 2019.1 h6bb024c_0 +------------------------- +file name : gromacs-2019.1-h6bb024c_0.tar.bz2 +name : gromacs +version : 2019.1 +build : h6bb024c_0 +build number: 0 +size : 18.2 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2019.1-h6bb024c_0.tar.bz2 +md5 : 9f7515fc0df3fa29b4603883ede25dd4 +timestamp : 2019-02-15 17:24:33 UTC +dependencies: + - fftw + - libgcc-ng >=7.3.0 + - libhwloc 2.* + - libstdcxx-ng >=7.3.0 + - ocl-icd + - openmp + + +gromacs 2019.1 h6bb024c_1 +------------------------- +file name : gromacs-2019.1-h6bb024c_1.tar.bz2 +name : gromacs +version : 2019.1 +build : h6bb024c_1 +build number: 1 +size : 18.2 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2019.1-h6bb024c_1.tar.bz2 +md5 : 9f4e086c71cfc8514b77626d867f2bd2 +timestamp : 2019-02-25 16:23:02 UTC +dependencies: + - fftw + - libgcc-ng >=7.3.0 + - libhwloc 2.* + - libstdcxx-ng >=7.3.0 + - ocl-icd + - openmp + + +gromacs 2019.1 h6bb024c_2 +------------------------- +file name : gromacs-2019.1-h6bb024c_2.tar.bz2 +name : gromacs +version : 2019.1 +build : h6bb024c_2 +build number: 2 +size : 18.1 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2019.1-h6bb024c_2.tar.bz2 +md5 : e0a2c1aa19a65ef9f5447b90b191f7f4 +timestamp : 2019-05-12 21:12:23 UTC +dependencies: + - fftw + - libgcc-ng >=7.3.0 + - libhwloc 2.* + - libhwloc >=2.0.3,<2.0.4.0a0 + - libstdcxx-ng >=7.3.0 + - ocl-icd + - openmp + + +gromacs 2019.1 hc9558a2_3 +------------------------- +file name : gromacs-2019.1-hc9558a2_3.tar.bz2 +name : gromacs +version : 2019.1 +build : hc9558a2_3 +build number: 3 +size : 18.1 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2019.1-hc9558a2_3.tar.bz2 +md5 : ac3675fb1681835c310321f30aa2048b +timestamp : 2019-10-26 12:56:43 UTC +dependencies: + - fftw + - libgcc-ng >=7.3.0 + - libhwloc 2.* + - libhwloc >=2.0.3,<2.0.4.0a0 + - libstdcxx-ng >=7.3.0 + - ocl-icd + - openmp + + +gromacs 2019.5 h3ddc34e_1 +------------------------- +file name : gromacs-2019.5-h3ddc34e_1.tar.bz2 +name : gromacs +version : 2019.5 +build : h3ddc34e_1 +build number: 1 +size : 18.2 MB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2019.5-h3ddc34e_1.tar.bz2 +md5 : 60785ad0cfe4e654e8aa710ebc7e44d8 +timestamp : 2020-07-03 09:43:10 UTC +dependencies: + - fftw >=3.3.8,<4.0a0 + - libgcc-ng >=7.5.0 + - libhwloc 2.* + - libhwloc >=2.1.0,<2.1.1.0a0 + - libstdcxx-ng >=7.5.0 + - ocl-icd >=2.2.12,<3.0a0 + - openmp + - python_abi 2.7.* *_cp27mu + + +gromacs 2019.5 hc9558a2_0 +------------------------- +file name : gromacs-2019.5-hc9558a2_0.tar.bz2 +name : gromacs +version : 2019.5 +build : hc9558a2_0 +build number: 0 +size : 18.0 MB +license : GNU Lesser General Public License (LGPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gromacs-2019.5-hc9558a2_0.tar.bz2 +md5 : 7fdd388313aa447571e8aa8e19b7eb8a +timestamp : 2020-01-10 08:53:44 UTC +dependencies: + - fftw + - libgcc-ng >=7.3.0 + - libhwloc 2.* + - libhwloc >=2.1.0,<2.1.1.0a0 + - libstdcxx-ng >=7.3.0 + - ocl-icd >=2.2.12,<3.0a0 + - openmp + + +gromacs 2019.6 mpi_openmpi_dblprec_h8652d4b_0 +--------------------------------------------- +file name : gromacs-2019.6-mpi_openmpi_dblprec_h8652d4b_0.conda +name : gromacs +version : 2019.6 +build : mpi_openmpi_dblprec_h8652d4b_0 +build number: 0 +size : 22.3 MB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gromacs-2019.6-mpi_openmpi_dblprec_h8652d4b_0.conda +md5 : 531f7142a74a23cc8bf48bb2c55e73f0 +timestamp : 2025-01-29 11:03:43 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - _openmp_mutex >=4.5 + - fftw >=3.3.10,<4.0a0 + - libgcc >=13 + - libstdcxx >=13 + - ocl-icd >=2.3.2,<3.0a0 + - openmpi >=5.0.6,<6.0a0 + + +gromacs 2019.6 mpi_openmpi_h9e48474_0 +------------------------------------- +file name : gromacs-2019.6-mpi_openmpi_h9e48474_0.conda +name : gromacs +version : 2019.6 +build : mpi_openmpi_h9e48474_0 +build number: 0 +size : 23.9 MB +license : LGPL-2.1-or-later +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/gromacs-2019.6-mpi_openmpi_h9e48474_0.conda +md5 : 537c6f1a520fde2b763e5d372f75a9d4 +timestamp : 2025-01-29 11:03:37 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - _openmp_mutex >=4.5 + - fft diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gseapy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gseapy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..bb143a32b34906ae2ccb30e7e1affe1168fffd94 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gseapy.manual_bundle.txt @@ -0,0 +1,530 @@ +# Tool: gseapy +software_name: gseapy +tier: T1 +domain: t1_backfill_overall +downloads: 265964 +summary: Gene Set Enrichment Analysis in Python. +description: Gene Set Enrichment Analysis in Python. +dependencies: matplotlib-base >=2.2, numpy >=1.13.0, pandas, pyopengl, python >=3.10,<3.11.0a0, python_abi 3.10.* *_cp310, requests, scipy +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/zqfang/gseapy +doc_url: https://gseapy.readthedocs.io/en/latest +dev_url: https://github.com/zqfang/gseapy + +## URL Docs Extract +### https://gseapy.readthedocs.io/en/latest +Welcome to GSEAPY’s documentation! — GSEApy 1.1.8 documentation GSEApy Table of Contents 1. Welcome to GSEAPY’s documentation! 2. GSEAPY Example 3. GSVA example 4. scRNA-seq Example 5. A Protocol to Prepare files for GSEApy 6. Developmental Guide 7. Frequently Asked Questions GSEApy Welcome to GSEAPY’s documentation! View page source Welcome to GSEAPY’s documentation!  GSEAPY: Gene Set Enrichment Analysis in Python.  Release notes : https://github.com/zqfang/GSEApy/releases Citation  Zhuoqing Fang , Xinyuan Liu , Gary Peltz , GSEApy : a comprehensive package for performing gene set enrichment analysis in Python , Bioinformatics , 2022 ;, btac757 , https : // doi . org / 10.1093 / bioinformatics / btac757 Installation  Install gseapy package from bioconda or pypi. # if you have conda (MacOS_x86-64 and Linux only) $ conda install -c bioconda gseapy # or use pip to install the latest release $ pip install gseapy GSEApy is a Python/Rust implementation of GSEA and wrapper for Enrichr .  GSEApy has multiple subcommands: gsea , prerank , ssgsea , gsva , replot enrichr , biomart . 1. The gsea module produces GSEA results. The input requries a txt file(FPKM, Expected Counts, TPM, et.al), a cls file, and gene_sets file in gmt format. 2. The prerank module produces Prerank tool results. The input expects a pre-ranked gene list dataset with correlation values, which in .rnk format, and gene_sets file in gmt format. prerank module is an API to GSEA pre-rank tools. 3. The ssgsea module performs single sample GSEA(ssGSEA) analysis. The input expects a gene list with expression values(same with .rnk file, and gene_sets file in gmt format. ssGSEA enrichment score for the gene set as described by D. Barbie et al 2009 . The gsva module performs GSVA analysis, which described by Hänzelmann et al . 5. The replot module reproduces GSEA desktop version results. The only input for GSEAPY is the location to GSEA Desktop output results. 6. The enrichr module enables you to perform gene set enrichment analysis using Enrichr API. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr . It runs very fast and generates results in txt format. The biomart module helps you convert gene ids using BioMart API. GSEApy could be used for RNA-seq, ChIP-seq, Microarry data. It’s used for convenient GO enrichments and produce publishable quality figures in python. The full GSEA is far too extensive to describe here; see GSEA documentation for more information. All files’ formats for GSEApy are identical to GSEA desktop version. Why GSEAPY  I would like to use Pandas to explore my data, but I did not find a convenient tool to do gene set enrichment analysis in python. So, here are my reasons: Ability to run inside python interactive console without having to switch to R!!! User friendly for both wet and dry lab users. Produce or reproduce publishable figures. Perform batch jobs easy. Easy to use in bash shell or your data analysis workflow, e.g. snakemake. Table of Contents 1. Welcome to GSEAPY’s documentation! 2. GSEAPY Example 3. GSVA example 4. scRNA-seq Example 5. A Protocol to Prepare files for GSEApy 6. Developmental Guide 7. Frequently Asked Questions Indices and tables  Index Module Index Search Page Next © Copyright 2017-2025, Zhuoqing Fang. Built with Sphinx using a theme provided by Read the Docs . + +### https://github.com/zqfang/gseapy +GitHub - zqfang/GSEApy: Gene Set Enrichment Analysis in Python · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} zqfang / GSEApy Public Notifications You must be signed in to change notification settings Fork 136 Star 696 Code Issues 8 Pull requests 1 Discussions Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Wiki Security and quality Insights zqfang/GSEApy master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,400 Commits 1,400 Commits .github .github docs docs gseapy gseapy src src tests tests .gitignore .gitignore .readthedocs.yaml .readthedocs.yaml Cargo.toml Cargo.toml LICENSE LICENSE MANIFEST.in MANIFEST.in README-rust.md README-rust.md README.rst README.rst pyproject.toml pyproject.toml requirements.txt requirements.txt setup.py setup.py test-requirements.txt test-requirements.txt tox.ini tox.ini View all files Repository files navigation README BSD-3-Clause license GSEApy GSEApy: Gene Set Enrichment Analysis in Python. Release notes : https://github.com/zqfang/GSEApy/releases Tutorial for scRNA-seq datasets Tutorial for general usage Citation Zhuoqing Fang, Xinyuan Liu, Gary Peltz, GSEApy: a comprehensive package for performing gene set enrichment analysis in Python, Bioinformatics, 2022;, btac757, https://doi.org/10.1093/bioinformatics/btac757 GSEApy is a Python/Rust implementation for GSEA and wrapper for Enrichr . GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It can be used for convenient GO enrichment and to produce publication quality figures in python. GSEApy has 7 sub-commands available: gsea , prerank , ssgsea , gsva , replot enrichr , biomart . gsea: The gsea module produces GSEA results. The input requries a txt file(FPKM, Expected Counts, TPM, et.al), a cls file, and gene_sets file in gmt format. prerank: The prerank module produces Prerank tool results. The input expects a pre-ranked gene list dataset with correlation values, provided in .rnk format, and gene_sets file in gmt format. prerank module is an API to GSEA pre-rank tools. ssgsea: The ssgsea module performs single sample GSEA(ssGSEA) analysis. The input expects a pd.Series (indexed by gene name), or a pd.DataFrame (include GCT file) with expression values and a GMT file. For multiple sample input, ssGSEA reconigzes gct format, too. ssGSEA enrichment score for the gene set is described by D. Barbie et al 2009 . gsva: The gsva module performs GSVA method by Hänzelmann et al . The input is same to ssgsea. replot: The replot module reproduce GSEA desktop version results. The only input for GSEApy is the location to GSEA Desktop output results. enrichr: The enrichr module enable you perform gene set enrichment analysis using Enrichr API. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr . It runs very fast. biomart: The biomart module helps you convert gene ids using BioMart API. Please use 'gseapy COMMAND -h' to see the detail description for each option of each module. The full GSEA is far too extensive to describe here; see GSEA documentation for more information. All files' formats for GSEApy are identical to GSEA desktop version. Why GSEApy I would like to use Pandas to explore my data, but I did not find a convenient tool to do gene set enrichment analysis in python. So, here are my reasons: Ability to run inside python interactive console without having to switch to R!!! User friendly for both wet and dry lab users. Produce or reproduce publishable figures. Perform batch jobs easy. Easy to use in bash shell or your data analysis workflow, e.g. snakemake. GSEApy vs GSEA(Broad) output Using the same data for GSEAPreranked , and GSEApy reproduce similar results. See more output here: Example Installation Install gseapy package from bioconda or pip. # if you have conda/mamba $ conda install -c bioconda gseapy # or pip $ pip install gseapy # or uv $ uv add gseapy If pip install failed, install Rust first and build from source: # install rust toolchain curl https://sh.rustup.rs -sSf | sh -s -- -y export PATH= " $PATH : $HOME /.cargo/bin " # then install via pip or uv $ pip install gseapy # or $ uv add gseapy Dependency Python 3.8+ Mandatory build Rust: For gseapy > 0.11.0, Rust compiler is needed setuptools-rust run Numpy >= 1.13.0 Scipy Pandas Matplotlib Requests Run GSEApy For command line usage: # An example to reproduce figures using replot module. $ gseapy replot -i ./Gsea.reports -o test # An example to run GSEA using gseapy gsea module $ gseapy gsea -d exptable.txt -c test.cls -g gene_sets.gmt -o test # An example to run Prerank using gseapy prerank module $ gseapy prerank -r gsea_data.rnk -g gene_sets.gmt -o test # An example to run ssGSEA using gseapy ssgsea module $ gseapy ssgsea -d expression.txt -g gene_sets.gmt -o test # An example to run GSVA using gseapy ssgsea module $ gseapy gsva -d expression.txt -g gene_sets.gmt -o test # An example to use enrichr api # see details for -g input -> ``get_library_name`` $ gseapy enrichr -i gene_list.txt -g KEGG_2016 -o test Run gseapy inside python console: Prepare expression.txt, gene_sets.gmt and test.cls required by GSEA, you could do this import gseapy # run GSEA. gseapy . gsea ( data = 'expression.txt' , gene_sets = 'gene_sets.gmt' , cls = 'test.cls' , outdir = 'test' ) # run prerank gseapy . prerank ( rnk = 'gsea_data.rnk' , gene_sets = 'gene_sets.gmt' , outdir = 'test' ) # run ssGSEA gseapy . ssgsea ( data = "expression.txt" , gene_sets = "gene_sets.gmt" , outdir = 'test' ) # run GSVA gseapy . gsva ( data = "expression.txt" , gene_sets = "gene_sets.gmt" , outdir = 'test' ) # An example to reproduce figures using replot module. gseapy . replot ( indir = './Gsea.reports' , outdir = 'test' ) If you prefer to use Dataframe, dict, list in interactive python console, you could do this. see detail here: Example # assign dataframe, and use enrichr library data set 'KEGG_2016' expression_dataframe = pd . DataFrame () sample_name = [ 'A' , 'A' , 'A' , 'B' , 'B' , 'B' ] # always only two group,any names you like # assign gene_sets parameter with enrichr library name or gmt file on your local computer. gseapy . gsea ( data = expression_dataframe , gene_sets = 'KEGG_2016' , cls = sample_names , outdir = 'test' ) # prerank tool gene_ranked_dataframe = pd . DataFrame () gseapy . prerank ( rnk = gene_ranked_dataframe , gene_sets = 'KEGG_2016' , outdir = 'test' ) # ssGSEA gseapy . ssgsea ( data = expression_dataframe , gene_sets = 'KEGG_2016' , outdir = 'test' ) # gsva gseapy . gsva ( data = expression_dataframe , gene_sets = 'KEGG_2016' , outdir = 'test' ) For enrichr , you could assign a list, pd.Series, pd.DataFrame object, or a txt file (should be one gene name per row.) # assign a list object to enrichr gl = [ 'SCARA3' , 'LOC100044683' , 'CMBL' , 'CLIC6' , 'IL13RA1' , 'TACSTD2' , 'DKKL1' , 'CSF1' , 'SYNPO2L' , 'TINAGL1' , 'PTX3' , 'BGN' , 'HERC1' , 'EFNA1' , 'CIB2' , 'PMP22' , 'TMEM173' ] gseapy . enrichr ( gene_list = gl , gene_sets = 'KEGG_2016' , outdir = 'test' ) # or a txt file path. gseapy . enrichr ( gene_list = 'gene_list.txt' , gene_sets = 'KEGG_2016' , outdir = 'test' , cutoff = 0.05 , format = 'png' ) GSEApy supported gene set libaries : To see the full list of gseapy supported gene set libraries, please click here: Library Or use get_library_name function inside python console. #see full list of latest enrichr library names, which will pass to -g parameter: names = gseapy . get_library_name () # show top 20 entries. print ( names [: 20 ]) [ 'Genome_Browser_PWMs' , 'TRANSFAC_and_JASPAR_PWMs' , 'ChEA_2013' , 'Drug_Perturbations_from_GEO_2014' , 'ENCODE_TF_ChIP-seq_2014' , 'BioCarta_2013' , 'Reactome_2013' , 'WikiPathways_2013' , 'Disease_Signatures_from_GEO_up_2014' , 'KEGG_2016' , 'TF-LOF_Expression_from_GEO' , 'TargetScan_microRNA' , 'PPI_Hub_Proteins' , 'GO_Molecular_Function_2015' , 'GeneSigDB' , 'Chromosome_Location' , 'Human_Gene_Atlas' , 'Mouse_Gene_Atlas' , 'GO_Cellular_Component_2015' , 'GO_Biological_Process_2015' , 'Human_Phenotype_Ontology' ,] Dev # clone and set up dev environment (requires Rust toolchain) $ git clone https://github.com/zqfang/GSEApy.git $ cd GSEApy $ uv sync --extra dev # run tests $ uv run pytest # lint and format $ uv run ruff format gseapy $ uv run ruff check gseapy # test rust extension only $ cargo test --features=extension-module # build wheel + sdist locally $ uv build Bug Report If you would like to report any bugs when use gseapy, don't hesitate to create an issue on github here. To get help of GSEApy See Frequently Asked Questions Visit the document site at Examples The GSEApy discussion channel: Q&A About Gene Set Enrichment Analysis in Python gseapy.rtfd.io/ Topics rust python3 enrichment-analysis gsea Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Stars 696 stars Watchers 11 watching Forks 136 forks Report repository Releases 45 gseapy-v1.2.1 Latest Apr 27, 2026 + 44 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 67.6% Rust 31.8% Other 0.6% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/zqfang/gseapy +GitHub - zqfang/GSEApy: Gene Set Enrichment Analysis in Python · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} zqfang / GSEApy Public Notifications You must be signed in to change notification settings Fork 136 Star 696 Code Issues 8 Pull requests 1 Discussions Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Wiki Security and quality Insights zqfang/GSEApy master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,400 Commits 1,400 Commits .github .github docs docs gseapy gseapy src src tests tests .gitignore .gitignore .readthedocs.yaml .readthedocs.yaml Cargo.toml Cargo.toml LICENSE LICENSE MANIFEST.in MANIFEST.in README-rust.md README-rust.md README.rst README.rst pyproject.toml pyproject.toml requirements.txt requirements.txt setup.py setup.py test-requirements.txt test-requirements.txt tox.ini tox.ini View all files Repository files navigation README BSD-3-Clause license GSEApy GSEApy: Gene Set Enrichment Analysis in Python. Release notes : https://github.com/zqfang/GSEApy/releases Tutorial for scRNA-seq datasets Tutorial for general usage Citation Zhuoqing Fang, Xinyuan Liu, Gary Peltz, GSEApy: a comprehensive package for performing gene set enrichment analysis in Python, Bioinformatics, 2022;, btac757, https://doi.org/10.1093/bioinformatics/btac757 GSEApy is a Python/Rust implementation for GSEA and wrapper for Enrichr . GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It can be used for convenient GO enrichment and to produce publication quality figures in python. GSEApy has 7 sub-commands available: gsea , prerank , ssgsea , gsva , replot enrichr , biomart . gsea: The gsea module produces GSEA results. The input requries a txt file(FPKM, Expected Counts, TPM, et.al), a cls file, and gene_sets file in gmt format. prerank: The prerank module produces Prerank tool results. The input expects a pre-ranked gene list dataset with correlation values, provided in .rnk format, and gene_sets file in gmt format. prerank module is an API to GSEA pre-rank tools. ssgsea: The ssgsea module performs single sample GSEA(ssGSEA) analysis. The input expects a pd.Series (indexed by gene name), or a pd.DataFrame (include GCT file) with expression values and a GMT file. For multiple sample input, ssGSEA reconigzes gct format, too. ssGSEA enrichment score for the gene set is described by D. Barbie et al 2009 . gsva: The gsva module performs GSVA method by Hänzelmann et al . The input is same to ssgsea. replot: The replot module reproduce GSEA desktop version results. The only input for GSEApy is the location to GSEA Desktop output results. enrichr: The enrichr module enable you perform gene set enrichment analysis using Enrichr API. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr . It runs very fast. biomart: The biomart module helps you convert gene ids using BioMart API. Please use 'gseapy COMMAND -h' to see the detail description for each option of each module. The full GSEA is far too extensive to describe here; see GSEA documentation for more information. All files' formats for GSEApy are identical to GSEA desktop version. Why GSEApy I would like to use Pandas to explore my data, but I did not find a convenient tool to do gene set enrichment analysis in python. So, here are my reasons: Ability to run inside python interactive console without having to switch to R!!! User friendly for both wet and dry lab users. Produce or reproduce publishable figures. Perform batch jobs easy. Easy to use in bash shell or your data analysis workflow, e.g. snakemake. GSEApy vs GSEA(Broad) output Using the same data for GSEAPreranked , and GSEApy reproduce similar results. See more output here: Example Installation Install gseapy package from bioconda or pip. # if you have conda/mamba $ conda install -c bioconda gseapy # or pip $ pip install gseapy # or uv $ uv add gseapy If pip install failed, install Rust first and build from source: # install rust toolchain curl https://sh.rustup.rs -sSf | sh -s -- -y export PATH= " $PATH : $HOME /.cargo/bin " # then install via pip or uv $ pip install gseapy # or $ uv add gseapy Dependency Python 3.8+ Mandatory build Rust: For gseapy > 0.11.0, Rust compiler is needed setuptools-rust run Numpy >= 1.13.0 Scipy Pandas Matplotlib Requests Run GSEApy For command line usage: # An example to reproduce figures using replot module. $ gseapy replot -i ./Gsea.reports -o test # An example to run GSEA using gseapy gsea module $ gseapy gsea -d exptable.txt -c test.cls -g gene_sets.gmt -o test # An example to run Prerank using gseapy prerank module $ gseapy prerank -r gsea_data.rnk -g gene_sets.gmt -o test # An example to run ssGSEA using gseapy ssgsea module $ gseapy ssgsea -d expression.txt -g gene_sets.gmt -o test # An example to run GSVA using gseapy ssgsea module $ gseapy gsva -d expression.txt -g gene_sets.gmt -o test # An example to use enrichr api # see details for -g input -> ``get_library_name`` $ gseapy enrichr -i gene_list.txt -g KEGG_2016 -o test Run gseapy inside python console: Prepare expression.txt, gene_sets.gmt and test.cls required by GSEA, you could do this import gseapy # run GSEA. gseapy . gsea ( data = 'expression.txt' , gene_sets = 'gene_sets.gmt' , cls = 'test.cls' , outdir = 'test' ) # run prerank gseapy . prerank ( rnk = 'gsea_data.rnk' , gene_sets = 'gene_sets.gmt' , outdir = 'test' ) # run ssGSEA gseapy . ssgsea ( data = "expression.txt" , gene_sets = "gene_sets.gmt" , outdir = 'test' ) # run GSVA gseapy . gsva ( data = "expression.txt" , gene_sets = "gene_sets.gmt" , outdir = 'test' ) # An example to reproduce figures using replot module. gseapy . replot ( indir = './Gsea.reports' , outdir = 'test' ) If you prefer to use Dataframe, dict, list in interactive python console, you could do this. see detail here: Example # assign dataframe, and use enrichr library data set 'KEGG_2016' expression_dataframe = pd . DataFrame () sample_name = [ 'A' , 'A' , 'A' , 'B' , 'B' , 'B' ] # always only two group,any names you like # assign gene_sets parameter with enrichr library name or gmt file on your local computer. gseapy . gsea ( data = expression_dataframe , gene_sets = 'KEGG_2016' , cls = sample_names , outdir = 'test' ) # prerank tool gene_ranked_dataframe = pd . DataFrame () gseapy . prerank ( rnk = gene_ranked_dataframe , gene_sets = 'KEGG_2016' , outdir = 'test' ) # ssGSEA gseapy . ssgsea ( data = expression_dataframe , gene_sets = 'KEGG_2016' , outdir = 'test' ) # gsva gseapy . gsva ( data = expression_dataframe , gene_sets = 'KEGG_2016' , outdir = 'test' ) For enrichr , you could assign a list, pd.Series, pd.DataFrame object, or a txt file (should be one gene name per row.) # assign a list object to enrichr gl = [ 'SCARA3' , 'LOC100044683' , 'CMBL' , 'CLIC6' , 'IL13RA1' , 'TACSTD2' , 'DKKL1' , 'CSF1' , 'SYNPO2L' , 'TINAGL1' , 'PTX3' , 'BGN' , 'HERC1' , 'EFNA1' , 'CIB2' , 'PMP22' , 'TMEM173' ] gseapy . enrichr ( gene_list = gl , gene_sets = 'KEGG_2016' , outdir = 'test' ) # or a txt file path. gseapy . enrichr ( gene_list = 'gene_list.txt' , gene_sets = 'KEGG_2016' , outdir = 'test' , cutoff = 0.05 , format = 'png' ) GSEApy supported gene set libaries : To see the full list of gseapy supported gene set libraries, please click here: Library Or use get_library_name function inside python console. #see full list of latest enrichr library names, which will pass to -g parameter: names = gseapy . get_library_name () # show top 20 entries. print ( names [: 20 ]) [ 'Genome_Browser_PWMs' , 'TRANSFAC_and_JASPAR_PWMs' , 'ChEA_2013' , 'Drug_Perturbations_from_GEO_2014' , 'ENCODE_TF_ChIP-seq_2014' , 'BioCarta_2013' , 'Reactome_2013' , 'WikiPathways_2013' , 'Disease_Signatures_from_GEO_up_2014' , 'KEGG_2016' , 'TF-LOF_Expression_from_GEO' , 'TargetScan_microRNA' , 'PPI_Hub_Proteins' , 'GO_Molecular_Function_2015' , 'GeneSigDB' , 'Chromosome_Location' , 'Human_Gene_Atlas' , 'Mouse_Gene_Atlas' , 'GO_Cellular_Component_2015' , 'GO_Biological_Process_2015' , 'Human_Phenotype_Ontology' ,] Dev # clone and set up dev environment (requires Rust toolchain) $ git clone https://github.com/zqfang/GSEApy.git $ cd GSEApy $ uv sync --extra dev # run tests $ uv run pytest # lint and format $ uv run ruff format gseapy $ uv run ruff check gseapy # test rust extension only $ cargo test --features=extension-module # build wheel + sdist locally $ uv build Bug Report If you would like to report any bugs when use gseapy, don't hesitate to create an issue on github here. To get help of GSEApy See Frequently Asked Questions Visit the document site at Examples The GSEApy discussion channel: Q&A About Gene Set Enrichment Analysis in Python gseapy.rtfd.io/ Topics rust python3 enrichment-analysis gsea Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Stars 696 stars Watchers 11 watching Forks 136 forks Report repository Releases 45 gseapy-v1.2.1 Latest Apr 27, 2026 + 44 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 67.6% Rust 31.8% Other 0.6% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gseapy --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +gseapy 0.4.2 py27_0 +------------------- +file name : gseapy-0.4.2-py27_0.tar.bz2 +name : gseapy +version : 0.4.2 +build : py27_0 +build number: 0 +size : 29 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.4.2-py27_0.tar.bz2 +md5 : cb72c2a319e1678ab01abd523d88c0a2 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 2.7* + + +gseapy 0.4.2 py34_0 +------------------- +file name : gseapy-0.4.2-py34_0.tar.bz2 +name : gseapy +version : 0.4.2 +build : py34_0 +build number: 0 +size : 29 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.4.2-py34_0.tar.bz2 +md5 : 2e9dac2dc4803529520e9a858a61ea00 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.4* + + +gseapy 0.4.2 py35_0 +------------------- +file name : gseapy-0.4.2-py35_0.tar.bz2 +name : gseapy +version : 0.4.2 +build : py35_0 +build number: 0 +size : 29 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.4.2-py35_0.tar.bz2 +md5 : ec28dfe2ae1b52d0ab7011ae3e673df9 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.5* + + +gseapy 0.5.2a0 py27_0 +--------------------- +file name : gseapy-0.5.2a0-py27_0.tar.bz2 +name : gseapy +version : 0.5.2a0 +build : py27_0 +build number: 0 +size : 32 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.5.2a0-py27_0.tar.bz2 +md5 : 3da6e5274030a69a01d4d4b072aa7724 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 2.7* + - requests + + +gseapy 0.5.2a0 py34_0 +--------------------- +file name : gseapy-0.5.2a0-py34_0.tar.bz2 +name : gseapy +version : 0.5.2a0 +build : py34_0 +build number: 0 +size : 32 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.5.2a0-py34_0.tar.bz2 +md5 : 516d75f83010e134143fa641cfd402ec +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.4* + - requests + + +gseapy 0.5.2a0 py35_0 +--------------------- +file name : gseapy-0.5.2a0-py35_0.tar.bz2 +name : gseapy +version : 0.5.2a0 +build : py35_0 +build number: 0 +size : 32 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.5.2a0-py35_0.tar.bz2 +md5 : 9f7aa010ac1731af4a2b867e55ce7755 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.5* + - requests + + +gseapy 0.5.3 py27_0 +------------------- +file name : gseapy-0.5.3-py27_0.tar.bz2 +name : gseapy +version : 0.5.3 +build : py27_0 +build number: 0 +size : 33 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.5.3-py27_0.tar.bz2 +md5 : a341be400e57cf64e523f8e21f6b822b +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 2.7* + - requests + + +gseapy 0.5.3 py34_0 +------------------- +file name : gseapy-0.5.3-py34_0.tar.bz2 +name : gseapy +version : 0.5.3 +build : py34_0 +build number: 0 +size : 33 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.5.3-py34_0.tar.bz2 +md5 : 00029fb71699c147067841e4b740abd1 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.4* + - requests + + +gseapy 0.5.3 py35_0 +------------------- +file name : gseapy-0.5.3-py35_0.tar.bz2 +name : gseapy +version : 0.5.3 +build : py35_0 +build number: 0 +size : 33 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.5.3-py35_0.tar.bz2 +md5 : bb63bf6dec07211f80dd67da62424c25 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.5* + - requests + + +gseapy 0.6.0 py27_0 +------------------- +file name : gseapy-0.6.0-py27_0.tar.bz2 +name : gseapy +version : 0.6.0 +build : py27_0 +build number: 0 +size : 35 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.6.0-py27_0.tar.bz2 +md5 : 0e413930d073b9a8cc18db8c99bd4a22 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 2.7* + - requests + + +gseapy 0.6.0 py34_0 +------------------- +file name : gseapy-0.6.0-py34_0.tar.bz2 +name : gseapy +version : 0.6.0 +build : py34_0 +build number: 0 +size : 35 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.6.0-py34_0.tar.bz2 +md5 : e07726f1531891d4773019fb9868a32e +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.4* + - requests + + +gseapy 0.6.0 py35_0 +------------------- +file name : gseapy-0.6.0-py35_0.tar.bz2 +name : gseapy +version : 0.6.0 +build : py35_0 +build number: 0 +size : 35 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.6.0-py35_0.tar.bz2 +md5 : 064743bdf6d1eeac18df7861cb8a9865 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.5* + - requests + + +gseapy 0.6.2 py27_0 +------------------- +file name : gseapy-0.6.2-py27_0.tar.bz2 +name : gseapy +version : 0.6.2 +build : py27_0 +build number: 0 +size : 35 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.6.2-py27_0.tar.bz2 +md5 : e9f7f8ef70938e0d8928ae09017cdce0 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 2.7* + - requests + + +gseapy 0.6.2 py34_0 +------------------- +file name : gseapy-0.6.2-py34_0.tar.bz2 +name : gseapy +version : 0.6.2 +build : py34_0 +build number: 0 +size : 35 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.6.2-py34_0.tar.bz2 +md5 : c6fc7128a6d4cd5c9d7bbdde992b4fdc +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.4* + - requests + + +gseapy 0.6.2 py35_0 +------------------- +file name : gseapy-0.6.2-py35_0.tar.bz2 +name : gseapy +version : 0.6.2 +build : py35_0 +build number: 0 +size : 35 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.6.2-py35_0.tar.bz2 +md5 : a3801c1e3b13b881d51be188f5513b96 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.5* + - requests + + +gseapy 0.7.2 py27_0 +------------------- +file name : gseapy-0.7.2-py27_0.tar.bz2 +name : gseapy +version : 0.7.2 +build : py27_0 +build number: 0 +size : 41 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.7.2-py27_0.tar.bz2 +md5 : 343b69380ab7d87a1e6f4c1501e9a51e +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 2.7* + - requests + + +gseapy 0.7.2 py34_0 +------------------- +file name : gseapy-0.7.2-py34_0.tar.bz2 +name : gseapy +version : 0.7.2 +build : py34_0 +build number: 0 +size : 41 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.7.2-py34_0.tar.bz2 +md5 : 0ef569a9ce62f43951423d1568686e58 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.4* + - requests + + +gseapy 0.7.2 py35_0 +------------------- +file name : gseapy-0.7.2-py35_0.tar.bz2 +name : gseapy +version : 0.7.2 +build : py35_0 +build number: 0 +size : 41 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.7.2-py35_0.tar.bz2 +md5 : a13b03507193e679456dd8f66faa5246 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.5* + - requests + + +gseapy 0.7.3 py27_0 +------------------- +file name : gseapy-0.7.3-py27_0.tar.bz2 +name : gseapy +version : 0.7.3 +build : py27_0 +build number: 0 +size : 40 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.7.3-py27_0.tar.bz2 +md5 : 6df48044f33afecbe8e30cf8547f1b3a +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 2.7* + - requests + + +gseapy 0.7.3 py34_0 +------------------- +file name : gseapy-0.7.3-py34_0.tar.bz2 +name : gseapy +version : 0.7.3 +build : py34_0 +build number: 0 +size : 41 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.7.3-py34_0.tar.bz2 +md5 : 3e5805e3884d22f31c7d731b18afbfec +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.4* + - requests + + +gseapy 0.7.3 py35_0 +------------------- +file name : gseapy-0.7.3-py35_0.tar.bz2 +name : gseapy +version : 0.7.3 +build : py35_0 +build number: 0 +size : 41 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.7.3-py35_0.tar.bz2 +md5 : c11710e6c4f39749db6dc7166d135ea0 +dependencies: + - beautifulsoup4 >=4.4.1 + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 3.5* + - requests + + +gseapy 0.7.4 py27_0 +------------------- +file name : gseapy-0.7.4-py27_0.tar.bz2 +name : gseapy +version : 0.7.4 +build : py27_0 +build number: 0 +size : 42 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.7.4-py27_0.tar.bz2 +md5 : 416f31382b155890e14e5b5b942ece25 +dependencies: + - beautifulsoup4 >=4.4.1 + - html5lib + - lxml + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 2.7* + - requests + + +gseapy 0.7.4 py27_3 +------------------- +file name : gseapy-0.7.4-py27_3.tar.bz2 +name : gseapy +version : 0.7.4 +build : py27_3 +build number: 3 +size : 42 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.7.4-py27_3.tar.bz2 +md5 : 0db520de25d1c349bcb5730f3df07f1c +dependencies: + - beautifulsoup4 >=4.4.1 + - html5lib + - lxml + - matplotlib >=1.4.3 + - numpy >=1.8.0 + - pandas >=0.16 + - python 2.7* + - requests + + +gseapy 0.7.4 py34_0 +------------------- +file name : gseapy-0.7.4-py34_0.tar.bz2 +name : gseapy +version : 0.7.4 +build : py34_0 +build number: 0 +size : 42 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gseapy-0.7.4-py34_0.tar.bz2 +md5 : 2b1b68eb49915269e013 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gtdbtk.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gtdbtk.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..cebdc6b0b73bb4c627c56d24786db949e4b1d49d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/gtdbtk.manual_bundle.txt @@ -0,0 +1,538 @@ +# Tool: gtdbtk +software_name: gtdbtk +tier: T1 +domain: t1_backfill_overall +downloads: 215266 +summary: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. +description: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. +dependencies: dendropy >=4.1.0, fastani >=1.32, fasttree >=2.1.9, hmmer 3.*, numpy >=1.9.0, pplacer 1.1.alpha19.*, prodigal >=2.6.2, pydantic >=1.9.2,<2, python >=3.6,<3.14, skani >=0.3.0, tqdm >=4.35.0 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: http://pypi.python.org/pypi/gtdbtk/ +doc_url: https://ecogenomics.github.io/GTDBTk +dev_url: https://github.com/Ecogenomics/GTDBTk + +## CLI Help Source +cli:gtdbtk +## CLI Help Content +$ conda run -n bioenv_cli gtdbtk --help +[rc=1] + +================================================================================ + ERROR +________________________________________________________________________________ + + The GTDB-Tk reference data does not exist or is corrupted. + GTDBTK_DATA_PATH=/225040511/miniconda3/envs/bioenv_cli/share/gtdbtk-1.1.1/db/ + + Please compare the checksum to those provided in the download repository. + https://github.com/Ecogenomics/GTDBTk#gtdb-tk-reference-data +================================================================================ + + +ERROR conda.cli.main_run:execute(127): `conda run gtdbtk --help` failed. (See above for error) + + +## URL Docs Extract +### https://ecogenomics.github.io/GTDBTk +GTDB-Tk — GTDB-Tk 2.7.1 documentation 2.7.1 Getting started Announcements Installing GTDB-Tk FAQ Running GTDB-Tk Performance and Accuracy Commands Files Example About Change log References GTDB-Tk » GTDB-Tk Edit on GitHub GTDB-Tk ¶ GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB . It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3) . Notifications about GTDB-Tk releases will be available through the GTDB Bluesky account https://bsky.app/profile/ace-gtdb.bsky.social . Please post questions and issues related to GTDB-Tk on the Issues section of the GitHub repository. Questions related to the GTDB should be sent to the GTDB team . Running GTDB-Tk ¶ Install GTDB-Tk (or use the third-party web application) ( Installing GTDB-Tk ) Access the help documentation Commands , or view the program help menu: gtdbtk -h Note: Individual help can be accessed via the specific command, e.g.: gtdbtk classify_wf -h Citing GTDB-Tk ¶ We encourage you to cite GTDB-Tk and the third-party dependencies as described in References . Getting started Announcements Installing GTDB-Tk FAQ Running GTDB-Tk Performance and Accuracy Commands Files Example About Change log References Next © Copyright 2026, Pierre-Alain Chaumeil, Aaron Mussig and Donovan Parks. Built with Sphinx using a theme provided by Read the Docs . + +### http://pypi.python.org/pypi/gtdbtk/ +gtdbtk · PyPI Skip to main content Switch to mobile version Warning You are using an unsupported browser, upgrade to a newer version. Warning Some features may not work without JavaScript. Please try enabling it if you encounter problems. Search PyPI search-focus#focusSearchField" data-search-focus-target="searchField"> Search Help Docs Sponsors Log in Register Menu Help Docs Sponsors Log in Register Search PyPI Search gtdbtk 2.7.1 pip install gtdbtk Copy PIP instructions Latest version Released: Apr 17, 2026 A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. Navigation Project description Release history Download files Verified details These details have been verified by PyPI Maintainers aaronmussig dparks pierrec Unverified details These details have not been verified by PyPI Project links Homepage Meta License: GNU General Public License v3 (GPLv3) (GPL3) Author: Pierre-Alain Chaumeil, Aaron Mussig and Donovan Parks Maintainer: Pierre-Alain Chaumeil, Aaron Mussig and Donovan Parks Requires: Python >=3.6 Classifiers Development Status 5 - Production/Stable Intended Audience Science/Research License OSI Approved :: GNU General Public License v3 (GPLv3) Natural Language English Programming Language Python :: 3 Python :: 3.6 Python :: 3.7 Python :: 3.8 Python :: 3.9 Python :: 3.10 Python :: 3.11 Python :: 3.12 Python :: 3.13 Topic Scientific/Engineering :: Bio-Informatics Report project as malware Project description Project details Release history Download files Project description GTDB-Tk GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy ( GTDB ). It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3) . Notifications about GTDB-Tk releases will be available through the GTDB Twitter account and the GTDB Announcements Forum . Please post questions and issues related to GTDB-Tk on the Issues section of the GitHub repository. Questions related to the GTDB can be posted on the GTDB Forum or sent to the GTDB team . 🚀 Getting started Be sure to check the hardware requirements , then choose your preferred method: Bioconda Docker pip 📖 Documentation Documentation for GTDB-Tk can be found here . ✨ New Features GTDB-Tk v2.7.0+ includes the following new features: Pre-sketched skani database: GTDB-Tk now uses a skani pre-sketched database of the GTDB representative genomes. This significantly reduces the database storage footprint from 198 GB (in Release 232) down to 98 GB. Representative genomes availability: The GTDB representative genomes are now available via the "Download" page on the GTDB website. Deprecated flag: Because the database is already sketched natively, the --skani_sketch_dir flag is now deprecated. Replaced --skip_ani_screen with --place_species : The --skip_ani_screen flag is now deprecated in v2.7.0 and has been replaced by the --place_species flag. The logic has been updated to reflect the new database structure: Previously: Using --skip_ani_screen , genomes placed in a genus by pplacer were only compared to representative genomes within that specific genus. Now: Because the database is a single skani sketch, user genomes are compared against all GTDB reference genomes once at the very beginning of the pipeline. When the new --place_species flag is selected, the genomes are still explicitly placed in the reference tree. ⚠️ IMPORTANT MEMORY WARNING: The divide-and-conquer approach now requires more than 128 GB of RAM. Specifically, you will need at least 140 GB of RAM for R232. 📈 Performance Using ANI screen "can" reduce computation by >50%, although it depends on the set of input genomes. A set of input genomes consisting primarily of new species will not benefit from ANI screen as much as a set of genomes that are largely assigned to GTDB species clusters. In the latter case, the ANI screen will reduce the number of genomes that need to be classified by pplacer which reduces computation time substantially (between 25% and 60% in our testing). 📚 References GTDB-Tk is described in: Chaumeil PA, et al. 2022. GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database . Bioinformatics , btac672. Chaumeil PA, et al. 2019. GTDB-Tk: A toolkit to classify genomes with the Genome Taxonomy Database . Bioinformatics , btz848. The Genome Taxonomy Database (GTDB) is described in: Parks, D.H., et al. (2021). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy . Nucleic Acids Research , 50 : D785–D794. Rinke, C, et al. (2021). A standardized archaeal taxonomy for the Genome Taxonomy Database . Nature Microbiology , 6 : 946–959. Parks, D.H., et al. 2020. A complete domain-to-species taxonomy for Bacteria and Archaea . Nature Biotechnology , https://doi.org/10.1038/s41587-020-0501-8 . Parks DH, et al. 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life . Nature Biotechnology , http://dx.doi.org/10.1038/nbt.4229 . We strongly encourage you to cite the following 3rd party dependencies: Matsen FA, et al. 2010. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree . BMC Bioinformatics , 11:538. Shaw J. and Yu Y.W. 2023. Fast and robust metagenomic sequence comparison through sparse chaining with skani . Nature Methods , 20, pages1661–1665 (2023). Hyatt D, et al. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification . BMC Bioinformatics , 11:119. doi: 10.1186/1471-2105-11-119. Price MN, et al. 2010. FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments . PLoS One , 5, e9490. Eddy SR. 2011. Accelerated profile HMM searches . PLOS Comp. Biol. , 7:e1002195. © Copyright Copyright 2017 Pierre-Alain Chaumeil. See LICENSE for further details. Project details Verified details These details have been verified by PyPI Maintainers aaronmussig dparks pierrec Unverified details These details have not been verified by PyPI Project links Homepage Meta License: GNU General Public License v3 (GPLv3) (GPL3) Author: Pierre-Alain Chaumeil, Aaron Mussig and Donovan Parks Maintainer: Pierre-Alain Chaumeil, Aaron Mussig and Donovan Parks Requires: Python >=3.6 Classifiers Development Status 5 - Production/Stable Intended Audience Science/Research License OSI Approved :: GNU General Public License v3 (GPLv3) Natural Language English Programming Language Python :: 3 Python :: 3.6 Python :: 3.7 Python :: 3.8 Python :: 3.9 Python :: 3.10 Python :: 3.11 Python :: 3.12 Python :: 3.13 Topic Scientific/Engineering :: Bio-Informatics Release history Release notifications | RSS feed This version 2.7.1 Apr 17, 2026 2.7.0 Apr 15, 2026 2.6.1 Dec 12, 2025 2.6.0 Dec 10, 2025 2.5.2 Sep 12, 2025 2.5.1 Sep 9, 2025 2.5.0 Sep 8, 2025 2.4.1 Apr 18, 2025 2.4.0 Apr 24, 2024 2.3.2 Jul 5, 2023 2.3.0 May 9, 2023 2.2.6 Mar 23, 2023 2.2.5 Mar 16, 2023 2.2.4 Feb 28, 2023 2.2.3 Feb 15, 2023 2.2.2 Feb 14, 2023 2.2.1 Feb 14, 2023 2.2.0 Feb 14, 2023 2.1.1 Jul 11, 2022 2.1.0 May 12, 2022 2.0.0 Apr 8, 2022 1.7.0 Oct 15, 2021 1.6.0 Aug 20, 2021 1.5.1 Jun 24, 2021 1.5.0 Apr 26, 2021 1.4.1 Feb 3, 2021 1.4.0 Nov 30, 2020 1.3.0 Jul 18, 2020 1.2.0 May 29, 2020 1.1.1 Apr 22, 2020 1.1.0 Apr 14, 2020 1.0.2 Dec 12, 2019 1.0.1 Dec 5, 2019 1.0.0 Dec 5, 2019 0.3.3 Nov 15, 2019 0.3.2 Jul 12, 2019 0.3.1 Jul 8, 2019 0.3.0 Jun 21, 2019 0.2.2 Mar 18, 2019 0.2.1 Mar 8, 2019 0.1.6 Jan 14, 2019 0.1.3 Sep 21, 2018 0.1.2 Sep 18, 2018 0.1.1 Aug 30, 2018 0.1.0 Aug 30, 2018 0.0.8b1 pre-release Jun 20, 2018 0.0.7 Apr 19, 2018 0.0.6 Apr 19, 2018 0.0.5 Mar 16, 2018 0.0.4b3 pre-release Mar 8, 2018 0.0.4b2 pre-release Mar 8, 2018 0.0.4b1 pre-release Mar 1, 2018 0.0.4b0 pre-release Feb 28, 2018 0.0.3 Feb 27, 2018 0.0.2 Feb 27, 2018 0.0.1 Aug 22, 2017 Download files Download the file for your platform. If you're not sure which to choose, learn more about installing packages . Source Distribution gtdbtk-2.7.1.tar.gz (1.7 MB view details ) Uploaded Apr 17, 2026 Source Built Distribution Filter files by name, interpreter, ABI, and platform. If you're not sure about the file name format, learn more about wheel file names . The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files. Copy a direct link to the current filters Copy File name Interpreter Interpreter py3 ABI ABI none Platform Platform any gtdbtk-2.7.1-py3-none-any.whl (1.8 MB view details ) Uploaded Apr 17, 2026 Python 3 File details Details for the file gtdbtk-2.7.1.tar.gz . File metadata Download URL: gtdbtk-2.7.1.tar.gz Upload date: Apr 17, 2026 Size: 1.7 MB Tags: Source Uploaded using Trusted Publishing? No Uploaded via: twine/6.1.0 CPython/3.8.18 File hashes Hashes for gtdbtk-2.7.1.tar.gz Algorithm Hash digest SHA256 657c6b63b7d2fa7e875acbc075ff8d0b20e2a0d761125f527cded90c0c957c0a Copy MD5 10c55817ee59c8f3c06e4f00d46f0318 Copy BLAKE2b-256 8c863e58e4af7aab2bf4d819390bbfa74688fc93b06483534948465a18dcf7f5 Copy See more details on using hashes here. File details Details for the file gtdbtk-2.7.1-py3-none-any.whl . File metadata Download URL: gtdbtk-2.7.1-py3-none-any.whl Upload date: Apr 17, 2026 Size: 1.8 MB Tags: Python 3 Uploaded using Trusted Publishing? No Uploaded via: twine/6.1.0 CPython/3.8.18 File hashes Hashes for gtdbtk-2.7.1-py3-none-any.whl Algorithm Hash digest SHA256 9279bb39ca5e6c386d655616d31d82b7a587f6b357beb1f99fafd8965ade24da Copy MD5 10c64436e4d508bbb834f80a8e19deba Copy BLAKE2b-256 4411b91c8c2ac8bdf59e55ae4efa026ffbfe18141aa910de6f5b17150a47e6c7 Copy See more details on using hashes here. Help Installing packages Uploading packages User guide Project name retention FAQs About PyPI PyPI Blog Infrastructure dashboard Statistics Logos & trademarks Our sponsors Contributing to PyPI Bugs and feedback Contribute on GitHub Translate PyPI Sponsor PyPI Development credits Using PyPI Terms of Service Report security issue Code of conduct Privacy Notice Acceptable Use Policy Status: all systems operational Developed and maintained by the Python community, for the Python community. Donate today! "PyPI", "Python Package Index", and the blocks logos are registered trademarks of the Python Software Foundation . © 2026 Python Software Foundation Site map Switch to desktop version English español français 日本語 português (Brasil) українська Ελληνικά Deutsch 中文 (简体) 中文 (繁體) русский עברית Esperanto 한국어 Supported by AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page + +### https://github.com/Ecogenomics/GTDBTk +GitHub - Ecogenomics/GTDBTk: GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Ecogenomics / GTDBTk Public Notifications You must be signed in to change notification settings Fork 97 Star 597 Code Issues 28 Pull requests 0 Actions Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Wiki Security and quality Insights Ecogenomics/GTDBTk master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,062 Commits 1,062 Commits .github .github docs docs gtdbtk gtdbtk scripts scripts tests tests .gitignore .gitignore CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md CONTRIBUTING.md CONTRIBUTING.md Dockerfile Dockerfile LICENSE LICENSE README.md README.md setup.py setup.py View all files Repository files navigation README Code of conduct Contributing GPL-3.0 license GTDB-Tk GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy ( GTDB ). It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3) . Notifications about GTDB-Tk releases will be available through the GTDB Twitter account and the GTDB Announcements Forum . Please post questions and issues related to GTDB-Tk on the Issues section of the GitHub repository. Questions related to the GTDB can be posted on the GTDB Forum or sent to the GTDB team . 🚀 Getting started Be sure to check the hardware requirements , then choose your preferred method: Bioconda Docker pip 📖 Documentation Documentation for GTDB-Tk can be found here . ✨ New Features GTDB-Tk v2.7.0+ includes the following new features: Pre-sketched skani database: GTDB-Tk now uses a skani pre-sketched database of the GTDB representative genomes. This significantly reduces the database storage footprint from 198 GB (in Release 232) down to 98 GB. Representative genomes availability: The GTDB representative genomes are now available via the "Download" page on the GTDB website. Deprecated flag: Because the database is already sketched natively, the --skani_sketch_dir flag is now deprecated. Replaced --skip_ani_screen with --place_species : The --skip_ani_screen flag is now deprecated in v2.7.0 and has been replaced by the --place_species flag. The logic has been updated to reflect the new database structure: Previously: Using --skip_ani_screen , genomes placed in a genus by pplacer were only compared to representative genomes within that specific genus. Now: Because the database is a single skani sketch, user genomes are compared against all GTDB reference genomes once at the very beginning of the pipeline. When the new --place_species flag is selected, the genomes are still explicitly placed in the reference tree. ⚠️ IMPORTANT MEMORY WARNING: The divide-and-conquer approach now requires more than 128 GB of RAM. Specifically, you will need at least 140 GB of RAM for R232. 📈 Performance Using ANI screen "can" reduce computation by >50%, although it depends on the set of input genomes. A set of input genomes consisting primarily of new species will not benefit from ANI screen as much as a set of genomes that are largely assigned to GTDB species clusters. In the latter case, the ANI screen will reduce the number of genomes that need to be classified by pplacer which reduces computation time substantially (between 25% and 60% in our testing). 📚 References GTDB-Tk is described in: Chaumeil PA, et al. 2022. GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database . Bioinformatics , btac672. Chaumeil PA, et al. 2019. GTDB-Tk: A toolkit to classify genomes with the Genome Taxonomy Database . Bioinformatics , btz848. The Genome Taxonomy Database (GTDB) is described in: Parks, D.H., et al. (2021). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy . Nucleic Acids Research , 50 : D785–D794. Rinke, C, et al. (2021). A standardized archaeal taxonomy for the Genome Taxonomy Database . Nature Microbiology , 6 : 946–959. Parks, D.H., et al. 2020. A complete domain-to-species taxonomy for Bacteria and Archaea . Nature Biotechnology , https://doi.org/10.1038/s41587-020-0501-8 . Parks DH, et al. 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life . Nature Biotechnology , http://dx.doi.org/10.1038/nbt.4229 . We strongly encourage you to cite the following 3rd party dependencies: Matsen FA, et al. 2010. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree . BMC Bioinformatics , 11:538. Shaw J. and Yu Y.W. 2023. Fast and robust metagenomic sequence comparison through sparse chaining with skani . Nature Methods , 20, pages1661–1665 (2023). Hyatt D, et al. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification . BMC Bioinformatics , 11:119. doi: 10.1186/1471-2105-11-119. Price MN, et al. 2010. FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments . PLoS One , 5, e9490. Eddy SR. 2011. Accelerated profile HMM searches . PLOS Comp. Biol. , 7:e1002195. © Copyright Copyright 2017 Pierre-Alain Chaumeil. See LICENSE for further details. About GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. ecogenomics.github.io/GTDBTk/ Topics bioinformatics nomenclature taxonomy metagenomics phylogenetics bacteria archaea species-assignments Resources Readme License GPL-3.0 license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 597 stars Watchers 20 watching Forks 97 forks Report repository Releases 50 2.7.1 Latest Apr 17, 2026 + 49 releases Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.6% Other 0.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge gtdbtk --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +gtdbtk 0.1.3 py27_0 +------------------- +file name : gtdbtk-0.1.3-py27_0.tar.bz2 +name : gtdbtk +version : 0.1.3 +build : py27_0 +build number: 0 +size : 116 KB +license : GNU General Public v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gtdbtk-0.1.3-py27_0.tar.bz2 +md5 : 61c93f612de8032cf78955f04921d3bf +timestamp : 2018-10-05 06:21:40 UTC +dependencies: + - biolib >=0.0.43 + - dendropy >=4.1.0 + - fastani + - fasttree + - hmmer + - jinja2 >=2.7.3 + - mpld3 >=0.2 + - perl-gtdbtk + - pplacer + - prodigal + - python >=2.7,<2.8.0a0 + - scipy + + +gtdbtk 0.1.5 py27_0 +------------------- +file name : gtdbtk-0.1.5-py27_0.tar.bz2 +name : gtdbtk +version : 0.1.5 +build : py27_0 +build number: 0 +size : 123 KB +license : GNU General Public v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gtdbtk-0.1.5-py27_0.tar.bz2 +md5 : 042b69dc70678372fe2e730944e2d765 +timestamp : 2019-01-12 21:33:53 UTC +dependencies: + - biolib >=0.0.43 + - dendropy >=4.1.0 + - fastani + - fasttree + - hmmer + - jinja2 >=2.7.3 + - mpld3 >=0.2 + - perl-gtdbtk + - pplacer + - prodigal + - python >=2.7,<2.8.0a0 + - scipy + + +gtdbtk 0.1.6 py27_0 +------------------- +file name : gtdbtk-0.1.6-py27_0.tar.bz2 +name : gtdbtk +version : 0.1.6 +build : py27_0 +build number: 0 +size : 123 KB +license : GNU General Public v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gtdbtk-0.1.6-py27_0.tar.bz2 +md5 : 415596cc3add3e94528654a48caff52b +timestamp : 2019-02-08 07:49:36 UTC +dependencies: + - biolib >=0.0.43 + - dendropy >=4.1.0 + - fastani + - fasttree + - hmmer + - jinja2 >=2.7.3 + - mpld3 >=0.2 + - perl-gtdbtk + - pplacer + - prodigal + - python >=2.7,<2.8.0a0 + - scipy + + +gtdbtk 0.2.2 py27_0 +------------------- +file name : gtdbtk-0.2.2-py27_0.tar.bz2 +name : gtdbtk +version : 0.2.2 +build : py27_0 +build number: 0 +size : 1.6 MB +license : GNU General Public v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gtdbtk-0.2.2-py27_0.tar.bz2 +md5 : 493bbbd3f355b60873a66ecc629b8ad8 +timestamp : 2019-03-19 15:43:31 UTC +dependencies: + - dendropy >=4.1.0 + - fastani + - fasttree + - future >=0.15.2 + - hmmer + - pplacer + - prodigal + - python >=2.7,<2.8.0a0 + + +gtdbtk 0.3.0 py_0 +----------------- +file name : gtdbtk-0.3.0-py_0.tar.bz2 +name : gtdbtk +version : 0.3.0 +build : py_0 +build number: 0 +size : 1.5 MB +license : GNU General Public v3 (GPLv3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gtdbtk-0.3.0-py_0.tar.bz2 +md5 : 458520374bab0e14dcaaf13de1d4377b +timestamp : 2019-06-25 06:24:24 UTC +dependencies: + - dendropy >=4.1.0 + - fastani + - fasttree + - future >=0.15.2 + - hmmer + - pplacer + - prodigal + - python <3 + + +gtdbtk 0.3.0 py_1 +----------------- +file name : gtdbtk-0.3.0-py_1.tar.bz2 +name : gtdbtk +version : 0.3.0 +build : py_1 +build number: 1 +size : 1.5 MB +license : GNU General Public v3 (GPLv3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gtdbtk-0.3.0-py_1.tar.bz2 +md5 : 67b1d3912a8208fc029fd0a89d337fbc +timestamp : 2019-06-25 22:50:41 UTC +dependencies: + - dendropy >=4.1.0 + - fastani + - fasttree + - future >=0.15.2 + - hmmer + - pplacer + - prodigal + - python <3 + + +gtdbtk 0.3.1 py_0 +----------------- +file name : gtdbtk-0.3.1-py_0.tar.bz2 +name : gtdbtk +version : 0.3.1 +build : py_0 +build number: 0 +size : 1.5 MB +license : GNU General Public v3 (GPLv3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gtdbtk-0.3.1-py_0.tar.bz2 +md5 : 759cc4d1d49d9355d8607cb7f8e29c9a +timestamp : 2019-07-08 19:39:08 UTC +dependencies: + - dendropy >=4.1.0 + - fastani + - fasttree + - future >=0.15.2 + - hmmer + - pplacer + - prodigal + - python <3 + + +gtdbtk 0.3.2 py27_1 +------------------- +file name : gtdbtk-0.3.2-py27_1.tar.bz2 +name : gtdbtk +version : 0.3.2 +build : py27_1 +build number: 1 +size : 1.6 MB +license : GNU General Public v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gtdbtk-0.3.2-py27_1.tar.bz2 +md5 : 5287b092de206af8648fcbf1670ec3c4 +timestamp : 2019-08-07 19:00:45 UTC +dependencies: + - dendropy >=4.1.0 + - fastani + - fasttree + - future >=0.15.2 + - hmmer + - pplacer + - prodigal + - python >=2.7,<2.8.0a0 + + +gtdbtk 0.3.2 py27_2 +------------------- +file name : gtdbtk-0.3.2-py27_2.tar.bz2 +name : gtdbtk +version : 0.3.2 +build : py27_2 +build number: 2 +size : 1.6 MB +license : GNU General Public v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gtdbtk-0.3.2-py27_2.tar.bz2 +md5 : 7dcef17dfba6e9f0efe1fb362c0967e0 +timestamp : 2019-11-08 13:29:44 UTC +dependencies: + - dendropy >=4.1.0 + - fastani >=1.2 + - fasttree >=2.1.9 + - future >=0.15.2 + - hmmer >=3.1 + - pplacer >=1.1.alpha17 + - prodigal >=2.6.2 + - python >=2.7,<2.8.0a0 + + +gtdbtk 0.3.2 py_0 +----------------- +file name : gtdbtk-0.3.2-py_0.tar.bz2 +name : gtdbtk +version : 0.3.2 +build : py_0 +build number: 0 +size : 1.5 MB +license : GNU General Public v3 (GPLv3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gtdbtk-0.3.2-py_0.tar.bz2 +md5 : f2b1b6915ddd312abd7ec750f904222e +timestamp : 2019-07-12 08:27:13 UTC +dependencies: + - dendropy >=4.1.0 + - fastani + - fasttree + - future >=0.15.2 + - hmmer + - pplacer + - prodigal + - python <3 + + +gtdbtk 0.3.3 py27_0 +------------------- +file name : gtdbtk-0.3.3-py27_0.tar.bz2 +name : gtdbtk +version : 0.3.3 +build : py27_0 +build number: 0 +size : 1.6 MB +license : GNU General Public v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gtdbtk-0.3.3-py27_0.tar.bz2 +md5 : 47961130e06819daabce8c7b48baad9a +timestamp : 2019-11-15 07:12:10 UTC +dependencies: + - dendropy >=4.1.0 + - fastani >=1.2 + - fasttree >=2.1.9 + - future >=0.15.2 + - hmmer >=3.1 + - pplacer >=1.1.alpha17 + - prodigal >=2.6.2 + - python >=2.7,<2.8.0a0 + + +gtdbtk 1.0.0 py_0 +----------------- +file name : gtdbtk-1.0.0-py_0.tar.bz2 +name : gtdbtk +version : 1.0.0 +build : py_0 +build number: 0 +size : 1.5 MB +license : GNU General Public v3 (GPLv3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gtdbtk-1.0.0-py_0.tar.bz2 +md5 : a1f7ddbc2d48af2f86d2d5c0d72ebe69 +timestamp : 2019-12-05 08:03:24 UTC +dependencies: + - dendropy >=4.1.0 + - fastani >=1.2 + - fasttree >=2.1.9 + - future >=0.15.2 + - hmmer >=3.1 + - pplacer >=1.1.alpha17 + - prodigal >=2.6.2 + - python >=3.6 + + +gtdbtk 1.0.1 py38_1 +------------------- +file name : gtdbtk-1.0.1-py38_1.tar.bz2 +name : gtdbtk +version : 1.0.1 +build : py38_1 +build number: 1 +size : 1.6 MB +license : GNU General Public v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gtdbtk-1.0.1-py38_1.tar.bz2 +md5 : c50d11d9245f031911f100c584195009 +timestamp : 2019-12-06 00:10:51 UTC +dependencies: + - dendropy >=4.1.0 + - fastani >=1.2 + - fasttree >=2.1.9 + - hmmer >=3.1 + - pplacer >=1.1.alpha17 + - prodigal >=2.6.2 + - python >=3.8,<3.9.0a0 + + +gtdbtk 1.0.1 py_0 +----------------- +file name : gtdbtk-1.0.1-py_0.tar.bz2 +name : gtdbtk +version : 1.0.1 +build : py_0 +build number: 0 +size : 1.5 MB +license : GNU General Public v3 (GPLv3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gtdbtk-1.0.1-py_0.tar.bz2 +md5 : d50f33b0694150c20a0184604cff12c7 +timestamp : 2019-12-05 11:14:24 UTC +dependencies: + - dendropy >=4.1.0 + - fastani >=1.2 + - fasttree >=2.1.9 + - future >=0.15.2 + - hmmer >=3.1 + - pplacer >=1.1.alpha17 + - prodigal >=2.6.2 + - python >=3.6 + + +gtdbtk 1.0.2 py38_0 +------------------- +file name : gtdbtk-1.0.2-py38_0.tar.bz2 +name : gtdbtk +version : 1.0.2 +build : py38_0 +build number: 0 +size : 1.6 MB +license : GNU General Public v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gtdbtk-1.0.2-py38_0.tar.bz2 +md5 : 3716ccc71a0b105075a72f0d105a4018 +timestamp : 2019-12-12 06:10:04 UTC +dependencies: + - dendropy >=4.1.0 + - fastani >=1.2 + - fasttree >=2.1.9 + - hmmer >=3.1 + - pplacer >=1.1.alpha17 + - prodigal >=2.6.2 + - python >=3.8,<3.9.0a0 + + +gtdbtk 1.0.2 py38_1 +------------------- +file name : gtdbtk-1.0.2-py38_1.tar.bz2 +name : gtdbtk +version : 1.0.2 +build : py38_1 +build number: 1 +size : 1.6 MB +license : GNU General Public v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/gtdbtk-1.0.2-py38_1.tar.bz2 +md5 : 85fc711e46dc8ca1eaf22134021353a8 +timestamp : 2019-12-13 01:06:48 UTC +dependencies: + - dendropy >=4.1.0 + - fastani >=1.2 + - fasttree >=2.1.9 + - hmmer >=3.1 + - matplotlib + - numpy + - pplacer >=1.1.alpha17 + - prodigal >=2.6.2 + - python >=3.8,<3.9.0a0 + - scipy + + +gtdbtk 1.0.2 py_2 +----------------- +file name : gtdbtk-1.0.2-py_2.tar.bz2 +name : gtdbtk +version : 1.0.2 +build : py_2 +build number: 2 +size : 1.5 MB +license : GNU General Public v3 (GPLv3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gtdbtk-1.0.2-py_2.tar.bz2 +md5 : 32082a3663fb4b8004129e1634b95298 +timestamp : 2020-02-05 22:07:25 UTC +dependencies: + - dendropy >=4.1.0 + - fastani >=1.2 + - fasttree >=2.1.9 + - hmmer >=3.1 + - matplotlib-base + - numpy + - pplacer >=1.1.alpha17 + - prodigal >=2.6.2 + - python >=3.6 + - scipy + + +gtdbtk 1.0.2 py_3 +----------------- +file name : gtdbtk-1.0.2-py_3.tar.bz2 +name : gtdbtk +version : 1.0.2 +build : py_3 +build number: 3 +size : 1.5 MB +license : GNU General Public v3 (GPLv3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gtdbtk-1.0.2-py_3.tar.bz2 +md5 : aa4ef8dc82293ebfd9f3ac58d315ea13 +timestamp : 2020-03-12 00:22:16 UTC +dependencies: + - dendropy >=4.1.0 + - fastani >=1.2 + - fasttree >=2.1.9 + - hmmer 3.1b2 + - matplotlib-base + - numpy + - pplacer >=1.1.alpha17 + - prodigal >=2.6.2 + - python >=3.6 + - scipy + + +gtdbtk 1.1.0 py_0 +----------------- +file name : gtdbtk-1.1.0-py_0.tar.bz2 +name : gtdbtk +version : 1.1.0 +build : py_0 +build number: 0 +size : 1.5 MB +license : GNU General Public v3 (GPLv3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gtdbtk-1.1.0-py_0.tar.bz2 +md5 : a598541b6e89d672f4c3537ec107a8ab +timestamp : 2020-04-14 06:02:46 UTC +dependencies: + - dendropy >=4.1.0 + - fastani >=1.2 + - fasttree >=2.1.9 + - hmmer 3.1b2 + - mash >=2.0 + - numpy >=1.9.0 + - pplacer >=1.1.alpha17 + - prodigal >=2.6.2 + - python >=3.6 + + +gtdbtk 1.1.1 py_0 +----------------- +file name : gtdbtk-1.1.1-py_0.tar.bz2 +name : gtdbtk +version : 1.1.1 +build : py_0 +build number: 0 +size : 1.5 MB +license : GNU General Public v3 (GPLv3) +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/gtdbtk-1.1.1-py_0.tar.bz2 +md5 : 3f5c6313b3bcac9d1b3a3d02013e6b76 +timestamp : 2020-04-22 08:1 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/hicexplorer.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/hicexplorer.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..396673d18f23f1b3c2ffdafb312daf3fd1d32251 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/hicexplorer.manual_bundle.txt @@ -0,0 +1,530 @@ +# Tool: hicexplorer +software_name: hicexplorer +tier: T1 +domain: t1_backfill_overall +downloads: 214136 +summary: Set of programs to process, analyze and visualize Hi-C and capture Hi-C data +description: Set of programs to process, analyze and visualize Hi-C and capture Hi-C data +dependencies: biopython, cleanlab >=2.5, cooler >=0.9.3, fit_nbinom >=1.2, future, hic2cool >=0.8.3, hicmatrix >=17, hyperopt >=0.2.7, imbalanced-learn >=0.11, intervaltree, ipykernel >=6.25.2, jinja2, krbalancing >=0.0.5, matplotlib-base >=3.6, numpy >=1.19, pandas >=2.0, psutil, pybedtools >=0.9, pybigwig, pygenometracks >=3.8, pysam, pytables, python >=3.8, python-graphviz >=0.20, scikit-learn >=1.3,<1.4, scipy >=1.10, tqdm >=4.66, unidecode +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/deeptools/HiCExplorer +doc_url: https://hicexplorer.readthedocs.org/ +dev_url: https://github.com/deeptools/HiCExplorer + +## URL Docs Extract +### https://github.com/deeptools/HiCExplorer +GitHub - deeptools/HiCExplorer: HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} deeptools / HiCExplorer Public Notifications You must be signed in to change notification settings Fork 75 Star 271 Code Issues 160 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights deeptools/HiCExplorer master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 3,138 Commits 3,138 Commits .github .github bin bin docs docs examples examples hicexplorer hicexplorer .gitignore .gitignore .readthedocs.yml .readthedocs.yml .travis.yml .travis.yml CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE MANIFEST.in MANIFEST.in Makefile Makefile README.rst README.rst azure-pipelines.yml azure-pipelines.yml dev-requirements.txt dev-requirements.txt hicPlotTADS_template.ini hicPlotTADS_template.ini pytest.ini pytest.ini requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README Contributing GPL-3.0 license HiCExplorer Set of programs to process, analyze and visualize Hi-C, Micro-C and cHi-C data Sequencing techniques that probe the 3D organization of the genome generate large amounts of data whose processing, analysis and visualization is challenging. Here, we present HiCExplorer, a set of tools for the analysis and visualization of chromosome conformation data. HiCExplorer facilitates the creation of contact matrices, correction of contacts, TAD detection, A/B compartments, merging, reordering or chromosomes, conversion from different formats including cooler and detection of long-range contacts. Moreover, it allows the visualization of multiple contact matrices along with other types of data like genes, compartments, ChIP-seq coverage tracks (and in general any type of genomic scores), long range contacts and the visualization of viewpoints. With version 3.7.6 we introduce the support for Micro-C data for the build of matrices. Single-cell Hi-C data We provide the scHiCExplorer to create, manipulate, analyse and visualize single-cell Hi-C data in its own software: The scHiCExplorer . Citation: Joachim Wolff, Rolf Backofen, Björn Grüning. Loop detection using Hi-C data with HiCExplorer , GigaScience, Volume 11, 2022, giac061, https://doi.org/10.1093/gigascience/giac061 Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A Grüning. Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization, Nucleic Acids Research , Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W177–W184, https://doi.org/10.1093/nar/gkaa220 Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A Grüning. "Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization", Nucleic Acids Research , Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi: https://doi.org/10.1093/nar/gky504 Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening, Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke. "High-resolution TADs reveal DNA sequences underlying genome organization in flies". Nature Communications , Volume 9, Article number: 189 (2018), doi: https://doi.org/10.1038/s41467-017-02525-w Availability HiCExplorer is available as a command line suite of tools on this very GitHub repository and also on other platforms (detailed in Installation below). A Galaxy HiCExplorer version is directly available to users at http://hicexplorer.usegalaxy.eu . Training material is available at the Galaxy Training Network , while a Galaxy Tour is available here for users not familiar with this platform. Galaxy HiCExplorer is also available as a Docker image at the Docker Galaxy HiCExplorer GitHub repository . Finally, this Galaxy version is available on the Galaxy Tool Shed and on the corresponding GitHub repository . Installation With version 3.0, HiCExplorer is available for Python 3 only, the Python 2 support is discontinued. HiCExplorer can be installed with conda. Anaconda and GitHub for command line usage. Toolshed and Docker image for its integration on Galaxy servers. There are many easy ways to install HiCExplorer. Details can be found here . We strongly recommended to use conda to install HiCExplorer. Command line version Install with conda The easiest way to install HiCExplorer is using BioConda $ conda install hicexplorer -c bioconda -c conda-forge We highly recommend conda environments to separate software from each other. With it, different versions of dependencies do not interfere with each other. $ conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge $ conda activate hicexplorer To deactivate the environment use: $ conda deactivate To learn more about conda and environments, please consider the following documentation . Install by cloning this repository You can install any one of the HiCExplorer branches on command line (linux/mac) by cloning this git repository : $ git clone https://github.com/deeptools/HiCExplorer.git $ cd HiCExplorer $ python setup.py install If you don't have root permission, you can set a specific folder using the --prefix option $ python setup.py install --prefix /User/Tools/hicexplorer If you don't use conda, please take care of all dependencies on your own. Galaxy version Install with Docker Installation instructions as a Docker image can be followed at https://github.com/deeptools/docker-galaxy-hicexplorer . Install with Tool Shed Galaxy HiCExplorer is part of the Galaxy Tool Shed and can be installed from there to any Galaxy server following this link . Documentation: Please visit our complete documentation Here . This documentation is also available directly within Galaxy . About HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data. hicexplorer.readthedocs.org Topics python bioinformatics genomics galaxy hic chromosome-conformation-capture Resources Readme License GPL-3.0 license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 271 stars Watchers 11 watching Forks 75 forks Report repository Releases 47 November release 2024 Latest Nov 28, 2024 + 46 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 88.1% HTML 11.5% Other 0.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/deeptools/HiCExplorer +GitHub - deeptools/HiCExplorer: HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} deeptools / HiCExplorer Public Notifications You must be signed in to change notification settings Fork 75 Star 271 Code Issues 160 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights deeptools/HiCExplorer master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 3,138 Commits 3,138 Commits .github .github bin bin docs docs examples examples hicexplorer hicexplorer .gitignore .gitignore .readthedocs.yml .readthedocs.yml .travis.yml .travis.yml CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE MANIFEST.in MANIFEST.in Makefile Makefile README.rst README.rst azure-pipelines.yml azure-pipelines.yml dev-requirements.txt dev-requirements.txt hicPlotTADS_template.ini hicPlotTADS_template.ini pytest.ini pytest.ini requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README Contributing GPL-3.0 license HiCExplorer Set of programs to process, analyze and visualize Hi-C, Micro-C and cHi-C data Sequencing techniques that probe the 3D organization of the genome generate large amounts of data whose processing, analysis and visualization is challenging. Here, we present HiCExplorer, a set of tools for the analysis and visualization of chromosome conformation data. HiCExplorer facilitates the creation of contact matrices, correction of contacts, TAD detection, A/B compartments, merging, reordering or chromosomes, conversion from different formats including cooler and detection of long-range contacts. Moreover, it allows the visualization of multiple contact matrices along with other types of data like genes, compartments, ChIP-seq coverage tracks (and in general any type of genomic scores), long range contacts and the visualization of viewpoints. With version 3.7.6 we introduce the support for Micro-C data for the build of matrices. Single-cell Hi-C data We provide the scHiCExplorer to create, manipulate, analyse and visualize single-cell Hi-C data in its own software: The scHiCExplorer . Citation: Joachim Wolff, Rolf Backofen, Björn Grüning. Loop detection using Hi-C data with HiCExplorer , GigaScience, Volume 11, 2022, giac061, https://doi.org/10.1093/gigascience/giac061 Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A Grüning. Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization, Nucleic Acids Research , Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W177–W184, https://doi.org/10.1093/nar/gkaa220 Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A Grüning. "Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization", Nucleic Acids Research , Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi: https://doi.org/10.1093/nar/gky504 Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening, Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke. "High-resolution TADs reveal DNA sequences underlying genome organization in flies". Nature Communications , Volume 9, Article number: 189 (2018), doi: https://doi.org/10.1038/s41467-017-02525-w Availability HiCExplorer is available as a command line suite of tools on this very GitHub repository and also on other platforms (detailed in Installation below). A Galaxy HiCExplorer version is directly available to users at http://hicexplorer.usegalaxy.eu . Training material is available at the Galaxy Training Network , while a Galaxy Tour is available here for users not familiar with this platform. Galaxy HiCExplorer is also available as a Docker image at the Docker Galaxy HiCExplorer GitHub repository . Finally, this Galaxy version is available on the Galaxy Tool Shed and on the corresponding GitHub repository . Installation With version 3.0, HiCExplorer is available for Python 3 only, the Python 2 support is discontinued. HiCExplorer can be installed with conda. Anaconda and GitHub for command line usage. Toolshed and Docker image for its integration on Galaxy servers. There are many easy ways to install HiCExplorer. Details can be found here . We strongly recommended to use conda to install HiCExplorer. Command line version Install with conda The easiest way to install HiCExplorer is using BioConda $ conda install hicexplorer -c bioconda -c conda-forge We highly recommend conda environments to separate software from each other. With it, different versions of dependencies do not interfere with each other. $ conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge $ conda activate hicexplorer To deactivate the environment use: $ conda deactivate To learn more about conda and environments, please consider the following documentation . Install by cloning this repository You can install any one of the HiCExplorer branches on command line (linux/mac) by cloning this git repository : $ git clone https://github.com/deeptools/HiCExplorer.git $ cd HiCExplorer $ python setup.py install If you don't have root permission, you can set a specific folder using the --prefix option $ python setup.py install --prefix /User/Tools/hicexplorer If you don't use conda, please take care of all dependencies on your own. Galaxy version Install with Docker Installation instructions as a Docker image can be followed at https://github.com/deeptools/docker-galaxy-hicexplorer . Install with Tool Shed Galaxy HiCExplorer is part of the Galaxy Tool Shed and can be installed from there to any Galaxy server following this link . Documentation: Please visit our complete documentation Here . This documentation is also available directly within Galaxy . About HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data. hicexplorer.readthedocs.org Topics python bioinformatics genomics galaxy hic chromosome-conformation-capture Resources Readme License GPL-3.0 license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 271 stars Watchers 11 watching Forks 75 forks Report repository Releases 47 November release 2024 Latest Nov 28, 2024 + 46 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 88.1% HTML 11.5% Other 0.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge hicexplorer --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +hicexplorer 0.1 py27_0 +---------------------- +file name : hicexplorer-0.1-py27_0.tar.bz2 +name : hicexplorer +version : 0.1 +build : py27_0 +build number: 0 +size : 128 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-0.1-py27_0.tar.bz2 +md5 : e335b41f97715121cae61622343577de +dependencies: + - biopython + - bx-python >=0.7.2 + - matplotlib >=1.4.0 + - numpy >=1.8.0 + - pybigwig >=0.2.3 + - pysam >=0.8.2 + - python 2.7* + - scipy >=0.15.0 + + +hicexplorer 1.1a py27_0 +----------------------- +file name : hicexplorer-1.1a-py27_0.tar.bz2 +name : hicexplorer +version : 1.1a +build : py27_0 +build number: 0 +size : 135 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.1a-py27_0.tar.bz2 +md5 : 51c086a25b8f29bb66ce266e40b3fe01 +dependencies: + - biopython + - bx-python >=0.7.2 + - matplotlib >=1.4.0 + - numpy >=1.8.0 + - pybigwig >=0.2.3 + - pysam >=0.8.2 + - pytables + - python 2.7* + - scipy >=0.15.0 + + +hicexplorer 1.2 py27_0 +---------------------- +file name : hicexplorer-1.2-py27_0.tar.bz2 +name : hicexplorer +version : 1.2 +build : py27_0 +build number: 0 +size : 139 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.2-py27_0.tar.bz2 +md5 : 0f96794efdb8f87790c59a62547861c2 +dependencies: + - biopython + - bx-python >=0.7.2 + - matplotlib >=1.4.0 + - numpy >=1.8.0 + - pybigwig >=0.2.3 + - pysam >=0.8.2 + - pytables + - python 2.7* + - scipy >=0.15.0 + + +hicexplorer 1.3 py27_0 +---------------------- +file name : hicexplorer-1.3-py27_0.tar.bz2 +name : hicexplorer +version : 1.3 +build : py27_0 +build number: 0 +size : 192 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.3-py27_0.tar.bz2 +md5 : ea4a07f4785d45aa2317db7d4eb78e87 +dependencies: + - biopython >=1.65 + - bx-python >=0.7.2 + - matplotlib >=1.4.0 + - numpy >=1.10.4 + - pybigwig + - pybigwig >=0.2.8 + - pysam >=0.8.3 + - pytables >=3.2.2 + - python 2.7* + - scipy >=0.17.1 + + +hicexplorer 1.4 py27_0 +---------------------- +file name : hicexplorer-1.4-py27_0.tar.bz2 +name : hicexplorer +version : 1.4 +build : py27_0 +build number: 0 +size : 145 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.4-py27_0.tar.bz2 +md5 : fdc236aeb2a71d928092ba7135e12e6b +dependencies: + - biopython >=1.65 + - intervaltree >=2.1.0 + - matplotlib >=1.5.3 + - numpy >=1.10.4 + - pybigwig + - pybigwig >=0.2.8 + - pysam >=0.8.3 + - pytables >=3.2.2 + - python 2.7* + - scipy >=0.17.1 + + +hicexplorer 1.6 py27_0 +---------------------- +file name : hicexplorer-1.6-py27_0.tar.bz2 +name : hicexplorer +version : 1.6 +build : py27_0 +build number: 0 +size : 151 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.6-py27_0.tar.bz2 +md5 : a02c14ccc167020fb44b687fe0342802 +dependencies: + - biopython >=1.65 + - intervaltree >=2.1.0 + - matplotlib >=1.5.3 + - numpy >=1.10.4 + - pybigwig >=0.2.8 + - pybigwig >=0.2.8 + - pysam >=0.8.3 + - pytables >=3.2.2 + - python 2.7* + - scipy >=0.17.1 + + +hicexplorer 1.6.1 py27_0 +------------------------ +file name : hicexplorer-1.6.1-py27_0.tar.bz2 +name : hicexplorer +version : 1.6.1 +build : py27_0 +build number: 0 +size : 152 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.6.1-py27_0.tar.bz2 +md5 : 4119eb39b8354f47d1280d19ded4774c +dependencies: + - biopython >=1.65 + - intervaltree >=2.1.0 + - matplotlib >=1.5.3 + - numpy >=1.10.4 + - pybigwig >=0.2.8 + - pybigwig >=0.2.8 + - pysam >=0.8.3 + - pytables >=3.2.2 + - python 2.7* + - scipy >=0.17.1 + + +hicexplorer 1.7.1 py27_0 +------------------------ +file name : hicexplorer-1.7.1-py27_0.tar.bz2 +name : hicexplorer +version : 1.7.1 +build : py27_0 +build number: 0 +size : 157 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.7.1-py27_0.tar.bz2 +md5 : cda8c76cd6823b90cbb16a900948b13a +dependencies: + - biopython >=1.65 + - htslib >=1.3,<1.4 + - intervaltree >=2.1.0 + - matplotlib >=1.5.3 + - numpy >=1.10.4 + - pandas + - pybigwig >=0.2.8 + - pybigwig >=0.2.8 + - pysam + - pytables >=3.2.2 + - python 2.7* + - scipy >=0.17.1 + + +hicexplorer 1.7.2 py27_0 +------------------------ +file name : hicexplorer-1.7.2-py27_0.tar.bz2 +name : hicexplorer +version : 1.7.2 +build : py27_0 +build number: 0 +size : 159 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.7.2-py27_0.tar.bz2 +md5 : abb2f76af1f29e8c9b903f5817345cfb +dependencies: + - biopython >=1.65 + - htslib >=1.3,<1.4 + - intervaltree >=2.1.0 + - matplotlib >=1.5.3 + - numpy >=1.10.4 + - pandas + - pybigwig >=0.2.8 + - pybigwig >=0.2.8 + - pysam + - pytables >=3.2.2 + - python 2.7* + - scipy >=0.17.1 + + +hicexplorer 1.8 py27_0 +---------------------- +file name : hicexplorer-1.8-py27_0.tar.bz2 +name : hicexplorer +version : 1.8 +build : py27_0 +build number: 0 +size : 175 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.8-py27_0.tar.bz2 +md5 : fab24a3623d2351c25df652391fb7463 +dependencies: + - biopython >=1.68 + - intervaltree >=2.1.0 + - jinja2 >=2.9.6 + - matplotlib >=2.0.0,<2.1 + - numpy >=1.12.1 + - pandas >=0.20.2 + - pybigwig >=0.3.4 + - pybigwig >=0.3.4 + - pysam >=0.11.2 + - pytables >=3.3.0 + - python 2.7* + - scipy >=0.19.0 + + +hicexplorer 1.8 py27_1 +---------------------- +file name : hicexplorer-1.8-py27_1.tar.bz2 +name : hicexplorer +version : 1.8 +build : py27_1 +build number: 1 +size : 176 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.8-py27_1.tar.bz2 +md5 : 47a09f373ffa9cb31025bdcc01e0dd2e +dependencies: + - biopython >=1.68 + - intervaltree >=2.1.0 + - jinja2 >=2.9.6 + - matplotlib >=2.0.0,<2.1 + - numpy + - pandas >=0.20.2 + - pybigwig >=0.3.4 + - pybigwig >=0.3.4 + - pysam >=0.11.2 + - pytables >=3.3.0 + - python 2.7* + - scipy >=0.19.0 + + +hicexplorer 1.8 py27_2 +---------------------- +file name : hicexplorer-1.8-py27_2.tar.bz2 +name : hicexplorer +version : 1.8 +build : py27_2 +build number: 2 +size : 176 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.8-py27_2.tar.bz2 +md5 : 691083e56c8f53621cc17f74bb469d31 +dependencies: + - biopython >=1.68 + - intervaltree >=2.1.0 + - jinja2 >=2.9.6 + - matplotlib >=2.0.0,<2.1 + - numpy + - pandas >=0.20.2 + - pybigwig >=0.3.4 + - pybigwig >=0.3.4 + - pysam >=0.11.2 + - pytables >=3.3.0 + - python 2.7* + - scipy >=0.19.0 + + +hicexplorer 1.8.1 py27_0 +------------------------ +file name : hicexplorer-1.8.1-py27_0.tar.bz2 +name : hicexplorer +version : 1.8.1 +build : py27_0 +build number: 0 +size : 177 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-1.8.1-py27_0.tar.bz2 +md5 : 41f4f66e104396f1271b8cb1c03c3458 +dependencies: + - biopython >=1.68 + - intervaltree >=2.1.0 + - jinja2 >=2.9.6 + - matplotlib >=2.0.0,<2.1 + - numpy + - pandas >=0.20.2 + - pybigwig >=0.3.4 + - pybigwig >=0.3.4 + - pysam >=0.11.2 + - pytables >=3.3.0 + - python 2.7* + - scipy >=0.19.0 + + +hicexplorer 2.0 py27_0 +---------------------- +file name : hicexplorer-2.0-py27_0.tar.bz2 +name : hicexplorer +version : 2.0 +build : py27_0 +build number: 0 +size : 198 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-2.0-py27_0.tar.bz2 +md5 : cee630cb3605eb169c69a36dd98986b6 +dependencies: + - biopython >=1.68 + - configparser >=3.5.0 + - cooler >=0.7.6 + - future >=0.16.0 + - intervaltree >=2.1.0 + - jinja2 >=2.9.6 + - matplotlib >=2.0.0 + - numpy >=1.12.* + - pandas >=0.20.2 + - pybigwig >=0.3.4 + - pybigwig >=0.3.4 + - pysam >=0.11.2 + - pytables >=3.3.0 + - python 2.7* + - scipy >=0.19.0 + - six >=1.10.0 + + +hicexplorer 2.0 py27_1 +---------------------- +file name : hicexplorer-2.0-py27_1.tar.bz2 +name : hicexplorer +version : 2.0 +build : py27_1 +build number: 1 +size : 199 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-2.0-py27_1.tar.bz2 +md5 : 008c97521ac2f0901bf6cb065e0beac4 +dependencies: + - biopython >=1.68 + - configparser >=3.5.0 + - cooler >=0.7.6 + - future >=0.16.0 + - intervaltree >=2.1.0 + - jinja2 >=2.9.6 + - matplotlib ==2.1.1 + - numpy >=1.12.* + - pandas >=0.20.2 + - pybigwig >=0.3.4 + - pybigwig >=0.3.4 + - pysam >=0.11.2 + - pytables >=3.3.0 + - python 2.7* + - scipy >=0.19.0 + - six >=1.10.0 + + +hicexplorer 2.0 py35_0 +---------------------- +file name : hicexplorer-2.0-py35_0.tar.bz2 +name : hicexplorer +version : 2.0 +build : py35_0 +build number: 0 +size : 198 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-2.0-py35_0.tar.bz2 +md5 : 5c47a5fd6e5fb83a2196373a124f99f8 +dependencies: + - biopython >=1.68 + - cooler >=0.7.6 + - future >=0.16.0 + - intervaltree >=2.1.0 + - jinja2 >=2.9.6 + - matplotlib >=2.0.0 + - numpy >=1.12.* + - pandas >=0.20.2 + - pybigwig >=0.3.4 + - pybigwig >=0.3.4 + - pysam >=0.11.2 + - pytables >=3.3.0 + - python 3.5* + - scipy >=0.19.0 + - six >=1.10.0 + + +hicexplorer 2.0 py35_1 +---------------------- +file name : hicexplorer-2.0-py35_1.tar.bz2 +name : hicexplorer +version : 2.0 +build : py35_1 +build number: 1 +size : 199 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-2.0-py35_1.tar.bz2 +md5 : f2b1ea30495e3d68ef504dc99693c8f0 +dependencies: + - biopython >=1.68 + - cooler >=0.7.6 + - future >=0.16.0 + - intervaltree >=2.1.0 + - jinja2 >=2.9.6 + - matplotlib ==2.1.1 + - numpy >=1.12.* + - pandas >=0.20.2 + - pybigwig >=0.3.4 + - pybigwig >=0.3.4 + - pysam >=0.11.2 + - pytables >=3.3.0 + - python 3.5* + - scipy >=0.19.0 + - six >=1.10.0 + + +hicexplorer 2.0 py36_0 +---------------------- +file name : hicexplorer-2.0-py36_0.tar.bz2 +name : hicexplorer +version : 2.0 +build : py36_0 +build number: 0 +size : 197 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-2.0-py36_0.tar.bz2 +md5 : dc2b6ea18eac4db69250f7ca85894f44 +dependencies: + - biopython >=1.68 + - cooler >=0.7.6 + - future >=0.16.0 + - intervaltree >=2.1.0 + - jinja2 >=2.9.6 + - matplotlib >=2.0.0 + - numpy >=1.12.* + - pandas >=0.20.2 + - pybigwig >=0.3.4 + - pybigwig >=0.3.4 + - pysam >=0.11.2 + - pytables >=3.3.0 + - python 3.6* + - scipy >=0.19.0 + - six >=1.10.0 + + +hicexplorer 2.0 py36_1 +---------------------- +file name : hicexplorer-2.0-py36_1.tar.bz2 +name : hicexplorer +version : 2.0 +build : py36_1 +build number: 1 +size : 198 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hicexplorer-2.0-py36_1.tar.bz2 +md5 : 3ea02778112964e3cbb34c33992f0d7a +dependencies: + - biopython >=1.68 + - cooler >=0.7.6 + - future >=0.16.0 + - intervaltree >=2.1.0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/htseq.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/htseq.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..58f13d732d74775bb3f4fde31bd20942fd136cff --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/htseq.manual_bundle.txt @@ -0,0 +1,460 @@ +# Tool: htseq +software_name: htseq +tier: T1 +domain: t1_backfill_overall +downloads: 879068 +summary: HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. +description: HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. +dependencies: anndata, libgcc >=14, libstdcxx >=14, loompy, matplotlib-base, numpy >=1.23,<3, pysam >=0.23.3,<0.24.0a0, python >=3.12,<3.13.0a0, python_abi 3.12.* *_cp312, scipy +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/htseq/htseq +doc_url: https://htseq.readthedocs.io/en/latest +dev_url: https://github.com/htseq/htseq + +## URL Docs Extract +### https://htseq.readthedocs.io/en/latest +HTSeq: High-throughput sequence analysis in Python — HTSeq 2.0.5 documentation --> HTSeq latest Home Overview Installation A tour through HTSeq Tutorials Counting reads Reference API Sequences and FASTA/FASTQ files Positions, intervals and arrays Read alignments Features Other parsers Miscellaneous htseq-count : counting reads within features htseq-count-barcodes : counting reads with cell barcodes and UMIs Quality Assessment with htseq-qa Version history Contributing HTSeq HTSeq: High-throughput sequence analysis in Python Edit on GitHub HTSeq: High-throughput sequence analysis in Python  Author Fabio Zanini, Simon Anders, Givanna Putri and contributors Date Dec 14, 2023 Version 2.0.5 HTSeq is a Python package for analysis of high-throughput sequencing data. For a high-level description of the package, see the Overview . For downloads and installation instructions, see Installation . For a thorough example, see A tour through HTSeq . For tutorials about specific analyses, see Tutorials . For documentation on htseq-count , see htseq-count: counting reads within features . Reference API documentation is available on the other pages. Citation  If you use HTSeq in your research, please cite this paper: G Putri, S Anders, PT Pyl, JE Pimanda, F Zanini Analysing high-throughput sequencing data in Python with HTSeq 2.0 https://doi.org/10.1093/bioinformatics/btac166 (2022) Note bioRxiv previously rejected this preprint saying it’s not proper research. Thankfully, the arXiv was a little more supportive of open source and open science. HTSeq 1.0 was described in: Simon Anders, Paul Theodor Pyl, Wolfgang Huber HTSeq — A Python framework to work with high-throughput sequencing data Bioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638 Indices and tables  Index Module Index Search Page Authors  HTSeq is currently developed by: Givanna Putri at UNSW Sydney (g dot putri at unsw dot edu dot au) Simon Anders (anders at embl dot de) at EMBL Heidelberg ( Genome Biology Unit ). Fabio Zanini at UNSW Sydney (fabio dot zanini at unsw dot edu dot au) License  HTSeq is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. The full text of the GNU General Public License, version 3, can be found here: http://www.gnu.org/licenses/gpl-3.0-standalone.html Sitemap  Home Overview Installation A tour through HTSeq Tutorials Counting reads Reference API Sequences and FASTA/FASTQ files Positions, intervals and arrays Read alignments Features Other parsers Miscellaneous htseq-count : counting reads within features htseq-count-barcodes : counting reads with cell barcodes and UMIs Quality Assessment with htseq-qa Version history Contributing Next © Copyright 2010-2022, the HTSeq team. Revision 726a1432 . Built with Sphinx using a theme provided by Read the Docs . + +### https://github.com/htseq/htseq +GitHub - htseq/htseq: HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} htseq / htseq Public forked from simon-anders/htseq Notifications You must be signed in to change notification settings Fork 31 Star 106 Code Issues 9 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights htseq/htseq main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 835 Commits 835 Commits .github .github HTSeq HTSeq doc doc example_data example_data src src test test .ci_deploy.sh .ci_deploy.sh .ci_deps.sh .ci_deps.sh .ci_install.sh .ci_install.sh .ci_postdeploy_install.sh .ci_postdeploy_install.sh .ci_test.sh .ci_test.sh .gitignore .gitignore .readthedocs.yaml .readthedocs.yaml .travis.yml .travis.yml .travis_pypirc .travis_pypirc LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md RELEASE_CHECKOUT RELEASE_CHECKOUT buildwheels.sh buildwheels.sh deploywheels.sh deploywheels.sh installwheels.sh installwheels.sh prepare_docker.sh prepare_docker.sh pyproject.toml pyproject.toml requirements.txt requirements.txt setup.py setup.py test.sh test.sh testwheels.sh testwheels.sh todo.txt todo.txt View all files Repository files navigation README GPL-3.0 license HTSeq DEVS : https://github.com/htseq/htseq DOCS : https://htseq.readthedocs.io CITATION (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, https://doi.org/10.1093/bioinformatics/btac166 (2022). A Python library to facilitate programmatic analysis of data from high-throughput sequencing (HTS) experiments. A popular component of HTSeq is htseq-count , a script to quantify gene expression in bulk and single-cell RNA-Seq and similar experiments. Requirements To use HTSeq you need: Python >= 3.10 ( note : Python 2 support has been dropped) numpy pysam To manipulate BigWig files, you also need: pyBigWig To run the htseq-qa script, you also need: matplotlib To run htseq-count and htseq-count-barcodes with custom output formats for the counts table, you need: mtx file: scipy h5ad file: anndata loom file: loompy Both Linux and OSX are supported and binaries are provided on Pypi. We would like to support Windows but currently lack the expertise to do so. If you would like to take on the Windows release and maintenance, please open an issue and we'll try to help. A source package which should not require Cython nor SWIG is also provided on Pypi. To develop HTSeq you will also need: Cython >=0.29.5 SWIG >=3.0.8 Installation PIP To install directly from PyPI: pip install HTSeq To install a specific version: pip install ' HTSeq==2.0.0 ' If this fails, please install all dependencies first: pip install matplotlib pip install Cython pip install pysam pip install HTSeq setup.py (distutils/setuptools) Install the dependencies with your favourite tool ( pip , conda , etc.). To install HTSeq itself, run: python setup.py build install Testing To test locally, run ./test.sh To test htseq-count alone, run it with the -o option. A virtual environment is created in the .venv folder and HTSeq is installed inside it, including all modules and scripts. Authors 2021-: Givanna Putri ( ghar1821 ) 2016-: Fabio Zanini ( iosonofabio )@ https://fabilab.org 2010-2015: Simon Anders ( simon-anders ), Wolfgang Huber About HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. htseq.readthedocs.io Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 106 stars Watchers 3 watching Forks 31 forks Report repository Releases 109 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 72.9% Cython 18.5% SWIG 3.9% Shell 3.5% C++ 1.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/htseq/htseq +GitHub - htseq/htseq: HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} htseq / htseq Public forked from simon-anders/htseq Notifications You must be signed in to change notification settings Fork 31 Star 106 Code Issues 9 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights htseq/htseq main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 835 Commits 835 Commits .github .github HTSeq HTSeq doc doc example_data example_data src src test test .ci_deploy.sh .ci_deploy.sh .ci_deps.sh .ci_deps.sh .ci_install.sh .ci_install.sh .ci_postdeploy_install.sh .ci_postdeploy_install.sh .ci_test.sh .ci_test.sh .gitignore .gitignore .readthedocs.yaml .readthedocs.yaml .travis.yml .travis.yml .travis_pypirc .travis_pypirc LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md RELEASE_CHECKOUT RELEASE_CHECKOUT buildwheels.sh buildwheels.sh deploywheels.sh deploywheels.sh installwheels.sh installwheels.sh prepare_docker.sh prepare_docker.sh pyproject.toml pyproject.toml requirements.txt requirements.txt setup.py setup.py test.sh test.sh testwheels.sh testwheels.sh todo.txt todo.txt View all files Repository files navigation README GPL-3.0 license HTSeq DEVS : https://github.com/htseq/htseq DOCS : https://htseq.readthedocs.io CITATION (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, https://doi.org/10.1093/bioinformatics/btac166 (2022). A Python library to facilitate programmatic analysis of data from high-throughput sequencing (HTS) experiments. A popular component of HTSeq is htseq-count , a script to quantify gene expression in bulk and single-cell RNA-Seq and similar experiments. Requirements To use HTSeq you need: Python >= 3.10 ( note : Python 2 support has been dropped) numpy pysam To manipulate BigWig files, you also need: pyBigWig To run the htseq-qa script, you also need: matplotlib To run htseq-count and htseq-count-barcodes with custom output formats for the counts table, you need: mtx file: scipy h5ad file: anndata loom file: loompy Both Linux and OSX are supported and binaries are provided on Pypi. We would like to support Windows but currently lack the expertise to do so. If you would like to take on the Windows release and maintenance, please open an issue and we'll try to help. A source package which should not require Cython nor SWIG is also provided on Pypi. To develop HTSeq you will also need: Cython >=0.29.5 SWIG >=3.0.8 Installation PIP To install directly from PyPI: pip install HTSeq To install a specific version: pip install ' HTSeq==2.0.0 ' If this fails, please install all dependencies first: pip install matplotlib pip install Cython pip install pysam pip install HTSeq setup.py (distutils/setuptools) Install the dependencies with your favourite tool ( pip , conda , etc.). To install HTSeq itself, run: python setup.py build install Testing To test locally, run ./test.sh To test htseq-count alone, run it with the -o option. A virtual environment is created in the .venv folder and HTSeq is installed inside it, including all modules and scripts. Authors 2021-: Givanna Putri ( ghar1821 ) 2016-: Fabio Zanini ( iosonofabio )@ https://fabilab.org 2010-2015: Simon Anders ( simon-anders ), Wolfgang Huber About HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. htseq.readthedocs.io Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 106 stars Watchers 3 watching Forks 31 forks Report repository Releases 109 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 72.9% Cython 18.5% SWIG 3.9% Shell 3.5% C++ 1.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge htseq --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +htseq 0.6.1p1 py27_0 +-------------------- +file name : htseq-0.6.1p1-py27_0.tar.bz2 +name : htseq +version : 0.6.1p1 +build : py27_0 +build number: 0 +size : 805 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.6.1p1-py27_0.tar.bz2 +md5 : 101e7ffcad52af6a2c653c318f64e762 +dependencies: + - matplotlib + - numpy + - python 2.7* + - setuptools + + +htseq 0.6.1p1 py27_1 +-------------------- +file name : htseq-0.6.1p1-py27_1.tar.bz2 +name : htseq +version : 0.6.1p1 +build : py27_1 +build number: 1 +size : 800 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.6.1p1-py27_1.tar.bz2 +md5 : 99e6b5e580cde55c5f416bf58eb5a129 +dependencies: + - matplotlib + - numpy + - python 2.7* + - setuptools + + +htseq 0.6.1 np17py27_0 +---------------------- +file name : htseq-0.6.1-np17py27_0.tar.bz2 +name : htseq +version : 0.6.1 +build : np17py27_0 +build number: 0 +size : 805 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.6.1-np17py27_0.tar.bz2 +md5 : 9710d290ec98a0373dcd01449c837824 +dependencies: + - matplotlib ==1.2.1 + - numpy ==1.7.1 + - python 2.7* + + +htseq 0.6.1 py27_1 +------------------ +file name : htseq-0.6.1-py27_1.tar.bz2 +name : htseq +version : 0.6.1 +build : py27_1 +build number: 1 +size : 775 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.6.1-py27_1.tar.bz2 +md5 : f7e92aa0ef6cf97524ec9aae87571536 +timestamp : 2018-08-06 00:13:50 UTC +dependencies: + - matplotlib 1.2.1 + - numpy 1.7.1 + - python >=2.7,<2.8.0a0 + + +htseq 0.6.1 py27h470a237_2 +-------------------------- +file name : htseq-0.6.1-py27h470a237_2.tar.bz2 +name : htseq +version : 0.6.1 +build : py27h470a237_2 +build number: 2 +size : 772 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.6.1-py27h470a237_2.tar.bz2 +md5 : ada23654366a5145ae9f7539c0e93c3e +timestamp : 2018-12-05 19:08:54 UTC +dependencies: + - libgcc-ng >=4.9 + - matplotlib 1.2.1 + - numpy 1.7.1 + - python >=2.7,<2.8.0a0 + + +htseq 0.6.1 py27h76bc9d7_4 +-------------------------- +file name : htseq-0.6.1-py27h76bc9d7_4.tar.bz2 +name : htseq +version : 0.6.1 +build : py27h76bc9d7_4 +build number: 4 +size : 237 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.6.1-py27h76bc9d7_4.tar.bz2 +md5 : 3b687cad72b58203f6564c22720aab42 +timestamp : 2020-09-01 11:53:29 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - matplotlib-base + - numpy >=1.16.5,<2.0a0 + - pysam + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + + +htseq 0.6.1 py27hfd4ddd4_3 +-------------------------- +file name : htseq-0.6.1-py27hfd4ddd4_3.tar.bz2 +name : htseq +version : 0.6.1 +build : py27hfd4ddd4_3 +build number: 3 +size : 237 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.6.1-py27hfd4ddd4_3.tar.bz2 +md5 : 1d6b44f5a6e31d0a07a684694c06ec78 +timestamp : 2020-07-30 03:50:10 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - matplotlib-base + - numpy >=1.14.6,<2.0a0 + - pysam + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + + +htseq 0.6.1.post1 py27h76bc9d7_5 +-------------------------------- +file name : htseq-0.6.1.post1-py27h76bc9d7_5.tar.bz2 +name : htseq +version : 0.6.1.post1 +build : py27h76bc9d7_5 +build number: 5 +size : 237 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.6.1.post1-py27h76bc9d7_5.tar.bz2 +md5 : 0fbbfe73ed8aa514bb2bca0c9e5ccac9 +timestamp : 2020-09-01 12:29:00 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - matplotlib-base + - numpy >=1.16.5,<2.0a0 + - pysam + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + + +htseq 0.6.1.post1 py27hfd4ddd4_4 +-------------------------------- +file name : htseq-0.6.1.post1-py27hfd4ddd4_4.tar.bz2 +name : htseq +version : 0.6.1.post1 +build : py27hfd4ddd4_4 +build number: 4 +size : 237 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.6.1.post1-py27hfd4ddd4_4.tar.bz2 +md5 : 11d5d5dfc2ad67e1995736157ce276dd +timestamp : 2020-07-30 04:27:22 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - matplotlib-base + - numpy >=1.14.6,<2.0a0 + - pysam + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + + +htseq 0.7.2 py27_0 +------------------ +file name : htseq-0.7.2-py27_0.tar.bz2 +name : htseq +version : 0.7.2 +build : py27_0 +build number: 0 +size : 956 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py27_0.tar.bz2 +md5 : 6393e5152c4f73695beaebab3c195655 +dependencies: + - matplotlib + - numpy + - pysam >=0.9.0 + - python 2.7* + + +htseq 0.7.2 py27h24bf2e0_1 +-------------------------- +file name : htseq-0.7.2-py27h24bf2e0_1.tar.bz2 +name : htseq +version : 0.7.2 +build : py27h24bf2e0_1 +build number: 1 +size : 1.0 MB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py27h24bf2e0_1.tar.bz2 +md5 : 2a52cd20e9cb5574b00cb0ebeaae1db4 +timestamp : 2018-06-25 22:47:26 UTC +dependencies: + - matplotlib + - numpy + - pysam >=0.9.0 + - python >=2.7,<2.8.0a0 + + +htseq 0.7.2 py27h76bc9d7_4 +-------------------------- +file name : htseq-0.7.2-py27h76bc9d7_4.tar.bz2 +name : htseq +version : 0.7.2 +build : py27h76bc9d7_4 +build number: 4 +size : 315 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py27h76bc9d7_4.tar.bz2 +md5 : 51384350f248355bdffc50d9d3c9aa69 +timestamp : 2020-09-01 11:30:58 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - matplotlib-base + - numpy >=1.16.5,<2.0a0 + - pysam >=0.9.0 + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + + +htseq 0.7.2 py27h7eb728f_2 +-------------------------- +file name : htseq-0.7.2-py27h7eb728f_2.tar.bz2 +name : htseq +version : 0.7.2 +build : py27h7eb728f_2 +build number: 2 +size : 1.0 MB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py27h7eb728f_2.tar.bz2 +md5 : d98cfa3b163b53f0c21055ef961ea9e6 +timestamp : 2018-12-05 19:18:41 UTC +dependencies: + - libgcc-ng >=4.9 + - matplotlib + - numpy >=1.9.3,<2.0a0 + - pysam >=0.9.0 + - python >=2.7,<2.8.0a0 + + +htseq 0.7.2 py27hfd4ddd4_3 +-------------------------- +file name : htseq-0.7.2-py27hfd4ddd4_3.tar.bz2 +name : htseq +version : 0.7.2 +build : py27hfd4ddd4_3 +build number: 3 +size : 313 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py27hfd4ddd4_3.tar.bz2 +md5 : 1c9bc710f78a7ccc0520f7ec54068994 +timestamp : 2020-07-30 04:09:15 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - matplotlib-base + - numpy >=1.14.6,<2.0a0 + - pysam >=0.9.0 + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + + +htseq 0.7.2 py34_0 +------------------ +file name : htseq-0.7.2-py34_0.tar.bz2 +name : htseq +version : 0.7.2 +build : py34_0 +build number: 0 +size : 1.0 MB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py34_0.tar.bz2 +md5 : b62c4d3f210638967b7b4232f29df461 +dependencies: + - matplotlib + - numpy + - pysam >=0.9.0 + - python 3.4* + + +htseq 0.7.2 py35_0 +------------------ +file name : htseq-0.7.2-py35_0.tar.bz2 +name : htseq +version : 0.7.2 +build : py35_0 +build number: 0 +size : 1.0 MB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py35_0.tar.bz2 +md5 : 24fa09686325e254442602b14b0bc02a +dependencies: + - matplotlib + - numpy + - pysam >=0.9.0 + - python 3.5* + + +htseq 0.7.2 py35h24bf2e0_1 +-------------------------- +file name : htseq-0.7.2-py35h24bf2e0_1.tar.bz2 +name : htseq +version : 0.7.2 +build : py35h24bf2e0_1 +build number: 1 +size : 1.2 MB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py35h24bf2e0_1.tar.bz2 +md5 : 2086836c181cac927ae509974f0fdc77 +timestamp : 2018-06-25 22:45:14 UTC +dependencies: + - matplotlib + - numpy + - pysam >=0.9.0 + - python >=3.5,<3.6.0a0 + + +htseq 0.7.2 py35h7eb728f_2 +-------------------------- +file name : htseq-0.7.2-py35h7eb728f_2.tar.bz2 +name : htseq +version : 0.7.2 +build : py35h7eb728f_2 +build number: 2 +size : 1.2 MB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py35h7eb728f_2.tar.bz2 +md5 : c6f170ed7ad5f521ce4bb45c9dbe76ce +timestamp : 2018-12-05 19:16:22 UTC +dependencies: + - libgcc-ng >=4.9 + - matplotlib + - numpy >=1.9.3,<2.0a0 + - pysam >=0.9.0 + - python >=3.5,<3.6.0a0 + + +htseq 0.7.2 py36_0 +------------------ +file name : htseq-0.7.2-py36_0.tar.bz2 +name : htseq +version : 0.7.2 +build : py36_0 +build number: 0 +size : 1.0 MB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py36_0.tar.bz2 +md5 : bb4e41b16e52a3c50dc6f400f0eb673d +dependencies: + - matplotlib + - numpy + - pysam >=0.9.0 + - python 3.6* + + +htseq 0.7.2 py36h0234e80_4 +-------------------------- +file name : htseq-0.7.2-py36h0234e80_4.tar.bz2 +name : htseq +version : 0.7.2 +build : py36h0234e80_4 +build number: 4 +size : 282 KB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py36h0234e80_4.tar.bz2 +md5 : e232835c3a528510a68832293e1935c8 +timestamp : 2020-09-01 11:24:45 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - matplotlib-base + - numpy >=1.16.5,<2.0a0 + - pysam >=0.9.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + + +htseq 0.7.2 py36h24bf2e0_1 +-------------------------- +file name : htseq-0.7.2-py36h24bf2e0_1.tar.bz2 +name : htseq +version : 0.7.2 +build : py36h24bf2e0_1 +build number: 1 +size : 1.2 MB +license : GNU General Public License (GPL) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/htseq-0.7.2-py36h24bf2e0_1.tar.bz2 +md5 : c2344a97facb diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/hyphy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/hyphy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..f60f50b2bda7154294d8469d4e6f8039940dcfb3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/hyphy.manual_bundle.txt @@ -0,0 +1,599 @@ +# Tool: hyphy +software_name: hyphy +tier: T1 +domain: t1_backfill_overall +downloads: 968101 +summary: An open-source software package for comparative sequence analysis using stochastic evolutionary models. +description: HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences +(in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning. +dependencies: _openmp_mutex >=4.5, libblas >=3.9.0,<4.0a0, libcurl >=8.19.0,<9.0a0, libgcc >=14, libgomp, libstdcxx >=14, libzlib >=1.3.2,<2.0a0, openmpi >=4.1.6,<5.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://hyphy.org/ +doc_url: https://hyphy.org +dev_url: https://github.com/veg/hyphy + +## CLI Help Source +cli:hyphy +## CLI Help Content +$ conda run -n bioenv_cli hyphy --help +[rc=0] +usage: hyphy or HYPHYMPI [-h] [--help][-c] [-d] [-i] [-p] [BASEPATH=directory path] [CPU=integer] [LIBPATH=library path] [USEPATH=library path] [ or ] [--keyword value ...] [positional arguments ...] + +Execute a HyPhy analysis, either interactively, or in batch mode +optional flags: + -h --help show this help message and exit + -c calculator mode; causes HyPhy to drop into an expression evaluation until 'exit' is typed + -d debug mode; causes HyPhy to drop into an expression evaluation mode upon script error + -i interactive mode; causes HyPhy to always prompt the user for analysis options, even when defaults are available + -p postprocessor mode; drops HyPhy into an interactive mode where general post-processing scripts can be selected + upon analysis completion + +optional global arguments: + BASEPATH=directory path defines the base directory for all path operations (default is pwd) + CPU=integer if compiled with OpenMP multithreading support, requests this many threads; HyPhy could use fewer than this + but never more; default is the number of CPU cores (as computed by OpenMP) on the system + LIBPATH=directory path defines the directory where HyPhy library files are located (default installed location is /usr/local/lib/hyphy + or as configured during CMake installation + USEPATH=directory path specifies the optional working and relative path directory (default is BASEPATH) + + batch file to run if specified, execute this file, otherwise drop into an interactive mode + analysis arguments if batch file is present, all remaining positional arguments are interpreted as inputs to analysis prompts + +optional keyword arguments (can appear anywhere); will be consumed by the requested analysis + --keyword value will be passed to the analysis (which uses KeywordArgument directives) + multiple values for the same keywords are treated as an array of values for multiple selectors + +usage examples: + +Select a standard analysis from the list : + hyphy -i +Run a standard analysis with default options and one required user argument; + hyphy busted --alignment path/to/file +Run a standard analysis with additional keyword arguments + hyphy busted --alignment path/to/file --srv No +See whcih arguments are understood by a standard analysis + hyphy busted --help +Run a custom analysis and pass it some arguments + hyphy path/to/hyphy.script argument1 'argument 2' +Available standard keyword analyses (located in /225040511/miniconda3/envs/bioenv_cli/lib/hyphy/) + meme [MEME] Test for episodic site-level selection using MEME (Mixed Effects Model of Evolution). + mh Merge two datafiles by combining sites (horizontal merge). + mv Merge two datafiles by combining sequences (vertical merge). + mcc Compare mean within-clade branch length or pairwise divergence between two or more non-nested cladesd in a tree + mclk Test for the presence of a global molecular clock on the tree using its root (the resulting clock tree is unrooted, but one of the root branches can be divided in such a way as to enforce the clock). + mgvsgy Compare the fits of MG94 and GY94 models (crossed with an arbitrary nucleotide bias) on codon data. + mt Select an evolutionary model for nucleotide data, using the methods of 'ModelTest' - a program by David Posada and Keith Crandall. + fel [FEL] Test for pervasive site-level selection using FEL (Fixed Effects Likelihood). + fubar [FUBAR] Test for pervasive site-level selection using FUBAR (Fast Unconstrained Bayesian AppRoximation for inferring selection). + fade [FADE] Test a protein alignment for directional selection towards specific amino acids along a specified set of test branches using FADE (a FUBAR Approach to Directional Evolution). + faa Fit a multiple fitness class model to amino acid data. + fst Compute various measures of F_ST and (optionally) perform permutation tests. + slac [SLAC] Test for pervasive site-level selection using SLAC (Single Likelihood Ancestor Counting). + sm Peform a classic and structured Slatkin-Maddison test for the number migrations. + sns Parse a codon alignment for ambiguous codons and output a complete list/resolutions/syn and ns counts by sequence/position + sw Perform a sliding window analysis of sequence data. + sa Perform a phylogeny reconstuction for nucleotide, protein or codon data with user-selectable models using the method of sequential addition. + sbl Search an alignment for a single breakpoint. + spl Plot genetic distances (similarity) of one sequence against all others in an alignment, using a sliding window. Optionally, determine NJ-based clustering and bootstrap support in every window. This is a HyPhy adaptation of the excellent (but Windows only tool) SimPlot (and/or VarPlot) written by Stuart Ray (http://sray.med.som.jhmi.edu/SCRoftware/simplot/) + busted [BUSTED] Test for episodic gene-wide selection using BUSTED (Branch-site Unrestricted Statistical Test of Episodic Diversification). + bgm [BGM] Apply Bayesian Graphical Model inference to substitution histories at individual sites. + bva Run a selection analysis using a general discrete bivariate (dN AND dS) distribution; the appropriate number of rate classes is determined automatically. + brp Interpret bivariate codon rate analysis results. + bsel Split a tree into two clades (compartments) and a separating branch and test for equality of dN/dS between compartments and for selection along the separating branch using a series of Likelihood Ratio Tests. + bst Use the improved branch-site REL method of Yang and Nielsen (2005) to look for episodic selection in sequences. + bt Test whether a branch (or branches) in the tree evolves under different dN and dS than the rest of the tree. + absrel [aBSREL] Test for lineage-specific evolution using the branch-site method aBS-REL (Adaptive Branch-Site Random Effects Likelihood). + acd Analyse codon data with a variery of standard models using given tree. + ad Analyse nucleotide or aminoacid data with a variery of standard models using given tree. + adn Analyse di-nucleotide data with a variery of standard models using given tree. + afd Analyse nucleotide data with a variery of standard models using given tree, estimating equilibrium frequencies as parameters + ana Run a selection analysis. + ai Peter Simmonds' Association Index (AI). + relax [RELAX] Test for relaxation of selection pressure along a specified set of test branches using RELAX (a random effects test of selection relaxation). + red Replace sufficiently close sequence with their MRCA + rpc Interpret analysis results. + rmv Remove sequences with stop codons from the data. + rble Use a series of random effects branch-site models to perform robust model-averaged branch length estimation under a codon model with episodic selection. + rclk Test for the presence of a global molecular clock on the tree. The tree is rooted at every possible branch. + rr Use relative rate test on three species and a variety of standard models + rrt Use relative ratio test on 2 datasets and a variety of standard models + contrast-fel Use a FEL method to test which sites in a gene may be associated with adaptation to a different environment. + conv Translate an in-frame codon alignment to proteins. + corr Assess the correlation between phylogenetic and compartment segregation using generalized correlation coefficients and permutation tests. + cod Compare all 203 reversible nucleotide models composed with MG94 to extend them to codon data, and perform LRT and AIC model selection. + cmp Use a series of LR tests to decide if dN and dS rate distributions are the same or different between two codon alignments. + caln Align coding sequences to reference (assuming star topology) using a codon-based dynamic programming algorithm (good for fixing multiple frameshifts). Designed with within-patient HIV sequences in mind. + clg Remove 'gappy' sites from alignments based on a user-specified gap threshold. + cln Convert sequence names to HyPhy valid identifiers if needed and replace stop codons with gaps in codon data if any are present. + clsr Partition sequences into clusters based on a distance matrix. + clst Apply clustering methods for phylogeny reconstruction (UPGMA,WPGMA,complete or minimal linkage) to nucleotide, protein and codon data, using MLE of pairwise distances with user-selectable models. These methods produce trees with global molecular clock. + leisr Infer relative evolutionary rates on a nucleotide or protein alignment, in a spirit similar to Rate4Site (PMID: 12169533). + lz Compute Lempel-Ziv complexity and entropy of (possibly unaligned) sequences + lclk Test for the presence of a local molecular clock. Every subtree of the given tree is subjected to the clock constraint, while the remainder of the tree is free of the clock constraint. + lht A Likelihood Ratio Test to detect conflicting phylogenetic signal Huelsenbeck and Bull, 1996. [Contributed by Olivier Fedrigo]. + tc Test whether a group of sequences in a sample cluster together + ts Perform an exhaustive tree space search for nucleotide or protein data with user-selectable models. Should only be used for data sets with less than 10 taxa! + dtr Read sequence data (#,PHYLIP,NEXUS) and convert to a different format + dist Generate a pairwise sequence distance matrix in PHYLIP format. + pdf Read sequence data, select a contiguous subset of sites and save it to another datafile. + phb Run an example file from our book chapter in 'The Phylogentic Handbook' (2nd edition). + protein Compare the fit of several amino-acid substitution models to an alignment using AIC and c-AIC. + prr Using the model and the outgroup provided by the user, perform relative rate tests with all possible pair of species from the data file. + prrti Given a list of files (and optinally genetic code tables), perform relative ratio tests on all possible pair of the data files. + psm Test for positive selection using the approach of Nielsen and Yang, by sampling global dN/dS from an array of distributions, and using Bayesian posterior to identify the sites with dN/dS>1. Multiple subsets of one data set with shared dN/dS. + parris A PARtitioning approach for Robust Inference of Selection (written by K. Scheffler) + kh Perform a Kishino-Hasegawa test on two competing phylogenies + ub Obtain an upper bound on the likelihood score of a dataset. + nuc Compare all 203 reversible nucleotide models and perform LRT and AIC model selection. + nj Perform a phylogeny reconstuction for nucleotide, protein or codon data with user-selectable models using the method of neighbor joining. + ny Test for positive selection using the approach of Nielsen and Yabg, by sampling global dN/dS from an array of distributions, and using Bayesian posterior to identify the sites with dN/dS>1. + gard [GARD] Screen an alignment using GARD (requires an MPI environment). + grdr Process GARD results. + + + + +## URL Docs Extract +### http://hyphy.org/ +HyPhy - Hypothesis Testing using Phylogenies - Information, documentation, and news about the HyPhy software package HyPhy Hypothesis Testing using Phylogenies HyPhy Home News and Releases About Installation Getting Started Methods Selection Tutorials CLI Tutorial CL Prompt Tutorial Batch Language Reference Library Resources Hypothesis Testing using Phylogenies An open-source software package for comparative sequence analysis using stochastic evolutionary models Install --> HyPhy development has received support from the NIH ( R01GM151683 , U01GM110749 , U24AI183870 , R01GM093939 ), and the NSF ( 2027196 , 2419522 ). + +### https://github.com/veg/hyphy +GitHub - veg/hyphy: HyPhy: Hypothesis testing using Phylogenies · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} veg / hyphy Public Notifications You must be signed in to change notification settings Fork 70 Star 254 Code Issues 7 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights veg/hyphy master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 4,103 Commits 4,103 Commits .github/ workflows .github/ workflows cmake cmake contrib contrib res res src src tests tests .gitattributes .gitattributes .gitignore .gitignore .travis.yml .travis.yml CMakeLists.txt CMakeLists.txt CONTRIBUTING.md CONTRIBUTING.md Dockerfile Dockerfile LICENSE LICENSE README.md README.md run_unit_tests.sh run_unit_tests.sh View all files Repository files navigation README Contributing License HyPhy - Hypothesis testing using Phylogenies HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as Python and R. HyPhy is the computational backbone powering datamonkey.org. Additional information is available at hyphy.org. Quick Start Install conda install -c bioconda hyphy Running with Docker You can also run HyPhy without having to install it on your system using the provided Dockerfile. Following the below instructions starts an interactive Docker container where HyPhy is already available. If you don't have Docker installed, first look at Docker Desktop . Please note you must change this code snippet to point to the appropriate location for your input data. This will be made available inside the container at /hyphy/data . git clone https://github.com/veg/hyphy.git cd hyphy docker build -t hyphy:latest . docker run --rm -v [path-to-your-input-data]:/hyphy/data -it hyphy:latest Run with Command Line Arguments hyphy <method_name> --alignment <path_to_alignment_file> <additional_method_specific_arguments> <method_name> is the name of the analysis you wish to run (can be: absrel, bgm, busted, fade, fel, fubar, gard, meme, relax or slac) <path_to_alignment_file> is the relative or absolute path to a FASTA , NEXUS , Phylip , or MEGA file containing an alignment and tree A list of the available <additional_method_specific_arguments> can be seen by running hyphy <method_name> --help or Run in Interactive Mode hyphy -i Building from Source Requirements cmake >= 3.12 gcc >= 4.9 libcurl libpthread openmp (can be installed on mac via brew install libomp ) Download You can download a specific release here or clone this repo with git clone https://github.com/veg/hyphy.git Change your directory to the downloaded/cloned directory cd hyphy Build cmake . make install Additional Options for Building from Source Build Systems If you prefer to use other build systems, such as Xcode, configure using the -G switch cmake -G Xcode . CMake supports a number of build system generators, feel free to peruse these and use them if you wish. If you are on an OS X platform, you can specify which OS X SDK to use cmake -DCMAKE_OSX_SYSROOT=/Developer/SDKs/MacOSX10.9.sdk/ . If building on a heterogeneous cluster with some nodes that do not support auto-vectorization cmake -DNOAVX=ON . . If you're on a UNIX-compatible system, and you're comfortable with GNU make, then run make with one of the following build targets: MP or hyphy - build a HyPhy executable (This used to be "HYPHYMP" but is now just "hyphy") using pthreads to do multiprocessing MPI or HYPHYMPI - build a HyPhy executable (HYPHYMPI) using openMPI to do multiprocessing LIB - build a HyPhy library (libhyphy_mp) using pthreads to do multiprocessing GTEST - build HyPhy's gtest testing executable (HYPHYGTEST) Example (MPI build of hyphy using openMPI) Ensure that you have openmpi installed and available on your path. You can check if this is the case after running cmake . you should see something similar to this in your output -- Found MPI_C: /opt/scyld/openmpi/1.6.3/gnu/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libtorque.so;/usr/lib64/libm.so;/usr/lib64/libnuma.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so -- Found MPI_CXX: /opt/scyld/openmpi/1.6.3/gnu/lib/libmpi_cxx.so;/opt/scyld/openmpi/1.6.3/gnu/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libtorque.so;/usr/lib64/libm.so;/usr/lib64/libnuma.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so Then run make HYPHYMPI And then run make install to install the software make install hyphy will be installed at /location/of/choice/bin libhyphy_mp.(so/dylib/dll) will be installed at /location/of/choice/lib HyPhy's standard library of batchfiles will go into /location/of/choice/lib/hyphy WebAssembly Build HyPhy provides WebAssembly builds that can run in modern browsers without installation. Using Pre-built WebAssembly Files The latest WebAssembly build can be downloaded from the GitHub Actions artifacts. Go to the GitHub Actions page , select the most recent successful workflow run, and download the hyphy-wasm artifact. The artifact contains: hyphy.js hyphy.wasm hyphy.data hyphy_resources.tar.gz Extract the resources tarball ( hyphy_resources.tar.gz ) in the same directory as the other files. All files should be served from the same directory on your web server. For an example of HyPhy running in the browser, see https://observablehq.com/@spond/hyphy-biowasm . Building WebAssembly Files Locally To build the WebAssembly files yourself, you'll need Emscripten . Configure the build - note that we don't use preload flags during configuration to avoid CMake test issues: emcmake cmake -DCMAKE_EXE_LINKER_FLAGS="-sTOTAL_STACK=2097152 -O2 -sASSERTIONS=1 -sMODULARIZE=1 -sALLOW_MEMORY_GROWTH -sFORCE_FILESYSTEM=1 -sEXIT_RUNTIME=0 -s EXPORTED_RUNTIME_METHODS=[\"callMain\",\"FS\",\"PROXYFS\",\"WORKERFS\",\"UTF8ToString\",\"getValue\",\"AsciiToString\"] -lworkerfs.js -lproxyfs.js -s INVOKE_RUN=0 -s ENVIRONMENT=\"web,worker\" ${EM_FLAGS//-s /-s} -fwasm-exceptions" Build the target: emmake make -j hyphy This will create the following files: hyphy.js hyphy.wasm hyphy.data You'll also need to copy the resource files to serve alongside the WebAssembly files: mkdir -p hyphy_resources cp -r res hyphy_resources/ cp -r tests/hbltests hyphy_resources/tests All files should be served from the same directory on your web server. Testing Use make test after running cmake . . Benchmarks for CMake Tests Benchmarks, using Github Actions, can be found at http://hyphy.org/bench Executable Location By default, HyPhy installs into /usr/local but it can be installed on any location of your system by providing an installation prefix cmake -DCMAKE_INSTALL_PREFIX:PATH=/location/of/choice For example, this configuration will install hyphy at /opt/hyphy mkdir -p /opt/hyphy cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/hyphy . Building Documentation make docs cd docs python3 -m http.server CLI notes As noted in the documentation here hyphy can be run as a command line tool. Indeed for many analyses the hyphy CLI will return useful help messages, showing which parameter values can be set to specify your analysis. For example, running hyphy gard --help hyphy gard --help Available analysis command line options --------------------------------------- Use --option VALUE syntax to invoke If a [reqired] option is not provided on the command line, the analysis will prompt for its value [conditionally required] options may or not be required based on the values of other options type The type of data to perform screening on default value: nucleotide code Genetic code to use (for codon alignments) default value: Universal applies to: Choose Genetic Code alignment [required] Sequence alignment to screen for recombination model The substitution model to use default value: JTT rv Site to site rate variation default value: None max-breakpoints Maximum number of breakpoints to consider default value: 10000 rate-classes How many site rate classes to use default value: 4 output Write the resulting JSON to this file (default is to save to the same path as the alignment file + 'GARD.json') default value: gard.defaultJsonFilePath [computed at run time] mode Run mode (Normal or Faster) default value: Normal output-lf Write the best fitting HyPhy analysis snapshot to (default is to save to the same path as the alignment file + 'best-gard') default value: gard.defaultFitFilePath [computed at run time] will show you the options that can be set for the gard analysis. So for instance one could specify a gard run on the command line with the following command hyphy gard --alignment /path/to/file --rv GDD --mode Faster --rate-classes 3 While this is a useful feature, it is not always the case that older analyses will have the same level of support for command line. For instance, the acd analysis does not have CLI support and so if one runs the help command hyphy acd --help Available analysis command line options --------------------------------------- Use --option VALUE syntax to invoke If a [reqired] option is not provided on the command line, the analysis will prompt for its value [conditionally required] options may or not be required based on the values of other options No annotated keyword arguments are available for this analysis one will see that there are no options available. In this case, you can use a different CLI specification. Indeed the CLI will accept all of the options that are asked for in an interactive session, as positional arguments. In this case I could run the acd analysis with hyphy acd Universal <alignment.fa> MG94CUSTOMCF3X4 Global 012345 <treefile> Estimate where the options are specified in the exact order that they are asked for in the interactive session. This will work for all hyphy analyses and provides a less readable but more flexible way to run hyphy analyses. About HyPhy: Hypothesis testing using Phylogenies www.hyphy.org Topics science c-plus-plus bioinformatics evolution statistical-methods phylogenetics comparative-genomics Resources Readme License View license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 254 stars Watchers 17 watching Forks 70 forks Report repository Releases 117 2.5.98 Latest Apr 28, 2026 + 116 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages HyPhy 75.8% C++ 23.8% Other 0.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge hyphy --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +hyphy 2.3.11 h396f500_1 +----------------------- +file name : hyphy-2.3.11-h396f500_1.tar.bz2 +name : hyphy +version : 2.3.11 +build : h396f500_1 +build number: 1 +size : 3.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.3.11-h396f500_1.tar.bz2 +md5 : dba641a45307edd6655147185d4abe9c +timestamp : 2019-03-14 15:50:03 UTC +dependencies: + - curl >=7.64.0,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=3.1.3,<3.2.0a0 + - openssl >=1.1.1b,<1.1.2a + + +hyphy 2.3.11 h5466e78_0 +----------------------- +file name : hyphy-2.3.11-h5466e78_0.tar.bz2 +name : hyphy +version : 2.3.11 +build : h5466e78_0 +build number: 0 +size : 3.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.3.11-h5466e78_0.tar.bz2 +md5 : b7c70919dfe02315ba5e8fd3bb20fa9f +timestamp : 2019-02-28 16:14:50 UTC +dependencies: + - curl >=7.59.0,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=3.1.3,<3.2.0a0 + - openssl 1.0.* + + +hyphy 2.3.11 h82996af_2 +----------------------- +file name : hyphy-2.3.11-h82996af_2.tar.bz2 +name : hyphy +version : 2.3.11 +build : h82996af_2 +build number: 2 +size : 3.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.3.11-h82996af_2.tar.bz2 +md5 : 62b0d6f96dc7632314fdd34a68666388 +timestamp : 2020-07-03 04:48:02 UTC +dependencies: + - curl >=7.71.1,<8.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - openmpi >=4.0.4,<4.1.0a0 + - openssl >=1.1.1g,<1.1.2a + + +hyphy 2.3.12 0 +-------------- +file name : hyphy-2.3.12-0.tar.bz2 +name : hyphy +version : 2.3.12 +build : 0 +build number: 0 +size : 3.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.3.12-0.tar.bz2 +md5 : d34d8b12ddbc0cf65afec323fe382a25 +dependencies: + - curl 7.59.* + - libgcc + - openmpi 3.0.* + + +hyphy 2.3.12 h5466e78_1 +----------------------- +file name : hyphy-2.3.12-h5466e78_1.tar.bz2 +name : hyphy +version : 2.3.12 +build : h5466e78_1 +build number: 1 +size : 3.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.3.12-h5466e78_1.tar.bz2 +md5 : 570496383dbf2e8bc344b3892962919a +timestamp : 2018-07-13 09:08:04 UTC +dependencies: + - curl >=7.59.0,<8.0a0 + - libgcc-ng >=7.2.0 + - libstdcxx-ng >=7.2.0 + - openmpi >=3.1,<3.2.0a0 + + +hyphy 2.3.14 h396f500_1 +----------------------- +file name : hyphy-2.3.14-h396f500_1.tar.bz2 +name : hyphy +version : 2.3.14 +build : h396f500_1 +build number: 1 +size : 2.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.3.14-h396f500_1.tar.bz2 +md5 : 4b00c538ec2a2a59e8041f60876a3a9f +timestamp : 2019-04-18 07:14:23 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +hyphy 2.3.14 h5466e78_0 +----------------------- +file name : hyphy-2.3.14-h5466e78_0.tar.bz2 +name : hyphy +version : 2.3.14 +build : h5466e78_0 +build number: 0 +size : 3.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.3.14-h5466e78_0.tar.bz2 +md5 : 4eb4b7872691e156e043abaadcfa1a44 +timestamp : 2018-08-09 12:18:09 UTC +dependencies: + - curl >=7.59.0,<8.0a0 + - libgcc-ng >=7.2.0 + - libstdcxx-ng >=7.2.0 + - openmpi >=3.1,<3.2.0a0 + + +hyphy 2.5.0 h396f500_0 +---------------------- +file name : hyphy-2.5.0-h396f500_0.tar.bz2 +name : hyphy +version : 2.5.0 +build : h396f500_0 +build number: 0 +size : 5.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.0-h396f500_0.tar.bz2 +md5 : 73299a89c9ae9cab7a337bc6be5de2e8 +timestamp : 2019-06-04 10:43:52 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +hyphy 2.5.0 h396f500_1 +---------------------- +file name : hyphy-2.5.0-h396f500_1.tar.bz2 +name : hyphy +version : 2.5.0 +build : h396f500_1 +build number: 1 +size : 5.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.0-h396f500_1.tar.bz2 +md5 : ff7e6c15ed2b33359a85bdcd1141d771 +timestamp : 2019-06-05 17:32:28 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +hyphy 2.5.1 h7d38c80_0 +---------------------- +file name : hyphy-2.5.1-h7d38c80_0.tar.bz2 +name : hyphy +version : 2.5.1 +build : h7d38c80_0 +build number: 0 +size : 5.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.1-h7d38c80_0.tar.bz2 +md5 : 16a032018913b49b558367f9a58f524f +timestamp : 2019-08-22 21:27:36 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +hyphy 2.5.1 h7d38c80_1 +---------------------- +file name : hyphy-2.5.1-h7d38c80_1.tar.bz2 +name : hyphy +version : 2.5.1 +build : h7d38c80_1 +build number: 1 +size : 5.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.1-h7d38c80_1.tar.bz2 +md5 : fa2ea9cfe206e04021512ddc3680e0a8 +timestamp : 2019-10-26 14:39:13 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +hyphy 2.5.2 h7d38c80_0 +---------------------- +file name : hyphy-2.5.2-h7d38c80_0.tar.bz2 +name : hyphy +version : 2.5.2 +build : h7d38c80_0 +build number: 0 +size : 5.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.2-h7d38c80_0.tar.bz2 +md5 : a022eedde41145f09132c61dc910dd21 +timestamp : 2020-02-06 16:13:48 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +hyphy 2.5.2 ha076c6e_1 +---------------------- +file name : hyphy-2.5.2-ha076c6e_1.tar.bz2 +name : hyphy +version : 2.5.2 +build : ha076c6e_1 +build number: 1 +size : 6.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.2-ha076c6e_1.tar.bz2 +md5 : 75a02dbb56e02acea001d91f25c493a2 +timestamp : 2020-02-14 14:45:09 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=4.0.2,<4.1.0a0 + + +hyphy 2.5.3 ha076c6e_0 +---------------------- +file name : hyphy-2.5.3-ha076c6e_0.tar.bz2 +name : hyphy +version : 2.5.3 +build : ha076c6e_0 +build number: 0 +size : 6.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.3-ha076c6e_0.tar.bz2 +md5 : 28bd0009cd18802620e4e2b9a5905bdd +timestamp : 2020-02-16 02:48:22 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=4.0.2,<4.1.0a0 + + +hyphy 2.5.4 ha076c6e_0 +---------------------- +file name : hyphy-2.5.4-ha076c6e_0.tar.bz2 +name : hyphy +version : 2.5.4 +build : ha076c6e_0 +build number: 0 +size : 6.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.4-ha076c6e_0.tar.bz2 +md5 : 1ca15e15bcfbb90afeddb3920b38b924 +timestamp : 2020-02-18 20:04:04 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=4.0.2,<4.1.0a0 + + +hyphy 2.5.4 ha076c6e_1 +---------------------- +file name : hyphy-2.5.4-ha076c6e_1.tar.bz2 +name : hyphy +version : 2.5.4 +build : ha076c6e_1 +build number: 1 +size : 6.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.4-ha076c6e_1.tar.bz2 +md5 : f39d675f705eaf3822163a444ac1c5cb +timestamp : 2020-02-20 18:36:30 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=4.0.2,<4.1.0a0 + + +hyphy 2.5.5 ha076c6e_0 +---------------------- +file name : hyphy-2.5.5-ha076c6e_0.tar.bz2 +name : hyphy +version : 2.5.5 +build : ha076c6e_0 +build number: 0 +size : 6.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.5-ha076c6e_0.tar.bz2 +md5 : 768925c5da7e8576f4da802c8f9a1b51 +timestamp : 2020-02-29 17:17:18 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=4.0.2,<4.1.0a0 + + +hyphy 2.5.6 ha076c6e_0 +---------------------- +file name : hyphy-2.5.6-ha076c6e_0.tar.bz2 +name : hyphy +version : 2.5.6 +build : ha076c6e_0 +build number: 0 +size : 6.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.6-ha076c6e_0.tar.bz2 +md5 : 4bb1169246b603ccc91bca03d85f34b8 +timestamp : 2020-03-14 13:19:05 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=4.0.2,<4.1.0a0 + + +hyphy 2.5.7 ha076c6e_0 +---------------------- +file name : hyphy-2.5.7-ha076c6e_0.tar.bz2 +name : hyphy +version : 2.5.7 +build : ha076c6e_0 +build number: 0 +size : 6.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.7-ha076c6e_0.tar.bz2 +md5 : cd6d87cccbe8928ca30b52042309f5ac +timestamp : 2020-03-19 04:20:31 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=4.0.2,<4.1.0a0 + + +hyphy 2.5.8 ha076c6e_0 +---------------------- +file name : hyphy-2.5.8-ha076c6e_0.tar.bz2 +name : hyphy +version : 2.5.8 +build : ha076c6e_0 +build number: 0 +size : 6.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.8-ha076c6e_0.tar.bz2 +md5 : 5dddf84b9a02da243d2d00c0a1593bf7 +timestamp : 2020-03-24 02:12:22 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=4.0.2,<4.1.0a0 + + +hyphy 2.5.8 ha076c6e_1 +---------------------- +file name : hyphy-2.5.8-ha076c6e_1.tar.bz2 +name : hyphy +version : 2.5.8 +build : ha076c6e_1 +build number: 1 +size : 6.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.8-ha076c6e_1.tar.bz2 +md5 : 06a9b17c9f4b0eba01e7bb58b0b8534c +timestamp : 2020-03-25 16:05:46 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=4.0.2,<4.1.0a0 + + +hyphy 2.5.9 ha076c6e_0 +---------------------- +file name : hyphy-2.5.9-ha076c6e_0.tar.bz2 +name : hyphy +version : 2.5.9 +build : ha076c6e_0 +build number: 0 +size : 6.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.9-ha076c6e_0.tar.bz2 +md5 : 3a491d175718abe6990e2cff187e9c58 +timestamp : 2020-04-21 12:16:13 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openmpi >=4.0.3,<4.1.0a0 + + +hyphy 2.5.10 ha076c6e_0 +----------------------- +file name : hyphy-2.5.10-ha076c6e_0.tar.bz2 +name : hyphy +version : 2.5.10 +build : ha076c6e_0 +build number: 0 +size : 6.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/hyphy-2.5.10-ha076c6e_0.tar.bz2 +md5 : c8541d81ac8cb7b8289b8eabd2087229 +timestamp diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/involucro.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/involucro.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0cc8e1893a148f24597f5a7b1dc833bb51843613 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/involucro.manual_bundle.txt @@ -0,0 +1,163 @@ +# Tool: involucro +software_name: involucro +tier: T1 +domain: t1_backfill_overall +downloads: 130830 +summary: +description: +dependencies: +execution_environment: Other +execution_environment_reason: fallback runtime classification + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +cli:involucro +## CLI Help Content +$ conda run -n bioenv_cli involucro --help +[rc=0] + +Usage of involucro 1.1.2: + -H string + Set the URL of the Docker instance (default "unix:///var/run/docker.sock") + -T Shorthand for --tasks + -e string + Evaluate the given script directly, not evaluating the control file + -f string + Set the control file (default "invfile.lua") + -host string + Long form for -H (default "unix:///var/run/docker.sock") + -s value + Shorthand for --set + -set value + Used as KEY=VALUE, makes VAR[KEY] available with value VALUE in Lua script + -tasks + Show available tasks and then exit + -v int + Set verbosity, 3 logs everything, 2 shows standard output (default 1) + -version + Show version and the exit + -w string + Set working dir, being the base for all operations. Also settable via environment variable $INVOLUCRO_WORKDIR (default ".") + -wrap string + Execute encoded wrap task + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge involucro --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +involucro 1.1.2 0 +----------------- +file name : involucro-1.1.2-0.tar.bz2 +name : involucro +version : 1.1.2 +build : 0 +build number: 0 +size : 2.1 MB +license : Apache 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/involucro-1.1.2-0.tar.bz2 +md5 : c0f215b0a8405981effd4cdec00522bc +dependencies: [] + + +involucro 1.1.2 1 +----------------- +file name : involucro-1.1.2-1.tar.bz2 +name : involucro +version : 1.1.2 +build : 1 +build number: 1 +size : 2.1 MB +license : Apache 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/involucro-1.1.2-1.tar.bz2 +md5 : aa7c66e6e3499edd5a960a0a46053d8f +timestamp : 2018-07-06 17:11:46 UTC +dependencies: [] + + +involucro 1.1.2 h375a9b1_2 +-------------------------- +file name : involucro-1.1.2-h375a9b1_2.tar.bz2 +name : involucro +version : 1.1.2 +build : h375a9b1_2 +build number: 2 +size : 2.5 MB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/involucro-1.1.2-h375a9b1_2.tar.bz2 +md5 : 3e6de46646cb1bee8933ddc3b7c76e30 +timestamp : 2020-12-05 10:28:47 UTC +dependencies: [] + + +involucro 1.1.2 ha8f183a_0 +-------------------------- +file name : involucro-1.1.2-ha8f183a_0.conda +name : involucro +version : 1.1.2 +build : ha8f183a_0 +build number: 0 +size : 2.1 MB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/involucro-1.1.2-ha8f183a_0.conda +md5 : 58decacfd3089abf524910c97437987d +timestamp : 2023-04-10 16:26:00 UTC +dependencies: [] + + +involucro 1.1.2 he881be0_3 +-------------------------- +file name : involucro-1.1.2-he881be0_3.tar.bz2 +name : involucro +version : 1.1.2 +build : he881be0_3 +build number: 3 +size : 2.3 MB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/involucro-1.1.2-he881be0_3.tar.bz2 +md5 : fbf0715e3e211c4491eb69a0b9eb01d2 +timestamp : 2021-03-26 15:34:29 UTC +dependencies: [] + + +involucro 1.1.2 he881be0_4 +-------------------------- +file name : involucro-1.1.2-he881be0_4.tar.bz2 +name : involucro +version : 1.1.2 +build : he881be0_4 +build number: 4 +size : 2.4 MB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/involucro-1.1.2-he881be0_4.tar.bz2 +md5 : 43d14fa1ddeff559dd74f3c35392f650 +timestamp : 2023-03-30 08:26:46 UTC +dependencies: [] + + +involucro 1.1.3 ha8f183a_0 +-------------------------- +file name : involucro-1.1.3-ha8f183a_0.conda +name : involucro +version : 1.1.3 +build : ha8f183a_0 +build number: 0 +size : 2.2 MB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/involucro-1.1.3-ha8f183a_0.conda +md5 : 06c462a040db3ff1e9c05fe9b7253d09 +timestamp : 2023-11-24 20:32:02 UTC +dependencies: [] diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/iqtree.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/iqtree.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ea4d754397a294ad5f9029e3eda917fca26e887 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/iqtree.manual_bundle.txt @@ -0,0 +1,689 @@ +# Tool: iqtree +software_name: iqtree +tier: T1 +domain: t1_backfill_overall +downloads: 1028577 +summary: Efficient phylogenomic software by maximum likelihood. +description: Efficient phylogenomic software by maximum likelihood. +dependencies: _openmp_mutex >=4.5, libgcc >=14, libgomp, libstdcxx >=14 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://www.iqtree.org +doc_url: http://www.iqtree.org/doc +dev_url: https://github.com/iqtree/iqtree3 + +## CLI Help Source +cli:iqtree +## CLI Help Content +$ conda run -n bioenv_cli iqtree --help +[rc=0] +IQ-TREE version 3.1.1 for Linux x86 64-bit built Apr 8 2026 +Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren +Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow, +Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt + +Usage: iqtree [-s ALIGNMENT] [-p PARTITION] [-m MODEL] [-t TREE] ... + +GENERAL OPTIONS: + -h, --help Print (more) help usages + -s FILE[,...,FILE] PHYLIP/FASTA/NEXUS/CLUSTAL/MSF alignment file(s) + -s DIR Directory of alignment files + --seqtype STRING BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect) + -t FILE|PARS|RAND Starting tree (default: 99 parsimony and BIONJ) + -o TAX[,...,TAX] Outgroup taxon (list) for writing .treefile + --prefix STRING Prefix for all output files (default: aln/partition) + --seed NUM Random seed number, normally used for debugging purpose + --safe Safe likelihood kernel to avoid numerical underflow + --mem NUM[G|M|%] Maximal RAM usage in GB | MB | % + --runs NUM Number of indepedent runs (default: 1) + -v, --verbose Verbose mode, printing more messages to screen + -V, --version Display version number + --quiet Quiet mode, suppress printing to screen (stdout) + -fconst f1,...,fN Add constant patterns into alignment (N=no. states) + --epsilon NUM Likelihood epsilon for parameter estimate (default 0.01) + -T NUM|AUTO No. cores/threads or AUTO-detect (default: 1) + --threads-max NUM Max number of threads for -T AUTO (default: all cores) + +CHECKPOINT: + --redo Redo both ModelFinder and tree search + --redo-tree Restore ModelFinder and only redo tree search + --undo Revoke finished run, used when changing some options + --cptime NUM Minimum checkpoint interval (default: 60 sec and adapt) + +PARTITION MODEL: + -p FILE|DIR NEXUS/RAxML partition file or directory with alignments + Edge-linked proportional partition model + -q FILE|DIR Like -p but edge-linked equal partition model + -Q FILE|DIR Like -p but edge-unlinked partition model + -S FILE|DIR Like -p but separate tree inference + --subsample NUM Randomly sub-sample partitions (negative for complement) + --subsample-seed NUM Random number seed for --subsample + +LIKELIHOOD/QUARTET MAPPING: + --lmap NUM Number of quartets for likelihood mapping analysis + --lmclust FILE NEXUS file containing clusters for likelihood mapping + --quartetlh Print quartet log-likelihoods to .quartetlh file + +TREE SEARCH ALGORITHM: + --ninit NUM Number of initial parsimony trees (default: 100) + --ntop NUM Number of top initial trees (default: 20) + --nbest NUM Number of best trees retained during search (default: 5) + -n NUM Fix number of iterations to stop (default: OFF) + --nstop NUM Number of unsuccessful iterations to stop (default: 100) + --perturb NUM Perturbation strength for randomized NNI (default: 0.5) + --radius NUM Radius for parsimony SPR search (default: 6) + --allnni Perform more thorough NNI search (default: OFF) + -g FILE (Multifurcating) topological constraint tree file + --fast Fast search to resemble FastTree + --polytomy Collapse near-zero branches into polytomy + --tree-fix Fix -t tree (no tree search performed) + --treels Write locally optimal trees into .treels file + --show-lh Compute tree likelihood without optimisation + --terrace Check if the tree lies on a phylogenetic terrace + +ULTRAFAST BOOTSTRAP/JACKKNIFE: + -B, --ufboot NUM Replicates for ultrafast bootstrap (>=1000) + -J, --ufjack NUM Replicates for ultrafast jackknife (>=1000) + --jack-prop NUM Subsampling proportion for jackknife (default: 0.5) + --sampling STRING GENE|GENESITE resampling for partitions (default: SITE) + --boot-trees Write bootstrap trees to .ufboot file (default: none) + --wbtl Like --boot-trees but also writing branch lengths + --nmax NUM Maximum number of iterations (default: 1000) + --nstep NUM Iterations for UFBoot stopping rule (default: 100) + --bcor NUM Minimum correlation coefficient (default: 0.99) + --beps NUM RELL epsilon to break tie (default: 0.5) + --bnni Optimize UFBoot trees by NNI on bootstrap alignment + +NON-PARAMETRIC BOOTSTRAP/JACKKNIFE: + -b, --boot NUM Replicates for bootstrap + ML tree + consensus tree + -j, --jack NUM Replicates for jackknife + ML tree + consensus tree + --jack-prop NUM Subsampling proportion for jackknife (default: 0.5) + --bcon NUM Replicates for bootstrap + consensus tree + --bonly NUM Replicates for bootstrap only + --tbe Transfer bootstrap expectation + +SINGLE BRANCH TEST: + --alrt NUM Replicates for SH approximate likelihood ratio test + --alrt 0 Parametric aLRT test (Anisimova and Gascuel 2006) + --abayes approximate Bayes test (Anisimova et al. 2011) + --lbp NUM Replicates for fast local bootstrap probabilities + +MODEL-FINDER: + --use-nn-model Use neural network for tree inference + --nn-path-model Neural network file for substitution model (onnx format) + --nn-path-rates Neural network file for alpha value (onnx format) + -m TESTONLY Standard model selection (like jModelTest, ProtTest) + -m TEST Standard model selection followed by tree inference + -m MF Extended model selection with FreeRate heterogeneity + -m MFP Extended model selection followed by tree inference + -m ...+LM Additionally test Lie Markov models + -m ...+LMRY Additionally test Lie Markov models with RY symmetry + -m ...+LMWS Additionally test Lie Markov models with WS symmetry + -m ...+LMMK Additionally test Lie Markov models with MK symmetry + -m ...+LMSS Additionally test strand-symmetric models + --mset STRING Restrict search to models supported by other programs + (raxml, phyml, mrbayes, beast1 or beast2) + If 'mrbayes' is selected, will output a MrBayes + Block File if Data Type is supported. + --mset STR,... Comma-separated model list (e.g. -mset WAG,LG,JTT) + --msub STRING Amino-acid model source + (nuclear, mitochondrial, chloroplast or viral) + --mfreq STR,... List of state frequencies + --mrate STR,... List of rate heterogeneity among sites + (e.g. -mrate E,I,G,I+G,R is used for -m MF) + --cmin NUM Min categories for FreeRate model [+R] (default: 2) + --cmax NUM Max categories for FreeRate model [+R] (default: 10) + --merit AIC|AICc|BIC Akaike|Bayesian information criterion (default: BIC) + --mtree Perform full tree search for every model + --madd STR,... List of mixture models to consider + --mdef FILE Model definition NEXUS file (see Manual) + --modelomatic Find best codon/protein/DNA models (Whelan et al. 2015) + +PARTITION-FINDER: + --merge Merge partitions to increase model fit + --merge greedy|rcluster|rclusterf + Set merging algorithm (default: rclusterf) + --merge-model 1|all Use only 1 or all models for merging (default: 1) + --merge-model STR,... + Comma-separated model list for merging + --merge-rate 1|all Use only 1 or all rate heterogeneity (default: 1) + --merge-rate STR,... + Comma-separated rate list for merging + --rcluster NUM Percentage of partition pairs for rcluster algorithm + --rclusterf NUM Percentage of partition pairs for rclusterf algorithm + --rcluster-max NUM Max number of partition pairs (default: 10*partitions) + +SUBSTITUTION MODEL: + -m STRING Model name string (e.g. GTR+F+I+G) + DNA: HKY (default), JC, F81, K2P, K3P, K81uf, TN/TrN, TNef, + TIM, TIMef, TVM, TVMef, SYM, GTR, or 6-digit model + specification (e.g., 010010 = HKY) + Protein: LG (default), Poisson, cpREV, mtREV, Dayhoff, mtMAM, + JTT, WAG, mtART, mtZOA, VT, rtREV, DCMut, PMB, HIVb, + HIVw, JTTDCMut, FLU, Blosum62, GTR20, mtMet, mtVer, mtInv, FLAVI, + Q.LG, Q.pfam, Q.pfam_gb, Q.bird, Q.mammal, Q.insect, Q.plant, Q.yeast + Protein mixture: C10,...,C60, EX2, EX3, EHO, UL2, UL3, EX_EHO, LG4M, LG4X + Binary: JC2 (default), GTR2 + Empirical codon: KOSI07, SCHN05 + Mechanistic codon: GY (default), MG, MGK, GY0K, GY1KTS, GY1KTV, GY2K, + MG1KTS, MG1KTV, MG2K +Semi-empirical codon: XX_YY where XX is empirical and YY is mechanistic model + Morphology/SNP: MK (default), ORDERED, GTR + Lie Markov DNA: 1.1, 2.2b, 3.3a, 3.3b, 3.3c, 3.4, 4.4a, 4.4b, 4.5a, + 4.5b, 5.6a, 5.6b, 5.7a, 5.7b, 5.7c, 5.11a, 5.11b, 5.11c, + 5.16, 6.6, 6.7a, 6.7b, 6.8a, 6.8b, 6.17a, 6.17b, 8.8, + 8.10a, 8.10b, 8.16, 8.17, 8.18, 9.20a, 9.20b, 10.12, + 10.34, 12.12 (optionally prefixed by RY, WS or MK) + Non-reversible: STRSYM (strand symmetric model, equiv. WS6.6), + NONREV, UNREST (unrestricted model, equiv. 12.12) + NQ.pfam, NQ.bird, NQ.mammal, NQ.insect, NQ.plant, NQ.yeast + Otherwise: Name of file containing user-model parameters + +STATE FREQUENCY: + -m ...+F Empirically counted frequencies from alignment + -m ...+FO Optimized frequencies by maximum-likelihood + -m ...+FQ Equal frequencies + -m ...+FRY For DNA, freq(A+G)=1/2=freq(C+T) + -m ...+FWS For DNA, freq(A+T)=1/2=freq(C+G) + -m ...+FMK For DNA, freq(A+C)=1/2=freq(G+T) + -m ...+Fabcd 4-digit constraint on ACGT frequency + (e.g. +F1221 means f_A=f_T, f_C=f_G) + -m ...+FU Amino-acid frequencies given protein matrix + -m ...+F1x4 Equal NT frequencies over three codon positions + -m ...+F3x4 Unequal NT frequencies over three codon positions + +RATE HETEROGENEITY AMONG SITES: + -m ...+I A proportion of invariable sites + -m ...+G[n] Discrete Gamma model with n categories (default n=4) + -m ...*G[n] Discrete Gamma model with unlinked model parameters + -m ...+I+G[n] Invariable sites plus Gamma model with n categories + -m ...+R[n] FreeRate model with n categories (default n=4) + -m ...*R[n] FreeRate model with unlinked model parameters + -m ...+I+R[n] Invariable sites plus FreeRate model with n categories + -m ...+Hn Heterotachy model with n classes + -m ...*Hn Heterotachy model with n classes and unlinked parameters + --alpha-min NUM Min Gamma shape parameter for site rates (default: 0.02) + --gamma-median Median approximation for +G site rates (default: mean) + --rate Write empirical Bayesian site rates to .rate file + --mlrate Write maximum likelihood site rates to .mlrate file + +POLYMORPHISM AWARE MODELS (PoMo): + -s FILE Input counts file (see manual) + -m ...+P DNA substitution model (see above) used with PoMo + -m ...+N Virtual population size (default: 9) + -m ...+WB|WH|S] Weighted binomial sampling + -m ...+WH Weighted hypergeometric sampling + -m ...+S Sampled sampling + -m ...+G[n] Discrete Gamma rate with n categories (default n=4) + +COMPLEX MODELS: + -m "MIX{m1,...,mK}" Mixture model with K components + -m "FMIX{f1,...fK}" Frequency mixture model with K components + --mix-opt Optimize mixture weights (defaul + +## URL Docs Extract +### http://www.iqtree.org/doc +Page Redirection If you are not redirected automatically, follow this link . + +### http://www.iqtree.org +Page Redirection If you are not redirected automatically, follow this link . + +### https://github.com/iqtree/iqtree3 +GitHub - iqtree/iqtree3: IQ-TREE version 3: software for phylogenetics · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} iqtree / iqtree3 Public Notifications You must be signed in to change notification settings Fork 34 Star 125 Code Issues 50 Pull requests 2 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights iqtree/iqtree3 master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 5,901 Commits 5,901 Commits .github/ workflows .github/ workflows .vscode .vscode alignment alignment booster booster cmaple @ 3d45b1a cmaple @ 3d45b1a doc doc example example gsl gsl lbfgsb lbfgsb lib lib liblinux_arm liblinux_arm libmac libmac libmac26 libmac26 libmac26_m1 libmac26_m1 libmac_m1 libmac_m1 lsd2 @ c61110f lsd2 @ c61110f main main model model ncl ncl nclextra nclextra nn nn nn_models nn_models obsolete obsolete pda pda phylo-yaml phylo-yaml pll pll simulator simulator sprng sprng terrace terrace terracetphast terracetphast terraphast terraphast test_scripts test_scripts tree tree utils utils vectorclass vectorclass whtest whtest yaml-cpp yaml-cpp zlib-1.2.7 zlib-1.2.7 .gitignore .gitignore .gitmodules .gitmodules .ycm_extra_conf.py .ycm_extra_conf.py CMakeLists.txt CMakeLists.txt CMakeSettings.json CMakeSettings.json CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md FindEigen3.cmake FindEigen3.cmake LICENSE LICENSE README.md README.md flake.lock flake.lock flake.nix flake.nix iqtree.doxy iqtree.doxy iqtree_config.h.in iqtree_config.h.in onnxruntimeConfig.cmake onnxruntimeConfig.cmake View all files Repository files navigation README Code of conduct GPL-2.0 license IQ-TREE Efficient and versatile phylogenomic software by maximum likelihood http://www.iqtree.org Introduction The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis. As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree ), a NEWICK tree file ( .treefile ) which can be visualized by tree viewer programs such as FigTree , Dendroscope or iTOL . Key features of IQ-TREE Efficient search algorithm : Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihood while requiring similar amount of computing time ( Nguyen et al., 2015 ). Ultrafast bootstrap : An ultrafast bootstrap approximation (UFBoot) to assess branch supports. UFBoot is 10 to 40 times faster than RAxML rapid bootstrap and obtains less biased support values ( Minh et al., 2013 ). Accurate model selection : An ultrafast and automatic model selection (ModelFinder) which is 10 to 100 times faster than jModelTest and ProtTest. ModelFinder also finds best-fit partitioning scheme like PartitionFinder ( Kalyaanamoorthy et al., 2017 ). Alignment simulation : A flexible simulator (AliSim) which allows to simulate sequence alignments under more realistic models than Seq-Gen and INDELible ( Ly-Trong et al., 2023 ). Phylogenetic testing : Several fast branch tests like SH-aLRT and aBayes test ( Anisimova et al., 2011 ) and tree topology tests like the approximately unbiased (AU) test ( Shimodaira, 2002 ). The strength of IQ-TREE is the availability of a wide variety of phylogenetic models: Common models : All common substitution models for DNA, protein, codon, binary and morphological data with rate heterogeneity among sites and ascertainment bias correction for e.g. SNP data. Partition models : Allowing individual models for different genomic loci (e.g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions. Mixture Models : fully customizable mixture models and empirical protein mixture models and. Polymorphism-aware models (PoMo) : http://www.iqtree.org/doc/Polymorphism-Aware-Models IQ-TREE web service For a quick start you can also try the IQ-TREE web server, which performs online computation using a dedicated computing cluster. It is very easy to use with as few as just 3 clicks! Try it out at: Vienna Bioinformatics Cluster: http://iqtree.cibiv.univie.ac.at CIPRES Gateway: https://www.phylo.org Los Alamos Laboratories: https://www.hiv.lanl.gov/content/sequence/IQTREE/iqtree.html User support Please refer to the user documentation and frequently asked questions . If you have further questions and feedback, please create a topic at Github discussions . For feature requests bug reports please post a topic at Github issues . Citations General citation for IQ-TREE 3: T.K.F. Wong, N. Ly-Trong, H. Ren, H. Banos, A.J. Roger, E. Susko, C. Bielow, N. De Maio, N. Goldman, M.W. Hahn, G. Huttley, R. Lanfear, B.Q. Minh (2025) IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models. Submitted, https://doi.org/10.32942/X2P62N . Moreover, there are other papers associated with notable features in IQ-TREE, which are normally mentioned in the corresponding documentation. We ask that you also cite these papers, which are important for us to obtain fundings to continuously maintain the code of IQ-TREE. These papers are also listed below. NOTE : You can also obtain the citations in .iqtree output file. When using MixtureFinder please cite: H. Ren, T.K.F. Wong, B.Q. Minh, R. Lanfear (2025) MixtureFinder: Estimating DNA mixture models for phylogenetic analyses. Mol. Biol. Evol. , 42:msae264. https://doi.org/10.1093/molbev/msae264 When using GTRpmix model please cite: H. Banos, T.K.F. Wong, J. Daneau, E. Susko, B.Q. Minh, R. Lanfear, M.W. Brown, L. Eme, A.J. Roger (2024) GTRpmix: A linked general-time reversible model for profile mixture models. Mol. Biol. Evol. , 92:msae174. https://doi.org/10.1093/molbev/msae174 When using CMAPLE please cite: N. Ly-Trong, C. Bielow, N. De Maio, B.Q. Minh (2024) CMAPLE: Efficient phylogenetic inference in the pandemic era. Mol. Biol. Evol. , 41:msae134. https://doi.org/10.1093/molbev/msae134 When using tree mixture models (MAST) please cite: T.K.F. Wong, C. Cherryh, A.G. Rodrigo, M.W. Hahn, B.Q. Minh, R. Lanfear (2024) MAST: Phylogenetic Inference with Mixtures Across Sites and Trees. Syst. Biol. , 73:375–391. https://doi.org/10.1093/sysbio/syae008 When computing concordance factors please cite: Y.K. Mo, R. Lanfear, M.W. Hahn, B.Q. Minh (2023) Updated site concordance factors minimize effects of homoplasy and taxon sampling. Bioinformatics , 39:btac741. https://doi.org/10.1093/bioinformatics/btac741 When using AliSim to simulate alignments please cite: N. Ly-Trong, G.M.J. Barca, B.Q. Minh (2023) AliSim-HPC: parallel sequence simulator for phylogenetics. Bioinformatics , 39:btad540. https://doi.org/10.1093/bioinformatics/btad540 When estimating amino-acid Q matrix please cite: B.Q. Minh, C. Cao Dang, L.S. Vinh, R. Lanfear (2021) QMaker: Fast and accurate method to estimate empirical models of protein evolution. Syst. Biol. , 70:1046–1060. https://doi.org/10.1093/sysbio/syab010 When using the heterotachy GHOST model "+H" please cite: S.M. Crotty, B.Q. Minh, N.G. Bean, B.R. Holland, J. Tuke, L.S. Jermiin, A. von Haeseler (2020) GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments. Syst. Biol. , 69:249-264. https://doi.org/10.1093/sysbio/syz051 When using the tests of symmetry please cite: S. Naser-Khdour, B.Q. Minh, W. Zhang, E.A. Stone, R. Lanfear (2019) The Prevalence and Impact of Model Violations in Phylogenetic Analysis. Genome Biol. Evol. , 11:3341-3352. https://doi.org/10.1093/gbe/evz193 When using polymorphism-aware models please cite: D. Schrempf, B.Q. Minh, A. von Haeseler, C. Kosiol (2019) Polymorphism-aware species trees with advanced mutation models, bootstrap, and rate heterogeneity. Mol. Biol. Evol. , 36:1294–1301. https://doi.org/10.1093/molbev/msz043 For the ultrafast bootstrap (UFBoot) please cite: D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, and L.S. Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol. , 35:518–522. https://doi.org/10.1093/molbev/msx281 When using posterior mean site frequency model (PMSF) please cite: H.C. Wang, B.Q. Minh, S. Susko, A.J. Roger (2018) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol. , 67:216–235. https://doi.org/10.1093/sysbio/syx068 When using ModelFinder please cite: S. Kalyaanamoorthy, B.Q. Minh, T.K.F. Wong, A. von Haeseler, L.S. Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods , 14:587-589. https://doi.org/10.1038/nmeth.4285 When using partition models please cite: O. Chernomor, A. von Haeseler, B.Q. Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol. , 65:997-1008. https://doi.org/10.1093/sysbio/syw037 When using IQ-TREE web server please cite: J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. , 44:W232-W235. https://doi.org/10.1093/nar/gkw256 When using IQ-TREE version 1 please cite: L. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Mol. Biol. and Evol. , 32:268-274. https://doi.org/10.1093/molbev/msu300 When using IQ-TREE version 2 please cite: B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. , 37:1530-1534. https://doi.org/10.1093/molbev/msaa015 Credits and Acknowledgements Some parts of the code were taken from the following packages/libraries: Phylogenetic likelihood library , TREE-PUZZLE , BIONJ , Nexus Class Libary , Eigen library , SPRNG library , Zlib library , gzstream library , vectorclass library , GNU scientific library . IQ-TREE was funded by the Austrian Science Fund - FWF (grant no. I 760-B17 from 2012-2015 and and I 2508-B29 from 2016-2019), the University of Vienna (Initiativkolleg I059-N), the Australian National University , Chan-Zuckerberg Initiative (open source software for science grants), Simons Foundation , Moore Foundation , and Australian Research Council . About IQ-TREE version 3: software for phylogenetics iqtree.github.io Resources Readme License GPL-2.0 license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 125 stars Watchers 9 watching Forks 34 forks Report repository Releases 4 Release version 3.1.1 Latest Apr 2, 2026 + 3 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 69.4% C 26.7% Assembly 1.0% CMake 0.6% Ada 0.6% C# 0.4% Other 1.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge iqtree --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +iqtree 1.5.3 0 +-------------- +file name : iqtree-1.5.3-0.tar.bz2 +name : iqtree +version : 1.5.3 +build : 0 +build number: 0 +size : 1.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.5.3-0.tar.bz2 +md5 : 5ef0f9b5f1e0f7cd02e7e7a9c7344840 +dependencies: + - libgcc + - zlib + + +iqtree 1.5.3 1 +-------------- +file name : iqtree-1.5.3-1.tar.bz2 +name : iqtree +version : 1.5.3 +build : 1 +build number: 1 +size : 1.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.5.3-1.tar.bz2 +md5 : 7c8923f34ddb829c191bf561b547ddda +dependencies: + - libgcc + - zlib 1.2.11* + + +iqtree 1.5.3 he941832_2 +----------------------- +file name : iqtree-1.5.3-he941832_2.tar.bz2 +name : iqtree +version : 1.5.3 +build : he941832_2 +build number: 2 +size : 1.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.5.3-he941832_2.tar.bz2 +md5 : f47e35a41c1b17ddf4f1c9aad98f12d3 +timestamp : 2018-07-08 00:26:49 UTC +dependencies: + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.5.5 0 +-------------- +file name : iqtree-1.5.5-0.tar.bz2 +name : iqtree +version : 1.5.5 +build : 0 +build number: 0 +size : 1.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.5.5-0.tar.bz2 +md5 : 60cd02946d49f4ecab0302c1e3dbe671 +dependencies: + - libgcc + - zlib + + +iqtree 1.5.5 1 +-------------- +file name : iqtree-1.5.5-1.tar.bz2 +name : iqtree +version : 1.5.5 +build : 1 +build number: 1 +size : 1.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.5.5-1.tar.bz2 +md5 : fefe73509e422761c01b90c092567a91 +dependencies: + - libgcc + - zlib 1.2.11* + + +iqtree 1.5.5 he941832_2 +----------------------- +file name : iqtree-1.5.5-he941832_2.tar.bz2 +name : iqtree +version : 1.5.5 +build : he941832_2 +build number: 2 +size : 1.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.5.5-he941832_2.tar.bz2 +md5 : ccdd805e5bd647842f038db44a550bbd +timestamp : 2018-07-08 00:34:03 UTC +dependencies: + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.6 he941832_0 +----------------------- +file name : iqtree-1.6.6-he941832_0.tar.bz2 +name : iqtree +version : 1.6.6 +build : he941832_0 +build number: 0 +size : 2.2 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.6-he941832_0.tar.bz2 +md5 : ed961005c89db7589bac3f08ac6763f1 +timestamp : 2018-08-18 20:03:19 UTC +dependencies: + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.7 he941832_0 +----------------------- +file name : iqtree-1.6.7-he941832_0.tar.bz2 +name : iqtree +version : 1.6.7 +build : he941832_0 +build number: 0 +size : 2.2 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.7-he941832_0.tar.bz2 +md5 : 1f58fb464e3b31c238fa245c9c3284e2 +timestamp : 2018-08-24 03:48:22 UTC +dependencies: + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.7 he941832_1 +----------------------- +file name : iqtree-1.6.7-he941832_1.tar.bz2 +name : iqtree +version : 1.6.7 +build : he941832_1 +build number: 1 +size : 2.2 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.7-he941832_1.tar.bz2 +md5 : 7995af036c7db0d3d9793dc868ef77f2 +timestamp : 2018-09-04 20:11:45 UTC +dependencies: + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.7.1 he941832_0 +------------------------- +file name : iqtree-1.6.7.1-he941832_0.tar.bz2 +name : iqtree +version : 1.6.7.1 +build : he941832_0 +build number: 0 +size : 2.3 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.7.1-he941832_0.tar.bz2 +md5 : cfc7f2b6d339c2d44e9aca9eb60963f6 +timestamp : 2018-10-19 16:40:59 UTC +dependencies: + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.7.2 he941832_0 +------------------------- +file name : iqtree-1.6.7.2-he941832_0.tar.bz2 +name : iqtree +version : 1.6.7.2 +build : he941832_0 +build number: 0 +size : 2.3 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.7.2-he941832_0.tar.bz2 +md5 : d2e6ed7b2c75d99cfbad55066babf6e6 +timestamp : 2018-10-24 00:23:04 UTC +dependencies: + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.8 he941832_0 +----------------------- +file name : iqtree-1.6.8-he941832_0.tar.bz2 +name : iqtree +version : 1.6.8 +build : he941832_0 +build number: 0 +size : 2.3 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.8-he941832_0.tar.bz2 +md5 : a1f3249f21340bf57f626445c00b58c6 +timestamp : 2018-10-29 01:02:16 UTC +dependencies: + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.9 he860b03_1 +----------------------- +file name : iqtree-1.6.9-he860b03_1.tar.bz2 +name : iqtree +version : 1.6.9 +build : he860b03_1 +build number: 1 +size : 2.4 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.9-he860b03_1.tar.bz2 +md5 : cc2327a75b678071ca19a3314a9b086c +timestamp : 2019-03-09 17:05:09 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.9 he941832_0 +----------------------- +file name : iqtree-1.6.9-he941832_0.tar.bz2 +name : iqtree +version : 1.6.9 +build : he941832_0 +build number: 0 +size : 2.3 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.9-he941832_0.tar.bz2 +md5 : c72ccc7d230e2925a17afad84f709f8f +timestamp : 2018-12-19 21:44:15 UTC +dependencies: + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.10 he860b03_0 +------------------------ +file name : iqtree-1.6.10-he860b03_0.tar.bz2 +name : iqtree +version : 1.6.10 +build : he860b03_0 +build number: 0 +size : 2.4 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.10-he860b03_0.tar.bz2 +md5 : 6f4299ebd667d88fab30483f29b24609 +timestamp : 2019-03-21 13:06:42 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.11 he860b03_0 +------------------------ +file name : iqtree-1.6.11-he860b03_0.tar.bz2 +name : iqtree +version : 1.6.11 +build : he860b03_0 +build number: 0 +size : 2.4 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.11-he860b03_0.tar.bz2 +md5 : 11f11423319ea6d142e644f4e1eeb573 +timestamp : 2019-06-15 21:45:34 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.11.1 he513fc3_0 +-------------------------- +file name : iqtree-1.6.11.1-he513fc3_0.tar.bz2 +name : iqtree +version : 1.6.11.1 +build : he513fc3_0 +build number: 0 +size : 2.4 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.11.1-he513fc3_0.tar.bz2 +md5 : 17c743f769b3d97f56c4080293e7f350 +timestamp : 2019-08-14 07:21:21 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.12 he513fc3_0 +------------------------ +file name : iqtree-1.6.12-he513fc3_0.tar.bz2 +name : iqtree +version : 1.6.12 +build : he513fc3_0 +build number: 0 +size : 2.4 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.12-he513fc3_0.tar.bz2 +md5 : 1673819b8f48b948aeddb733af73fd33 +timestamp : 2019-08-15 07:19:11 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 1.6.12 he513fc3_1 +------------------------ +file name : iqtree-1.6.12-he513fc3_1.tar.bz2 +name : iqtree +version : 1.6.12 +build : he513fc3_1 +build number: 1 +size : 2.4 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-1.6.12-he513fc3_1.tar.bz2 +md5 : 78af0f9d6853266439b725cb39416397 +timestamp : 2020-03-16 20:47:10 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 2.0.3 h176a8bc_0 +----------------------- +file name : iqtree-2.0.3-h176a8bc_0.tar.bz2 +name : iqtree +version : 2.0.3 +build : h176a8bc_0 +build number: 0 +size : 2.8 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-2.0.3-h176a8bc_0.tar.bz2 +md5 : 66f360c44a040eb8ff2a5426cdfebe30 +timestamp : 2020-04-26 21:28:24 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 2.0.3 h176a8bc_1 +----------------------- +file name : iqtree-2.0.3-h176a8bc_1.tar.bz2 +name : iqtree +version : 2.0.3 +build : h176a8bc_1 +build number: 1 +size : 3.0 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-2.0.3-h176a8bc_1.tar.bz2 +md5 : 977514abd01b05f6e1a4c214c607c91b +timestamp : 2020-12-20 07:03:37 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 2.1.2 h56fc30b_0 +----------------------- +file name : iqtree-2.1.2-h56fc30b_0.tar.bz2 +name : iqtree +version : 2.1.2 +build : h56fc30b_0 +build number: 0 +size : 5.9 MB +license : GPL-2.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-2.1.2-h56fc30b_0.tar.bz2 +md5 : bca65c7d10fd1f3ff0f4a0d4b63b3908 +timestamp : 2021-03-30 20:44:15 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 2.1.4_beta hdcc8f71_0 +---------------------------- +file name : iqtree-2.1.4_beta-hdcc8f71_0.tar.bz2 +name : iqtree +version : 2.1.4_beta +build : hdcc8f71_0 +build number: 0 +size : 6.4 MB +license : GPL-2.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-2.1.4_beta-hdcc8f71_0.tar.bz2 +md5 : 0fb0479dcbd0bb7745a4b09976c2886d +timestamp : 2021-06-24 16:16:18 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +iqtree 2.2.0_beta hb97b32f_1 +---------------------------- +file name : iqtree-2.2.0_beta-hb97b32f_1.tar.bz2 +name : iqtree +version : 2.2.0_beta +build : hb97b32f_1 +build number: 1 +size : 6.9 MB +license : GPL-2.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/iqtree-2.2.0_beta-hb97b32f_1.tar.bz2 +md5 : 9fe98a963dafdf8c336ed6b3086f4901 +timestamp : 2022-03-03 13:52:42 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + + +iqtree 2.2.0_beta hdcc8f71_0 +---------------------------- +file name : iqtree-2.2.0_beta-hdcc8f71_0.tar.bz2 +name : iqtree +version : 2.2.0_beta +build : hdcc8f71_0 +b diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/jbrowse2.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/jbrowse2.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2eedac70f0fb78e0876af45bd679b1d0ef4b2d3e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/jbrowse2.manual_bundle.txt @@ -0,0 +1,514 @@ +# Tool: jbrowse2 +software_name: jbrowse2 +tier: T1 +domain: t1_backfill_overall +downloads: 184424 +summary: The JBrowse 2 Genome Browser +description: The JBrowse 2 Genome Browser +dependencies: bcftools, gff3sort, htslib, nodejs, samtools +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://jbrowse.org/ +doc_url: +dev_url: + +## URL Docs Extract +### https://jbrowse.org/ +JBrowse Skip to main content JBrowse Genomes Docs Blog Download Plugins Features Gallery Demos Contact Looking for JBrowse 1? JBrowse The next-generation genome browser JBrowse is a genome browser that runs on the web, on your desktop, or embedded in your app. Download Browse demo Check out our latest release blogpost , our embedded components , and our command line tools . Features Improved visualization of structural variants and genome synteny with tightly-integrated linear, circular, dotplot, and synteny views In-browser protein 3D structure displays with integrated alignment and phylogenetic tree views. Mouse over a genomic variant to see where it lands on the structure! Support for many common data types including BAM, CRAM, tabix indexed VCF, GFF, BED, BigBed, BigWig, and several specialized formats Powerful extensibility with a plugin ecosytem which can add additional view types, track types, data adapters, and more! See a summary of new features and a comparison to JBrowse 1 Citation We at the JBrowse Consortium are working to make JBrowse a pluggable, open-source computational platform for integrating many kinds of biological data from many different places. Research citations are one of the main metrics the consortium uses to demonstrate our relevance and utility when applying for funding to continue our work. If you use JBrowse in research that you publish, please cite the most recent JBrowse paper: Diesh et al , 2023. JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biology 24:74. https://doi.org/10.1186/s13059-023-02914-z License JBrowse is released under the Apache License, Version 2.0 . Funding and Collaboration JBrowse development has received support from the US National Institutes of Health (U41 HG003751), The Chan Zuckerberg Initiative, The Ontario Institute for Cancer Research (OICR), and the University of California, Berkeley. Docs Documentation Cancer resources Community Gitter chat Bluesky Mastodon More Blog Contact GitHub Looking for JBrowse 1? Copyright © 2020 Evolutionary Software Foundation, Inc. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge jbrowse2 --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +jbrowse2 1.3.2 hdfd78af_0 +------------------------- +file name : jbrowse2-1.3.2-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.3.2 +build : hdfd78af_0 +build number: 0 +size : 17.7 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.3.2-hdfd78af_0.tar.bz2 +md5 : be7f269157f510cd14be8f7e0b5ff9fd +timestamp : 2021-07-07 08:56:24 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.3.3 hdfd78af_0 +------------------------- +file name : jbrowse2-1.3.3-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.3.3 +build : hdfd78af_0 +build number: 0 +size : 17.7 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.3.3-hdfd78af_0.tar.bz2 +md5 : bbad1db558e72106efa6f9a4d60d08d1 +timestamp : 2021-08-02 21:26:06 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.3.5 hdfd78af_0 +------------------------- +file name : jbrowse2-1.3.5-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.3.5 +build : hdfd78af_0 +build number: 0 +size : 17.7 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.3.5-hdfd78af_0.tar.bz2 +md5 : 62e72862f4689e5245709368b5679a58 +timestamp : 2021-08-25 06:50:39 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.4.1 hdfd78af_0 +------------------------- +file name : jbrowse2-1.4.1-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.4.1 +build : hdfd78af_0 +build number: 0 +size : 18.9 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.4.1-hdfd78af_0.tar.bz2 +md5 : c334838e6cdc9bd41cb1be1ae2cff3e5 +timestamp : 2021-09-14 08:59:39 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.4.4 hdfd78af_0 +------------------------- +file name : jbrowse2-1.4.4-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.4.4 +build : hdfd78af_0 +build number: 0 +size : 18.8 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.4.4-hdfd78af_0.tar.bz2 +md5 : 7cf123428ed9be9c7b786bbd98bb7b12 +timestamp : 2021-09-14 13:26:03 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.5.0 hdfd78af_0 +------------------------- +file name : jbrowse2-1.5.0-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.5.0 +build : hdfd78af_0 +build number: 0 +size : 20.8 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.5.0-hdfd78af_0.tar.bz2 +md5 : 3930dbff611a93705f65afe090f2346b +timestamp : 2021-10-18 20:28:57 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.5.1 hdfd78af_0 +------------------------- +file name : jbrowse2-1.5.1-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.5.1 +build : hdfd78af_0 +build number: 0 +size : 21.5 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.5.1-hdfd78af_0.tar.bz2 +md5 : fd530f08ec3b6332f208c7c3d8effc50 +timestamp : 2021-11-04 18:30:28 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.5.3 hdfd78af_0 +------------------------- +file name : jbrowse2-1.5.3-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.5.3 +build : hdfd78af_0 +build number: 0 +size : 20.7 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.5.3-hdfd78af_0.tar.bz2 +md5 : a25a0f76f401a956bcbd62f7e7bd49cf +timestamp : 2021-12-21 19:18:48 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.5.5 hdfd78af_0 +------------------------- +file name : jbrowse2-1.5.5-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.5.5 +build : hdfd78af_0 +build number: 0 +size : 20.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.5.5-hdfd78af_0.tar.bz2 +md5 : dd15068539cc9d3fcf8cfb7140a0a6b9 +timestamp : 2022-01-08 11:26:22 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.5.8 hdfd78af_0 +------------------------- +file name : jbrowse2-1.5.8-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.5.8 +build : hdfd78af_0 +build number: 0 +size : 20.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.5.8-hdfd78af_0.tar.bz2 +md5 : 902b880ba2e8acd5ab75bf7ed9b3e350 +timestamp : 2022-01-13 10:28:18 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.5.9 h9d45583_1 +------------------------- +file name : jbrowse2-1.5.9-h9d45583_1.tar.bz2 +name : jbrowse2 +version : 1.5.9 +build : h9d45583_1 +build number: 1 +size : 20.3 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.5.9-h9d45583_1.tar.bz2 +md5 : ab2d5d9eb09a70475ed062ecaafb17a6 +timestamp : 2022-01-14 17:53:05 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.5.9 hbcef4ee_1 +------------------------- +file name : jbrowse2-1.5.9-hbcef4ee_1.tar.bz2 +name : jbrowse2 +version : 1.5.9 +build : hbcef4ee_1 +build number: 1 +size : 20.3 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.5.9-hbcef4ee_1.tar.bz2 +md5 : 36f0cd1c71ae8809ee12963697501b1f +timestamp : 2022-01-14 17:56:21 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.5.9 hd6180af_1 +------------------------- +file name : jbrowse2-1.5.9-hd6180af_1.tar.bz2 +name : jbrowse2 +version : 1.5.9 +build : hd6180af_1 +build number: 1 +size : 20.3 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.5.9-hd6180af_1.tar.bz2 +md5 : a08cfba159de050c87d236d8368126f6 +timestamp : 2022-01-14 17:49:35 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.5.9 hdfd78af_0 +------------------------- +file name : jbrowse2-1.5.9-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.5.9 +build : hdfd78af_0 +build number: 0 +size : 20.3 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.5.9-hdfd78af_0.tar.bz2 +md5 : 58825995698fa40f54642145698fc6ac +timestamp : 2022-01-14 08:23:20 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.6.4 h9d45583_1 +------------------------- +file name : jbrowse2-1.6.4-h9d45583_1.tar.bz2 +name : jbrowse2 +version : 1.6.4 +build : h9d45583_1 +build number: 1 +size : 20.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.6.4-h9d45583_1.tar.bz2 +md5 : a6819afbbe662e0f8b2c716eeb8f8511 +timestamp : 2022-02-08 09:34:27 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.6.4 hbcef4ee_1 +------------------------- +file name : jbrowse2-1.6.4-hbcef4ee_1.tar.bz2 +name : jbrowse2 +version : 1.6.4 +build : hbcef4ee_1 +build number: 1 +size : 20.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.6.4-hbcef4ee_1.tar.bz2 +md5 : 6bc169d056835aeb20b77cf2f7462bcf +timestamp : 2022-02-08 09:38:10 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.6.4 hd6180af_1 +------------------------- +file name : jbrowse2-1.6.4-hd6180af_1.tar.bz2 +name : jbrowse2 +version : 1.6.4 +build : hd6180af_1 +build number: 1 +size : 20.5 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.6.4-hd6180af_1.tar.bz2 +md5 : 43ae4fa1cc462594621fd86d08f61412 +timestamp : 2022-02-08 09:41:51 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.6.4 hdfd78af_0 +------------------------- +file name : jbrowse2-1.6.4-hdfd78af_0.tar.bz2 +name : jbrowse2 +version : 1.6.4 +build : hdfd78af_0 +build number: 0 +size : 20.4 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.6.4-hdfd78af_0.tar.bz2 +md5 : a87506d48c8fd4d8df90c4cda76f50b1 +timestamp : 2022-01-29 12:26:48 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.6.5 h9d45583_0 +------------------------- +file name : jbrowse2-1.6.5-h9d45583_0.tar.bz2 +name : jbrowse2 +version : 1.6.5 +build : h9d45583_0 +build number: 0 +size : 19.0 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.6.5-h9d45583_0.tar.bz2 +md5 : 6d5c7f4db856d106271d863108de6983 +timestamp : 2022-02-22 14:13:08 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.6.5 hbcef4ee_0 +------------------------- +file name : jbrowse2-1.6.5-hbcef4ee_0.tar.bz2 +name : jbrowse2 +version : 1.6.5 +build : hbcef4ee_0 +build number: 0 +size : 19.0 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.6.5-hbcef4ee_0.tar.bz2 +md5 : 8114a779051d0f62a6c3c4b8c992f7a2 +timestamp : 2022-02-22 14:09:41 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.6.5 hd6180af_0 +------------------------- +file name : jbrowse2-1.6.5-hd6180af_0.tar.bz2 +name : jbrowse2 +version : 1.6.5 +build : hd6180af_0 +build number: 0 +size : 19.0 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.6.5-hd6180af_0.tar.bz2 +md5 : 728912620b0e465b522886e2cbc84040 +timestamp : 2022-02-22 14:06:09 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.6.6 h9d45583_0 +------------------------- +file name : jbrowse2-1.6.6-h9d45583_0.tar.bz2 +name : jbrowse2 +version : 1.6.6 +build : h9d45583_0 +build number: 0 +size : 18.8 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.6.6-h9d45583_0.tar.bz2 +md5 : 3dc98184ea433de68330e9074cb1b98d +timestamp : 2022-03-16 06:21:56 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.6.6 hbcef4ee_0 +------------------------- +file name : jbrowse2-1.6.6-hbcef4ee_0.tar.bz2 +name : jbrowse2 +version : 1.6.6 +build : hbcef4ee_0 +build number: 0 +size : 18.8 MB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/jbrowse2-1.6.6-hbcef4ee_0.tar.bz2 +md5 : dbf3e3a192d3b42509ffa1ad5ba3f2a1 +timestamp : 2022-03-16 06:15:12 UTC +dependencies: + - bcftools + - gff3sort + - htslib + - nodejs + - samtools + + +jbrowse2 1.6.6 hd6180af_0 +------------------------- +file name : jbrowse2-1.6.6-hd6180af_0.tar.bz2 +name : jbrowse2 +version : 1.6.6 +build diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/jellyfish.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/jellyfish.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa1340baca7f7d15e5ced9d11eebe885be880ba4 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/jellyfish.manual_bundle.txt @@ -0,0 +1,477 @@ +# Tool: jellyfish +software_name: jellyfish +tier: T1 +domain: t1_backfill_overall +downloads: 174001 +summary: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence +description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence +dependencies: jemalloc, libgcc-ng >=7.3.0, libstdcxx-ng >=7.3.0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://www.genome.umd.edu/jellyfish.html +doc_url: +dev_url: https://github.com/gmarcais/Jellyfish + +## CLI Help Source +cli:jellyfish +## CLI Help Content +$ conda run -n bioenv_cli jellyfish --help +[rc=0] +Usage: jellyfish [options] arg... +Where is one of: count, bc, info, stats, histo, dump, merge, query, cite, mem, jf. +Options: + --version Display version + --help Display this message + + + +## URL Docs Extract +### https://github.com/gmarcais/Jellyfish +GitHub - gmarcais/Jellyfish: A fast multi-threaded k-mer counter · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} gmarcais / Jellyfish Public Notifications You must be signed in to change notification settings Fork 140 Star 538 Code Issues 99 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights gmarcais/Jellyfish master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 660 Commits 660 Commits .github/ workflows .github/ workflows doc doc examples examples include/ jellyfish include/ jellyfish jellyfish jellyfish lib lib m4 m4 sub_commands sub_commands swig swig tests tests unit_tests unit_tests .gitignore .gitignore .gitmod .gitmod .travis.yml .travis.yml CHANGES CHANGES CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md HalfLICENSE HalfLICENSE LICENSE LICENSE LICENSE-BSD-3-Clause LICENSE-BSD-3-Clause LICENSE-GPL-3.0 LICENSE-GPL-3.0 Makefile.am Makefile.am README README README.md README.md compat.sh.in compat.sh.in config.rpath config.rpath configure.ac configure.ac development.mk development.mk gtest.mk gtest.mk header-license header-license jellyfish-2.0.pc.in jellyfish-2.0.pc.in jellyfish.spec.in jellyfish.spec.in local.mk local.mk View all files Repository files navigation README Code of conduct License BSD-3-Clause license GPL-3.0 license Jellyfish Overview Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the documentation for details. If you use Jellyfish in your research, please cite: Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 ( first published online January 7, 2011 ) doi:10.1093/bioinformatics/btr011 Installation Linux Binaries On Debian and Ubuntu with apt : sudo apt update sudo apt install jellyfish On Arch, it is available from AUR . FreeBSD Jellyfish can be installed on FreeBSD via the FreeBSD ports system. To install via the binary package, simply run: pkg install Jellyfish To install from source: cd /usr/ports/biology/jellyfish make install Windows With Cygwin , Jellyfish can be compiled from source as explained below . The simpler way on Windows 10 is to first install WSL and then install a Linux distribution that carries Jellyfish (e.g., Ubuntu) from the Windows Store. Finally, install with: sudo apt update sudo apt install jellyfish From source To get an easier to compiled packaged tar ball of the source code, download a release from the github release . You need make and g++ version 4.4 or higher. To install in your home directory, do: ./configure --prefix= $HOME make -j 4 make install To compile from the git tree, you will also need autoconf, automake, libool, gettext, pkg-config and yaggo . Then to compile and install (in /usr/local in that example) with: autoreconf -i ./configure make -j 4 sudo make install If the software is installed in system directories (hint: you needed to use sudo to install), like the example above, then the system library cache must be updated like such: sudo ldconfig Usage Instruction of use are available in the doc directory. Extra / Examples In the examples directory are potentially useful extra programs to query/manipulates output files of Jellyfish, using the shared library of Jellyfish in C++ or with scripting languages. The examples are not compiled by default. Each subdirectory of examples is independent and is compiled with a simple invocation of 'make'. Binding to script languages Bindings to Ruby, Python and Perl are provided. This binding allows to read the output file of Jellyfish directly in a scripting language. Compilation of the bindings is easier from the release tarball . The development files of the target scripting language are required. Compilation of the bindings from the git tree requires SWIG version 3 and adding the switch --enable-swig to the configure command lines show below. To compile all three bindings, configure and compile with: ./configure --enable-ruby-binding --enable-python-binding --enable-perl-binding make -j 4 sudo make install By default, Jellyfish is installed in /usr/local and the bindings are installed in the proper system location. When the --prefix switch is passed, the bindings are installed in the given directory. For example: ./configure --prefix= $HOME --enable-python-binding make -j 4 make install This will install the python binding in $HOME/lib/python2.7/site-packages (adjust based on your Python version). Then, for Python, Ruby or Perl to find the binding, an environment variable may need to be adjusted ( PYTHONPATH , RUBYLIB and PERL5LIB respectively). For example: export PYTHONPATH= $HOME /lib/python2.7/site-packages See the swig directory for examples on how to use the bindings. About A fast multi-threaded k-mer counter Resources Readme License Unknown and 2 other licenses found Licenses found Unknown LICENSE BSD-3-Clause LICENSE-BSD-3-Clause GPL-3.0 LICENSE-GPL-3.0 Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Stars 538 stars Watchers 29 watching Forks 140 forks Report repository Releases 12 Version 2.3.1 Latest Dec 7, 2023 + 11 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 92.0% M4 3.4% Shell 2.0% SWIG 1.0% Makefile 0.8% Python 0.4% Other 0.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge jellyfish --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +jellyfish 0.5.1 py27_0 +---------------------- +file name : jellyfish-0.5.1-py27_0.tar.bz2 +name : jellyfish +version : 0.5.1 +build : py27_0 +build number: 0 +size : 65 KB +license : LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.5.1-py27_0.tar.bz2 +md5 : bfe3c9b2685e8738e8ab9cb649196ffb +constraints : + - python_abi * *_cp27mu +dependencies: + - python 2.7* + + +jellyfish 0.5.1 py34_0 +---------------------- +file name : jellyfish-0.5.1-py34_0.tar.bz2 +name : jellyfish +version : 0.5.1 +build : py34_0 +build number: 0 +size : 66 KB +license : LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.5.1-py34_0.tar.bz2 +md5 : a044b7a087ae41d1c859aa8d3442d93a +constraints : + - python_abi * *_cp34m +dependencies: + - python 3.4* + + +jellyfish 0.5.1 py35_0 +---------------------- +file name : jellyfish-0.5.1-py35_0.tar.bz2 +name : jellyfish +version : 0.5.1 +build : py35_0 +build number: 0 +size : 267 KB +license : LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.5.1-py35_0.tar.bz2 +md5 : f52236550dd0f203847dfdf1c73c6d97 +constraints : + - python_abi * *_cp35m +dependencies: + - python 3.5* + + +jellyfish 0.5.6 py27_0 +---------------------- +file name : jellyfish-0.5.6-py27_0.tar.bz2 +name : jellyfish +version : 0.5.6 +build : py27_0 +build number: 0 +size : 66 KB +license : LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.5.6-py27_0.tar.bz2 +md5 : 353ca74ef20e31237f75334e4249eba2 +constraints : + - python_abi * *_cp27mu +dependencies: + - python 2.7* + + +jellyfish 0.5.6 py27_1 +---------------------- +file name : jellyfish-0.5.6-py27_1.tar.bz2 +name : jellyfish +version : 0.5.6 +build : py27_1 +build number: 1 +size : 68 KB +license : LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.5.6-py27_1.tar.bz2 +md5 : c3f4b6802c00cee13ea9fc1bb326b598 +constraints : + - python_abi * *_cp27mu +dependencies: + - python 2.7* + + +jellyfish 0.5.6 py34_0 +---------------------- +file name : jellyfish-0.5.6-py34_0.tar.bz2 +name : jellyfish +version : 0.5.6 +build : py34_0 +build number: 0 +size : 67 KB +license : LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.5.6-py34_0.tar.bz2 +md5 : 78d70d9e83ba8ffb88861cab3affe842 +constraints : + - python_abi * *_cp34m +dependencies: + - python 3.4* + + +jellyfish 0.5.6 py35_0 +---------------------- +file name : jellyfish-0.5.6-py35_0.tar.bz2 +name : jellyfish +version : 0.5.6 +build : py35_0 +build number: 0 +size : 268 KB +license : LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.5.6-py35_0.tar.bz2 +md5 : 7f6da659dcd5f7ef17cca83f433da8fc +constraints : + - python_abi * *_cp35m +dependencies: + - python 3.5* + + +jellyfish 0.5.6 py35_1 +---------------------- +file name : jellyfish-0.5.6-py35_1.tar.bz2 +name : jellyfish +version : 0.5.6 +build : py35_1 +build number: 1 +size : 70 KB +license : LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.5.6-py35_1.tar.bz2 +md5 : 25fbab34f4c8df2cc20a81b5aae4e868 +constraints : + - python_abi * *_cp35m +dependencies: + - python 3.5* + + +jellyfish 0.5.6 py36_1 +---------------------- +file name : jellyfish-0.5.6-py36_1.tar.bz2 +name : jellyfish +version : 0.5.6 +build : py36_1 +build number: 1 +size : 70 KB +license : LICENSE +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.5.6-py36_1.tar.bz2 +md5 : ae4f4bdb1d3a4a9c014c55ffca0a2fad +constraints : + - python_abi * *_cp36m +dependencies: + - python 3.6* + + +jellyfish 0.6.0 py27_0 +---------------------- +file name : jellyfish-0.6.0-py27_0.tar.bz2 +name : jellyfish +version : 0.6.0 +build : py27_0 +build number: 0 +size : 70 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.0-py27_0.tar.bz2 +md5 : a8809f57c22876a0fec67a1863b01f6a +constraints : + - python_abi * *_cp27mu +dependencies: + - python 2.7* + + +jellyfish 0.6.0 py35_0 +---------------------- +file name : jellyfish-0.6.0-py35_0.tar.bz2 +name : jellyfish +version : 0.6.0 +build : py35_0 +build number: 0 +size : 72 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.0-py35_0.tar.bz2 +md5 : af8c3e8e674e832ac8666536319cd818 +constraints : + - python_abi * *_cp35m +dependencies: + - python 3.5* + + +jellyfish 0.6.0 py36_0 +---------------------- +file name : jellyfish-0.6.0-py36_0.tar.bz2 +name : jellyfish +version : 0.6.0 +build : py36_0 +build number: 0 +size : 71 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.0-py36_0.tar.bz2 +md5 : 6ab790cf69b31c480aec05273831860b +constraints : + - python_abi * *_cp36m +dependencies: + - python 3.6* + + +jellyfish 0.6.1 py27_0 +---------------------- +file name : jellyfish-0.6.1-py27_0.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py27_0 +build number: 0 +size : 70 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py27_0.tar.bz2 +md5 : b8bcb395dfa57490130984c837b65340 +constraints : + - python_abi * *_cp27mu +dependencies: + - python 2.7* + + +jellyfish 0.6.1 py27h14c3975_1000 +--------------------------------- +file name : jellyfish-0.6.1-py27h14c3975_1000.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py27h14c3975_1000 +build number: 1000 +size : 35 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py27h14c3975_1000.tar.bz2 +md5 : 4cf9b3c1d4ea46c955e22db164734095 +timestamp : 2018-10-06 23:18:12 UTC +constraints : + - python_abi * *_cp27mu +dependencies: + - libgcc-ng >=7.3.0 + - python >=2.7,<2.8.0a0 + + +jellyfish 0.6.1 py27h470a237_0 +------------------------------ +file name : jellyfish-0.6.1-py27h470a237_0.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py27h470a237_0 +build number: 0 +size : 37 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py27h470a237_0.tar.bz2 +md5 : 87789a28f7cf90ef32871a79de9f46ee +timestamp : 2018-10-06 23:20:07 UTC +constraints : + - python_abi * *_cp27mu +dependencies: + - libgcc-ng >=4.9 + - python >=2.7,<2.8.0a0 + + +jellyfish 0.6.1 py35_0 +---------------------- +file name : jellyfish-0.6.1-py35_0.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py35_0 +build number: 0 +size : 72 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py35_0.tar.bz2 +md5 : 7b0bd674886fbd698494cf6fbf7e7bea +constraints : + - python_abi * *_cp35m +dependencies: + - python 3.5* + + +jellyfish 0.6.1 py36_0 +---------------------- +file name : jellyfish-0.6.1-py36_0.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py36_0 +build number: 0 +size : 71 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py36_0.tar.bz2 +md5 : bde662ec1828a0de1d989c209a5fd57d +constraints : + - python_abi * *_cp36m +dependencies: + - python 3.6* + + +jellyfish 0.6.1 py36h14c3975_1000 +--------------------------------- +file name : jellyfish-0.6.1-py36h14c3975_1000.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py36h14c3975_1000 +build number: 1000 +size : 35 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py36h14c3975_1000.tar.bz2 +md5 : cbb8603ff89c507ff45d1231f7c6ee81 +timestamp : 2018-10-06 23:17:12 UTC +constraints : + - python_abi * *_cp36m +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + + +jellyfish 0.6.1 py36h470a237_0 +------------------------------ +file name : jellyfish-0.6.1-py36h470a237_0.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py36h470a237_0 +build number: 0 +size : 72 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py36h470a237_0.tar.bz2 +md5 : ccea0604c34253cdfc0ed32e112fd795 +timestamp : 2018-10-06 23:17:37 UTC +constraints : + - python_abi * *_cp36m +dependencies: + - libgcc-ng >=4.9 + - python >=3.6,<3.7.0a0 + + +jellyfish 0.6.1 py36h8c4c3a4_1000 +--------------------------------- +file name : jellyfish-0.6.1-py36h8c4c3a4_1000.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py36h8c4c3a4_1000 +build number: 1000 +size : 36 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py36h8c4c3a4_1000.tar.bz2 +md5 : 7d66629bc80af7431a640d54323ef044 +timestamp : 2020-03-25 17:28:43 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + + +jellyfish 0.6.1 py37h14c3975_1000 +--------------------------------- +file name : jellyfish-0.6.1-py37h14c3975_1000.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py37h14c3975_1000 +build number: 1000 +size : 35 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py37h14c3975_1000.tar.bz2 +md5 : 26538fa905f6a6b4ae024e0bf5fd2665 +timestamp : 2018-10-06 23:16:43 UTC +constraints : + - python_abi * *_cp37m +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + + +jellyfish 0.6.1 py37h470a237_0 +------------------------------ +file name : jellyfish-0.6.1-py37h470a237_0.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py37h470a237_0 +build number: 0 +size : 35 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py37h470a237_0.tar.bz2 +md5 : c3d00bf50a37c7e838c2830f9b3d1c36 +timestamp : 2018-10-06 23:19:41 UTC +constraints : + - python_abi * *_cp37m +dependencies: + - libgcc-ng >=4.9 + - python >=3.7,<3.8.0a0 + + +jellyfish 0.6.1 py37h8f50634_1000 +--------------------------------- +file name : jellyfish-0.6.1-py37h8f50634_1000.tar.bz2 +name : jellyfish +version : 0.6.1 +build : py37h8f50634_1000 +build number: 1000 +size : 36 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.6.1-py37h8f50634_1000.tar.bz2 +md5 : da333aab9133f0d7dfede6fd1f723f2f +timestamp : 2020-03-25 17:28:19 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + + +jellyfish 0.7.1 py36h8c4c3a4_1000 +--------------------------------- +file name : jellyfish-0.7.1-py36h8c4c3a4_1000.tar.bz2 +name : jellyfish +version : 0.7.1 +build : py36h8c4c3a4_1000 +build number: 1000 +size : 35 KB +license : BSD 2-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jellyfish-0.7.1-py36h8c4c3a4_1000.t diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/jq.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/jq.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1db612270bd7c37ec9c148e5614be012d7d64559 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/jq.manual_bundle.txt @@ -0,0 +1,416 @@ +# Tool: jq +software_name: jq +tier: T1 +domain: t1_backfill_overall +downloads: 121509 +summary: jq is a lightweight and flexible command-line JSON processor. +description: jq is a lightweight and flexible command-line JSON processor. +dependencies: libgcc +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +cli:jq +## CLI Help Content +$ conda run -n bioenv_cli jq --help +[rc=0] +jq - commandline JSON processor [version 1.5] +Usage: jq [options] [file...] + + jq is a tool for processing JSON inputs, applying the + given filter to its JSON text inputs and producing the + filter's results as JSON on standard output. + The simplest filter is ., which is the identity filter, + copying jq's input to its output unmodified (except for + formatting). + For more advanced filters see the jq(1) manpage ("man jq") + and/or https://stedolan.github.io/jq + + Some of the options include: + -c compact instead of pretty-printed output; + -n use `null` as the single input value; + -e set the exit status code based on the output; + -s read (slurp) all inputs into an array; apply filter to it; + -r output raw strings, not JSON texts; + -R read raw strings, not JSON texts; + -C colorize JSON; + -M monochrome (don't colorize JSON); + -S sort keys of objects on output; + --tab use tabs for indentation; + --arg a v set variable $a to value ; + --argjson a v set variable $a to JSON value ; + --slurpfile a f set variable $a to an array of JSON texts read from ; + See the manpage for more options. + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge jq --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +jq 1.5 0 +-------- +file name : jq-1.5-0.tar.bz2 +name : jq +version : 1.5 +build : 0 +build number: 0 +size : 1.1 MB +license : MIT (code), CC-BY-3.0 (docs) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/jq-1.5-0.tar.bz2 +md5 : f380e0813e0752164752d9a9c63667d7 +dependencies: + - libgcc + + +jq 1.5 1 +-------- +file name : jq-1.5-1.tar.bz2 +name : jq +version : 1.5 +build : 1 +build number: 1 +size : 1.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.5-1.tar.bz2 +md5 : 5248f2a360252a864b3919fb631b8933 +dependencies: + - oniguruma 5.9.* + + +jq 1.5 2 +-------- +file name : jq-1.5-2.tar.bz2 +name : jq +version : 1.5 +build : 2 +build number: 2 +size : 1.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.5-2.tar.bz2 +md5 : f19ac85b92159679c3d7b1cf13796fa2 +dependencies: + - oniguruma 6.0.* + + +jq 1.5 3 +-------- +file name : jq-1.5-3.tar.bz2 +name : jq +version : 1.5 +build : 3 +build number: 3 +size : 1.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.5-3.tar.bz2 +md5 : 19d3fb3fbc733486a64702bdac80d9b6 +dependencies: + - oniguruma 6.1.* + + +jq 1.5 4 +-------- +file name : jq-1.5-4.tar.bz2 +name : jq +version : 1.5 +build : 4 +build number: 4 +size : 1.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.5-4.tar.bz2 +md5 : 5b947b0ef16a7b99fd5c8db70249bc4e +dependencies: + - oniguruma 6.8.* + + +jq 1.5 h14c3975_1005 +-------------------- +file name : jq-1.5-h14c3975_1005.tar.bz2 +name : jq +version : 1.5 +build : h14c3975_1005 +build number: 1005 +size : 477 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.5-h14c3975_1005.tar.bz2 +md5 : dd39b4c901c1eb1ee0c71bb1ee3a3956 +timestamp : 2018-11-11 02:03:37 UTC +dependencies: + - libgcc-ng >=7.3.0 + - oniguruma 6.8.* + + +jq 1.5 h14c3975_5 +----------------- +file name : jq-1.5-h14c3975_5.tar.bz2 +name : jq +version : 1.5 +build : h14c3975_5 +build number: 5 +size : 501 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.5-h14c3975_5.tar.bz2 +md5 : 6fa09d00bc22187a4f0597e6abc773cc +timestamp : 2018-11-10 21:55:37 UTC +dependencies: + - libgcc-ng >=7.3.0 + - oniguruma 6.8.* + + +jq 1.5 h470a237_5 +----------------- +file name : jq-1.5-h470a237_5.tar.bz2 +name : jq +version : 1.5 +build : h470a237_5 +build number: 5 +size : 507 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.5-h470a237_5.tar.bz2 +md5 : 8db8ee4a73a8b128f8304301e82a6bc4 +timestamp : 2018-11-10 21:57:34 UTC +dependencies: + - libgcc-ng >=4.9 + - oniguruma 6.8.* + + +jq 1.6 h14c3975_1000 +-------------------- +file name : jq-1.6-h14c3975_1000.tar.bz2 +name : jq +version : 1.6 +build : h14c3975_1000 +build number: 1000 +size : 358 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.6-h14c3975_1000.tar.bz2 +md5 : 3d0d3e5b46fe2856358ebd195fe23e6a +timestamp : 2018-12-19 02:34:12 UTC +dependencies: + - libgcc-ng >=7.3.0 + - oniguruma 6.9.* + + +jq 1.6 h27cfd23_1 +----------------- +file name : jq-1.6-h27cfd23_1.conda +name : jq +version : 1.6 +build : h27cfd23_1 +build number: 1 +size : 260 KB +license : MIT +subdir : linux-64 +url : https://repo.anaconda.com/pkgs/main/linux-64/jq-1.6-h27cfd23_1.conda +md5 : ca6e88c5049e0741b7868a2af36ed74f +timestamp : 2020-11-07 11:28:12 UTC +dependencies: + - libgcc-ng >=7.3.0 + - oniguruma 6.9.* + - oniguruma >=6.9.3,<6.10.0a0 + + +jq 1.6 h27cfd23_1000 +-------------------- +file name : jq-1.6-h27cfd23_1000.conda +name : jq +version : 1.6 +build : h27cfd23_1000 +build number: 1000 +size : 257 KB +license : MIT +subdir : linux-64 +url : https://repo.anaconda.com/pkgs/main/linux-64/jq-1.6-h27cfd23_1000.conda +md5 : e3959b747ad5c51cbb8e0c2b0374e9d1 +timestamp : 2020-11-02 16:37:25 UTC +dependencies: + - libgcc-ng >=7.3.0 + - oniguruma 6.9.* + - oniguruma >=6.9.3,<6.10.0a0 + + +jq 1.6 h36c2ea0_1000 +-------------------- +file name : jq-1.6-h36c2ea0_1000.tar.bz2 +name : jq +version : 1.6 +build : h36c2ea0_1000 +build number: 1000 +size : 346 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.6-h36c2ea0_1000.tar.bz2 +md5 : 8578ae83310b8c9f5717f1aa65054f36 +timestamp : 2020-12-02 20:24:07 UTC +dependencies: + - libgcc-ng >=7.5.0 + - oniguruma 6.9.* + - oniguruma >=6.9.3,<6.10.0a0 + + +jq 1.6 h470a237_0 +----------------- +file name : jq-1.6-h470a237_0.tar.bz2 +name : jq +version : 1.6 +build : h470a237_0 +build number: 0 +size : 370 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.6-h470a237_0.tar.bz2 +md5 : f6c9c1f6905ea3b103626f8be4231d5a +timestamp : 2018-12-19 02:33:42 UTC +dependencies: + - libgcc-ng >=4.9 + - oniguruma 6.9.* + + +jq 1.7 hd590300_0 +----------------- +file name : jq-1.7-hd590300_0.conda +name : jq +version : 1.7 +build : hd590300_0 +build number: 0 +size : 313 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.7-hd590300_0.conda +md5 : c29cbd5ee663325f9bed9a2b2488ef3a +timestamp : 2023-11-24 09:35:47 UTC +dependencies: + - libgcc-ng >=12 + - oniguruma 6.9.* + - oniguruma >=6.9.9,<6.10.0a0 + + +jq 1.7.1 h5eee18b_0 +------------------- +file name : jq-1.7.1-h5eee18b_0.conda +name : jq +version : 1.7.1 +build : h5eee18b_0 +build number: 0 +size : 349 KB +license : MIT +subdir : linux-64 +url : https://repo.anaconda.com/pkgs/main/linux-64/jq-1.7.1-h5eee18b_0.conda +md5 : 5c8e7392aa854e42f6dd9d99e4e20722 +timestamp : 2024-10-23 15:38:57 UTC +dependencies: + - libgcc-ng >=11.2.0 + - oniguruma 6.9.* + - oniguruma >=6.9.7.1,<6.10.0a0 + + +jq 1.7.1 hd590300_0 +------------------- +file name : jq-1.7.1-hd590300_0.conda +name : jq +version : 1.7.1 +build : hd590300_0 +build number: 0 +size : 311 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.7.1-hd590300_0.conda +md5 : 80814f94713e35df60aad6c4b235de87 +timestamp : 2023-12-13 20:53:13 UTC +dependencies: + - libgcc-ng >=12 + - oniguruma 6.9.* + - oniguruma >=6.9.9,<6.10.0a0 + + +jq 1.8.0 h73b1eb8_0 +------------------- +file name : jq-1.8.0-h73b1eb8_0.conda +name : jq +version : 1.8.0 +build : h73b1eb8_0 +build number: 0 +size : 305 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.8.0-h73b1eb8_0.conda +md5 : 4ba48f239e4c4941e0a1ca393cb580c7 +timestamp : 2025-06-01 18:52:25 UTC +dependencies: + - oniguruma 6.9.* + - libgcc >=13 + - __glibc >=2.17,<3.0.a0 + - oniguruma >=6.9.10,<6.10.0a0 + + +jq 1.8.1 h5eee18b_0 +------------------- +file name : jq-1.8.1-h5eee18b_0.conda +name : jq +version : 1.8.1 +build : h5eee18b_0 +build number: 0 +size : 336 KB +license : MIT +subdir : linux-64 +url : https://repo.anaconda.com/pkgs/main/linux-64/jq-1.8.1-h5eee18b_0.conda +md5 : 9cbb074f0474efd8748aab75e47152c0 +timestamp : 2025-07-10 09:26:34 UTC +dependencies: + - libgcc-ng >=11.2.0 + - oniguruma 6.9.* + - oniguruma >=6.9.7.1,<6.10.0a0 + + +jq 1.8.1 h73b1eb8_0 +------------------- +file name : jq-1.8.1-h73b1eb8_0.conda +name : jq +version : 1.8.1 +build : h73b1eb8_0 +build number: 0 +size : 306 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/jq-1.8.1-h73b1eb8_0.conda +md5 : 2714e43bfc035f7ef26796632aa1b523 +timestamp : 2025-07-02 09:08:30 UTC +dependencies: + - oniguruma 6.9.* + - libgcc >=13 + - __glibc >=2.17,<3.0.a0 + - oniguruma >=6.9.10,<6.10.0a0 + + +jq 1.8.1 hfdf79b4_1 +------------------- +file name : jq-1.8.1-hfdf79b4_1.conda +name : jq +version : 1.8.1 +build : hfdf79b4_1 +build number: 1 +size : 307 KB +license : MIT +subdir : linux-64 +url : https://repo.anaconda.com/pkgs/main/linux-64/jq-1.8.1-hfdf79b4_1.conda +md5 : e65f88519afc284bb565add6e69707c1 +timestamp : 2026-04-06 14:46:09 UTC +dependencies: + - libgcc >=14 + - oniguruma 6.9.* + - oniguruma >=6.9.10,<6.10.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/k8.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/k8.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..30d0c9f039e9127d83ffaef1cb52d6bd43147515 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/k8.manual_bundle.txt @@ -0,0 +1,559 @@ +# Tool: k8 +software_name: k8 +tier: T1 +domain: t1_backfill_overall +downloads: 988054 +summary: Lightweight JavaScript shell based on Google's V8 JavaScript engine +description: Lightweight JavaScript shell based on Google's V8 JavaScript engine +dependencies: __glibc >=2.17,<3.0.a0, libgcc >=13, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, sysroot_linux-64 >=2.17 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/attractivechaos/k8 +doc_url: +dev_url: https://github.com/attractivechaos/k8 + +## CLI Help Source +cli:k8 +## CLI Help Content +$ conda run -n bioenv_cli k8 --help +[rc=0] +Usage: + shell [options] -e string + execute string in V8 + shell [options] file1 file2 ... filek + run JavaScript scripts in file1, file2, ..., filek + shell [options] + shell [options] --shell [file1 file2 ... filek] + run an interactive JavaScript shell + d8 [options] file1 file2 ... filek + d8 [options] + d8 [options] --shell [file1 file2 ... filek] + run the new debugging shell + +Options: + --use_strict (enforce strict mode) + type: bool default: false + --es5_readonly (activate correct semantics for inheriting readonliness) + type: bool default: true + --es52_globals (activate new semantics for global var declarations) + type: bool default: true + --harmony_typeof (enable harmony semantics for typeof) + type: bool default: false + --harmony_scoping (enable harmony block scoping) + type: bool default: false + --harmony_modules (enable harmony modules (implies block scoping)) + type: bool default: false + --harmony_proxies (enable harmony proxies) + type: bool default: false + --harmony_collections (enable harmony collections (sets, maps, and weak maps)) + type: bool default: false + --harmony_observation (enable harmony object observation (implies harmony collections) + type: bool default: false + --harmony (enable all harmony features (except typeof)) + type: bool default: false + --packed_arrays (optimizes arrays that have no holes) + type: bool default: true + --smi_only_arrays (tracks arrays with only smi values) + type: bool default: true + --clever_optimizations (Optimize object size, Array shift, DOM strings and string +) + type: bool default: true + --unbox_double_arrays (automatically unbox arrays of doubles) + type: bool default: true + --string_slices (use string slices) + type: bool default: true + --crankshaft (use crankshaft) + type: bool default: true + --hydrogen_filter (optimization filter) + type: string default: + --use_range (use hydrogen range analysis) + type: bool default: true + --eliminate_dead_phis (eliminate dead phis) + type: bool default: true + --use_gvn (use hydrogen global value numbering) + type: bool default: true + --use_canonicalizing (use hydrogen instruction canonicalizing) + type: bool default: true + --use_inlining (use function inlining) + type: bool default: true + --max_inlined_source_size (maximum source size in bytes considered for a single inlining) + type: int default: 600 + --max_inlined_nodes (maximum number of AST nodes considered for a single inlining) + type: int default: 196 + --max_inlined_nodes_cumulative (maximum cumulative number of AST nodes considered for inlining) + type: int default: 196 + --loop_invariant_code_motion (loop invariant code motion) + type: bool default: true + --fast_math (faster (but maybe less accurate) math functions) + type: bool default: true + --collect_megamorphic_maps_from_stub_cache (crankshaft harvests type feedback from stub cache) + type: bool default: true + --hydrogen_stats (print statistics for hydrogen) + type: bool default: false + --trace_hydrogen (trace generated hydrogen to file) + type: bool default: false + --trace_phase (trace generated IR for specified phases) + type: string default: Z + --trace_inlining (trace inlining decisions) + type: bool default: false + --trace_alloc (trace register allocator) + type: bool default: false + --trace_all_uses (trace all use positions) + type: bool default: false + --trace_range (trace range analysis) + type: bool default: false + --trace_gvn (trace global value numbering) + type: bool default: false + --trace_representation (trace representation types) + type: bool default: false + --stress_pointer_maps (pointer map for every instruction) + type: bool default: false + --stress_environments (environment for every instruction) + type: bool default: false + --deopt_every_n_times (deoptimize every n times a deopt point is passed) + type: int default: 0 + --trap_on_deopt (put a break point before deoptimizing) + type: bool default: false + --deoptimize_uncommon_cases (deoptimize uncommon cases) + type: bool default: true + --polymorphic_inlining (polymorphic inlining) + type: bool default: true + --use_osr (use on-stack replacement) + type: bool default: true + --array_bounds_checks_elimination (perform array bounds checks elimination) + type: bool default: true + --array_index_dehoisting (perform array index dehoisting) + type: bool default: true + --dead_code_elimination (use dead code elimination) + type: bool default: true + --trace_dead_code_elimination (trace dead code elimination) + type: bool default: false + --track_allocation_sites (Use allocation site info to reduce transitions) + type: bool default: true + --trace_osr (trace on-stack replacement) + type: bool default: false + --stress_runs (number of stress runs) + type: int default: 0 + --optimize_closures (optimize closures) + type: bool default: true + --lookup_sample_by_shared (when picking a function to optimize, watch for shared function info, not JSFunction itself) + type: bool default: true + --cache_optimized_code (cache optimized code for closures) + type: bool default: true + --inline_construct (inline constructor calls) + type: bool default: true + --inline_arguments (inline functions with arguments object) + type: bool default: true + --inline_accessors (inline JavaScript accessors) + type: bool default: true + --loop_weight (loop weight for representation inference) + type: int default: 1 + --optimize_for_in (optimize functions containing for-in loops) + type: bool default: true + --opt_safe_uint32_operations (allow uint32 values on optimize frames if they are used only in safe operations) + type: bool default: true + --parallel_recompilation (optimizing hot functions asynchronously on a separate thread) + type: bool default: false + --trace_parallel_recompilation (track parallel recompilation) + type: bool default: false + --parallel_recompilation_queue_length (the length of the parallel compilation queue) + type: int default: 2 + --manual_parallel_recompilation (disable automatic optimization) + type: bool default: false + --experimental_profiler (enable all profiler experiments) + type: bool default: true + --watch_ic_patching (profiler considers IC stability) + type: bool default: false + --frame_count (number of stack frames inspected by the profiler) + type: int default: 1 + --self_optimization (primitive functions trigger their own optimization) + type: bool default: false + --direct_self_opt (call recompile stub directly when self-optimizing) + type: bool default: false + --retry_self_opt (re-try self-optimization if it failed) + type: bool default: false + --interrupt_at_exit (insert an interrupt check at function exit) + type: bool default: false + --weighted_back_edges (weight back edges by jump distance for interrupt triggering) + type: bool default: false + --interrupt_budget (execution budget before interrupt is triggered) + type: int default: 5888 + --type_info_threshold (percentage of ICs that must have type info to allow optimization) + type: int default: 15 + --self_opt_count (call count before self-optimization) + type: int default: 130 + --trace_opt_verbose (extra verbose compilation tracing) + type: bool default: false + --debug_code (generate extra code (assertions) for debugging) + type: bool default: false + --code_comments (emit comments in code disassembly) + type: bool default: false + --enable_sse2 (enable use of SSE2 instructions if available) + type: bool default: true + --enable_sse3 (enable use of SSE3 instructions if available) + type: bool default: true + --enable_sse4_1 (enable use of SSE4.1 instructions if available) + type: bool default: true + --enable_cmov (enable use of CMOV instruction if available) + type: bool default: true + --enable_rdtsc (enable use of RDTSC instruction if available) + type: bool default: true + --enable_sahf (enable use of SAHF instruction if available (X64 only)) + type: bool default: true + --enable_vfp3 (enable use of VFP3 instructions if available - this implies enabling ARMv7 and VFP2 instructions (ARM only)) + type: bool default: true + --enable_vfp2 (enable use of VFP2 instructions if available) + type: bool default: true + --enable_armv7 (enable use of ARMv7 instructions if available (ARM only)) + type: bool default: true + --enable_sudiv (enable use of SDIV and UDIV instructions if available (ARM only)) + type: bool default: true + --enable_movw_movt (enable loading 32-bit constant by means of movw/movt instruction pairs (ARM only)) + type: bool default: false + --enable_unaligned_accesses (enable unaligned accesses for ARMv7 (ARM only)) + type: bool default: true + --enable_fpu (enable use of MIPS FPU instructions if available (MIPS only)) + type: bool default: true + --enable_vldr_imm (enable use of constant pools for double immediate (ARM only)) + type: bool default: false + --expose_natives_as (expose natives in global object) + type: string default: NULL + --expose_debug_as (expose debug in global object) + type: string default: NULL + --expose_gc (expose gc extension) + type: bool default: false + --expose_externalize_string (expose externalize string extension) + type: bool default: false + --stack_trace_limit (number of stack frames to capture) + type: int default: 10 + --builtins_in_stack_traces (show built-in functions in stack traces) + type: bool default: false + --disable_native_files (disable builtin natives files) + type: bool default: false + --inline_new (use fast inline allocation) + type: bool default: true + --stack_trace_on_abort (print a stack trace if an assertion failure occurs) + type: bool default: true + --trace (trace function calls) + type: bool default: false + --mask_constants_with_cookie (use random jit cookie to mask large constants) + type: bool default: true + --lazy (use lazy compilation) + type: bool default: true + --trace_opt (trace lazy optimization) + type: bool default: false + --trace_opt_stats (trace lazy optimization statistics) + type: bool default: false + --opt (use adaptive optimizations) + type: bool default: true + --always_opt (always try to optimize functions) + type: bool default: false + --prepare_always_opt (prepare for turning on always opt) + type: bool default: false + --trace_deopt (trace deoptimization) + type: bool default: false + --min_preparse_length (minimum length for automatic enable preparsing) + type: int default: 1024 + --always_full_compiler (try to use the dedicated run-once backend for all code) + type: bool default: false + --max_opt_count (maximum number of optimization attempts before giving up.) + type: int default: 10 + --compilation_cache (enable compilation cache) + type: bool default: true + --cache_prototype_transitions (cache prototype transitions) + type: bool default: true + --trace_debug_json (trace debugging JSON request/response) + type: bool default: false + --debugger_auto_break (automatically set the debug break flag when debugger commands are in the queue) + type: bool default: true + --enable_liveedit (enable liveedit experimental feature) + type: bool default: true + --break_on_abort (always cause a debug break before aborting) + type: bool default: true + --stack_size + +## URL Docs Extract +### https://github.com/attractivechaos/k8 +GitHub - attractivechaos/k8: k8 Javascript shell · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} attractivechaos / k8 Public Notifications You must be signed in to change notification settings Fork 6 Star 158 Code Issues 0 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights attractivechaos/k8 master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 143 Commits 143 Commits .circleci .circleci scripts-old scripts-old scripts scripts test test .gitignore .gitignore LICENSE.txt LICENSE.txt Makefile Makefile NEWS.md NEWS.md README.md README.md k8.cc k8.cc View all files Repository files navigation README License Getting Started # Download precomiplied binaries wget -O- https://github.com/attractivechaos/k8/releases/download/v1.2/k8-1.2.tar.bz2 | tar -jxf - k8-1.2/k8-x86_64-Linux -e ' print(Math.log(2)) ' # Compile from source code. This requires to compile node.js first (or v18.20.3 on Mac): wget -O- https://nodejs.org/dist/v18.19.1/node-v18.19.1.tar.gz | tar -zxf - cd node-v18.19.1 && ./configure && make -j16 # Then compile k8 git clone https://github.com/attractivechaos/k8 cd k8 && make The following example counts the number of lines: if ( arguments . length == 0 ) { // test command-line arguments warn ( "Usage: k8 lc.js <in.txt>" ) ; exit ( 1 ) ; } let buf = new Bytes ( ) ; let n = 0 , file = new File ( arguments [ 0 ] ) ; while ( file . readline ( buf ) >= 0 ) ++ n ; file . close ( ) ; buf . destroy ( ) ; print ( n ) ; Introduction K8 is a JavaScript runtime built on top of Google's v8 JavaScript engine . It provides a resizable binary buffer and synchronous APIs for plain file writing and gzip'd file reading. Motivations JavaScript is among the fastest scripting languages. It is essential for web development but not often used for large-scale text processing or command-line utilities, in my opinion, due to the lack of sensible file I/O. Current JavaScript runtimes such as Node.js and Deno focus on asynchronous I/O and whole-file reading. Even reading a file line by line, which is required to work with large files, becomes a cumbersome effort. K8 aims to solve this problem. With synchronous I/O APIs, JavaScript can be a powerful language for developing command-line tools. Installation It is recommended to download precompiled binaries (also available from Zenodo ). If you want to compile k8, you need to compile Node.js which bundles v8 and provides a more convenient way build v8. As the v8 APIs are fast changing, both Node.js and k8 only work with specific versions of v8. The k8-1.x branch is known to work with node-18.x but not 19.x or higher. It is also worth noting that node-18.20.x upgraded c-ares which is now incompatible with older glibc. Node-18.19.1 is the most recent version that can be compiled on CentOS 7. On the other hand, Node-18.19.x cannot be compiled on MacOS with clang-15. Node-18.20.3 is known to work. API Documentations Functions // Print to stdout (print) or stderr (warn). TAB delimited if multiple arguments. function print ( data : any ) function warn ( data : any ) // Exit function exit ( code : number ) // Load a JavaScript file and execute. It searches the working directory, the // script directory and then the K8_PATH environment variable in order. function load ( fileName : string ) // Read entire file as an ArrayBuffer function k8_read_file ( fileName : string ) : ArrayBuffer // Decode $buf to string under the $enc encoding; only "utf-8" is supported for now // Missing or unknown encoding is treated as Latin-1 function k8_decode ( buf : ArrayBuffer | Bytes , enc ?: string ) : string // Encode $str into an ArrayBuffer function k8_encode ( str : string , enc ?: string ) : ArrayBuffer // Reverse complement a DNA sequence in string function k8_revcomp ( seq : string ) : string // Reverse complement a DNA sequence in place function k8_revcomp ( seq : ArrayBuffer | Bytes ) // Get version string function k8_version ( ) : string The Bytes Object Bytes provides a resizable byte array. // Create an array of byte buffer of $len in size. new Bytes ( len ? : number = 0 ) // Property: get/set length of the array . length : number // Property: get/set the max capacity of the array . capacity : number // Property: get ArrayBuffer of the underlying data, not allocated from v8 . buffer : ArrayBuffer // Deallocate the array. This is necessary as the memory is not managed by the v8 GC. Bytes . prototype . destroy ( ) // Replace the byte array starting from $offset to $data, where $data can be a number, // a string, an array or Bytes. The size of the array is modified if the new array // is larger. Return the number of modified bytes. Bytes . prototype . set ( data : number | string | Array | ArrayBuffer , offset ? : number ) : number // Convert the byte array to string Bytes . prototype . toString ( ) The File Object File provides buffered file I/O. // Open a plain or gzip'd file for reading or a plain file for writing. $file // is file descriptor if it is an integer or file name if string. Each File // object can only be read or only be written, not mixed new File ( file ? : string | number = 0 , mode ? : string = "r" ) // Read a byte and return it File . prototype . read ( ) : number // Read the rest of the file into $buf at offset 0. Return the number of bytes read. File . prototype . read ( buf : Bytes ) : number // Read $len bytes into $buf at $offset. // Return the number of bytes read on success; 0 on file end; <0 on errors File . prototype . read ( buf : Bytes , offset : number , len : number ) : number // Read a line or a token to $buf at $offset. $sep=0 for SPACE, 1 for TAB and 2 // for newline. If $sep is a string, only the first character is considered. // Return the delimiter if non-negative, -1 upon EOF, or <-1 for errors File . prototype . readline ( buf : Bytes , sep ? : number | string = 2 , offset ? : number = 0 ) : number // Write data File . prototype . write ( data : string | ArrayBuffer ) : number // Close a file File . prototype . close ( ) About k8 Javascript shell Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Stars 158 stars Watchers 9 watching Forks 6 forks Report repository Releases 8 k8-1.2 (r137) Latest May 27, 2024 + 7 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages JavaScript 58.0% C++ 41.1% Makefile 0.9% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/attractivechaos/k8 +GitHub - attractivechaos/k8: k8 Javascript shell · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} attractivechaos / k8 Public Notifications You must be signed in to change notification settings Fork 6 Star 158 Code Issues 0 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights attractivechaos/k8 master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 143 Commits 143 Commits .circleci .circleci scripts-old scripts-old scripts scripts test test .gitignore .gitignore LICENSE.txt LICENSE.txt Makefile Makefile NEWS.md NEWS.md README.md README.md k8.cc k8.cc View all files Repository files navigation README License Getting Started # Download precomiplied binaries wget -O- https://github.com/attractivechaos/k8/releases/download/v1.2/k8-1.2.tar.bz2 | tar -jxf - k8-1.2/k8-x86_64-Linux -e ' print(Math.log(2)) ' # Compile from source code. This requires to compile node.js first (or v18.20.3 on Mac): wget -O- https://nodejs.org/dist/v18.19.1/node-v18.19.1.tar.gz | tar -zxf - cd node-v18.19.1 && ./configure && make -j16 # Then compile k8 git clone https://github.com/attractivechaos/k8 cd k8 && make The following example counts the number of lines: if ( arguments . length == 0 ) { // test command-line arguments warn ( "Usage: k8 lc.js <in.txt>" ) ; exit ( 1 ) ; } let buf = new Bytes ( ) ; let n = 0 , file = new File ( arguments [ 0 ] ) ; while ( file . readline ( buf ) >= 0 ) ++ n ; file . close ( ) ; buf . destroy ( ) ; print ( n ) ; Introduction K8 is a JavaScript runtime built on top of Google's v8 JavaScript engine . It provides a resizable binary buffer and synchronous APIs for plain file writing and gzip'd file reading. Motivations JavaScript is among the fastest scripting languages. It is essential for web development but not often used for large-scale text processing or command-line utilities, in my opinion, due to the lack of sensible file I/O. Current JavaScript runtimes such as Node.js and Deno focus on asynchronous I/O and whole-file reading. Even reading a file line by line, which is required to work with large files, becomes a cumbersome effort. K8 aims to solve this problem. With synchronous I/O APIs, JavaScript can be a powerful language for developing command-line tools. Installation It is recommended to download precompiled binaries (also available from Zenodo ). If you want to compile k8, you need to compile Node.js which bundles v8 and provides a more convenient way build v8. As the v8 APIs are fast changing, both Node.js and k8 only work with specific versions of v8. The k8-1.x branch is known to work with node-18.x but not 19.x or higher. It is also worth noting that node-18.20.x upgraded c-ares which is now incompatible with older glibc. Node-18.19.1 is the most recent version that can be compiled on CentOS 7. On the other hand, Node-18.19.x cannot be compiled on MacOS with clang-15. Node-18.20.3 is known to work. API Documentations Functions // Print to stdout (print) or stderr (warn). TAB delimited if multiple arguments. function print ( data : any ) function warn ( data : any ) // Exit function exit ( code : number ) // Load a JavaScript file and execute. It searches the working directory, the // script directory and then the K8_PATH environment variable in order. function load ( fileName : string ) // Read entire file as an ArrayBuffer function k8_read_file ( fileName : string ) : ArrayBuffer // Decode $buf to string under the $enc encoding; only "utf-8" is supported for now // Missing or unknown encoding is treated as Latin-1 function k8_decode ( buf : ArrayBuffer | Bytes , enc ?: string ) : string // Encode $str into an ArrayBuffer function k8_encode ( str : string , enc ?: string ) : ArrayBuffer // Reverse complement a DNA sequence in string function k8_revcomp ( seq : string ) : string // Reverse complement a DNA sequence in place function k8_revcomp ( seq : ArrayBuffer | Bytes ) // Get version string function k8_version ( ) : string The Bytes Object Bytes provides a resizable byte array. // Create an array of byte buffer of $len in size. new Bytes ( len ? : number = 0 ) // Property: get/set length of the array . length : number // Property: get/set the max capacity of the array . capacity : number // Property: get ArrayBuffer of the underlying data, not allocated from v8 . buffer : ArrayBuffer // Deallocate the array. This is necessary as the memory is not managed by the v8 GC. Bytes . prototype . destroy ( ) // Replace the byte array starting from $offset to $data, where $data can be a number, // a string, an array or Bytes. The size of the array is modified if the new array // is larger. Return the number of modified bytes. Bytes . prototype . set ( data : number | string | Array | ArrayBuffer , offset ? : number ) : number // Convert the byte array to string Bytes . prototype . toString ( ) The File Object File provides buffered file I/O. // Open a plain or gzip'd file for reading or a plain file for writing. $file // is file descriptor if it is an integer or file name if string. Each File // object can only be read or only be written, not mixed new File ( file ? : string | number = 0 , mode ? : string = "r" ) // Read a byte and return it File . prototype . read ( ) : number // Read the rest of the file into $buf at offset 0. Return the number of bytes read. File . prototype . read ( buf : Bytes ) : number // Read $len bytes into $buf at $offset. // Return the number of bytes read on success; 0 on file end; <0 on errors File . prototype . read ( buf : Bytes , offset : number , len : number ) : number // Read a line or a token to $buf at $offset. $sep=0 for SPACE, 1 for TAB and 2 // for newline. If $sep is a string, only the first character is considered. // Return the delimiter if non-negative, -1 upon EOF, or <-1 for errors File . prototype . readline ( buf : Bytes , sep ? : number | string = 2 , offset ? : number = 0 ) : number // Write data File . prototype . write ( data : string | ArrayBuffer ) : number // Close a file File . prototype . close ( ) About k8 Javascript shell Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Stars 158 stars Watchers 9 watching Forks 6 forks Report repository Releases 8 k8-1.2 (r137) Latest May 27, 2024 + 7 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages JavaScript 58.0% C++ 41.1% Makefile 0.9% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge k8 --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +k8 0.2.5 h9a82719_1 +------------------- +file name : k8-0.2.5-h9a82719_1.tar.bz2 +name : k8 +version : 0.2.5 +build : h9a82719_1 +build number: 1 +size : 1.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-h9a82719_1.tar.bz2 +md5 : 8700d84f57171e0d92bb5e7178aca95c +timestamp : 2021-03-24 20:06:41 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +k8 0.2.5 hd03093a_2 +------------------- +file name : k8-0.2.5-hd03093a_2.tar.bz2 +name : k8 +version : 0.2.5 +build : hd03093a_2 +build number: 2 +size : 1.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hd03093a_2.tar.bz2 +md5 : 37e8cc3b610f6e0e91715fa4ad553c24 +timestamp : 2022-02-23 12:36:24 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +k8 0.2.5 hd03093a_3 +------------------- +file name : k8-0.2.5-hd03093a_3.tar.bz2 +name : k8 +version : 0.2.5 +build : hd03093a_3 +build number: 3 +size : 1.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hd03093a_3.tar.bz2 +md5 : ca494930ce35ba3755469f6ec8d86f27 +timestamp : 2023-05-13 15:01:41 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +k8 0.2.5 hdcf5f25_3 +------------------- +file name : k8-0.2.5-hdcf5f25_3.tar.bz2 +name : k8 +version : 0.2.5 +build : hdcf5f25_3 +build number: 3 +size : 1.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_3.tar.bz2 +md5 : d4018f538d778a5bbdbf590b2a3cdbc5 +timestamp : 2023-05-15 00:19:17 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +k8 0.2.5 hdcf5f25_4 +------------------- +file name : k8-0.2.5-hdcf5f25_4.tar.bz2 +name : k8 +version : 0.2.5 +build : hdcf5f25_4 +build number: 4 +size : 1.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2 +md5 : d3c49a96ae45864706037702775ca7c2 +timestamp : 2023-05-16 01:35:15 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +k8 0.2.5 he513fc3_0 +------------------- +file name : k8-0.2.5-he513fc3_0.tar.bz2 +name : k8 +version : 0.2.5 +build : he513fc3_0 +build number: 0 +size : 1.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-he513fc3_0.tar.bz2 +md5 : fc3928fa64e02482eb70a8b7a27adb8a +timestamp : 2020-06-18 13:35:21 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +k8 1.0 h6618dc6_0 +----------------- +file name : k8-1.0-h6618dc6_0.tar.bz2 +name : k8 +version : 1.0 +build : h6618dc6_0 +build number: 0 +size : 7.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-1.0-h6618dc6_0.tar.bz2 +md5 : b43ec67ac9997bfe775cbba4780214af +timestamp : 2024-05-07 04:09:07 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - python_abi 3.8.* *_cp38 + - sysroot_linux-64 >=2.17 + + +k8 1.2 h6618dc6_0 +----------------- +file name : k8-1.2-h6618dc6_0.tar.bz2 +name : k8 +version : 1.2 +build : h6618dc6_0 +build number: 0 +size : 7.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-1.2-h6618dc6_0.tar.bz2 +md5 : 9a08735b32b4d69f88db55364c5ed51a +timestamp : 2024-05-27 20:25:42 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - python_abi 3.8.* *_cp38 + - sysroot_linux-64 >=2.17 + + +k8 1.2 h6618dc6_1 +----------------- +file name : k8-1.2-h6618dc6_1.tar.bz2 +name : k8 +version : 1.2 +build : h6618dc6_1 +build number: 1 +size : 7.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-1.2-h6618dc6_1.tar.bz2 +md5 : 809d962752f1843dde1c26aee4f033d3 +timestamp : 2024-06-04 20:53:17 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<2.0a0 + - python_abi 3.8.* *_cp38 + - sysroot_linux-64 >=2.17 + + +k8 1.2 h6618dc6_3 +----------------- +file name : k8-1.2-h6618dc6_3.tar.bz2 +name : k8 +version : 1.2 +build : h6618dc6_3 +build number: 3 +size : 7.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-1.2-h6618dc6_3.tar.bz2 +md5 : 7121e62d9fcd82071086350b7ddc846f +timestamp : 2024-10-02 22:44:46 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - libgcc >=12 + - libstdcxx >=12 + - libzlib >=1.2.13,<2.0a0 + - python_abi 3.12.* *_cp312 + - sysroot_linux-64 >=2.17 + + +k8 1.2 he8db53b_4 +----------------- +file name : k8-1.2-he8db53b_4.tar.bz2 +name : k8 +version : 1.2 +build : he8db53b_4 +build number: 4 +size : 7.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-1.2-he8db53b_4.tar.bz2 +md5 : 3b2d3fbb442002b0436e2c5ebf3de212 +timestamp : 2024-12-13 23:31:19 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - libgcc >=13 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + - python_abi 3.13.* *_cp313 + - sysroot_linux-64 >=2.17 + + +k8 1.2 he8db53b_5 +----------------- +file name : k8-1.2-he8db53b_5.tar.bz2 +name : k8 +version : 1.2 +build : he8db53b_5 +build number: 5 +size : 7.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-1.2-he8db53b_5.tar.bz2 +md5 : 090bfaefc98c4e7b72a083ec1b9cf525 +timestamp : 2024-12-17 04:06:50 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - libgcc >=13 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + - python_abi 3.13.* *_cp313 + - sysroot_linux-64 >=2.17 + + +k8 1.2 he8db53b_6 +----------------- +file name : k8-1.2-he8db53b_6.tar.bz2 +name : k8 +version : 1.2 +build : he8db53b_6 +build number: 6 +size : 7.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/k8-1.2-he8db53b_6.tar.bz2 +md5 : 6c44663f234185cc54d7a90c4d7a555a +timestamp : 2025-06-03 09:21:19 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - libgcc >=13 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + - sysroot_linux-64 >=2.17 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kaiju.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kaiju.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..95d572f18fecbe9f2d6a83eb23e864f8f588ab39 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kaiju.manual_bundle.txt @@ -0,0 +1,549 @@ +# Tool: kaiju +software_name: kaiju +tier: T1 +domain: t1_backfill_overall +downloads: 136312 +summary: Fast and sensitive taxonomic classification for metagenomics +description: Fast and sensitive taxonomic classification for metagenomics +dependencies: curl, libgcc >=13, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, perl, python, wget +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://kaiju.binf.ku.dk/ +doc_url: +dev_url: https://github.com/bioinformatics-centre/kaiju + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://kaiju.binf.ku.dk/ +Kaiju: Fast and sensitive taxonomic classification for metagenomics Home Downloads Source Fast and sensitive taxonomic classification for metagenomics About Kaiju Kaiju is a program for fast and sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing or metatranscriptomics experiments. Each sequencing read is assigned to a taxon in the NCBI taxonomy by comparing it to a reference protein database containing microbial and viral protein sequences . By using protein-level classification, Kaiju achieves a higher sensitivity compared with methods based on nucleotide comparison. Several reference protein databases can be used, such as complete genomes from NCBI RefSeq or the microbial subset of the NCBI BLAST non-redundant protein database nr , optionally also including fungi and microbial eukaryotes. Reads are translated into amino acid sequences, which are then searched in the database using a modified backward search on a memory-efficient implementation of the Burrows-Wheeler transform by finding maximum exact matches (MEMs), optionally allowing mismatches. Kaiju can also be used for querying any custom protein database without taxonomic classification, using either protein or nucleotide queries. Kaiju is described in Menzel, P. et al. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257 (open access). Pre-built kaiju indexes for various reference databases can also be downloaded . Download The latest version of Kaiju's source code can be downloaded from GitHub either as compressed archive or by cloning the repository via git : git clone https://github.com/bioinformatics-centre/kaiju.git Please refer to the README file for installation and usage instructions. The source code is available under the GNU General Public License 3. News and Release notes 2024-07-31 The web server at kaiju.binf.ku.dk was shut down after more than 8 years of operation. Version 1.10.1 2024-03-03 fix download of refseq_nr files in kaiju-makedb Version 1.10.0 2023-11-25 update proGenomes to v3 update RVDB-prot to v26.0 add refseq_nr and refseq_ref databases remove Mar databases statically linked Linux binaries are available on GitHub 2023-07-01 Pre-built indexes are now hosted on AWS S3 through the Open Data Sponsorship Program 2023-06-01 Kaiju indexes for 2023 are available Version 1.9.2 2022-11-19 small bugfixes regarding using command line option -a statically linked Linux binaries are available on GitHub Version 1.9.0 2022-05-12 set default E-value to 0.01 in Greedy mode fix MAR databases downloads fix RefSeq plasmid downloads update RVDB-prot to v23.0 statically linked Linux binaries are available on GitHub Version 1.8.2 2021-10-26 make downloading RefSeq genomes work again in kaiju-makedb statically linked Linux binaries are available on GitHub Version 1.8.1 2021-10-13 update RVDB-prot to v22.0 use curl for downloading virus/plasmid sequences from RefSeq FTP server statically linked Linux binaries are available on GitHub 2021-08-05 new web server with updated databases and option for setting E-value Version 1.8 2021-08-05 add kaiju-multi add option -l to kaiju2krona update RVDB-prot to v21.0 better handling of downloading virus and plasmid sequences from RefSeq statically linked Linux binaries are available on GitHub Version 1.7.4 2020-11-04 update RVDB-prot to v20.0 fix bug in RefSeq download statically linked Linux binaries are available on GitHub Version 1.7.3 2020-01-16 update RVDB-prot to v17.0 add list with excluded accession numbers for NR database, based on Breitwieser et al., 2019 add option -s to kaiju-mergeOutputs statically linked Linux binaries are available on GitHub Version 1.7.2 2019-07-12 fix download of virus genomes for source databases viruses , refseq , progenomes add source database fungi , which contains all fungi assemblies from NCBI RefSeq statically linked Linux binaries are available on GitHub Version 1.7.1 2019-06-27 update download of virus genomes for source databases viruses , refseq , progenomes statically linked Linux binaries are available on GitHub Version 1.7.0 2019-04-28 replace makeDB.sh with kaiju-makedb replace kaijuReport with kaiju2table rename addTaxonNames to kaiju-addTaxonNames rename mergeOutputs to kaiju-mergeOutputs add RVDB-prot as reference database statically linked Linux binaries are available on GitHub Version 1.6.3 2018-10-01 new options for makeDB.sh to only download plasmids ( -l ) or viruses ( -v ) extend list of downloaded files for viruses and plasmids in makeDB.sh updates to marDB statically linked Linux binaries are available on GitHub Version 1.6.2 2018-02-24 fixed crash of makeDB.sh on MacOS statically linked Linux binaries are available on GitHub Version 1.6.1 2018-02-16 fixed bug in MacOS compilation statically linked Linux binaries are available on GitHub Version 1.6.0 2018-01-09 changed default search parameters to Greedy mode with 3 allowed mismatches and enabled SEG filter (can be disabled with the new option -X ) E-value is calculated in Greedy mode and can be used as a threshold for classification using option -E Kaiju can now also open gzip-compressed FASTQ/A input files the MarDB database can be selected in makeDB.sh using option -m statically linked Linux binaries are available on GitHub Version 1.5.0 2017-02-20 add accession numbers to database identifiers Kaiju's long output format via option -v will now print the accession numbers of the matched database sequences in column 6 Important: Kaiju 1.5.0 does not work with index files ( .fmi ) from previous versions and previous versions will not work with index files made with Kaiju 1.5.0 statically linked Linux binaries are available on GitHub Version 1.4.5 2017-01-27 various small bug fixes and improvements add option -c lowest to mergeOutputs add option -p to kaijuReport for printing the full taxon path in the report add option -l to kaijuReport for selecting specific ranks for taxon path statically linked Linux binaries are available on GitHub Version 1.4.4 2016-10-31 add option -p to makeDB.sh for using the representative set from proGenomes as a reference database add option -r to makeDB.sh for using RefSeq complete genomes as a reference database remove default option in makeDB.sh . Now, one of the options -r , -p , -n , or -e has to be used. add option for static linking statically linked Linux binaries are available on GitHub Version 1.4.3 2016-10-19 adjust makeDB.sh to the new folder structure of RefSeq genomes on the NCBI FTP server increase precision of percentage numbers in kaijuReport Version 1.4.2 2016-09-03 change makeDB.sh and convertNR to accommodate the removal of GI numbers from the NCBI BLAST nr database Version 1.4.1 2016-07-06 fix bug in calculation of percentage of unassigned reads in kaijuReport fix parsing of names of taxon ranks from nodes.dmp in kaijuReport and addTaxonNames Version 1.4 2016-05-17 add BLAST's SEG low complexity filter via option -x add option -p to kaiju for protein sequence input, which disables the translation from nucleotide to amino acids add option -e to makeDB.sh for including proteins from fungi and microbial eukaryotes when using the nr database add program addTaxonNames for extending the output file by taxon names or taxon paths Version 1.3.1 2016-04-19 fix read name detection on PE reads for newer Illumina name standard Version 1.3 2016-04-13 add makeDB.sh for downloading genomes and building reference database and Kaiju index add convertNR for using the BLAST nr database fix overflow bug for large DBs improved file type detection update README and minor cosmetic changes Paper published 2016-02-23 web server launched Version 1.2 2016-01-11 update for Greedy mode, which is now approximately twice as fast without change of accuracy. add kaijup , for searching protein queries against a protein database without taxonomy classification, so that the database names of best matches are printed. Version 1.1 2015-12-18 new implementation of the FM-index, which improves query speed to the BWT. the distance between suffix array checkpoints can be set using the -e option for mkbwt , which allows trading off database size vs speed. MEM mode now only prints the matching sequence(s) in verbose mode instead of the full query sequence. add kaijux , for searching translated reads against a protein database without taxonomy classification, so that the database names of best matches are printed. Version 1.0.1 2015-11-24 add kaijuReport bugfix in kaiju for FASTA input files, which caused the last input line to be read twice Version 1.0 2015-11-16 initial release preprint paper on bioRxiv published Previous releases can be downloaded here . Contact For questions, bug reports or more information about Kaiju, please contact Peter Menzel . Bug reports can also be filed in GitHub's issue tracker . Citation Menzel P., Ng K.L., Krogh A. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257 Read the behind the paper post on Nature Microbiology Community. The program is being developed by Peter Menzel and Anders Krogh at the Bioinformatics Centre, a part of the Section for Computational and RNA Biology at the University of Copenhagen . This page is maintained by pmenzel + +### https://github.com/bioinformatics-centre/kaiju +GitHub - bioinformatics-centre/kaiju: Fast taxonomic classification of metagenomic sequencing reads using a protein reference database · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bioinformatics-centre / kaiju Public Notifications You must be signed in to change notification settings Fork 70 Star 302 Code Issues 61 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights bioinformatics-centre/kaiju master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 252 Commits 252 Commits .github/ workflows .github/ workflows src src test/ viruses test/ viruses util util .gitignore .gitignore LICENSE LICENSE Quickstart.md Quickstart.md README.md README.md View all files Repository files navigation README GPL-3.0 license Kaiju Kaiju is a program for the taxonomic classification of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from microbial and viral genomes. The program is described in Menzel, P. et al. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257 (open access). See the release notes for all releases here . Authors Peter Menzel pmenzel@gmail.com Anders Krogh krogh@binf.ku.dk License Copyright (c) 2015-2024 Peter Menzel and Anders Krogh Kaiju is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Kaiju is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the file LICENSE for more details. You should have received a copy of the GNU General Public License along with the source code. If not, see http://www.gnu.org/licenses/ . Installation Compiling Kaiju from source Kaiju's source code can be downloaded directly from GitHub either as a compressed archive or using the git command line client: git clone https://github.com/bioinformatics-centre/kaiju.git This will create the directory kaiju in the current directory. Kaiju is written in C/C++11 for Linux. It uses the zlib library for reading gzip-compressed files. If not already installed, it is necessary to install the zlib development library, e.g. on Ubuntu using: sudo apt install libz-dev For compiling Kaiju and its associated programs, type: cd kaiju/src make After compilation, Kaiju's executable files are available in the kaiju/bin directory. You can add this directory to your shell's $PATH variable or copy all files from kaiju/bin to a directory in your $PATH . Installation via Bioconda Kaiju is also available via the bioconda channel and can be installed via conda install -c bioconda kaiju # or mamba install -c bioconda kaiju Creating the Kaiju index Before classification of reads, Kaiju's database index needs to be built from the reference protein database. You can either create a local index based on the currently available reference databases, or download a pre-built index . For creating a local index, the program kaiju-makedb in the bin/ directory will download a source database and the taxonomy files from the NCBI FTP server, convert them into a protein database and construct Kaiju's index (the Burrows-Wheeler transform and the FM-index) in one go. kaiju-makedb needs curl and wget for downloading the reference databases. The downloaded files can be very large, depending on the selected reference database. It is therefore recommended to run kaiju-makedb in a directory with at least 500 GB of free space. Example usage: mkdir kaijudb cd kaijudb kaiju-makedb -s <DB> The table below lists the available source databases. Use the database name shown in the first column as argument to option -s in kaiju-makedb . The last column denotes the required memory for running Kaiju with the respective index and for creating the index (in brackets). Index name Description Sequences * RAM in GB (makedb) * refseq Completely assembled and annotated reference genomes of Archaea, Bacteria, and viruses from the NCBI RefSeq database. 164 M 111 (144) refseq_nr Sequences for Archaea, Bacteria, viruses and microbial eukaryotes from the NCBI RefSeq non-redundant protein collection . 276 M 153 (263) refseq_ref Protein sequences from representative assemblies of Archaea and bacteria from NCBI RefSeq plus viruses from NCBI RefSeq. 76.9 M 54 (70) progenomes Representative set of genomes from the proGenomes v3 database and viruses from the NCBI RefSeq database. 141 M 102 (120) viruses Only viruses from the NCBI RefSeq database. 0.68 M 0.5 (0.6) plasmids Plasmid sequences from the NCBI RefSeq database. 7 M 4 (6) fungi Fungi sequences from the NCBI RefSeq database. 6.5 M 6 (9) nr Subset of NCBI BLAST nr database containing all proteins belonging to Archaea, bacteria and viruses. 353 M 219 (491) nr_euk Like option -s nr and additionally include proteins from fungi and microbial eukaryotes, see taxon list in bin/kaiju-taxonlistEuk.tsv . 397 M 250 (432) rvdb Protein sequences from RVDB-prot 39 M 86 (253) * as of late 2024. Pre-built indexes for each reference database can be downloaded . By default, kaiju-makedb uses 5 parallel threads for constructing the index, which can be changed by using the option -t . Note that a higher number of threads increases the memory usage during index construction, while reducing the number of threads decreases memory usage. After kaiju-makedb is finished, only the files kaiju_db_*.fmi , nodes.dmp , and names.dmp are needed to run Kaiju. Custom database It is also possible to make a custom database from a collection of protein sequences. The format needs to be a FASTA file in which the headers are the numeric NCBI taxon identifiers of the protein sequences, which can optionally be prefixed by another identifier (e.g. a counter) followed by an underscore, for example: >1_1358 MAQQRRGGFKRRKKVDFIAANKIEVVDYKDTELLKRFISERGKILPRRVTGTSAKNQRKVVNAIKRARVMALLPFVAEDQN >2_44689 MASTQNIVEEVQKMLDTYDTNKDGEITKAEAVEYFKGKKAFNPERSAIYLFQVYDKDNDGKITIKELAGDIDFDKALKEYKEKQAKSKQQEAEVEEDIEAFILRHNKDDNTDITKDELIQGFKETGAKDPEKSANFILTEMDTNKDGTITVKELRVYYQKVQKLLNPDQ >3_352472 MKTKSSNNIKKIYYISSILVGIYLCWQIIIQIIFLMDNSIAILEAIGMVVFISVYSLAVAINGWILVGRMKKSSKKAQYEDFYKKMILKSKILLSTIIIVIIVVVVQDIVINFILPQNPQPYVYMIISNFIVGIADSFQMIMVIFVMGELSFKNYFKFKRIEKQKNHIVIGGSSLNSLPVSLPTVKSNESNESNTISINSENNNSKVSTDDTINNVM >4_91061 MTNPFENDNYTYKVLKNEEGQYSLWPAFLDVPIGWNVVHKEASRNDCLQYVENNWEDLNPKSNQVGKKILVGKR ... The taxon identifiers must be contained in the NCBI taxonomy files nodes.dmp and names.dmp. Then, Kaiju's index is created using the programs kaiju-mkbwt and kaiju-mkfmi . For example, if the database FASTA file is called proteins.faa , then run: kaiju-mkbwt -n 5 -a ACDEFGHIKLMNPQRSTVWY -o proteins proteins.faa kaiju-mkfmi proteins which creates the file proteins.fmi that is used by Kaiju. Note that the protein sequences may only contain the uppercase characters of the standard 20 amino acids, all other characters need to be removed. Running Kaiju Kaiju requires at least three arguments: kaiju -t nodes.dmp -f kaiju_db_*.fmi -i inputfile.fastq Replace kaiju_db_*.fmi by the actual .fmi file depending on the selected database. For example, when running kaiju-makedb -s refseq , the corresponding index file is refseq/kaiju_db_refseq.fmi . For paired-end reads use -i firstfile.fastq and -j secondfile.fastq . The reads must be in the same order in both files. Kaiju will strip suffixes from the read names by deleting all characters after a / or space. The read names are then compared between the first and second file and an error is issued if they are not identical. Kaiju can read input files in FASTQ and FASTA format, which may also be gzip-compressed. By default, Kaiju will print the output to the terminal (STDOUT). The output can also be written to a file using the -o option: kaiju -t nodes.dmp -f kaiju_db.fmi -i inputfile.fastq -o kaiju.out Kaiju can use multiple parallel threads, which can be specified with the -z option, e.g. for using 25 parallel threads: kaiju -z 25 -t nodes.dmp -f kaiju_db.fmi -i inputfile.fastq -o kaiju.out kaiju-multi While kaiju can only process one input, kaiju-multi can take a comma-separated list of input files (and optionally output files) for processing multiple samples at once: kaiju-multi -z 25 -t nodes.dmp -f kaiju_db.fmi -i sample1_R1.fastq,sample2_R1.fastq,sample3_R1.fastq -j sample1_R2.fastq,sample2_R2.fastq,sample3_R2.fastq -o sample1.out,sample2.out,sample3.out These lists must have the same length. It's also possible to merge all outputs into one file using output redirection: kaiju-multi -z 25 -t nodes.dmp -f kaiju_db.fmi -i sample1_R1.fastq,sample2_R1.fastq,sample3_R1.fastq -j sample1_R2.fastq,sample2_R2.fastq,sample3_R2.fastq > all_samples.out Run modes The default run mode is Greedy with three allowed mismatches. The number of allowed mismatches can be changed using option -e . In Greedy mode, matches are filtered by a minimum length and score, but also by their E-value (similar to blastp), which can be adjusted with the option -E . The default value is 0.01. The cutoffs for minimum required match length and match score can be changed using the options -m (default: 11) and -s (default: 65). The run mode can be changed to MEM using option -a : kaiju -t nodes.dmp -f kaiju_db.fmi -i inputfile.fastq -a mem If the input sequences are already protein sequences, use option -p to disable translation of the input. Option -x enables filtering of query sequences containing low-complexity regions by using the SEG algorithm from the blast+ package. It is enabled by default and can be disabled by the -X option. SEG filtering is always recommended in order to avoid false positive taxon assignments that are caused by spurious matches due to simple repeat patterns or other sequencing noise. Output format Kaiju will print one line for each read or read pair. The default output format contains three columns separated by tabs. Using the option -v enables the verbose output, which will print additional columns: either C or U, indicating whether the read is classified or unclassified. name of the read NCBI taxon identifier of the assigned taxon the length or score of the best match used for classification the taxon identifiers of all database sequences with the best match the accession numbers of all database sequences with the best match matching fragment sequence(s) NB: Since the nr database aggregates multiple genes of identical sequences, only the first accession number for each sequence in the nr source file is kept in Kaiju's database and therefore also in the output file. The number of taxon identifiers (column 5) and accession numbers (column 5) is limited to 20 entries each in order to reduce large outputs produced by highly abundant protein sequences in nr , e.g. from HIV. Classification accuracy The accuracy of the classification depends both on the choice of the reference database and the chosen options when running Kaiju. These choices also affect the speed and memory usage of Kaiju. For highest sensitivity, it is recommended to use the nr database (+eukaryotes) as a reference database because it is the most comprehensive set of protein sequences. Alternatively, use proGenomes over Refseq for increased sensitivity. Greedy run mode yields a higher sensitivity compared with MEM mode. For fastest classification, use MEM mode and multiple parallel threads ( -z ); and for lowest memory usage use the proGenomes reference database. The number of parallel threads has only little impact on memory usage. Further, the choice of the minimum required match length ( -m ) in MEM mode or match score ( -s ) in Greedy mode governs the trade-off between sensitivity and precision of the classification. Please refer to the paper for a discussion on this topic. Helper programs Creating input file for Krona The program kaiju2krona can be used to convert Kaiju's tab-separated output file into a tab-separated text file, which can be imported into Krona . It requires the nodes.dmp and names.dmp files from the NCBI taxonomy for mapping the taxon identifiers from Kaiju's output to the corresponding taxon names. kaiju2krona -t nodes.dmp -n names.dmp -i kaiju.out -o kaiju.out.krona The file kaiju.out.krona can then be imported into Krona and converted into an HTML file using Krona's ktImportText program: ktImportText -o kaiju.out.html kaiju.out.krona Creating classification summary The program kaiju2table converts Kaiju's output file(s) into a summary table for a given taxonomic rank, e.g., genus. It requires the nodes.dmp and names.dmp files for mapping the taxon identifiers from the third column in the Kaiju output to the corresponding taxon names. Basic usage: kaiju2table -t nodes.dmp -n names.dmp -r genus -o kaiju_summary.tsv kaiju.out [kaiju2.out, ...] The program can also filter out taxa with low abundances, e.g. for only showing genera that comprise at least 1 percent of the total reads: kaiju2table -t nodes.dmp -n names.dmp -r genus -m 1.0 -o kaiju_summary.tsv kaiju.out [kaiju2.out, ...] Similarly, option -c can be used to specify the threshold by absolute read count. Option -u disables counting unclassified reads towards the total number of reads when calculating percentages. Option -p will print the full taxon path instead of just the taxon name. Instead of printing the full taxon path, option -l can be used to specify the ranks to be printed by supplying a comma-separated list, for example: -l superkingdom,phylum,class,order,family,genus,species . Adding taxa names to output file The program kaiju-addTaxonNames appends the name that corresponds to the taxon id in Kaiju's output file as an additional last column to the output. kaiju-addTaxonNames -t nodes.dmp -n names.dmp -i kaiju.out -o kaiju.names.out Option -u will omit unclassified reads. Option -p will print the full taxon path instead of just the taxon name. Option -r will print the path containing only to the specified ranks. For example, -r phylum,genus will append the names of phylum and genus to the end of each line. Merging outputs The program kaiju-mergeOutputs can merge two tab-separated output files in the column format (see above) used by Kaiju and Kraken. Only the first three columns are used. The files need to be sorted by the read name in the second column, for example by: sort -k2,2 kaiju.out >kaiju.out.sort sort -k2,2 kraken.out >kraken.out.sort Then both files can be merged: kaiju-mergeOutputs -i kaiju.out.sort -j kraken.out.sort -o combined.out -v The shell's process substitution can be used for sorting without creating intermediate files: kaiju-mergeOutputs -i <(sort -k2,2 kaiju.out) -j <(sort -k2,2 kraken.out) -o combined.out -v The output file will be in the same column format as the input files (but only contain the first three columns) and it will have the same length as the input files (which also have to be of same length). In the case of conflicting taxon identifiers for a classified read in both input files, kaiju-mergeOutputs will use the identifier found in the first input file (specified by -i ). This behavior can be changed using the -c option, which can take four possible values: 1 : use taxon identifier from the first input file. 2 : use taxon identifier from the second input file. lca : use the least common ancestor of the taxon identifiers from both files (default). lowest : use the lowest ranking of the two taxon identifiers if they are within the same lineage. Otherwise use the LCA. Options lca and lowest require the path to the file nodes.dmp by using the -t option. When the two tab-separated output files contain the classification score in the 4th column (by running kaiju -v ), then option -s can be used to give precedence to the classification result with the higher score. KaijuX and KaijuP The programs kaijux and kaijup can be used for finding the best matching database sequence for each query sequence without taxonomic classification, i.e., they will just print the name of the database sequence. Thus, both programs do not use the nodes.dmp file containing the taxonomy, but only need the .fmi database file. While kaijux takes nucleotide sequences as input and translates them into the six reading frames like standard kaiju , kaijup takes protein sequences as input, which are directly searched in the database. All other parameters remain the same as in standard kaiju . In case of paired-end reads, both mates are searched independently. To build an index for a custom database, all sequences need to be in a single FASTA file and may only contain the 20 letters from the standard protein alphabet ACDEFGHIKLMNPQRSTVWY . For example, building the index (the Burrows-Wheeler transform and FM-index) from the file with the protein sequences proteins.faa is done in two steps by the programs kaiju-mkbwt and kaiju-mkfmi : kaiju-mkbwt -n 5 -a ACDEFGHIKLMNPQRSTVWY -o proteins proteins.faa kaiju-mkfmi proteins This will create two intermediate files proteins.bwt and proteins.sa , and finally the file proteins.fmi , which is used by Kaiju. The option -n for kaiju-mkbwt specifies the number of parallel threads. The more threads are used, the higher the memory consumpt + +## Conda Search Info +$ conda search -c bioconda -c conda-forge kaiju --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +kaiju 1.0 0 +----------- +file name : kaiju-1.0-0.tar.bz2 +name : kaiju +version : 1.0 +build : 0 +build number: 0 +size : 3.8 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.0-0.tar.bz2 +md5 : bffcfb19805d26678da0791e02e0fe73 +dependencies: + - libgcc + + +kaiju 1.4.4 0 +------------- +file name : kaiju-1.4.4-0.tar.bz2 +name : kaiju +version : 1.4.4 +build : 0 +build number: 0 +size : 3.8 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.4.4-0.tar.bz2 +md5 : af68055ceb6334cd2bd7c2c4f0404337 +dependencies: + - libgcc + - perl-threaded + + +kaiju 1.4.4 1 +------------- +file name : kaiju-1.4.4-1.tar.bz2 +name : kaiju +version : 1.4.4 +build : 1 +build number: 1 +size : 3.8 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.4.4-1.tar.bz2 +md5 : f184fd432d398bdaf78c59496f8e439c +dependencies: + - libgcc + - perl-threaded + + +kaiju 1.4.4 2 +------------- +file name : kaiju-1.4.4-2.tar.bz2 +name : kaiju +version : 1.4.4 +build : 2 +build number: 2 +size : 3.8 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.4.4-2.tar.bz2 +md5 : c9580c86960b308ea17bcbfcdcff2184 +dependencies: + - gnu-wget >=1.16 + - libgcc + - perl-threaded + + +kaiju 1.4.4 3 +------------- +file name : kaiju-1.4.4-3.tar.bz2 +name : kaiju +version : 1.4.4 +build : 3 +build number: 3 +size : 3.8 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.4.4-3.tar.bz2 +md5 : 09226ce756751f0dc2ea0e486f38ae50 +dependencies: + - gnu-wget >=1.16 + - libgcc + - perl-threaded + + +kaiju 1.4.5 pl5.22.0_0 +---------------------- +file name : kaiju-1.4.5-pl5.22.0_0.tar.bz2 +name : kaiju +version : 1.4.5 +build : pl5.22.0_0 +build number: 0 +size : 4.3 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.4.5-pl5.22.0_0.tar.bz2 +md5 : 4b8c9a2667071748543247b5bf2ed19f +dependencies: + - gnu-wget >=1.16 + - libgcc + - perl 5.22.0* + + +kaiju 1.5.0 pl5.22.0_0 +---------------------- +file name : kaiju-1.5.0-pl5.22.0_0.tar.bz2 +name : kaiju +version : 1.5.0 +build : pl5.22.0_0 +build number: 0 +size : 4.5 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.5.0-pl5.22.0_0.tar.bz2 +md5 : 38a368380a5b011f6b3e1cba66ea0c2e +dependencies: + - gnu-wget >=1.16 + - libgcc + - perl 5.22.0* + + +kaiju 1.6.1 pl5.22.0_0 +---------------------- +file name : kaiju-1.6.1-pl5.22.0_0.tar.bz2 +name : kaiju +version : 1.6.1 +build : pl5.22.0_0 +build number: 0 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.6.1-pl5.22.0_0.tar.bz2 +md5 : f098f16471d7cff9e448c2a654b9b378 +dependencies: + - gnu-wget >=1.16 + - libgcc + - perl 5.22.0* + - zlib 1.2.11* + + +kaiju 1.6.2 hd28b015_1 +---------------------- +file name : kaiju-1.6.2-hd28b015_1.tar.bz2 +name : kaiju +version : 1.6.2 +build : hd28b015_1 +build number: 1 +size : 1.1 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.6.2-hd28b015_1.tar.bz2 +md5 : 4a297265cb20b22d491e6db5b0c521e8 +timestamp : 2018-07-16 20:29:56 UTC +dependencies: + - gnu-wget >=1.16 + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.6.2 pl5.22.0_0 +---------------------- +file name : kaiju-1.6.2-pl5.22.0_0.tar.bz2 +name : kaiju +version : 1.6.2 +build : pl5.22.0_0 +build number: 0 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.6.2-pl5.22.0_0.tar.bz2 +md5 : 2261c3975c624d4d83a88afaee1f6345 +dependencies: + - gnu-wget >=1.16 + - libgcc + - perl 5.22.0* + - zlib 1.2.11* + + +kaiju 1.6.3 hd28b015_0 +---------------------- +file name : kaiju-1.6.3-hd28b015_0.tar.bz2 +name : kaiju +version : 1.6.3 +build : hd28b015_0 +build number: 0 +size : 1.1 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.6.3-hd28b015_0.tar.bz2 +md5 : 9353e461a223ef7f2473c23f695fbbb9 +timestamp : 2018-10-10 20:49:51 UTC +dependencies: + - gnu-wget >=1.16 + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.6.3 hdbcaa40_1 +---------------------- +file name : kaiju-1.6.3-hdbcaa40_1.tar.bz2 +name : kaiju +version : 1.6.3 +build : hdbcaa40_1 +build number: 1 +size : 1.1 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.6.3-hdbcaa40_1.tar.bz2 +md5 : eb46d998f6e48f7811f6a02e3e03768b +timestamp : 2019-02-16 17:29:39 UTC +dependencies: + - gnu-wget >=1.16 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.6.3 hdbcaa40_2 +---------------------- +file name : kaiju-1.6.3-hdbcaa40_2.tar.bz2 +name : kaiju +version : 1.6.3 +build : hdbcaa40_2 +build number: 2 +size : 1.1 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.6.3-hdbcaa40_2.tar.bz2 +md5 : 458c87469ec4114f5784015a91ce3083 +timestamp : 2019-04-03 11:31:08 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.7.0 hdbcaa40_2 +---------------------- +file name : kaiju-1.7.0-hdbcaa40_2.tar.bz2 +name : kaiju +version : 1.7.0 +build : hdbcaa40_2 +build number: 2 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.7.0-hdbcaa40_2.tar.bz2 +md5 : e26c9c7efcf4eea1efc438307a020acb +timestamp : 2019-05-10 09:58:09 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.7.1 hdbcaa40_0 +---------------------- +file name : kaiju-1.7.1-hdbcaa40_0.tar.bz2 +name : kaiju +version : 1.7.1 +build : hdbcaa40_0 +build number: 0 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.7.1-hdbcaa40_0.tar.bz2 +md5 : ad700916a1780ca4aa3f2a9a92957ffb +timestamp : 2019-06-27 07:52:42 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.7.2 hdbcaa40_0 +---------------------- +file name : kaiju-1.7.2-hdbcaa40_0.tar.bz2 +name : kaiju +version : 1.7.2 +build : hdbcaa40_0 +build number: 0 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.7.2-hdbcaa40_0.tar.bz2 +md5 : ccbb29a70e57c7d3cb994fec48d73a09 +timestamp : 2019-07-12 17:49:11 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.7.3 h8b12597_0 +---------------------- +file name : kaiju-1.7.3-h8b12597_0.tar.bz2 +name : kaiju +version : 1.7.3 +build : h8b12597_0 +build number: 0 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.7.3-h8b12597_0.tar.bz2 +md5 : 8491f6440857d357c131796536573a49 +timestamp : 2020-01-16 11:13:47 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.7.3 h8b12597_1 +---------------------- +file name : kaiju-1.7.3-h8b12597_1.tar.bz2 +name : kaiju +version : 1.7.3 +build : h8b12597_1 +build number: 1 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.7.3-h8b12597_1.tar.bz2 +md5 : a5c59332e7b48270791d53e49cdcebf2 +timestamp : 2020-01-26 15:26:48 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.7.4 h2e03b76_1 +---------------------- +file name : kaiju-1.7.4-h2e03b76_1.tar.bz2 +name : kaiju +version : 1.7.4 +build : h2e03b76_1 +build number: 1 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.7.4-h2e03b76_1.tar.bz2 +md5 : 0292f246bf2dee77a847e8665d1759b4 +timestamp : 2021-03-25 02:12:20 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.7.4 h8b12597_0 +---------------------- +file name : kaiju-1.7.4-h8b12597_0.tar.bz2 +name : kaiju +version : 1.7.4 +build : h8b12597_0 +build number: 0 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.7.4-h8b12597_0.tar.bz2 +md5 : be050825d55b362f1b06ac1ff13179a7 +timestamp : 2020-11-04 12:18:51 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.8.0 h2e03b76_0 +---------------------- +file name : kaiju-1.8.0-h2e03b76_0.tar.bz2 +name : kaiju +version : 1.8.0 +build : h2e03b76_0 +build number: 0 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.8.0-h2e03b76_0.tar.bz2 +md5 : b63c5c2b7a0d04cfeefd87d8c9a5f5eb +timestamp : 2021-08-05 11:25:49 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.8.1 h2e03b76_0 +---------------------- +file name : kaiju-1.8.1-h2e03b76_0.tar.bz2 +name : kaiju +version : 1.8.1 +build : h2e03b76_0 +build number: 0 +size : 1.2 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.8.1-h2e03b76_0.tar.bz2 +md5 : 32292d8540df479adb705805624109f0 +timestamp : 2021-10-13 15:31:39 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - libzlib >=1.2.11,<1.3.0a0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.8.1 h2e03b76_1 +---------------------- +file name : kaiju-1.8.1-h2e03b76_1.tar.bz2 +name : kaiju +version : 1.8.1 +build : h2e03b76_1 +build number: 1 +size : 1.4 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.8.1-h2e03b76_1.tar.bz2 +md5 : ef1ca58b30501492208a3615a10f100c +timestamp : 2021-10-13 18:19:57 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - libzlib >=1.2.11,<1.3.0a0 + - perl + - python + - wget + - zlib >=1.2.11,<1.3.0a0 + + +kaiju 1.8.2 h2e03b76_0 +---------------------- +file name : kaiju-1.8.2-h2e03b76_0.tar.bz2 +name : kaiju +version : 1.8.2 +build : h2e03b76_0 +build number: 0 +size : 1.4 MB +license : GNU GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kaiju-1.8.2-h2e03b76_0.tar.bz2 +md5 : 505e diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kb-python.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kb-python.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..7fac7b50c7f8ac3cc90675a5acd965e7c2769cca --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kb-python.manual_bundle.txt @@ -0,0 +1,441 @@ +# Tool: kb-python +software_name: kb-python +tier: T1 +domain: single_cell +downloads: 41638 +summary: A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing. +description: A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing. +dependencies: anndata >=0.9.2, biopython >=1.8, h5py >=2.10.0, jinja2 >2.10.1, loompy >=3.0.6, nbconvert >=5.6.0, nbformat >=4.4.0, ngs-tools >=1.8.6, numpy >=1.17.2, pandas >=1.5.3, plotly >=4.5.0, python >=3.8, requests >=2.22.0, scanpy >=1.4.4.post1, scikit-learn >=0.21.3, tqdm >=4.39.0, typing-extensions >=3.7.4 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/pachterlab/kb_python +doc_url: https://www.kallistobus.tools/ +dev_url: https://github.com/pachterlab/kb_python + +## URL Docs Extract +### https://www.kallistobus.tools/ +Redirecting... Redirecting to https://kallisto.readthedocs.io/en/latest/ + +### https://github.com/pachterlab/kb_python +GitHub - pachterlab/kb_python: A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} pachterlab / kb_python Public Notifications You must be signed in to change notification settings Fork 29 Star 187 Code Issues 1 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights pachterlab/kb_python master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 649 Commits 649 Commits .github .github docs docs kb_python kb_python tests tests .gitattributes .gitattributes .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml LICENSE LICENSE MANIFEST.in MANIFEST.in Makefile Makefile README.md README.md codecov.yml codecov.yml dev-requirements.txt dev-requirements.txt readthedocs.yml readthedocs.yml requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README BSD-2-Clause license kb-python kb-python is a python package for processing single-cell RNA-sequencing. It wraps the kallisto | bustools single-cell RNA-seq command line tools in order to unify multiple processing workflows. kb-python was first developed by Kyung Hoi (Joseph) Min and A. Sina Booeshaghi while in Lior Pachter 's lab at Caltech. If you use kb-python in a publication please cite* : Melsted, P., Booeshaghi, A.S., et al. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nat Biotechnol 39, 813–818 (2021). https://doi.org/10.1038/s41587-021-00870-2 Installation The latest release can be installed with pip install kb-python The development version can be installed with pip install git+https://github.com/pachterlab/kb_python There are no prerequisite packages to install. The kallisto and bustools binaries are included with the package. Usage kb consists of five subcommands $ kb usage: kb [-h] [--list] < CMD > ... positional arguments: < CMD > info Display package and citation information compile Compile ` kallisto ` and ` bustools ` binaries from source ref Build a kallisto index and transcript-to-gene mapping count Generate count matrices from a set of single-cell FASTQ files extract Extract reads that were pseudoaligned to specific genes/transcripts (or extract all reads that were / were not pseudoaligned) kb ref : generate a pseudoalignment index The kb ref command takes in a species annotation file (GTF) and associated genome (FASTA) and builds a species-specific index for pseudoalignment of reads. This must be run before kb count . Internally, kb ref extracts the coding regions from the GTF and builds a transcriptome FASTA that is then indexed with kallisto index . kb ref -i index.idx -g t2g.txt -f1 transcriptome.fa < GENOME > < GENOME_ANNOTATION > <GENOME> refers to a genome file (FASTA). For example, the zebrafish genome is hosted by ensembl and can be downloaded here <GENOME_ANNOTATION> refers to a genome annotation file (GTF) For example, the zebrafish genome annotation file is hosted by ensembl and can be downloaded here Note: The latest genome annotation and genome file for every species on ensembl can be found with the gget command-line tool. Prebuilt indices are available at https://github.com/pachterlab/kallisto-transcriptome-indices Examples # Index the transcriptome from genome FASTA (genome.fa.gz) and GTF (annotation.gtf.gz) $ kb ref -i index.idx -g t2g.txt -f1 transcriptome.fa genome.fa.gz annotation.gtf.gz # An example for downloading a prebuilt reference for mouse $ kb ref -d mouse -i index.idx -g t2g.txt kb count : pseudoalign and count reads The kb count command takes in the pseudoalignment index (built with kb ref ) and sequencing reads generated by a sequencing machine to generate a count matrix. Internally, kb count runs numerous kallisto and bustools commands comprising a single-cell workflow for the specified technology that generated the sequencing reads. kb count -i index.idx -g t2g.txt -o out/ -x < TECHNOLOGY > < FASTQ FILE[s] > <TECHNOLOGY> refers to the assay that generated the sequencing reads. For a list of supported assays run kb --list <FASTQ FILE[s]> refers to the a list of FASTQ files generated Different assays will have a different number of FASTQ files Different assays will place the different features in different FASTQ files For example, sequencing a 10xv3 library on a NextSeq Illumina sequencer usually results in two FASTQ files. The R1.fastq.gz file (colloquially called "read 1") contains a 16 basepair cell barcode and a 12 basepair unique molecular identifier (UMI). The R2.fastq.gz file (colloquially called "read 2") contains the cDNA associated with the cell barcode-UMI pair in read 1. Examples # Quantify 10xv3 reads read1.fastq.gz and read2.fastq.gz $ kb count -i index.idx -g t2g.txt -o out/ -x 10xv3 read1.fastq.gz read2.fastq.gz kb info : display package and citation information The kb info command prints out package information including the version of kb-python , kallisto , and bustools along with their installation location. $ kb info kb_python 0.30.1 ... kallisto: 0.52.0 ... bustools: 0.45.1 ... ... kb compile : compile kallisto and bustools binaries from source The kb compile command grabs the latest kallisto and bustools source and compiles the binaries. Note : this is not required to run kb-python . Use cases kb-python facilitates fast and uniform pre-processing of single-cell sequencing data to answer relevant research questions. $ pip install kb-python gget ffq # Goal: quantify publicly available scRNAseq data $ kb ref -i index.idx -g t2g.txt -f1 transcriptome.fa $( gget ref --ftp -w dna,gtf homo_sapiens ) $ kb count -i index.idx -g t2g.txt -x 10xv3 -o out $( ffq --ftp SRR10668798 | jq -r ' .[] | .url ' | tr ' \n ' ' ' ) # -> count matrix in out/ folder # Goal: quantify 10xv2 feature barcode data, feature_barcodes.txt is a tab-delimited file # containing barcode_sequence<tab>barcode_name $ kb ref -i index.idx -g f2g.txt -f1 features.fa --workflow kite feature_barcodes.txt $ kb count -i index.idx -g f2b.txt -x 10xv2 -o out/ --workflow kite --h5ad R1.fastq.gz R2.fastq.gz # -> count matrix in out/ folder Submitted by @sbooeshaghi . Do you have a cool use case for kb-python ? Submit a PR (including the goal, code snippet, and your username) so that we can feature it here. Documentation and Tutorials Documentation and tutorials for kb-python usage are available at https://kallisto.readthedocs.io/en/latest/ . Contributing Thank you for wanting to improve kb-python ! If you have believe you've found a bug, please submit an issue. If you have a new feature you'd like to add to kb-python please create a pull request. Pull requests should contain a message detailing the exact changes made, the reasons for the change, and tests that check for the correctness of those changes. Cite If you use kb-python in a publication, please cite the following papers: kb-python & kallisto and/or bustools @article{sullivan2023kallisto, title={kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq}, author={Sullivan, Delaney K and Min, Kyung Hoi and Hj{\"o}rleifsson, Kristj{\'a}n Eldj{\'a}rn and Luebbert, Laura and Holley, Guillaume and Moses, Lambda and Gustafsson, Johan and Bray, Nicolas L and Pimentel, Harold and Booeshaghi, A Sina and others}, journal={bioRxiv}, pages={2023--11}, year={2023}, publisher={Cold Spring Harbor Laboratory} } bustools @article{melsted2021modular, title={ \href {https://doi.org/10.1038/s41587-021-00870-2}{Modular, efficient and constant-memory single-cell RNA-seq preprocessing}}, author={Melsted, P{ \' a}ll and Booeshaghi, A. Sina and Liu, Lauren and Gao, Fan and Lu, Lambda and Min, Kyung Hoi Joseph and da Veiga Beltrame, Eduardo and Hj{ \" o}rleifsson, Kristj{ \' a}n Eldj{ \' a}rn and Gehring, Jase and Pachter, Lior}, author+an={1=first;2=first,highlight}, journal={Nature biotechnology}, year={2021}, month={4}, day={1}, doi={https://doi.org/10.1038/s41587-021-00870-2} } kallisto @article{bray2016near, title={Near-optimal probabilistic RNA-seq quantification}, author={Bray, Nicolas L and Pimentel, Harold and Melsted, P{ \' a}ll and Pachter, Lior}, journal={Nature biotechnology}, volume={34}, number={5}, pages={525--527}, year={2016}, publisher={Nature Publishing Group} } kITE @article{booeshaghi2024quantifying, title={Quantifying orthogonal barcodes for sequence census assays}, author={Booeshaghi, A Sina and Min, Kyung Hoi and Gehring, Jase and Pachter, Lior}, journal={Bioinformatics Advances}, volume={4}, number={1}, pages={vbad181}, year={2024}, publisher={Oxford University Press} } BUS format @article{melsted2019barcode, title={The barcode, UMI, set format and BUStools}, author={Melsted, P{ \' a}ll and Ntranos, Vasilis and Pachter, Lior}, journal={Bioinformatics}, volume={35}, number={21}, pages={4472--4473}, year={2019}, publisher={Oxford University Press} } kb-python was inspired by Sten Linnarsson’s loompy fromfq command ( http://linnarssonlab.org/loompy/kallisto/index.html ) About A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing www.kallistobus.tools/ Topics scrna-seq kallisto single-cell-rna-seq rna-velocity-estimation bustools kb-python Resources Readme License BSD-2-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 187 stars Watchers 10 watching Forks 29 forks Report repository Releases 37 v0.30.1 Latest Mar 8, 2026 + 36 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 98.6% Jupyter Notebook 1.2% Other 0.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/pachterlab/kb_python +GitHub - pachterlab/kb_python: A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} pachterlab / kb_python Public Notifications You must be signed in to change notification settings Fork 29 Star 187 Code Issues 1 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights pachterlab/kb_python master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 649 Commits 649 Commits .github .github docs docs kb_python kb_python tests tests .gitattributes .gitattributes .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml LICENSE LICENSE MANIFEST.in MANIFEST.in Makefile Makefile README.md README.md codecov.yml codecov.yml dev-requirements.txt dev-requirements.txt readthedocs.yml readthedocs.yml requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README BSD-2-Clause license kb-python kb-python is a python package for processing single-cell RNA-sequencing. It wraps the kallisto | bustools single-cell RNA-seq command line tools in order to unify multiple processing workflows. kb-python was first developed by Kyung Hoi (Joseph) Min and A. Sina Booeshaghi while in Lior Pachter 's lab at Caltech. If you use kb-python in a publication please cite* : Melsted, P., Booeshaghi, A.S., et al. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nat Biotechnol 39, 813–818 (2021). https://doi.org/10.1038/s41587-021-00870-2 Installation The latest release can be installed with pip install kb-python The development version can be installed with pip install git+https://github.com/pachterlab/kb_python There are no prerequisite packages to install. The kallisto and bustools binaries are included with the package. Usage kb consists of five subcommands $ kb usage: kb [-h] [--list] < CMD > ... positional arguments: < CMD > info Display package and citation information compile Compile ` kallisto ` and ` bustools ` binaries from source ref Build a kallisto index and transcript-to-gene mapping count Generate count matrices from a set of single-cell FASTQ files extract Extract reads that were pseudoaligned to specific genes/transcripts (or extract all reads that were / were not pseudoaligned) kb ref : generate a pseudoalignment index The kb ref command takes in a species annotation file (GTF) and associated genome (FASTA) and builds a species-specific index for pseudoalignment of reads. This must be run before kb count . Internally, kb ref extracts the coding regions from the GTF and builds a transcriptome FASTA that is then indexed with kallisto index . kb ref -i index.idx -g t2g.txt -f1 transcriptome.fa < GENOME > < GENOME_ANNOTATION > <GENOME> refers to a genome file (FASTA). For example, the zebrafish genome is hosted by ensembl and can be downloaded here <GENOME_ANNOTATION> refers to a genome annotation file (GTF) For example, the zebrafish genome annotation file is hosted by ensembl and can be downloaded here Note: The latest genome annotation and genome file for every species on ensembl can be found with the gget command-line tool. Prebuilt indices are available at https://github.com/pachterlab/kallisto-transcriptome-indices Examples # Index the transcriptome from genome FASTA (genome.fa.gz) and GTF (annotation.gtf.gz) $ kb ref -i index.idx -g t2g.txt -f1 transcriptome.fa genome.fa.gz annotation.gtf.gz # An example for downloading a prebuilt reference for mouse $ kb ref -d mouse -i index.idx -g t2g.txt kb count : pseudoalign and count reads The kb count command takes in the pseudoalignment index (built with kb ref ) and sequencing reads generated by a sequencing machine to generate a count matrix. Internally, kb count runs numerous kallisto and bustools commands comprising a single-cell workflow for the specified technology that generated the sequencing reads. kb count -i index.idx -g t2g.txt -o out/ -x < TECHNOLOGY > < FASTQ FILE[s] > <TECHNOLOGY> refers to the assay that generated the sequencing reads. For a list of supported assays run kb --list <FASTQ FILE[s]> refers to the a list of FASTQ files generated Different assays will have a different number of FASTQ files Different assays will place the different features in different FASTQ files For example, sequencing a 10xv3 library on a NextSeq Illumina sequencer usually results in two FASTQ files. The R1.fastq.gz file (colloquially called "read 1") contains a 16 basepair cell barcode and a 12 basepair unique molecular identifier (UMI). The R2.fastq.gz file (colloquially called "read 2") contains the cDNA associated with the cell barcode-UMI pair in read 1. Examples # Quantify 10xv3 reads read1.fastq.gz and read2.fastq.gz $ kb count -i index.idx -g t2g.txt -o out/ -x 10xv3 read1.fastq.gz read2.fastq.gz kb info : display package and citation information The kb info command prints out package information including the version of kb-python , kallisto , and bustools along with their installation location. $ kb info kb_python 0.30.1 ... kallisto: 0.52.0 ... bustools: 0.45.1 ... ... kb compile : compile kallisto and bustools binaries from source The kb compile command grabs the latest kallisto and bustools source and compiles the binaries. Note : this is not required to run kb-python . Use cases kb-python facilitates fast and uniform pre-processing of single-cell sequencing data to answer relevant research questions. $ pip install kb-python gget ffq # Goal: quantify publicly available scRNAseq data $ kb ref -i index.idx -g t2g.txt -f1 transcriptome.fa $( gget ref --ftp -w dna,gtf homo_sapiens ) $ kb count -i index.idx -g t2g.txt -x 10xv3 -o out $( ffq --ftp SRR10668798 | jq -r ' .[] | .url ' | tr ' \n ' ' ' ) # -> count matrix in out/ folder # Goal: quantify 10xv2 feature barcode data, feature_barcodes.txt is a tab-delimited file # containing barcode_sequence<tab>barcode_name $ kb ref -i index.idx -g f2g.txt -f1 features.fa --workflow kite feature_barcodes.txt $ kb count -i index.idx -g f2b.txt -x 10xv2 -o out/ --workflow kite --h5ad R1.fastq.gz R2.fastq.gz # -> count matrix in out/ folder Submitted by @sbooeshaghi . Do you have a cool use case for kb-python ? Submit a PR (including the goal, code snippet, and your username) so that we can feature it here. Documentation and Tutorials Documentation and tutorials for kb-python usage are available at https://kallisto.readthedocs.io/en/latest/ . Contributing Thank you for wanting to improve kb-python ! If you have believe you've found a bug, please submit an issue. If you have a new feature you'd like to add to kb-python please create a pull request. Pull requests should contain a message detailing the exact changes made, the reasons for the change, and tests that check for the correctness of those changes. Cite If you use kb-python in a publication, please cite the following papers: kb-python & kallisto and/or bustools @article{sullivan2023kallisto, title={kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq}, author={Sullivan, Delaney K and Min, Kyung Hoi and Hj{\"o}rleifsson, Kristj{\'a}n Eldj{\'a}rn and Luebbert, Laura and Holley, Guillaume and Moses, Lambda and Gustafsson, Johan and Bray, Nicolas L and Pimentel, Harold and Booeshaghi, A Sina and others}, journal={bioRxiv}, pages={2023--11}, year={2023}, publisher={Cold Spring Harbor Laboratory} } bustools @article{melsted2021modular, title={ \href {https://doi.org/10.1038/s41587-021-00870-2}{Modular, efficient and constant-memory single-cell RNA-seq preprocessing}}, author={Melsted, P{ \' a}ll and Booeshaghi, A. Sina and Liu, Lauren and Gao, Fan and Lu, Lambda and Min, Kyung Hoi Joseph and da Veiga Beltrame, Eduardo and Hj{ \" o}rleifsson, Kristj{ \' a}n Eldj{ \' a}rn and Gehring, Jase and Pachter, Lior}, author+an={1=first;2=first,highlight}, journal={Nature biotechnology}, year={2021}, month={4}, day={1}, doi={https://doi.org/10.1038/s41587-021-00870-2} } kallisto @article{bray2016near, title={Near-optimal probabilistic RNA-seq quantification}, author={Bray, Nicolas L and Pimentel, Harold and Melsted, P{ \' a}ll and Pachter, Lior}, journal={Nature biotechnology}, volume={34}, number={5}, pages={525--527}, year={2016}, publisher={Nature Publishing Group} } kITE @article{booeshaghi2024quantifying, title={Quantifying orthogonal barcodes for sequence census assays}, author={Booeshaghi, A Sina and Min, Kyung Hoi and Gehring, Jase and Pachter, Lior}, journal={Bioinformatics Advances}, volume={4}, number={1}, pages={vbad181}, year={2024}, publisher={Oxford University Press} } BUS format @article{melsted2019barcode, title={The barcode, UMI, set format and BUStools}, author={Melsted, P{ \' a}ll and Ntranos, Vasilis and Pachter, Lior}, journal={Bioinformatics}, volume={35}, number={21}, pages={4472--4473}, year={2019}, publisher={Oxford University Press} } kb-python was inspired by Sten Linnarsson’s loompy fromfq command ( http://linnarssonlab.org/loompy/kallisto/index.html ) About A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing www.kallistobus.tools/ Topics scrna-seq kallisto single-cell-rna-seq rna-velocity-estimation bustools kb-python Resources Readme License BSD-2-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 187 stars Watchers 10 watching Forks 29 forks Report repository Releases 37 v0.30.1 Latest Mar 8, 2026 + 36 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 98.6% Jupyter Notebook 1.2% Other 0.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge kb-python --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +kb-python 0.24.4 py_0 +--------------------- +file name : kb-python-0.24.4-py_0.tar.bz2 +name : kb-python +version : 0.24.4 +build : py_0 +build number: 0 +size : 28.2 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.24.4-py_0.tar.bz2 +md5 : 1afbd9c39debd37e9b607d3423054a00 +timestamp : 2020-10-21 12:12:46 UTC +dependencies: + - anndata >=0.6.22.post1 + - loompy >=3.0.6 + - python >=3.6 + - requests >=2.19.0 + - tqdm >=4.39.0 + + +kb-python 0.25.0 py_0 +--------------------- +file name : kb-python-0.25.0-py_0.tar.bz2 +name : kb-python +version : 0.25.0 +build : py_0 +build number: 0 +size : 41.1 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.25.0-py_0.tar.bz2 +md5 : caab1a8b9dfbb4c472ce4d25af269c6d +timestamp : 2020-11-19 15:28:52 UTC +dependencies: + - anndata >=0.6.22.post1 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - numpy >=1.17.2 + - plotly >=4.5.0 + - python >=3.6 + - requests >=2.19.0 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.25.1 py_0 +--------------------- +file name : kb-python-0.25.1-py_0.tar.bz2 +name : kb-python +version : 0.25.1 +build : py_0 +build number: 0 +size : 41.1 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.25.1-py_0.tar.bz2 +md5 : 9ec21d2ebc695cb6ce89a6816afcc9f9 +timestamp : 2021-01-08 21:27:48 UTC +dependencies: + - anndata >=0.6.22.post1 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - numpy >=1.17.2 + - plotly >=4.5.0 + - python >=3.6 + - requests >=2.19.0 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.26.0 pyhdfd78af_0 +----------------------------- +file name : kb-python-0.26.0-pyhdfd78af_0.tar.bz2 +name : kb-python +version : 0.26.0 +build : pyhdfd78af_0 +build number: 0 +size : 41.2 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.26.0-pyhdfd78af_0.tar.bz2 +md5 : 2eb864fe653dfef60190dbc0953f7304 +timestamp : 2021-04-14 08:05:58 UTC +dependencies: + - anndata >=0.6.22.post1 + - bustools >=0.40.0 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - kallisto >=0.46.2 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - numpy >=1.17.2 + - plotly >=4.5.0 + - python >=3.6 + - requests >=2.19.0 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.26.1 pyhdfd78af_0 +----------------------------- +file name : kb-python-0.26.1-pyhdfd78af_0.tar.bz2 +name : kb-python +version : 0.26.1 +build : pyhdfd78af_0 +build number: 0 +size : 6.7 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.26.1-pyhdfd78af_0.tar.bz2 +md5 : 3e6753ee7927d517ec4e4e423c126ffb +timestamp : 2021-06-03 09:22:35 UTC +dependencies: + - anndata >=0.6.22.post1 + - bustools >=0.40.0 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - kallisto >=0.46.2 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - ngs-tools >=1.3.0 + - numpy >=1.17.2 + - pandas >=1.0.0 + - plotly >=4.5.0 + - python >=3.6 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.26.2 pyhdfd78af_0 +----------------------------- +file name : kb-python-0.26.2-pyhdfd78af_0.tar.bz2 +name : kb-python +version : 0.26.2 +build : pyhdfd78af_0 +build number: 0 +size : 6.7 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.26.2-pyhdfd78af_0.tar.bz2 +md5 : 14dc62f0f553f027305522124b081a97 +timestamp : 2021-06-04 19:25:04 UTC +dependencies: + - anndata >=0.6.22.post1 + - bustools >=0.40.0 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - kallisto >=0.46.2 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - ngs-tools >=1.3.0 + - numpy >=1.17.2 + - pandas >=1.0.0 + - plotly >=4.5.0 + - python >=3.6 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.26.3 pyhdfd78af_0 +----------------------------- +file name : kb-python-0.26.3-pyhdfd78af_0.tar.bz2 +name : kb-python +version : 0.26.3 +build : pyhdfd78af_0 +build number: 0 +size : 6.7 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.26.3-pyhdfd78af_0.tar.bz2 +md5 : 813b83fdec28a23dc3f705361e235a22 +timestamp : 2021-06-10 14:23:18 UTC +dependencies: + - anndata >=0.6.22.post1 + - bustools >=0.40.0 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - kallisto >=0.46.2 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - ngs-tools >=1.3.0 + - numpy >=1.17.2 + - pandas >=1.0.0 + - plotly >=4.5.0 + - python >=3.6 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.26.4 pyhdfd78af_0 +----------------------------- +file name : kb-python-0.26.4-pyhdfd78af_0.tar.bz2 +name : kb-python +version : 0.26.4 +build : pyhdfd78af_0 +build number: 0 +size : 6.7 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.26.4-pyhdfd78af_0.tar.bz2 +md5 : 6cc283957468e0752c00fe664a0dde32 +timestamp : 2021-09-24 20:21:21 UTC +dependencies: + - anndata >=0.6.22.post1 + - bustools >=0.40.0 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - kallisto >=0.46.2 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - ngs-tools >=1.3.0 + - numpy >=1.17.2 + - pandas >=1.0.0 + - plotly >=4.5.0 + - python >=3.6 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.27.0 pyhdfd78af_0 +----------------------------- +file name : kb-python-0.27.0-pyhdfd78af_0.tar.bz2 +name : kb-python +version : 0.27.0 +build : pyhdfd78af_0 +build number: 0 +size : 6.8 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.27.0-pyhdfd78af_0.tar.bz2 +md5 : 270f8347cbd9cba02a0d16951a18a424 +timestamp : 2022-01-19 10:04:15 UTC +dependencies: + - anndata >=0.6.22.post1 + - bustools >=0.40.0 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - kallisto >=0.46.2 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - ngs-tools >=1.5.11 + - numpy >=1.17.2 + - pandas >=1.0.0 + - plotly >=4.5.0 + - python >=3.6 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.27.1 pyhdfd78af_0 +----------------------------- +file name : kb-python-0.27.1-pyhdfd78af_0.tar.bz2 +name : kb-python +version : 0.27.1 +build : pyhdfd78af_0 +build number: 0 +size : 6.8 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.27.1-pyhdfd78af_0.tar.bz2 +md5 : ca6d9dfa801ff97529b7e20356d6e6cd +timestamp : 2022-03-08 08:28:11 UTC +dependencies: + - anndata >=0.6.22.post1 + - bustools >=0.40.0 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - kallisto >=0.46.2 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - ngs-tools >=1.5.11 + - numpy >=1.17.2 + - pandas >=1.0.0 + - plotly >=4.5.0 + - python >=3.6 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.27.2 pyhdfd78af_0 +----------------------------- +file name : kb-python-0.27.2-pyhdfd78af_0.tar.bz2 +name : kb-python +version : 0.27.2 +build : pyhdfd78af_0 +build number: 0 +size : 6.9 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.27.2-pyhdfd78af_0.tar.bz2 +md5 : f8a57f4bbd46dc2fb2b96ce31dd0f135 +timestamp : 2022-03-28 15:37:22 UTC +dependencies: + - anndata >=0.6.22.post1 + - bustools >=0.40.0 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - kallisto >=0.46.2 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - ngs-tools >=1.5.11 + - numpy >=1.17.2 + - pandas >=1.0.0 + - plotly >=4.5.0 + - python >=3.6 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.27.3 pyhdfd78af_0 +----------------------------- +file name : kb-python-0.27.3-pyhdfd78af_0.tar.bz2 +name : kb-python +version : 0.27.3 +build : pyhdfd78af_0 +build number: 0 +size : 6.8 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.27.3-pyhdfd78af_0.tar.bz2 +md5 : 7f9ad8f23c28dad52f5a95f39ce9665a +timestamp : 2022-07-08 07:37:30 UTC +dependencies: + - anndata >=0.6.22.post1 + - bustools >=0.40.0 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - kallisto >=0.46.2 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - ngs-tools >=1.5.11 + - numpy >=1.17.2 + - pandas >=1.0.0 + - plotly >=4.5.0 + - python >=3.6 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.27.3 pyhdfd78af_1 +----------------------------- +file name : kb-python-0.27.3-pyhdfd78af_1.tar.bz2 +name : kb-python +version : 0.27.3 +build : pyhdfd78af_1 +build number: 1 +size : 6.8 MB +license : BSD +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/kb-python-0.27.3-pyhdfd78af_1.tar.bz2 +md5 : 6d0b093923c381de863d6755a0790b12 +timestamp : 2022-11-23 08:40:16 UTC +dependencies: + - anndata >=0.6.22.post1 + - bustools >=0.40.0 + - h5py >=2.10.0 + - jinja2 >2.10.1 + - kallisto >=0.46.2 + - loompy >=3.0.6 + - nbconvert >=5.6.0 + - nbformat >=4.4.0 + - ngs-tools >=1.5.11 + - numpy >=1.17.2 + - pandas >=1.0.0 + - plotly >=4.5.0 + - python >=3.6 + - requests >=2.22.0 + - scanpy >=1.4.4.post1 + - scikit-learn >=0.21.3 + - tqdm >=4.39.0 + + +kb-python 0.28.0 pyhdfd78af_0 +----------------------------- +file name : kb-python-0.28.0-pyhdfd78af_0.tar.bz2 +name : kb-python +version : 0.28.0 +build : pyhdfd78af_0 +build number: 0 +size : 11.9 MB +license : BSD-2-Clause +subdir : noarch +url : https:/ diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/khipu-metabolomics.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/khipu-metabolomics.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8861400dafbff8bf106b6b188bef4729be8321e5 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/khipu-metabolomics.manual_bundle.txt @@ -0,0 +1,128 @@ +# Tool: khipu-metabolomics +software_name: khipu-metabolomics +tier: T1 +domain: metabolomics +downloads: 3359 +summary: Python library for generalized, low-level annotation of MS metabolomics. +description: Python library for generalized, low-level annotation of MS metabolomics. +dependencies: intervaltree, isocor, mass2chem, matplotlib-base, networkx, numpy, pandas, python >=3.7, requests, scipy, treelib +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/shuzhao-li/khipu +doc_url: +dev_url: https://github.com/shuzhao-li/khipu + +## URL Docs Extract +### https://github.com/shuzhao-li/khipu +GitHub - shuzhao-li-lab/khipu: a Python library for generalized, low-level annotation of MS metabolomics · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} shuzhao-li-lab / khipu Public Notifications You must be signed in to change notification settings Fork 3 Star 9 Code Issues 25 Pull requests 0 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights shuzhao-li-lab/khipu main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 106 Commits 106 Commits doc doc docs docs khipu khipu notebooks notebooks testdata testdata LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md requirements.txt requirements.txt setup.py setup.py View all files Repository files navigation README License khipu: generalized tree structure to annotate untargeted metabolomics and stable isotope tracing data Pre-annotation tool to annotate degenerate ions in relationships to the original compound and infer neutral mass. The initial version was described in Li and Zheng (2023). Analytical chemistry, 95(15), pp.6212-6217 . This applies to regular LC-MS data, but also enables easy analysis of isotope tracing and chemical labeling data. Different applications may require different parameters. A web server for isotope tracing data (described in [Mitchell et al (2024) Journal of the American Society for Mass Spectrometry. https://doi.org/10.1021/jasms.4c00175 ]) is now available at https://metabolomics.cloud/khipu/ . Implementation overview Khipu is developed as an open source Python 3 package, and available to install from the standard PyPi repository via the pip tool. It is freely available on GitHub ( https://github.com/shuzhao-li/khipu ) under a BSD 3-Clause License. The graph operations are supported by the networkx library, tree visualization aided by the treelib library. Khipu uses our package mass2chem for search functions. The data model of “empirical compound” is described in the metDataModel package. The package is designed in a modular way to encourage reuse. The classes of Weavor and Khipu contain main algorithms, supported by numerous utility functions. All functions are documented in the source via docstrings. Examples of reuse are given in wrapper functions and in Jupyter notebooks. It can be run as a standalone command line tool. Users can use a feature table from any preprocessing tool as input and get annotated empirical compounds in JSON and tab delimited formats. Installation and Use Install as a package (some systems may require pip3): pip install khipu-metabolomics Run as a command line tool after installation: khipu -i testdata/ecoli_pos.tsv -o this_test This will output pre-annotation to two files of JSON and tab delimited formats, this_test.json and this_test.tsv. Run from source code: python3 -m khipu.main -i testdata/ecoli_pos.tsv -o this_test Run test: python3 -m khipu.test (This downloads and uses test data from GitHub.) Best used as a library for software development or in a Jupyter Notebook for data analysis. Demo notebooks We have provided multiple demo notebooks under notebooks/ They include algorithm demostrations, data analysis examples, use of custom isotope and adduct patterns. Algorithm overview Start with an initial list of isotope patterns and adduct patterns (see khipu grid below). Search feature list to get all pairs that match any of the pattern. The initial adduct patterns are trimmed to reduce ambiguity. Connect all pattern-matched feature pairs to an overall network, which is further partitioned into connected subnetworks. Each subnetwork becomes a khipu instance. The subnetwork is inspected, redundant nodes removed, and converted to an optimal tree structure (see below). A khipu is essentially an 'empirical compound' that is used for downstream annotation and analysis. This library supports tree and grid visualization in plain text. Once imported to a Jupyter Notebook, one can use enhanced visualization schemes. The library can also be used by others for extended tools. Our data processing tool, asari, uses khipu for preannotation. Additional documentation, more for developers, is provided under doc/ . Assignment of ion species in a khipu to grid Separate isotope edges and adduct edges. The isotope edges form their own groups by shared nodes, each group belong to one adduct type. Each group of connected isotope edges is treated as one "branch". Establish a "trunk" of adducts with a root and a path for adducts, by optimizing the number of nodes explained. Assign each isotopic branch to the adduct trunk. Re-align isotopes in all branches to establish optimal match to the khipu grid. Based on available ions and the theoretical "khipu grid", the neutral mass can be obtained via linear regression. Some ions may come into the initial network by mistakes or unresolved signals. The are removed from the established khipu, and sent off to form a new khipu. The khipu grid Initial grid may look like this: M+H[+] M+NH4[+] M+Na[+] M+HCl+H[+] M+K[+] M+ACN+H[+] M0 1.007276 18.033826 22.989276 36.983976 38.963158 42.033825 13C/12C 2.010631 19.037181 23.992631 37.987331 39.966513 43.037180 13C/12C*2 3.013986 20.040536 24.995986 38.990686 40.969868 44.040535 13C/12C*3 4.017341 21.043891 25.999341 39.994041 41.973223 45.043890 13C/12C*4 5.020696 22.047246 27.002696 40.997396 42.976578 46.047245 13C/12C*5 6.024051 23.050601 28.006051 42.000751 43.979933 47.050600 13C/12C*6 7.027406 24.053956 29.009406 43.004106 44.983288 48.053955 This can be extended by searching for additional ions. But the core construction should be done first. Applicable to isotope tracing The search pattern for isotopes is often dependent on the biochemical experiment. Users can overwrite the default by supplying their search patterns (see demo notebooks). Search patterns are separate from search functions, lending flexibility to data analysis. The next step is to apply Khipu to chemical derivatization experiments. In chemical derivatization experiments, the origin compound and derivatized compound can be both measured in the LC-MS data. We have separate khipu trees for each, then link them by the m/z shift from derivatization. Because derivatization is a reaction that occurs before LC-MS, and LC-MS measures whatever compounds that are present in samples. Test data Three datasets are included under testdata/. All three tables were generated by asari v1.9.2. The automated khipu.test downloads ecoli_pos.tsv from GitHub remotely. The ecoli_pos.tsv was generated by Li lab using the credentialed E. coli sample from Cambridge Isotopes. The yeast datasets were from the NetID paper by Rabinowitz lab. The yeast_neg table is features that are filted by SNR > 100 to serve as a cleaner demo. Input tables are tab delimited text files. The first columns are feature ID, m/z, rtime, followed by intensities. Users can specify the start column and end column of intensity data. Detailed use of command and parameters >>> khipu -h usage: main.py [-h] [-v] [-m MODE] [--ppm PPM] [--rtol RTOL] [-i INPUT] [-s START] [-e END] [-o OUTPUT] khipu, annotating metabolomics features to empCpds optional arguments: -h, --help show this help message and exit -v, --version print version and exit -m MODE, --mode MODE mode of ionization, pos or neg --ppm PPM mass precision in ppm (part per million), same as mz_tolerance_ppm --rtol RTOL tolerance of retention time match, arbitrary unit dependent on preprocessing tool -i INPUT, --input INPUT input file as feature table -s START, --start START start column for intensity in input table -e END, --end END end column for intensity in input table -o OUTPUT, --output OUTPUT prefix of output files What's "khipu"? Khipu is a recording device using knots, often 2-level of strings, historically used by people in Andean South America, includign Inca ( https://en.wikipedia.org/wiki/Quipu ). The format is similar to how we represent isotopes and adducts in our data. We chose "khipu" over the spelling of "quipu", to pay respect to the indigenous people. Khipu is part of The Asari Project. asari (Source code: https://github.com/shuzhao-li/asari , Package Repository: https://pypi.org/project/asari-metabolomics/ ) metDataModel: data models for metabolomics ( https://github.com/shuzhao-li-lab/metDataModel ) mass2chem: common utilities in interpreting mass spectrometry data, annotation ( https://github.com/shuzhao-li-lab/mass2chem ) khipu: a Python library for generalized, low-level annotation of MS metabolomics ( https://github.com/shuzhao-li-lab/khipu ) JMS: Json's Metabolite Services. Search functions, annotation and metabolic models ( https://github.com/shuzhao-li-lab/JMS ) pcpfm pipeline ( https://github.com/shuzhao-li-lab/PythonCentricPipelineForMetabolomics ) asari-x: the eXposome miner (to be released) About a Python library for generalized, low-level annotation of MS metabolomics Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 9 stars Watchers 1 watching Forks 3 forks Report repository Releases No releases published Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 92.1% Jupyter Notebook 7.9% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/shuzhao-li/khipu +GitHub - shuzhao-li-lab/khipu: a Python library for generalized, low-level annotation of MS metabolomics · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} shuzhao-li-lab / khipu Public Notifications You must be signed in to change notification settings Fork 3 Star 9 Code Issues 25 Pull requests 0 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights shuzhao-li-lab/khipu main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 106 Commits 106 Commits doc doc docs docs khipu khipu notebooks notebooks testdata testdata LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md requirements.txt requirements.txt setup.py setup.py View all files Repository files navigation README License khipu: generalized tree structure to annotate untargeted metabolomics and stable isotope tracing data Pre-annotation tool to annotate degenerate ions in relationships to the original compound and infer neutral mass. The initial version was described in Li and Zheng (2023). Analytical chemistry, 95(15), pp.6212-6217 . This applies to regular LC-MS data, but also enables easy analysis of isotope tracing and chemical labeling data. Different applications may require different parameters. A web server for isotope tracing data (described in [Mitchell et al (2024) Journal of the American Society for Mass Spectrometry. https://doi.org/10.1021/jasms.4c00175 ]) is now available at https://metabolomics.cloud/khipu/ . Implementation overview Khipu is developed as an open source Python 3 package, and available to install from the standard PyPi repository via the pip tool. It is freely available on GitHub ( https://github.com/shuzhao-li/khipu ) under a BSD 3-Clause License. The graph operations are supported by the networkx library, tree visualization aided by the treelib library. Khipu uses our package mass2chem for search functions. The data model of “empirical compound” is described in the metDataModel package. The package is designed in a modular way to encourage reuse. The classes of Weavor and Khipu contain main algorithms, supported by numerous utility functions. All functions are documented in the source via docstrings. Examples of reuse are given in wrapper functions and in Jupyter notebooks. It can be run as a standalone command line tool. Users can use a feature table from any preprocessing tool as input and get annotated empirical compounds in JSON and tab delimited formats. Installation and Use Install as a package (some systems may require pip3): pip install khipu-metabolomics Run as a command line tool after installation: khipu -i testdata/ecoli_pos.tsv -o this_test This will output pre-annotation to two files of JSON and tab delimited formats, this_test.json and this_test.tsv. Run from source code: python3 -m khipu.main -i testdata/ecoli_pos.tsv -o this_test Run test: python3 -m khipu.test (This downloads and uses test data from GitHub.) Best used as a library for software development or in a Jupyter Notebook for data analysis. Demo notebooks We have provided multiple demo notebooks under notebooks/ They include algorithm demostrations, data analysis examples, use of custom isotope and adduct patterns. Algorithm overview Start with an initial list of isotope patterns and adduct patterns (see khipu grid below). Search feature list to get all pairs that match any of the pattern. The initial adduct patterns are trimmed to reduce ambiguity. Connect all pattern-matched feature pairs to an overall network, which is further partitioned into connected subnetworks. Each subnetwork becomes a khipu instance. The subnetwork is inspected, redundant nodes removed, and converted to an optimal tree structure (see below). A khipu is essentially an 'empirical compound' that is used for downstream annotation and analysis. This library supports tree and grid visualization in plain text. Once imported to a Jupyter Notebook, one can use enhanced visualization schemes. The library can also be used by others for extended tools. Our data processing tool, asari, uses khipu for preannotation. Additional documentation, more for developers, is provided under doc/ . Assignment of ion species in a khipu to grid Separate isotope edges and adduct edges. The isotope edges form their own groups by shared nodes, each group belong to one adduct type. Each group of connected isotope edges is treated as one "branch". Establish a "trunk" of adducts with a root and a path for adducts, by optimizing the number of nodes explained. Assign each isotopic branch to the adduct trunk. Re-align isotopes in all branches to establish optimal match to the khipu grid. Based on available ions and the theoretical "khipu grid", the neutral mass can be obtained via linear regression. Some ions may come into the initial network by mistakes or unresolved signals. The are removed from the established khipu, and sent off to form a new khipu. The khipu grid Initial grid may look like this: M+H[+] M+NH4[+] M+Na[+] M+HCl+H[+] M+K[+] M+ACN+H[+] M0 1.007276 18.033826 22.989276 36.983976 38.963158 42.033825 13C/12C 2.010631 19.037181 23.992631 37.987331 39.966513 43.037180 13C/12C*2 3.013986 20.040536 24.995986 38.990686 40.969868 44.040535 13C/12C*3 4.017341 21.043891 25.999341 39.994041 41.973223 45.043890 13C/12C*4 5.020696 22.047246 27.002696 40.997396 42.976578 46.047245 13C/12C*5 6.024051 23.050601 28.006051 42.000751 43.979933 47.050600 13C/12C*6 7.027406 24.053956 29.009406 43.004106 44.983288 48.053955 This can be extended by searching for additional ions. But the core construction should be done first. Applicable to isotope tracing The search pattern for isotopes is often dependent on the biochemical experiment. Users can overwrite the default by supplying their search patterns (see demo notebooks). Search patterns are separate from search functions, lending flexibility to data analysis. The next step is to apply Khipu to chemical derivatization experiments. In chemical derivatization experiments, the origin compound and derivatized compound can be both measured in the LC-MS data. We have separate khipu trees for each, then link them by the m/z shift from derivatization. Because derivatization is a reaction that occurs before LC-MS, and LC-MS measures whatever compounds that are present in samples. Test data Three datasets are included under testdata/. All three tables were generated by asari v1.9.2. The automated khipu.test downloads ecoli_pos.tsv from GitHub remotely. The ecoli_pos.tsv was generated by Li lab using the credentialed E. coli sample from Cambridge Isotopes. The yeast datasets were from the NetID paper by Rabinowitz lab. The yeast_neg table is features that are filted by SNR > 100 to serve as a cleaner demo. Input tables are tab delimited text files. The first columns are feature ID, m/z, rtime, followed by intensities. Users can specify the start column and end column of intensity data. Detailed use of command and parameters >>> khipu -h usage: main.py [-h] [-v] [-m MODE] [--ppm PPM] [--rtol RTOL] [-i INPUT] [-s START] [-e END] [-o OUTPUT] khipu, annotating metabolomics features to empCpds optional arguments: -h, --help show this help message and exit -v, --version print version and exit -m MODE, --mode MODE mode of ionization, pos or neg --ppm PPM mass precision in ppm (part per million), same as mz_tolerance_ppm --rtol RTOL tolerance of retention time match, arbitrary unit dependent on preprocessing tool -i INPUT, --input INPUT input file as feature table -s START, --start START start column for intensity in input table -e END, --end END end column for intensity in input table -o OUTPUT, --output OUTPUT prefix of output files What's "khipu"? Khipu is a recording device using knots, often 2-level of strings, historically used by people in Andean South America, includign Inca ( https://en.wikipedia.org/wiki/Quipu ). The format is similar to how we represent isotopes and adducts in our data. We chose "khipu" over the spelling of "quipu", to pay respect to the indigenous people. Khipu is part of The Asari Project. asari (Source code: https://github.com/shuzhao-li/asari , Package Repository: https://pypi.org/project/asari-metabolomics/ ) metDataModel: data models for metabolomics ( https://github.com/shuzhao-li-lab/metDataModel ) mass2chem: common utilities in interpreting mass spectrometry data, annotation ( https://github.com/shuzhao-li-lab/mass2chem ) khipu: a Python library for generalized, low-level annotation of MS metabolomics ( https://github.com/shuzhao-li-lab/khipu ) JMS: Json's Metabolite Services. Search functions, annotation and metabolic models ( https://github.com/shuzhao-li-lab/JMS ) pcpfm pipeline ( https://github.com/shuzhao-li-lab/PythonCentricPipelineForMetabolomics ) asari-x: the eXposome miner (to be released) About a Python library for generalized, low-level annotation of MS metabolomics Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 9 stars Watchers 1 watching Forks 3 forks Report repository Releases No releases published Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 92.1% Jupyter Notebook 7.9% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge khipu-metabolomics --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +khipu-metabolomics 0.7.5 pyhdfd78af_0 +------------------------------------- +file name : khipu-metabolomics-0.7.5-pyhdfd78af_0.tar.bz2 +name : khipu-metabolomics +version : 0.7.5 +build : pyhdfd78af_0 +build number: 0 +size : 1.4 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/khipu-metabolomics-0.7.5-pyhdfd78af_0.tar.bz2 +md5 : e1695267679aa9ab0232fe4a46d1d6ef +timestamp : 2023-10-09 07:42:40 UTC +dependencies: + - mass2chem + - networkx + - pandas + - python >=3.7 + - treelib + + +khipu-metabolomics 2.0.1 pyhdfd78af_0 +------------------------------------- +file name : khipu-metabolomics-2.0.1-pyhdfd78af_0.tar.bz2 +name : khipu-metabolomics +version : 2.0.1 +build : pyhdfd78af_0 +build number: 0 +size : 1.4 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/khipu-metabolomics-2.0.1-pyhdfd78af_0.tar.bz2 +md5 : 8f9e3f27f0ed7c81c4cb4269e9d58d90 +timestamp : 2024-07-14 15:43:41 UTC +dependencies: + - intervaltree + - isocor + - mass2chem + - matplotlib + - networkx + - numpy + - pandas + - python >=3.7 + - requests + - scipy + - treelib + + +khipu-metabolomics 2.0.2 pyhdfd78af_0 +------------------------------------- +file name : khipu-metabolomics-2.0.2-pyhdfd78af_0.tar.bz2 +name : khipu-metabolomics +version : 2.0.2 +build : pyhdfd78af_0 +build number: 0 +size : 1.4 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/khipu-metabolomics-2.0.2-pyhdfd78af_0.tar.bz2 +md5 : 85efffd7f8eedff070347e0e4599dec8 +timestamp : 2024-07-19 02:07:12 UTC +dependencies: + - intervaltree + - isocor + - mass2chem + - matplotlib-base + - networkx + - numpy + - pandas + - python >=3.7 + - requests + - scipy + - treelib + + +khipu-metabolomics 2.0.4 pyhdfd78af_0 +------------------------------------- +file name : khipu-metabolomics-2.0.4-pyhdfd78af_0.tar.bz2 +name : khipu-metabolomics +version : 2.0.4 +build : pyhdfd78af_0 +build number: 0 +size : 1.4 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/khipu-metabolomics-2.0.4-pyhdfd78af_0.tar.bz2 +md5 : 442f5a9da5aa59c08cbe521fbd4f0fe3 +timestamp : 2025-07-30 21:41:31 UTC +dependencies: + - intervaltree + - isocor + - mass2chem + - matplotlib-base + - networkx + - numpy + - pandas + - python >=3.7 + - requests + - scipy + - treelib diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kmc.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kmc.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f38a100a32d0cd4b5d43421d3d36e537a2a0714 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kmc.manual_bundle.txt @@ -0,0 +1,530 @@ +# Tool: kmc +software_name: kmc +tier: T1 +domain: t1_backfill_overall +downloads: 123799 +summary: Tools for efficient k-mer counting and filtering of reads based on k-mer content. +description: KMC is a utility designed for counting k-mers (sequences +of consecutive k symbols) in a set of DNA sequences. KMC tools allow performing various operations on k-mers sets. +dependencies: libgcc >=13, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, python <3.11 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/refresh-bio/kmc +doc_url: +dev_url: https://github.com/refresh-bio/kmc + +## CLI Help Source +cli:kmc +## CLI Help Content +$ conda run -n bioenv_cli kmc --help +[rc=0] +K-Mer Counter (KMC) ver. 3.2.4 (2024-02-09) +Usage: + kmc [options] + kmc [options] <@input_file_names> +Parameters: + input_file_name - single file in specified (-f switch) format (gziped or not) + @input_file_names - file name with list of input files in specified (-f switch) format (gziped or not) +Options: + -v - verbose mode (shows all parameter settings); default: false + -k - k-mer length (k from 1 to 256; default: 25) + -m - max amount of RAM in GB (from 1 to 1024); default: 12 + -sm - use strict memory mode (memory limit from -m switch will not be exceeded) + -hc - count homopolymer compressed k-mers (approximate and experimental) + -p - signature length (5, 6, 7, 8, 9, 10, 11); default: 9 + -f - input in FASTA format (-fa), FASTQ format (-fq), multi FASTA (-fm) or BAM (-fbam) or KMC(-fkmc); default: FASTQ + -ci - exclude k-mers occurring less than times (default: 2) + -cs - maximal value of a counter (default: 255) + -cx - exclude k-mers occurring more of than times (default: 1e9) + -b - turn off transformation of k-mers into canonical form + -r - turn on RAM-only mode + -n - number of bins + -t - total number of threads (default: no. of CPU cores) + -sf - number of FASTQ reading threads + -sp - number of splitting threads + -sr - number of threads for 2nd stage + -j - file name with execution summary in JSON format + -w - without output + -o - output in KMC of KFF format; default: KMC + -hp - hide percentage progress (default: false) + -e - only estimate histogram of k-mers occurrences instead of exact k-mer counting + --opt-out-size - optimize output database size (may increase running time) +Example: +kmc -k27 -m24 NA19238.fastq NA.res /data/kmc_tmp_dir/ +kmc -k27 -m24 @files.lst NA.res /data/kmc_tmp_dir/ + + + +## URL Docs Extract +### https://github.com/refresh-bio/kmc +GitHub - refresh-bio/KMC: Fast and frugal disk based k-mer counter · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} refresh-bio / KMC Public Notifications You must be signed in to change notification settings Fork 83 Star 331 Code Issues 96 Pull requests 5 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights refresh-bio/KMC master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 320 Commits 320 Commits .github/ workflows .github/ workflows 3rd_party 3rd_party doc/ kmc_tools doc/ kmc_tools kmc_CLI kmc_CLI kmc_api kmc_api kmc_core kmc_core kmc_dump kmc_dump kmc_dump_sample kmc_dump_sample kmc_tools kmc_tools py_kmc_api py_kmc_api tests tests .gitattributes .gitattributes .gitignore .gitignore .gitmodules .gitmodules API.pdf API.pdf Makefile Makefile README.md README.md build_release.py build_release.py kmc.sln kmc.sln kmc_tools.pdf kmc_tools.pdf View all files Repository files navigation README KMC KMC is a disk-based program for counting k-mers from (possibly gzipped) FASTQ/FASTA files. KMC is one of many projects developed by REFRESH Bioinformatics Group . For accessing k-mers stored in database produced by KMC there is an API (kmc_api directory). Note that for KMC versions 0.x and 1.x dababase format differs from produced by KMC version 2.x. From version 2.2.0 API is unified for both formats and all new features/bug fixes are present only for 2.x branch (standalone API for older KMC version is not longer under development, so new version of API should be used even for databases produced by older KMC version). Quick start Getting the executable The simplest way to get the KMC is to download newest release for appropriate operating system from KMC releases . Counting the k-mers from a single fastq file ./kmc -k27 input.fastq 27mers . The command above will count all the 27-mers occurring in input.fastq at least twice (configurable with -ci switch). The result will be stored in a KMC database, which is split into two files: 27mers.kmc_pre and 27mers.kmc_suf . KMC will create hundreds of intermediate files. In the case of the above command, those will be created in the current working directory(the . at the end of the command). It may be more convinient to use dedicated directory for KMC temporary files, for example: mkdir kmc_tmp # create directory for kmc temporary files ./kmc -k27 input.fastq 27mers kmc_tmp Create text dump from KMC database binary format Having the k-mers counted it is possible to dump KMC binary database to textual form with kmc_tools . ./kmc_tools transform 27mers dump 27mers.txt Installation details Compile from sources git clone --recurse-submodules https://github.com/refresh-bio/kmc.git cd kmc make -j32 = The following libraries come with KMC in a binary (64-bit compiled for x86 platform) form. If your system needs other binary formats, you should put the following libraries in kmc_core/libs: zlib - for support for gzip-compressed input FASTQ/FASTA files The following libraries come with KMC in a source coude form. pybind11 - used to create python wrapper of KMC API ( https://github.com/pybind/pybind11 ) If needed, you can also redefine maximal length of k-mer, which is 256 in the current version. Note: KMC is highly optimized and spends only as many bytes for k-mer (rounded up to 8) as necessary, so using large values of MAX_K does not affect the KMC performance for short k-mers. Some parts of KMC use C++17 features, so you need a compatible C++ compiler After that, you can run make to compile kmc and kmc_dump applications. Additional infromation for MAC OS installation There might be a need to change g++ path in makefile_mac. If needed we recommend install g++ with brew ( http://brew.sh/ ). Note that KMC creates a hundreds of temporary files, while default limit for opened files is small for under MAC OS platform. To increase this number use following command before running KMC: ulimit -n 2048 Directory structure bin - after compilation executables and libraries after compilation will be stored here include - after compilation header file to use kmc core through the C++ API will be stored here kmc_core - source code of kmc core library kmc_CLI - source code of kmc command line interface kmc_tools - source codes of kmc_tools program kmc_core/libs - libraries used by KMC kmc_api - C++ source codes implementing API to access KMC databases; must be used by any program that wants to process databases produced by kmc kmc_dump - source codes of kmc_dump program listing k-mers in databases produced by kmc (deprecated, use kmc_tools instead) py_kmc_api - python wrapper for kmc API tests - tests files Use the KMC directly from code through the API It is possible to use the KMC directly from C++ code through. Detailed API description is available at wiki Python wrapper for KMC API Python wrapper for KMC API was created using pybind11. Warning: python binding is experimental. The library used to create binding as well as public interface may change in the future. Warning 2: python wrapper for C++ KMC API is much slower (much, much more than I have been expecting) than native C++ API. In fact the first attempt to create python wrapper was to use ctypes , but it turned out it was even slower than in case when pybind11 is used. The wrapper is designed and was tested only for python3. The main goal was to make it as similar to C++ API as possible. For this reason the API may be not [pythonic] ( https://blog.startifact.com/posts/older/what-is-pythonic.html ) enough for regular python programmer. Suggestions or pull requests to make it more robust are welcome. Python module wrapping KMC API must be compiled. for windows there is a visual studio project (note that there will be probably the need to change include directories and library directories to point python include and libs location) for linux or mac one should run make py_kmc_api As a result of pybind11 *.so file (for linux and mac os) or *.pyd (for windows) is created and may be used as a python module. *.pyd file is in fact DLL file, the only difference is its extension. for windows following file is created: x64/Release/py_kmc_api.pyd for linux/mac os the following file is created: bin/py_kmc_api python3-config --extension-suffix To be able to use this file one should make it visible for python. One way to do this is to extend PYTHONPATH environment variable. For linux/mac os one may just source py_kmc_api/set_path.sh while, for windows: py_kmc_api\set_path.bat it will export apropriate file. The example of Python wrapper for KMC API is presented in file: py_kmc_api/py_kmc_dump.py Detailed API description is available at wiki Binaries After compilation you will obtain two binaries: bin/kmc - the main program for counting k-mer occurrences bin/kmc_dump - the program listing k-mers in a database produced by kmc bin/kmc_tools - the program allowing to manipulate kmc databases (set operations, transformations, etc.) bin/libkmc_core.a - compiled KMC code sources py_kmc_api.cpython-39-x86_64-linux-gnu.so - compiled python wrapper for KMC API License KMC software distributed under GNU GPL 3 licence. gzip is free, open-source pybind11 ( https://github.com/pybind/pybind11 ) is open-source (BDS-style license) In case of doubt, please consult the original documentations. Archival source codes, binaries and documentation Archival source codes, binaries and documentation are available at wiki . Warranty THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Citing Marek Kokot, Maciej Długosz, Sebastian Deorowicz, KMC 3: counting and manipulating k-mer statistics, Bioinformatics, Volume 33, Issue 17, 01 September 2017, Pages 2759–2761, https://doi.org/10.1093/bioinformatics/btx304 Sebastian Deorowicz, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz, KMC 2: fast and resource-frugal k-mer counting, Bioinformatics, Volume 31, Issue 10, 15 May 2015, Pages 1569–1576, https://doi.org/10.1093/bioinformatics/btv022 Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. Disk-based k-mer counting on a PC. BMC Bioinformatics 14, 160 (2013). https://doi.org/10.1186/1471-2105-14-160 About Fast and frugal disk based k-mer counter Resources Readme Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 331 stars Watchers 8 watching Forks 83 forks Report repository Releases 13 KMC 3.2.4 Latest Feb 9, 2024 + 12 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 97.8% Python 1.6% Other 0.6% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/refresh-bio/kmc +GitHub - refresh-bio/KMC: Fast and frugal disk based k-mer counter · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} refresh-bio / KMC Public Notifications You must be signed in to change notification settings Fork 83 Star 331 Code Issues 96 Pull requests 5 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights refresh-bio/KMC master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 320 Commits 320 Commits .github/ workflows .github/ workflows 3rd_party 3rd_party doc/ kmc_tools doc/ kmc_tools kmc_CLI kmc_CLI kmc_api kmc_api kmc_core kmc_core kmc_dump kmc_dump kmc_dump_sample kmc_dump_sample kmc_tools kmc_tools py_kmc_api py_kmc_api tests tests .gitattributes .gitattributes .gitignore .gitignore .gitmodules .gitmodules API.pdf API.pdf Makefile Makefile README.md README.md build_release.py build_release.py kmc.sln kmc.sln kmc_tools.pdf kmc_tools.pdf View all files Repository files navigation README KMC KMC is a disk-based program for counting k-mers from (possibly gzipped) FASTQ/FASTA files. KMC is one of many projects developed by REFRESH Bioinformatics Group . For accessing k-mers stored in database produced by KMC there is an API (kmc_api directory). Note that for KMC versions 0.x and 1.x dababase format differs from produced by KMC version 2.x. From version 2.2.0 API is unified for both formats and all new features/bug fixes are present only for 2.x branch (standalone API for older KMC version is not longer under development, so new version of API should be used even for databases produced by older KMC version). Quick start Getting the executable The simplest way to get the KMC is to download newest release for appropriate operating system from KMC releases . Counting the k-mers from a single fastq file ./kmc -k27 input.fastq 27mers . The command above will count all the 27-mers occurring in input.fastq at least twice (configurable with -ci switch). The result will be stored in a KMC database, which is split into two files: 27mers.kmc_pre and 27mers.kmc_suf . KMC will create hundreds of intermediate files. In the case of the above command, those will be created in the current working directory(the . at the end of the command). It may be more convinient to use dedicated directory for KMC temporary files, for example: mkdir kmc_tmp # create directory for kmc temporary files ./kmc -k27 input.fastq 27mers kmc_tmp Create text dump from KMC database binary format Having the k-mers counted it is possible to dump KMC binary database to textual form with kmc_tools . ./kmc_tools transform 27mers dump 27mers.txt Installation details Compile from sources git clone --recurse-submodules https://github.com/refresh-bio/kmc.git cd kmc make -j32 = The following libraries come with KMC in a binary (64-bit compiled for x86 platform) form. If your system needs other binary formats, you should put the following libraries in kmc_core/libs: zlib - for support for gzip-compressed input FASTQ/FASTA files The following libraries come with KMC in a source coude form. pybind11 - used to create python wrapper of KMC API ( https://github.com/pybind/pybind11 ) If needed, you can also redefine maximal length of k-mer, which is 256 in the current version. Note: KMC is highly optimized and spends only as many bytes for k-mer (rounded up to 8) as necessary, so using large values of MAX_K does not affect the KMC performance for short k-mers. Some parts of KMC use C++17 features, so you need a compatible C++ compiler After that, you can run make to compile kmc and kmc_dump applications. Additional infromation for MAC OS installation There might be a need to change g++ path in makefile_mac. If needed we recommend install g++ with brew ( http://brew.sh/ ). Note that KMC creates a hundreds of temporary files, while default limit for opened files is small for under MAC OS platform. To increase this number use following command before running KMC: ulimit -n 2048 Directory structure bin - after compilation executables and libraries after compilation will be stored here include - after compilation header file to use kmc core through the C++ API will be stored here kmc_core - source code of kmc core library kmc_CLI - source code of kmc command line interface kmc_tools - source codes of kmc_tools program kmc_core/libs - libraries used by KMC kmc_api - C++ source codes implementing API to access KMC databases; must be used by any program that wants to process databases produced by kmc kmc_dump - source codes of kmc_dump program listing k-mers in databases produced by kmc (deprecated, use kmc_tools instead) py_kmc_api - python wrapper for kmc API tests - tests files Use the KMC directly from code through the API It is possible to use the KMC directly from C++ code through. Detailed API description is available at wiki Python wrapper for KMC API Python wrapper for KMC API was created using pybind11. Warning: python binding is experimental. The library used to create binding as well as public interface may change in the future. Warning 2: python wrapper for C++ KMC API is much slower (much, much more than I have been expecting) than native C++ API. In fact the first attempt to create python wrapper was to use ctypes , but it turned out it was even slower than in case when pybind11 is used. The wrapper is designed and was tested only for python3. The main goal was to make it as similar to C++ API as possible. For this reason the API may be not [pythonic] ( https://blog.startifact.com/posts/older/what-is-pythonic.html ) enough for regular python programmer. Suggestions or pull requests to make it more robust are welcome. Python module wrapping KMC API must be compiled. for windows there is a visual studio project (note that there will be probably the need to change include directories and library directories to point python include and libs location) for linux or mac one should run make py_kmc_api As a result of pybind11 *.so file (for linux and mac os) or *.pyd (for windows) is created and may be used as a python module. *.pyd file is in fact DLL file, the only difference is its extension. for windows following file is created: x64/Release/py_kmc_api.pyd for linux/mac os the following file is created: bin/py_kmc_api python3-config --extension-suffix To be able to use this file one should make it visible for python. One way to do this is to extend PYTHONPATH environment variable. For linux/mac os one may just source py_kmc_api/set_path.sh while, for windows: py_kmc_api\set_path.bat it will export apropriate file. The example of Python wrapper for KMC API is presented in file: py_kmc_api/py_kmc_dump.py Detailed API description is available at wiki Binaries After compilation you will obtain two binaries: bin/kmc - the main program for counting k-mer occurrences bin/kmc_dump - the program listing k-mers in a database produced by kmc bin/kmc_tools - the program allowing to manipulate kmc databases (set operations, transformations, etc.) bin/libkmc_core.a - compiled KMC code sources py_kmc_api.cpython-39-x86_64-linux-gnu.so - compiled python wrapper for KMC API License KMC software distributed under GNU GPL 3 licence. gzip is free, open-source pybind11 ( https://github.com/pybind/pybind11 ) is open-source (BDS-style license) In case of doubt, please consult the original documentations. Archival source codes, binaries and documentation Archival source codes, binaries and documentation are available at wiki . Warranty THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Citing Marek Kokot, Maciej Długosz, Sebastian Deorowicz, KMC 3: counting and manipulating k-mer statistics, Bioinformatics, Volume 33, Issue 17, 01 September 2017, Pages 2759–2761, https://doi.org/10.1093/bioinformatics/btx304 Sebastian Deorowicz, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz, KMC 2: fast and resource-frugal k-mer counting, Bioinformatics, Volume 31, Issue 10, 15 May 2015, Pages 1569–1576, https://doi.org/10.1093/bioinformatics/btv022 Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. Disk-based k-mer counting on a PC. BMC Bioinformatics 14, 160 (2013). https://doi.org/10.1186/1471-2105-14-160 About Fast and frugal disk based k-mer counter Resources Readme Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 331 stars Watchers 8 watching Forks 83 forks Report repository Releases 13 KMC 3.2.4 Latest Feb 9, 2024 + 12 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 97.8% Python 1.6% Other 0.6% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge kmc --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +kmc 2.3.0 noasmlib +------------------ +file name : kmc-2.3.0-noasmlib.tar.bz2 +name : kmc +version : 2.3.0 +build : noasmlib +build number: 1 +size : 5.0 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-2.3.0-noasmlib.tar.bz2 +md5 : e298c93ab1ed8728b89b685f734e5217 +dependencies: + - bzip2 + - libgcc + - zlib + + +kmc 2.3.0 noasmlib_2 +-------------------- +file name : kmc-2.3.0-noasmlib_2.tar.bz2 +name : kmc +version : 2.3.0 +build : noasmlib_2 +build number: 2 +size : 5.0 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-2.3.0-noasmlib_2.tar.bz2 +md5 : 0cc32072db6b44109184f192c04b707e +dependencies: + - bzip2 + - libgcc + - zlib + + +kmc 2.3.0 noasmlib_3 +-------------------- +file name : kmc-2.3.0-noasmlib_3.tar.bz2 +name : kmc +version : 2.3.0 +build : noasmlib_3 +build number: 3 +size : 6.1 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-2.3.0-noasmlib_3.tar.bz2 +md5 : 29a460931ae01eb7483bd3de53d205ea +dependencies: + - bzip2 + - libgcc + - zlib + + +kmc 3.0.0 1 +----------- +file name : kmc-3.0.0-1.tar.bz2 +name : kmc +version : 3.0.0 +build : 1 +build number: 1 +size : 10.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.0.0-1.tar.bz2 +md5 : d5463b9fd83f10448a6180945ac9b6c2 +timestamp : 2018-06-25 22:28:58 UTC +dependencies: [] + + +kmc 3.0.0 2 +----------- +file name : kmc-3.0.0-2.tar.bz2 +name : kmc +version : 3.0.0 +build : 2 +build number: 2 +size : 10.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.0.0-2.tar.bz2 +md5 : 1812dba09168ca7b7ad610f3bebf9a59 +timestamp : 2019-10-26 12:50:59 UTC +dependencies: [] + + +kmc 3.0.0 h9ee0642_3 +-------------------- +file name : kmc-3.0.0-h9ee0642_3.tar.bz2 +name : kmc +version : 3.0.0 +build : h9ee0642_3 +build number: 3 +size : 10.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.0.0-h9ee0642_3.tar.bz2 +md5 : 13ed2430e2366344e85cca85672bbc15 +timestamp : 2021-03-26 02:21:39 UTC +dependencies: [] + + +kmc 3.0.0 static_0 +------------------ +file name : kmc-3.0.0-static_0.tar.bz2 +name : kmc +version : 3.0.0 +build : static_0 +build number: 0 +size : 10.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.0.0-static_0.tar.bz2 +md5 : 74afbf346157fd71e7850051a06e6c39 +dependencies: [] + + +kmc 3.0.1 noasmlib_0 +-------------------- +file name : kmc-3.0.1-noasmlib_0.tar.bz2 +name : kmc +version : 3.0.1 +build : noasmlib_0 +build number: 0 +size : 1.1 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.0.1-noasmlib_0.tar.bz2 +md5 : b01f94ecb3e24d9bd9a5aae0f6a1375d +dependencies: + - bzip2 1.0* + - libgcc + - zlib 1.2.8* + + +kmc 3.0.1 noasmlib_1 +-------------------- +file name : kmc-3.0.1-noasmlib_1.tar.bz2 +name : kmc +version : 3.0.1 +build : noasmlib_1 +build number: 1 +size : 1.1 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.0.1-noasmlib_1.tar.bz2 +md5 : 6ce68a23f5ddf895ba14dc55965d3b24 +dependencies: + - bzip2 1.0* + - libgcc + - zlib 1.2.11* + + +kmc 3.0.1 noasmlib_2 +-------------------- +file name : kmc-3.0.1-noasmlib_2.tar.bz2 +name : kmc +version : 3.0.1 +build : noasmlib_2 +build number: 2 +size : 1.1 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.0.1-noasmlib_2.tar.bz2 +md5 : 1b5f41ae7e720d391ea7e405fd0c0cc3 +dependencies: + - bzip2 1.0* + - libgcc + - zlib 1.2.11* + + +kmc 3.1.0 0 +----------- +file name : kmc-3.1.0-0.tar.bz2 +name : kmc +version : 3.1.0 +build : 0 +build number: 0 +size : 10.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.1.0-0.tar.bz2 +md5 : ef18b8b657467f67a1505b2eed6f89bf +dependencies: [] + + +kmc 3.1.1rc1 h76f5088_0 +----------------------- +file name : kmc-3.1.1rc1-h76f5088_0.tar.bz2 +name : kmc +version : 3.1.1rc1 +build : h76f5088_0 +build number: 0 +size : 1.3 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.1.1rc1-h76f5088_0.tar.bz2 +md5 : 42044baef5182b921c61e23035796c41 +timestamp : 2018-07-18 09:32:25 UTC +dependencies: + - bzip2 >=1.0.6,<2.0a0 + - libgcc-ng >=7.2.0 + - libstdcxx-ng >=7.2.0 + - zlib >=1.2.11,<1.3.0a0 + + +kmc 3.1.1rc1 h76f5088_1 +----------------------- +file name : kmc-3.1.1rc1-h76f5088_1.tar.bz2 +name : kmc +version : 3.1.1rc1 +build : h76f5088_1 +build number: 1 +size : 13.0 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.1.1rc1-h76f5088_1.tar.bz2 +md5 : b78ee6916188cbd1b7e21e5ff0d583bf +timestamp : 2019-03-29 13:00:41 UTC +dependencies: + - bzip2 >=1.0.6,<2.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +kmc 3.1.1rc1 h76f5088_2 +----------------------- +file name : kmc-3.1.1rc1-h76f5088_2.tar.bz2 +name : kmc +version : 3.1.1rc1 +build : h76f5088_2 +build number: 2 +size : 13.1 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.1.1rc1-h76f5088_2.tar.bz2 +md5 : 1b205d198d35b8e9ae3dabc7a368e75f +timestamp : 2019-04-01 11:23:33 UTC +dependencies: + - bzip2 >=1.0.6,<2.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +kmc 3.1.1 h2d02072_1 +-------------------- +file name : kmc-3.1.1-h2d02072_1.tar.bz2 +name : kmc +version : 3.1.1 +build : h2d02072_1 +build number: 1 +size : 13.0 MB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.1.1-h2d02072_1.tar.bz2 +md5 : e200de2c4983be3d1844328af1c1189b +timestamp : 2019-10-26 13:00:16 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +kmc 3.1.1 h76f5088_0 +-------------------- +file name : kmc-3.1.1-h76f5088_0.tar.bz2 +name : kmc +version : 3.1.1 +build : h76f5088_0 +build number: 0 +size : 13.1 MB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.1.1-h76f5088_0.tar.bz2 +md5 : 1b5ea4a0c5e9120f9672bd3708bae30f +timestamp : 2019-05-29 17:30:16 UTC +dependencies: + - bzip2 >=1.0.6,<2.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +kmc 3.1.2rc1 h2d02072_0 +----------------------- +file name : kmc-3.1.2rc1-h2d02072_0.tar.bz2 +name : kmc +version : 3.1.2rc1 +build : h2d02072_0 +build number: 0 +size : 13.1 MB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.1.2rc1-h2d02072_0.tar.bz2 +md5 : da17fd1317af11696a44cf00482e4d21 +timestamp : 2020-01-14 17:21:09 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +kmc 3.2.1 h95f258a_1 +-------------------- +file name : kmc-3.2.1-h95f258a_1.tar.bz2 +name : kmc +version : 3.2.1 +build : h95f258a_1 +build number: 1 +size : 2.8 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.2.1-h95f258a_1.tar.bz2 +md5 : eedd0769c43380260050d44a5bb61652 +timestamp : 2022-01-22 11:02:59 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +kmc 3.2.1 h9ee0642_0 +-------------------- +file name : kmc-3.2.1-h9ee0642_0.tar.bz2 +name : kmc +version : 3.2.1 +build : h9ee0642_0 +build number: 0 +size : 4.9 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.2.1-h9ee0642_0.tar.bz2 +md5 : b72fbcee9b93444629b7bad42ef628e7 +timestamp : 2022-01-05 11:57:13 UTC +dependencies: [] + + +kmc 3.2.1 hf1761c0_2 +-------------------- +file name : kmc-3.2.1-hf1761c0_2.tar.bz2 +name : kmc +version : 3.2.1 +build : hf1761c0_2 +build number: 2 +size : 2.7 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.2.1-hf1761c0_2.tar.bz2 +md5 : 9b78c0ab811b65d22d8372a95cda8bcd +timestamp : 2022-02-23 01:44:32 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +kmc 3.2.4 h5ca1c30_4 +-------------------- +file name : kmc-3.2.4-h5ca1c30_4.tar.bz2 +name : kmc +version : 3.2.4 +build : h5ca1c30_4 +build number: 4 +size : 1.7 MB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.2.4-h5ca1c30_4.tar.bz2 +md5 : 95bc42b419ebbb828c8f5926f7dd3c77 +timestamp : 2025-06-17 23:25:18 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + - python <3.11 + + +kmc 3.2.4 h6dccd9a_0 +-------------------- +file name : kmc-3.2.4-h6dccd9a_0.tar.bz2 +name : kmc +version : 3.2.4 +build : h6dccd9a_0 +build number: 0 +size : 5.0 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.2.4-h6dccd9a_0.tar.bz2 +md5 : 8393fd4e2a22e9a5b2c5b5175239deba +timestamp : 2024-04-12 04:45:58 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +kmc 3.2.4 h6dccd9a_1 +-------------------- +file name : kmc-3.2.4-h6dccd9a_1.tar.bz2 +name : kmc +version : 3.2.4 +build : h6dccd9a_1 +build number: 1 +size : 5.0 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.2.4-h6dccd9a_1.tar.bz2 +md5 : 45ae659acd79624655e813255b4e7539 +timestamp : 2024-04-23 12:41:04 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +kmc 3.2.4 h6dccd9a_2 +-------------------- +file name : kmc-3.2.4-h6dccd9a_2.tar.bz2 +name : kmc +version : 3.2.4 +build : h6dccd9a_2 +build number: 2 +size : 5.0 MB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.2.4-h6dccd9a_2.tar.bz2 +md5 : 25d6b0de5d6473d755ef18dfe160bf83 +timestamp : 2024-10-09 19:53:21 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc >=12 + - libstdcxx >=12 + - libzlib >=1.2.13,<2.0a0 + + +kmc 3.2.4 haf24da9_3 +-------------------- +file name : kmc-3.2.4-haf24da9_3.tar.bz2 +name : kmc +version : 3.2.4 +build : haf24da9_3 +build number: 3 +size : 5.0 MB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmc-3.2.4-haf24da9_3.tar.bz2 +md5 : 7e363a4eb4202c02326c894583fd960e +timestamp diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kmer-jellyfish.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kmer-jellyfish.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..06903dcf23d3ffafc77c5ae5d160f17f5e53b399 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/kmer-jellyfish.manual_bundle.txt @@ -0,0 +1,419 @@ +# Tool: kmer-jellyfish +software_name: kmer-jellyfish +tier: T1 +domain: t1_backfill_overall +downloads: 126037 +summary: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence +description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence +dependencies: libgcc >=13, libstdcxx >=13, perl >=5.32.1,<5.33.0a0 *_perl5, python >=3.9,<3.10.0a0, python_abi 3.9.* *_cp39 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: http://www.genome.umd.edu/jellyfish.html +doc_url: +dev_url: https://github.com/gmarcais/Jellyfish + +## URL Docs Extract +### https://github.com/gmarcais/Jellyfish +GitHub - gmarcais/Jellyfish: A fast multi-threaded k-mer counter · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} gmarcais / Jellyfish Public Notifications You must be signed in to change notification settings Fork 140 Star 538 Code Issues 99 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights gmarcais/Jellyfish master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 660 Commits 660 Commits .github/ workflows .github/ workflows doc doc examples examples include/ jellyfish include/ jellyfish jellyfish jellyfish lib lib m4 m4 sub_commands sub_commands swig swig tests tests unit_tests unit_tests .gitignore .gitignore .gitmod .gitmod .travis.yml .travis.yml CHANGES CHANGES CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md HalfLICENSE HalfLICENSE LICENSE LICENSE LICENSE-BSD-3-Clause LICENSE-BSD-3-Clause LICENSE-GPL-3.0 LICENSE-GPL-3.0 Makefile.am Makefile.am README README README.md README.md compat.sh.in compat.sh.in config.rpath config.rpath configure.ac configure.ac development.mk development.mk gtest.mk gtest.mk header-license header-license jellyfish-2.0.pc.in jellyfish-2.0.pc.in jellyfish.spec.in jellyfish.spec.in local.mk local.mk View all files Repository files navigation README Code of conduct License BSD-3-Clause license GPL-3.0 license Jellyfish Overview Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the documentation for details. If you use Jellyfish in your research, please cite: Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 ( first published online January 7, 2011 ) doi:10.1093/bioinformatics/btr011 Installation Linux Binaries On Debian and Ubuntu with apt : sudo apt update sudo apt install jellyfish On Arch, it is available from AUR . FreeBSD Jellyfish can be installed on FreeBSD via the FreeBSD ports system. To install via the binary package, simply run: pkg install Jellyfish To install from source: cd /usr/ports/biology/jellyfish make install Windows With Cygwin , Jellyfish can be compiled from source as explained below . The simpler way on Windows 10 is to first install WSL and then install a Linux distribution that carries Jellyfish (e.g., Ubuntu) from the Windows Store. Finally, install with: sudo apt update sudo apt install jellyfish From source To get an easier to compiled packaged tar ball of the source code, download a release from the github release . You need make and g++ version 4.4 or higher. To install in your home directory, do: ./configure --prefix= $HOME make -j 4 make install To compile from the git tree, you will also need autoconf, automake, libool, gettext, pkg-config and yaggo . Then to compile and install (in /usr/local in that example) with: autoreconf -i ./configure make -j 4 sudo make install If the software is installed in system directories (hint: you needed to use sudo to install), like the example above, then the system library cache must be updated like such: sudo ldconfig Usage Instruction of use are available in the doc directory. Extra / Examples In the examples directory are potentially useful extra programs to query/manipulates output files of Jellyfish, using the shared library of Jellyfish in C++ or with scripting languages. The examples are not compiled by default. Each subdirectory of examples is independent and is compiled with a simple invocation of 'make'. Binding to script languages Bindings to Ruby, Python and Perl are provided. This binding allows to read the output file of Jellyfish directly in a scripting language. Compilation of the bindings is easier from the release tarball . The development files of the target scripting language are required. Compilation of the bindings from the git tree requires SWIG version 3 and adding the switch --enable-swig to the configure command lines show below. To compile all three bindings, configure and compile with: ./configure --enable-ruby-binding --enable-python-binding --enable-perl-binding make -j 4 sudo make install By default, Jellyfish is installed in /usr/local and the bindings are installed in the proper system location. When the --prefix switch is passed, the bindings are installed in the given directory. For example: ./configure --prefix= $HOME --enable-python-binding make -j 4 make install This will install the python binding in $HOME/lib/python2.7/site-packages (adjust based on your Python version). Then, for Python, Ruby or Perl to find the binding, an environment variable may need to be adjusted ( PYTHONPATH , RUBYLIB and PERL5LIB respectively). For example: export PYTHONPATH= $HOME /lib/python2.7/site-packages See the swig directory for examples on how to use the bindings. About A fast multi-threaded k-mer counter Resources Readme License Unknown and 2 other licenses found Licenses found Unknown LICENSE BSD-3-Clause LICENSE-BSD-3-Clause GPL-3.0 LICENSE-GPL-3.0 Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Stars 538 stars Watchers 29 watching Forks 140 forks Report repository Releases 12 Version 2.3.1 Latest Dec 7, 2023 + 11 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 92.0% M4 3.4% Shell 2.0% SWIG 1.0% Makefile 0.8% Python 0.4% Other 0.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge kmer-jellyfish --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +kmer-jellyfish 1.1.12 h7d875b9_1 +-------------------------------- +file name : kmer-jellyfish-1.1.12-h7d875b9_1.tar.bz2 +name : kmer-jellyfish +version : 1.1.12 +build : h7d875b9_1 +build number: 1 +size : 3.4 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-1.1.12-h7d875b9_1.tar.bz2 +md5 : f5eb49e2cba9e0a2705e81412cbad62f +timestamp : 2021-03-25 12:43:02 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + + +kmer-jellyfish 1.1.12 h9948957_4 +-------------------------------- +file name : kmer-jellyfish-1.1.12-h9948957_4.tar.bz2 +name : kmer-jellyfish +version : 1.1.12 +build : h9948957_4 +build number: 4 +size : 2.4 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-1.1.12-h9948957_4.tar.bz2 +md5 : 5f5aebeed95af448a4897821783c54e9 +timestamp : 2025-01-31 09:19:35 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + + +kmer-jellyfish 1.1.12 h9948957_6 +-------------------------------- +file name : kmer-jellyfish-1.1.12-h9948957_6.conda +name : kmer-jellyfish +version : 1.1.12 +build : h9948957_6 +build number: 6 +size : 1.8 MB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-1.1.12-h9948957_6.conda +md5 : d3876ad64922f9213ecc6fafcc7041fa +timestamp : 2025-09-30 11:33:07 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + + +kmer-jellyfish 1.1.12 h9f5acd7_2 +-------------------------------- +file name : kmer-jellyfish-1.1.12-h9f5acd7_2.tar.bz2 +name : kmer-jellyfish +version : 1.1.12 +build : h9f5acd7_2 +build number: 2 +size : 2.6 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-1.1.12-h9f5acd7_2.tar.bz2 +md5 : aa93b899c86192ebd022003249e902a0 +timestamp : 2022-02-22 03:39:30 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + + +kmer-jellyfish 1.1.12 hc9558a2_0 +-------------------------------- +file name : kmer-jellyfish-1.1.12-hc9558a2_0.tar.bz2 +name : kmer-jellyfish +version : 1.1.12 +build : hc9558a2_0 +build number: 0 +size : 3.1 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-1.1.12-hc9558a2_0.tar.bz2 +md5 : d7529ad4bdc024a3cc0f94a6999780e5 +timestamp : 2019-10-09 16:35:57 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +kmer-jellyfish 2.3.0 h7d875b9_2 +------------------------------- +file name : kmer-jellyfish-2.3.0-h7d875b9_2.tar.bz2 +name : kmer-jellyfish +version : 2.3.0 +build : h7d875b9_2 +build number: 2 +size : 362 KB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.0-h7d875b9_2.tar.bz2 +md5 : 5a12964c7347a9501b03bf3c814ed81a +timestamp : 2021-03-27 00:05:04 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + + +kmer-jellyfish 2.3.0 h9f5acd7_3 +------------------------------- +file name : kmer-jellyfish-2.3.0-h9f5acd7_3.tar.bz2 +name : kmer-jellyfish +version : 2.3.0 +build : h9f5acd7_3 +build number: 3 +size : 364 KB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.0-h9f5acd7_3.tar.bz2 +md5 : 03b16a793a0f59b66e0c0f663e6837cd +timestamp : 2022-02-22 03:29:02 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + + +kmer-jellyfish 2.3.0 hc9558a2_0 +------------------------------- +file name : kmer-jellyfish-2.3.0-hc9558a2_0.tar.bz2 +name : kmer-jellyfish +version : 2.3.0 +build : hc9558a2_0 +build number: 0 +size : 364 KB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.0-hc9558a2_0.tar.bz2 +md5 : fe5a02f36e6803c0dd284a92e7fcfc83 +timestamp : 2019-10-09 16:41:23 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +kmer-jellyfish 2.3.0 hc9558a2_1 +------------------------------- +file name : kmer-jellyfish-2.3.0-hc9558a2_1.tar.bz2 +name : kmer-jellyfish +version : 2.3.0 +build : hc9558a2_1 +build number: 1 +size : 382 KB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.0-hc9558a2_1.tar.bz2 +md5 : d866365e90a2ff5a14a479a51deb233c +timestamp : 2019-10-26 11:59:07 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +kmer-jellyfish 2.3.1 h4ac6f70_0 +------------------------------- +file name : kmer-jellyfish-2.3.1-h4ac6f70_0.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : h4ac6f70_0 +build number: 0 +size : 345 KB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-h4ac6f70_0.tar.bz2 +md5 : 579b4c45a8eacbb37487078a5aa40739 +timestamp : 2024-02-06 09:41:46 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +kmer-jellyfish 2.3.1 h4ac6f70_1 +------------------------------- +file name : kmer-jellyfish-2.3.1-h4ac6f70_1.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : h4ac6f70_1 +build number: 1 +size : 518 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-h4ac6f70_1.tar.bz2 +md5 : 88655f88b4125050b3ae41c877ed0796 +timestamp : 2024-05-08 17:09:32 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +kmer-jellyfish 2.3.1 h4ac6f70_2 +------------------------------- +file name : kmer-jellyfish-2.3.1-h4ac6f70_2.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : h4ac6f70_2 +build number: 2 +size : 510 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-h4ac6f70_2.tar.bz2 +md5 : dfe74da922649f9457549ac2650959a1 +timestamp : 2024-06-06 15:57:16 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +kmer-jellyfish 2.3.1 py310h184ae93_5 +------------------------------------ +file name : kmer-jellyfish-2.3.1-py310h184ae93_5.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : py310h184ae93_5 +build number: 5 +size : 582 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-py310h184ae93_5.tar.bz2 +md5 : da1ee0c765d47568fa7b807c2f33a9ab +timestamp : 2024-12-15 02:35:00 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - yaggo >=1.5.10,<1.6.0a0 + + +kmer-jellyfish 2.3.1 py310h84f13bb_4 +------------------------------------ +file name : kmer-jellyfish-2.3.1-py310h84f13bb_4.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : py310h84f13bb_4 +build number: 4 +size : 567 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-py310h84f13bb_4.tar.bz2 +md5 : e0b8deac6efb2db0c1635cedb7f0d8db +timestamp : 2024-10-28 08:28:58 UTC +dependencies: + - libgcc >=12 + - libstdcxx >=12 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - yaggo >=1.5.10,<1.6.0a0 + + +kmer-jellyfish 2.3.1 py310pl5321h184ae93_6 +------------------------------------------ +file name : kmer-jellyfish-2.3.1-py310pl5321h184ae93_6.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : py310pl5321h184ae93_6 +build number: 6 +size : 626 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-py310pl5321h184ae93_6.tar.bz2 +md5 : eaad7935fea48ec83382ddd7e07e68fd +timestamp : 2025-05-27 06:47:41 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + + +kmer-jellyfish 2.3.1 py311h2a4ad6c_4 +------------------------------------ +file name : kmer-jellyfish-2.3.1-py311h2a4ad6c_4.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : py311h2a4ad6c_4 +build number: 4 +size : 570 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-py311h2a4ad6c_4.tar.bz2 +md5 : ce4dc271b1c04bea04c88593df6f3041 +timestamp : 2024-10-28 08:23:24 UTC +dependencies: + - libgcc >=12 + - libstdcxx >=12 + - python >=3.11,<3.12.0a0 + - python_abi 3.11.* *_cp311 + - yaggo >=1.5.10,<1.6.0a0 + + +kmer-jellyfish 2.3.1 py311he264feb_5 +------------------------------------ +file name : kmer-jellyfish-2.3.1-py311he264feb_5.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : py311he264feb_5 +build number: 5 +size : 583 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-py311he264feb_5.tar.bz2 +md5 : ca068abdda3768c91daab60ec407fd82 +timestamp : 2024-12-15 02:34:01 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + - python >=3.11,<3.12.0a0 + - python_abi 3.11.* *_cp311 + - yaggo >=1.5.10,<1.6.0a0 + + +kmer-jellyfish 2.3.1 py311pl5321he264feb_6 +------------------------------------------ +file name : kmer-jellyfish-2.3.1-py311pl5321he264feb_6.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : py311pl5321he264feb_6 +build number: 6 +size : 628 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-py311pl5321he264feb_6.tar.bz2 +md5 : 710d637c78780cf668a19e859403b16a +timestamp : 2025-05-27 06:49:49 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - python >=3.11,<3.12.0a0 + - python_abi 3.11.* *_cp311 + + +kmer-jellyfish 2.3.1 py312h28adbb1_4 +------------------------------------ +file name : kmer-jellyfish-2.3.1-py312h28adbb1_4.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : py312h28adbb1_4 +build number: 4 +size : 569 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-py312h28adbb1_4.tar.bz2 +md5 : 51075f9c428bcc6b31a1e695543dba4f +timestamp : 2024-10-28 08:27:16 UTC +dependencies: + - libgcc >=12 + - libstdcxx >=12 + - python >=3.12,<3.13.0a0 + - python_abi 3.12.* *_cp312 + - yaggo >=1.5.10,<1.6.0a0 + + +kmer-jellyfish 2.3.1 py312h4ac6f70_3 +------------------------------------ +file name : kmer-jellyfish-2.3.1-py312h4ac6f70_3.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : py312h4ac6f70_3 +build number: 3 +size : 572 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/kmer-jellyfish-2.3.1-py312h4ac6f70_3.tar.bz2 +md5 : a7cd3f41e634d8901c547a2b20954390 +timestamp : 2024-07-22 14:20:04 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - python >=3.12,<3.13.0a0 + - python_abi 3.12.* *_cp312 + + +kmer-jellyfish 2.3.1 py312hf731ba3_5 +------------------------------------ +file name : kmer-jellyfish-2.3.1-py312hf731ba3_5.tar.bz2 +name : kmer-jellyfish +version : 2.3.1 +build : py312hf731ba3_5 +build number: 5 +size : 583 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.an diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/lastz.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/lastz.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..540172350473f67849935fab7d21c3a52ac8426a --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/lastz.manual_bundle.txt @@ -0,0 +1,516 @@ +# Tool: lastz +software_name: lastz +tier: T1 +domain: t1_backfill_overall +downloads: 119952 +summary: LASTZ is a program for aligning DNA sequences, a pairwise aligner. +description: LASTZ is a program for aligning DNA sequences, a pairwise aligner. +dependencies: libgcc >=13 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://www.bx.psu.edu/~rsharris/lastz/ +doc_url: +dev_url: + +## CLI Help Source +cli:lastz +## CLI Help Content +$ conda run -n bioenv_cli lastz --help +[rc=1] +NOTE: the following list is not comprehensive. The most up-to-date list is + available at http://www.bx.psu.edu/~rsharris/lastz + + target[[start..end]] spec/file containing target sequence (fasta, fastq, + nib, 2bit or hsx); [start..end] defines a subrange of + the file + (use --help=files for more details) + query[[start..end]] spec/file containing query sequences; if absent, + queries come from stdin (if needed) + --self the target sequence is also the query + (this replaces the query file) + --seed=match use a word with no gaps instead of a seed pattern + --[no]transition[=2] allow one or two transitions in a seed hit + (by default a transition is allowed) + --step= set step length (default is 1) + --strand=both search both strands + --strand=plus search + strand only (matching strand of query spec) + --strand=minus search - strand only (opposite strand of query spec) + (by default both strands are searched) + --ambiguous=n[,] treat N as an ambiguous nucleotide + (by default N is treated as a sequence splicing + character) + --ambiguous=iupac[,] treat any ambiguous IUPAC-IUB character as a + completely ambiguous nucleotide + (by default any sequence file with B,D,H,K,M,R,S,V,W,Y + is rejected) + --[no]gfextend perform gap-free extension of seed hits to HSPs + (by default extension is performed) + --[no]chain perform chaining + --chain= perform chaining with given penalties for diagonal and + anti-diagonal + (by default no chaining is performed) + --[no]gapped perform gapped alignment (instead of gap-free) + (by default gapped alignment is performed) + --notrivial do not output a trivial self-alignment block if the + target and query happen to be identical + --scores= read substitution scores from a file + (default is HOXD70) + --match=,

scores are +R/-P for match/mismatch + --gap= set gap open and extend penalties (default is 400,30) + --xdrop= set x-drop threshold (default is 10*sub[A][A]) + --ydrop= set y-drop threshold (default is open+300extend) + --noxtrim if x-drop extension encounters end of sequence, don't + trim back to peak score (use this for short reads) + --noytrim if y-drop extension encounters end of sequence, don't + trim back to peak score (use this for short reads) + --hspthresh= set threshold for high scoring pairs (default is 3000) + ungapped extensions scoring lower are discarded + can also be a percentage or base count + --exact= set threshold for exact matches + if specified, exact matches are found rather than high + scoring pairs (replaces --hspthresh) + --inner= set threshold for HSPs during interpolation + (default is no interpolation) + --gappedthresh= set threshold for gapped alignments + gapped extensions scoring lower are discarded + can also be a percentage or base count + (default is to use same value as --hspthresh) + --[no]entropy involve entropy in filtering high scoring pairs + (default is "entropy") + --nomirror don't report mirror-image alignments when using --self + (default is to skip processing them, but recreate them + in the output) + --allocate:traceback= space for trace-back information + (default is 80.0M) + --masking= mask any position in target hit this many times + zero indicates no masking + (default is no masking) + --identity=[..] filter alignments by percent identity + 0<=min<=max<=100; blocks (or HSPs) outside min..max + are discarded + (default is no identity filtering) + --coverage=[..] filter alignments by percentage of query covered + 0<=min<=max<=100; blocks (or HSPs) outside min..max + are discarded + (default is no query coverage filtering) + --output= specify output alignment file; otherwise alignments + are written to stdout + --format= specify output format; one of lav, axt, maf, cigar, + rdotplot, text or general + (use --help=formats for more details) + (by default output is LAV) + --rdotplot= create an output file suitable for plotting in R. + --axt= create an output file in AXT format. + --maf= create an output file in MAF format. + --progress= report processing of every nth query + --version report the program version and quit + --help list all options + --help=files list information about file specifiers + --help=formats list information about output file formats + --help=shortcuts list blastz-compatible shortcuts + --help=defaults list scoring defaults for your current settings + --help=yasra list yasra-specific shortcuts + +NOTE: the preceding list is not comprehensive. The most up-to-date list is + available at http://www.bx.psu.edu/~rsharris/lastz + + +ERROR conda.cli.main_run:execute(127): `conda run lastz --help` failed. (See above for error) + + +## URL Docs Extract +### http://www.bx.psu.edu/~rsharris/lastz/ +CCGB: Miller Lab, LASTZ Penn State University Center for Comparative Genomics and Bioinformatics Miller Lab, LASTZ Introduction LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. Citing LASTZ Harris, R.S. (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University. That Ph.D. thesis is here . Links Source code for release 1.04.15   (gzipped tar file of source code; 1.04.15, 2021-Aug-26)          ↑↑ Note that that is NOT the latest official release. Official releases are now distributed via github. LASTZ documentation   ( what’s new in lastz-1.04.15 ) LASTZ repository on github .          ↑↑ That is where the latest official release can be found. Documentation for the LAV alignment format   (default output from LASTZ) Bob Harris’s Ph.D. Thesis , describing LASTZ. Older releases, including the long time "official" release 1.02.00 Other releases, between Jan/2010 and Aug/2021   (Some not officially released) Related tools   (As is, with little or no documentation) I feel lucky   (Other versions, usually for a specific user) --> Miller Lab main page Contact Bob Harris: + +## Conda Search Info +$ conda search -c bioconda -c conda-forge lastz --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +lastz 1.0.2 0 +------------- +file name : lastz-1.0.2-0.tar.bz2 +name : lastz +version : 1.0.2 +build : 0 +build number: 0 +size : 306 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.2-0.tar.bz2 +md5 : d52d564b2663e12c8d48cb1d29998b71 +dependencies: + - libgcc + + +lastz 1.0.2 1 +------------- +file name : lastz-1.0.2-1.tar.bz2 +name : lastz +version : 1.0.2 +build : 1 +build number: 1 +size : 306 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.2-1.tar.bz2 +md5 : 4ec379ebd9858fdf8d485c62f397d501 +dependencies: + - libgcc + + +lastz 1.0.2 2 +------------- +file name : lastz-1.0.2-2.tar.bz2 +name : lastz +version : 1.0.2 +build : 2 +build number: 2 +size : 311 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.2-2.tar.bz2 +md5 : 9483629d51588494f3b976f5c4b95c0e +dependencies: + - libgcc + + +lastz 1.0.2 h470a237_3 +---------------------- +file name : lastz-1.0.2-h470a237_3.tar.bz2 +name : lastz +version : 1.0.2 +build : h470a237_3 +build number: 3 +size : 308 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.2-h470a237_3.tar.bz2 +md5 : 91a235f90485a1496c86e9a863dcd423 +timestamp : 2018-07-06 02:31:57 UTC +dependencies: + - libgcc-ng >=4.9 + + +lastz 1.0.2 h516909a_4 +---------------------- +file name : lastz-1.0.2-h516909a_4.tar.bz2 +name : lastz +version : 1.0.2 +build : h516909a_4 +build number: 4 +size : 298 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.2-h516909a_4.tar.bz2 +md5 : f25343f5b1a1608197a0f7d89915df48 +timestamp : 2020-07-13 22:04:32 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +lastz 1.0.2 h779adbc_5 +---------------------- +file name : lastz-1.0.2-h779adbc_5.tar.bz2 +name : lastz +version : 1.0.2 +build : h779adbc_5 +build number: 5 +size : 298 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.2-h779adbc_5.tar.bz2 +md5 : 8b30547b0eb576daa025d22a1b3391f2 +timestamp : 2021-03-26 23:45:35 UTC +dependencies: + - libgcc-ng >=9.3.0 + + +lastz 1.0.4 1 +------------- +file name : lastz-1.0.4-1.tar.bz2 +name : lastz +version : 1.0.4 +build : 1 +build number: 1 +size : 429 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.4-1.tar.bz2 +md5 : 6a3225f0eee6f64978dbfca1b92d3616 +dependencies: + - libgcc + + +lastz 1.0.4 h14c3975_3 +---------------------- +file name : lastz-1.0.4-h14c3975_3.tar.bz2 +name : lastz +version : 1.0.4 +build : h14c3975_3 +build number: 3 +size : 606 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.4-h14c3975_3.tar.bz2 +md5 : 0819c9414517ca74ba4c55cca83d0548 +timestamp : 2019-03-08 09:45:18 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +lastz 1.0.4 h470a237_2 +---------------------- +file name : lastz-1.0.4-h470a237_2.tar.bz2 +name : lastz +version : 1.0.4 +build : h470a237_2 +build number: 2 +size : 418 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.4-h470a237_2.tar.bz2 +md5 : a66efa7f7cb0c4f3aad2f29cbee330fe +timestamp : 2018-07-06 02:35:08 UTC +dependencies: + - libgcc-ng >=4.9 + + +lastz 1.0.4 h516909a_4 +---------------------- +file name : lastz-1.0.4-h516909a_4.tar.bz2 +name : lastz +version : 1.0.4 +build : h516909a_4 +build number: 4 +size : 654 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.4-h516909a_4.tar.bz2 +md5 : 610549471c5ff50d4c9994ce90944d92 +timestamp : 2020-07-10 20:58:46 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +lastz 1.0.4 h779adbc_5 +---------------------- +file name : lastz-1.0.4-h779adbc_5.tar.bz2 +name : lastz +version : 1.0.4 +build : h779adbc_5 +build number: 5 +size : 627 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.0.4-h779adbc_5.tar.bz2 +md5 : a0db334f0b0791573ae7f57129db1041 +timestamp : 2021-03-26 23:52:52 UTC +dependencies: + - libgcc-ng >=9.3.0 + + +lastz 1.04.15 h031d066_2 +------------------------ +file name : lastz-1.04.15-h031d066_2.tar.bz2 +name : lastz +version : 1.04.15 +build : h031d066_2 +build number: 2 +size : 619 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.15-h031d066_2.tar.bz2 +md5 : dcf91a34646322d3b2a8cd48ecdac1e4 +timestamp : 2023-05-15 03:39:12 UTC +dependencies: + - libgcc-ng >=12 + + +lastz 1.04.15 h031d066_3 +------------------------ +file name : lastz-1.04.15-h031d066_3.tar.bz2 +name : lastz +version : 1.04.15 +build : h031d066_3 +build number: 3 +size : 618 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.15-h031d066_3.tar.bz2 +md5 : 017577e977b7b8e0b4525f150801ce41 +timestamp : 2023-05-16 00:47:07 UTC +dependencies: + - libgcc-ng >=12 + + +lastz 1.04.15 h779adbc_0 +------------------------ +file name : lastz-1.04.15-h779adbc_0.tar.bz2 +name : lastz +version : 1.04.15 +build : h779adbc_0 +build number: 0 +size : 629 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.15-h779adbc_0.tar.bz2 +md5 : 1334928014739f0e0c1b9894c92b6d1c +timestamp : 2021-11-26 10:32:36 UTC +dependencies: + - libgcc-ng >=9.4.0 + + +lastz 1.04.15 hec16e2b_1 +------------------------ +file name : lastz-1.04.15-hec16e2b_1.tar.bz2 +name : lastz +version : 1.04.15 +build : hec16e2b_1 +build number: 1 +size : 619 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.15-hec16e2b_1.tar.bz2 +md5 : 0f15187427b4ad3c50f83a892127b6ec +timestamp : 2022-03-03 23:51:01 UTC +dependencies: + - libgcc-ng >=10.3.0 + + +lastz 1.04.15 hec16e2b_2 +------------------------ +file name : lastz-1.04.15-hec16e2b_2.tar.bz2 +name : lastz +version : 1.04.15 +build : hec16e2b_2 +build number: 2 +size : 621 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.15-hec16e2b_2.tar.bz2 +md5 : 830aefd3c7fcb24c096c13e0fab7991d +timestamp : 2023-05-13 09:41:32 UTC +dependencies: + - libgcc-ng >=12 + + +lastz 1.04.22 h031d066_0 +------------------------ +file name : lastz-1.04.22-h031d066_0.tar.bz2 +name : lastz +version : 1.04.22 +build : h031d066_0 +build number: 0 +size : 621 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.22-h031d066_0.tar.bz2 +md5 : f8e980494d5f7bf1739123fbae8d5e4c +timestamp : 2023-06-29 21:11:43 UTC +dependencies: + - libgcc-ng >=12 + + +lastz 1.04.22 h031d066_1 +------------------------ +file name : lastz-1.04.22-h031d066_1.tar.bz2 +name : lastz +version : 1.04.22 +build : h031d066_1 +build number: 1 +size : 622 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.22-h031d066_1.tar.bz2 +md5 : 38b6221582a6254b7be38f4c51f99120 +timestamp : 2024-08-13 11:10:18 UTC +dependencies: + - libgcc-ng >=12 + + +lastz 1.04.22 h7b50bb2_2 +------------------------ +file name : lastz-1.04.22-h7b50bb2_2.tar.bz2 +name : lastz +version : 1.04.22 +build : h7b50bb2_2 +build number: 2 +size : 630 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.22-h7b50bb2_2.tar.bz2 +md5 : 0c3aec7f3731fd3fc57713e848141e3d +timestamp : 2024-12-14 03:21:59 UTC +dependencies: + - libgcc >=13 + + +lastz 1.04.41 h7b50bb2_0 +------------------------ +file name : lastz-1.04.41-h7b50bb2_0.tar.bz2 +name : lastz +version : 1.04.41 +build : h7b50bb2_0 +build number: 0 +size : 639 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.41-h7b50bb2_0.tar.bz2 +md5 : 153f1ec7d064560bc7a269c395ae6193 +timestamp : 2024-12-18 16:26:07 UTC +dependencies: + - libgcc >=13 + + +lastz 1.04.45 h7b50bb2_0 +------------------------ +file name : lastz-1.04.45-h7b50bb2_0.tar.bz2 +name : lastz +version : 1.04.45 +build : h7b50bb2_0 +build number: 0 +size : 643 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.45-h7b50bb2_0.tar.bz2 +md5 : 86394a0c22183ade4da793ff378ef3ac +timestamp : 2025-02-24 17:15:36 UTC +dependencies: + - libgcc >=13 + + +lastz 1.04.52 h7b50bb2_0 +------------------------ +file name : lastz-1.04.52-h7b50bb2_0.tar.bz2 +name : lastz +version : 1.04.52 +build : h7b50bb2_0 +build number: 0 +size : 645 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.52-h7b50bb2_0.tar.bz2 +md5 : 91e6e99a11610bc906e48247d20dc421 +timestamp : 2025-04-02 22:26:32 UTC +dependencies: + - libgcc >=13 + + +lastz 1.04.52 h7b50bb2_1 +------------------------ +file name : lastz-1.04.52-h7b50bb2_1.tar.bz2 +name : lastz +version : 1.04.52 +build : h7b50bb2_1 +build number: 1 +size : 890 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/lastz-1.04.52-h7b50bb2_1.tar.bz2 +md5 : 8ac6f1ddab21d1ff519a8b5135c4d8a7 +timestamp : 2025-04-16 07:36:20 UTC +dependencies: + - libgcc >=13 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/liana.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/liana.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6714da67792cd4f1c57ba5e1805e3f3ddedf7aee --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/liana.manual_bundle.txt @@ -0,0 +1,285 @@ +# Tool: liana +software_name: liana +tier: T1 +domain: single_cell +downloads: 1386 +summary: LIANA+: a one-stop-shop framework for cell-cell communication. +description: LIANA+: a one-stop-shop framework for cell-cell communication. +dependencies: anndata >=0.7.4, cell2cell, corneto, cvxpy >=1.6,<2, decoupler-py >=1.5.1, docrep >=0.3.1, mofapy2 >=0.7.0, mofax, mudata, muon, numba >=0.60.0,<0.61.0, omnipath >=1.0.6, pandas >2.0.1, plotnine >=0.10.1, pre-commit >=3.0.0, pydeseq2 >=0.3.5, python >=3.10,<3.14, requests >=2.25.1,<3.0.0, scanpy >=1.8.0, session-info2, tqdm >=4.0.0 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://liana-py.readthedocs.io +doc_url: https://liana-py.readthedocs.io +dev_url: https://github.com/saezlab/liana-py + +## URL Docs Extract +### https://liana-py.readthedocs.io +LIANA+: an all-in-one cell-cell communication framework — liana Skip to main content Back to top Ctrl + K Installation API liana.method.cellchat.__call__ liana.method.cellphonedb.__call__ liana.method.connectome.__call__ liana.method.logfc.__call__ liana.method.natmi.__call__ liana.method.singlecellsignalr.__call__ liana.method.geometric_mean.__call__ liana.method.rank_aggregate.__call__ liana.method.bivariate.__call__ liana.method.MistyData liana.method.genericMistyData liana.method.lrMistyData liana.multi.df_to_lr liana.multi.to_tensor_c2c liana.multi.adata_to_views liana.multi.lrs_to_views liana.multi.nmf liana.multi.estimate_elbow liana.plotting.dotplot liana.plotting.dotplot_by_sample liana.plotting.tileplot liana.plotting.connectivity liana.plotting.target_metrics liana.plotting.contributions liana.plotting.interactions liana.utils.obsm_to_adata liana.utils.mdata_to_anndata liana.utils.zi_minmax liana.utils.neg_to_zero liana.utils.spatial_neighbors liana.utils.get_factor_scores liana.utils.get_variable_loadings liana.utils.interpolate_adata liana.resource.select_resource liana.resource.show_resources liana.resource.generate_lr_geneset liana.resource.explode_complexes liana.resource.get_metalinks liana.resource.describe_metalinks liana.resource.get_metalinks_values liana.method.find_causalnet liana.method.build_prior_network liana.method.estimate_metalinks Changelog Contributing guide References Tutorials Steady-state Ligand-Receptor inference Multi-Modal Ligand-Receptor Inference Prior Knowledge Spatially-informed Bivariate Metrics Integrating Multi-Modal Spatially-Resolved Technologies with LIANA+ Learning Spatial Relationships with MISTy Differential Expression Analysis for CCC & Downstream Signalling Networks Intercellular Context Factorization with Tensor-Cell2cell MOFAcellular - Multicellular Factor Analysis Intercellular Context Factorization with MOFA Inferring Cell–Cell Interactions at Single Cell Resolution .md .pdf LIANA+: an all-in-one cell-cell communication framework Contents Contributions Vignettes Decision Tree API Cite LIANA+: LIANA+: an all-in-one cell-cell communication framework # LIANA+ is a scalable framework that adapts and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. It is part of the scverse ecosystem , and relies on AnnData & MuData objects as input. Contributions # We welcome suggestions, ideas, and contributions! Please do not hesitate to contact us, open issues, and check the contributions guide . Vignettes # A set of extensive vignettes can be found in the LIANA+ documentation . Decision Tree # flowchart TD Start[What type of data?] --> Spatial{Spatial<br/>coordinates?} Start --> Modal{Multi-modal?} %% Spatial branch Spatial -->|Yes| SpatialRes{Resolution?} SpatialRes -->|Single-cell| Inflow[Inflow Score] SpatialRes -->|Spot-based| SpatialType{Analysis type?} SpatialType -->|Bivariate| LocalQ{Local<br/>interactions?} LocalQ -->|Yes| Local[Local Bivariate Metrics] LocalQ -->|No| Global[Global Bivariate Metrics] SpatialType -->|Unsupervised| MISTy[Multi-view Learning] %% Non-spatial branch Spatial -->|No| Compare{Compare across<br/>samples?} Compare -->|Yes| Contrast{Specific<br/>contrast?} Contrast -->|Yes| Targeted[Differential Contrasts] Contrast -->|No| MOFA[MOFA+] Contrast -->|No| Tensor[Tensor-cell2cell] Tensor --> TensorExt[Extended Tutorials] Compare -->|No| Steady[Steady-state LR Inference] %% Multi-modal branch Modal -->|Spatial| SMA[Multi-Modal Spatial] Modal -->|Non-Spatial| SCMulti[Multi-Modal Single-Cell] %% Metabolite sub-branch SCMulti --> Metab[Metabolite-mediated CCC] %% Links (click events) click Inflow "https://liana-py.readthedocs.io/en/latest/notebooks/inflow_score.html" click Local "https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html" click Global "https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html" click MISTy "https://liana-py.readthedocs.io/en/latest/notebooks/misty.html" click Targeted "https://liana-py.readthedocs.io/en/latest/notebooks/targeted.html" click MOFA "https://liana-py.readthedocs.io/en/latest/notebooks/mofatalk.html" click Tensor "https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html" click TensorExt "https://ccc-protocols.readthedocs.io/en/latest/" click Steady "https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html" click SMA "https://liana-py.readthedocs.io/en/latest/notebooks/sma.html" click SCMulti "https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html" click Metab "https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html#metabolite-mediated-ccc-from-transcriptomics-data" API # For further information please check LIANA’s API documentation . Cite LIANA+: # Dimitrov D., Schäfer P.S.L, Farr E., Rodriguez Mier P., Lobentanzer S., Badia-i-Mompel P., Dugourd A., Tanevski J., Ramirez Flores R.O. and Saez-Rodriguez J. LIANA+ provides an all-in-one framework for cell–cell communication inference. Nat Cell Biol (2024). https://doi.org/10.1038/s41556-024-01469-w Dimitrov, D., Türei, D., Garrido-Rodriguez M., Burmedi P.L., Nagai, J.S., Boys, C., Flores, R.O.R., Kim, H., Szalai, B., Costa, I.G., Valdeolivas, A., Dugourd, A. and Saez-Rodriguez, J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13, 3224 (2022). https://doi.org/10.1038/s41467-022-30755-0 Please also consider citing any of the methods and/or resources that were particularly relevant for your research! next Installation Contents Contributions Vignettes Decision Tree API Cite LIANA+: By Daniel Dimitrov, Philipp Sven Lars Schäfer, Elias Farr, Pablo Rodriguez-Mier, Sebastian Lobentanzer, Pau Badia-i-Mompel, Aurelien Dugourd, Jovan Tanevski, Ricardo Omar Ramirez Flores, Julio Saez-Rodriguez © Copyright 2026, Daniel Dimitrov, Philipp Sven Lars Schäfer, Elias Farr, Pablo Rodriguez-Mier, Sebastian Lobentanzer, Pau Badia-i-Mompel, Aurelien Dugourd, Jovan Tanevski, Ricardo Omar Ramirez Flores, Julio Saez-Rodriguez.. so the DOM is not blocked --> + +### https://liana-py.readthedocs.io +LIANA+: an all-in-one cell-cell communication framework — liana Skip to main content Back to top Ctrl + K Installation API liana.method.cellchat.__call__ liana.method.cellphonedb.__call__ liana.method.connectome.__call__ liana.method.logfc.__call__ liana.method.natmi.__call__ liana.method.singlecellsignalr.__call__ liana.method.geometric_mean.__call__ liana.method.rank_aggregate.__call__ liana.method.bivariate.__call__ liana.method.MistyData liana.method.genericMistyData liana.method.lrMistyData liana.multi.df_to_lr liana.multi.to_tensor_c2c liana.multi.adata_to_views liana.multi.lrs_to_views liana.multi.nmf liana.multi.estimate_elbow liana.plotting.dotplot liana.plotting.dotplot_by_sample liana.plotting.tileplot liana.plotting.connectivity liana.plotting.target_metrics liana.plotting.contributions liana.plotting.interactions liana.utils.obsm_to_adata liana.utils.mdata_to_anndata liana.utils.zi_minmax liana.utils.neg_to_zero liana.utils.spatial_neighbors liana.utils.get_factor_scores liana.utils.get_variable_loadings liana.utils.interpolate_adata liana.resource.select_resource liana.resource.show_resources liana.resource.generate_lr_geneset liana.resource.explode_complexes liana.resource.get_metalinks liana.resource.describe_metalinks liana.resource.get_metalinks_values liana.method.find_causalnet liana.method.build_prior_network liana.method.estimate_metalinks Changelog Contributing guide References Tutorials Steady-state Ligand-Receptor inference Multi-Modal Ligand-Receptor Inference Prior Knowledge Spatially-informed Bivariate Metrics Integrating Multi-Modal Spatially-Resolved Technologies with LIANA+ Learning Spatial Relationships with MISTy Differential Expression Analysis for CCC & Downstream Signalling Networks Intercellular Context Factorization with Tensor-Cell2cell MOFAcellular - Multicellular Factor Analysis Intercellular Context Factorization with MOFA Inferring Cell–Cell Interactions at Single Cell Resolution .md .pdf LIANA+: an all-in-one cell-cell communication framework Contents Contributions Vignettes Decision Tree API Cite LIANA+: LIANA+: an all-in-one cell-cell communication framework # LIANA+ is a scalable framework that adapts and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. It is part of the scverse ecosystem , and relies on AnnData & MuData objects as input. Contributions # We welcome suggestions, ideas, and contributions! Please do not hesitate to contact us, open issues, and check the contributions guide . Vignettes # A set of extensive vignettes can be found in the LIANA+ documentation . Decision Tree # flowchart TD Start[What type of data?] --> Spatial{Spatial<br/>coordinates?} Start --> Modal{Multi-modal?} %% Spatial branch Spatial -->|Yes| SpatialRes{Resolution?} SpatialRes -->|Single-cell| Inflow[Inflow Score] SpatialRes -->|Spot-based| SpatialType{Analysis type?} SpatialType -->|Bivariate| LocalQ{Local<br/>interactions?} LocalQ -->|Yes| Local[Local Bivariate Metrics] LocalQ -->|No| Global[Global Bivariate Metrics] SpatialType -->|Unsupervised| MISTy[Multi-view Learning] %% Non-spatial branch Spatial -->|No| Compare{Compare across<br/>samples?} Compare -->|Yes| Contrast{Specific<br/>contrast?} Contrast -->|Yes| Targeted[Differential Contrasts] Contrast -->|No| MOFA[MOFA+] Contrast -->|No| Tensor[Tensor-cell2cell] Tensor --> TensorExt[Extended Tutorials] Compare -->|No| Steady[Steady-state LR Inference] %% Multi-modal branch Modal -->|Spatial| SMA[Multi-Modal Spatial] Modal -->|Non-Spatial| SCMulti[Multi-Modal Single-Cell] %% Metabolite sub-branch SCMulti --> Metab[Metabolite-mediated CCC] %% Links (click events) click Inflow "https://liana-py.readthedocs.io/en/latest/notebooks/inflow_score.html" click Local "https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html" click Global "https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html" click MISTy "https://liana-py.readthedocs.io/en/latest/notebooks/misty.html" click Targeted "https://liana-py.readthedocs.io/en/latest/notebooks/targeted.html" click MOFA "https://liana-py.readthedocs.io/en/latest/notebooks/mofatalk.html" click Tensor "https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html" click TensorExt "https://ccc-protocols.readthedocs.io/en/latest/" click Steady "https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html" click SMA "https://liana-py.readthedocs.io/en/latest/notebooks/sma.html" click SCMulti "https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html" click Metab "https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html#metabolite-mediated-ccc-from-transcriptomics-data" API # For further information please check LIANA’s API documentation . Cite LIANA+: # Dimitrov D., Schäfer P.S.L, Farr E., Rodriguez Mier P., Lobentanzer S., Badia-i-Mompel P., Dugourd A., Tanevski J., Ramirez Flores R.O. and Saez-Rodriguez J. LIANA+ provides an all-in-one framework for cell–cell communication inference. Nat Cell Biol (2024). https://doi.org/10.1038/s41556-024-01469-w Dimitrov, D., Türei, D., Garrido-Rodriguez M., Burmedi P.L., Nagai, J.S., Boys, C., Flores, R.O.R., Kim, H., Szalai, B., Costa, I.G., Valdeolivas, A., Dugourd, A. and Saez-Rodriguez, J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13, 3224 (2022). https://doi.org/10.1038/s41467-022-30755-0 Please also consider citing any of the methods and/or resources that were particularly relevant for your research! next Installation Contents Contributions Vignettes Decision Tree API Cite LIANA+: By Daniel Dimitrov, Philipp Sven Lars Schäfer, Elias Farr, Pablo Rodriguez-Mier, Sebastian Lobentanzer, Pau Badia-i-Mompel, Aurelien Dugourd, Jovan Tanevski, Ricardo Omar Ramirez Flores, Julio Saez-Rodriguez © Copyright 2026, Daniel Dimitrov, Philipp Sven Lars Schäfer, Elias Farr, Pablo Rodriguez-Mier, Sebastian Lobentanzer, Pau Badia-i-Mompel, Aurelien Dugourd, Jovan Tanevski, Ricardo Omar Ramirez Flores, Julio Saez-Rodriguez.. so the DOM is not blocked --> + +### https://github.com/saezlab/liana-py +GitHub - saezlab/liana-py: LIANA+: an all-in-one framework for cell-cell communication · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} saezlab / liana-py Public Notifications You must be signed in to change notification settings Fork 32 Star 283 Code Issues 29 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights saezlab/liana-py main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 983 Commits 983 Commits .github .github docs docs src/ liana src/ liana tests tests .bumpversion.cfg .bumpversion.cfg .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml .readthedocs.yml .readthedocs.yml CHANGELOG.md CHANGELOG.md LICENSE LICENSE README.md README.md biome.jsonc biome.jsonc bumpversion.cfg bumpversion.cfg pyproject.toml pyproject.toml View all files Repository files navigation README Contributing BSD-3-Clause license LIANA+: an all-in-one cell-cell communication framework LIANA+ is a scalable framework that adapts and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. It is part of the scverse ecosystem , and relies on AnnData & MuData objects as input. Contributions We welcome suggestions, ideas, and contributions! Please do not hesitate to contact us, open issues, and check the contributions guide . Vignettes A set of extensive vignettes can be found in the LIANA+ documentation . Decision Tree flowchart TD Start[What type of data?] --> Spatial{Spatial<br/>coordinates?} Start --> Modal{Multi-modal?} %% Spatial branch Spatial -->|Yes| SpatialRes{Resolution?} SpatialRes -->|Single-cell| Inflow[Inflow Score] SpatialRes -->|Spot-based| SpatialType{Analysis type?} SpatialType -->|Bivariate| LocalQ{Local<br/>interactions?} LocalQ -->|Yes| Local[Local Bivariate Metrics] LocalQ -->|No| Global[Global Bivariate Metrics] SpatialType -->|Unsupervised| MISTy[Multi-view Learning] %% Non-spatial branch Spatial -->|No| Compare{Compare across<br/>samples?} Compare -->|Yes| Contrast{Specific<br/>contrast?} Contrast -->|Yes| Targeted[Differential Contrasts] Contrast -->|No| MOFA[MOFA+] Contrast -->|No| Tensor[Tensor-cell2cell] Tensor --> TensorExt[Extended Tutorials] Compare -->|No| Steady[Steady-state LR Inference] %% Multi-modal branch Modal -->|Spatial| SMA[Multi-Modal Spatial] Modal -->|Non-Spatial| SCMulti[Multi-Modal Single-Cell] %% Metabolite sub-branch SCMulti --> Metab[Metabolite-mediated CCC] %% Links (click events) click Inflow "https://liana-py.readthedocs.io/en/latest/notebooks/inflow_score.html" click Local "https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html" click Global "https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html" click MISTy "https://liana-py.readthedocs.io/en/latest/notebooks/misty.html" click Targeted "https://liana-py.readthedocs.io/en/latest/notebooks/targeted.html" click MOFA "https://liana-py.readthedocs.io/en/latest/notebooks/mofatalk.html" click Tensor "https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html" click TensorExt "https://ccc-protocols.readthedocs.io/en/latest/" click Steady "https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html" click SMA "https://liana-py.readthedocs.io/en/latest/notebooks/sma.html" click SCMulti "https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html" click Metab "https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html#metabolite-mediated-ccc-from-transcriptomics-data" Loading API For further information please check LIANA's API documentation . Cite LIANA+: Dimitrov D., Schäfer P.S.L, Farr E., Rodriguez Mier P., Lobentanzer S., Badia-i-Mompel P., Dugourd A., Tanevski J., Ramirez Flores R.O. and Saez-Rodriguez J. LIANA+ provides an all-in-one framework for cell–cell communication inference. Nat Cell Biol (2024). https://doi.org/10.1038/s41556-024-01469-w Dimitrov, D., Türei, D., Garrido-Rodriguez M., Burmedi P.L., Nagai, J.S., Boys, C., Flores, R.O.R., Kim, H., Szalai, B., Costa, I.G., Valdeolivas, A., Dugourd, A. and Saez-Rodriguez, J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13, 3224 (2022). https://doi.org/10.1038/s41467-022-30755-0 Please also consider citing any of the methods and/or resources that were particularly relevant for your research! About LIANA+: an all-in-one framework for cell-cell communication liana-py.readthedocs.io/ Topics python spatial single-cell single-cell-rna-seq ligand-receptor cell-cell-communication spatialomics Resources Readme License BSD-3-Clause license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 283 stars Watchers 1 watching Forks 32 forks Report repository Releases 21 v1.7.1 Latest Jan 24, 2026 + 20 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge liana --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +liana 1.4.0 pyhdfd78af_0 +------------------------ +file name : liana-1.4.0-pyhdfd78af_0.tar.bz2 +name : liana +version : 1.4.0 +build : pyhdfd78af_0 +build number: 0 +size : 841 KB +license : GPL-3.0-or-later +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/liana-1.4.0-pyhdfd78af_0.tar.bz2 +md5 : 08f050fb1ecea68fcc4fb2b2d538e699 +timestamp : 2024-10-31 13:27:12 UTC +dependencies: + - anndata >=0.7.4 + - cell2cell + - corneto + - cvxpy >=1.4,<2 + - cylp >=0.91.5,<0.92.0 + - decoupler >=1.4.0 + - docrep >=0.3.1 + - mofapy2 >=0.7.0 + - mofax + - mudata + - muon + - numba >=0.54.0 + - omnipath >=1.0.6 + - plotnine >=0.10.0 + - pre-commit >=3.0.0 + - pydeseq2 >=0.3.5 + - python >=3.8,<3.12 + - requests >=2.25.1,<3.0.0 + - scanpy >=1.8.0 + - tqdm >=4.0.0,<5.0.0 + + +liana 1.4.0 pyhdfd78af_1 +------------------------ +file name : liana-1.4.0-pyhdfd78af_1.tar.bz2 +name : liana +version : 1.4.0 +build : pyhdfd78af_1 +build number: 1 +size : 841 KB +license : GPL-3.0-or-later +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/liana-1.4.0-pyhdfd78af_1.tar.bz2 +md5 : 9922a0f9e95b8e437e3a803f8c488706 +timestamp : 2024-11-20 22:39:35 UTC +dependencies: + - anndata >=0.7.4,<=0.10.8 + - cell2cell + - corneto + - cvxpy >=1.4,<2 + - cylp >=0.91.5,<0.92.0 + - decoupler-py >=1.4.0 + - docrep >=0.3.1 + - mofapy2 >=0.7.0 + - mofax + - mudata + - muon + - numba >=0.54.0 + - omnipath >=1.0.6 + - pandas >=2.2.2,<3.0.0 + - plotnine >=0.10.0 + - pre-commit >=3.0.0 + - pydeseq2 >=0.3.5 + - python >=3.8,<3.12 + - requests >=2.25.1,<3.0.0 + - scanpy >=1.8.0 + - tqdm >=4.0.0,<5.0.0 + + +liana 1.5.1 pyhdfd78af_0 +------------------------ +file name : liana-1.5.1-pyhdfd78af_0.tar.bz2 +name : liana +version : 1.5.1 +build : pyhdfd78af_0 +build number: 0 +size : 5.3 MB +license : GPL-3.0-or-later +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/liana-1.5.1-pyhdfd78af_0.tar.bz2 +md5 : befbaa892337c074f0065afee16debcb +timestamp : 2025-03-17 14:57:07 UTC +dependencies: + - anndata >=0.7.4 + - cell2cell + - corneto + - cvxpy >=1.6,<2 + - decoupler-py >=1.5.1 + - docrep >=0.3.1 + - mofapy2 >=0.7.0 + - mofax + - mudata + - muon + - numba >=0.60.0,<0.61.0 + - omnipath >=1.0.6 + - pandas >2.0.1 + - plotnine >=0.10.0 + - pre-commit >=3.0.0 + - pydeseq2 >=0.3.5 + - python >=3.10,<3.12 + - requests >=2.25.1,<3.0.0 + - scanpy >=1.8.0 + - tqdm >=4.0.0,<5.0.0 + + +liana 1.5.1 pyhdfd78af_1 +------------------------ +file name : liana-1.5.1-pyhdfd78af_1.tar.bz2 +name : liana +version : 1.5.1 +build : pyhdfd78af_1 +build number: 1 +size : 5.3 MB +license : GPL-3.0-or-later +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/liana-1.5.1-pyhdfd78af_1.tar.bz2 +md5 : ba345862f36d3b3b6ee3193c989c610e +timestamp : 2025-07-31 02:24:32 UTC +dependencies: + - anndata >=0.7.4 + - cell2cell + - corneto + - cvxpy >=1.6,<2 + - decoupler-py >=1.5.1 + - docrep >=0.3.1 + - mofapy2 >=0.7.0 + - mofax + - mudata + - muon + - numba >=0.60.0,<0.61.0 + - omnipath >=1.0.6 + - pandas >2.0.1 + - plotnine >=0.10.0 + - pre-commit >=3.0.0 + - pydeseq2 >=0.3.5 + - python >=3.10,<3.12 + - requests >=2.25.1,<3.0.0 + - scanpy >=1.8.0 + - tqdm >=4.0.0,<5.0.0 + + +liana 1.6.1 pyhdfd78af_0 +------------------------ +file name : liana-1.6.1-pyhdfd78af_0.conda +name : liana +version : 1.6.1 +build : pyhdfd78af_0 +build number: 0 +size : 287 KB +license : GPL-3.0-or-later +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/liana-1.6.1-pyhdfd78af_0.conda +md5 : 1a5423f95a3efc57187393c109a2f898 +timestamp : 2025-09-29 22:23:34 UTC +dependencies: + - anndata >=0.7.4 + - cell2cell + - corneto + - cvxpy >=1.6,<2 + - decoupler-py >=1.5.1 + - docrep >=0.3.1 + - mofapy2 >=0.7.0 + - mofax + - mudata + - muon + - numba >=0.60.0,<0.61.0 + - omnipath >=1.0.6 + - pandas >2.0.1 + - plotnine >=0.10.1 + - pre-commit >=3.0.0 + - pydeseq2 >=0.3.5 + - python >=3.10,<3.14 + - requests >=2.25.1,<3.0.0 + - scanpy >=1.8.0 + - session-info2 + - tqdm >=4.0.0 + + +liana 1.7.0 pyhdfd78af_0 +------------------------ +file name : liana-1.7.0-pyhdfd78af_0.conda +name : liana +version : 1.7.0 +build : pyhdfd78af_0 +build number: 0 +size : 295 KB +license : GPL-3.0-or-later +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/liana-1.7.0-pyhdfd78af_0.conda +md5 : 3d612796db00f5abbb39fcc7b804cfcc +timestamp : 2026-01-11 10:14:13 UTC +dependencies: + - anndata >=0.7.4 + - cell2cell + - corneto + - cvxpy >=1.6,<2 + - decoupler-py >=1.5.1 + - docrep >=0.3.1 + - mofapy2 >=0.7.0 + - mofax + - mudata + - muon + - numba >=0.60.0,<0.61.0 + - omnipath >=1.0.6 + - pandas >2.0.1 + - plotnine >=0.10.1 + - pre-commit >=3.0.0 + - pydeseq2 >=0.3.5 + - python >=3.10,<3.14 + - requests >=2.25.1,<3.0.0 + - scanpy >=1.8.0 + - session-info2 + - tqdm >=4.0.0 + + +liana 1.7.1 pyhdfd78af_0 +------------------------ +file name : liana-1.7.1-pyhdfd78af_0.conda +name : liana +version : 1.7.1 +build : pyhdfd78af_0 +build number: 0 +size : 296 KB +license : GPL-3.0-or-later +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/liana-1.7.1-pyhdfd78af_0.conda +md5 : f3fa65be00ce1cbcf917cd9eb112c56c +timestamp : 2026-01-24 12:22:06 UTC +dependencies: + - anndata >=0.7.4 + - cell2cell + - corneto + - cvxpy >=1.6,<2 + - decoupler-py >=1.5.1 + - docrep >=0.3.1 + - mofapy2 >=0.7.0 + - mofax + - mudata + - muon + - numba >=0.60.0,<0.61.0 + - omnipath >=1.0.6 + - pandas >2.0.1 + - plotnine >=0.10.1 + - pre-commit >=3.0.0 + - pydeseq2 >=0.3.5 + - python >=3.10,<3.14 + - requests >=2.25.1,<3.0.0 + - scanpy >=1.8.0 + - session-info2 + - tqdm >=4.0.0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/locarna.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/locarna.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..72178b440d2f6cdef0816b5457331c4761c7bc5c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/locarna.manual_bundle.txt @@ -0,0 +1,727 @@ +# Tool: locarna +software_name: locarna +tier: T1 +domain: t1_backfill_overall +downloads: 153126 +summary: Multiple alignment of RNAs +description: Multiple alignment of RNAs +dependencies: libgcc >=13, libstdcxx >=13, perl >=5.32.1,<5.33.0a0 *_perl5, viennarna >=2.5.1,<3, viennarna >=2.7.0,<2.8.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://s-will.github.io/LocARNA +doc_url: +dev_url: + +## CLI Help Source +cli:locarna +## CLI Help Content +$ conda run -n bioenv_cli locarna --help +[rc=0] +locarna - pairwise (global and local) alignment of RNA. + +USAGE: locarna [options] + +Options: + -h, --help Print this help. + + --galaxy-xml Print galaxy xml wrapper. + + -V, --version Print only version string. + + -v, --verbose Be verbose. Prints input parameters, + sequences and size information. + + -q, --quiet Be quiet. + + +Scoring parameters: + -i, --indel=(-150) Indel score. Score contribution of each + single base insertion or deletion. + Indel opening score and indel score + define the affine scoring of gaps. + + --indel-opening=(-750) Indel opening score. Score contribution + of opening an insertion or deletion, + i.e. score for a consecutive run of + deletions or insertions. Indel opening + score and indel score define the affine + scoring of gaps. + + --ribosum-file=(RIBOSUM85_60) File specifying the Ribosum base and + base-pair similarities. [default: use + RIBOSUM85_60 without requiring a + Ribosum file.] + + --use-ribosum=(true) Use ribosum scores for scoring base + matches and base pair matches; note + that tau=0 suppresses any effect on the + latter. + + -m, --match=(50) Set score contribution of a base match + (unless ribosum scoring). + + -M, --mismatch=(0) Set score contribution of a base + mismatch (unless ribosum scoring). + + --unpaired-penalty=(0) Penalty for unpaired bases + + -s, --struct-weight=(200) Maximal weight of 1/2 arc match. + Balances structure vs. sequence score + contributions. + + -e, --exp-prob= Expected base pair probability. Used as + background probability for base pair + scoring [default: calculated from + sequence length]. + + -t, --tau=(50) Tau factor. Factor for contribution of + sequence similarity in an arc match (in + percent). tau=0 does not penalize any + sequence information including + compensatory mutations at arc matches, + while tau=100 scores sequence + similarity at ends of base matches (if + a scoring matrix like ribosum is used, + this adds the contributions for base + pair match from the matrix). [default + tau=0!] + + -E, --exclusion=(0) Score contribution per exclusion in + structure local alignment. Set to zero + for unrestricted structure locality. + + --stacking Use stacking terms (requires + stack-probs by RNAfold -p2) + + --new-stacking Use new stacking terms (requires + stack-probs by RNAfold -p2) + + +Partition function representation (for sequence envelopes): + --extended-pf Use extended precision for the + computation of sequence envelopes. This + enables handling significantly larger + instances. [default] + + --quad-pf Use quad precision for partition + function values. Even more precision + than extended pf, but usually much + slower (overrides extended-pf). + + +Locality: + --struct-local=(false) Turn on/off structure locality. Allow + exclusions in alignments of connected + substructures. + + --sequ-local=(false) Turn on/off sequence locality. Find + best alignment of arbitrary + subsequences of the input sequences. + + --free-endgaps=(----) Control where end gaps are allowed for + free. String of four +/- symbols, + allowing/disallowing free end gaps at + the four sequence ends in the order + left end of first sequence, right end + of first sequence, left end of second + sequence, right end of second sequence. + For example, "+---" allows free end + gaps at the left end of the first + alignment string; "----" forbids free + end gaps [default]. + + --normalized=(0) Perform normalized local alignment with + parameter L. This causes locarna to + compute the best local alignment + according to 'Score' / ( L + 'length' + ), where length is the sum of the + lengths of the two locally aligned + subsequences. Thus, the larger L, the + larger the local alignment; the size of + value L is in the order of local + alignment lengths. Verbose yields info + on the iterative optimizations. + + --penalized=(0) Penalized local alignment with penalty + PP + + +Output: + -w, --width=(120) Width of alignment output. + + --clustal= Write alignment in ClustalW (aln) + format to given file. + + --stockholm= Write alignment Stockholm format to + given file. + + --pp= Write alignment in PP format to given + file. + + --alifold-consensus-dp Compute consensus dot plot by alifold + (warning: this may fail for long + sequences). + + --consensus-structure=(none) Type of consensus structures written to + screen and stockholm output + [alifold|mea|none] (default: none). + + --consensus-gamma=(1.0) Base pair weight for mea consensus + computation. For MEA, base pairs are + scored by their pair probability times + 2 gamma; unpaired bases, by their + unpaired probability. + + -L, --local-output Output only local sub-alignment (to std + out). + + --local-file-output Write only local sub-alignment to + output files. + + -P, --pos-output Output only local sub-alignment + positions. + + --write-structure Write guidance structure in output. + + --score-components Output components of the score + (experimental). + + --stopwatch Print run time informations. + + +Heuristics for speed accuracy trade off: + -p, --min-prob=(0.001) Minimal probability. Only base pairs of + at least this probability are taken + into account. + + --max-bps-length-ratio=(0.0) Maximal ratio of #base pairs divided by + sequence length. This serves as a + second filter on the "significant" base + pairs. [default: 0.0 = no effect]. + + -D, --max-diff-am=(-1) Maximal difference for sizes of matched + arcs. [-1=off] + + -d, --max-diff=(-1) Maximal difference for positions of + alignment traces (and aligned bases). + [-1=off] + + --max-diff-at-am=(-1) Maximal difference for positions of + alignment traces at arc match ends. + [-1=off] + + --max-diff-aln=() Maximal difference relative to given + alignment (file in clustalw format) + + --max-diff-pw-aln=() Maximal difference relative to given + alignment (string, delim=AMPERSAND) + + --max-diff-relax Relax deviation constraints in multiple + aligmnent + + --min-trace-probability=(1e-4) Minimal sequence alignment + probability of potential traces + (probability-based sequence alignment + envelope) [default=1e-4]. + + +Special sauce options: + --kbest=(-1) Enumerate k-best alignments + + --better=(-1000000) Enumerate alignments better threshold t + + +MEA score: + --mea-alignment Perform maximum expected accuracy + alignment (instead of using the default + similarity scoring). + + --match-prob-method=(0) Select method for computing + sequence-based base match probablities + (to be used for mea-type alignment + scores). Methods: 1=probcons-style from + HMM, 2=probalign-style from PFs, 3=from + PFs, local + + --probcons-file= Read parameters for probcons-like + calculation of match probabilities from + probcons parameter file. + + --temperature-alipf=(300) Temperature for the /sequence + alignment/ partition functions used by + the probcons-like sequence-based + match/trace probability computation + (this temperature is different from the + 'physical' temperature of RNA + folding!). + + --pf-struct-weight=(200) Structure weight in PF com + +## URL Docs Extract +### https://s-will.github.io/LocARNA +LocARNA-2.0.0: Main Page LocARNA-2.0.0 LocARNA-2.0.0 Documentation Table of Contents LocARNA: Alignment of RNAs Example of standard usage More on features and alignment variants Installation Installation from Conda package (recommended) Alternative installation from source Installation from source distribution Installation from the git repository Usage Web server Contact References LocARNA: Alignment of RNAs The LocARNA package provides several tools for the structural analysis of RNA. LocARNA's main functionality is to align a set of a priori unaligned RNAs sequences and at the same time predict their common structure. In this way, LocARNA performs simultaneous alignment and folding in the spirit of the classical Sankoff algorithm, but implements strategies to perform this computationally challenging task efficiently and comparably fast. Due to the central ability to simultaneously assess sequence similarity and the similarity of predicted structure, LocARNA is recommends itself for the analysis of RNAs in the twilight zone (around or below 60% sequence identity), where alignments based on only sequence similarity are unreliable. Thus, it could be sometimes easier and typically faster to align highly similar RNAs using pure sequence alignment tools; similarily, RNAs with existing trusted alignments can be more efficiently analyzed based on specialized tools like RNAalifold, R-scape, or Infernal. Example of standard usage Most of the package's functionality is accessible via the command-line tool mlocarna through its various options. In the simplest case, we provide the input sequences in a fasta file. $ mlocarna archaea.fa yields text output and writes results (and intermediary results) to disk; here to folder archaea.out . As main result, it produces the alignment of the seven short RNA sequences in archaea.fa together with a consensus structure: The graphical RNAalifold-generated output shows the aligned RNAs (with gaps), the consensus structure as dot-bracket string on top, and the column similarities by bars at the bottom. In the way of alifold, columns are color-coded to visualize compensatory and incompatible mutations at predicted base pairs. More on features and alignment variants LocARNA distinguishes itself from many other Sankoff-style multiple alignment programs by its high performance (strongly improved in the 2.x line) and low memory complexity, high accuracy, and a broad set of features. As unique features, it offers structure-local alignment, flexible structure constraints and anchor constraints, specialized realignment modes for refining existing alignments, and provides efficient computation of reliabilities in sequence-structure alignment. The package offers a robust core of features and is used as experimental platform for new RNA alignment related methods. Multiple alignment can be performed in one of several different ways: progressive alignment using sequence-structure alignment of profiles progressive alignment after consistency transformation using T-Coffee progressive alignment using probabilistic consistency transformation and sequence-structure profile alignments, optionally followed by iterative refinement. Besides of global alignment, LocARNA supports two kinds of locality. Local alignment as it is known from sequence alignment, identifies and aligns the best matching subsequences. This form of locality is called sequence local to distinguish it from structural locality. When performing structure local alignment, LocARNA identifies and aligns the best matching substructures in the RNAs. The sequences of those substructures can be discontinuous on the sequence level, but remain connected via structural bonds. Alignment Reliabilities (LocARNA-P). In this special, probabilistic mode of operation LocARNA supports the efficient computation of match probabilities, probabilistic consistency transformation for more accurate multiple alignment, and generates reliability profiles of multiple alignments. Installation The software can be installed on recent Linux or MacOSX systems; Windows is untested but should be supported via WSL. Installation from Conda package (recommended) On Mac/Linux, LocARNA is installed most easily via Conda from a pre-compiled package. For this purpose, install Conda and run from the command line: conda install -c conda-forge -c bioconda locarna Alternative installation from source Installing from source requires a C++ compiler (GNU C++, Clang, ...) and Autotools. Moreover, it depends on the Vienna RNA package. Installation from source distribution Obtain the tar.gz source distribution, e.g. from Github https://github.com/s-will/LocARNA/releases Then, build and install like tar xzf locarna-xxx.tar.gz cd locarna-xxx ./configure --prefix=/usr/local make make install Is Vienna RNA installed in a non-standard location, this has to be specified by configure option ` --with-vrna=path-to-vrna . Installing from source furthermore allows testing via make check and building documentation locally by make doxygen-doc Building documentation requires additional tools: doxygen, pod2markdown and pandoc. Installation from the git repository Installing from repository is possible after cloning and setting up the autotools suite. This is most easily achieved by running autoreconf -i in the cloned repository. Then, the installation essentially works like installing from source distribution. Note that, we will however require additional tools to build the documentation: help2man, pod2man. Usage For instructions on the use of the tools, please see the documentation / man pages of the single tools mlocarna — for multiple alignment of RNAs. This program supports most of the functionality of the package via a high level interface. locarna — for pairwise alignment locarna_p — for pairwise computation of alignment partition function and (sequence and structure) match probabilities sparse — for structurally stronger sparsified pairwise alignment For additional functionality and special purposes, see exparna_p — for generating exact matches from the ensembles of two RNAs locarnate — for multiple alignment of RNAs via T-Coffee. This script offers multiple alignment of RNAs that is performed by sequence-structurally aligning all pairs of RNAs and then using T-Coffee to construct a common multiple alignment out of all pairwise ones. Web server The core functionality of the package is accessible through a web interface at http://rna.informatik.uni-freiburg.de Contact Main author and contact: Sebastian Will sebastian.will (at) polytechnique.edu References Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Computational Biology, 3 no. 4 pp. e65, 2007. doi:10.1371/journal.pcbi.0030065 Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA, 18 no. 5 pp. 900-914, 2012. doi:10.1261/rna.029041.111 Sebastian Will, Michael Yu, and Bonnie Berger. Structure-based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. Genome Research, no. 23 pp. 1018-1027, 2013. doi:10.1101/gr.137091.111 Sebastian Will, Christina Otto, Milad Miladi, Mathias Mohl, and Rolf Backofen. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics, 31(15):2489–2496, 2015. doi:10.1093/bioinformatics/btv185 Generated on Sat Nov 19 2022 11:24:48 for LocARNA-2.0.0 by  1.9.1 + +## Conda Search Info +$ conda search -c bioconda -c conda-forge locarna --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +locarna 1.8.7 0 +--------------- +file name : locarna-1.8.7-0.tar.bz2 +name : locarna +version : 1.8.7 +build : 0 +build number: 0 +size : 2.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.8.7-0.tar.bz2 +md5 : 9fbf4c45076498592c0bc5e029cfed42 +dependencies: + - perl-threaded + - viennarna <=2.1.9 + + +locarna 1.8.7 1 +--------------- +file name : locarna-1.8.7-1.tar.bz2 +name : locarna +version : 1.8.7 +build : 1 +build number: 1 +size : 10.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.8.7-1.tar.bz2 +md5 : 02e5e3046a7ff910466f33a3a186e12a +dependencies: + - perl-threaded + - viennarna <=2.1.9 + + +locarna 1.8.9 1 +--------------- +file name : locarna-1.8.9-1.tar.bz2 +name : locarna +version : 1.8.9 +build : 1 +build number: 1 +size : 22.9 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.8.9-1.tar.bz2 +md5 : adaf7c75b73a6f1d32c3904d768b30a6 +dependencies: + - libgcc + - perl-threaded + - viennarna >=2.2.5 + + +locarna 1.8.9 2 +--------------- +file name : locarna-1.8.9-2.tar.bz2 +name : locarna +version : 1.8.9 +build : 2 +build number: 2 +size : 22.9 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.8.9-2.tar.bz2 +md5 : b61660567540eab1c86d9937c937f660 +dependencies: + - libgcc + - perl-threaded + - viennarna >=2.2.5 + + +locarna 1.8.9 3 +--------------- +file name : locarna-1.8.9-3.tar.bz2 +name : locarna +version : 1.8.9 +build : 3 +build number: 3 +size : 22.9 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.8.9-3.tar.bz2 +md5 : 97a8df612ea59bce3bd8556ab02746d7 +dependencies: + - libgcc + - perl-threaded + - viennarna >=2.2.5 + + +locarna 1.8.10 0 +---------------- +file name : locarna-1.8.10-0.tar.bz2 +name : locarna +version : 1.8.10 +build : 0 +build number: 0 +size : 23.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.8.10-0.tar.bz2 +md5 : 3f1868dc76f3ad346d9f8790b197bd62 +dependencies: + - libgcc + - perl-threaded + - viennarna >=2.2.7 + + +locarna 1.8.11 1 +---------------- +file name : locarna-1.8.11-1.tar.bz2 +name : locarna +version : 1.8.11 +build : 1 +build number: 1 +size : 23.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.8.11-1.tar.bz2 +md5 : 3173a4aae738a8e5ecd891bbcdc5a91c +dependencies: + - libgcc + - perl-threaded + - viennarna >=2.2.8 + + +locarna 1.8.12 0 +---------------- +file name : locarna-1.8.12-0.tar.bz2 +name : locarna +version : 1.8.12 +build : 0 +build number: 0 +size : 24.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.8.12-0.tar.bz2 +md5 : c90cd4df52170aacbcda215bf49db43d +dependencies: + - libgcc + - perl-threaded + - viennarna ==2.3.1 + + +locarna 1.9.0 0 +--------------- +file name : locarna-1.9.0-0.tar.bz2 +name : locarna +version : 1.9.0 +build : 0 +build number: 0 +size : 24.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.9.0-0.tar.bz2 +md5 : 06ce17086dd04b3f9fc1a2ad58a4324d +dependencies: + - libgcc + - perl-threaded + - viennarna ==2.3.1 + + +locarna 1.9.1 0 +--------------- +file name : locarna-1.9.1-0.tar.bz2 +name : locarna +version : 1.9.1 +build : 0 +build number: 0 +size : 24.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.9.1-0.tar.bz2 +md5 : 6ade8cf773b45b614dc8c6ac4dee91fa +dependencies: + - libgcc + - perl-threaded + - viennarna ==2.3.2 + + +locarna 1.9.1 1 +--------------- +file name : locarna-1.9.1-1.tar.bz2 +name : locarna +version : 1.9.1 +build : 1 +build number: 1 +size : 24.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.9.1-1.tar.bz2 +md5 : 74c04c393716738af7ac92149b65a226 +dependencies: + - libgcc + - perl-threaded + - viennarna ==2.3.3 + + +locarna 1.9.1 pl5.22.0_2 +------------------------ +file name : locarna-1.9.1-pl5.22.0_2.tar.bz2 +name : locarna +version : 1.9.1 +build : pl5.22.0_2 +build number: 2 +size : 24.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.9.1-pl5.22.0_2.tar.bz2 +md5 : 739b6251fd5a35799041c426973e0a03 +dependencies: + - libgcc + - perl 5.22.0* + - viennarna ==2.3.3 + + +locarna 1.9.2 h2d50403_1 +------------------------ +file name : locarna-1.9.2-h2d50403_1.tar.bz2 +name : locarna +version : 1.9.2 +build : h2d50403_1 +build number: 1 +size : 7.6 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.9.2-h2d50403_1.tar.bz2 +md5 : 8f48343e5fd5e2eaaed6dcd05ca68aee +timestamp : 2018-07-06 08:55:10 UTC +dependencies: + - libstdcxx-ng >=4.9 + - perl + - viennarna 2.3.5 + + +locarna 1.9.2 pl5.22.0_0 +------------------------ +file name : locarna-1.9.2-pl5.22.0_0.tar.bz2 +name : locarna +version : 1.9.2 +build : pl5.22.0_0 +build number: 0 +size : 24.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.9.2-pl5.22.0_0.tar.bz2 +md5 : 3bea034be7263af7bf1a0bd579eb1378 +dependencies: + - libgcc + - perl 5.22.0* + - viennarna ==2.3.5 + + +locarna 1.9.2.3 h7d875b9_1 +-------------------------- +file name : locarna-1.9.2.3-h7d875b9_1.tar.bz2 +name : locarna +version : 1.9.2.3 +build : h7d875b9_1 +build number: 1 +size : 3.7 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.9.2.3-h7d875b9_1.tar.bz2 +md5 : 2f03859308e7d759b375a80fa52dd243 +timestamp : 2021-03-26 19:25:47 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + - viennarna 2.4.13 + - viennarna >=2.4.13,<2.5.0a0 + + +locarna 1.9.2.3 h9f5acd7_2 +-------------------------- +file name : locarna-1.9.2.3-h9f5acd7_2.tar.bz2 +name : locarna +version : 1.9.2.3 +build : h9f5acd7_2 +build number: 2 +size : 3.7 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.9.2.3-h9f5acd7_2.tar.bz2 +md5 : 218e1f6d24f8d8e0009e04b6ba3a133a +timestamp : 2022-02-24 20:30:23 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - perl + - viennarna 2.4.13 + - viennarna >=2.4.13,<2.5.0a0 + + +locarna 1.9.2.3 hc9558a2_0 +-------------------------- +file name : locarna-1.9.2.3-hc9558a2_0.tar.bz2 +name : locarna +version : 1.9.2.3 +build : hc9558a2_0 +build number: 0 +size : 3.7 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-1.9.2.3-hc9558a2_0.tar.bz2 +md5 : 410204f6b7382ca8cc227613d8351f6a +timestamp : 2019-08-05 10:18:05 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - viennarna 2.4.13 + - viennarna >=2.4.13,<2.5.0a0 + + +locarna 2.0.0RC6 h7d875b9_1 +--------------------------- +file name : locarna-2.0.0RC6-h7d875b9_1.tar.bz2 +name : locarna +version : 2.0.0RC6 +build : h7d875b9_1 +build number: 1 +size : 3.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-2.0.0RC6-h7d875b9_1.tar.bz2 +md5 : 0284cff24855a03b5131a459d5f6cfdd +timestamp : 2021-03-26 19:36:42 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + - viennarna 2.4.13 + - viennarna >=2.4.13,<2.5.0a0 + + +locarna 2.0.0RC6 h9f5acd7_2 +--------------------------- +file name : locarna-2.0.0RC6-h9f5acd7_2.tar.bz2 +name : locarna +version : 2.0.0RC6 +build : h9f5acd7_2 +build number: 2 +size : 3.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-2.0.0RC6-h9f5acd7_2.tar.bz2 +md5 : d00c8950a8ab41d103486205420c9c19 +timestamp : 2022-02-24 20:56:52 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - perl + - viennarna 2.4.13 + - viennarna >=2.4.13,<2.5.0a0 + + +locarna 2.0.0RC6 hc9558a2_0 +--------------------------- +file name : locarna-2.0.0RC6-hc9558a2_0.tar.bz2 +name : locarna +version : 2.0.0RC6 +build : hc9558a2_0 +build number: 0 +size : 3.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-2.0.0RC6-hc9558a2_0.tar.bz2 +md5 : 6369f4c69539d352b77338e00343c918 +timestamp : 2020-03-26 16:41:17 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - viennarna 2.4.13 + - viennarna >=2.4.13,<2.5.0a0 + + +locarna 2.0.0RC8 h7d875b9_1 +--------------------------- +file name : locarna-2.0.0RC8-h7d875b9_1.tar.bz2 +name : locarna +version : 2.0.0RC8 +build : h7d875b9_1 +build number: 1 +size : 3.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-2.0.0RC8-h7d875b9_1.tar.bz2 +md5 : ab176ecbd964cf2785c89b029a07ec5f +timestamp : 2021-03-26 19:47:40 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + - viennarna 2.4.13 + - viennarna >=2.4.13,<2.5.0a0 + + +locarna 2.0.0RC8 h9f5acd7_2 +--------------------------- +file name : locarna-2.0.0RC8-h9f5acd7_2.tar.bz2 +name : locarna +version : 2.0.0RC8 +build : h9f5acd7_2 +build number: 2 +size : 3.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-2.0.0RC8-h9f5acd7_2.tar.bz2 +md5 : a4cd96ff25e69a249f87b173ecb38cbd +timestamp : 2022-02-24 20:43:52 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - perl + - viennarna 2.4.13 + - viennarna >=2.4.13,<2.5.0a0 + + +locarna 2.0.0RC8 hc9558a2_0 +--------------------------- +file name : locarna-2.0.0RC8-hc9558a2_0.tar.bz2 +name : locarna +version : 2.0.0RC8 +build : hc9558a2_0 +build number: 0 +size : 3.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-2.0.0RC8-hc9558a2_0.tar.bz2 +md5 : 32a466e5ea57344bd8b6967fbde4b549 +timestamp : 2019-08-05 10:25:37 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - viennarna 2.4.13 + - viennarna >=2.4.13,<2.5.0a0 + + +locarna 2.0.0RC10 pl5321h9f5acd7_0 +---------------------------------- +file name : locarna-2.0.0RC10-pl5321h9f5acd7_0.tar.bz2 +name : locarna +version : 2.0.0RC10 +build : pl5321h9f5acd7_0 +build number: 0 +size : 3.9 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/locarna-2.0.0RC10-pl5321h9f5acd7_0.tar.bz2 +md5 : 8aa3457f3db80a0c6228462368018535 +timestamp : 2022-04-04 10:13:22 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - perl diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mafft.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mafft.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..96f676b0e9b5785b910e8db5bf23650a1783b43d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mafft.manual_bundle.txt @@ -0,0 +1,518 @@ +# Tool: mafft +software_name: mafft +tier: T1 +domain: t1_backfill_overall +downloads: 1361725 +summary: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform +description: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform +dependencies: __glibc >=2.17, gawk, libgcc-ng >=12 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://mafft.cbrc.jp/alignment/software/ +doc_url: +dev_url: + +## CLI Help Source +cli:mafft +## CLI Help Content +$ conda run -n bioenv_cli mafft --help +[rc=1] + +------------------------------------------------------------------------------ + MAFFT v7.525 (2024/Mar/13) + https://mafft.cbrc.jp/alignment/software/ + MBE 30:772-780 (2013), NAR 30:3059-3066 (2002) +------------------------------------------------------------------------------ +High speed: + % mafft in > out + % mafft --retree 1 in > out (fast) + +High accuracy (for <~200 sequences x <~2,000 aa/nt): + % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok) + % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out) + % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out) + +If unsure which option to use: + % mafft --auto in > out + +--op # : Gap opening penalty, default: 1.53 +--ep # : Offset (works like gap extension penalty), default: 0.0 +--maxiterate # : Maximum number of iterative refinement, default: 0 +--clustalout : Output: clustal format, default: fasta +--reorder : Outorder: aligned, default: input order +--quiet : Do not report progress +--thread # : Number of threads (if unsure, --thread -1) +--dash : Add structural information (Rozewicki et al, submitted) + +ERROR conda.cli.main_run:execute(127): `conda run mafft --help` failed. (See above for error) + + +## URL Docs Extract +### http://mafft.cbrc.jp/alignment/software/ +MAFFT - a multiple sequence alignment program --> MAFFT version 7 Multiple alignment program for amino acid or nucleotide sequences This server is in the process of switching from HTTP to HTTPS.  No change is necessary for links, bookmarks, etc. in most cases, as they are redirected to HTTPS.  However, if you are automatically downloading packages (.zip, .tgz, etc) using cURL or other tools, please change the URL from: http://mafft.cbrc.jp/... to: http s ://mafft.cbrc.jp/... See here for detailed information. Contact email address, kazutaka.katoh@aist.go.jp , is temporarily unavailable from 2018/Feb/7.  If you sent an email to this address but have received no response, then please re-send the email to katoh@ifrec.osaka-u.ac.jp . --> About MAFFT is a multiple sequence alignment program for unix-like operating systems.  It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc . Download and Installation Mac OS X Linux Windows Source Changelog The latest version is 7.526 (2024/Apr) This version supports full-length MSA of closely-related viral geonmes .   New!   (2020/May/14) --> Versions 7.463 – 7.486 had a serious bug in the FFT-NS-i option; unnecessarily much memory was requested and the calculation sometimes failed.  This bug also affected the --auto option.  Please use 7.487 or higher.  (2021/Jul/25) Input Format Fasta format.  example1 (LSU rRNA) , example2 (protein) The type of input sequences (amino acid or nucleotide) is automatically recognized. Usage % mafft [ arguments ] input > output An alias for an accurate option (L-INS-i) for an alignment of up to ∼200 sequences × ∼2,000 sites: % mafft-linsi input > output A fast option (FFT-NS-2) for a larger sequence alignment: % mafft input > output If not sure which option to use, % mafft --auto input > output Manual (v6.240) Tips (not yet included in the manual) for large alignment, ncRNA alignment, profile alignment, etc . Related Resources MAFFT server at EBI MAFFT server at the MPI Bioinformatics Toolkit ClustalW / MAFFT / PRRN at GenomeNet ClustalW / TCoffee / MAFFT in MyHits, SIB MAFFT service in Mobyle@Pasteur --> MAFFT service in T-REX web server MAFFT service in WABI, DDBJ CIPRES Science Gateway : TeraGrid resources for Phyogenetic tree inference Jalview : an alignment editor written in Java Pfam : Protein families database of alignments and HMMs Strap : Editor for multiple sequence alignment written in JAVA BioRuby : Ruby tools for bioinformatics aLeaves collects amino acid sequences from diverse animal genomes References Rozewicki, Li, Amada, Standley, Katoh 2019 ( Nucleic Acids Research 47 :W5-W10 ) New! MAFFT-DASH: integrated protein sequence and structural alignment (describes web interface for sequence and structural alignments) Nakamura, Yamada, Tomii, Katoh 2018 ( Bioinformatics 34 :2490–2492 ) Parallelization of MAFFT for large-scale multiple sequence alignments. (describes MPI parallelization of accurate progressive options) Katoh, Rozewicki, Yamada 2019 ( Briefings in Bioinformatics 20 :1160-1166 ) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. (explains online service) Yamada, Tomii, Katoh 2016 ( Bioinformatics 32 :3246-3251 ) additional information Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees. (explains some options for aligning a large number of short sequences) Katoh, Standley 2016 ( Bioinformatics 32 :1933-1942 ) A simple method to control over-alignment in the MAFFT multiple sequence alignment program. (describes some options to avoid over-alignment) Katoh, Standley 2013 ( Molecular Biology and Evolution 30 :772-780 ) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. (outlines version 7) Kuraku, Zmasek, Nishimura, Katoh 2013 ( Nucleic Acids Research 41 :W22-W28 ) aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. (describes an interactive sequence collection/selection service by aLeaves , MAFFT and Archaeopteryx ) Katoh, Frith 2012 ( Bioinformatics 28 :3144-3146 ) Adding unaligned sequences into an existing alignment using MAFFT and LAST. (describes the --add and --addfragments options) Katoh, Toh 2010 ( Bioinformatics 26 :1899-1900 ) Parallelization of the MAFFT multiple sequence alignment program. (describes the multithread version) Katoh, Asimenos, Toh 2009 ( Methods in Molecular Biology 537 :39-64 ) Multiple Alignment of DNA Sequences with MAFFT. In Bioinformatics for DNA Sequence Analysis edited by D. Posada (outlines DNA alignment methods and several tips including group-to-group alignment and rough clustering of a large number of sequences) Katoh, Toh 2008 ( BMC Bioinformatics 9 :212 ) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. (describes RNA structural alignment methods) Katoh, Toh 2008 ( Briefings in Bioinformatics 9 :286-298 ) Recent developments in the MAFFT multiple sequence alignment program. (outlines version 6; Fast Breaking Paper in Thomson Reuters' ScienceWatch ) Katoh, Toh 2007 ( Bioinformatics 23 :372-374 )  Errata PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. (describes the PartTree algorithm) Katoh, Kuma, Toh, Miyata 2005 ( Nucleic Acids Res. 33 :511-518 ) MAFFT version 5: improvement in accuracy of multiple sequence alignment. (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies) Katoh, Misawa, Kuma, Miyata 2002 ( Nucleic Acids Res. 30 :3059-3066 ) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. (describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies) Contact kazutaka.katoh@aist.go.jp Temporarily unavailable since 2018/Feb/7.  If you sent an email to the above address but have received no response, then re-send the email to: katoh@ifrec.osaka-u.ac.jp License mafft-*-without-extensions-src.tgz: BSD mafft-*-win*.zip: GPL Other packages include the codes of the Vienna RNA package , MXSCARNA and ProbConsRNA , for RNA structural alignment.  See their license notices . © 2013 Kazutaka Katoh Download version Mac OS X Windows Linux Source Online version Alignment mafft --add Merge Phylogeny Rough tree Merits / limitations Algorithms Tips Benchmarks Feedback --> + +## Conda Search Info +$ conda search -c bioconda -c conda-forge mafft --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +mafft 7.221 0 +------------- +file name : mafft-7.221-0.tar.bz2 +name : mafft +version : 7.221 +build : 0 +build number: 0 +size : 2.8 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.221-0.tar.bz2 +md5 : 899894cb0d634ad4c555fe9c3649b71f +dependencies: [] + + +mafft 7.305 0 +------------- +file name : mafft-7.305-0.tar.bz2 +name : mafft +version : 7.305 +build : 0 +build number: 0 +size : 3.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.305-0.tar.bz2 +md5 : 52287b2fa78d02c007445ff32a4de77c +dependencies: [] + + +mafft 7.305 1 +------------- +file name : mafft-7.305-1.tar.bz2 +name : mafft +version : 7.305 +build : 1 +build number: 1 +size : 3.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.305-1.tar.bz2 +md5 : 936d44f99d86cd417c7a681c59b54d16 +timestamp : 2018-06-25 23:06:06 UTC +dependencies: [] + + +mafft 7.310 0 +------------- +file name : mafft-7.310-0.tar.bz2 +name : mafft +version : 7.310 +build : 0 +build number: 0 +size : 3.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.310-0.tar.bz2 +md5 : 216ba2dea93134d29b9577dfc3d6bac5 +dependencies: [] + + +mafft 7.310 1 +------------- +file name : mafft-7.310-1.tar.bz2 +name : mafft +version : 7.310 +build : 1 +build number: 1 +size : 3.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.310-1.tar.bz2 +md5 : 3e58942993b837e28cd6597f2859e400 +timestamp : 2018-06-25 23:12:52 UTC +dependencies: [] + + +mafft 7.310 h1b792b2_4 +---------------------- +file name : mafft-7.310-h1b792b2_4.tar.bz2 +name : mafft +version : 7.310 +build : h1b792b2_4 +build number: 4 +size : 2.7 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.310-h1b792b2_4.tar.bz2 +md5 : 4cb555eaa3736e9dca76de12cf7aba31 +timestamp : 2021-03-26 03:12:35 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + + +mafft 7.310 h87f3376_5 +---------------------- +file name : mafft-7.310-h87f3376_5.tar.bz2 +name : mafft +version : 7.310 +build : h87f3376_5 +build number: 5 +size : 2.6 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.310-h87f3376_5.tar.bz2 +md5 : 526f40f1385d80d330d16b59495c8f7e +timestamp : 2022-02-21 20:47:51 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + + +mafft 7.310 h87f3376_6 +---------------------- +file name : mafft-7.310-h87f3376_6.tar.bz2 +name : mafft +version : 7.310 +build : h87f3376_6 +build number: 6 +size : 2.6 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.310-h87f3376_6.tar.bz2 +md5 : 81ab5b258f9eda5c2e295f74dc165649 +timestamp : 2023-05-11 17:21:03 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +mafft 7.310 hdbdd923_7 +---------------------- +file name : mafft-7.310-hdbdd923_7.tar.bz2 +name : mafft +version : 7.310 +build : hdbdd923_7 +build number: 7 +size : 2.7 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.310-hdbdd923_7.tar.bz2 +md5 : 57a2714fe41eee3a6952aabfa0ebb197 +timestamp : 2023-05-16 07:35:21 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +mafft 7.310 he1b5a44_3 +---------------------- +file name : mafft-7.310-he1b5a44_3.tar.bz2 +name : mafft +version : 7.310 +build : he1b5a44_3 +build number: 3 +size : 2.9 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.310-he1b5a44_3.tar.bz2 +md5 : 23add428a87591feb648f89aeaf0bc72 +timestamp : 2019-10-26 13:31:02 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +mafft 7.310 hf484d3e_2 +---------------------- +file name : mafft-7.310-hf484d3e_2.tar.bz2 +name : mafft +version : 7.310 +build : hf484d3e_2 +build number: 2 +size : 3.6 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.310-hf484d3e_2.tar.bz2 +md5 : 0965c4ee8f2bc3a5eee54d91e81820a3 +timestamp : 2019-05-09 10:33:10 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +mafft 7.313 0 +------------- +file name : mafft-7.313-0.tar.bz2 +name : mafft +version : 7.313 +build : 0 +build number: 0 +size : 3.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.313-0.tar.bz2 +md5 : b9f432e67fcaccaf3382a236872d7f1c +dependencies: [] + + +mafft 7.313 1 +------------- +file name : mafft-7.313-1.tar.bz2 +name : mafft +version : 7.313 +build : 1 +build number: 1 +size : 3.3 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.313-1.tar.bz2 +md5 : 0cd8adfe3220bb04df87e0062a949aaa +timestamp : 2018-06-25 23:09:20 UTC +dependencies: [] + + +mafft 7.402 0 +------------- +file name : mafft-7.402-0.tar.bz2 +name : mafft +version : 7.402 +build : 0 +build number: 0 +size : 4.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.402-0.tar.bz2 +md5 : 3fe3911ae2467e672418b7848070af30 +timestamp : 2018-07-23 22:06:35 UTC +dependencies: [] + + +mafft 7.407 0 +------------- +file name : mafft-7.407-0.tar.bz2 +name : mafft +version : 7.407 +build : 0 +build number: 0 +size : 4.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.407-0.tar.bz2 +md5 : 5d2a0e04ae4f60989db7abc66950b612 +timestamp : 2018-08-22 17:11:19 UTC +dependencies: [] + + +mafft 7.407 1 +------------- +file name : mafft-7.407-1.tar.bz2 +name : mafft +version : 7.407 +build : 1 +build number: 1 +size : 4.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.407-1.tar.bz2 +md5 : fb720ae5f39f9ed0693a2616dd6c72bf +timestamp : 2019-03-09 15:47:42 UTC +dependencies: [] + + +mafft 7.407 hf484d3e_2 +---------------------- +file name : mafft-7.407-hf484d3e_2.tar.bz2 +name : mafft +version : 7.407 +build : hf484d3e_2 +build number: 2 +size : 4.5 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.407-hf484d3e_2.tar.bz2 +md5 : c7ac2004b8a41672f5ee51efef5f9689 +timestamp : 2019-05-09 10:38:23 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +mafft 7.453 h516909a_0 +---------------------- +file name : mafft-7.453-h516909a_0.tar.bz2 +name : mafft +version : 7.453 +build : h516909a_0 +build number: 0 +size : 1.2 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.453-h516909a_0.tar.bz2 +md5 : 69bf572b5060a640c7b5d01e025c384e +timestamp : 2019-12-01 23:32:02 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +mafft 7.453 h516909a_1 +---------------------- +file name : mafft-7.453-h516909a_1.tar.bz2 +name : mafft +version : 7.453 +build : h516909a_1 +build number: 1 +size : 1.2 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.453-h516909a_1.tar.bz2 +md5 : 3f05213686df1e7bfd79e29706eaceff +timestamp : 2019-12-06 05:52:43 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +mafft 7.455 h516909a_0 +---------------------- +file name : mafft-7.455-h516909a_0.tar.bz2 +name : mafft +version : 7.455 +build : h516909a_0 +build number: 0 +size : 3.1 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.455-h516909a_0.tar.bz2 +md5 : 2aeabfcbb5c304937cf784df5b050f90 +timestamp : 2019-12-07 15:02:01 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +mafft 7.458 h516909a_0 +---------------------- +file name : mafft-7.458-h516909a_0.tar.bz2 +name : mafft +version : 7.458 +build : h516909a_0 +build number: 0 +size : 3.2 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.458-h516909a_0.tar.bz2 +md5 : 5a05a3f2543a847174c8bb24c7edbd56 +timestamp : 2020-03-31 08:26:43 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +mafft 7.463 h516909a_0 +---------------------- +file name : mafft-7.463-h516909a_0.tar.bz2 +name : mafft +version : 7.463 +build : h516909a_0 +build number: 0 +size : 3.2 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.463-h516909a_0.tar.bz2 +md5 : 3aa81b60e32bc12236125db39620468d +timestamp : 2020-04-18 07:51:05 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +mafft 7.464 h516909a_0 +---------------------- +file name : mafft-7.464-h516909a_0.tar.bz2 +name : mafft +version : 7.464 +build : h516909a_0 +build number: 0 +size : 3.2 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.464-h516909a_0.tar.bz2 +md5 : 917a635f8ba602479e79c27be703e1cf +timestamp : 2020-04-22 01:07:28 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +mafft 7.467 h516909a_0 +---------------------- +file name : mafft-7.467-h516909a_0.tar.bz2 +name : mafft +version : 7.467 +build : h516909a_0 +build number: 0 +size : 3.2 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.467-h516909a_0.tar.bz2 +md5 : c4f6e682378b88829debebbc1d3df2d7 +timestamp : 2020-05-23 05:08:00 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +mafft 7.470 h516909a_0 +---------------------- +file name : mafft-7.470-h516909a_0.tar.bz2 +name : mafft +version : 7.470 +build : h516909a_0 +build number: 0 +size : 3.2 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.470-h516909a_0.tar.bz2 +md5 : cca0739dcf774c907ca513ef4aae0d5d +timestamp : 2020-06-20 03:30:10 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +mafft 7.471 h516909a_0 +---------------------- +file name : mafft-7.471-h516909a_0.tar.bz2 +name : mafft +version : 7.471 +build : h516909a_0 +build number: 0 +size : 3.2 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.471-h516909a_0.tar.bz2 +md5 : b26b9dac54861cb577e2f6267c9360f0 +timestamp : 2020-07-03 06:02:38 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +mafft 7.475 h516909a_0 +---------------------- +file name : mafft-7.475-h516909a_0.tar.bz2 +name : mafft +version : 7.475 +build : h516909a_0 +build number: 0 +size : 3.2 MB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mafft-7.475-h516909a_0.tar.bz2 +md5 : 8cdb1b1911877e4898696d4c10b40d8b +timestamp : 2020-11-26 01:58:58 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +mafft 7.475 h779adbc_1 +---------------------- +file name : diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mameshiba.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mameshiba.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e5bd34a502f2c92230d0cf49b4770275186191a5 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mameshiba.manual_bundle.txt @@ -0,0 +1,300 @@ +# Tool: mameshiba +software_name: mameshiba +tier: T1 +domain: single_cell +downloads: 1872 +summary: mameshiba installs only the dependencies needed to run MameShiba. +description: mameshiba is a minimal conda meta-package that installs all dependencies required +for running MameShiba (https://github.com/Sika-Zheng-Lab/Shiba). +dependencies: numexpr >=2.8.4,<3.0.0, numpy >=1.26.4,<2.0.0, pandas >=1.5.3,<3.0.0, pysam >=0.23.0,<1.0.0, python >=3.11.0,<3.13.0, pyyaml >=6.0.2,<7.0.0, regtools >=1.0.0,<2.0.0, scanpy >=1.9.5,<2.0.0, statsmodels >=0.13.5,<1.0.0, stringtie >=3.0.0,<4.0.0, subread >=2.0.8,<3.0.0 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/Sika-Zheng-Lab/Shiba +doc_url: https://sika-zheng-lab.github.io/Shiba +dev_url: https://github.com/Sika-Zheng-Lab/Shiba + +## URL Docs Extract +### https://sika-zheng-lab.github.io/Shiba +Shiba Skip to content Shiba Home Initializing search Sika-Zheng-Lab/Shiba Home Installation Quick start Output Usage Shiba Sika-Zheng-Lab/Shiba Home Home Table of contents Contents Citation Installation Quick start Quick start With bulk RNA-seq data With single-cell RNA-seq data Output Output Shiba/SnakeShiba scShiba/SnakeScShiba Usage Usage Shiba scShiba SnakeShiba SnakeScShiba Table of contents Contents Citation Shiba ¶ A versatile computational method for systematic identification of differential RNA splicing. Shiba / scShiba can quantify and identify differential splicing events from bulk RNA-seq data and single-cell RNA-seq data. Shiba and scShiba are also implemented as Snakemake workflows, SnakeShiba and SnakeScShiba , respectively. See CHANGELOG.md for the latest updates. Report a bug If you continue to encounter issues, please don't hesitate to open an issue on GitHub. The community and developers are here to help! Contents ¶ Installation Quick Start With bulk RNA-seq data With single-cell RNA-seq data Output Shiba/SnakeShiba scShiba/SnakeScShiba Usage shiba.py snakeshiba.smk scshiba.py snakescshiba.smk Citation ¶ Kubota N, Chen L, Zheng S. Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms . Nucleic Acids Research 53(4), 2025, gkaf098. Next Installation © 2024 Naoto Kubota Made with Material for MkDocs + +### https://github.com/Sika-Zheng-Lab/Shiba +GitHub - Sika-Zheng-Lab/Shiba: A versatile method for systematic identification of differential RNA splicing across platforms · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Sika-Zheng-Lab / Shiba Public Notifications You must be signed in to change notification settings Fork 3 Star 16 Code Issues 10 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Sika-Zheng-Lab/Shiba main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 426 Commits 426 Commits .github .github docker docker docs docs example example img img src src test test .coveragerc .coveragerc .gitignore .gitignore CHANGELOG.md CHANGELOG.md LICENSE LICENSE README.md README.md VERSION VERSION codecov.yml codecov.yml mkdocs.yml mkdocs.yml scshiba.py scshiba.py shiba.py shiba.py snakescshiba.smk snakescshiba.smk snakeshiba.smk snakeshiba.smk View all files Repository files navigation README MIT license Shiba (v0.8.2) A versatile computational method for systematic identification of differential RNA splicing. Shiba/scShiba can quantify and identify differential splicing events (DSEs) from bulk RNA-seq data and single-cell RNA-seq data. Shiba and scShiba are also implemented as Snakemake workflows, SnakeShiba and SnakeScShiba, respectively. See CHANGELOG.md for the latest updates. Important Shiba now supports long-read RNA-seq data analysis! Please check the manual for more details. Overview Shiba comprises four main steps: Transcript assembly : Assemble transcripts from RNA-seq reads using StringTie Splicing event identification : Identify alternative mRNA splicing events from assembled transcripts Read counting : Count reads mapped to each splicing event using RegTools and featureCounts Statistical analysis : Identify DSEs based on Fisher's exact test Installation Conda conda create -n shiba -c conda-forge -c bioconda shiba conda activate shiba pip install styleframe==4.2 # optional, for generating outputs in Excel format. If you want to perform only splicing analysis, you can install minimal dependencies and run MameShiba , a lightweight version of Shiba. conda create -n mameshiba -c conda-forge -c bioconda mameshiba Docker docker pull naotokubota/shiba:v0.8.2 Usage Manual for Shiba is available at https://sika-zheng-lab.github.io/Shiba/ . Shiba shiba.py -p 4 config.yaml MameShiba , a lightweight version of Shiba shiba.py --mame -p 4 config.yaml SnakeShiba , Snakemake-based workflow of Shiba snakemake -s snakeshiba.smk --configfile config.yaml --cores 4 --use-singularity scShiba , a single-cell RNA-seq version of Shiba scshiba.py -p 4 config.yaml SnakeScShiba , Snakemake-based workflow of scShiba snakemake -s snakescshiba.smk --configfile config.yaml --cores 4 --use-singularity Visualization Do you want to visualize the results of Shiba analysis? Try 🐕 shiba2sashimi 🍣 ! Contributing Thank you for wanting to improve Shiba! If you have any bugs or questions, feel free to open an issue or pull request. Citation Kubota N, Chen L, Zheng S. Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms . Nucleic Acids Research 53(4), 2025, gkaf098. Authors Naoto Kubota ( 0000-0003-0612-2300 ) Liang Chen ( 0000-0001-6164-4553 ) Sika Zheng ( 0000-0002-0573-4981 ) About A versatile method for systematic identification of differential RNA splicing across platforms sika-zheng-lab.github.io/Shiba/ Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 16 stars Watchers 3 watching Forks 3 forks Report repository Releases 23 v0.8.2 Latest Feb 24, 2026 + 22 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 80.6% HTML 15.3% CSS 2.2% JavaScript 1.2% Other 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/Sika-Zheng-Lab/Shiba +GitHub - Sika-Zheng-Lab/Shiba: A versatile method for systematic identification of differential RNA splicing across platforms · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Sika-Zheng-Lab / Shiba Public Notifications You must be signed in to change notification settings Fork 3 Star 16 Code Issues 10 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Sika-Zheng-Lab/Shiba main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 426 Commits 426 Commits .github .github docker docker docs docs example example img img src src test test .coveragerc .coveragerc .gitignore .gitignore CHANGELOG.md CHANGELOG.md LICENSE LICENSE README.md README.md VERSION VERSION codecov.yml codecov.yml mkdocs.yml mkdocs.yml scshiba.py scshiba.py shiba.py shiba.py snakescshiba.smk snakescshiba.smk snakeshiba.smk snakeshiba.smk View all files Repository files navigation README MIT license Shiba (v0.8.2) A versatile computational method for systematic identification of differential RNA splicing. Shiba/scShiba can quantify and identify differential splicing events (DSEs) from bulk RNA-seq data and single-cell RNA-seq data. Shiba and scShiba are also implemented as Snakemake workflows, SnakeShiba and SnakeScShiba, respectively. See CHANGELOG.md for the latest updates. Important Shiba now supports long-read RNA-seq data analysis! Please check the manual for more details. Overview Shiba comprises four main steps: Transcript assembly : Assemble transcripts from RNA-seq reads using StringTie Splicing event identification : Identify alternative mRNA splicing events from assembled transcripts Read counting : Count reads mapped to each splicing event using RegTools and featureCounts Statistical analysis : Identify DSEs based on Fisher's exact test Installation Conda conda create -n shiba -c conda-forge -c bioconda shiba conda activate shiba pip install styleframe==4.2 # optional, for generating outputs in Excel format. If you want to perform only splicing analysis, you can install minimal dependencies and run MameShiba , a lightweight version of Shiba. conda create -n mameshiba -c conda-forge -c bioconda mameshiba Docker docker pull naotokubota/shiba:v0.8.2 Usage Manual for Shiba is available at https://sika-zheng-lab.github.io/Shiba/ . Shiba shiba.py -p 4 config.yaml MameShiba , a lightweight version of Shiba shiba.py --mame -p 4 config.yaml SnakeShiba , Snakemake-based workflow of Shiba snakemake -s snakeshiba.smk --configfile config.yaml --cores 4 --use-singularity scShiba , a single-cell RNA-seq version of Shiba scshiba.py -p 4 config.yaml SnakeScShiba , Snakemake-based workflow of scShiba snakemake -s snakescshiba.smk --configfile config.yaml --cores 4 --use-singularity Visualization Do you want to visualize the results of Shiba analysis? Try 🐕 shiba2sashimi 🍣 ! Contributing Thank you for wanting to improve Shiba! If you have any bugs or questions, feel free to open an issue or pull request. Citation Kubota N, Chen L, Zheng S. Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms . Nucleic Acids Research 53(4), 2025, gkaf098. Authors Naoto Kubota ( 0000-0003-0612-2300 ) Liang Chen ( 0000-0001-6164-4553 ) Sika Zheng ( 0000-0002-0573-4981 ) About A versatile method for systematic identification of differential RNA splicing across platforms sika-zheng-lab.github.io/Shiba/ Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 16 stars Watchers 3 watching Forks 3 forks Report repository Releases 23 v0.8.2 Latest Feb 24, 2026 + 22 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 80.6% HTML 15.3% CSS 2.2% JavaScript 1.2% Other 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge mameshiba --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +mameshiba 0.6.0 hdfd78af_0 +-------------------------- +file name : mameshiba-0.6.0-hdfd78af_0.tar.bz2 +name : mameshiba +version : 0.6.0 +build : hdfd78af_0 +build number: 0 +size : 1.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mameshiba-0.6.0-hdfd78af_0.tar.bz2 +md5 : b447450d6bffa3294ea1c1ec3bf753dd +timestamp : 2025-05-03 03:35:08 UTC +dependencies: + - numexpr 2.8.4 + - numpy 1.26.4 + - pandas 1.5.3 + - pysam 0.23.0 + - python 3.11.0.* + - pyyaml 6.0.2 + - regtools 1.0.0 + - scanpy 1.9.5 + - statsmodels 0.13.5 + - stringtie 3.0.0 + - subread 2.0.8 + + +mameshiba 0.6.1 hdfd78af_0 +-------------------------- +file name : mameshiba-0.6.1-hdfd78af_0.tar.bz2 +name : mameshiba +version : 0.6.1 +build : hdfd78af_0 +build number: 0 +size : 1.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mameshiba-0.6.1-hdfd78af_0.tar.bz2 +md5 : 67143b6f6785dfe3977f8c8d44005746 +timestamp : 2025-05-04 00:15:25 UTC +dependencies: + - numexpr 2.8.4 + - numpy 1.26.4 + - pandas 1.5.3 + - pysam 0.23.0 + - python 3.11.0.* + - pyyaml 6.0.2 + - regtools 1.0.0 + - scanpy 1.9.5 + - statsmodels 0.13.5 + - stringtie 3.0.0 + - subread 2.0.8 + + +mameshiba 0.6.2 hdfd78af_0 +-------------------------- +file name : mameshiba-0.6.2-hdfd78af_0.tar.bz2 +name : mameshiba +version : 0.6.2 +build : hdfd78af_0 +build number: 0 +size : 1.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mameshiba-0.6.2-hdfd78af_0.tar.bz2 +md5 : 68140b6ca4e51b50038e23f04ceea349 +timestamp : 2025-06-25 02:21:17 UTC +dependencies: + - numexpr 2.8.4 + - numpy 1.26.4 + - pandas 1.5.3 + - pysam 0.23.0 + - python 3.11.0.* + - pyyaml 6.0.2 + - regtools 1.0.0 + - scanpy 1.9.5 + - statsmodels 0.13.5 + - stringtie 3.0.0 + - subread 2.0.8 + + +mameshiba 0.6.3 hdfd78af_0 +-------------------------- +file name : mameshiba-0.6.3-hdfd78af_0.tar.bz2 +name : mameshiba +version : 0.6.3 +build : hdfd78af_0 +build number: 0 +size : 1.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mameshiba-0.6.3-hdfd78af_0.tar.bz2 +md5 : 7700ff9ec29055f73e916e3b372dcf20 +timestamp : 2025-07-05 18:17:35 UTC +dependencies: + - numexpr 2.8.4 + - numpy 1.26.4 + - pandas 1.5.3 + - pysam 0.23.0 + - python 3.11.0.* + - pyyaml 6.0.2 + - regtools 1.0.0 + - scanpy 1.9.5 + - statsmodels 0.13.5 + - stringtie 3.0.0 + - subread 2.0.8 + + +mameshiba 0.7.0 hdfd78af_0 +-------------------------- +file name : mameshiba-0.7.0-hdfd78af_0.tar.bz2 +name : mameshiba +version : 0.7.0 +build : hdfd78af_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mameshiba-0.7.0-hdfd78af_0.tar.bz2 +md5 : 191c30e6c1298e7a3b00fc7b60d266df +timestamp : 2025-08-07 03:16:52 UTC +dependencies: + - numexpr 2.8.4 + - numpy 1.26.4 + - pandas 1.5.3 + - pysam 0.23.0 + - python 3.11.0.* + - pyyaml 6.0.2 + - regtools 1.0.0 + - scanpy 1.9.5 + - statsmodels 0.13.5 + - stringtie 3.0.0 + - subread 2.0.8 + + +mameshiba 0.7.1 hdfd78af_0 +-------------------------- +file name : mameshiba-0.7.1-hdfd78af_0.conda +name : mameshiba +version : 0.7.1 +build : hdfd78af_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mameshiba-0.7.1-hdfd78af_0.conda +md5 : 9fe9521523424abd7dccfb8773d2ba39 +timestamp : 2025-08-21 00:16:29 UTC +dependencies: + - numexpr 2.8.4 + - numpy 1.26.4 + - pandas 1.5.3 + - pysam 0.23.0 + - python 3.11.0.* + - pyyaml 6.0.2 + - regtools 1.0.0 + - scanpy 1.9.5 + - statsmodels 0.13.5 + - stringtie 3.0.0 + - subread 2.0.8 + + +mameshiba 0.8.0 hdfd78af_0 +-------------------------- +file name : mameshiba-0.8.0-hdfd78af_0.conda +name : mameshiba +version : 0.8.0 +build : hdfd78af_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mameshiba-0.8.0-hdfd78af_0.conda +md5 : 616c8536ef48013cf5b18760ffeb7890 +timestamp : 2025-11-27 01:18:17 UTC +dependencies: + - numexpr 2.8.4 + - numpy 1.26.4 + - pandas 1.5.3 + - pysam 0.23.0 + - python 3.11.0.* + - pyyaml 6.0.2 + - regtools 1.0.0 + - scanpy 1.9.5 + - statsmodels 0.13.5 + - stringtie 3.0.0 + - subread 2.0.8 + + +mameshiba 0.8.1 hdfd78af_0 +-------------------------- +file name : mameshiba-0.8.1-hdfd78af_0.conda +name : mameshiba +version : 0.8.1 +build : hdfd78af_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mameshiba-0.8.1-hdfd78af_0.conda +md5 : 4c9e22f7509e2e818214c45fedb68b6b +timestamp : 2025-12-02 03:23:45 UTC +dependencies: + - numexpr 2.8.4 + - numpy 1.26.4 + - pandas 1.5.3 + - pysam 0.23.0 + - python 3.11.0.* + - pyyaml 6.0.2 + - regtools 1.0.0 + - scanpy 1.9.5 + - statsmodels 0.13.5 + - stringtie 3.0.0 + - subread 2.0.8 + + +mameshiba 0.8.1 hdfd78af_1 +-------------------------- +file name : mameshiba-0.8.1-hdfd78af_1.conda +name : mameshiba +version : 0.8.1 +build : hdfd78af_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mameshiba-0.8.1-hdfd78af_1.conda +md5 : 5bc691d65252955efa3b080d761b84fa +timestamp : 2026-02-19 22:35:15 UTC +dependencies: + - numexpr >=2.8.4,<3.0.0 + - numpy >=1.26.4,<2.0.0 + - pandas >=1.5.3,<3.0.0 + - pysam >=0.23.0,<1.0.0 + - python >=3.11.0,<3.13.0 + - pyyaml >=6.0.2,<7.0.0 + - regtools >=1.0.0,<2.0.0 + - scanpy >=1.9.5,<2.0.0 + - statsmodels >=0.13.5,<1.0.0 + - stringtie >=3.0.0,<4.0.0 + - subread >=2.0.8,<3.0.0 + + +mameshiba 0.8.2 hdfd78af_0 +-------------------------- +file name : mameshiba-0.8.2-hdfd78af_0.conda +name : mameshiba +version : 0.8.2 +build : hdfd78af_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mameshiba-0.8.2-hdfd78af_0.conda +md5 : 1f3f481566bf497b08c6884ebb6e27c0 +timestamp : 2026-02-24 03:18:20 UTC +dependencies: + - numexpr >=2.8.4,<3.0.0 + - numpy >=1.26.4,<2.0.0 + - pandas >=1.5.3,<3.0.0 + - pysam >=0.23.0,<1.0.0 + - python >=3.11.0,<3.13.0 + - pyyaml >=6.0.2,<7.0.0 + - regtools >=1.0.0,<2.0.0 + - scanpy >=1.9.5,<2.0.0 + - statsmodels >=0.13.5,<1.0.0 + - stringtie >=3.0.0,<4.0.0 + - subread >=2.0.8,<3.0.0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mappy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mappy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..a2ec6a6efa960ddbc38b11f34feceb00ac7bd52e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mappy.manual_bundle.txt @@ -0,0 +1,531 @@ +# Tool: mappy +software_name: mappy +tier: T1 +domain: t1_backfill_overall +downloads: 272733 +summary: Minimap2 Python binding +description: Minimap2 Python binding +dependencies: libgcc >=13, libzlib >=1.3.1,<2.0a0, python >=3.9,<3.10.0a0, python_abi 3.9.* *_cp39 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/lh3/minimap2 +doc_url: +dev_url: + +## CLI Help Source +module:mappy +## CLI Help Content +$ conda run -n bioenv_cli python -m mappy --help +[rc=1] + +/225040511/miniconda3/envs/bioenv_cli/bin/python: No code object available for mappy + +ERROR conda.cli.main_run:execute(127): `conda run python -m mappy --help` failed. (See above for error) + + +## URL Docs Extract +### https://github.com/lh3/minimap2 +GitHub - lh3/minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} lh3 / minimap2 Public Notifications You must be signed in to change notification settings Fork 461 Star 2.2k Code Issues 51 Pull requests 17 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights lh3/minimap2 master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,222 Commits 1,222 Commits .github/ workflows .github/ workflows misc misc python python sse2neon sse2neon test test tex tex .gitignore .gitignore .gitmodules .gitmodules FAQ.md FAQ.md LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in Makefile Makefile Makefile.simde Makefile.simde NEWS.md NEWS.md README.md README.md align.c align.c bseq.c bseq.c bseq.h bseq.h code_of_conduct.md code_of_conduct.md cookbook.md cookbook.md esterr.c esterr.c example.c example.c format.c format.c hit.c hit.c index.c index.c jump.c jump.c kalloc.c kalloc.c kalloc.h kalloc.h kdq.h kdq.h ketopt.h ketopt.h khash.h khash.h krmq.h krmq.h kseq.h kseq.h ksort.h ksort.h ksw2.h ksw2.h ksw2_dispatch.c ksw2_dispatch.c ksw2_extd2_sse.c ksw2_extd2_sse.c ksw2_exts2_sse.c ksw2_exts2_sse.c ksw2_extz2_sse.c ksw2_extz2_sse.c ksw2_ll_sse.c ksw2_ll_sse.c kthread.c kthread.c kthread.h kthread.h kvec.h kvec.h lchain.c lchain.c main.c main.c map.c map.c minimap.h minimap.h minimap2.1 minimap2.1 misc.c misc.c mmpriv.h mmpriv.h options.c options.c pe.c pe.c pyproject.toml pyproject.toml sdust.c sdust.c sdust.h sdust.h seed.c seed.c setup.py setup.py sketch.c sketch.c splitidx.c splitidx.c View all files Repository files navigation README Code of conduct License Getting Started ALERT: minimap2.com is a phishing site . Please don't use anything from that website. git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and then map ./minimap2 -x map-ont -d MT-human-ont.mmi test/MT-human.fa ./minimap2 -a MT-human-ont.mmi test/MT-orang.fa > test.sam # use presets (no test data) ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio CLR genomic reads ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads ./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19+) ./minimap2 -ax lr:hq ref.fa ont-Q20.fq.gz > aln.sam # Nanopore Q20 genomic reads (v2.27+) ./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam # short genomic paired-end reads ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads (strand unknown) ./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam # noisy Nanopore direct RNA-seq ./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam # PacBio Kinnex/Iso-seq (RNA-seq) ./minimap2 -ax splice --junc-bed=anno.bed12 ref.fa query.fa > aln.sam # use annotated junctions ./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # short-read RNA-seq (v2.29+) ./minimap2 -ax splice:sr -j anno.bed12 ref.fa r1.fq r2.fq > aln.sam ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap ./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf # Nanopore read overlap # man page for detailed command line options man ./minimap2.1 Table of Contents Getting Started Users' Guide Installation General usage Use cases Map long noisy genomic reads Map long mRNA/cDNA reads Find overlaps between long reads Map short genomic reads Map short RNA-seq reads Full genome/assembly alignment Advanced features Working with >65535 CIGAR operations The cs optional tag Working with the PAF format Algorithm overview Getting help Citing minimap2 Developers' Guide Limitations Users' Guide Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2) finding overlaps between long reads with error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome; (4) aligning Illumina single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-genome alignment between two closely related species with divergence below ~15%. For ~10kb noisy reads sequences, minimap2 is tens of times faster than mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more accurate on simulated long reads and produces biologically meaningful alignment ready for downstream analyses. For >100bp Illumina short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data. Detailed evaluations are available from the minimap2 paper or the preprint . Installation Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from the release page with: curl -L https://github.com/lh3/minimap2/releases/download/v2.30/minimap2-2.30_x64-linux.tar.bz2 | tar -jxvf - ./minimap2-2.30_x64-linux/minimap2 If you want to compile from the source, you need to have a C compiler, GNU make and zlib development files installed. Then type make in the source code directory to compile. If you see compilation errors, try make sse2only=1 to disable SSE4 code, which will make minimap2 slightly slower. Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To compile for 32 bit ARM architectures (such as ARMv7), use make arm_neon=1 . To compile for for 64 bit ARM architectures (such as ARMv8), use make arm_neon=1 aarch64=1 . Minimap2 can use SIMD Everywhere (SIMDe) library for porting implementation to the different SIMD instruction sets. To compile using SIMDe, use make -f Makefile.simde . To compile for ARM CPUs, use Makefile.simde with the ARM related command lines given above. General usage Without any options, minimap2 takes a reference database and a query sequence file as input and produce approximate mapping, without base-level alignment (i.e. coordinates are only approximate and no CIGAR in output), in the PAF format : minimap2 ref.fa query.fq > approx-mapping.paf You can ask minimap2 to generate CIGAR at the cg tag of PAF with: minimap2 -c ref.fa query.fq > alignment.paf or to output alignments in the SAM format : minimap2 -a ref.fa query.fq > alignment.sam Minimap2 seamlessly works with gzip'd FASTA and FASTQ formats as input. You don't need to convert between FASTA and FASTQ or decompress gzip'd files first. For the human reference genome, minimap2 takes a few minutes to generate a minimizer index for the reference before mapping. To reduce indexing time, you can optionally save the index with option -d and replace the reference sequence file with the index file on the minimap2 command line: minimap2 -d ref.mmi ref.fa # indexing minimap2 -a ref.mmi reads.fq > alignment.sam # alignment Importantly , it should be noted that once you build the index, indexing parameters such as -k , -w , -H and -I can't be changed during mapping. If you are running minimap2 for different data types, you will probably need to keep multiple indexes generated with different parameters. This makes minimap2 different from BWA which always uses the same index regardless of query data types. Use cases Minimap2 uses the same base algorithm for all applications. However, due to the different data types it supports (e.g. short vs long reads; DNA vs mRNA reads), minimap2 needs to be tuned for optimal performance and accuracy. It is usually recommended to choose a preset with option -x , which sets multiple parameters at the same time. The default setting is the same as map-ont . Map long noisy genomic reads minimap2 -ax map-pb ref.fa pacbio-reads.fq > aln.sam # for PacBio CLR reads minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam # for Oxford Nanopore reads minimap2 -ax map-iclr ref.fa iclr-reads.fq > aln.sam # for Illumina Complete Long Reads The difference between map-pb and map-ont is that map-pb uses homopolymer-compressed (HPC) minimizers as seeds, while map-ont uses ordinary minimizers as seeds. Empirical evaluation suggests HPC minimizers improve performance and sensitivity when aligning PacBio CLR reads, but hurt when aligning Nanopore reads. map-iclr uses an adjusted alignment scoring matrix that accounts for the low overall error rate in the reads, with transversion errors being less frequent than transitions. Map long mRNA/cDNA reads minimap2 -ax splice:hq -uf ref.fa iso-seq.fq > aln.sam # PacBio Iso-seq/traditional cDNA minimap2 -ax splice ref.fa nanopore-cdna.fa > aln.sam # Nanopore 2D cDNA-seq minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam # Nanopore Direct RNA-seq minimap2 -ax splice --splice-flank=no SIRV.fa SIRV-seq.fa # mapping against SIRV control There are different long-read RNA-seq technologies, including tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq and Direct RNA-seq. They produce data of varying quality and properties. By default, -x splice assumes the read orientation relative to the transcript strand is unknown. It tries two rounds of alignment to infer the orientation and write the strand to the ts SAM/PAF tag if possible. For Iso-seq, Direct RNA-seq and tranditional full-length cDNAs, it would be desired to apply -u f to force minimap2 to consider the forward transcript strand only. This speeds up alignment with slight improvement to accuracy. For noisy Nanopore Direct RNA-seq reads, it is recommended to use a smaller k-mer size for increased sensitivity to the first or the last exons. Minimap2 rates an alignment by the score of the max-scoring sub-segment, excluding introns, and marks the best alignment as primary in SAM. When a spliced gene also has unspliced pseudogenes, minimap2 slightly prefers the spliced alignment. By default, minimap2 outputs up to five secondary alignments (i.e. likely pseudogenes in the context of RNA-seq mapping). This can be tuned with option -N . For long RNA-seq reads, minimap2 may produce chimeric alignments potentially caused by gene fusions/structural variations or by an intron longer than the max intron length -G (200k by default). For now, it is not recommended to apply an excessively large -G as this slows down minimap2 and sometimes leads to false alignments. It is worth noting that by default -x splice prefers GT[A/G]..[C/T]AG over GT[C/T]..[A/G]AG, and then over other splicing signals. Considering one additional base improves the junction accuracy for noisy reads, but reduces the accuracy when aligning against the widely used SIRV control data. This is because SIRV does not honor the evolutionarily conservative splicing signal. If you are studying SIRV, you may apply --splice-flank=no to let minimap2 only model GT..AG, ignoring the additional base. Since v2.17, minimap2 can optionally take annotated genes as input and prioritize on annotated splice junctions. To use this feature, you can paftools.js gff2bed anno.gff > anno.bed minimap2 -ax splice --junc-bed anno.bed ref.fa query.fa > aln.sam Here, anno.gff is the gene annotation in the GTF or GFF3 format ( gff2bed automatically tests the format). The output of gff2bed is in the 12-column BED format, or the BED12 format. With the --junc-bed option, minimap2 adds a bonus score (tuned by --junc-bonus ) if an aligned junction matches a junction in the annotation. Option --junc-bed also takes 5-column BED, including the strand field. In this case, each line indicates an oriented junction. Note: --junc-bed is intended for long noisy RNA-seq reads only. Applying the option to short RNA-seq reads would increase run time with little improvement to junction accuracy. Find overlaps between long reads minimap2 -x ava-pb reads.fq reads.fq > ovlp.paf # PacBio CLR read overlap minimap2 -x ava-ont reads.fq reads.fq > ovlp.paf # Oxford Nanopore read overlap Similarly, ava-pb uses HPC minimizers while ava-ont uses ordinary minimizers. It is usually not recommended to perform base-level alignment in the overlapping mode because it is slow and may produce false positive overlaps. However, if performance is not a concern, you may try to add -a or -c anyway. Map short genomic reads minimap2 -ax sr ref.fa reads-se.fq > aln.sam # single-end alignment minimap2 -ax sr ref.fa read1.fq read2.fq > aln.sam # paired-end alignment minimap2 -ax sr ref.fa reads-interleaved.fq > aln.sam # paired-end alignment When two read files are specified, minimap2 reads from each file in turn and merge them into an interleaved stream internally. Two reads are considered to be paired if they are adjacent in the input stream and have the same name (with the /[0-9] suffix trimmed if present). Single- and paired-end reads can be mixed. Map short RNA-seq reads minimap2 -ax splice:sr ref.fa reads-se.fq.gz > aln.sam # single-end minimap2 -ax splice:sr ref.fa r1.fq.gz r2.fq.gz > aln.sam # paired-end minimap2 -ax splice:sr -j anno.bed ref.fa r1.fq r2.fq > aln.sam # use annotation # 2-pass alignment minimap2 -x splice:sr -j anno.bed --write-junc ref.fa r1.fq r2.fq > junc.bed minimap2 -ax splice:sr -j anno.bed --pass1=junc.bed ref.fa r1.fq r2.fq > aln.sam The new preset splice:sr was added in v2.29. It functions similarly to sr except that it performs spliced alignment. Full genome/assembly alignment minimap2 -ax asm5 ref.fa asm.fa > aln.sam # assembly to assembly/ref alignment For cross-species full-genome alignment, the scoring system needs to be tuned according to the sequence divergence. Advanced features Working with >65535 CIGAR operations Due to a design flaw, BAM does not work with CIGAR strings with >65535 operations (SAM and CRAM work). However, for ultra-long nanopore reads minimap2 may align ~1% of read bases with long CIGARs beyond the capability of BAM. If you convert such SAM/CRAM to BAM, Picard and recent samtools will throw an error and abort. Older samtools and other tools may create corrupted BAM. To avoid this issue, you can add option -L at the minimap2 command line. This option moves a long CIGAR to the CG tag and leaves a fully clipped CIGAR at the SAM CIGAR column. Current tools that don't read CIGAR (e.g. merging and sorting) still work with such BAM records; tools that read CIGAR will effectively ignore these records. It has been decided that future tools will seamlessly recognize long-cigar records generated by option -L . TL;DR : if you work with ultra-long reads and use tools that only process BAM files, please add option -L . The cs optional tag The cs SAM/PAF tag encodes bases at mismatches and INDELs. It matches regular expression /(:[0-9]+|\*[a-z][a-z]|[=\+\-][A-Za-z]+)+/ . Like CIGAR, cs consists of series of operations. Each leading character specifies the operation; the following sequence is the one involved in the operation. The cs tag is enabled by command line option --cs . The following alignment, for example: CGATCGATAAATAGAGTAG---GAATAGCA || |||| |||||||||| |||| || | CGATCG---AATAGAGTAGGTCGAATtGCA is represented as :6-ata:10+gtc:4*at:3 , where :[0-9]+ represents an identical block, -ata represents a deletion, +gtc an insertion and *at indicates reference base a is substituted with a query base t . It is similar to the MD SAM tag but is standalone and easier to parse. If --cs=long is used, the cs string also contains identical sequences in the alignment. The above example will become =CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA . The long form of cs encodes both reference and query sequences in one string. The cs tag also encodes intron positions and splicing signals (see the minimap2 manpage for details). Working with the PAF format Minimap2 also comes with a (java)script paftools.js that processes alignments in the PAF format. It calls variants from assembly-to-reference alignment, lifts over BED files based on alignment, converts between formats and provides utilities for various evaluations. For details, please see misc/README.md . Algorithm overview In the following, minimap2 command line options have a dash ahead and are highlighted in bold. The description may help to tune minimap2 parameters. Read -I [= 4G ] reference bases, extract ( -k , -w )-minimizers and index them in a hash table. Read -K [= 200M ] query bases. For each query sequence, do step 3 through 7: For each ( -k , -w )-minimizer on the query, check against the reference index. If a reference minimizer is not among the top -f [= 2e-4 ] most frequent, collect its the occurrences in the reference, which are called seeds . Sort seeds by position in the reference. Chain them with dynamic programming. Each chain represents a potential mapping. For read overlapping, report all chains and then go to step 8. For reference mapping, do step 5 through 7: Let P be the set of primary mappings, which is an empty set initially. For each chain from the best to the worst according to their chaining scores: if on the query, the chain overlaps with a chain in P by --mask-level [= 0.5 ] or higher fraction of the shorter chain, mark the chain as secondary to the chain in P ; otherwise, add the chain to P . Retain all primary mappings. Also retain up to -N [= 5 ] top secondary mappings if their chaining scores are higher than -p [= 0.8 ] of their corresponding primary mappings. If alignment is requested, + +## Conda Search Info +$ conda search -c bioconda -c conda-forge mappy --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +mappy 2.2 py35_0 +---------------- +file name : mappy-2.2-py35_0.tar.bz2 +name : mappy +version : 2.2 +build : py35_0 +build number: 0 +size : 358 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.2-py35_0.tar.bz2 +md5 : f782d845a48b0cc89f333a4622720aab +dependencies: + - python 3.5* + - zlib 1.2.8* + + +mappy 2.2 py36_0 +---------------- +file name : mappy-2.2-py36_0.tar.bz2 +name : mappy +version : 2.2 +build : py36_0 +build number: 0 +size : 360 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.2-py36_0.tar.bz2 +md5 : 6c2b2b390e06424146ccefae23dfa91a +dependencies: + - python 3.6* + - zlib 1.2.8* + + +mappy 2.4 py27_0 +---------------- +file name : mappy-2.4-py27_0.tar.bz2 +name : mappy +version : 2.4 +build : py27_0 +build number: 0 +size : 383 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.4-py27_0.tar.bz2 +md5 : 1c78b1de3ad14523fc142fa9610a32c6 +dependencies: + - python 2.7* + - zlib 1.2.8* + + +mappy 2.4 py35_0 +---------------- +file name : mappy-2.4-py35_0.tar.bz2 +name : mappy +version : 2.4 +build : py35_0 +build number: 0 +size : 399 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.4-py35_0.tar.bz2 +md5 : daf06200b8aafe6b56b1828d23ccbf4c +dependencies: + - python 3.5* + - zlib 1.2.8* + + +mappy 2.4 py36_0 +---------------- +file name : mappy-2.4-py36_0.tar.bz2 +name : mappy +version : 2.4 +build : py36_0 +build number: 0 +size : 401 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.4-py36_0.tar.bz2 +md5 : 8afa7ee79db1100bd1f18fea6af06586 +dependencies: + - python 3.6* + - zlib 1.2.8* + + +mappy 2.5 py27_0 +---------------- +file name : mappy-2.5-py27_0.tar.bz2 +name : mappy +version : 2.5 +build : py27_0 +build number: 0 +size : 385 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.5-py27_0.tar.bz2 +md5 : d305a4c0fc3e27157777a303e62a0292 +dependencies: + - python 2.7* + - zlib 1.2.8* + + +mappy 2.5 py35_0 +---------------- +file name : mappy-2.5-py35_0.tar.bz2 +name : mappy +version : 2.5 +build : py35_0 +build number: 0 +size : 403 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.5-py35_0.tar.bz2 +md5 : 04ee848f57d1f2312ed7a5255bc16bb0 +dependencies: + - python 3.5* + - zlib 1.2.8* + + +mappy 2.5 py36_0 +---------------- +file name : mappy-2.5-py36_0.tar.bz2 +name : mappy +version : 2.5 +build : py36_0 +build number: 0 +size : 405 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.5-py36_0.tar.bz2 +md5 : c78f3836b9ccfa3331955e60e79cd654 +dependencies: + - python 3.6* + - zlib 1.2.8* + + +mappy 2.6 py27_0 +---------------- +file name : mappy-2.6-py27_0.tar.bz2 +name : mappy +version : 2.6 +build : py27_0 +build number: 0 +size : 391 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.6-py27_0.tar.bz2 +md5 : 7266985379bc06ca03fd86336d1d3c75 +dependencies: + - python 2.7* + - zlib 1.2.8* + + +mappy 2.6 py35_0 +---------------- +file name : mappy-2.6-py35_0.tar.bz2 +name : mappy +version : 2.6 +build : py35_0 +build number: 0 +size : 409 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.6-py35_0.tar.bz2 +md5 : b80ad006611f327cb10f72355d3fefaa +dependencies: + - python 3.5* + - zlib 1.2.8* + + +mappy 2.6 py36_0 +---------------- +file name : mappy-2.6-py36_0.tar.bz2 +name : mappy +version : 2.6 +build : py36_0 +build number: 0 +size : 411 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.6-py36_0.tar.bz2 +md5 : 0776e06e5e4d773b27352f11cc13691e +dependencies: + - python 3.6* + - zlib 1.2.8* + + +mappy 2.7 py27_0 +---------------- +file name : mappy-2.7-py27_0.tar.bz2 +name : mappy +version : 2.7 +build : py27_0 +build number: 0 +size : 394 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.7-py27_0.tar.bz2 +md5 : 903c9ae4b214f954edf96d3554356ea5 +dependencies: + - python 2.7* + - zlib 1.2.8* + + +mappy 2.7 py35_0 +---------------- +file name : mappy-2.7-py35_0.tar.bz2 +name : mappy +version : 2.7 +build : py35_0 +build number: 0 +size : 413 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.7-py35_0.tar.bz2 +md5 : 41885db76345570466e2d5b9c63d406a +dependencies: + - python 3.5* + - zlib 1.2.8* + + +mappy 2.7 py36_0 +---------------- +file name : mappy-2.7-py36_0.tar.bz2 +name : mappy +version : 2.7 +build : py36_0 +build number: 0 +size : 415 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.7-py36_0.tar.bz2 +md5 : 00259b4313f80240b42efaa1c1663825 +dependencies: + - python 3.6* + - zlib 1.2.8* + + +mappy 2.8 py27_0 +---------------- +file name : mappy-2.8-py27_0.tar.bz2 +name : mappy +version : 2.8 +build : py27_0 +build number: 0 +size : 408 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.8-py27_0.tar.bz2 +md5 : b10019e875b71fa8d07fd7526ae30669 +dependencies: + - python 2.7* + - zlib 1.2.8* + + +mappy 2.8 py27_1 +---------------- +file name : mappy-2.8-py27_1.tar.bz2 +name : mappy +version : 2.8 +build : py27_1 +build number: 1 +size : 408 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.8-py27_1.tar.bz2 +md5 : ac99cf0e400f28b1d5a99ad12f417dbd +dependencies: + - python 2.7* + - zlib 1.2.11* + + +mappy 2.8 py35_0 +---------------- +file name : mappy-2.8-py35_0.tar.bz2 +name : mappy +version : 2.8 +build : py35_0 +build number: 0 +size : 424 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.8-py35_0.tar.bz2 +md5 : f17df77314029ddf1f12f71d7e558b08 +dependencies: + - python 3.5* + - zlib 1.2.8* + + +mappy 2.8 py35_1 +---------------- +file name : mappy-2.8-py35_1.tar.bz2 +name : mappy +version : 2.8 +build : py35_1 +build number: 1 +size : 424 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.8-py35_1.tar.bz2 +md5 : aa5ce24632dbc96b3ffb941643ba7a84 +dependencies: + - python 3.5* + - zlib 1.2.11* + + +mappy 2.8 py36_0 +---------------- +file name : mappy-2.8-py36_0.tar.bz2 +name : mappy +version : 2.8 +build : py36_0 +build number: 0 +size : 427 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.8-py36_0.tar.bz2 +md5 : d9ab07d3aca2f898c6b3450d5f76c771 +dependencies: + - python 3.6* + - zlib 1.2.8* + + +mappy 2.8 py36_1 +---------------- +file name : mappy-2.8-py36_1.tar.bz2 +name : mappy +version : 2.8 +build : py36_1 +build number: 1 +size : 427 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.8-py36_1.tar.bz2 +md5 : 2db157e71e2e29ff20d8301a0685076e +dependencies: + - python 3.6* + - zlib 1.2.11* + + +mappy 2.9 py27_1 +---------------- +file name : mappy-2.9-py27_1.tar.bz2 +name : mappy +version : 2.9 +build : py27_1 +build number: 1 +size : 428 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.9-py27_1.tar.bz2 +md5 : 3d07b8f25d177903eb9c5edaa4906065 +dependencies: + - python 2.7* + - zlib 1.2.11* + + +mappy 2.9 py35_1 +---------------- +file name : mappy-2.9-py35_1.tar.bz2 +name : mappy +version : 2.9 +build : py35_1 +build number: 1 +size : 446 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.9-py35_1.tar.bz2 +md5 : 5bbcb6d0e75720d0885bd1c007ce0566 +dependencies: + - python 3.5* + - zlib 1.2.11* + + +mappy 2.9 py36_1 +---------------- +file name : mappy-2.9-py36_1.tar.bz2 +name : mappy +version : 2.9 +build : py36_1 +build number: 1 +size : 449 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.9-py36_1.tar.bz2 +md5 : 50faf81a6465b38fce6a417255992a12 +dependencies: + - python 3.6* + - zlib 1.2.11* + + +mappy 2.10 py27_1 +----------------- +file name : mappy-2.10-py27_1.tar.bz2 +name : mappy +version : 2.10 +build : py27_1 +build number: 1 +size : 437 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.10-py27_1.tar.bz2 +md5 : dc72fc770d3a0167db7b101cc382edcb +dependencies: + - python 2.7* + - zlib 1.2.11* + + +mappy 2.10 py35_1 +----------------- +file name : mappy-2.10-py35_1.tar.bz2 +name : mappy +version : 2.10 +build : py35_1 +build number: 1 +size : 452 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.10-py35_1.tar.bz2 +md5 : 858339a6774dc347d226de65e4193b3b +dependencies: + - python 3.5* + - zlib 1.2.11* + + +mappy 2.10 py36_1 +----------------- +file name : mappy-2.10-py36_1.tar.bz2 +name : mappy +version : 2.10 +build : py36_1 +build number: 1 +size : 454 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.10-py36_1.tar.bz2 +md5 : 3a6a19708ad125929129b0127ec61fa7 +dependencies: + - python 3.6* + - zlib 1.2.11* + + +mappy 2.11 py27ha92aebf_0 +------------------------- +file name : mappy-2.11-py27ha92aebf_0.tar.bz2 +name : mappy +version : 2.11 +build : py27ha92aebf_0 +build number: 0 +size : 444 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.11-py27ha92aebf_0.tar.bz2 +md5 : 44997c31c847150f3713ab7d285df7f6 +timestamp : 2018-06-21 15:30:02 UTC +dependencies: + - libgcc-ng >=4.9 + - python >=2.7,<2.8.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +mappy 2.11 py35ha92aebf_0 +------------------------- +file name : mappy-2.11-py35ha92aebf_0.tar.bz2 +name : mappy +version : 2.11 +build : py35ha92aebf_0 +build number: 0 +size : 459 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.11-py35ha92aebf_0.tar.bz2 +md5 : 94552b9666824acf463e9a3277bedada +timestamp : 2018-06-21 15:30:40 UTC +dependencies: + - libgcc-ng >=4.9 + - python >=3.5,<3.6.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +mappy 2.11 py36ha92aebf_0 +------------------------- +file name : mappy-2.11-py36ha92aebf_0.tar.bz2 +name : mappy +version : 2.11 +build : py36ha92aebf_0 +build number: 0 +size : 461 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mappy-2.11-py36ha92aebf_0.tar.bz2 +md5 : d4342c3485cf549f092dc5c3f diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/markerrepo.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/markerrepo.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d7cdb8606fbad7d9b38edcf646dc6c597ddb147 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/markerrepo.manual_bundle.txt @@ -0,0 +1,81 @@ +# Tool: markerrepo +software_name: markerrepo +tier: T1 +domain: single_cell +downloads: 60 +summary: A tool for marker list management and annotation in the single cell context. +description: A tool for marker list management and annotation in the single cell context. +dependencies: apybiomart, gitpython, intervaltree, ipython, matplotlib-base >=3.7.1, numpy, pandas >=1.5.3, python, pyyaml >=6.0, requests, scanpy, scikit-learn >=1.2.2, seaborn >=0.12.2 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://pypi.org/project/markerrepo/ +doc_url: +dev_url: + +## URL Docs Extract +### https://pypi.org/project/markerrepo/ +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge markerrepo --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +markerrepo 0.1.5 pyh106432d_0 +----------------------------- +file name : markerrepo-0.1.5-pyh106432d_0.conda +name : markerrepo +version : 0.1.5 +build : pyh106432d_0 +build number: 0 +size : 63 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/markerrepo-0.1.5-pyh106432d_0.conda +md5 : 42e831cb755ddb776cae2fa6844cff71 +timestamp : 2026-02-13 10:39:39 UTC +dependencies: + - apybiomart + - gitpython + - intervaltree + - ipython + - matplotlib-base >=3.7.1 + - numpy + - pandas >=1.5.3 + - python + - pyyaml >=6.0 + - requests + - scanpy + - scikit-learn >=1.2.2 + - seaborn >=0.12.2 + + +markerrepo 0.1.6 pyh106432d_0 +----------------------------- +file name : markerrepo-0.1.6-pyh106432d_0.conda +name : markerrepo +version : 0.1.6 +build : pyh106432d_0 +build number: 0 +size : 63 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/markerrepo-0.1.6-pyh106432d_0.conda +md5 : 664c1064ed4b5ae2b53065d431f2ea4c +timestamp : 2026-04-27 14:25:08 UTC +dependencies: + - apybiomart + - gitpython + - intervaltree + - ipython + - matplotlib-base >=3.7.1 + - numpy + - pandas >=1.5.3 + - python + - pyyaml >=6.0 + - requests + - scanpy + - scikit-learn >=1.2.2 + - seaborn >=0.12.2 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mash.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mash.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f4fe048053e36fb9ea337d501830b3c796d0fd3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mash.manual_bundle.txt @@ -0,0 +1,502 @@ +# Tool: mash +software_name: mash +tier: T1 +domain: t1_backfill_overall +downloads: 261042 +summary: Fast sequence distance estimator that uses MinHash +description: Fast sequence distance estimator that uses MinHash +dependencies: capnproto >=1.0.2,<1.0.3.0a0, gsl >=2.8,<2.9.0a0, libcblas >=3.9.0,<4.0a0, libgcc, libgcc-ng >=12, libstdcxx, libstdcxx-ng >=12, libzlib >=1.3.1,<2.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/marbl/Mash +doc_url: +dev_url: + +## CLI Help Source +cli:mash +## CLI Help Content +$ conda run -n bioenv_cli mash --help +[rc=0] + +Mash version 2.3 + +Type 'mash --license' for license and copyright information. + +Usage: + + mash [options] [arguments ...] + +Commands: + + bounds + Print a table of Mash error bounds. + + dist + Estimate the distance of query sequences to references. + + info + Display information about sketch files. + + paste + Create a single sketch file from multiple sketch files. + + screen + Determine whether query sequences are within a larger mixture of sequences. + + sketch + Create sketches (reduced representations for fast operations). + + taxscreen + Create Kraken-style taxonomic report based on mash screen. + + triangle + Estimate a lower-triangular distance matrix. + + + + +## URL Docs Extract +### https://github.com/marbl/Mash +GitHub - marbl/Mash: Fast genome and metagenome distance estimation using MinHash · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} marbl / Mash Public Notifications You must be signed in to change notification settings Fork 94 Star 441 Code Issues 85 Pull requests 3 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights marbl/Mash master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 430 Commits 430 Commits data data doc doc src/ mash src/ mash test test .gitignore .gitignore .readthedocs.yaml .readthedocs.yaml INSTALL.txt INSTALL.txt LICENSE.txt LICENSE.txt Makefile.in Makefile.in README.md README.md bootstrap.sh bootstrap.sh configure.ac configure.ac View all files Repository files navigation README License Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases ). This source distribution is intended for other operating systems or for development. Mash requires c++14 to build, which is available in and GCC >= 5 and XCode >= 6. See http://mash.readthedocs.org for more information. About Fast genome and metagenome distance estimation using MinHash mash.readthedocs.org Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 441 stars Watchers 31 watching Forks 94 forks Report repository Releases 10 Mash v2.3 Latest Feb 26, 2021 + 9 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 94.3% C 4.0% Other 1.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge mash --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +mash 1.0.2 1 +------------ +file name : mash-1.0.2-1.tar.bz2 +name : mash +version : 1.0.2 +build : 1 +build number: 1 +size : 1.7 MB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-1.0.2-1.tar.bz2 +md5 : 5ef07b881fa6379d372e1716d882e612 +dependencies: + - boost + - libgcc + - zlib + + +mash 1.0.2 2 +------------ +file name : mash-1.0.2-2.tar.bz2 +name : mash +version : 1.0.2 +build : 2 +build number: 2 +size : 1.7 MB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-1.0.2-2.tar.bz2 +md5 : 9a316f3666e4121adcd7be80e46d1158 +dependencies: + - libgcc + - zlib + + +mash 1.1 0 +---------- +file name : mash-1.1-0.tar.bz2 +name : mash +version : 1.1 +build : 0 +build number: 0 +size : 1.7 MB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-1.1-0.tar.bz2 +md5 : 675afd4b18a1d252c4d8772dc15d940f +dependencies: + - libgcc + - zlib + + +mash 2.0 gsl1.16_0 +------------------ +file name : mash-2.0-gsl1.16_0.tar.bz2 +name : mash +version : 2.0 +build : gsl1.16_0 +build number: 0 +size : 223 KB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.0-gsl1.16_0.tar.bz2 +md5 : bfcffb72fac3aed2444e68d843f60ffa +dependencies: + - capnproto + - gsl 1.16* + - libgcc + - zlib 1.2.8* + + +mash 2.0 gsl1.16_1 +------------------ +file name : mash-2.0-gsl1.16_1.tar.bz2 +name : mash +version : 2.0 +build : gsl1.16_1 +build number: 1 +size : 223 KB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.0-gsl1.16_1.tar.bz2 +md5 : 4a4ec83ecc97b88451d9de462d93ccb4 +dependencies: + - capnproto + - gsl 1.16* + - libgcc + - zlib 1.2.11* + + +mash 2.0 gsl2.2_2 +----------------- +file name : mash-2.0-gsl2.2_2.tar.bz2 +name : mash +version : 2.0 +build : gsl2.2_2 +build number: 2 +size : 253 KB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.0-gsl2.2_2.tar.bz2 +md5 : 090723d8a43f33c8ff6356660d103843 +dependencies: + - capnproto + - gsl 2.2* + - libgcc + - openblas + - zlib 1.2.11* + + +mash 2.0 h9dd4a16_3 +------------------- +file name : mash-2.0-h9dd4a16_3.tar.bz2 +name : mash +version : 2.0 +build : h9dd4a16_3 +build number: 3 +size : 257 KB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.0-h9dd4a16_3.tar.bz2 +md5 : 584a85b832bd70403c772a140dc9a2e3 +timestamp : 2018-07-06 08:36:19 UTC +dependencies: + - capnproto + - gsl >=2.2.1,<2.3.0a0 + - libstdcxx-ng >=4.9 + - openblas >=0.2.20,<0.2.21.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.1 h9dd4a16_0 +------------------- +file name : mash-2.1-h9dd4a16_0.tar.bz2 +name : mash +version : 2.1 +build : h9dd4a16_0 +build number: 0 +size : 264 KB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.1-h9dd4a16_0.tar.bz2 +md5 : f84e9dc7ca3f95f51b73050c098ba708 +timestamp : 2018-10-08 20:19:03 UTC +dependencies: + - capnproto + - gsl >=2.2.1,<2.3.0a0 + - libstdcxx-ng >=4.9 + - openblas >=0.2.20,<0.2.21.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.1 hf69f6b5_1 +------------------- +file name : mash-2.1-hf69f6b5_1.tar.bz2 +name : mash +version : 2.1 +build : hf69f6b5_1 +build number: 1 +size : 253 KB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.1-hf69f6b5_1.tar.bz2 +md5 : f272faddb19d874f539e54eb27bc0dd6 +timestamp : 2019-02-21 20:11:31 UTC +dependencies: + - capnproto + - gsl >=2.4,<2.5.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.3,<0.3.4.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.1.1 he518ae8_0 +--------------------- +file name : mash-2.1.1-he518ae8_0.tar.bz2 +name : mash +version : 2.1.1 +build : he518ae8_0 +build number: 0 +size : 253 KB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.1.1-he518ae8_0.tar.bz2 +md5 : 99b2cbbe6ba0c26beb9ce007361c37d1 +timestamp : 2019-05-09 05:06:29 UTC +dependencies: + - capnproto + - gsl >=2.4,<2.5.0a0 + - libcblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.2 h3d38be6_0 +------------------- +file name : mash-2.2-h3d38be6_0.tar.bz2 +name : mash +version : 2.2 +build : h3d38be6_0 +build number: 0 +size : 256 KB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.2-h3d38be6_0.tar.bz2 +md5 : 8468399c038dd472bfc7563c227dda72 +timestamp : 2019-07-27 15:46:34 UTC +dependencies: + - capnproto + - gsl >=2.5,<2.6.0a0 + - libcblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.2.1 h3d38be6_0 +--------------------- +file name : mash-2.2.1-h3d38be6_0.tar.bz2 +name : mash +version : 2.2.1 +build : h3d38be6_0 +build number: 0 +size : 256 KB +license : https://raw.githubusercontent.com/marbl/Mash/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.2.1-h3d38be6_0.tar.bz2 +md5 : 221f6f3ed2d2e551c684b0afd2cdcc17 +timestamp : 2019-09-12 02:13:37 UTC +dependencies: + - capnproto + - gsl >=2.5,<2.6.0a0 + - libcblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.2.1 h3d38be6_1 +--------------------- +file name : mash-2.2.1-h3d38be6_1.tar.bz2 +name : mash +version : 2.2.1 +build : h3d38be6_1 +build number: 1 +size : 449 KB +license : https://github.com/marbl/Mash/blob/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.2.1-h3d38be6_1.tar.bz2 +md5 : e3fc0764517ac57e660a6dfc7e891d67 +timestamp : 2019-10-15 19:33:30 UTC +dependencies: + - capnproto + - gsl >=2.5,<2.6.0a0 + - libcblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.2.2 h3d38be6_0 +--------------------- +file name : mash-2.2.2-h3d38be6_0.tar.bz2 +name : mash +version : 2.2.2 +build : h3d38be6_0 +build number: 0 +size : 451 KB +license : https://github.com/marbl/Mash/blob/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.2.2-h3d38be6_0.tar.bz2 +md5 : 7d21f0c542784e6992a739fe12877198 +timestamp : 2019-10-18 07:23:08 UTC +dependencies: + - capnproto + - gsl >=2.5,<2.6.0a0 + - libcblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.2.2 h3d38be6_1 +--------------------- +file name : mash-2.2.2-h3d38be6_1.tar.bz2 +name : mash +version : 2.2.2 +build : h3d38be6_1 +build number: 1 +size : 449 KB +license : https://github.com/marbl/Mash/blob/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.2.2-h3d38be6_1.tar.bz2 +md5 : 9bd97a8bf27438804be711405acc9b88 +timestamp : 2019-10-26 15:01:45 UTC +dependencies: + - capnproto + - gsl >=2.5,<2.6.0a0 + - libcblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.2.2 ha61e061_2 +--------------------- +file name : mash-2.2.2-ha61e061_2.tar.bz2 +name : mash +version : 2.2.2 +build : ha61e061_2 +build number: 2 +size : 448 KB +license : https://github.com/marbl/Mash/blob/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.2.2-ha61e061_2.tar.bz2 +md5 : a314c4b6677a719b902ee7c3df4eee78 +timestamp : 2020-07-03 04:54:13 UTC +dependencies: + - capnproto + - gsl >=2.6,<2.7.0a0 + - libcblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.3 h7c2a333_8 +------------------- +file name : mash-2.3-h7c2a333_8.tar.bz2 +name : mash +version : 2.3 +build : h7c2a333_8 +build number: 8 +size : 612 KB +license : https://github.com/marbl/Mash/blob/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.3-h7c2a333_8.tar.bz2 +md5 : 96339a537ff80bc4882ff9750eb5ecbf +timestamp : 2024-12-11 17:04:12 UTC +dependencies: + - capnproto >=1.0.2,<1.0.3.0a0 + - gsl >=2.7,<2.8.0a0 + - libcblas >=3.9.0,<4.0a0 + - libgcc + - libgcc-ng >=12 + - libstdcxx + - libstdcxx-ng >=12 + - libzlib >=1.3.1,<2.0a0 + - zlib + + +mash 2.3 ha61e061_0 +------------------- +file name : mash-2.3-ha61e061_0.tar.bz2 +name : mash +version : 2.3 +build : ha61e061_0 +build number: 0 +size : 570 KB +license : https://github.com/marbl/Mash/blob/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.3-ha61e061_0.tar.bz2 +md5 : e5016ada8d55d8b65db57cf38dc9e486 +timestamp : 2021-02-27 00:36:11 UTC +dependencies: + - capnproto + - gsl >=2.6,<2.7.0a0 + - libcblas >=3.8.0,<4.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.3 ha9a2dd8_3 +------------------- +file name : mash-2.3-ha9a2dd8_3.tar.bz2 +name : mash +version : 2.3 +build : ha9a2dd8_3 +build number: 3 +size : 595 KB +license : https://github.com/marbl/Mash/blob/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.3-ha9a2dd8_3.tar.bz2 +md5 : 272e9719f69a9846e49f8292b7f4c965 +timestamp : 2022-02-22 20:14:44 UTC +dependencies: + - capnproto >=0.9.1,<0.9.2.0a0 + - gsl >=2.7,<2.8.0a0 + - libcblas >=3.8.0,<4.0a0 + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +mash 2.3 hb105d93_10 +-------------------- +file name : mash-2.3-hb105d93_10.tar.bz2 +name : mash +version : 2.3 +build : hb105d93_10 +build number: 10 +size : 620 KB +license : https://github.com/marbl/Mash/blob/master/LICENSE.txt +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mash-2.3-hb105d93_10.tar.bz2 +md5 : 9d22da2dbc61776f6e10cca4fae96f52 +timestamp : 2025-08-05 20:30:07 UTC +dependencies: + - capnproto >=1.0.2,<1.0.3.0a0 + - gsl >=2.8,<2.9.0a0 + - libcblas >=3.9.0,<4.0a0 + - libgcc + - libgcc-ng >=12 + - libstdcxx + - libstdcxx-ng >=12 + - libzlib >=1.3.1,<2.0a0 + + +mash 2.3 hb105d93_9 +------------------- +file name : mash-2.3-hb105d93_9.tar.bz2 +name : mash +version : 2.3 +build : hb105d93_9 +build number: 9 +size : 589 KB +license : https://github.com/marbl/Mash/blo diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/metaphlan.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/metaphlan.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..66aeda15e0d5c669e032dacc1c71026b7874a074 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/metaphlan.manual_bundle.txt @@ -0,0 +1,566 @@ +# Tool: metaphlan +software_name: metaphlan +tier: T1 +domain: t1_backfill_overall +downloads: 394200 +summary: Metagenomic Phylogenetic Analysis. +description: MetaPhlAn is a computational tool for profiling the composition of microbial +communities (Bacteria, Archaea and Eukaryotes) from metagenomic +shotgun sequencing data with species level resolution. From version 2.0 +MetaPhlAn is also able to identify specific strains (in the not-so-frequent +cases in which the sample contains a previously sequenced strains) and to +track strains across samples for all species. +dependencies: bioconductor-microbiome, biom-format, biopython, blast, bowtie2 >=2.3.0, cmseq, dendropy, h5py, hclust2, matplotlib-base, minimap2 >=2.26, muscle >=3.8.1551, numpy, pandas, phylophlan, pysam, python >=3.7, r-ape, r-base >=4, r-biocmanager, r-compositions, r-essentials, r-optparse, r-rbiom, raxml >=8.2.10, requests, samtools, scipy +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://github.com/biobakery/metaphlan +doc_url: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4 +dev_url: https://github.com/biobakery/metaphlan + +## URL Docs Extract +### https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4 +MetaPhlAn 4 · biobakery/MetaPhlAn Wiki · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} biobakery / MetaPhlAn Public Notifications You must be signed in to change notification settings Fork 91 Star 403 Code Issues 0 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights MetaPhlAn 4 Jump to bottom Claudia Mengoni edited this page Apr 16, 2025 · 20 revisions MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With StrainPhlAn, it is possible to perform accurate strain-level microbial profiling. MetaPhlAn 4 relies on ~5.1M unique clade-specific marker genes (the latest marker information file can be found here ) identified from ~1M microbial genomes (~236,600 references and 771,500 metagenomic assembled genomes) spanning 26,970 species-level genome bins (SGBs, http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html ), 4,992 of them taxonomically unidentified at the species level (the full list of the species included in the latest database can be found here ), allowing: unambiguous taxonomic assignments; an accurate estimation of organismal relative abundance; SGB-level resolution for bacteria, archaea and eukaryotes; strain identification and tracking orders of magnitude speedups compared to existing methods. metagenomic strain-level population genomics Pre-requisites MetaPhlAn requires python 3 or newer with numpy , and Biopython libraries installed. Python libraries are automatically installed by pip . MetaPhlAn relies on BowTie2 (version 2.3 or higher) to map reads against marker genes. Check that bowtie2 is present in the system path with execute and read permissions. If MetaPhlAn is installed using conda, no pre-requisites are needed. MetaPhlAn is integrated with advanced heatmap plotting with hclust2 and cladogram visualization with GraPhlAn . If you use such visualization tools please refer to their prerequisites. The best way to install MetaPhlAn is through conda via the Bioconda channel. If you have not configured your Anaconda installation to fetch packages from Bioconda, please follow these steps to set up the channels. You can install MetaPhlAn by running $ conda install -c bioconda metaphlan It is recommended to create an isolated conda environment and install MetaPhlAn into it. $ conda create --name mpa -c bioconda python=3.7 metaphlan If during the installation you encounter an incompatibility error with the glibc package, we suggest you to add the conda-forge channel to conda or run one of the following commands. $ conda install -c conda-forge -c bioconda metaphlan $ conda create --name mpa -c conda-forge -c bioconda python=3.7 metaphlan This allows having the correct version of all the dependencies isolated from the system's python installation. Before using MetaPhlAn, you should activate the mpa environment: $ conda activate mpa MetaPhlAn is also available in PyPi $ pip install metaphlan Alternatively, you can manually download from GitHub or clone the repository using the following command $ git clone https://github.com/biobakery/MetaPhlAn.git and install MetaPhlAn by running $ pip install . If you choose this way, you'll need to install manually some dependencies! MetaPhlAn needs the clade markers and the database to be downloaded locally. To obtain them: $ metaphlan --install Important! The MetaPhlAn 4 database has been substantially increased in comparison with the previous 3.1 version. Thus, for running MetaPhlAn 4, a minimum of 15GB or memory is needed. If you have installed MetaPhlAn using Anaconda, it is advised to install the database in a folder outside the Conda environment. To do this, run $ metaphlan --install --bowtie2db <database folder> If you install the database in a different location, remember to run MetaPhlAn using --bowtie2db <database folder> ! By default, the latest MetaPhlAn database is downloaded and built. You can download a specific version with the --index parameter $ metaphlan --install --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db <database folder> When --index is specified, MetaPhlAn skips the check for the latest database version and run the analysis using the database version provided by --index located in --bowtie2db . This option is recommended when MetaPhlAn is run on HPC clusters or containerized If you have issues in downloading the database, you can get it from: Segatalab FTP Just download the .tar, .md5, and the mpa_latest files and place them in the metaphlan_databases folder. Basic Usage Important! The MetaPhlAn 4 database has been substantially increased in comparison with the previous 3.1 version. Thus, for running MetaPhlAn 4, a minimum of 15GB or memory is needed. $ metaphlan metagenome.fastq --input_type fastq -o profiled_metagenome.txt It is highly recommended to save the intermediate BowTie2 output for re-running MetaPhlAn extremely quickly ( --bowtie2out ), and use multiple CPUs ( --nproc ) if available: $ metaphlan metagenome.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_metagenome.txt If you already mapped your metagenome against the marker DB (using a previous MetaPhlAn run), you can obtain the results in few seconds by using the previously saved --bowtie2out file and specifying the input ( --input_type bowtie2out ): $ metaphlan metagenome.bowtie2.bz2 --nproc 5 --input_type bowtie2out -o profiled_metagenome.txt bowtie2out files generated with MetaPhlAn versions below 3.0 are not compatible . Starting from MetaPhlAn 3, the BowTie2 output now includes the size of the profiled metagenome. You can also provide an externally BowTie2-mapped SAM if you specify this format with --input_type . Two steps here: first map your metagenome with BowTie2 and then feed MetaPhlAn with the obtained SAM: $ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103 -U metagenome.fastq $ metaphlan metagenome.sam --input_type sam -o profiled_metagenome.txt MetaPhlAn can also natively handle paired-end metagenomes (but does not use the paired-end information), and, more generally, metagenomes stored in multiple files (but you need to specify the --bowtie2out parameter): $ metaphlan metagenome_1.fastq,metagenome_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_metagenome.txt Starting from version 3, MetaPhlAn can estimate the unclassified fraction of the metagenome. The relative abundance profile is scaled according to the percentage of reads mapping to a clade in the database. $ metaphlan metagenome.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq --unclassified_estimation -o profiled_metagenome.txt If you want to estimate the unknown fraction of a metagenome and your input file is a SAM file, remember to specify the metagenome size using --nreads . You can get easily get the metagenome size from a SAM file if you have run bowtie2 without the --no-unal parameter by running $ wc -l metagenome.sam Otherwise, read_fastx.py is your choice: this will print on the standard error the metagenome size. $ read_fastx.py metagenome.fastq > /dev/null You can provide the specific database version with --index . By default MetaPhlAn is run with --index latest : the latest version of the database is used; if it is not available, MetaPhlAn will try to download it. When --index is specified, MetaPhlAn skips the check for the latest database version and run the analysis using the database version provided by --index located in --bowtie2db . For advanced options and other analysis types (such as strain tracking) please refer to the full command-line options metaphlan --help . Utility Scripts MetaPhlAn's repository features a few utility scripts to aid in the manipulation of sample output and its visualization. These scripts can be found under the utils folder in the MetaPhlAn directory. Merging Tables The script merge_metaphlan_tables.py allows to combine MetaPhlAn output from several samples to be merged into one table Bugs (rows) vs Samples (columns) with the table enlisting the relative normalized abundances per sample per bug. To merge multiple output files, run the script as below $ merge_metaphlan_tables.py metaphlan_output1.txt metaphlan_output2.txt metaphlan_output3.txt > output/merged_abundance_table.txt Wildcards can be used as needed: $ merge_metaphlan_tables.py metaphlan_output*.txt > output/merged_abundance_table.txt Output files can be merged only if the profiling was performed with the same version of the MetaPhlAn database. There is no limit to how many files you can merge. Converting SGB profiles to the GTDB taxonomy The script sgb_to_gtdb_profile.py allows to convert a SGB-based MetaPhlAn 4 output into a GTDB-taxonomy-based profile. To do so, run the script as below $ sgb_to_gtdb_profile.py -i metaphlan_output.txt -o metaphlan_output_gtdb.txt Alpha and beta diversity calculation The script calculate_diversity.R allows to compute alpha and/or beta diversity, with different metrics of choice, starting from a merged MetaPhlAn table. Available alpha-diversity metrics are richness , shannon , simpson , and gini . Available beta-diversity distance functions are bray-curtis , jaccard , weighted-unifrac , unweighted-unifrac , centered log-ratio , and aitchison . For example, to generate a beta diversity distance matrix with bray-curtis, you need to run the script as below: Rscript calculate_diversity.R -f merged_mpa4_profiles.tsv -d beta -m bray-curtis To compute UniFrac distances, the SGB tree in the Newick format (available here ) must be provided. For the full list of options, please run: Rscript calculate_diversity.R Heatmap Visualization The hclust2 script generates a hierarchically-clustered heatmap from MetaPhlAn abundance profiles. To generate the heatmap for a merged MetaPhlAn output table (as described above), you need to run the script as below: hclust2.py \ -i HMP.species.txt \ -o HMP.sqrt_scale.png \ --skip_rows 1 \ --ftop 50 \ --f_dist_f correlation \ --s_dist_f braycurtis \ --cell_aspect_ratio 9 \ -s --fperc 99 \ --flabel_size 4 \ --metadata_rows 2,3,4 \ --legend_file HMP.sqrt_scale.legend.png \ --max_flabel_len 100 \ --metadata_height 0.075 \ --minv 0.01 \ --no_slabels \ --dpi 300 \ --slinkage complete GraPhlAn Visualization The tutorial of using GraPhlAn can be found from the GraPhlAn wiki . Customizing the database In order to add a marker to the database, the user needs the following steps: Reconstruct the marker sequences (in fasta format) from the MetaPhlAn BowTie2 database by: bowtie2-inspect metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103 > metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_markers.fasta Add the marker sequence stored in a file new_marker.fasta to the marker set: cat new_marker.fasta >> metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_markers.fasta Rebuild the bowtie2 database: bowtie2-build metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_markers.fasta metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_NEW Assume that the new marker was extracted from genome1, genome2. Update the taxonomy file from the Python console as follows: import pickle import bz2 db = pickle.load(bz2.open('metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103.pkl', 'r')) # Add the taxonomy of the new genomes db['taxonomy']['7-levels taxonomy with clade names of genome1'] = ('7-levels NCBI taxonomy id of genome1', length of genome1) db['taxonomy']['7-levels taxonomy with clade names of genome2'] = ('7-levels NCBI taxonomy id of genome1', length of genome2) # Add the information of the new marker as the other markers db['markers'][new_marker_name] = { 'clade': the clade that the marker belongs to, 'ext': {the GCA of the first external genome where the marker appears, the GCA of the second external genome where the marker appears, }, 'len': length of the marker, 'taxon': the taxon of the marker } To see an example, try to print the first marker information: print list(db['markers'].items())[0] # Save the new mpa_pkl file with bz2.BZ2File('metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_NEW.pkl', 'w') as ofile: pickle.dump(db, ofile, pickle.HIGHEST_PROTOCOL) To use the new database, remember to run metaphlan.py with the "--index mpa_vJan21_CHOCOPhlAnSGB_NEW" parameter. Toggle table of contents Pages 15 Loading Home Uh oh! There was an error while loading. Please reload this page . Loading HUMAnN Workshop on Genomics 2023 Uh oh! There was an error while loading. Please reload this page . Loading MetaPhlAn 3.0 Uh oh! There was an error while loading. Please reload this page . Loading MetaPhlAn 3.1 Uh oh! There was an error while loading. Please reload this page . Loading MetaPhlAn 4 Pre-requisites Basic Usage Utility Scripts Merging Tables Converting SGB profiles to the GTDB taxonomy Alpha and beta diversity calculation Heatmap Visualization GraPhlAn Visualization Customizing the database Loading MetaPhlAn 4.1 Uh oh! There was an error while loading. Please reload this page . Loading MetaPhlAn 4.2 Uh oh! There was an error while loading. Please reload this page . Loading MetaPhlAn Workshop on Genomics 2023 Uh oh! There was an error while loading. Please reload this page . Loading MetaPhlAn2 Uh oh! There was an error while loading. Please reload this page . Loading Strain Sharing Inference Uh oh! There was an error while loading. Please reload this page . Loading Strain Sharing Inference (StrainPhlan 4.1) Uh oh! There was an error while loading. Please reload this page . Loading StrainPhlAn 3 Uh oh! There was an error while loading. Please reload this page . Loading StrainPhlAn 4 Uh oh! There was an error while loading. Please reload this page . Loading StrainPhlAn 4.1 Uh oh! There was an error while loading. Please reload this page . Loading WoM_2023_workshop Uh oh! There was an error while loading. Please reload this page . Home MetaPhlAn documentation MetaPhlAn 4.2 MetaPhlAn 4.1 MetaPhlAn 4 MetaPhlAn 3.1 MetaPhlAn 3.0 MetaPhlAn2 StrainPhlAn documentation StrainPhlAn 4.1 StrainPhlAn 4 StrainPhlAn 3 StrainPhlAn Strain Sharing Inference (StrainPhlAn 4.0) Strain Sharing Inference (StrainPhlAn 4.1) Workshop on Genomics 2023 MetaPhlAn workshop HUMAnN workshop Workshop at World of Microbiome 2023 MetaPhlAn, StrainPhlAn, and cMD Clone this wiki locally Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/biobakery/metaphlan +GitHub - biobakery/MetaPhlAn: MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} biobakery / MetaPhlAn Public Notifications You must be signed in to change notification settings Fork 91 Star 403 Code Issues 0 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights biobakery/MetaPhlAn master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 899 Commits 899 Commits .github .github bioconda_recipe bioconda_recipe metaphlan metaphlan .gitmodules .gitmodules CHANGELOG.md CHANGELOG.md README.md README.md license.txt license.txt setup.py setup.py View all files Repository files navigation README MIT license MetaPhlAn: Metagenomic Phylogenetic Analysis MetaPhlAn is a computational tool for species-level microbial profiling (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing data. StrainPhlAn (available within MetaPhlAn) allows strain-level microbial population genomics. Installation To install MetaPhlan through conda run: $ conda install -c bioconda metaphlan For further installation instructions and alternative installation methods check the MetaPhlAn documentation . Citation If you use MetaPhlAn, please cite: Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Aitor Blanco-Miguez, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D. Huang, Andrew Maltez Thomas, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E. Berry, Tim D. Spector, Eric A. Franzosa, Edoardo Pasolli, Francesco Asnicar, Curtis Huttenhower, Nicola Segata. Nature Biotechnology (2023) If you use StrainPhlAn, please cite the MetaPhlAn paper and the StrainPhlAn paper: Microbial strain-level population structure and genetic diversity from metagenomes. Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, Nicola Segata. Genome Research (2017) If you use the MetaPhlAn viral module, please cite the MetaPhlAn paper and the MetaPhlan viral module paper: Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples. Moreno Zolfo, Andrea Silverj, Aitor Blanco-Míguez, Paolo Manghi, Omar Rota-Stabelli, Vitor Heidrich, Jordan Jensen, Sagun Maharjan, Eric Franzosa, Cristina Menni, Alessia Visconti, Federica Pinto, Matteo Ciciani, Curtis Huttenhower, Anna Cereseto, Francesco Asnicar, Hiroaki Kitano, Takuji Yamada, Nicola Segata. bioRxiv (2024) Tutorials and resources MetaPhlan webpage MetaPhlAn documentation MetaPhlan tutorial MetaPhlan user support MetaPhlan change log StrainPhlAn webpage StrainPhlAn documentation StrainPhlan tutorial StrainPhlan user support MetaPhlAn and StrainPhlAn are part of the bioBakery suite. For further bioBakery tools and tutorials visit the bioBakery wiki . About MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data segatalab.cibio.unitn.it/tools/metaphlan/index.html Topics python tools public metagenomics python-tools biobakery Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 403 stars Watchers 20 watching Forks 91 forks Report repository Releases 30 4.2.4 Latest Oct 21, 2025 + 29 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 92.3% R 5.1% HTML 1.8% Other 0.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/biobakery/metaphlan +GitHub - biobakery/MetaPhlAn: MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} biobakery / MetaPhlAn Public Notifications You must be signed in to change notification settings Fork 91 Star 403 Code Issues 0 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights biobakery/MetaPhlAn master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 899 Commits 899 Commits .github .github bioconda_recipe bioconda_recipe metaphlan metaphlan .gitmodules .gitmodules CHANGELOG.md CHANGELOG.md README.md README.md license.txt license.txt setup.py setup.py View all files Repository files navigation README MIT license MetaPhlAn: Metagenomic Phylogenetic Analysis MetaPhlAn is a computational tool for species-level microbial profiling (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing data. StrainPhlAn (available within MetaPhlAn) allows strain-level microbial population genomics. Installation To install MetaPhlan through conda run: $ conda install -c bioconda metaphlan For further installation instructions and alternative installation methods check the MetaPhlAn documentation . Citation If you use MetaPhlAn, please cite: Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Aitor Blanco-Miguez, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D. Huang, Andrew Maltez Thomas, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E. Berry, Tim D. Spector, Eric A. Franzosa, Edoardo Pasolli, Francesco Asnicar, Curtis Huttenhower, Nicola Segata. Nature Biotechnology (2023) If you use StrainPhlAn, please cite the MetaPhlAn paper and the StrainPhlAn paper: Microbial strain-level population structure and genetic diversity from metagenomes. Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, Nicola Segata. Genome Research (2017) If you use the MetaPhlAn viral module, please cite the MetaPhlAn paper and the MetaPhlan viral module paper: Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples. Moreno Zolfo, Andrea Silverj, Aitor Blanco-Míguez, Paolo Manghi, Omar Rota-Stabelli, Vitor Heidrich, Jordan Jensen, Sagun Maharjan, Eric Franzosa, Cristina Menni, Alessia Visconti, Federica Pinto, Matteo Ciciani, Curtis Huttenhower, Anna Cereseto, Francesco Asnicar, Hiroaki Kitano, Takuji Yamada, Nicola Segata. bioRxiv (2024) Tutorials and resources MetaPhlan webpage MetaPhlAn documentation MetaPhlan tutorial MetaPhlan user support MetaPhlan change log StrainPhlAn webpage StrainPhlAn documentation StrainPhlan tutorial StrainPhlan user support MetaPhlAn and StrainPhlAn are part of the bioBakery suite. For further bioBakery tools and tutorials visit the bioBakery wiki . About MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data segatalab.cibio.unitn.it/tools/metaphlan/index.html Topics python tools public metagenomics python-tools biobakery Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 403 stars Watchers 20 watching Forks 91 forks Report repository Releases 30 4.2.4 Latest Oct 21, 2025 + 29 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 92.3% R 5.1% HTML 1.8% Other 0.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge metaphlan --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +metaphlan 2.8.1 py_0 +-------------------- +file name : metaphlan-2.8.1-py_0.tar.bz2 +name : metaphlan +version : 2.8.1 +build : py_0 +build number: 0 +size : 50 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-2.8.1-py_0.tar.bz2 +md5 : 02838b609aef629a98d710853cb7fc69 +timestamp : 2021-01-04 10:56:50 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.0.0 + - dendropy + - matplotlib-base + - msgpack-python + - muscle >=3.8.1551 + - numpy + - pandas + - pysam >=0.8.3 + - python 2.7.* + - raxml >=8.2.10 + - requests + - samtools >=0.1.19,<1.0 + - scipy + + +metaphlan 2.8.1 py_1 +-------------------- +file name : metaphlan-2.8.1-py_1.tar.bz2 +name : metaphlan +version : 2.8.1 +build : py_1 +build number: 1 +size : 50 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-2.8.1-py_1.tar.bz2 +md5 : bd66ac6965d15bbf904a72fff2198ba6 +timestamp : 2021-03-11 06:04:11 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.0.0 + - dendropy + - matplotlib-base >=2.0,<3.0 + - msgpack-python + - muscle >=3.8.1551 + - numpy + - pandas + - pysam >=0.8.3 + - python 2.7.* + - raxml >=8.2.10 + - requests + - samtools >=0.1.19,<1.0 + - scipy + + +metaphlan 3.0.0.alpha pyh5ca1d4c_0 +---------------------------------- +file name : metaphlan-3.0.0.alpha-pyh5ca1d4c_0.tar.bz2 +name : metaphlan +version : 3.0.0.alpha +build : pyh5ca1d4c_0 +build number: 0 +size : 54 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0.0.alpha-pyh5ca1d4c_0.tar.bz2 +md5 : 36d9d55ae02af7826f7a9a747eaa9a1e +timestamp : 2020-04-24 16:21:24 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0.0.alpha pyh5ca1d4c_1 +---------------------------------- +file name : metaphlan-3.0.0.alpha-pyh5ca1d4c_1.tar.bz2 +name : metaphlan +version : 3.0.0.alpha +build : pyh5ca1d4c_1 +build number: 1 +size : 54 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0.0.alpha-pyh5ca1d4c_1.tar.bz2 +md5 : 4dd2d01d9d2ebd4df59bf50c97ac6dbf +timestamp : 2020-04-27 14:42:51 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3.7 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0 pyh5ca1d4c_0 +-------------------------- +file name : metaphlan-3.0-pyh5ca1d4c_0.tar.bz2 +name : metaphlan +version : 3.0 +build : pyh5ca1d4c_0 +build number: 0 +size : 62 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0-pyh5ca1d4c_0.tar.bz2 +md5 : 0510d045087e28a794131aba329a943c +timestamp : 2020-03-14 20:26:26 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.0.0 + - dendropy + - matplotlib-base + - msgpack-python + - muscle >=3.8.1551 + - numpy + - pandas + - pysam >=0.8.3 + - python >=3 + - raxml >=8.2.10 + - requests + - samtools >=0.1.19,<1.0 + - scipy + + +metaphlan 3.0 pyh5ca1d4c_1 +-------------------------- +file name : metaphlan-3.0-pyh5ca1d4c_1.tar.bz2 +name : metaphlan +version : 3.0 +build : pyh5ca1d4c_1 +build number: 1 +size : 62 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0-pyh5ca1d4c_1.tar.bz2 +md5 : 0ebaa2cdfae5fe288248e41260859c2d +timestamp : 2020-03-16 12:04:39 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.0.0 + - dendropy + - matplotlib-base + - msgpack-python + - muscle >=3.8.1551 + - numpy + - pandas + - pysam >=0.8.3 + - python >=3 + - raxml >=8.2.10 + - requests + - samtools >=0.1.19,<1.0 + - scipy + + +metaphlan 3.0 pyh5ca1d4c_2 +-------------------------- +file name : metaphlan-3.0-pyh5ca1d4c_2.tar.bz2 +name : metaphlan +version : 3.0 +build : pyh5ca1d4c_2 +build number: 2 +size : 54 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0-pyh5ca1d4c_2.tar.bz2 +md5 : e5567bf9da5501b49e63bdfef6c0dff6 +timestamp : 2020-03-31 12:00:26 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0 pyh5ca1d4c_3 +-------------------------- +file name : metaphlan-3.0-pyh5ca1d4c_3.tar.bz2 +name : metaphlan +version : 3.0 +build : pyh5ca1d4c_3 +build number: 3 +size : 54 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0-pyh5ca1d4c_3.tar.bz2 +md5 : c8107e30a2603b22442c8f0ab4585a7f +timestamp : 2020-04-21 11:58:58 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0 pyh5ca1d4c_4 +-------------------------- +file name : metaphlan-3.0-pyh5ca1d4c_4.tar.bz2 +name : metaphlan +version : 3.0 +build : pyh5ca1d4c_4 +build number: 4 +size : 54 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0-pyh5ca1d4c_4.tar.bz2 +md5 : 4b2f62b4d7198b5cc6ee5d4a48090259 +timestamp : 2020-04-27 14:32:27 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3.7 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0.1 pyh5ca1d4c_0 +---------------------------- +file name : metaphlan-3.0.1-pyh5ca1d4c_0.tar.bz2 +name : metaphlan +version : 3.0.1 +build : pyh5ca1d4c_0 +build number: 0 +size : 55 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0.1-pyh5ca1d4c_0.tar.bz2 +md5 : 4c3399ba465172f242d053fd25067d9a +timestamp : 2020-06-25 09:08:33 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3.7 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0.2 pyh5ca1d4c_0 +---------------------------- +file name : metaphlan-3.0.2-pyh5ca1d4c_0.tar.bz2 +name : metaphlan +version : 3.0.2 +build : pyh5ca1d4c_0 +build number: 0 +size : 55 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0.2-pyh5ca1d4c_0.tar.bz2 +md5 : df3239199fe2d89538f5cf3b01a74d27 +timestamp : 2020-07-29 08:22:39 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3.7 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0.3 pyh5ca1d4c_0 +---------------------------- +file name : metaphlan-3.0.3-pyh5ca1d4c_0.tar.bz2 +name : metaphlan +version : 3.0.3 +build : pyh5ca1d4c_0 +build number: 0 +size : 55 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0.3-pyh5ca1d4c_0.tar.bz2 +md5 : 783a5247638fcfc11b931e99c471ec81 +timestamp : 2020-08-28 15:16:00 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3.7 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0.4 pyh7b7c402_0 +---------------------------- +file name : metaphlan-3.0.4-pyh7b7c402_0.tar.bz2 +name : metaphlan +version : 3.0.4 +build : pyh7b7c402_0 +build number: 0 +size : 55 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0.4-pyh7b7c402_0.tar.bz2 +md5 : 1675217badc57b65f3c31b6c036db77f +timestamp : 2020-09-23 09:20:18 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3.7 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0.4 pyh7b7c402_1 +---------------------------- +file name : metaphlan-3.0.4-pyh7b7c402_1.tar.bz2 +name : metaphlan +version : 3.0.4 +build : pyh7b7c402_1 +build number: 1 +size : 55 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0.4-pyh7b7c402_1.tar.bz2 +md5 : a716fbbadf18130e437cb802b05943ae +timestamp : 2020-10-12 14:39:20 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3.7 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0.5 pyh7b7c402_0 +---------------------------- +file name : metaphlan-3.0.5-pyh7b7c402_0.tar.bz2 +name : metaphlan +version : 3.0.5 +build : pyh7b7c402_0 +build number: 0 +size : 55 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0.5-pyh7b7c402_0.tar.bz2 +md5 : d4fff6fed4e7ea0c9bbbc651398e7353 +timestamp : 2020-11-10 19:34:04 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3.7 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0.6 pyh7b7c402_0 +---------------------------- +file name : metaphlan-3.0.6-pyh7b7c402_0.tar.bz2 +name : metaphlan +version : 3.0.6 +build : pyh7b7c402_0 +build number: 0 +size : 56 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/metaphlan-3.0.6-pyh7b7c402_0.tar.bz2 +md5 : bbdcea8b0df8fcc9c45c4c4b2b222073 +timestamp : 2020-11-24 21:37:55 UTC +dependencies: + - biom-format + - biopython + - blast >=2.6.0 + - bowtie2 >=2.3.0 + - cmseq + - dendropy + - matplotlib-base + - muscle >=3.8.1551 + - numpy + - pandas + - phylophlan + - pysam + - python >=3.7 + - raxml >=8.2.10 + - requests + - samtools >=1.9 + - scipy + + +metaphlan 3.0.7 pyh7b7c402_0 +---------------------------- +file name : metaphlan-3.0.7 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/minced.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/minced.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..aefc886bc3e63fe68b62bd6c29f460539dfa24c7 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/minced.manual_bundle.txt @@ -0,0 +1,302 @@ +# Tool: minced +software_name: minced +tier: T1 +domain: t1_backfill_overall +downloads: 180559 +summary: MinCED - Mining CRISPRs in Environmental Datasets +description: MinCED - Mining CRISPRs in Environmental Datasets +dependencies: openjdk >=8 +execution_environment: Java +execution_environment_reason: inferred from Java runtime dependencies + +## URLs +home_url: https://github.com/ctSkennerton/minced +doc_url: +dev_url: + +## CLI Help Source +java:-help +## CLI Help Content +$ conda run -n bioenv_java java -help +[rc=0] + +Usage: java [-options] class [args...] + (to execute a class) + or java [-options] -jar jarfile [args...] + (to execute a jar file) +where options include: + -d32 use a 32-bit data model if available + -d64 use a 64-bit data model if available + -server to select the "server" VM + The default VM is server, + because you are running on a server-class machine. + + + -cp + -classpath + A : separated list of directories, JAR archives, + and ZIP archives to search for class files. + -D= + set a system property + -verbose:[class|gc|jni] + enable verbose output + -version print product version and exit + -version: + Warning: this feature is deprecated and will be removed + in a future release. + require the specified version to run + -showversion print product version and continue + -jre-restrict-search | -no-jre-restrict-search + Warning: this feature is deprecated and will be removed + in a future release. + include/exclude user private JREs in the version search + -? -help print this help message + -X print help on non-standard options + -ea[:...|:] + -enableassertions[:...|:] + enable assertions with specified granularity + -da[:...|:] + -disableassertions[:...|:] + disable assertions with specified granularity + -esa | -enablesystemassertions + enable system assertions + -dsa | -disablesystemassertions + disable system assertions + -agentlib:[=] + load native agent library , e.g. -agentlib:hprof + see also, -agentlib:jdwp=help and -agentlib:hprof=help + -agentpath:[=] + load native agent library by full pathname + -javaagent:[=] + load Java programming language agent, see java.lang.instrument + -splash: + show splash screen with specified image +See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details. + + + +## URL Docs Extract +### https://github.com/ctSkennerton/minced +GitHub - ctSkennerton/minced: Mining CRISPRs in Environmental Datasets · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} ctSkennerton / minced Public Notifications You must be signed in to change notification settings Fork 20 Star 122 Code Issues 7 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights ctSkennerton/minced master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 59 Commits 59 Commits t t .gitignore .gitignore CHANGES CHANGES CRISPR.java CRISPR.java CRISPRFinder.java CRISPRFinder.java CRISPRUtil.java CRISPRUtil.java DNASequence.java DNASequence.java FASTAReader.java FASTAReader.java IntervalSearchTree.java IntervalSearchTree.java LICENSE LICENSE MANIFEST.txt MANIFEST.txt Makefile Makefile README.md README.md SearchUtil.java SearchUtil.java minced minced minced.java minced.java View all files Repository files navigation README GPL-3.0 license MinCED - Mining CRISPRs in Environmental Datasets MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as assembled contigs from metagenomes. Iff you want to identify CRISPRs in raw short read data, in the size range of 100-200bp try using Crass ( https://github.com/ctskennerton/Crass ) MinCED runs from the command-line and was derived from CRT ( http://www.room220.com/crt/ ): Charles Bland et al., CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats, BMC Bioinformatics 8, no. 1 (2007): 209. INSTALLATION You need to install these dependencies first: Java ( http://www.java.com/en/download/ ) there is a Makefile in the source directory so installation should be as simple as: cd <download_folder> make To run MinCED: ./minced [options] file.fa The help page can be obtained by typing: ./minced --help You can get the MinCED version this way: ./minced --version NOTE: Always keep minced and minced.jar in the same folder! EXAMPLES Finding CRISPRs in the E. coli genome: ./minced ecoli.fna To find repeats in short sequences, we need to decrease the minimum number of repeats to find. For example, in 100 bp reads, we could not possibly find more than 2 repeats: minced -minNR 2 metagenome.fna The output can be large, so save it in a file: minced -minNR 2 metagenome.fna metagenome.crisprs You can also save both the table output and the gff output at the same time: minced ecoli.fna out.txt out.gff COPYRIGHT AND LICENSE Copyright 2011 Florent ANGLY <florent.angly@gmail.com> 2013-2019 Connor SKENNERTON <c.skennerton@gmail.com> MinCED is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. MinCED is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with MinCED. If not, see <http://www.gnu.org/licenses/>. BUGS All complex software has bugs lurking in it, and this program is no exception. If you find a bug please post an issue on github https://github.com/ctSkennerton/minced/issues About Mining CRISPRs in Environmental Datasets Topics bioinformatics crispr Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 122 stars Watchers 5 watching Forks 20 forks Report repository Releases 15 Version 0.4.2 Latest Sep 3, 2019 + 14 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Java 97.9% Shell 1.2% Makefile 0.9% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge minced --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +minced 0.2.0 0 +-------------- +file name : minced-0.2.0-0.tar.bz2 +name : minced +version : 0.2.0 +build : 0 +build number: 0 +size : 26 KB +license : GPL (>= 3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minced-0.2.0-0.tar.bz2 +md5 : 2c10e5b02555ea962951934289ccce43 +dependencies: + - java-jdk + + +minced 0.2.0 1 +-------------- +file name : minced-0.2.0-1.tar.bz2 +name : minced +version : 0.2.0 +build : 1 +build number: 1 +size : 29 KB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minced-0.2.0-1.tar.bz2 +md5 : 4025dd29617255ed6fe4026095e3d850 +dependencies: + - openjdk + + +minced 0.2.0 2 +-------------- +file name : minced-0.2.0-2.tar.bz2 +name : minced +version : 0.2.0 +build : 2 +build number: 2 +size : 29 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/minced-0.2.0-2.tar.bz2 +md5 : 00869206f46c3dd1a6390174df4d50ec +timestamp : 2018-07-06 00:21:59 UTC +dependencies: + - openjdk + + +minced 0.2.0 hdfd78af_3 +----------------------- +file name : minced-0.2.0-hdfd78af_3.tar.bz2 +name : minced +version : 0.2.0 +build : hdfd78af_3 +build number: 3 +size : 32 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/minced-0.2.0-hdfd78af_3.tar.bz2 +md5 : d27ec0853eb897391c700a6b8da6cfeb +timestamp : 2021-03-25 10:11:36 UTC +dependencies: + - openjdk + + +minced 0.3.0 0 +-------------- +file name : minced-0.3.0-0.tar.bz2 +name : minced +version : 0.3.0 +build : 0 +build number: 0 +size : 29 KB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minced-0.3.0-0.tar.bz2 +md5 : 8b38cc9b194efa2ad3d758e39f6d6700 +dependencies: + - openjdk + + +minced 0.3.0 1 +-------------- +file name : minced-0.3.0-1.tar.bz2 +name : minced +version : 0.3.0 +build : 1 +build number: 1 +size : 29 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/minced-0.3.0-1.tar.bz2 +md5 : 3042a64e851052cf99ff066f11bc07e1 +timestamp : 2018-07-06 00:18:30 UTC +dependencies: + - openjdk + + +minced 0.3.2 0 +-------------- +file name : minced-0.3.2-0.tar.bz2 +name : minced +version : 0.3.2 +build : 0 +build number: 0 +size : 30 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/minced-0.3.2-0.tar.bz2 +md5 : 7970d344b7b5bde9e3005b460c1f92fb +timestamp : 2018-10-24 07:31:46 UTC +dependencies: + - openjdk + + +minced 0.4.0 0 +-------------- +file name : minced-0.4.0-0.tar.bz2 +name : minced +version : 0.4.0 +build : 0 +build number: 0 +size : 31 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/minced-0.4.0-0.tar.bz2 +md5 : 9929d0ac8a5948995a52ea8d2b34a5ed +timestamp : 2019-04-26 14:20:16 UTC +dependencies: + - openjdk + + +minced 0.4.0 1 +-------------- +file name : minced-0.4.0-1.tar.bz2 +name : minced +version : 0.4.0 +build : 1 +build number: 1 +size : 31 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/minced-0.4.0-1.tar.bz2 +md5 : 338fe6b6be7bcb12b73007573cfccec3 +timestamp : 2019-05-15 21:42:39 UTC +dependencies: + - openjdk 11.* + + +minced 0.4.0 2 +-------------- +file name : minced-0.4.0-2.tar.bz2 +name : minced +version : 0.4.0 +build : 2 +build number: 2 +size : 46 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/minced-0.4.0-2.tar.bz2 +md5 : 2d5c9c318d62ea2f793ebdf544b531e8 +timestamp : 2019-08-29 07:38:36 UTC +dependencies: + - openjdk >=8 + + +minced 0.4.1 0 +-------------- +file name : minced-0.4.1-0.tar.bz2 +name : minced +version : 0.4.1 +build : 0 +build number: 0 +size : 46 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/minced-0.4.1-0.tar.bz2 +md5 : e0152730eda570538a856f85087c49df +timestamp : 2019-08-30 07:44:48 UTC +dependencies: + - openjdk >=8 + + +minced 0.4.2 0 +-------------- +file name : minced-0.4.2-0.tar.bz2 +name : minced +version : 0.4.2 +build : 0 +build number: 0 +size : 46 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/minced-0.4.2-0.tar.bz2 +md5 : 7f474fdc72cc49ef332df1daa5687b11 +timestamp : 2019-09-03 07:07:14 UTC +dependencies: + - openjdk >=8 + + +minced 0.4.2 hdfd78af_1 +----------------------- +file name : minced-0.4.2-hdfd78af_1.tar.bz2 +name : minced +version : 0.4.2 +build : hdfd78af_1 +build number: 1 +size : 47 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/minced-0.4.2-hdfd78af_1.tar.bz2 +md5 : eee6ac504430c045623a6616e13ba833 +timestamp : 2021-03-27 10:46:20 UTC +dependencies: + - openjdk >=8 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/miniasm.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/miniasm.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..67fd6d29e7988456f92a40abcb6110a4162122d8 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/miniasm.manual_bundle.txt @@ -0,0 +1,386 @@ +# Tool: miniasm +software_name: miniasm +tier: T1 +domain: t1_backfill_overall +downloads: 116937 +summary: Ultrafast de novo assembly for long noisy reads (though having no consensus step) +description: Ultrafast de novo assembly for long noisy reads (though having no consensus step) +dependencies: libgcc-ng >=10.3.0, libzlib >=1.2.11,<1.3.0a0, zlib >=1.2.11,<1.3.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/lh3/miniasm +doc_url: +dev_url: + +## CLI Help Source +cli:miniasm +## CLI Help Content +$ conda run -n bioenv_cli miniasm --help +[rc=1] + +miniasm: invalid option -- '-' +Usage: miniasm [options] +Options: + Pre-selection: + -R prefilter clearly contained reads (2-pass required) + -m INT min match length [100] + -i FLOAT min identity [0.05] + -s INT min span [2000] + -c INT min coverage [3] + Overlap: + -o INT min overlap [same as -s] + -h INT max over hang length [0] + -I FLOAT min end-to-end match ratio [0.8] + Layout: + -g INT max gap differences between reads for trans-reduction [1000] + -d INT max distance for bubble popping [50000] + -e INT small unitig threshold [4] + -f FILE read sequences [] + -n INT rounds of short overlap removal [3] + -r FLOAT[,FLOAT] + max and min overlap drop ratio [0.7,0.5] + -F FLOAT aggressive overlap drop ratio in the end [0.8] + Miscellaneous: + -p STR output information: bed, paf, sg or ug [ug] + -b both directions of an arc are present in input + -1 skip 1-pass read selection + -2 skip 2-pass read selection + -V print version number + +See miniasm.1 for detailed description of the command-line options. + +ERROR conda.cli.main_run:execute(127): `conda run miniasm --help` failed. (See above for error) + + +## URL Docs Extract +### https://github.com/lh3/miniasm +GitHub - lh3/miniasm: Ultrafast de novo assembly for long noisy reads (though having no consensus step) · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} lh3 / miniasm Public Notifications You must be signed in to change notification settings Fork 69 Star 353 Code Issues 53 Pull requests 4 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights lh3/miniasm master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 176 Commits 176 Commits misc misc tex tex .gitignore .gitignore LICENSE.txt LICENSE.txt Makefile Makefile PAF.md PAF.md README.md README.md asg.c asg.c asg.h asg.h asm.c asm.c common.c common.c dotter.c dotter.c eps.h eps.h hit.c hit.c kdq.h kdq.h khash.h khash.h kseq.h kseq.h ksort.h ksort.h kvec.h kvec.h main.c main.c miniasm.1 miniasm.1 miniasm.h miniasm.h paf.c paf.c paf.h paf.h sdict.c sdict.c sdict.h sdict.h sys.c sys.c sys.h sys.h View all files Repository files navigation README MIT license Getting Started # Download sample PacBio from the PBcR website wget -O- http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz | tar zxf - ln -s selfSampleData/pacbio_filtered.fastq reads.fq # Install minimap and miniasm (requiring gcc and zlib) git clone https://github.com/lh3/minimap2 && (cd minimap2 && make) git clone https://github.com/lh3/miniasm && (cd miniasm && make) # Overlap for PacBio reads (or use "-x ava-ont" for nanopore read overlapping) minimap2/minimap2 -x ava-pb -t8 pb-reads.fq pb-reads.fq | gzip -1 > reads.paf.gz # Layout miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa Introduction Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap ) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads. So far miniasm is in early development stage. It has only been tested on a dozen of PacBio and Oxford Nanopore (ONT) bacterial data sets. Including the mapping step, it takes about 3 minutes to assemble a bacterial genome. Under the default setting, miniasm assembles 9 out of 12 PacBio datasets and 3 out of 4 ONT datasets into a single contig. The 12 PacBio data sets are PacBio E. coli sample , ERS473430 , ERS544009 , ERS554120 , ERS605484 , ERS617393 , ERS646601 , ERS659581 , ERS670327 , ERS685285 , ERS743109 and a deprecated PacBio E. coli data set . ONT data are acquired from the Loman Lab . For a C. elegans PacBio data set (only 40X are used, not the whole dataset), miniasm finishes the assembly, including reads overlapping, in ~10 minutes with 16 CPUs. The total assembly size is 105Mb; the N50 is 1.94Mb. In comparison, the HGAP3 produces a 104Mb assembly with N50 1.61Mb. This dotter plot gives a global view of the miniasm assembly (on the X axis) and the HGAP3 assembly (on Y). They are broadly comparable. Of course, the HGAP3 consensus sequences are much more accurate. In addition, on the whole data set (assembled in ~30 min), the miniasm N50 is reduced to 1.79Mb. Miniasm still needs improvements. Miniasm confirms that at least for high-coverage bacterial genomes, it is possible to generate long contigs from raw PacBio or ONT reads without error correction. It also shows that minimap can be used as a read overlapper, even though it is probably not as sensitive as the more sophisticated overlapers such as MHAP and DALIGNER . Coupled with long-read error correctors and consensus tools, miniasm may also be useful to produce high-quality assemblies. Algorithm Overview Crude read selection. For each read, find the longest contiguous region covered by three good mappings. Get an approximate estimate of read coverage. Fine read selection. Use the coverage information to find the good regions again but with more stringent thresholds. Discard contained reads. Generate a string graph . Prune tips, drop weak overlaps and collapse short bubbles. These procedures are similar to those implemented in short-read assemblers. Merge unambiguous overlaps to produce unitig sequences. Limitations Consensus base quality is similar to input reads (may be fixed with a consensus tool). Only tested on a dozen of high-coverage PacBio/ONT data sets (more testing needed). Prone to collapse repeats or segmental duplications longer than input reads (hard to fix without error correction). About Ultrafast de novo assembly for long noisy reads (though having no consensus step) Topics bioinformatics genomics denovo-assembly Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 353 stars Watchers 27 watching Forks 69 forks Report repository Releases 3 Miniasm-0.3 (r179) Latest Jul 24, 2018 + 2 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages TeX 41.0% C 36.2% BibTeX Style 9.3% JavaScript 6.8% Shell 2.7% Roff 2.2% Other 1.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge miniasm --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +miniasm 0.2_r137 0 +------------------ +file name : miniasm-0.2_r137-0.tar.bz2 +name : miniasm +version : 0.2_r137 +build : 0 +build number: 0 +size : 109 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.2_r137-0.tar.bz2 +md5 : 0ee378e80d5260ab37d9b16b6afbcdc5 +dependencies: + - libgcc + + +miniasm 0.2_r159 0 +------------------ +file name : miniasm-0.2_r159-0.tar.bz2 +name : miniasm +version : 0.2_r159 +build : 0 +build number: 0 +size : 106 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.2_r159-0.tar.bz2 +md5 : 33134135dcd5d0306cd0d0c39f7849d5 +dependencies: + - libgcc + - zlib + + +miniasm 0.2_r168 0 +------------------ +file name : miniasm-0.2_r168-0.tar.bz2 +name : miniasm +version : 0.2_r168 +build : 0 +build number: 0 +size : 108 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.2_r168-0.tar.bz2 +md5 : fa4f2d728a963cee4f4687af1cc159aa +dependencies: + - libgcc + - zlib + + +miniasm 0.2_r168 1 +------------------ +file name : miniasm-0.2_r168-1.tar.bz2 +name : miniasm +version : 0.2_r168 +build : 1 +build number: 1 +size : 108 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.2_r168-1.tar.bz2 +md5 : 98971727a4c2724ce4c29038317822ea +dependencies: + - libgcc + - zlib 1.2.11* + + +miniasm 0.2_r168 2 +------------------ +file name : miniasm-0.2_r168-2.tar.bz2 +name : miniasm +version : 0.2_r168 +build : 2 +build number: 2 +size : 108 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.2_r168-2.tar.bz2 +md5 : faa98759fad53b91a2e53a0f9dbffc8d +dependencies: + - libgcc + - zlib 1.2.11* + + +miniasm 0.2_r168 ha92aebf_3 +--------------------------- +file name : miniasm-0.2_r168-ha92aebf_3.tar.bz2 +name : miniasm +version : 0.2_r168 +build : ha92aebf_3 +build number: 3 +size : 109 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.2_r168-ha92aebf_3.tar.bz2 +md5 : c76ee9d7079129c8411146569d24cf63 +timestamp : 2018-07-06 13:46:53 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +miniasm 0.2 0 +------------- +file name : miniasm-0.2-0.tar.bz2 +name : miniasm +version : 0.2 +build : 0 +build number: 0 +size : 105 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.2-0.tar.bz2 +md5 : 842e7e7c3557e66bd5467c72e0c3e3e3 +dependencies: + - libgcc + + +miniasm 0.3_r179 h5bf99c6_2 +--------------------------- +file name : miniasm-0.3_r179-h5bf99c6_2.tar.bz2 +name : miniasm +version : 0.3_r179 +build : h5bf99c6_2 +build number: 2 +size : 134 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3_r179-h5bf99c6_2.tar.bz2 +md5 : 89d659f167c9d681a5490d1179bbd375 +timestamp : 2021-03-25 18:32:13 UTC +dependencies: + - libgcc-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +miniasm 0.3_r179 h7132678_3 +--------------------------- +file name : miniasm-0.3_r179-h7132678_3.tar.bz2 +name : miniasm +version : 0.3_r179 +build : h7132678_3 +build number: 3 +size : 124 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3_r179-h7132678_3.tar.bz2 +md5 : 831a2376949b1138ea7e201152da8787 +timestamp : 2022-02-23 15:55:47 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +miniasm 0.3_r179 ha92aebf_0 +--------------------------- +file name : miniasm-0.3_r179-ha92aebf_0.tar.bz2 +name : miniasm +version : 0.3_r179 +build : ha92aebf_0 +build number: 0 +size : 109 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3_r179-ha92aebf_0.tar.bz2 +md5 : d54e7be02d9ef3298cdd071060677d8f +timestamp : 2018-08-17 19:59:29 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +miniasm 0.3_r179 hed695b0_1 +--------------------------- +file name : miniasm-0.3_r179-hed695b0_1.tar.bz2 +name : miniasm +version : 0.3_r179 +build : hed695b0_1 +build number: 1 +size : 116 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3_r179-hed695b0_1.tar.bz2 +md5 : 475ab0fe8afb1e88e3af1f9e231b6fc7 +timestamp : 2020-07-13 22:26:38 UTC +dependencies: + - libgcc-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +miniasm 0.3 h577a1d6_4 +---------------------- +file name : miniasm-0.3-h577a1d6_4.tar.bz2 +name : miniasm +version : 0.3 +build : h577a1d6_4 +build number: 4 +size : 125 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3-h577a1d6_4.tar.bz2 +md5 : 5737eac2f364afb068b91cf96eaa994c +timestamp : 2024-12-12 06:12:44 UTC +dependencies: + - libgcc >=13 + - libzlib >=1.3.1,<2.0a0 + - zlib + + +miniasm 0.3 h577a1d6_5 +---------------------- +file name : miniasm-0.3-h577a1d6_5.tar.bz2 +name : miniasm +version : 0.3 +build : h577a1d6_5 +build number: 5 +size : 44 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3-h577a1d6_5.tar.bz2 +md5 : 4ceaff059c5a5322862bdce4e912e69c +timestamp : 2025-01-27 08:30:37 UTC +dependencies: + - libgcc >=13 + - libzlib >=1.3.1,<2.0a0 + + +miniasm 0.3 h7132678_0 +---------------------- +file name : miniasm-0.3-h7132678_0.tar.bz2 +name : miniasm +version : 0.3 +build : h7132678_0 +build number: 0 +size : 124 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3-h7132678_0.tar.bz2 +md5 : 2bd98c2f32737912df37e740f7812d06 +timestamp : 2023-01-31 03:53:21 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +miniasm 0.3 h7132678_1 +---------------------- +file name : miniasm-0.3-h7132678_1.tar.bz2 +name : miniasm +version : 0.3 +build : h7132678_1 +build number: 1 +size : 125 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3-h7132678_1.tar.bz2 +md5 : 71855fda5d1d4558a657c233827d017d +timestamp : 2023-05-12 15:41:28 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +miniasm 0.3 he4a0461_1 +---------------------- +file name : miniasm-0.3-he4a0461_1.tar.bz2 +name : miniasm +version : 0.3 +build : he4a0461_1 +build number: 1 +size : 127 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3-he4a0461_1.tar.bz2 +md5 : ec406acb4457162e3ce1b1b4055c1cce +timestamp : 2023-05-14 23:48:53 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +miniasm 0.3 he4a0461_2 +---------------------- +file name : miniasm-0.3-he4a0461_2.tar.bz2 +name : miniasm +version : 0.3 +build : he4a0461_2 +build number: 2 +size : 127 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3-he4a0461_2.tar.bz2 +md5 : 9c1070344fdd87ee7e0a8bddfb143069 +timestamp : 2023-05-15 22:38:01 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +miniasm 0.3 he4a0461_3 +---------------------- +file name : miniasm-0.3-he4a0461_3.tar.bz2 +name : miniasm +version : 0.3 +build : he4a0461_3 +build number: 3 +size : 127 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/miniasm-0.3-he4a0461_3.tar.bz2 +md5 : 48b210aced98d578b8153ed997a7b69c +timestamp : 2024-04-18 12:33:15 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/minimap2.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/minimap2.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..22be60a10eca54deafb5e511d5347780dc1afce5 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/minimap2.manual_bundle.txt @@ -0,0 +1,571 @@ +# Tool: minimap2 +software_name: minimap2 +tier: T1 +domain: t1_backfill_overall +downloads: 1311993 +summary: A versatile pairwise aligner for genomic and spliced nucleotide sequences. +description: A versatile pairwise aligner for genomic and spliced nucleotide sequences. +dependencies: k8, libgcc >=13, libzlib >=1.3.1,<2.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/lh3/minimap2 +doc_url: https://lh3.github.io/minimap2/minimap2.html +dev_url: https://github.com/lh3/minimap2 + +## CLI Help Source +cli:minimap2 +## CLI Help Content +$ conda run -n bioenv_cli minimap2 --help +[rc=0] +Usage: minimap2 [options] | [query.fa] [...] +Options: + Indexing: + -H use homopolymer-compressed k-mer (preferrable for PacBio) + -k INT k-mer size (no larger than 28) [15] + -w INT minimizer window size [10] + -I NUM split index for every ~NUM input bases [8G] + -d FILE dump index to FILE [] + Mapping: + -f FLOAT filter out top FLOAT fraction of repetitive minimizers [0.0002] + -g NUM stop chain enlongation if there are no minimizers in INT-bp [5000] + -G NUM max intron length (effective with -xsplice; changing -r) [200k] + -F NUM max fragment length (effective with -xsr or in the fragment mode) [800] + -r NUM[,NUM] chaining/alignment bandwidth and long-join bandwidth [500,20000] + -n INT minimal number of minimizers on a chain [3] + -m INT minimal chaining score (matching bases minus log gap penalty) [40] + -X skip self and dual mappings (for the all-vs-all mode) + -p FLOAT min secondary-to-primary score ratio [0.8] + -N INT retain at most INT secondary alignments [5] + Alignment: + -A INT matching score [2] + -B INT mismatch penalty (larger value for lower divergence) [4] + -O INT[,INT] gap open penalty [4,24] + -E INT[,INT] gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [2,1] + -z INT[,INT] Z-drop score and inversion Z-drop score [400,200] + -s INT minimal peak DP alignment score [80] + -u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n] + -J INT splice mode. 0: original minimap2 model; 1: miniprot model [1] + Input/Output: + -a output in the SAM format (PAF by default) + -o FILE output alignments to FILE [stdout] + -L write CIGAR with >65535 ops at the CG tag + -R STR SAM read group line in a format like '@RG\tID:foo\tSM:bar' [] + -c output CIGAR in PAF + --cs[=STR] output the cs tag; STR is 'short' (if absent) or 'long' [none] + --ds output the ds tag, which is an extension to cs + --MD output the MD tag + --eqx write =/X CIGAR operators + -Y use soft clipping for supplementary alignments + -t INT number of threads [3] + -K NUM minibatch size for mapping [500M] + --version show version number + Preset: + -x STR preset (always applied before other options; see minimap2.1 for details) [] + - lr:hq - accurate long reads (error rate <1%) against a reference genome + - splice/splice:hq - spliced alignment for long reads/accurate long reads + - asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5% sequence divergence + - sr - short reads against a reference + - map-pb/map-hifi/map-ont/map-iclr - CLR/HiFi/Nanopore/ICLR vs reference mapping + - ava-pb/ava-ont - PacBio CLR/Nanopore read overlap + +See `man ./minimap2.1' for detailed description of these and other advanced command-line options. + + + +## URL Docs Extract +### https://lh3.github.io/minimap2/minimap2.html +minimap2.1 Manual Reference Pages  -  minimap2 (1) NAME minimap2 - mapping and alignment between collections of DNA sequences CONTENTS Synopsis Description Options       Indexing options       Mapping options       Alignment options       Input/output options       Preset options       Miscellaneous options Output Format Limitations See Also SYNOPSIS * Indexing the target sequences (optional): minimap2 [ -x preset ] -d target.mmi target.fa minimap2 [ -H ] [ -k kmer ] [ -w miniWinSize ] [ -I batchSize ] -d target.mmi target.fa * Long-read alignment with CIGAR: minimap2 -a [ -x preset ] target.mmi query.fa > output.sam minimap2 -c [ -H ] [ -k kmer ] [ -w miniWinSize ] [ ... ] target.fa query.fa > output.paf * Long-read overlap without CIGAR: minimap2 -x ava-ont [ -t nThreads ] target.fa query.fa > output.paf DESCRIPTION Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the SAM format. OPTIONS     Indexing options -k INT Minimizer k-mer length [15] -w INT Minimizer window size [10]. A minimizer is the smallest k-mer in a window of w consecutive k-mers. -j INT Syncmer submer size [10]. Option -j and -w will override each: if -w is applied after -j , -j will have no effect, and vice versa. -H Use homopolymer-compressed (HPC) minimizers. An HPC sequence is constructed by contracting homopolymer runs to a single base. An HPC minimizer is a minimizer on the HPC sequence. -I NUM Load at most NUM target bases into RAM for indexing [8G]. If there are more than NUM bases in target.fa , minimap2 needs to read query.fa multiple times to map it against each batch of target sequences. This would create a multi-part index. NUM may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a multi-part index. See also option --split-prefix . --idx-no-seq   Don’t store target sequences in the index. It saves disk space and memory but the index generated with this option will not work with -a or -c . When base-level alignment is not requested, this option is automatically applied. -d FILE Save the minimizer index of target.fa to FILE [no dump]. Minimap2 indexing is fast. It can index the human genome in a couple of minutes. If even shorter startup time is desired, use this option to save the index. Indexing options are fixed in the index file. When an index file is provided as the target sequences, options -H , -k , -w , -I will be effectively overridden by the options stored in the index file. --alt FILE List of ALT contigs [null] --alt-drop FLOAT   Drop ALT hits by FLOAT fraction when ranking and computing mapping quality [0.15]     Mapping options -f FLOAT | INT1 [, INT2 ]   If fraction, ignore top FLOAT fraction of most frequent minimizers [0.0002]. If integer, ignore minimizers occuring more than INT1 times. INT2 is only effective in the --sr or -xsr mode, which sets the threshold for a second round of seeding. -U INT1 [, INT2 ]   Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold is max{ INT1 , min{ INT2 , -f }}. This option prevents excessively small or large -f estimated from the input reference. Available since r1034 and deprecating --min-occ-floor in earlier versions of minimap2. --q-occ-frac FLOAT   Discard a query minimizer if its occurrence is higher than FLOAT fraction of query minimizers and than the reference occurrence threshold [0.01]. Set 0 to disable. Available since r1105. -e INT Sample a high-frequency minimizer every INT basepairs [500]. -g NUM Stop chain enlongation if there are no minimizers within NUM -bp [10k]. -r NUM1 [, NUM2 ]   Bandwidth for chaining and base alignment [500,20k]. NUM1 is used for initial chaining and alignment extension; NUM2 for RMQ-based re-chaining and closing gaps in alignments. -n INT Discard chains consisting of < INT number of minimizers [3] -m INT Discard chains with chaining score < INT [40]. Chaining score equals the approximate number of matching bases minus a concave gap penalty. It is computed with dynamic programming. -D If query sequence name/length are identical to the target name/length, ignore diagonal anchors. This option also reduces DP-based extension along the diagonal. -P Retain all chains and don’t attempt to set primary chains. Options -p and -N have no effect when this option is in use. --dual = yes | no   If no , skip query-target pairs wherein the query name is lexicographically greater than the target name [yes] -X Equivalent to ’ -DP --dual = no --no-long-join ’. Primarily used for all-vs-all read overlapping. -p FLOAT Minimal secondary-to-primary score ratio to output secondary mappings [0.8]. Between two chains overlaping over half of the shorter chain (controlled by -M ), the chain with a lower score is secondary to the chain with a higher score. If the ratio of the scores is below FLOAT , the secondary chain will not be outputted or extended with DP alignment later. This option has no effect when -X is applied. -N INT Output at most INT secondary alignments [5]. This option has no effect when -X is applied. -G NUM Maximum gap on the reference (effective with -xsplice / --splice ). This option also changes the chaining and alignment band width to NUM . Increasing this option slows down spliced alignment. [200k] -F NUM Maximum fragment length (aka insert size; effective with -xsr / --frag = yes ) [800] -M FLOAT Mark as secondary a chain that overlaps with a better chain by FLOAT or more of the shorter chain [0.5] --rmq = no | yes   Use the minigraph chaining algorithm [no]. The minigraph algorithm is better for aligning contigs through long INDELs. --rmq-inner NUM   Apply full dynamic programming for anchors within distance NUM [1000]. --hard-mask-level   Honor option -M and disable a heurstic to save unmapped subsequences and disables --mask-len . --mask-len NUM   Keep an alignment if dropping it leaves an unaligned region on query longer than INT [inf]. Effective without --hard-mask-level . --max-chain-skip INT   A heuristics that stops chaining early [25]. Minimap2 uses dynamic programming for chaining. The time complexity is quadratic in the number of seeds. This option makes minimap2 exits the inner loop if it repeatedly sees seeds already on chains. Set INT to a large number to switch off this heurstics. --max-chain-iter INT   Check up to INT partial chains during chaining [5000]. This is a heuristic to avoid quadratic time complexity in the worst case. --chain-gap-scale FLOAT   Scale of gap cost during chaining [1.0] --no-long-join   Disable the long gap patching heuristic. When this option is applied, the maximum alignment gap is mostly controlled by -r . --splice Enable the splice alignment mode. --sr Enable short-read alignment heuristics. In the short-read mode, minimap2 applies a second round of chaining with a higher minimizer occurrence threshold if no good chain is found. In addition, minimap2 attempts to patch gaps between seeds with ungapped alignment. --split-prefix STR   Prefix to create temporary files. Typically used for a multi-part index. --frag = no | yes   Whether to enable the fragment mode [no] --for-only Only map to the forward strand of the reference sequences. For paired-end reads in the forward-reverse orientation, the first read is mapped to forward strand of the reference and the second read to the reverse stand. --rev-only Only map to the reverse complement strand of the reference sequences. --heap-sort = no | yes   If yes, sort anchors with heap merge, instead of radix sort. Heap merge is faster for short reads, but slower for long reads. [no] --no-pairing   Treat two reads in a pair as independent reads. The mate related fields in SAM are still properly populated. --no-hash-name   Produce the same alignment for identical sequences regardless of their sequence names.     Alignment options -A INT Matching score [2] -B INT Mismatching penalty [4] -b INT Mismatching penalty for transitions [same as -B ]. -O INT1[,INT2]   Gap open penalty [4,24]. If INT2 is not specified, it is set to INT1 . -E INT1[,INT2]   Gap extension penalty [2,1]. A gap of length k costs min{ O1 + k * E1 , O2 + k * E2 }. In the splice mode, the second gap penalties are not used. -J INT Splice model [1]. 0 for the original minimap2 splice model that always penalizes non-GT-AG splicing; 1 for the miniprot model that considers non-GT-AG. Option -C has no effect with the default -J1 . -J0 . -C INT Cost for a non-canonical GT-AG splicing (effective with --splice -J0 ) [0]. -z INT1[,INT2]   Truncate an alignment if the running alignment score drops too quickly along the diagonal of the DP matrix (diagonal X-drop, or Z-drop) [400,200]. If the drop of score is above INT2 , minimap2 will reverse complement the query in the related region and align again to test small inversions. Minimap2 truncates alignment if there is an inversion or the drop of score is greater than INT1 . Decrease INT2 to find small inversions at the cost of performance and false positives. Increase INT1 to improves the contiguity of alignment at the cost of poor alignment in the middle. -s INT Minimal peak DP alignment score to output [40]. The peak score is computed from the final CIGAR. It is the score of the max scoring segment in the alignment and may be different from the total alignment score. -u CHAR How to find canonical splicing sites GT-AG - f : transcript strand; b : both strands; n : no attempt to match GT-AG [n] --end-bonus INT   Score bonus when alignment extends to the end of the query sequence [0]. --score-N INT   Score of a mismatch involving ambiguous bases [1]. --pe-ind-chain   For paired-end short reads, perform chaining for each end independently. By default, minimap2 chains the two ends together. --splice-flank = yes | no   Assume the next base to a GT donor site tends to be A/G (91% in human and 92% in mouse) and the preceding base to a AG acceptor tends to be C/T [no]. This trend is evolutionarily conservative, all the way to S. cerevisiae (PMID:18688272). Specifying this option generally leads to higher junction accuracy by several percents, so it is applied by default with --splice . However, the SIRV control does not honor this trend (only ~60%). This option reduces accuracy. If you are benchmarking minimap2 on SIRV data, please add --splice-flank=no to the command line. --spsc FILE Splice scores []. Each line consists of five fields: 1) contig, 2) offset, 3) ‘+’ or ‘-’, 4) ‘D’ or ‘A’, and 5) score, where offset is the number of bases before a splice junction, ‘D’ indicates the line corresponds to a donor site and ‘A’ for an acceptor site. A positive score suggests the junction is preferred and a negative score suggests the junction is not preferred. --junc-pen INT   Penalty for a position not in FILE specified by --spsc [5]. Effective with --spsc but not --junc-bed . --junc-bed FILE   Gene annotations in the BED12 format (aka 12-column BED), or intron positions in 5-column BED. With this option, minimap2 prefers splicing in annotations. BED12 file can be converted from GTF/GFF3 with ‘paftools.js gff2bed anno.gtf’ []. --junc-bonus INT   Score bonus for a splice donor or acceptor found in annotation [9]. Effective with --junc-bed but not --spsc . --end-seed-pen INT   Drop a terminal anchor if s <log( g )+ INT , where s is the local alignment score around the anchor and g the length of the terminal gap in the chain. This option is only effective with --splice . It helps to avoid tiny terminal exons. [6] --no-end-flt   Don’t filter seeds towards the ends of chains before performing base-level alignment. --cap-sw-mem NUM   Skip alignment if the DP matrix size is above NUM . Set 0 to disable [100m]. --cap-kalloc NUM   Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir above NUM . Set 0 to disable [500m].     Input/output options -a Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF by default. -o FILE Output alignments to FILE [stdout]. -Q Ignore base quality in the input file. -L Write CIGAR with >65535 operators at the CG tag. Older tools are unable to convert alignments with >65535 CIGAR ops to BAM. This option makes minimap2 SAM compatible with older tools. Newer tools recognizes this tag and reconstruct the real CIGAR in memory. -R STR SAM read group line in a format like @RG\\tID:foo\\tSM:bar []. -y Copy input FASTA/Q comments to output. -c Generate CIGAR. In PAF, the CIGAR is written to the ‘cg’ custom tag. --cs[= STR ]   Output the cs tag. STR can be either short or long . If no STR is given, short is assumed. [none] --MD Output the MD tag (see the SAM spec). --eqx Output =/X CIGAR operators for sequence match/mismatch. -Y In SAM output, use soft clipping for supplementary alignments. --secondary-seq   In SAM output, show query sequences for secondary alignments. --seed INT Integer seed for randomizing equally best hits. Minimap2 hashes INT and read name when choosing between equally best hits. [11] -t INT Number of threads [3]. Minimap2 uses at most three threads when indexing target sequences, and uses up to INT +1 threads when mapping (the extra thread is for I/O, which is frequently idle and takes little CPU time). -2 Use two I/O threads during mapping. By default, minimap2 uses one I/O thread. When I/O is slow (e.g. piping to gzip, or reading from a slow pipe), the I/O thread may become the bottleneck. Apply this option to use one thread for input and another thread for output, at the cost of increased peak RAM. -K NUM Number of bases loaded into memory to process in a mini-batch [500M]. Similar to option -I , K/M/G/k/m/g suffix is accepted. A large NUM helps load balancing in the multi-threading mode, at the cost of increased memory. --secondary = yes | no   Whether to output secondary alignments [yes] --max-qlen NUM   Filter out query sequences longer than NUM . --paf-no-hit   In PAF, output unmapped queries; the strand and the reference name fields are set to ‘*’. Warning: some paftools.js commands may not work with such output for the moment. --sam-hit-only   In SAM, don’t output unmapped reads. --version Print version number to stdout     Preset options -x STR Preset []. This option applies multiple options at the same time. It should be applied before other options because options applied later will overwrite the values set by -x . Available STR are: map-ont Align noisy long reads of ~10% error rate to a reference genome. This is the default mode. lr:hq Align accurate long reads (error rate <1%) to a reference genome ( -k19 -w19 -U50,500 -g10k ). This was recommended by ONT developers for recent Nanopore reads produced with chemistry v14 that can reach ~99% in accuracy. It was shown to work better for accurate Nanopore reads than map-hifi . map-hifi Align PacBio high-fidelity (HiFi) reads to a reference genome ( -xlr:hq -A1 -B4 -O6,26 -E2,1 -s200 ). It differs from lr:hq only in scoring. It has not been tested whether lr:hq would work better for PacBio HiFi reads. map-pb Align older PacBio continuous long (CLR) reads to a reference genome ( -Hk19 ). Note that this data type is effectively deprecated by HiFi. Unless you work on very old data, you probably want to use map-hifi or lr:hq . map-iclr Align Illumina Complete Long Reads (ICLR) to a reference genome ( -k19 -B6 -b4 -O10,50 ). This was recommended by Illumina developers. asm5 Long assembly to reference mapping ( -k19 -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50 ). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Use this preset if the average divergence is not much higher than 0.1%. asm10 Long assembly to reference mapping ( -k19 -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200 -N50 ). Use this if the average divergence is around 1%. asm20 Long assembly to reference mapping ( -k19 -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50 ). Use this if the average divergence is around several percent. splice Long-read spliced alignment ( -k15 -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0 --splice-flank=yes ). In the splice mode, 1) long deletions are taken as introns and represented as the ‘ N ’ CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap costs are different during chaining; 4) the computation of the ‘ ms ’ tag ignores introns to demote hits to pseudogenes. splice:hq Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq ( -xsplice -C5 -O6,24 -B4 ). splice:sr Spliced alignment for short RNA-seq reads ( -xsplice:hq --frag=yes --end-bonus=10 -2K50m --heap-sort=yes --pe-ind-chain --secondary=no ). sr Short-read alignment without splicing ( -k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m25 -s40 -g100 -2K50m --heap-sort=yes --secondary=no ). ava-pb PacBio CLR all-vs-all overlap mapping ( -Hk19 -Xw5 -e0 -m100 ). ava-ont Oxford Nanopore all-vs-all overlap mapping ( -k15 -Xw5 -e0 -m100 -r2k ).     Miscellaneous options --no-kalloc   Use the libc default allocator instead of the kalloc thread-local allocator. This debugging option is mostly used with Valgrind to detect invalid memory accesses. Minimap2 runs slower with this option, especially in the multi-threading mode. --print-qname   Print query names to stderr, mostly to see which query is crashing minimap2. --print-seeds   Print seed positions to stderr, for debugging only. OUTPUT FORMAT Minimap2 outputs mapping positions in the Pairwise mApping Format (PAF) by default. PAF is a TAB-delimited text format with each line consisting of at least 12 fields as are described in the following table: Col Type Description 1 string Query sequence name 2 int Query sequence length 3 int Query start coordinate (0-based) 4 int Query end coordinate (0-based) 5 char ‘+’ if query/target on the same strand; ‘-’ if opposite 6 string Target sequence name 7 int Target sequence length 8 int Target start coordinate on the original strand 9 int Target end coordinate on the original strand 10 int Number of matching bases in the mapping 11 int Number bases, including gaps, in the mapping 12 int Mapping quality (0-255 with 255 for missing) When alignment is available, column 11 gives the total number of sequence matches, mismatches and gaps in the alignment; column 10 divided by column 11 gives the BLAST-like alignment identity. When alignment is unavailable, these two columns are approximate. PAF may optionally have additional fields in the SAM-like typed key-value format. Minimap2 may output the following tags: Tag Type Description tp A Type of aln: P/primary, S/secondary and I,i/inversion cm i Number of minimizers on the chain s1 i Chaining score s2 i Chaining score of the best secondary chain NM i Total number of mismatches and gaps in the alignment MD Z To generate the ref sequence in the alignment AS i DP alignment score SA Z List of other supplementary alignments (with approximate CIGAR strings) ms i DP score of the max scoring segment in the alignment nn i Number of ambiguous bases in the alignment ts A Transcript strand (splice mode only) cg Z + +### https://github.com/lh3/minimap2 +GitHub - lh3/minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} lh3 / minimap2 Public Notifications You must be signed in to change notification settings Fork 461 Star 2.2k Code Issues 51 Pull requests 17 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights lh3/minimap2 master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,222 Commits 1,222 Commits .github/ workflows .github/ workflows misc misc python python sse2neon sse2neon test test tex tex .gitignore .gitignore .gitmodules .gitmodules FAQ.md FAQ.md LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in Makefile Makefile Makefile.simde Makefile.simde NEWS.md NEWS.md README.md README.md align.c align.c bseq.c bseq.c bseq.h bseq.h code_of_conduct.md code_of_conduct.md cookbook.md cookbook.md esterr.c esterr.c example.c example.c format.c format.c hit.c hit.c index.c index.c jump.c jump.c kalloc.c kalloc.c kalloc.h kalloc.h kdq.h kdq.h ketopt.h ketopt.h khash.h khash.h krmq.h krmq.h kseq.h kseq.h ksort.h ksort.h ksw2.h ksw2.h ksw2_dispatch.c ksw2_dispatch.c ksw2_extd2_sse.c ksw2_extd2_sse.c ksw2_exts2_sse.c ksw2_exts2_sse.c ksw2_extz2_sse.c ksw2_extz2_sse.c ksw2_ll_sse.c ksw2_ll_sse.c kthread.c kthread.c kthread.h kthread.h kvec.h kvec.h lchain.c lchain.c main.c main.c map.c map.c minimap.h minimap.h minimap2.1 minimap2.1 misc.c misc.c mmpriv.h mmpriv.h options.c options.c pe.c pe.c pyproject.toml pyproject.toml sdust.c sdust.c sdust.h sdust.h seed.c seed.c setup.py setup.py sketch.c sketch.c splitidx.c splitidx.c View all files Repository files navigation README Code of conduct License Getting Started ALERT: minimap2.com is a phishing site . Please don't use anything from that website. git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and then map ./minimap2 -x map-ont -d MT-human-ont.mmi test/MT-human.fa ./minimap2 -a MT-human-ont.mmi test/MT-orang.fa > test.sam # use presets (no test data) ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio CLR genomic reads ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads ./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19+) ./minimap2 -ax lr:hq ref.fa ont-Q20.fq.gz > aln.sam # Nanopore Q20 genomic reads (v2.27+) ./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam # short genomic paired-end reads ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads (strand unknown) ./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam # noisy Nanopore direct RNA-seq ./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam # PacBio Kinnex/Iso-seq (RNA-seq) ./minimap2 -ax splice --junc-bed=anno.bed12 ref.fa query.fa > aln.sam # use annotated junctions ./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # short-read RNA-seq (v2.29+) ./minimap2 -ax splice:sr -j anno.bed12 ref.fa r1.fq r2.fq > aln.sam ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap ./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf # Nanopore read overlap # man page for detailed command line options man ./minimap2.1 Table of Contents Getting Started Users' Guide Installation General usage Use cases Map long noisy genomic reads Map long mRNA/cDNA reads Find overlaps between long reads Map short genomic reads Map short RNA-seq reads Full genome/assembly alignment Advanced features Working with >65535 CIGAR operations The cs optional tag Working with the PAF format Algorithm overview Getting help Citing minimap2 Developers' Guide Limitations Users' Guide Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2) finding overlaps between long reads with error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome; (4) aligning Illumina single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-genome alignment between two closely related species with divergence below ~15%. For ~10kb noisy reads sequences, minimap2 is tens of times faster than mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more accurate on simulated long reads and produces biologically meaningful alignment ready for downstream analyses. For >100bp Illumina short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data. Detailed evaluations are available from the minimap2 paper or the preprint . Installation Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from the release page with: curl -L https://github.com/lh3/minimap2/releases/download/v2.30/minimap2-2.30_x64-linux.tar.bz2 | tar -jxvf - ./minimap2-2.30_x64-linux/minimap2 If you want to compile from the source, you need to have a C compiler, GNU make and zlib development files installed. Then type make in the source code directory to compile. If you see compilation errors, try make sse2only=1 to disable SSE4 code, which will make minimap2 slightly slower. Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To compile for 32 bit ARM architectures (such as ARMv7), use make arm_neon=1 . To compile for for 64 bit ARM architectures (such as ARMv8), use make arm_neon=1 aarch64=1 . Minimap2 can use SIMD Everywhere (SIMDe) library for porting implementation to the different SIMD instruction sets. To compile using SIMDe, use make -f Makefile.simde . To compile for ARM CPUs, use Makefile.simde with the ARM related command lines given above. General usage Without any options, minimap2 takes a reference database and a query sequence file as input and produce approximate mapping, without base-level alignment (i.e. coordinates are only approximate and no CIGAR in output), in the PAF format : minimap2 ref.fa query.fq > approx-mapping.paf You can ask minimap2 to generate CIGAR at the cg tag of PAF with: minimap2 -c ref.fa query.fq > alignment.paf or to output alignments in the SAM format : minimap2 -a ref.fa query.fq > alignment.sam Minimap2 seamlessly works with gzip'd FASTA and FASTQ formats as input. You don't need to convert between FASTA and FASTQ or decompress gzip'd files first. For the human reference genome, minimap2 takes a few minutes to generate a minimizer index for the reference before mapping. To reduce indexing time, you can optionally save the index with option -d and replace the reference sequence file with the index file on the minimap2 command line: minimap2 -d ref.mmi ref.fa # indexing minimap2 -a ref.mmi reads.fq > alignment.sam # alignment Importantly , it should be noted that once you build the index, indexing parameters such as -k , -w , -H and -I can't be changed during mapping. If you are running minimap2 for different data types, you will probably need to keep multiple indexes generated with different parameters. This makes minimap2 different from BWA which always uses the same index regardless of query data types. Use cases Minimap2 uses the same base algorithm for all applications. However, due to the different data types it supports (e.g. short vs long reads; DNA vs mRNA reads), minimap2 needs to be tuned for optimal performance and accuracy. It is usually recommended to choose a preset with option -x , which sets multiple parameters at the same time. The default setting is the same as map-ont . Map long noisy genomic reads minimap2 -ax map-pb ref.fa pacbio-reads.fq > aln.sam # for PacBio CLR reads minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam # for Oxford Nanopore reads minimap2 -ax map-iclr ref.fa iclr-reads.fq > aln.sam # for Illumina Complete Long Reads The difference between map-pb and map-ont is that map-pb uses homopolymer-compressed (HPC) minimizers as seeds, while map-ont uses ordinary minimizers as seeds. Empirical evaluation suggests HPC minimizers improve performance and sensitivity when aligning PacBio CLR reads, but hurt when aligning Nanopore reads. map-iclr uses an adjusted alignment scoring matrix that accounts for the low overall error rate in the reads, with transversion errors being less frequent than transitions. Map long mRNA/cDNA reads minimap2 -ax splice:hq -uf ref.fa iso-seq.fq > aln.sam # PacBio Iso-seq/traditional cDNA minimap2 -ax splice ref.fa nanopore-cdna.fa > aln.sam # Nanopore 2D cDNA-seq minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam # Nanopore Direct RNA-seq minimap2 -ax splice --splice-flank=no SIRV.fa SIRV-seq.fa # mapping against SIRV control There are different long-read RNA-seq technologies, including tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq and Direct RNA-seq. They produce data of varying quality and properties. By default, -x splice assumes the read orientation relative to the transcript strand is unknown. It tries two rounds of alignment to infer the orientation and write the strand to the ts SAM/PAF tag if possible. For Iso-seq, Direct RNA-seq and tranditional full-length cDNAs, it would be desired to apply -u f to force minimap2 to consider the forward transcript strand only. This speeds up alignment with slight improvement to accuracy. For noisy Nanopore Direct RNA-seq reads, it is recommended to use a smaller k-mer size for increased sensitivity to the first or the last exons. Minimap2 rates an alignment by the score of the max-scoring sub-segment, excluding introns, and marks the best alignment as primary in SAM. When a spliced gene also has unspliced pseudogenes, minimap2 slightly prefers the spliced alignment. By default, minimap2 outputs up to five secondary alignments (i.e. likely pseudogenes in the context of RNA-seq mapping). This can be tuned with option -N . For long RNA-seq reads, minimap2 may produce chimeric alignments potentially caused by gene fusions/structural variations or by an intron longer than the max intron length -G (200k by default). For now, it is not recommended to apply an excessively large -G as this slows down minimap2 and sometimes leads to false alignments. It is worth noting that by default -x splice prefers GT[A/G]..[C/T]AG over GT[C/T]..[A/G]AG, and then over other splicing signals. Considering one additional base improves the junction accuracy for noisy reads, but reduces the accuracy when aligning against the widely used SIRV control data. This is because SIRV does not honor the evolutionarily conservative splicing signal. If you are studying SIRV, you may apply --splice-flank=no to let minimap2 only model GT..AG, ignoring the additional base. Since v2.17, minimap2 can optionally take annotated genes as input and prioritize on annotated splice junctions. To use this feature, you can paftools.js gff2bed anno.gff > anno.bed minimap2 -ax splice --junc-bed anno.bed ref.fa query.fa > aln.sam Here, anno.gff is the gene annotation in the GTF or GFF3 format ( gff2bed automatically tests the format). The output of gff2bed is in the 12-column BED format, or the BED12 format. With the --junc-bed option, minimap2 adds a bonus score (tuned by --junc-bonus ) if an aligned junction matches a junction in the annotation. Option --junc-bed also takes 5-column BED, including the strand field. In this case, each line indicates an oriented junction. Note: --junc-bed is intended for long noisy RNA-seq reads only. Applying the option to short RNA-seq reads would increase run time with little improvement to junction accuracy. Find overlaps between long reads minimap2 -x ava-pb reads.fq reads.fq > ovlp.paf # PacBio CLR read overlap minimap2 -x ava-ont reads.fq reads.fq > ovlp.paf # Oxford Nanopore read overlap Similarly, ava-pb uses HPC minimizers while ava-ont uses ordinary minimizers. It is usually not recommended to perform base-level alignment in the overlapping mode because it is slow and may produce false positive overlaps. However, if performance is not a concern, you may try to add -a or -c anyway. Map short genomic reads minimap2 -ax sr ref.fa reads-se.fq > aln.sam # single-end alignment minimap2 -ax sr ref.fa read1.fq read2.fq > aln.sam # paired-end alignment minimap2 -ax sr ref.fa reads-interleaved.fq > aln.sam # paired-end alignment When two read files are specified, minimap2 reads from each file in turn and merge them into an interleaved stream internally. Two reads are considered to be paired if they are adjacent in the input stream and have the same name (with the /[0-9] suffix trimmed if present). Single- and paired-end reads can be mixed. Map short RNA-seq reads minimap2 -ax splice:sr ref.fa reads-se.fq.gz > aln.sam # single-end minimap2 -ax splice:sr ref.fa r1.fq.gz r2.fq.gz > aln.sam # paired-end minimap2 -ax splice:sr -j anno.bed ref.fa r1.fq r2.fq > aln.sam # use annotation # 2-pass alignment minimap2 -x splice:sr -j anno.bed --write-junc ref.fa r1.fq r2.fq > junc.bed minimap2 -ax splice:sr -j anno.bed --pass1=junc.bed ref.fa r1.fq r2.fq > aln.sam The new preset splice:sr was added in v2.29. It functions similarly to sr except that it performs spliced alignment. Full genome/assembly alignment minimap2 -ax asm5 ref.fa asm.fa > aln.sam # assembly to assembly/ref alignment For cross-species full-genome alignment, the scoring system needs to be tuned according to the sequence divergence. Advanced features Working with >65535 CIGAR operations Due to a design flaw, BAM does not work with CIGAR strings with >65535 operations (SAM and CRAM work). However, for ultra-long nanopore reads minimap2 may align ~1% of read bases with long CIGARs beyond the capability of BAM. If you convert such SAM/CRAM to BAM, Picard and recent samtools will throw an error and abort. Older samtools and other tools may create corrupted BAM. To avoid this issue, you can add option -L at the minimap2 command line. This option moves a long CIGAR to the CG tag and leaves a fully clipped CIGAR at the SAM CIGAR column. Current tools that don't read CIGAR (e.g. merging and sorting) still work with such BAM records; tools that read CIGAR will effectively ignore these records. It has been decided that future tools will seamlessly recognize long-cigar records generated by option -L . TL;DR : if you work with ultra-long reads and use tools that only process BAM files, please add option -L . The cs optional tag The cs SAM/PAF tag encodes bases at mismatches and INDELs. It matches regular expression /(:[0-9]+|\*[a-z][a-z]|[=\+\-][A-Za-z]+)+/ . Like CIGAR, cs consists of series of operations. Each leading character specifies the operation; the following sequence is the one involved in the operation. The cs tag is enabled by command line option --cs . The following alignment, for example: CGATCGATAAATAGAGTAG---GAATAGCA || |||| |||||||||| |||| || | CGATCG---AATAGAGTAGGTCGAATtGCA is represented as :6-ata:10+gtc:4*at:3 , where :[0-9]+ represents an identical block, -ata represents a deletion, +gtc an insertion and *at indicates reference base a is substituted with a query base t . It is similar to the MD SAM tag but is standalone and easier to parse. If --cs=long is used, the cs string also contains identical sequences in the alignment. The above example will become =CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA . The long form of cs encodes both reference and query sequences in one string. The cs tag also encodes intron positions and splicing signals (see the minimap2 manpage for details). Working with the PAF format Minimap2 also comes with a (java)script paftools.js that processes alignments in the PAF format. It calls variants from assembly-to-reference alignment, lifts over BED files based on alignment, converts between formats and provides utilities for various evaluations. For details, please see misc/README.md . Algorithm overview In the following, minimap2 command line options have a dash ahead and are highlighted in bold. The description may help to tune minimap2 parameters. Read -I [= 4G ] reference bases, extract ( -k , -w )-minimizers and index them in a hash table. Read -K [= 200M ] query bases. For each query sequence, do step 3 through 7: For each ( -k , -w )-minimizer on the query, check against the reference index. If a reference minimizer is not among the top -f [= 2e-4 ] most frequent, collect its the occurrences in the reference, which are called seeds . Sort seeds by position in the reference. Chain them with dynamic programming. Each chain represents a potential mapping. For read overlapping, report all chains and then go to step 8. For reference mapping, do step 5 through 7: Let P be the set of primary mappings, which is an empty set initially. For each chain from the best to the worst according to their chaining scores: if on the query, the chain overlaps with a chain in P by --mask-level [= 0.5 ] or higher fraction of the shorter chain, mark the chain as secondary to the chain in P ; otherwise, add the chain to P . Retain all primary mappings. Also retain up to -N [= 5 ] top secondary mappings if their chaining scores are higher than -p [= 0.8 ] of their corresponding primary mappings. If alignment is requested, + +### https://github.com/lh3/minimap2 +GitHub - lh3/minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} lh3 / minimap2 Public Notifications You must be signed in to change notification settings Fork 461 Star 2.2k Code Issues 51 Pull requests 17 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights lh3/minimap2 master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,222 Commits 1,222 Commits .github/ workflows .github/ workflows misc misc python python sse2neon sse2neon test test tex tex .gitignore .gitignore .gitmodules .gitmodules FAQ.md FAQ.md LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in Makefile Makefile Makefile.simde Makefile.simde NEWS.md NEWS.md README.md README.md align.c align.c bseq.c bseq.c bseq.h bseq.h code_of_conduct.md code_of_conduct.md cookbook.md cookbook.md esterr.c esterr.c example.c example.c format.c format.c hit.c hit.c index.c index.c jump.c jump.c kalloc.c kalloc.c kalloc.h kalloc.h kdq.h kdq.h ketopt.h ketopt.h khash.h khash.h krmq.h krmq.h kseq.h kseq.h ksort.h ksort.h ksw2.h ksw2.h ksw2_dispatch.c ksw2_dispatch.c ksw2_extd2_sse.c ksw2_extd2_sse.c ksw2_exts2_sse.c ksw2_exts2_sse.c ksw2_extz2_sse.c ksw2_extz2_sse.c ksw2_ll_sse.c ksw2_ll_sse.c kthread.c kthread.c kthread.h kthread.h kvec.h kvec.h lchain.c lchain.c main.c main.c map.c map.c minimap.h minimap.h minimap2.1 minimap2.1 misc.c misc.c mmpriv.h mmpriv.h options.c options.c pe.c pe.c pyproject.toml pyproject.toml sdust.c sdust.c sdust.h sdust.h seed.c seed.c setup.py setup.py sketch.c sketch.c splitidx.c splitidx.c View all files Repository files navigation README Code of conduct License Getting Started ALERT: minimap2.com is a phishing site . Please don't use anything from that website. git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and then map ./minimap2 -x map-ont -d MT-human-ont.mmi test/MT-human.fa ./minimap2 -a MT-human-ont.mmi test/MT-orang.fa > test.sam # use presets (no test data) ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio CLR genomic reads ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads ./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19+) ./minimap2 -ax lr:hq ref.fa ont-Q20.fq.gz > aln.sam # Nanopore Q20 genomic reads (v2.27+) ./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam # short genomic paired-end reads ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads (strand unknown) ./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam # noisy Nanopore direct RNA-seq ./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam # PacBio Kinnex/Iso-seq (RNA-seq) ./minimap2 -ax splice --junc-bed=anno.bed12 ref.fa query.fa > aln.sam # use annotated junctions ./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # short-read RNA-seq (v2.29+) ./minimap2 -ax splice:sr -j anno.bed12 ref.fa r1.fq r2.fq > aln.sam ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap ./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf # Nanopore read overlap # man page for detailed command line options man ./minimap2.1 Table of Contents Getting Started Users' Guide Installation General usage Use cases Map long noisy genomic reads Map long mRNA/cDNA reads Find overlaps between long reads Map short genomic reads Map short RNA-seq reads Full genome/assembly alignment Advanced features Working with >65535 CIGAR operations The cs optional tag Working with the PAF format Algorithm overview Getting help Citing minimap2 Developers' Guide Limitations Users' Guide Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2) finding overlaps between long reads with error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome; (4) aligning Illumina single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-genome alignment between two closely related species with divergence below ~15%. For ~10kb noisy reads sequences, minimap2 is tens of times faster than mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more accurate on simulated long reads and produces biologically meaningful alignment ready for downstream analyses. For >100bp Illumina short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data. Detailed evaluations are available from the minimap2 paper or the preprint . Installation Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from the release page with: curl -L https://github.com/lh3/minimap2/releases/download/v2.30/minimap2-2.30_x64-linux.tar.bz2 | tar -jxvf - ./minimap2-2.30_x64-linux/minimap2 If you want to compile from the source, you need to have a C compiler, GNU make and zlib development files installed. Then type make in the source code directory to compile. If you see compilation errors, try make sse2only=1 to disable SSE4 code, which will make minimap2 slightly slower. Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To compile for 32 bit ARM architectures (such as ARMv7), use make arm_neon=1 . To compile for for 64 bit ARM architectures (such as ARMv8), use make arm_neon=1 aarch64=1 . Minimap2 can use SIMD Everywhere (SIMDe) library for porting implementation to the different SIMD instruction sets. To compile using SIMDe, use make -f Makefile.simde . To compile for ARM CPUs, use Makefile.simde with the ARM related command lines given above. General usage Without any options, minimap2 takes a reference database and a query sequence file as input and produce approximate mapping, without base-level alignment (i.e. coordinates are only approximate and no CIGAR in output), in the PAF format : minimap2 ref.fa query.fq > approx-mapping.paf You can ask minimap2 to generate CIGAR at the cg tag of PAF with: minimap2 -c ref.fa query.fq > alignment.paf or to output alignments in the SAM format : minimap2 -a ref.fa query.fq > alignment.sam Minimap2 seamlessly works with gzip'd FASTA and FASTQ formats as input. You don't need to convert between FASTA and FASTQ or decompress gzip'd files first. For the human reference genome, minimap2 takes a few minutes to generate a minimizer index for the reference before mapping. To reduce indexing time, you can optionally save the index with option -d and replace the reference sequence file with the index file on the minimap2 command line: minimap2 -d ref.mmi ref.fa # indexing minimap2 -a ref.mmi reads.fq > alignment.sam # alignment Importantly , it should be noted that once you build the index, indexing parameters such as -k , -w , -H and -I can't be changed during mapping. If you are running minimap2 for different data types, you will probably need to keep multiple indexes generated with different parameters. This makes minimap2 different from BWA which always uses the same index regardless of query data types. Use cases Minimap2 uses the same base algorithm for all applications. However, due to the different data types it supports (e.g. short vs long reads; DNA vs mRNA reads), minimap2 needs to be tuned for optimal performance and accuracy. It is usually recommended to choose a preset with option -x , which sets multiple parameters at the same time. The default setting is the same as map-ont . Map long noisy genomic reads minimap2 -ax map-pb ref.fa pacbio-reads.fq > aln.sam # for PacBio CLR reads minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam # for Oxford Nanopore reads minimap2 -ax map-iclr ref.fa iclr-reads.fq > aln.sam # for Illumina Complete Long Reads The difference between map-pb and map-ont is that map-pb uses homopolymer-compressed (HPC) minimizers as seeds, while map-ont uses ordinary minimizers as seeds. Empirical evaluation suggests HPC minimizers improve performance and sensitivity when aligning PacBio CLR reads, but hurt when aligning Nanopore reads. map-iclr uses an adjusted alignment scoring matrix that accounts for the low overall error rate in the reads, with transversion errors being less frequent than transitions. Map long mRNA/cDNA reads minimap2 -ax splice:hq -uf ref.fa iso-seq.fq > aln.sam # PacBio Iso-seq/traditional cDNA minimap2 -ax splice ref.fa nanopore-cdna.fa > aln.sam # Nanopore 2D cDNA-seq minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam # Nanopore Direct RNA-seq minimap2 -ax splice --splice-flank=no SIRV.fa SIRV-seq.fa # mapping against SIRV control There are different long-read RNA-seq technologies, including tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq and Direct RNA-seq. They produce data of varying quality and properties. By default, -x splice assumes the read orientation relative to the transcript strand is unknown. It tries two rounds of alignment to infer the orientation and write the strand to the ts SAM/PAF tag if possible. For Iso-seq, Direct RNA-seq and tranditional full-length cDNAs, it would be desired to apply -u f to force minimap2 to consider the forward transcript strand only. This speeds up alignment with slight improvement to accuracy. For noisy Nanopore Direct RNA-seq reads, it is recommended to use a smaller k-mer size for increased sensitivity to the first or the last exons. Minimap2 rates an alignment by the score of the max-scoring sub-segment, excluding introns, and marks the best alignment as primary in SAM. When a spliced gene also has unspliced pseudogenes, minimap2 slightly prefers the spliced alignment. By default, minimap2 outputs up to five secondary alignments (i.e. likely pseudogenes in the context of RNA-seq mapping). This can be tuned with option -N . For long RNA-seq reads, minimap2 may produce chimeric alignments potentially caused by gene fusions/structural variations or by an intron longer than the max intron length -G (200k by default). For now, it is not recommended to apply an excessively large -G as this slows down minimap2 and sometimes leads to false alignments. It is worth noting that by default -x splice prefers GT[A/G]..[C/T]AG over GT[C/T]..[A/G]AG, and then over other splicing signals. Considering one additional base improves the junction accuracy for noisy reads, but reduces the accuracy when aligning against the widely used SIRV control data. This is because SIRV does not honor the evolutionarily conservative splicing signal. If you are studying SIRV, you may apply --splice-flank=no to let minimap2 only model GT..AG, ignoring the additional base. Since v2.17, minimap2 can optionally take annotated genes as input and prioritize on annotated splice junctions. To use this feature, you can paftools.js gff2bed anno.gff > anno.bed minimap2 -ax splice --junc-bed anno.bed ref.fa query.fa > aln.sam Here, anno.gff is the gene annotation in the GTF or GFF3 format ( gff2bed automatically tests the format). The output of gff2bed is in the 12-column BED format, or the BED12 format. With the --junc-bed option, minimap2 adds a bonus score (tuned by --junc-bonus ) if an aligned junction matches a junction in the annotation. Option --junc-bed also takes 5-column BED, including the strand field. In this case, each line indicates an oriented junction. Note: --junc-bed is intended for long noisy RNA-seq reads only. Applying the option to short RNA-seq reads would increase run time with little improvement to junction accuracy. Find overlaps between long reads minimap2 -x ava-pb reads.fq reads.fq > ovlp.paf # PacBio CLR read overlap minimap2 -x ava-ont reads.fq reads.fq > ovlp.paf # Oxford Nanopore read overlap Similarly, ava-pb uses HPC minimizers while ava-ont uses ordinary minimizers. It is usually not recommended to perform base-level alignment in the overlapping mode because it is slow and may produce false positive overlaps. However, if performance is not a concern, you may try to add -a or -c anyway. Map short genomic reads minimap2 -ax sr ref.fa reads-se.fq > aln.sam # single-end alignment minimap2 -ax sr ref.fa read1.fq read2.fq > aln.sam # paired-end alignment minimap2 -ax sr ref.fa reads-interleaved.fq > aln.sam # paired-end alignment When two read files are specified, minimap2 reads from each file in turn and merge them into an interleaved stream internally. Two reads are considered to be paired if they are adjacent in the input stream and have the same name (with the /[0-9] suffix trimmed if present). Single- and paired-end reads can be mixed. Map short RNA-seq reads minimap2 -ax splice:sr ref.fa reads-se.fq.gz > aln.sam # single-end minimap2 -ax splice:sr ref.fa r1.fq.gz r2.fq.gz > aln.sam # paired-end minimap2 -ax splice:sr -j anno.bed ref.fa r1.fq r2.fq > aln.sam # use annotation # 2-pass alignment minimap2 -x splice:sr -j anno.bed --write-junc ref.fa r1.fq r2.fq > junc.bed minimap2 -ax splice:sr -j anno.bed --pass1=junc.bed ref.fa r1.fq r2.fq > aln.sam The new preset splice:sr was added in v2.29. It functions similarly to sr except that it performs spliced alignment. Full genome/assembly alignment minimap2 -ax asm5 ref.fa asm.fa > aln.sam # assembly to assembly/ref alignment For cross-species full-genome alignment, the scoring system needs to be tuned according to the sequence divergence. Advanced features Working with >65535 CIGAR operations Due to a design flaw, BAM does not work with CIGAR strings with >65535 operations (SAM and CRAM work). However, for ultra-long nanopore reads minimap2 may align ~1% of read bases with long CIGARs beyond the capability of BAM. If you convert such SAM/CRAM to BAM, Picard and recent samtools will throw an error and abort. Older samtools and other tools may create corrupted BAM. To avoid this issue, you can add option -L at the minimap2 command line. This option moves a long CIGAR to the CG tag and leaves a fully clipped CIGAR at the SAM CIGAR column. Current tools that don't read CIGAR (e.g. merging and sorting) still work with such BAM records; tools that read CIGAR will effectively ignore these records. It has been decided that future tools will seamlessly recognize long-cigar records generated by option -L . TL;DR : if you work with ultra-long reads and use tools that only process BAM files, please add option -L . The cs optional tag The cs SAM/PAF tag encodes bases at mismatches and INDELs. It matches regular expression /(:[0-9]+|\*[a-z][a-z]|[=\+\-][A-Za-z]+)+/ . Like CIGAR, cs consists of series of operations. Each leading character specifies the operation; the following sequence is the one involved in the operation. The cs tag is enabled by command line option --cs . The following alignment, for example: CGATCGATAAATAGAGTAG---GAATAGCA || |||| |||||||||| |||| || | CGATCG---AATAGAGTAGGTCGAATtGCA is represented as :6-ata:10+gtc:4*at:3 , where :[0-9]+ represents an identical block, -ata represents a deletion, +gtc an insertion and *at indicates reference base a is substituted with a query base t . It is similar to the MD SAM tag but is standalone and easier to parse. If --cs=long is used, the cs string also contains identical sequences in the alignment. The above example will become =CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA . The long form of cs encodes both reference and query sequences in one string. The cs tag also encodes intron positions and splicing signals (see the minimap2 manpage for details). Working with the PAF format Minimap2 also comes with a (java)script paftools.js that processes alignments in the PAF format. It calls variants from assembly-to-reference alignment, lifts over BED files based on alignment, converts between formats and provides utilities for various evaluations. For details, please see misc/README.md . Algorithm overview In the following, minimap2 command line options have a dash ahead and are highlighted in bold. The description may help to tune minimap2 parameters. Read -I [= 4G ] reference bases, extract ( -k , -w )-minimizers and index them in a hash table. Read -K [= 200M ] query bases. For each query sequence, do step 3 through 7: For each ( -k , -w )-minimizer on the query, check against the reference index. If a reference minimizer is not among the top -f [= 2e-4 ] most frequent, collect its the occurrences in the reference, which are called seeds . Sort seeds by position in the reference. Chain them with dynamic programming. Each chain represents a potential mapping. For read overlapping, report all chains and then go to step 8. For reference mapping, do step 5 through 7: Let P be the set of primary mappings, which is an empty set initially. For each chain from the best to the worst according to their chaining scores: if on the query, the chain overlaps with a chain in P by --mask-level [= 0.5 ] or higher fraction of the shorter chain, mark the chain as secondary to the chain in P ; otherwise, add the chain to P . Retain all primary mappings. Also retain up to -N [= 5 ] top secondary mappings if their chaining scores are higher than -p [= 0.8 ] of their corresponding primary mappings. If alignment is requested, + +## Conda Search Info +$ conda search -c bioconda -c conda-forge minimap2 --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +minimap2 2.0.r191 0 +------------------- +file name : minimap2-2.0.r191-0.tar.bz2 +name : minimap2 +version : 2.0.r191 +build : 0 +build number: 0 +size : 155 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.0.r191-0.tar.bz2 +md5 : 07aff15193b144aea790acdf5f013284 +dependencies: + - libgcc + - zlib + + +minimap2 2.1.r311 0 +------------------- +file name : minimap2-2.1.r311-0.tar.bz2 +name : minimap2 +version : 2.1.r311 +build : 0 +build number: 0 +size : 196 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.1.r311-0.tar.bz2 +md5 : eddc5f9fe2b023be9c9a0a7ba2fd400e +dependencies: + - libgcc + - zlib + + +minimap2 2.1.1 0 +---------------- +file name : minimap2-2.1.1-0.tar.bz2 +name : minimap2 +version : 2.1.1 +build : 0 +build number: 0 +size : 255 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.1.1-0.tar.bz2 +md5 : 45a7acda90b05c7a44493e6742d8d82f +dependencies: + - libgcc + - zlib + + +minimap2 2.3 0 +-------------- +file name : minimap2-2.3-0.tar.bz2 +name : minimap2 +version : 2.3 +build : 0 +build number: 0 +size : 306 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.3-0.tar.bz2 +md5 : b9a877f05c94b32eb8957afae2171824 +dependencies: + - libgcc + - zlib 1.2.8* + + +minimap2 2.4 0 +-------------- +file name : minimap2-2.4-0.tar.bz2 +name : minimap2 +version : 2.4 +build : 0 +build number: 0 +size : 306 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.4-0.tar.bz2 +md5 : ca875cd58e6a6863cb013bfa692d2a79 +dependencies: + - libgcc + - zlib 1.2.8* + + +minimap2 2.5 0 +-------------- +file name : minimap2-2.5-0.tar.bz2 +name : minimap2 +version : 2.5 +build : 0 +build number: 0 +size : 306 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.5-0.tar.bz2 +md5 : fb4f00abfbd4f52ae07be3387b6e1cde +dependencies: + - libgcc + - zlib 1.2.8* + + +minimap2 2.6 0 +-------------- +file name : minimap2-2.6-0.tar.bz2 +name : minimap2 +version : 2.6 +build : 0 +build number: 0 +size : 313 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.6-0.tar.bz2 +md5 : 318190517393c126c9218dc668bb9d25 +dependencies: + - libgcc + - zlib 1.2.8* + + +minimap2 2.6.1 0 +---------------- +file name : minimap2-2.6.1-0.tar.bz2 +name : minimap2 +version : 2.6.1 +build : 0 +build number: 0 +size : 314 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.6.1-0.tar.bz2 +md5 : a77952028b6e2a7be8e30cdd3caceb34 +dependencies: + - libgcc + - zlib 1.2.8* + + +minimap2 2.7 0 +-------------- +file name : minimap2-2.7-0.tar.bz2 +name : minimap2 +version : 2.7 +build : 0 +build number: 0 +size : 316 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.7-0.tar.bz2 +md5 : 4816ef1c46275ab51fe5645eb7ca1534 +dependencies: + - libgcc + - zlib 1.2.8* + + +minimap2 2.8 0 +-------------- +file name : minimap2-2.8-0.tar.bz2 +name : minimap2 +version : 2.8 +build : 0 +build number: 0 +size : 323 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.8-0.tar.bz2 +md5 : 8a451740bf3f8bb549910fb72761d5b1 +dependencies: + - libgcc + - zlib 1.2.8* + + +minimap2 2.8 1 +-------------- +file name : minimap2-2.8-1.tar.bz2 +name : minimap2 +version : 2.8 +build : 1 +build number: 1 +size : 323 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.8-1.tar.bz2 +md5 : d43a346ea9bb677ae3b00102763b7df5 +dependencies: + - libgcc + - zlib 1.2.11* + + +minimap2 2.9 1 +-------------- +file name : minimap2-2.9-1.tar.bz2 +name : minimap2 +version : 2.9 +build : 1 +build number: 1 +size : 332 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.9-1.tar.bz2 +md5 : 02557a540207b9a04ea8290e2e06852e +dependencies: + - libgcc + - zlib 1.2.11* + + +minimap2 2.10 1 +--------------- +file name : minimap2-2.10-1.tar.bz2 +name : minimap2 +version : 2.10 +build : 1 +build number: 1 +size : 335 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.10-1.tar.bz2 +md5 : ccbb67818c82f33ff7dfcc5163fd61bb +dependencies: + - libgcc + - zlib 1.2.11* + + +minimap2 2.11 ha92aebf_0 +------------------------ +file name : minimap2-2.11-ha92aebf_0.tar.bz2 +name : minimap2 +version : 2.11 +build : ha92aebf_0 +build number: 0 +size : 342 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.11-ha92aebf_0.tar.bz2 +md5 : 90f0e5086f98660b7edb741d22aa578b +timestamp : 2018-06-21 15:25:19 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.12 ha92aebf_0 +------------------------ +file name : minimap2-2.12-ha92aebf_0.tar.bz2 +name : minimap2 +version : 2.12 +build : ha92aebf_0 +build number: 0 +size : 354 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.12-ha92aebf_0.tar.bz2 +md5 : 9f09e94f877f9b55c4c26fc6d47b13b3 +timestamp : 2018-08-06 18:57:09 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.13 ha92aebf_0 +------------------------ +file name : minimap2-2.13-ha92aebf_0.tar.bz2 +name : minimap2 +version : 2.13 +build : ha92aebf_0 +build number: 0 +size : 2.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.13-ha92aebf_0.tar.bz2 +md5 : ae7246d5ff182fbf020abb8d6ef21ec7 +timestamp : 2018-10-11 18:54:17 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.14 ha92aebf_0 +------------------------ +file name : minimap2-2.14-ha92aebf_0.tar.bz2 +name : minimap2 +version : 2.14 +build : ha92aebf_0 +build number: 0 +size : 2.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.14-ha92aebf_0.tar.bz2 +md5 : 4180294d8977fff77126a559b5affc37 +timestamp : 2018-11-06 06:07:42 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.15 h84994c4_1 +------------------------ +file name : minimap2-2.15-h84994c4_1.tar.bz2 +name : minimap2 +version : 2.15 +build : h84994c4_1 +build number: 1 +size : 367 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.15-h84994c4_1.tar.bz2 +md5 : 316133eba9b304471d975663be1b02bb +timestamp : 2019-02-08 12:30:47 UTC +dependencies: + - libgcc-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.15 ha92aebf_0 +------------------------ +file name : minimap2-2.15-ha92aebf_0.tar.bz2 +name : minimap2 +version : 2.15 +build : ha92aebf_0 +build number: 0 +size : 2.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.15-ha92aebf_0.tar.bz2 +md5 : 4ed6518709f9961ba56ce411c603f611 +timestamp : 2019-01-10 19:21:11 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.16 h84994c4_0 +------------------------ +file name : minimap2-2.16-h84994c4_0.tar.bz2 +name : minimap2 +version : 2.16 +build : h84994c4_0 +build number: 0 +size : 369 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.16-h84994c4_0.tar.bz2 +md5 : 1ec8d27d850770c4375d5a1744681771 +timestamp : 2019-03-01 04:27:34 UTC +dependencies: + - libgcc-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.16 h84994c4_1 +------------------------ +file name : minimap2-2.16-h84994c4_1.tar.bz2 +name : minimap2 +version : 2.16 +build : h84994c4_1 +build number: 1 +size : 2.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.16-h84994c4_1.tar.bz2 +md5 : dbe4f9fcd1221e7967dfa6067beceeec +timestamp : 2019-03-01 16:20:30 UTC +dependencies: + - libgcc-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.17 h5bf99c6_4 +------------------------ +file name : minimap2-2.17-h5bf99c6_4.tar.bz2 +name : minimap2 +version : 2.17 +build : h5bf99c6_4 +build number: 4 +size : 448 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.17-h5bf99c6_4.tar.bz2 +md5 : b20098e12fa32a92087a69e982e4755e +timestamp : 2021-03-26 03:57:02 UTC +dependencies: + - k8 + - libgcc-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.17 h84994c4_0 +------------------------ +file name : minimap2-2.17-h84994c4_0.tar.bz2 +name : minimap2 +version : 2.17 +build : h84994c4_0 +build number: 0 +size : 2.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.17-h84994c4_0.tar.bz2 +md5 : 9ca9f076d6a2dbe8b20fec6bce35fe93 +timestamp : 2019-05-05 04:39:10 UTC +dependencies: + - libgcc-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.17 h8b12597_1 +------------------------ +file name : minimap2-2.17-h8b12597_1.tar.bz2 +name : minimap2 +version : 2.17 +build : h8b12597_1 +build number: 1 +size : 2.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.17-h8b12597_1.tar.bz2 +md5 : d8c1f4e82c2511a41c700ee2115f27dc +timestamp : 2019-10-11 06:46:16 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.17 hed695b0_2 +------------------------ +file name : minimap2-2.17-hed695b0_2.tar.bz2 +name : minimap2 +version : 2.17 +build : hed695b0_2 +build number: 2 +size : 378 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.17-hed695b0_2.tar.bz2 +md5 : af8a5d73f42a2d60acee016f8973e0e3 +timestamp : 2020-06-18 13:39:41 UTC +dependencies: + - k8 + - libgcc-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.17 hed695b0_3 +------------------------ +file name : minimap2-2.17-hed695b0_3.tar.bz2 +name : minimap2 +version : 2.17 +build : hed695b0_3 +build number: 3 +size : 393 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.17-hed695b0_3.tar.bz2 +md5 : bb253837433882f2e87e0af5f066537a +timestamp : 2020-07-21 15:51:20 UTC +dependencies: + - k8 + - libgcc-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2.18 h5bf99c6_0 +------------------------ +file name : minimap2-2.18-h5bf99c6_0.tar.bz2 +name : minimap2 +version : 2.18 +build : h5bf99c6_0 +build number: 0 +size : 457 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/minimap2-2.18-h5bf99c6_0.tar.bz2 +md5 : 34c015cc1084f36a40779d6f68359d7d +timestamp : 2021-04-09 18:36:48 UTC +dependencies: + - k8 + - libgcc-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +minimap2 2. diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mitos.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mitos.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..eb189e650e3ad8a5ea3e7367f6d219d11cc3f69c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mitos.manual_bundle.txt @@ -0,0 +1,564 @@ +# Tool: mitos +software_name: mitos +tier: T1 +domain: t1_backfill_overall +downloads: 137048 +summary: MITOS is a tool for the annotation of metazoan mitochondrial genomes. +description: MITOS is a tool for the annotation of metazoan mitochondrial genomes. +dependencies: biopython <1.82, blast >=2.9,<3, hmmer 3.4.*, infernal >=1.1.5,<2, libtiff, openjdk >8, pillow, python >=3.10,<3.14, r-base, r-ggplot2, r-reshape2, reportlab, typing-extensions, viennarna <2 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: http://mitos.bioinf.uni-leipzig.de +doc_url: +dev_url: https://gitlab.com/Bernt/MITOS + +## URL Docs Extract +### http://mitos.bioinf.uni-leipzig.de +MITOS Web Server MITOS WebServer Bioinformatik MITOS (webserver) is dead - long live MITOS 🤙 MITOS and MITOS2 are now available as Galaxy tool (our recommendation for most users) and command line application (for power users with Linux experience). In order to make switching as easy as possible we provide tutorial videos for both cases. Feel free to contact us in case of problems/questions by mail (mitos (at) bioinf (dot) uni-leipzig (dot) de) or open an issue in the MITOS source code repository Using MITOS on usegalaxy.eu Your browser does not support the video tag, you may download it here . Using MITOS on the command line (conda/containers) Your browser does not support the video tag, you may download it here . In our opinion for most MITOS users the Galaxy platform is the way to go. At the moment there are usegalaxy.eu hosts MITOS MITOS2 usegalaxy.org hosts MITOS2 usegalaxy.org.au hosts MITOS2 Besides this the MITOS Galaxy tool can be installed in any Galaxy (for instance, any of the national usegalaxy instances which may provide more resources for you). One big advantage of the Galaxy platform is that it integrates a wide variety of bioinformatics tools. Interesting for mitochondrial data are for instance getorganelle, mitobim, and plasmidspades. If you want to learn more about Galaxy check out the Galaxy training network , The Galaxy community help forum , or The Galaxy community hub . The command line option is only suggested for power users with experience with Linux. Background: Why the MITOS service can't be provided as a web-service anymore: The current implementation of the webserver had serious security issues The webserver part of MITOS needs to be ported to python 3 Maintenance of the webserver consumed quite a bit of time Citation : M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz, G. Fritzsch, J. Pütz, M. Middendorf, P. F. Stadler MITOS: Improved de novo Metazoan Mitochondrial Genome Annotation Molecular Phylogenetics and Evolution 2013, 69(2):313-319 link Data Privacy Statement : The data privacy statement of the University of Leipzig applies to the mitos websites. --> Data Collection : In connection with your access to the web-service provided by Leipzig University, for reason of security, some data might be temporarily stored within server log files that might enable user identification. This includes name of the files, date and time of access, IP address, used browser and OS. You can voluntary provide your email address to this web-service, which is only used to send you a link to the results once the analysis is complete. Uploaded data is deleted after 8 weeks. Processing of the provided data is not performed, except for the following cases: suspicion of criminal offense, statistical purposes, optimization of the web-service and research use. Please consider that data transfer over the internet is largely unsecured. It cannot be excluded that transferred data can be read and possibly altered by unauthorized third parties. --> + +### https://gitlab.com/Bernt/MITOS +Matthias Bernt / MITOS · GitLab M MITOS Project information MITOS Read more 912 Commits 8 Branches 25 Tags 5 Releases README MIT License CHANGELOG Created on February 20, 2017 Loading + +## Conda Search Info +$ conda search -c bioconda -c conda-forge mitos --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +mitos 1.0.1 py27_0 +------------------ +file name : mitos-1.0.1-py27_0.tar.bz2 +name : mitos +version : 1.0.1 +build : py27_0 +build number: 0 +size : 231 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.0.1-py27_0.tar.bz2 +md5 : 23ade48ee24c514055609e3a834c02e4 +timestamp : 2019-04-23 20:51:20 UTC +dependencies: + - biopython 1.73 + - blast-legacy 2.2.26 + - ete2 2.3.10 + - infernal 1.0.2 + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.1 + - reportlab + - viennarna <2 + + +mitos 1.0.1 py27_1 +------------------ +file name : mitos-1.0.1-py27_1.tar.bz2 +name : mitos +version : 1.0.1 +build : py27_1 +build number: 1 +size : 234 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.0.1-py27_1.tar.bz2 +md5 : 632add69652cd48e187a3fae8e21b2e8 +timestamp : 2019-05-07 20:05:33 UTC +dependencies: + - biopython 1.73 + - blast-legacy 2.2.* + - ete2 2.3.* + - infernal 1.0.* + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.* + - reportlab + - viennarna <2 + + +mitos 1.0.2 py27_0 +------------------ +file name : mitos-1.0.2-py27_0.tar.bz2 +name : mitos +version : 1.0.2 +build : py27_0 +build number: 0 +size : 231 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.0.2-py27_0.tar.bz2 +md5 : bbbdeb4d3de6fff11b1be92039162c8a +timestamp : 2019-10-16 07:40:25 UTC +dependencies: + - biopython 1.73 + - blast-legacy 2.2.* + - ete2 2.3.* + - infernal 1.0.* + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.* + - reportlab + - viennarna <2 + + +mitos 1.0.4 py27_0 +------------------ +file name : mitos-1.0.4-py27_0.tar.bz2 +name : mitos +version : 1.0.4 +build : py27_0 +build number: 0 +size : 234 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.0.4-py27_0.tar.bz2 +md5 : 2feb76515a5b9f2e03c521786ccc369e +timestamp : 2020-02-09 16:49:42 UTC +dependencies: + - biopython 1.73 + - blast-legacy 2.2.* + - ete2 2.3.* + - infernal 1.0.* + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.* + - reportlab + - viennarna <2 + + +mitos 1.0.5 py_0 +---------------- +file name : mitos-1.0.5-py_0.tar.bz2 +name : mitos +version : 1.0.5 +build : py_0 +build number: 0 +size : 232 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.0.5-py_0.tar.bz2 +md5 : ef3d656b5c933a60486f8a52d5e56a4a +timestamp : 2020-02-17 09:03:25 UTC +dependencies: + - biopython 1.73 + - blast-legacy 2.2.* + - ete2 2.3.* + - infernal 1.0.* + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.* + - reportlab + - viennarna <2 + + +mitos 1.0.5 pyhdfd78af_1 +------------------------ +file name : mitos-1.0.5-pyhdfd78af_1.tar.bz2 +name : mitos +version : 1.0.5 +build : pyhdfd78af_1 +build number: 1 +size : 235 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.0.5-pyhdfd78af_1.tar.bz2 +md5 : 6b4d35873f58240899fd6823b09f8010 +timestamp : 2021-08-26 14:57:23 UTC +dependencies: + - biopython + - blast-legacy 2.2.* + - infernal 1.0.* + - openjdk + - python <3 + - r-base >=4 + - r-ggplot2 + - viennarna <2 + + +mitos 1.1.0 pyhdfd78af_0 +------------------------ +file name : mitos-1.1.0-pyhdfd78af_0.tar.bz2 +name : mitos +version : 1.1.0 +build : pyhdfd78af_0 +build number: 0 +size : 228 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.1.0-pyhdfd78af_0.tar.bz2 +md5 : a40f346f7ccab045d24192699e98086b +timestamp : 2022-09-10 13:34:06 UTC +dependencies: + - biopython <1.68 + - blast-legacy 2.2.* + - infernal 1.0.* + - openjdk >8 + - python >=3 + - r-base >=4 + - r-ggplot2 + - viennarna <2 + + +mitos 1.1.1 pyhdfd78af_0 +------------------------ +file name : mitos-1.1.1-pyhdfd78af_0.tar.bz2 +name : mitos +version : 1.1.1 +build : pyhdfd78af_0 +build number: 0 +size : 224 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.1.1-pyhdfd78af_0.tar.bz2 +md5 : 2fcd0f3c14a8a8d6955e3d63916f5401 +timestamp : 2023-02-23 14:11:41 UTC +dependencies: + - biopython <1.68 + - blast-legacy 2.2.* + - infernal 1.0.* + - openjdk >8 + - python >=3 + - r-base >=4 + - r-ggplot2 + - viennarna <2 + + +mitos 1.1.1 pyhdfd78af_1 +------------------------ +file name : mitos-1.1.1-pyhdfd78af_1.tar.bz2 +name : mitos +version : 1.1.1 +build : pyhdfd78af_1 +build number: 1 +size : 224 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.1.1-pyhdfd78af_1.tar.bz2 +md5 : d7e8918ff12a9cdcafb309f24995b845 +timestamp : 2023-02-25 16:23:45 UTC +dependencies: + - biopython <1.68 + - blast-legacy 2.2.* + - infernal 1.0.* + - libtiff <4.5 + - openjdk >8 + - pillow + - python >=3 + - r-base >=4 + - r-ggplot2 + - viennarna <2 + + +mitos 1.1.3 pyhdfd78af_0 +------------------------ +file name : mitos-1.1.3-pyhdfd78af_0.tar.bz2 +name : mitos +version : 1.1.3 +build : pyhdfd78af_0 +build number: 0 +size : 228 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.1.3-pyhdfd78af_0.tar.bz2 +md5 : 03ab97f005b7fb2455829440a783f4d9 +timestamp : 2023-12-22 13:40:21 UTC +dependencies: + - biopython <1.82 + - blast-legacy 2.2.* + - infernal 1.0.* + - libtiff + - openjdk >8 + - pillow + - python >=3 + - r-base >=4 + - r-ggplot2 + - r-reshape2 + - reportlab + - viennarna <2 + + +mitos 1.1.4 pyhdfd78af_0 +------------------------ +file name : mitos-1.1.4-pyhdfd78af_0.tar.bz2 +name : mitos +version : 1.1.4 +build : pyhdfd78af_0 +build number: 0 +size : 224 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.1.4-pyhdfd78af_0.tar.bz2 +md5 : c44c42c1abddb36d51b38112fc58c356 +timestamp : 2024-01-09 01:56:47 UTC +dependencies: + - biopython <1.82 + - blast-legacy 2.2.* + - infernal 1.0.* + - libtiff + - openjdk >8 + - pillow + - python >=3 + - r-ggplot2 + - r-reshape2 + - reportlab + - viennarna + + +mitos 1.1.5 pyhdfd78af_0 +------------------------ +file name : mitos-1.1.5-pyhdfd78af_0.tar.bz2 +name : mitos +version : 1.1.5 +build : pyhdfd78af_0 +build number: 0 +size : 221 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.1.5-pyhdfd78af_0.tar.bz2 +md5 : 50c40757006e4edadae828f812fd22fa +timestamp : 2024-01-24 21:45:56 UTC +dependencies: + - biopython <1.82 + - blast-legacy 2.2.* + - infernal 1.0.* + - libtiff + - openjdk >8 + - pillow + - python >=3 + - r-ggplot2 + - r-reshape2 + - reportlab + - viennarna + + +mitos 1.1.6 pyhdfd78af_0 +------------------------ +file name : mitos-1.1.6-pyhdfd78af_0.tar.bz2 +name : mitos +version : 1.1.6 +build : pyhdfd78af_0 +build number: 0 +size : 223 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.1.6-pyhdfd78af_0.tar.bz2 +md5 : 34436363c902241162bb93806a165cf8 +timestamp : 2024-03-22 01:46:37 UTC +dependencies: + - biopython <1.82 + - blast-legacy 2.2.* + - infernal 1.0.* + - libtiff + - openjdk >8 + - pillow + - python >=3 + - r-ggplot2 + - r-reshape2 + - reportlab + - viennarna + + +mitos 1.1.7 pyhdfd78af_0 +------------------------ +file name : mitos-1.1.7-pyhdfd78af_0.tar.bz2 +name : mitos +version : 1.1.7 +build : pyhdfd78af_0 +build number: 0 +size : 223 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-1.1.7-pyhdfd78af_0.tar.bz2 +md5 : 1ee6af14a4d722adef743098ead85c3a +timestamp : 2024-04-30 09:50:59 UTC +dependencies: + - biopython <1.82 + - blast-legacy 2.2.* + - infernal 1.0.* + - libtiff + - openjdk >8 + - pillow + - python >=3 + - r-ggplot2 + - r-reshape2 + - reportlab + - viennarna + + +mitos 2.0.1 py27_0 +------------------ +file name : mitos-2.0.1-py27_0.tar.bz2 +name : mitos +version : 2.0.1 +build : py27_0 +build number: 0 +size : 269 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-2.0.1-py27_0.tar.bz2 +md5 : 9ba11c4c577ec265ab72df3f35bf89d6 +timestamp : 2019-05-07 19:53:49 UTC +dependencies: + - biopython 1.73 + - blast-legacy 2.2.* + - ete2 2.3.* + - hmmer 3.2.* + - infernal 1.1.* + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.* + - reportlab + - viennarna <2 + + +mitos 2.0.2 py27_0 +------------------ +file name : mitos-2.0.2-py27_0.tar.bz2 +name : mitos +version : 2.0.2 +build : py27_0 +build number: 0 +size : 272 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-2.0.2-py27_0.tar.bz2 +md5 : 160c638e77de886b8ca88530d37db90b +timestamp : 2019-10-16 07:21:25 UTC +dependencies: + - biopython 1.73 + - blast-legacy 2.2.* + - ete2 2.3.* + - hmmer 3.2.* + - infernal 1.1.* + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.* + - reportlab + - viennarna <2 + + +mitos 2.0.2 py_1 +---------------- +file name : mitos-2.0.2-py_1.tar.bz2 +name : mitos +version : 2.0.2 +build : py_1 +build number: 1 +size : 262 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-2.0.2-py_1.tar.bz2 +md5 : 7cfac9bb4a6ae408843aa9b7a8050a43 +timestamp : 2019-10-16 12:25:43 UTC +dependencies: + - biopython 1.73 + - blast 2.9.* + - ete2 2.3.* + - hmmer 3.2.* + - infernal 1.1.* + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.* + - reportlab + - viennarna <2 + + +mitos 2.0.3 py_0 +---------------- +file name : mitos-2.0.3-py_0.tar.bz2 +name : mitos +version : 2.0.3 +build : py_0 +build number: 0 +size : 270 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-2.0.3-py_0.tar.bz2 +md5 : 2ec15ec40181dc485ae51c1e61c9eda7 +timestamp : 2020-01-07 22:11:17 UTC +dependencies: + - biopython 1.73 + - blast 2.9.* + - ete2 2.3.* + - hmmer 3.2.* + - infernal 1.1.* + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.* + - reportlab + - viennarna <2 + + +mitos 2.0.4 py_0 +---------------- +file name : mitos-2.0.4-py_0.tar.bz2 +name : mitos +version : 2.0.4 +build : py_0 +build number: 0 +size : 269 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-2.0.4-py_0.tar.bz2 +md5 : 030a424394115df84189fe5bb8132ab0 +timestamp : 2020-02-09 16:35:39 UTC +dependencies: + - biopython 1.73 + - blast 2.9.* + - ete2 2.3.* + - hmmer 3.2.* + - infernal 1.1.* + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.* + - reportlab + - viennarna <2 + + +mitos 2.0.5 py_0 +---------------- +file name : mitos-2.0.5-py_0.tar.bz2 +name : mitos +version : 2.0.5 +build : py_0 +build number: 0 +size : 273 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mitos-2.0.5-py_0.tar.bz2 +md5 : dd4298fa1c0461cbcdfef862ba5fa240 +timestamp : 2020-03-26 17:20:49 UTC +dependencies: + - biopython 1.73 + - blast 2.9.* + - ete2 2.3.* + - hmmer 3.2.* + - infernal 1.1.* + - openjdk + - python <3 + - r-base + - r-ggplot2 3.1.* + - reportlab + - viennarna <2 + + +mitos 2.0.6 py_0 +---------------- +file name : mitos-2.0.6-py_0.tar.bz2 +name : mitos +version : 2.0.6 +build : py_0 +build number: 0 +size : 262 KB +license : MIT +subdir diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mlst.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mlst.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..06d625382f12174d8ec7b072d76d9dcd1d67b3ed --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mlst.manual_bundle.txt @@ -0,0 +1,589 @@ +# Tool: mlst +software_name: mlst +tier: T1 +domain: t1_backfill_overall +downloads: 249697 +summary: Scan contig files against PubMLST typing schemes +description: Scan contig files against PubMLST typing schemes +dependencies: any2fasta, blast >=2.16.0, perl, perl-bioperl >=1.7.2, perl-file-which, perl-json, perl-list-moreutils, perl-moo, zlib +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/tseemann/mlst +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/tseemann/mlst +GitHub - tseemann/mlst: :id: Scan contig files against PubMLST typing schemes · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} tseemann / mlst Public Notifications You must be signed in to change notification settings Fork 58 Star 279 Code Issues 31 Pull requests 3 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights tseemann/mlst master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 327 Commits 327 Commits .github/ workflows .github/ workflows bin bin db db perl5 perl5 scripts scripts test test .gitignore .gitignore CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md LICENSE LICENSE README.md README.md environment.yml environment.yml View all files Repository files navigation README Code of conduct GPL-2.0 license mlst Scan contig files against traditional PubMLST typing schemes Quick Start % mlst contigs.fa contigs.fa neisseria 11149 abcZ(672) adk(3) aroE(4) fumC(3) gdh(8) pdhC(4) pgm(6) % mlst genome.gbk.gz genome.gbk.gz sepidermidis 184 arcC(16) aroE(1) gtr(2) mutS(1) pyrR(2) tpiA(1) yqiL(1) % mlst --full new.fa FILE SCHEME ST STATUS SCORE ALLELES new.fa mgenitalium - NOVEL 90 MLST_adk(7);MLST_atpA(1);MLST_gmk(1);MLST_gyrB(1);MLST_pgm(3);MLST_ppa(1) % mlst --label Anthrax GCF_001941925.1_ASM194192v1_genomic.fna.bz2 Anthrax bcereus - glp(24) gmk(1) ilv(~83) pta(1) pur(~71) pyc(37) tpi(41) % mlst --nopath /opt/data/refseq/S_pyogenes/*.fna NC_018936.fna spyogenes 28 gki(4) gtr(3) murI(4) mutS(4) recP(4) xpt(2) yqiL(4) NC_017596.fna spyogenes 11 gki(2) gtr(6) murI(1) mutS(2) recP(2) xpt(2) yqiL(2) NC_008022.fna spyogenes 55 gki(11) gtr(9) murI(1) mutS(9) recP(2) xpt(3) yqiL(4) NC_006086.fna spyogenes 382 gki(5) gtr(52) murI(5) mutS(5) recP(5) xpt(4) yqiL(3) NC_008024.fna spyogenes - gki(5) gtr(11) murI(8) mutS(5) recP(15?) xpt(2) yqiL(1) NC_017040.fna spyogenes 172 gki(56) gtr(24) murI(39) mutS(7) recP(30) xpt(2) yqiL(33) % mlst --full --fofn files.txt --csv --outfile mlst.csv # data saved in 'mlst.csv' Installation Conda If you are using Conda % conda install -c conda-forge -c bioconda mlst Source % cd $HOME % git clone https://github.com/tseemann/mlst.git % $HOME/mlst/bin/mlst --help Usage Simply just give it a genome file in FASTA/GenBank/EMBL format, optionally compressed with gzip, zip or bzip2. % mlst contigs.fa contigs.fa neisseria 11149 abcZ(672) adk(3) aroE(4) fumC(3) gdh(8) pdhC(4) pgm(6) It returns a tab-separated line containing the filename the matching PubMLST scheme name the ST (sequence type) the allele IDs You can give it multiple files at once, and they can be in FASTA/GenBank/EMBL format, and even compressed with gzip, bzip2 or zip. % mlst genomes/* genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3) genomes/strep.fasta.gz ssuis 1 aroA(1) cpn60(1) dpr(1) gki(1) mutS(1) recA(1) thrA(1) genomes/NC_002973.gbk lmonocytogenes 1 abcZ(3) bglA(1) cat(1) dapE(1) dat(3) ldh(1) lhkA(3) genomes/L550.gbk.bz2 leptospira 152 glmU(26) pntA(30) sucA(28) tpiA(35) pfkB(39) mreA(29) caiB(29) Without auto-detection You can force a particular scheme (useful for reporting systems): % mlst --scheme neisseria NM* NM003.fa neisseria 4821 abcZ(222) adk(3) aroE(58) fumC(275) gdh(30) pdhC(5) pgm(255) NM005.gbk neisseria 177 abcZ(7) adk(8) aroE(10) fumC(38) gdh(10) pdhC(1) pgm(20) NM011.fa neisseria 11 abcZ(2) adk(3) aroE(4) fumC(3) gdh(8) pdhC(4) pgm(6) NMC.gbk.gz neisseria 8 abcZ(2) adk(3) aroE(7) fumC(2) gdh(8) pdhC(5) pgm(2) You can make mlst behave like older version before auto-detection existed by providing the --legacy parameter with the --scheme parameter. In that case it will print a fixed tabular output with a heading containing allele names specific to that scheme: % mlst --legacy --scheme neisseria *.fa FILE SCHEME ST abcZ adk aroE fumC gdh pdhC pgm NM003.fa neisseria 11 2 3 4 3 8 4 6 NM009.fa neisseria 11149 672 3 4 3 8 4 6 MN043.fa neisseria 11 2 3 4 3 8 4 6 NM051.fa neisseria 11 2 3 4 3 8 4 6 NM099.fa neisseria 1287 2 3 4 17 8 4 6 NM110.fa neisseria 11 2 3 4 3 8 4 6 Available schemes To see which MLST schemes are supported: % mlst --info | csvtk -t pretty CHEME LOCII TYPES ALLELES DATE LOCII_NAMES -------------- ----- ----- ------- ---------- -------------------------------------------------- mbovis 7 193 154 2025-06-25 adh1 gltX gpsA gyrB pta2 tdk tkt mhominis_3 11 43 190 2023-11-05 eST uvrA gyrB ftsY tuf gap p120' vaa lmp1 lmp3 p60 mhyopneumoniae 3 255 254 2025-12-14 adk rpoB tpiA mcanis 7 83 153 2019-10-21 ack cpn60 fdh pta purA sar tuf mhyorhinis 6 265 148 2025-08-20 dnaA rpoB gyrB gltX adk gmk mgallisepticum 7 119 249 2025-12-05 atpG dppC DUF3196 lgT mraW plsC ugpA mflocculare 3 8 22 2018-07-03 adk rpoB tpiA ... This outpuit is TSV by default but will honour the --csv option. The older --list and --longlist are still available for backward compatibility. Missing data mlst does not just look for exact matches to full length alleles. It attempts to tell you as much as possible about what it found using the notation below: Symbol Meaning Length Identity n exact intact allele 100% 100% ~n novel full length allele similar to n 100% ≥ --minid n? partial match to known allele ≥ --mincov ≥ --minid - allele missing < --mincov < --minid n,m multiple alleles Scoring system Each MLST prediction gets a score out of 100. The score for a scheme with N alleles is as follows: Points For Example +90/N exact allele match 42 +63/N novel allele match (50% of an exact allele) ~42 +18/N partial allele match (20% of an exact alelle) 42? 0 missing allele - +10 a matching ST type for the allele combination 248 It is possible to filter results using the --minscore option which takes a value between 1 and 100. If you only want to report known ST types, then use --minscore 100 . To also include novel combinations of existing alleles with no ST type, use --minscore 90 . The default is --minscore 50 which is an ad hoc value I have found allows for genuine partial ST matches but eliminates false positives. Output formats There are 3 output formats. I recommened using --full mode. By default they are TSV, but CSV can be enabled with --csv . Default This format does not have any column headings. Column Description Example 1 Filename genome.gbk 2 Scheme mgenitalium 3 Sequence Type 148 4 Alelle 1 adk(7) 5 Allele 2 atpA(1) 6 + Allele 3 ... ... Full --full (recommended) This preferred format has 6 columns: Column Description Example FILE Input filename genome.gbk SCHEME Auto-detected scheme mgenitalium ST Sequence Type assined 148 STATUS Quality of genotype NOVEL (read more ) SCORE Score of genotype 90 ALLELES Indetified alleles adk(7);atpA(1);gmk(1);gyrB(1);pgm(3);ppa(1) Status These codes are in development. Some of them are stable, but others are subject to change. STATUS Meaning Stable? PERFECT Exact matches to a known ST YES NOVEL Exact matches, but not ST yet YES NONE No allele matches whatsoever YES MIXED Has at least one mixed allele YES MISSING Has at least one missing allele no BAD If none of the above & score below 70 no OK If none of the above no Legacy --legacy This format has a variable number of columns per line, depending on how many allees are in the scheme found. This makes it hard to use for mixtures of species, so you should use --full for that mode. Column Description Example FILE Input filename genome.gbk SCHEME From --scheme mgenitalium ST Sequence Type 148 ALLELE_1 Allele 1 numner 7 ALLELE_2 Allele 2 numbner 1 ALLELE_n Allele number integer Tweaking the output The output is TSV (tab-separated values). This makes it easy to parse and manipulate with Unix utilities like cut and sort etc. For example, if you only want the filename and ST you can do the following: % mlst --scheme abaumanii AB*.fasta | cut -f1,3 > ST.tsv If you prefer CSV because it loads more smoothly into MS Excel, use the --csv option: % mlst --csv Peptobismol.fna.gz > mlst.csv JSON output is available too; it returns an array of dictionaries, one per input file. The id will be the same as filename unless --label is used, but that only works when scanning a single file. % mlst -q --json out.json test/example.gbk.gz test/novel.fasta.bz2 % cat out.json [ { "scheme" : "sepidermidis", "alleles" : { "mutS" : "1", "yqiL" : "1", "tpiA" : "1", "pyrR" : "2", "gtr" : "2", "aroE" : "1", "arcC" : "16" }, "sequence_type" : "184", "filename" : "test/example.gbk.gz", "id" : "test/example.gbk.gz" }, { "sequence_type" : "-", "filename" : "test/novel.fasta.bz2", "scheme" : "spneumoniae", "alleles" : { "gki" : "2", "aroE" : "7", "ddl" : "22", "gdh" : "15", "xpt" : "1", "recP" : "~10", "spi" : "6" }, "id" : "test/novel.fasta.bz2" } ] You can also save the "novel" alleles for submission to PubMLST:: % mlst -q --novel nouveau.fa s_myces.fasta % cat nouveau.fa >streptomyces.recA-e562a2cd93e701e3b58ba0670bcbba0c s_myces.fasta GACGTGGCCCTCGGCGTCGGCGGTCTGCCGCGCGGCCGCGTCGTCGAGATCTACGGACCGGAGTCCTCC... The format of the sequence IDs is scheme.allele-hash filename where hash is the hexadecimal MD5 digest of the allele DNA sequence. Mapping to genus/species Included is a file called db/scheme_species_map.tab which has 3 tab-separated columns as follows: #SCHEME GENUS SPECIES abaumannii Acinetobacter baumannii abaumannii_2 Acinetobacter baumannii achromobacter Achromobacter aeromonas Aeromonas afumigatus Aspergillus afumigatus arcobacter Arcobacter bburgdorferi Borrelia burgdorferi bhampsonii Brachyspira hampsonii bhenselae Bartonella henselae borrelia Borrelia bpilosicoli Brachyspira pilosicoli <snip> Note that that some schemes are species specific, and others are genus specific, so the SPECIES column is empty. Note that the same species/genus can apply to multiple schemes, see abaumanii above. Updating the bundled database The mlst software no longer provides a script to update the database. This is because PubMLST now requires a user account and a private key to access data through the PubMLST API . You can use the mlstdb tool to help you do this. If you do download a new database, make sure it's in /path/to/mlst/db/pubmlst and run scripts/mlst-make_blast_db before attempting to run mlst . Adding a scheme If you want to add a custom private scheme with mlst you can The directory structure Each MLST scheme exists in a folder withing the mlst/db/pubmlst folder. The name of the folder is the scheme name, say saureus for Staphylococcus aureus . It contains files like this: % cd mlst/db/pubmlst/sareus % ls -1 saureus.txt arcC.tfa aroE.tfa glpF.tfa gmk.tfa pta.tfa tpi.tfa yqiL.tfa The folder name (ie. saureus ) must be the same name as the scheme file (ie. saureus.txt ) or it will not work. The scheme file The saureus.txt is a tab-separated file containing one ST definition per row. The header line must be present. Extra columns with names mlst_clade,clonal_complex,species,CC,Lineage are ignored. % head -n 5 saureus.txt ST arcC aroE glpF gmk pta tpi yqiL clonal_complex 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 26 3 1 1 1 9 1 1 12 4 10 10 8 6 10 3 2 The allele sequence files Each of the .tfa files are nucleotide FASTA files with the allele sequences for each locus. There must be a .tfa file for each and every allele locus in the TSV scheme .txt file. Here is what the arcC.tfa file looks like: % head -n 20 arcC.tfa >arcC_1 TTATTAATCCAACAAGCTAAATCGAACAGTGACACAACGCCGGCAATGCCATTGGATACT TGTGGTGCAATGTCACAGGGTATGATAGGCTATTGGTTGGAAACTGAAATCAATCGCATT TTAACTGAAATGAATAGTGATAGAACTGTAGGCACAATCGTTACACGTGTGGAAGTAGAT AAAGATGATCCACGATTCAATAACCCAACCAAACCAATTGGTCCTTTTTATACGAAAGAA GAAGTTGAAGAATTACAAAAAGAACAGCCAGACTCAGTCTTTAAAGAAGATGCAGGACGT GGTTATAGAAAAGTAGTTGCGTCACCACTACCTCAATCTATACTAGAACACCAGTTAATT CGAACTTTAGCAGACGGTAAAAATATTGTCATTGCATGCGGTGGTGGCGGTATTCCAGTT ATAAAAAAAGAAAATACCTATGAAGGTGTTGAAGCG >arcC_2 TTATTAATCCAACAAGCTAAATCGAACAGTGACACAACGCCGGCAATGCCATTGGATACT TGTGGTGCAATGTCACAAGGTATGATAGGCTATTGGTTGGAAACTGAAATCAATCGCATT TTAACTGAAATGAATAGTGATAGAACTGTAGGCACAATCGTAACACGTGTGGAAGTAGAT AAAGATGATCCACGATTTGATAACCCAACTAAACCAATTGGTCCTTTTTATACGAAAGAA GAAGTTGAAGAATTACAAAAAGAACAGCCAGGCTCAGTCTTTAAAGAAGATGCAGGACGT GGTTATAGAAAAGTAGTTGCGTCACCACTACCTCAATCTATACTAGAACACCAGTTAATT CGAACTTTAGCAGACGGTAAAAATATTGTCATTGCATGCGGTGGTGGCGGTATTCCAGTT ATAAAAAAAGAAAATACCTATGAAGGTGTTGAAGCG The FASTA sequence IDs must be named as >allele_number or >allele-number . Ideally the sequences will not contain any ambiguous IUPAC symbols. i.e. just A,T,C,G . Adding a new scheme Make a new folder in mlst/db/pubmlst/SCHEME Put your SCHEME.txt file in there Put your ALLELE.tfa files in there Run mlst/scripts/mlst-make_blast_db to update the BLAST indices Run mlst --info | grep SCHEME to see if it exists Run mlst --scheme SCHEME file.fasta to see if it works If it doesn't - go back and check you really did do Step 4 above. Citations The mlst software incorporates components of the PubMLST database which must be cited in any publications that use mlst : "This publication made use of the PubMLST website ( https://pubmlst.org/ ) developed by Keith Jolley Wellcome Open Res. 2018 Sep 24:3:124 and sited at the University of Oxford. The development of that website was funded by the Wellcome Trust". You should also cite this software (currently unpublished) as: Seemann T, mlst Github https://github.com/tseemann/mlst Feedback Please submit via the Github Issues page Licence GPL v2 Author Torsten Seemann About 🆔 Scan contig files against PubMLST typing schemes Resources Readme License GPL-2.0 license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Stars 279 stars Watchers 20 watching Forks 58 forks Report repository Releases 29 Let's rewind to 2024 Latest Mar 22, 2026 + 28 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 96.7% Shell 3.0% Other 0.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge mlst --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +mlst 2.6 0 +---------- +file name : mlst-2.6-0.tar.bz2 +name : mlst +version : 2.6 +build : 0 +build number: 0 +size : 7.2 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.6-0.tar.bz2 +md5 : 18d7725c62b77f7e0025d01a6650b750 +dependencies: + - blast + - libgcc + - perl-bioperl + - perl-list-moreutils + - perl-moo + - perl-threaded + + +mlst 2.9 h031d066_5 +------------------- +file name : mlst-2.9-h031d066_5.tar.bz2 +name : mlst +version : 2.9 +build : h031d066_5 +build number: 5 +size : 8.2 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.9-h031d066_5.tar.bz2 +md5 : 6781326f0bf49a0135f00454c0273cc3 +timestamp : 2023-05-15 07:25:22 UTC +dependencies: + - blast + - libgcc-ng >=12 + - perl + - perl-bioperl + - perl-list-moreutils + - perl-moo + + +mlst 2.9 h470a237_1 +------------------- +file name : mlst-2.9-h470a237_1.tar.bz2 +name : mlst +version : 2.9 +build : h470a237_1 +build number: 1 +size : 8.0 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.9-h470a237_1.tar.bz2 +md5 : 8f2a3df96482385ed679d02ac3340696 +timestamp : 2018-09-25 16:02:59 UTC +dependencies: + - blast + - libgcc-ng >=4.9 + - perl + - perl-bioperl + - perl-list-moreutils + - perl-moo + + +mlst 2.9 h516909a_2 +------------------- +file name : mlst-2.9-h516909a_2.tar.bz2 +name : mlst +version : 2.9 +build : h516909a_2 +build number: 2 +size : 8.1 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.9-h516909a_2.tar.bz2 +md5 : 63f87951722dab273cd6c471eb27e334 +timestamp : 2019-10-26 18:04:52 UTC +dependencies: + - blast + - libgcc-ng >=7.3.0 + - perl + - perl-bioperl + - perl-list-moreutils + - perl-moo + + +mlst 2.9 h779adbc_3 +------------------- +file name : mlst-2.9-h779adbc_3.tar.bz2 +name : mlst +version : 2.9 +build : h779adbc_3 +build number: 3 +size : 8.0 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.9-h779adbc_3.tar.bz2 +md5 : df8d2af3134ac7e943f43647b72123c6 +timestamp : 2021-03-28 04:19:20 UTC +dependencies: + - blast + - libgcc-ng >=9.3.0 + - perl + - perl-bioperl + - perl-list-moreutils + - perl-moo + + +mlst 2.9 h7b50bb2_6 +------------------- +file name : mlst-2.9-h7b50bb2_6.tar.bz2 +name : mlst +version : 2.9 +build : h7b50bb2_6 +build number: 6 +size : 8.2 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.9-h7b50bb2_6.tar.bz2 +md5 : cce3b0b6f1e951f133cee2ba31d6debe +timestamp : 2024-12-15 04:18:08 UTC +dependencies: + - blast + - libgcc >=13 + - perl + - perl-bioperl + - perl-list-moreutils + - perl-moo + + +mlst 2.9 hec16e2b_4 +------------------- +file name : mlst-2.9-hec16e2b_4.tar.bz2 +name : mlst +version : 2.9 +build : hec16e2b_4 +build number: 4 +size : 8.0 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.9-hec16e2b_4.tar.bz2 +md5 : e64b0c7dc0d1e98b787ce0bf8f708493 +timestamp : 2022-02-21 18:14:38 UTC +dependencies: + - blast + - libgcc-ng >=10.3.0 + - perl + - perl-bioperl + - perl-list-moreutils + - perl-moo + + +mlst 2.9 pl5.22.0_0 +------------------- +file name : mlst-2.9-pl5.22.0_0.tar.bz2 +name : mlst +version : 2.9 +build : pl5.22.0_0 +build number: 0 +size : 8.1 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.9-pl5.22.0_0.tar.bz2 +md5 : 23aabe089b687f3a98d40b6d1d27f61d +dependencies: + - blast + - libgcc + - perl 5.22.0* + - perl-bioperl + - perl-list-moreutils + - perl-moo + + +mlst 2.10 pl5.22.0_0 +-------------------- +file name : mlst-2.10-pl5.22.0_0.tar.bz2 +name : mlst +version : 2.10 +build : pl5.22.0_0 +build number: 0 +size : 11.0 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.10-pl5.22.0_0.tar.bz2 +md5 : 9491f95f2c5eb55d9abc191006831cd9 +dependencies: + - blast + - libgcc + - perl 5.22.0* + - perl-bioperl + - perl-file-slurp + - perl-json + - perl-list-moreutils + - perl-moo + - zlib 1.2.8* + + +mlst 2.10 pl5.22.0_1 +-------------------- +file name : mlst-2.10-pl5.22.0_1.tar.bz2 +name : mlst +version : 2.10 +build : pl5.22.0_1 +build number: 1 +size : 11.0 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.10-pl5.22.0_1.tar.bz2 +md5 : 64f84dfd92100ec55edaf2fe1da3ac26 +dependencies: + - blast + - libgcc + - perl 5.22.0* + - perl-bioperl + - perl-file-slurp + - perl-json + - perl-list-moreutils + - perl-moo + - zlib 1.2.11* + + +mlst 2.11 0 +----------- +file name : mlst-2.11-0.tar.bz2 +name : mlst +version : 2.11 +build : 0 +build number: 0 +size : 10.8 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.11-0.tar.bz2 +md5 : c4a648f24e88737bc3cf74020083d472 +timestamp : 2018-08-07 05:33:07 UTC +dependencies: + - blast + - perl + - perl-bioperl + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.12 0 +----------- +file name : mlst-2.12-0.tar.bz2 +name : mlst +version : 2.12 +build : 0 +build number: 0 +size : 11.3 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.12-0.tar.bz2 +md5 : ba6f430d84794482acdadd602e75613a +timestamp : 2018-08-19 04:17:07 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.13 0 +----------- +file name : mlst-2.13-0.tar.bz2 +name : mlst +version : 2.13 +build : 0 +build number: 0 +size : 11.2 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.13-0.tar.bz2 +md5 : 45566753b0146026f0df7c10ec6b4d6b +timestamp : 2018-08-28 05:50:00 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.14 0 +----------- +file name : mlst-2.14-0.tar.bz2 +name : mlst +version : 2.14 +build : 0 +build number: 0 +size : 11.2 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.14-0.tar.bz2 +md5 : 2d6ed18f53437d286162861d286b50a4 +timestamp : 2018-08-28 09:17:59 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.15 0 +----------- +file name : mlst-2.15-0.tar.bz2 +name : mlst +version : 2.15 +build : 0 +build number: 0 +size : 11.2 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.15-0.tar.bz2 +md5 : f5bd6921b20d77841f325ce2e0688a84 +timestamp : 2018-08-30 05:42:27 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.15.1 0 +------------- +file name : mlst-2.15.1-0.tar.bz2 +name : mlst +version : 2.15.1 +build : 0 +build number: 0 +size : 11.1 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.15.1-0.tar.bz2 +md5 : 93571939e3d189ba2fe95abf89be107b +timestamp : 2018-09-05 17:43:58 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.15.2 0 +------------- +file name : mlst-2.15.2-0.tar.bz2 +name : mlst +version : 2.15.2 +build : 0 +build number: 0 +size : 11.1 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.15.2-0.tar.bz2 +md5 : 6bdee28b67415fa445ddd2396a9e5e7d +timestamp : 2018-10-24 06:51:14 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.16 0 +----------- +file name : mlst-2.16-0.tar.bz2 +name : mlst +version : 2.16 +build : 0 +build number: 0 +size : 11.7 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.16-0.tar.bz2 +md5 : 9b0236e14f2ad02211e32ef8e55b9378 +timestamp : 2018-12-11 21:46:55 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.16.1 0 +------------- +file name : mlst-2.16.1-0.tar.bz2 +name : mlst +version : 2.16.1 +build : 0 +build number: 0 +size : 11.8 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mlst-2.16.1-0.tar.bz2 +md5 : 660ab9e51f6a48e9653e1418218ae8c4 +timestamp : 2018-12-12 08:54:05 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.16.2 0 +------------- +file name : mlst-2.16.2-0.tar.bz2 +name : mlst +version : 2.16.2 +build : 0 +build number: 0 +size : 12.2 MB +license : GPL-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mlst-2.16.2-0.tar.bz2 +md5 : 0b1916fd4fe49252ec13d28c955ca5e5 +timestamp : 2019-06-11 06:50:28 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.16.2 h1341992_1 +---------------------- +file name : mlst-2.16.2-h1341992_1.tar.bz2 +name : mlst +version : 2.16.2 +build : h1341992_1 +build number: 1 +size : 12.0 MB +license : GPL-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mlst-2.16.2-h1341992_1.tar.bz2 +md5 : 191a968b88bad48e7d34072fa25f8aaf +timestamp : 2019-08-04 06:46:52 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib >=1.2.11,<1.3.0a0 + + +mlst 2.16.4 h1341992_0 +---------------------- +file name : mlst-2.16.4-h1341992_0.tar.bz2 +name : mlst +version : 2.16.4 +build : h1341992_0 +build number: 0 +size : 12.4 MB +license : GPL-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mlst-2.16.4-h1341992_0.tar.bz2 +md5 : 72b46b47cdac850f20eb6a21a027b853 +timestamp : 2019-08-04 18:11:37 UTC +dependencies: + - blast >=2.7.1 + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib >=1.2.11,<1.3.0a0 + + +mlst 2.17.6 1 +------------- +file name : mlst-2.17.6-1.tar.bz2 +name : mlst +version : 2.17.6 +build : 1 +build number: 1 +size : 12.9 MB +license : GPL-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mlst-2.17.6-1.tar.bz2 +md5 : 9f06760e8eb00bd3e07311a941e4fbe2 +timestamp : 2019-10-26 18:18:30 UTC +dependencies: + - any2fasta + - blast >=2.9.0 + - perl + - perl-bioperl >=1.7.2 + - perl-json + - perl-list-moreutils + - perl-moo + - zlib + + +mlst 2.17.6 pl526h1341992_0 +--------------------------- +file name : mlst-2.17.6-pl526h1341992_0.tar.bz2 +name : mlst +version : 2.17.6 +build : pl526h1341992_0 +build number: 0 +size : 12.8 MB +license : GPL-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/mlst-2.17.6-pl526h1341992_0.tar.bz2 +md5 : ce492e2f558b7017753064dd651a592d diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mmtf-python.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mmtf-python.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..11b59fa3362f34d2228779df72ea8a3122c7ee15 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/mmtf-python.manual_bundle.txt @@ -0,0 +1,404 @@ +# Tool: mmtf-python +software_name: mmtf-python +tier: T1 +domain: t1_backfill_overall +downloads: 137074 +summary: A decoding libary for the PDB mmtf format +description: A decoding libary for the PDB mmtf format +dependencies: msgpack-python, python 2.7* +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: +doc_url: +dev_url: + +## Conda Search Info +$ conda search -c bioconda -c conda-forge mmtf-python --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +mmtf-python 1.0.2 py27_0 +------------------------ +file name : mmtf-python-1.0.2-py27_0.tar.bz2 +name : mmtf-python +version : 1.0.2 +build : py27_0 +build number: 0 +size : 34 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mmtf-python-1.0.2-py27_0.tar.bz2 +md5 : fbdb3ee1ffebcb66ac895fefd9132772 +dependencies: + - msgpack-python + - python 2.7* + + +mmtf-python 1.0.2 py34_0 +------------------------ +file name : mmtf-python-1.0.2-py34_0.tar.bz2 +name : mmtf-python +version : 1.0.2 +build : py34_0 +build number: 0 +size : 35 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mmtf-python-1.0.2-py34_0.tar.bz2 +md5 : aab7a980a86c3130053aa01c5d4b1b55 +dependencies: + - msgpack-python + - python 3.4* + + +mmtf-python 1.0.2 py35_0 +------------------------ +file name : mmtf-python-1.0.2-py35_0.tar.bz2 +name : mmtf-python +version : 1.0.2 +build : py35_0 +build number: 0 +size : 35 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/mmtf-python-1.0.2-py35_0.tar.bz2 +md5 : 3cd3a98a05ee5c136064518f8a229cf0 +dependencies: + - msgpack-python + - python 3.5* + + +mmtf-python 1.0.4 py27_0 +------------------------ +file name : mmtf-python-1.0.4-py27_0.tar.bz2 +name : mmtf-python +version : 1.0.4 +build : py27_0 +build number: 0 +size : 34 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.4-py27_0.tar.bz2 +md5 : c531411f1aad82459fc91f1b6acb86e5 +constraints : + - python_abi * *_cp27mu +dependencies: + - msgpack-python + - python 2.7* + + +mmtf-python 1.0.4 py34_0 +------------------------ +file name : mmtf-python-1.0.4-py34_0.tar.bz2 +name : mmtf-python +version : 1.0.4 +build : py34_0 +build number: 0 +size : 35 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.4-py34_0.tar.bz2 +md5 : d87acfefd03aaaf9165ac025fa852bca +constraints : + - python_abi * *_cp34m +dependencies: + - msgpack-python + - python 3.4* + + +mmtf-python 1.0.4 py35_0 +------------------------ +file name : mmtf-python-1.0.4-py35_0.tar.bz2 +name : mmtf-python +version : 1.0.4 +build : py35_0 +build number: 0 +size : 989 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.4-py35_0.tar.bz2 +md5 : de6538295202d840568b8cbb60d5f622 +constraints : + - python_abi * *_cp35m +dependencies: + - msgpack-python + - python 3.5* + + +mmtf-python 1.0.5 py27_0 +------------------------ +file name : mmtf-python-1.0.5-py27_0.tar.bz2 +name : mmtf-python +version : 1.0.5 +build : py27_0 +build number: 0 +size : 34 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.5-py27_0.tar.bz2 +md5 : 0a6315c54204850952c92d87e3bb24cf +constraints : + - python_abi * *_cp27mu +dependencies: + - msgpack-python + - python 2.7* + + +mmtf-python 1.0.5 py34_0 +------------------------ +file name : mmtf-python-1.0.5-py34_0.tar.bz2 +name : mmtf-python +version : 1.0.5 +build : py34_0 +build number: 0 +size : 35 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.5-py34_0.tar.bz2 +md5 : 6ab74bc07b23f1fce203a1393f6190ad +constraints : + - python_abi * *_cp34m +dependencies: + - msgpack-python + - python 3.4* + + +mmtf-python 1.0.5 py35_0 +------------------------ +file name : mmtf-python-1.0.5-py35_0.tar.bz2 +name : mmtf-python +version : 1.0.5 +build : py35_0 +build number: 0 +size : 238 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.5-py35_0.tar.bz2 +md5 : 723a7817c1893a3902dd72a9cb5623b6 +constraints : + - python_abi * *_cp35m +dependencies: + - msgpack-python + - python 3.5* + + +mmtf-python 1.0.5 py36_0 +------------------------ +file name : mmtf-python-1.0.5-py36_0.tar.bz2 +name : mmtf-python +version : 1.0.5 +build : py36_0 +build number: 0 +size : 38 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.5-py36_0.tar.bz2 +md5 : 943740aa6f4802d57823f548414b6bd0 +constraints : + - python_abi * *_cp36m +dependencies: + - msgpack-python + - python 3.6* + + +mmtf-python 1.0.6 py27_0 +------------------------ +file name : mmtf-python-1.0.6-py27_0.tar.bz2 +name : mmtf-python +version : 1.0.6 +build : py27_0 +build number: 0 +size : 38 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.6-py27_0.tar.bz2 +md5 : 0c6ab67c10fd3cda88719aaaf6841da0 +constraints : + - python_abi * *_cp27mu +dependencies: + - msgpack-python + - python 2.7* + + +mmtf-python 1.0.6 py35_0 +------------------------ +file name : mmtf-python-1.0.6-py35_0.tar.bz2 +name : mmtf-python +version : 1.0.6 +build : py35_0 +build number: 0 +size : 39 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.6-py35_0.tar.bz2 +md5 : 8e1ebffdc6139496a07580c57534356f +constraints : + - python_abi * *_cp35m +dependencies: + - msgpack-python + - python 3.5* + + +mmtf-python 1.0.6 py36_0 +------------------------ +file name : mmtf-python-1.0.6-py36_0.tar.bz2 +name : mmtf-python +version : 1.0.6 +build : py36_0 +build number: 0 +size : 39 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.6-py36_0.tar.bz2 +md5 : aa17eb8be743ed446fb4166d3e70b9ef +constraints : + - python_abi * *_cp36m +dependencies: + - msgpack-python + - python 3.6* + + +mmtf-python 1.0.7 py27_0 +------------------------ +file name : mmtf-python-1.0.7-py27_0.tar.bz2 +name : mmtf-python +version : 1.0.7 +build : py27_0 +build number: 0 +size : 37 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.7-py27_0.tar.bz2 +md5 : a2b482a92c3ed8877c3c3dad6849942d +constraints : + - python_abi * *_cp27mu +dependencies: + - msgpack-python + - python 2.7* + + +mmtf-python 1.0.7 py35_0 +------------------------ +file name : mmtf-python-1.0.7-py35_0.tar.bz2 +name : mmtf-python +version : 1.0.7 +build : py35_0 +build number: 0 +size : 39 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.7-py35_0.tar.bz2 +md5 : 62993a9f577d68381912082d78880215 +constraints : + - python_abi * *_cp35m +dependencies: + - msgpack-python + - python 3.5* + + +mmtf-python 1.0.7 py36_0 +------------------------ +file name : mmtf-python-1.0.7-py36_0.tar.bz2 +name : mmtf-python +version : 1.0.7 +build : py36_0 +build number: 0 +size : 39 KB +license : Apache-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/mmtf-python-1.0.7-py36_0.tar.bz2 +md5 : af55adec0ec0e711da0a8d8ef93a7855 +constraints : + - python_abi * *_cp36m +dependencies: + - msgpack-python + - python 3.6* + + +mmtf-python 1.0.9 py_0 +---------------------- +file name : mmtf-python-1.0.9-py_0.tar.bz2 +name : mmtf-python +version : 1.0.9 +build : py_0 +build number: 0 +size : 22 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/mmtf-python-1.0.9-py_0.tar.bz2 +md5 : 9ba1850401d69f4a2052835d8c09948d +dependencies: + - msgpack-python + - python + + +mmtf-python 1.0.10 py_0 +----------------------- +file name : mmtf-python-1.0.10-py_0.tar.bz2 +name : mmtf-python +version : 1.0.10 +build : py_0 +build number: 0 +size : 22 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/mmtf-python-1.0.10-py_0.tar.bz2 +md5 : dcf4ade764d2dfe89b59a4b10bc27c14 +dependencies: + - msgpack-python + - python + + +mmtf-python 1.1.0 py_0 +---------------------- +file name : mmtf-python-1.1.0-py_0.tar.bz2 +name : mmtf-python +version : 1.1.0 +build : py_0 +build number: 0 +size : 22 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/mmtf-python-1.1.0-py_0.tar.bz2 +md5 : 7c67919674937349a3a6774405feb883 +dependencies: + - msgpack-python + - python + + +mmtf-python 1.1.2 py_0 +---------------------- +file name : mmtf-python-1.1.2-py_0.tar.bz2 +name : mmtf-python +version : 1.1.2 +build : py_0 +build number: 0 +size : 21 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/mmtf-python-1.1.2-py_0.tar.bz2 +md5 : 27a1195e80daae02aa143599eacb1535 +timestamp : 2018-05-22 08:31:03 UTC +dependencies: + - msgpack-python + - python + + +mmtf-python 1.1.3 pyhd8ed1ab_0 +------------------------------ +file name : mmtf-python-1.1.3-pyhd8ed1ab_0.tar.bz2 +name : mmtf-python +version : 1.1.3 +build : pyhd8ed1ab_0 +build number: 0 +size : 25 KB +license : Apache-2.0 +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/mmtf-python-1.1.3-pyhd8ed1ab_0.tar.bz2 +md5 : 2e68d973b43ff50b76ffe35f227bdc73 +timestamp : 2022-07-06 08:16:05 UTC +dependencies: + - msgpack-python + - python >=3.6 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/moments.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/moments.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..07a671fddbe58b63338c887f2413baf205d5e755 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/moments.manual_bundle.txt @@ -0,0 +1,496 @@ +# Tool: moments +software_name: moments +tier: T1 +domain: t1_backfill_overall +downloads: 240300 +summary: Evolutionary inference using SFS and LD statistics. +description: Evolutionary inference using SFS and LD statistics. +dependencies: demes >=0.2, libgcc >=14, mpmath >=1.0,<1.4, numpy >=1.23,<3, python >=3.12,<3.13.0a0, python_abi 3.12.* *_cp312, scipy >=1.3,<1.17 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://bitbucket.org/simon-gravel/moments +doc_url: https://momentsld.github.io/moments +dev_url: https://github.com/MomentsLD/moments + +## URL Docs Extract +### https://momentsld.github.io/moments +Welcome to moments’s documentation! — moments 1.1.0 documentation moments Getting started Introduction Installation SFS The Site Frequency Spectrum Parsing the SFS from a VCF file SFS Inference Linkage disequilibrium Multi-population LD statistics Parsing LD statistics Inferring demography with LD Extensions Specifying models with demes Two-locus frequency spectrum Triallele frequency spectrum Modules Demography and genetic diversity DFE inference Linkage disequilibrium and recombination Selection at two loci Data types and functions API for site frequency spectra API for linkage disequilibrium API for demes functions moments Welcome to moments’s documentation! View page source Welcome to moments’s documentation!  Getting started Introduction Installation SFS The Site Frequency Spectrum Parsing the SFS from a VCF file SFS Inference Linkage disequilibrium Multi-population LD statistics Parsing LD statistics Inferring demography with LD Extensions Specifying models with demes Two-locus frequency spectrum Triallele frequency spectrum Modules Demography and genetic diversity DFE inference Linkage disequilibrium and recombination Selection at two loci Data types and functions API for site frequency spectra API for linkage disequilibrium API for demes functions Next © Copyright 2020, Aaron Ragsdale. Built with Sphinx using a theme provided by Read the Docs . + +### https://github.com/MomentsLD/moments +GitHub - MomentsLD/moments · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} MomentsLD / moments Public Notifications You must be signed in to change notification settings Fork 6 Star 15 Code Issues 27 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights MomentsLD/moments main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,051 Commits 1,051 Commits .github/ workflows .github/ workflows bench bench docs docs examples examples moments moments requirements requirements tests tests .gitignore .gitignore LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in README.md README.md epydoc.config epydoc.config pyproject.toml pyproject.toml requirements.txt requirements.txt setup.py setup.py View all files Repository files navigation README MIT license moments: population genetic analyses and inference using diversity statistics Please see the documentation for more details, examples, tutorials and API usage. moments provides a suite of methods for demographic history and selection inference from genetic data, based on diffusion approximations to the one- and two-locus allele frequency spectrum. moments is modeled after the ∂a∂i open source package developed by Ryan Gutenkunst . For SFS-based methdos, we largely reuse ∂a∂i 's API, but introduce a new simulation engine. This new method is based on the direct computation of the frequency spectrum without solving the diffusion system, removing the need for frequency grids as used in ∂a∂i . moments.LD , packaged within moments , implements methods for computing linkage disequilibrium statistics and running multi-population demographic inference using patterns of LD. Getting started moments now supports Python 3, and we no longer guarantee compatibility with Python 2. The simplest way to install moments is using pip : pip install moments-popgen moments can then be imported using import moments . Important note: pip install moments installs a different package named moments, and our pypi package is named moments-popgen . We can install the development branch directly from Github by running pip install git+https://github.com/MomentsLD/moments.git@devel Alternatively, you can clone the git repository to make an editable or development build. git clone https://github.com/MomentsLD/moments.git and then from within the moments directory ( cd moments ), run pip install -r requirements.txt pip install . If you use conda , moments is available via bioconda : conda config --add channels bioconda conda install moments Citing moments If you use moments in your research, please cite: Jouganous, J., Long, W., Ragsdale, A. P., & Gravel, S. (2017). Inferring the joint demographic history of multiple populations: beyond the diffusion approximation. Genetics, 206(3), 1549-1567. If you use moments.LD in your research, please cite: Ragsdale, A. P. & Gravel, S. (2019). Models of archaic admixture and recent history from two-locus statistics. PLoS Genetics, 15(6), e1008204. Ragsdale, A. P. & Gravel, S. (2020). Unbiased estimation of linkage disequilibrium from unphased data. Mol Biol Evol, 37(3), 923-932. If you use moments.TwoLocus in your research, please cite: Ragsdale, A. P. (2021). Can we distinguish modes of selective interactions from linkage disequilibrium? BioRxiv, doi: https://doi.org/10.1101/2021.03.25.437004 moments is developed in the Simon Gravel and Aaron Ragsdale research groups, at McGill University and UW-Madison, respectively. For any issues, questions or bug reports, please open an issue on Github . Dependencies If you install moments from source (e.g., after cloning the repository), you will need to install the dependencies. These are all listed in requirements.txt , and can be installed via pip after navigating to the moments directory: pip install -r requirements.txt A few more details: moments and moments.LD requires a handful of dependencies. At a minimum, these include numpy scipy cython mpmath demes We also strongly recommend installing ipython . If you are using conda , all dependencies can be installed by navigating to the moments directory and then running conda install --file requirements.txt Once dependencies are installed, to install moments , run the following command in the moments directory: python -m pip install -e . You should then be able to import moments in your python scripts. Entering an ipython or python session, try to import moments . More details on installation can be found in the documentation . If, for any reason, you have trouble installing moments after following these steps, please submit an issue . If you use Parsing from moments.LD , which reads VCF files and computes LD statistics to compare to predictions from moments.LD , you will need to additionally install hdf5 scikit-allel pandas Changelog All changes are detailed in the documentation . About No description, website, or topics provided. Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 15 stars Watchers 2 watching Forks 6 forks Report repository Releases 19 v1.5.3 Latest Apr 16, 2026 + 18 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages F# 56.9% Python 40.7% Cython 2.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge moments --info +[rc=0] +2 channel Terms of Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +moments 1.0.6 py36h29c9776_1 +---------------------------- +file name : moments-1.0.6-py36h29c9776_1.tar.bz2 +name : moments +version : 1.0.6 +build : py36h29c9776_1 +build number: 1 +size : 438 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.6-py36h29c9776_1.tar.bz2 +md5 : 84f5cfcdf1923da6f946a5eb0167fade +timestamp : 2020-10-29 18:08:53 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - scipy + + +moments 1.0.6 py37h97743b1_1 +---------------------------- +file name : moments-1.0.6-py37h97743b1_1.tar.bz2 +name : moments +version : 1.0.6 +build : py37h97743b1_1 +build number: 1 +size : 438 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.6-py37h97743b1_1.tar.bz2 +md5 : 9d7ee82848e5a6097f1624ac00f46905 +timestamp : 2020-10-29 18:02:24 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - scipy + + +moments 1.0.6 py38h29c9776_0 +---------------------------- +file name : moments-1.0.6-py38h29c9776_0.tar.bz2 +name : moments +version : 1.0.6 +build : py38h29c9776_0 +build number: 0 +size : 438 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.6-py38h29c9776_0.tar.bz2 +md5 : b0a8f5a21a2b20a52b7fdf1d045e4927 +timestamp : 2020-10-28 17:42:59 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.6 py38h97743b1_0 +---------------------------- +file name : moments-1.0.6-py38h97743b1_0.tar.bz2 +name : moments +version : 1.0.6 +build : py38h97743b1_0 +build number: 0 +size : 439 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.6-py38h97743b1_0.tar.bz2 +md5 : 97a416f35a10589333c6acfbc100ccc3 +timestamp : 2020-10-28 17:41:47 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.6 py38hd504320_0 +---------------------------- +file name : moments-1.0.6-py38hd504320_0.tar.bz2 +name : moments +version : 1.0.6 +build : py38hd504320_0 +build number: 0 +size : 439 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.6-py38hd504320_0.tar.bz2 +md5 : 853916e3bbe87a48d2c33ec10afc8552 +timestamp : 2020-10-28 17:43:59 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.6 py38hd504320_1 +---------------------------- +file name : moments-1.0.6-py38hd504320_1.tar.bz2 +name : moments +version : 1.0.6 +build : py38hd504320_1 +build number: 1 +size : 451 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.6-py38hd504320_1.tar.bz2 +md5 : 3d982a137312ce2d6a6b346ddd22a717 +timestamp : 2020-10-29 18:05:37 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.7 py36h29c9776_0 +---------------------------- +file name : moments-1.0.7-py36h29c9776_0.tar.bz2 +name : moments +version : 1.0.7 +build : py36h29c9776_0 +build number: 0 +size : 422 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.7-py36h29c9776_0.tar.bz2 +md5 : a23d4d5a2e600e6f96e56d4bcaa90c83 +timestamp : 2020-11-24 20:30:27 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - scipy + + +moments 1.0.7 py37h97743b1_0 +---------------------------- +file name : moments-1.0.7-py37h97743b1_0.tar.bz2 +name : moments +version : 1.0.7 +build : py37h97743b1_0 +build number: 0 +size : 421 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.7-py37h97743b1_0.tar.bz2 +md5 : d533e43d42ec15062be8dfd94818420b +timestamp : 2020-11-24 20:33:57 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - scipy + + +moments 1.0.7 py38hd504320_0 +---------------------------- +file name : moments-1.0.7-py38hd504320_0.tar.bz2 +name : moments +version : 1.0.7 +build : py38hd504320_0 +build number: 0 +size : 433 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.7-py38hd504320_0.tar.bz2 +md5 : f8b80c8b1d3c000f7ddd6b0ff42cd6b0 +timestamp : 2020-11-24 20:37:10 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.8 py36h29c9776_0 +---------------------------- +file name : moments-1.0.8-py36h29c9776_0.tar.bz2 +name : moments +version : 1.0.8 +build : py36h29c9776_0 +build number: 0 +size : 439 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.8-py36h29c9776_0.tar.bz2 +md5 : ace3fc92f9bb353699b45123c7035416 +timestamp : 2020-12-29 02:23:40 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - scipy + + +moments 1.0.8 py37h97743b1_0 +---------------------------- +file name : moments-1.0.8-py37h97743b1_0.tar.bz2 +name : moments +version : 1.0.8 +build : py37h97743b1_0 +build number: 0 +size : 440 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.8-py37h97743b1_0.tar.bz2 +md5 : 3431afde2a318221799753a39fd24c07 +timestamp : 2020-12-29 02:27:02 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - scipy + + +moments 1.0.8 py38h0a581ac_1 +---------------------------- +file name : moments-1.0.8-py38h0a581ac_1.tar.bz2 +name : moments +version : 1.0.8 +build : py38h0a581ac_1 +build number: 1 +size : 449 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.8-py38h0a581ac_1.tar.bz2 +md5 : 16f89e13a981b8c91b45730f93c40ba4 +timestamp : 2021-01-13 17:49:51 UTC +dependencies: + - libgcc-ng >=7.5.0 + - mpmath + - numpy + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.8 py38h29c9776_1 +---------------------------- +file name : moments-1.0.8-py38h29c9776_1.tar.bz2 +name : moments +version : 1.0.8 +build : py38h29c9776_1 +build number: 1 +size : 449 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.8-py38h29c9776_1.tar.bz2 +md5 : 4d597cc6657f22eb6e7b01885928f030 +timestamp : 2021-01-13 17:52:11 UTC +dependencies: + - libgcc-ng >=7.5.0 + - mpmath + - numpy + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.8 py38h97743b1_1 +---------------------------- +file name : moments-1.0.8-py38h97743b1_1.tar.bz2 +name : moments +version : 1.0.8 +build : py38h97743b1_1 +build number: 1 +size : 449 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.8-py38h97743b1_1.tar.bz2 +md5 : 2d6ac1663ba630519088f25bc886c2bd +timestamp : 2021-01-13 17:51:00 UTC +dependencies: + - libgcc-ng >=7.5.0 + - mpmath + - numpy + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.8 py38hd504320_0 +---------------------------- +file name : moments-1.0.8-py38hd504320_0.tar.bz2 +name : moments +version : 1.0.8 +build : py38hd504320_0 +build number: 0 +size : 451 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.8-py38hd504320_0.tar.bz2 +md5 : c2e4176cd1674fc8752a662d7a80a76d +timestamp : 2020-12-29 02:20:22 UTC +dependencies: + - libgcc-ng >=7.5.0 + - matplotlib-base + - mpmath + - networkx + - numpy + - pandas + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.8 py38hd504320_1 +---------------------------- +file name : moments-1.0.8-py38hd504320_1.tar.bz2 +name : moments +version : 1.0.8 +build : py38hd504320_1 +build number: 1 +size : 449 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.8-py38hd504320_1.tar.bz2 +md5 : 2849e9eb9e839d995dc65c1291c326e1 +timestamp : 2021-01-13 17:53:19 UTC +dependencies: + - libgcc-ng >=7.5.0 + - mpmath + - numpy + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.9 py38h0152933_1 +---------------------------- +file name : moments-1.0.9-py38h0152933_1.tar.bz2 +name : moments +version : 1.0.9 +build : py38h0152933_1 +build number: 1 +size : 466 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.9-py38h0152933_1.tar.bz2 +md5 : 71ce8866b10ffa2febe92d08ea7c0176 +timestamp : 2021-03-28 15:42:02 UTC +dependencies: + - libgcc-ng >=9.3.0 + - mpmath + - numpy + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.9 py38h0a581ac_0 +---------------------------- +file name : moments-1.0.9-py38h0a581ac_0.tar.bz2 +name : moments +version : 1.0.9 +build : py38h0a581ac_0 +build number: 0 +size : 453 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.9-py38h0a581ac_0.tar.bz2 +md5 : 51c6976754978f640faa3e6c0f673879 +timestamp : 2021-02-03 23:45:50 UTC +dependencies: + - libgcc-ng >=7.5.0 + - mpmath + - numpy + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.9 py38h29c9776_0 +---------------------------- +file name : moments-1.0.9-py38h29c9776_0.tar.bz2 +name : moments +version : 1.0.9 +build : py38h29c9776_0 +build number: 0 +size : 453 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.9-py38h29c9776_0.tar.bz2 +md5 : 21bd34743bb5b0bd23380758c6e3933b +timestamp : 2021-02-03 23:46:54 UTC +dependencies: + - libgcc-ng >=7.5.0 + - mpmath + - numpy + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - scipy + + +moments 1.0.9 py38h4f025d9_1 +---------------------------- +file name : moments-1.0.9-py38h4f025d9_1.tar.bz2 +name : moments +version : 1.0.9 +build : py38h4f025d9_1 +build number: 1 +size : 467 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/moments-1.0.9-py38h4f025d9_1.tar.bz2 +md5 : d9e6778d7e183da4d04b7a83683c668e +time diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/multiqc.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/multiqc.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b038d6b0b5608a300fcaea5d6f2d95e72b9094cf --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/multiqc.manual_bundle.txt @@ -0,0 +1,548 @@ +# Tool: multiqc +software_name: multiqc +tier: T1 +domain: t1_backfill_overall +downloads: 804493 +summary: Aggregate results from bioinformatics analyses across many samples into a single report. +description: Aggregate results from bioinformatics analyses across many samples into a single report. +dependencies: click, coloredlogs, humanize, importlib-metadata, jinja2 >=3.0.0, jsonschema, markdown, natsort, numpy, packaging, pillow >=10.2.0, plotly >=5.18, polars-lts-cpu, pyaml-env, pydantic >=2.7.1, python >=3.8,!=3.14.1, python-dotenv, python-kaleido 0.2.1, pyyaml >=4, requests, rich >=10, rich-click, spectra >=0.0.10, tiktoken, tqdm, typeguard +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://seqera.io/multiqc +doc_url: https://docs.seqera.io/multiqc/ +dev_url: https://github.com/MultiQC/MultiQC + +## URL Docs Extract +### https://docs.seqera.io/multiqc/ +MultiQC overview | Seqera Docs Skip to main content Seqera Search Log In Sign Up Help Forum Support Portal Nextflow Slack Seqera AI Company Seqera.io Contact us Submit Feedback Cloud Enterprise Nextflow MultiQC Wave Fusion Platform API Changelog MultiQC overview Getting started Reports Custom content AI summaries Usage Development Supported Tools Changelog Home MultiQC overview MultiQC overview MultiQC is a reporting tool that parses results and statistics from bioinformatics tool outputs, such as log files and console outputs. It helps to summarise experiments containing multiple samples and multiple analysis steps. It's designed to be placed at the end of pipelines or to be run manually when you've finished running your tools. eyJ2ZXJzaW9uIjoiMSIsImVuY29kaW5nIjoiYnN0cmluZyIsImNvbXByZXNzZWQiOnRydWUsImVuY29kZWQiOiJ4nO19aVMqy7L29/0rVqz79VinqrLGXHUwMDEzceNcclFwnlx1MDAxMFx1MDAxMX3PXHKDeVx1MDAxZWRcdTAwMTDwxvnvN5M1MEhcdTAwMGJcYq7dKu5cdTAwMWR77UVD03Y/T+VQmU/+71/fvn3vXHUwMDBlW/nv//r2PT/IpmvlXFw73f/+XHUwMDBmev0p3+6Um1xyPCRHf+80e+3s6J2lbrfV+dc//1lPt6v5bquWzubZU7nTS9c63V6u3GTZZv2f5W6+3vl/9N/zdD3/361mPddts/GX7ORz5W6z/eO78rV8Pd/odvDs/1x1MDAxZv/+7dv/jv47cXXtfLabblx1MDAxNGv50Vx1MDAwN0aHJi6Q89lXz5uN0cVcblx1MDAwMyCtN0b8fke5s4/f183n8HBcdTAwMDGvOT8+Qi99vzSF+kmPN611jcj9WbNw12rx8ddcdTAwMTbKtdp1d1j7cSvS2VKvPXFRnW67Wc3flnPdXHUwMDEyffvM678/12niXVx1MDAxOH+q3excdTAwMTVLjXyn8+tuj15tttLZcndI55n4XHUwMDA1f9yFf31cdTAwMWK/MqBPeWDOK1xyQurfXHUwMDA3Rlx1MDAxZvWeKemNs3rmYvaaNbz/eDH/xUc/48vJpLPVXCJeUyM3fk82n1O59Pg9/Z+/XCKe3mmtps5fypeLpS59uVx1MDAwMMY9WOV//YyvIT96XHUwMDAwXHUwMDFhnFx1MDAwNy3s+E7RXHUwMDE3t45yYyyMXlXDVqHTr1x1MDAxN7y9XHUwMDE1d3V9l7ftw9L3n8f/Z/JGNnI/b2SjV6uNfyU6XHUwMDEwnYDZ+DO9Vi79XHUwMDAzXHLCWK8l3S1pxldaKzeqs6erNbPVMYBGr/7nXHUwMDFm85GLXHUwMDFmn1x1MDAwYlohXTBopXTArdZLg7ZcdTAwMTR96Fx1MDAxNm9S7XSqedPUteHF4b5cdTAwMTVhXHUwMDA3LXDPtHZcdTAwMWFcdTAwMTEyXHJa/PWZXHUwMDA0XHUwMDA162G22043Oq10XHUwMDFiXHUwMDFm+UvcXHUwMDFhyaTTQlx1MDAxYjlcdTAwMDe3nE199Vx1MDAwZqhcbodAtsY4/ZGxOnFD0+1upNzIlVx1MDAxYsXZj+RcdTAwMWK5gCO1dKe716zXy128jMtmudGdfcfovLvtdrNfyqdzc85cdTAwMWN4rEWnm76X4//7NsbO6C+///9//jH33XOe7+hz9GTHn/1r8s9VXHUwMDE5LLmcffU3gz1H/Fx1MDAxYc3Hj2ZcdTAwMTGDu/VqtnRdXHUwMDE2XXE/jMR470Tlojb8XGa2XGa4kyCslNrAXGaNlWZ4XHUwMDBiLCjlwThcdTAwMGVcdTAwMTBcIjorrq1E62i3bN6yeVx1MDAwMZutsVpZpVdg88l+oXzSz+/vn93LXruWLtxcdTAwMWSWw89mj7eZO2e9ncNmY5hcdTAwMTBacpBqxOZcdTAwMTCRWVhruJFebm3z12Lzq3Gh0mL21Vx0XHUwMDAzbZRDJC/vYvdcdTAwMGLZxJ6rJSulu2GqdZaI+2L7IeyUpriQwkJDMZbQs442gGaecGpcdTAwMWRcdTAwMWXD21x1MDAxMcZcdTAwMThRXG7goJ1cdTAwMTLjXHUwMDE1Zz654Sjx8NhwXHUwMDA11yvK+lOqNlSVllx1MDAwZlx1MDAwYrnfZJTA+kBcdTAwMDRb0F5cdTAwMGKjl89sJLOP8fvTm8555zzWj4jhw1HH7YVcdTAwMWTBZJRcZvdKolx1MDAxMZ6HYKNcdTAwMTg6mIBH1kfwpq2SdN5phMtHxu3WKG3MxcR1OJDNILjkXFytkKfc3z2omLP09SM/873o8UPuYS/zXHUwMDAxUj5cdTAwMTgwajS+2iiwXHUwMDE4NZppNjvJOPfGKof+tpB25sL+TjZb4aRQzn9oK7Rl81x1MDAxZmEzul1cXHiA5dmcOG/E756Oqr14VttCXCJ60jT5dvjZ7Fx1MDAxOVDuRyAtXrJZccmM0EIh48PGZimk1JZcdTAwMDOM2bOl81eg8+s7iTYwYnRWgEPQLJ9cdTAwMDPKXHUwMDE2Lyu357eNs8fHXHUwMDFinb6NN1x1MDAwZfPFdNgpjVx1MDAxMGRcdTAwMDadXHUwMDEx2pRcdTAwMDGKMKZcdTAwMTltPFx1MDAxM9JIh+GaXHUwMDA0bdzMdYVcIl5cdTAwMTTaXHUwMDEysYVe5HeXXHUwMDEzXHUwMDE3Z/nDXFxP7NbiunqQ2qnxXFwvLNR+k01cdTAwMTI+OF50yCCrV7FJN8V8sV04XHUwMDE1Z4N0uqCyJ7p5XHUwMDE3a4VcdTAwMWTAIHCtwMBcdTAwMTht0jxcdTAwMDB7y9A2e4LP2lx1MDAwMN6wSUK3l9M/i/bCQ1xy261F2tyOhH3FwXTGc2n48unLwln3yFV3rlx1MDAwZVx1MDAxMmc78d3G8HxQi4c/+SM440pZ7Z3SSNgpLuPdZ5JcdTAwMWJcdTAwMDClnOFgZy/rb039XHUwMDE4Ya1cdTAwMTawMPezJfOWzN6AUeD5OD5aRObHyOBSQFx1MDAxY8RzOXXXqFSi7cjJSfjJLFx1MDAxOVx1MDAxN1x1MDAxOFxiXHUwMDFh7l+SXHUwMDE5NHNCOFx1MDAwZVx1MDAxMkJHZo3M8drJrWX+WmR+NVZcdTAwMDSuZl/9zWglcfmnXGJqaUaDi9li0z89qWQmefGQNJXc7mXYXHUwMDE5rSRnXluKXHUwMDA2uVx1MDAxNlPx2qhigEtcdTAwMDbgXHUwMDExq1Y5p8DImStbLVxczORVJpfZfLjorZdysdt9Z1Oxk8huN6tz7f5FqdYoNSP1sJD7bTZcdIL3x+lcdTAwMTK8kH75dEepkEg97ZxcXOyU42JcdTAwMTCt+E57eJtcdTAwMGY9gsEwI1x1MDAwNVx1MDAwMWQugkEwgaZcdTAwMTm43Fx1MDAwMII3bZa88FxuwJhFJWyhRu7WLG3Mx4SJcHCWz9wr4YTny2d/om15vVx1MDAxYos+ZWKlxFW7fdB8aHZuws9nhTdUUKLLWlx1MDAwYnJmR1x1MDAwMlnMlPDSeauklmibQsVnhe4vhruLYsYtn788nyVXwnLE8PL2+eA0eniQgVQuqu/y1dpj9IyHv6+J7DMohXbYyHl8Np6habbaKT/ic5jorFx1MDAwNf5oI1x1MDAxNu0w/mk62/Et3tL518+filx1MDAxYbVcdTAwMGXktEFzhNcgl8/pXHUwMDFlxiOtgjxLXHUwMDE1nNORVDf2XFxuJ0JfNICxMePcWe6cNMjo2YpUx1x1MDAxY3jhqCBKW8PXK0l9r5jRUOmwsW5R0OhcdTAwMWLVSO6xnfBcdTAwMGaFx8izu2p0Xf80LNx+k1FSLrhPQmjNcS1cdTAwMTbLO5ntp+huqnhyXT+O5578ZSV7e3C6XHUwMDFielx1MDAwNFPQaNFcdTAwMWVcdJiHYGOZUYBcdTAwMDA3XHUwMDFiQPCGjZLG93rtXHUwMDE3Vr2EXHUwMDFht1ubtDFcdTAwMTdcdTAwMTPxXHUwMDEwyGZcXFx1MDAxZbXwVi+/LfGwn7KlcjWjXHUwMDEzpajakalM8iZ9XHUwMDE0fjYrpqRU3EvvnJstSFXMY8BcYlSVSj1RYVwis8PlXHUwMDA10IQtyv9sybwlM3qWhjrYlzfNMrLfu29cdTAwMGVjl8dP/ZPDSPOpVr2uhp/MXHUwMDE4L3rNXHI6dy/IrLhmXGJRgzRXoSOzcOhZOWndls1fi82vbzLaYEpb6byBVTZcdTAwMTlbkKh2z8VzoZ+tPVx1MDAwZc77e3u3PvRcdTAwMTWpSlx1MDAwMjNeKVx1MDAwZZyiYzddN6CsZFx1MDAwMmmDYTNHxJr1iszfLV7Eq5NaXHUwMDBisYjc9/d8eO3j+81T/ERuL+dcXDleXHRcdTAwMGK532SUgFx1MDAwN1x1MDAxN75cYlx1MDAwMG9IXHUwMDAwZmlcdTAwMDRXW7HT4oWNqez1Y+1AVVxuXHUwMDBmmUYh9FxiXHUwMDA2z6iBXHUwMDE1jdJcdTAwMWNcdTAwMDRrzpl3XHUwMDE2XHUwMDAxzn8gOERGiZo7qD94Uc9TqGG7tUmb25GYiDVmyKxcdTAwMTDcVnuxfLTYTl1cdTAwMGYqJ9fd7nWS63SvX0hcdTAwMWPf9sPPZctcdTAwMDR3goPmgnsxLiD/UZLqXHUwMDE42SCPLihIbszMdf2tgjeaasvdoszPlspfnspcdTAwMDJdLiPwXHUwMDAxLe9Z7veyXHUwMDBmz4ma7+0nTlx1MDAwYkVZTlx1MDAwZVx1MDAxM5VS+LnsXHUwMDE5d1x1MDAxY1ctq+dwmXZcIoyT+K9cdTAwMGVcdTAwMWKXqVx1MDAxNVnbxcpcdTAwMDJbMn8uMr/evOhcdTAwMDKbv1xmXHUwMDA2INRcdTAwMGW1NJ9vxKl8Vvv53t5F9CxXu+7XzrOVsPNZK2r9QmIgpYWaSf5QMarn4KVcdTAwMTWWO6XX1ENVPMu1fYdA0WuHP7CI2akuelwip37YfqpcdTAwMTQvVeaqPHQtXHUwMDFlXHUwMDE2Zr/JIElcdTAwMTGY6pDcSYfRkV9+a1xcRerHpeNo9kYmLy/S53F3lUlkQlx1MDAwZmBtmdeaNIvnXHUwMDAwXHUwMDE4XHUwMDA0Q+RcdTAwMWGhzFx1MDAwNlx1MDAwMLz52jV8s1x1MDAwNrVoQzzUuN1apM31O/lgTW6l3Gqd9LxQiOtUfXDUyV3apo+mU7d3Kvxk1shXXGaKXHUwMDA1bS6qmUZkqkT1XHUwMDBlSFx1MDAxN8MoPdXJXHUwMDE5XHUwMDAyNlup8LpgYVx1MDAwN/2WzVs2I0q4smKFncXqzsFRWcqbRraY7OVv+8/F2t0g/HS2zGDIJa2yc+hsPNPOK0SpXGJcdTAwMWSdXHIut17yhXVcdTAwMDJbNn8uNr9eiFxuwVIhSlwipbleofJHXHUwMDFklMvPXHTTg2RbXGZUKrvbvS9cdTAwMWOHntJcdTAwMTgvglwi42ysNOCn8z9cdTAwMDBIaSW011xuJDgw61WivlPASFInXHUwMDFlXHUwMDE5tchSJ6B6r2PD3J7qXHUwMDFkdSCRLtZcdTAwMGJcIlx1MDAxZVx1MDAxNm6/ySYp81q8XGLe21U2XHUwMDE2y4enULxKnZzsXFw+uvuj47JJXGZcdTAwMGVCXHUwMDBmYO1cdTAwMTjnXHUwMDA24SvmXHUwMDAx2DiEt5FO+lxyXHUwMDAweNNiN8ooJ2ChYHeocbu1SZurXVOBXHUwMDFlJrJZidVcdTAwMWEjcumbfrl7WcBgcT9cdTAwMTE5zcidw93T8LNcdTAwMTlcdTAwMDNGbVx1MDAwNNfkQk5Oy/hRiaqpU9mgvUL3XHUwMDEyyVx1MDAxZSY201BcdTAwMDBPw1x1MDAwMVx1MDAxNlx1MDAxNVxubOn8Vej8ivQ+qUUghJf3Lnd7ei/RLpRK2YvrZt/2XHUwMDEy0WS2XHUwMDE4fjpbZqWzhlSgXtBZccO482iWR1x1MDAxYoxOh2qcXHUwMDA2Xp1cdTAwMDMxWVq4pfNXoPPrtag6OGI0XHUwMDEyXHUwMDFmkpB2eU7X1P1e/E731c7l1U5W3Vx1MDAxZCNcdTAwMTlC3yuilWZcXDrunSOJcj1TX24ls4Bs1tziudyavYvvtcWITJLOc7koXHUwMDFkxJPJ3U4ud3Ltu5enXHUwMDE3TyXuM6f9sJD7TVZJuuBqak/tTn5cdTAwMTXBm0dz4K5bcKrjLnNZubo5dlaGvppcdTAwMWFcci8zXHUwMDFl/UhcXN1fXCJYc8E0PlxmJfVcdTAwMDZcdTAwMTC8aavEOYazwFx1MDAxN8qwhVx1MDAxYbhbq7S5XHUwMDEyNlx1MDAxM7wroYVFrOhcdTAwMTX0blwiZ91cdTAwMWR+dvH4oHdL94mhN1dnz1x1MDAxZqBiwDGlhPVcdTAwMWVoW8KPv/lXOapcdTAwMTNcdTAwMGUpQ0lcIufCJMAvjPGOXHUwMDFirrds3rJ5XHUwMDAxm73hXHUwMDFlXSpYIZ07TD1mfPxSVJ9cdTAwMDZcdTAwMTd7+51oob57XHUwMDFmejKjbVZCKa1pXsZcdTAwMGIyXHUwMDAzTfJcdTAwMDZruVx1MDAxM6Ejs+U030PBh/Ypt2TecMBcdTAwMTg84lxcKS9Gg9+XZvRzfL9VM43rdKvSalx1MDAxZqd3oH8lrsLOaGMsc8ZS7zXJXHUwMDA3T7jTP0pSgTnQzlx1MDAxOS7AUEfyWvFiIZ3hXFxvfofRgjY0aHBcdTAwMDG1L4/2TqqZwW4qWo3tXHUwMDAxN89wlHZhofabLJJcZtZqklxcalDOrVx1MDAxMC7GXHUwMDFlq9Wj9EBe3excdTAwMGUv4s3efvRGNEJcdTAwMGZgXHUwMDA3TIPAX9XMXHUwMDAzMEhmaJA2Mnl9XHUwMDAwb7p30VkhnVjYu1x1MDAxOGrcbk3S5vxL+VrBXHUwMDBiXHUwMDE46dRcbiWpncQl7N5cdTAwMWZGXHUwMDFlXCJ9v9sud5M+1lxifbRonGCj7KUxwK2d8Kd/lKR65oX2XHUwMDAwnFtQk8myv5/NwnFcdTAwMDegXHUwMDE2T/je0vnL01x1MDAxOX1LQdpry7O5ecW74knGTLxS3uW6dVx1MDAxNq1cdTAwMGZCXy9Atlx1MDAxOb1cdTAwMTCDTHVz2Gw501IoLqxcdTAwMGVcdTAwMWabwdCsZrVQXHUwMDFidcvmz8Xm10tSg6eda8Q36YUuT+lh5/C+dlVN7jzf89yA79rBbS787jbGi144IdFcdTAwMDJ7ZPZ0XHUwMDA2XGJcdTAwMTTecoxcdTAwMTelIfpMVKCHKFpcdTAwMTSglcbYfqHSTfNgt3vnq736TW/QzFx1MDAxNVJPvYeH+7Aw+01cdTAwMTZJ8+DdRY5cdTAwMWVcdTAwMTeaJb18XHRbs3pjs27n1lxyr1x1MDAxMlx1MDAwN/Kpfyj244ehxy+Fi1x1MDAxOCeSMuFcdTAwMWP80vRQmrNcdTAwMDFubfxuulx1MDAxY1UqXHUwMDEwSLtFwWKoUbu1R5urX3OBm1x1MDAxMZYrzSX3yzfTn7R14mnwvHdx3Mn3yslC5PAqk1xiP5VcdTAwMDXN9naSay28tLO6qIYpMdJcdTAwMTQwgttwVa9cdTAwMDHHx+dcdTAwMTdnLLdk/vJkXHUwMDE2Rlx1MDAxOG+0WEHq5rJykLwuJnJcdTAwMTeZ+oXaafibZK1cdTAwMTJ+x1x1MDAxMlxyM42Wscbxl2xW3DIuXHUwMDA1RolChI7NVKyEXHUwMDBmaOGUqy2bP1x1MDAxN5tf31pcZlx1MDAxZXROXHUwMDFhulKs0CxSPMveJiuNlrD++F7mQcVkIfTqXHUwMDAyxnJmODihpFx1MDAxM1x1MDAxM42aP+pQadNG0lRkbpDua9H53Vx1MDAwMkUjvFx1MDAxMdYsnHZ1XHUwMDEzK99nS6lEVSn/+Jg4uN2HaDssvH6TPVx1MDAwMlx1MDAxOVx1MDAxYyhcdTAwMWFtwHK9gtLNcTbiirH+rSxXa1wicpsvwYFcdTAwMTiGXHUwMDFlvug/4pLuLM1QmYGvXHUwMDFljVxytcKCXHUwMDFlwTdUNahkXCJhXHRljFCjdmuNNuZbKlx1MDAxZexbWi6kl6u00Vx1MDAwZncjxXhcZi7i6WEt2T86yaWenvbDz2VFc721UFYrXHUwMDAxXHUwMDEz0mU/alA9I/k5kGhcdTAwMDTMlCH429msSLGKK78o67Ml85bMpFx1MDAxYVxipLm5NJlT5XaVV072eHc34bORZ7TOuzr8ZNbMe6QzvnVcdTAwMGWZXHUwMDE1Z1I4jsdV2MgsXHUwMDE1xvlcdTAwMWNcdTAwMTa2IG/J/LnI3M1cdTAwMGa688gsXqveo6JMMCvkcCPHZlx1MDAxZu5cdTAwMGZcdTAwMGZijXbpIH00NNVu7Vwi7GTGNYs5I1x1MDAwNeC90JTLnZ084Fx1MDAxOVx1MDAwN+NcdTAwMWNIx5X171R+Or6m31x1MDAwNJYv2ItcdTAwMGaE6lx1MDAwYs38goDQ0LLQbHSvy88/QDT1aixdL9eGU493hEy8NdfpequW/1x1MDAwNpP3r5NcdTAwMWZcdTAwMTkhKmyaev9urVxcbIxsVL4wXHLrbjmbrv0+3G22xkez+P1pPF376Fx1MDAwNWub7XKx3EjXXHUwMDEys9fyNk7JQE5p4ZzVYFaYRlO7Kj/fVkx3kJNcdTAwMGYnN5nHnbJccr3kjjCk8I/hK8df13JvpitiwUqm8C54a4lQer1cdTAwMGXg9ShFI2cseJhvXHUwMDEwP1x1MDAwNaVkiCgl30YpXHUwMDE5rMOmXHUwMDAx7Vx1MDAxNEdPa2lKndT2+3eHd1x1MDAxMV/LZCqd+3i0dSe6oaeUVcySiJVcdTAwMTNcdTAwMTYtkbXTVkrS9Fx1MDAxY1x06Cog7TS5pu/CqYmxtq9wivZ9XHUwMDA1mlI/fzfiU5BKhIhU4q12KnjoXHUwMDE0XHUwMDA2/IB3VS1vqI6ig/3Lx9RjpJE5rtVcdTAwMWWf/bUph15cZlx1MDAxZoRgXHUwMDEyfT50rEhrx05cdTAwMDdyXHUwMDAyLHNcdTAwMWGs0WSlXHUwMDA0X686NJBURixDKo9fr5VcdTAwMGXo1PjYnEo0m7VwMOrnlbyNT8GjJVx1MDAxY1x1MDAxN7gqO7f8hsX5XmU/XT3eP2/0o53hcyxcdTAwMTUrXHUwMDFkhr6yTdE0XHUwMDE4a0j6lyNrlLEzfPLoXHUwMDE2UlsueOq4n8ibbJJPdinHXHUwMDBmvMflXHJcdTAwMWTQz8qnULh9P6/kbU5cdTAwMWZcdTAwMGbkXHUwMDEzXHUwMDAwOjt2ckjgXCI+XHIye0l1Ws2qg2ZOx+7yiW587ynsfFwi4Vxu6zTyhXvuXHUwMDE1l9N0Ulx1MDAwMtmmuVx1MDAwM8nBmElzvlHz5JehXHUwMDEzzVx1MDAxZbHaXHUwMDA2TE77XHUwMDA0dFxuRWLi55W8zTxN7Fx1MDAxMb+ovFaKXG6RV5iS69xcdTAwMDOUMJBKNndcdTAwMGVS2au7TrZcXFx1MDAxMWHnXHUwMDEzlWtS4bXR2msxU99F1lx0vFx1MDAxMcpcbunBq3dKS1x1MDAxOLdcdTAwMTSdwFuMbPn8XHUwMDFk9E9AJ1x1MDAxNVx1MDAxYTqp1+lcdTAwMTRYLzkxy2G2+FlwdH5WiJ3sUfMqdlSqZ2/6PJ04haKRw3jYySSdZlTZRIlzYfSkczs6XHUwMDAxhlZOkZtntHFGcfcudMJvYFxu2Vxu5Fx1MDAxMlx1MDAxOO4nXHUwMDA0+37TS0tcdTAwMWF3bzxcdTAwMDLdclx1MDAwZS/rVYyXTngzXHUwMDExiIWSbZ98u0t6hk9TO4Ngsfigxq45/excYsWsXHUwMDA0qkJ2XHUwMDE2NPVrLjyhNIzCXGahldXOTnR3jk4oKVx1MDAwYq1Be3SkvDSgXHUwMDE3nk9cdTAwMTmGb8NPaMtcdTAwMWTHS5k6n1x1MDAxNoxLheGPliRcdTAwMDThxcLzUZqcXHUwMDFiXHUwMDEyXHUwMDA1ssogTdT09Vx1MDAwMaOpR5aAidbZebPohPhupjHSXHUwMDE0eKVmQtThx/3TzFx1MDAxOPlzJ8tYI93C01x1MDAwNXKLflx1MDAwNFx1MDAwM4uv4ZlcdTAwMWMohfy34/P9Nfnnyo5cblx1MDAwNOelXHUwMDAw15LpyX+L1lZ/p/pP4mFHdPKNndgzl41KN/R9JbhaMisszaxw1Fx1MDAxNmenN1BwaVVcdTAwMTKDbbrzXHUwMDE0XHUwMDAwrDdcdTAwMGU9cG2Vavy1v1x1MDAxN1OYSIL9XFw+XHUwMDExuMpcdTAwMDWK34Rm+Zx0VtzUq6+le7v5Vudbs/AtjX7DsFPuzPVbJlx1MDAxY7g/kvd9cVFvcmF8cMJcbl1g47lcXCFh1b/unnZ1f/fq9OS8u5u76PYuTFxi1Vx1MDAwMdCIkFx1MDAwNXHecXBqXCK2JdrtKMW4XHUwMDAxietcdTAwMTngXHUwMDEyKvi0Wlx1MDAwMHWAOGdAXGLjOImDvE+EXHUwMDAwoJhcdTAwMWJJ+WE8bTzMK1x1MDAxZNeaUa1cdTAwMTX6VVT8y19ua1x1MDAxYdLIXHUwMDBiXHUwMDE4kFx1MDAxYVx1MDAxYUZ+codGeIbPxmPgjVacO6unynh2pGCEJDT+uNDTzLSF51OagbG40EojqYF8xl9A74Rj+OpImEZbr1x1MDAxNp7PaDZcdTAwMWF65oH2wGdON1x1MDAwYrGFZ3NcdTAwMTbdbC5J4UpIaoecvjrLrMdcdTAwMTjbaVx1MDAxMtZGd2bhXHSRYMwrq/DCXHUwMDE0TWb20+dD71xykMuWNFLxa1x1MDAxN58ukFY/zofeXHUwMDExXHUwMDE1XHUwMDAycKpXsKS9sSF3RtpAgT/06vCWoH+69CqbjVx1MDAxNjKn3URq//bs9rF34WO1XHUwMDFiXGL9XGKxXHUwMDFk4OSHXHUwMDBicjpcdTAwMDWCU87sXHUwMDBiXHUwMDAwYoNrXHUwMDBlXHUwMDE4mknu1lx1MDAxZDpcdTAwMWS0rFxuNWfzXHUwMDFhL+eFO2PR5VIm9Ivn29yZ0Y5x59+NcuPfjfyglW+X61OlpVx1MDAxM07NRKnblFOTxVx1MDAwZuTb77ad/fLiXqVdmpbyuXXKXHUwMDEzxVxuL5UmPE2oXFxBKeUofXhcdTAwMTWHlC1cdTAwMWP640fZPnncsZHQK2s6yTHAXHUwMDE0XFwrNEMw2Y8zqlx1MDAxOcEwXHUwMDAyQ21DW/1cdTAwMTgqK/k+NSMgJPNcdTAwMTiSUuJVo3mYk/9cdTAwMTRcdTAwMWVNXHUwMDE3xpm0KCu0XHLgXpBSWImGcnLHJ5SkXGaFRzPLic06NdwzoFmpXHUwMDFhhHJ8orx9dFR7pvAxcsCn7YVcXOyDeM5INdN4xFx1MDAwNpryqVx1MDAxNFxyek7ojytcdEDGgbbAXHUwMDE2XHUwMDFh+SCw/TjdLMxWNPGBa41cZu60XHUwMDE1kkqyXHUwMDA0uOXXmkxz0EdcdTAwMDepUrh/XHUwMDEwp+3+fvK08CxDv9ZcYss0PiiNLuhIm3tqraGZMFx1MDAxYSGDXHUwMDBmhorY3knEXHUwMDE3z87QzaC2XuqKtH5O5IQrXHRz5EFz9PNcdTAwMDRlpl/ETlx1MDAxY1x1MDAxZphcZnuR9edfaZRhQlOeXHUwMDE1XHUwMDAzXHUwMDFhpYRz0/GJXHUwMDA3Nlx1MDAxYdEz2iZbZm1AO8ik1KBcdTAwMTHM9IeaXHUwMDBlKPBVhiaRXHUwMDBi/D5cdTAwMTJ0WSbiXHUwMDExTGpFXHUwMDE1xIamrpjpiGeENEmz67k23lx1MDAxOL4wf1x1MDAxYozf8Vx0p6C7qfVLyMDNLG0xXCLC+7J8jJIq7l3r53L/klx1MDAxZU3ft3vVo51s6JcvqVx1MDAxOMlAKsp0OzRcXNNcdTAwMTGKlsxymimplNfUlP9OIVxuhfBcdTAwMTTAO/w2M1x1MDAxOVx1MDAxOP5ev1xmxyvBaMo5hCnn7oVmXHUwMDAwhlhUK1xisF3A/uZcdTAwMDWM0iu05WhITFx1MDAwNlx1MDAxZICp7Vx1MDAxM82Zo71TZJellpDFy1cgOEbfNVx1MDAwYotcdTAwMTWXhqDsxUSo/kKFgVx1MDAxYlxuLiYmcCxaXHUwMDE5XHUwMDFhlrvmoOdcdTAwMWGtWq/flZdcdTAwMDf31VroXHUwMDFkXHUwMDFifIdnXHUwMDE4e1x1MDAxOLRcdTAwMWQkbDCzz42uXHUwMDFmU1x1MDAwZVdJj89cdTAwMDTUO61cZkjql0vBRFx1MDAwNcLvnWy8WFx1MDAwZfrPVN6DsCD+XFzu4qxX65av9r610u1cdTAwMGVlXHS6VL3R7HVbve78XVx1MDAxOTN9jvdPYLx6ha/S71VcdTAwMWRcdTAwMWahXHUwMDAzpVDIICnaa16ag63jSCpykVx1MDAxNHl3U7o6L1x1MDAwZVx1MDAwNr2n8Fx1MDAxN1x1MDAxNlx1MDAwYqRcdTAwMWV6Rui30Vx1MDAxOFx1MDAxMIw7Z8yzlLg0OuvQ3Vx1MDAwMmudfD9cdTAwMTln0vTT0mOEo0ZKYWpOvYnkNOLSe0t9OFx1MDAxYe3jXHUwMDFj9T1Lsj6wUtvZL9CMYfOrXHUwMDAy4j9vN91iXHUwMDA1+r6K4KBNRlx1MDAxYizjozzeQHxiy1x1MDAxN0rtJa/OjlI7XZWKXHUwMDFjps73bD1cdTAwMTkt3X1cdTAwMDDwolx1MDAwMUHHXfhcdTAwMTFcdTAwMWFmRFwi8SCiRNNkcOpEeT/BV3CKYZQuhDRcdTAwMTimXHUwMDFisPOgS1tIXHUwMDE2jVx1MDAxZNVHXG5ydmehS6j1gYpUy1wiV/5Z5IbL6Xy/XHUwMDFkx+BHTD8vXHUwMDFm7opOYlx1MDAxMMeNXHTc4lwi5TNlxFxu2S+o+qTt7V2Lhr52J9epVrqUqlx1MDAwNXA82252OjuldDdb2iTPx59ZjefeIZVccnqJXHUwMDFjTbbR0y2a4Fx1MDAwNd5/Q2pcdTAwMGVWaKfWq9ZcdTAwMTcy45x5SfI5bqLgwPBxXHUwMDBikIr6rZV6kV03XHUwMDE20IWdrGidr1xucpTtRLKdxF5lUO/bwVHuXHUwMDEwrvfhdVWQLfX/XHUwMDEw9afe/fKRb4rpNjhcdTAwMWVcdTAwMDSMdT1MjsxeRPVS2lx1MDAxZfb7cTdsJYZcdTAwMTeRk4fnhEvsfFx1MDAxOKpzrpzUXHUwMDE4iiPlp2NCXFxZmVx1MDAxZKUm8SBX6ylcdTAwMDBcdTAwMDVSXVxuXFzsR21cdTAwMWKShlXbedmi8WX/8jzxU3hZsHD0wJbr4eV68JOf+fhSXFx/PfY0wfNGJOfUN23t8tFn/ziVsPuJm/N6U8dNJFc+iF6k/pxcdTAwMDO/LNtcdTAwMDWjtLc3VKrilfNcdTAwMTPqhCP6XHUwMDAzOKbx1uDaSsXlfsbSW0A/gDQw7WhOyZqdRFK6TH5cdTAwMGX/LVPcXHQtQSBPSM33Jf2tYlx1MDAxM29cdTAwMTFzxP1cdTAwMWPSTGv+XHUwMDBlq8Hb00rccrNKWmlcdTAwMWR0u2B75ijhb1xmX37nY/D8ZJsnO1etXHUwMDBiMzy9LHd1dZ/7XHUwMDBmiG6J3lx1MDAwM6eeQElZz4lcZt2PKljJSFx0S9JzXHUwMDAyqderPV9cdTAwMGXcYmKJ+VxybqVcdTAwMTg6NlRTKCim4S82coX3XHUwMDE4p4JcYsiyfH50W1x1MDAxOYhuRcPuhTHLO2umJfq7uUjBXHUwMDE3XHUwMDBm91x1MDAwYj2rXHUwMDFhXHUwMDBm5vTsXHUwMDAzglto5qibxlLvz8w8OFxcXHUwMDBimdKGZsGBlFx1MDAxOMmtXHUwMDE3pFx1MDAwNYPboKM8slxm3jsp54BbesYpcyioXHUwMDE3XG5ccvxcdTAwMDSGf1x0XHUwMDE4oFx1MDAxM+r15ISgL1x1MDAwNm5cYtyz9pxrWjdWmG1YP+/19jqRa39+dVx1MDAxOblrdXP30T8oQ7o5v1x1MDAwNFx1MDAxOL7onPJcdTAwMTiDaCVn0C2ZQuiTpjx3dr1yv2BsXHUwMDBiidxBXHUwMDBmXHTJZNU8cVx1MDAxYqOYwWs0XHUwMDBlI0Zu0Et6sXDzkTI/LFx1MDAxY07zabGtg1vgrDHKS7nClk81Vz0qqOdcdTAwMWWPNVwiN8e2unORtXtcdTAwMWZcdTAwMTDcwlFcdTAwMWFcdTAwMWS9bVxmuoWbLjCj1kczXHUwMDFhXCJvaVA8l+tcdTAwMTWRXHUwMDA3odtg3OWkV+h4OJrrNCfkRlxu4upj0Ypw6fWkhf09pVdcdTAwMDKeYfHQ7c+KbidcdTAwMDKVKCTNXHUwMDFhsnaFwSTRei1bjkTvn07POnzYi+f2XHUwMDFmXHUwMDEysVx1MDAwZlxi7td9biPRXHUwMDFk8Fx1MDAxZUEjR1x1MDAxM1x1MDAxZtarMljW6Z7Yqlxu9LrnLN5WcS9UQFx1MDAwMeXnh7dxgbshuGrhXHUwMDAypcRcbtNcdTAwMGX42XX8qjJcdTAwMTB7kUEjXHUwMDE50bG73F4/KEdcdTAwMWFmfL+eMdGOobugXHUwMDA0hpWK6lx1MDAxZt9n9d5ExoSccVx1MDAxN9hcdTAwMWT0d6Fb+IlChHd2u4MzJpxLzqk1YGl0l+TJbbychIeSXHUwMDE5QKI4aOy1LkK62bdcdTAwMTDhztEscUtcdTAwMTlR6p6e3f2zzFx0p9BcdTAwMWZA90SpdXvctNRykXsyWWY/oTXEkG0kUqFIXWBymuvv8T3gnTdGvsN24Hp1plx1MDAxYitWWeR9vzJcblx1MDAxMVx1MDAwMK2eWt75vmw+ukLPVvL3p3VRbVx1MDAxZT/tXGZvbj4owrViXHUwMDE4Wo/GQXppZ4JLYdDvRa/AkeertFi3OX4+wpdxUYTFIJhrjJEkhZhzXHUwMDA0f/BcdTAwMDFcdTAwMTL+32PD+2Mg3Fx1MDAwNeZOXHUwMDFjd6PRXSsorHhz2Lgx+c5JrfJ4XHUwMDA2ceNunoJaI0OPcGBATUxSo5NcdTAwMDJ6Zlx1MDAwMihcdTAwMDKLOpgladprJ9Yt9V1cbuHz5Fx1MDAxN2d98JdzXHUwMDAz0Vxmo8elbZhCzD9cdTAwMGLwwF1LXHUwMDBiuHZ5qZZcdTAwMDe4PWrV987FVfMweq+uL1SslLK9XHUwMDBmXG5wXHUwMDEybVx1MDAwM/TTpNTox4qZMFx1MDAxM1xmuuFk4tCDwPesV7ewXHUwMDE0wO1kxfw4h2LZSEJYaO+Emmwx+OWFe1x1MDAwNdODNL5cdTAwMTa+XHUwMDFkf0XMU0hDe1x1MDAxOMtnv08zrVitqXb2jvKZuD7PXHUwMDBmk610UE142Fx1MDAwMa4kQ9tP4pkknDWbXHUwMDAxN4JcdTAwMDR16Vx1MDAwZXnhXHUwMDFkn73S91jB5by6XHUwMDFjKuBAX5L6eLzEhyXlLMKFt5I0fUO1eflHIT7ht83u75Br58VcboXj5vHw/PS56lxup1eR/d1a2V3lq1x1MDAxZjXORFxma6+9J1x1MDAxNSo1M7JAXHUwMDE50lx1MDAxY6JcdTAwMWVSLoThbl1J6OVcdTAwMDA+r5DcM/NTNJD0XGLtSydcXCvlyVx1MDAxNn9VfE/W672Yo4jLXHUwMDAyLlIr6JvHXHUwMDBlRMm1bo8u9q/V83G6fnB9fFx1MDAxOCRcZlx1MDAxNHaAe4uLNOmxKjuqr5xC+IaLq5aF+JxU4Vx1MDAxMvUn1IwnJ4OtL1x1MDAwNnFcdTAwMWJcYnFJXHUwMDE4x1x1MDAwYlmhWLj8cNhcdTAwMTXH5Vx1MDAwM9G7PyqmVeOsXHUwMDE1+6BhppJUXHUwMDAx4lx0286Am+1cYqImXHUwMDBlalwi4CRM67Ves1NAp9OZwptcdTAwMTCuXHUwMDA1o85Wko3FldrKXHUwMDE3bjjSU+NcdTAwMTm+7lx1MDAxYW6CNaZcdTAwMTRQdeFcbrWxXaVcdTAwMGbKmWTp/j560En53ZvK7WGQUm3YXHUwMDAxzjUjZVplrcQ/Jip1flx1MDAwMVxcXHUwMDFi9FxmhCRsTdU2vVx1MDAxYsDnllx1MDAxMJLAsfPGalxmhnGx9nO8cKAwNKjd7fMj3PHgJVx1MDAxY903XGY07fJL+ONN0tUvOs3IjXouVmy2Uo9kLz8mwqmby3pHutd4XHUwMDFmpJ2pRpGKWVKtXHUwMDE03IODNUVcdTAwMDGWXHUwMDA0+NxBLTNuuJyjrEZcdTAwMGWQkeqrruEuWPuGlEI9xuDLp1xuT7LJm6e0tEf1ii2m7Vx1MDAwM48+XHUwMDFjPX9MhCtcdTAwMDBmXHUwMDFjcCrnw1hTzVwiXFwzQP+Ek5ardvxvW8Kpt9poknvDX0fShLxZhCNDSfc1VMWEf1x1MDAxNODqXHUwMDE1J1x1MDAwNdcnkj1aPtAsVOJnV/nqZSH56PYzw3T0IXpcdTAwMWU0PTXkXGKnTFxul4ZqUzjasplAXHUwMDEzUc04XHUwMDFlXHUwMDAwqkdcdTAwMTFTfSDv6YbPSVx1MDAxNkrJpFSIbI/WximYU1IoOTpTckJh+qthPLhcdTAwMDNdYJDCV5JIKe6eR4fFu0H/Xl9WS73jxFna9D8mxFx1MDAxNTeMNMswTPNcdTAwMGUxNJNcdTAwMGUnVVx1MDAxNUtzuoFGq6zXybMswOdccuiZWcNf4lx1MDAxYlx1MDAxND5hkl/6ovi2r1xmb3MjXHUwMDAxeblCt1x1MDAwM0RrspjpRop7N2Xd60SeVeUk80FcdTAwMDFcdTAwMGWkoj9cdTAwMTJXQV9cdTAwMDTEjDBcdTAwMTBGmlx1MDAxMldMJSnY1Gq9XHUwMDE5VEtcInxiUzJoXHTX8DJZqEjKXHUwMDFlXHUwMDFm5OeFeKBCvlxmzoTDSHZxXHUwMDE1jSDVzLVcXLR3tr97XHUwMDE0K10nL4vVhFx1MDAwYr9GXHUwMDEwcGDcc1x1MDAxYdBEdd4zfWlcdTAwMTJcdTAwMTTTgqbVWlx1MDAwYk5PrZCbVJnzc8S556nMXHUwMDE5jvHkXHUwMDFmUsincpxcdCn3d1fIL9NcdTAwMDP6dtirp1x1MDAxYjvtfDqXztTy/25cdTAwMWMmzk6/tfOtZnu+WP5cdTAwMWbXmlviOt9ExkmV+FkpWHSF0cuE5Vx1MDAxMz7Ht2dHNd7jtty4P7hcdTAwMTGRKm/kXHUwMDFmQs9FaT2zuJY7qySCb8ZpXHUwMDAysjiGNPW9XHUwMDFmtdK9XHUwMDBiXHUwMDE154pzzZlcXOhcdTAwMWNcdTAwMTUyqj+i9VxuiiYlrsvEpeeE/lRTnEu3oEGh7y3t+JNTf/20tN/TrdZ1XHUwMDE379L3X+oneP/LuZ+/6viE35/K+X5k3uNcdTAwMWb90FlHPCVG5EdSKv/56z//XHUwMDA3sqY+NiJ9 Sample 3 Sample 2 Sample 1 Tool 1 Tool 2 Tool 3 Tool 4 Steps of analysis Samples in experiment MultiQC parses tool outputs Single Human-readable HTML report MultiQC note MultiQC doesn't do any analysis for you - it just finds results from other tools that you have already run and generates nice reports. When you launch MultiQC, it recursively searches through any provided file paths and finds files that it recognises. It parses relevant information from these and generates a single stand-alone HTML report file. In addition to the HTML report, MultiQC generates a directory of parsed data files with consistent data structure. This can be useful for further downstream analysis. Edit this page on Github Next Getting started Nextflow Training Support Portal Forum Blog Podcast Contact Us Seqera.io Copyright © 2026 Seqera. All rights reserved. User Agreement Privacy Statement + +### https://seqera.io/multiqc +MultiQC | Seqera Platform Open Source Resources Solutions Company Co-Scientist Pipelines Containers Open-source tool to aggregate bioinformatic analyses results. Read documentation MultiQC/MultiQC Ready to get started? Built-in support for 150+ tools, enabling you to search results and compile a single report across all samples and analyses. See all the supported tools Quick install Copied! pip install multiqc # Install multiqc . # Run pip conda docker Gold Standard MultiQC is the standard in bioinformatics reporting Taught in genomic courses globally, MultiQC has become a fixture at the end of most biological data analysis pipelines. Bioinformaticians and data scientists choose MultiQC because it "just works" Simplify QC analysis with user-friendly HTML reports and convenient data exports Plot outputs from most popular bioinformatics tools, or bring your own with "custom content" Enable collaboration and boost research productivity by easily sharing QC data Detect outliers, anomalies, and batch effects with built-in visualizations See all samples at once, enabling comparisons without looking at individual reports See all tools at once, tracking your data through the analysis process Trusted by researchers worldwide Loading... citations Dimensions Loading... GitHub stars GitHub +1.5M downloads PyPI Bioconda +25K runs per day Internal metrics Join the community Daniel Pass @passDan "Legitimately one of the most indispensable bioinformatics packages" Devon Ryan @dpryan79 "I've said it before and I'll say it again; your pipeline isn't complete until you've added MultiQC." James Ashmore @jma1991 "Hard to remember life without MultiQC" Gaurav Jain @gauravjain49 "For NGS analysis, MultiQC has just become an intrinsic tool ... It's like breathing ... just happens naturally" Saugat Poudel @insilicomicro "Well deserved milestone for #MultiQC. It takes the pain out running QC/QA on large sequencing pipelines. As another tweet once put it: "It just works."" Daniel Pass @passDan "Legitimately one of the most indispensable bioinformatics packages" Devon Ryan @dpryan79 "I've said it before and I'll say it again; your pipeline isn't complete until you've added MultiQC." James Ashmore @jma1991 "Hard to remember life without MultiQC" Gaurav Jain @gauravjain49 "For NGS analysis, MultiQC has just become an intrinsic tool ... It's like breathing ... just happens naturally" Saugat Poudel @insilicomicro "Well deserved milestone for #MultiQC. It takes the pain out running QC/QA on large sequencing pipelines. As another tweet once put it: "It just works."" Follow @MultiQC Follow @MultiQC Sample reports MultiQC collects numerical stats from each module at the top the report, so that you can track how your data behaves as it proceeds through your analysis. RNA-Seq Whole-Genome Seq Bisulfite Seq Hi-C MultiQC_NGI Jupyter Notebook RNA-Seq This report was generated using logs from an analysis accidentally run on ChIP-Seq data from the BI Human Reference Epigenome Mapping Project. This report was generated using logs from an analysis accidentally run on ChIP-Seq data from the BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject dataset ( SRP001534 ). Initial QC was done using FastQC , followed by trimming with TrimGalore ! (a wrapper around cutadapt ). Reads were aligned using STAR and overlaps counted with featureCounts . You can download this report and / or the logs used to generate it, to try running MultiQC yourself. Open report Download full report Download input data Your report Try MultiQC in your browser This MultiQC runner uses WebAssembly to process your data entirely in your browser. No data leaves your computer for the analysis. Note that this feature is experimental and requires a modern browser with WebAssembly support. Try MultiQC in your browser Features No setup required MultiQC works out of the box, with no setup or configuration required. Data is gathered into a single interactive report, automatically extracting sample names from reports and log files for downstream analysis. Easily scan key statistics across samples without switching files or accessing multiple QC tools. Interactive browser-based analysis More than just a reporting tool, MultiQC provides rich visualizations, enabling analysts to explore results from multiple QC tools interactively. Use the intuitive MultiQC interface to visualize data, sort, filter, and customize results, export visualizations to third-party tools, and visualize samples side by side. Support for 150+ tools MultiQC automatically recognizes outputs from the most commonly used bioinformatics tools, including FastQC, Samtools, Picard, GATK, RSeQC, SnpEff, DRAGEN and many more, enabling easy analysis in a single place. Better yet, with a vibrant, engaged open-source community and extensive documentation, the list of supported tools continues to grow, providing support for the latest tools and file formats. Built for the Seqera Platform Built with open science in mind, MultiQC integrates seamlessly with the Seqera Platform enabling analysts in shared workspaces to easily access interactive MultiQC reports directly from the Seqera UI. MultiQC can be used in a variety of ways and is ideally suited to being embedded as a final analysis step in analysis pipelines written in Nextflow or other workflow languages. Ready for downstream analysis Every bioinformatics tool generates output in its own format. MultiQC standardises these, exporting data as TSV / YAML / JSON in a directory alongside the HTML report. Easily import data generated by MultiQC for downstream analysis, for example working with single-cell filtering based on QC metrics, or creating custom analysis reports with aggregate data. Ready for MultiQC? Set it up in no time with our step-by-step installation guide. View Installation Guide Install from the Python Package Index or Bioconda. To install MultiQC, simply run pip install multiqc on the command line. If you use conda, run conda install multiqc instead. View on GitHub View on PyPI View on Bioconda Log in Sign up Platform Overview Pipelines Studios Fusion Compute Co-Scientist Pricing Professional Services Book a demo Open Source Nextflow MultiQC Wave Scientists Pipelines Containers Ask Seqera AI Resources Documentation Podcast Blog Whitepapers Case Studies Support Portal Solutions Genomics Image Processing Protein Analysis Drug Discovery Biopharma Clinical Diagnostics Public Research Agriculture GxP Community Events Forum Partners Submit Feedback Company About Careers Newsletter Contact Trust Center Social Media LinkedIn Bluesky Twitter / X GitHub © 2026 Seqera. All Rights Reserved. User agreement Privacy statement + +### https://github.com/MultiQC/MultiQC +GitHub - MultiQC/MultiQC: Aggregate results from bioinformatics analyses across many samples into a single report. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} MultiQC / MultiQC Public Notifications You must be signed in to change notification settings Fork 659 Star 1.4k Code Issues 229 Pull requests 75 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights MultiQC/MultiQC main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 6,972 Commits 6,972 Commits .claude .claude .github .github docs docs multiqc multiqc scripts scripts tests tests .cursorignore .cursorignore .cursorrules .cursorrules .dockerignore .dockerignore .gitattributes .gitattributes .gitignore .gitignore .gitmodules .gitmodules .markdownlint.yaml .markdownlint.yaml .pre-commit-config.yaml .pre-commit-config.yaml .prettierignore .prettierignore .prettierrc.js .prettierrc.js CHANGELOG.md CHANGELOG.md CITATION.cff CITATION.cff CLAUDE.md CLAUDE.md CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md Dockerfile Dockerfile LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md codecov.yml codecov.yml flake.lock flake.lock flake.nix flake.nix pyproject.toml pyproject.toml setup.py setup.py View all files Repository files navigation README Code of conduct Contributing GPL-3.0 license Aggregate bioinformatics results across many samples into a single report Find documentation and example reports at https://seqera.io/multiqc/ MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples. Reports are generated by scanning given directories for recognised log files. These are parsed and a single HTML report is generated summarising the statistics for all logs found. MultiQC reports can describe multiple analysis steps and large numbers of samples within a single plot, and multiple analysis tools making it ideal for routine fast quality control. A very large number of Bioinformatics tools are supported by MultiQC. Please see the MultiQC website for a complete list . MultiQC can also easily parse data from custom scripts, if correctly formatted / configured - a feature called Custom Content . More modules are being written all the time. Please suggest any ideas as a new issue (please include example log files) . Installation You can install MultiQC using uv (no separate Python installation required): uv tool install multiqc Alternatively, install from PyPI using pip : pip install multiqc Or install using Conda from Bioconda ( set up your channels first): conda install multiqc If you would like the development version from GitHub instead, you can install it with uv or pip : uv tool install git+https://github.com/MultiQC/MultiQC.git pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC.git MultiQC is also available via Docker and Singularity images, Galaxy wrappers, and many more distribution methods. See the documentation for details. Usage Once installed, you can use MultiQC by navigating to your analysis directory (or a parent directory) and running the tool: multiqc . That's it! MultiQC will scan the specified directory ( . is the current dir) and produce a report detailing whatever it finds. The report is created in multiqc_report.html by default. Tab-delimited data files are also created in multiqc_data/ , containing extra information. These can be easily inspected using Excel (use --data-format to get yaml or json instead). For more detailed instructions, run multiqc -h or see the documentation . Citation Please consider citing MultiQC if you use it in your analysis. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller Bioinformatics (2016) doi: 10.1093/bioinformatics/btw354 PMID: 27312411 @article { doi:10.1093/bioinformatics/btw354 , author = { Ewels, Philip and Magnusson, Måns and Lundin, Sverker and Käller, Max } , title = { MultiQC: summarize analysis results for multiple tools and samples in a single report } , journal = { Bioinformatics } , volume = { 32 } , number = { 19 } , pages = { 3047 } , year = { 2016 } , doi = { 10.1093/bioinformatics/btw354 } , URL = { + http://dx.doi.org/10.1093/bioinformatics/btw354 } , eprint = { /oup/backfile/Content_public/Journal/bioinformatics/32/19/10.1093_bioinformatics_btw354/3/btw354.pdf } } Contributions & Support Contributions and suggestions for new features are welcome, as are bug reports! Please create a new issue for any of these, including example reports where possible. Pull-requests for fixes and additions are very welcome. Please see the contributing notes for more information about how the process works. MultiQC has extensive documentation describing how to write new modules, plugins and templates. If in doubt, feel free to get in touch with the author directly: @ewels ( phil.ewels@seqera.io ) Contributors MultiQC is developed and maintained by Phil Ewels ( @ewels ) at Seqera Labs . It was originally written at the National Genomics Infrastructure , part of SciLifeLab in Sweden. A huge thank you to all code contributors - there are a lot of you! See the Contributors Graph for details. MultiQC is released under the GPL v3 or later licence. About Aggregate results from bioinformatics analyses across many samples into a single report. seqera.io/multiqc/ Topics python bioinformatics quality-control analysis reporting pypi data-visualization bioconda multiqc vizualisation seqera Resources Readme License GPL-3.0 license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1.4k stars Watchers 30 watching Forks 659 forks Report repository Releases 54 v1.34 Latest Apr 21, 2026 + 53 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages JavaScript 68.7% Python 29.9% HTML 1.0% SCSS 0.2% CSS 0.2% Dockerfile 0.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge multiqc --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +multiqc 0.4 py27_0 +------------------ +file name : multiqc-0.4-py27_0.tar.bz2 +name : multiqc +version : 0.4 +build : py27_0 +build number: 0 +size : 860 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.4-py27_0.tar.bz2 +md5 : 1db9798677229ca09b2308d92078b571 +dependencies: + - click + - jinja2 + - python 2.7* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.4 py34_0 +------------------ +file name : multiqc-0.4-py34_0.tar.bz2 +name : multiqc +version : 0.4 +build : py34_0 +build number: 0 +size : 860 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.4-py34_0.tar.bz2 +md5 : 82108fa9b0e1590ed0e55b660cba5272 +dependencies: + - click + - jinja2 + - python 3.4* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.4 py35_0 +------------------ +file name : multiqc-0.4-py35_0.tar.bz2 +name : multiqc +version : 0.4 +build : py35_0 +build number: 0 +size : 876 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.4-py35_0.tar.bz2 +md5 : e06ea0a3cfd6e1aca6b62438d3b64dba +dependencies: + - click + - jinja2 + - python 3.5* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.5 py27_0 +------------------ +file name : multiqc-0.5-py27_0.tar.bz2 +name : multiqc +version : 0.5 +build : py27_0 +build number: 0 +size : 666 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.5-py27_0.tar.bz2 +md5 : 0d4c97d054a3b600f3d7f160a7a7a18d +dependencies: + - click + - jinja2 + - matplotlib + - python 2.7* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.5 py34_0 +------------------ +file name : multiqc-0.5-py34_0.tar.bz2 +name : multiqc +version : 0.5 +build : py34_0 +build number: 0 +size : 673 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.5-py34_0.tar.bz2 +md5 : 345e87924b6f7ef47cf2f084c75bdca8 +dependencies: + - click + - jinja2 + - matplotlib + - python 3.4* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.5 py35_0 +------------------ +file name : multiqc-0.5-py35_0.tar.bz2 +name : multiqc +version : 0.5 +build : py35_0 +build number: 0 +size : 688 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.5-py35_0.tar.bz2 +md5 : 404caf68761b00895d9e5724648cb02e +dependencies: + - click + - jinja2 + - matplotlib + - python 3.5* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.6 py27_0 +------------------ +file name : multiqc-0.6-py27_0.tar.bz2 +name : multiqc +version : 0.6 +build : py27_0 +build number: 0 +size : 719 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.6-py27_0.tar.bz2 +md5 : cd70dbba19a086b7a1eaf704228913b3 +dependencies: + - click + - jinja2 + - matplotlib + - python 2.7* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.6 py34_0 +------------------ +file name : multiqc-0.6-py34_0.tar.bz2 +name : multiqc +version : 0.6 +build : py34_0 +build number: 0 +size : 750 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.6-py34_0.tar.bz2 +md5 : 7686cb74b0c7ea1d39e5809844bc0808 +dependencies: + - click + - jinja2 + - matplotlib + - python 3.4* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.6 py35_0 +------------------ +file name : multiqc-0.6-py35_0.tar.bz2 +name : multiqc +version : 0.6 +build : py35_0 +build number: 0 +size : 720 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.6-py35_0.tar.bz2 +md5 : a6275b10bfac4c6c4367ff337a1c1e3c +dependencies: + - click + - jinja2 + - matplotlib + - python 3.5* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.7 py27_0 +------------------ +file name : multiqc-0.7-py27_0.tar.bz2 +name : multiqc +version : 0.7 +build : py27_0 +build number: 0 +size : 740 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.7-py27_0.tar.bz2 +md5 : 472490107980f64f50ecb9e4c3373d37 +dependencies: + - click + - jinja2 + - matplotlib + - python 2.7* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.7 py34_0 +------------------ +file name : multiqc-0.7-py34_0.tar.bz2 +name : multiqc +version : 0.7 +build : py34_0 +build number: 0 +size : 741 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.7-py34_0.tar.bz2 +md5 : 3364cce30179c29a8cd4dc9751bca940 +dependencies: + - click + - jinja2 + - matplotlib + - python 3.4* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.7 py35_0 +------------------ +file name : multiqc-0.7-py35_0.tar.bz2 +name : multiqc +version : 0.7 +build : py35_0 +build number: 0 +size : 781 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.7-py35_0.tar.bz2 +md5 : fb859c43eb5a1651e197079c7c0775d1 +dependencies: + - click + - jinja2 + - matplotlib + - python 3.5* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.7.1dev0 py27_0 +------------------------ +file name : multiqc-0.7.1dev0-py27_0.tar.bz2 +name : multiqc +version : 0.7.1dev0 +build : py27_0 +build number: 0 +size : 685 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.7.1dev0-py27_0.tar.bz2 +md5 : a204eb1960e384e060cdad2f93aac659 +dependencies: + - click + - jinja2 + - matplotlib + - python 2.7* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.7.1dev0 py27_1 +------------------------ +file name : multiqc-0.7.1dev0-py27_1.tar.bz2 +name : multiqc +version : 0.7.1dev0 +build : py27_1 +build number: 1 +size : 686 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.7.1dev0-py27_1.tar.bz2 +md5 : 299aebfccce30735d3e237c3227399a0 +dependencies: + - click + - jinja2 + - matplotlib + - python 2.7* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.7.1dev0 py34_0 +------------------------ +file name : multiqc-0.7.1dev0-py34_0.tar.bz2 +name : multiqc +version : 0.7.1dev0 +build : py34_0 +build number: 0 +size : 688 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.7.1dev0-py34_0.tar.bz2 +md5 : 22b10134864804b2edc7fee132b3d5a5 +dependencies: + - click + - jinja2 + - matplotlib + - python 3.4* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.7.1dev0 py34_1 +------------------------ +file name : multiqc-0.7.1dev0-py34_1.tar.bz2 +name : multiqc +version : 0.7.1dev0 +build : py34_1 +build number: 1 +size : 690 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.7.1dev0-py34_1.tar.bz2 +md5 : b3979eac7b5cf319677b1ad2300f7d72 +dependencies: + - click + - jinja2 + - matplotlib + - python 3.4* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.7.1dev0 py35_0 +------------------------ +file name : multiqc-0.7.1dev0-py35_0.tar.bz2 +name : multiqc +version : 0.7.1dev0 +build : py35_0 +build number: 0 +size : 687 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.7.1dev0-py35_0.tar.bz2 +md5 : 7efbc61c5b9a054a83afabb803c23041 +dependencies: + - click + - jinja2 + - matplotlib + - python 3.5* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.7.1dev0 py35_1 +------------------------ +file name : multiqc-0.7.1dev0-py35_1.tar.bz2 +name : multiqc +version : 0.7.1dev0 +build : py35_1 +build number: 1 +size : 689 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.7.1dev0-py35_1.tar.bz2 +md5 : ea8c95ffcfc9bdf8b35dff0acc9449c0 +dependencies: + - click + - jinja2 + - matplotlib + - python 3.5* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.8dev0 py27_0 +---------------------- +file name : multiqc-0.8dev0-py27_0.tar.bz2 +name : multiqc +version : 0.8dev0 +build : py27_0 +build number: 0 +size : 700 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.8dev0-py27_0.tar.bz2 +md5 : 40cd538401341a3052de33fc059416bc +dependencies: + - click + - jinja2 + - matplotlib + - python 2.7* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.8dev0 py34_0 +---------------------- +file name : multiqc-0.8dev0-py34_0.tar.bz2 +name : multiqc +version : 0.8dev0 +build : py34_0 +build number: 0 +size : 703 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.8dev0-py34_0.tar.bz2 +md5 : 700c86233bd0045678926ee06cf334d8 +dependencies: + - click + - jinja2 + - matplotlib + - python 3.4* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.8dev0 py35_0 +---------------------- +file name : multiqc-0.8dev0-py35_0.tar.bz2 +name : multiqc +version : 0.8dev0 +build : py35_0 +build number: 0 +size : 702 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.8dev0-py35_0.tar.bz2 +md5 : ef643a482cfdefc51e8026a85b86ea0f +dependencies: + - click + - jinja2 + - matplotlib + - python 3.5* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.8 py27_0 +------------------ +file name : multiqc-0.8-py27_0.tar.bz2 +name : multiqc +version : 0.8 +build : py27_0 +build number: 0 +size : 771 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.8-py27_0.tar.bz2 +md5 : 56427048bc47978b81bdbe148fb4a15c +dependencies: + - click + - jinja2 + - matplotlib + - python 2.7* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.8 py34_0 +------------------ +file name : multiqc-0.8-py34_0.tar.bz2 +name : multiqc +version : 0.8 +build : py34_0 +build number: 0 +size : 777 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/multiqc-0.8-py34_0.tar.bz2 +md5 : 323ba988ee80a2f14cb5605b9ecc6e76 +dependencies: + - click + - jinja2 + - matplotlib + - python 3.4* + - pyyaml + - setuptools + - simplejson + + +multiqc 0.8 py35_0 +------------------ +file name : multiqc-0.8-py35_0.tar.bz2 +name : multiqc +version : 0.8 +build : py35_0 +build number: 0 +size : 829 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nanomath.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nanomath.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..eb43f8f7239d3b213618e498849ca15195421b84 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nanomath.manual_bundle.txt @@ -0,0 +1,505 @@ +# Tool: nanomath +software_name: nanomath +tier: T1 +domain: t1_backfill_overall +downloads: 124765 +summary: A few simple math function for other Oxford Nanopore processing scripts +description: A few simple math function for other Oxford Nanopore processing scripts +dependencies: deprecated, numpy >1.8, pandas, python >=3 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/wdecoster/nanomath +doc_url: +dev_url: https://github.com/wdecoster/nanomath + +## URL Docs Extract +### https://github.com/wdecoster/nanomath +GitHub - wdecoster/nanomath: A few simple math function for other Oxford Nanopore processing scripts · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} This repository was archived by the owner on Jun 19, 2024. It is now read-only. wdecoster / nanomath Public archive Notifications You must be signed in to change notification settings Fork 3 Star 9 Code Issues 1 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights wdecoster/nanomath master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 115 Commits 115 Commits nanomath nanomath .gitignore .gitignore .travis.yml .travis.yml LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README GPL-3.0 license nanomath - DEPRECATED AS OF 2024-06-20, THIS REPOSITORY IS DEPRECATED. ITS CODE IS INTEGRATED INTO NANOPLOT. This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data FUNCTIONS Calculate read N50 from a set of lengths get_N50(readlenghts) Remove extreme length outliers from a dataset remove_length_outliers(dataframe, columname) Calculate the average Phred quality of a read ave_qual(qualscores) Write out the statistics report after calling readstats function write_stats(dataframe, outputname) Compute a number of statistics, return a dictionary calc_read_stats(dataframe) As of v1.3.0 , nanomath calculates the average quality differently, by first converting per-read phred scale averages to error rates, take the average, and converting back ( nanostat#40 ) INSTALLATION pip install nanomath or conda install -c bioconda nanomath CONTRIBUTORS @alexomics for fixing the indentation of the printed stats CITATION If you use this tool, please consider citing our publication . About A few simple math function for other Oxford Nanopore processing scripts Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 9 stars Watchers 1 watching Forks 3 forks Report repository Releases 2 Version with stats enabling --tsv Latest Sep 1, 2020 + 1 release Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/wdecoster/nanomath +GitHub - wdecoster/nanomath: A few simple math function for other Oxford Nanopore processing scripts · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} This repository was archived by the owner on Jun 19, 2024. It is now read-only. wdecoster / nanomath Public archive Notifications You must be signed in to change notification settings Fork 3 Star 9 Code Issues 1 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights wdecoster/nanomath master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 115 Commits 115 Commits nanomath nanomath .gitignore .gitignore .travis.yml .travis.yml LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README GPL-3.0 license nanomath - DEPRECATED AS OF 2024-06-20, THIS REPOSITORY IS DEPRECATED. ITS CODE IS INTEGRATED INTO NANOPLOT. This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data FUNCTIONS Calculate read N50 from a set of lengths get_N50(readlenghts) Remove extreme length outliers from a dataset remove_length_outliers(dataframe, columname) Calculate the average Phred quality of a read ave_qual(qualscores) Write out the statistics report after calling readstats function write_stats(dataframe, outputname) Compute a number of statistics, return a dictionary calc_read_stats(dataframe) As of v1.3.0 , nanomath calculates the average quality differently, by first converting per-read phred scale averages to error rates, take the average, and converting back ( nanostat#40 ) INSTALLATION pip install nanomath or conda install -c bioconda nanomath CONTRIBUTORS @alexomics for fixing the indentation of the printed stats CITATION If you use this tool, please consider citing our publication . About A few simple math function for other Oxford Nanopore processing scripts Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 9 stars Watchers 1 watching Forks 3 forks Report repository Releases 2 Version with stats enabling --tsv Latest Sep 1, 2020 + 1 release Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge nanomath --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +nanomath 0.12.5 py35_0 +---------------------- +file name : nanomath-0.12.5-py35_0.tar.bz2 +name : nanomath +version : 0.12.5 +build : py35_0 +build number: 0 +size : 8 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.12.5-py35_0.tar.bz2 +md5 : f5a3c23d1be2d4f1e84a490551ba0890 +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.5* + + +nanomath 0.12.5 py36_0 +---------------------- +file name : nanomath-0.12.5-py36_0.tar.bz2 +name : nanomath +version : 0.12.5 +build : py36_0 +build number: 0 +size : 8 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.12.5-py36_0.tar.bz2 +md5 : 74ec2ecce9164553f4f012db6a5a6f44 +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.6* + + +nanomath 0.14.2 py35_0 +---------------------- +file name : nanomath-0.14.2-py35_0.tar.bz2 +name : nanomath +version : 0.14.2 +build : py35_0 +build number: 0 +size : 9 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.14.2-py35_0.tar.bz2 +md5 : a64fba450006103e4af3f5ca34e8c81c +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.5* + + +nanomath 0.14.2 py36_0 +---------------------- +file name : nanomath-0.14.2-py36_0.tar.bz2 +name : nanomath +version : 0.14.2 +build : py36_0 +build number: 0 +size : 9 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.14.2-py36_0.tar.bz2 +md5 : 9dd1810320967c13c4d4d7abe9411411 +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.6* + + +nanomath 0.16.2 py35_0 +---------------------- +file name : nanomath-0.16.2-py35_0.tar.bz2 +name : nanomath +version : 0.16.2 +build : py35_0 +build number: 0 +size : 9 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.16.2-py35_0.tar.bz2 +md5 : 0ac41bed9fedab87d9958434d77904a5 +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.5* + + +nanomath 0.16.2 py36_0 +---------------------- +file name : nanomath-0.16.2-py36_0.tar.bz2 +name : nanomath +version : 0.16.2 +build : py36_0 +build number: 0 +size : 9 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.16.2-py36_0.tar.bz2 +md5 : fa623a0e46dd3651503c9978fcb60e41 +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.6* + + +nanomath 0.18.1 py35_0 +---------------------- +file name : nanomath-0.18.1-py35_0.tar.bz2 +name : nanomath +version : 0.18.1 +build : py35_0 +build number: 0 +size : 10 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.18.1-py35_0.tar.bz2 +md5 : 59da168e3634d8bbfad764686a0145d8 +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.5* + + +nanomath 0.18.1 py36_0 +---------------------- +file name : nanomath-0.18.1-py36_0.tar.bz2 +name : nanomath +version : 0.18.1 +build : py36_0 +build number: 0 +size : 10 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.18.1-py36_0.tar.bz2 +md5 : 21eda2a93ffec71f400198afe80d7f55 +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.6* + + +nanomath 0.20.0 py35_0 +---------------------- +file name : nanomath-0.20.0-py35_0.tar.bz2 +name : nanomath +version : 0.20.0 +build : py35_0 +build number: 0 +size : 10 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.20.0-py35_0.tar.bz2 +md5 : 9f7db92f7df6576d01048d5431d4a2fd +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.5* + + +nanomath 0.20.0 py36_0 +---------------------- +file name : nanomath-0.20.0-py36_0.tar.bz2 +name : nanomath +version : 0.20.0 +build : py36_0 +build number: 0 +size : 10 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.20.0-py36_0.tar.bz2 +md5 : c79eedf19560d64fde984f5da7c8a7ae +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.6* + + +nanomath 0.21.0 py35_0 +---------------------- +file name : nanomath-0.21.0-py35_0.tar.bz2 +name : nanomath +version : 0.21.0 +build : py35_0 +build number: 0 +size : 10 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.21.0-py35_0.tar.bz2 +md5 : 1abefcceb2596196f6a169cce8600da9 +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.5* + + +nanomath 0.21.0 py35_2 +---------------------- +file name : nanomath-0.21.0-py35_2.tar.bz2 +name : nanomath +version : 0.21.0 +build : py35_2 +build number: 2 +size : 10 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.21.0-py35_2.tar.bz2 +md5 : d7b00bd10b53d8eb192a7f6dacefba6b +timestamp : 2018-07-05 23:39:44 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3.5,<3.6.0a0 + + +nanomath 0.21.0 py36_0 +---------------------- +file name : nanomath-0.21.0-py36_0.tar.bz2 +name : nanomath +version : 0.21.0 +build : py36_0 +build number: 0 +size : 10 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.21.0-py36_0.tar.bz2 +md5 : f3b0dee51ca70f19f0509c23c129e05d +dependencies: + - libgcc + - numpy >1.8 + - pandas + - python 3.6* + + +nanomath 0.21.0 py36_2 +---------------------- +file name : nanomath-0.21.0-py36_2.tar.bz2 +name : nanomath +version : 0.21.0 +build : py36_2 +build number: 2 +size : 10 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.21.0-py36_2.tar.bz2 +md5 : 2e52b455022865b5769b64db78b813df +timestamp : 2018-07-05 23:40:45 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3.6,<3.7.0a0 + + +nanomath 0.22.0 py35_0 +---------------------- +file name : nanomath-0.22.0-py35_0.tar.bz2 +name : nanomath +version : 0.22.0 +build : py35_0 +build number: 0 +size : 11 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.22.0-py35_0.tar.bz2 +md5 : e3a4c91d5c50f3419569e8aaf5e5eb88 +timestamp : 2018-11-19 01:38:26 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3.5,<3.6.0a0 + + +nanomath 0.22.0 py36_0 +---------------------- +file name : nanomath-0.22.0-py36_0.tar.bz2 +name : nanomath +version : 0.22.0 +build : py36_0 +build number: 0 +size : 11 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.22.0-py36_0.tar.bz2 +md5 : 9a7cd631bffd008ca9a1eb989a9226b1 +timestamp : 2018-11-19 01:36:49 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3.6,<3.7.0a0 + + +nanomath 0.22.0 py36_1 +---------------------- +file name : nanomath-0.22.0-py36_1.tar.bz2 +name : nanomath +version : 0.22.0 +build : py36_1 +build number: 1 +size : 12 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.22.0-py36_1.tar.bz2 +md5 : be03bb7f6adcb773f29983ec9c523d32 +timestamp : 2019-03-09 14:26:50 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3.6,<3.7.0a0 + + +nanomath 0.22.0 py37_1 +---------------------- +file name : nanomath-0.22.0-py37_1.tar.bz2 +name : nanomath +version : 0.22.0 +build : py37_1 +build number: 1 +size : 12 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.22.0-py37_1.tar.bz2 +md5 : 5c81efa139d97973680925416014580c +timestamp : 2019-03-09 14:25:27 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3.7,<3.8.0a0 + + +nanomath 0.23.1 py36_0 +---------------------- +file name : nanomath-0.23.1-py36_0.tar.bz2 +name : nanomath +version : 0.23.1 +build : py36_0 +build number: 0 +size : 12 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.23.1-py36_0.tar.bz2 +md5 : de4ecd611bae1287078ede6fc8bf1483 +timestamp : 2019-04-24 03:12:51 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3.6,<3.7.0a0 + + +nanomath 0.23.1 py37_0 +---------------------- +file name : nanomath-0.23.1-py37_0.tar.bz2 +name : nanomath +version : 0.23.1 +build : py37_0 +build number: 0 +size : 12 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanomath-0.23.1-py37_0.tar.bz2 +md5 : 8c18b71e8193c03336ef338d54e2ae53 +timestamp : 2019-04-24 03:11:21 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3.7,<3.8.0a0 + + +nanomath 0.23.1 py_1 +-------------------- +file name : nanomath-0.23.1-py_1.tar.bz2 +name : nanomath +version : 0.23.1 +build : py_1 +build number: 1 +size : 9 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nanomath-0.23.1-py_1.tar.bz2 +md5 : 5d02835c98d93307f959593dd74c6b91 +timestamp : 2019-10-26 22:49:30 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3 + + +nanomath 0.23.2 py_0 +-------------------- +file name : nanomath-0.23.2-py_0.tar.bz2 +name : nanomath +version : 0.23.2 +build : py_0 +build number: 0 +size : 24 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nanomath-0.23.2-py_0.tar.bz2 +md5 : 2212d5824a33ac6ded19415c47b19ab6 +timestamp : 2020-04-25 09:14:26 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3 + + +nanomath 0.23.3 py_0 +-------------------- +file name : nanomath-0.23.3-py_0.tar.bz2 +name : nanomath +version : 0.23.3 +build : py_0 +build number: 0 +size : 24 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nanomath-0.23.3-py_0.tar.bz2 +md5 : 85c2d24e0851344df0db3b08c598090b +timestamp : 2020-06-17 11:43:24 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3 + + +nanomath 1.0.0 py_0 +------------------- +file name : nanomath-1.0.0-py_0.tar.bz2 +name : nanomath +version : 1.0.0 +build : py_0 +build number: 0 +size : 25 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nanomath-1.0.0-py_0.tar.bz2 +md5 : 2d0eb054a9600448f08135b5e19ed573 +timestamp : 2020-08-19 08:25:25 UTC +dependencies: + - numpy >1.8 + - pandas + - python >=3 + + +nanomath 1.2.0 py_0 +------------------- +file name : nanomath-1.2.0-py_0.tar.bz2 +name : nanomath +version : 1.2.0 +build : py_0 +build number: 0 +size : 25 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nanomath-1.2.0-py_0.tar.bz2 +md5 : 9ba962d6826665f4e02facfcd78da463 +timestamp : 2020-12-30 11:23:06 UTC +dependencies: + - deprecated + - numpy >1.8 + - pandas + - python >=3 + + +nanomath 1. diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nanoplot.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nanoplot.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..26100352dc6b1316957378c6307894cbc8c53a52 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nanoplot.manual_bundle.txt @@ -0,0 +1,545 @@ +# Tool: nanoplot +software_name: nanoplot +tier: T1 +domain: t1_backfill_overall +downloads: 225649 +summary: Plotting suite for long read sequencing data and alignments. +description: Plotting suite for long read sequencing data and alignments. +dependencies: biopython, libpng, nanoget >=1.19.1, numpy >=1.16.5, pandas >=1.1.0, plotly >=6.1.1, pyarrow, pysam >0.10.0.0, python >=3, python-dateutil, python-kaleido >=1.0.0, scipy +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/wdecoster/NanoPlot +doc_url: +dev_url: https://github.com/wdecoster/NanoPlot + +## URL Docs Extract +### https://github.com/wdecoster/NanoPlot +GitHub - wdecoster/NanoPlot: Plotting scripts for long read sequencing data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} wdecoster / NanoPlot Public Notifications You must be signed in to change notification settings Fork 52 Star 548 Code Issues 19 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights wdecoster/NanoPlot master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 648 Commits 648 Commits .github/ workflows .github/ workflows examples examples extra extra nanomath nanomath nanoplot nanoplot nanoplotter nanoplotter scripts scripts .DS_Store .DS_Store .gitignore .gitignore .travis.yml .travis.yml CHANGES.md CHANGES.md LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md setup.py setup.py View all files Repository files navigation README MIT license NanoPlot Plotting tool for long read sequencing data and alignments. NanoPlot is also available as a web service . The example plot above shows a bivariate plot comparing log transformed read length with average basecall Phred quality score. More examples can be found in the gallery on my blog 'Gigabase Or Gigabyte'. In addition to various plots also a NanoStats file is created summarizing key features of the dataset. This script performs data extraction from Oxford Nanopore sequencing data in the following formats: fastq files (can be bgzip, bzip2 or gzip compressed) fastq files generated by albacore, guppy or MinKNOW containing additional information (can be bgzip, bzip2 or gzip compressed) sorted bam files sequencing_summary.txt output table generated by albacore, guppy or MinKnow basecalling (can be gzip, bz2, zip and xz compressed) fasta files (can be bgzip, bzip2 or gzip compressed) arrow files (as created by other tools I have developed) Multiple files of the same type can be provided simultaneously INSTALLATION pip install NanoPlot Upgrade to a newer version using: pip install NanoPlot --upgrade or conda install -c bioconda nanoplot The script is written for python3. OUTPUT NanoPlot creates: a statistical summary a number of plots a html summary file USAGE usage: NanoPlot [-h] [-v] [-t THREADS] [--verbose] [--store] [--raw] [--huge] [-o OUTDIR] [--no_static] [-p PREFIX] [--tsv_stats] [--info_in_report] [--maxlength N] [--minlength N] [--drop_outliers] [--downsample N] [--loglength] [--percentqual] [--alength] [--minqual N] [--runtime_until N] [--readtype {1D,2D,1D2}] [--barcoded] [--no_supplementary] [-c COLOR] [-cm COLORMAP] [-f [{png,jpg,jpeg,webp,svg,pdf,eps,json} ...]] [--plots [{kde,hex,dot} ...]] [--legacy [{kde,dot,hex} ...]] [--listcolors] [--listcolormaps] [--no-N50] [--N50] [--title TITLE] [--font_scale FONT_SCALE] [--dpi DPI] [--hide_stats] (--fastq file [file ...] | --fasta file [file ...] | --fastq_rich file [file ...] | --fastq_minimal file [file ...] | --summary file [file ...] | --bam file [file ...] | --ubam file [file ...] | --cram file [file ...] | --pickle pickle | --feather file [file ...]) CREATES VARIOUS PLOTS FOR LONG READ SEQUENCING DATA. General options: -h, --help show the help and exit -v, --version Print version and exit. -t, --threads THREADS Set the allowed number of threads to be used by the script --verbose Write log messages also to terminal. --store Store the extracted data in a pickle file for future plotting. --raw Store the extracted data in tab separated file. --huge Input data is one very large file. -o, --outdir OUTDIR Specify directory in which output has to be created. --no_static Do not make static (png) plots. -p, --prefix PREFIX Specify an optional prefix to be used for the output files. --tsv_stats Output the stats file as a properly formatted TSV. --info_in_report Add NanoPlot run info in the report. Options for filtering or transforming input prior to plotting: --maxlength N Hide reads longer than length specified. --minlength N Hide reads shorter than length specified. --drop_outliers Drop outlier reads with extreme long length. --downsample N Reduce dataset to N reads by random sampling. --loglength Additionally show logarithmic scaling of lengths in plots. --percentqual Use qualities as theoretical percent identities. --alength Use aligned read lengths rather than sequenced length (bam mode) --minqual N Drop reads with an average quality lower than specified. --runtime_until N Only take the N first hours of a run --readtype {1D,2D,1D2} Which read type to extract information about from summary. Options are 1D, 2D, 1D2 --barcoded Use if you want to split the summary file by barcode --no_supplementary Use if you want to remove supplementary alignments Options for customizing the plots created: -c, --color COLOR Specify a valid matplotlib color for the plots -cm, --colormap COLORMAP Specify a valid matplotlib colormap for the heatmap -f, --format [{png,jpg,jpeg,webp,svg,pdf,eps,json} ...] Specify the output format of the plots, which are in addition to the html files --plots [{kde,hex,dot} ...] Specify which bivariate plots have to be made. --legacy [{kde,dot,hex} ...] Specify which bivariate plots have to be made (legacy mode). --listcolors List the colors which are available for plotting and exit. --listcolormaps List the colors which are available for plotting and exit. --no-N50 Hide the N50 mark in the read length histogram --N50 Show the N50 mark in the read length histogram --title TITLE Add a title to all plots, requires quoting if using spaces --font_scale FONT_SCALE Scale the font of the plots by a factor --dpi DPI Set the dpi for saving images --hide_stats Not adding Pearson R stats in some bivariate plots Input data sources, one of these is required.: --fastq file [file ...] Data is in one or more default fastq file(s). --fasta file [file ...] Data is in one or more fasta file(s). --fastq_rich file [file ...] Data is in one or more fastq file(s) generated by albacore, MinKNOW or guppy with additional information concerning channel and time. --fastq_minimal file [file ...] Data is in one or more fastq file(s) generated by albacore, MinKNOW or guppy with additional information concerning channel and time. Is extracted swiftly without elaborate checks. --summary file [file ...] Data is in one or more summary file(s) generated by albacore or guppy. --bam file [file ...] Data is in one or more sorted bam file(s). --ubam file [file ...] Data is in one or more unmapped bam file(s). --cram file [file ...] Data is in one or more sorted cram file(s). --pickle pickle Data is a pickle file stored earlier. --feather/--arrow file [file ...] Data is in one or more feather/arrow file(s). EXAMPLES: NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots hex dot NanoPlot --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000 NOTES --downsample won't save you tons of time, as down sampling is only done after collecting all data and probably would only make a difference for a huge amount of data. If you want to save time you could down sample your data upfront. Note also that extracting information from a summary file is faster than other formats, and that you can extract from multiple files simultaneously (which will happen in parallel then). Some plot types (especially kde) are slower than others and you can take a look at the input for --plots to speed things up (default is to make both kde and dot plot). If you are only interested in say the read length histogram it is possible to write a script to just get you that and avoid wasting time on the rest. Let me know if you need any help here. --plots uses the plotly package to plot kde and dot plots. Hex option will be ignored. --legacy plotting of a hex plot currently is only possible using this option,which uses the seaborn and matplotlib package, since there is no support for it in plotly (yet). Plots like kde and dot are also possible with this option. EXAMPLE USAGE NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots dot --legacy hex NanoPlot -t 12 --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000 -o bamplots_downsampled ACKNOWLEDGMENTS/CONTRIBUTORS Ilias Bukraa for tremendous improvements and maintenance of the code Andreas Sjödin for building and maintaining conda recipes Darrin Schultz @conchoecia for Pauvre code @alexomics for fixing the indentation of the printed stats Botond Sipos @bsipos for speeding up the calculation of average quality scores CONTRIBUTING I welcome all suggestions, bug reports, feature requests and contributions. Please leave an issue or open a pull request. I will usually respond within a day, or rarely within a few days. PLOTS GENERATED Plot Fastq Fastq_rich Fastq_minimal Bam Summary Options Style Histogram of read length x x x x x N50 Histogram of (log transformed) read length x x x x x N50 Bivariate plot of length against base call quality x x x x log transformation dot, hex, kde Heatmap of reads per channel x x Cumulative yield plot x x x Violin plot of read length over time x x x Violin plot of base call quality over time x x Bivariate plot of aligned read length against sequenced read length x dot, hex, kde Bivariate plot of percent reference identity against read length x log transformation dot, hex, kde Bivariate plot of percent reference identity against base call quality x dot, hex, kde Bivariate plot of mapping quality against read length x log transformation dot, hex, kde Bivariate plot of mapping quality against basecall quality x dot, hex, kde COMPANION SCRIPTS NanoComp : comparing multiple runs NanoStat : statistic summary report of reads or alignments NanoFilt : filtering and trimming of reads NanoLyse : removing contaminant reads (e.g. lambda control DNA) from fastq CITATION If you use this tool, please consider citing our publication . Copyright: 2016-2020 Wouter De Coster decosterwouter@gmail.com About Plotting scripts for long read sequencing data nanoplot.bioinf.be Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 548 stars Watchers 9 watching Forks 52 forks Report repository Releases 6 v1.46.2 Latest Dec 4, 2025 + 5 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages HTML 95.1% Python 4.8% Shell 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/wdecoster/NanoPlot +GitHub - wdecoster/NanoPlot: Plotting scripts for long read sequencing data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} wdecoster / NanoPlot Public Notifications You must be signed in to change notification settings Fork 52 Star 548 Code Issues 19 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights wdecoster/NanoPlot master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 648 Commits 648 Commits .github/ workflows .github/ workflows examples examples extra extra nanomath nanomath nanoplot nanoplot nanoplotter nanoplotter scripts scripts .DS_Store .DS_Store .gitignore .gitignore .travis.yml .travis.yml CHANGES.md CHANGES.md LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md setup.py setup.py View all files Repository files navigation README MIT license NanoPlot Plotting tool for long read sequencing data and alignments. NanoPlot is also available as a web service . The example plot above shows a bivariate plot comparing log transformed read length with average basecall Phred quality score. More examples can be found in the gallery on my blog 'Gigabase Or Gigabyte'. In addition to various plots also a NanoStats file is created summarizing key features of the dataset. This script performs data extraction from Oxford Nanopore sequencing data in the following formats: fastq files (can be bgzip, bzip2 or gzip compressed) fastq files generated by albacore, guppy or MinKNOW containing additional information (can be bgzip, bzip2 or gzip compressed) sorted bam files sequencing_summary.txt output table generated by albacore, guppy or MinKnow basecalling (can be gzip, bz2, zip and xz compressed) fasta files (can be bgzip, bzip2 or gzip compressed) arrow files (as created by other tools I have developed) Multiple files of the same type can be provided simultaneously INSTALLATION pip install NanoPlot Upgrade to a newer version using: pip install NanoPlot --upgrade or conda install -c bioconda nanoplot The script is written for python3. OUTPUT NanoPlot creates: a statistical summary a number of plots a html summary file USAGE usage: NanoPlot [-h] [-v] [-t THREADS] [--verbose] [--store] [--raw] [--huge] [-o OUTDIR] [--no_static] [-p PREFIX] [--tsv_stats] [--info_in_report] [--maxlength N] [--minlength N] [--drop_outliers] [--downsample N] [--loglength] [--percentqual] [--alength] [--minqual N] [--runtime_until N] [--readtype {1D,2D,1D2}] [--barcoded] [--no_supplementary] [-c COLOR] [-cm COLORMAP] [-f [{png,jpg,jpeg,webp,svg,pdf,eps,json} ...]] [--plots [{kde,hex,dot} ...]] [--legacy [{kde,dot,hex} ...]] [--listcolors] [--listcolormaps] [--no-N50] [--N50] [--title TITLE] [--font_scale FONT_SCALE] [--dpi DPI] [--hide_stats] (--fastq file [file ...] | --fasta file [file ...] | --fastq_rich file [file ...] | --fastq_minimal file [file ...] | --summary file [file ...] | --bam file [file ...] | --ubam file [file ...] | --cram file [file ...] | --pickle pickle | --feather file [file ...]) CREATES VARIOUS PLOTS FOR LONG READ SEQUENCING DATA. General options: -h, --help show the help and exit -v, --version Print version and exit. -t, --threads THREADS Set the allowed number of threads to be used by the script --verbose Write log messages also to terminal. --store Store the extracted data in a pickle file for future plotting. --raw Store the extracted data in tab separated file. --huge Input data is one very large file. -o, --outdir OUTDIR Specify directory in which output has to be created. --no_static Do not make static (png) plots. -p, --prefix PREFIX Specify an optional prefix to be used for the output files. --tsv_stats Output the stats file as a properly formatted TSV. --info_in_report Add NanoPlot run info in the report. Options for filtering or transforming input prior to plotting: --maxlength N Hide reads longer than length specified. --minlength N Hide reads shorter than length specified. --drop_outliers Drop outlier reads with extreme long length. --downsample N Reduce dataset to N reads by random sampling. --loglength Additionally show logarithmic scaling of lengths in plots. --percentqual Use qualities as theoretical percent identities. --alength Use aligned read lengths rather than sequenced length (bam mode) --minqual N Drop reads with an average quality lower than specified. --runtime_until N Only take the N first hours of a run --readtype {1D,2D,1D2} Which read type to extract information about from summary. Options are 1D, 2D, 1D2 --barcoded Use if you want to split the summary file by barcode --no_supplementary Use if you want to remove supplementary alignments Options for customizing the plots created: -c, --color COLOR Specify a valid matplotlib color for the plots -cm, --colormap COLORMAP Specify a valid matplotlib colormap for the heatmap -f, --format [{png,jpg,jpeg,webp,svg,pdf,eps,json} ...] Specify the output format of the plots, which are in addition to the html files --plots [{kde,hex,dot} ...] Specify which bivariate plots have to be made. --legacy [{kde,dot,hex} ...] Specify which bivariate plots have to be made (legacy mode). --listcolors List the colors which are available for plotting and exit. --listcolormaps List the colors which are available for plotting and exit. --no-N50 Hide the N50 mark in the read length histogram --N50 Show the N50 mark in the read length histogram --title TITLE Add a title to all plots, requires quoting if using spaces --font_scale FONT_SCALE Scale the font of the plots by a factor --dpi DPI Set the dpi for saving images --hide_stats Not adding Pearson R stats in some bivariate plots Input data sources, one of these is required.: --fastq file [file ...] Data is in one or more default fastq file(s). --fasta file [file ...] Data is in one or more fasta file(s). --fastq_rich file [file ...] Data is in one or more fastq file(s) generated by albacore, MinKNOW or guppy with additional information concerning channel and time. --fastq_minimal file [file ...] Data is in one or more fastq file(s) generated by albacore, MinKNOW or guppy with additional information concerning channel and time. Is extracted swiftly without elaborate checks. --summary file [file ...] Data is in one or more summary file(s) generated by albacore or guppy. --bam file [file ...] Data is in one or more sorted bam file(s). --ubam file [file ...] Data is in one or more unmapped bam file(s). --cram file [file ...] Data is in one or more sorted cram file(s). --pickle pickle Data is a pickle file stored earlier. --feather/--arrow file [file ...] Data is in one or more feather/arrow file(s). EXAMPLES: NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots hex dot NanoPlot --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000 NOTES --downsample won't save you tons of time, as down sampling is only done after collecting all data and probably would only make a difference for a huge amount of data. If you want to save time you could down sample your data upfront. Note also that extracting information from a summary file is faster than other formats, and that you can extract from multiple files simultaneously (which will happen in parallel then). Some plot types (especially kde) are slower than others and you can take a look at the input for --plots to speed things up (default is to make both kde and dot plot). If you are only interested in say the read length histogram it is possible to write a script to just get you that and avoid wasting time on the rest. Let me know if you need any help here. --plots uses the plotly package to plot kde and dot plots. Hex option will be ignored. --legacy plotting of a hex plot currently is only possible using this option,which uses the seaborn and matplotlib package, since there is no support for it in plotly (yet). Plots like kde and dot are also possible with this option. EXAMPLE USAGE NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots dot --legacy hex NanoPlot -t 12 --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000 -o bamplots_downsampled ACKNOWLEDGMENTS/CONTRIBUTORS Ilias Bukraa for tremendous improvements and maintenance of the code Andreas Sjödin for building and maintaining conda recipes Darrin Schultz @conchoecia for Pauvre code @alexomics for fixing the indentation of the printed stats Botond Sipos @bsipos for speeding up the calculation of average quality scores CONTRIBUTING I welcome all suggestions, bug reports, feature requests and contributions. Please leave an issue or open a pull request. I will usually respond within a day, or rarely within a few days. PLOTS GENERATED Plot Fastq Fastq_rich Fastq_minimal Bam Summary Options Style Histogram of read length x x x x x N50 Histogram of (log transformed) read length x x x x x N50 Bivariate plot of length against base call quality x x x x log transformation dot, hex, kde Heatmap of reads per channel x x Cumulative yield plot x x x Violin plot of read length over time x x x Violin plot of base call quality over time x x Bivariate plot of aligned read length against sequenced read length x dot, hex, kde Bivariate plot of percent reference identity against read length x log transformation dot, hex, kde Bivariate plot of percent reference identity against base call quality x dot, hex, kde Bivariate plot of mapping quality against read length x log transformation dot, hex, kde Bivariate plot of mapping quality against basecall quality x dot, hex, kde COMPANION SCRIPTS NanoComp : comparing multiple runs NanoStat : statistic summary report of reads or alignments NanoFilt : filtering and trimming of reads NanoLyse : removing contaminant reads (e.g. lambda control DNA) from fastq CITATION If you use this tool, please consider citing our publication . Copyright: 2016-2020 Wouter De Coster decosterwouter@gmail.com About Plotting scripts for long read sequencing data nanoplot.bioinf.be Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 548 stars Watchers 9 watching Forks 52 forks Report repository Releases 6 v1.46.2 Latest Dec 4, 2025 + 5 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages HTML 95.1% Python 4.8% Shell 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge nanoplot --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +nanoplot 0.16.2 py35_0 +---------------------- +file name : nanoplot-0.16.2-py35_0.tar.bz2 +name : nanoplot +version : 0.16.2 +build : py35_0 +build number: 0 +size : 14 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-0.16.2-py35_0.tar.bz2 +md5 : 28c6c3327c1361b71e7a7be6ee88d878 +dependencies: + - biopython + - matplotlib + - nanoget >=0.11.0 + - nanomath >=0.12.0 + - nanoplotter >=0.13.1 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.5* + - python-dateutil + - scipy + - seaborn + + +nanoplot 0.16.2 py36_0 +---------------------- +file name : nanoplot-0.16.2-py36_0.tar.bz2 +name : nanoplot +version : 0.16.2 +build : py36_0 +build number: 0 +size : 14 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-0.16.2-py36_0.tar.bz2 +md5 : c0ff2fa0b1ef84027af0c688cbc3b097 +dependencies: + - biopython + - matplotlib + - nanoget >=0.11.0 + - nanomath >=0.12.0 + - nanoplotter >=0.13.1 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.6* + - python-dateutil + - scipy + - seaborn + + +nanoplot 0.16.4 py35_0 +---------------------- +file name : nanoplot-0.16.4-py35_0.tar.bz2 +name : nanoplot +version : 0.16.4 +build : py35_0 +build number: 0 +size : 14 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-0.16.4-py35_0.tar.bz2 +md5 : 7d5891e089502312052a815dc42ccb5c +dependencies: + - biopython + - matplotlib + - nanoget >=0.11.0 + - nanomath >=0.12.0 + - nanoplotter >=0.13.1 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.5* + - python-dateutil + - scipy + - seaborn + + +nanoplot 0.16.4 py36_0 +---------------------- +file name : nanoplot-0.16.4-py36_0.tar.bz2 +name : nanoplot +version : 0.16.4 +build : py36_0 +build number: 0 +size : 14 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-0.16.4-py36_0.tar.bz2 +md5 : c7b96e75d61cfa54b6f672938df06a4a +dependencies: + - biopython + - matplotlib + - nanoget >=0.11.0 + - nanomath >=0.12.0 + - nanoplotter >=0.13.1 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.6* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.0.0 py35_0 +--------------------- +file name : nanoplot-1.0.0-py35_0.tar.bz2 +name : nanoplot +version : 1.0.0 +build : py35_0 +build number: 0 +size : 21 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.0.0-py35_0.tar.bz2 +md5 : f5e15b00fad8237aa6b3a47e79dd153f +dependencies: + - biopython + - matplotlib + - nanoget >=0.19.3 + - nanomath >=0.14.2 + - nanoplotter >=0.22.0 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.5* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.0.0 py36_0 +--------------------- +file name : nanoplot-1.0.0-py36_0.tar.bz2 +name : nanoplot +version : 1.0.0 +build : py36_0 +build number: 0 +size : 21 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.0.0-py36_0.tar.bz2 +md5 : 6caae603d30a9ce52c5d93602e9bb850 +dependencies: + - biopython + - matplotlib + - nanoget >=0.19.3 + - nanomath >=0.14.2 + - nanoplotter >=0.22.0 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.6* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.1.0 py35_0 +--------------------- +file name : nanoplot-1.1.0-py35_0.tar.bz2 +name : nanoplot +version : 1.1.0 +build : py35_0 +build number: 0 +size : 21 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.1.0-py35_0.tar.bz2 +md5 : 566a5eeacd5175700907b80113168e85 +dependencies: + - biopython + - matplotlib + - nanoget >=0.19.3 + - nanomath >=0.14.2 + - nanoplotter >=0.22.0 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.5* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.1.0 py36_0 +--------------------- +file name : nanoplot-1.1.0-py36_0.tar.bz2 +name : nanoplot +version : 1.1.0 +build : py36_0 +build number: 0 +size : 21 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.1.0-py36_0.tar.bz2 +md5 : 59983051514a3acb48e1fd719a0724f6 +dependencies: + - biopython + - matplotlib + - nanoget >=0.19.3 + - nanomath >=0.14.2 + - nanoplotter >=0.22.0 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.6* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.2.2 py35_0 +--------------------- +file name : nanoplot-1.2.2-py35_0.tar.bz2 +name : nanoplot +version : 1.2.2 +build : py35_0 +build number: 0 +size : 21 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.2.2-py35_0.tar.bz2 +md5 : f4141a0517f692834559f0a3384c59df +dependencies: + - biopython + - matplotlib + - nanoget >=0.19.3 + - nanomath >=0.14.2 + - nanoplotter >=0.22.0 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.5* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.2.2 py36_0 +--------------------- +file name : nanoplot-1.2.2-py36_0.tar.bz2 +name : nanoplot +version : 1.2.2 +build : py36_0 +build number: 0 +size : 21 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.2.2-py36_0.tar.bz2 +md5 : 2b51b735dec3454ee632310376446889 +dependencies: + - biopython + - matplotlib + - nanoget >=0.19.3 + - nanomath >=0.14.2 + - nanoplotter >=0.22.0 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.6* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.8.1 py35_0 +--------------------- +file name : nanoplot-1.8.1-py35_0.tar.bz2 +name : nanoplot +version : 1.8.1 +build : py35_0 +build number: 0 +size : 21 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.8.1-py35_0.tar.bz2 +md5 : 1d399808161083d260461b9f448d7382 +dependencies: + - biopython + - nanoget >=1.2.0 + - nanomath >=0.14.2 + - nanoplotter >=0.25.0 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.5* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.8.1 py36_0 +--------------------- +file name : nanoplot-1.8.1-py36_0.tar.bz2 +name : nanoplot +version : 1.8.1 +build : py36_0 +build number: 0 +size : 22 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.8.1-py36_0.tar.bz2 +md5 : 55bd1bb9969a1bc31bd53b0a6064f1e4 +dependencies: + - biopython + - nanoget >=1.2.0 + - nanomath >=0.14.2 + - nanoplotter >=0.25.0 + - numpy + - pandas + - pysam >0.10.0.0 + - python 3.6* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.10.4 py35_0 +---------------------- +file name : nanoplot-1.10.4-py35_0.tar.bz2 +name : nanoplot +version : 1.10.4 +build : py35_0 +build number: 0 +size : 22 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.10.4-py35_0.tar.bz2 +md5 : 33cb31884a7f19529e56c4e7ca1d6def +dependencies: + - biopython + - nanoget >=1.4.0 + - nanomath >=0.18.1 + - nanoplotter >=0.35.1 + - numpy + - pandas >=0.22.0 + - pysam >0.10.0.0 + - python 3.5* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.10.4 py36_0 +---------------------- +file name : nanoplot-1.10.4-py36_0.tar.bz2 +name : nanoplot +version : 1.10.4 +build : py36_0 +build number: 0 +size : 22 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.10.4-py36_0.tar.bz2 +md5 : b18ed2ceefea2391b82b537baf21a411 +dependencies: + - biopython + - nanoget >=1.4.0 + - nanomath >=0.18.1 + - nanoplotter >=0.35.1 + - numpy + - pandas >=0.22.0 + - pysam >0.10.0.0 + - python 3.6* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.11.0 py35_0 +---------------------- +file name : nanoplot-1.11.0-py35_0.tar.bz2 +name : nanoplot +version : 1.11.0 +build : py35_0 +build number: 0 +size : 23 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.11.0-py35_0.tar.bz2 +md5 : 7cc9f0bc4fce81853dae6f54442dbf19 +dependencies: + - biopython + - nanoget >=1.4.0 + - nanomath >=0.19.1 + - nanoplotter >=0.35.1 + - numpy + - pandas >=0.22.0 + - pysam >0.10.0.0 + - python 3.5* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.11.0 py36_0 +---------------------- +file name : nanoplot-1.11.0-py36_0.tar.bz2 +name : nanoplot +version : 1.11.0 +build : py36_0 +build number: 0 +size : 23 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.11.0-py36_0.tar.bz2 +md5 : 1fc3d404b783de042e6c4795fe0e8aa0 +dependencies: + - biopython + - nanoget >=1.4.0 + - nanomath >=0.19.1 + - nanoplotter >=0.35.1 + - numpy + - pandas >=0.22.0 + - pysam >0.10.0.0 + - python 3.6* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.13.0 py35_0 +---------------------- +file name : nanoplot-1.13.0-py35_0.tar.bz2 +name : nanoplot +version : 1.13.0 +build : py35_0 +build number: 0 +size : 22 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.13.0-py35_0.tar.bz2 +md5 : 99a1aca5714132c1609f3712e8b1cab5 +dependencies: + - biopython + - nanoget >=1.4.0 + - nanomath >=0.21.0 + - nanoplotter >=0.38.0 + - numpy + - pandas >=0.22.0 + - pysam >0.10.0.0 + - python 3.5* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.13.0 py35_1 +---------------------- +file name : nanoplot-1.13.0-py35_1.tar.bz2 +name : nanoplot +version : 1.13.0 +build : py35_1 +build number: 1 +size : 22 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.13.0-py35_1.tar.bz2 +md5 : cdd0eb40d4699967cb35e9c7f4bcc6a3 +timestamp : 2018-07-08 10:47:25 UTC +dependencies: + - biopython + - nanoget >=1.4.0 + - nanomath >=0.21.0 + - nanoplotter >=0.38.0 + - numpy + - pandas >=0.22.0 + - pysam >0.10.0.0 + - python >=3.5,<3.6.0a0 + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.13.0 py36_0 +---------------------- +file name : nanoplot-1.13.0-py36_0.tar.bz2 +name : nanoplot +version : 1.13.0 +build : py36_0 +build number: 0 +size : 22 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.13.0-py36_0.tar.bz2 +md5 : 8ec2b5fa43d9fdc2bec51e96163fc2ae +dependencies: + - biopython + - nanoget >=1.4.0 + - nanomath >=0.21.0 + - nanoplotter >=0.38.0 + - numpy + - pandas >=0.22.0 + - pysam >0.10.0.0 + - python 3.6* + - python-dateutil + - scipy + - seaborn + + +nanoplot 1.13.0 py36_1 +---------------------- +file name : nanoplot-1.13.0-py36_1.tar.bz2 +name : nanoplot +version : 1.13.0 +build : py36_1 +build number: 1 +size : 22 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nanoplot-1.13.0-py36_1.tar.bz2 +md5 : 99f6205b4496f3a1c401a1a5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ncbi-datasets-pylib.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ncbi-datasets-pylib.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e94b4a4fbab7115aabb6434b257b145c63868631 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ncbi-datasets-pylib.manual_bundle.txt @@ -0,0 +1,450 @@ +# Tool: ncbi-datasets-pylib +software_name: ncbi-datasets-pylib +tier: T1 +domain: t1_backfill_overall +downloads: 125426 +summary: Easily gather data from across NCBI databases +description: Easily gather data from across NCBI databases +dependencies: gffutils 0.10.*, jinja2 3.1.*, jsonlines 3.0.*, protobuf 3.20.*, python >=3.8, python-dateutil 2.8.*, urllib3 1.26.* +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://www.ncbi.nlm.nih.gov/datasets +doc_url: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/ +dev_url: https://github.com/ncbi/datasets + +## URL Docs Extract +### https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/ +/datasets/docs/v2/command-line-tools/download-and-install/ + +### https://www.ncbi.nlm.nih.gov/datasets +Datasets - NCBI - NLM Skip to main page content An official website of the United States government Here's how you know The .gov means it’s official. Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site. The site is secure. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely. Log in Show account info Close Account Logged in as: username Dashboard Publications Account settings Log out Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation NCBI Datasets A one-stop shop for finding, browsing, and downloading genomic sequences, annotations, and metadata Examples: NIH Comparative Genomics Resource (CGR) This resource is part of the NIH Comparative Genomics Resource (CGR) Toolkit About CGR Data resources Analysis tools Data quality tools Follow NCBI Twitter Facebook LinkedIn GitHub Connect with NLM Twitter SM-Facebook SM-Youtube National Library of Medicine 8600 Rockville Pike Bethesda, MD 20894 Web Policies FOIA HHS Vulnerability Disclosure Help Accessibility Careers NLM NIH HHS USA.gov + +### https://github.com/ncbi/datasets +GitHub - ncbi/datasets: NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} ncbi / datasets Public Notifications You must be signed in to change notification settings Fork 61 Star 529 Code Issues 21 Pull requests 2 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights ncbi/datasets master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 692 Commits 692 Commits .github/ ISSUE_TEMPLATE .github/ ISSUE_TEMPLATE client client training training CONTRIBUTING.md CONTRIBUTING.md LICENSE.md LICENSE.md README.md README.md datasets.openapi.yaml datasets.openapi.yaml View all files Repository files navigation README Contributing License NCBI Datasets NCBI Datasets is a resource that lets you easily gather data from across NCBI databases. You can use it to find and download sequence, annotation, and metadata for genes and genomes using our command-line interface (CLI) tools or NCBI Datasets web interface. NCBI Datasets tools are under active development. To submit feedback, please create a GitHub issue or contact NCBI directly with your questions, comments or feature requests. Install the NCBI Datasets command-line tools Install the latest version (CLI v16.x) of the NCBI Datasets CLI tools, datasets and dataformat , using conda: conda install -c conda-forge ncbi-datasets-cli For other installation options, see our CLI tools download and install instructions. Use the NCBI Datasets command-line tools Use datasets to download biological sequence data across all domains of life from NCBI. Use dataformat to convert metadata included as part of the data package from JSON Lines format to other formats. Examples: Use datasets to download a genome data package for the human reference genome GRCh38: datasets download genome taxon human --reference --filename human-reference.zip Use dataformat to extract selected fields of metadata from the downloaded data package for the human reference genome, GRCh38: dataformat tsv genome --package human-reference.zip --fields organism-name,assminfo-name,accession,assminfo-submitter Organism name Assembly Name Assembly Accession Assembly Submitter Homo sapiens GRCh38.p14 GCF_000001405.40 Genome Reference Consortium The Datasets CLI schematic below also outlines the available commands for the datasets CLI. Download large numbers of genomes Download large numbers of genomes by first downloading a dehydrated zip archive and then accessing the data in three steps. Download the dehydrated zip archive Unzip the downloaded zip archive Rehydrate to access the data Try this example for the human reference genome: Download the dehydrated zip archive: datasets download genome accession GCF_000001405.40 --dehydrated --filename human_GRCh38_dataset.zip Unzip the downloaded zip archive: unzip human_GRCh38_dataset.zip -d my_human_dataset Rehydrate to access the data: datasets rehydrate --directory my_human_dataset/ For more information, see how to download large genome data packages . Use your API key with the NCBI Datasets command-line tools NCBI Datasets API and command-line tool requests are rate-limited. By default, this rate limit is set at 5 requests per second (rps). By using your API key, you can increase this rate limit to 10 rps. For more information, see our documentation on how to get an API key and how to use your API key. NCBI Datasets data packages NCBI Datasets provides sequence, annotation, metadata and other biological data as NCBI Datasets Data Package zip archives . We currently offer four types of data package: An NCBI Datasets Gene Data Package An NCBI Datasets Genome Data Package A specialized NCBI Datasets Virus Data Package . An NCBI Datasets Taxonomy Data Package NCBI Datasets data reports NCBI Datasets data packages include data report files that contain metadata about the requested records. Data report schemas describe each type of data report, including available fields, with descriptions and examples. Citing NCBI Datasets Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets O'Leary NA, Cox E, Holmes JB, Anderson WR, Falk R, Hem V, Tsuchiya MTN, Schuler GD, Zhang X, Torcivia J, Ketter A, Breen L, Cothran J, Bajwa H, Tinne J, Meric PA, Hlavina W, Schneider VA. Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets. Sci Data. 2024 Jul 5;11(1):732. doi: 10.1038/s41597-024-03571-y. PMID: 38969627; PMCID: PMC11226681. About NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. www.ncbi.nlm.nih.gov/datasets Topics ncbi genomics-data Resources Readme License View license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 529 stars Watchers 28 watching Forks 61 forks Report repository Releases 228 v18.25.0 Latest Apr 29, 2026 + 227 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 52.4% Go 40.7% Mustache 5.7% Other 1.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge ncbi-datasets-pylib --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +ncbi-datasets-pylib 14.13.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.13.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.13.0 +build : pyhdfd78af_0 +build number: 0 +size : 233 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.13.0-pyhdfd78af_0.tar.bz2 +md5 : d76ba70038d209bc5a9a80bb705326fa +timestamp : 2023-03-06 19:28:52 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.15.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.15.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.15.0 +build : pyhdfd78af_0 +build number: 0 +size : 233 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.15.0-pyhdfd78af_0.tar.bz2 +md5 : 785e819c6cfed53568c5ef2c81d79a73 +timestamp : 2023-03-09 18:28:04 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.16.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.16.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.16.0 +build : pyhdfd78af_0 +build number: 0 +size : 234 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.16.0-pyhdfd78af_0.tar.bz2 +md5 : b5df9dfc27d51fbde5def91d35eb9ffc +timestamp : 2023-03-13 20:28:12 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.17.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.17.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.17.0 +build : pyhdfd78af_0 +build number: 0 +size : 234 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.17.0-pyhdfd78af_0.tar.bz2 +md5 : 1dc4cf816b973457080ea22d524c69a1 +timestamp : 2023-03-16 15:35:15 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.18.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.18.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.18.0 +build : pyhdfd78af_0 +build number: 0 +size : 236 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.18.0-pyhdfd78af_0.tar.bz2 +md5 : 48885f73902aecff4cffdb4d69b397a7 +timestamp : 2023-03-22 01:55:20 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.19.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.19.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.19.0 +build : pyhdfd78af_0 +build number: 0 +size : 236 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.19.0-pyhdfd78af_0.tar.bz2 +md5 : cfad82c884aa613b7cf0eff3d55caa9d +timestamp : 2023-03-28 22:26:54 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.20.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.20.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.20.0 +build : pyhdfd78af_0 +build number: 0 +size : 237 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.20.0-pyhdfd78af_0.tar.bz2 +md5 : 59905a6c74aa4bda714be18216a2f2d2 +timestamp : 2023-04-04 03:33:33 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.21.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.21.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.21.0 +build : pyhdfd78af_0 +build number: 0 +size : 234 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.21.0-pyhdfd78af_0.tar.bz2 +md5 : d6041d5cda0989e134a7b520cc32fbfb +timestamp : 2023-04-07 20:31:29 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.22.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.22.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.22.0 +build : pyhdfd78af_0 +build number: 0 +size : 237 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.22.0-pyhdfd78af_0.tar.bz2 +md5 : c734eeb5ba8c52467c1e8670a0f14b88 +timestamp : 2023-04-11 08:57:35 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.22.1 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.22.1-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.22.1 +build : pyhdfd78af_0 +build number: 0 +size : 237 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.22.1-pyhdfd78af_0.tar.bz2 +md5 : 72db9578e05239ce1dea0adf75aec8ff +timestamp : 2023-04-13 15:30:37 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.23.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.23.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.23.0 +build : pyhdfd78af_0 +build number: 0 +size : 238 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.23.0-pyhdfd78af_0.tar.bz2 +md5 : fe574fb22b0715ddeee6993642fa1422 +timestamp : 2023-04-20 21:26:01 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.25.1 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.25.1-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.25.1 +build : pyhdfd78af_0 +build number: 0 +size : 234 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.25.1-pyhdfd78af_0.tar.bz2 +md5 : 0c575cacca39aeb1f0fce933373d189a +timestamp : 2023-04-25 22:15:57 UTC +dependencies: + - gffutils 0.10.* + - jinja2 + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil + - urllib3 + + +ncbi-datasets-pylib 14.26.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.26.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.26.0 +build : pyhdfd78af_0 +build number: 0 +size : 234 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.26.0-pyhdfd78af_0.tar.bz2 +md5 : 125087c094fdb4110062f535005caf84 +timestamp : 2023-05-03 18:12:55 UTC +dependencies: + - gffutils 0.10.* + - jinja2 3.1.* + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil 2.8.* + - setuptools >=21.0.0 + - urllib3 1.26.* + + +ncbi-datasets-pylib 14.27.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-14.27.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 14.27.0 +build : pyhdfd78af_0 +build number: 0 +size : 234 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-14.27.0-pyhdfd78af_0.tar.bz2 +md5 : 1a63e1992de499ba36570a7c3cd85d95 +timestamp : 2023-05-08 16:21:19 UTC +dependencies: + - gffutils 0.10.* + - jinja2 3.1.* + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil 2.8.* + - setuptools >=21.0.0 + - urllib3 1.26.* + + +ncbi-datasets-pylib 15.11.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-15.11.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 15.11.0 +build : pyhdfd78af_0 +build number: 0 +size : 238 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-15.11.0-pyhdfd78af_0.tar.bz2 +md5 : d80d43049a27f9efef0f3b1b5131aee4 +timestamp : 2023-08-01 22:49:29 UTC +dependencies: + - gffutils 0.10.* + - jinja2 3.1.* + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil 2.8.* + - urllib3 1.26.* + + +ncbi-datasets-pylib 15.12.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-15.12.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 15.12.0 +build : pyhdfd78af_0 +build number: 0 +size : 236 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-15.12.0-pyhdfd78af_0.tar.bz2 +md5 : 1d3f12997c55fa0f98eaf7fcc5cfd05a +timestamp : 2023-08-02 11:21:55 UTC +dependencies: + - gffutils 0.10.* + - jinja2 3.1.* + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil 2.8.* + - urllib3 1.26.* + + +ncbi-datasets-pylib 15.13.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-15.13.0-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 15.13.0 +build : pyhdfd78af_0 +build number: 0 +size : 236 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-15.13.0-pyhdfd78af_0.tar.bz2 +md5 : 48f3422b24e8424e7c76c8ccbefedf56 +timestamp : 2023-08-17 12:28:30 UTC +dependencies: + - gffutils 0.10.* + - jinja2 3.1.* + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil 2.8.* + - urllib3 1.26.* + + +ncbi-datasets-pylib 15.13.1 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-15.13.1-pyhdfd78af_0.tar.bz2 +name : ncbi-datasets-pylib +version : 15.13.1 +build : pyhdfd78af_0 +build number: 0 +size : 235 KB +license : Unlicense +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ncbi-datasets-pylib-15.13.1-pyhdfd78af_0.tar.bz2 +md5 : f75e334a85299268603eab63482bb8fc +timestamp : 2023-08-22 00:25:26 UTC +dependencies: + - gffutils 0.10.* + - jinja2 3.1.* + - jsonlines 3.0.* + - protobuf 3.20.* + - python >=3.8 + - python-dateutil 2.8.* + - urllib3 1.26.* + + +ncbi-datasets-pylib 15.14.0 pyhdfd78af_0 +---------------------------------------- +file name : ncbi-datasets-pylib-15.14.0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ncbi-ngs-sdk.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ncbi-ngs-sdk.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c8764ac3d61c188d51e40295fdcc88b0a794d76 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ncbi-ngs-sdk.manual_bundle.txt @@ -0,0 +1,425 @@ +# Tool: ncbi-ngs-sdk +software_name: ncbi-ngs-sdk +tier: T1 +domain: t1_backfill_overall +downloads: 208657 +summary: NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. +description: NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. +dependencies: libgcc >=13, libiconv >=1.17,<2.0a0, libstdcxx >=13, libxml2 >=2.13.5,<3.0a0, perl >=5.32.1,<5.33.0a0 *_perl5 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/ncbi/ngs +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/ncbi/ngs +GitHub - ncbi/ngs: NGS Language Bindings · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} ncbi / ngs Public Notifications You must be signed in to change notification settings Fork 53 Star 122 Code Issues 5 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights ncbi/ngs master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 959 Commits 959 Commits ngs-bam ngs-bam ngs-java ngs-java ngs-python ngs-python ngs-sdk ngs-sdk .gitignore .gitignore CHANGES.md CHANGES.md LICENSE LICENSE Makefile Makefile README.md README.md configure configure View all files Repository files navigation README License ngs ANNOUNCEMENTS: This repository is now frozen. The NGS project has moved to https://github.com/ncbi/sra-tools/ngs . See the full announcement below. February 10, 2022 NCBI's SRA changed the source build system to use CMake in toolkit release 3.0.0. This change is an important step to improve developers' productivity as it provides unified cross platform access to support multiple build systems. This change affects developers building NCBI SRA tools from source. Old makefiles and build systems are no longer supported. This change also includes the structure of GitHub repositories, which underwent consolidation to provide an easier environment for building tools and libraries (NGS libs and dependencies are consolidated). Consolidation of NGS libraries and dependencies provides better usage scope isolation and makes building more straightforward. Affected repositories ncbi/ngs (This repository) This repository is frozen. All future development will take place in GitHub repository ncbi/sra-tools (this repository), under subdirectory ngs/ . ncbi/ncbi-vdb This project's build system is based on CMake. The libraries providing access to SRA data in VDB format via the NGS API have moved to GitHub repository ncbi/sra-tools . Old (base URL: https://github.com/ncbi/ncbi-vdb ) New (base URL: https://github.com/ncbi/sra-tools ) libs/ngs ngs/ncbi/ngs libs/ngs-c++ ngs/ncbi/ngs-c++ libs/ngs-jni ngs/ncbi/ngs-jni libs/ngs-py ngs/ncbi/ngs-py libs/vdb-sqlite libs/vdb-sqlite test/ngs-java test/ngs-java test/ngs-python test/ngs-python ncbi/sra-tools This project's build system is based on CMake. The project acquired some new components, as listed in the table above. NGS Language Bindings NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb . The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java. Distribution of NGS APIs and Examples You can find information about building and running examples in README file located in tar archives . Documentation Further documentation is available on the wiki . About NGS Language Bindings Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 122 stars Watchers 27 watching Forks 53 forks Report repository Releases 32 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 46.7% Perl 21.0% Java 16.7% Python 6.6% C 5.9% Makefile 2.3% Shell 0.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge ncbi-ngs-sdk --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +ncbi-ngs-sdk 2.9.0 0 +-------------------- +file name : ncbi-ngs-sdk-2.9.0-0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.9.0 +build : 0 +build number: 0 +size : 560 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.9.0-0.tar.bz2 +md5 : bf584333acf578aa113f6d03e25f22e4 +dependencies: [] + + +ncbi-ngs-sdk 2.9.1 h550f44e_0 +----------------------------- +file name : ncbi-ngs-sdk-2.9.1-h550f44e_0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.9.1 +build : h550f44e_0 +build number: 0 +size : 151 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.9.1-h550f44e_0.tar.bz2 +md5 : 0c2f48eae65e14c8f0b083b256da8474 +timestamp : 2018-06-26 15:04:44 UTC +dependencies: + - libgcc-ng >=4.9 + - libiconv >=1.15,<1.16.0a0 + + +ncbi-ngs-sdk 2.9.3 h550f44e_0 +----------------------------- +file name : ncbi-ngs-sdk-2.9.3-h550f44e_0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.9.3 +build : h550f44e_0 +build number: 0 +size : 152 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.9.3-h550f44e_0.tar.bz2 +md5 : 0fdbff7974a00672f4a1adb663e94bc8 +timestamp : 2018-10-21 20:27:43 UTC +dependencies: + - libgcc-ng >=4.9 + - libiconv >=1.15,<1.16.0a0 + - libxml2 >=2.9.8,<2.10.0a0 + + +ncbi-ngs-sdk 2.10.0 hdf6179e_0 +------------------------------ +file name : ncbi-ngs-sdk-2.10.0-hdf6179e_0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.10.0 +build : hdf6179e_0 +build number: 0 +size : 139 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.10.0-hdf6179e_0.tar.bz2 +md5 : 894b9adc66f6ef58535f00b4f327cbd1 +timestamp : 2019-09-07 23:55:47 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libiconv >=1.15,<1.16.0a0 + - libstdcxx-ng >=7.3.0 + - libxml2 >=2.9.9,<2.10.0a0 + + +ncbi-ngs-sdk 2.10.1 hdf6179e_0 +------------------------------ +file name : ncbi-ngs-sdk-2.10.1-hdf6179e_0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.10.1 +build : hdf6179e_0 +build number: 0 +size : 140 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.10.1-hdf6179e_0.tar.bz2 +md5 : 41f00b642247a0faafa2658b0c1f6ddd +timestamp : 2019-12-16 19:16:45 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libiconv >=1.15,<1.16.0a0 + - libstdcxx-ng >=7.3.0 + - libxml2 >=2.9.10,<2.10.0a0 + + +ncbi-ngs-sdk 2.10.2 hdf6179e_0 +------------------------------ +file name : ncbi-ngs-sdk-2.10.2-hdf6179e_0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.10.2 +build : hdf6179e_0 +build number: 0 +size : 140 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.10.2-hdf6179e_0.tar.bz2 +md5 : 8d64a8efb2191f27841f40029ad46092 +timestamp : 2020-01-15 22:08:38 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libiconv >=1.15,<1.16.0a0 + - libstdcxx-ng >=7.3.0 + - libxml2 >=2.9.10,<2.10.0a0 + + +ncbi-ngs-sdk 2.10.4 h3e72335_1 +------------------------------ +file name : ncbi-ngs-sdk-2.10.4-h3e72335_1.tar.bz2 +name : ncbi-ngs-sdk +version : 2.10.4 +build : h3e72335_1 +build number: 1 +size : 140 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.10.4-h3e72335_1.tar.bz2 +md5 : abfbe1085fa37ee03c94befd3db993a2 +timestamp : 2020-08-30 14:30:04 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libiconv >=1.16,<1.17.0a0 + - libstdcxx-ng >=7.5.0 + - libxml2 >=2.9.10,<2.10.0a0 + + +ncbi-ngs-sdk 2.10.4 hdf6179e_0 +------------------------------ +file name : ncbi-ngs-sdk-2.10.4-hdf6179e_0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.10.4 +build : hdf6179e_0 +build number: 0 +size : 141 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.10.4-hdf6179e_0.tar.bz2 +md5 : 21a03b21c3b98a76257e4c7a3bbe1187 +timestamp : 2020-02-26 16:11:22 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libiconv >=1.15,<1.16.0a0 + - libstdcxx-ng >=7.3.0 + - libxml2 >=2.9.10,<2.10.0a0 + + +ncbi-ngs-sdk 2.10.9 h3e72335_0 +------------------------------ +file name : ncbi-ngs-sdk-2.10.9-h3e72335_0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.10.9 +build : h3e72335_0 +build number: 0 +size : 141 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.10.9-h3e72335_0.tar.bz2 +md5 : 91fe1b3e9998b2dae1ec7bacbe3948dd +timestamp : 2020-12-30 13:33:07 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libiconv >=1.16,<1.17.0a0 + - libstdcxx-ng >=7.5.0 + - libxml2 >=2.9.10,<2.10.0a0 + + +ncbi-ngs-sdk 2.10.9 hff44eed_1 +------------------------------ +file name : ncbi-ngs-sdk-2.10.9-hff44eed_1.tar.bz2 +name : ncbi-ngs-sdk +version : 2.10.9 +build : hff44eed_1 +build number: 1 +size : 166 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.10.9-hff44eed_1.tar.bz2 +md5 : a08394e9acc368b545ac9405f6c7157c +timestamp : 2021-03-24 23:47:32 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libiconv >=1.16,<1.17.0a0 + - libstdcxx-ng >=9.3.0 + - libxml2 >=2.9.10,<2.10.0a0 + + +ncbi-ngs-sdk 2.11.0 hff44eed_0 +------------------------------ +file name : ncbi-ngs-sdk-2.11.0-hff44eed_0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.11.0 +build : hff44eed_0 +build number: 0 +size : 167 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.11.0-hff44eed_0.tar.bz2 +md5 : 620fcdc0188ef9302c12d76d5a2517ea +timestamp : 2021-04-04 21:35:49 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libiconv >=1.16,<1.17.0a0 + - libstdcxx-ng >=9.3.0 + - libxml2 >=2.9.10,<2.10.0a0 + + +ncbi-ngs-sdk 2.11.1 hff44eed_0 +------------------------------ +file name : ncbi-ngs-sdk-2.11.1-hff44eed_0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.11.1 +build : hff44eed_0 +build number: 0 +size : 2.3 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.11.1-hff44eed_0.tar.bz2 +md5 : 6449408b58a13153f3677c6ba29a57af +timestamp : 2021-08-17 20:22:02 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libiconv >=1.16,<1.17.0a0 + - libstdcxx-ng >=9.4.0 + - libxml2 >=2.9.12,<2.10.0a0 + + +ncbi-ngs-sdk 2.11.2 hff44eed_0 +------------------------------ +file name : ncbi-ngs-sdk-2.11.2-hff44eed_0.tar.bz2 +name : ncbi-ngs-sdk +version : 2.11.2 +build : hff44eed_0 +build number: 0 +size : 2.3 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.11.2-hff44eed_0.tar.bz2 +md5 : efae1372bc1c31a266df0bd2086e1e8b +timestamp : 2021-10-07 20:31:16 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libiconv >=1.16,<1.17.0a0 + - libstdcxx-ng >=9.4.0 + - libxml2 >=2.9.12,<2.10.0a0 + + +ncbi-ngs-sdk 2.11.2 pl5321h629fbf0_1 +------------------------------------ +file name : ncbi-ngs-sdk-2.11.2-pl5321h629fbf0_1.tar.bz2 +name : ncbi-ngs-sdk +version : 2.11.2 +build : pl5321h629fbf0_1 +build number: 1 +size : 168 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-2.11.2-pl5321h629fbf0_1.tar.bz2 +md5 : 748754eb6afe73cb7c3f8865977581ff +timestamp : 2022-02-23 00:56:52 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libiconv >=1.16,<1.17.0a0 + - libstdcxx-ng >=10.3.0 + - libxml2 >=2.9.12,<2.10.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +ncbi-ngs-sdk 3.0.1 pl5321h0ff018f_5 +----------------------------------- +file name : ncbi-ngs-sdk-3.0.1-pl5321h0ff018f_5.tar.bz2 +name : ncbi-ngs-sdk +version : 3.0.1 +build : pl5321h0ff018f_5 +build number: 5 +size : 166 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-3.0.1-pl5321h0ff018f_5.tar.bz2 +md5 : e722a8788094bb1d1440a5f49305ee22 +timestamp : 2024-12-13 11:25:01 UTC +dependencies: + - libgcc >=13 + - libiconv >=1.17,<2.0a0 + - libstdcxx >=13 + - libxml2 >=2.13.5,<3.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +ncbi-ngs-sdk 3.0.1 pl5321h629fbf0_0 +----------------------------------- +file name : ncbi-ngs-sdk-3.0.1-pl5321h629fbf0_0.tar.bz2 +name : ncbi-ngs-sdk +version : 3.0.1 +build : pl5321h629fbf0_0 +build number: 0 +size : 168 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-3.0.1-pl5321h629fbf0_0.tar.bz2 +md5 : fa655c58510f1103861c84501262c10a +timestamp : 2022-11-15 18:29:57 UTC +dependencies: + - libgcc-ng >=12 + - libiconv >=1.16,<1.17.0a0 + - libstdcxx-ng >=12 + - libxml2 >=2.9.14,<2.10.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +ncbi-ngs-sdk 3.0.1 pl5321h629fbf0_1 +----------------------------------- +file name : ncbi-ngs-sdk-3.0.1-pl5321h629fbf0_1.tar.bz2 +name : ncbi-ngs-sdk +version : 3.0.1 +build : pl5321h629fbf0_1 +build number: 1 +size : 167 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-3.0.1-pl5321h629fbf0_1.tar.bz2 +md5 : 223a72a2ff651ce96ab0d06d0a0b5e64 +timestamp : 2023-05-12 17:48:30 UTC +dependencies: + - libgcc-ng >=12 + - libiconv >=1.16,<1.17.0a0 + - libstdcxx-ng >=12 + - libxml2 >=2.9.14,<2.10.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +ncbi-ngs-sdk 3.0.1 pl5321ha72442d_1 +----------------------------------- +file name : ncbi-ngs-sdk-3.0.1-pl5321ha72442d_1.tar.bz2 +name : ncbi-ngs-sdk +version : 3.0.1 +build : pl5321ha72442d_1 +build number: 1 +size : 167 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-3.0.1-pl5321ha72442d_1.tar.bz2 +md5 : 7dc1db633e59e303a46bb240485bd72e +timestamp : 2023-05-14 21:54:42 UTC +dependencies: + - libgcc-ng >=12 + - libiconv >=1.17,<2.0a0 + - libstdcxx-ng >=12 + - libxml2 >=2.10.4,<2.11.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +ncbi-ngs-sdk 3.0.1 pl5321ha72442d_2 +----------------------------------- +file name : ncbi-ngs-sdk-3.0.1-pl5321ha72442d_2.tar.bz2 +name : ncbi-ngs-sdk +version : 3.0.1 +build : pl5321ha72442d_2 +build number: 2 +size : 167 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-3.0.1-pl5321ha72442d_2.tar.bz2 +md5 : b5e8c0aca3175e5d4140aac576e8ee60 +timestamp : 2023-05-16 12:10:44 UTC +dependencies: + - libgcc-ng >=12 + - libiconv >=1.17,<2.0a0 + - libstdcxx-ng >=12 + - libxml2 >=2.10.4,<2.11.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +ncbi-ngs-sdk 3.0.1 pl5321ha7a0b76_3 +----------------------------------- +file name : ncbi-ngs-sdk-3.0.1-pl5321ha7a0b76_3.tar.bz2 +name : ncbi-ngs-sdk +version : 3.0.1 +build : pl5321ha7a0b76_3 +build number: 3 +size : 168 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ncbi-ngs-sdk-3.0.1-pl5321ha7a0b76_3.tar.bz2 +md5 : 229bd88ee93e346c86694fdfe02afa8a +timestamp : 2024-04-08 12:35:02 UTC +dependencies: + - libgcc-ng >=12 + - libiconv >=1.17,<2.0a0 + - libstdcxx-ng >=12 + - libxml2 >=2.11.6,<2.12.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +ncbi-ngs-sdk 3.0.1 pl5321he diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nf-core.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nf-core.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..88775112cbc40109de901d6e0a2ac18c71e43c9e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nf-core.manual_bundle.txt @@ -0,0 +1,593 @@ +# Tool: nf-core +software_name: nf-core +tier: T1 +domain: t1_backfill_overall +downloads: 142131 +summary: Python package with helper tools for the nf-core community. +description: Python package with helper tools for the nf-core community. +dependencies: click, filetype, git, gitpython, jinja2, jsonschema >=4.0, linkify-it-py >=1,<3, markdown >=3.3, nextflow >=25.04.2, nf-test, packaging, pillow, pre-commit, prompt_toolkit >=3.0.52, pydantic >=2.2.1, pygithub, python >=3.10, pyyaml, questionary >=2.0.1, refgenie, repo2rocrate, requests, requests-cache, rich >=13.3.1, rich-click 1.9.*, rocrate, ruamel.yaml, tabulate, textual 6.2.1, trogon +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: http://nf-co.re/ +doc_url: https://nf-co.re +dev_url: https://github.com/nf-core/tools + +## URL Docs Extract +### https://nf-co.re +nf-core Search Home Pipelines Resources Components Modules Subworkflows Configs Shared configs Plugins & Actions nft-utils setup-nextflow setup-nf-test Docs Community What's happening Advisories Blog new post Events Bytesize Talks Hackathons Training Talks Weekly Helpdesks Programs and groups Special interest groups In-progress RFCs Mentorships Contributors Shop new Connect game 👾 About About nf-core nf-core Lore Stickers Governance Marketing Code of conduct Publications Statistics Join nf-core Search Select theme Light Dark System Select theme Light Dark System Join nf-core Join nf-core A global community collaborating to build open-source Nextflow components and pipelines View Pipelines For organisations Highly optimised pipelines with excellent reporting. Validated releases ensure reproducibility. For users Portable, documented and easy to use workflows. Pipelines that you can trust. For developers Companion templates and tools help to validate your code and simplify common tasks. nf-core is published in Nature Biotechnology! Nat Biotechnol 38 , 276-278 (2020). Nextflow is an incredibly powerful and flexible workflow language. nf-core pipelines adhere to strict guidelines - if one works, they all will. Fully featured pipelines Documentation Extensive documentation covering installation, usage and description of output files ensures that you won't be left in the dark. Stable Releases nf-core pipelines use GitHub releases to tag stable versions of the code and software. Pipelines are exceptionally well tested and easy to run. Open source All nf-core code is licensed under the MIT license and is available on GitHub. Pipelines can be used, modified, and forked - by anyone. CI Testing Every time a change is made to the pipeline code, nf-core pipelines use continuous-integration testing to ensure that nothing has broken. Run anywhere Pipelines are ultra-portable and run on most laptops, HPCs and clouds. Tests run on AWS after every release: you can browse results on the website and use for your own benchmarking. Packaged software Pipeline dependencies are automatically downloaded and handled using Docker, Singularity, Conda or others. No need for any software installations. All nf-core code is community owned . Everyone is welcome to use, contribute to, and help maintain nf-core. How to get involved Everyone is welcome to contribute, in any way! Contribute ideas and code directly via GitHub , or come talk to us in Slack . Start small or go big You start wherever you like: Typo fixes in docs? No module for your favourite tool? Missing a pipeline? We are looking for all types of contributions! Get started Develop with the community Join forces with others! We promote collaboration over duplication: before you start coding, please propose your idea in Slack. Join Slack Start from the template Pipelines, modules and subworkflows are based on a template, created using nf-core tools . An automated sync keeps pipelines up to date. Read the docs Introduction to nf-core Play nf-core YouTube channel Past Events Hackathon - April 2026 (Boston) April 28, 2026 at 14:00 - April 29, 2026 at 21:00 April 28, 2026 at 14:00 - April 29, 2026 at 21:00 See details Bytesize: Claude code plugin for nf-core modules April 21, 2026 at 11:00 - 11:30 April 21, 2026 at 11:00 - 11:30 See details #animal-genomics: April Meeting April 15, 2026 at 14:00 - 15:00 April 15, 2026 at 14:00 - 15:00 See details Latest bytesize Our weekly series of short talks. Play Get started in minutes Nextflow lets you run nf-core pipelines on virtually any computing environment. The nf-core companion tool makes it easy to list all available nf-core pipelines and shows which are available locally. Local versions are checked against the latest available release. The nf-core companion tool also provides a range of helper functions to make it easier to work with nf-core pipelines, such as downloading pipelines for offline use, an interactive command-line launch wizard and helper functions to generate commented config file templates for any pipeline. # Install nextflow curl -s https://get.nextflow.io | bash mv nextflow ~/bin/ # Launch the RNAseq pipeline nextflow run nf-core/rnaseq \ --input samplesheet.csv \ --output ./results/ \ --genome GRCh37 \ -profile docker # Install nf-core tools pip install nf-core # List all nf-core pipelines and show available updates nf-core pipelines list See what's available Check out the available pipelines to see if we have what you need. Each comes with release details, keywords and a description. Available pipelines Run a pipeline Read the quickstart tutorial to learn how to get set up with the required software and tools, and how to launch a nf-core pipeline. Quickstart Tutorial Get into the code If you're interested in contributing to nf-core, take a look at the developer documentation to see what's required. Developer docs See a complete list » Used by groups all over the world The nf-core community is spread all over the globe and includes a large number of contributing users. See a complete list » Making awesome workflows since 2018. Supported by: + + + See the source code for this website on GitHub: https://github.com/nf-core/website + +### https://github.com/nf-core/tools +GitHub - nf-core/tools: Python package with helper tools for the nf-core community. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} nf-core / tools Public Notifications You must be signed in to change notification settings Fork 239 Star 304 Code Issues 335 Pull requests 34 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights nf-core/tools main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 14,460 Commits 14,460 Commits .devcontainer .devcontainer .github .github .vscode .vscode docs docs nf_core nf_core tests tests .gitattributes .gitattributes .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml .prettierignore .prettierignore .prettierrc.yml .prettierrc.yml CHANGELOG.md CHANGELOG.md CITATION.cff CITATION.cff CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md CONTRIBUTING.md CONTRIBUTING.md Dockerfile Dockerfile LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md codecov.yml codecov.yml mypy.ini mypy.ini pyproject.toml pyproject.toml uv.lock uv.lock View all files Repository files navigation README Code of conduct Contributing MIT license A python package with helper tools for the nf-core community. The nf-core tools package is written in Python and can be imported and used within other packages. For documentation of the internal Python functions, please refer to the Tools Python API docs . Installation For full installation instructions, please see the nf-core documentation . Below is a quick-start for those who know what they're doing: Bioconda Install from Bioconda : conda install nf-core Alternatively, you can create a new environment with both nf-core/tools and nextflow: conda create --name nf-core python=3.14 nf-core nextflow conda activate nf-core Python Package Index Install from PyPI : pip install nf-core Development version pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev If editing, fork and clone the repo, then install as follows: uv sync --all-extras # Activate the virtual environment source .venv/bin/activate # Or use uv run to run commands without activating uv run nf-core --help Contributions and Support If you would like to contribute to this package, please see the contributing guidelines . For further information or help, don't hesitate to get in touch on the Slack #tools channel (you can join with this invite ). Citation If you use nf-core tools in your work, please cite the nf-core publication as follows: The nf-core framework for community-curated bioinformatics pipelines. Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x . About Python package with helper tools for the nf-core community. nf-co.re Topics python workflow bioinformatics pipeline nextflow linting linter nf-core Resources Readme License MIT license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 304 stars Watchers 152 watching Forks 239 forks Report repository Releases 66 v4.0.1 - Bold Boa Patch Latest Apr 29, 2026 + 65 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 92.4% Nextflow 6.9% Other 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge nf-core --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +nf-core 1.1 py_0 +---------------- +file name : nf-core-1.1-py_0.tar.bz2 +name : nf-core +version : 1.1 +build : py_0 +build number: 0 +size : 46 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.1-py_0.tar.bz2 +md5 : a7a60f33b852fc48d3edb0760add9951 +timestamp : 2018-10-02 12:32:29 UTC +dependencies: + - arrow + - binaryornot + - certifi + - chardet + - click + - cookiecutter + - future + - git + - gitdb2 + - gitpython + - idna + - jinja2 + - jinja2-time + - markupsafe + - poyo + - python + - python-dateutil + - pyyaml + - requests + - requests-cache + - six + - smmap2 + - tabulate + - urllib3 + - whichcraft + + +nf-core 1.2 py_0 +---------------- +file name : nf-core-1.2-py_0.tar.bz2 +name : nf-core +version : 1.2 +build : py_0 +build number: 0 +size : 47 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.2-py_0.tar.bz2 +md5 : bf5cc283a85b4d2375f01f76eda7d031 +timestamp : 2018-10-03 07:35:42 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - python + - pyyaml + - requests + - requests-cache + - tabulate + + +nf-core 1.3 py_0 +---------------- +file name : nf-core-1.3-py_0.tar.bz2 +name : nf-core +version : 1.3 +build : py_0 +build number: 0 +size : 48 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.3-py_0.tar.bz2 +md5 : 664723a4920b803343bd2f7661b453f4 +timestamp : 2018-11-22 09:00:33 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - python + - pyyaml + - requests + - requests-cache + - tabulate + + +nf-core 1.4 py_0 +---------------- +file name : nf-core-1.4-py_0.tar.bz2 +name : nf-core +version : 1.4 +build : py_0 +build number: 0 +size : 49 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.4-py_0.tar.bz2 +md5 : 85398dbee52e6c0288ee28699b384355 +timestamp : 2018-12-12 19:45:13 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - python + - pyyaml + - requests + - requests-cache + - tabulate + + +nf-core 1.5 py_0 +---------------- +file name : nf-core-1.5-py_0.tar.bz2 +name : nf-core +version : 1.5 +build : py_0 +build number: 0 +size : 59 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.5-py_0.tar.bz2 +md5 : b6e15c272cf34898b2d12c4b5c2eea58 +timestamp : 2019-03-14 07:56:29 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - jsonschema + - python + - pyyaml + - requests + - requests-cache + - tabulate + + +nf-core 1.6 py_0 +---------------- +file name : nf-core-1.6-py_0.tar.bz2 +name : nf-core +version : 1.6 +build : py_0 +build number: 0 +size : 56 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.6-py_0.tar.bz2 +md5 : 39fc1b6f5cade8c6c387086229f7cada +timestamp : 2019-04-09 12:46:08 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - jsonschema + - python + - pyyaml + - requests + - requests-cache + - tabulate + + +nf-core 1.7 py_0 +---------------- +file name : nf-core-1.7-py_0.tar.bz2 +name : nf-core +version : 1.7 +build : py_0 +build number: 0 +size : 62 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.7-py_0.tar.bz2 +md5 : bab163aea4a26d5178f141f749f22f23 +timestamp : 2019-10-07 14:50:23 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - jsonschema + - python + - pyyaml + - requests + - requests-cache + - tabulate + + +nf-core 1.8 py_0 +---------------- +file name : nf-core-1.8-py_0.tar.bz2 +name : nf-core +version : 1.8 +build : py_0 +build number: 0 +size : 70 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.8-py_0.tar.bz2 +md5 : 1f4bc7a82f65b7f57988f736f84a8ee1 +timestamp : 2020-01-31 11:26:40 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - jsonschema + - python + - pyyaml + - requests + - requests-cache + - tabulate + + +nf-core 1.9 py_0 +---------------- +file name : nf-core-1.9-py_0.tar.bz2 +name : nf-core +version : 1.9 +build : py_0 +build number: 0 +size : 70 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.9-py_0.tar.bz2 +md5 : 82eebf4dd4bc45d089092513e4f057db +timestamp : 2020-02-20 16:12:49 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - jsonschema + - python + - pyyaml + - requests + - requests-cache + - tabulate + + +nf-core 1.10.2 pyh864c0ab_0 +--------------------------- +file name : nf-core-1.10.2-pyh864c0ab_0.tar.bz2 +name : nf-core +version : 1.10.2 +build : pyh864c0ab_0 +build number: 0 +size : 88 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.10.2-pyh864c0ab_0.tar.bz2 +md5 : 5078d89c9693e254b83e65b6c83f3b79 +timestamp : 2020-07-31 20:21:11 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - jinja2 + - jsonschema + - pyinquirer 1.0.2.* + - python + - pyyaml + - requests + - requests-cache + - rich >=4.0.0 + - tabulate + + +nf-core 1.11 pyh3252c3a_0 +------------------------- +file name : nf-core-1.11-pyh3252c3a_0.tar.bz2 +name : nf-core +version : 1.11 +build : pyh3252c3a_0 +build number: 0 +size : 89 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.11-pyh3252c3a_0.tar.bz2 +md5 : 7bb35be0dde4b4e35a047d698fa065c0 +timestamp : 2020-10-27 10:39:42 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - jinja2 + - jsonschema + - pyinquirer 1.0.2.* + - python + - pyyaml + - requests + - requests-cache + - rich >=9 + - tabulate + + +nf-core 1.12 pyh3252c3a_0 +------------------------- +file name : nf-core-1.12-pyh3252c3a_0.tar.bz2 +name : nf-core +version : 1.12 +build : pyh3252c3a_0 +build number: 0 +size : 89 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.12-pyh3252c3a_0.tar.bz2 +md5 : 22686e4044b118655127b170dd85c78e +timestamp : 2020-11-22 06:21:47 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - jinja2 + - jsonschema + - pyinquirer 1.0.2.* + - python + - pyyaml + - requests + - requests-cache + - rich >=9 + - tabulate + + +nf-core 1.12.1 pyh3252c3a_0 +--------------------------- +file name : nf-core-1.12.1-pyh3252c3a_0.tar.bz2 +name : nf-core +version : 1.12.1 +build : pyh3252c3a_0 +build number: 0 +size : 91 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.12.1-pyh3252c3a_0.tar.bz2 +md5 : efc6dc12e127a7ca49d4de7a9c562317 +timestamp : 2020-12-10 08:52:32 UTC +dependencies: + - click + - cookiecutter + - git + - gitpython + - jinja2 + - jsonschema + - prompt_toolkit >=3.0.3 + - python + - pyyaml + - questionary >=1.8.0 + - requests + - requests-cache + - rich >=9 + - tabulate + + +nf-core 1.13 pyh3252c3a_0 +------------------------- +file name : nf-core-1.13-pyh3252c3a_0.tar.bz2 +name : nf-core +version : 1.13 +build : pyh3252c3a_0 +build number: 0 +size : 2.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.13-pyh3252c3a_0.tar.bz2 +md5 : ce5148a3ee49299619d3f57a0dfb6682 +timestamp : 2021-03-18 12:44:42 UTC +dependencies: + - click + - git + - gitpython + - jinja2 + - jsonschema + - packaging + - prompt_toolkit >=3.0.3 + - python + - pyyaml + - questionary >=1.8.0 + - requests + - requests-cache + - rich >=9.8.2 + - tabulate + + +nf-core 1.13.1 pyh3252c3a_0 +--------------------------- +file name : nf-core-1.13.1-pyh3252c3a_0.tar.bz2 +name : nf-core +version : 1.13.1 +build : pyh3252c3a_0 +build number: 0 +size : 2.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.13.1-pyh3252c3a_0.tar.bz2 +md5 : 6e3cbf023182bbf23c83392f250a2a60 +timestamp : 2021-03-19 13:22:43 UTC +dependencies: + - click + - git + - gitpython + - jinja2 + - jsonschema + - packaging + - prompt_toolkit >=3.0.3 + - python + - pyyaml + - questionary >=1.8.0 + - requests + - requests-cache + - rich >=9.8.2 + - tabulate + + +nf-core 1.13.2 pyh3252c3a_0 +--------------------------- +file name : nf-core-1.13.2-pyh3252c3a_0.tar.bz2 +name : nf-core +version : 1.13.2 +build : pyh3252c3a_0 +build number: 0 +size : 2.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.13.2-pyh3252c3a_0.tar.bz2 +md5 : 9eee3d959f1e23f79a483afd5d1135b4 +timestamp : 2021-03-23 16:18:33 UTC +dependencies: + - click + - git + - gitpython + - jinja2 + - jsonschema + - packaging + - prompt_toolkit >=3.0.3 + - python + - pyyaml + - questionary >=1.8.0 + - requests + - requests-cache + - rich >=9.8.2 + - tabulate + + +nf-core 1.13.3 pyh3252c3a_0 +--------------------------- +file name : nf-core-1.13.3-pyh3252c3a_0.tar.bz2 +name : nf-core +version : 1.13.3 +build : pyh3252c3a_0 +build number: 0 +size : 2.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.13.3-pyh3252c3a_0.tar.bz2 +md5 : d8f2648b186f44e0019e0c1a99860a47 +timestamp : 2021-03-25 19:25:53 UTC +dependencies: + - click + - git + - gitpython + - jinja2 + - jsonschema + - packaging + - prompt_toolkit >=3.0.3 + - python + - pyyaml + - questionary >=1.8.0 + - requests + - requests-cache + - rich >=9.8.2 + - tabulate + + +nf-core 1.14 pyh5e36f6f_0 +------------------------- +file name : nf-core-1.14-pyh5e36f6f_0.tar.bz2 +name : nf-core +version : 1.14 +build : pyh5e36f6f_0 +build number: 0 +size : 2.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-1.14-pyh5e36f6f_0.tar.bz2 +md5 : 51d704ea6411d26fc13ddd828c376352 +timestamp : 2021-05-11 19:11:51 UTC +dependencies: + - click + - git + - gitpython + - jinja2 + - jsonschema + - packaging + - prompt_toolkit >=3.0.3 + - python + - pyyaml + - questionary >=1.8.0 + - requests + - requests-cache + - rich >=9.8.2 + - tabulate + + +nf-core 2.0.1 pyh5e36f6f_0 +-------------------------- +file name : nf-core-2.0.1-pyh5e36f6f_0.tar.bz2 +name : nf-core +version : 2.0.1 +build : pyh5e36f6f_0 +build number: 0 +size : 2.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-2.0.1-pyh5e36f6f_0.tar.bz2 +md5 : 9dd1f3962da1b13cc8de5ae6832476a7 +timestamp : 2021-07-13 16:00:17 UTC +dependencies: + - click + - git + - gitpython + - jinja2 + - jsonschema + - packaging + - prompt_toolkit >=3.0.3 + - python + - pyyaml + - questionary >=1.8.0 + - requests + - requests-cache + - rich >=9.8.2 + - tabulate + + +nf-core 2.1 pyh5e36f6f_0 +------------------------ +file name : nf-core-2.1-pyh5e36f6f_0.tar.bz2 +name : nf-core +version : 2.1 +build : pyh5e36f6f_0 +build number: 0 +size : 2.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/nf-core-2.1-pyh5e36f6f_0.tar.bz2 +md5 : 4a4af7e057d5f4d279f14da36c93e66f +timestamp : 2021-07-27 15:28:43 UTC +dependencies: + - click + - git + - gitpython + - jinja2 + - jsonschema + - packaging + - prompt_toolkit >=3.0.3 + - python diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nglview.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nglview.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c95bae66723392802b80bea6431eb999f44c32c5 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/nglview.manual_bundle.txt @@ -0,0 +1,535 @@ +# Tool: nglview +software_name: nglview +tier: T1 +domain: t1_backfill_overall +downloads: 120773 +summary: An IPython widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering. +description: An IPython widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering. +dependencies: ipywidgets >=7, notebook, numpy, python +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/arose/nglview +doc_url: https://arose.github.io/nglview/latest/ +dev_url: https://github.com/arose/nglview + +## URL Docs Extract +### https://github.com/arose/nglview +GitHub - nglviewer/nglview: Jupyter widget to interactively view molecular structures and trajectories · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} nglviewer / nglview Public Notifications You must be signed in to change notification settings Fork 140 Star 919 Code Issues 44 Pull requests 1 Discussions Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Wiki Security and quality Insights nglviewer/nglview master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,482 Commits 1,482 Commits .github .github devtools devtools docs docs examples examples js js nglview nglview notebooks notebooks tests tests .coveragerc .coveragerc .gitattributes .gitattributes .gitignore .gitignore .style.yapf .style.yapf CHANGELOG.md CHANGELOG.md CONTRIBUTING.md CONTRIBUTING.md Dockerfile Dockerfile Dockerfile-jupyterlab Dockerfile-jupyterlab LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md circle.yml circle.yml conda-requirements-test.sh conda-requirements-test.sh environment.yml environment.yml nglview-js-widgets.json nglview-js-widgets.json nglview.gif nglview.gif nglview.png nglview.png nightwatch.json nightwatch.json pip-requirements-test.txt pip-requirements-test.txt pyproject.toml pyproject.toml run_tests.sh run_tests.sh setup.py setup.py talks.md talks.md View all files Repository files navigation README Contributing License Citation | Installation | Example | Usage | Command line | API doc | Interface classes | Website | Acknowledgment An IPython/Jupyter widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering. Support for showing data from the file-system, RCSB PDB , simpletraj and from objects of analysis libraries mdtraj , pytraj , mdanalysis , ParmEd , rdkit , ase , HTMD , biopython , cctbx , pyrosetta , schrodinger's Structure Should work with Python 3. If you experience problems, please file an issue . Ask question about usage? Please post here Table of contents Installation Example Showcase from users Usage Contributing Command line API doc Interface classes Changelog FAQ Website Acknowledgment Cite License Installation Released version Available on conda-forge channel conda install nglview -c conda-forge Available on PyPI pip install nglview Jupyterlab: nglview works best with jupyterlab >= 3.0 and no further steps needed. Known to work versions nglview lab notebook ipywidgets Known issue(s) VSCode 3.1.0 4.0.10 7.0.6 8.1.1 HTML embed doesn't work No 3.0.8 4.0.10 7.0.6 8.1.1 show_pdbid doesn't work Yes Notes If you are using notebook v5.0, you need to increase the iopub_data_rate_limit to visualize big structure (e.g: solvated system) jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 Development version Requirement: ipywidgets >= 7.0 , notebook >= 4.2 The development version can be installed directly from github: notebook user git clone https://github.com/arose/nglview cd nglview python setup.py install # if you edit files in ./js folder, make sure to rebuild the code cd js npm install # probably need to activate widgetsnbextension # python -m ipykernel install --sys-prefix # jupyter nbextension enable --py --sys-prefix widgetsnbextension # jupyter nbextension enable --py --sys-prefix nglview # tested with ipywidgets 5.2.2, notebook 4.2.1 Example Notebooks: please see our Jupyter notebook examples Simple demo for trajectory (take time to load): biomembrane Showcase from users Please check user examples . Feel free to contribute. Also check a series of excelent tutorials about/using nglview from volkamerlab Usage Open a notebook jupyter notebook and issue import nglview view = nglview . show_pdbid ( "3pqr" ) # load "3pqr" from RCSB PDB and display viewer widget view A number of convenience functions are available to quickly display data from the file-system, RCSB PDB , simpletraj and from objects of analysis libraries mdtraj , pytraj , mdanalysis , ParmEd , rdkit , HTMD , biopython . Function Description show_file(path) Shows any NGL supported file formats (pdb, gro, mol2, sdf, dx, ..) in path show_pdbid(pdbid) Shows pdbid fetched from RCSB PDB show_simpletraj(struc_path, traj_path) Shows structure & trajectory loaded with simpletraj show_mdtraj(traj) Shows MDTraj trajectory traj show_pytraj(traj) Shows PyTraj trajectory traj show_parmed(structure) Shows ParmEd structure show_mdanalysis(univ) Shows MDAnalysis Universe or AtomGroup univ show_rdkit(mol) Shows rdkit rdkit.Chem.rdchem.Mol show_ase(atoms) Shows ase Atoms show_asetraj(traj) Shows ase trajectory traj show_pymatgen(struct) Shows pymatgen Structure show_htmd(mol) Shows HTMD Molecules show_biopython(mol) Shows Biopython structural entities show_iotbx(mol) Shows cctbx's iotbx structure show_rosetta(pose) Shows pyrosetta's Pose show_iodata(obj) Shows iodata's IOData show_psi4(obj) Shows psi4's Molecule show_qcelemental Shows QCelementary's Molecule show_openbabel Shows openbabel's OMol show_prody Shows prody's Ensemble or AtomGroup API Representations view . add_representation ( 'cartoon' , selection = 'protein' ) # or shorter view . add_cartoon ( selection = "protein" ) view . add_surface ( selection = "protein" , opacity = 0.3 ) # specify color view . add_cartoon ( selection = "protein" , color = 'blue' ) # specify residue view . add_licorice ( 'ALA, GLU' ) # clear representations view . clear_representations () # update parameters for ALL cartoons of component 0 (default) view . update_cartoon ( opacity = 0.4 , component = 0 ) # remove ALL cartoons of component 0 (default) view . remove_cartoon ( opacity = 0.4 , component = 0 ) # Not using default representation view = nv . show_file ( 'your.pdb' , default = False ) view . center () view . add_rope () Representations can also be changed by overwriting the representations property of the widget instance view . The available type and params are described in the NGL Viewer documentation . view . representations = [ { "type" : "cartoon" , "params" : { "sele" : "protein" , "color" : "residueindex" }}, { "type" : "ball+stick" , "params" : { "sele" : "hetero" }} ] The widget constructor also accepts a representation argument: initial_repr = [ { "type" : "cartoon" , "params" : { "sele" : "protein" , "color" : "sstruc" }} ] view = nglview . NGLWidget ( struc , representation = initial_repr ) view Properties # set the frame number view . frame = 100 # parameters for the NGL stage object view . stage . set_parameters ( ** { # "percentages, "dist" is distance to camera in Angstrom "clipNear" : 0 , "clipFar" : 100 , "clipDist" : 10 , # percentages, start of fog and where on full effect "fogNear" : 0 , "fogFar" : 100 , # background color "backgroundColor" : "black" , }) # note: NGLView accepts both origin camel NGL keywords (e.g. "clipNear") # and snake keywords (e.g "clip_near") # parameters to control the `delay` between snapshots # change `step` to play forward (positive value) or backward (negative value) # note: experimental code view . player . parameters = dict ( delay = 0.04 , step = - 1 ) # update camera type view . camera = 'orthographic' # change background color view . background = 'black' Trajectory # adding new trajectory view . add_trajectory ( traj ) # traj could be a `pytraj.Trajectory`, `mdtraj.Trajectory`, `MDAnalysis.Universe`, # `parmed.Structure`, `htmd.Molecule` or derived class of `nglview.Trajectory` # change representation view [ 0 ]. add_cartoon (...) # equal to view.add_cartoon(component=0) view [ 1 ]. add_licorice (...) # equal to view.add_licorice(component=1) Add extra component # Density volumes (MRC/MAP/CCP4, DX/DXBIN, CUBE) # Or adding derived class of `nglview.Structure` view . add_component ( 'my.ccp4' ) # add component from url view . add_component ( 'rcsb://1tsu.pdb' ) # NOTE: Trajectory is a special case of component. Mouse # coot mouse style (https://en.wikipedia.org/wiki/Coot_(software)) view . stage . set_parameters ( mouse_preset = 'coot' ) Interaction controls Mouse Keyboard Movie making Require: moviepy ( pip install moviepy ) from nglview . contrib . movie import MovieMaker movie = MovieMaker ( view , output = 'my.gif' , in_memory = True ) movie . make () Embed widget embed API doc Latest version All releases versions Development version Command line # open a notebook and import nglview nglview # Require installing pytraj (PR for other backends is welcome) # open notebook, load `my.pdb` to pytraj's trajectory then display `view` nglview my.pdb # load density data nglview my.ccp4 # open notebook, create trajectory with given topology `my.parm7` and trajecotry file `traj.nc`, # then display `view` nglview my.parm7 -c traj.nc # load all trajectories with filename ending with 'nc' # make sure to use quote " " nglview my.parm7 -c " *.nc " # open notebook, copy content from `myscript.py` nglview myscript.py # create a remote notebook # just follow its instruction nglview my.pdb --remote nglview my.parm7 -c traj.nc --remote nglview mynotebook.ipynb --remote # demo (don't need pytraj) nglview demo # specify web browser nglview my.pdb --browser=google-chrome FAQ Q&A Website http://nglviewer.github.io/nglview/latest http://nglviewer.github.io/nglview/dev Talks Talks about NGL and nglview Contributing Join us here Projects integrating NGLView (Feel free to make a PR to add/remove your project here. Thanks.) AMBER - A package of programs for molecular dynamics simulations of proteins and nucleic acids mbuild - A hierarchical, component based molecule builder deepchem - Deep-learning models for Drug Discovery and Quantum Chemistry htmd - High throughput molecular dynamics simulations Moleidoscope - Molecular kaleidoscope ssbio - Tools for enabling structural systems biology hublib - hublib is a Python library for the HUBzero science gateway platform. molPX : ipython API to visualize MD-trajectories along projected trajectories nanoribbon ase : Atomic Simulation Environment pida : Software for analyzing multiple protein-protein interaction docking solutions, pytim MobleyLab/drug-computing Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course. pyiron : an integrated development environment for implementing, testing, and running simulations in computational materials science. BioSimSpace : An interoperable framework for biomolecular simulation pyrod : PyRod - Tracing water molecules in molecular dynamics simulations kugupu : kugupu - a molecular network generator to study charge transport pathways in amorphous materials pnab : proto-Nucleic Acid Builder opencadd : A Python library for structural cheminformatics teachopencadd : TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data query.libretexts.org : query.libretexts.org datamol : A python library to work with molecules. dynophores : Dynamic pharmacophore modeling of molecular interactions pychemcurv : Discrete and local curvature applied to chemistry and chemical reactivity AutoSolvate : Automated workflow for generating quantum chemistry calculation of explicitly solvated molecules plipify : PLIPify: Protein-Ligand Interaction Frequencies across Multiple Structures Melodia : Differential Geometry of Proteins Backbones pyrosetta_viewer3d : Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab py4vasp : Python interface for VASP eminus : A plane wave density functional theory code. MolSysMT : Molecular Systems Multi-Tool Acknowledgment Funding: Hai Nguyen is supported by NIH Grant GM103297, "The Center for HIV RNA Studies" (2015 to 02-2017). Many thanks to nglview contributors Cite If you would like to acknowledge our work, feel free to cite: Hai Nguyen, David A Case, Alexander S Rose; NGLview - Interactive molecular graphics for Jupyter notebooks, Bioinformatics, , btx789, https://doi.org/10.1093/bioinformatics/btx789 License Generally MIT, see the LICENSE file for details. About Jupyter widget to interactively view molecular structures and trajectories nglviewer.org/nglview/latest/ Resources Readme License View license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 919 stars Watchers 21 watching Forks 140 forks Report repository Releases 88 v4.0 Latest Oct 2, 2025 + 87 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 96.8% Python 1.3% JavaScript 0.8% CSS 0.7% TypeScript 0.4% Shell 0.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/arose/nglview +GitHub - nglviewer/nglview: Jupyter widget to interactively view molecular structures and trajectories · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} nglviewer / nglview Public Notifications You must be signed in to change notification settings Fork 140 Star 919 Code Issues 44 Pull requests 1 Discussions Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Wiki Security and quality Insights nglviewer/nglview master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,482 Commits 1,482 Commits .github .github devtools devtools docs docs examples examples js js nglview nglview notebooks notebooks tests tests .coveragerc .coveragerc .gitattributes .gitattributes .gitignore .gitignore .style.yapf .style.yapf CHANGELOG.md CHANGELOG.md CONTRIBUTING.md CONTRIBUTING.md Dockerfile Dockerfile Dockerfile-jupyterlab Dockerfile-jupyterlab LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md circle.yml circle.yml conda-requirements-test.sh conda-requirements-test.sh environment.yml environment.yml nglview-js-widgets.json nglview-js-widgets.json nglview.gif nglview.gif nglview.png nglview.png nightwatch.json nightwatch.json pip-requirements-test.txt pip-requirements-test.txt pyproject.toml pyproject.toml run_tests.sh run_tests.sh setup.py setup.py talks.md talks.md View all files Repository files navigation README Contributing License Citation | Installation | Example | Usage | Command line | API doc | Interface classes | Website | Acknowledgment An IPython/Jupyter widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering. Support for showing data from the file-system, RCSB PDB , simpletraj and from objects of analysis libraries mdtraj , pytraj , mdanalysis , ParmEd , rdkit , ase , HTMD , biopython , cctbx , pyrosetta , schrodinger's Structure Should work with Python 3. If you experience problems, please file an issue . Ask question about usage? Please post here Table of contents Installation Example Showcase from users Usage Contributing Command line API doc Interface classes Changelog FAQ Website Acknowledgment Cite License Installation Released version Available on conda-forge channel conda install nglview -c conda-forge Available on PyPI pip install nglview Jupyterlab: nglview works best with jupyterlab >= 3.0 and no further steps needed. Known to work versions nglview lab notebook ipywidgets Known issue(s) VSCode 3.1.0 4.0.10 7.0.6 8.1.1 HTML embed doesn't work No 3.0.8 4.0.10 7.0.6 8.1.1 show_pdbid doesn't work Yes Notes If you are using notebook v5.0, you need to increase the iopub_data_rate_limit to visualize big structure (e.g: solvated system) jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 Development version Requirement: ipywidgets >= 7.0 , notebook >= 4.2 The development version can be installed directly from github: notebook user git clone https://github.com/arose/nglview cd nglview python setup.py install # if you edit files in ./js folder, make sure to rebuild the code cd js npm install # probably need to activate widgetsnbextension # python -m ipykernel install --sys-prefix # jupyter nbextension enable --py --sys-prefix widgetsnbextension # jupyter nbextension enable --py --sys-prefix nglview # tested with ipywidgets 5.2.2, notebook 4.2.1 Example Notebooks: please see our Jupyter notebook examples Simple demo for trajectory (take time to load): biomembrane Showcase from users Please check user examples . Feel free to contribute. Also check a series of excelent tutorials about/using nglview from volkamerlab Usage Open a notebook jupyter notebook and issue import nglview view = nglview . show_pdbid ( "3pqr" ) # load "3pqr" from RCSB PDB and display viewer widget view A number of convenience functions are available to quickly display data from the file-system, RCSB PDB , simpletraj and from objects of analysis libraries mdtraj , pytraj , mdanalysis , ParmEd , rdkit , HTMD , biopython . Function Description show_file(path) Shows any NGL supported file formats (pdb, gro, mol2, sdf, dx, ..) in path show_pdbid(pdbid) Shows pdbid fetched from RCSB PDB show_simpletraj(struc_path, traj_path) Shows structure & trajectory loaded with simpletraj show_mdtraj(traj) Shows MDTraj trajectory traj show_pytraj(traj) Shows PyTraj trajectory traj show_parmed(structure) Shows ParmEd structure show_mdanalysis(univ) Shows MDAnalysis Universe or AtomGroup univ show_rdkit(mol) Shows rdkit rdkit.Chem.rdchem.Mol show_ase(atoms) Shows ase Atoms show_asetraj(traj) Shows ase trajectory traj show_pymatgen(struct) Shows pymatgen Structure show_htmd(mol) Shows HTMD Molecules show_biopython(mol) Shows Biopython structural entities show_iotbx(mol) Shows cctbx's iotbx structure show_rosetta(pose) Shows pyrosetta's Pose show_iodata(obj) Shows iodata's IOData show_psi4(obj) Shows psi4's Molecule show_qcelemental Shows QCelementary's Molecule show_openbabel Shows openbabel's OMol show_prody Shows prody's Ensemble or AtomGroup API Representations view . add_representation ( 'cartoon' , selection = 'protein' ) # or shorter view . add_cartoon ( selection = "protein" ) view . add_surface ( selection = "protein" , opacity = 0.3 ) # specify color view . add_cartoon ( selection = "protein" , color = 'blue' ) # specify residue view . add_licorice ( 'ALA, GLU' ) # clear representations view . clear_representations () # update parameters for ALL cartoons of component 0 (default) view . update_cartoon ( opacity = 0.4 , component = 0 ) # remove ALL cartoons of component 0 (default) view . remove_cartoon ( opacity = 0.4 , component = 0 ) # Not using default representation view = nv . show_file ( 'your.pdb' , default = False ) view . center () view . add_rope () Representations can also be changed by overwriting the representations property of the widget instance view . The available type and params are described in the NGL Viewer documentation . view . representations = [ { "type" : "cartoon" , "params" : { "sele" : "protein" , "color" : "residueindex" }}, { "type" : "ball+stick" , "params" : { "sele" : "hetero" }} ] The widget constructor also accepts a representation argument: initial_repr = [ { "type" : "cartoon" , "params" : { "sele" : "protein" , "color" : "sstruc" }} ] view = nglview . NGLWidget ( struc , representation = initial_repr ) view Properties # set the frame number view . frame = 100 # parameters for the NGL stage object view . stage . set_parameters ( ** { # "percentages, "dist" is distance to camera in Angstrom "clipNear" : 0 , "clipFar" : 100 , "clipDist" : 10 , # percentages, start of fog and where on full effect "fogNear" : 0 , "fogFar" : 100 , # background color "backgroundColor" : "black" , }) # note: NGLView accepts both origin camel NGL keywords (e.g. "clipNear") # and snake keywords (e.g "clip_near") # parameters to control the `delay` between snapshots # change `step` to play forward (positive value) or backward (negative value) # note: experimental code view . player . parameters = dict ( delay = 0.04 , step = - 1 ) # update camera type view . camera = 'orthographic' # change background color view . background = 'black' Trajectory # adding new trajectory view . add_trajectory ( traj ) # traj could be a `pytraj.Trajectory`, `mdtraj.Trajectory`, `MDAnalysis.Universe`, # `parmed.Structure`, `htmd.Molecule` or derived class of `nglview.Trajectory` # change representation view [ 0 ]. add_cartoon (...) # equal to view.add_cartoon(component=0) view [ 1 ]. add_licorice (...) # equal to view.add_licorice(component=1) Add extra component # Density volumes (MRC/MAP/CCP4, DX/DXBIN, CUBE) # Or adding derived class of `nglview.Structure` view . add_component ( 'my.ccp4' ) # add component from url view . add_component ( 'rcsb://1tsu.pdb' ) # NOTE: Trajectory is a special case of component. Mouse # coot mouse style (https://en.wikipedia.org/wiki/Coot_(software)) view . stage . set_parameters ( mouse_preset = 'coot' ) Interaction controls Mouse Keyboard Movie making Require: moviepy ( pip install moviepy ) from nglview . contrib . movie import MovieMaker movie = MovieMaker ( view , output = 'my.gif' , in_memory = True ) movie . make () Embed widget embed API doc Latest version All releases versions Development version Command line # open a notebook and import nglview nglview # Require installing pytraj (PR for other backends is welcome) # open notebook, load `my.pdb` to pytraj's trajectory then display `view` nglview my.pdb # load density data nglview my.ccp4 # open notebook, create trajectory with given topology `my.parm7` and trajecotry file `traj.nc`, # then display `view` nglview my.parm7 -c traj.nc # load all trajectories with filename ending with 'nc' # make sure to use quote " " nglview my.parm7 -c " *.nc " # open notebook, copy content from `myscript.py` nglview myscript.py # create a remote notebook # just follow its instruction nglview my.pdb --remote nglview my.parm7 -c traj.nc --remote nglview mynotebook.ipynb --remote # demo (don't need pytraj) nglview demo # specify web browser nglview my.pdb --browser=google-chrome FAQ Q&A Website http://nglviewer.github.io/nglview/latest http://nglviewer.github.io/nglview/dev Talks Talks about NGL and nglview Contributing Join us here Projects integrating NGLView (Feel free to make a PR to add/remove your project here. Thanks.) AMBER - A package of programs for molecular dynamics simulations of proteins and nucleic acids mbuild - A hierarchical, component based molecule builder deepchem - Deep-learning models for Drug Discovery and Quantum Chemistry htmd - High throughput molecular dynamics simulations Moleidoscope - Molecular kaleidoscope ssbio - Tools for enabling structural systems biology hublib - hublib is a Python library for the HUBzero science gateway platform. molPX : ipython API to visualize MD-trajectories along projected trajectories nanoribbon ase : Atomic Simulation Environment pida : Software for analyzing multiple protein-protein interaction docking solutions, pytim MobleyLab/drug-computing Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course. pyiron : an integrated development environment for implementing, testing, and running simulations in computational materials science. BioSimSpace : An interoperable framework for biomolecular simulation pyrod : PyRod - Tracing water molecules in molecular dynamics simulations kugupu : kugupu - a molecular network generator to study charge transport pathways in amorphous materials pnab : proto-Nucleic Acid Builder opencadd : A Python library for structural cheminformatics teachopencadd : TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data query.libretexts.org : query.libretexts.org datamol : A python library to work with molecules. dynophores : Dynamic pharmacophore modeling of molecular interactions pychemcurv : Discrete and local curvature applied to chemistry and chemical reactivity AutoSolvate : Automated workflow for generating quantum chemistry calculation of explicitly solvated molecules plipify : PLIPify: Protein-Ligand Interaction Frequencies across Multiple Structures Melodia : Differential Geometry of Proteins Backbones pyrosetta_viewer3d : Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab py4vasp : Python interface for VASP eminus : A plane wave density functional theory code. MolSysMT : Molecular Systems Multi-Tool Acknowledgment Funding: Hai Nguyen is supported by NIH Grant GM103297, "The Center for HIV RNA Studies" (2015 to 02-2017). Many thanks to nglview contributors Cite If you would like to acknowledge our work, feel free to cite: Hai Nguyen, David A Case, Alexander S Rose; NGLview - Interactive molecular graphics for Jupyter notebooks, Bioinformatics, , btx789, https://doi.org/10.1093/bioinformatics/btx789 License Generally MIT, see the LICENSE file for details. About Jupyter widget to interactively view molecular structures and trajectories nglviewer.org/nglview/latest/ Resources Readme License View license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 919 stars Watchers 21 watching Forks 140 forks Report repository Releases 88 v4.0 Latest Oct 2, 2025 + 87 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 96.8% Python 1.3% JavaScript 0.8% CSS 0.7% TypeScript 0.4% Shell 0.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge nglview --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +nglview 0.5.1 py27_0 +-------------------- +file name : nglview-0.5.1-py27_0.tar.bz2 +name : nglview +version : 0.5.1 +build : py27_0 +build number: 0 +size : 2.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.5.1-py27_0.tar.bz2 +md5 : 3f897145bc98a0ba8ca67dc5bdc2dc6a +dependencies: + - ipython <=4.1.2 + - ipywidgets <=4.1.1 + - jupyter + - notebook + - numpy + - python 2.7* + - traitlets + + +nglview 0.5.1 py34_0 +-------------------- +file name : nglview-0.5.1-py34_0.tar.bz2 +name : nglview +version : 0.5.1 +build : py34_0 +build number: 0 +size : 2.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.5.1-py34_0.tar.bz2 +md5 : 1f9e5fbb0ba56e893aeb5c6b979a3734 +dependencies: + - ipython <=4.1.2 + - ipywidgets <=4.1.1 + - jupyter + - notebook + - numpy + - python 3.4* + - traitlets + + +nglview 0.5.1 py35_0 +-------------------- +file name : nglview-0.5.1-py35_0.tar.bz2 +name : nglview +version : 0.5.1 +build : py35_0 +build number: 0 +size : 2.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.5.1-py35_0.tar.bz2 +md5 : 13ff562adc4abbf86ca0adfd06033a50 +dependencies: + - ipython <=4.1.2 + - ipywidgets <=4.1.1 + - jupyter + - notebook + - numpy + - python 3.5* + - traitlets + + +nglview 0.5.2 py27_0 +-------------------- +file name : nglview-0.5.2-py27_0.tar.bz2 +name : nglview +version : 0.5.2 +build : py27_0 +build number: 0 +size : 2.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.5.2-py27_0.tar.bz2 +md5 : 3b5291800be70d2445cf3062ec1d5bdf +dependencies: + - ipython <=4.1.2 + - ipywidgets <=4.1.1 + - jupyter + - notebook + - numpy + - python 2.7* + - traitlets + + +nglview 0.5.2 py34_0 +-------------------- +file name : nglview-0.5.2-py34_0.tar.bz2 +name : nglview +version : 0.5.2 +build : py34_0 +build number: 0 +size : 2.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.5.2-py34_0.tar.bz2 +md5 : 4df9b1ae022454773c09fda98a14667f +dependencies: + - ipython <=4.1.2 + - ipywidgets <=4.1.1 + - jupyter + - notebook + - numpy + - python 3.4* + - traitlets + + +nglview 0.5.2 py35_0 +-------------------- +file name : nglview-0.5.2-py35_0.tar.bz2 +name : nglview +version : 0.5.2 +build : py35_0 +build number: 0 +size : 2.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.5.2-py35_0.tar.bz2 +md5 : d3efe2a0e043cf4fb5db60258676ac41 +dependencies: + - ipython <=4.1.2 + - ipywidgets <=4.1.1 + - jupyter + - notebook + - numpy + - python 3.5* + - traitlets + + +nglview 0.6.1 py27_0 +-------------------- +file name : nglview-0.6.1-py27_0.tar.bz2 +name : nglview +version : 0.6.1 +build : py27_0 +build number: 0 +size : 3.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.1-py27_0.tar.bz2 +md5 : a77ff356917eb440f2bfdf9069a71eee +dependencies: + - ipywidgets >=5.2.2 + - numpy + - python 2.7* + + +nglview 0.6.1 py34_0 +-------------------- +file name : nglview-0.6.1-py34_0.tar.bz2 +name : nglview +version : 0.6.1 +build : py34_0 +build number: 0 +size : 3.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.1-py34_0.tar.bz2 +md5 : 634bf2979cdeae7a10809909bff84541 +dependencies: + - ipywidgets >=5.2.2 + - numpy + - python 3.4* + + +nglview 0.6.1 py35_0 +-------------------- +file name : nglview-0.6.1-py35_0.tar.bz2 +name : nglview +version : 0.6.1 +build : py35_0 +build number: 0 +size : 3.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.1-py35_0.tar.bz2 +md5 : 9dce9656337005b0e2a0d838b280182d +dependencies: + - ipywidgets >=5.2.2 + - numpy + - python 3.5* + + +nglview 0.6.2.1 py27_0 +---------------------- +file name : nglview-0.6.2.1-py27_0.tar.bz2 +name : nglview +version : 0.6.2.1 +build : py27_0 +build number: 0 +size : 5.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.2.1-py27_0.tar.bz2 +md5 : 4a722c09d7d8ab1028e0aacae0504d87 +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 2.7* + + +nglview 0.6.2.1 py34_0 +---------------------- +file name : nglview-0.6.2.1-py34_0.tar.bz2 +name : nglview +version : 0.6.2.1 +build : py34_0 +build number: 0 +size : 5.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.2.1-py34_0.tar.bz2 +md5 : fda5be5e04152eb90bfb83907c8e38dc +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 3.4* + + +nglview 0.6.2.1 py35_0 +---------------------- +file name : nglview-0.6.2.1-py35_0.tar.bz2 +name : nglview +version : 0.6.2.1 +build : py35_0 +build number: 0 +size : 5.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.2.1-py35_0.tar.bz2 +md5 : 5bba7590ff6f4d864bb5863437d5159c +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 3.5* + + +nglview 0.6.2.2 1 +----------------- +file name : nglview-0.6.2.2-1.tar.bz2 +name : nglview +version : 0.6.2.2 +build : 1 +build number: 1 +size : 5.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.2.2-1.tar.bz2 +md5 : c1fff7f0f4206d1c9daee4e3f6efc367 +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + + +nglview 0.6.2.2 py27_0 +---------------------- +file name : nglview-0.6.2.2-py27_0.tar.bz2 +name : nglview +version : 0.6.2.2 +build : py27_0 +build number: 0 +size : 5.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.2.2-py27_0.tar.bz2 +md5 : caa61fe2d698efed9ebb52f266306928 +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 2.7* + + +nglview 0.6.2.2 py27_0 +---------------------- +file name : nglview-0.6.2.2-py27_0.tar.bz2 +name : nglview +version : 0.6.2.2 +build : py27_0 +build number: 0 +size : 5.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/nglview-0.6.2.2-py27_0.tar.bz2 +md5 : b113b228de037da93dc024ef36b5b683 +constraints : + - python_abi * *_cp27mu +dependencies: + - ipywidgets >=5.2.2,<6 + - notebook + - numpy + - python 2.7* + + +nglview 0.6.2.2 py34_0 +---------------------- +file name : nglview-0.6.2.2-py34_0.tar.bz2 +name : nglview +version : 0.6.2.2 +build : py34_0 +build number: 0 +size : 5.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.2.2-py34_0.tar.bz2 +md5 : fbbf05f731c15d0e77a490c5af93b9ac +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 3.4* + + +nglview 0.6.2.2 py35_0 +---------------------- +file name : nglview-0.6.2.2-py35_0.tar.bz2 +name : nglview +version : 0.6.2.2 +build : py35_0 +build number: 0 +size : 5.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.2.2-py35_0.tar.bz2 +md5 : a074f630b0dbca946cce92c73893d1c0 +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 3.5* + + +nglview 0.6.2.2 py35_0 +---------------------- +file name : nglview-0.6.2.2-py35_0.tar.bz2 +name : nglview +version : 0.6.2.2 +build : py35_0 +build number: 0 +size : 5.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/nglview-0.6.2.2-py35_0.tar.bz2 +md5 : bb3aa1fcde3ef55322ef51ce41bb1a43 +constraints : + - python_abi * *_cp35m +dependencies: + - ipywidgets >=5.2.2,<6 + - notebook + - numpy + - python 3.5* + + +nglview 0.6.2.2 py36_0 +---------------------- +file name : nglview-0.6.2.2-py36_0.tar.bz2 +name : nglview +version : 0.6.2.2 +build : py36_0 +build number: 0 +size : 5.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/nglview-0.6.2.2-py36_0.tar.bz2 +md5 : 3cb35115be53fa8f54bd32fd1f7ba34d +constraints : + - python_abi * *_cp36m +dependencies: + - ipywidgets >=5.2.2,<6 + - notebook + - numpy + - python 3.6* + + +nglview 0.6.2.3 py27_0 +---------------------- +file name : nglview-0.6.2.3-py27_0.tar.bz2 +name : nglview +version : 0.6.2.3 +build : py27_0 +build number: 0 +size : 5.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.2.3-py27_0.tar.bz2 +md5 : 0dfc5994e74304871870a98eae8891d5 +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 2.7* + + +nglview 0.6.2.3 py27_0 +---------------------- +file name : nglview-0.6.2.3-py27_0.tar.bz2 +name : nglview +version : 0.6.2.3 +build : py27_0 +build number: 0 +size : 5.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/nglview-0.6.2.3-py27_0.tar.bz2 +md5 : 5d4bdd5eb6983d5026f26d5f637b05cb +constraints : + - python_abi * *_cp27mu +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 2.7* + + +nglview 0.6.2.3 py27_1 +---------------------- +file name : nglview-0.6.2.3-py27_1.tar.bz2 +name : nglview +version : 0.6.2.3 +build : py27_1 +build number: 1 +size : 5.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/nglview-0.6.2.3-py27_1.tar.bz2 +md5 : de9807a8bd4092aa02a7c43f894b1565 +constraints : + - python_abi * *_cp27mu +dependencies: + - ipywidgets >=5.2.2,<6 + - notebook + - numpy + - python 2.7* + + +nglview 0.6.2.3 py34_0 +---------------------- +file name : nglview-0.6.2.3-py34_0.tar.bz2 +name : nglview +version : 0.6.2.3 +build : py34_0 +build number: 0 +size : 5.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.2.3-py34_0.tar.bz2 +md5 : 86cd903fca1bc7effcef1caf3d9f479e +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 3.4* + + +nglview 0.6.2.3 py35_0 +---------------------- +file name : nglview-0.6.2.3-py35_0.tar.bz2 +name : nglview +version : 0.6.2.3 +build : py35_0 +build number: 0 +size : 5.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/nglview-0.6.2.3-py35_0.tar.bz2 +md5 : 2c58c9627a301d4cd35c008e44e1a33e +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 3.5* + + +nglview 0.6.2.3 py35_0 +---------------------- +file name : nglview-0.6.2.3-py35_0.tar.bz2 +name : nglview +version : 0.6.2.3 +build : py35_0 +build number: 0 +size : 5.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/nglview-0.6.2.3-py35_0.tar.bz2 +md5 : 74e26fb0c7e71dfa7e1bcd13c0592b2a +constraints : + - python_abi * *_cp35m +dependencies: + - ipywidgets >=5.2.2 + - notebook + - numpy + - python 3.5* + + +nglview 0.6.2.3 py35_1 +---------------------- +file name : nglview-0.6.2.3-py35_1.tar.bz2 +name : nglview +version : 0.6.2.3 +build diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ngs-tools.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ngs-tools.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..98b8f607ac638f7e0c3fe853c8c3bd97be0dacc4 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ngs-tools.manual_bundle.txt @@ -0,0 +1,469 @@ +# Tool: ngs-tools +software_name: ngs-tools +tier: T1 +domain: t1_backfill_overall +downloads: 124360 +summary: Reusable tools for working with next-generation sequencing (NGS) data +description: Reusable tools for working with next-generation sequencing (NGS) data +dependencies: joblib >=1.0.1, numba >=0.53.1, numpy >=1.19.0, pysam >=0.16.0.1, pyseq-align >=1.0.0, python >=3.6, shortuuid >=1.0.1, tqdm >=4.50.0, typing-extensions >=3.7.4 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/Lioscro/ngs-tools +doc_url: https://ngs-tools.readthedocs.io/en/latest/ +dev_url: https://github.com/Lioscro/ngs-tools + +## URL Docs Extract +### https://ngs-tools.readthedocs.io/en/latest/ +ngs-tools: Reusable tools for working with next-generation sequencing (NGS) data — ngs-tools 1.8.4 documentation --> ngs-tools latest Contents: API ngs-tools ngs-tools: Reusable tools for working with next-generation sequencing (NGS) data Edit on GitHub ngs-tools: Reusable tools for working with next-generation sequencing (NGS) data  Contents: API Subpackages Submodules Package Contents Indices and tables  Index Module Index Search Page Next © Copyright 2021, Kyung Hoi (Joseph) Min. Revision 6662460d . Built with Sphinx using a theme provided by Read the Docs . + +### https://github.com/Lioscro/ngs-tools +GitHub - Lioscro/ngs-tools: Reusable tools for working with next-generation sequencing (NGS) data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Lioscro / ngs-tools Public Notifications You must be signed in to change notification settings Fork 7 Star 12 Code Issues 1 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Lioscro/ngs-tools main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 196 Commits 196 Commits .github/ workflows .github/ workflows docs docs ngs_tools ngs_tools tests tests .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml LICENSE LICENSE MANIFEST.in MANIFEST.in Makefile Makefile README.md README.md codecov.yml codecov.yml dev-requirements.txt dev-requirements.txt requirements-levenshtein.txt requirements-levenshtein.txt requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README MIT license ngs_tools Reusable tools for working with next-generation sequencing (NGS) data Documentation: https://ngs-tools.readthedocs.io/en/latest/ About Reusable tools for working with next-generation sequencing (NGS) data Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 12 stars Watchers 2 watching Forks 7 forks Report repository Releases 2 v1.8.6 Latest Oct 7, 2024 + 1 release Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.8% Makefile 0.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/Lioscro/ngs-tools +GitHub - Lioscro/ngs-tools: Reusable tools for working with next-generation sequencing (NGS) data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Lioscro / ngs-tools Public Notifications You must be signed in to change notification settings Fork 7 Star 12 Code Issues 1 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Lioscro/ngs-tools main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 196 Commits 196 Commits .github/ workflows .github/ workflows docs docs ngs_tools ngs_tools tests tests .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml LICENSE LICENSE MANIFEST.in MANIFEST.in Makefile Makefile README.md README.md codecov.yml codecov.yml dev-requirements.txt dev-requirements.txt requirements-levenshtein.txt requirements-levenshtein.txt requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README MIT license ngs_tools Reusable tools for working with next-generation sequencing (NGS) data Documentation: https://ngs-tools.readthedocs.io/en/latest/ About Reusable tools for working with next-generation sequencing (NGS) data Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 12 stars Watchers 2 watching Forks 7 forks Report repository Releases 2 v1.8.6 Latest Oct 7, 2024 + 1 release Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.8% Makefile 0.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge ngs-tools --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +ngs-tools 1.3.0 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.3.0-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.3.0 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.3.0-py39hdfd78af_0.tar.bz2 +md5 : 25906c3e383933493b1fe8071961df90 +timestamp : 2021-06-03 07:56:29 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.4.0 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.4.0-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.4.0 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.4.0-py39hdfd78af_0.tar.bz2 +md5 : fa3b85066d64a71916ee452a5afa0070 +timestamp : 2021-06-09 20:19:58 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.0 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.5.0-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.0 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.0-py39hdfd78af_0.tar.bz2 +md5 : 366575162019e25fb4a199f5e8057d12 +timestamp : 2021-07-11 11:25:22 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.2 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.5.2-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.2 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.2-py39hdfd78af_0.tar.bz2 +md5 : 3002c3cdd1e85758b7f8d75bf8912494 +timestamp : 2021-07-15 18:31:00 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.3 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.5.3-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.3 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.3-py39hdfd78af_0.tar.bz2 +md5 : b8e267f58d22ab2b0d538d4d81782a87 +timestamp : 2021-07-20 02:23:03 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.4 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.5.4-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.4 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.4-py39hdfd78af_0.tar.bz2 +md5 : 7c239fb6a1584dc3629f53585d57a31c +timestamp : 2021-07-28 16:22:50 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.5 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.5.5-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.5 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.5-py39hdfd78af_0.tar.bz2 +md5 : 1b3acc084e6aeec6d2de565b512065c4 +timestamp : 2021-08-02 20:30:08 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.6 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.5.6-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.6 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.6-py39hdfd78af_0.tar.bz2 +md5 : b00e17d28b9fabe48861d46ed9f9de0a +timestamp : 2021-08-13 18:21:09 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.7 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.5.7-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.7 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.7-py39hdfd78af_0.tar.bz2 +md5 : 2d9eaf853803a1ecd24dbf66671dbe26 +timestamp : 2021-08-26 20:21:01 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.8 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.5.8-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.8 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.8-py39hdfd78af_0.tar.bz2 +md5 : 403dac78f45732144ca826a73308766f +timestamp : 2021-10-19 16:32:49 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.9 py39hdfd78af_0 +------------------------------ +file name : ngs-tools-1.5.9-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.9 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.9-py39hdfd78af_0.tar.bz2 +md5 : bc40350c73786a261fa46d7b8b02d03e +timestamp : 2021-12-05 19:28:41 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.9 pyhdfd78af_1 +---------------------------- +file name : ngs-tools-1.5.9-pyhdfd78af_1.tar.bz2 +name : ngs-tools +version : 1.5.9 +build : pyhdfd78af_1 +build number: 1 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.9-pyhdfd78af_1.tar.bz2 +md5 : f169c116fed6b33fb27269555463ea41 +timestamp : 2022-01-20 23:09:41 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.10 py39hdfd78af_0 +------------------------------- +file name : ngs-tools-1.5.10-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.10 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.10-py39hdfd78af_0.tar.bz2 +md5 : ddb93f727b416386aa96d29440396ed6 +timestamp : 2022-01-18 09:59:04 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.11 py39hdfd78af_0 +------------------------------- +file name : ngs-tools-1.5.11-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.11 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.11-py39hdfd78af_0.tar.bz2 +md5 : 9cb77b65545d231230372ea52b88e499 +timestamp : 2022-01-19 08:31:59 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.12 py39hdfd78af_0 +------------------------------- +file name : ngs-tools-1.5.12-py39hdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.12 +build : py39hdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.12-py39hdfd78af_0.tar.bz2 +md5 : c27d50b3b3581ead1229bc66dc4738cc +timestamp : 2022-01-20 19:39:06 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.12 pyhdfd78af_1 +----------------------------- +file name : ngs-tools-1.5.12-pyhdfd78af_1.tar.bz2 +name : ngs-tools +version : 1.5.12 +build : pyhdfd78af_1 +build number: 1 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.12-pyhdfd78af_1.tar.bz2 +md5 : a27bd32605dc0e67a0bbb919c6ef81ca +timestamp : 2022-02-08 16:06:48 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.13 pyhdfd78af_0 +----------------------------- +file name : ngs-tools-1.5.13-pyhdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.13 +build : pyhdfd78af_0 +build number: 0 +size : 34.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.13-pyhdfd78af_0.tar.bz2 +md5 : 86f36db337478ca0a5017dcb969817a7 +timestamp : 2022-03-05 04:26:23 UTC +dependencies: + - joblib >=1.0.1 + - numba >=0.53.1 + - numpy >=1.19.0 + - pysam >=0.16.0.1 + - pyseq-align >=1.0.0 + - python >=3.6 + - shortuuid >=1.0.1 + - tqdm >=4.50.0 + - typing-extensions >=3.7.4 + + +ngs-tools 1.5.14 pyhdfd78af_0 +----------------------------- +file name : ngs-tools-1.5.14-pyhdfd78af_0.tar.bz2 +name : ngs-tools +version : 1.5.14 +build : pyhdfd78af_0 +build number: 0 +size : 35.7 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ngs-tools-1.5.14-pyhdfd78af_0.tar.bz2 +md5 : bd8737e3804370278c2e5a273c9c79b0 +tim diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/novoalign.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/novoalign.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..9815837405f3d7825929dfe885ef9663e8a43d39 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/novoalign.manual_bundle.txt @@ -0,0 +1,429 @@ +# Tool: novoalign +software_name: novoalign +tier: T1 +domain: t1_backfill_overall +downloads: 122001 +summary: Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms +description: Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms +dependencies: curl, libgcc >=13, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, util-linux +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://www.novocraft.com/products/novoalign/ +doc_url: +dev_url: + +## CLI Help Source +cli:novoalign +## CLI Help Content +$ conda run -n bioenv_cli novoalign --help +[rc=255] + +/bin/bash: /225040511/miniconda3/envs/bioenv_cli/lib/libtinfo.so.6: no version information available (required by /bin/bash) +Error - You need a valid current license to use this product. +You can purchase a license or request a trial license from http://www.novocraft.com/buy-now/ +Novoalign V3 and earlier can be used by non-profit organisations without a license with some limitations on functionality. + +ERROR conda.cli.main_run:execute(127): `conda run novoalign --help` failed. (See above for error) + + +## URL Docs Extract +### http://www.novocraft.com/products/novoalign/ +novoAlign | Novocraft full border #666666 http://www.novocraft.com/wp-content/themes/smartbox-installable/ http://www.novocraft.com/ #0397c9 style1 Home Products novoAlign novoHLA novoWorx novoClinic novoAlignCS novoSort novoSplice Services Bioinformatics Consultancy Pipeline and Software Development Services Bioinformatics Contract Research Services Support Download FAQ User Forum News About Us Clients Opportunities Investor Contact Us Try/Buy Open Menu Home Products novoAlign novoHLA novoWorx novoClinic novoAlignCS novoSort novoSplice Services Bioinformatics Consultancy Pipeline and Software Development Services Bioinformatics Contract Research Services Support Download FAQ User Forum News About Us Clients Opportunities Investor Contact Us Try/Buy A powerful tool for mapping of short reads onto a reference genome   Introducing novoAlign, a powerful tool for mapping short reads onto reference genomes from Illumina and MGI Tech platforms. Designed to streamline and optimize this critical process, novoAlign ensures precise alignments and deeper genetic insights. Elevate your research and unlock data potential with our advanced technology. Request trial Download brochure Higher precision alignment Better SV calling performance_line Superior sensitivity tool_line Extensive technical support Trusted by more than 200 institutions, research centers, universities, and corporations Why novoAlign novoAlign+GATK pipeline scores a higher AUC value, higher recall, and higher precision than BWA+GATK High AUC for SNPs   ROC-like PR curves from hap.py results comparing GIAB benchmark SNPs with Novoalign+GATK and BWA+GATK pipeline SNPs. The graph focuses on high-quality SNPs, and the AUC value is calculated using the “bayestestR” library in R. High AUC for INDELs   ROC-like PR curves from hap.py results comparing GIAB benchmark INDELS with Novoalign+GATK and BWA+GATK pipeline INDELs. The graph focuses on high-quality INDELs, and the AUC value is calculated using the “bayestestR” library in R. Why novoAlign Superior Precision and Recall for Structural Variants   Achieve unparalleled accuracy in detecting variants with our novoAlign, delivering superior precision and recall rates. Whether identifying deletions, duplications, or structural variants, novoAlign ensures reliable results, minimizing false positives and capturing critical genomic alterations with confidence. Benchmarking Results Request Trial High sensitivity Unlocking Precision: High Sensitivity in Sequence Alignment   Discover the power of high sensitivity in sequence alignment. Our advanced aligner, novoAlign, ensures precision and accuracy in your genomics and bioinformatics projects, providing a detailed view of your data. No more missed variations or incomplete alignments. This figure is obtained from a study on reads alignment or contigs assembly against a large reference genome. It shows that novoAlign has scored highest in sensitivity compared to other aligners. (Source: https://doi.org/10.48550/arXiv.1303.3997 ) Technical support Fully backed up by extensive technical support   We give you the assurance and confidence in your research needs. Explore, and post questions in our information rich support forum to seek the best answers to all your technical questions from a community of experts and fellow users. Visit forum Documentation How novoAlign Works   novoAlign streamlines your genomic analysis from start to finish. It begins with NGS data and a reference genome, then performs precise read alignment, followed by variant calling and annotation. The process concludes with variant selection and validation assessment, ensuring accurate and reliable results for your research. Testimonial “novoAlign showed the highest accuracy in all alignments. It is also reached the best mapping score for uniquely aligned coding sequences in WGS analysis”   Neural Computing and Applications, 32(22), 15669-15692 (2021) Request trial Download Other unsurpassed features Mapping with base quality values Bisulphite alignment mode for analysis of methylation status Alignment quality scores using posterior alignment probability Automatic base quality calibration Paired end alignment Handles single end and paired end reads up to 950bp/read Mismatches and gaps of up to 50% of read length In built adapter trimming and base quality trimming. Use of ambiguous codes in reference sequences can be used to reduce allelic bias Option for amplicon primer trimming. Applications Unleashing novoAlign in diverse applications Whole exome sequence RNA Whole genome sequence Human Leukocyte Antigen (HLA) typing Amplicon miRNA Publications What others are saying? “GATK worked best on alignments produced by novoAlign.” Schilbert et. al. Plants. 2020; 9(4):439 “novoAlign + GATK detects more variants than the other.” Park et. al. Genes & Genomics. 2023; 1-10 “We observed that Novoalign was the leading aligner with the highest accuracy.” Adam et. al. Pertanika. 2022; 30 (4): 2727 - 2745 Unlocking the potentials in various research areas novoAlign can be used in numerous fields in the biological sciences. Genomics Transcriptomics Metagenomics Pharmacology Cancer Research Human Genetics Plant Genomics Microbiology Ready to elevate your research? Get started with novoAlign today! Contact us Request trial LATEST NEWS Novocraft and Basepair Inc. Announce Strategic Partnership to Deliver Advanced Genomic Pipelines in the Cloud April 9, 2025 The collaboration aims to expand access to advanced bioinformatics tools through innovative cloud... read more » Novoalign V4.03.01 October 13, 2020 A 25-35% performance improvement for mate pair alignments when using long & short fragment... read more » Novoalign V4.03.00 and Novosort V3.00.00 October 13, 2020 This release is primarily about better UMI support with changes in Novoalign for extracting... read more » Contact Us Novocraft Technologies Sdn Bhd C-23A-05, 3 Two Square Seksyen 19 46300 Petaling Jaya Selangor, Malaysia Tel: +603 7960 0541 Fax: +603 7960 0540 office@novocraft.com © 2023 Novocraft Technologies Sdn Bhd. All rights reserved. default No more posts to load. Load More Posts Loading posts... 333333 link_magnifier #6E787E on fadeInDown /%postname%/ #6E787E on + +## Conda Search Info +$ conda search -c bioconda -c conda-forge novoalign --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +novoalign 3.03.02 0 +------------------- +file name : novoalign-3.03.02-0.tar.bz2 +name : novoalign +version : 3.03.02 +build : 0 +build number: 0 +size : 12.1 MB +license : Commercial (requires license for multithreaded use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.03.02-0.tar.bz2 +md5 : 2c0c161adc5dedbea2b44409956038d6 +dependencies: [] + + +novoalign 3.04.04 0 +------------------- +file name : novoalign-3.04.04-0.tar.bz2 +name : novoalign +version : 3.04.04 +build : 0 +build number: 0 +size : 12.1 MB +license : Commercial (requires license for multithreaded use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.04.04-0.tar.bz2 +md5 : a24ed420d9c65439dbcc32546d472353 +dependencies: [] + + +novoalign 3.04.04 2 +------------------- +file name : novoalign-3.04.04-2.tar.bz2 +name : novoalign +version : 3.04.04 +build : 2 +build number: 2 +size : 12.1 MB +license : Commercial (requires license for multithreaded use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.04.04-2.tar.bz2 +md5 : 4215e84e606be518ef9759fdf20ff333 +dependencies: [] + + +novoalign 3.04.04 3 +------------------- +file name : novoalign-3.04.04-3.tar.bz2 +name : novoalign +version : 3.04.04 +build : 3 +build number: 3 +size : 12.1 MB +license : Commercial (requires license for multithreaded use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.04.04-3.tar.bz2 +md5 : f852f726b54490fe8417b9477317cb45 +dependencies: [] + + +novoalign 3.06.05 0 +------------------- +file name : novoalign-3.06.05-0.tar.bz2 +name : novoalign +version : 3.06.05 +build : 0 +build number: 0 +size : 11.9 MB +license : Commercial (requires license for multithreaded use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.06.05-0.tar.bz2 +md5 : 23a0f0678ce986649f01b2786b6a5420 +dependencies: [] + + +novoalign 3.07.00 0 +------------------- +file name : novoalign-3.07.00-0.tar.bz2 +name : novoalign +version : 3.07.00 +build : 0 +build number: 0 +size : 12.0 MB +license : Commercial (requires license for multithreaded use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.07.00-0.tar.bz2 +md5 : 1852cbe26b4861d7b267e5e48a70c8ae +dependencies: [] + + +novoalign 3.07.00 1 +------------------- +file name : novoalign-3.07.00-1.tar.bz2 +name : novoalign +version : 3.07.00 +build : 1 +build number: 1 +size : 12.0 MB +license : Commercial (requires license for multithreaded use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.07.00-1.tar.bz2 +md5 : 3e4b9d9440045ab1dd05990cac95eace +timestamp : 2018-07-05 22:49:59 UTC +dependencies: [] + + +novoalign 3.09.00 0 +------------------- +file name : novoalign-3.09.00-0.tar.bz2 +name : novoalign +version : 3.09.00 +build : 0 +build number: 0 +size : 16.3 MB +license : Commercial (requires license for multithreaded use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.00-0.tar.bz2 +md5 : ce2d0227f023a16af5ed2b4af53edac2 +timestamp : 2018-08-14 12:12:17 UTC +dependencies: [] + + +novoalign 3.09.00 h7311fa2_1 +---------------------------- +file name : novoalign-3.09.00-h7311fa2_1.tar.bz2 +name : novoalign +version : 3.09.00 +build : h7311fa2_1 +build number: 1 +size : 30.0 MB +license : Commercial (requires license for commercial use or for features likes multi-threading) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.00-h7311fa2_1.tar.bz2 +md5 : 8509947f7551f4ddeb7c34c9ab357ee5 +timestamp : 2018-08-23 09:53:01 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +novoalign 3.09.00 h7311fa2_2 +---------------------------- +file name : novoalign-3.09.00-h7311fa2_2.tar.bz2 +name : novoalign +version : 3.09.00 +build : h7311fa2_2 +build number: 2 +size : 30.0 MB +license : Commercial (requires license for commercial use or for features likes multi-threading) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.00-h7311fa2_2.tar.bz2 +md5 : 0e9270dffa5fa698b01e97289d008630 +timestamp : 2018-09-02 18:50:41 UTC +dependencies: + - curl >=7.59.0,<8.0a0 + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +novoalign 3.09.04 h02d2503_4 +---------------------------- +file name : novoalign-3.09.04-h02d2503_4.tar.bz2 +name : novoalign +version : 3.09.04 +build : h02d2503_4 +build number: 4 +size : 35.7 MB +license : Commercial (requires license for commercial use or for features likes multi-threading) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.04-h02d2503_4.tar.bz2 +md5 : fb721dd7af82aae63b483de244eb3a05 +timestamp : 2022-02-22 20:29:22 UTC +dependencies: + - curl >=7.81.0,<8.0a0 + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +novoalign 3.09.04 h02d2503_5 +---------------------------- +file name : novoalign-3.09.04-h02d2503_5.tar.bz2 +name : novoalign +version : 3.09.04 +build : h02d2503_5 +build number: 5 +size : 35.4 MB +license : Commercial (requires license for commercial use or for features likes multi-threading) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.04-h02d2503_5.tar.bz2 +md5 : b441d7c180d669b774e8e22bf6139c79 +timestamp : 2023-05-13 10:38:45 UTC +dependencies: + - curl >=7.88.1,<8.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +novoalign 3.09.04 h82c745c_3 +---------------------------- +file name : novoalign-3.09.04-h82c745c_3.tar.bz2 +name : novoalign +version : 3.09.04 +build : h82c745c_3 +build number: 3 +size : 35.8 MB +license : Commercial (requires license for commercial use or for features likes multi-threading) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.04-h82c745c_3.tar.bz2 +md5 : 8bf28cc9372dea27f2f6200e0fb7180e +timestamp : 2021-03-24 16:29:20 UTC +dependencies: + - curl >=7.75.0,<8.0a0 + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +novoalign 3.09.04 h8456db6_7 +---------------------------- +file name : novoalign-3.09.04-h8456db6_7.tar.bz2 +name : novoalign +version : 3.09.04 +build : h8456db6_7 +build number: 7 +size : 35.7 MB +license : Commercial (requires license for commercial use or for features likes multi-threading) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.04-h8456db6_7.tar.bz2 +md5 : be1998f30b3641ebdd818f2c9a9f1c01 +timestamp : 2024-12-12 03:41:08 UTC +dependencies: + - curl + - libgcc >=13 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + - zlib + + +novoalign 3.09.04 h9c0d1ba_2 +---------------------------- +file name : novoalign-3.09.04-h9c0d1ba_2.tar.bz2 +name : novoalign +version : 3.09.04 +build : h9c0d1ba_2 +build number: 2 +size : 35.6 MB +license : Commercial (requires license for commercial use or for features likes multi-threading) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.04-h9c0d1ba_2.tar.bz2 +md5 : db60c63b7acf70a064cd90ea036c8ace +timestamp : 2020-07-03 02:58:42 UTC +dependencies: + - curl >=7.71.1,<8.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +novoalign 3.09.04 hb0d03b7_6 +---------------------------- +file name : novoalign-3.09.04-hb0d03b7_6.tar.bz2 +name : novoalign +version : 3.09.04 +build : hb0d03b7_6 +build number: 6 +size : 35.6 MB +license : Commercial (requires license for commercial use or for features likes multi-threading) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.04-hb0d03b7_6.tar.bz2 +md5 : 2dece941feb51a00ad5e6c1f9512fb66 +timestamp : 2023-05-16 11:37:29 UTC +dependencies: + - curl + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +novoalign 3.09.04 hc900ff6_0 +---------------------------- +file name : novoalign-3.09.04-hc900ff6_0.tar.bz2 +name : novoalign +version : 3.09.04 +build : hc900ff6_0 +build number: 0 +size : 35.5 MB +license : Commercial (requires license for commercial use or for features likes multi-threading) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.04-hc900ff6_0.tar.bz2 +md5 : 3a2431e763a7f546e0f8b3f787b29b98 +timestamp : 2020-01-14 23:27:09 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +novoalign 3.09.04 hc900ff6_1 +---------------------------- +file name : novoalign-3.09.04-hc900ff6_1.tar.bz2 +name : novoalign +version : 3.09.04 +build : hc900ff6_1 +build number: 1 +size : 35.7 MB +license : Commercial (requires license for commercial use or for features likes multi-threading) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-3.09.04-hc900ff6_1.tar.bz2 +md5 : dc8c730cb8abc079b1d031521128f5c4 +timestamp : 2020-01-15 00:48:02 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +novoalign 4.02.00 hc900ff6_0 +---------------------------- +file name : novoalign-4.02.00-hc900ff6_0.tar.bz2 +name : novoalign +version : 4.02.00 +build : hc900ff6_0 +build number: 0 +size : 27.3 MB +license : Commercial (requires license for use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-4.02.00-hc900ff6_0.tar.bz2 +md5 : 4cb36da410145b336c02f076ae57f301 +timestamp : 2020-01-15 00:53:54 UTC +dependencies: + - curl >=7.64.1,<8.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +novoalign 4.02.02 h82c745c_2 +---------------------------- +file name : novoalign-4.02.02-h82c745c_2.tar.bz2 +name : novoalign +version : 4.02.02 +build : h82c745c_2 +build number: 2 +size : 27.5 MB +license : Commercial (requires license for use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-4.02.02-h82c745c_2.tar.bz2 +md5 : 9204126f77e330cb787f729dd82a80c4 +timestamp : 2021-03-24 16:39:35 UTC +dependencies: + - curl >=7.75.0,<8.0a0 + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +novoalign 4.02.02 h82c745c_4 +---------------------------- +file name : novoalign-4.02.02-h82c745c_4.tar.bz2 +name : novoalign +version : 4.02.02 +build : h82c745c_4 +build number: 4 +size : 27.6 MB +license : Commercial (requires license for use) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/novoalign-4.02.02-h82c745c_4.tar.bz2 +md5 : 08920007d8f05e1bbb3c921b9d5b35cc +timestamp : 2021-11-03 01:15:02 UTC +dependencies: + - curl >=7.79.1,<8.0a0 + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +novoalign 4.02.02 h9c0d1ba_1 +---------------------------- +file name : novoalign-4.02.02-h9c0d1ba_1.tar.bz2 +name diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/orthofinder.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/orthofinder.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..04714c0196555e99127d98c4f5e740173721aeae --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/orthofinder.manual_bundle.txt @@ -0,0 +1,672 @@ +# Tool: orthofinder +software_name: orthofinder +tier: T1 +domain: t1_backfill_overall +downloads: 136989 +summary: Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy! +description: Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy! +dependencies: aster, biopython, blast, bzip2, diamond <2.2|>=2.1.7, ete4, famsa, fastme, fasttree, iqtree, mafft, mcl, mmseqs2, muscle, numpy, python >=3.11,<=3.14, raxml, raxml-ng, rich, scikit-learn, scipy +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/OrthoFinder/OrthoFinder +doc_url: https://orthofinder.github.io/OrthoFinder +dev_url: https://github.com/OrthoFinder/OrthoFinder + +## CLI Help Source +cli:orthofinder +## CLI Help Content +$ conda run -n bioenv_py_sc orthofinder --help +[rc=0] + +OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms + +SIMPLE USAGE: +Run full OrthoFinder analysis on FASTA format proteomes in

+ orthofinder [options] -f + +Add new species in to previous run in and run new analysis + orthofinder [options] -f -b + +OPTIONS: + -t Number of parallel sequence search threads [Default = 112] + -a Number of parallel analysis threads + -d Input is DNA sequences + -M Method for gene tree inference. Options 'dendroblast' & 'msa' + [Default = dendroblast] + -S Sequence search program [Default = diamond] + Options: blast, diamond, diamond_ultra_sens, blast_gz, mmseqs, blast_nucl + -A MSA program, requires '-M msa' [Default = mafft] + Options: mafft, muscle + -T Tree inference method, requires '-M msa' [Default = fasttree] + Options: fasttree, raxml, raxml-ng, iqtree + -s User-specified rooted species tree + -I MCL inflation parameter [Default = 1.5] + --fewer-files Only create one orthologs file per species + -x Info for outputting results in OrthoXML format + -p Write the temporary pickle files to + -1 Only perform one-way sequence search + -X Don't add species names to sequence IDs + -y Split paralogous clades below root of a HOG into separate HOGs + -z Don't trim MSAs (columns>=90% gap, min. alignment length 500) + -n Name to append to the results directory + -o Non-default results directory + -h Print this help text + +WORKFLOW STOPPING OPTIONS: + -op Stop after preparing input files for BLAST + -og Stop after inferring orthogroups + -os Stop after writing sequence files for orthogroups + (requires '-M msa') + -oa Stop after inferring alignments for orthogroups + (requires '-M msa') + -ot Stop after inferring gene trees for orthogroups + +WORKFLOW RESTART COMMANDS: + -b Start OrthoFinder from pre-computed BLAST results in + -fg Start OrthoFinder from pre-computed orthogroups in + -ft Start OrthoFinder from pre-computed gene trees in + +LICENSE: + Distributed under the GNU General Public License (GPLv3). See License.md + +CITATION: + When publishing work that uses OrthoFinder please cite: + Emms D.M. & Kelly S. (2019), Genome Biology 20:238 + + If you use the species tree in your work then please also cite: + Emms D.M. & Kelly S. (2017), MBE 34(12): 3267-3278 + Emms D.M. & Kelly S. (2018), bioRxiv https://doi.org/10.1101/267914 + + + +## URL Docs Extract +### https://orthofinder.github.io/OrthoFinder +Home | OrthoFinder OrthoFinder --> OrthoFinder Home About Download & Install Tutorials FAQ --> Home About Download & Install Tutorials FAQ GitHub Home --> Home OrthoFinder identifies orthogroups, infers gene trees for all orthogroups, and analyzes the gene trees to identify the rooted species tree. The method subsequently identifies all gene duplication events in the complete set of gene trees, and analyses them at both gene tree and species tree level. OrthoFinder further analyzes all of this phylogenetic information to identify the complete set of orthologs between all species, and provides extensive comparative genomics statistics. --> Home OrthoFinder identifies orthogroups, infers gene trees for all orthogroups, and analyzes the gene trees to identify the rooted species tree. The method subsequently identifies all gene duplication events in the complete set of gene trees, and analyses them at both gene tree and species tree level. OrthoFinder further analyzes all of this phylogenetic information to identify the complete set of orthologs between all species, and provides extensive comparative genomics statistics. Apr 2, 2026 OrthoFinder-v3.1.3 📦 orthofinder-linux-intel-3.1.3.tar.gz Feb 17, 2026 OrthoFinder-v3.1.2 📦 orthofinder-linux-intel-3.1.2.tar.gz Jan 5, 2026 OrthoFinder-v3.1.1 📦 orthofinder-linux-intel-3.1.1.tar.gz May 7, 2025 OrthoFinder-v3.1.0 📦 orthofinder-linux-intel-3.1.0.tar.gz --> Subscribe --> --> GitHub Link to the team section instead of listing every author Meet the Team --> Meet the Team This is a software developed by the [Steven Kelly Lab](http://www.stevekellylab.com/). --> This is a software developed by the Steven Kelly Lab . --> + +### https://github.com/OrthoFinder/OrthoFinder +GitHub - OrthoFinder/OrthoFinder: Phylogenetic orthology inference for comparative genomics · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} OrthoFinder / OrthoFinder Public forked from davidemms/OrthoFinder Notifications You must be signed in to change notification settings Fork 8 Star 121 Code Issues 23 Pull requests 2 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights OrthoFinder/OrthoFinder main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 932 Commits 932 Commits .github/ workflows .github/ workflows ExampleData ExampleData assets assets src/ orthofinder src/ orthofinder tests tests tools tools .gitignore .gitignore CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE MANIFEST.in MANIFEST.in Makefile Makefile README.md README.md orthofinder.py orthofinder.py pyproject.toml pyproject.toml requirements.txt requirements.txt requirements_dev.txt requirements_dev.txt setup.py setup.py user_config.json user_config.json View all files Repository files navigation README Contributing GPL-3.0 license OrthoFinder OrthoFinder identifies orthogroups, infers gene trees for all orthogroups, and analyzes the gene trees to identify the rooted species tree. The method subsequently identifies all gene duplication events in the complete set of gene trees, and analyses them at both gene tree and species tree level. OrthoFinder further analyzes all of this phylogenetic information to identify the complete set of orthologs between all species, and provides extensive comparative genomics statistics. Table of contents Installation Simple Usage Advanced Usage - Scaling to Thousands of Species Command line Options Output files Latest additions Citation System Requirements For more information please visit our website . Installation Install in conda (recommended) The simplest way to install OrthoFinder is through conda . If you're unfamiliar with conda, this tutorial offers a beginner-friendly introduction. conda create -n of3_env python=3.12 conda activate of3_env conda install orthofinder Alternatively, you could install via github, or download the source code and install locally. Install via github python3 -m venv of3_env . of3_env/bin/activate pip install git+https://github.com/OrthoFinder/OrthoFinder.git Install locally from source code The following commands provide three ways to download the source code of OrthoFinder locally into a directory named OrthoFinder . # Download via git git clone https://github.com/OrthoFinder/OrthoFinder.git # or download the orthofinder-linux-intel-3.1.4.tar.gz and unzip it into OrthoFinder if you are on a Linux Intel machine mkdir OrthoFinder && \ wget -qO- https://github.com/OrthoFinder/OrthoFinder/releases/download/v3.1.4/orthofinder-linux-intel-3.1.4.tar.gz | \ tar -xz --strip-components=1 -C OrthoFinder Next, you can run the following commands to install OrthoFinder inside the of3_env virtural environment. cd OrthoFinder python3 -m venv of3_env # Create an virtural environment named of3_env . of3_env/bin/activate # Activate of3_env pip install . Whether you've installed OrthoFinder directly from GitHub or downloaded and set it up locally, the OrthoFinder package will only be available within the of3_env virtual environment. This avoids potential conflicts with Python dependencies. To deactivate the virtual environment when you are finished, run: deactivate To activate the virtual environment you have created, run: . of3_env/bin/activate Test your installation Once you have installed OrthoFinder, you can print the help information and version, and test it on the example data . orthofinder --help # Print out help informatioin orthofinder --version # Check the version orthofinder -f ExampleData # Test OrthoFinder on an example dataset - this should take a few minutes to run. Uninstalling To uninstall on conda: conda deactivate conda remove -n of3_env --all To remove the virtual environment where OrthoFinder is installed: deactivate cd .. rm -rf OrthoFinder Simple Usage Run OrthoFinder on FASTA format proteomes in <dir> orthofinder [ options ] - f < dir > OrthoFinder requires one FASTA file for each species. Each file should contain the complete set of protein sequences from that species' genome, with a single representative sequence for each gene. If your files have multiple transcript variants for each gene, then we provide a script primary_transcripts.py to extract the longest variant per gene. This script should be run on your files prior to running OrthoFinder; for f in * fa ; do python primary_transcript.py $f ; done Advanced Usage - Scaling to Thousands of Species If you are analysing >100 species, we recommend that you use the scalable implementation. Add the files for 64 species into one directory <core> Add the remaining files into another directory <additional> First, run OrthoFinder on the subset of 64 species orthofinder [ options ] - f < core > Then, add the additional species to the results of the core run orthofinder [ options ] - - assign < additional > - - core < Results_Dir > To choose which 64 species to include in the core, aim to capture a broad range of the evolutionary diversity of your species. Note that this alternative way of running OrthoFinder requires that the core species are run using the multiple sequence alignment option. You cannot add additional species to OrthoFinder results that were run with the -M dendroblast option, which was the default for OrthoFinder2 Command-line options Command-line options for OrthoFinder Adding additional species Parameter Description --assign <dir1> --core <dir2> Assign species from <dir1> to existing orthogroups in <dir2> . Method choices Parameter Description Default Options -M Method for gene tree inference. msa dendroblast , msa -S Sequence search program diamond blast , diamond , diamond_ultra_sens , blastp , mmseqs , blastn -A MSA program, requires -M msa famsa famsa , mafft , muscle , -T Tree inference method, requires -M msa fasttree fasttree , fasttree_fastest , raxml , iqtree -I MCL inflation parameter 1.2 1-10 Input options Parameter Description -d Input is DNA sequences. -s User-specified rooted species tree. Output options Parameter Description -X Don’t add species names to sequence IDs. -n <txt> Name to append to the results directory. -o <txt> Specify a non-default results directory. Parallel processing options Parameter Description Default -t Number of parallel sequence search threads. All available -a Number of parallel analysis threads. 16 or t/8 (whichever lower) Workflow stopping options Parameter Description -op Stop after preparing input files for BLAST. Workflow restart options Parameter Description -b <dir> Start OrthoFinder from pre-computed BLAST results in <dir> . Other options Parameter Description -1 Only perform one-way sequence search. -z Don’t trim MSAs (columns >= 90% gap, min. alignment length 500). -y Split paralogous clades below the root of a HOG into separate HOGs. -h Print this help text. -v Print version. Output files From OrthoFinder v3.1.4 , N0.tsv is removed from /Phylogenetic_Hierarchical_Orthogroups . Instead, Orthogroups/Orthogroups.tsv contains the orthogroups from N0.tsv . A standard OrthoFinder run produces a set of files describing the orthogroups, orthologs, gene trees, resolve gene trees, the rooted species tree, gene duplication events, and comparative genomic statistics for the set of species being analysed. These files are located in an intuitive directory structure. Full details on the output files and directories can be found here . The directories that are useful for most users are /Orthogroups Orthogroups.tsv is the main orthogroup file. Each row contains the genes belonging to a single orthogroup. The genes from each orthogroup are organized into columns, one per species. Orthogroups.txt is a text file with each line showing the genes in a single orthogroup. It differs from Orthogroups.tsv in that it doesn’t show the species which each gene belongs to. Orthogroups.GeneCount.tsv is a tab separated text file that contains counts of the number of genes for each species in each orthogroup. Orthogroups_SingleCopyOrthologues.txt is a list of orthogroups that contain exactly one gene per species Orthogrouops_UnassignedGenes.tsv is a tab separated text file that contains all of the genes that were not assigned to any orthogroup. /Phylogenetic_Hierarchical_Orthogroups Each file is a phylogenetic hierarchical orthogroup (HOG) for a different node of the species tree. Each row of a file contain the genes belonging to a single orthogroup. Each species is represented by a single column. N0.tsv from the old version is now Orthogroups/Orthogroups.tsv /Orthologues Each species has a sub-directory that in turn contains a file for each pairwise species comparison, listing the orthologs between that species pair. /Comparative_Genomics_Statistics Files containing summary statistics across all orthogroups, as well as comparisons between each pair of species. /Resolved_Gene_Trees A rooted phylogenetic tree inferred for each orthogroup with 4 or more sequences and resolved using the OrthoFinder hybrid species-overlap/duplication-loss coalescent model. /Species_Tree SpeciesTree_rooted.txt is a species tree inferred using STAG or ASTRAL-Pro. SpeciesTree_rooted_node_labels.txt is the same tree, but with nodes labels instead of support values. This labelled version is useful for interpreting and analysing the results of the gene duplication analyses. /Gene_Duplication_Events Duplications.tsv has a row for each gene duplication event, with information on orthogroup in which it occured, the species that contain the duplicated gene, the node in the species tree on which the gene duplication event occured, and the support score for the gene duplication event. SpeciesTree_Gene_Duplications_0.5_Support.txt provides a summation of the above duplications over the branches of the species tree. /Orthogroup_Sequences A FASTA file for each orthogroup giving the amino acid sequences for each gene in the orthogroup. Latest additions The current version of OrthoFinder has several major changes compared to OrthoFinder version 2 (Emms & Kelly 2019). New workflow for scalability The --core --assign workflow uses the SHOOT algorithm to create profiles for previously computed orthogroups, and adds new genes to these orthogroups without requiring a costly all-versus-all sequence search. Genes that cannot be assigned using the SHOOT approach are analysed using a standard OrthoFinder workflow. Phylogenetic Hierarchical Orthogroups OrthoFinder has now extended its phylogenetic approach to orthogroups, allowing orthogroups to be defined for each node within the species tree. This significantly increases the accuracy of orthogroups, and enables users to perform orthogroup analyses for any clade of species in the species tree. Citation Latest [1] David M Emms, Yi Liu, Laurence Belcher, Jonathan Holmes, Steven Kelly, 2025. OrthoFinder: scalable phylogenetic orthology inference for comparative genomics . bioRxiv. Introduced the SHOOT method to perform phylogenetic gene search [2] Emms, D.M., Kelly, S . SHOOT: phylogenetic gene search and ortholog inference . Genome Biol 23, 85 (2022). Introduced the phylogenetic inference of orthologs, including rooted gene and species trees, and gene duplication events [3] Emms, D.M., Kelly, S . OrthoFinder: phylogenetic orthology inference for comparative genomics . Genome Biol 20, 238 (2019). Introduced the STRIDE method to root an unrooted species tree. [4] Emms DM, Kelly S . STRIDE: Species Tree Root Inference from Gene Duplication Events . Mol Biol Evol. 2017 Dec 1;34(12):3267-3278. Introduced the STAG method of species tree inference [5] D.M. Emms, S. Kelly, 2017 . STAG: Species Tree Inference from All Genes bioRxiv. Introduced the orthogroup inference method [6] Emms, D.M., Kelly, S . OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy . Genome Biol 16, 157 (2015). System Requirements Operating system OrthoFinder was designed to run on Linux (including WSL2). We have tested OrthoFinder v3.1 on debian 12.9, centOS v8, macOS 14.4.1, macOS 13.2.1. Dependencies Python >=3.11 Diamond >=2.1.7,<2.2 Famsa >=2.2.3 Fasttree >=2.1.11 Numpy >=2.3.2 Scipy >=1.16 Biopython >=1.85 Rich >=14.1.0 Scikit-learn >=1.7.1 Meet the team OrthoFinder was developed by David Emms & Steve Kelly Current members of the OrthoFinder team: Yi Liu, Jonathan Holmes, Laurie Belcher About Phylogenetic orthology inference for comparative genomics orthofinder.github.io/OrthoFinder/ Resources Readme License GPL-3.0 license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 121 stars Watchers 1 watching Forks 8 forks Report repository Releases 6 OrthoFinder v3.1.4 Latest Apr 2, 2026 + 5 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 84.6% Shell 9.3% Makefile 4.5% Roff 1.6% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/OrthoFinder/OrthoFinder +GitHub - OrthoFinder/OrthoFinder: Phylogenetic orthology inference for comparative genomics · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} OrthoFinder / OrthoFinder Public forked from davidemms/OrthoFinder Notifications You must be signed in to change notification settings Fork 8 Star 121 Code Issues 23 Pull requests 2 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights OrthoFinder/OrthoFinder main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 932 Commits 932 Commits .github/ workflows .github/ workflows ExampleData ExampleData assets assets src/ orthofinder src/ orthofinder tests tests tools tools .gitignore .gitignore CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE MANIFEST.in MANIFEST.in Makefile Makefile README.md README.md orthofinder.py orthofinder.py pyproject.toml pyproject.toml requirements.txt requirements.txt requirements_dev.txt requirements_dev.txt setup.py setup.py user_config.json user_config.json View all files Repository files navigation README Contributing GPL-3.0 license OrthoFinder OrthoFinder identifies orthogroups, infers gene trees for all orthogroups, and analyzes the gene trees to identify the rooted species tree. The method subsequently identifies all gene duplication events in the complete set of gene trees, and analyses them at both gene tree and species tree level. OrthoFinder further analyzes all of this phylogenetic information to identify the complete set of orthologs between all species, and provides extensive comparative genomics statistics. Table of contents Installation Simple Usage Advanced Usage - Scaling to Thousands of Species Command line Options Output files Latest additions Citation System Requirements For more information please visit our website . Installation Install in conda (recommended) The simplest way to install OrthoFinder is through conda . If you're unfamiliar with conda, this tutorial offers a beginner-friendly introduction. conda create -n of3_env python=3.12 conda activate of3_env conda install orthofinder Alternatively, you could install via github, or download the source code and install locally. Install via github python3 -m venv of3_env . of3_env/bin/activate pip install git+https://github.com/OrthoFinder/OrthoFinder.git Install locally from source code The following commands provide three ways to download the source code of OrthoFinder locally into a directory named OrthoFinder . # Download via git git clone https://github.com/OrthoFinder/OrthoFinder.git # or download the orthofinder-linux-intel-3.1.4.tar.gz and unzip it into OrthoFinder if you are on a Linux Intel machine mkdir OrthoFinder && \ wget -qO- https://github.com/OrthoFinder/OrthoFinder/releases/download/v3.1.4/orthofinder-linux-intel-3.1.4.tar.gz | \ tar -xz --strip-components=1 -C OrthoFinder Next, you can run the following commands to install OrthoFinder inside the of3_env virtural environment. cd OrthoFinder python3 -m venv of3_env # Create an virtural environment named of3_env . of3_env/bin/activate # Activate of3_env pip install . Whether you've installed OrthoFinder directly from GitHub or downloaded and set it up locally, the OrthoFinder package will only be available within the of3_env virtual environment. This avoids potential conflicts with Python dependencies. To deactivate the virtual environment when you are finished, run: deactivate To activate the virtual environment you have created, run: . of3_env/bin/activate Test your installation Once you have installed OrthoFinder, you can print the help information and version, and test it on the example data . orthofinder --help # Print out help informatioin orthofinder --version # Check the version orthofinder -f ExampleData # Test OrthoFinder on an example dataset - this should take a few minutes to run. Uninstalling To uninstall on conda: conda deactivate conda remove -n of3_env --all To remove the virtual environment where OrthoFinder is installed: deactivate cd .. rm -rf OrthoFinder Simple Usage Run OrthoFinder on FASTA format proteomes in <dir> orthofinder [ options ] - f < dir > OrthoFinder requires one FASTA file for each species. Each file should contain the complete set of protein sequences from that species' genome, with a single representative sequence for each gene. If your files have multiple transcript variants for each gene, then we provide a script primary_transcripts.py to extract the longest variant per gene. This script should be run on your files prior to running OrthoFinder; for f in * fa ; do python primary_transcript.py $f ; done Advanced Usage - Scaling to Thousands of Species If you are analysing >100 species, we recommend that you use the scalable implementation. Add the files for 64 species into one directory <core> Add the remaining files into another directory <additional> First, run OrthoFinder on the subset of 64 species orthofinder [ options ] - f < core > Then, add the additional species to the results of the core run orthofinder [ options ] - - assign < additional > - - core < Results_Dir > To choose which 64 species to include in the core, aim to capture a broad range of the evolutionary diversity of your species. Note that this alternative way of running OrthoFinder requires that the core species are run using the multiple sequence alignment option. You cannot add additional species to OrthoFinder results that were run with the -M dendroblast option, which was the default for OrthoFinder2 Command-line options Command-line options for OrthoFinder Adding additional species Parameter Description --assign <dir1> --core <dir2> Assign species from <dir1> to existing orthogroups in <dir2> . Method choices Parameter Description Default Options -M Method for gene tree inference. msa dendroblast , msa -S Sequence search program diamond blast , diamond , diamond_ultra_sens , blastp , mmseqs , blastn -A MSA program, requires -M msa famsa famsa , mafft , muscle , -T Tree inference method, requires -M msa fasttree fasttree , fasttree_fastest , raxml , iqtree -I MCL inflation parameter 1.2 1-10 Input options Parameter Description -d Input is DNA sequences. -s User-specified rooted species tree. Output options Parameter Description -X Don’t add species names to sequence IDs. -n <txt> Name to append to the results directory. -o <txt> Specify a non-default results directory. Parallel processing options Parameter Description Default -t Number of parallel sequence search threads. All available -a Number of parallel analysis threads. 16 or t/8 (whichever lower) Workflow stopping options Parameter Description -op Stop after preparing input files for BLAST. Workflow restart options Parameter Description -b <dir> Start OrthoFinder from pre-computed BLAST results in <dir> . Other options Parameter Description -1 Only perform one-way sequence search. -z Don’t trim MSAs (columns >= 90% gap, min. alignment length 500). -y Split paralogous clades below the root of a HOG into separate HOGs. -h Print this help text. -v Print version. Output files From OrthoFinder v3.1.4 , N0.tsv is removed from /Phylogenetic_Hierarchical_Orthogroups . Instead, Orthogroups/Orthogroups.tsv contains the orthogroups from N0.tsv . A standard OrthoFinder run produces a set of files describing the orthogroups, orthologs, gene trees, resolve gene trees, the rooted species tree, gene duplication events, and comparative genomic statistics for the set of species being analysed. These files are located in an intuitive directory structure. Full details on the output files and directories can be found here . The directories that are useful for most users are /Orthogroups Orthogroups.tsv is the main orthogroup file. Each row contains the genes belonging to a single orthogroup. The genes from each orthogroup are organized into columns, one per species. Orthogroups.txt is a text file with each line showing the genes in a single orthogroup. It differs from Orthogroups.tsv in that it doesn’t show the species which each gene belongs to. Orthogroups.GeneCount.tsv is a tab separated text file that contains counts of the number of genes for each species in each orthogroup. Orthogroups_SingleCopyOrthologues.txt is a list of orthogroups that contain exactly one gene per species Orthogrouops_UnassignedGenes.tsv is a tab separated text file that contains all of the genes that were not assigned to any orthogroup. /Phylogenetic_Hierarchical_Orthogroups Each file is a phylogenetic hierarchical orthogroup (HOG) for a different node of the species tree. Each row of a file contain the genes belonging to a single orthogroup. Each species is represented by a single column. N0.tsv from the old version is now Orthogroups/Orthogroups.tsv /Orthologues Each species has a sub-directory that in turn contains a file for each pairwise species comparison, listing the orthologs between that species pair. /Comparative_Genomics_Statistics Files containing summary statistics across all orthogroups, as well as comparisons between each pair of species. /Resolved_Gene_Trees A rooted phylogenetic tree inferred for each orthogroup with 4 or more sequences and resolved using the OrthoFinder hybrid species-overlap/duplication-loss coalescent model. /Species_Tree SpeciesTree_rooted.txt is a species tree inferred using STAG or ASTRAL-Pro. SpeciesTree_rooted_node_labels.txt is the same tree, but with nodes labels instead of support values. This labelled version is useful for interpreting and analysing the results of the gene duplication analyses. /Gene_Duplication_Events Duplications.tsv has a row for each gene duplication event, with information on orthogroup in which it occured, the species that contain the duplicated gene, the node in the species tree on which the gene duplication event occured, and the support score for the gene duplication event. SpeciesTree_Gene_Duplications_0.5_Support.txt provides a summation of the above duplications over the branches of the species tree. /Orthogroup_Sequences A FASTA file for each orthogroup giving the amino acid sequences for each gene in the orthogroup. Latest additions The current version of OrthoFinder has several major changes compared to OrthoFinder version 2 (Emms & Kelly 2019). New workflow for scalability The --core --assign workflow uses the SHOOT algorithm to create profiles for previously computed orthogroups, and adds new genes to these orthogroups without requiring a costly all-versus-all sequence search. Genes that cannot be assigned using the SHOOT approach are analysed using a standard OrthoFinder workflow. Phylogenetic Hierarchical Orthogroups OrthoFinder has now extended its phylogenetic approach to orthogroups, allowing orthogroups to be defined for each node within the species tree. This significantly increases the accuracy of orthogroups, and enables users to perform orthogroup analyses for any clade of species in the species tree. Citation Latest [1] David M Emms, Yi Liu, Laurence Belcher, Jonathan Holmes, Steven Kelly, 2025. OrthoFinder: scalable phylogenetic orthology inference for comparative genomics . bioRxiv. Introduced the SHOOT method to perform phylogenetic gene search [2] Emms, D.M., Kelly, S . SHOOT: phylogenetic gene search and ortholog inference . Genome Biol 23, 85 (2022). Introduced the phylogenetic inference of orthologs, including rooted gene and species trees, and gene duplication events [3] Emms, D.M., Kelly, S . OrthoFinder: phylogenetic orthology inference for comparative genomics . Genome Biol 20, 238 (2019). Introduced the STRIDE method to root an unrooted species tree. [4] Emms DM, Kelly S . STRIDE: Species Tree Root Inference from Gene Duplication Events . Mol Biol Evol. 2017 Dec 1;34(12):3267-3278. Introduced the STAG method of species tree inference [5] D.M. Emms, S. Kelly, 2017 . STAG: Species Tree Inference from All Genes bioRxiv. Introduced the orthogroup inference method [6] Emms, D.M., Kelly, S . OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy . Genome Biol 16, 157 (2015). System Requirements Operating system OrthoFinder was designed to run on Linux (including WSL2). We have tested OrthoFinder v3.1 on debian 12.9, centOS v8, macOS 14.4.1, macOS 13.2.1. Dependencies Python >=3.11 Diamond >=2.1.7,<2.2 Famsa >=2.2.3 Fasttree >=2.1.11 Numpy >=2.3.2 Scipy >=1.16 Biopython >=1.85 Rich >=14.1.0 Scikit-learn >=1.7.1 Meet the team OrthoFinder was developed by David Emms & Steve Kelly Current members of the OrthoFinder team: Yi Liu, Jonathan Holmes, Laurie Belcher About Phylogenetic orthology inference for comparative genomics orthofinder.github.io/OrthoFinder/ Resources Readme License GPL-3.0 license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 121 stars Watchers 1 watching Forks 8 forks Report repository Releases 6 OrthoFinder v3.1.4 Latest Apr 2, 2026 + 5 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 84.6% Shell 9.3% Makefile 4.5% Roff 1.6% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge orthofinder --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +orthofinder 1.1.2 py27_0 +------------------------ +file name : orthofinder-1.1.2-py27_0.tar.bz2 +name : orthofinder +version : 1.1.2 +build : py27_0 +build number: 0 +size : 55 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/orthofinder-1.1.2-py27_0.tar.bz2 +md5 : 0d845a9806813c3cafed65effc071378 +dependencies: + - blast + - dlcpar + - fastme + - mcl + - python 2.7* + - scipy + + +orthofinder 1.1.4 py27_0 +------------------------ +file name : orthofinder-1.1.4-py27_0.tar.bz2 +name : orthofinder +version : 1.1.4 +build : py27_0 +build number: 0 +size : 55 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/orthofinder-1.1.4-py27_0.tar.bz2 +md5 : 58cd08c3178da78d7883e8072cd7a8dc +dependencies: + - blast + - dlcpar + - fastme + - mcl + - python 2.7* + - scipy + + +orthofinder 1.1.8 py27_0 +------------------------ +file name : orthofinder-1.1.8-py27_0.tar.bz2 +name : orthofinder +version : 1.1.8 +build : py27_0 +build number: 0 +size : 62 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/orthofinder-1.1.8-py27_0.tar.bz2 +md5 : 9b3eb966690d486ac03abd72860456e1 +dependencies: + - blast + - dlcpar + - fastme + - mcl + - python 2.7* + - scipy + + +orthofinder 1.1.10 py27_0 +------------------------- +file name : orthofinder-1.1.10-py27_0.tar.bz2 +name : orthofinder +version : 1.1.10 +build : py27_0 +build number: 0 +size : 63 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/orthofinder-1.1.10-py27_0.tar.bz2 +md5 : b2ae6b19268322ce1b64f18acacf0721 +dependencies: + - blast + - diamond + - dlcpar + - fastme + - fasttree + - mafft + - mcl + - python 2.7* + - scipy + + +orthofinder 2.1.2 py27_0 +------------------------ +file name : orthofinder-2.1.2-py27_0.tar.bz2 +name : orthofinder +version : 2.1.2 +build : py27_0 +build number: 0 +size : 84 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/orthofinder-2.1.2-py27_0.tar.bz2 +md5 : 5a3ec14f37fb6a92d7cabae0c6419816 +dependencies: + - blast + - diamond + - dlcpar + - fastme + - fasttree + - mafft + - mcl + - python 2.7* + - scipy + + +orthofinder 2.1.2 py27_1 +------------------------ +file name : orthofinder-2.1.2-py27_1.tar.bz2 +name : orthofinder +version : 2.1.2 +build : py27_1 +build number: 1 +size : 85 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/orthofinder-2.1.2-py27_1.tar.bz2 +md5 : 1a29a8d0d8d5c9662c10294df060b196 +dependencies: + - blast + - diamond + - dlcpar + - fastme + - fasttree + - iqtree + - mafft + - mcl + - muscle + - python 2.7* + - raxml + - scipy + + +orthofinder 2.2.0 py27_0 +------------------------ +file name : orthofinder-2.2.0-py27_0.tar.bz2 +name : orthofinder +version : 2.2.0 +build : py27_0 +build number: 0 +size : 93 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/orthofinder-2.2.0-py27_0.tar.bz2 +md5 : 24b03cce5a97f691735bcc3384441f6d +dependencies: + - blast + - diamond + - dlcpar + - fastme + - fasttree + - iqtree + - mafft + - mcl + - muscle + - python 2.7* + - raxml + - scipy + + +orthofinder 2.2.1 py27_0 +------------------------ +file name : orthofinder-2.2.1-py27_0.tar.bz2 +name : orthofinder +version : 2.2.1 +build : py27_0 +build number: 0 +size : 91 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/orthofinder-2.2.1-py27_0.tar.bz2 +md5 : fd2102ac6da6c0b0fda93d287123adad +dependencies: + - blast + - diamond + - dlcpar + - fastme + - fasttree + - iqtree + - mafft + - mcl + - muscle + - python 2.7* + - raxml + - scipy + + +orthofinder 2.2.6 py27_0 +------------------------ +file name : orthofinder-2.2.6-py27_0.tar.bz2 +name : orthofinder +version : 2.2.6 +build : py27_0 +build number: 0 +size : 94 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/orthofinder-2.2.6-py27_0.tar.bz2 +md5 : 5f5209449e9b198cec63e3e71a0cbd1a +dependencies: + - blast + - diamond + - dlcpar + - fastme + - fasttree + - iqtree + - mafft + - mcl + - muscle + - python 2.7* + - raxml + - scipy + + +orthofinder 2.2.7 0 +------------------- +file name : orthofinder-2.2.7-0.tar.bz2 +name : orthofinder +version : 2.2.7 +build : 0 +build number: 0 +size : 94 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/orthofinder-2.2.7-0.tar.bz2 +md5 : 3a28f97afcd9f509875df41fd635784e +timestamp : 2018-09-24 20:22:08 UTC +dependencies: + - blast + - bzip2 + - diamond + - dlcpar + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python 2.7.* + - raxml + - scipy + + +orthofinder 2.3.3 0 +------------------- +file name : orthofinder-2.3.3-0.tar.bz2 +name : orthofinder +version : 2.3.3 +build : 0 +build number: 0 +size : 111 KB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.3.3-0.tar.bz2 +md5 : 4c1de82ef4d127dfea820c9c34446156 +timestamp : 2019-05-27 15:15:09 UTC +dependencies: + - blast + - bzip2 + - diamond + - dlcpar + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python 2.7.* + - raxml + - scipy + + +orthofinder 2.3.3 1 +------------------- +file name : orthofinder-2.3.3-1.tar.bz2 +name : orthofinder +version : 2.3.3 +build : 1 +build number: 1 +size : 112 KB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.3.3-1.tar.bz2 +md5 : ff80b10101bf1b829c5223c93d8ecd75 +timestamp : 2019-10-26 17:57:13 UTC +dependencies: + - blast + - bzip2 + - diamond + - dlcpar + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python 2.7.* + - raxml + - scipy + + +orthofinder 2.3.8 0 +------------------- +file name : orthofinder-2.3.8-0.tar.bz2 +name : orthofinder +version : 2.3.8 +build : 0 +build number: 0 +size : 2.6 MB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.3.8-0.tar.bz2 +md5 : 9c1fd42237fc3f32343e744c2e3a3f53 +timestamp : 2019-11-29 11:31:16 UTC +dependencies: + - blast + - bzip2 + - diamond + - dlcpar + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python >=2.7 + - raxml + - scipy + + +orthofinder 2.3.8 1 +------------------- +file name : orthofinder-2.3.8-1.tar.bz2 +name : orthofinder +version : 2.3.8 +build : 1 +build number: 1 +size : 2.6 MB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.3.8-1.tar.bz2 +md5 : c6234be274e077fd0008a70fc2dc760e +timestamp : 2019-12-02 22:17:54 UTC +dependencies: + - blast + - bzip2 + - diamond + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python >=2.7 + - raxml + - scipy + + +orthofinder 2.3.8 2 +------------------- +file name : orthofinder-2.3.8-2.tar.bz2 +name : orthofinder +version : 2.3.8 +build : 2 +build number: 2 +size : 116 KB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.3.8-2.tar.bz2 +md5 : 39893141924bbeac9d2ba7a02c200221 +timestamp : 2020-02-05 12:27:54 UTC +dependencies: + - blast + - bzip2 + - diamond <=0.9.24 + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python >=2.7 + - raxml + - scipy + + +orthofinder 2.3.10 0 +-------------------- +file name : orthofinder-2.3.10-0.tar.bz2 +name : orthofinder +version : 2.3.10 +build : 0 +build number: 0 +size : 116 KB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.3.10-0.tar.bz2 +md5 : a42714c27d26050e80a7d7934534a7c3 +timestamp : 2020-02-06 16:44:11 UTC +dependencies: + - blast + - bzip2 + - diamond <=0.9.24 + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python >=2.7 + - raxml + - scipy + + +orthofinder 2.3.11 0 +-------------------- +file name : orthofinder-2.3.11-0.tar.bz2 +name : orthofinder +version : 2.3.11 +build : 0 +build number: 0 +size : 116 KB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.3.11-0.tar.bz2 +md5 : 2c3b9d8abc2ca09311565d8a83448d6e +timestamp : 2020-02-11 11:31:48 UTC +dependencies: + - blast + - bzip2 + - diamond <=0.9.24 + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python >=2.7 + - raxml + - scipy + + +orthofinder 2.3.11 1 +-------------------- +file name : orthofinder-2.3.11-1.tar.bz2 +name : orthofinder +version : 2.3.11 +build : 1 +build number: 1 +size : 116 KB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.3.11-1.tar.bz2 +md5 : f6360daa78476d22257d14172255a347 +timestamp : 2020-04-19 00:56:41 UTC +dependencies: + - blast + - bzip2 + - diamond <=0.9.24 + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python >=2.7 + - raxml + - scipy + + +orthofinder 2.3.12 0 +-------------------- +file name : orthofinder-2.3.12-0.tar.bz2 +name : orthofinder +version : 2.3.12 +build : 0 +build number: 0 +size : 117 KB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.3.12-0.tar.bz2 +md5 : 7a890cec58f1dd86c3bd796c8da49916 +timestamp : 2020-05-07 17:16:02 UTC +dependencies: + - blast + - bzip2 + - diamond <=0.9.24 + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python >=2.7 + - raxml + - scipy + + +orthofinder 2.4.0 0 +------------------- +file name : orthofinder-2.4.0-0.tar.bz2 +name : orthofinder +version : 2.4.0 +build : 0 +build number: 0 +size : 120 KB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.4.0-0.tar.bz2 +md5 : a5ec81a287e4827eaacbfb6f49491add +timestamp : 2020-07-15 18:52:20 UTC +dependencies: + - blast + - bzip2 + - diamond <=0.9.24 + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python >=2.7 + - raxml + - scipy + + +orthofinder 2.4.0 1 +------------------- +file name : orthofinder-2.4.0-1.tar.bz2 +name : orthofinder +version : 2.4.0 +build : 1 +build number: 1 +size : 120 KB +license : GPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/orthofinder-2.4.0-1.tar.bz2 +md5 : cb9b3860a9c945b92c118c550237f351 +timestamp : 2020-08-14 10:56:54 UTC +dependencies: + - blast + - bzip2 + - diamond <=0.9.24 + - fastme + - fasttree + - iqtree + - mafft + - mcl + - mmseqs2 + - muscle + - python >=2.7 + - raxml + - raxml-ng + - scipy + + +orthofinder 2.4.1 0 +------ diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ourotools.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ourotools.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2440bc8da2e143f94104f8567c4fd081c8f07568 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/ourotools.manual_bundle.txt @@ -0,0 +1,135 @@ +# Tool: ourotools +software_name: ourotools +tier: T1 +domain: single_cell +downloads: 998 +summary: A comprehensive toolkit for quality control and analysis of single-cell long-read RNA-seq data +description: Ouro-Tools is a novel, comprehensive computational pipeline for long-read scRNA-seq with the following key features. Ouro-Tools (1) normalizes mRNA size distributions and (2) detects mRNA 7-methylguanosine caps to integrate multiple single-cell long-read RNA-sequencing experiments across modalities and characterize full-length transcripts, respectively. +dependencies: bitarray >=2.5.1, h5py >=3.8.0, intervaltree >=3.1.0, joblib >=1.2.0, mappy >=2.24, matplotlib-base >=3.5.2, minimap2 >=2.28, nest-asyncio >=1.5.6, numpy >=1.26.4, owlready2 >=0.46, pandas >=1.5.2, plotly >=5.18.0, pybigwig >=0.3.22, pysam >=0.18.0, python >=3.11, regex >=2.5.135, samtools >=1.10, scanpy >=1.10.2, scipy >=1.9.1, tqdm >=4.64.1 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/ahs2202/ouro-tools +doc_url: https://pypi.org/project/ourotools/ +dev_url: https://github.com/ahs2202/ouro-tools + +## URL Docs Extract +### https://pypi.org/project/ourotools/ +ourotools · PyPI Skip to main content Switch to mobile version Warning You are using an unsupported browser, upgrade to a newer version. Warning Some features may not work without JavaScript. Please try enabling it if you encounter problems. Search PyPI search-focus#focusSearchField" data-search-focus-target="searchField"> Search Help Docs Sponsors Log in Register Menu Help Docs Sponsors Log in Register Search PyPI Search ourotools 0.2.9 pip install ourotools Copy PIP instructions Latest version Released: Dec 6, 2025 A comprehensive toolkit for quality control and analysis of single-cell long-read RNA-seq data Navigation Project description Release history Download files Verified details These details have been verified by PyPI Maintainers hyunsu_an Unverified details These details have not been verified by PyPI Project links Homepage Meta License: MIT Author: Hyunsu An Requires: Python >=3.11 Report project as malware Project description Project details Release history Download files Project description Ouro-Tools - long-read scRNA-seq toolkit Up-to-date README.md can be found on the GitHub repo. Ouro-Tools is a novel, comprehensive computational pipeline for long-read scRNA-seq with the following key features. Ouro-Tools (1) normalizes mRNA size distributions and (2) detects mRNA 7-methylguanosine caps to integrate multiple single-cell long-read RNA-sequencing experiments across modalities and characterize full-length transcripts, respectively. Table of Contents Table of Contents Introduction What is long-read scRNA-seq? Installation Before starting the tutorial Download our toy long-read scRNA-seq datasets Basic settings for running the entire pipeline step 1) Raw long-read pre-processing module step 2) Spliced alignment step 3) Barcode extraction module step 4) Biological full-length molecule identification module step 5) Size distribution normalization module step 6) Single-cell count module step 7) Visualization wrap-up) Running the entire pipeline using a wrapper function Pre-built indices of unwanted genomic sequences for pre-processing An Ouro-Tools count module index Pre-built count module index Building index from scratch optional input annotations SAM Tags Bitwise flags Introduction The Ouro-Tools pipeline comprises five main modules, allowing seamless integration with existing bulk and single-cell long-read RNA-seq pipelines and tools. Every main module of Ouro-Tools utilizes efficient parallelization for compute-intensive tasks to facilitate the processing of large datasets. Additionally, each Ouro-Tools module employs filesystem-based locks for parallel processing of a large number of samples across multiple machines for scalability. What is long-read scRNA-seq? (Figure adapted from Volden & Vollmers, Genome Biol. 23:47 (2022), and made available under Creative Commons license 4.0 by Oxford Nanopore Technologies plc.) In 2013, 2019, and 2022, “single-cell sequencing,” “single-cell multimodal omics,” and “long-read sequencing” were chosen as “Method of the Year” by Nature Methods journal, respectively, highlighting the urgent need to understand biology at the resolution of individual cells and individual biological molecules. Long-read scRNA-seq is a method that combines the single-cell RNA sequencing and long-read sequencing ( Nanopore and PacBio ) methods. Installation The latest stable version of Ouro-Tools is available in PyPI , BioConda , and BioContainers . PyPI Installation (as a Python package) pip install ourotools Bioconda Installation (as an Anaconda package) conda install bioconda::ourotools BioContainers Installation (as a Docker container) # Download the latest Ouro-Tools Docker image from BioContainers docker pull quay.io/biocontainers/ourotools:0.2.8--pyhdfd78af_0 # Run the Ouro-Tools Docker image # please change '/your/local/folder' to the local path containing the input files docker run -v /your/local/folder:/data -it quay.io/biocontainers/ourotools:0.2.8--pyhdfd78af_0 Install the latest (but possibly unstable) version via GitHub git clone https://github.com/ahs2202/ouro-tools.git cd ouro-tools pip install . Test the installation Ouro-Tools can be used in command line, in a Python script, or in an interactive Python interpreter (e.g., Jupyter Notebook). To print the command line usage example of each module from the bash shell, please type the following command. Bash shell ourotools LongFilterNSplit -h IPython environment (Jupyter Notebook) ourotools . LongFilterNSplit ? Before starting the tutorial Download our toy long-read scRNA-seq datasets Each toy dataset contains a subsampled long-read sequencing (ONT R10.4.1) result of an Ouro-Seq library (please check our BioRxiv pre-print for more details). 3 cell types (100 cells are sampled for each cell type) and 3 chromosomes are selected for subsampling. Additionally, the artifact molecules were subsampled and included in the toy dataset. # download toy datasets from mouse ovary and testis wget https://ouro-tools.s3.amazonaws.com/tutorial/mOvary.subsampled.fastq.gz wget https://ouro-tools.s3.amazonaws.com/tutorial/mTestis2.subsampled.fastq.gz Alternatively, you can download directly using your browser using the following links: mOvary and mTestis Basic settings for running the entire pipeline import ourotools # global multiprocessing settings ourotools . bk . int_max_num_batches_in_a_queue_for_each_worker = 1 # [NOTE] For WSL, changing this variable to 1 is necessary to prevent deadlock(s) during IPC. n_workers = 2 # employ 2 workers (since there are two samples, 2 workers are sufficient) n_threads_for_each_worker = 8 # use 8 CPU cores for each worker # datasets-specific setting path_folder_data = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20220331_Ouroboros_Project/pipeline/20230208_Mouse_Long_Read_Single_Cell_Atlas/pipeline/20230811_mouse_long_read_single_cell_atlas_v202308/tutorial_data/20240728_ovary_testis_tutorial/' l_name_sample = [ 'mOvary.subsampled' , 'mTestis2.subsampled' , ] # scRNA-seq technology-specific settings path_file_valid_barcode_list = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20210728_development_ouroboros_qc/example/3M-february-2018.txt.gz' # GEX v3 CB # species-specific settings path_file_minimap_index_genome = '/home/shared/ensembl/Mus_musculus/index/minimap2/Mus_musculus.GRCm38.dna.primary_assembly.k_14.idx' path_file_minimap_splice_junction = '/home/shared/ensembl/Mus_musculus/Mus_musculus.GRCm38.102.paftools.bed' path_file_minimap_unwanted = '/home/project/Single_Cell_Full_Length_Atlas/data/accessory_data/cDNA_depletion/index/minimap2/MT_and_rRNA_GRCm38.fa.ont.mmi' path_folder_count_module_index = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20211116_ouroboros_short_read_public_data_mining/scarab_annotations/Mus_musculus.GRCm38.102.v0.2.4/' # path to the Ouro-Tools count module index To find the barcode whitelist specific to your scRNA-seq experiment, please refer to the official 10x Genomics article . Pre-built Ouro-Tools count module index can be downloaded here . Pre-built indices of unwanted sequences (ribosomal DNA repeats and mitochondrial DNAs) can be downloaded here . step 1) Raw long-read pre-processing module (QC module) # run LongFilterNSplit ourotools . LongFilterNSplit ( path_file_minimap_index_genome = path_file_minimap_index_genome , l_path_file_minimap_index_unwanted = [ path_file_minimap_unwanted ], l_path_file_fastq_input = list ( f " { path_folder_data }{ name_sample } .fastq.gz" for name_sample in l_name_sample ), l_path_folder_output = list ( f " { path_folder_data } LongFilterNSplit_out/ { name_sample } /" for name_sample in l_name_sample ), int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) As the first module of the Ouro-Tools pipeline, the raw long-read pre-processing module LongFilterNSplit has a dual function for (1) providing comprehensive quality control metrics of a long-read scRNA-seq experiment and (2) pre-processing of raw long-read sequencing data for the downstream analysis. According to the classification results, cDNA molecules are organized into separate output FASTQ files. For the cDNA molecules that contains a single (external or internal) poly(A) tail, the read is re-oriented so that it has the same orientation as its original mRNA transcript, with the poly(A) tail at its 3’ end; the resulting long-reads of cDNAs can be utilized for strand-specific long-read RNA-seq analysis. step 2) Spliced alignment # align using minimap2 (require that minimap2 executable can be found in PATH) # below is a wrapper function for minimap2 ourotools . Workers ( ourotools . ONT . Minimap2_Align , # function to deploy int_num_workers_for_Workers = n_workers , # create 'n_workers' number of workers # below are arguments for the function 'ourotools.ONT.Minimap2_Align' path_file_fastq = list ( f " { path_folder_data } LongFilterNSplit_out/ { name_sample } /aligned_to_genome__non_chimeric__poly_A__plus_strand.fastq.gz" for name_sample in l_name_sample ), path_folder_minimap2_output = list ( f " { path_folder_data } minimap2_bam_genome/ { name_sample } /" for name_sample in l_name_sample ), path_file_junc_bed = path_file_minimap_splice_junction , path_file_minimap2_index = path_file_minimap_index_genome , n_threads = n_threads_for_each_worker , ) Minimap2 can be used for annotation-guided alignment based on the transcript annotations prepared by the researcher. Here, the reference annotation from Ensembl ( Ensembl release 102 ) was utilized. step 3) Barcode extraction module # run LongExtractBarcodeFromBAM l_path_folder_barcodedbam = list ( f " { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /" for name_sample in l_name_sample ) ourotools . LongExtractBarcodeFromBAM ( path_file_valid_cb = path_file_valid_barcode_list , l_path_file_bam_input = list ( f " { path_folder_data } minimap2_bam_genome/ { name_sample } /aligned_to_genome__non_chimeric__poly_A__plus_strand.fastq.gz.minimap2_aligned.bam" for name_sample in l_name_sample ), l_path_folder_output = l_path_folder_barcodedbam , int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) The barcode extraction module LongExtractBarcodeFromBAM identifies cell barcode ( CB ) and unique molecular identifier ( UMI ) sequences for each read and exports the results as a “barcoded” BAM file , a BAM file containing corrected CB and UMI sequences for each read using the predefined SAM tags . step 4) Biological full-length molecule identification module # run full-length ID module # survey 5' sites for each sample ourotools . LongSurvey5pSiteFromBAM ( l_path_folder_input = l_path_folder_barcodedbam , int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) # combine 5' site profiles across samples and classify each 5' profile ourotools . LongClassify5pSiteProfiles ( l_path_folder_input = l_path_folder_barcodedbam , path_folder_output = f " { path_folder_data } LongClassify5pSiteProfiles_out/" , n_threads = n_threads_for_each_worker , ) # append 5' site classification results to each BAM file ourotools . LongAdd5pSiteClassificationResultToBAM ( path_folder_input_5p_sites = f ' { path_folder_data } LongClassify5pSiteProfiles_out/' , l_path_folder_input_barcodedbam = l_path_folder_barcodedbam , int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) # filter artifact reads from each BAM file ourotools . Workers ( ourotools . FilterArtifactReadFromBAM , # function to deploy int_num_workers_for_Workers = n_workers , # create 'n_workers' number of workers # below are arguments for the function 'ourotools.FilterArtifactReadFromBAM' path_file_bam_input = list ( f ' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/barcoded.bam' for name_sample in l_name_sample ), path_folder_output = list ( f ' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/' for name_sample in l_name_sample ), ) The biological full-length identification module collects the lengths of guanosine homopolymers at the 5’ ends of cDNAs to identify genuine TSSs that produce capped mRNAs, depleting truncated cDNA molecules in silico . The module is implemented as a workflow consisting of LongSurvey5pSiteFromBAM , LongClassify5pSiteProfiles , LongAdd5pSiteClassificationResultToBAM , and FilterArtifactReadFromBAM . step 5) Size distribution normalization module # run mRNA size distribution normalization module # survey the size distribution of full-length mRNAs for each sample l_full_length_bam = list ( f ' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/valid_3p_valid_5p.bam' for name_sample in l_name_sample ) ourotools . Workers ( ourotools . LongSummarizeSizeDistributions , int_num_workers_for_Workers = n_workers , # create 'n_workers' number of workers path_file_bam_input = l_full_length_bam , path_folder_output = list ( f ' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/valid_3p_valid_5p.LongSummarizeSizeDistributions_out/' for name_sample in l_name_sample ), ) # normalize size distributions path_folder_size_norm = f " { path_folder_data } LongCreateReferenceSizeDistribution_out/" ourotools . LongCreateReferenceSizeDistribution ( l_path_file_distributions = list ( f ' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/valid_3p_valid_5p.LongSummarizeSizeDistributions_out/dict_arr_dist.pkl' for name_sample in l_name_sample ), l_name_file_distributions = l_name_sample , path_folder_output = path_folder_size_norm , float_max_ratio_to_arr_dist_guassian_filter_min_sigma_for_dynamic_gaussian_filter_selection = 2 , float_sigma_gaussian_filter_min = 8 , int_min_total_read_count_for_a_peak = 30 , ) # based on the output, set the confident size range str_confident_size_range = ourotools . get_confident_size_range ( path_folder_size_norm ) The size distribution normalization module is implemented using the LongSummarizeSizeDistributions and LongCreateReferenceSizeDistribution workflows. First, using the LongSummarizeSizeDistributions workflow, a full-length, UMI-deduplicated cDNA size distribution is obtained from the valid_3p_valid_5p barcoded BAM file (representing in vivo full-length mRNAs ) for each sample. Next, the reference mRNA size distribution is constructed for all the samples using the LongCreateReferenceSizeDistribution workflow. step 6) Single-cell count module # run the single-cell count module ourotools . LongExportNormalizedCountMatrix ( path_folder_ref = path_folder_count_module_index , l_path_file_bam_input = l_full_length_bam , l_path_folder_output = list ( f ' { path_folder_data } LongExportNormalizedCountMatrix_out/ { name_sample } /' for name_sample in l_name_sample ), l_name_distribution = l_name_sample , path_folder_reference_distribution = path_folder_size_norm , l_str_l_t_distribution_range_of_interest = [ ',' . join ( [ "raw" , str_confident_size_range ] ) ], flag_enforce_transcript_start_site_matching_for_long_read_during_realignment = True , flag_enforce_transcript_end_site_matching_for_long_read_during_realignment = True , ) The single-cell long-read count module LongExportNormalizedCountMatrix is largely composed of three parts: constructing an index (only required once for each set of genes, transcripts, repeat elements, regulatory elements and the reference genome), assigning each read to various buckets (each bucket represent one of the genes, transcripts, exons, splice junctions, TEs, tCREs, and individual genomic tiles), and exporting a size distribution-normalized count matrix for each bucket (later these count matrixes are combined into a single size distribution-normalized count matrix as an output). step 7) Visualization # TBD wrap-up) Running the entire pipeline using a wrapper function # version 2025-01-25 by Hyunsu An @ GIST-FGL import ourotools ourotools . bk . int_max_num_batches_in_a_queue_for_each_worker = 1 # [NOTE] For WSL, changing this variable to 1 is necessary to prevent deadlock(s) during IPC. ourotools . run_pipeline ( # dataset setting path_folder_data = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20220331_Ouroboros_Project/pipeline/20230208_Mouse_Long_Read_Single_Cell_Atlas/pipeline/20230811_mouse_long_read_single_cell_atlas_v202308/tutorial_data/20240813_ovary_testis_tutorial2/' , l_name_sample = [ 'mOvary.subsampled' , 'mTestis2.subsampled' , ], # scRNA-seq technology-specific path_file_valid_barcode_list = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20210728_development_ouroboros_qc/example/3M-february-2018.txt.gz' , # GEX v3 CB # species-specific settings path_file_minimap_index_genome = '/home/shared/ensembl/Mus_musculus/index/minimap2/Mus_musculus.GRCm38.dna.primary_assembly.k_14.idx' , path_file_minimap_splice_junction = '/home/shared/ensembl/Mus_musculus/Mus_musculus.GRCm38.102.paftools.bed' , path_file_minimap_unwanted = '/home/project/Single_Cell_Full_Length_Atlas/data/accessory_data/cDNA_depletion/index/minimap2/MT_and_rRNA_GRCm38.fa.ont.mmi' , path_folder_count_module_index = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20211116_ouroboros_short_read_public_data_mining/scarab_annotations/Mus_musculus.GRCm38.102.v0.2.4/' , # path to the Ouro-Tools reference # run setting n_workers = 2 , # employ 2 workers (since there are two samples, 2 workers are sufficient) n_threads_for_each_worker = 8 , # use 8 CPU cores for each worker # additional settings args = dict ( LongCreateReferenceSizeDistribution = dict ( float_max_ratio_to_arr_dist_guassian_filter_min_sigma_for_dynamic_gaussian_filter_selection = 2 , float_sigma_gaussian_filter_min = 8 , int_min_total_read_count_for_a_peak = 30 , ), LongExportNormalizedCountMatrix = dict ( flag_enforce_transcript_start_site_matching_for_long_read_during_realignment = True , flag_enforce_transcript_end_site_matching_for_long_read_during_realignment = True , ), ), ) Pre-built indices of unwanted genomic sequences for pre-processing The pre-built indices of unwanted sequences can be downloaded using the following links: Human (GRCh38) : Minimap2-index-file , FASTA-file , GTF-file Mouse (GRCm38) : Minimap2-index-file , FASTA-file , GTF-file An Ouro-Tools count module index The single-cell count module of Ouro-Tools utilizes genome, transcriptome, and gene annotations to assign reads to genes, isoforms, and genomic bins (tiles across the genome) . The index building process is automatic; there is no needs to run a separate command in order to build the index. Once Ouro-Tools processes these information before analyzing an input BAM file(s), the program saves an index in order to load the information much faster next time. We recommends using Ensembl reference genome, transcriptome, and gene annotations of the same version (release number). [Latest] Pre-built index The latest pre-built index can be downloaded using the following links (should be extracted to a folder using tar -xf command): Human (GRCh38, Ensembl version 114) Mouse (GRCm39, Ensembl version 114) Zebrafish (GRCz11, Ensembl version 114) Arabidopsis thaliana (Thale cress) (TAIR10, Ensembl Plant version 61) Building index from scratch An Ouro-Tools index can be built on-the-fly from the input genome, transcriptome, and gene annotation files. For example, below are the list of files that were used for the pre-built Ouro-Tools index " Human (GRCh38, Ensembl version 114) ". The list of [required] annotations ( Ensemble version 114 and Ensemble-Plant version 61 , as of 2025-05-15 ): path_file_fa_genome : Human/GRCh38 , Mouse/GRCm39 A genome FASTA file. Either gzipped or plain FASTA file can be accepted. path_file_gtf_genome : Human/GRCh38 , Mouse/GRCm3 + +### https://github.com/ahs2202/ouro-tools +GitHub - ahs2202/ouro-tools: A comprehensive toolkit for quality control and analysis of single-cell long-read RNA-seq data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} ahs2202 / ouro-tools Public Notifications You must be signed in to change notification settings Fork 1 Star 9 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights ahs2202/ouro-tools main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 68 Commits 68 Commits conda conda doc/ img doc/ img docker docker ourotools ourotools .gitignore .gitignore LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md setup.py setup.py View all files Repository files navigation README MIT license Ouro-Tools - long-read scRNA-seq toolkit Up-to-date README.md can be found on the GitHub repo. Ouro-Tools is a novel, comprehensive computational pipeline for long-read scRNA-seq with the following key features. Ouro-Tools (1) normalizes mRNA size distributions and (2) detects mRNA 7-methylguanosine caps to integrate multiple single-cell long-read RNA-sequencing experiments across modalities and characterize full-length transcripts, respectively. Table of Contents Table of Contents Introduction What is long-read scRNA-seq? Installation Before starting the tutorial Download our toy long-read scRNA-seq datasets Basic settings for running the entire pipeline step 1) Raw long-read pre-processing module step 2) Spliced alignment step 3) Barcode extraction module step 4) Biological full-length molecule identification module step 5) Size distribution normalization module step 6) Single-cell count module step 7) Visualization wrap-up) Running the entire pipeline using a wrapper function Pre-built indices of unwanted genomic sequences for pre-processing An Ouro-Tools count module index Pre-built count module index Building index from scratch optional input annotations SAM Tags Bitwise flags Introduction The Ouro-Tools pipeline comprises five main modules, allowing seamless integration with existing bulk and single-cell long-read RNA-seq pipelines and tools. Every main module of Ouro-Tools utilizes efficient parallelization for compute-intensive tasks to facilitate the processing of large datasets. Additionally, each Ouro-Tools module employs filesystem-based locks for parallel processing of a large number of samples across multiple machines for scalability. What is long-read scRNA-seq? (Figure adapted from Volden & Vollmers, Genome Biol. 23:47 (2022), and made available under Creative Commons license 4.0 by Oxford Nanopore Technologies plc.) In 2013, 2019, and 2022, “single-cell sequencing,” “single-cell multimodal omics,” and “long-read sequencing” were chosen as “Method of the Year” by Nature Methods journal, respectively, highlighting the urgent need to understand biology at the resolution of individual cells and individual biological molecules. Long-read scRNA-seq is a method that combines the single-cell RNA sequencing and long-read sequencing ( Nanopore and PacBio ) methods. Installation The latest stable version of Ouro-Tools is available in PyPI , BioConda , and BioContainers . PyPI Installation (as a Python package) pip install ourotools Bioconda Installation (as an Anaconda package) conda install bioconda::ourotools BioContainers Installation (as a Docker container) # Download the latest Ouro-Tools Docker image from BioContainers docker pull quay.io/biocontainers/ourotools:0.2.8--pyhdfd78af_0 # Run the Ouro-Tools Docker image # please change '/your/local/folder' to the local path containing the input files docker run -v /your/local/folder:/data -it quay.io/biocontainers/ourotools:0.2.8--pyhdfd78af_0 Install the latest (but possibly unstable) version via GitHub git clone https://github.com/ahs2202/ouro-tools.git cd ouro-tools pip install . Test the installation Ouro-Tools can be used in command line, in a Python script, or in an interactive Python interpreter (e.g., Jupyter Notebook). To print the command line usage example of each module from the bash shell, please type the following command. Bash shell ourotools LongFilterNSplit -h IPython environment (Jupyter Notebook) ourotools . LongFilterNSplit ? Before starting the tutorial Download our toy long-read scRNA-seq datasets Each toy dataset contains a subsampled long-read sequencing (ONT R10.4.1) result of an Ouro-Seq library (please check our BioRxiv pre-print for more details). 3 cell types (100 cells are sampled for each cell type) and 3 chromosomes are selected for subsampling. Additionally, the artifact molecules were subsampled and included in the toy dataset. # download toy datasets from mouse ovary and testis wget https://ouro-tools.s3.amazonaws.com/tutorial/mOvary.subsampled.fastq.gz wget https://ouro-tools.s3.amazonaws.com/tutorial/mTestis2.subsampled.fastq.gz Alternatively, you can download directly using your browser using the following links: mOvary and mTestis Basic settings for running the entire pipeline import ourotools # global multiprocessing settings ourotools . bk . int_max_num_batches_in_a_queue_for_each_worker = 1 # [NOTE] For WSL, changing this variable to 1 is necessary to prevent deadlock(s) during IPC. n_workers = 2 # employ 2 workers (since there are two samples, 2 workers are sufficient) n_threads_for_each_worker = 8 # use 8 CPU cores for each worker # datasets-specific setting path_folder_data = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20220331_Ouroboros_Project/pipeline/20230208_Mouse_Long_Read_Single_Cell_Atlas/pipeline/20230811_mouse_long_read_single_cell_atlas_v202308/tutorial_data/20240728_ovary_testis_tutorial/' l_name_sample = [ 'mOvary.subsampled' , 'mTestis2.subsampled' , ] # scRNA-seq technology-specific settings path_file_valid_barcode_list = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20210728_development_ouroboros_qc/example/3M-february-2018.txt.gz' # GEX v3 CB # species-specific settings path_file_minimap_index_genome = '/home/shared/ensembl/Mus_musculus/index/minimap2/Mus_musculus.GRCm38.dna.primary_assembly.k_14.idx' path_file_minimap_splice_junction = '/home/shared/ensembl/Mus_musculus/Mus_musculus.GRCm38.102.paftools.bed' path_file_minimap_unwanted = '/home/project/Single_Cell_Full_Length_Atlas/data/accessory_data/cDNA_depletion/index/minimap2/MT_and_rRNA_GRCm38.fa.ont.mmi' path_folder_count_module_index = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20211116_ouroboros_short_read_public_data_mining/scarab_annotations/Mus_musculus.GRCm38.102.v0.2.4/' # path to the Ouro-Tools count module index To find the barcode whitelist specific to your scRNA-seq experiment, please refer to the official 10x Genomics article . Pre-built Ouro-Tools count module index can be downloaded here . Pre-built indices of unwanted sequences (ribosomal DNA repeats and mitochondrial DNAs) can be downloaded here . step 1) Raw long-read pre-processing module (QC module) # run LongFilterNSplit ourotools . LongFilterNSplit ( path_file_minimap_index_genome = path_file_minimap_index_genome , l_path_file_minimap_index_unwanted = [ path_file_minimap_unwanted ], l_path_file_fastq_input = list ( f" { path_folder_data } { name_sample } .fastq.gz" for name_sample in l_name_sample ), l_path_folder_output = list ( f" { path_folder_data } LongFilterNSplit_out/ { name_sample } /" for name_sample in l_name_sample ), int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) As the first module of the Ouro-Tools pipeline, the raw long-read pre-processing module LongFilterNSplit has a dual function for (1) providing comprehensive quality control metrics of a long-read scRNA-seq experiment and (2) pre-processing of raw long-read sequencing data for the downstream analysis. According to the classification results, cDNA molecules are organized into separate output FASTQ files. For the cDNA molecules that contains a single (external or internal) poly(A) tail, the read is re-oriented so that it has the same orientation as its original mRNA transcript, with the poly(A) tail at its 3’ end; the resulting long-reads of cDNAs can be utilized for strand-specific long-read RNA-seq analysis. step 2) Spliced alignment # align using minimap2 (require that minimap2 executable can be found in PATH) # below is a wrapper function for minimap2 ourotools . Workers ( ourotools . ONT . Minimap2_Align , # function to deploy int_num_workers_for_Workers = n_workers , # create 'n_workers' number of workers # below are arguments for the function 'ourotools.ONT.Minimap2_Align' path_file_fastq = list ( f" { path_folder_data } LongFilterNSplit_out/ { name_sample } /aligned_to_genome__non_chimeric__poly_A__plus_strand.fastq.gz" for name_sample in l_name_sample ), path_folder_minimap2_output = list ( f" { path_folder_data } minimap2_bam_genome/ { name_sample } /" for name_sample in l_name_sample ), path_file_junc_bed = path_file_minimap_splice_junction , path_file_minimap2_index = path_file_minimap_index_genome , n_threads = n_threads_for_each_worker , ) Minimap2 can be used for annotation-guided alignment based on the transcript annotations prepared by the researcher. Here, the reference annotation from Ensembl ( Ensembl release 102 ) was utilized. step 3) Barcode extraction module # run LongExtractBarcodeFromBAM l_path_folder_barcodedbam = list ( f" { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /" for name_sample in l_name_sample ) ourotools . LongExtractBarcodeFromBAM ( path_file_valid_cb = path_file_valid_barcode_list , l_path_file_bam_input = list ( f" { path_folder_data } minimap2_bam_genome/ { name_sample } /aligned_to_genome__non_chimeric__poly_A__plus_strand.fastq.gz.minimap2_aligned.bam" for name_sample in l_name_sample ), l_path_folder_output = l_path_folder_barcodedbam , int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) The barcode extraction module LongExtractBarcodeFromBAM identifies cell barcode ( CB ) and unique molecular identifier ( UMI ) sequences for each read and exports the results as a “barcoded” BAM file , a BAM file containing corrected CB and UMI sequences for each read using the predefined SAM tags . step 4) Biological full-length molecule identification module # run full-length ID module # survey 5' sites for each sample ourotools . LongSurvey5pSiteFromBAM ( l_path_folder_input = l_path_folder_barcodedbam , int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) # combine 5' site profiles across samples and classify each 5' profile ourotools . LongClassify5pSiteProfiles ( l_path_folder_input = l_path_folder_barcodedbam , path_folder_output = f" { path_folder_data } LongClassify5pSiteProfiles_out/" , n_threads = n_threads_for_each_worker , ) # append 5' site classification results to each BAM file ourotools . LongAdd5pSiteClassificationResultToBAM ( path_folder_input_5p_sites = f' { path_folder_data } LongClassify5pSiteProfiles_out/' , l_path_folder_input_barcodedbam = l_path_folder_barcodedbam , int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) # filter artifact reads from each BAM file ourotools . Workers ( ourotools . FilterArtifactReadFromBAM , # function to deploy int_num_workers_for_Workers = n_workers , # create 'n_workers' number of workers # below are arguments for the function 'ourotools.FilterArtifactReadFromBAM' path_file_bam_input = list ( f' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/barcoded.bam' for name_sample in l_name_sample ), path_folder_output = list ( f' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/' for name_sample in l_name_sample ), ) The biological full-length identification module collects the lengths of guanosine homopolymers at the 5’ ends of cDNAs to identify genuine TSSs that produce capped mRNAs, depleting truncated cDNA molecules in silico . The module is implemented as a workflow consisting of LongSurvey5pSiteFromBAM , LongClassify5pSiteProfiles , LongAdd5pSiteClassificationResultToBAM , and FilterArtifactReadFromBAM . step 5) Size distribution normalization module # run mRNA size distribution normalization module # survey the size distribution of full-length mRNAs for each sample l_full_length_bam = list ( f' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/valid_3p_valid_5p.bam' for name_sample in l_name_sample ) ourotools . Workers ( ourotools . LongSummarizeSizeDistributions , int_num_workers_for_Workers = n_workers , # create 'n_workers' number of workers path_file_bam_input = l_full_length_bam , path_folder_output = list ( f' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/valid_3p_valid_5p.LongSummarizeSizeDistributions_out/' for name_sample in l_name_sample ), ) # normalize size distributions path_folder_size_norm = f" { path_folder_data } LongCreateReferenceSizeDistribution_out/" ourotools . LongCreateReferenceSizeDistribution ( l_path_file_distributions = list ( f' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/valid_3p_valid_5p.LongSummarizeSizeDistributions_out/dict_arr_dist.pkl' for name_sample in l_name_sample ), l_name_file_distributions = l_name_sample , path_folder_output = path_folder_size_norm , float_max_ratio_to_arr_dist_guassian_filter_min_sigma_for_dynamic_gaussian_filter_selection = 2 , float_sigma_gaussian_filter_min = 8 , int_min_total_read_count_for_a_peak = 30 , ) # based on the output, set the confident size range str_confident_size_range = ourotools . get_confident_size_range ( path_folder_size_norm ) The size distribution normalization module is implemented using the LongSummarizeSizeDistributions and LongCreateReferenceSizeDistribution workflows. First, using the LongSummarizeSizeDistributions workflow, a full-length, UMI-deduplicated cDNA size distribution is obtained from the valid_3p_valid_5p barcoded BAM file (representing in vivo full-length mRNAs ) for each sample. Next, the reference mRNA size distribution is constructed for all the samples using the LongCreateReferenceSizeDistribution workflow. step 6) Single-cell count module # run the single-cell count module ourotools . LongExportNormalizedCountMatrix ( path_folder_ref = path_folder_count_module_index , l_path_file_bam_input = l_full_length_bam , l_path_folder_output = list ( f' { path_folder_data } LongExportNormalizedCountMatrix_out/ { name_sample } /' for name_sample in l_name_sample ), l_name_distribution = l_name_sample , path_folder_reference_distribution = path_folder_size_norm , l_str_l_t_distribution_range_of_interest = [ ',' . join ( [ "raw" , str_confident_size_range ] ) ], flag_enforce_transcript_start_site_matching_for_long_read_during_realignment = True , flag_enforce_transcript_end_site_matching_for_long_read_during_realignment = True , ) The single-cell long-read count module LongExportNormalizedCountMatrix is largely composed of three parts: constructing an index (only required once for each set of genes, transcripts, repeat elements, regulatory elements and the reference genome), assigning each read to various buckets (each bucket represent one of the genes, transcripts, exons, splice junctions, TEs, tCREs, and individual genomic tiles), and exporting a size distribution-normalized count matrix for each bucket (later these count matrixes are combined into a single size distribution-normalized count matrix as an output). step 7) Visualization # TBD wrap-up) Running the entire pipeline using a wrapper function # version 2025-01-25 by Hyunsu An @ GIST-FGL import ourotools ourotools . bk . int_max_num_batches_in_a_queue_for_each_worker = 1 # [NOTE] For WSL, changing this variable to 1 is necessary to prevent deadlock(s) during IPC. ourotools . run_pipeline ( # dataset setting path_folder_data = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20220331_Ouroboros_Project/pipeline/20230208_Mouse_Long_Read_Single_Cell_Atlas/pipeline/20230811_mouse_long_read_single_cell_atlas_v202308/tutorial_data/20240813_ovary_testis_tutorial2/' , l_name_sample = [ 'mOvary.subsampled' , 'mTestis2.subsampled' , ], # scRNA-seq technology-specific path_file_valid_barcode_list = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20210728_development_ouroboros_qc/example/3M-february-2018.txt.gz' , # GEX v3 CB # species-specific settings path_file_minimap_index_genome = '/home/shared/ensembl/Mus_musculus/index/minimap2/Mus_musculus.GRCm38.dna.primary_assembly.k_14.idx' , path_file_minimap_splice_junction = '/home/shared/ensembl/Mus_musculus/Mus_musculus.GRCm38.102.paftools.bed' , path_file_minimap_unwanted = '/home/project/Single_Cell_Full_Length_Atlas/data/accessory_data/cDNA_depletion/index/minimap2/MT_and_rRNA_GRCm38.fa.ont.mmi' , path_folder_count_module_index = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20211116_ouroboros_short_read_public_data_mining/scarab_annotations/Mus_musculus.GRCm38.102.v0.2.4/' , # path to the Ouro-Tools reference # run setting n_workers = 2 , # employ 2 workers (since there are two samples, 2 workers are sufficient) n_threads_for_each_worker = 8 , # use 8 CPU cores for each worker # additional settings ar + +### https://github.com/ahs2202/ouro-tools +GitHub - ahs2202/ouro-tools: A comprehensive toolkit for quality control and analysis of single-cell long-read RNA-seq data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} ahs2202 / ouro-tools Public Notifications You must be signed in to change notification settings Fork 1 Star 9 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights ahs2202/ouro-tools main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 68 Commits 68 Commits conda conda doc/ img doc/ img docker docker ourotools ourotools .gitignore .gitignore LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md setup.py setup.py View all files Repository files navigation README MIT license Ouro-Tools - long-read scRNA-seq toolkit Up-to-date README.md can be found on the GitHub repo. Ouro-Tools is a novel, comprehensive computational pipeline for long-read scRNA-seq with the following key features. Ouro-Tools (1) normalizes mRNA size distributions and (2) detects mRNA 7-methylguanosine caps to integrate multiple single-cell long-read RNA-sequencing experiments across modalities and characterize full-length transcripts, respectively. Table of Contents Table of Contents Introduction What is long-read scRNA-seq? Installation Before starting the tutorial Download our toy long-read scRNA-seq datasets Basic settings for running the entire pipeline step 1) Raw long-read pre-processing module step 2) Spliced alignment step 3) Barcode extraction module step 4) Biological full-length molecule identification module step 5) Size distribution normalization module step 6) Single-cell count module step 7) Visualization wrap-up) Running the entire pipeline using a wrapper function Pre-built indices of unwanted genomic sequences for pre-processing An Ouro-Tools count module index Pre-built count module index Building index from scratch optional input annotations SAM Tags Bitwise flags Introduction The Ouro-Tools pipeline comprises five main modules, allowing seamless integration with existing bulk and single-cell long-read RNA-seq pipelines and tools. Every main module of Ouro-Tools utilizes efficient parallelization for compute-intensive tasks to facilitate the processing of large datasets. Additionally, each Ouro-Tools module employs filesystem-based locks for parallel processing of a large number of samples across multiple machines for scalability. What is long-read scRNA-seq? (Figure adapted from Volden & Vollmers, Genome Biol. 23:47 (2022), and made available under Creative Commons license 4.0 by Oxford Nanopore Technologies plc.) In 2013, 2019, and 2022, “single-cell sequencing,” “single-cell multimodal omics,” and “long-read sequencing” were chosen as “Method of the Year” by Nature Methods journal, respectively, highlighting the urgent need to understand biology at the resolution of individual cells and individual biological molecules. Long-read scRNA-seq is a method that combines the single-cell RNA sequencing and long-read sequencing ( Nanopore and PacBio ) methods. Installation The latest stable version of Ouro-Tools is available in PyPI , BioConda , and BioContainers . PyPI Installation (as a Python package) pip install ourotools Bioconda Installation (as an Anaconda package) conda install bioconda::ourotools BioContainers Installation (as a Docker container) # Download the latest Ouro-Tools Docker image from BioContainers docker pull quay.io/biocontainers/ourotools:0.2.8--pyhdfd78af_0 # Run the Ouro-Tools Docker image # please change '/your/local/folder' to the local path containing the input files docker run -v /your/local/folder:/data -it quay.io/biocontainers/ourotools:0.2.8--pyhdfd78af_0 Install the latest (but possibly unstable) version via GitHub git clone https://github.com/ahs2202/ouro-tools.git cd ouro-tools pip install . Test the installation Ouro-Tools can be used in command line, in a Python script, or in an interactive Python interpreter (e.g., Jupyter Notebook). To print the command line usage example of each module from the bash shell, please type the following command. Bash shell ourotools LongFilterNSplit -h IPython environment (Jupyter Notebook) ourotools . LongFilterNSplit ? Before starting the tutorial Download our toy long-read scRNA-seq datasets Each toy dataset contains a subsampled long-read sequencing (ONT R10.4.1) result of an Ouro-Seq library (please check our BioRxiv pre-print for more details). 3 cell types (100 cells are sampled for each cell type) and 3 chromosomes are selected for subsampling. Additionally, the artifact molecules were subsampled and included in the toy dataset. # download toy datasets from mouse ovary and testis wget https://ouro-tools.s3.amazonaws.com/tutorial/mOvary.subsampled.fastq.gz wget https://ouro-tools.s3.amazonaws.com/tutorial/mTestis2.subsampled.fastq.gz Alternatively, you can download directly using your browser using the following links: mOvary and mTestis Basic settings for running the entire pipeline import ourotools # global multiprocessing settings ourotools . bk . int_max_num_batches_in_a_queue_for_each_worker = 1 # [NOTE] For WSL, changing this variable to 1 is necessary to prevent deadlock(s) during IPC. n_workers = 2 # employ 2 workers (since there are two samples, 2 workers are sufficient) n_threads_for_each_worker = 8 # use 8 CPU cores for each worker # datasets-specific setting path_folder_data = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20220331_Ouroboros_Project/pipeline/20230208_Mouse_Long_Read_Single_Cell_Atlas/pipeline/20230811_mouse_long_read_single_cell_atlas_v202308/tutorial_data/20240728_ovary_testis_tutorial/' l_name_sample = [ 'mOvary.subsampled' , 'mTestis2.subsampled' , ] # scRNA-seq technology-specific settings path_file_valid_barcode_list = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20210728_development_ouroboros_qc/example/3M-february-2018.txt.gz' # GEX v3 CB # species-specific settings path_file_minimap_index_genome = '/home/shared/ensembl/Mus_musculus/index/minimap2/Mus_musculus.GRCm38.dna.primary_assembly.k_14.idx' path_file_minimap_splice_junction = '/home/shared/ensembl/Mus_musculus/Mus_musculus.GRCm38.102.paftools.bed' path_file_minimap_unwanted = '/home/project/Single_Cell_Full_Length_Atlas/data/accessory_data/cDNA_depletion/index/minimap2/MT_and_rRNA_GRCm38.fa.ont.mmi' path_folder_count_module_index = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20211116_ouroboros_short_read_public_data_mining/scarab_annotations/Mus_musculus.GRCm38.102.v0.2.4/' # path to the Ouro-Tools count module index To find the barcode whitelist specific to your scRNA-seq experiment, please refer to the official 10x Genomics article . Pre-built Ouro-Tools count module index can be downloaded here . Pre-built indices of unwanted sequences (ribosomal DNA repeats and mitochondrial DNAs) can be downloaded here . step 1) Raw long-read pre-processing module (QC module) # run LongFilterNSplit ourotools . LongFilterNSplit ( path_file_minimap_index_genome = path_file_minimap_index_genome , l_path_file_minimap_index_unwanted = [ path_file_minimap_unwanted ], l_path_file_fastq_input = list ( f" { path_folder_data } { name_sample } .fastq.gz" for name_sample in l_name_sample ), l_path_folder_output = list ( f" { path_folder_data } LongFilterNSplit_out/ { name_sample } /" for name_sample in l_name_sample ), int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) As the first module of the Ouro-Tools pipeline, the raw long-read pre-processing module LongFilterNSplit has a dual function for (1) providing comprehensive quality control metrics of a long-read scRNA-seq experiment and (2) pre-processing of raw long-read sequencing data for the downstream analysis. According to the classification results, cDNA molecules are organized into separate output FASTQ files. For the cDNA molecules that contains a single (external or internal) poly(A) tail, the read is re-oriented so that it has the same orientation as its original mRNA transcript, with the poly(A) tail at its 3’ end; the resulting long-reads of cDNAs can be utilized for strand-specific long-read RNA-seq analysis. step 2) Spliced alignment # align using minimap2 (require that minimap2 executable can be found in PATH) # below is a wrapper function for minimap2 ourotools . Workers ( ourotools . ONT . Minimap2_Align , # function to deploy int_num_workers_for_Workers = n_workers , # create 'n_workers' number of workers # below are arguments for the function 'ourotools.ONT.Minimap2_Align' path_file_fastq = list ( f" { path_folder_data } LongFilterNSplit_out/ { name_sample } /aligned_to_genome__non_chimeric__poly_A__plus_strand.fastq.gz" for name_sample in l_name_sample ), path_folder_minimap2_output = list ( f" { path_folder_data } minimap2_bam_genome/ { name_sample } /" for name_sample in l_name_sample ), path_file_junc_bed = path_file_minimap_splice_junction , path_file_minimap2_index = path_file_minimap_index_genome , n_threads = n_threads_for_each_worker , ) Minimap2 can be used for annotation-guided alignment based on the transcript annotations prepared by the researcher. Here, the reference annotation from Ensembl ( Ensembl release 102 ) was utilized. step 3) Barcode extraction module # run LongExtractBarcodeFromBAM l_path_folder_barcodedbam = list ( f" { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /" for name_sample in l_name_sample ) ourotools . LongExtractBarcodeFromBAM ( path_file_valid_cb = path_file_valid_barcode_list , l_path_file_bam_input = list ( f" { path_folder_data } minimap2_bam_genome/ { name_sample } /aligned_to_genome__non_chimeric__poly_A__plus_strand.fastq.gz.minimap2_aligned.bam" for name_sample in l_name_sample ), l_path_folder_output = l_path_folder_barcodedbam , int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) The barcode extraction module LongExtractBarcodeFromBAM identifies cell barcode ( CB ) and unique molecular identifier ( UMI ) sequences for each read and exports the results as a “barcoded” BAM file , a BAM file containing corrected CB and UMI sequences for each read using the predefined SAM tags . step 4) Biological full-length molecule identification module # run full-length ID module # survey 5' sites for each sample ourotools . LongSurvey5pSiteFromBAM ( l_path_folder_input = l_path_folder_barcodedbam , int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) # combine 5' site profiles across samples and classify each 5' profile ourotools . LongClassify5pSiteProfiles ( l_path_folder_input = l_path_folder_barcodedbam , path_folder_output = f" { path_folder_data } LongClassify5pSiteProfiles_out/" , n_threads = n_threads_for_each_worker , ) # append 5' site classification results to each BAM file ourotools . LongAdd5pSiteClassificationResultToBAM ( path_folder_input_5p_sites = f' { path_folder_data } LongClassify5pSiteProfiles_out/' , l_path_folder_input_barcodedbam = l_path_folder_barcodedbam , int_num_samples_analyzed_concurrently = n_workers , n_threads = n_workers * n_threads_for_each_worker , ) # filter artifact reads from each BAM file ourotools . Workers ( ourotools . FilterArtifactReadFromBAM , # function to deploy int_num_workers_for_Workers = n_workers , # create 'n_workers' number of workers # below are arguments for the function 'ourotools.FilterArtifactReadFromBAM' path_file_bam_input = list ( f' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/barcoded.bam' for name_sample in l_name_sample ), path_folder_output = list ( f' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/' for name_sample in l_name_sample ), ) The biological full-length identification module collects the lengths of guanosine homopolymers at the 5’ ends of cDNAs to identify genuine TSSs that produce capped mRNAs, depleting truncated cDNA molecules in silico . The module is implemented as a workflow consisting of LongSurvey5pSiteFromBAM , LongClassify5pSiteProfiles , LongAdd5pSiteClassificationResultToBAM , and FilterArtifactReadFromBAM . step 5) Size distribution normalization module # run mRNA size distribution normalization module # survey the size distribution of full-length mRNAs for each sample l_full_length_bam = list ( f' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/valid_3p_valid_5p.bam' for name_sample in l_name_sample ) ourotools . Workers ( ourotools . LongSummarizeSizeDistributions , int_num_workers_for_Workers = n_workers , # create 'n_workers' number of workers path_file_bam_input = l_full_length_bam , path_folder_output = list ( f' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/valid_3p_valid_5p.LongSummarizeSizeDistributions_out/' for name_sample in l_name_sample ), ) # normalize size distributions path_folder_size_norm = f" { path_folder_data } LongCreateReferenceSizeDistribution_out/" ourotools . LongCreateReferenceSizeDistribution ( l_path_file_distributions = list ( f' { path_folder_data } LongExtractBarcodeFromBAM_out/ { name_sample } /5pSiteTagAdded/FilterArtifactReadFromBAM_out/valid_3p_valid_5p.LongSummarizeSizeDistributions_out/dict_arr_dist.pkl' for name_sample in l_name_sample ), l_name_file_distributions = l_name_sample , path_folder_output = path_folder_size_norm , float_max_ratio_to_arr_dist_guassian_filter_min_sigma_for_dynamic_gaussian_filter_selection = 2 , float_sigma_gaussian_filter_min = 8 , int_min_total_read_count_for_a_peak = 30 , ) # based on the output, set the confident size range str_confident_size_range = ourotools . get_confident_size_range ( path_folder_size_norm ) The size distribution normalization module is implemented using the LongSummarizeSizeDistributions and LongCreateReferenceSizeDistribution workflows. First, using the LongSummarizeSizeDistributions workflow, a full-length, UMI-deduplicated cDNA size distribution is obtained from the valid_3p_valid_5p barcoded BAM file (representing in vivo full-length mRNAs ) for each sample. Next, the reference mRNA size distribution is constructed for all the samples using the LongCreateReferenceSizeDistribution workflow. step 6) Single-cell count module # run the single-cell count module ourotools . LongExportNormalizedCountMatrix ( path_folder_ref = path_folder_count_module_index , l_path_file_bam_input = l_full_length_bam , l_path_folder_output = list ( f' { path_folder_data } LongExportNormalizedCountMatrix_out/ { name_sample } /' for name_sample in l_name_sample ), l_name_distribution = l_name_sample , path_folder_reference_distribution = path_folder_size_norm , l_str_l_t_distribution_range_of_interest = [ ',' . join ( [ "raw" , str_confident_size_range ] ) ], flag_enforce_transcript_start_site_matching_for_long_read_during_realignment = True , flag_enforce_transcript_end_site_matching_for_long_read_during_realignment = True , ) The single-cell long-read count module LongExportNormalizedCountMatrix is largely composed of three parts: constructing an index (only required once for each set of genes, transcripts, repeat elements, regulatory elements and the reference genome), assigning each read to various buckets (each bucket represent one of the genes, transcripts, exons, splice junctions, TEs, tCREs, and individual genomic tiles), and exporting a size distribution-normalized count matrix for each bucket (later these count matrixes are combined into a single size distribution-normalized count matrix as an output). step 7) Visualization # TBD wrap-up) Running the entire pipeline using a wrapper function # version 2025-01-25 by Hyunsu An @ GIST-FGL import ourotools ourotools . bk . int_max_num_batches_in_a_queue_for_each_worker = 1 # [NOTE] For WSL, changing this variable to 1 is necessary to prevent deadlock(s) during IPC. ourotools . run_pipeline ( # dataset setting path_folder_data = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20220331_Ouroboros_Project/pipeline/20230208_Mouse_Long_Read_Single_Cell_Atlas/pipeline/20230811_mouse_long_read_single_cell_atlas_v202308/tutorial_data/20240813_ovary_testis_tutorial2/' , l_name_sample = [ 'mOvary.subsampled' , 'mTestis2.subsampled' , ], # scRNA-seq technology-specific path_file_valid_barcode_list = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20210728_development_ouroboros_qc/example/3M-february-2018.txt.gz' , # GEX v3 CB # species-specific settings path_file_minimap_index_genome = '/home/shared/ensembl/Mus_musculus/index/minimap2/Mus_musculus.GRCm38.dna.primary_assembly.k_14.idx' , path_file_minimap_splice_junction = '/home/shared/ensembl/Mus_musculus/Mus_musculus.GRCm38.102.paftools.bed' , path_file_minimap_unwanted = '/home/project/Single_Cell_Full_Length_Atlas/data/accessory_data/cDNA_depletion/index/minimap2/MT_and_rRNA_GRCm38.fa.ont.mmi' , path_folder_count_module_index = '/home/project/Single_Cell_Full_Length_Atlas/data/pipeline/20211116_ouroboros_short_read_public_data_mining/scarab_annotations/Mus_musculus.GRCm38.102.v0.2.4/' , # path to the Ouro-Tools reference # run setting n_workers = 2 , # employ 2 workers (since there are two samples, 2 workers are sufficient) n_threads_for_each_worker = 8 , # use 8 CPU cores for each worker # additional settings ar + +## Conda Search Info +$ conda search -c bioconda -c conda-forge ourotools --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +ourotools 0.2.7 pyhdfd78af_0 +---------------------------- +file name : ourotools-0.2.7-pyhdfd78af_0.tar.bz2 +name : ourotools +version : 0.2.7 +build : pyhdfd78af_0 +build number: 0 +size : 169 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ourotools-0.2.7-pyhdfd78af_0.tar.bz2 +md5 : abaa8895f8a466776bd0039d0c222c12 +timestamp : 2025-01-20 01:26:56 UTC +dependencies: + - bitarray >=2.5.1 + - h5py >=3.8.0 + - intervaltree >=3.1.0 + - joblib >=1.2.0 + - mappy >=2.24 + - matplotlib-base >=3.5.2 + - nest-asyncio >=1.5.6 + - numpy >=1.26.4 + - owlready2 >=0.46 + - pandas >=1.5.2 + - plotly >=5.18.0 + - pybigwig >=0.3.22 + - pysam >=0.18.0 + - python >=3.11,<4.0 + - regex >=2.5.135 + - scanpy >=1.10.2 + - scipy >=1.9.1 + - tqdm >=4.64.1 + + +ourotools 0.2.8 pyhdfd78af_0 +---------------------------- +file name : ourotools-0.2.8-pyhdfd78af_0.tar.bz2 +name : ourotools +version : 0.2.8 +build : pyhdfd78af_0 +build number: 0 +size : 169 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ourotools-0.2.8-pyhdfd78af_0.tar.bz2 +md5 : 3ae544d21ca11c7969b3ce1f2075a5dd +timestamp : 2025-01-20 08:12:07 UTC +dependencies: + - bitarray >=2.5.1 + - h5py >=3.8.0 + - intervaltree >=3.1.0 + - joblib >=1.2.0 + - mappy >=2.24 + - matplotlib-base >=3.5.2 + - minimap2 >=2.28 + - nest-asyncio >=1.5.6 + - numpy >=1.26.4 + - owlready2 >=0.46 + - pandas >=1.5.2 + - plotly >=5.18.0 + - pybigwig >=0.3.22 + - pysam >=0.18.0 + - python >=3.11 + - regex >=2.5.135 + - samtools >=1.10 + - scanpy >=1.10.2 + - scipy >=1.9.1 + - tqdm >=4.64.1 + + +ourotools 0.2.9 pyhdfd78af_0 +---------------------------- +file name : ourotools-0.2.9-pyhdfd78af_0.conda +name : ourotools +version : 0.2.9 +build : pyhdfd78af_0 +build number: 0 +size : 165 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/ourotools-0.2.9-pyhdfd78af_0.conda +md5 : 1dbaf63d32419c04755a83e4774798e1 +timestamp : 2025-12-06 06:13:28 UTC +dependencies: + - bitarray >=2.5.1 + - h5py >=3.8.0 + - intervaltree >=3.1.0 + - joblib >=1.2.0 + - mappy >=2.24 + - matplotlib-base >=3.5.2 + - minimap2 >=2.28 + - nest-asyncio >=1.5.6 + - numpy >=1.26.4 + - owlready2 >=0.46 + - pandas >=1.5.2 + - plotly >=5.18.0 + - pybigwig >=0.3.22 + - pysam >=0.18.0 + - python >=3.11 + - regex >=2.5.135 + - samtools >=1.10 + - scanpy >=1.10.2 + - scipy >=1.9.1 + - tqdm >=4.64.1 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/paml.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/paml.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e2d6a10c7e1b3602e3f6f3d72afde316f77dfac0 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/paml.manual_bundle.txt @@ -0,0 +1,366 @@ +# Tool: paml +software_name: paml +tier: T1 +domain: t1_backfill_overall +downloads: 331958 +summary: A package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. +description: A package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. +dependencies: libgcc >=14 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://evomics.org/resources/software/molecular-evolution-software/paml +doc_url: https://github.com/abacus-gene/paml/wiki +dev_url: https://github.com/abacus-gene/paml + +## URL Docs Extract +### https://github.com/abacus-gene/paml/wiki +HOME · abacus-gene/paml Wiki · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} abacus-gene / paml Public Notifications You must be signed in to change notification settings Fork 32 Star 192 Code Issues 2 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights HOME Jump to bottom sabifo4 edited this page Apr 21, 2025 · 10 revisions PAML Wiki PAML (for Phylogenetic Analysis by Maximum Likelihood ) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained by Ziheng Yang and distributed under the GNU GPL v3. Before running any of the programs included in the PAML software, please go through the different sections of this Wiki, where a detailed explanation of how to install and run the programs is given. One of the main problems users face is related to data formatting . In that way, please make sure that you go through the section Data formatting before running any PAML program and format your input data files and control files accordingly. Important Problems with input data, control files, error/warning messages output by the PAML programs (which inform users about formatting issues in their input files or wrong settings in their control files), and general questions should be posted in the PAML discussion group . Before posting a message, please use the search tool in the PAML discussion group to check whether your question/s have already been asked by other PAML users. You should also refer to the FAQs document . If you still cannot find an answer to your question/s, please post them in the PAML discussion group . Please, do not paste the screen output and the error/warning that you get without any reference when you are requesting help. Instead, make sure that you attach the input data and the control files you are using, explain how you ran PAML , which PAML version you are using, etc. In that way, your issue will be much easier and faster to troubleshoot . You can find more information about how to report your warning/error message on this website . Please, only raise an issue on this GitHub repository when you experience technical problems such as compiling issues, programs aborting or not running at all, etc. Installation ANSI C source codes and executable files are distributed for UNIX, Linux, and Mac OS X (see the latest stable release available on this GitHub repository ). PAML is not good for tree making, although it may be used to estimate parameters and test hypotheses to study the evolutionary process once you have reconstructed trees using other programs such as RAxML-NG , IQ-TREE , PAUP* , PHYLIP , PhyML , etc. To download and install PAML software, please follow the next links in the wiki: Downloading and installing PAML PAML for Linux How to export paths in Linux PAML for Mac OS X How to export paths in Mac OS X PAML for Windows 10 or later How to export paths using the Windows Subsystem for Linux Old compiled versions of PAML PAML for Mac OS X PAML for Windows 9x/NT/2000/XP/Vista 7 Graphical user interface: PAML-X Documentation Overview PAML documentation What PAML programs can do What PAML programs cannot do Data formatting Sequence data file format Sequential and interleaved formats Species/sequence names Option G Option G for codon sequences ( codeml with seqtype = 1 ) Site pattern counts Tree file format and representations of tree topology Parenthesis notation Tree files produced by PAUP and MacClade Branch or node labels Divergence date symbol @ Branch representation of tree topology Substitution models Nucleotide substitution models Codon substitution models Branch models Site models Suzuki and Gojobori’s (1999) method for detecting sites under positive selection Branch-site models Clade models Mutation-selection models Amino acid substitution models PAML programs BASEML BASEMLG CODEML Evolver yn00 MCMCtree Infinitesites Citing PAML If you use PAML , please cite the following: Yang, Z (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556 . Yang, Z (2007). PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24, 1586-1591 . In addition... If you use the PAML program MCMCtree , please cite the following papers if you have used/run... ... the approximate likelihood calculation to speed up analyses with phylogenomic datasets (calculating branch lengths, Hessian, and gradient): dos Reis M and Yang Z (2011). Approximate likelihood calculation for Bayesian estimation of divergence times. Mol. Biol. Evol. 28, 2161-2172 . ... Bayesian model selection analyses: dos Reis M, et al. (2018). Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: Primates as a test case. Syst. Biol. 67, 594–615 . Also, please cite the mcmc3r R package if you use it ( see tutorial via this link ). ... the models for continuous morphological characters implemented in MCMCtree : Álvarez-Carretero S, et al. (2019). Bayesian estimation of species divergence times using correlated quantitative characters. Syst. Biol. 68, 967–986 . Also, please cite the mcmc3r R package if you use it ( see tutorial via this link ). ... the protocol Bayesian Molecular Clock Dating Using Genome-Scale Datasets : dos Reis M and Yang, Z (2019). Bayesian Molecular Clock Dating Using Genome-Scale Datasets. In : Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 1910. Humana, New York, NY . You can also access this chapter and the code used throughout the protocol on the divtime GitHub repository maintained by Mario dos Reis . ... the protocol Environmental Microbial Evolution: Methods and Protocols : dos Reis M (2022) In : Haiwei Luo (ed.) Environmental Microbial Evolution: Methods and Protocols. Methods in Molecular Biology, vol 2569. Humana, New York, NY . You can access the code used throughout the protocol on the microdiv GitHub repository maintained by Mario dos Reis . ... the Bayesian sequential-subtree (BSS) approach and/or the scripts to fit skew- t distributions to fossil calibrations : Álvarez-Carretero S, et al. (2022) A species-level timeline of mammal evolution integrating phylogenomic data. Nature 602, 263–267 . You can find the tutorial to reproduce these analyses on the mammals_dating GitHub repository maintained by Sandra Álvarez-Carretero . If you use the PAML program CODEML , please cite the following papers if you have used/run... ... the protocol A Beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome : Jeffares DC, Tomiczek B, Sojo V, dos Reis M (2015). A Beginners Guide to Estimating the Non-synonymous to Synonymous Rate Ratio of all Protein-Coding Genes in a Genome. In : Peacock, C. (eds) Parasite Genomics Protocols. Methods in Molecular Biology, vol 1201. Humana Press, New York, NY. . ... the protocol Beginner's guide on the use of PAML to detect positive selection and/or the corresponding GitHub tutorial on the positive-selection repository : Álvarez-Carretero S, Kapli P, Yang Z (2023). Beginner's guide on the use of PAML to detect positive selection, Mol Biol Evol, 40(4):msad041. . Remember to read the supplementary material where we discuss (i) analyses and checks you should carry out before running tests of positive selection with CODEML, (ii) gene tree VS species tree, and (iii) the usage of rooted and unrooted trees . Additional information Changes and bug fixes until v4.10.1 were documented in the file doc/pamlHistory.txt . Changes in later versions have been documented for each release in the releases section of this GitHub repository . © Copyright 1993-2023 by Ziheng Yang The software package is provided "as is" without warranty of any kind. In no event shall the author or their employer be held responsible for any damage resulting from the use of this software, including but not limited to the frustration that you may experience in using the package. The program package, including source codes, example data sets, executables, and this documentation is maintained by Ziheng Yang and distributed under the GNU GPL v3. Ziheng Yang Department of Genetics, Evolution, and Environment University College London Gower Street WC1E 6BT, London, United Kingdom Toggle table of contents Pages 12 Loading HOME PAML Wiki Installation Documentation Citing PAML In addition... Additional information Loading BASEML Uh oh! There was an error while loading. Please reload this page . Loading BASEMLG Uh oh! There was an error while loading. Please reload this page . Loading CODEML Uh oh! There was an error while loading. Please reload this page . Loading Data formatting Uh oh! There was an error while loading. Please reload this page . Loading Evolver Uh oh! There was an error while loading. Please reload this page . Loading Infinitesites Uh oh! There was an error while loading. Please reload this page . Loading Installation Uh oh! There was an error while loading. Please reload this page . Loading MCMCtree Uh oh! There was an error while loading. Please reload this page . Loading Overview Uh oh! There was an error while loading. Please reload this page . Loading Substitution models Uh oh! There was an error while loading. Please reload this page . Loading yn00 Uh oh! There was an error while loading. Please reload this page . Clone this wiki locally Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/abacus-gene/paml +GitHub - abacus-gene/paml: PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **technical issues** on this repository (e.g., compiling, programs abort, etc.). Problems with input data (e.g., error/warning messages) & general questions should be posted at https://groups.google.com/g/pamlsoftware?pli · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} abacus-gene / paml Public Notifications You must be signed in to change notification settings Fork 32 Star 192 Code Issues 2 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights abacus-gene/paml master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 97 Commits 97 Commits Technical Technical dat dat doc doc examples examples src src .gitignore .gitignore LICENSE LICENSE README.md README.md View all files Repository files navigation README GPL-3.0 license Phylogenetic Analysis by Maximum Likelihood PAML (for Phylogenetic Analysis by Maximum Likelihood ) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained by Ziheng Yang and distributed under the GNU GPL v3. Before running any of the programs included in the PAML software, please go through the different sections of this Wiki, where a detailed explanation of how to install and run the programs is given. One of the main problems users face is related to data formatting . In that way, please make sure that you go through the section Data formatting in the PAML Wiki before running any PAML program and format your input data files and control files accordingly. Important Problems with input data, control files, error/warning messages output by the PAML programs (which inform users about formatting issues in their input files or wrong settings in their control files), and general questions should be posted in the PAML discussion group . Before posting a message, please use the search tool in the PAML discussion group to check whether your question/s have already been asked by other PAML users. You should also refer to the FAQs document . If you still cannot find an answer to your question/s, please post them in the PAML discussion group . Please, do not paste the screen output and the error/warning that you get without any reference when you are requesting help. Instead, make sure that you attach the input data and the control files you are using, explain how you ran PAML , which PAML version you are using, etc. In that way, your issue will be much easier and faster to troubleshoot . You can find more information about how to report your warning/error message on this website . Please, only raise an issue on this GitHub repository when you experience technical problems such as compiling issues, programs aborting or not running at all, etc. Installation ANSI C source codes and executable files are distributed for UNIX, Linux, and Mac OS X (see the latest stable release available on this GitHub repository ). PAML is not good for tree making, although it may be used to estimate parameters and test hypotheses to study the evolutionary process once you have reconstructed trees using other programs such as RAxML-NG , IQ-TREE , PAUP* , PHYLIP , PhyML , etc. To download and install PAML software, please follow the next links in the wiki: Downloading and installing PAML PAML for Linux How to export paths in Linux PAML for Mac OS X How to export paths in Mac OS X PAML for Windows 10 or later How to export paths using the Windows Subsystem for Linux Old compiled versions of PAML PAML for Mac OS X PAML for Windows 9x/NT/2000/XP/Vista 7 Graphical user interface: PAML-X Documentation The PAML Wiki is still under construction 🔧 -- we are slowly migrating the PAML documentation in PDF format to a more interactive and engaging tutorial! In the meantime, you can access the following sections, which are also detailed in the PAML Wiki home section: Overview PAML documentation What PAML programs can do What PAML programs cannot do Data formatting Sequence data file format Sequential and interleaved formats Species/sequence names Option G Option G for codon sequences ( codeml with seqtype = 1 ) Site pattern counts Tree file format and representations of tree topology Parenthesis notation Tree files produced by PAUP and MacClade Branch or node labels Divergence date symbol @ Branch representation of tree topology Substitution models Nucleotide substitution models Codon substitution models Branch models Site models Suzuki and Gojobori’s (1999) method for detecting sites under positive selection Branch-site models Clade models Mutation-selection models Amino acid substitution models PAML programs BASEML BASEMLG CODEML Evolver Infinitesites MCMCtree yn00 Citing PAML If you use PAML , please cite the following: Yang, Z (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556 . Yang, Z (2007). PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24, 1586-1591 . In addition... If you use the PAML program MCMCtree , please cite the following papers if you have used/run... ... the approximate likelihood calculation to speed up analyses with phylogenomic datasets (calculating branch lengths, Hessian, and gradient): dos Reis M and Yang Z (2011). Approximate likelihood calculation for Bayesian estimation of divergence times. Mol. Biol. Evol. 28, 2161-2172 . ... Bayesian model selection analyses: dos Reis M, et al. (2018). Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: Primates as a test case. Syst. Biol. 67, 594–615 . Also, please cite the mcmc3r R package if you use it ( see tutorial via this link ). ... the models for continuous morphological characters implemented in MCMCtree : Álvarez-Carretero S, et al. (2019). Bayesian estimation of species divergence times using correlated quantitative characters. Syst. Biol. 68, 967–986 . Also, please cite the mcmc3r R package if you use it ( see tutorial via this link ). ... the protocol Bayesian Molecular Clock Dating Using Genome-Scale Datasets : dos Reis M and Yang, Z (2019). Bayesian Molecular Clock Dating Using Genome-Scale Datasets. In : Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 1910. Humana, New York, NY . You can also access this chapter and the code used throughout the protocol on the divtime GitHub repository maintained by Mario dos Reis . ... the protocol Environmental Microbial Evolution: Methods and Protocols : dos Reis M (2022) In : Haiwei Luo (ed.) Environmental Microbial Evolution: Methods and Protocols. Methods in Molecular Biology, vol 2569. Humana, New York, NY . You can access the code used throughout the protocol on the microdiv GitHub repository maintained by Mario dos Reis . ... the Bayesian sequential-subtree (BSS) approach and/or the scripts to fit skew- t distributions to fossil calibrations : Álvarez-Carretero S, et al. (2022) A species-level timeline of mammal evolution integrating phylogenomic data. Nature 602, 263–267 . You can find the tutorial to reproduce these analyses on the mammals_dating GitHub repository maintained by Sandra Álvarez-Carretero . If you use the PAML program CODEML , please cite the following papers if you have used/run... ... the protocol A Beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome : Jeffares DC, Tomiczek B, Sojo V, dos Reis M (2015). A Beginners Guide to Estimating the Non-synonymous to Synonymous Rate Ratio of all Protein-Coding Genes in a Genome. In : Peacock, C. (eds) Parasite Genomics Protocols. Methods in Molecular Biology, vol 1201. Humana Press, New York, NY. . ... the protocol Beginner's guide on the use of PAML to detect positive selection and/or the corresponding GitHub tutorial on the positive-selection repository : Álvarez-Carretero S, Kapli P, Yang Z (2023). Beginner's guide on the use of PAML to detect positive selection, Mol Biol Evol, 40(4):msad041. . Remember to read the supplementary material where we discuss (i) analyses and checks you should carry out before running tests of positive selection with CODEML, (ii) gene tree VS species tree, and (iii) the usage of rooted and unrooted trees . Additional information Changes in all version from PAML v4.10.0 have been documented for each release in the releases section of this GitHub repository . Changes and bug fixes prior to v4.10.0 can only be found in doc/pamlHistory.txt . About PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **technical issues** on this repository (e.g., compiling, programs abort, etc.). Problems with input data (e.g., error/warning messages) & general questions should be posted at https://groups.google.com/g/pamlsoftware?pli Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 192 stars Watchers 7 watching Forks 32 forks Report repository Releases 11 4.10.10 Latest Jan 29, 2026 + 10 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C 99.1% Other 0.9% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge paml --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +paml 4.9 0 +---------- +file name : paml-4.9-0.tar.bz2 +name : paml +version : 4.9 +build : 0 +build number: 0 +size : 1.1 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.9-0.tar.bz2 +md5 : 7de782b2c5eb0ee4fe634513e91edeac +dependencies: [] + + +paml 4.9 1 +---------- +file name : paml-4.9-1.tar.bz2 +name : paml +version : 4.9 +build : 1 +build number: 1 +size : 1.1 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.9-1.tar.bz2 +md5 : 9fce143462da42c7743dde3d18e51cd8 +dependencies: + - libgcc + + +paml 4.9 h14c3975_4 +------------------- +file name : paml-4.9-h14c3975_4.tar.bz2 +name : paml +version : 4.9 +build : h14c3975_4 +build number: 4 +size : 1.2 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.9-h14c3975_4.tar.bz2 +md5 : ccfac7bb5d4357952a6de9e0329d9fc4 +timestamp : 2019-02-03 23:09:14 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +paml 4.9 h470a237_2 +------------------- +file name : paml-4.9-h470a237_2.tar.bz2 +name : paml +version : 4.9 +build : h470a237_2 +build number: 2 +size : 1.1 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.9-h470a237_2.tar.bz2 +md5 : 64dd1edcd12db1e9e72f6945bbcf39b1 +timestamp : 2018-07-05 22:16:58 UTC +dependencies: + - libgcc-ng >=4.9 + + +paml 4.9 h470a237_3 +------------------- +file name : paml-4.9-h470a237_3.tar.bz2 +name : paml +version : 4.9 +build : h470a237_3 +build number: 3 +size : 1.2 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.9-h470a237_3.tar.bz2 +md5 : 999a1bbe4d8c9dcddb8d2a7f2807e003 +timestamp : 2018-09-30 18:04:44 UTC +dependencies: + - libgcc-ng >=4.9 + + +paml 4.9 h516909a_5 +------------------- +file name : paml-4.9-h516909a_5.tar.bz2 +name : paml +version : 4.9 +build : h516909a_5 +build number: 5 +size : 1.5 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.9-h516909a_5.tar.bz2 +md5 : 22a8fafb58c6d2e04ca06309d6c6d560 +timestamp : 2019-10-26 22:56:23 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +paml 4.9 h779adbc_6 +------------------- +file name : paml-4.9-h779adbc_6.tar.bz2 +name : paml +version : 4.9 +build : h779adbc_6 +build number: 6 +size : 1.2 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.9-h779adbc_6.tar.bz2 +md5 : 55ee983b74c38377b419ca91ab601fce +timestamp : 2021-03-31 22:13:25 UTC +dependencies: + - libgcc-ng >=9.3.0 + + +paml 4.9 hec16e2b_7 +------------------- +file name : paml-4.9-hec16e2b_7.tar.bz2 +name : paml +version : 4.9 +build : hec16e2b_7 +build number: 7 +size : 994 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.9-hec16e2b_7.tar.bz2 +md5 : 41888eb05cc9da15d9e2ef3bb6950f40 +timestamp : 2022-02-23 01:07:29 UTC +dependencies: + - libgcc-ng >=10.3.0 + + +paml 4.10.6 h031d066_1 +---------------------- +file name : paml-4.10.6-h031d066_1.tar.bz2 +name : paml +version : 4.10.6 +build : h031d066_1 +build number: 1 +size : 1.0 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.6-h031d066_1.tar.bz2 +md5 : 9a6a8f263ec3a75312c48bed1cac577b +timestamp : 2023-05-15 01:11:34 UTC +dependencies: + - libgcc-ng >=12 + + +paml 4.10.6 h031d066_2 +---------------------- +file name : paml-4.10.6-h031d066_2.tar.bz2 +name : paml +version : 4.10.6 +build : h031d066_2 +build number: 2 +size : 1.0 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.6-h031d066_2.tar.bz2 +md5 : 2adac5d4627dacbf16552a5e677a2a0b +timestamp : 2023-05-15 23:51:16 UTC +dependencies: + - libgcc-ng >=12 + + +paml 4.10.6 hec16e2b_0 +---------------------- +file name : paml-4.10.6-hec16e2b_0.tar.bz2 +name : paml +version : 4.10.6 +build : hec16e2b_0 +build number: 0 +size : 1018 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.6-hec16e2b_0.tar.bz2 +md5 : d81d36901584c7a45f25458da42ebd9b +timestamp : 2023-02-22 11:33:35 UTC +dependencies: + - libgcc-ng >=12 + + +paml 4.10.6 hec16e2b_1 +---------------------- +file name : paml-4.10.6-hec16e2b_1.tar.bz2 +name : paml +version : 4.10.6 +build : hec16e2b_1 +build number: 1 +size : 1019 KB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.6-hec16e2b_1.tar.bz2 +md5 : 5faa8f602e81205b37d72ac96f245309 +timestamp : 2023-05-11 14:25:11 UTC +dependencies: + - libgcc-ng >=12 + + +paml 4.10.7 h031d066_0 +---------------------- +file name : paml-4.10.7-h031d066_0.tar.bz2 +name : paml +version : 4.10.7 +build : h031d066_0 +build number: 0 +size : 1.0 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.7-h031d066_0.tar.bz2 +md5 : e25a921ac5019b8e442ef789a403d49c +timestamp : 2023-11-17 13:04:56 UTC +dependencies: + - libgcc-ng >=12 + + +paml 4.10.7 h031d066_1 +---------------------- +file name : paml-4.10.7-h031d066_1.tar.bz2 +name : paml +version : 4.10.7 +build : h031d066_1 +build number: 1 +size : 1.0 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.7-h031d066_1.tar.bz2 +md5 : 627002991a379d013307808bf9b71676 +timestamp : 2024-04-03 13:01:06 UTC +dependencies: + - libgcc-ng >=12 + + +paml 4.10.7 h7b50bb2_2 +---------------------- +file name : paml-4.10.7-h7b50bb2_2.tar.bz2 +name : paml +version : 4.10.7 +build : h7b50bb2_2 +build number: 2 +size : 1.0 MB +license : GNU General Public License v3 (GPLv3) +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.7-h7b50bb2_2.tar.bz2 +md5 : e4bbd0dbc7801b5db4df04fe25bfe0b1 +timestamp : 2024-12-12 16:20:25 UTC +dependencies: + - libgcc >=13 + + +paml 4.10.9 h7b50bb2_0 +---------------------- +file name : paml-4.10.9-h7b50bb2_0.tar.bz2 +name : paml +version : 4.10.9 +build : h7b50bb2_0 +build number: 0 +size : 857 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.9-h7b50bb2_0.tar.bz2 +md5 : 32375f6d7505b178574d66d8db3a2429 +timestamp : 2025-07-31 18:14:25 UTC +dependencies: + - libgcc >=13 + + +paml 4.10.9 h7b50bb2_1 +---------------------- +file name : paml-4.10.9-h7b50bb2_1.conda +name : paml +version : 4.10.9 +build : h7b50bb2_1 +build number: 1 +size : 663 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.9-h7b50bb2_1.conda +md5 : ef02b401c5daaf104b3d1091f8ec37f5 +timestamp : 2025-08-20 16:18:48 UTC +dependencies: + - libgcc >=13 + + +paml 4.10.10 h7b50bb2_0 +----------------------- +file name : paml-4.10.10-h7b50bb2_0.conda +name : paml +version : 4.10.10 +build : h7b50bb2_0 +build number: 0 +size : 667 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.10-h7b50bb2_0.conda +md5 : 3836a92c8d78504890e074d92b33022f +timestamp : 2026-01-29 18:18:17 UTC +dependencies: + - libgcc >=13 + + +paml 4.10.10 h87e0c26_1 +----------------------- +file name : paml-4.10.10-h87e0c26_1.conda +name : paml +version : 4.10.10 +build : h87e0c26_1 +build number: 1 +size : 677 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.10-h87e0c26_1.conda +md5 : ef3f7b34622dc40c32f23d42cb757d89 +timestamp : 2026-04-06 08:48:10 UTC +dependencies: + - libgcc >=14 + + +paml 4.10.10 h87e0c26_2 +----------------------- +file name : paml-4.10.10-h87e0c26_2.conda +name : paml +version : 4.10.10 +build : h87e0c26_2 +build number: 2 +size : 675 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/paml-4.10.10-h87e0c26_2.conda +md5 : 126e7be483750ee719c882fb23d471f7 +timestamp : 2026-04-08 06:00:39 UTC +dependencies: + - libgcc >=14 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pandaseq.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pandaseq.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c86661b77b925494769e9f12768bf5f7bfa225d0 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pandaseq.manual_bundle.txt @@ -0,0 +1,420 @@ +# Tool: pandaseq +software_name: pandaseq +tier: T1 +domain: t1_backfill_overall +downloads: 174267 +summary: +description: +dependencies: bzip2 >=1.0.8,<2.0a0, libgcc >=13, libzlib >=1.3.1,<2.0a0, zlib +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +cli:pandaseq +## CLI Help Content +$ conda run -n bioenv_cli pandaseq --help +[rc=1] + +pandaseq: invalid option -- '-' +Unknown option `--'. + +ERROR conda.cli.main_run:execute(127): `conda run pandaseq --help` failed. (See above for error) + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge pandaseq --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +pandaseq 2.8.1 1 +---------------- +file name : pandaseq-2.8.1-1.tar.bz2 +name : pandaseq +version : 2.8.1 +build : 1 +build number: 1 +size : 590 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.8.1-1.tar.bz2 +md5 : 1cdc3062d3b11a8fa7c83f43d7e99314 +dependencies: + - bzip2 1.0* + - libgcc + - libtool + - zlib 1.2.11* + + +pandaseq 2.8.1 h2f06484_3 +------------------------- +file name : pandaseq-2.8.1-h2f06484_3.tar.bz2 +name : pandaseq +version : 2.8.1 +build : h2f06484_3 +build number: 3 +size : 776 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.8.1-h2f06484_3.tar.bz2 +md5 : b6299538c80384f1144e03421c9a516b +timestamp : 2020-08-13 10:37:12 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +pandaseq 2.8.1 h36cd882_4 +------------------------- +file name : pandaseq-2.8.1-h36cd882_4.tar.bz2 +name : pandaseq +version : 2.8.1 +build : h36cd882_4 +build number: 4 +size : 822 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.8.1-h36cd882_4.tar.bz2 +md5 : b487ade251a377534564fdbaca408f23 +timestamp : 2021-03-25 15:47:34 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +pandaseq 2.8.1 h67092d7_5 +------------------------- +file name : pandaseq-2.8.1-h67092d7_5.tar.bz2 +name : pandaseq +version : 2.8.1 +build : h67092d7_5 +build number: 5 +size : 679 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.8.1-h67092d7_5.tar.bz2 +md5 : 6da0abb547f299e83229f69295aa55cc +timestamp : 2022-02-22 02:12:57 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +pandaseq 2.8.1 h67092d7_6 +------------------------- +file name : pandaseq-2.8.1-h67092d7_6.tar.bz2 +name : pandaseq +version : 2.8.1 +build : h67092d7_6 +build number: 6 +size : 686 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.8.1-h67092d7_6.tar.bz2 +md5 : cc45725d2cbed169b859126310e8086a +timestamp : 2023-05-14 11:08:16 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +pandaseq 2.8.1 h9d449c0_6 +------------------------- +file name : pandaseq-2.8.1-h9d449c0_6.tar.bz2 +name : pandaseq +version : 2.8.1 +build : h9d449c0_6 +build number: 6 +size : 733 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.8.1-h9d449c0_6.tar.bz2 +md5 : 67702d234276fe9c0c8c1e94b1f99259 +timestamp : 2023-05-15 01:17:28 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +pandaseq 2.8.1 h9d449c0_7 +------------------------- +file name : pandaseq-2.8.1-h9d449c0_7.tar.bz2 +name : pandaseq +version : 2.8.1 +build : h9d449c0_7 +build number: 7 +size : 741 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.8.1-h9d449c0_7.tar.bz2 +md5 : a98fd4668e2d998faae0c8c581d5bc80 +timestamp : 2023-05-15 23:27:12 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +pandaseq 2.8.1 hb1d24b7_8 +------------------------- +file name : pandaseq-2.8.1-hb1d24b7_8.tar.bz2 +name : pandaseq +version : 2.8.1 +build : hb1d24b7_8 +build number: 8 +size : 669 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.8.1-hb1d24b7_8.tar.bz2 +md5 : 69a6ad9823edb17b17d5b90bd312aa4f +timestamp : 2024-12-11 15:32:05 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc >=13 + - libzlib >=1.3.1,<2.0a0 + - zlib + + +pandaseq 2.8.1 he4cf2ce_2 +------------------------- +file name : pandaseq-2.8.1-he4cf2ce_2.tar.bz2 +name : pandaseq +version : 2.8.1 +build : he4cf2ce_2 +build number: 2 +size : 454 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.8.1-he4cf2ce_2.tar.bz2 +md5 : 9f749245af5b6c71968a855728f00074 +timestamp : 2018-07-22 19:22:46 UTC +dependencies: + - bzip2 >=1.0.6,<2.0a0 + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +pandaseq 2.11 1 +--------------- +file name : pandaseq-2.11-1.tar.bz2 +name : pandaseq +version : 2.11 +build : 1 +build number: 1 +size : 680 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-1.tar.bz2 +md5 : 46cac32c9e48d88fc62f232e3115f41e +dependencies: + - libgcc + - libtool + + +pandaseq 2.11 2 +--------------- +file name : pandaseq-2.11-2.tar.bz2 +name : pandaseq +version : 2.11 +build : 2 +build number: 2 +size : 609 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-2.tar.bz2 +md5 : b8838590d9e5a3871d0166250ff27822 +dependencies: + - bzip2 1.0* + - libgcc + - libtool + - zlib 1.2.11* + + +pandaseq 2.11 h2f06484_4 +------------------------ +file name : pandaseq-2.11-h2f06484_4.tar.bz2 +name : pandaseq +version : 2.11 +build : h2f06484_4 +build number: 4 +size : 802 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-h2f06484_4.tar.bz2 +md5 : 04bf3c3f478be42f7490738d4a876659 +timestamp : 2020-08-13 10:43:34 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +pandaseq 2.11 h36cd882_5 +------------------------ +file name : pandaseq-2.11-h36cd882_5.tar.bz2 +name : pandaseq +version : 2.11 +build : h36cd882_5 +build number: 5 +size : 781 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-h36cd882_5.tar.bz2 +md5 : 257564202fed27baa7094f27046cbdf7 +timestamp : 2021-03-25 15:55:07 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=9.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +pandaseq 2.11 h67092d7_6 +------------------------ +file name : pandaseq-2.11-h67092d7_6.tar.bz2 +name : pandaseq +version : 2.11 +build : h67092d7_6 +build number: 6 +size : 707 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-h67092d7_6.tar.bz2 +md5 : e8d75a18fa241cad9731494814d2a09f +timestamp : 2022-02-22 02:23:51 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +pandaseq 2.11 h67092d7_7 +------------------------ +file name : pandaseq-2.11-h67092d7_7.tar.bz2 +name : pandaseq +version : 2.11 +build : h67092d7_7 +build number: 7 +size : 740 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-h67092d7_7.tar.bz2 +md5 : 0e9c363459501946775d397ea70502dd +timestamp : 2023-05-14 11:01:37 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +pandaseq 2.11 h9d449c0_7 +------------------------ +file name : pandaseq-2.11-h9d449c0_7.tar.bz2 +name : pandaseq +version : 2.11 +build : h9d449c0_7 +build number: 7 +size : 742 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-h9d449c0_7.tar.bz2 +md5 : 2599a0a2ce6954ef15c8014fee0cec87 +timestamp : 2023-05-15 01:11:18 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +pandaseq 2.11 h9d449c0_8 +------------------------ +file name : pandaseq-2.11-h9d449c0_8.tar.bz2 +name : pandaseq +version : 2.11 +build : h9d449c0_8 +build number: 8 +size : 751 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-h9d449c0_8.tar.bz2 +md5 : c0e96d0845da38f1eb23e6d8d1123733 +timestamp : 2023-05-15 23:18:21 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +pandaseq 2.11 hb1d24b7_10 +------------------------- +file name : pandaseq-2.11-hb1d24b7_10.tar.bz2 +name : pandaseq +version : 2.11 +build : hb1d24b7_10 +build number: 10 +size : 690 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-hb1d24b7_10.tar.bz2 +md5 : c714abb547f0bf63f0ccf66e2b47f688 +timestamp : 2025-04-29 10:06:03 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc >=13 + - libzlib >=1.3.1,<2.0a0 + - zlib + + +pandaseq 2.11 hb1d24b7_9 +------------------------ +file name : pandaseq-2.11-hb1d24b7_9.tar.bz2 +name : pandaseq +version : 2.11 +build : hb1d24b7_9 +build number: 9 +size : 764 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-hb1d24b7_9.tar.bz2 +md5 : 0f60dee19e1d283caa1a72a1285ccbda +timestamp : 2024-12-11 15:36:14 UTC +dependencies: + - bzip2 >=1.0.8,<2.0a0 + - libgcc >=13 + - libzlib >=1.3.1,<2.0a0 + - zlib + + +pandaseq 2.11 he4cf2ce_3 +------------------------ +file name : pandaseq-2.11-he4cf2ce_3.tar.bz2 +name : pandaseq +version : 2.11 +build : he4cf2ce_3 +build number: 3 +size : 477 KB +license : GPL3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pandaseq-2.11-he4cf2ce_3.tar.bz2 +md5 : 67bcc1e7de8c91b55f32eaec59aaaa7c +timestamp : 2018-07-22 19:26:12 UTC +dependencies: + - bzip2 >=1.0.6,<2.0a0 + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pango-designation.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pango-designation.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b4a24d6cf1e8dc4a7e27b9e42b25eecd7c165a31 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pango-designation.manual_bundle.txt @@ -0,0 +1,420 @@ +# Tool: pango-designation +software_name: pango-designation +tier: T1 +domain: t1_backfill_overall +downloads: 318521 +summary: Repository for suggesting new lineages that should be added to the current scheme. +description: Repository for suggesting new lineages that should be added to the current scheme. +dependencies: python >=3.7 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/cov-lineages/pango-designation +doc_url: +dev_url: https://github.com/cov-lineages/pango-designation + +## CLI Help Source +cli:pango_designation +## CLI Help Content +$ conda run -n bioenv_cli pango_designation --help +[rc=1] + +Traceback (most recent call last): + File "/225040511/miniconda3/envs/bioenv_cli/bin/pango_designation", line 6, in + from pango_designation.command import main +ModuleNotFoundError: No module named 'pango_designation.command' + +ERROR conda.cli.main_run:execute(127): `conda run pango_designation --help` failed. (See above for error) + + +## URL Docs Extract +### https://github.com/cov-lineages/pango-designation +GitHub - cov-lineages/pango-designation: Repository for suggesting new lineages that should be added to the current scheme · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} cov-lineages / pango-designation Public Notifications You must be signed in to change notification settings Fork 104 Star 1.1k Code Issues 66 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights cov-lineages/pango-designation master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 5,122 Commits 5,122 Commits .github .github anaconda_projects/ db anaconda_projects/ db autoref autoref curation_notes curation_notes docs docs lineage_constellations lineage_constellations misc misc pango_designation pango_designation scripts/ issue-milestone-collector scripts/ issue-milestone-collector tests tests utils utils .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml LICENSE.md LICENSE.md README.md README.md analyze_lineage_notes.py analyze_lineage_notes.py automated-issue-ref.ipynb automated-issue-ref.ipynb checkDups.sh checkDups.sh deduplicate_keeping_first.py deduplicate_keeping_first.py deduplicate_keeping_last.py deduplicate_keeping_last.py drop_duplicate_rows.py drop_duplicate_rows.py findDups.sh findDups.sh lineage_notes.txt lineage_notes.txt lineages.csv lineages.csv setup.py setup.py View all files Repository files navigation README License Pango designation The latest maintained Pango-lineage designations. Suggesting a new lineage Novel lineages or lineage refinements can be suggested by filing an issue with the respective sequence names, as found on GISAID, and any supporting information such as a phylogenetic tree for the putative lineage. Full details on how to suggest a new lineage can be found in the Pango lineage designation guide . Nomenclature rules can be found in the Pango statement of nomenclature rules . Resources available on this repository As detailed on the former pango.network website, we host the lineage description list (LDL) and sequence designation list (SDL) in this repository. Lineage description list: lineage_notes.txt Sequence designation list: lineages.csv Alias record: alias_key.json Other The lineage_constellations directory contains the mutations associated with each of the AY lineages. These are the mutations that were acquried along the phylogenetic path leading to the common ancestor of the lineage and remain conserved in the lineage (defined here as being in >70% of sequences designated to the lineage). This path is identified using the UShER phylogenetic tree. These constellations are different from those in constellations as they attempt to capture all of the associated mutations, not only the defining mutations for a lineage. These constellations are provided for reference and are not used by scorpio currently. However, they should be compatible with scorpio if researchers are interested in exploring them. Sites in the intermediate category drop in and out in the Delta clade so may be associated with the lineage but may be prone to artefacts. Developer docs It is recommended to clone this repo using --filter=blob:none for a blobless clone unless you want to download and put 15GB on your hard drive. The lineages.csv file is quite large and since git stores the state of each file at each commit, that creates a large repo. Git is good at downloading past blobs when necessary, so you shouldn't be impacted in your day to day work by doing this partial clone. Learn more about partial clone here: https://github.blog/2020-12-21-get-up-to-speed-with-partial-clone-and-shallow-clone/ Recommended commands to clone: git clone git clone --filter=blob:none git+https://github.com/cov-lineages/pango-designation.git gh repo clone cov-lineages/pango-designation -- --filter=blob:none About Repository for suggesting new lineages that should be added to the current scheme Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1.1k stars Watchers 75 watching Forks 104 forks Report repository Releases 221 pango designation v1.38 Latest Mar 13, 2026 + 220 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 67.6% Python 30.2% Shell 2.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/cov-lineages/pango-designation +GitHub - cov-lineages/pango-designation: Repository for suggesting new lineages that should be added to the current scheme · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} cov-lineages / pango-designation Public Notifications You must be signed in to change notification settings Fork 104 Star 1.1k Code Issues 66 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights cov-lineages/pango-designation master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 5,122 Commits 5,122 Commits .github .github anaconda_projects/ db anaconda_projects/ db autoref autoref curation_notes curation_notes docs docs lineage_constellations lineage_constellations misc misc pango_designation pango_designation scripts/ issue-milestone-collector scripts/ issue-milestone-collector tests tests utils utils .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml LICENSE.md LICENSE.md README.md README.md analyze_lineage_notes.py analyze_lineage_notes.py automated-issue-ref.ipynb automated-issue-ref.ipynb checkDups.sh checkDups.sh deduplicate_keeping_first.py deduplicate_keeping_first.py deduplicate_keeping_last.py deduplicate_keeping_last.py drop_duplicate_rows.py drop_duplicate_rows.py findDups.sh findDups.sh lineage_notes.txt lineage_notes.txt lineages.csv lineages.csv setup.py setup.py View all files Repository files navigation README License Pango designation The latest maintained Pango-lineage designations. Suggesting a new lineage Novel lineages or lineage refinements can be suggested by filing an issue with the respective sequence names, as found on GISAID, and any supporting information such as a phylogenetic tree for the putative lineage. Full details on how to suggest a new lineage can be found in the Pango lineage designation guide . Nomenclature rules can be found in the Pango statement of nomenclature rules . Resources available on this repository As detailed on the former pango.network website, we host the lineage description list (LDL) and sequence designation list (SDL) in this repository. Lineage description list: lineage_notes.txt Sequence designation list: lineages.csv Alias record: alias_key.json Other The lineage_constellations directory contains the mutations associated with each of the AY lineages. These are the mutations that were acquried along the phylogenetic path leading to the common ancestor of the lineage and remain conserved in the lineage (defined here as being in >70% of sequences designated to the lineage). This path is identified using the UShER phylogenetic tree. These constellations are different from those in constellations as they attempt to capture all of the associated mutations, not only the defining mutations for a lineage. These constellations are provided for reference and are not used by scorpio currently. However, they should be compatible with scorpio if researchers are interested in exploring them. Sites in the intermediate category drop in and out in the Delta clade so may be associated with the lineage but may be prone to artefacts. Developer docs It is recommended to clone this repo using --filter=blob:none for a blobless clone unless you want to download and put 15GB on your hard drive. The lineages.csv file is quite large and since git stores the state of each file at each commit, that creates a large repo. Git is good at downloading past blobs when necessary, so you shouldn't be impacted in your day to day work by doing this partial clone. Learn more about partial clone here: https://github.blog/2020-12-21-get-up-to-speed-with-partial-clone-and-shallow-clone/ Recommended commands to clone: git clone git clone --filter=blob:none git+https://github.com/cov-lineages/pango-designation.git gh repo clone cov-lineages/pango-designation -- --filter=blob:none About Repository for suggesting new lineages that should be added to the current scheme Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1.1k stars Watchers 75 watching Forks 104 forks Report repository Releases 221 pango designation v1.38 Latest Mar 13, 2026 + 220 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 67.6% Python 30.2% Shell 2.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge pango-designation --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +pango-designation 1.2.14 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.14-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.14 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.14-pyhdfd78af_0.tar.bz2 +md5 : 150ad3ab280c844a72ac43109aa0413f +timestamp : 2021-06-17 08:19:16 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.18 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.18-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.18 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.18-pyhdfd78af_0.tar.bz2 +md5 : f8f2eecf9b5b7bfb79ddb330233f43a4 +timestamp : 2021-06-19 15:21:37 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.20 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.20-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.20 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.20-pyhdfd78af_0.tar.bz2 +md5 : 0867275d65b6cd18c42e46c6ae199063 +timestamp : 2021-06-22 14:21:31 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.21 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.21-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.21 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.21-pyhdfd78af_0.tar.bz2 +md5 : 41f0b3ea58427a669a369c2812b44d9e +timestamp : 2021-06-23 16:18:35 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.22 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.22-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.22 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.22-pyhdfd78af_0.tar.bz2 +md5 : b9ecda3c1d11dd9370a184a12c339bdb +timestamp : 2021-06-23 17:26:24 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.23 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.23-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.23 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.23-pyhdfd78af_0.tar.bz2 +md5 : f5607853688fc4e16af1169766b9a43a +timestamp : 2021-06-24 17:20:42 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.25 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.25-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.25 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.25-pyhdfd78af_0.tar.bz2 +md5 : d090899f53f9488c3bf73dfc685590b6 +timestamp : 2021-06-25 17:43:27 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.26 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.26-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.26 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.26-pyhdfd78af_0.tar.bz2 +md5 : ec91d48eba41ef90bcb4776e77d499ea +timestamp : 2021-06-28 17:19:35 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.27 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.27-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.27 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.27-pyhdfd78af_0.tar.bz2 +md5 : 2433b8b1225592338468b5e328a530c4 +timestamp : 2021-06-29 10:20:45 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.29 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.29-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.29 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.29-pyhdfd78af_0.tar.bz2 +md5 : 906f0434c2e9fc8204464c50d13afdab +timestamp : 2021-06-30 12:20:16 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.32 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.32-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.32 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.32-pyhdfd78af_0.tar.bz2 +md5 : 48742690f494ad67ace57d71a128ad77 +timestamp : 2021-07-01 16:29:45 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.33 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.33-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.33 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.33-pyhdfd78af_0.tar.bz2 +md5 : 89a2f190922f79b9dc2e91e79ac9ff1f +timestamp : 2021-07-06 12:18:13 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.34 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.34-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.34 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.34-pyhdfd78af_0.tar.bz2 +md5 : bd94a8abc40eac1a37867b29d49ef7aa +timestamp : 2021-07-07 15:58:14 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.36 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.36-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.36 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.36-pyhdfd78af_0.tar.bz2 +md5 : 82b752dede221ceef6509306c7c8cdbc +timestamp : 2021-07-09 11:21:20 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.37 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.37-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.37 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.37-pyhdfd78af_0.tar.bz2 +md5 : 093729704c21ba2d61834ac5030e4c79 +timestamp : 2021-07-13 16:21:41 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.38 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.38-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.38 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.38-pyhdfd78af_0.tar.bz2 +md5 : 74d46fa11f9c5e5b03324f9ff70f6289 +timestamp : 2021-07-15 09:23:14 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.39 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.39-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.39 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.39-pyhdfd78af_0.tar.bz2 +md5 : ba03988c6098c82cec759d205c56ae9a +timestamp : 2021-07-21 13:27:11 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.41 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.41-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.41 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.41-pyhdfd78af_0.tar.bz2 +md5 : 6448c5ee335233325d3d2bda319b6b94 +timestamp : 2021-07-22 17:22:39 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.42 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.42-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.42 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.42-pyhdfd78af_0.tar.bz2 +md5 : 17040d4823e30c73371a4ec05a9b2ade +timestamp : 2021-07-23 17:28:21 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.43 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.43-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.43 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.43-pyhdfd78af_0.tar.bz2 +md5 : a448fb61c4a89c2e12217869c9fb5e22 +timestamp : 2021-07-26 09:27:33 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.44 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.44-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.44 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.44-pyhdfd78af_0.tar.bz2 +md5 : 0a6d12967287ad9f908041c3f1742813 +timestamp : 2021-07-27 12:25:38 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.46 pyhdfd78af_0 +------------------------------------- +file name : pango-designation-1.2.46-pyhdfd78af_0.tar.bz2 +name : pango-designation +version : 1.2.46 +build : pyhdfd78af_0 +build number: 0 +size : 8 KB +license : CC-BY-NC-4.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pango-designation-1.2.46-pyhdfd78af_0.tar.bz2 +md5 : bf7614712bd6f59dcb240e2b4b88daa9 +timestamp : 2021-07-28 11:26:08 UTC +dependencies: + - python >=3.7 + + +pango-designation 1.2.47 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pbmm2.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pbmm2.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..98e8fad403c73e6d97ba44def9dfd5fea0a39f75 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pbmm2.manual_bundle.txt @@ -0,0 +1,504 @@ +# Tool: pbmm2 +software_name: pbmm2 +tier: T1 +domain: t1_backfill_overall +downloads: 116188 +summary: A minimap2 frontend for PacBio native data formats +description: A minimap2 frontend for PacBio native data formats +dependencies: +execution_environment: Other +execution_environment_reason: fallback runtime classification + +## URLs +home_url: https://github.com/PacificBiosciences/pbmm2 +doc_url: +dev_url: + +## CLI Help Source +cli:pbmm2 +## CLI Help Content +$ conda run -n bioenv_cli pbmm2 --help +[rc=0] +pbmm2 - minimap2 with native PacBio BAM support + +Usage: + pbmm2 + + -h,--help Show this help and exit. + --version Show application version and exit. + +Tools: + index Index reference and store as .mmi file + align Align PacBio reads to reference sequences + +Examples: + pbmm2 index ref.referenceset.xml ref.mmi + pbmm2 align ref.referenceset.xml movie.hifi_reads.xml ref.movie.alignmentset.xml + +Typical workflows: + A. Generate index file for reference and reuse it to align reads + $ pbmm2 index ref.fasta ref.mmi + $ pbmm2 align ref.mmi movie.subreads.bam ref.movie.bam + + B. Align reads and sort on-the-fly, with 4 alignment and 2 sort threads + $ pbmm2 align ref.fasta movie.subreads.bam ref.movie.bam --sort -j 4 -J 2 + + C. Align reads, sort on-the-fly, and create PBI + $ pbmm2 align ref.fasta movie.subreadset.xml ref.movie.alignmentset.xml --sort + + D. Omit output file and stream BAM output to stdout + $ pbmm2 align hg38.mmi movie1.subreadset.xml | samtools sort > hg38.movie1.sorted.bam + + E. Align CCS fastq input and sort on-the-fly + $ pbmm2 align ref.fasta movie.Q20.fastq ref.movie.bam --preset CCS --sort --rg '@RG\tID:myid\tSM:mysample' + +Copyright (C) 2004-2025 Pacific Biosciences of California, Inc. +This program comes with ABSOLUTELY NO WARRANTY; it is intended for +Research Use Only and not for use in diagnostic procedures. + + + +## URL Docs Extract +### https://github.com/PacificBiosciences/pbmm2 +GitHub - PacificBiosciences/pbmm2: A minimap2 frontend for PacBio native data formats · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} PacificBiosciences / pbmm2 Public Notifications You must be signed in to change notification settings Fork 34 Star 215 Code Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Pull requests Actions Security and quality Insights PacificBiosciences/pbmm2 develop Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 542 Commits 542 Commits img img include include src src subprojects subprojects tests tests third-party third-party .gitignore .gitignore LICENSE LICENSE README.md README.md meson.build meson.build meson_options.txt meson_options.txt View all files Repository files navigation README BSD-3-Clause-Clear license pbmm2 A minimap2 SMRT wrapper for PacBio data: native PacBio data in ⇨ native PacBio BAM out. pbmm2 is a SMRT C++ wrapper for minimap2 's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2 . Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. Binary Availability Latest version can be installed via bioconda package pbmm2 . Please refer to our official pbbioconda page for information on Installation, Support, License, Copyright, and Disclaimer. Latest Version Version 26.1.99 : Full changelog here Usage pbmm2 offers following tools Tools: index Index reference and store as .mmi file align Align PacBio reads to reference sequences Typical workflows A. Generate index file for reference and reuse it to align reads $ pbmm2 index ref.fasta ref.mmi --preset SUBREAD $ pbmm2 align ref.mmi movie.subreads.bam ref.movie.bam --preset SUBREAD B. Align reads and sort on-the-fly, with 4 alignment and 2 sort threads $ pbmm2 align ref.fasta movie.subreads.bam ref.movie.bam --preset SUBREAD --sort -j 4 -J 2 C. Align reads, sort on-the-fly, and create PBI $ pbmm2 align ref.fasta movie.subreadset.xml ref.movie.alignmentset.xml --preset SUBREAD --sort D. Omit output file and stream BAM output to stdout $ pbmm2 align hg38.mmi movie1.subreadset.xml --preset SUBREAD | samtools sort > hg38.movie1.sorted.bam E. Align CCS fastq input and sort output $ pbmm2 align ref.fasta movie.Q20.fastq ref.movie.bam --sort --rg '@RG\tID:myid\tSM:mysample' Index Indexing is optional, but recommended if you use the same reference with the same --preset multiple times. Usage: pbmm2 index [options] <ref.fa|xml> <out.mmi> Notes: If you use an index file, you can't override parameters -k , -w , nor -u in pbmm2 align ! Minimap2 parameter -H (homopolymer-compressed k-mer) is always on for SUBREAD and UNROLLED presets and can be disabled with -u . You can also use existing minimap2 .mmi files in pbmm2 align . Align The output argument is optional. If not provided, BAM output is streamed to stdout. Usage: pbmm2 align [options] <ref.fa|xml|mmi> <in.bam|xml|fa|fq> [out.aligned.bam|xml] Alignment Parallelization The number of alignment threads can be specified with -j,--num-threads . If not specified, the maximum number of threads will be used, minus one thread for BAM IO and minus the number of threads specified for sorting. Sorting Sorted output can be generated using --sort . Percentage: By default, 25% of threads specified with -j , maximum 8, are used for sorting. Example: --sort -j 12 , 9 threads for alignment, 3 threads for sorting. Manual override: To override the default percentage, -J,--sort-threads defines the explicit number of threads used for on-the-fly sorting. Example: --sort -j 12 -J 4 , 12 threads for alignment, 4 threads for sorting. The memory allocated per sort thread can be defined with -m,--sort-memory , accepting suffixes M,G . Temporary files during sorting are stored in the current working directory, unless explicitly defined with environment variable TMPDIR . The path used for temporary files is also printed if --log-level DEBUG is set. Benchmarks on human data have shown that 4 sort threads are recommended, but no more than 8 threads can be effectively leveraged, even with 70 cores used for alignment. It is recommended to provide more memory to each of a few sort threads, to avoid disk IO pressure, than providing less memory to each of many sort threads. Input file types Following compatibility table shows allowed input file types, output file types, compatibility with GenomicConsensus, and recommended --preset choice. More info about our dataset XML specification . Input Output GC Preset .bam (aligned or unaliged) .bam Y .fasta / .fa / .fasta.gz / .fa.gz .bam N .fastq / .fq / .fastq.gz / .fq.gz .bam N .Q20.fastq / Q20.fastq.gz .bam N CCS bam.fofn .bam N fasta.fofn .bam N fastq.fofn .bam N .subreadset.xml .bam \ .alignmentset.xml Y .consensusreadset.xml .bam \ .consensusalignmentset.xml Y CCS .transcriptset.xml .bam \ .transcriptalignmentset.xml Y ISOSEQ FASTA/Q input In addition to native PacBio BAM input, reads can also be provided in FASTA and FASTQ formats, as shown above. With FASTA/Q input, option --rg sets the read group. Example call: pbmm2 align hg38.fasta movie.Q20.fastq hg38.movie.bam --rg '@RG\tID:myid\tSM:mysample' All three reference file formats .fasta , .referenceset.xml , and .mmi can be combined with FASTA/Q input. Multiple input files pbmm2 supports the .fofn file type (File Of File Names), containing the same datatype. Supported are .fofn files with FASTA, FASTQ, or BAM. Examples: echo "m64001_190131_212703.Q20.fastq.gz" > myfiles.fofn echo "m64001_190228_200412.Q20.fastq.gz" >> myfiles.fofn pbmm2 align hg38.fasta myfiles.fofn hg38.myfiles.bam --rg '@RG\tID:myid\tSM:mysample' ls *.subreads.bam > mymovies.fofn pbmm2 align hg38.fasta mymovies.fofn hg38.mymovies.bam FAQ Which minimap2 version is used? pbmm2 ≥v1.13.0: minimap2 v2.26 pbmm2 <v1.13.0: minimap2 v2.15 When are pbi files created? Whenever the output is of type xml , a pbi file is being generated. When are BAM index files created? For sorted output via --sort , a bai file is being generated per default. You can switch to csi for larger genomes with --bam-index CSI or skip index generation completely with --bam-index NONE . What are parameter sets and how can I override them? Per default, pbmm2 uses recommended parameter sets to simplify the plethora of possible combinations. For this, we currently offer: SUBREAD CCS or HIFI (default) ISOSEQ UNROLLED Parameter sets vary based on pbmm2 version and are explained in --help . If you want to override any of the parameters of your chosen set, please use the respective options: -k k-mer size (no larger than 28). [-1] -w Minimizer window size. [-1] -u Disable homopolymer-compressed k-mer (compression is active for SUBREAD & UNROLLED presets). -A Matching score. [-1] -B Mismatch penalty. [-1] -z Z-drop score. [-1] -Z Z-drop inversion score. [-1] -r Bandwidth used in chaining and DP-based alignment. [-1] -g Stop chain enlongation if there are no minimizers in N bp. [-1] For the piece-wise linear gap penalties, use the following overrides, whereas a k-long gap costs min{o+k e,O+k E}: -o,--gap-open-1 Gap open penalty 1. [-1] -O,--gap-open-2 Gap open penalty 2. [-1] -e,--gap-extend-1 Gap extension penalty 1. [-1] -E,--gap-extend-2 Gap extension penalty 2. [-1] -L,--lj-min-ratio Long join flank ratio. [-1] For ISOSEQ , you can override additional parameters: -G Max intron length (changes -r). [-1] -C Cost for a non-canonical GT-AG splicing. [-1] --no-splice-flank Do not prefer splice flanks GT-AG. If you have suggestions for our default parameters or ideas for a new parameter set, please open a GitHub issue! What other special parameters are used implicitly? To achieve similar alignment behavior like blasr, we implicitly use following minimap2 parameters: soft clipping with -Y long cigars for tag CG with -L X/= cigars instead of M with --eqx no overlapping query intervals with repeated matches trimming no secondary alignments are produced per default (overridable with --secondary ) What sequence identity filters does pbmm2 offer? The idea of removing spurious or low-quality alignments is straightforward, but the exact definition of a threshold is tricky and varies between tools and applications. More on sequence identity from Heng Li. pbmm2 offers following filters: --min-concordance-perc , legacy mapped concordance filter, inherited from its predecessor BLASR (hidden option) --min-id-perc , a sequence identity percentage filter defined as the BLAST identity (hidden option) --min-gap-comp-id-perc , a gap-compressed sequence identity filter accounting insertions and deletions as single events only (default) By default, (3) is set to 70%, (1) and (2) are deactivated. The problem with (1) the mapped concordance filter is that it also removes biological structural variations, such as true insertions and deletions w.r.t. used reference; it is only appropriate if applied to resequencing data of haploid organisms. The (2) sequence identity is the BLAST identity, a very natural metric for filtering. The (3) gap-compressed sequence identity filter is very similar to (2), but accounts insertions and deletions as single events only and is the fairest metric when it comes to assess the actual error rate. All three filters are combined with AND , meaning an alignment has to pass all three thresholds. How do you define mapped concordance? The --min-concordance-perc option, whereas concordance is defined as 100 - 100 * (#Deletions + #Insertions + #Mismatches) / (AlignEndInRead - AlignStartInRead) will remove alignments that do not pass the provided threshold in percent. You can deactivate this filter with --min-concordance-perc 0 . How do you define identity? The --min-id-perc option, whereas sequence identity is defined as the BLAST identity 100 * #Matches / (#Matches + #Mismatches + #Deletions + #Insertions) will remove alignments that do not pass the provided threshold in percent. You can deactivate this filter with --min-id-perc 0 . How do you define gap-compressed identity? The --min-gap-comp-id-perc, -y option, whereas gap-compressed identity is defined as 100 * #Matches / (#Matches + #Mismatches + #DeletionEvents + #InsertionEvents) will remove alignments that do not pass the provided threshold in percent. This is the default filter. You can deactivate this filter with --min-gap-comp-id-perc 0 . What is repeated matches trimming? A repeated match is, when the same query interval is shared between a primary and supplementary alignment. This can happen for translocations, where breakends share the same flanking sequence: And sometimes, when a LINE gets inserted, the flanks are/get duplicated leading to complicated alignments, where we see a split read sharing a duplication. The inserted region itself, mapping to a random other LINE in the reference genome, may also share sequence similarity to the flanks: To get the best alignments, minimap2 decides that two alignments may use up to 50% (default) of the same query bases. This does not work for PacBio, because we see pbmm2 as a blasr replacement and require that a single base may never be aligned twice. Minimap2 offers a feature to enforce a query interval overlap to 0%. What happens now if a query interval gets used in two alignments, one or both get flagged as secondary and get filtered. This leads to yield loss and more importantly missing SVs in the alignment. Papers like this present dynamic programming approaches to find the optimal split to uniquely map query intervals, while maximizing alignment scores. We don't have per base alignment scores available, thus our approach is much simpler. We align the read, find overlapping query intervals, and trim non-primary alignments in order as provided by minimap2; trimming here means that pbmm2 rewrites the cigar and the reference coordinates on-the-fly. This allows us to increase number of mapped bases, slightly reduce identity, but boost SV recall rate. What SAM tags are added by pbmm2? pbmm2 adds following tags to each aligned record: mc , stores mapped concordance percentage between 0.0 and 100.0, if the filter was used mg , stores gap-compressed sequence identity percentage between 0.0 and 100.0, if the filter was used mi , stores sequence identity percentage between 0.0 and 100.0, if the filter was used rm , is set to 1 if an alignment has been manipulated by repeated matches trimming Why is the output different from BLASR? As for any two alignments of the same data with different mappers, alignments will differ. This is because of many reasons, but mainly a combination of different scoring functions and seeding techniques. How does sorting work? We integrated samtools sort code into pbmm2 to use it as on-the-fly sorting. This allows pbmm2 to skip writing unsorted BAM as output and thus save one round-trip of writing and reading unsorted BAM to disk, minimizing disk IO pressure. Is pbmm2 unsorted + samtools sort faster than pbmm2 --sort ? This highly depends on your filesystem. Our tests are showing that there is no clear winner; runtimes differ up to 10% in either directions, depending on read length distribution, genome length and complexity, disk IO pressure, and possibly further unknown factors. For very small genomes post-alignment sorting is faster, but for larger genomes like rice or human on-the-fly sorting is faster. Keep in mind, scalability is not only about runtime, but also disk IO pressure. We recommend to use on-the-fly sorting via pbmm2 align --sort . Can I get alignment statistics? If you use --log-level INFO , after alignment is done, you get following alignment metrics: Mapped Reads: 1529671 Alignments: 3087717 Mapped Bases: 28020786811 Mean Sequence Identity: 88.4% Max Mapped Read Length : 122989 Mean Mapped Read Length : 35597.9 Is there any benchmark information, like timings and peak memory consumption? If you use --log-level INFO , after alignment is done, you get following timing and memory information: Index Build/Read Time: 22s 327ms Alignment Time: 5s 523ms Sort Merge Time: 344ms 927us BAI Generation Time: 150ms PBI Generation Time: 161ms 120us Run Time: 28s 392ms CPU Time: 39s 653ms Peak RSS: 12.5847 GB Can I get progress output? If you use --log-level DEBUG , you will following reports: #Reads, #Aln, #RPM: 1462688, 2941000, 37393 #Reads, #Aln, #RPM: 1465877, 2948000, 37379 #Reads, #Aln, #RPM: 1469103, 2955000, 37350 That is: number of reads processed, number of alignments generated, reads per minute processed. Can I perform unrolled alignment? If you are interested in unrolled alignments that is, align the full-length ZMW read or the HQ region of a ZMW against an unrolled template, please use --zmw or --hqregion with *.subreadset.xml as input that contains one *.subreads.bam and one *.scraps.bam file. Keep in mind, to unroll the reference on your own. This is beta feature and still in development. How can I set the sample name? You can override the sample name (SM field in RG tag) for all read groups with --sample . If not provided, sample names derive from the dataset input with order of precedence: SM field in input read group, biosample name, well sample name, UnnamedSample . If the input is a BAM file and --sample has not been used, the SM field will be populated with UnnamedSample . Can I split output by sample name? Yes, --split-by-sample generates one output BAM file per sample name, with the sample name as file name infix, if there is more than one aligned sample name. Can I remove all those extra per base and pulse tags? Yes, --strip removes following extraneous tags if the input is BAM, but the resulting output BAM file cannot be used as input into GenomicConsensus : dq, dt, ip, iq, mq, pa, pc, pd, pe, pg, pm, pq, pt, pv, pw, px, sf, sq, st Where are the unmapped reads? Per default, unmapped reads are omitted. You can add them to the output BAM file with --unmapped . Can I output secondary alignments? Use --secondary to enable secondary alignment output. Secondary alignments are independent alternate mappings that skip repeated matches trimming and do not participate in SA tag generation. Use --max-secondary-alns N to retain at most N secondary alignments prior to filtering (default: 5). This option is only effective with --secondary . Can I output at maximum the N best alignments per read? Use -N, --best-n . If set to 0 , default, maximum filtering is disabled. Is there a way to only align one subread per ZMW? Using --median-filter , only the subread closest to the median subread length per ZMW is being aligned. Preferably, full-length subreads flanked by adapters are chosen. What is --collapse-homopolymers ? The idea behind --collapse-homopolymers is to collapse any two or more consecutive bases of the same type. In this mode, the reference is collapsed and written to disk with the same prefix as your output alignment and appended with suffix .ref.collapsed.fasta . In addition, each read is collapsed before alignment. This mode cannot be combined with .mmi input. Known issues Due to multithreading the ouput alignment ordering can differ between multiple runs with the same input parameters. The same can occur even with option --sort for records that align to the same target sequence, the same position within t + +## Conda Search Info +$ conda search -c bioconda -c conda-forge pbmm2 --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +pbmm2 0.5.1 ha87ae23_0 +---------------------- +file name : pbmm2-0.5.1-ha87ae23_0.tar.bz2 +name : pbmm2 +version : 0.5.1 +build : ha87ae23_0 +build number: 0 +size : 178 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-0.5.1-ha87ae23_0.tar.bz2 +md5 : 5cbefd53c7d82240b4103a319cddcdac +timestamp : 2018-08-15 15:01:17 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pbbam 0.18.0.* + - pbcopper 0.4.1.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 0.6.0 ha87ae23_0 +---------------------- +file name : pbmm2-0.6.0-ha87ae23_0.tar.bz2 +name : pbmm2 +version : 0.6.0 +build : ha87ae23_0 +build number: 0 +size : 188 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-0.6.0-ha87ae23_0.tar.bz2 +md5 : 3207897ef0e38b7726d783affc4a2e1a +timestamp : 2018-08-21 11:42:13 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pbbam 0.18.0.* + - pbcopper 0.4.1.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 0.7.0 ha87ae23_0 +---------------------- +file name : pbmm2-0.7.0-ha87ae23_0.tar.bz2 +name : pbmm2 +version : 0.7.0 +build : ha87ae23_0 +build number: 0 +size : 188 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-0.7.0-ha87ae23_0.tar.bz2 +md5 : eca30f721bab106380b5a2f6bbb9ecc4 +timestamp : 2018-08-22 21:15:03 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pbbam 0.18.0.* + - pbcopper 0.4.1.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 0.8.1 ha87ae23_0 +---------------------- +file name : pbmm2-0.8.1-ha87ae23_0.tar.bz2 +name : pbmm2 +version : 0.8.1 +build : ha87ae23_0 +build number: 0 +size : 191 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-0.8.1-ha87ae23_0.tar.bz2 +md5 : 13e6ee04d8aec3593c83797d76bb8919 +timestamp : 2018-08-24 22:03:53 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pbbam 0.18.0.* + - pbcopper 0.4.2.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 0.9.0 ha87ae23_0 +---------------------- +file name : pbmm2-0.9.0-ha87ae23_0.tar.bz2 +name : pbmm2 +version : 0.9.0 +build : ha87ae23_0 +build number: 0 +size : 304 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-0.9.0-ha87ae23_0.tar.bz2 +md5 : b64b67fc71a4ab862ec3540de4535f13 +timestamp : 2018-09-18 12:50:51 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pbbam 0.19.0.* + - pbcopper 0.4.2.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 0.10.0 ha87ae23_0 +----------------------- +file name : pbmm2-0.10.0-ha87ae23_0.tar.bz2 +name : pbmm2 +version : 0.10.0 +build : ha87ae23_0 +build number: 0 +size : 325 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-0.10.0-ha87ae23_0.tar.bz2 +md5 : 2c699485ed4cf83bb5c5485bba6f5f5c +timestamp : 2018-10-05 10:06:38 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pbbam 0.19.0.* + - pbcopper 0.4.2.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 0.10.1 ha87ae23_0 +----------------------- +file name : pbmm2-0.10.1-ha87ae23_0.tar.bz2 +name : pbmm2 +version : 0.10.1 +build : ha87ae23_0 +build number: 0 +size : 327 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-0.10.1-ha87ae23_0.tar.bz2 +md5 : fadab0eb039bb00fe10f002bc424f859 +timestamp : 2018-10-08 12:45:02 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pbbam 0.19.0.* + - pbcopper 0.4.2.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 0.10.1 ha87ae23_1 +----------------------- +file name : pbmm2-0.10.1-ha87ae23_1.tar.bz2 +name : pbmm2 +version : 0.10.1 +build : ha87ae23_1 +build number: 1 +size : 327 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-0.10.1-ha87ae23_1.tar.bz2 +md5 : 22d41495e8a6c3efd25c9e28bf8a0492 +timestamp : 2018-10-08 13:17:25 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pbbam 0.19.0.* + - pbcopper 0.4.2.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 0.11.0 ha87ae23_0 +----------------------- +file name : pbmm2-0.11.0-ha87ae23_0.tar.bz2 +name : pbmm2 +version : 0.11.0 +build : ha87ae23_0 +build number: 0 +size : 363 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-0.11.0-ha87ae23_0.tar.bz2 +md5 : 92c4558fa582a966db795f1619e5d0ba +timestamp : 2018-11-19 22:39:54 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pbbam 0.19.0.* + - pbcopper 0.4.2.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 0.12.0 ha87ae23_0 +----------------------- +file name : pbmm2-0.12.0-ha87ae23_0.tar.bz2 +name : pbmm2 +version : 0.12.0 +build : ha87ae23_0 +build number: 0 +size : 376 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-0.12.0-ha87ae23_0.tar.bz2 +md5 : 5ba1be530114b7e7a74752f6a0c5afaf +timestamp : 2019-01-14 13:30:04 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - pbbam 0.19.0.* + - pbcopper 0.4.2.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 1.0.0 ha888412_0 +---------------------- +file name : pbmm2-1.0.0-ha888412_0.tar.bz2 +name : pbmm2 +version : 1.0.0 +build : ha888412_0 +build number: 0 +size : 370 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.0.0-ha888412_0.tar.bz2 +md5 : 24d65cfa76d1d08a962b3d9d5d9f644a +timestamp : 2019-03-11 23:32:25 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pbbam 0.23.0.* + - pbcopper 0.4.2.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 1.1.0 hfb76ee0_0 +---------------------- +file name : pbmm2-1.1.0-hfb76ee0_0.tar.bz2 +name : pbmm2 +version : 1.1.0 +build : hfb76ee0_0 +build number: 0 +size : 368 KB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.1.0-hfb76ee0_0.tar.bz2 +md5 : f1fa20c453abde7576d168b9fa02632e +timestamp : 2019-08-27 12:51:47 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pbbam 1.0.6.* + - pbcopper 1.3.0.* + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 1.2.1 h56fc30b_0 +---------------------- +file name : pbmm2-1.2.1-h56fc30b_0.tar.bz2 +name : pbmm2 +version : 1.2.1 +build : h56fc30b_0 +build number: 0 +size : 1.2 MB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.2.1-h56fc30b_0.tar.bz2 +md5 : 2ba331b4e651de1146b2d84b5ae2e3d2 +timestamp : 2020-02-19 08:43:04 UTC +dependencies: + - htslib >=1.9,<1.10.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 1.3.0 h56fc30b_0 +---------------------- +file name : pbmm2-1.3.0-h56fc30b_0.tar.bz2 +name : pbmm2 +version : 1.3.0 +build : h56fc30b_0 +build number: 0 +size : 1.2 MB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.3.0-h56fc30b_0.tar.bz2 +md5 : 96d772d8a7ab40d90dd46e1006ff67a8 +timestamp : 2020-05-04 10:58:12 UTC +dependencies: + - htslib >=1.9,<1.10.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 1.3.0 h56fc30b_1 +---------------------- +file name : pbmm2-1.3.0-h56fc30b_1.tar.bz2 +name : pbmm2 +version : 1.3.0 +build : h56fc30b_1 +build number: 1 +size : 1.2 MB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.3.0-h56fc30b_1.tar.bz2 +md5 : a4b5c6464e8550b05e783a8be817fef4 +timestamp : 2020-05-20 09:37:18 UTC +dependencies: + - htslib >=1.10.2,<1.24.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 1.4.0 h56fc30b_0 +---------------------- +file name : pbmm2-1.4.0-h56fc30b_0.tar.bz2 +name : pbmm2 +version : 1.4.0 +build : h56fc30b_0 +build number: 0 +size : 1.2 MB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.4.0-h56fc30b_0.tar.bz2 +md5 : 3dedf37b500ee25702334c196fea2104 +timestamp : 2020-09-23 10:04:40 UTC +dependencies: + - htslib >=1.10.2,<1.24.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 1.7.0 hb97b32f_1 +---------------------- +file name : pbmm2-1.7.0-hb97b32f_1.tar.bz2 +name : pbmm2 +version : 1.7.0 +build : hb97b32f_1 +build number: 1 +size : 1.2 MB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.7.0-hb97b32f_1.tar.bz2 +md5 : fdb99e2f8cb76487389bfdabe6d15a0f +timestamp : 2022-02-24 11:20:35 UTC +dependencies: + - htslib >=1.12,<1.24.0a0 + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + + +pbmm2 1.7.0 hdcc8f71_0 +---------------------- +file name : pbmm2-1.7.0-hdcc8f71_0.tar.bz2 +name : pbmm2 +version : 1.7.0 +build : hdcc8f71_0 +build number: 0 +size : 1.3 MB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.7.0-hdcc8f71_0.tar.bz2 +md5 : 880d42ed0343e5a3839c37619f319bbb +timestamp : 2021-09-27 15:18:33 UTC +dependencies: + - htslib >=1.12,<1.24.0a0 + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - zlib >=1.2.11,<1.3.0a0 + + +pbmm2 1.8.0 h87f3376_1 +---------------------- +file name : pbmm2-1.8.0-h87f3376_1.tar.bz2 +name : pbmm2 +version : 1.8.0 +build : h87f3376_1 +build number: 1 +size : 1.3 MB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.8.0-h87f3376_1.tar.bz2 +md5 : 03217dcac6dbe7d1310dd91f794cd93d +timestamp : 2022-03-02 00:04:18 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + + +pbmm2 1.9.0 h9ee0642_0 +---------------------- +file name : pbmm2-1.9.0-h9ee0642_0.tar.bz2 +name : pbmm2 +version : 1.9.0 +build : h9ee0642_0 +build number: 0 +size : 1.3 MB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.9.0-h9ee0642_0.tar.bz2 +md5 : 9f159a1cabea4ea26f0078cc0d175737 +timestamp : 2022-04-19 12:08:25 UTC +dependencies: [] + + +pbmm2 1.10.0 h9ee0642_0 +----------------------- +file name : pbmm2-1.10.0-h9ee0642_0.tar.bz2 +name : pbmm2 +version : 1.10.0 +build : h9ee0642_0 +build number: 0 +size : 1.4 MB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.10.0-h9ee0642_0.tar.bz2 +md5 : 52beeda0c4d0cabc1c0e0ba532e5fce6 +timestamp : 2023-01-10 12:36:48 UTC +dependencies: [] + + +pbmm2 1.12.0 h9ee0642_0 +----------------------- +file name : pbmm2-1.12.0-h9ee0642_0.tar.bz2 +name : pbmm2 +version : 1.12.0 +build : h9ee0642_0 +build number: 0 +size : 1.8 MB +license : BSD-3-Clause-Clear +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pbmm2-1.12.0-h9ee0642_0.tar.bz2 +md5 : e107f6d8135270b3a30e10a0f0695e8a +timestamp : 2023-06-09 08:41:02 U diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pcdl.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pcdl.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8e6eb6e53a9245dbc7415a3378bd8a6abdb5fbba --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pcdl.manual_bundle.txt @@ -0,0 +1,176 @@ +# Tool: pcdl +software_name: pcdl +tier: T1 +domain: spatial_transcriptomics +downloads: 1013 +summary: physicell data loader (pcdl) provides a platform independent, python3 based, pip installable interface to transform output, generated with the PhysiCell agent based modeling framework, into standard formats. +description: physicell data loader (pcdl) provides a platform independent, python3 based, pip installable interface to transform output, generated with the PhysiCell agent based modeling framework, into standard formats. +dependencies: anndata >=0.10.8, bioio, bioio-base, bioio-ome-tiff, ffmpeg, geopandas >=0.14, imagemagick, matplotlib-base, neuroglancer, numpy, pandas >=2.2.2, python >=3.11,<4.0, requests, scikit-image >=0.24.0, scipy >=1.13.0, shapely >=2.0.1, spatialdata >=0.7.2, vtk +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/elmbeech/physicelldataloader +doc_url: https://github.com/elmbeech/physicelldataloader/blob/v3.3.6/README.md +dev_url: https://github.com/elmbeech/physicelldataloader + +## URL Docs Extract +### https://github.com/elmbeech/physicelldataloader/blob/v3.3.6/README.md +physicelldataloader/README.md at v3.3.6 · elmbeech/physicelldataloader · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} elmbeech / physicelldataloader Public forked from PhysiCell-Tools/python-loader Notifications You must be signed in to change notification settings Fork 7 Star 11 Code Issues 4 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights Files Expand file tree v3.3.6 Breadcrumbs physicelldataloader / README.md Copy path Blame More file actions Blame More file actions Latest commit History History History 323 lines (261 loc) · 22.3 KB v3.3.6 Breadcrumbs physicelldataloader / README.md Top File metadata and controls Preview Code Blame 323 lines (261 loc) · 22.3 KB Raw Copy raw file Download raw file Outline Edit and raw actions Abstract: physicelldataloader (pcdl) provides a platform independent, python3 based, pip installable interface to load output, generated with the PhysiCell agent-based modeling and diffusion solver framework, into python3 . pcdl was forked from the original PhysiCell-Tools python-loader implementation. The pcdl python3 library maintains three branches: Branch version 1 is the original PhysiCell-Tools/python-loader code. Branch version 2 will be strictly compatible with the original PhysiCell-Tools/python-loader code, although pip installable. Branch version 3 might break with old habits, although tries to be as much downward compatible as possible. The aim of the v3 branch is to get a very lean and agile python3 physicell output interface for the ones coming from the python3 world. Header: Language: python >= 3.9 Library dependencies: anndata, matplotlib, numpy, pandas, (requests), scipy, vtk Date of origin original PhysiCell-Tools python-loader: 2019-09-02 Date of origin pcdl fork: 2022-08-30 Doi: https://doi.org/10.5281/ZENODO.8176399 License: BSD-3-Clause User manual: this README.md file Source code: https://github.com/elmbeech/physicelldataloader HowTo Guide: installation and troubleshooting Tutorial: Basics Tutorials: pcdl background pcdl processing mcds time steps in python3 pcdl processing mcds time series in python3 pcdl from the command line Extras tutorials python3 language: pcdl and python3 and json pcdl and python3 and pandas pcdl and python3 and scipy and scanpy pcdl and python3 and graphs pcdl and python3 and matplotlib pcdl and python3 and vtk pcdl and python3 and tiff, png, and jpeg pcdl and python3 and napari Extras tutorials for other languages than python3: pcdl and julia pcdl and matlab pcdl and R Extras tutorials for GUI software: pcdl and paraview pcdl and blender Slides: presentations given Reference Manual: API application interface Discussion: To be developed. About Documentation: Within the pcdl library, we tried to stick to the documentation policy laid out by Daniele Procida in his " what nobody tells you about documentation " talk at PyCon 2017 in Portland, Oregon. Contributions: original PhysiCell-Tools python-loader implementation: Patrick Wall, Randy Heiland, Paul Macklin fork pcdl implementation: Elmar Bucher fork pcdl co-programmer: Furkan Kurtoglu, Jennifer Eng, Heber Rocha fork pcdl continuous testing and feedbacks: Aneequa Sundus, John Metzcar student prj on pcdl: Benjamin Jacobs (make_gml), Katie Pletz (beta testing), Marshal Gress (plot_scatter), Nick Oldfather (unit test model), Thierry-Pascal Fleurant (plot_timeseries) Developers, please make pull requests to the https://github.com/elmbeech/physicelldataloader/tree/development branch. Thanks! Cite: @Misc { bucher2023 , author = { Bucher, Elmar and Wall, Patrick and Rocha, Heber and Kurtoglu, Furkan and Eng, Jennifer and Sundus, Aneequa, and Metzcar, John and Heiland, Randy and Macklin, Paul } , title = { elmbeech/physicelldataloader: pcdl platform-independent, pip-installable interface to load PhysiCell agent-based modeling framework output into python3. } , year = { 2023 } , copyright = { Open Access } , doi = { 10.5281/ZENODO.8176399 } , publisher = { Zenodo } , } Road Map: Release Notes: version 3.3.5 (2025-03-xx): elmbeech/physicelldataloader remove pyMCDS and pyMCDSts make_ome_tiff and pyCLI pcdl_make_ome_tiff removed to make pyMCS.py stand alone again. version 3.3.4 (2025-03-07): elmbeech/physicelldataloader replace the aicsimageio library dependency with its successor bioio . special thanks to Joel Eliason! make_ome_tiff can now handel generated file names with > 255 characters. special thank to Genevieve Stein-O'Brien and DanielBergman! get_mesh_spacing handels now an edge case correctly that would have resulted in a division by zero. special thanks to Randy Heiland! version 3.3.3 (2025-01-10): elmbeech/physicelldataloader bug fix plot_contour plot orientation. special thanks to Marco Ruscone! add test data for new improved unittest physicell model . special thanks to Nick Oldfather! add pyMCDS make_conc_vtk on the fly visualization. special thanks to Randy Heiland and Nick Oldfather! pyMCDS and pyMCDSts make_graph_gml and pyAnnData get_anndata handles now spring_attached_cells graph too. version 3.3.2 (2024-11-24): elmbeech/physicelldataloader Warnings will no longer be piped to standard output if verbose is set to False. pyMCDS make_ome_tiff function rewriten to be less RAM hungry and more versatile. version 3.3.1 (2024-09-22): elmbeech/physicelldataloader bugfix pyMCDS custom vectors loading. version 3.3.0 (2024-08-22): elmbeech/physicelldataloader pip install pcdl : will again install all library dependencies. The fine-tuned version was too confssing. pyMCDS handels now intracellular physinboss data too; data is stored in cell_df. rename pyMCDS get_cell_variables to get_celltype_list for conciseness and order list by ID. rename pyMCDS get_substrate_names to get_substrate_list for conciseness and order list by ID. rename pyMCDS get_scatter to plot_scatter for conciseness. rename pyMCDS get_contour to plot_contour for conciseness. rename pyMCDSts make_imgcell to plot_scatter for conciseness. rename pyMCDSts make_imgconc to plot_contour for conciseness. rename pyMCDSts get_cell_df_states to get_cell_attribute for conciseness. rename pyMCDSts get_conc_df_states to get_conc_attribute for conciseness. rewrite pyMCDS mcds.get_unit_se into mcds.get_unit_dict . new pyCLI pcdl_get_anndata command line interface function. new pyCLI pcdl_get_celltype_list command line interface function. new pyCLI pcdl_get_cell_attribute command line interface function. new pyCLI pcdl_get_cell_df command line interface function. new pyCLI pcdl_get_substrate_list command line interface function. new pyCLI pcdl_get_conc_attribute command line interface function. new pyCLI pcdl_get_conc_df command line interface function. new pyCLI pcdl_get_graph_gml command line interface function. new pyCLI pcdl_get_unit_dict command line interface function. new pyCLI pcdl_get_version command line interface function. new pyCLI pcdl_make_cell_vtk command line interface function. new pyCLI pcdl_make_conc_vtk command line interface function. new pyCLI pcdl_make_gif command line interface function. new pyCLI pcdl_make_movie command line interface function. new pyCLI pcdl_make_ome_tiff command line interface function. new pyCLI pcdl_plot_contour command line interface function. new pyCLI pcdl_plot_scatter command line interface function. new pyCLI pcdl_plot_timeseries command line interface function. new pyMCDS mcds.get_mesh_mnp function, the mesh version from mcds.get_voxel_ijk. new pyMCDS make_conc_vtk function, to save substrate data as rectilinear grid vtk file. new pyMCDS make_cell_vtk function, to save cell data as glyph vtk file. new pyMCDS make_graph_gml function, to save graphs in a networkx and igraph compatible file format. new pyMCDS make_ome_tiff function, to save the output data in ome tiff file format. new pyMCDS set_verbosity_true function, to complete pcdl.TimeStep(verbosity=True/False) experience. new pyMCDS set_verbosity_false function, to complete pcdl.TimeStep(verbosity=True/False) experience. new pyMCDSts get_cell_df function, to extract one big dataframe or a list of dataframes from the whole time series. new pyMCDSts get_conc_df function, to extract one big dataframe or a list of dataframes from the whole time series. new pyMCDSts make_cell_vtk function, to save substrate data as rectilinear grid vtk files. special thanks to Furkan Kurtoglu! new pyMCDSts make_conc_vtk function, to save cell data as glyph vtk files. special thanks to Furkan Kurtoglu! new pyMCDSts make_graph_gml function, to save graphs in a networkx and igraph compatible files format. special thanks to Benjamin Jacobs! new pyMCDSts make_ome_tiff function, to save the output data in ome tiff file format. new pyMCDSts plot_timeseries function, to plot time series. special thanks to Thierry-Pascal Fleurant! new pyMCDSts set_verbosity_true function, to complete the pcdl.TimeSeries(verbosity=True/False) experience. new pyMCDSts set_verbosity_false function to complete the pcdl.TimeSeries(verbosity=True/False) experience. version 3.2.13 (2023-09-18): elmbeech/physicelldataloader rename pyMCDSts make_imgsubs to make_imgconc for consistency. add man/lecture/20230917_pcdl_repl_programming_analysis_plots.pdf slide deck. version 3.2.12 (2023-08-12): elmbeech/physicelldataloader add man/jupyter/pcdl_repl_programming.ipynb : Jupyter notebook to give an idea about how to work with pcdl in a python3 REPL. add man/lecture/20230808_pcws2023_session07_pcdl.pdf slide deck. add github continuous integration for all supported python3 versions, all supported operating systems. version 3.2.11 (2023-08-08): elmbeech/physicelldataloader pip install pcdl : will only install the bare minimum library dependencies. pip install pcdl[data] : will install the minimum dependencies plus the dependencies to download the test dataset. pip install pcdl[scverse] : will install the minimum dependencies plus the dependencies needed to generate an anndata object. pip install pcdl[all] : will always install all dependencies. new TimeSeries get_annmcds_list function, which points to the self.l_annmcds object. new pyMCDS get_scatter function is split off from pyMCDSts make_imgcell. pyMCDSts make_imgcell and make_imgsubs bug fixes. TimeStep and TimeSeries get_anndata evolution. version 3.2.10 (2023-07-24): elmbeech/physicelldataloader rename pyMCDSts get_cell_df_columns_states to get_cell_df_states for conciseness. rename pyMCDSts get_conc_df_columns_states to get_conc_df_states for conciseness. version 3.2.9 (2023-07-23): elmbeech/physicelldataloader new class TimeStep can do everything pyMCDS can do and more. new class TimeSeries can do everything pyMCDSts can do and more. new TimeStep get_anndata function to transform physicell output into AnnData objects. new TimeSeries get_anndata function to transform physicell output into AnnData objects. internal pyAnnData scaler function. internal pyAnnData _anndextract function. pyMCDS __init__ seetingxml parameter changed from boolean to string to accept other PhysiCell_settings.xml filenames than the default. pyMCDS get_cell_df drop and keep parameters to declare a set of columns to be dropped or kept. pyMCDS get_conc_df drop and keep parameters to declare a set of columns to be dropped or kept. new pyMCDS get_conc_df shorthand for get_concentration_df. pyMCDSts get_cell_minstate_col reimplementation as get_cell_df_columns_states function. pyMCDSts get_concentartion_minstate_col reimplementation as get_conc_df_columns_states function. new pyMCDSts get_mcds_list function which points to the self.l_mcds object. version 3.2.8 (2023-06-21): elmbeech/physicelldataloader pyMCDS get_concentration_df states parameter to filter out non-informative variables. pyMCDS get_cell_df states parameter to filter out non-informative variables. pyMCDSts __init__ load parameter to specify if the whole time series data straight at object initialization should be loaded. new pyMCDSts get_cell_minstate_col function to scan the whole time series for informative attributes. new pyMCDSts get_concentartion_minstate_col function to scan the whole time series for informative attributes. version 3.2.7 (2023-06-20): elmbeech/physicelldataloader pyMCDS and pyMCDSts __init__ custom_type parameter to specify other custom_data variable types (int, bool, str) then the generic float. version 3.2.5 (2023-06-19): elmbeech/physicelldataloader pyMCDS resolves incompatibility with earlier PhysiCell and MultiCellDS versions. version 3.2.4 (2023-06-17): elmbeech/physicelldataloader pyMCDS __init__ seetingxml parameter for cases where in the output folder no PhysiCell_settings.xml can be found. pyMCDSts mcdsts.make_imgcell extrema parameter is replaced by the z_axis parameter to account for numerical and categorical variable types. version 3.2.2 (2023-06-16): elmbeech/physicelldataloader pyMCDS mcds.get_cell_df sets distinct boolean, categorical, integer number, and real number variable types. categorical number codes are translated. for all spatial variables, the vector length value is calculated and added automatically. new pyMCDS mcds.get_celltype_dict function. new pyMCDS mcds.get_substrate_dict function. pyMCDSts mcdsts.make_imgcell and mcdsts.make_imgsubs functions improved. version 3.2.1 (2023-06-12): elmbeech/physicelldataloader pypa odyssey is coming to an end. change build system from setuptools to hatching. change the library name from pcDataLoader to pcdl. to make the library installation more lightweight, test data was excluded from the basic installation. given the computer is connected to the internet, test data can easily be installed and removed with the pcdl.install_data() and pcdl.uninstall_data() functions now. version 3.0.7 (2023-06-08): elmbeech/physicelldataloader pyMCDSts: replaces the svg dependent mcdsts.make_jpeg , mcdsts.make_png , and mcdsts.make_tiff with mcdsts.make_imgcell and mcdsts.make_imgsubs which generate images straight out of the loaded data. the mcdsts.make_gif and mcdsts.make_movie functions were adjusted accordingly. special thanks to Marshal Gress! pyMCDSts: mcdsts.read_mcds loads now automatically all mcds snapshots if no xmlfile_list is provided (default). version 3.0.6 (2023-04-29): elmbeech/physicelldataloader pyMCDS _read_xml is now able to load time steps with zero cells. pyMCDS mcds.get_contour can handle more input parameters. version 3.0.5 (2023-02-26): elmbeech/physicelldataloader pyMCDS mcds.get_contour plots span now the whole domain and not only to the border voxel centers. version 3.0.4 (2023-02-21): elmbeech/physicelldataloader pyMCDS mcds.get_contour function, to easily generate for substrates matplotlib contourf and contour plots because they do not exist as pandas plots. version 3.0.3 (2023-02-19): elmbeech/physicelldataloader branch 3 has no longer anndata and, as such, hdf5 dependency. version 3.0.2 (2023-01-06): elmbeech/physicelldataloader bugfix installing package data. version 3.0.0 (2023-01-06): elmbeech/physicelldataloader pyMCDS parameter xml_file can now handle path/file.xml (unix) or path\file.xml (dos) input, as long output_path is the default. pyMCDS has a new additional boolean microenv parameter, to specify if the microenvironment (substrates) should be read (for completeness) or not (for speed increase and less memory usage). pyMCDS has a new additional boolean graph parameter, to specify if the attached and neighbor graph should be read. pyMCDS has a new additional boolean verbose parameter, to specify if there should be text output while processing. pyMCDS mcds.get_2D_mesh was renamed to mcds.get_mesh_2D for consistency. pyMCDS mcds.get_linear_voxels was renamed to mcds.get_mesh_coordinate for consistency. pyMCDS mcds.get_containing_voxel_ijk was renamed to mcds.get_voxel_ijk for briefness. pyMCDS mcds.get_voxel_spacing returns now 3 specific values, one for x, y, and z, instead of 1 general value. pyMCDS mcds.get_concentrations was renamed to mcds.get_concentration for consistency pyMCDS mcds.get_concentrations_at was renamed to mcds.get_concentration_at for consistency pyMCDS mcds.get_concentration_at if z_slice is not a mesh center value, the function will by default adjust to the nearest and no longer break. pyMCDS mcds.get_cell_variables and mcds.get_substrate_names return now a strictly alphabetically ordered list. pyMCDS mcds.get_cell_df returns now a pandas dataframe with the cell IDs as the index and not as a column. additionally, this dataframe contains now voxel, mesh_center, substrate parameter, substrate concentration, and cell density information too. new pyMCDS mcds.get_concentration_df function. new pyMCDS mcds.get_substrate_df function. new pyMCDS mcds.get_unit_se function. new pyMCDS mcds.get_multicellds_version function. new pyMCDS mcds.get_physicell_version function. new pyMCDS mcds.get_runtime function. new pyMCDS mcds.get_timestamp function. new pyMCDS mcds.get_voxel_ijk_range function. new pyMCDS mcds.get_voxel_ijk_axis function. new pyMCDS mcds.get_voxel_spacing function. new pyMCDS mcds.get_voxel_volume function. new pyMCDS mcds.get_mesh_mnp_range function. new pyMCDS mcds.get_mesh_mnp_axis function. new pyMCDS mcds.get_xyz_range function. new pyMCDS mcds.is_in_mesh function. new pyMCDS mcds.get_attached_graph_dict function. new pyMCDS mcds.get_neigbor_graph_dict function. class pyMCDS_timeseries was renamed to pyMCDSts and completely rewritten. new pyMCDSts get_xmlfile_list function. new pyMCDSts read_mcds function. new pyMCDSts make_jpeg function. new pyMCDSts make_png function. new pyMCDSts make_tiff function. new pyMCDSts make_gif f + +### https://github.com/elmbeech/physicelldataloader +GitHub - elmbeech/physicelldataloader: python3 physicell data output loader. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} elmbeech / physicelldataloader Public forked from PhysiCell-Tools/python-loader Notifications You must be signed in to change notification settings Fork 7 Star 11 Code Issues 4 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights elmbeech/physicelldataloader master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 693 Commits 693 Commits .github/ workflows .github/ workflows man man pcdl pcdl test test .gitignore .gitignore LICENSE LICENSE README.md README.md output_2d.tar.gz output_2d.tar.gz output_3d.tar.gz output_3d.tar.gz pyproject.toml pyproject.toml View all files Repository files navigation README BSD-3-Clause license Abstract: physicell data loader (pcdl) provides a platform-independent (Windows, MacOSX, Linux), python3 based, pip -installable set of commands to load output, generated with the PhysiCell agent-based modeling and diffusion solver framework, into python3 or transform PhysiCell output into more widely used data formats. pcdl can be loaded as a python3 module or run straight from the command line. pcdl was forked from the original PhysiCell-Tools python-loader implementation. The pcdl python3 library maintains four branches: Branch version 1 is the original PhysiCell-Tools/python-loader code. Branch version 2 will be strictly compatible with the original PhysiCell-Tools/python-loader code, although pip installable. Branch version 3 might break with old habits, although tries to be as much downward compatible as possible. The aim of the v3 branch is to get a very lean and agile python3 physicell output interface for the ones coming from the python3 world. Finally, Branch version 4 reimplemented the backend in a more python3, less C++ like manner. Header: Language: python >= 3.11 Library dependencies: anndata, bioio, geopandas, matplotlib, networkx, neuroglancer, numpy, pandas, (requests), scikit-image, scipy, shapely, spatialdata, vtk Date of origin original PhysiCell-Tools python-loader: 2019-09-02 Date of origin pcdl fork: 2022-08-30 Doi: https://doi.org/10.5281/ZENODO.8176399 License: BSD-3-Clause User manual: this README.md file Source code: https://github.com/elmbeech/physicelldataloader ✨ HowTo Guide: installation and troubleshooting ✨ Tutorial: Basics Tutorials: pcdl background pcdl processing mcds time steps in python3 pcdl processing mcds time series in python3 pcdl from the command line Extras tutorials python3 language: pcdl and python3 and json pcdl and python3 and pandas pcdl and python3 and scanpy and squidpy pcdl and python3 and muspan pcdl and python3 and graphs pcdl and python3 and matplotlib pcdl and python3 and vtk pcdl and python3 and ome.tiff, tiff, png, and jpeg pcdl and python3 and napari Extras tutorials for other languages than python3: pcdl and julia pcdl and matlab pcdl and R Extras tutorials for GUI software: pcdl and paraview pcdl and blender pcdl and napari pcdl and fiji imagej, icy, qupath pcdl and neuroglancer Slides: presentations given ✨ Reference Manual: API application interface Discussion: To be developed. About Documentation: Within the pcdl library, we tried to stick to the documentation policy laid out by Daniele Procida in his " what nobody tells you about documentation " talk at PyCon 2017 in Portland, Oregon. Contributions: original PhysiCell-Tools python-loader implementation: Patrick Wall, Randy Heiland, Paul Macklin fork pcdl implementation: Elmar Bucher fork pcdl co-programmer: Furkan Kurtoglu, Heber Rocha, Jennifer Eng fork pcdl continuous testing and feedbacks: Aneequa Sundus (python), John Metzcar (python), Raquel Arroya (matlab) student prj on pcdl: Benjamin Jacobs (make_graph_gml), Jason Lu (render_neuroglancer), Katie Pletz (beta testing), Leena Sohail (beta testing), Marshal Gress (plot_scatter), Nick Oldfather (unit test model), Thierry-Pascal Fleurant (plot_timeseries), Viviana Kwong (render_neuroglancer) Developers, please make pull requests to the https://github.com/elmbeech/physicelldataloader/tree/development branch. Thanks! Cite: @Misc { bucher2023 , author = { Bucher, Elmar and Wall, Patrick and Rocha, Heber and Kurtoglu, Furkan and Eng, Jennifer and Sundus, Aneequa, and Metzcar, John and Arroya, Raquel and Heiland, Randy and Macklin, Paul } , title = { elmbeech/physicelldataloader: pcdl platform-independent, pip-installable interface to load PhysiCell agent-based modeling framework output into python3. } , year = { 2023 } , copyright = { Open Access } , doi = { 10.5281/ZENODO.8176399 } , publisher = { Zenodo } , } Road Map: evt generate lineage tree graph output files. Release Notes: version 4.1.5 (2026-04-05) bugfix library dependencies and library versions. version 4.1.4 (2026-04-04) pyMCDSts mcdsts.make_contour extrema parameter is replaced by vmin and vmax to be compatible with mcds.make_contour and plt.contour. make_cell_vtk and make_conc_vtk now offer an ext parameter, allowing to manually specify the exact file extension. special thanks to Danyon Gedris! new make_muspan TimeStep class and TimeSeris class function and pcdl_get_muspan command line command. special thanks to Joshua Moore and Joshua Bull! version 4.1.3 (2026-03-21): new pcdl.pccmap color map. this is an adaptation of the physicell pathology paint by number color map. new TimeStep get_pcdl_version function. version 4.1.2 (2026-03-06): elmbeech/physicelldataloader new custom_data_astype TimeStep class and TimeSeries class function to set the dtype of custom_data variables even after the timestep or timeseries is loaded. TimeSeries __init__ function can now handle a list of TimeStep objects as input instead of a path. version 4.1.1 (2026-02-28): elmbeech/physicelldataloader reduced memory footprint. version 4.1.0 (2025-12-31): elmbeech/physicelldataloader new get_spatialdata TimeStep class and TimeSeris class function and pcdl_get_spatialdata command line command. special thanks to Luca Marconato! with this release, pcdl officially became an scverse ecosystem package. version 4.0.5 (2025-10-22): elmbeech/physicelldataloader settingxml default is now set to False, because the cell_type id label mapping can, in recent PhysiCell output, be retrieved from output*.xml too. plot_scatter and plot_timeseries now additionally have a cat_drop and cat_keep argument to filter categorical data. plot_timeseries(frame=conc) now plots by default all substrate concentrations over time. plot_timeseries(ext=) parameter offers to return a dataframe object, dafaframe csv file, image file, or a matplotlib fig object. special thanks to John Nardini and Edward Young! version 4.0.4 (2025-07-23): elmbeech/physicelldataloader command line commands now return error code 0 if the command runs successfully. version 4.0.3 (2025-07-20): elmbeech/physicelldataloader TimeStep and TimeSeris plot_contour , plot_scatter , and plot_timeseries handle now kwargs arguments. minor bugfixes. version 4.0.2 (2025-06-29): elmbeech/physicelldataloader minor bugfixes. version 4.0.1 (2025-06-24): elmbeech/physicelldataloader man updated. minor bugfixes. version 4.0.0 (2025-05-13): elmbeech/physicelldataloader v4 was forked from v3.3.4! mcds.data struct was rewritten in more python less c++ way. pyMCDS.py and part of pyAnnData.py was fused to timestep.py . pyMCDSts.py and part of pyAnnData.py was fused to timeseries.py . pyCLI.py was renames to commandline.py . data_timeseries.py was renamed to output_data.py . TimeStep function get_concentration was deprecated because pandas already has this functionlity. TimeStep function get_concentration_at was deprecated because pandas already has this functionlity. TimeStep function get_cell_df_at was deprecated because pandas already has this functionlity. make_conc_vtk and make_cell_vtk on the fly visualization was removed because paraview is good enough. new TimeStep get_cell_attribute_list function, to retrieve a list of all tracked cell attribute labels. new pcdl_get_cell_attribute_list function, to retrieve a list of all tracked cell attribute labels. new render_neuroglancer function, to render ome tiff image into neuroglancer. new pcdl_render_neuroglancer function, to render ome tiff images into neuroglancer. version 3.3.8 (2025-07-23): elmbeech/physicelldataloader command line commands now return error code 0 if the command runs successfully. version 3.3.7 (2025-06-01): elmbeech/physicelldataloader compatible with current (non end-of-life cycle) python versions. minor bugfixes. version 3.3.6 (2025-05-13): elmbeech/physicelldataloader compatible with numpy >= 2.0.0 and current (non end-of-life cycle) python versions. version 3.3.5 (2025-05-13): elmbeech/physicelldataloader compatible with numpy < 2.0.0 and current (non end-of-life cycle) python versions. remove pyMCDS and pyMCDSts make_ome_tiff and pyCLI pcdl_make_ome_tiff to make pyMCS.py stand alone again. new TimeStep get_cell_attribute_list function, to retrieve a list of all tracked cell attribute labels. new pcdl_get_cell_attribute_list function, to retrieve a list of all tracked cell attribute labels. version 3.3.4 (2025-03-07): elmbeech/physicelldataloader replace the aicsimageio library dependency with its successor bioio . special thanks to Joel Eliason! make_ome_tiff can now handel generated file names with > 255 characters. special thank to Genevieve Stein-O'Brien and DanielBergman! get_mesh_spacing handels now an edge case correctly that would have resulted in a division by zero. special thanks to Randy Heiland! version 3.3.3 (2025-01-10): elmbeech/physicelldataloader bug fix plot_contour plot orientation. special thanks to Marco Ruscone! add test data for new improved unittest physicell model . special thanks to Nick Oldfather! add pyMCDS make_conc_vtk on the fly visualization. special thanks to Randy Heiland and Nick Oldfather! pyMCDS and pyMCDSts make_graph_gml and pyAnnData get_anndata handles now spring_attached_cells graph too. version 3.3.2 (2024-11-24): elmbeech/physicelldataloader Warnings will no longer be piped to standard output if verbose is set to False. pyMCDS make_ome_tiff function rewriten to be less RAM hungry and more versatile. version 3.3.1 (2024-09-22): elmbeech/physicelldataloader bugfix pyMCDS custom vectors loading. version 3.3.0 (2024-08-22): elmbeech/physicelldataloader pip install pcdl : will again install all library dependencies. The fine-tuned version was too confssing. pyMCDS handels now intracellular physinboss data too; data is stored in cell_df. rename pyMCDS get_cell_variables to get_celltype_list for conciseness and order list by ID. rename pyMCDS get_substrate_names to get_substrate_list for conciseness and order list by ID. rename pyMCDS get_scatter to plot_scatter for conciseness. rename pyMCDS get_contour to plot_contour for conciseness. rename pyMCDSts make_imgcell to plot_scatter for conciseness. rename pyMCDSts make_imgconc to plot_contour for conciseness. rename pyMCDSts get_cell_df_states to get_cell_attribute for conciseness. rename pyMCDSts get_conc_df_states to get_conc_attribute for conciseness. rewrite pyMCDS mcds.get_unit_se into mcds.get_unit_dict . new pyCLI pcdl_get_anndata command line interface function. new pyCLI pcdl_get_celltype_list command line interface function. new pyCLI pcdl_get_cell_attribute command line interface function. new pyCLI pcdl_get_cell_df command line interface function. new pyCLI pcdl_get_substrate_list command line interface function. new pyCLI pcdl_get_conc_attribute command line interface function. new pyCLI pcdl_get_conc_df command line interface function. new pyCLI pcdl_get_graph_gml command line interface function. new pyCLI pcdl_get_unit_dict command line interface function. new pyCLI pcdl_get_version command line interface function. new pyCLI pcdl_make_cell_vtk command line interface function. new pyCLI pcdl_make_conc_vtk command line interface function. new pyCLI pcdl_make_gif command line interface function. new pyCLI pcdl_make_movie command line interface function. new pyCLI pcdl_make_ome_tiff command line interface function. new pyCLI pcdl_plot_contour command line interface function. new pyCLI pcdl_plot_scatter command line interface function. new pyCLI pcdl_plot_timeseries command line interface function. new pyMCDS mcds.get_mesh_mnp function, the mesh version from mcds.get_voxel_ijk. new pyMCDS make_conc_vtk function, to save substrate data as rectilinear grid vtk file. new pyMCDS make_cell_vtk function, to save cell data as glyph vtk file. new pyMCDS make_graph_gml function, to save graphs in a networkx and igraph compatible file format. new pyMCDS make_ome_tiff function, to save the output data in ome tiff file format. new pyMCDS set_verbosity_true function, to complete pcdl.TimeStep(verbosity=True/False) experience. new pyMCDS set_verbosity_false function, to complete pcdl.TimeStep(verbosity=True/False) experience. new pyMCDSts get_cell_df function, to extract one big dataframe or a list of dataframes from the whole time series. new pyMCDSts get_conc_df function, to extract one big dataframe or a list of dataframes from the whole time series. new pyMCDSts make_cell_vtk function, to save substrate data as rectilinear grid vtk files. special thanks to Furkan Kurtoglu! new pyMCDSts make_conc_vtk function, to save cell data as glyph vtk files. special thanks to Furkan Kurtoglu! new pyMCDSts make_graph_gml function, to save graphs in a networkx and igraph compatible files format. special thanks to Benjamin Jacobs! new pyMCDSts make_ome_tiff function, to save the output data in ome tiff file format. new pyMCDSts plot_timeseries function, to plot time series. special thanks to Thierry-Pascal Fleurant! new pyMCDSts set_verbosity_true function, to complete the pcdl.TimeSeries(verbosity=True/False) experience. new pyMCDSts set_verbosity_false function to complete the pcdl.TimeSeries(verbosity=True/False) experience. version 3.2.13 (2023-09-18): elmbeech/physicelldataloader rename pyMCDSts make_imgsubs to make_imgconc for consistency. add man/lecture/20230917_pcdl_repl_programming_analysis_plots.pdf slide deck. version 3.2.12 (2023-08-12): elmbeech/physicelldataloader add man/jupyter/pcdl_repl_programming.ipynb : Jupyter notebook to give an idea about how to work with pcdl in a python3 REPL. add man/lecture/20230808_pcws2023_session07_pcdl.pdf slide deck. add github continuous integration for all supported python3 versions, all supported operating systems. version 3.2.11 (2023-08-08): elmbeech/physicelldataloader pip install pcdl : will only install the bare minimum library dependencies. pip install pcdl[data] : will install the minimum dependencies plus the dependencies to download the test dataset. pip install pcdl[scverse] : will install the minimum dependencies plus the dependencies needed to generate an anndata object. pip install pcdl[all] : will always install all dependencies. new TimeSeries get_annmcds_list function, which points to the self.l_annmcds object. new pyMCDS get_scatter function is split off from pyMCDSts make_imgcell. pyMCDSts make_imgcell and make_imgsubs bug fixes. TimeStep and TimeSeries get_anndata evolution. version 3.2.10 (2023-07-24): elmbeech/physicelldataloader rename pyMCDSts get_cell_df_columns_states to get_cell_df_states for conciseness. rename pyMCDSts get_conc_df_columns_states to get_conc_df_states for conciseness. version 3.2.9 (2023-07-23): elmbeech/physicelldataloader new class TimeStep can do everything pyMCDS can do and more. new class TimeSeries can do everything pyMCDSts can do and more. new TimeStep get_anndata function to transform physicell output into AnnData objects. new TimeSeries get_anndata function to transform physicell output into AnnData objects. internal pyAnnData scaler function. internal pyAnnData _anndextract function. pyMCDS __init__ seetingxml parameter changed from boolean to string to accept other PhysiCell_settings.xml filenames than the default. pyMCDS get_cell_df drop and keep parameters to declare a set of columns to be dropped or kept. pyMCDS get_conc_df drop and keep parameters to declare a set of columns to be dropped or kept. new pyMCDS get_conc_df shorthand for get_concentration_df. pyMCDSts get_cell_minstate_col reimplementation as get_cell_df_columns_states function. pyMCDSts get_concentartion_minstate_col reimplementation as get_conc_df_columns_states function. new pyMCDSts get_mcds_list function which points to the self.l_mcds object. version 3.2.8 (2023-06-21): elmbeech/physicelldataloader pyMCDS get_concentration_df states parameter to filter out non-informative variables. pyMCDS get_cell_df states parameter to filter out non-informative variables. pyMCDSts __init__ load parameter to specify if the whole time series data straight at object initialization should be loaded. new pyMCDSts get_cell_minstate_col function to scan the whole time series for informative attributes. new pyMCDSts get_concentartion_minstate_col function to scan the whole time series for informative attributes. version 3.2.7 (2023-06-20): elmbeech/physicelldataloader pyMCDS and pyMCDSts __init__ custom_type parameter to specify other custom_data variable types (int, bool, str) then the generic float. version 3.2.5 (2023-06-19): elmbeech/physicelldataloader pyMCDS resolves incompatibility with earlier PhysiCell and MultiCellDS versions. version 3.2.4 (2023-06-17): elmbeech/physicelldataloader pyMCDS __init__ + +### https://github.com/elmbeech/physicelldataloader +GitHub - elmbeech/physicelldataloader: python3 physicell data output loader. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} elmbeech / physicelldataloader Public forked from PhysiCell-Tools/python-loader Notifications You must be signed in to change notification settings Fork 7 Star 11 Code Issues 4 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights elmbeech/physicelldataloader master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 693 Commits 693 Commits .github/ workflows .github/ workflows man man pcdl pcdl test test .gitignore .gitignore LICENSE LICENSE README.md README.md output_2d.tar.gz output_2d.tar.gz output_3d.tar.gz output_3d.tar.gz pyproject.toml pyproject.toml View all files Repository files navigation README BSD-3-Clause license Abstract: physicell data loader (pcdl) provides a platform-independent (Windows, MacOSX, Linux), python3 based, pip -installable set of commands to load output, generated with the PhysiCell agent-based modeling and diffusion solver framework, into python3 or transform PhysiCell output into more widely used data formats. pcdl can be loaded as a python3 module or run straight from the command line. pcdl was forked from the original PhysiCell-Tools python-loader implementation. The pcdl python3 library maintains four branches: Branch version 1 is the original PhysiCell-Tools/python-loader code. Branch version 2 will be strictly compatible with the original PhysiCell-Tools/python-loader code, although pip installable. Branch version 3 might break with old habits, although tries to be as much downward compatible as possible. The aim of the v3 branch is to get a very lean and agile python3 physicell output interface for the ones coming from the python3 world. Finally, Branch version 4 reimplemented the backend in a more python3, less C++ like manner. Header: Language: python >= 3.11 Library dependencies: anndata, bioio, geopandas, matplotlib, networkx, neuroglancer, numpy, pandas, (requests), scikit-image, scipy, shapely, spatialdata, vtk Date of origin original PhysiCell-Tools python-loader: 2019-09-02 Date of origin pcdl fork: 2022-08-30 Doi: https://doi.org/10.5281/ZENODO.8176399 License: BSD-3-Clause User manual: this README.md file Source code: https://github.com/elmbeech/physicelldataloader ✨ HowTo Guide: installation and troubleshooting ✨ Tutorial: Basics Tutorials: pcdl background pcdl processing mcds time steps in python3 pcdl processing mcds time series in python3 pcdl from the command line Extras tutorials python3 language: pcdl and python3 and json pcdl and python3 and pandas pcdl and python3 and scanpy and squidpy pcdl and python3 and muspan pcdl and python3 and graphs pcdl and python3 and matplotlib pcdl and python3 and vtk pcdl and python3 and ome.tiff, tiff, png, and jpeg pcdl and python3 and napari Extras tutorials for other languages than python3: pcdl and julia pcdl and matlab pcdl and R Extras tutorials for GUI software: pcdl and paraview pcdl and blender pcdl and napari pcdl and fiji imagej, icy, qupath pcdl and neuroglancer Slides: presentations given ✨ Reference Manual: API application interface Discussion: To be developed. About Documentation: Within the pcdl library, we tried to stick to the documentation policy laid out by Daniele Procida in his " what nobody tells you about documentation " talk at PyCon 2017 in Portland, Oregon. Contributions: original PhysiCell-Tools python-loader implementation: Patrick Wall, Randy Heiland, Paul Macklin fork pcdl implementation: Elmar Bucher fork pcdl co-programmer: Furkan Kurtoglu, Heber Rocha, Jennifer Eng fork pcdl continuous testing and feedbacks: Aneequa Sundus (python), John Metzcar (python), Raquel Arroya (matlab) student prj on pcdl: Benjamin Jacobs (make_graph_gml), Jason Lu (render_neuroglancer), Katie Pletz (beta testing), Leena Sohail (beta testing), Marshal Gress (plot_scatter), Nick Oldfather (unit test model), Thierry-Pascal Fleurant (plot_timeseries), Viviana Kwong (render_neuroglancer) Developers, please make pull requests to the https://github.com/elmbeech/physicelldataloader/tree/development branch. Thanks! Cite: @Misc { bucher2023 , author = { Bucher, Elmar and Wall, Patrick and Rocha, Heber and Kurtoglu, Furkan and Eng, Jennifer and Sundus, Aneequa, and Metzcar, John and Arroya, Raquel and Heiland, Randy and Macklin, Paul } , title = { elmbeech/physicelldataloader: pcdl platform-independent, pip-installable interface to load PhysiCell agent-based modeling framework output into python3. } , year = { 2023 } , copyright = { Open Access } , doi = { 10.5281/ZENODO.8176399 } , publisher = { Zenodo } , } Road Map: evt generate lineage tree graph output files. Release Notes: version 4.1.5 (2026-04-05) bugfix library dependencies and library versions. version 4.1.4 (2026-04-04) pyMCDSts mcdsts.make_contour extrema parameter is replaced by vmin and vmax to be compatible with mcds.make_contour and plt.contour. make_cell_vtk and make_conc_vtk now offer an ext parameter, allowing to manually specify the exact file extension. special thanks to Danyon Gedris! new make_muspan TimeStep class and TimeSeris class function and pcdl_get_muspan command line command. special thanks to Joshua Moore and Joshua Bull! version 4.1.3 (2026-03-21): new pcdl.pccmap color map. this is an adaptation of the physicell pathology paint by number color map. new TimeStep get_pcdl_version function. version 4.1.2 (2026-03-06): elmbeech/physicelldataloader new custom_data_astype TimeStep class and TimeSeries class function to set the dtype of custom_data variables even after the timestep or timeseries is loaded. TimeSeries __init__ function can now handle a list of TimeStep objects as input instead of a path. version 4.1.1 (2026-02-28): elmbeech/physicelldataloader reduced memory footprint. version 4.1.0 (2025-12-31): elmbeech/physicelldataloader new get_spatialdata TimeStep class and TimeSeris class function and pcdl_get_spatialdata command line command. special thanks to Luca Marconato! with this release, pcdl officially became an scverse ecosystem package. version 4.0.5 (2025-10-22): elmbeech/physicelldataloader settingxml default is now set to False, because the cell_type id label mapping can, in recent PhysiCell output, be retrieved from output*.xml too. plot_scatter and plot_timeseries now additionally have a cat_drop and cat_keep argument to filter categorical data. plot_timeseries(frame=conc) now plots by default all substrate concentrations over time. plot_timeseries(ext=) parameter offers to return a dataframe object, dafaframe csv file, image file, or a matplotlib fig object. special thanks to John Nardini and Edward Young! version 4.0.4 (2025-07-23): elmbeech/physicelldataloader command line commands now return error code 0 if the command runs successfully. version 4.0.3 (2025-07-20): elmbeech/physicelldataloader TimeStep and TimeSeris plot_contour , plot_scatter , and plot_timeseries handle now kwargs arguments. minor bugfixes. version 4.0.2 (2025-06-29): elmbeech/physicelldataloader minor bugfixes. version 4.0.1 (2025-06-24): elmbeech/physicelldataloader man updated. minor bugfixes. version 4.0.0 (2025-05-13): elmbeech/physicelldataloader v4 was forked from v3.3.4! mcds.data struct was rewritten in more python less c++ way. pyMCDS.py and part of pyAnnData.py was fused to timestep.py . pyMCDSts.py and part of pyAnnData.py was fused to timeseries.py . pyCLI.py was renames to commandline.py . data_timeseries.py was renamed to output_data.py . TimeStep function get_concentration was deprecated because pandas already has this functionlity. TimeStep function get_concentration_at was deprecated because pandas already has this functionlity. TimeStep function get_cell_df_at was deprecated because pandas already has this functionlity. make_conc_vtk and make_cell_vtk on the fly visualization was removed because paraview is good enough. new TimeStep get_cell_attribute_list function, to retrieve a list of all tracked cell attribute labels. new pcdl_get_cell_attribute_list function, to retrieve a list of all tracked cell attribute labels. new render_neuroglancer function, to render ome tiff image into neuroglancer. new pcdl_render_neuroglancer function, to render ome tiff images into neuroglancer. version 3.3.8 (2025-07-23): elmbeech/physicelldataloader command line commands now return error code 0 if the command runs successfully. version 3.3.7 (2025-06-01): elmbeech/physicelldataloader compatible with current (non end-of-life cycle) python versions. minor bugfixes. version 3.3.6 (2025-05-13): elmbeech/physicelldataloader compatible with numpy >= 2.0.0 and current (non end-of-life cycle) python versions. version 3.3.5 (2025-05-13): elmbeech/physicelldataloader compatible with numpy < 2.0.0 and current (non end-of-life cycle) python versions. remove pyMCDS and pyMCDSts make_ome_tiff and pyCLI pcdl_make_ome_tiff to make pyMCS.py stand alone again. new TimeStep get_cell_attribute_list function, to retrieve a list of all tracked cell attribute labels. new pcdl_get_cell_attribute_list function, to retrieve a list of all tracked cell attribute labels. version 3.3.4 (2025-03-07): elmbeech/physicelldataloader replace the aicsimageio library dependency with its successor bioio . special thanks to Joel Eliason! make_ome_tiff can now handel generated file names with > 255 characters. special thank to Genevieve Stein-O'Brien and DanielBergman! get_mesh_spacing handels now an edge case correctly that would have resulted in a division by zero. special thanks to Randy Heiland! version 3.3.3 (2025-01-10): elmbeech/physicelldataloader bug fix plot_contour plot orientation. special thanks to Marco Ruscone! add test data for new improved unittest physicell model . special thanks to Nick Oldfather! add pyMCDS make_conc_vtk on the fly visualization. special thanks to Randy Heiland and Nick Oldfather! pyMCDS and pyMCDSts make_graph_gml and pyAnnData get_anndata handles now spring_attached_cells graph too. version 3.3.2 (2024-11-24): elmbeech/physicelldataloader Warnings will no longer be piped to standard output if verbose is set to False. pyMCDS make_ome_tiff function rewriten to be less RAM hungry and more versatile. version 3.3.1 (2024-09-22): elmbeech/physicelldataloader bugfix pyMCDS custom vectors loading. version 3.3.0 (2024-08-22): elmbeech/physicelldataloader pip install pcdl : will again install all library dependencies. The fine-tuned version was too confssing. pyMCDS handels now intracellular physinboss data too; data is stored in cell_df. rename pyMCDS get_cell_variables to get_celltype_list for conciseness and order list by ID. rename pyMCDS get_substrate_names to get_substrate_list for conciseness and order list by ID. rename pyMCDS get_scatter to plot_scatter for conciseness. rename pyMCDS get_contour to plot_contour for conciseness. rename pyMCDSts make_imgcell to plot_scatter for conciseness. rename pyMCDSts make_imgconc to plot_contour for conciseness. rename pyMCDSts get_cell_df_states to get_cell_attribute for conciseness. rename pyMCDSts get_conc_df_states to get_conc_attribute for conciseness. rewrite pyMCDS mcds.get_unit_se into mcds.get_unit_dict . new pyCLI pcdl_get_anndata command line interface function. new pyCLI pcdl_get_celltype_list command line interface function. new pyCLI pcdl_get_cell_attribute command line interface function. new pyCLI pcdl_get_cell_df command line interface function. new pyCLI pcdl_get_substrate_list command line interface function. new pyCLI pcdl_get_conc_attribute command line interface function. new pyCLI pcdl_get_conc_df command line interface function. new pyCLI pcdl_get_graph_gml command line interface function. new pyCLI pcdl_get_unit_dict command line interface function. new pyCLI pcdl_get_version command line interface function. new pyCLI pcdl_make_cell_vtk command line interface function. new pyCLI pcdl_make_conc_vtk command line interface function. new pyCLI pcdl_make_gif command line interface function. new pyCLI pcdl_make_movie command line interface function. new pyCLI pcdl_make_ome_tiff command line interface function. new pyCLI pcdl_plot_contour command line interface function. new pyCLI pcdl_plot_scatter command line interface function. new pyCLI pcdl_plot_timeseries command line interface function. new pyMCDS mcds.get_mesh_mnp function, the mesh version from mcds.get_voxel_ijk. new pyMCDS make_conc_vtk function, to save substrate data as rectilinear grid vtk file. new pyMCDS make_cell_vtk function, to save cell data as glyph vtk file. new pyMCDS make_graph_gml function, to save graphs in a networkx and igraph compatible file format. new pyMCDS make_ome_tiff function, to save the output data in ome tiff file format. new pyMCDS set_verbosity_true function, to complete pcdl.TimeStep(verbosity=True/False) experience. new pyMCDS set_verbosity_false function, to complete pcdl.TimeStep(verbosity=True/False) experience. new pyMCDSts get_cell_df function, to extract one big dataframe or a list of dataframes from the whole time series. new pyMCDSts get_conc_df function, to extract one big dataframe or a list of dataframes from the whole time series. new pyMCDSts make_cell_vtk function, to save substrate data as rectilinear grid vtk files. special thanks to Furkan Kurtoglu! new pyMCDSts make_conc_vtk function, to save cell data as glyph vtk files. special thanks to Furkan Kurtoglu! new pyMCDSts make_graph_gml function, to save graphs in a networkx and igraph compatible files format. special thanks to Benjamin Jacobs! new pyMCDSts make_ome_tiff function, to save the output data in ome tiff file format. new pyMCDSts plot_timeseries function, to plot time series. special thanks to Thierry-Pascal Fleurant! new pyMCDSts set_verbosity_true function, to complete the pcdl.TimeSeries(verbosity=True/False) experience. new pyMCDSts set_verbosity_false function to complete the pcdl.TimeSeries(verbosity=True/False) experience. version 3.2.13 (2023-09-18): elmbeech/physicelldataloader rename pyMCDSts make_imgsubs to make_imgconc for consistency. add man/lecture/20230917_pcdl_repl_programming_analysis_plots.pdf slide deck. version 3.2.12 (2023-08-12): elmbeech/physicelldataloader add man/jupyter/pcdl_repl_programming.ipynb : Jupyter notebook to give an idea about how to work with pcdl in a python3 REPL. add man/lecture/20230808_pcws2023_session07_pcdl.pdf slide deck. add github continuous integration for all supported python3 versions, all supported operating systems. version 3.2.11 (2023-08-08): elmbeech/physicelldataloader pip install pcdl : will only install the bare minimum library dependencies. pip install pcdl[data] : will install the minimum dependencies plus the dependencies to download the test dataset. pip install pcdl[scverse] : will install the minimum dependencies plus the dependencies needed to generate an anndata object. pip install pcdl[all] : will always install all dependencies. new TimeSeries get_annmcds_list function, which points to the self.l_annmcds object. new pyMCDS get_scatter function is split off from pyMCDSts make_imgcell. pyMCDSts make_imgcell and make_imgsubs bug fixes. TimeStep and TimeSeries get_anndata evolution. version 3.2.10 (2023-07-24): elmbeech/physicelldataloader rename pyMCDSts get_cell_df_columns_states to get_cell_df_states for conciseness. rename pyMCDSts get_conc_df_columns_states to get_conc_df_states for conciseness. version 3.2.9 (2023-07-23): elmbeech/physicelldataloader new class TimeStep can do everything pyMCDS can do and more. new class TimeSeries can do everything pyMCDSts can do and more. new TimeStep get_anndata function to transform physicell output into AnnData objects. new TimeSeries get_anndata function to transform physicell output into AnnData objects. internal pyAnnData scaler function. internal pyAnnData _anndextract function. pyMCDS __init__ seetingxml parameter changed from boolean to string to accept other PhysiCell_settings.xml filenames than the default. pyMCDS get_cell_df drop and keep parameters to declare a set of columns to be dropped or kept. pyMCDS get_conc_df drop and keep parameters to declare a set of columns to be dropped or kept. new pyMCDS get_conc_df shorthand for get_concentration_df. pyMCDSts get_cell_minstate_col reimplementation as get_cell_df_columns_states function. pyMCDSts get_concentartion_minstate_col reimplementation as get_conc_df_columns_states function. new pyMCDSts get_mcds_list function which points to the self.l_mcds object. version 3.2.8 (2023-06-21): elmbeech/physicelldataloader pyMCDS get_concentration_df states parameter to filter out non-informative variables. pyMCDS get_cell_df states parameter to filter out non-informative variables. pyMCDSts __init__ load parameter to specify if the whole time series data straight at object initialization should be loaded. new pyMCDSts get_cell_minstate_col function to scan the whole time series for informative attributes. new pyMCDSts get_concentartion_minstate_col function to scan the whole time series for informative attributes. version 3.2.7 (2023-06-20): elmbeech/physicelldataloader pyMCDS and pyMCDSts __init__ custom_type parameter to specify other custom_data variable types (int, bool, str) then the generic float. version 3.2.5 (2023-06-19): elmbeech/physicelldataloader pyMCDS resolves incompatibility with earlier PhysiCell and MultiCellDS versions. version 3.2.4 (2023-06-17): elmbeech/physicelldataloader pyMCDS __init__ + +## Conda Search Info +$ conda search -c bioconda -c conda-forge pcdl --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +pcdl 3.3.6 pyhdfd78af_0 +----------------------- +file name : pcdl-3.3.6-pyhdfd78af_0.tar.bz2 +name : pcdl +version : 3.3.6 +build : pyhdfd78af_0 +build number: 0 +size : 56 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pcdl-3.3.6-pyhdfd78af_0.tar.bz2 +md5 : fea173ea9441df1ae80733a94e0f517d +timestamp : 2025-05-19 00:19:02 UTC +dependencies: + - anndata >=0.10.8 + - ffmpeg + - imagemagick + - matplotlib-base + - numpy >=2.0.0 + - pandas >=2.2.2 + - python >=3.8,<4.0 + - requests + - scipy >=1.13.0 + - vtk + + +pcdl 3.3.7 pyhdfd78af_0 +----------------------- +file name : pcdl-3.3.7-pyhdfd78af_0.tar.bz2 +name : pcdl +version : 3.3.7 +build : pyhdfd78af_0 +build number: 0 +size : 56 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pcdl-3.3.7-pyhdfd78af_0.tar.bz2 +md5 : d434ea3f9ae55d8406b16ef3cd8b1fcf +timestamp : 2025-06-01 21:40:58 UTC +dependencies: + - anndata >=0.10.8 + - ffmpeg + - imagemagick + - matplotlib-base + - numpy + - pandas >=2.2.2 + - python >=3.8,<4.0 + - requests + - scipy >=1.13.0 + - vtk + + +pcdl 3.3.8 pyhdfd78af_0 +----------------------- +file name : pcdl-3.3.8-pyhdfd78af_0.tar.bz2 +name : pcdl +version : 3.3.8 +build : pyhdfd78af_0 +build number: 0 +size : 56 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pcdl-3.3.8-pyhdfd78af_0.tar.bz2 +md5 : 90aec5621bdf4915cb07f62c8961a64f +timestamp : 2025-07-23 21:24:11 UTC +dependencies: + - anndata >=0.10.8 + - ffmpeg + - imagemagick + - matplotlib-base + - numpy + - pandas >=2.2.2 + - python >=3.9,<4.0 + - requests + - scipy >=1.13.0 + - vtk + + +pcdl 4.1.3 pyhdfd78af_0 +----------------------- +file name : pcdl-4.1.3-pyhdfd78af_0.conda +name : pcdl +version : 4.1.3 +build : pyhdfd78af_0 +build number: 0 +size : 68 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pcdl-4.1.3-pyhdfd78af_0.conda +md5 : c35a95614adfc8d1160da857c86bbc7f +timestamp : 2026-03-28 06:45:07 UTC +dependencies: + - anndata >=0.10.8 + - bioio + - bioio-base + - bioio-ome-tiff + - ffmpeg + - geopandas >=0.14 + - imagemagick + - matplotlib-base + - neuroglancer + - numpy + - pandas >=2.2.2 + - python >=3.11,<4.0 + - requests + - scikit-image >=0.24.0 + - scipy >=1.13.0 + - shapely >=2.0.1 + - spatialdata >=0.7.2 + - vtk + + +pcdl 4.1.5 pyhdfd78af_0 +----------------------- +file name : pcdl-4.1.5-pyhdfd78af_0.conda +name : pcdl +version : 4.1.5 +build : pyhdfd78af_0 +build number: 0 +size : 70 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pcdl-4.1.5-pyhdfd78af_0.conda +md5 : 571a2fa00ab9cd28872194f99459c6d7 +timestamp : 2026-04-05 17:27:48 UTC +dependencies: + - anndata >=0.10.8 + - bioio + - bioio-base + - bioio-ome-tiff + - ffmpeg + - geopandas >=0.14 + - imagemagick + - matplotlib-base + - neuroglancer + - numpy + - pandas >=2.2.2 + - python >=3.11,<4.0 + - requests + - scikit-image >=0.24.0 + - scipy >=1.13.0 + - shapely >=2.0.1 + - spatialdata >=0.7.2 + - vtk diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/peakqc.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/peakqc.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..49aacb8dab30f41bb6239f959babdfb29090f22e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/peakqc.manual_bundle.txt @@ -0,0 +1,51 @@ +# Tool: peakqc +software_name: peakqc +tier: T1 +domain: single_cell +downloads: 30 +summary: Quality control of single cell ATAC-seq data based on fragment length distributions. +description: Quality control of single cell ATAC-seq data based on fragment length distributions. +dependencies: beartype, pysam, python, scanpy >=1.9, scipy, tqdm +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/loosolab/PEAKQC +doc_url: https://loosolab.pages.gwdg.de/software/peakqc/ +dev_url: https://github.com/loosolab/PEAKQC + +## URL Docs Extract +### https://loosolab.pages.gwdg.de/software/peakqc/ +PEAKQC Documentation — PEAKQC documentation PEAKQC Getting Started Installation Quickstart Developer API Contents: PEAKQC PEAKQC Documentation View page source PEAKQC Documentation  Periodicity Evaluation in scATAC-seq data for quality assessment A Python tool for single-cell ATAC-seq QC, based on convolutional analysis of fragment length distribution. Main Features  Evaluate fragment length periodicity in single cells Detect low-quality cells based on FDL signal Visual and algorithmic QC for ATAC-seq Navigation  Getting Started Installation Install from PyPi: Install from Source: Quickstart Developer API Contents: Next © Copyright 2025, Loosolab. Built with Sphinx using a theme provided by Read the Docs . + +### https://github.com/loosolab/PEAKQC +GitHub - loosolab/PEAKQC: PEAK-QC: Periodicity Evaluation in ATAC-seq as Key aspect in Quality Control · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} loosolab / PEAKQC Public Notifications You must be signed in to change notification settings Fork 0 Star 2 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights loosolab/PEAKQC main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 260 Commits 260 Commits .gitlab .gitlab dist dist docs docs figures figures paper paper scripts scripts src/ peakqc src/ peakqc tests tests .gitignore .gitignore .gitlab-ci.yml .gitlab-ci.yml CHANGES.md CHANGES.md Dockerfile Dockerfile LICENSE LICENSE README.md README.md peakqc_env.yml peakqc_env.yml pyproject.toml pyproject.toml View all files Repository files navigation README MIT license Periodicity Evaluation in scATAC-seq data for quality assessment A python tool for ATAC-seq quality control in single cells. On the bulk level quality control approaches rely on four key aspects: - signal-to-noise ratio - library complexity - mitochondrial DNA nuclear DNA ratio - fragment length distribution Hereby relies PEAKQC on the evaluation of the fragment length distribution. While on the bulk level the evaluation is done visually, it is not possible to do that on the single cell level. PEAKQC solves this constraint with an convolution based algorithmic approach. API Documentation A detailed API documentation is provided by our read the docs page: https://loosolab.pages.gwdg.de/software/peakqc/ Workflow To execute the tool an anndata object and fragments, corresponding to the cells in the anndata have to be provided. The fragments can be either determined from a bamfile directly or by an fragments file in the bed format. If a fragments bedfile is available this is recommended to shorten the runtime. Installation PyPi pip install peakqc From Source 1. Enviroment & Package Installation Download the repository. This will download the repository to the current directory git@gitlab.gwdg.de:loosolab/software/peakqc.git Change the working directory to the newly created repository directory. cd sc_framework Install analysis environment. Note: using mamba is faster than conda , but this requires mamba to be installed. mamba env create -f peakqc_env.yml Activate the environment. conda activate peakqc Install PEAKQC into the enviroment. pip install . 2. Package Installation Download the repository. This will download the repository to the current directory git@gitlab.gwdg.de:loosolab/software/peakqc.git Change the working directory to the newly created repository directory. cd sc_framework Install PEAKQC into the enviroment. pip install . Quickstart Below is a minimal example showing how to integrate FLD scoring into a Jupyter Notebook. A fully worked example is available at paper/example_notebook.ipynb . Load your AnnData object import scanpy as sc # replace with your path to the .h5ad file anndata = sc . read_h5ad ( 'path/to/your_data.h5ad' ) Note: We recommend storing your cell barcodes as the .obs index in adata . If your barcodes are instead in a specific .obs column, you can override this via the barcode_col parameter (see below). Import FLD scoring function from peakqc . fld_scoring import add_fld_metrics Prepare fragment files Provide either a BED or BAM file via fragments=. BED files are recommended for faster runtime. Example: fragments = 'path/to/fragments.bed' # or .bam Run FLD scoring adata = add_fld_metrics ( adata = anndata , fragments = fragments , barcode_col = None , plot = True , save_density = None , save_overview = None , sample = 0 , n_threads = 8 , sample_size = 5000 , mc_seed = 42 , mc_samples = 1000 ) Filter on PEAKQC scores In our experience, PEAKQC scores above 100 are generally effective for filtering out low-quality cells. Hereby PEAKQC scores positively correlate with improving FLD patterns. However, it is important to note that optimal thresholds can vary between datasets and should be tuned to achieve reliable results. Threshold selection may also depend on the specific requirements of your downstream analysis, and should be adjusted accordingly. For a step-by-step walkthrough along with plotting examples, see the example notebook at paper/example_notebook.ipynb About PEAK-QC: Periodicity Evaluation in ATAC-seq as Key aspect in Quality Control Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 2 stars Watchers 1 watching Forks 0 forks Report repository Releases 4 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 99.6% Other 0.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/loosolab/PEAKQC +GitHub - loosolab/PEAKQC: PEAK-QC: Periodicity Evaluation in ATAC-seq as Key aspect in Quality Control · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} loosolab / PEAKQC Public Notifications You must be signed in to change notification settings Fork 0 Star 2 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights loosolab/PEAKQC main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 260 Commits 260 Commits .gitlab .gitlab dist dist docs docs figures figures paper paper scripts scripts src/ peakqc src/ peakqc tests tests .gitignore .gitignore .gitlab-ci.yml .gitlab-ci.yml CHANGES.md CHANGES.md Dockerfile Dockerfile LICENSE LICENSE README.md README.md peakqc_env.yml peakqc_env.yml pyproject.toml pyproject.toml View all files Repository files navigation README MIT license Periodicity Evaluation in scATAC-seq data for quality assessment A python tool for ATAC-seq quality control in single cells. On the bulk level quality control approaches rely on four key aspects: - signal-to-noise ratio - library complexity - mitochondrial DNA nuclear DNA ratio - fragment length distribution Hereby relies PEAKQC on the evaluation of the fragment length distribution. While on the bulk level the evaluation is done visually, it is not possible to do that on the single cell level. PEAKQC solves this constraint with an convolution based algorithmic approach. API Documentation A detailed API documentation is provided by our read the docs page: https://loosolab.pages.gwdg.de/software/peakqc/ Workflow To execute the tool an anndata object and fragments, corresponding to the cells in the anndata have to be provided. The fragments can be either determined from a bamfile directly or by an fragments file in the bed format. If a fragments bedfile is available this is recommended to shorten the runtime. Installation PyPi pip install peakqc From Source 1. Enviroment & Package Installation Download the repository. This will download the repository to the current directory git@gitlab.gwdg.de:loosolab/software/peakqc.git Change the working directory to the newly created repository directory. cd sc_framework Install analysis environment. Note: using mamba is faster than conda , but this requires mamba to be installed. mamba env create -f peakqc_env.yml Activate the environment. conda activate peakqc Install PEAKQC into the enviroment. pip install . 2. Package Installation Download the repository. This will download the repository to the current directory git@gitlab.gwdg.de:loosolab/software/peakqc.git Change the working directory to the newly created repository directory. cd sc_framework Install PEAKQC into the enviroment. pip install . Quickstart Below is a minimal example showing how to integrate FLD scoring into a Jupyter Notebook. A fully worked example is available at paper/example_notebook.ipynb . Load your AnnData object import scanpy as sc # replace with your path to the .h5ad file anndata = sc . read_h5ad ( 'path/to/your_data.h5ad' ) Note: We recommend storing your cell barcodes as the .obs index in adata . If your barcodes are instead in a specific .obs column, you can override this via the barcode_col parameter (see below). Import FLD scoring function from peakqc . fld_scoring import add_fld_metrics Prepare fragment files Provide either a BED or BAM file via fragments=. BED files are recommended for faster runtime. Example: fragments = 'path/to/fragments.bed' # or .bam Run FLD scoring adata = add_fld_metrics ( adata = anndata , fragments = fragments , barcode_col = None , plot = True , save_density = None , save_overview = None , sample = 0 , n_threads = 8 , sample_size = 5000 , mc_seed = 42 , mc_samples = 1000 ) Filter on PEAKQC scores In our experience, PEAKQC scores above 100 are generally effective for filtering out low-quality cells. Hereby PEAKQC scores positively correlate with improving FLD patterns. However, it is important to note that optimal thresholds can vary between datasets and should be tuned to achieve reliable results. Threshold selection may also depend on the specific requirements of your downstream analysis, and should be adjusted accordingly. For a step-by-step walkthrough along with plotting examples, see the example notebook at paper/example_notebook.ipynb About PEAK-QC: Periodicity Evaluation in ATAC-seq as Key aspect in Quality Control Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 2 stars Watchers 1 watching Forks 0 forks Report repository Releases 4 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 99.6% Other 0.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge peakqc --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +peakqc 0.1.6 pyh106432d_0 +------------------------- +file name : peakqc-0.1.6-pyh106432d_0.conda +name : peakqc +version : 0.1.6 +build : pyh106432d_0 +build number: 0 +size : 28 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/peakqc-0.1.6-pyh106432d_0.conda +md5 : cdeefa8a39ac78bf1337a3c4ba205001 +timestamp : 2026-03-12 07:43:03 UTC +dependencies: + - beartype + - pysam + - python + - scanpy >=1.9 + - scipy + - tqdm diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/peptides.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/peptides.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc94b65a0fc69fcf55bd70d206a238106f6debf8 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/peptides.manual_bundle.txt @@ -0,0 +1,94 @@ +# Tool: peptides +software_name: peptides +tier: T1 +domain: proteomics +downloads: 4255 +summary: Physicochemical properties, indices and descriptors for amino-acid sequences. +description: Physicochemical properties, indices and descriptors for amino-acid sequences. +dependencies: python +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://peptides.readthedocs.io/ +doc_url: +dev_url: + +## URL Docs Extract +### https://peptides.readthedocs.io/ +peptides.py — peptides 0.5.0 documentation Skip to main content Back to top Ctrl + K Peptides Choose version User Guide API Reference Search Ctrl + K GitHub PyPI Search Ctrl + K User Guide API Reference GitHub PyPI peptides.py # Physicochemical properties, indices and descriptors for amino-acid sequences. Overview # peptides.py is a pure-Python package to compute common descriptors for protein sequences. It started as a port of Peptides , the R package written by Daniel Osorio for the same purpose, but now also provides some more features from EMBOSS , ExPASy Protein Identification and Analysis Tools , and Rcpi . This library has no external dependency and is available for all modern Python versions (3.6+). A non-exhaustive list of available features: Amino-acid Statistics: Number of occurrences in the peptide sequence Frequency in the peptide sequence Longuest run of identical amino-acids Shannon Entropy QSAR descriptors: BLOSUM indices Cruciani properties FASGAI vectors Kidera factors Atchley factors MS-WHIM scores PCP descriptors ProtFP descriptors Sneath vectors ST-scales SVGER descriptors T-scales VHSE-scales Z-scales Sequence profiles: Hydrophobicity profile using one of 39 proposed scales. Hydrophobic moment profile based on Eisenberg, Weiss and Terwilliger (1984) . Membrane position based on Eisenberg (1984) . Physical-chemical properties: Aliphatic index proposed in Ikai (1980) . Instability index proposed in Boman (2003) . Theoretical net charge based on the Henderson-Hasselbach equation . Isoelectric point using one of 8 pKa scales. Molecular weight, taking into account isotope labelling, using one of 3 average weight tables. Biological properties: Structural class using methods and reference data from either Nakashima, Nishikawa & Ooi (1985) , Chou (1989) , Chou & Zhang (1992) , or Chou, Liu, Maggiora & Zhang (1998) . Sequence validation comparing several metrics against a reference distribution computed from the SwissProt database. Setup # peptides is a pure Python package available for all modern Python (3.6+). Run pip install peptides in a shell to download the latest release, or have a look at the Installation page to find other ways to install peptides.py . Library # User Guide Installation Contribution Guide Changelog Copyright Notice API Reference Peptide Descriptors Sequence Vetting Related Projects # The following Python libraries may be of interest for bioinformaticians. PyHMMER Profile Hidden Markov Models (with HMMER). https://pyhmmer.readthedocs.io Pyrodigal Prokaryotic Gene Finding (with Prodigal). https://pyrodigal.readthedocs.io Pyrodigal-gv Pyrodigal for Giant Viruses. https://pypi.org/project/pyrodigal-gv/ PyFAMSA Multiple Sequence Alignment (with FAMSA). https://pyfamsa.readthedocs.io PytrimAl Alignment Trimming (with trimAl). https://pytrimal.readthedocs.io LightMotif Platform-accelerated motif scoring. https://lightmotif.readthedocs.io Diced CRISPR Detection (with MinCED). https://diced.readthedocs.io Scoring Matrices Scoring matrices for Cython. https://scoring-matrices.readthedocs.io Pyskani Average Nucleotide Identity (with skani). https://pyskani.readthedocs.io PySylph ANI containment and taxonomic profiling (with sylph). https://pysylph.readthedocs.io PyFastANI Average Nucleotide Identity (with FastANI). https://pyfastani.readthedocs.io PyJess Geometric Template Matching (with Jess). https://pyjess.readthedocs.io PyTantan Tandem Repeat Masking (with Tantan). https://pytantan.readthedocs.io PyOpal Query/Database Aligner (with Opal). https://pyopal.readthedocs.io PySWRD Database Heuristic Filtering (with SWORD). https://pyswrd.readthedocs.io Mini3di Protein structure to 3di with NumPy. https://pypi.org/project/mini3di/ MiniNEAR Protein sequence to NEAR embedding with NumPy. https://pypi.org/project/mininear/ peptides.py Peptide descriptors for Python. https://peptides.readthedocs.io Pronto Open Biomedical Ontologies for Python. https://pronto.readthedocs.io NAFcodec Nucleotide Archival Format for Python (and Rust). https://pypi.org/project/nafcodec/ gb-io.py Fast GenBank parser for Python (with gb-io ). https://gb-io.readthedocs.io PyOrthoANI OrthoAni re-implementation in Python. https://pypi.org/project/pyorthoani/ PyCoMSA Multiple Sequence Alignment compression (with CoMSA). https://pycomsa.readthedocs.io PyARAGORN tRNA, tmRNA and mtRNA gene prediction (with ARAGORN). https://pyaragorn.readthedocs.io License # This library is provided under the GNU General Public License v3.0 . The original R Peptides package was written by Daniel Osorio , Paola Rondón-Villarreal and Rodrigo Torres , and is licensed under the terms of the GNU General Public License v2.0 . The EMBOSS applications are released under the GNU General Public License v1.0 . This project is in no way not affiliated, sponsored, or otherwise endorsed by the original Peptides authors. It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team . next User Guide On this page Overview Setup Library Related Projects License Edit on GitHub This Page Show Source so the DOM is not blocked --> © Copyright 2021-2025, Martin Larralde. Created using Sphinx 8.2.3. Built with the PyData Sphinx Theme 0.16.1. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge peptides --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +peptides 0.3.1 pyh5e36f6f_0 +--------------------------- +file name : peptides-0.3.1-pyh5e36f6f_0.tar.bz2 +name : peptides +version : 0.3.1 +build : pyh5e36f6f_0 +build number: 0 +size : 85 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/peptides-0.3.1-pyh5e36f6f_0.tar.bz2 +md5 : 70557ffa375abcc7e478000ba1447d83 +timestamp : 2022-09-03 09:27:46 UTC +dependencies: + - python + + +peptides 0.3.4 pyh7e72e81_0 +--------------------------- +file name : peptides-0.3.4-pyh7e72e81_0.tar.bz2 +name : peptides +version : 0.3.4 +build : pyh7e72e81_0 +build number: 0 +size : 94 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/peptides-0.3.4-pyh7e72e81_0.tar.bz2 +md5 : 17eb7d7a2558c911856fe9f60b451300 +timestamp : 2024-09-19 12:03:12 UTC +dependencies: + - python + + +peptides 0.4.0 pyh7e72e81_0 +--------------------------- +file name : peptides-0.4.0-pyh7e72e81_0.tar.bz2 +name : peptides +version : 0.4.0 +build : pyh7e72e81_0 +build number: 0 +size : 68 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/peptides-0.4.0-pyh7e72e81_0.tar.bz2 +md5 : f56c3986c9594f089312da7f4cd31a79 +timestamp : 2025-07-25 17:36:13 UTC +dependencies: + - python + + +peptides 0.5.0 pyh7e72e81_0 +--------------------------- +file name : peptides-0.5.0-pyh7e72e81_0.conda +name : peptides +version : 0.5.0 +build : pyh7e72e81_0 +build number: 0 +size : 68 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/peptides-0.5.0-pyh7e72e81_0.conda +md5 : 6f2844f53107635c46e81832aa3ad4a9 +timestamp : 2025-09-04 10:17:49 UTC +dependencies: + - python diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-aceperl.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-aceperl.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b4799bdb4d19122aafe7d9265d41a4d80149a6ba --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-aceperl.manual_bundle.txt @@ -0,0 +1,233 @@ +# Tool: perl-aceperl +software_name: perl-aceperl +tier: T1 +domain: t1_backfill_overall +downloads: 186779 +summary: Object-Oriented Access to ACEDB Databases +description: Object-Oriented Access to ACEDB Databases +dependencies: libgcc >=13, perl >=5.32.1,<5.33.0a0 *_perl5, perl-cache-cache, perl-digest-md5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-aceperl --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-aceperl 1.92 0 +------------------- +file name : perl-aceperl-1.92-0.tar.bz2 +name : perl-aceperl +version : 1.92 +build : 0 +build number: 0 +size : 110 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-aceperl-1.92-0.tar.bz2 +md5 : f3f6ae62e966f52bd89eeb56bf356165 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-aceperl 1.92 pl526_1 +------------------------- +file name : perl-aceperl-1.92-pl526_1.tar.bz2 +name : perl-aceperl +version : 1.92 +build : pl526_1 +build number: 1 +size : 149 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-aceperl-1.92-pl526_1.tar.bz2 +md5 : 2b0a417390e6d11346d994237ae86194 +timestamp : 2018-07-08 00:04:33 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-aceperl 1.92 pl526_2 +------------------------- +file name : perl-aceperl-1.92-pl526_2.tar.bz2 +name : perl-aceperl +version : 1.92 +build : pl526_2 +build number: 2 +size : 149 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-aceperl-1.92-pl526_2.tar.bz2 +md5 : 8f0932e2e264bebf85619c4ef2f166a8 +timestamp : 2018-07-29 22:18:47 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-cache-cache + - perl-digest-md5 + + +perl-aceperl 1.92 pl5321h031d066_5 +---------------------------------- +file name : perl-aceperl-1.92-pl5321h031d066_5.tar.bz2 +name : perl-aceperl +version : 1.92 +build : pl5321h031d066_5 +build number: 5 +size : 156 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-aceperl-1.92-pl5321h031d066_5.tar.bz2 +md5 : aba607017b0a6b6d06b666772321a4b1 +timestamp : 2023-05-16 17:50:01 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-cache-cache + - perl-digest-md5 + + +perl-aceperl 1.92 pl5321h779adbc_3 +---------------------------------- +file name : perl-aceperl-1.92-pl5321h779adbc_3.tar.bz2 +name : perl-aceperl +version : 1.92 +build : pl5321h779adbc_3 +build number: 3 +size : 151 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-aceperl-1.92-pl5321h779adbc_3.tar.bz2 +md5 : e00994c65a2e7fb13d9f310d31634105 +timestamp : 2022-01-24 22:14:49 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-cache-cache + - perl-digest-md5 + + +perl-aceperl 1.92 pl5321h7b50bb2_6 +---------------------------------- +file name : perl-aceperl-1.92-pl5321h7b50bb2_6.tar.bz2 +name : perl-aceperl +version : 1.92 +build : pl5321h7b50bb2_6 +build number: 6 +size : 153 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-aceperl-1.92-pl5321h7b50bb2_6.tar.bz2 +md5 : 7c08212a2faae57539ee73b83f7fba7e +timestamp : 2024-12-14 22:59:42 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-cache-cache + - perl-digest-md5 + + +perl-aceperl 1.92 pl5321h7b50bb2_7 +---------------------------------- +file name : perl-aceperl-1.92-pl5321h7b50bb2_7.tar.bz2 +name : perl-aceperl +version : 1.92 +build : pl5321h7b50bb2_7 +build number: 7 +size : 153 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-aceperl-1.92-pl5321h7b50bb2_7.tar.bz2 +md5 : 50c8c44c1cbb6f34bf307dc9e4c280c5 +timestamp : 2025-02-11 14:45:54 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-cache-cache + - perl-digest-md5 + + +perl-aceperl 1.92 pl5321h7b50bb2_8 +---------------------------------- +file name : perl-aceperl-1.92-pl5321h7b50bb2_8.tar.bz2 +name : perl-aceperl +version : 1.92 +build : pl5321h7b50bb2_8 +build number: 8 +size : 157 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-aceperl-1.92-pl5321h7b50bb2_8.tar.bz2 +md5 : 235e3b287244d3ae654be321516cbe66 +timestamp : 2025-04-21 21:37:35 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-cache-cache + - perl-digest-md5 + + +perl-aceperl 1.92 pl5321hec16e2b_4 +---------------------------------- +file name : perl-aceperl-1.92-pl5321hec16e2b_4.tar.bz2 +name : perl-aceperl +version : 1.92 +build : pl5321hec16e2b_4 +build number: 4 +size : 151 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-aceperl-1.92-pl5321hec16e2b_4.tar.bz2 +md5 : 11c9ea09d89028c68ecba2dd45f89135 +timestamp : 2022-02-25 13:42:31 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-cache-cache + - perl-digest-md5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-base.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-base.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3758082a3aa92d3ba4dacfdd74a6ab178e3cc599 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-base.manual_bundle.txt @@ -0,0 +1,146 @@ +# Tool: perl-base +software_name: perl-base +tier: T1 +domain: t1_backfill_overall +downloads: 443854 +summary: +description: +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-base --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-base 2.22 pl5.22.0_0 +------------------------- +file name : perl-base-2.22-pl5.22.0_0.tar.bz2 +name : perl-base +version : 2.22 +build : pl5.22.0_0 +build number: 0 +size : 2 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-base-2.22-pl5.22.0_0.tar.bz2 +md5 : d52639a154743401fc2020d7bd683462 +dependencies: + - perl 5.22.0* + + +perl-base 2.23 pl5.22.0_0 +------------------------- +file name : perl-base-2.23-pl5.22.0_0.tar.bz2 +name : perl-base +version : 2.23 +build : pl5.22.0_0 +build number: 0 +size : 8 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-base-2.23-pl5.22.0_0.tar.bz2 +md5 : 571d47af1e269c039bbbdb6c2c4adab0 +dependencies: + - perl 5.22.0* + + +perl-base 2.23 pl526_1 +---------------------- +file name : perl-base-2.23-pl526_1.tar.bz2 +name : perl-base +version : 2.23 +build : pl526_1 +build number: 1 +size : 10 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-base-2.23-pl526_1.tar.bz2 +md5 : 03db12873cdeb00d4e8d02bcbf583a04 +timestamp : 2018-07-08 22:02:35 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-base 2.23 pl5321hd8ed1ab_0 +------------------------------- +file name : perl-base-2.23-pl5321hd8ed1ab_0.tar.bz2 +name : perl-base +version : 2.23 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 19 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-base-2.23-pl5321hd8ed1ab_0.tar.bz2 +md5 : d0ae29661c8985b4e4a512e6973f7a3f +timestamp : 2022-10-09 21:54:04 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-base 2.23 pl5321hdfd78af_2 +------------------------------- +file name : perl-base-2.23-pl5321hdfd78af_2.tar.bz2 +name : perl-base +version : 2.23 +build : pl5321hdfd78af_2 +build number: 2 +size : 12 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-base-2.23-pl5321hdfd78af_2.tar.bz2 +md5 : 56bcf32d7efd3cb8f9bb6c3e4c592f48 +timestamp : 2022-01-20 07:56:16 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bio-asn1-entrezgene.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bio-asn1-entrezgene.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..973ca3848483f3fc3ca17bea6e7591f1f1b82951 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bio-asn1-entrezgene.manual_bundle.txt @@ -0,0 +1,213 @@ +# Tool: perl-bio-asn1-entrezgene +software_name: perl-bio-asn1-entrezgene +tier: T1 +domain: t1_backfill_overall +downloads: 331528 +summary: Regular expression-based Perl Parser for NCBI Entrez Gene +description: Regular expression-based Perl Parser for NCBI Entrez Gene +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-base, perl-bioperl-core, perl-carp, perl-data-dumper, perl-parent, perl-test-most +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://search.cpan.org/dist/Bio-ASN1-EntrezGene +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://search.cpan.org/dist/Bio-ASN1-EntrezGene +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-bio-asn1-entrezgene --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-bio-asn1-entrezgene 1.70 0 +------------------------------- +file name : perl-bio-asn1-entrezgene-1.70-0.tar.bz2 +name : perl-bio-asn1-entrezgene +version : 1.70 +build : 0 +build number: 0 +size : 12 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bio-asn1-entrezgene-1.70-0.tar.bz2 +md5 : 17e34777c547c74acc2ee4119676076a +dependencies: + - perl-bioperl-core + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-bio-asn1-entrezgene 1.72 1 +------------------------------- +file name : perl-bio-asn1-entrezgene-1.72-1.tar.bz2 +name : perl-bio-asn1-entrezgene +version : 1.72 +build : 1 +build number: 1 +size : 12 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bio-asn1-entrezgene-1.72-1.tar.bz2 +md5 : 3bd50cda1c070f15366b74a19cade593 +dependencies: + - perl-bioperl-core + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-bio-asn1-entrezgene 1.72 pl526_2 +------------------------------------- +file name : perl-bio-asn1-entrezgene-1.72-pl526_2.tar.bz2 +name : perl-bio-asn1-entrezgene +version : 1.72 +build : pl526_2 +build number: 2 +size : 21 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bio-asn1-entrezgene-1.72-pl526_2.tar.bz2 +md5 : d970f9843bc2335a7a11525d7f6228d4 +timestamp : 2018-08-09 08:54:17 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-bioperl-core + + +perl-bio-asn1-entrezgene 1.73 pl5262hdfd78af_2 +---------------------------------------------- +file name : perl-bio-asn1-entrezgene-1.73-pl5262hdfd78af_2.tar.bz2 +name : perl-bio-asn1-entrezgene +version : 1.73 +build : pl5262hdfd78af_2 +build number: 2 +size : 23 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-bio-asn1-entrezgene-1.73-pl5262hdfd78af_2.tar.bz2 +md5 : ae612dabb9d0b59ac2287f6eefa12b40 +timestamp : 2021-03-31 21:08:19 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-bioperl-core + - perl-carp + - perl-data-dumper + - perl-parent + - perl-test-most + + +perl-bio-asn1-entrezgene 1.73 pl526_0 +------------------------------------- +file name : perl-bio-asn1-entrezgene-1.73-pl526_0.tar.bz2 +name : perl-bio-asn1-entrezgene +version : 1.73 +build : pl526_0 +build number: 0 +size : 22 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bio-asn1-entrezgene-1.73-pl526_0.tar.bz2 +md5 : eb4508d7832a56b14b0be6aae26da212 +timestamp : 2018-11-17 03:02:48 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-bioperl-core + - perl-carp + - perl-data-dumper + - perl-parent + - perl-test-most + + +perl-bio-asn1-entrezgene 1.73 pl526_1 +------------------------------------- +file name : perl-bio-asn1-entrezgene-1.73-pl526_1.tar.bz2 +name : perl-bio-asn1-entrezgene +version : 1.73 +build : pl526_1 +build number: 1 +size : 23 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-bio-asn1-entrezgene-1.73-pl526_1.tar.bz2 +md5 : f20cd003a7a6a52c88305aa0608e0d78 +timestamp : 2019-10-27 23:43:04 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-bioperl-core + - perl-carp + - perl-data-dumper + - perl-parent + - perl-test-most + + +perl-bio-asn1-entrezgene 1.73 pl5321hdfd78af_3 +---------------------------------------------- +file name : perl-bio-asn1-entrezgene-1.73-pl5321hdfd78af_3.tar.bz2 +name : perl-bio-asn1-entrezgene +version : 1.73 +build : pl5321hdfd78af_3 +build number: 3 +size : 24 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-bio-asn1-entrezgene-1.73-pl5321hdfd78af_3.tar.bz2 +md5 : 1fa1e8f39aad93a6dc5a07b5bbb0d648 +timestamp : 2022-01-28 23:01:25 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-base + - perl-bioperl-core + - perl-carp + - perl-data-dumper + - perl-parent + - perl-test-most diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bio-searchio-hmmer.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bio-searchio-hmmer.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad460d3f67c5fd60c2de8643b6e5b66ce199cf6e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bio-searchio-hmmer.manual_bundle.txt @@ -0,0 +1,43 @@ +# Tool: perl-bio-searchio-hmmer +software_name: perl-bio-searchio-hmmer +tier: T1 +domain: t1_backfill_overall +downloads: 138928 +summary: A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) +description: A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-bioperl-core, perl-db_file, perl-io-string +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/release/Bio-SearchIO-hmmer +doc_url: +dev_url: + +## URL Docs Extract +### https://metacpan.org/release/Bio-SearchIO-hmmer +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-bio-searchio-hmmer --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-bio-searchio-hmmer 1.7.3 pl5321hdfd78af_0 +---------------------------------------------- +file name : perl-bio-searchio-hmmer-1.7.3-pl5321hdfd78af_0.tar.bz2 +name : perl-bio-searchio-hmmer +version : 1.7.3 +build : pl5321hdfd78af_0 +build number: 0 +size : 58 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-bio-searchio-hmmer-1.7.3-pl5321hdfd78af_0.tar.bz2 +md5 : 8251ea4d5dc4fd65272ac6700c1d8a21 +timestamp : 2022-03-21 23:14:18 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-bioperl-core + - perl-db_file + - perl-io-string diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bio-tools-run-alignment-clustalw.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bio-tools-run-alignment-clustalw.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3986c9ead81080bb16b3831d001c19abcb3e0440 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bio-tools-run-alignment-clustalw.manual_bundle.txt @@ -0,0 +1,106 @@ +# Tool: perl-bio-tools-run-alignment-clustalw +software_name: perl-bio-tools-run-alignment-clustalw +tier: T1 +domain: t1_backfill_overall +downloads: 283687 +summary: Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program +description: Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program +dependencies: clustalw, perl >=5.32.1,<6.0a0 *_perl5, perl-base, perl-bioperl-run +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/release/Bio-Tools-Run-Alignment-Clustalw +doc_url: +dev_url: + +## URL Docs Extract +### https://metacpan.org/release/Bio-Tools-Run-Alignment-Clustalw +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-bio-tools-run-alignment-clustalw --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-bio-tools-run-alignment-clustalw 1.7.4 pl5262hdfd78af_2 +------------------------------------------------------------ +file name : perl-bio-tools-run-alignment-clustalw-1.7.4-pl5262hdfd78af_2.tar.bz2 +name : perl-bio-tools-run-alignment-clustalw +version : 1.7.4 +build : pl5262hdfd78af_2 +build number: 2 +size : 25 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-run-alignment-clustalw-1.7.4-pl5262hdfd78af_2.tar.bz2 +md5 : 85f4d7898fc7911ff5f71c24c082075e +timestamp : 2021-03-29 16:07:52 UTC +dependencies: + - clustalw + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-bioperl-run + + +perl-bio-tools-run-alignment-clustalw 1.7.4 pl526_0 +--------------------------------------------------- +file name : perl-bio-tools-run-alignment-clustalw-1.7.4-pl526_0.tar.bz2 +name : perl-bio-tools-run-alignment-clustalw +version : 1.7.4 +build : pl526_0 +build number: 0 +size : 22 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bio-tools-run-alignment-clustalw-1.7.4-pl526_0.tar.bz2 +md5 : 3794d563f4a6b81063eaf4a7f8098a2e +timestamp : 2018-08-09 13:46:42 UTC +dependencies: + - clustalw + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-bioperl-run + + +perl-bio-tools-run-alignment-clustalw 1.7.4 pl526_1 +--------------------------------------------------- +file name : perl-bio-tools-run-alignment-clustalw-1.7.4-pl526_1.tar.bz2 +name : perl-bio-tools-run-alignment-clustalw +version : 1.7.4 +build : pl526_1 +build number: 1 +size : 24 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-run-alignment-clustalw-1.7.4-pl526_1.tar.bz2 +md5 : ed40aea3bead264ea48ba2faf88d1106 +timestamp : 2019-10-27 15:35:44 UTC +dependencies: + - clustalw + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-bioperl-run + + +perl-bio-tools-run-alignment-clustalw 1.7.4 pl5321hdfd78af_3 +------------------------------------------------------------ +file name : perl-bio-tools-run-alignment-clustalw-1.7.4-pl5321hdfd78af_3.tar.bz2 +name : perl-bio-tools-run-alignment-clustalw +version : 1.7.4 +build : pl5321hdfd78af_3 +build number: 3 +size : 25 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-run-alignment-clustalw-1.7.4-pl5321hdfd78af_3.tar.bz2 +md5 : f248e955dd6d2cac60b844cb6df7d68f +timestamp : 2022-01-30 13:16:15 UTC +dependencies: + - clustalw + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-base + - perl-bioperl-run diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bioperl.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bioperl.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ea26169b9f99f5fb1f5b3c5f58a942f8f6453822 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-bioperl.manual_bundle.txt @@ -0,0 +1,374 @@ +# Tool: perl-bioperl +software_name: perl-bioperl +tier: T1 +domain: t1_backfill_overall +downloads: 427644 +summary: Bioinformatics Toolkit +description: Bioinformatics Toolkit +dependencies: perl, perl-bio-asn1-entrezgene, perl-bio-coordinate, perl-bio-featureio, perl-bio-samtools, perl-bio-searchio-hmmer, perl-bio-tools-phylo-paml, perl-bio-tools-run-alignment-clustalw, perl-bio-tools-run-alignment-tcoffee, perl-bioperl-core 1.7.8.*, perl-bioperl-run +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/BioPerl +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/BioPerl +BioPerl - Perl modules for biology - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution BioPerl Module version: 1.7.8 03 Feb 2021 05:15:14 UTC License: perl_5 Code Download ( 7.18MB ) Source ( raw ) Browse ( raw ) Changes Project Homepage Repository Issues How to Contribute Quality Testers ( 1292 / 87 / 0 ) Testers (Magpie) Kwalitee Bus factor: 1 Activity 24 month 71 Dependencies AnyDBM_File Carp Cwd DB_File Data::Dumper and 66 more Data::Stag Digest::MD5 Dumpvalue Error Exporter Fcntl File::Basename File::Copy File::Path File::Spec File::Spec::Functions File::Temp FileHandle Getopt::Long Graph::Directed HTTP::Request::Common HTTP::Response IO::File IO::Handle IO::Pipe IO::Scalar IO::Socket IO::String IPC::Run LWP::UserAgent List::MoreUtils List::Util Math::BigFloat Module::Build POSIX Pod::Usage Scalar::Util Set::Scalar Storable Symbol Test::Builder Test::Builder::Module Test::Most Test::RequiresInternet Text::Balanced Text::Wrap Tie::Handle Tie::RefHash Time::HiRes UNIVERSAL URI XML::DOM XML::LibXML XML::LibXML::Reader XML::Parser::PerlSAX XML::SAX XML::SAX::Base XML::SAX::Writer XML::Twig XML::Writer YAML base constant integer overload parent strict utf8 vars version warnings and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 1.7.8 (CJFIELDS on 2021-02-03) 1.7.7 (CJFIELDS on 2019-12-07) 1.7.6 (CDRAUG on 2019-08-28) 1.7.5 (CDRAUG on 2019-02-11) 1.7.4 (CDRAUG on 2019-02-05) 1.7.3 (CDRAUG on 2019-01-30) 1.007002 (CJFIELDS on 2017-09-11) 1.007001 (CJFIELDS on 2016-11-06) 1.007000 (CJFIELDS on 2016-09-25) 1.007000_006 DEV (CJFIELDS on 2016-09-16) 1.007000_005 DEV (CJFIELDS on 2016-07-16) 1.007000_004 DEV (CJFIELDS on 2016-07-07) 1.007000_003 DEV (CJFIELDS on 2016-07-07) 1.6.924 (CJFIELDS on 2014-07-10) 1.7.0._2 (CJFIELDS on 2016-07-06) 1.7.0._1 (CJFIELDS on 2016-07-06) 1.6.923 (CJFIELDS on 2013-12-18) 1.6.922 (CJFIELDS on 2013-09-14) 1.6.921 (CJFIELDS on 2013-09-11) 1.6.920 (CJFIELDS on 2013-09-08) 1.6.910 (CJFIELDS on 2013-09-08) 1.6.901 (CJFIELDS on 2011-05-19) 1.6.900 (CJFIELDS on 2011-04-14) 1.6.1 (CJFIELDS on 2009-09-29) 1.6.0_6 DEV (CJFIELDS on 2009-09-28) 1.6.0_5 DEV (CJFIELDS on 2009-09-28) 1.6.0_4 DEV (CJFIELDS on 2009-09-25) 1.6.0_3 DEV (CJFIELDS on 2009-09-22) 1.6.0_2 DEV (CJFIELDS on 2009-09-22) 1.6.0_1 DEV (CJFIELDS on 2009-09-17) 1.6.0 (CJFIELDS on 2009-01-25) 1.5.9_4 DEV (CJFIELDS on 2009-01-21) 1.5.9_3 DEV (CJFIELDS on 2009-01-16) 1.5.9_2 DEV (CJFIELDS on 2009-01-06) 1.5.9_1 DEV (CJFIELDS on 2008-12-24) 1.5.9_001 DEV (CJFIELDS on 2008-12-24) Diff with version 1.7.8 (CJFIELDS on 2021-02-03) 1.7.7 (CJFIELDS on 2019-12-07) 1.7.6 (CDRAUG on 2019-08-28) 1.7.5 (CDRAUG on 2019-02-11) 1.7.4 (CDRAUG on 2019-02-05) 1.7.3 (CDRAUG on 2019-01-30) 1.007002 (CJFIELDS on 2017-09-11) 1.007001 (CJFIELDS on 2016-11-06) 1.007000 (CJFIELDS on 2016-09-25) 1.007000_006 DEV (CJFIELDS on 2016-09-16) 1.007000_005 DEV (CJFIELDS on 2016-07-16) 1.007000_004 DEV (CJFIELDS on 2016-07-07) 1.007000_003 DEV (CJFIELDS on 2016-07-07) 1.6.924 (CJFIELDS on 2014-07-10) 1.7.0._2 (CJFIELDS on 2016-07-06) 1.7.0._1 (CJFIELDS on 2016-07-06) 1.6.923 (CJFIELDS on 2013-12-18) 1.6.922 (CJFIELDS on 2013-09-14) 1.6.921 (CJFIELDS on 2013-09-11) 1.6.920 (CJFIELDS on 2013-09-08) 1.6.910 (CJFIELDS on 2013-09-08) 1.6.901 (CJFIELDS on 2011-05-19) 1.6.900 (CJFIELDS on 2011-04-14) 1.6.1 (CJFIELDS on 2009-09-29) 1.6.0_6 DEV (CJFIELDS on 2009-09-28) 1.6.0_5 DEV (CJFIELDS on 2009-09-28) 1.6.0_4 DEV (CJFIELDS on 2009-09-25) 1.6.0_3 DEV (CJFIELDS on 2009-09-22) 1.6.0_2 DEV (CJFIELDS on 2009-09-22) 1.6.0_1 DEV (CJFIELDS on 2009-09-17) 1.6.0 (CJFIELDS on 2009-01-25) 1.5.9_4 DEV (CJFIELDS on 2009-01-21) 1.5.9_3 DEV (CJFIELDS on 2009-01-16) 1.5.9_2 DEV (CJFIELDS on 2009-01-06) 1.5.9_1 DEV (CJFIELDS on 2008-12-24) 1.5.9_001 DEV (CJFIELDS on 2008-12-24) Permalinks This version Latest version ++ed by: 12 PAUSE users 24 non-PAUSE users Authors: See individual modules Released by: Christopher Fields Maintainers: BIOPERLML owner BOSBORNE CDRAUG CJFIELDS MAJENSEN Contributors: See individual modules Christopher Fields  /  1.7.8 (CJFIELDS on 2021-02-03) 1.7.7 (CJFIELDS on 2019-12-07) 1.7.6 (CDRAUG on 2019-08-28) 1.7.5 (CDRAUG on 2019-02-11) 1.7.4 (CDRAUG on 2019-02-05) 1.7.3 (CDRAUG on 2019-01-30) 1.007002 (CJFIELDS on 2017-09-11) 1.007001 (CJFIELDS on 2016-11-06) 1.007000 (CJFIELDS on 2016-09-25) 1.007000_006 DEV (CJFIELDS on 2016-09-16) 1.007000_005 DEV (CJFIELDS on 2016-07-16) 1.007000_004 DEV (CJFIELDS on 2016-07-07) 1.007000_003 DEV (CJFIELDS on 2016-07-07) 1.6.924 (CJFIELDS on 2014-07-10) 1.7.0._2 (CJFIELDS on 2016-07-06) 1.7.0._1 (CJFIELDS on 2016-07-06) 1.6.923 (CJFIELDS on 2013-12-18) 1.6.922 (CJFIELDS on 2013-09-14) 1.6.921 (CJFIELDS on 2013-09-11) 1.6.920 (CJFIELDS on 2013-09-08) 1.6.910 (CJFIELDS on 2013-09-08) 1.6.901 (CJFIELDS on 2011-05-19) 1.6.900 (CJFIELDS on 2011-04-14) 1.6.1 (CJFIELDS on 2009-09-29) 1.6.0_6 DEV (CJFIELDS on 2009-09-28) 1.6.0_5 DEV (CJFIELDS on 2009-09-28) 1.6.0_4 DEV (CJFIELDS on 2009-09-25) 1.6.0_3 DEV (CJFIELDS on 2009-09-22) 1.6.0_2 DEV (CJFIELDS on 2009-09-22) 1.6.0_1 DEV (CJFIELDS on 2009-09-17) 1.6.0 (CJFIELDS on 2009-01-25) 1.5.9_4 DEV (CJFIELDS on 2009-01-21) 1.5.9_3 DEV (CJFIELDS on 2009-01-16) 1.5.9_2 DEV (CJFIELDS on 2009-01-06) 1.5.9_1 DEV (CJFIELDS on 2008-12-24) 1.5.9_001 DEV (CJFIELDS on 2008-12-24) BioPerl-1.7.8 36 ++ 36 ++ ⭐ Starred 302 GitHub stars / BioPerl Contents NAME VERSION SYNOPSIS References for Individual Modules DESCRIPTION INSTALLATION GETTING STARTED GETTING INVOLVED Asking questions and telling us you used it Writing a script that uses it Find bugs! Suggest new functionality Make your own objects Writing documentation ACKNOWLEDGEMENTS FEEDBACK Mailing lists Support Reporting bugs AUTHOR COPYRIGHT NAME BioPerl - Perl modules for biology VERSION version 1.7.8 SYNOPSIS If you're new to BioPerl, you should start reading the BioPerl HOWTO's: http://bioperl.org/howtos/index.html References for Individual Modules For ease of maintenance and coordination amongst contributors, BioPerl code is maintained in a modular form, as is the documentation. Refer to the documentation for individual modules by using perldoc, i.e. perldoc Bio::Seq to get documentation for the Bio::Seq object. DESCRIPTION BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are advertised to do in the documentation, but they also interact - Alignment objects are made from the Sequence objects, Sequence objects have access to Annotation and SeqFeature objects and databases, Blast objects can be converted to Alignment objects, and so on. This means that the objects provide a coordinated and extensible framework to do computational biology. BioPerl development focuses on Perl classes, or code that is used to create objects representing biological entities. There are scripts provided in the scripts/ and examples/ directories but scripts are not the main focus of the BioPerl developers. Of course, as the objects do most of the hard work for you, all you have to do is combine a number of objects together sensibly to make useful scripts. The intent of the BioPerl development effort is to make reusable tools that aid people in creating their own sites or job-specific applications. The BioPerl website at http://bioperl.org also attempts to maintain links and archives of standalone bio-related Perl tools that are not affiliated or related to the core BioPerl effort. Check the site for useful code ideas and contribute your own if possible. INSTALLATION The BioPerl modules are distributed as a tar file that expands into a standard perl CPAN distribution. Detailed installation directions can be found in the distribution INSTALL file. Installing on windows using ActiveState Perl is covered in the INSTALL.WIN file. We highly suggest reading the installation instructions on the BioPerl website: http://bioperl.org/INSTALL.html Note that only the following are supported at this time with the current API: BioPerl-db BioPerl-network BioPerl-run BioPerl-pedigree Bio::Graphics GETTING STARTED The distribution scripts/ directory has working scripts for use with BioPerl, check the self-described examples/ directory as well. You are more than welcome to contribute your script! If you have installed BioPerl in the standard way, as detailed in the INSTALL in the distribution, these scripts should work by just running them. GETTING INVOLVED BioPerl is a completely open community of developers. We are not funded and we don't have a mission statement. We encourage collaborative code, in particular in Perl. You can help us in many different ways, from just a simple statement about how you have used BioPerl to doing something interesting to contributing a whole new object hierarchy. See http://bioperl.org for more information. Here are some ways of helping us: Asking questions and telling us you used it We are very interested to hear how you experienced using BioPerl. Did it install cleanly? Did you understand the documentation? Could you get the objects to do what you wanted them to do? If BioPerl was useless we want to know why, and if it was great - that too. Post a message to bioperl-l@bioperl.org , the BioPerl mailing list, where all the developers are. Only by getting people's feedback do we know whether we are providing anything useful. Writing a script that uses it By writing a good script that uses BioPerl you both show that BioPerl is useful and probably save someone elsewhere writing it. If you contribute it to the 'script central' at http://bioperl.org then other people can view and use it. Don't be nervous if you've never done this sort of work, advice is freely given and all are welcome! Find bugs! We know that there are bugs in this code. If you find something which you are pretty sure is a problem, post a bug report using our Bugzilla tracking system: https://github.com/bioperl/bioperl-live/issues Please read the main bug tracking ( http://www.bioperl.org/articles/Bugs.html ) for an overview of what we expect in a bug report. Specifically, having a code and data example where appropriate helps tremendously. We gladly accept all patches after a quick code review. Suggest new functionality You can suggest areas where the objects are not ideally written and could be done better. The best way is to find the main developer of the module (each module was written principally by one person, except for Seq.pm). Talk to him or her and suggest changes. Make your own objects If you can make a useful object we will happily include it into the core. Probably you will want to read a lot of the documentation in Bio::Root::Root and talk to people on the BioPerl mailing list, bioperl-l@bioperl.org . Writing documentation We appreciate good documentation. It's what tells the world what's in BioPerl, it's what instructs the user, it's what describes the rationale and inner workings of the package. Feel free to contribute. ACKNOWLEDGEMENTS For a more detailed history of the BioPerl project, we recommend the History of BioPerl: http://bioperl.org/articles/History_of_BioPerl.html FEEDBACK Mailing lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion https://bioperl.org/Support.html - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues AUTHOR See the individual modules for their authors. COPYRIGHT This software is copyright (c) by many people (see the individual modules for their copyright holders). This software is available under the same terms as the perl 5 programming language system itself. Module Install Instructions To install BioPerl, copy and paste the appropriate command in to your terminal. cpanm cpanm BioPerl CPAN shell perl -MCPAN -e shell install BioPerl For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-bioperl --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-bioperl 1.6.924 1 +---------------------- +file name : perl-bioperl-1.6.924-1.tar.bz2 +name : perl-bioperl +version : 1.6.924 +build : 1 +build number: 1 +size : 2.2 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.6.924-1.tar.bz2 +md5 : 5dd92ce79d36a65fb4a38d40dc702158 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-bioperl 1.6.924 2 +---------------------- +file name : perl-bioperl-1.6.924-2.tar.bz2 +name : perl-bioperl +version : 1.6.924 +build : 2 +build number: 2 +size : 2.2 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.6.924-2.tar.bz2 +md5 : 65eeecdacccfbcf45fb11ce145430deb +dependencies: + - libgcc + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-bioperl 1.6.924 3 +---------------------- +file name : perl-bioperl-1.6.924-3.tar.bz2 +name : perl-bioperl +version : 1.6.924 +build : 3 +build number: 3 +size : 2.2 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.6.924-3.tar.bz2 +md5 : c4ef2977953496ecd9439ae9777ea5c0 +dependencies: + - libgcc + - perl-threaded + - perl-yaml + - perl >=5.22.0,<5.23.0 + + +perl-bioperl 1.6.924 4 +---------------------- +file name : perl-bioperl-1.6.924-4.tar.bz2 +name : perl-bioperl +version : 1.6.924 +build : 4 +build number: 4 +size : 2.2 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.6.924-4.tar.bz2 +md5 : 5bdd6d5a398635a92afca1d4a0bd69ed +dependencies: + - libgcc + - perl-threaded + - perl-yaml + - perl >=5.22.0,<5.23.0 + + +perl-bioperl 1.6.924 6 +---------------------- +file name : perl-bioperl-1.6.924-6.tar.bz2 +name : perl-bioperl +version : 1.6.924 +build : 6 +build number: 6 +size : 6 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.6.924-6.tar.bz2 +md5 : d937cd094c85752fbcba6c6ba07b3f0f +dependencies: + - perl-bio-asn1-entrezgene + - perl-bio-featureio + - perl-bio-samtools + - perl-bioperl-core + - perl-bioperl-run + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-bioperl 1.6.924 pl5.22.0_0 +------------------------------- +file name : perl-bioperl-1.6.924-pl5.22.0_0.tar.bz2 +name : perl-bioperl +version : 1.6.924 +build : pl5.22.0_0 +build number: 0 +size : 2.2 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.6.924-pl5.22.0_0.tar.bz2 +md5 : 360e206f8554865d017f1b95105b3479 +dependencies: + - perl 5.22.0* + + +perl-bioperl 1.6.924 pl5.22.0_5 +------------------------------- +file name : perl-bioperl-1.6.924-pl5.22.0_5.tar.bz2 +name : perl-bioperl +version : 1.6.924 +build : pl5.22.0_5 +build number: 5 +size : 6 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.6.924-pl5.22.0_5.tar.bz2 +md5 : 4994b51ab6150d940952b078237460a9 +dependencies: + - perl 5.22.0* + - perl-bio-asn1-entrezgene + - perl-bio-featureio + - perl-bio-samtools + - perl-bioperl-core + - perl-bioperl-run + + +perl-bioperl 1.6.924 pl5.22.0_7 +------------------------------- +file name : perl-bioperl-1.6.924-pl5.22.0_7.tar.bz2 +name : perl-bioperl +version : 1.6.924 +build : pl5.22.0_7 +build number: 7 +size : 9 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.6.924-pl5.22.0_7.tar.bz2 +md5 : 39f199a2558231f502c3cc332407cb97 +dependencies: + - perl 5.22.0* + - perl-bioperl-core ==1.6.924 + - perl-bioperl-run + + +perl-bioperl 1.7.2 pl526_10 +--------------------------- +file name : perl-bioperl-1.7.2-pl526_10.tar.bz2 +name : perl-bioperl +version : 1.7.2 +build : pl526_10 +build number: 10 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.7.2-pl526_10.tar.bz2 +md5 : be14c93b15ee4f84b5cbdd25ebb757d0 +timestamp : 2019-05-16 15:03:59 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-bio-asn1-entrezgene + - perl-bio-coordinate + - perl-bio-featureio + - perl-bio-samtools + - perl-bio-tools-phylo-paml + - perl-bio-tools-run-alignment-clustalw + - perl-bio-tools-run-alignment-tcoffee + - perl-bioperl-core 1.007002 + - perl-bioperl-run + + +perl-bioperl 1.7.2 pl526_11 +--------------------------- +file name : perl-bioperl-1.7.2-pl526_11.tar.bz2 +name : perl-bioperl +version : 1.7.2 +build : pl526_11 +build number: 11 +size : 13 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-bioperl-1.7.2-pl526_11.tar.bz2 +md5 : 2fe21b69efb39401d28f27f398f7d26e +timestamp : 2019-10-28 11:09:06 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-bio-asn1-entrezgene + - perl-bio-coordinate + - perl-bio-featureio + - perl-bio-samtools + - perl-bio-tools-phylo-paml + - perl-bio-tools-run-alignment-clustalw + - perl-bio-tools-run-alignment-tcoffee + - perl-bioperl-core 1.007002 + - perl-bioperl-run + + +perl-bioperl 1.7.2 pl526_8 +-------------------------- +file name : perl-bioperl-1.7.2-pl526_8.tar.bz2 +name : perl-bioperl +version : 1.7.2 +build : pl526_8 +build number: 8 +size : 11 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.7.2-pl526_8.tar.bz2 +md5 : 6cc0ed7cb1f1b53a17f85e31f58d2f9d +timestamp : 2018-08-09 16:08:14 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-bio-asn1-entrezgene + - perl-bio-coordinate + - perl-bio-featureio + - perl-bio-samtools + - perl-bio-tools-phylo-paml + - perl-bio-tools-run-alignment-clustalw + - perl-bio-tools-run-alignment-tcoffee + - perl-bioperl-core 1.7.2 + - perl-bioperl-run + + +perl-bioperl 1.7.2 pl526_9 +-------------------------- +file name : perl-bioperl-1.7.2-pl526_9.tar.bz2 +name : perl-bioperl +version : 1.7.2 +build : pl526_9 +build number: 9 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-bioperl-1.7.2-pl526_9.tar.bz2 +md5 : d5fc7c8032dba2d2de8fe650567d3450 +timestamp : 2019-03-14 00:00:31 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-bio-asn1-entrezgene + - perl-bio-coordinate + - perl-bio-featureio + - perl-bio-samtools + - perl-bio-tools-phylo-paml + - perl-bio-tools-run-alignment-clustalw + - perl-bio-tools-run-alignment-tcoffee + - perl-bioperl-core 1.7.2 + - perl-bioperl-run + + +perl-bioperl 1.7.8 hdfd78af_0 +----------------------------- +file name : perl-bioperl-1.7.8-hdfd78af_0.tar.bz2 +name : perl-bioperl +version : 1.7.8 +build : hdfd78af_0 +build number: 0 +size : 8 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-bioperl-1.7.8-hdfd78af_0.tar.bz2 +md5 : fb452a4ab4fe1a3a6682ce14ee3290e2 +timestamp : 2022-01-31 22:14:53 UTC +dependencies: + - perl + - perl-bio-asn1-entrezgene + - perl-bio-coordinate + - perl-bio-featureio + - perl-bio-samtools + - perl-bio-tools-phylo-paml + - perl-bio-tools-run-alignment-clustalw + - perl-bio-tools-run-alignment-tcoffee + - perl-bioperl-core 1.7.8.* + - perl-bioperl-run + + +perl-bioperl 1.7.8 hdfd78af_1 +----------------------------- +file name : perl-bioperl-1.7.8-hdfd78af_1.tar.bz2 +name : perl-bioperl +version : 1.7.8 +build : hdfd78af_1 +build number: 1 +size : 6 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-bioperl-1.7.8-hdfd78af_1.tar.bz2 +md5 : a693939710e572d0f85f6058b534e319 +timestamp : 2022-03-21 23:21:34 UTC +dependencies: + - perl + - perl-bio-asn1-entrezgene + - perl-bio-coordinate + - perl-bio-featureio + - perl-bio-samtools + - perl-bio-searchio-hmmer + - perl-bio-tools-phylo-paml + - perl-bio-tools-run-alignment-clustalw + - perl-bio-tools-run-alignment-tcoffee + - perl-bioperl-core 1.7.8.* + - perl-bioperl-run diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-business-isbn.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-business-isbn.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1959e5ac4fdd78b67ae9c99eb39ed972cd2d7862 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-business-isbn.manual_bundle.txt @@ -0,0 +1,139 @@ +# Tool: perl-business-isbn +software_name: perl-business-isbn +tier: T1 +domain: t1_backfill_overall +downloads: 479172 +summary: work with International Standard Book Numbers +description: work with International Standard Book Numbers +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-business-isbn-data >=20191107 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/briandfoy/business-isbn +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/briandfoy/business-isbn +GitHub - briandfoy/business-isbn: (Perl) Deal with ISBNs · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} briandfoy / business-isbn Public Notifications You must be signed in to change notification settings Fork 5 Star 3 Code Issues 0 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights briandfoy/business-isbn master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 412 Commits 412 Commits .circleci .circleci .github/ workflows .github/ workflows dropbox dropbox examples examples lib/ Business lib/ Business scripts scripts t t xt xt .appveyor.yml .appveyor.yml .gitattributes .gitattributes .gitignore .gitignore .releaserc .releaserc Changes Changes INSTALL.SKIP INSTALL.SKIP LICENSE LICENSE MANIFEST MANIFEST MANIFEST.SKIP MANIFEST.SKIP Makefile.PL Makefile.PL README.pod README.pod SECURITY.md SECURITY.md bad-isbn13s.txt bad-isbn13s.txt bad-isbns.txt bad-isbns.txt isbn13s.txt isbn13s.txt isbns.txt isbns.txt objtest.pl objtest.pl select_tabledata.pl select_tabledata.pl stringtest.pl stringtest.pl View all files Repository files navigation README License Security The Business::ISBN module This is the README for the Business::ISBN Perl module, which handles International Standard Book Numbers. You're probably looking at this because you don't know where else to find what you're looking for. Read this once and you might never have to read one again for any Perl module. Documentation To read about Business::ISBN , look at the embedded documentation in the module itself. Inside the distribution, you can format it with perldoc : % perldoc lib/Business/ISBN.pm If you have already installed the module, you can specify the module name instead of the file location: % perldoc Business::ISBN You can read the documentation and inspect the meta data at MetaCPAN . The standard module documentation has example uses in the SYNOPSIS section, but you can also look in the examples/ directory (if it's there), or look at the test files in t/ . Installation You can install this module with a CPAN client, which will resolve and install the dependencies: % cpan Business::ISBN % cpanm Business::ISBN You can also install directly from the distribution directory, which will also install the dependencies: % cpan . % cpanm . You could install just this module manually: % perl Makefile.PL % make % make test % make install You probably don't want to do that unless you're fiddling with the module and only want to run the tests without installing anything. Source location The meta data, such as the source repository and bug tracker, is in Makefile.PL or the META.* files it creates. You can find that on those CPAN web interfaces, but you can also look at files directly in the source repository: https://github.com/briandfoy/business-isbn If you find a problem, file a ticket in the issue tracker . There are also backup repositories hosted on other services. These reflect the state of the main repo and exist only for redundancy: https://bitbucket.com/briandfoy/business-isbn https://codeberg.org/briandfoy/business-isbn https://gitlab.com/briandfoy/business-isbn GitHub Attestations This distribution now uses GitHub Attestations , which allow you to verify that the archive file you have was made from the official repo. You need a GitHub account and the gh tool . # download the distro file from GitHub, MetaCPAN, or a CPAN mirror $ gh auth login ...follow instructions... $ gh attestation verify Business-ISBN-1.23.tar.gz --owner briandfoy Getting help Although I'm happy to hear from module users in private email, that's the best way for me to forget to do something. Besides the issue trackers, you can find help at Perlmonks or Stackoverflow , both of which have many competent Perlers who can answer your question, almost in real time. They might not know the particulars of this module, but they can help you diagnose your problem. You might like to read brian's Guide to Solving Any Perl Problem . Copyright and License You should have received a LICENSE file, but the license is also noted in the module files. About the only thing you can't do is pretend that you wrote code that you didn't. Good luck! Enjoy, brian d foy, briandfoy@pobox.com About (Perl) Deal with ISBNs Topics books perl isbn perl-module Resources Readme License View license Security policy Security policy Uh oh! There was an error while loading. Please reload this page . Activity Stars 3 stars Watchers 3 watching Forks 5 forks Report repository Releases 6 Business-ISBN-3.013 Latest Mar 11, 2026 + 5 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-business-isbn --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-business-isbn 3.004 pl526_0 +-------------------------------- +file name : perl-business-isbn-3.004-pl526_0.tar.bz2 +name : perl-business-isbn +version : 3.004 +build : pl526_0 +build number: 0 +size : 15 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-business-isbn-3.004-pl526_0.tar.bz2 +md5 : 982a9766a06c69ce335cbd8567e98e7a +timestamp : 2018-08-24 03:14:45 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-business-isbn-data + + +perl-business-isbn 3.004 pl5321hdfd78af_1 +----------------------------------------- +file name : perl-business-isbn-3.004-pl5321hdfd78af_1.tar.bz2 +name : perl-business-isbn +version : 3.004 +build : pl5321hdfd78af_1 +build number: 1 +size : 17 KB +license : artistic_2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-business-isbn-3.004-pl5321hdfd78af_1.tar.bz2 +md5 : 9e872137d4d608b5f23917d88443b79d +timestamp : 2022-01-19 12:22:46 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-business-isbn-data + + +perl-business-isbn 3.007 pl5321hd8ed1ab_0 +----------------------------------------- +file name : perl-business-isbn-3.007-pl5321hd8ed1ab_0.tar.bz2 +name : perl-business-isbn +version : 3.007 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 18 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-3.007-pl5321hd8ed1ab_0.tar.bz2 +md5 : a7a3d7614e1a73b8d9c20030651d6006 +timestamp : 2022-10-10 14:10:30 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-business-isbn-data >=20191107 + + +perl-business-isbn 3.007 pl5321hdfd78af_0 +----------------------------------------- +file name : perl-business-isbn-3.007-pl5321hdfd78af_0.tar.bz2 +name : perl-business-isbn +version : 3.007 +build : pl5321hdfd78af_0 +build number: 0 +size : 18 KB +license : artistic_2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-business-isbn-3.007-pl5321hdfd78af_0.tar.bz2 +md5 : 3cdaa3f73497365e08346443d81dac81 +timestamp : 2022-02-14 23:40:32 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-business-isbn-data >=20191107 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-cgi.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-cgi.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6e9cff604f5f1901928fbdf79c6e45850557484 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-cgi.manual_bundle.txt @@ -0,0 +1,533 @@ +# Tool: perl-cgi +software_name: perl-cgi +tier: T1 +domain: t1_backfill_overall +downloads: 300748 +summary: A generic file fetching mechanism. +description: A generic file fetching mechanism. +dependencies: libgcc >=13, perl >=5.32.1,<5.33.0a0 *_perl5, perl-base, perl-carp, perl-encode, perl-exporter, perl-file-temp, perl-html-parser >=3.83,<4.0a0, perl-parent, perl-test-nowarnings 1.06.*, perl-uri +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/distribution/CGI/lib/CGI.pod +doc_url: https://metacpan.org/pod/distribution/CGI/lib/CGI.pod +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/distribution/CGI/lib/CGI.pod +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +### https://metacpan.org/pod/distribution/CGI/lib/CGI.pod +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-cgi --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-cgi 4.22 1 +--------------- +file name : perl-cgi-4.22-1.tar.bz2 +name : perl-cgi +version : 4.22 +build : 1 +build number: 1 +size : 162 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.22-1.tar.bz2 +md5 : 9345c13fdb67be29953f39e8588702bc +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-cgi 4.22 2 +--------------- +file name : perl-cgi-4.22-2.tar.bz2 +name : perl-cgi +version : 4.22 +build : 2 +build number: 2 +size : 162 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.22-2.tar.bz2 +md5 : c25050bcd597a0fee322f497011cad1d +dependencies: + - libgcc + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-cgi 4.22 3 +--------------- +file name : perl-cgi-4.22-3.tar.bz2 +name : perl-cgi +version : 4.22 +build : 3 +build number: 3 +size : 162 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.22-3.tar.bz2 +md5 : da8a3a015df22005ba06ee23a5312342 +dependencies: + - libgcc + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-cgi 4.22 pl5.22.0_0 +------------------------ +file name : perl-cgi-4.22-pl5.22.0_0.tar.bz2 +name : perl-cgi +version : 4.22 +build : pl5.22.0_0 +build number: 0 +size : 161 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.22-pl5.22.0_0.tar.bz2 +md5 : 907cc1126cafd3cc9c3042726216c939 +dependencies: + - perl 5.22.0* + + +perl-cgi 4.22 pl526h470a237_4 +----------------------------- +file name : perl-cgi-4.22-pl526h470a237_4.tar.bz2 +name : perl-cgi +version : 4.22 +build : pl526h470a237_4 +build number: 4 +size : 225 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.22-pl526h470a237_4.tar.bz2 +md5 : 1e6ea92923d2d6d7edee8b9e9401b1f1 +timestamp : 2018-07-07 23:15:49 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.27.0a0 + + +perl-cgi 4.40 pl526h14c3975_1 +----------------------------- +file name : perl-cgi-4.40-pl526h14c3975_1.tar.bz2 +name : perl-cgi +version : 4.40 +build : pl526h14c3975_1 +build number: 1 +size : 113 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.40-pl526h14c3975_1.tar.bz2 +md5 : 49c6a7515902d078e393ea00ddc5f9dd +timestamp : 2019-05-02 23:50:23 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + + +perl-cgi 4.40 pl526h14c3975_2 +----------------------------- +file name : perl-cgi-4.40-pl526h14c3975_2.tar.bz2 +name : perl-cgi +version : 4.40 +build : pl526h14c3975_2 +build number: 2 +size : 113 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.40-pl526h14c3975_2.tar.bz2 +md5 : 57f3be3548150d22a06a9e5b40cb108a +timestamp : 2019-05-03 21:17:11 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + + +perl-cgi 4.40 pl526h470a237_0 +----------------------------- +file name : perl-cgi-4.40-pl526h470a237_0.tar.bz2 +name : perl-cgi +version : 4.40 +build : pl526h470a237_0 +build number: 0 +size : 227 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.40-pl526h470a237_0.tar.bz2 +md5 : 881b76bf423983ca57105f010a969735 +timestamp : 2018-11-11 05:57:12 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + + +perl-cgi 4.43 pl526h14c3975_0 +----------------------------- +file name : perl-cgi-4.43-pl526h14c3975_0.tar.bz2 +name : perl-cgi +version : 4.43 +build : pl526h14c3975_0 +build number: 0 +size : 113 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.43-pl526h14c3975_0.tar.bz2 +md5 : 4f9c0aee6401a093447f28ea7525b86a +timestamp : 2019-05-11 13:09:25 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + + +perl-cgi 4.44 pl526h14c3975_0 +----------------------------- +file name : perl-cgi-4.44-pl526h14c3975_0.tar.bz2 +name : perl-cgi +version : 4.44 +build : pl526h14c3975_0 +build number: 0 +size : 113 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.44-pl526h14c3975_0.tar.bz2 +md5 : b4262425b694a6af8d18d8898bfbebcc +timestamp : 2019-06-04 06:14:41 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + + +perl-cgi 4.44 pl526h14c3975_1 +----------------------------- +file name : perl-cgi-4.44-pl526h14c3975_1.tar.bz2 +name : perl-cgi +version : 4.44 +build : pl526h14c3975_1 +build number: 1 +size : 116 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.44-pl526h14c3975_1.tar.bz2 +md5 : abf86df04595969e49c5ac3f295e2a20 +timestamp : 2019-06-05 17:38:15 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + + +perl-cgi 4.44 pl5321h779adbc_2 +------------------------------ +file name : perl-cgi-4.44-pl5321h779adbc_2.tar.bz2 +name : perl-cgi +version : 4.44 +build : pl5321h779adbc_2 +build number: 2 +size : 118 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.44-pl5321h779adbc_2.tar.bz2 +md5 : 3a7cde6a0cc78fa8afc6e1a055b80e96 +timestamp : 2022-01-21 08:50:16 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + + +perl-cgi 4.54 pl5321h779adbc_0 +------------------------------ +file name : perl-cgi-4.54-pl5321h779adbc_0.tar.bz2 +name : perl-cgi +version : 4.54 +build : pl5321h779adbc_0 +build number: 0 +size : 118 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.54-pl5321h779adbc_0.tar.bz2 +md5 : c40c59c7ffda61291f22b4cf4b04d10c +timestamp : 2022-02-09 14:07:28 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + + +perl-cgi 4.54 pl5321hec16e2b_1 +------------------------------ +file name : perl-cgi-4.54-pl5321hec16e2b_1.tar.bz2 +name : perl-cgi +version : 4.54 +build : pl5321hec16e2b_1 +build number: 1 +size : 118 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.54-pl5321hec16e2b_1.tar.bz2 +md5 : 4e8bc1390b8bad947b9ec042b228a29a +timestamp : 2022-02-24 14:09:59 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + + +perl-cgi 4.55 pl5321hec16e2b_0 +------------------------------ +file name : perl-cgi-4.55-pl5321hec16e2b_0.tar.bz2 +name : perl-cgi +version : 4.55 +build : pl5321hec16e2b_0 +build number: 0 +size : 119 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.55-pl5321hec16e2b_0.tar.bz2 +md5 : 427993d3ff1288c1fb9b6e27ae995b13 +timestamp : 2023-01-03 08:32:51 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + - perl-test-nowarnings 1.06.* + + +perl-cgi 4.56 pl5321h031d066_1 +------------------------------ +file name : perl-cgi-4.56-pl5321h031d066_1.tar.bz2 +name : perl-cgi +version : 4.56 +build : pl5321h031d066_1 +build number: 1 +size : 120 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.56-pl5321h031d066_1.tar.bz2 +md5 : 411c24e86d674eda1d99237f7a038262 +timestamp : 2023-05-15 09:22:31 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + - perl-test-nowarnings 1.06.* + + +perl-cgi 4.56 pl5321h7b50bb2_2 +------------------------------ +file name : perl-cgi-4.56-pl5321h7b50bb2_2.tar.bz2 +name : perl-cgi +version : 4.56 +build : pl5321h7b50bb2_2 +build number: 2 +size : 120 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.56-pl5321h7b50bb2_2.tar.bz2 +md5 : 942c138c06720777cdba2a52c2edadb9 +timestamp : 2024-12-16 19:23:56 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + - perl-test-nowarnings 1.06.* + + +perl-cgi 4.56 pl5321hec16e2b_0 +------------------------------ +file name : perl-cgi-4.56-pl5321hec16e2b_0.tar.bz2 +name : perl-cgi +version : 4.56 +build : pl5321hec16e2b_0 +build number: 0 +size : 119 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.56-pl5321hec16e2b_0.tar.bz2 +md5 : 77f265775e65db37598f9df00fe95c12 +timestamp : 2023-03-03 13:45:22 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser + - perl-parent + - perl-test-nowarnings 1.06.* + + +perl-cgi 4.67 pl5321h7b50bb2_0 +------------------------------ +file name : perl-cgi-4.67-pl5321h7b50bb2_0.tar.bz2 +name : perl-cgi +version : 4.67 +build : pl5321h7b50bb2_0 +build number: 0 +size : 120 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.67-pl5321h7b50bb2_0.tar.bz2 +md5 : ca31b3ea6395eb93aac95fd0879f7d51 +timestamp : 2025-02-05 06:58:35 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser >=3.83,<4.0a0 + - perl-parent + - perl-test-nowarnings 1.06.* + - perl-uri + + +perl-cgi 4.67 pl5321h7b50bb2_1 +------------------------------ +file name : perl-cgi-4.67-pl5321h7b50bb2_1.tar.bz2 +name : perl-cgi +version : 4.67 +build : pl5321h7b50bb2_1 +build number: 1 +size : 120 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.67-pl5321h7b50bb2_1.tar.bz2 +md5 : a253b43c98ce236f5d391265e3b33ba6 +timestamp : 2025-03-10 09:50:13 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-base + - perl-carp + - perl-encode + - perl-exporter + - perl-file-temp + - perl-html-parser >=3.83,<4.0a0 + - perl-parent + - perl-test-nowarnings 1.06.* + - diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-class-load.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-class-load.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b9fed714ad95792a27619dbe2c1a7362aa89f2b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-class-load.manual_bundle.txt @@ -0,0 +1,229 @@ +# Tool: perl-class-load +software_name: perl-class-load +tier: T1 +domain: t1_backfill_overall +downloads: 248680 +summary: A working (require "Class::Name") and more +description: A working (require "Class::Name") and more +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-base, perl-carp, perl-data-optlist, perl-exporter, perl-module-implementation, perl-module-runtime, perl-package-stash, perl-try-tiny +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/moose/Class-Load +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/moose/Class-Load +GitHub - moose/Class-Load: A working (require "Class::Name") and more · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} moose / Class-Load Public Notifications You must be signed in to change notification settings Fork 4 Star 1 Code Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Pull requests Actions Projects Wiki Security and quality Insights moose/Class-Load master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 231 Commits 231 Commits lib/ Class lib/ Class t t .gitignore .gitignore .mailmap .mailmap .travis.yml .travis.yml CONTRIBUTING CONTRIBUTING Changes Changes INSTALL INSTALL LICENSE LICENSE README.pod README.pod dist.ini dist.ini View all files Repository files navigation README Contributing License NAME Class::Load - A working (require "Class::Name") and more VERSION version 0.25 SYNOPSIS use Class::Load ':all'; try_load_class('Class::Name') or plan skip_all => "Class::Name required to run these tests"; load_class('Class::Name'); is_class_loaded('Class::Name'); my $baseclass = load_optional_class('Class::Name::MightExist') ? 'Class::Name::MightExist' : 'Class::Name::Default'; DESCRIPTION require EXPR only accepts Class/Name.pm style module names, not Class::Name . How frustrating! For that, we provide load_class 'Class::Name' . It's often useful to test whether a module can be loaded, instead of throwing an error when it's not available. For that, we provide try_load_class 'Class::Name' . Finally, sometimes we need to know whether a particular class has been loaded. Asking %INC is an option, but that will miss inner packages and any class for which the filename does not correspond to the package name. For that, we provide is_class_loaded 'Class::Name' . FUNCTIONS load_class Class::Name, \%options load_class will load Class::Name or throw an error, much like require . If Class::Name is already loaded (checked with is_class_loaded ) then it will not try to load the class. This is useful when you have inner packages which require does not check. The %options hash currently accepts one key, -version . If you specify a version, then this subroutine will call Class::Name->VERSION( $options{-version} ) internally, which will throw an error if the class's version is not equal to or greater than the version you requested. This method will return the name of the class on success. try_load_class Class::Name, \%options -> (0|1, error message) Returns 1 if the class was loaded, 0 if it was not. If the class was not loaded, the error will be returned as a second return value in list context. Again, if Class::Name is already loaded (checked with is_class_loaded ) then it will not try to load the class. This is useful when you have inner packages which require does not check. Like load_class , you can pass a -version in %options . If the version is not sufficient, then this subroutine will return false. is_class_loaded Class::Name, \%options -> 0|1 This uses a number of heuristics to determine if the class Class::Name is loaded. There heuristics were taken from Class::MOP 's old pure-perl implementation. Like load_class , you can pass a -version in %options . If the version is not sufficient, then this subroutine will return false. load_first_existing_class Class::Name, \%options, ... This attempts to load the first loadable class in the list of classes given. Each class name can be followed by an options hash reference. If any one of the classes loads and passes the optional version check, that class name will be returned. If none of the classes can be loaded (or none pass their version check), then an error will be thrown. If, when attempting to load a class, it fails to load because of a syntax error, then an error will be thrown immediately. load_optional_class Class::Name, \%options -> 0|1 load_optional_class is a lot like try_load_class , but also a lot like load_class . If the class exists, and it works, then it will return 1. If you specify a version in %options , then the version check must succeed or it will return 0. If the class doesn't exist, and it appears to not exist on disk either, it will return 0. If the class exists on disk, but loading from disk results in an error (e.g.: a syntax error), then it will croak with that error. This is useful for using if you want a fallback module system, i.e.: my $class = load_optional_class($foo) ? $foo : $default; That way, if $foo does exist, but can't be loaded due to error, you won't get the behaviour of it simply not existing. CAVEATS Because of some of the heuristics that this module uses to infer whether a module has been loaded, some false positives may occur in is_class_loaded checks (which are also performed internally in other interfaces) -- if a class has started to be loaded but then dies, it may appear that it has already been loaded, which can cause other things to make the wrong decision. Module::Runtime doesn't have this issue, but it also doesn't do some things that this module does -- for example gracefully handle packages that have been defined inline in the same file as another package. SEE ALSO http://blog.fox.geek.nz/2010/11/searching-design-spec-for-ultimate.html This blog post is a good overview of the current state of the existing modules for loading other modules in various ways. http://blog.fox.geek.nz/2010/11/handling-optional-requirements-with.html This blog post describes how to handle optional modules with Class::Load . http://d.hatena.ne.jp/tokuhirom/20110202/1296598578 This Japanese blog post describes why DBIx::Skinny now uses Class::Load over its competitors. Moose , Jifty , Prophet , etc This module was designed to be used anywhere you have if (eval "require $module"; 1) , which occurs in many large projects. Module::Runtime A leaner approach to loading modules SUPPORT Bugs may be submitted through the RT bug tracker (or bug-Class-Load@rt.cpan.org ). There is also a mailing list available for users of this distribution, at http://lists.perl.org/list/moose.html . There is also an irc channel available for users of this distribution, at #moose on irc.perl.org . AUTHOR Shawn M Moore <sartak at bestpractical.com> CONTRIBUTORS Dave Rolsky <autarch@urth.org> Karen Etheridge <ether@cpan.org> Shawn Moore <sartak@bestpractical.com> Jesse Luehrs <doy@tozt.net> Kent Fredric <kentfredric@gmail.com> Paul Howarth <paul@city-fan.org> Olivier Mengué <dolmen@cpan.org> Caleb Cushing <xenoterracide@gmail.com> COPYRIGHT AND LICENSE This software is copyright (c) 2008 by Shawn M Moore. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. About A working (require "Class::Name") and more metacpan.org/release/Class-Load/ Resources Readme License View license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1 star Watchers 8 watching Forks 4 forks Report repository Releases 21 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-class-load --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-class-load 0.23 pl5.22.0_0 +------------------------------- +file name : perl-class-load-0.23-pl5.22.0_0.tar.bz2 +name : perl-class-load +version : 0.23 +build : pl5.22.0_0 +build number: 0 +size : 9 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-class-load-0.23-pl5.22.0_0.tar.bz2 +md5 : 720b1a8cdfb6f175d54c2c5115aefc61 +dependencies: + - perl 5.22.0* + - perl-apache-test + - perl-data-optlist + - perl-module-implementation + - perl-module-runtime + - perl-package-stash + - perl-scalar-list-utils + - perl-try-tiny + + +perl-class-load 0.23 pl526h2d50403_1 +------------------------------------ +file name : perl-class-load-0.23-pl526h2d50403_1.tar.bz2 +name : perl-class-load +version : 0.23 +build : pl526h2d50403_1 +build number: 1 +size : 11 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-class-load-0.23-pl526h2d50403_1.tar.bz2 +md5 : 1542a8e207b94a170832059b8dc65d5e +timestamp : 2018-07-19 11:06:56 UTC +dependencies: + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.27.0a0 + - perl-apache-test + - perl-app-cpanminus + - perl-data-optlist + - perl-module-implementation + - perl-module-runtime + - perl-package-stash + - perl-scalar-list-utils + - perl-try-tiny + + +perl-class-load 0.25 pl526_0 +---------------------------- +file name : perl-class-load-0.25-pl526_0.tar.bz2 +name : perl-class-load +version : 0.25 +build : pl526_0 +build number: 0 +size : 12 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-class-load-0.25-pl526_0.tar.bz2 +md5 : 03c73103dc5e4f7daabd6bb0931193b6 +timestamp : 2018-08-17 21:52:21 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-carp + - perl-data-optlist + - perl-exporter + - perl-module-implementation + - perl-module-runtime + - perl-package-stash + - perl-try-tiny + + +perl-class-load 0.25 pl5321ha770c72_0 +------------------------------------- +file name : perl-class-load-0.25-pl5321ha770c72_0.conda +name : perl-class-load +version : 0.25 +build : pl5321ha770c72_0 +build number: 0 +size : 21 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-class-load-0.25-pl5321ha770c72_0.conda +md5 : f05ed9d80da4a1db91f281072d00a276 +timestamp : 2023-01-23 13:20:58 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-data-optlist 0.113.* + - perl-module-implementation 0.09.* + - perl-module-runtime 0.016.* + - perl-package-stash 0.40.* + - perl-try-tiny 0.31.* + + +perl-class-load 0.25 pl5321ha770c72_1 +------------------------------------- +file name : perl-class-load-0.25-pl5321ha770c72_1.conda +name : perl-class-load +version : 0.25 +build : pl5321ha770c72_1 +build number: 1 +size : 21 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-class-load-0.25-pl5321ha770c72_1.conda +md5 : 3b395c1ceca87d3052caad8c85b3faba +timestamp : 2025-02-28 09:40:06 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-data-optlist 0.114.* + - perl-module-implementation 0.09.* + - perl-module-runtime 0.016.* + - perl-package-stash 0.40.* + - perl-try-tiny 0.31.* + + +perl-class-load 0.25 pl5321ha770c72_2 +------------------------------------- +file name : perl-class-load-0.25-pl5321ha770c72_2.conda +name : perl-class-load +version : 0.25 +build : pl5321ha770c72_2 +build number: 2 +size : 21 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-class-load-0.25-pl5321ha770c72_2.conda +md5 : 0a6d6182c3d6379e1810b4632edd8000 +timestamp : 2025-04-25 19:56:34 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-data-optlist 0.114.* + - perl-module-implementation 0.09.* + - perl-module-runtime 0.016.* + - perl-package-stash 0.40.* + - perl-try-tiny 0.31.* + + +perl-class-load 0.25 pl5321hdfd78af_1 +------------------------------------- +file name : perl-class-load-0.25-pl5321hdfd78af_1.tar.bz2 +name : perl-class-load +version : 0.25 +build : pl5321hdfd78af_1 +build number: 1 +size : 14 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-class-load-0.25-pl5321hdfd78af_1.tar.bz2 +md5 : 1aa9bd26f4856a406b48a008e2e72630 +timestamp : 2022-01-24 22:43:11 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-base + - perl-carp + - perl-data-optlist + - perl-exporter + - perl-module-implementation + - perl-module-runtime + - perl-package-stash + - perl-try-tiny diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-constant.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-constant.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1aa1e638e1365f484be6f2bbe49ae20d47084b8d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-constant.manual_bundle.txt @@ -0,0 +1,130 @@ +# Tool: perl-constant +software_name: perl-constant +tier: T1 +domain: t1_backfill_overall +downloads: 577226 +summary: +description: +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-constant --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-constant 1.33 pl5.22.0_0 +----------------------------- +file name : perl-constant-1.33-pl5.22.0_0.tar.bz2 +name : perl-constant +version : 1.33 +build : pl5.22.0_0 +build number: 0 +size : 8 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-constant-1.33-pl5.22.0_0.tar.bz2 +md5 : 4e514918988fc65afc529d984a2d3e05 +dependencies: + - perl 5.22.0* + + +perl-constant 1.33 pl526_1 +-------------------------- +file name : perl-constant-1.33-pl526_1.tar.bz2 +name : perl-constant +version : 1.33 +build : pl526_1 +build number: 1 +size : 10 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-constant-1.33-pl526_1.tar.bz2 +md5 : 5037eea2bb962fab567d2d5ea43bc81a +timestamp : 2018-07-08 18:40:32 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-constant 1.33 pl5321hd8ed1ab_0 +----------------------------------- +file name : perl-constant-1.33-pl5321hd8ed1ab_0.tar.bz2 +name : perl-constant +version : 1.33 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 15 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-constant-1.33-pl5321hd8ed1ab_0.tar.bz2 +md5 : 7f9fc9cfa08a3fe36ffcff820c65c3ac +timestamp : 2021-11-11 15:38:27 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-constant 1.33 pl5321hdfd78af_2 +----------------------------------- +file name : perl-constant-1.33-pl5321hdfd78af_2.tar.bz2 +name : perl-constant +version : 1.33 +build : pl5321hdfd78af_2 +build number: 2 +size : 12 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-constant-1.33-pl5321hdfd78af_2.tar.bz2 +md5 : bda05b652c9a6d069ccf520149e1c171 +timestamp : 2022-01-17 23:02:01 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-cpan-meta-requirements.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-cpan-meta-requirements.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f808535d9c86e4c55b1f74feabffb0903bd31b0 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-cpan-meta-requirements.manual_bundle.txt @@ -0,0 +1,118 @@ +# Tool: perl-cpan-meta-requirements +software_name: perl-cpan-meta-requirements +tier: T1 +domain: t1_backfill_overall +downloads: 147593 +summary: A set of version requirements for a CPAN dist. +description: A set of version requirements for a CPAN dist. +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-carp, perl-version +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/Perl-Toolchain-Gang/CPAN-Meta-Requirements +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/Perl-Toolchain-Gang/CPAN-Meta-Requirements +GitHub - Perl-Toolchain-Gang/CPAN-Meta-Requirements: a set of version requirements for a CPAN dist · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Perl-Toolchain-Gang / CPAN-Meta-Requirements Public Notifications You must be signed in to change notification settings Fork 15 Star 5 Code Issues 5 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights Perl-Toolchain-Gang/CPAN-Meta-Requirements main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 160 Commits 160 Commits .github/ workflows .github/ workflows lib/ CPAN/ Meta lib/ CPAN/ Meta t t .gitattributes .gitattributes .gitignore .gitignore .mailmap .mailmap CONTRIBUTING.mkdn CONTRIBUTING.mkdn Changes Changes Makefile.PL Makefile.PL README.mkdn README.mkdn dist.ini dist.ini perlcritic.rc perlcritic.rc View all files Repository files navigation README Contributing HOW TO CONTRIBUTE Thank you for considering contributing to this distribution. This file contains instructions that will help you work with the source code. The distribution is managed with Dist::Zilla. This means than many of the usual files you might expect are not in the repository, but are generated at release time, as is much of the documentation. Some generated files are kept in the repository as a convenience (e.g. Makefile.PL or cpanfile). Generally, you do not need Dist::Zilla to contribute patches . You do need Dist::Zilla to create a tarball. See below for guidance. Getting dependencies If you have App::cpanminus 1.6 or later installed, you can use cpanm to satisfy dependencies like this: $ cpanm --installdeps . Otherwise, look for either a Makefile.PL or cpanfile file for a list of dependencies to satisfy. Running tests You can run tests directly using the prove tool: $ prove -l $ prove -lv t/some_test_file.t For most of my distributions, prove is entirely sufficient for you to test any patches you have. I use prove for 99% of my testing during development. Code style and tidying Please try to match any existing coding style. If there is a .perltidyrc file, please install Perl::Tidy and use perltidy before submitting patches. If there is a tidyall.ini file, you can also install Code::TidyAll and run tidyall on a file or tidyall -a to tidy all files. Patching documentation Much of the documentation Pod is generated at release time. Some is generated boilerplate; other documentation is built from pseudo-POD directives in the source like C<=method> or C<=func>. If you would like to submit a documentation edit, please limit yourself to the documentation you see. If you see typos or documentation issues in the generated docs, please email or open a bug ticket instead of patching. Installing and using Dist::Zilla Dist::Zilla is a very powerful authoring tool, optimized for maintaining a large number of distributions with a high degree of automation, but it has a large dependency chain, a bit of a learning curve and requires a number of author-specific plugins. To install it from CPAN, I recommend one of the following approaches for the quickest installation: # using CPAN.pm, but bypassing non-functional pod tests $ cpan TAP::Harness::Restricted $ PERL_MM_USE_DEFAULT=1 HARNESS_CLASS=TAP::Harness::Restricted cpan Dist::Zilla # using cpanm, bypassing *all* tests $ cpanm -n Dist::Zilla In either case, it's probably going to take about 10 minutes. Go for a walk, go get a cup of your favorite beverage, take a bathroom break, or whatever. When you get back, Dist::Zilla should be ready for you. Then you need to install any plugins specific to this distribution: $ cpan `dzil authordeps` $ dzil authordeps | cpanm Once installed, here are some dzil commands you might try: $ dzil build $ dzil test $ dzil xtest You can learn more about Dist::Zilla at http://dzil.org/ About a set of version requirements for a CPAN dist Resources Readme Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 5 stars Watchers 27 watching Forks 15 forks Report repository Releases 25 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-cpan-meta-requirements --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-cpan-meta-requirements 2.140 pl526_0 +----------------------------------------- +file name : perl-cpan-meta-requirements-2.140-pl526_0.tar.bz2 +name : perl-cpan-meta-requirements +version : 2.140 +build : pl526_0 +build number: 0 +size : 12 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-cpan-meta-requirements-2.140-pl526_0.tar.bz2 +md5 : 0fc9e88c5a1675c665e1e186ea34afc9 +timestamp : 2018-08-17 22:28:44 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-carp + - perl-version + + +perl-cpan-meta-requirements 2.140 pl5321hdfd78af_1 +-------------------------------------------------- +file name : perl-cpan-meta-requirements-2.140-pl5321hdfd78af_1.tar.bz2 +name : perl-cpan-meta-requirements +version : 2.140 +build : pl5321hdfd78af_1 +build number: 1 +size : 13 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-cpan-meta-requirements-2.140-pl5321hdfd78af_1.tar.bz2 +md5 : f2dfcf0fe21adcd671df28028db5e948 +timestamp : 2022-01-20 12:43:38 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-version + + +perl-cpan-meta-requirements 2.142 pl5321hdfd78af_0 +-------------------------------------------------- +file name : perl-cpan-meta-requirements-2.142-pl5321hdfd78af_0.tar.bz2 +name : perl-cpan-meta-requirements +version : 2.142 +build : pl5321hdfd78af_0 +build number: 0 +size : 18 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-cpan-meta-requirements-2.142-pl5321hdfd78af_0.tar.bz2 +md5 : 021c0fc2720683ddd41140f09b028ce9 +timestamp : 2023-05-09 13:28:12 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-version + + +perl-cpan-meta-requirements 2.143 pl5321hdfd78af_0 +-------------------------------------------------- +file name : perl-cpan-meta-requirements-2.143-pl5321hdfd78af_0.tar.bz2 +name : perl-cpan-meta-requirements +version : 2.143 +build : pl5321hdfd78af_0 +build number: 0 +size : 18 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-cpan-meta-requirements-2.143-pl5321hdfd78af_0.tar.bz2 +md5 : 42dcfa3f6ccd74bcc3ec405c5bb7f335 +timestamp : 2023-07-07 07:29:33 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-version + + +perl-cpan-meta-requirements 2.145 pl5321hdfd78af_0 +-------------------------------------------------- +file name : perl-cpan-meta-requirements-2.145-pl5321hdfd78af_0.conda +name : perl-cpan-meta-requirements +version : 2.145 +build : pl5321hdfd78af_0 +build number: 0 +size : 19 KB +license : Perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-cpan-meta-requirements-2.145-pl5321hdfd78af_0.conda +md5 : 93ce5b22b5f897c9aac62f0031a6b154 +timestamp : 2026-03-23 22:34:10 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-version diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-data-stag.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-data-stag.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1dae5ae04c0e0d707c38254557c4b4db01c1a88c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-data-stag.manual_bundle.txt @@ -0,0 +1,132 @@ +# Tool: perl-data-stag +software_name: perl-data-stag +tier: T1 +domain: t1_backfill_overall +downloads: 185845 +summary: Structured Tags +description: Structured Tags +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-graph, perl-io-string, perl-json, perl-libxml-perl, perl-mldbm, perl-xml-libxml, perl-xml-libxslt +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-data-stag --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-data-stag 0.14 0 +--------------------- +file name : perl-data-stag-0.14-0.tar.bz2 +name : perl-data-stag +version : 0.14 +build : 0 +build number: 0 +size : 53 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-data-stag-0.14-0.tar.bz2 +md5 : c001098b32ae1a034fb3a298f3da44dd +dependencies: + - perl-graph + - perl-io-string + - perl-json + - perl-libxml-perl + - perl-mldbm + - perl-threaded + - perl-xml-libxml + - perl-xml-libxslt + - perl >=5.22.0,<5.23.0 + + +perl-data-stag 0.14 pl526_1 +--------------------------- +file name : perl-data-stag-0.14-pl526_1.tar.bz2 +name : perl-data-stag +version : 0.14 +build : pl526_1 +build number: 1 +size : 78 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-data-stag-0.14-pl526_1.tar.bz2 +md5 : 3a50f48ef514466c9288b3151df08d8a +timestamp : 2018-08-08 11:01:20 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-graph + - perl-io-string + - perl-json + - perl-libxml-perl + - perl-mldbm + - perl-xml-libxml + - perl-xml-libxslt + + +perl-data-stag 0.14 pl5321hdfd78af_2 +------------------------------------ +file name : perl-data-stag-0.14-pl5321hdfd78af_2.tar.bz2 +name : perl-data-stag +version : 0.14 +build : pl5321hdfd78af_2 +build number: 2 +size : 81 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-data-stag-0.14-pl5321hdfd78af_2.tar.bz2 +md5 : 4ad6d4c9dddc6df0653abd3539ea4416 +timestamp : 2022-01-26 07:58:14 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-graph + - perl-io-string + - perl-json + - perl-libxml-perl + - perl-mldbm + - perl-xml-libxml + - perl-xml-libxslt diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-db-file.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-db-file.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..04a06f4861ba4bacc9c6858b277b8596c9122748 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-db-file.manual_bundle.txt @@ -0,0 +1,281 @@ +# Tool: perl-db-file +software_name: perl-db-file +tier: T1 +domain: t1_backfill_overall +downloads: 244495 +summary: Perl5 access to Berkeley DB version 1.x. +description: Perl5 access to Berkeley DB version 1.x. +dependencies: libdb >=6.2.32,<6.3.0a0, libgcc-ng >=9.4.0, perl >=5.32.1,<5.33.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/Set::IntervalTree +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/Set::IntervalTree +Set::IntervalTree - Perform range-based lookups on sets of ranges - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Set-IntervalTree Module version: 0.12 10 Jun 2018 05:21:32 UTC License: perl_5 Perl: v5.6.1 Code Download ( 69.04KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (1) How to Contribute Quality Testers ( 1760 / 0 / 0 ) Testers (Magpie) Kwalitee % Coverage Bus factor: 0 Activity 24 month 6 Dependencies AutoLoader Carp Exporter XSLoader strict and 1 more warnings Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 0.12 (SLOYD on 2018-06-10) 0.10 (BENBOOTH on 2014-04-17) 0.09 (BENBOOTH on 2013-12-04) 0.08 (BENBOOTH on 2013-10-22) 0.07 (BENBOOTH on 2013-02-28) 0.06 (BENBOOTH on 2012-12-12) 0.05 (BENBOOTH on 2012-11-26) 0.04 (BENBOOTH on 2012-11-16) 0.03 (BENBOOTH on 2012-11-15) 0.02 (BENBOOTH on 2011-05-09) 0.01 (BENBOOTH on 2010-09-08) 0.11_01 DEV (SLOYD on 2018-06-09) 0.11 (SLOYD on 2017-07-23) 0.10_01 DEV (SLOYD on 2017-07-21) Diff with version 0.12 (SLOYD on 2018-06-10) 0.10 (BENBOOTH on 2014-04-17) 0.09 (BENBOOTH on 2013-12-04) 0.08 (BENBOOTH on 2013-10-22) 0.07 (BENBOOTH on 2013-02-28) 0.06 (BENBOOTH on 2012-12-12) 0.05 (BENBOOTH on 2012-11-26) 0.04 (BENBOOTH on 2012-11-16) 0.03 (BENBOOTH on 2012-11-15) 0.02 (BENBOOTH on 2011-05-09) 0.01 (BENBOOTH on 2010-09-08) 0.11_01 DEV (SLOYD on 2018-06-09) 0.11 (SLOYD on 2017-07-23) 0.10_01 DEV (SLOYD on 2017-07-21) Permalinks This version Latest version ++ed by: 1 PAUSE user 1 non-PAUSE user Authors: Benjamin Booth Stephan Loyd Released by: Stephan Loyd Maintainers: BENBOOTH owner SLOYD Contributors: Benjamin Booth Stephan Loyd  /  0.12 (SLOYD on 2018-06-10) 0.10 (BENBOOTH on 2014-04-17) 0.09 (BENBOOTH on 2013-12-04) 0.08 (BENBOOTH on 2013-10-22) 0.07 (BENBOOTH on 2013-02-28) 0.06 (BENBOOTH on 2012-12-12) 0.05 (BENBOOTH on 2012-11-26) 0.04 (BENBOOTH on 2012-11-16) 0.03 (BENBOOTH on 2012-11-15) 0.02 (BENBOOTH on 2011-05-09) 0.01 (BENBOOTH on 2010-09-08) 0.11_01 DEV (SLOYD on 2018-06-09) 0.11 (SLOYD on 2017-07-23) 0.10_01 DEV (SLOYD on 2017-07-21) Set-IntervalTree-0.12 2 ++ 2 ++ / Set::IntervalTree Contents NAME VERSION SYNOPSIS DESCRIPTION EXPORTS METHODS LIMITATIONS SEE ALSO AUTHORS COPYRIGHT AND LICENSE NAME Set::IntervalTree - Perform range-based lookups on sets of ranges VERSION version 0.12 SYNOPSIS use Set::IntervalTree; my $tree = Set::IntervalTree->new; $tree->insert("ID1",100,200); $tree->insert(2,50,100); $tree->insert({id=>3},520,700); $tree->insert($some_obj,1000,1100); my $results = $tree->fetch(400,800); my $window = $tree->fetch_window(100,200); print scalar(@$results)." intervals found.\n"; # remove only items overlapping location 100..200 with values # less than 100; my $removed = $tree->remove(100,200 sub { my ($item, $low, $high) = @_; return $item < 100; }); DESCRIPTION Set::IntervalTree uses Interval Trees to store and efficiently look up ranges using a range-based lookup. All intervals are half-open, i.e. [1,3), [2,6), etc. EXPORTS Nothing. METHODS my $tree = Set::IntervalTree->new; Creates a new interval tree object. $tree->insert($object, $low, $high); Insert a range into the interval tree and associate it with a perl scalar. $object can be any perl scalar. This is what will be returned by fetch(). $low is the lower bound of the range. $high is the upper bound of the range. Ranges are represented as half-closed integer intervals. my $results = $tree->fetch($low, $high) Return an arrayref of perl objects whose ranges overlap the specified range. $low is the lower bound of the region to query. $high is the upper bound of the region to query. my $results = $tree->fetch_window($low, $high) Return an arrayref of perl objects whose ranges are completely contained witin the specified range. $low is the lower bound of the region to query. $high is the upper bound of the region to query. my $nearest_up = $tree->fetch_nearest_up($query) Search for the closest interval in upstream that does not contain the query and returns the perl object associated with it. $query is the position to use for the search my $nearest_down = $tree->fetch_nearest_down($query) Search for the closest interval in downstream that does not contain the query and returns the perl object associated with it. $query is the position to use for the search my $removed = $tree->remove($low, $high [, optional \&coderef]); Remove items in the tree that overlap the region from $low to $high. A coderef can be passed in as an optional third argument for filtering what is removed. The coderef receives the stored item, the low point, and the high point as its arguments. If the result value of the coderef is true, the item is removed, otherwise the item remains in the tree. Returns the list of removed items. my $removed = $tree->remove_window($low, $high [, optional \&coderef]); Remove items in the tree that are contained within the region from $low to $high. A coderef can be passed in as an optional third argument for filtering what is removed. The coderef receives the stored item, the low point, and the high point as its arguments. If the result value of the coderef is true, the item is removed, otherwise the item remains in the tree. Returns the list of removed items. LIMITATIONS A $tree->print() serialization method might be useful for debugging. SEE ALSO The source code for this module contains a reusable template-based C++ header for Interval trees that might be useful. AUTHORS Benjamin Booth <benbooth@cpan.org> Stephan Loyd <sloyd@cpan.org> COPYRIGHT AND LICENSE This software is copyright (c) 2012 by Benjamin Booth. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. Module Install Instructions To install Set::IntervalTree, copy and paste the appropriate command in to your terminal. cpanm cpanm Set::IntervalTree CPAN shell perl -MCPAN -e shell install Set::IntervalTree For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-db-file --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-db-file 1.835 4 +-------------------- +file name : perl-db-file-1.835-4.tar.bz2 +name : perl-db-file +version : 1.835 +build : 4 +build number: 4 +size : 38 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.835-4.tar.bz2 +md5 : d5dac7521fea1c377b2d9b7d3510eb9e +dependencies: + - libdb + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-db-file 1.835 5 +-------------------- +file name : perl-db-file-1.835-5.tar.bz2 +name : perl-db-file +version : 1.835 +build : 5 +build number: 5 +size : 38 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.835-5.tar.bz2 +md5 : 2cf57fa7e165dced6188635a8123785c +dependencies: + - libdb + - libgcc + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-db-file 1.835 pl5.18.2_0 +----------------------------- +file name : perl-db-file-1.835-pl5.18.2_0.tar.bz2 +name : perl-db-file +version : 1.835 +build : pl5.18.2_0 +build number: 0 +size : 49 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.835-pl5.18.2_0.tar.bz2 +md5 : 0271217472d139ee61cd216e93ce1592 +dependencies: + - perl 5.18.2* + + +perl-db-file 1.835 pl5.22.0_1 +----------------------------- +file name : perl-db-file-1.835-pl5.22.0_1.tar.bz2 +name : perl-db-file +version : 1.835 +build : pl5.22.0_1 +build number: 1 +size : 40 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.835-pl5.22.0_1.tar.bz2 +md5 : c3b0ca7925ef32f16f9c159eaa3e184b +dependencies: + - perl 5.22.0* + + +perl-db-file 1.835 pl5.22.0_2 +----------------------------- +file name : perl-db-file-1.835-pl5.22.0_2.tar.bz2 +name : perl-db-file +version : 1.835 +build : pl5.22.0_2 +build number: 2 +size : 40 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.835-pl5.22.0_2.tar.bz2 +md5 : 3a1f96607fde8e8f34c78415fa2f9f33 +dependencies: + - libdb + - perl 5.22.0* + + +perl-db-file 1.835 pl5.22.0_3 +----------------------------- +file name : perl-db-file-1.835-pl5.22.0_3.tar.bz2 +name : perl-db-file +version : 1.835 +build : pl5.22.0_3 +build number: 3 +size : 40 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.835-pl5.22.0_3.tar.bz2 +md5 : 27574d95b290fb82b83f94e2c9c3e236 +dependencies: + - libdb + - perl 5.22.0* + + +perl-db-file 1.835 pl526h470a237_6 +---------------------------------- +file name : perl-db-file-1.835-pl526h470a237_6.tar.bz2 +name : perl-db-file +version : 1.835 +build : pl526h470a237_6 +build number: 6 +size : 51 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.835-pl526h470a237_6.tar.bz2 +md5 : 9a3009d9bbc203f47536f3e58c43b7bc +timestamp : 2018-07-07 17:07:04 UTC +dependencies: + - libdb + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.27.0a0 + + +perl-db-file 1.843 pl526h470a237_0 +---------------------------------- +file name : perl-db-file-1.843-pl526h470a237_0.tar.bz2 +name : perl-db-file +version : 1.843 +build : pl526h470a237_0 +build number: 0 +size : 52 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.843-pl526h470a237_0.tar.bz2 +md5 : 4c1719138d86c9c2c545af338487b4ab +timestamp : 2018-11-11 06:11:28 UTC +dependencies: + - libdb + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + + +perl-db-file 1.852 pl526h14c3975_0 +---------------------------------- +file name : perl-db-file-1.852-pl526h14c3975_0.tar.bz2 +name : perl-db-file +version : 1.852 +build : pl526h14c3975_0 +build number: 0 +size : 52 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.852-pl526h14c3975_0.tar.bz2 +md5 : 579f23bc8317249bf2df9d3840af79c3 +timestamp : 2019-04-22 04:41:00 UTC +dependencies: + - libdb + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + + +perl-db-file 1.852 pl526h516909a_1 +---------------------------------- +file name : perl-db-file-1.852-pl526h516909a_1.tar.bz2 +name : perl-db-file +version : 1.852 +build : pl526h516909a_1 +build number: 1 +size : 53 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.852-pl526h516909a_1.tar.bz2 +md5 : d33bcdf85d56fb91e7d4efe580af071e +timestamp : 2020-10-21 12:57:49 UTC +dependencies: + - libdb >=6.2.32,<6.3.0a0 + - libgcc-ng >=7.5.0 + - perl >=5.26.2,<5.26.3.0a0 + + +perl-db-file 1.855 pl526h516909a_0 +---------------------------------- +file name : perl-db-file-1.855-pl526h516909a_0.tar.bz2 +name : perl-db-file +version : 1.855 +build : pl526h516909a_0 +build number: 0 +size : 53 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.855-pl526h516909a_0.tar.bz2 +md5 : a234abd4c1aa57ef1f52f9b2d9be9b2c +timestamp : 2020-10-21 14:21:06 UTC +dependencies: + - libdb >=6.2.32,<6.3.0a0 + - libgcc-ng >=7.5.0 + - perl >=5.26.2,<5.26.3.0a0 + + +perl-db-file 1.855 pl5321h779adbc_1 +----------------------------------- +file name : perl-db-file-1.855-pl5321h779adbc_1.tar.bz2 +name : perl-db-file +version : 1.855 +build : pl5321h779adbc_1 +build number: 1 +size : 54 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.855-pl5321h779adbc_1.tar.bz2 +md5 : 031a9a57deaa73c090267cd29b545482 +timestamp : 2022-01-17 07:43:53 UTC +dependencies: + - libdb >=6.2.32,<6.3.0a0 + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-dbd-sqlite.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-dbd-sqlite.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..5fcc7d8a2b764d5832a463fd593bca3e9dc0cf92 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-dbd-sqlite.manual_bundle.txt @@ -0,0 +1,430 @@ +# Tool: perl-dbd-sqlite +software_name: perl-dbd-sqlite +tier: T1 +domain: t1_backfill_overall +downloads: 280749 +summary: Self Contained RDBMS in a DBI Driver. +description: Self Contained RDBMS in a DBI Driver. +dependencies: libgcc >=13, perl >=5.32.1,<5.33.0a0 *_perl5, perl-dbi +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/DBD::SQLite +doc_url: https://metacpan.org/pod/DBD::SQLite +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/DBD::SQLite +DBD::SQLite - Self-contained RDBMS in a DBI Driver - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution DBD-SQLite Module version: 1.78 02 Jan 2026 01:23:08 UTC License: perl_5 Code Download ( 2.7MB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (15) How to Contribute Quality Testers ( 903 / 0 / 0 ) Testers (Magpie) Kwalitee % Coverage Bus factor: 2 Activity 24 month Dependencies DBI Scalar::Util Tie::Hash and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 1.78 (ISHIGAKI on 2026-01-02) 1.77_03 DEV (ISHIGAKI on 2025-12-27) 1.77_02 DEV (ISHIGAKI on 2025-11-24) 1.77_01 DEV (ISHIGAKI on 2025-11-24) 1.76 (ISHIGAKI on 2024-10-19) 1.75_01 DEV (ISHIGAKI on 2024-09-17) 1.74 (ISHIGAKI on 2023-09-19) 1.73_01 DEV (ISHIGAKI on 2023-07-09) 1.72 (ISHIGAKI on 2022-11-03) 1.71_07 DEV (ISHIGAKI on 2022-10-25) 1.71_06 DEV (ISHIGAKI on 2022-03-12) 1.71_05 DEV (ISHIGAKI on 2022-02-26) 1.71_04 DEV (ISHIGAKI on 2022-02-26) 1.71_03 DEV (ISHIGAKI on 2022-02-23) 1.71_02 DEV (ISHIGAKI on 2022-01-06) 1.71_01 DEV (ISHIGAKI on 2021-12-01) 1.70 (ISHIGAKI on 2021-08-01) 1.69_02 DEV (ISHIGAKI on 2021-07-30) 1.69_01 DEV (ISHIGAKI on 2021-07-29) 1.68 (ISHIGAKI on 2021-07-22) 1.67_07 DEV (ISHIGAKI on 2021-06-19) 1.67_06 DEV (ISHIGAKI on 2021-06-14) 1.67_05 DEV (ISHIGAKI on 2021-06-12) 1.67_04 DEV (ISHIGAKI on 2021-05-30) 1.67_03 DEV (ISHIGAKI on 2021-03-30) 1.67_02 DEV (ISHIGAKI on 2020-12-05) 1.67_01 DEV (ISHIGAKI on 2020-11-24) 1.66 (ISHIGAKI on 2020-08-30) 1.65_03 DEV (ISHIGAKI on 2020-07-26) 1.65_02 DEV (ISHIGAKI on 2020-02-08) 1.65_01 DEV (ISHIGAKI on 2020-01-18) 1.64 (ISHIGAKI on 2019-08-12) 1.62 (ISHIGAKI on 2018-12-28) 1.60 (ISHIGAKI on 2018-12-01) 1.63_05 DEV (ISHIGAKI on 2019-07-11) 1.63_04 DEV (ISHIGAKI on 2019-05-24) 1.63_03 DEV (ISHIGAKI on 2019-02-14) 1.63_02 DEV (ISHIGAKI on 2019-02-13) 1.63_01 DEV (ISHIGAKI on 2019-01-25) 1.61_04 DEV (ISHIGAKI on 2018-12-22) 1.61_03 DEV (ISHIGAKI on 2018-12-19) 1.61_02 DEV (ISHIGAKI on 2018-12-01) 1.61_01 DEV (ISHIGAKI on 2018-12-01) 1.59_03 DEV (ISHIGAKI on 2018-11-03) 1.59_02 DEV (ISHIGAKI on 2018-09-30) 1.59_01 DEV (ISHIGAKI on 2018-09-16) 1.58 (ISHIGAKI on 2018-03-28) 1.57_01 DEV (ISHIGAKI on 2018-03-21) 1.56 (ISHIGAKI on 2018-02-28) 1.55_07 DEV (ISHIGAKI on 2018-01-27) 1.55_06 DEV (ISHIGAKI on 2018-01-27) 1.55_05 DEV (ISHIGAKI on 2017-12-15) 1.55_04 DEV (ISHIGAKI on 2017-11-21) 1.55_03 DEV (ISHIGAKI on 2017-02-14) 1.55_02 DEV (ISHIGAKI on 2017-01-07) 1.55_01 DEV (ISHIGAKI on 2017-01-03) 1.54 (ISHIGAKI on 2016-12-24) 1.53_01 DEV (ISHIGAKI on 2016-11-26) 1.52 (ISHIGAKI on 2016-11-15) 1.51_07 DEV (ISHIGAKI on 2016-10-16) 1.51_06 DEV (ISHIGAKI on 2016-10-15) 1.51_05 DEV (ISHIGAKI on 2016-06-23) 1.51_04 DEV (ISHIGAKI on 2016-03-07) 1.51_03 DEV (ISHIGAKI on 2016-02-20) 1.51_02 DEV (ISHIGAKI on 2016-02-20) 1.51_01 DEV (ISHIGAKI on 2016-02-20) 1.50 (ISHIGAKI on 2016-02-10) 1.49_08 DEV (ISHIGAKI on 2016-01-30) 1.49_07 DEV (ISHIGAKI on 2016-01-21) 1.49_06 DEV (ISHIGAKI on 2016-01-15) 1.49_05 DEV (ISHIGAKI on 2016-01-11) 1.49_04 DEV (ISHIGAKI on 2015-11-24) 1.49_03 DEV (ISHIGAKI on 2015-11-05) 1.49_02 DEV (ISHIGAKI on 2015-10-10) 1.49_01 DEV (ISHIGAKI on 2015-08-04) 1.48 (ISHIGAKI on 2015-06-11) 1.47_05 DEV (ISHIGAKI on 2015-05-08) 1.47_04 DEV (ISHIGAKI on 2015-05-01) 1.47_03 DEV (ISHIGAKI on 2015-04-16) 1.47_02 DEV (ISHIGAKI on 2015-04-16) 1.47_01 DEV (ISHIGAKI on 2015-02-17) 1.46 (ISHIGAKI on 2014-12-10) 1.45_06 DEV (ISHIGAKI on 2014-11-26) 1.45_05 DEV (ISHIGAKI on 2014-11-25) 1.45_04 DEV (ISHIGAKI on 2014-10-28) 1.45_03 DEV (ISHIGAKI on 2014-10-24) 1.45_02 DEV (ISHIGAKI on 2014-10-23) 1.45_01 DEV (ISHIGAKI on 2014-10-22) 1.44 (ISHIGAKI on 2014-10-22) 1.43_09 DEV (ISHIGAKI on 2014-10-20) 1.43_08 DEV (ISHIGAKI on 2014-08-21) 1.43_07 DEV (ISHIGAKI on 2014-07-29) 1.43_06 DEV (ISHIGAKI on 2014-07-22) 1.43_05 DEV (ISHIGAKI on 2014-07-21) 1.43_04 DEV (ISHIGAKI on 2014-07-21) 1.43_03 DEV (ISHIGAKI on 2014-06-12) 1.43_02 DEV (ISHIGAKI on 2014-03-25) 1.43_01 DEV (ISHIGAKI on 2014-03-25) 1.42 (ISHIGAKI on 2014-03-19) 1.41_07 DEV (ISHIGAKI on 2014-03-13) 1.41_06 DEV (ISHIGAKI on 2014-02-12) 1.41_05 DEV (ISHIGAKI on 2014-01-22) 1.41_04 DEV (ISHIGAKI on 2014-01-12) 1.41_03 DEV (ISHIGAKI on 2013-09-04) 1.41_02 DEV (ISHIGAKI on 2013-08-29) 1.41_01 DEV (ISHIGAKI on 2013-08-27) 1.40 (ISHIGAKI on 2013-07-28) 1.39 (ISHIGAKI on 2013-06-09) 1.38_05 DEV (ISHIGAKI on 2013-05-31) 1.38_04 DEV (ISHIGAKI on 2013-05-29) 1.38_03 DEV (ADAMK on 2013-05-21) 1.38_02 DEV (ADAMK on 2013-04-09) 1.38_01 DEV (ADAMK on 2012-09-24) 1.37 (ADAMK on 2012-06-09) 1.36_04 DEV (ADAMK on 2012-05-19) 1.36_03 DEV (ADAMK on 2012-05-07) 1.36_02 DEV (ADAMK on 2012-02-23) 1.36_01 DEV (ADAMK on 2012-01-19) 1.35 (ADAMK on 2011-11-29) 1.34_03 DEV (ADAMK on 2011-11-01) 1.34_02 DEV (ADAMK on 2011-10-21) 1.34_01 DEV (ADAMK on 2011-09-21) 1.33 (ADAMK on 2011-05-30) 1.32_04 DEV (ADAMK on 2011-05-20) 1.32_03 DEV (ADAMK on 2011-05-12) 1.32_02 DEV (ADAMK on 2011-03-07) 1.32_01 DEV (ADAMK on 2010-12-10) 1.31 (ADAMK on 2010-09-15) 1.30_06 DEV (ADAMK on 2010-09-09) 1.30_05 DEV (ADAMK on 2010-08-27) 1.30_04 DEV (ADAMK on 2010-08-25) 1.30_03 DEV (ADAMK on 2010-05-31) 1.30_02 DEV (ADAMK on 2010-03-30) 1.30_01 DEV (ADAMK on 2010-03-10) 1.29 (ADAMK on 2010-01-08) 1.28_02 DEV (ADAMK on 2010-01-03) 1.28_01 DEV (ADAMK on 2009-12-23) 1.27 (ADAMK on 2009-11-23) 1.26_07 DEV (ADAMK on 2009-11-16) 1.26_06 DEV (ADAMK on 2009-10-28) 1.26_05 DEV (ADAMK on 2009-10-15) 1.26_04 DEV (ADAMK on 2009-10-06) 1.26_03 DEV (ADAMK on 2009-08-12) 1.26_02 DEV (ADAMK on 2009-06-19) 1.26_01 DEV (ADAMK on 2009-05-05) 1.25 (ADAMK on 2009-04-23) 1.24_02 DEV (ADAMK on 2009-04-23) 1.24_01 DEV (ADAMK on 2009-04-22) 1.23 (ADAMK on 2009-04-19) 1.22_08 DEV (ADAMK on 2009-04-17) 1.22_07 DEV (ADAMK on 2009-04-16) 1.22_06 DEV (ADAMK on 2009-04-15) 1.22_05 DEV (ADAMK on 2009-04-14) 1.22_04 DEV (ADAMK on 2009-04-11) 1.22_03 DEV (ADAMK on 2009-04-09) 1.22_02 DEV (ADAMK on 2009-04-08) 1.22_01 DEV (ADAMK on 2009-04-08) 1.21 (ADAMK on 2009-04-08) 1.20 (ADAMK on 2009-04-07) 1.19_10 DEV (ADAMK on 2009-04-05) 1.19_09 DEV (ADAMK on 2009-04-05) 1.19_08 DEV (ADAMK on 2009-04-04) 1.19_07 DEV (ADAMK on 2009-04-04) 1.19_06 DEV (ADAMK on 2009-04-03) 1.19_05 DEV (ADAMK on 2009-04-02) 1.19_04 DEV (ADAMK on 2009-03-31) 1.19_03 DEV (ADAMK on 2009-03-30) 1.19_02 DEV (ADAMK on 2009-03-28) 1.19_01 DEV (ADAMK on 2009-03-27) 1.14 (MSERGEANT on 2007-09-19) 1.13 (MSERGEANT on 2006-09-08) 1.12 (MSERGEANT on 2006-04-10) 1.11 (MSERGEANT on 2005-12-02) 1.10 (MSERGEANT on 2005-12-01) 1.09 (MSERGEANT on 2005-06-20) 1.08 (MSERGEANT on 2005-02-26) 1.07 (MSERGEANT on 2004-10-12) 1.06 (MSERGEANT on 2004-09-21) 1.05 (MSERGEANT on 2004-09-10) 1.04 (MSERGEANT on 2004-08-23) 1.03 (MSERGEANT on 2004-08-09) 1.02 (MSERGEANT on 2004-08-02) 1.01 (MSERGEANT on 2004-08-01) 1.00 (MSERGEANT on 2004-07-21) 0.31 (MSERGEANT on 2004-02-14) 0.30 (MSERGEANT on 2004-02-08) 0.29 (MSERGEANT on 2003-12-05) 0.28 (MSERGEANT on 2003-08-25) 0.27 (MSERGEANT on 2003-08-18) 0.26 (MSERGEANT on 2003-07-31) 0.25 (MSERGEANT on 2003-03-06) 0.24 (MSERGEANT on 2003-01-29) 0.23 (MSERGEANT on 2002-12-29) 0.22 (MSERGEANT on 2002-12-18) 0.21 (MSERGEANT on 2002-10-18) 0.20 (MSERGEANT on 2002-10-17) 0.19 (MSERGEANT on 2002-08-13) 0.18 (MSERGEANT on 2002-07-12) 0.17 (MSERGEANT on 2002-06-26) 0.16 (MSERGEANT on 2002-06-17) 0.15 (MSERGEANT on 2002-04-02) 0.14 (MSERGEANT on 2002-03-28) 0.13 (MSERGEANT on 2002-03-26) 0.12 (MSERGEANT on 2002-03-21) 0.11 (MSERGEANT on 2002-03-13) 0.10 (MSERGEANT on 2002-02-28) 0.09 (MSERGEANT on 2002-02-27) 0.08 (MSERGEANT on 2002-02-25) 0.07 (MSERGEANT on 2002-02-23) 0.06 (MSERGEANT on 2002-02-22) 0.05 (MSERGEANT on 2002-02-19) Diff with version 1.78 (ISHIGAKI on 2026-01-02) 1.77_03 DEV (ISHIGAKI on 2025-12-27) 1.77_02 DEV (ISHIGAKI on 2025-11-24) 1.77_01 DEV (ISHIGAKI on 2025-11-24) 1.76 (ISHIGAKI on 2024-10-19) 1.75_01 DEV (ISHIGAKI on 2024-09-17) 1.74 (ISHIGAKI on 2023-09-19) 1.73_01 DEV (ISHIGAKI on 2023-07-09) 1.72 (ISHIGAKI on 2022-11-03) 1.71_07 DEV (ISHIGAKI on 2022-10-25) 1.71_06 DEV (ISHIGAKI on 2022-03-12) 1.71_05 DEV (ISHIGAKI on 2022-02-26) 1.71_04 DEV (ISHIGAKI on 2022-02-26) 1.71_03 DEV (ISHIGAKI on 2022-02-23) 1.71_02 DEV (ISHIGAKI on 2022-01-06) 1.71_01 DEV (ISHIGAKI on 2021-12-01) 1.70 (ISHIGAKI on 2021-08-01) 1.69_02 DEV (ISHIGAKI on 2021-07-30) 1.69_01 DEV (ISHIGAKI on 2021-07-29) 1.68 (ISHIGAKI on 2021-07-22) 1.67_07 DEV (ISHIGAKI on 2021-06-19) 1.67_06 DEV (ISHIGAKI on 2021-06-14) 1.67_05 DEV (ISHIGAKI on 2021-06-12) 1.67_04 DEV (ISHIGAKI on 2021-05-30) 1.67_03 DEV (ISHIGAKI on 2021-03-30) 1.67_02 DEV (ISHIGAKI on 2020-12-05) 1.67_01 DEV (ISHIGAKI on 2020-11-24) 1.66 (ISHIGAKI on 2020-08-30) 1.65_03 DEV (ISHIGAKI on 2020-07-26) 1.65_02 DEV (ISHIGAKI on 2020-02-08) 1.65_01 DEV (ISHIGAKI on 2020-01-18) 1.64 (ISHIGAKI on 2019-08-12) 1.62 (ISHIGAKI on 2018-12-28) 1.60 (ISHIGAKI on 2018-12-01) 1.63_05 DEV (ISHIGAKI on 2019-07-11) 1.63_04 DEV (ISHIGAKI on 2019-05-24) 1.63_03 DEV (ISHIGAKI on 2019-02-14) 1.63_02 DEV (ISHIGAKI on 2019-02-13) 1.63_01 DEV (ISHIGAKI on 2019-01-25) 1.61_04 DEV (ISHIGAKI on 2018-12-22) 1.61_03 DEV (ISHIGAKI on 2018-12-19) 1.61_02 DEV (ISHIGAKI on 2018-12-01) 1.61_01 DEV (ISHIGAKI on 2018-12-01) 1.59_03 DEV (ISHIGAKI on 2018-11-03) 1.59_02 DEV (ISHIGAKI on 2018-09-30) 1.59_01 DEV (ISHIGAKI on 2018-09-16) 1.58 (ISHIGAKI on 2018-03-28) 1.57_01 DEV (ISHIGAKI on 2018-03-21) 1.56 (ISHIGAKI on 2018-02-28) 1.55_07 DEV (ISHIGAKI on 2018-01-27) 1.55_06 DEV (ISHIGAKI on 2018-01-27) 1.55_05 DEV (ISHIGAKI on 2017-12-15) 1.55_04 DEV (ISHIGAKI on 2017-11-21) 1.55_03 DEV (ISHIGAKI on 2017-02-14) 1.55_02 DEV (ISHIGAKI on 2017-01-07) 1.55_01 DEV (ISHIGAKI on 2017-01-03) 1.54 (ISHIGAKI on 2016-12-24) 1.53_01 DEV (ISHIGAKI on 2016-11-26) 1.52 (ISHIGAKI on 2016-11-15) 1.51_07 DEV (ISHIGAKI on 2016-10-16) 1.51_06 DEV (ISHIGAKI on 2016-10-15) 1.51_05 DEV (ISHIGAKI on 2016-06-23) 1.51_04 DEV (ISHIGAKI on 2016-03-07) 1.51_03 DEV (ISHIGAKI on 2016-02-20) 1.51_02 DEV (ISHIGAKI on 2016-02-20) 1.51_01 DEV (ISHIGAKI on 2016-02-20) 1.50 (ISHIGAKI on 2016-02-10) 1.49_08 DEV (ISHIGAKI on 2016-01-30) 1.49_07 DEV (ISHIGAKI on 2016-01-21) 1.49_06 DEV (ISHIGAKI on 2016-01-15) 1.49_05 DEV (ISHIGAKI on 2016-01-11) 1.49_04 DEV (ISHIGAKI on 2015-11-24) 1.49_03 DEV (ISHIGAKI on 2015-11-05) 1.49_02 DEV (ISHIGAKI on 2015-10-10) 1.49_01 DEV (ISHIGAKI on 2015-08-04) 1.48 (ISHIGAKI on 2015-06-11) 1.47_05 DEV (ISHIGAKI on 2015-05-08) 1.47_04 DEV (ISHIGAKI on 2015-05-01) 1.47_03 DEV (ISHIGAKI on 2015-04-16) 1.47_02 DEV (ISHIGAKI on 2015-04-16) 1.47_01 DEV (ISHIGAKI on 2015-02-17) 1.46 (ISHIGAKI on 2014-12-10) 1.45_06 DEV (ISHIGAKI on 2014-11-26) 1.45_05 DEV (ISHIGAKI on 2014-11-25) 1.45_04 DEV (ISHIGAKI on 2014-10-28) 1.45_03 DEV (ISHIGAKI on 2014-10-24) 1.45_02 DEV (ISHIGAKI on 2014-10-23) 1.45_01 DEV (ISHIGAKI on 2014-10-22) 1.44 (ISHIGAKI on 2014-10-22) 1.43_09 DEV (ISHIGAKI on 2014-10-20) 1.43_08 DEV (ISHIGAKI on 2014-08-21) 1.43_07 DEV (ISHIGAKI on 2014-07-29) 1.43_06 DEV (ISHIGAKI on 2014-07-22) 1.43_05 DEV (ISHIGAKI on 2014-07-21) 1.43_04 DEV (ISHIGAKI on 2014-07-21) 1.43_03 DEV (ISHIGAKI on 2014-06-12) 1.43_02 DEV (ISHIGAKI on 2014-03-25) 1.43_01 DEV (ISHIGAKI on 2014-03-25) 1.42 (ISHIGAKI on 2014-03-19) 1.41_07 DEV (ISHIGAKI on 2014-03-13) 1.41_06 DEV (ISHIGAKI on 2014-02-12) 1.41_05 DEV (ISHIGAKI on 2014-01-22) 1.41_04 DEV (ISHIGAKI on 2014-01-12) 1.41_03 DEV (ISHIGAKI on 2013-09-04) 1.41_02 DEV (ISHIGAKI on 2013-08-29) 1.41_01 DEV (ISHIGAKI on 2013-08-27) 1.40 (ISHIGAKI on 2013-07-28) 1.39 (ISHIGAKI on 2013-06-09) 1.38_05 DEV (ISHIGAKI on 2013-05-31) 1.38_04 DEV (ISHIGAKI on 2013-05-29) 1.38_03 DEV (ADAMK on 2013-05-21) 1.38_02 DEV (ADAMK on 2013-04-09) 1.38_01 DEV (ADAMK on 2012-09-24) 1.37 (ADAMK on 2012-06-09) 1.36_04 DEV (ADAMK on 2012-05-19) 1.36_03 DEV (ADAMK on 2012-05-07) 1.36_02 DEV (ADAMK on 2012-02-23) 1.36_01 DEV (ADAMK on 2012-01-19) 1.35 (ADAMK on 2011-11-29) 1.34_03 DEV (ADAMK on 2011-11-01) 1.34_02 DEV (ADAMK on 2011-10-21) 1.34_01 DEV (ADAMK on 2011-09-21) 1.33 (ADAMK on 2011-05-30) 1.32_04 DEV (ADAMK on 2011-05-20) 1.32_03 DEV (ADAMK on 2011-05-12) 1.32_02 DEV (ADAMK on 2011-03-07) 1.32_01 DEV (ADAMK on 2010-12-10) 1.31 (ADAMK on 2010-09-15) 1.30_06 DEV (ADAMK on 2010-09-09) 1.30_05 DEV (ADAMK on 2010-08-27) 1.30_04 DEV (ADAMK on 2010-08-25) 1.30_03 DEV (ADAMK on 2010-05-31) 1.30_02 DEV (ADAMK on 2010-03-30) 1.30_01 DEV (ADAMK on 2010-03-10) 1.29 (ADAMK on 2010-01-08) 1.28_02 DEV (ADAMK on 2010-01-03) 1.28_01 DEV (ADAMK on 2009-12-23) 1.27 (ADAMK on 2009-11-23) 1.26_07 DEV (ADAMK on 2009-11-16) 1.26_06 DEV (ADAMK on 2009-10-28) 1.26_05 DEV (ADAMK on 2009-10-15) 1.26_04 DEV (ADAMK on 2009-10-06) 1.26_03 DEV (ADAMK on 2009-08-12) 1.26_02 DEV (ADAMK on 2009-06-19) 1.26_01 DEV (ADAMK on 2009-05-05) 1.25 (ADAMK on 2009-04-23) 1.24_02 DEV (ADAMK on 2009-04-23) 1.24_01 DEV (ADAMK on 2009-04-22) 1.23 (ADAMK on 2009-04-19) 1.22_08 DEV (ADAMK on 2009-04-17) 1.22_07 DEV (ADAMK on 2009-04-16) 1.22_06 DEV (ADAMK on 2009-04-15) 1.22_05 DEV (ADAMK on 2009-04-14) 1.22_04 DEV (ADAMK on 2009-04-11) 1.22_03 DEV (ADAMK on 2009-04-09) 1.22_02 DEV (ADAMK on 2009-04-08) 1.22_01 DEV (ADAMK on 2009-04-08) 1.21 (ADAMK on 2009-04-08) 1.20 (ADAMK on 2009-04-07) 1.19_10 DEV (ADAMK on 2009-04-05) 1.19_09 DEV (ADAMK on 2009-04-05) 1.19_08 DEV (ADAMK on 2009-04-04) 1.19_07 DEV (ADAMK on 2009-04-04) 1.19_06 DEV (ADAMK on 2009-04-03) 1.19_05 DEV (ADAMK on 2009-04-02) 1.19_04 DEV (ADAMK on 2009-03-31) 1.19_03 DEV (ADAMK on 2009-03-30) 1.19_02 DEV (ADAMK on 2009-03-28) 1.19_01 DEV (ADAMK on 2009-03-27) 1.14 (MSERGEANT on 2007-09-19) 1.13 (MSERGEANT on 2006-09-08) 1.12 (MSERGEANT on 2006-04-10) 1.11 (MSERGEANT on 2005-12-02) 1.10 (MSERGEANT on 2005-12-01) 1.09 (MSERGEANT on 2005-06-20) 1.08 (MSERGEANT on 2005-02-26) 1.07 (MSERGEANT on 2004-10-12) 1.06 (MSERGEANT on 2004-09-21) 1.05 (MSERGEANT on 2004-09-10) 1.04 (MSERGEANT on 2004-08-23) 1.03 (MSERGEANT on 2004-08-09) 1.02 (MSERGEANT on 2004-08-02) 1.01 (MSERGEANT on 2004-08-01) 1.00 (MSERGEANT on 2004-07-21) 0.31 (MSERGEANT on 2004-02-14) 0.30 (MSERGEANT on 2004-02-08) 0.29 (MSERGEANT on 2003-12-05) 0.28 (MSERGEANT on 2003-08-25) 0.27 (MSERGEANT on 2003-08-18) 0.26 (MSERGEANT on 2003-07-31) 0.25 (MSERGEANT on 2003-03-06) 0.24 (MSERGEANT on 2003-01-29) 0.23 (MSERGEANT on 2002-12-29) 0.22 (MSERGEANT on 2002-12-18) 0.21 (MSERGEANT on 2002-10-18) 0.20 (MSERGEANT on 2002-10-17) 0.19 (MSERGEANT on 2002-08-13) 0.18 (MSERGEANT on 2002-07-12) 0.17 (MSERGEANT on 2002-06-26) 0.16 (MSERGEANT on 2002-06-17) 0.15 (MSERGEANT on 2002-04-02) 0.14 (MSERGEANT on 2002-03-28) 0.13 (MSERGEANT on 2002-03-26) 0.12 (MSERGEANT on 2002-03-21) 0.11 (MSERGEANT on 2002-03-13) 0.10 (MSERGEANT on 2002-02-28) 0.09 (MSERGEANT on 2002-02-27) 0.08 (MSERGEANT on 2002-02-25) 0.07 (MSERGEANT on 2002-02-23) 0.06 (MSERGEANT on 2002-02-22) 0.05 (MSERGEANT on 2002-02-19) Permalinks This version Latest version ++ed by: 56 PAUSE users 50 non-PAUSE users Authors: Adam Kennedy Released by: Kenichi Ishigaki Maintainers: ISHIGAKI owner ADAMK DUNCAND MSERGEANT Contributors: Adam Kennedy Kenichi Ishigaki  /  1.78 (ISHIGAKI on 2026-01-02) 1.77_03 DEV (ISHIGAKI on 2025-12-27) 1.77_02 DEV (ISHIGAKI on 2025-11-24) 1.77_01 DEV (ISHIGAKI on 2025-11-24) 1.76 (ISHIGAKI on 2024-10-19) 1.75_01 DEV (ISHIGAKI on 2024-09-17) 1.74 (ISHIGAKI on 2023-09-19) 1.73_01 DEV (ISHIGAKI on 2023-07-09) 1.72 (ISHIGAKI on 2022-11-03) 1.71_07 DEV (ISHIGAKI on 2022-10-25) 1.71_06 DEV (ISHIGAKI on 2022-03-12) 1.71_05 DEV (ISHIGAKI on 2022-02-26) 1.71_04 DEV (ISHIGAKI on 2022-02-26) 1.71_03 DEV (ISHIGAKI on 2022-02-23) 1.71_02 DEV (ISHIGAKI on 2022-01-06) 1.71_01 DEV (ISHIGAKI on 2021-12-01) 1.70 (ISHIGAKI on 2021-08-01) 1.69_02 DEV (ISHIGAKI on 2021-07-30) 1.69_01 DEV (ISHIGAKI on 2021-07-29) 1.68 (ISHIGAKI on 2021-07-22) 1.67_07 DEV (ISHIGAKI on 2021-06-19) 1.67_06 DEV (ISHIGAKI on 2021-06-14) 1.67_05 DEV (ISHIGAKI on 2021-06-12) 1.67_04 DEV (ISHIGAKI on 2021-05-30) 1.67_03 DEV (ISHIGAKI on 2021-03-30) 1.67_02 DEV (ISHIGAKI on 2020-12-05) 1.67_01 DEV (ISHIGAKI on 2020-11-24) 1.66 (ISHIGAKI on 2020-08-30) 1.65_03 DEV (ISHIGAKI on 2020-07-26) 1.65_02 DEV (ISHIGAKI on 2020-02-08) 1.65_01 DEV (ISHIGAKI on 2020-01-18) 1.64 (ISHIGAKI on 2019-08-12) 1.62 (ISHIGAKI on 2018-12-28) 1.60 (ISHIGAKI on 2018-12-01) 1.63_05 DEV (ISHIGAKI on 2019-07-11) 1.63_04 DEV (ISHIGAKI on 2019-05-24) 1.63_03 DEV (ISHIGAKI on 2019-02-14) 1.63_02 DEV (ISHIGAKI on 2019-02-13) 1.63_01 DEV (ISHIGAKI on 2019-01-25) 1.61_04 DEV (ISHIGAKI on 2018-12-22) 1.61_03 DEV (ISHIGAKI on 2018-12-19) 1.61_02 DEV (ISHIGAKI on 2018-12-01) 1.61_01 DEV (ISHIGAKI on 2018-12-01) 1.59_03 DEV (ISHIGAKI on 2018-11-03) 1.59_02 DEV (ISHIGAKI on 2018-09-30) 1.59_01 DEV (ISHIGAKI on 2018-09-16) 1.58 (ISHIGAKI on 2018-03-28) 1.57_01 DEV (ISHIGAKI on 2018-03-21) 1.56 (ISHIGAKI on 2018-02-28) 1.55_07 DEV (ISHIGAKI on 2018-01-27) 1.55_06 DEV (ISHIGAKI on 2018-01-27) 1.55_05 DEV (ISHIGAKI on 2017-12-15) 1.55_04 DEV (ISHIGAKI on 2017-11-21) 1.55_03 DEV (ISHIGAKI on 2017-02-14) 1.55_02 DEV (ISHIGAKI on 2017-01-07) 1.55_01 DEV (ISHIGAKI on 2017-01-03) 1.54 (ISHIGAKI on 2016-12-24) 1.53_01 DEV (ISHIGAKI on 2016-11-26) 1.52 (ISHIGAKI on 2016-11-15) 1.51_07 DEV (ISHIGAKI on 2016-10-16) 1.51_06 DEV (ISHIGAKI on 2016-10-15) 1.51_05 DEV (ISHIGAKI on 2016-06-23) 1.51_04 DEV (ISHIGAKI on 2016-03-07) 1.51_03 DEV (ISHIGAKI on 2016-02-20) 1.51_02 DEV (ISHIGAKI on 2016-02-20) 1.51_01 DEV (ISHIGAKI on 2016-02-20) 1.50 (ISHIGAKI on 2016-02-10) 1.49_08 DEV (ISHIGAKI on 2016-01-30) 1.49_07 DEV (ISHIGAKI on 2016-01-21) 1.49_06 DEV (ISHIGAKI on 2016-01-15) 1.49_05 DEV (ISHIGAKI on 2016-01-11) 1.49_04 DEV (ISHIGAKI on 2015-11-24) 1.49_03 DEV (ISHIGAKI on 2015-11-05) 1.49_02 DEV (ISHIGAKI on 2015-10-10) 1.49_01 DEV (ISHIGAKI on 2015-08-04) 1.48 (ISHIGAKI on 2015-06-11) 1.47_05 DEV (ISHIGAKI on 2015-05-08) 1.47_04 DEV (ISHIGAKI on 2015-05-01) 1.47_03 DEV (ISHIGAKI on 2015-04-16) 1.47_02 DEV (ISHIGAKI on 2015-04-16) 1.47_01 DEV (ISHIGAKI on 2015-02-17) 1.46 (ISHIGAKI on 2014-12-10) 1.45_06 DEV (ISHIGAKI on 2014-11-26) 1.45_05 DEV (ISHIGAKI on 2014-11-25) 1.45_04 DEV (ISHIGAKI on 2014-10-28) 1.45_03 DEV (ISHIGAKI on 2014-10-24) 1.45_02 DEV (ISHIGAKI on 2014-10-23) 1.45_01 DEV (ISHIGAKI on 2014-10-22) 1.44 (ISHIGAKI on 2014-10-22) 1.43_09 DEV (ISHIGAKI on 2014-10-20) 1.43_08 DEV (ISHIGAKI on 2014-08-21) 1.43_07 DEV (ISHIGAKI on 2014-07-29) 1.43_06 DEV (ISHIGAKI on 2014-07-22) 1.43_05 DEV (ISHIGAKI on 2014-07-21) 1.43_04 DEV (ISHIGAKI on 2014-07-21) 1.43_03 DEV (ISHIGAKI on 2014-06-12) 1.43_02 DEV (ISHIGAKI on 2014-03-25) 1.43_01 DEV (ISHIGAKI on 2014-03-25) 1.42 (ISHIGAKI on 2014-03-19) 1.41_07 DEV (ISHIGAKI on 2014-03-13) 1.41_06 DEV (ISHIGAKI on 2014-02-12) 1.41_05 DEV (ISHIGAKI on 2014-01-22) 1.41_04 DEV (ISHIGAKI on 2014-01-12) 1.41_03 DEV (ISHIGAKI on 2013-09-04) 1.41_02 DEV (ISHIGAKI on 2013-08-29) 1.41_01 DEV (ISHIGAKI on 2013-08-27) 1.40 (ISHIGAKI on 2013-07-28) 1.39 (ISHIGAKI on 2013-06-09) 1.38_05 DEV (ISHIGAKI on 2013-05-31) 1.38_04 DEV (ISHIGAKI on 2013-05-29) 1.38_03 DEV (ADAMK on 2013-05-21) 1.38_02 DEV (ADAMK on 2013-04-09) 1.38_01 DEV (ADAMK on 2012-09-24) 1.37 (ADAMK on 2012-06-09) 1.36_04 DEV (ADAMK on 2012-05-19) 1.36_03 DEV (ADAMK on 2012-05-07) 1.36_02 DEV (ADAMK on 2012-02-23) 1.36_01 DEV (ADAMK on 2012-01-19) 1.35 (ADAMK on 2011-11-29) 1.34_03 DEV (ADAMK on 2011-11-01) 1.34_02 DEV (ADAMK on 2011-10-21) 1.34_01 DEV (ADAMK on 2011-09-21) 1.33 (ADAMK on 2011-05-30) 1.32_04 DEV (ADAMK on 2011-05-20) 1.32_03 DEV (ADAMK on 2011-05-12) 1.32_02 DEV (ADAMK on 2011-03-07) 1.32_01 DEV (ADAMK on 2010-12-10) 1.31 (ADAMK on 2010-09-15) 1.30_06 DEV (ADAMK on 2010-09-09) 1.30_05 DEV (ADAMK on 2010-08-27) 1.30_04 DEV (ADAMK on 2010-08-25) 1.30_03 DEV (ADAMK on 2010-05-31) 1.30_02 DEV (ADAMK on 2010-03-30) 1.30_01 DEV (ADAMK on + +### https://metacpan.org/pod/DBD::SQLite +DBD::SQLite - Self-contained RDBMS in a DBI Driver - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution DBD-SQLite Module version: 1.78 02 Jan 2026 01:23:08 UTC License: perl_5 Code Download ( 2.7MB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (15) How to Contribute Quality Testers ( 903 / 0 / 0 ) Testers (Magpie) Kwalitee % Coverage Bus factor: 2 Activity 24 month Dependencies DBI Scalar::Util Tie::Hash and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 1.78 (ISHIGAKI on 2026-01-02) 1.77_03 DEV (ISHIGAKI on 2025-12-27) 1.77_02 DEV (ISHIGAKI on 2025-11-24) 1.77_01 DEV (ISHIGAKI on 2025-11-24) 1.76 (ISHIGAKI on 2024-10-19) 1.75_01 DEV (ISHIGAKI on 2024-09-17) 1.74 (ISHIGAKI on 2023-09-19) 1.73_01 DEV (ISHIGAKI on 2023-07-09) 1.72 (ISHIGAKI on 2022-11-03) 1.71_07 DEV (ISHIGAKI on 2022-10-25) 1.71_06 DEV (ISHIGAKI on 2022-03-12) 1.71_05 DEV (ISHIGAKI on 2022-02-26) 1.71_04 DEV (ISHIGAKI on 2022-02-26) 1.71_03 DEV (ISHIGAKI on 2022-02-23) 1.71_02 DEV (ISHIGAKI on 2022-01-06) 1.71_01 DEV (ISHIGAKI on 2021-12-01) 1.70 (ISHIGAKI on 2021-08-01) 1.69_02 DEV (ISHIGAKI on 2021-07-30) 1.69_01 DEV (ISHIGAKI on 2021-07-29) 1.68 (ISHIGAKI on 2021-07-22) 1.67_07 DEV (ISHIGAKI on 2021-06-19) 1.67_06 DEV (ISHIGAKI on 2021-06-14) 1.67_05 DEV (ISHIGAKI on 2021-06-12) 1.67_04 DEV (ISHIGAKI on 2021-05-30) 1.67_03 DEV (ISHIGAKI on 2021-03-30) 1.67_02 DEV (ISHIGAKI on 2020-12-05) 1.67_01 DEV (ISHIGAKI on 2020-11-24) 1.66 (ISHIGAKI on 2020-08-30) 1.65_03 DEV (ISHIGAKI on 2020-07-26) 1.65_02 DEV (ISHIGAKI on 2020-02-08) 1.65_01 DEV (ISHIGAKI on 2020-01-18) 1.64 (ISHIGAKI on 2019-08-12) 1.62 (ISHIGAKI on 2018-12-28) 1.60 (ISHIGAKI on 2018-12-01) 1.63_05 DEV (ISHIGAKI on 2019-07-11) 1.63_04 DEV (ISHIGAKI on 2019-05-24) 1.63_03 DEV (ISHIGAKI on 2019-02-14) 1.63_02 DEV (ISHIGAKI on 2019-02-13) 1.63_01 DEV (ISHIGAKI on 2019-01-25) 1.61_04 DEV (ISHIGAKI on 2018-12-22) 1.61_03 DEV (ISHIGAKI on 2018-12-19) 1.61_02 DEV (ISHIGAKI on 2018-12-01) 1.61_01 DEV (ISHIGAKI on 2018-12-01) 1.59_03 DEV (ISHIGAKI on 2018-11-03) 1.59_02 DEV (ISHIGAKI on 2018-09-30) 1.59_01 DEV (ISHIGAKI on 2018-09-16) 1.58 (ISHIGAKI on 2018-03-28) 1.57_01 DEV (ISHIGAKI on 2018-03-21) 1.56 (ISHIGAKI on 2018-02-28) 1.55_07 DEV (ISHIGAKI on 2018-01-27) 1.55_06 DEV (ISHIGAKI on 2018-01-27) 1.55_05 DEV (ISHIGAKI on 2017-12-15) 1.55_04 DEV (ISHIGAKI on 2017-11-21) 1.55_03 DEV (ISHIGAKI on 2017-02-14) 1.55_02 DEV (ISHIGAKI on 2017-01-07) 1.55_01 DEV (ISHIGAKI on 2017-01-03) 1.54 (ISHIGAKI on 2016-12-24) 1.53_01 DEV (ISHIGAKI on 2016-11-26) 1.52 (ISHIGAKI on 2016-11-15) 1.51_07 DEV (ISHIGAKI on 2016-10-16) 1.51_06 DEV (ISHIGAKI on 2016-10-15) 1.51_05 DEV (ISHIGAKI on 2016-06-23) 1.51_04 DEV (ISHIGAKI on 2016-03-07) 1.51_03 DEV (ISHIGAKI on 2016-02-20) 1.51_02 DEV (ISHIGAKI on 2016-02-20) 1.51_01 DEV (ISHIGAKI on 2016-02-20) 1.50 (ISHIGAKI on 2016-02-10) 1.49_08 DEV (ISHIGAKI on 2016-01-30) 1.49_07 DEV (ISHIGAKI on 2016-01-21) 1.49_06 DEV (ISHIGAKI on 2016-01-15) 1.49_05 DEV (ISHIGAKI on 2016-01-11) 1.49_04 DEV (ISHIGAKI on 2015-11-24) 1.49_03 DEV (ISHIGAKI on 2015-11-05) 1.49_02 DEV (ISHIGAKI on 2015-10-10) 1.49_01 DEV (ISHIGAKI on 2015-08-04) 1.48 (ISHIGAKI on 2015-06-11) 1.47_05 DEV (ISHIGAKI on 2015-05-08) 1.47_04 DEV (ISHIGAKI on 2015-05-01) 1.47_03 DEV (ISHIGAKI on 2015-04-16) 1.47_02 DEV (ISHIGAKI on 2015-04-16) 1.47_01 DEV (ISHIGAKI on 2015-02-17) 1.46 (ISHIGAKI on 2014-12-10) 1.45_06 DEV (ISHIGAKI on 2014-11-26) 1.45_05 DEV (ISHIGAKI on 2014-11-25) 1.45_04 DEV (ISHIGAKI on 2014-10-28) 1.45_03 DEV (ISHIGAKI on 2014-10-24) 1.45_02 DEV (ISHIGAKI on 2014-10-23) 1.45_01 DEV (ISHIGAKI on 2014-10-22) 1.44 (ISHIGAKI on 2014-10-22) 1.43_09 DEV (ISHIGAKI on 2014-10-20) 1.43_08 DEV (ISHIGAKI on 2014-08-21) 1.43_07 DEV (ISHIGAKI on 2014-07-29) 1.43_06 DEV (ISHIGAKI on 2014-07-22) 1.43_05 DEV (ISHIGAKI on 2014-07-21) 1.43_04 DEV (ISHIGAKI on 2014-07-21) 1.43_03 DEV (ISHIGAKI on 2014-06-12) 1.43_02 DEV (ISHIGAKI on 2014-03-25) 1.43_01 DEV (ISHIGAKI on 2014-03-25) 1.42 (ISHIGAKI on 2014-03-19) 1.41_07 DEV (ISHIGAKI on 2014-03-13) 1.41_06 DEV (ISHIGAKI on 2014-02-12) 1.41_05 DEV (ISHIGAKI on 2014-01-22) 1.41_04 DEV (ISHIGAKI on 2014-01-12) 1.41_03 DEV (ISHIGAKI on 2013-09-04) 1.41_02 DEV (ISHIGAKI on 2013-08-29) 1.41_01 DEV (ISHIGAKI on 2013-08-27) 1.40 (ISHIGAKI on 2013-07-28) 1.39 (ISHIGAKI on 2013-06-09) 1.38_05 DEV (ISHIGAKI on 2013-05-31) 1.38_04 DEV (ISHIGAKI on 2013-05-29) 1.38_03 DEV (ADAMK on 2013-05-21) 1.38_02 DEV (ADAMK on 2013-04-09) 1.38_01 DEV (ADAMK on 2012-09-24) 1.37 (ADAMK on 2012-06-09) 1.36_04 DEV (ADAMK on 2012-05-19) 1.36_03 DEV (ADAMK on 2012-05-07) 1.36_02 DEV (ADAMK on 2012-02-23) 1.36_01 DEV (ADAMK on 2012-01-19) 1.35 (ADAMK on 2011-11-29) 1.34_03 DEV (ADAMK on 2011-11-01) 1.34_02 DEV (ADAMK on 2011-10-21) 1.34_01 DEV (ADAMK on 2011-09-21) 1.33 (ADAMK on 2011-05-30) 1.32_04 DEV (ADAMK on 2011-05-20) 1.32_03 DEV (ADAMK on 2011-05-12) 1.32_02 DEV (ADAMK on 2011-03-07) 1.32_01 DEV (ADAMK on 2010-12-10) 1.31 (ADAMK on 2010-09-15) 1.30_06 DEV (ADAMK on 2010-09-09) 1.30_05 DEV (ADAMK on 2010-08-27) 1.30_04 DEV (ADAMK on 2010-08-25) 1.30_03 DEV (ADAMK on 2010-05-31) 1.30_02 DEV (ADAMK on 2010-03-30) 1.30_01 DEV (ADAMK on 2010-03-10) 1.29 (ADAMK on 2010-01-08) 1.28_02 DEV (ADAMK on 2010-01-03) 1.28_01 DEV (ADAMK on 2009-12-23) 1.27 (ADAMK on 2009-11-23) 1.26_07 DEV (ADAMK on 2009-11-16) 1.26_06 DEV (ADAMK on 2009-10-28) 1.26_05 DEV (ADAMK on 2009-10-15) 1.26_04 DEV (ADAMK on 2009-10-06) 1.26_03 DEV (ADAMK on 2009-08-12) 1.26_02 DEV (ADAMK on 2009-06-19) 1.26_01 DEV (ADAMK on 2009-05-05) 1.25 (ADAMK on 2009-04-23) 1.24_02 DEV (ADAMK on 2009-04-23) 1.24_01 DEV (ADAMK on 2009-04-22) 1.23 (ADAMK on 2009-04-19) 1.22_08 DEV (ADAMK on 2009-04-17) 1.22_07 DEV (ADAMK on 2009-04-16) 1.22_06 DEV (ADAMK on 2009-04-15) 1.22_05 DEV (ADAMK on 2009-04-14) 1.22_04 DEV (ADAMK on 2009-04-11) 1.22_03 DEV (ADAMK on 2009-04-09) 1.22_02 DEV (ADAMK on 2009-04-08) 1.22_01 DEV (ADAMK on 2009-04-08) 1.21 (ADAMK on 2009-04-08) 1.20 (ADAMK on 2009-04-07) 1.19_10 DEV (ADAMK on 2009-04-05) 1.19_09 DEV (ADAMK on 2009-04-05) 1.19_08 DEV (ADAMK on 2009-04-04) 1.19_07 DEV (ADAMK on 2009-04-04) 1.19_06 DEV (ADAMK on 2009-04-03) 1.19_05 DEV (ADAMK on 2009-04-02) 1.19_04 DEV (ADAMK on 2009-03-31) 1.19_03 DEV (ADAMK on 2009-03-30) 1.19_02 DEV (ADAMK on 2009-03-28) 1.19_01 DEV (ADAMK on 2009-03-27) 1.14 (MSERGEANT on 2007-09-19) 1.13 (MSERGEANT on 2006-09-08) 1.12 (MSERGEANT on 2006-04-10) 1.11 (MSERGEANT on 2005-12-02) 1.10 (MSERGEANT on 2005-12-01) 1.09 (MSERGEANT on 2005-06-20) 1.08 (MSERGEANT on 2005-02-26) 1.07 (MSERGEANT on 2004-10-12) 1.06 (MSERGEANT on 2004-09-21) 1.05 (MSERGEANT on 2004-09-10) 1.04 (MSERGEANT on 2004-08-23) 1.03 (MSERGEANT on 2004-08-09) 1.02 (MSERGEANT on 2004-08-02) 1.01 (MSERGEANT on 2004-08-01) 1.00 (MSERGEANT on 2004-07-21) 0.31 (MSERGEANT on 2004-02-14) 0.30 (MSERGEANT on 2004-02-08) 0.29 (MSERGEANT on 2003-12-05) 0.28 (MSERGEANT on 2003-08-25) 0.27 (MSERGEANT on 2003-08-18) 0.26 (MSERGEANT on 2003-07-31) 0.25 (MSERGEANT on 2003-03-06) 0.24 (MSERGEANT on 2003-01-29) 0.23 (MSERGEANT on 2002-12-29) 0.22 (MSERGEANT on 2002-12-18) 0.21 (MSERGEANT on 2002-10-18) 0.20 (MSERGEANT on 2002-10-17) 0.19 (MSERGEANT on 2002-08-13) 0.18 (MSERGEANT on 2002-07-12) 0.17 (MSERGEANT on 2002-06-26) 0.16 (MSERGEANT on 2002-06-17) 0.15 (MSERGEANT on 2002-04-02) 0.14 (MSERGEANT on 2002-03-28) 0.13 (MSERGEANT on 2002-03-26) 0.12 (MSERGEANT on 2002-03-21) 0.11 (MSERGEANT on 2002-03-13) 0.10 (MSERGEANT on 2002-02-28) 0.09 (MSERGEANT on 2002-02-27) 0.08 (MSERGEANT on 2002-02-25) 0.07 (MSERGEANT on 2002-02-23) 0.06 (MSERGEANT on 2002-02-22) 0.05 (MSERGEANT on 2002-02-19) Diff with version 1.78 (ISHIGAKI on 2026-01-02) 1.77_03 DEV (ISHIGAKI on 2025-12-27) 1.77_02 DEV (ISHIGAKI on 2025-11-24) 1.77_01 DEV (ISHIGAKI on 2025-11-24) 1.76 (ISHIGAKI on 2024-10-19) 1.75_01 DEV (ISHIGAKI on 2024-09-17) 1.74 (ISHIGAKI on 2023-09-19) 1.73_01 DEV (ISHIGAKI on 2023-07-09) 1.72 (ISHIGAKI on 2022-11-03) 1.71_07 DEV (ISHIGAKI on 2022-10-25) 1.71_06 DEV (ISHIGAKI on 2022-03-12) 1.71_05 DEV (ISHIGAKI on 2022-02-26) 1.71_04 DEV (ISHIGAKI on 2022-02-26) 1.71_03 DEV (ISHIGAKI on 2022-02-23) 1.71_02 DEV (ISHIGAKI on 2022-01-06) 1.71_01 DEV (ISHIGAKI on 2021-12-01) 1.70 (ISHIGAKI on 2021-08-01) 1.69_02 DEV (ISHIGAKI on 2021-07-30) 1.69_01 DEV (ISHIGAKI on 2021-07-29) 1.68 (ISHIGAKI on 2021-07-22) 1.67_07 DEV (ISHIGAKI on 2021-06-19) 1.67_06 DEV (ISHIGAKI on 2021-06-14) 1.67_05 DEV (ISHIGAKI on 2021-06-12) 1.67_04 DEV (ISHIGAKI on 2021-05-30) 1.67_03 DEV (ISHIGAKI on 2021-03-30) 1.67_02 DEV (ISHIGAKI on 2020-12-05) 1.67_01 DEV (ISHIGAKI on 2020-11-24) 1.66 (ISHIGAKI on 2020-08-30) 1.65_03 DEV (ISHIGAKI on 2020-07-26) 1.65_02 DEV (ISHIGAKI on 2020-02-08) 1.65_01 DEV (ISHIGAKI on 2020-01-18) 1.64 (ISHIGAKI on 2019-08-12) 1.62 (ISHIGAKI on 2018-12-28) 1.60 (ISHIGAKI on 2018-12-01) 1.63_05 DEV (ISHIGAKI on 2019-07-11) 1.63_04 DEV (ISHIGAKI on 2019-05-24) 1.63_03 DEV (ISHIGAKI on 2019-02-14) 1.63_02 DEV (ISHIGAKI on 2019-02-13) 1.63_01 DEV (ISHIGAKI on 2019-01-25) 1.61_04 DEV (ISHIGAKI on 2018-12-22) 1.61_03 DEV (ISHIGAKI on 2018-12-19) 1.61_02 DEV (ISHIGAKI on 2018-12-01) 1.61_01 DEV (ISHIGAKI on 2018-12-01) 1.59_03 DEV (ISHIGAKI on 2018-11-03) 1.59_02 DEV (ISHIGAKI on 2018-09-30) 1.59_01 DEV (ISHIGAKI on 2018-09-16) 1.58 (ISHIGAKI on 2018-03-28) 1.57_01 DEV (ISHIGAKI on 2018-03-21) 1.56 (ISHIGAKI on 2018-02-28) 1.55_07 DEV (ISHIGAKI on 2018-01-27) 1.55_06 DEV (ISHIGAKI on 2018-01-27) 1.55_05 DEV (ISHIGAKI on 2017-12-15) 1.55_04 DEV (ISHIGAKI on 2017-11-21) 1.55_03 DEV (ISHIGAKI on 2017-02-14) 1.55_02 DEV (ISHIGAKI on 2017-01-07) 1.55_01 DEV (ISHIGAKI on 2017-01-03) 1.54 (ISHIGAKI on 2016-12-24) 1.53_01 DEV (ISHIGAKI on 2016-11-26) 1.52 (ISHIGAKI on 2016-11-15) 1.51_07 DEV (ISHIGAKI on 2016-10-16) 1.51_06 DEV (ISHIGAKI on 2016-10-15) 1.51_05 DEV (ISHIGAKI on 2016-06-23) 1.51_04 DEV (ISHIGAKI on 2016-03-07) 1.51_03 DEV (ISHIGAKI on 2016-02-20) 1.51_02 DEV (ISHIGAKI on 2016-02-20) 1.51_01 DEV (ISHIGAKI on 2016-02-20) 1.50 (ISHIGAKI on 2016-02-10) 1.49_08 DEV (ISHIGAKI on 2016-01-30) 1.49_07 DEV (ISHIGAKI on 2016-01-21) 1.49_06 DEV (ISHIGAKI on 2016-01-15) 1.49_05 DEV (ISHIGAKI on 2016-01-11) 1.49_04 DEV (ISHIGAKI on 2015-11-24) 1.49_03 DEV (ISHIGAKI on 2015-11-05) 1.49_02 DEV (ISHIGAKI on 2015-10-10) 1.49_01 DEV (ISHIGAKI on 2015-08-04) 1.48 (ISHIGAKI on 2015-06-11) 1.47_05 DEV (ISHIGAKI on 2015-05-08) 1.47_04 DEV (ISHIGAKI on 2015-05-01) 1.47_03 DEV (ISHIGAKI on 2015-04-16) 1.47_02 DEV (ISHIGAKI on 2015-04-16) 1.47_01 DEV (ISHIGAKI on 2015-02-17) 1.46 (ISHIGAKI on 2014-12-10) 1.45_06 DEV (ISHIGAKI on 2014-11-26) 1.45_05 DEV (ISHIGAKI on 2014-11-25) 1.45_04 DEV (ISHIGAKI on 2014-10-28) 1.45_03 DEV (ISHIGAKI on 2014-10-24) 1.45_02 DEV (ISHIGAKI on 2014-10-23) 1.45_01 DEV (ISHIGAKI on 2014-10-22) 1.44 (ISHIGAKI on 2014-10-22) 1.43_09 DEV (ISHIGAKI on 2014-10-20) 1.43_08 DEV (ISHIGAKI on 2014-08-21) 1.43_07 DEV (ISHIGAKI on 2014-07-29) 1.43_06 DEV (ISHIGAKI on 2014-07-22) 1.43_05 DEV (ISHIGAKI on 2014-07-21) 1.43_04 DEV (ISHIGAKI on 2014-07-21) 1.43_03 DEV (ISHIGAKI on 2014-06-12) 1.43_02 DEV (ISHIGAKI on 2014-03-25) 1.43_01 DEV (ISHIGAKI on 2014-03-25) 1.42 (ISHIGAKI on 2014-03-19) 1.41_07 DEV (ISHIGAKI on 2014-03-13) 1.41_06 DEV (ISHIGAKI on 2014-02-12) 1.41_05 DEV (ISHIGAKI on 2014-01-22) 1.41_04 DEV (ISHIGAKI on 2014-01-12) 1.41_03 DEV (ISHIGAKI on 2013-09-04) 1.41_02 DEV (ISHIGAKI on 2013-08-29) 1.41_01 DEV (ISHIGAKI on 2013-08-27) 1.40 (ISHIGAKI on 2013-07-28) 1.39 (ISHIGAKI on 2013-06-09) 1.38_05 DEV (ISHIGAKI on 2013-05-31) 1.38_04 DEV (ISHIGAKI on 2013-05-29) 1.38_03 DEV (ADAMK on 2013-05-21) 1.38_02 DEV (ADAMK on 2013-04-09) 1.38_01 DEV (ADAMK on 2012-09-24) 1.37 (ADAMK on 2012-06-09) 1.36_04 DEV (ADAMK on 2012-05-19) 1.36_03 DEV (ADAMK on 2012-05-07) 1.36_02 DEV (ADAMK on 2012-02-23) 1.36_01 DEV (ADAMK on 2012-01-19) 1.35 (ADAMK on 2011-11-29) 1.34_03 DEV (ADAMK on 2011-11-01) 1.34_02 DEV (ADAMK on 2011-10-21) 1.34_01 DEV (ADAMK on 2011-09-21) 1.33 (ADAMK on 2011-05-30) 1.32_04 DEV (ADAMK on 2011-05-20) 1.32_03 DEV (ADAMK on 2011-05-12) 1.32_02 DEV (ADAMK on 2011-03-07) 1.32_01 DEV (ADAMK on 2010-12-10) 1.31 (ADAMK on 2010-09-15) 1.30_06 DEV (ADAMK on 2010-09-09) 1.30_05 DEV (ADAMK on 2010-08-27) 1.30_04 DEV (ADAMK on 2010-08-25) 1.30_03 DEV (ADAMK on 2010-05-31) 1.30_02 DEV (ADAMK on 2010-03-30) 1.30_01 DEV (ADAMK on 2010-03-10) 1.29 (ADAMK on 2010-01-08) 1.28_02 DEV (ADAMK on 2010-01-03) 1.28_01 DEV (ADAMK on 2009-12-23) 1.27 (ADAMK on 2009-11-23) 1.26_07 DEV (ADAMK on 2009-11-16) 1.26_06 DEV (ADAMK on 2009-10-28) 1.26_05 DEV (ADAMK on 2009-10-15) 1.26_04 DEV (ADAMK on 2009-10-06) 1.26_03 DEV (ADAMK on 2009-08-12) 1.26_02 DEV (ADAMK on 2009-06-19) 1.26_01 DEV (ADAMK on 2009-05-05) 1.25 (ADAMK on 2009-04-23) 1.24_02 DEV (ADAMK on 2009-04-23) 1.24_01 DEV (ADAMK on 2009-04-22) 1.23 (ADAMK on 2009-04-19) 1.22_08 DEV (ADAMK on 2009-04-17) 1.22_07 DEV (ADAMK on 2009-04-16) 1.22_06 DEV (ADAMK on 2009-04-15) 1.22_05 DEV (ADAMK on 2009-04-14) 1.22_04 DEV (ADAMK on 2009-04-11) 1.22_03 DEV (ADAMK on 2009-04-09) 1.22_02 DEV (ADAMK on 2009-04-08) 1.22_01 DEV (ADAMK on 2009-04-08) 1.21 (ADAMK on 2009-04-08) 1.20 (ADAMK on 2009-04-07) 1.19_10 DEV (ADAMK on 2009-04-05) 1.19_09 DEV (ADAMK on 2009-04-05) 1.19_08 DEV (ADAMK on 2009-04-04) 1.19_07 DEV (ADAMK on 2009-04-04) 1.19_06 DEV (ADAMK on 2009-04-03) 1.19_05 DEV (ADAMK on 2009-04-02) 1.19_04 DEV (ADAMK on 2009-03-31) 1.19_03 DEV (ADAMK on 2009-03-30) 1.19_02 DEV (ADAMK on 2009-03-28) 1.19_01 DEV (ADAMK on 2009-03-27) 1.14 (MSERGEANT on 2007-09-19) 1.13 (MSERGEANT on 2006-09-08) 1.12 (MSERGEANT on 2006-04-10) 1.11 (MSERGEANT on 2005-12-02) 1.10 (MSERGEANT on 2005-12-01) 1.09 (MSERGEANT on 2005-06-20) 1.08 (MSERGEANT on 2005-02-26) 1.07 (MSERGEANT on 2004-10-12) 1.06 (MSERGEANT on 2004-09-21) 1.05 (MSERGEANT on 2004-09-10) 1.04 (MSERGEANT on 2004-08-23) 1.03 (MSERGEANT on 2004-08-09) 1.02 (MSERGEANT on 2004-08-02) 1.01 (MSERGEANT on 2004-08-01) 1.00 (MSERGEANT on 2004-07-21) 0.31 (MSERGEANT on 2004-02-14) 0.30 (MSERGEANT on 2004-02-08) 0.29 (MSERGEANT on 2003-12-05) 0.28 (MSERGEANT on 2003-08-25) 0.27 (MSERGEANT on 2003-08-18) 0.26 (MSERGEANT on 2003-07-31) 0.25 (MSERGEANT on 2003-03-06) 0.24 (MSERGEANT on 2003-01-29) 0.23 (MSERGEANT on 2002-12-29) 0.22 (MSERGEANT on 2002-12-18) 0.21 (MSERGEANT on 2002-10-18) 0.20 (MSERGEANT on 2002-10-17) 0.19 (MSERGEANT on 2002-08-13) 0.18 (MSERGEANT on 2002-07-12) 0.17 (MSERGEANT on 2002-06-26) 0.16 (MSERGEANT on 2002-06-17) 0.15 (MSERGEANT on 2002-04-02) 0.14 (MSERGEANT on 2002-03-28) 0.13 (MSERGEANT on 2002-03-26) 0.12 (MSERGEANT on 2002-03-21) 0.11 (MSERGEANT on 2002-03-13) 0.10 (MSERGEANT on 2002-02-28) 0.09 (MSERGEANT on 2002-02-27) 0.08 (MSERGEANT on 2002-02-25) 0.07 (MSERGEANT on 2002-02-23) 0.06 (MSERGEANT on 2002-02-22) 0.05 (MSERGEANT on 2002-02-19) Permalinks This version Latest version ++ed by: 56 PAUSE users 50 non-PAUSE users Authors: Adam Kennedy Released by: Kenichi Ishigaki Maintainers: ISHIGAKI owner ADAMK DUNCAND MSERGEANT Contributors: Adam Kennedy Kenichi Ishigaki  /  1.78 (ISHIGAKI on 2026-01-02) 1.77_03 DEV (ISHIGAKI on 2025-12-27) 1.77_02 DEV (ISHIGAKI on 2025-11-24) 1.77_01 DEV (ISHIGAKI on 2025-11-24) 1.76 (ISHIGAKI on 2024-10-19) 1.75_01 DEV (ISHIGAKI on 2024-09-17) 1.74 (ISHIGAKI on 2023-09-19) 1.73_01 DEV (ISHIGAKI on 2023-07-09) 1.72 (ISHIGAKI on 2022-11-03) 1.71_07 DEV (ISHIGAKI on 2022-10-25) 1.71_06 DEV (ISHIGAKI on 2022-03-12) 1.71_05 DEV (ISHIGAKI on 2022-02-26) 1.71_04 DEV (ISHIGAKI on 2022-02-26) 1.71_03 DEV (ISHIGAKI on 2022-02-23) 1.71_02 DEV (ISHIGAKI on 2022-01-06) 1.71_01 DEV (ISHIGAKI on 2021-12-01) 1.70 (ISHIGAKI on 2021-08-01) 1.69_02 DEV (ISHIGAKI on 2021-07-30) 1.69_01 DEV (ISHIGAKI on 2021-07-29) 1.68 (ISHIGAKI on 2021-07-22) 1.67_07 DEV (ISHIGAKI on 2021-06-19) 1.67_06 DEV (ISHIGAKI on 2021-06-14) 1.67_05 DEV (ISHIGAKI on 2021-06-12) 1.67_04 DEV (ISHIGAKI on 2021-05-30) 1.67_03 DEV (ISHIGAKI on 2021-03-30) 1.67_02 DEV (ISHIGAKI on 2020-12-05) 1.67_01 DEV (ISHIGAKI on 2020-11-24) 1.66 (ISHIGAKI on 2020-08-30) 1.65_03 DEV (ISHIGAKI on 2020-07-26) 1.65_02 DEV (ISHIGAKI on 2020-02-08) 1.65_01 DEV (ISHIGAKI on 2020-01-18) 1.64 (ISHIGAKI on 2019-08-12) 1.62 (ISHIGAKI on 2018-12-28) 1.60 (ISHIGAKI on 2018-12-01) 1.63_05 DEV (ISHIGAKI on 2019-07-11) 1.63_04 DEV (ISHIGAKI on 2019-05-24) 1.63_03 DEV (ISHIGAKI on 2019-02-14) 1.63_02 DEV (ISHIGAKI on 2019-02-13) 1.63_01 DEV (ISHIGAKI on 2019-01-25) 1.61_04 DEV (ISHIGAKI on 2018-12-22) 1.61_03 DEV (ISHIGAKI on 2018-12-19) 1.61_02 DEV (ISHIGAKI on 2018-12-01) 1.61_01 DEV (ISHIGAKI on 2018-12-01) 1.59_03 DEV (ISHIGAKI on 2018-11-03) 1.59_02 DEV (ISHIGAKI on 2018-09-30) 1.59_01 DEV (ISHIGAKI on 2018-09-16) 1.58 (ISHIGAKI on 2018-03-28) 1.57_01 DEV (ISHIGAKI on 2018-03-21) 1.56 (ISHIGAKI on 2018-02-28) 1.55_07 DEV (ISHIGAKI on 2018-01-27) 1.55_06 DEV (ISHIGAKI on 2018-01-27) 1.55_05 DEV (ISHIGAKI on 2017-12-15) 1.55_04 DEV (ISHIGAKI on 2017-11-21) 1.55_03 DEV (ISHIGAKI on 2017-02-14) 1.55_02 DEV (ISHIGAKI on 2017-01-07) 1.55_01 DEV (ISHIGAKI on 2017-01-03) 1.54 (ISHIGAKI on 2016-12-24) 1.53_01 DEV (ISHIGAKI on 2016-11-26) 1.52 (ISHIGAKI on 2016-11-15) 1.51_07 DEV (ISHIGAKI on 2016-10-16) 1.51_06 DEV (ISHIGAKI on 2016-10-15) 1.51_05 DEV (ISHIGAKI on 2016-06-23) 1.51_04 DEV (ISHIGAKI on 2016-03-07) 1.51_03 DEV (ISHIGAKI on 2016-02-20) 1.51_02 DEV (ISHIGAKI on 2016-02-20) 1.51_01 DEV (ISHIGAKI on 2016-02-20) 1.50 (ISHIGAKI on 2016-02-10) 1.49_08 DEV (ISHIGAKI on 2016-01-30) 1.49_07 DEV (ISHIGAKI on 2016-01-21) 1.49_06 DEV (ISHIGAKI on 2016-01-15) 1.49_05 DEV (ISHIGAKI on 2016-01-11) 1.49_04 DEV (ISHIGAKI on 2015-11-24) 1.49_03 DEV (ISHIGAKI on 2015-11-05) 1.49_02 DEV (ISHIGAKI on 2015-10-10) 1.49_01 DEV (ISHIGAKI on 2015-08-04) 1.48 (ISHIGAKI on 2015-06-11) 1.47_05 DEV (ISHIGAKI on 2015-05-08) 1.47_04 DEV (ISHIGAKI on 2015-05-01) 1.47_03 DEV (ISHIGAKI on 2015-04-16) 1.47_02 DEV (ISHIGAKI on 2015-04-16) 1.47_01 DEV (ISHIGAKI on 2015-02-17) 1.46 (ISHIGAKI on 2014-12-10) 1.45_06 DEV (ISHIGAKI on 2014-11-26) 1.45_05 DEV (ISHIGAKI on 2014-11-25) 1.45_04 DEV (ISHIGAKI on 2014-10-28) 1.45_03 DEV (ISHIGAKI on 2014-10-24) 1.45_02 DEV (ISHIGAKI on 2014-10-23) 1.45_01 DEV (ISHIGAKI on 2014-10-22) 1.44 (ISHIGAKI on 2014-10-22) 1.43_09 DEV (ISHIGAKI on 2014-10-20) 1.43_08 DEV (ISHIGAKI on 2014-08-21) 1.43_07 DEV (ISHIGAKI on 2014-07-29) 1.43_06 DEV (ISHIGAKI on 2014-07-22) 1.43_05 DEV (ISHIGAKI on 2014-07-21) 1.43_04 DEV (ISHIGAKI on 2014-07-21) 1.43_03 DEV (ISHIGAKI on 2014-06-12) 1.43_02 DEV (ISHIGAKI on 2014-03-25) 1.43_01 DEV (ISHIGAKI on 2014-03-25) 1.42 (ISHIGAKI on 2014-03-19) 1.41_07 DEV (ISHIGAKI on 2014-03-13) 1.41_06 DEV (ISHIGAKI on 2014-02-12) 1.41_05 DEV (ISHIGAKI on 2014-01-22) 1.41_04 DEV (ISHIGAKI on 2014-01-12) 1.41_03 DEV (ISHIGAKI on 2013-09-04) 1.41_02 DEV (ISHIGAKI on 2013-08-29) 1.41_01 DEV (ISHIGAKI on 2013-08-27) 1.40 (ISHIGAKI on 2013-07-28) 1.39 (ISHIGAKI on 2013-06-09) 1.38_05 DEV (ISHIGAKI on 2013-05-31) 1.38_04 DEV (ISHIGAKI on 2013-05-29) 1.38_03 DEV (ADAMK on 2013-05-21) 1.38_02 DEV (ADAMK on 2013-04-09) 1.38_01 DEV (ADAMK on 2012-09-24) 1.37 (ADAMK on 2012-06-09) 1.36_04 DEV (ADAMK on 2012-05-19) 1.36_03 DEV (ADAMK on 2012-05-07) 1.36_02 DEV (ADAMK on 2012-02-23) 1.36_01 DEV (ADAMK on 2012-01-19) 1.35 (ADAMK on 2011-11-29) 1.34_03 DEV (ADAMK on 2011-11-01) 1.34_02 DEV (ADAMK on 2011-10-21) 1.34_01 DEV (ADAMK on 2011-09-21) 1.33 (ADAMK on 2011-05-30) 1.32_04 DEV (ADAMK on 2011-05-20) 1.32_03 DEV (ADAMK on 2011-05-12) 1.32_02 DEV (ADAMK on 2011-03-07) 1.32_01 DEV (ADAMK on 2010-12-10) 1.31 (ADAMK on 2010-09-15) 1.30_06 DEV (ADAMK on 2010-09-09) 1.30_05 DEV (ADAMK on 2010-08-27) 1.30_04 DEV (ADAMK on 2010-08-25) 1.30_03 DEV (ADAMK on 2010-05-31) 1.30_02 DEV (ADAMK on 2010-03-30) 1.30_01 DEV (ADAMK on + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-dbd-sqlite --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-dbd-sqlite 1.50 1 +---------------------- +file name : perl-dbd-sqlite-1.50-1.tar.bz2 +name : perl-dbd-sqlite +version : 1.50 +build : 1 +build number: 1 +size : 1.8 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.50-1.tar.bz2 +md5 : 4b2e60fe36352b556aad78ca69a5677e +dependencies: + - perl-dbi + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-dbd-sqlite 1.50 pl526h470a237_2 +------------------------------------ +file name : perl-dbd-sqlite-1.50-pl526h470a237_2.tar.bz2 +name : perl-dbd-sqlite +version : 1.50 +build : pl526h470a237_2 +build number: 2 +size : 1.8 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.50-pl526h470a237_2.tar.bz2 +md5 : c24147d1f833a554adf757677b430f2c +timestamp : 2018-07-08 18:06:34 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.27.0a0 + - perl-dbi + + +perl-dbd-sqlite 1.50 pl526h470a237_3 +------------------------------------ +file name : perl-dbd-sqlite-1.50-pl526h470a237_3.tar.bz2 +name : perl-dbd-sqlite +version : 1.50 +build : pl526h470a237_3 +build number: 3 +size : 1.8 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.50-pl526h470a237_3.tar.bz2 +md5 : 786488cab04254423601ae98408ab910 +timestamp : 2018-08-03 13:42:43 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-dbi + + +perl-dbd-sqlite 1.58 pl526h470a237_0 +------------------------------------ +file name : perl-dbd-sqlite-1.58-pl526h470a237_0.tar.bz2 +name : perl-dbd-sqlite +version : 1.58 +build : pl526h470a237_0 +build number: 0 +size : 2.1 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.58-pl526h470a237_0.tar.bz2 +md5 : a6671063472ff5598850f2f4ce0bf795 +timestamp : 2018-11-11 06:38:13 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-dbi + + +perl-dbd-sqlite 1.60 pl526h470a237_0 +------------------------------------ +file name : perl-dbd-sqlite-1.60-pl526h470a237_0.tar.bz2 +name : perl-dbd-sqlite +version : 1.60 +build : pl526h470a237_0 +build number: 0 +size : 2.2 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.60-pl526h470a237_0.tar.bz2 +md5 : f639f151a2bdcc033b22c127adeed4df +timestamp : 2018-12-07 02:37:37 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-dbi + + +perl-dbd-sqlite 1.62 pl526h14c3975_0 +------------------------------------ +file name : perl-dbd-sqlite-1.62-pl526h14c3975_0.tar.bz2 +name : perl-dbd-sqlite +version : 1.62 +build : pl526h14c3975_0 +build number: 0 +size : 2.2 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.62-pl526h14c3975_0.tar.bz2 +md5 : 031a764f1188f69621a1b6d30b850eb3 +timestamp : 2019-05-07 20:30:38 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-dbi + + +perl-dbd-sqlite 1.62 pl526h14c3975_1 +------------------------------------ +file name : perl-dbd-sqlite-1.62-pl526h14c3975_1.tar.bz2 +name : perl-dbd-sqlite +version : 1.62 +build : pl526h14c3975_1 +build number: 1 +size : 2.2 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.62-pl526h14c3975_1.tar.bz2 +md5 : 7c445460d9cec2360f0246d8a0b4275b +timestamp : 2019-05-07 04:28:45 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-dbi + + +perl-dbd-sqlite 1.64 pl526h516909a_0 +------------------------------------ +file name : perl-dbd-sqlite-1.64-pl526h516909a_0.tar.bz2 +name : perl-dbd-sqlite +version : 1.64 +build : pl526h516909a_0 +build number: 0 +size : 2.3 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.64-pl526h516909a_0.tar.bz2 +md5 : e174559d63638b9b1ff18e063f0b3173 +timestamp : 2019-08-12 12:53:17 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-dbi + + +perl-dbd-sqlite 1.64 pl5321h779adbc_1 +------------------------------------- +file name : perl-dbd-sqlite-1.64-pl5321h779adbc_1.tar.bz2 +name : perl-dbd-sqlite +version : 1.64 +build : pl5321h779adbc_1 +build number: 1 +size : 2.3 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.64-pl5321h779adbc_1.tar.bz2 +md5 : 7196fd6a5d74f3a1f1059bfffa8405b8 +timestamp : 2022-01-20 01:36:40 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi + + +perl-dbd-sqlite 1.70 pl5321h779adbc_0 +------------------------------------- +file name : perl-dbd-sqlite-1.70-pl5321h779adbc_0.tar.bz2 +name : perl-dbd-sqlite +version : 1.70 +build : pl5321h779adbc_0 +build number: 0 +size : 2.4 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.70-pl5321h779adbc_0.tar.bz2 +md5 : e662977a22b59c4502771cf69a79406c +timestamp : 2022-02-09 17:44:46 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi + + +perl-dbd-sqlite 1.70 pl5321h779adbc_1 +------------------------------------- +file name : perl-dbd-sqlite-1.70-pl5321h779adbc_1.tar.bz2 +name : perl-dbd-sqlite +version : 1.70 +build : pl5321h779adbc_1 +build number: 1 +size : 2.4 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.70-pl5321h779adbc_1.tar.bz2 +md5 : ffc01ad775939d47fb45dcce7d896f17 +timestamp : 2022-02-11 11:11:01 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi + + +perl-dbd-sqlite 1.70 pl5321hec16e2b_2 +------------------------------------- +file name : perl-dbd-sqlite-1.70-pl5321hec16e2b_2.tar.bz2 +name : perl-dbd-sqlite +version : 1.70 +build : pl5321hec16e2b_2 +build number: 2 +size : 2.4 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.70-pl5321hec16e2b_2.tar.bz2 +md5 : c4f838110498c065f6e1981ece1a2991 +timestamp : 2022-02-24 08:02:05 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi + + +perl-dbd-sqlite 1.72 pl5321h031d066_1 +------------------------------------- +file name : perl-dbd-sqlite-1.72-pl5321h031d066_1.tar.bz2 +name : perl-dbd-sqlite +version : 1.72 +build : pl5321h031d066_1 +build number: 1 +size : 2.5 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.72-pl5321h031d066_1.tar.bz2 +md5 : 11d1a1260ab40084bb6b8130b4b7ecef +timestamp : 2023-05-15 21:57:49 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi + + +perl-dbd-sqlite 1.72 pl5321h031d066_2 +------------------------------------- +file name : perl-dbd-sqlite-1.72-pl5321h031d066_2.tar.bz2 +name : perl-dbd-sqlite +version : 1.72 +build : pl5321h031d066_2 +build number: 2 +size : 2.5 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.72-pl5321h031d066_2.tar.bz2 +md5 : 3fa910311761f388a2722f7f6fd7d67d +timestamp : 2024-11-28 11:19:15 UTC +dependencies: + - libgcc >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi + + +perl-dbd-sqlite 1.72 pl5321hec16e2b_0 +------------------------------------- +file name : perl-dbd-sqlite-1.72-pl5321hec16e2b_0.tar.bz2 +name : perl-dbd-sqlite +version : 1.72 +build : pl5321hec16e2b_0 +build number: 0 +size : 2.5 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.72-pl5321hec16e2b_0.tar.bz2 +md5 : 9cc9271d6c8746258ae0efb6f2a716b6 +timestamp : 2022-11-03 17:27:49 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi + + +perl-dbd-sqlite 1.76 pl5321h031d066_0 +------------------------------------- +file name : perl-dbd-sqlite-1.76-pl5321h031d066_0.tar.bz2 +name : perl-dbd-sqlite +version : 1.76 +build : pl5321h031d066_0 +build number: 0 +size : 2.6 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.76-pl5321h031d066_0.tar.bz2 +md5 : f10a34631b3071da94310f802ed32313 +timestamp : 2024-11-28 19:25:47 UTC +dependencies: + - libgcc >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi + + +perl-dbd-sqlite 1.76 pl5321h7b50bb2_1 +------------------------------------- +file name : perl-dbd-sqlite-1.76-pl5321h7b50bb2_1.tar.bz2 +name : perl-dbd-sqlite +version : 1.76 +build : pl5321h7b50bb2_1 +build number: 1 +size : 2.6 MB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.76-pl5321h7b50bb2_1.tar.bz2 +md5 : 078f37aa0685137badc1b77f438380ea +timestamp : 2024-12-14 03:55:01 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi + + +perl-dbd-sqlite 1.76 pl5321h7b50bb2_2 +------------------------------------- +file name : perl-dbd-sqlite-1.76-pl5321h7b50bb2_2.tar.bz2 +name : perl-dbd-sqlite +version : 1.76 +build : pl5321h7b50bb2_2 +build number: 2 +size : 2.6 MB +license : Perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.76-pl5321h7b50bb2_2.tar.bz2 +md5 : dc7f1724a4ddfdecec5786a23b5e1036 +timestamp : 2025-07-24 09:37:34 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi + + +perl-dbd-sqlite 1.78 pl5321h6709bd3_0 +------------------------------------- +file name : perl-dbd-sqlite-1.78-pl5321h6709bd3_0.conda +name : perl-dbd-sqlite +version : 1.78 +build : pl5321h6709bd3_0 +build number: 0 +size : 2.5 MB +license : Perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.78-pl5321h6709bd3_0.conda +md5 : 36a7da8d7887a0b2bb82e5b809be784f +timestamp : 2026-01-15 05:17:22 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dbi diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-devel-stacktrace.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-devel-stacktrace.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b58a8b44ba30e8c766a176931437b4fbe99ec5e5 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-devel-stacktrace.manual_bundle.txt @@ -0,0 +1,185 @@ +# Tool: perl-devel-stacktrace +software_name: perl-devel-stacktrace +tier: T1 +domain: t1_backfill_overall +downloads: 320118 +summary: An object representing a stack trace +description: An object representing a stack trace +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/release/Devel-StackTrace +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/release/Devel-StackTrace +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-devel-stacktrace --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-devel-stacktrace 2.00 0 +---------------------------- +file name : perl-devel-stacktrace-2.00-0.tar.bz2 +name : perl-devel-stacktrace +version : 2.00 +build : 0 +build number: 0 +size : 7 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-devel-stacktrace-2.00-0.tar.bz2 +md5 : 9b405bfb4a583a34b8fe27ef7f5247a3 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-devel-stacktrace 2.03 pl5.22.0_0 +------------------------------------- +file name : perl-devel-stacktrace-2.03-pl5.22.0_0.tar.bz2 +name : perl-devel-stacktrace +version : 2.03 +build : pl5.22.0_0 +build number: 0 +size : 14 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-devel-stacktrace-2.03-pl5.22.0_0.tar.bz2 +md5 : 3a8ea61ceffc9c3cbb281cf257c5fa2d +dependencies: + - perl 5.22.0* + + +perl-devel-stacktrace 2.03 pl526_1 +---------------------------------- +file name : perl-devel-stacktrace-2.03-pl526_1.tar.bz2 +name : perl-devel-stacktrace +version : 2.03 +build : pl526_1 +build number: 1 +size : 14 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-devel-stacktrace-2.03-pl526_1.tar.bz2 +md5 : cd9158b3c11b5cccecc7ea0bc7daddbd +timestamp : 2018-07-07 17:00:15 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-devel-stacktrace 2.04 pl526_0 +---------------------------------- +file name : perl-devel-stacktrace-2.04-pl526_0.tar.bz2 +name : perl-devel-stacktrace +version : 2.04 +build : pl526_0 +build number: 0 +size : 16 KB +license : artistic_2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-devel-stacktrace-2.04-pl526_0.tar.bz2 +md5 : c26d7ca3e81c27cf6b1883fc16bc98eb +timestamp : 2019-05-26 20:27:46 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-devel-stacktrace 2.04 pl5321h296ab09_0 +------------------------------------------- +file name : perl-devel-stacktrace-2.04-pl5321h296ab09_0.conda +name : perl-devel-stacktrace +version : 2.04 +build : pl5321h296ab09_0 +build number: 0 +size : 20 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-devel-stacktrace-2.04-pl5321h296ab09_0.conda +md5 : dd8fdb871a43e20da8d419e08a25aabc +timestamp : 2025-04-23 07:50:19 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-devel-stacktrace 2.04 pl5321ha770c72_0 +------------------------------------------- +file name : perl-devel-stacktrace-2.04-pl5321ha770c72_0.conda +name : perl-devel-stacktrace +version : 2.04 +build : pl5321ha770c72_0 +build number: 0 +size : 18 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-devel-stacktrace-2.04-pl5321ha770c72_0.conda +md5 : 66856471d98bc726af849694a7f6ea0f +timestamp : 2022-11-23 21:46:49 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-devel-stacktrace 2.04 pl5321hdfd78af_1 +------------------------------------------- +file name : perl-devel-stacktrace-2.04-pl5321hdfd78af_1.tar.bz2 +name : perl-devel-stacktrace +version : 2.04 +build : pl5321hdfd78af_1 +build number: 1 +size : 17 KB +license : artistic_2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-devel-stacktrace-2.04-pl5321hdfd78af_1.tar.bz2 +md5 : 7446f526072f9ed4518e90d0575f962e +timestamp : 2022-01-18 12:28:24 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-dynaloader.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-dynaloader.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ff903b3ee7048f9313d07fd7caa6b016db5f9023 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-dynaloader.manual_bundle.txt @@ -0,0 +1,110 @@ +# Tool: perl-dynaloader +software_name: perl-dynaloader +tier: T1 +domain: t1_backfill_overall +downloads: 225942 +summary: +description: +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-dynaloader --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-dynaloader 1.25 pl5.22.0_0 +------------------------------- +file name : perl-dynaloader-1.25-pl5.22.0_0.tar.bz2 +name : perl-dynaloader +version : 1.25 +build : pl5.22.0_0 +build number: 0 +size : 2 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dynaloader-1.25-pl5.22.0_0.tar.bz2 +md5 : 3eefc9828af124f4118a31a050c22a9d +dependencies: + - perl 5.22.0* + + +perl-dynaloader 1.25 pl526_1 +---------------------------- +file name : perl-dynaloader-1.25-pl526_1.tar.bz2 +name : perl-dynaloader +version : 1.25 +build : pl526_1 +build number: 1 +size : 3 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-dynaloader-1.25-pl526_1.tar.bz2 +md5 : f8ef9b13d527c472a2a33a9218043f47 +timestamp : 2018-07-15 11:01:35 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-dynaloader 1.25 pl5321hdfd78af_2 +------------------------------------- +file name : perl-dynaloader-1.25-pl5321hdfd78af_2.tar.bz2 +name : perl-dynaloader +version : 1.25 +build : pl5321hdfd78af_2 +build number: 2 +size : 6 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-dynaloader-1.25-pl5321hdfd78af_2.tar.bz2 +md5 : 567e5714e227fec42659a2bc3fbc0031 +timestamp : 2022-01-16 23:52:48 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-email-date-format.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-email-date-format.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..efce1c15753344df15f12761963dafeb87717148 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-email-date-format.manual_bundle.txt @@ -0,0 +1,145 @@ +# Tool: perl-email-date-format +software_name: perl-email-date-format +tier: T1 +domain: t1_backfill_overall +downloads: 185813 +summary: produce RFC 2822 date strings +description: produce RFC 2822 date strings +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-email-date-format --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-email-date-format 1.005 0 +------------------------------ +file name : perl-email-date-format-1.005-0.tar.bz2 +name : perl-email-date-format +version : 1.005 +build : 0 +build number: 0 +size : 3 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-email-date-format-1.005-0.tar.bz2 +md5 : 1a0decded428932e3131937fffd8b238 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-email-date-format 1.005 pl526_1 +------------------------------------ +file name : perl-email-date-format-1.005-pl526_1.tar.bz2 +name : perl-email-date-format +version : 1.005 +build : pl526_1 +build number: 1 +size : 7 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-email-date-format-1.005-pl526_1.tar.bz2 +md5 : 7280b44a80e6eaddae0e88d2531ca5b2 +timestamp : 2018-07-07 16:38:45 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-email-date-format 1.005 pl526_2 +------------------------------------ +file name : perl-email-date-format-1.005-pl526_2.tar.bz2 +name : perl-email-date-format +version : 1.005 +build : pl526_2 +build number: 2 +size : 8 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-email-date-format-1.005-pl526_2.tar.bz2 +md5 : 7c2c2c488712dd3ae36a829a9db2e3cf +timestamp : 2019-03-09 11:47:07 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-email-date-format 1.005 pl5321hdfd78af_3 +--------------------------------------------- +file name : perl-email-date-format-1.005-pl5321hdfd78af_3.tar.bz2 +name : perl-email-date-format +version : 1.005 +build : pl5321hdfd78af_3 +build number: 3 +size : 9 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-email-date-format-1.005-pl5321hdfd78af_3.tar.bz2 +md5 : d27b88f0c08de0693f5a4661a5ae7496 +timestamp : 2022-01-17 11:38:05 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-email-date-format 1.006 pl5321hd8ed1ab_0 +--------------------------------------------- +file name : perl-email-date-format-1.006-pl5321hd8ed1ab_0.tar.bz2 +name : perl-email-date-format +version : 1.006 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 18 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-email-date-format-1.006-pl5321hd8ed1ab_0.tar.bz2 +md5 : 0999c7c51f78d426cafd3cfbdb7ee2b9 +timestamp : 2022-10-23 12:53:20 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-eval-closure.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-eval-closure.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..7876a5a694e866b11da0fbf907561427c93f8a04 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-eval-closure.manual_bundle.txt @@ -0,0 +1,204 @@ +# Tool: perl-eval-closure +software_name: perl-eval-closure +tier: T1 +domain: t1_backfill_overall +downloads: 258042 +summary: +description: +dependencies: libgcc-ng >=10.3.0, libstdcxx-ng >=10.3.0, perl >=5.32.1,<5.33.0a0 *_perl5, perl-carp, perl-constant, perl-exporter +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-eval-closure --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-eval-closure 0.14 pl5.22.0_0 +--------------------------------- +file name : perl-eval-closure-0.14-pl5.22.0_0.tar.bz2 +name : perl-eval-closure +version : 0.14 +build : pl5.22.0_0 +build number: 0 +size : 90 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-eval-closure-0.14-pl5.22.0_0.tar.bz2 +md5 : 6d220740c66feb3268ab548576d63953 +dependencies: + - perl 5.22.0* + - perl-app-cpanminus + - perl-test2-suite + + +perl-eval-closure 0.14 pl526_1 +------------------------------ +file name : perl-eval-closure-0.14-pl526_1.tar.bz2 +name : perl-eval-closure +version : 0.14 +build : pl526_1 +build number: 1 +size : 121 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-eval-closure-0.14-pl526_1.tar.bz2 +md5 : ffe94b2bb1f9500d20a9ebedd6fbe121 +timestamp : 2018-07-08 22:07:52 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-app-cpanminus + - perl-test2-suite + + +perl-eval-closure 0.14 pl526h2d50403_3 +-------------------------------------- +file name : perl-eval-closure-0.14-pl526h2d50403_3.tar.bz2 +name : perl-eval-closure +version : 0.14 +build : pl526h2d50403_3 +build number: 3 +size : 121 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-eval-closure-0.14-pl526h2d50403_3.tar.bz2 +md5 : 6c0e981c940fec88246df04bcc478c02 +timestamp : 2018-07-24 17:27:22 UTC +dependencies: + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-app-cpanminus + - perl-test2-suite + + +perl-eval-closure 0.14 pl526h6bb024c_4 +-------------------------------------- +file name : perl-eval-closure-0.14-pl526h6bb024c_4.tar.bz2 +name : perl-eval-closure +version : 0.14 +build : pl526h6bb024c_4 +build number: 4 +size : 11 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-eval-closure-0.14-pl526h6bb024c_4.tar.bz2 +md5 : 156f357c5abfa8690d8591ac8724235b +timestamp : 2019-05-02 22:18:54 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-carp + - perl-constant + - perl-exporter + + +perl-eval-closure 0.14 pl5321h7d875b9_5 +--------------------------------------- +file name : perl-eval-closure-0.14-pl5321h7d875b9_5.tar.bz2 +name : perl-eval-closure +version : 0.14 +build : pl5321h7d875b9_5 +build number: 5 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-eval-closure-0.14-pl5321h7d875b9_5.tar.bz2 +md5 : 34fc2851b72b45e3a10a36de02c38353 +timestamp : 2022-01-19 20:42:44 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-constant + - perl-exporter + + +perl-eval-closure 0.14 pl5321h9f5acd7_6 +--------------------------------------- +file name : perl-eval-closure-0.14-pl5321h9f5acd7_6.tar.bz2 +name : perl-eval-closure +version : 0.14 +build : pl5321h9f5acd7_6 +build number: 6 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-eval-closure-0.14-pl5321h9f5acd7_6.tar.bz2 +md5 : 1339fd6a2aa5fd2a58b94934e36d8fcf +timestamp : 2022-02-24 12:07:32 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-constant + - perl-exporter + + +perl-eval-closure 0.14 pl5321ha770c72_0 +--------------------------------------- +file name : perl-eval-closure-0.14-pl5321ha770c72_0.conda +name : perl-eval-closure +version : 0.14 +build : pl5321ha770c72_0 +build number: 0 +size : 19 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-eval-closure-0.14-pl5321ha770c72_0.conda +md5 : d4accc3fd843c55e5cca569b88b6fe1d +timestamp : 2023-01-23 13:38:23 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-test-fatal 0.016.* diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-exporter.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-exporter.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c91f58cb3bb9ec284248b36624deef40e8ecc072 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-exporter.manual_bundle.txt @@ -0,0 +1,165 @@ +# Tool: perl-exporter +software_name: perl-exporter +tier: T1 +domain: t1_backfill_overall +downloads: 977491 +summary: +description: +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-exporter --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-exporter 5.72 pl5.22.0_0 +----------------------------- +file name : perl-exporter-5.72-pl5.22.0_0.tar.bz2 +name : perl-exporter +version : 5.72 +build : pl5.22.0_0 +build number: 0 +size : 12 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-exporter-5.72-pl5.22.0_0.tar.bz2 +md5 : d0b76a9b093554c552209b174a3cda32 +dependencies: + - perl 5.22.0* + + +perl-exporter 5.72 pl526_1 +-------------------------- +file name : perl-exporter-5.72-pl526_1.tar.bz2 +name : perl-exporter +version : 5.72 +build : pl526_1 +build number: 1 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-exporter-5.72-pl526_1.tar.bz2 +md5 : 5ecf4d143181f4a4d71349811ea29177 +timestamp : 2018-07-08 17:32:10 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-exporter 5.72 pl5321hd8ed1ab_0 +----------------------------------- +file name : perl-exporter-5.72-pl5321hd8ed1ab_0.tar.bz2 +name : perl-exporter +version : 5.72 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 19 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-exporter-5.72-pl5321hd8ed1ab_0.tar.bz2 +md5 : 9d5668af1c317b6042ece034562254f6 +timestamp : 2021-11-11 15:41:18 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-exporter 5.72 pl5321hdfd78af_2 +----------------------------------- +file name : perl-exporter-5.72-pl5321hdfd78af_2.tar.bz2 +name : perl-exporter +version : 5.72 +build : pl5321hdfd78af_2 +build number: 2 +size : 16 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-exporter-5.72-pl5321hdfd78af_2.tar.bz2 +md5 : 7353e88329199d78b6e4c7bef4fc835e +timestamp : 2022-01-17 22:02:56 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-exporter 5.74 pl5321hd8ed1ab_0 +----------------------------------- +file name : perl-exporter-5.74-pl5321hd8ed1ab_0.tar.bz2 +name : perl-exporter +version : 5.74 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 19 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-exporter-5.74-pl5321hd8ed1ab_0.tar.bz2 +md5 : fd2eac4e35f8c970870a3961c1df3e29 +timestamp : 2021-11-12 05:46:49 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-exporter 5.79 pl5422h06a4308_0 +----------------------------------- +file name : perl-exporter-5.79-pl5422h06a4308_0.conda +name : perl-exporter +version : 5.79 +build : pl5422h06a4308_0 +build number: 0 +size : 15 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://repo.anaconda.com/pkgs/main/linux-64/perl-exporter-5.79-pl5422h06a4308_0.conda +md5 : 1cd227188ddf7d03c7460d1a5a990afe +timestamp : 2026-04-08 21:31:56 UTC +dependencies: + - perl + - perl-carp diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-extutils-cbuilder.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-extutils-cbuilder.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..844ca387adf10b5b7b3b42c4e2b650f7cb1f0782 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-extutils-cbuilder.manual_bundle.txt @@ -0,0 +1,129 @@ +# Tool: perl-extutils-cbuilder +software_name: perl-extutils-cbuilder +tier: T1 +domain: t1_backfill_overall +downloads: 126083 +summary: Compile and link C code for Perl modules +description: Compile and link C code for Perl modules +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-extutils-makemaker, perl-file-temp, perl-ipc-cmd, perl-perl-ostype, perl-text-parsewords +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://search.cpan.org/dist/ExtUtils-CBuilder +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://search.cpan.org/dist/ExtUtils-CBuilder +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-extutils-cbuilder --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-extutils-cbuilder 0.280230 pl5.22.0_0 +------------------------------------------ +file name : perl-extutils-cbuilder-0.280230-pl5.22.0_0.tar.bz2 +name : perl-extutils-cbuilder +version : 0.280230 +build : pl5.22.0_0 +build number: 0 +size : 20 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-cbuilder-0.280230-pl5.22.0_0.tar.bz2 +md5 : 9eb0f68bd045576af10130d23118399a +dependencies: + - perl 5.22.0* + - perl-extutils-makemaker + - perl-file-temp + - perl-ipc-cmd + - perl-perl-ostype + - perl-text-parsewords + + +perl-extutils-cbuilder 0.280230 pl526_1 +--------------------------------------- +file name : perl-extutils-cbuilder-0.280230-pl526_1.tar.bz2 +name : perl-extutils-cbuilder +version : 0.280230 +build : pl526_1 +build number: 1 +size : 21 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-cbuilder-0.280230-pl526_1.tar.bz2 +md5 : 36f24339ddf929bfb872574b27a6b313 +timestamp : 2018-07-15 05:05:09 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-extutils-makemaker + - perl-file-temp + - perl-ipc-cmd + - perl-perl-ostype + - perl-text-parsewords + + +perl-extutils-cbuilder 0.280230 pl5321hdfd78af_2 +------------------------------------------------ +file name : perl-extutils-cbuilder-0.280230-pl5321hdfd78af_2.tar.bz2 +name : perl-extutils-cbuilder +version : 0.280230 +build : pl5321hdfd78af_2 +build number: 2 +size : 22 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-extutils-cbuilder-0.280230-pl5321hdfd78af_2.tar.bz2 +md5 : 20be49da07a719e441eee54f00cf0bb6 +timestamp : 2022-01-20 11:59:48 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-extutils-makemaker + - perl-file-temp + - perl-ipc-cmd + - perl-perl-ostype + - perl-text-parsewords diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-extutils-makemaker.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-extutils-makemaker.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab9771f21ba153e264624ac9858c8ef7163b950c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-extutils-makemaker.manual_bundle.txt @@ -0,0 +1,378 @@ +# Tool: perl-extutils-makemaker +software_name: perl-extutils-makemaker +tier: T1 +domain: t1_backfill_overall +downloads: 840123 +summary: Create a module Makefile +description: Create a module Makefile +dependencies: perl >=5.26.2,<5.26.3.0a0 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/release/ExtUtils-MakeMaker +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/release/ExtUtils-MakeMaker +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-extutils-makemaker --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-extutils-makemaker 6.66 0 +------------------------------ +file name : perl-extutils-makemaker-6.66-0.tar.bz2 +name : perl-extutils-makemaker +version : 6.66 +build : 0 +build number: 0 +size : 2 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-6.66-0.tar.bz2 +md5 : 56c35ad78add099d6a2bfc9792f10b3e +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-extutils-makemaker 6.66 pl5.22.0_1 +--------------------------------------- +file name : perl-extutils-makemaker-6.66-pl5.22.0_1.tar.bz2 +name : perl-extutils-makemaker +version : 6.66 +build : pl5.22.0_1 +build number: 1 +size : 2 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-6.66-pl5.22.0_1.tar.bz2 +md5 : 04024c8d0b19582c18bbbb336d066bc2 +dependencies: + - perl 5.22.0* + + +perl-extutils-makemaker 6.66 pl5.22.0_2 +--------------------------------------- +file name : perl-extutils-makemaker-6.66-pl5.22.0_2.tar.bz2 +name : perl-extutils-makemaker +version : 6.66 +build : pl5.22.0_2 +build number: 2 +size : 2 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-6.66-pl5.22.0_2.tar.bz2 +md5 : c2d3ee7e1b7a4bf1e9fa895c54ec25db +dependencies: + - perl 5.22.0* + + +perl-extutils-makemaker 7.24 pl5.22.0_0 +--------------------------------------- +file name : perl-extutils-makemaker-7.24-pl5.22.0_0.tar.bz2 +name : perl-extutils-makemaker +version : 7.24 +build : pl5.22.0_0 +build number: 0 +size : 131 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.24-pl5.22.0_0.tar.bz2 +md5 : 7c35d0c5fc73c2b1a01acc54aac1569e +dependencies: + - perl 5.22.0* + - perl-app-cpanminus + - perl-data-dumper + + +perl-extutils-makemaker 7.24 pl5.22.0_1 +--------------------------------------- +file name : perl-extutils-makemaker-7.24-pl5.22.0_1.tar.bz2 +name : perl-extutils-makemaker +version : 7.24 +build : pl5.22.0_1 +build number: 1 +size : 134 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.24-pl5.22.0_1.tar.bz2 +md5 : 6712cd7fa12d1384ac0ee34fd50fbcad +dependencies: + - perl 5.22.0* + - perl-app-cpanminus + - perl-data-dumper + + +perl-extutils-makemaker 7.24 pl526_3 +------------------------------------ +file name : perl-extutils-makemaker-7.24-pl526_3.tar.bz2 +name : perl-extutils-makemaker +version : 7.24 +build : pl526_3 +build number: 3 +size : 134 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.24-pl526_3.tar.bz2 +md5 : eac434e5d3bb8538322059483f289415 +timestamp : 2018-07-08 06:24:32 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-app-cpanminus + + +perl-extutils-makemaker 7.34 pl526_0 +------------------------------------ +file name : perl-extutils-makemaker-7.34-pl526_0.tar.bz2 +name : perl-extutils-makemaker +version : 7.34 +build : pl526_0 +build number: 0 +size : 150 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.34-pl526_0.tar.bz2 +md5 : c181a2d2142bcc7251eb4ae41e9bc106 +timestamp : 2018-07-08 06:29:14 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-extutils-makemaker 7.34 pl526_1 +------------------------------------ +file name : perl-extutils-makemaker-7.34-pl526_1.tar.bz2 +name : perl-extutils-makemaker +version : 7.34 +build : pl526_1 +build number: 1 +size : 150 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.34-pl526_1.tar.bz2 +md5 : 2a8d82313d623d9ce3845535a9819ae7 +timestamp : 2018-08-09 16:15:10 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-extutils-makemaker 7.34 pl526_2 +------------------------------------ +file name : perl-extutils-makemaker-7.34-pl526_2.tar.bz2 +name : perl-extutils-makemaker +version : 7.34 +build : pl526_2 +build number: 2 +size : 151 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.34-pl526_2.tar.bz2 +md5 : 86bad5005beec505220fa0bf8760d05a +timestamp : 2018-08-21 20:50:39 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-data-dumper + - perl-encode + + +perl-extutils-makemaker 7.34 pl526_3 +------------------------------------ +file name : perl-extutils-makemaker-7.34-pl526_3.tar.bz2 +name : perl-extutils-makemaker +version : 7.34 +build : pl526_3 +build number: 3 +size : 152 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.34-pl526_3.tar.bz2 +md5 : 37f7a3cc24250d37d786329c487ccdcb +timestamp : 2018-12-17 16:40:43 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-extutils-makemaker 7.36 pl526_0 +------------------------------------ +file name : perl-extutils-makemaker-7.36-pl526_0.tar.bz2 +name : perl-extutils-makemaker +version : 7.36 +build : pl526_0 +build number: 0 +size : 153 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.36-pl526_0.tar.bz2 +md5 : eb96f5d86bb5828f1a24cccb9f847a69 +timestamp : 2019-04-29 06:27:38 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-extutils-makemaker 7.36 pl526_1 +------------------------------------ +file name : perl-extutils-makemaker-7.36-pl526_1.tar.bz2 +name : perl-extutils-makemaker +version : 7.36 +build : pl526_1 +build number: 1 +size : 153 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.36-pl526_1.tar.bz2 +md5 : 32d1b791177a614aeae12e67bca620b0 +timestamp : 2019-05-02 20:57:15 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-extutils-makemaker 7.36 pl5321hd8ed1ab_0 +--------------------------------------------- +file name : perl-extutils-makemaker-7.36-pl5321hd8ed1ab_0.tar.bz2 +name : perl-extutils-makemaker +version : 7.36 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 142 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-extutils-makemaker-7.36-pl5321hd8ed1ab_0.tar.bz2 +md5 : fa5b9075b78ccaf8a2514ad9dcab7238 +timestamp : 2021-11-11 11:02:50 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-extutils-makemaker 7.56 pl5321hd8ed1ab_0 +--------------------------------------------- +file name : perl-extutils-makemaker-7.56-pl5321hd8ed1ab_0.tar.bz2 +name : perl-extutils-makemaker +version : 7.56 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 144 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-extutils-makemaker-7.56-pl5321hd8ed1ab_0.tar.bz2 +md5 : 85a04cff4032382d931555edf20029b7 +timestamp : 2022-01-02 10:18:32 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-extutils-makemaker 7.64 pl5321hd8ed1ab_0 +--------------------------------------------- +file name : perl-extutils-makemaker-7.64-pl5321hd8ed1ab_0.tar.bz2 +name : perl-extutils-makemaker +version : 7.64 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 145 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-extutils-makemaker-7.64-pl5321hd8ed1ab_0.tar.bz2 +md5 : b61f36ed03ccf6a4981e0f7517db8ec7 +timestamp : 2022-01-02 20:30:16 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-extutils-makemaker 7.66 pl5321hd8ed1ab_0 +--------------------------------------------- +file name : perl-extutils-makemaker-7.66-pl5321hd8ed1ab_0.conda +name : perl-extutils-makemaker +version : 7.66 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 154 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-extutils-makemaker-7.66-pl5321hd8ed1ab_0.conda +md5 : 1b11fdf0ba127d26811377c1500e5482 +timestamp : 2022-12-25 13:53:31 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 +--------------------------------------------- +file name : perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0.conda +name : perl-extutils-makemaker +version : 7.70 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 154 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0.conda +md5 : ec3e57ed34f7765bfc7054a05868ce5d +timestamp : 2023-03-26 16:23:56 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-extutils-makemaker 7.78 pl5422h47b2149_0 +--------------------------------------------- +file name : perl-extutils-makemaker-7.78-pl5422h47b2149_0.conda +name : perl-extutils-makemaker +version : 7.78 +build : pl5422h47b2149_0 +build number: 0 +size : 148 KB +license : Artistic-1.0-Perl +subdir : linux-64 +url : https://repo.anaconda.com/pkgs/main/linux-64/perl-extutils-makemaker-7.78-pl5422h47b2149_0.conda +md5 : 07ad44649b12214a1cbfc30a3155400d +timestamp : 2026-04-08 20:41:41 UTC +dependencies: + - __glibc >=2.28,<3.0.a0 + - libgcc >=14 + - perl diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-file-slurp-tiny.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-file-slurp-tiny.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..f22c045bd4419a5c374a31a9c2ff8d21a8347f15 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-file-slurp-tiny.manual_bundle.txt @@ -0,0 +1,114 @@ +# Tool: perl-file-slurp-tiny +software_name: perl-file-slurp-tiny +tier: T1 +domain: t1_backfill_overall +downloads: 273658 +summary: A simple, sane and efficient file slurper [DISCOURAGED] +description: A simple, sane and efficient file slurper [DISCOURAGED] +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-file-slurp-tiny --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-file-slurp-tiny 0.004 0 +---------------------------- +file name : perl-file-slurp-tiny-0.004-0.tar.bz2 +name : perl-file-slurp-tiny +version : 0.004 +build : 0 +build number: 0 +size : 3 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-file-slurp-tiny-0.004-0.tar.bz2 +md5 : a935919fad685d77ae7514db9948874b +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-file-slurp-tiny 0.004 pl526_1 +---------------------------------- +file name : perl-file-slurp-tiny-0.004-pl526_1.tar.bz2 +name : perl-file-slurp-tiny +version : 0.004 +build : pl526_1 +build number: 1 +size : 8 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-file-slurp-tiny-0.004-pl526_1.tar.bz2 +md5 : 1cf79bd3a86d7dbc00837771705beea3 +timestamp : 2018-07-07 16:12:59 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-file-slurp-tiny 0.004 pl5321hdfd78af_2 +------------------------------------------- +file name : perl-file-slurp-tiny-0.004-pl5321hdfd78af_2.tar.bz2 +name : perl-file-slurp-tiny +version : 0.004 +build : pl5321hdfd78af_2 +build number: 2 +size : 10 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-file-slurp-tiny-0.004-pl5321hdfd78af_2.tar.bz2 +md5 : 67f2e04a41c08c7faab45ffd890a653b +timestamp : 2022-01-17 12:18:42 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-file-spec.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-file-spec.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b49b098f39522056e36e1ead04eac9b4e15a1445 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-file-spec.manual_bundle.txt @@ -0,0 +1,110 @@ +# Tool: perl-file-spec +software_name: perl-file-spec +tier: T1 +domain: t1_backfill_overall +downloads: 280454 +summary: +description: +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-file-spec --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-file-spec 3.48_01 pl5.22.0_0 +--------------------------------- +file name : perl-file-spec-3.48_01-pl5.22.0_0.tar.bz2 +name : perl-file-spec +version : 3.48_01 +build : pl5.22.0_0 +build number: 0 +size : 2 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-file-spec-3.48_01-pl5.22.0_0.tar.bz2 +md5 : d55eba45cceb11bb01349712f7d2ebfa +dependencies: + - perl 5.22.0* + + +perl-file-spec 3.48_01 pl526_1 +------------------------------ +file name : perl-file-spec-3.48_01-pl526_1.tar.bz2 +name : perl-file-spec +version : 3.48_01 +build : pl526_1 +build number: 1 +size : 3 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-file-spec-3.48_01-pl526_1.tar.bz2 +md5 : ab31b69400cd2dc979c12d6ea29c8ee8 +timestamp : 2018-07-07 16:06:55 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-file-spec 3.48_01 pl5321hdfd78af_2 +--------------------------------------- +file name : perl-file-spec-3.48_01-pl5321hdfd78af_2.tar.bz2 +name : perl-file-spec +version : 3.48_01 +build : pl5321hdfd78af_2 +build number: 2 +size : 6 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-file-spec-3.48_01-pl5321hdfd78af_2.tar.bz2 +md5 : aab3e394e9759fffdbd042d98d30aeb8 +timestamp : 2022-01-17 08:34:13 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-font-afm.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-font-afm.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8d7ba55c043e1219361048a9ea53af4cab7a1640 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-font-afm.manual_bundle.txt @@ -0,0 +1,111 @@ +# Tool: perl-font-afm +software_name: perl-font-afm +tier: T1 +domain: t1_backfill_overall +downloads: 185674 +summary: Interface to Adobe Font Metrics files +description: Interface to Adobe Font Metrics files +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-font-afm --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-font-afm 1.20 0 +-------------------- +file name : perl-font-afm-1.20-0.tar.bz2 +name : perl-font-afm +version : 1.20 +build : 0 +build number: 0 +size : 8 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-font-afm-1.20-0.tar.bz2 +md5 : 0bc7bf9a78e268e552f3199253012e29 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-font-afm 1.20 pl526_2 +-------------------------- +file name : perl-font-afm-1.20-pl526_2.tar.bz2 +name : perl-font-afm +version : 1.20 +build : pl526_2 +build number: 2 +size : 14 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-font-afm-1.20-pl526_2.tar.bz2 +md5 : abb160a30f5f6fd49ab1f5c9fcc6491e +timestamp : 2018-07-20 23:03:22 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-font-afm 1.20 pl5321hdfd78af_3 +----------------------------------- +file name : perl-font-afm-1.20-pl5321hdfd78af_3.tar.bz2 +name : perl-font-afm +version : 1.20 +build : pl5321hdfd78af_3 +build number: 3 +size : 16 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-font-afm-1.20-pl5321hdfd78af_3.tar.bz2 +md5 : fe86e3374a3b442e005477cd54de6d0f +timestamp : 2022-01-17 12:37:40 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-font-ttf.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-font-ttf.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..55903da3efe79873e60461603684c0c18bde717a --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-font-ttf.manual_bundle.txt @@ -0,0 +1,124 @@ +# Tool: perl-font-ttf +software_name: perl-font-ttf +tier: T1 +domain: t1_backfill_overall +downloads: 348671 +summary: TTF font support for Perl +description: TTF font support for Perl +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-io-string, perl-xml-parser +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Font-TTF +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Font-TTF +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-font-ttf --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-font-ttf 1.05 0 +-------------------- +file name : perl-font-ttf-1.05-0.tar.bz2 +name : perl-font-ttf +version : 1.05 +build : 0 +build number: 0 +size : 156 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-font-ttf-1.05-0.tar.bz2 +md5 : a5cdf78684a64ec1bd8e96065b7a5327 +dependencies: + - perl-io-string + - perl-threaded + - perl-xml-parser + - perl >=5.22.0,<5.23.0 + + +perl-font-ttf 1.06 pl526_0 +-------------------------- +file name : perl-font-ttf-1.06-pl526_0.tar.bz2 +name : perl-font-ttf +version : 1.06 +build : pl526_0 +build number: 0 +size : 200 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-font-ttf-1.06-pl526_0.tar.bz2 +md5 : 27f80e8d4202b360fbb0646fa31ee101 +timestamp : 2018-08-05 20:21:56 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-io-string + - perl-xml-parser + + +perl-font-ttf 1.06 pl5321hdfd78af_1 +----------------------------------- +file name : perl-font-ttf-1.06-pl5321hdfd78af_1.tar.bz2 +name : perl-font-ttf +version : 1.06 +build : pl5321hdfd78af_1 +build number: 1 +size : 202 KB +license : artistic_2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-font-ttf-1.06-pl5321hdfd78af_1.tar.bz2 +md5 : 7bdabdc54e5f3c8914c993d3799e56c1 +timestamp : 2022-01-19 10:05:17 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-io-string + - perl-xml-parser diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-getopt-long.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-getopt-long.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..4474edae794b2d211b607ef7f67d341a3621b1f1 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-getopt-long.manual_bundle.txt @@ -0,0 +1,202 @@ +# Tool: perl-getopt-long +software_name: perl-getopt-long +tier: T1 +domain: t1_backfill_overall +downloads: 471358 +summary: Module to handle parsing command line options +description: Module to handle parsing command line options +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Getopt::Long +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Getopt::Long +Getopt::Long - Extended processing of command line options - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Getopt-Long Module version: 2.58 11 Jun 2024 11:20:58 UTC License: unknown Code Download ( 44.57KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues How to Contribute Quality Testers ( 4022 / 0 / 0 ) Testers (Magpie) Kwalitee 44.37% Coverage Bus factor: 5 Activity 24 month Dependencies Pod::Usage and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 2.58 (JV on 2024-06-11) 2.57 (JV on 2023-11-11) 2.56 (JV on 2023-11-10) 2.55_01 DEV (JV on 2023-11-10) 2.55 (JV on 2023-11-09) 2.54 (JV on 2022-11-17) 2.53 (JV on 2022-11-15) 2.52_002 DEV (JV on 2022-08-19) 2.52 (JV on 2020-08-18) 2.51 (JV on 2019-08-12) 2.50 (JV on 2017-05-27) 2.49.1 (JV on 2016-06-17) 2.49 (JV on 2016-06-09) 2.48 (JV on 2015-11-02) 2.47 (JV on 2015-06-16) 2.46_01 DEV (JV on 2015-06-10) 2.46 (JV on 2015-06-02) 2.45 (JV on 2015-02-23) 2.44 (JV on 2015-02-19) 2.43 (JV on 2015-01-14) 2.42 (JV on 2013-10-01) 2.41_01 DEV (JV on 2013-09-16) 2.41 (JV on 2013-07-08) 2.40 (JV on 2013-06-16) 2.39 (JV on 2013-03-12) 2.38_02 DEV (JV on 2010-07-09) 2.38 (JV on 2009-03-30) 2.37_03 DEV (JV on 2009-03-08) 2.37_02 DEV (JV on 2008-06-25) 2.37_01 DEV (JV on 2008-05-12) 2.37 (JV on 2007-09-29) 2.36_02 DEV (JV on 2007-09-16) 2.36_01 DEV (JV on 2007-09-14) 2.36 (JV on 2007-01-27) 2.35_02 DEV (JV on 2006-11-16) 2.35_01 DEV (JV on 2006-03-20) 2.35 (JV on 2005-12-14) 2.34_04 DEV (JV on 2005-04-28) 2.34_03 DEV (JV on 2005-02-04) 2.34_02 DEV (JV on 2004-08-16) 2.34_01 DEV (JV on 2003-12-31) 2.34 (JV on 2003-09-23) 2.33_03 DEV (JV on 2003-09-21) 2.33_02 DEV (JV on 2003-07-04) 2.33 (JV on 2003-05-19) 2.32_05 DEV (JV on 2003-05-15) 2.32_02a DEV (JV on 2003-05-10) 2.32_04 DEV (JV on 2003-05-10) 2.32_03 DEV (JV on 2003-05-09) 2.32_02 DEV (JV on 2003-05-09) 2.32_01 DEV (JV on 2002-06-29) 2.32 (JV on 2002-06-20) 2.31 (JV on 2002-05-03) 2.30 (JV on 2002-04-30) 2.29 (JV on 2002-03-13) 2.28 (JV on 2002-02-20) 2.26_03 DEV (JV on 2001-11-15) 2.26_02 DEV (JV on 2001-10-15) 2.26_01 DEV (JV on 2001-09-22) 2.26 (JV on 2001-08-05) 2.25 (JV on 2001-01-31) 2.24_02 DEV (JV on 2001-01-06) 2.24_01 DEV (JV on 2000-12-26) 2.24 (JV on 2000-08-28) 2.23_05 DEV (JV on 2000-08-02) 2.23_04 DEV (JV on 2000-07-29) 2.23_03 DEV (JV on 2000-07-28) 2.23 (JV on 2000-03-20) 2.21a (JV on 2000-03-06) 2.21 (JV on 2000-03-05) 2.20 (JV on 1999-08-04) Diff with version 2.58 (JV on 2024-06-11) 2.57 (JV on 2023-11-11) 2.56 (JV on 2023-11-10) 2.55_01 DEV (JV on 2023-11-10) 2.55 (JV on 2023-11-09) 2.54 (JV on 2022-11-17) 2.53 (JV on 2022-11-15) 2.52_002 DEV (JV on 2022-08-19) 2.52 (JV on 2020-08-18) 2.51 (JV on 2019-08-12) 2.50 (JV on 2017-05-27) 2.49.1 (JV on 2016-06-17) 2.49 (JV on 2016-06-09) 2.48 (JV on 2015-11-02) 2.47 (JV on 2015-06-16) 2.46_01 DEV (JV on 2015-06-10) 2.46 (JV on 2015-06-02) 2.45 (JV on 2015-02-23) 2.44 (JV on 2015-02-19) 2.43 (JV on 2015-01-14) 2.42 (JV on 2013-10-01) 2.41_01 DEV (JV on 2013-09-16) 2.41 (JV on 2013-07-08) 2.40 (JV on 2013-06-16) 2.39 (JV on 2013-03-12) 2.38_02 DEV (JV on 2010-07-09) 2.38 (JV on 2009-03-30) 2.37_03 DEV (JV on 2009-03-08) 2.37_02 DEV (JV on 2008-06-25) 2.37_01 DEV (JV on 2008-05-12) 2.37 (JV on 2007-09-29) 2.36_02 DEV (JV on 2007-09-16) 2.36_01 DEV (JV on 2007-09-14) 2.36 (JV on 2007-01-27) 2.35_02 DEV (JV on 2006-11-16) 2.35_01 DEV (JV on 2006-03-20) 2.35 (JV on 2005-12-14) 2.34_04 DEV (JV on 2005-04-28) 2.34_03 DEV (JV on 2005-02-04) 2.34_02 DEV (JV on 2004-08-16) 2.34_01 DEV (JV on 2003-12-31) 2.34 (JV on 2003-09-23) 2.33_03 DEV (JV on 2003-09-21) 2.33_02 DEV (JV on 2003-07-04) 2.33 (JV on 2003-05-19) 2.32_05 DEV (JV on 2003-05-15) 2.32_02a DEV (JV on 2003-05-10) 2.32_04 DEV (JV on 2003-05-10) 2.32_03 DEV (JV on 2003-05-09) 2.32_02 DEV (JV on 2003-05-09) 2.32_01 DEV (JV on 2002-06-29) 2.32 (JV on 2002-06-20) 2.31 (JV on 2002-05-03) 2.30 (JV on 2002-04-30) 2.29 (JV on 2002-03-13) 2.28 (JV on 2002-02-20) 2.26_03 DEV (JV on 2001-11-15) 2.26_02 DEV (JV on 2001-10-15) 2.26_01 DEV (JV on 2001-09-22) 2.26 (JV on 2001-08-05) 2.25 (JV on 2001-01-31) 2.24_02 DEV (JV on 2001-01-06) 2.24_01 DEV (JV on 2000-12-26) 2.24 (JV on 2000-08-28) 2.23_05 DEV (JV on 2000-08-02) 2.23_04 DEV (JV on 2000-07-29) 2.23_03 DEV (JV on 2000-07-28) 2.23 (JV on 2000-03-20) 2.21a (JV on 2000-03-06) 2.21 (JV on 2000-03-05) 2.20 (JV on 1999-08-04) Permalinks This version Latest version ++ed by: 66 PAUSE users 63 non-PAUSE users Authors: Johan Vromans (jvromans@squirrel.nl) Released by: Johan Vromans Maintainers: JV owner Contributors: Johan Vromans (jvromans@squirrel.nl) Johan Vromans  /  2.58 (JV on 2024-06-11) 2.57 (JV on 2023-11-11) 2.56 (JV on 2023-11-10) 2.55_01 DEV (JV on 2023-11-10) 2.55 (JV on 2023-11-09) 2.54 (JV on 2022-11-17) 2.53 (JV on 2022-11-15) 2.52_002 DEV (JV on 2022-08-19) 2.52 (JV on 2020-08-18) 2.51 (JV on 2019-08-12) 2.50 (JV on 2017-05-27) 2.49.1 (JV on 2016-06-17) 2.49 (JV on 2016-06-09) 2.48 (JV on 2015-11-02) 2.47 (JV on 2015-06-16) 2.46_01 DEV (JV on 2015-06-10) 2.46 (JV on 2015-06-02) 2.45 (JV on 2015-02-23) 2.44 (JV on 2015-02-19) 2.43 (JV on 2015-01-14) 2.42 (JV on 2013-10-01) 2.41_01 DEV (JV on 2013-09-16) 2.41 (JV on 2013-07-08) 2.40 (JV on 2013-06-16) 2.39 (JV on 2013-03-12) 2.38_02 DEV (JV on 2010-07-09) 2.38 (JV on 2009-03-30) 2.37_03 DEV (JV on 2009-03-08) 2.37_02 DEV (JV on 2008-06-25) 2.37_01 DEV (JV on 2008-05-12) 2.37 (JV on 2007-09-29) 2.36_02 DEV (JV on 2007-09-16) 2.36_01 DEV (JV on 2007-09-14) 2.36 (JV on 2007-01-27) 2.35_02 DEV (JV on 2006-11-16) 2.35_01 DEV (JV on 2006-03-20) 2.35 (JV on 2005-12-14) 2.34_04 DEV (JV on 2005-04-28) 2.34_03 DEV (JV on 2005-02-04) 2.34_02 DEV (JV on 2004-08-16) 2.34_01 DEV (JV on 2003-12-31) 2.34 (JV on 2003-09-23) 2.33_03 DEV (JV on 2003-09-21) 2.33_02 DEV (JV on 2003-07-04) 2.33 (JV on 2003-05-19) 2.32_05 DEV (JV on 2003-05-15) 2.32_02a DEV (JV on 2003-05-10) 2.32_04 DEV (JV on 2003-05-10) 2.32_03 DEV (JV on 2003-05-09) 2.32_02 DEV (JV on 2003-05-09) 2.32_01 DEV (JV on 2002-06-29) 2.32 (JV on 2002-06-20) 2.31 (JV on 2002-05-03) 2.30 (JV on 2002-04-30) 2.29 (JV on 2002-03-13) 2.28 (JV on 2002-02-20) 2.26_03 DEV (JV on 2001-11-15) 2.26_02 DEV (JV on 2001-10-15) 2.26_01 DEV (JV on 2001-09-22) 2.26 (JV on 2001-08-05) 2.25 (JV on 2001-01-31) 2.24_02 DEV (JV on 2001-01-06) 2.24_01 DEV (JV on 2000-12-26) 2.24 (JV on 2000-08-28) 2.23_05 DEV (JV on 2000-08-02) 2.23_04 DEV (JV on 2000-07-29) 2.23_03 DEV (JV on 2000-07-28) 2.23 (JV on 2000-03-20) 2.21a (JV on 2000-03-06) 2.21 (JV on 2000-03-05) 2.20 (JV on 1999-08-04) Getopt-Long-2.58 129 ++ 129 ++ ⭐ Starred 13 GitHub stars / Getopt::Long Contents NAME SYNOPSIS DESCRIPTION Command Line Options, an Introduction Getting Started with Getopt::Long Simple options A little bit less simple options Mixing command line option with other arguments Options with values Options with multiple values Options with hash values User-defined subroutines to handle options Options with multiple names Case and abbreviations Summary of Option Specifications Advanced Possibilities Object oriented interface Callback object Thread Safety Documentation and help texts Parsing options from an arbitrary array Parsing options from an arbitrary string Storing options values in a hash Bundling The lonesome dash Argument callback Configuring Getopt::Long Exportable Methods Return values and Errors Legacy Default destinations Alternative option starters Configuration variables Tips and Techniques Pushing multiple values in a hash option Troubleshooting GetOptions does not return a false result when an option is not supplied GetOptions does not split the command line correctly Undefined subroutine &main::GetOptions called How do I put a "-?" option into a Getopt::Long? AUTHOR COPYRIGHT AND DISCLAIMER NAME Getopt::Long - Extended processing of command line options SYNOPSIS use Getopt::Long; my $data = "file.dat"; my $length = 24; my $verbose; GetOptions ("length=i" => \$length, # numeric "file=s" => \$data, # string "verbose" => \$verbose) # flag or die("Error in command line arguments\n"); DESCRIPTION The Getopt::Long module implements an extended getopt function called GetOptions(). It parses the command line from @ARGV , recognizing and removing specified options and their possible values. This function adheres to the POSIX syntax for command line options, with GNU extensions. In general, this means that options have long names instead of single letters, and are introduced with a double dash "--". Support for bundling of command line options, as was the case with the more traditional single-letter approach, is provided but not enabled by default. Command Line Options, an Introduction Command line operated programs traditionally take their arguments from the command line, for example filenames or other information that the program needs to know. Besides arguments, these programs often take command line options as well. Options are not necessary for the program to work, hence the name 'option', but are used to modify its default behaviour. For example, a program could do its job quietly, but with a suitable option it could provide verbose information about what it did. Command line options come in several flavours. Historically, they are preceded by a single dash - , and consist of a single letter. -l -a -c Usually, these single-character options can be bundled: -lac Options can have values, the value is placed after the option character. Sometimes with whitespace in between, sometimes not: -s 24 -s24 Due to the very cryptic nature of these options, another style was developed that used long names. So instead of a cryptic -l one could use the more descriptive --long . To distinguish between a bundle of single-character options and a long one, two dashes are used to precede the option name. Early implementations of long options used a plus + instead. Also, option values could be specified either like --size=24 or --size 24 The + form is now obsolete and strongly deprecated. Getting Started with Getopt::Long Getopt::Long is the Perl5 successor of newgetopt.pl . This was the first Perl module that provided support for handling the new style of command line options, in particular long option names, hence the Perl5 name Getopt::Long. This module also supports single-character options and bundling. To use Getopt::Long from a Perl program, you must include the following line in your Perl program: use Getopt::Long; This will load the core of the Getopt::Long module and prepare your program for using it. Most of the actual Getopt::Long code is not loaded until you really call one of its functions. In the default configuration, options names may be abbreviated to uniqueness, case does not matter, and a single dash is sufficient, even for long option names. Also, options may be placed between non-option arguments. See "Configuring Getopt::Long" for more details on how to configure Getopt::Long. Simple options The most simple options are the ones that take no values. Their mere presence on the command line enables the option. Popular examples are: --all --verbose --quiet --debug Handling simple options is straightforward: my $verbose = ''; # option variable with default value (false) my $all = ''; # option variable with default value (false) GetOptions ('verbose' => \$verbose, 'all' => \$all); The call to GetOptions() parses the command line arguments that are present in @ARGV and sets the option variable to the value 1 if the option did occur on the command line. Otherwise, the option variable is not touched. Setting the option value to true is often called enabling the option. The option name as specified to the GetOptions() function is called the option specification . Later we'll see that this specification can contain more than just the option name. The reference to the variable is called the option destination . GetOptions() will return a true value if the command line could be processed successfully. Otherwise, it will write error messages using die() and warn(), and return a false result. A little bit less simple options Getopt::Long supports two useful variants of simple options: negatable options and incremental options. A negatable option is specified with an exclamation mark ! after the option name: my $verbose = ''; # option variable with default value (false) GetOptions ('verbose!' => \$verbose); Now, using --verbose on the command line will enable $verbose , as expected. But it is also allowed to use --noverbose , which will disable $verbose by setting its value to 0 . Using a suitable default value, the program can find out whether $verbose is false by default, or disabled by using --noverbose . (If both --verbose and --noverbose are given, whichever is given last takes precedence.) An incremental option is specified with a plus + after the option name: my $verbose = ''; # option variable with default value (false) GetOptions ('verbose+' => \$verbose); Using --verbose on the command line will increment the value of $verbose . This way the program can keep track of how many times the option occurred on the command line. For example, each occurrence of --verbose could increase the verbosity level of the program. Mixing command line option with other arguments Usually programs take command line options as well as other arguments, for example, file names. It is good practice to always specify the options first, and the other arguments last. Getopt::Long will, however, allow the options and arguments to be mixed and 'filter out' all the options before passing the rest of the arguments to the program. To stop Getopt::Long from processing further arguments, insert a double dash -- on the command line: --size 24 -- --all In this example, --all will not be treated as an option, but passed to the program unharmed, in @ARGV . Options with values For options that take values it must be specified whether the option value is required or not, and what kind of value the option expects. Three kinds of values are supported: integer numbers, floating point numbers, and strings. If the option value is required, Getopt::Long will take the command line argument that follows the option and assign this to the option variable. If, however, the option value is specified as optional, this will only be done if that value does not look like a valid command line option itself. my $tag = ''; # option variable with default value GetOptions ('tag=s' => \$tag); In the option specification, the option name is followed by an equals sign = and the letter s . The equals sign indicates that this option requires a value. The letter s indicates that this value is an arbitrary string. Other possible value types are i for integer values, and f for floating point values. Using a colon : instead of the equals sign indicates that the option value is optional. In this case, if no suitable value is supplied, string valued options get an empty string '' assigned, while numeric options are set to 0 . (If the same option appears more than once on the command line, the last given value is used. If you want to take all the values, see below.) Options with multiple values Options sometimes take several values. For example, a program could use multiple directories to search for library files: --library lib/stdlib --library lib/extlib To accomplish this behaviour, simply specify an array reference as the destination for the option: GetOptions ("library=s" => \@libfiles); Alternatively, you can specify that the option can have multiple values by adding a "@", and pass a reference to a scalar as the destination: GetOptions ("library=s@" => \$libfiles); Used with the example above, @libfiles c.q. @$libfiles would contain two strings upon completion: "lib/stdlib" and "lib/extlib" , in that order. It is also possible to specify that only integer or floating point numbers are acceptable values. Often it is useful to allow comma-separated lists of values as well as multiple occurrences of the options. This is easy using Perl's split() and join() operators: GetOptions ("library=s" => \@libfiles); @libfiles = split(/,/,join(',',@libfiles)); Of course, it is important to choose the right separator string for each purpose. Warning: What follows is an experimental feature. Options can take multiple values at once, for example --coordinates 52.2 16.4 --rgbcolor 255 255 149 This can be accomplished by adding a repeat specifier to the option specification. Repeat specifiers are very similar to the {...} repeat specifiers that can be used with regular expression patterns. For example, the above command line would be handled as follows: GetOptions('coordinates=f{2}' => \@coor, 'rgbcolor=i{3}' => \@color); The destination for the option must be an array or array reference. It is also possible to specify the minimal and maximal number of arguments an option takes. foo=s{2,4} indicates an option that takes at least two and at most 4 arguments. foo=s{1,} indicates one or more values; foo:s{,} indicates zero or more option values. Options with hash values If the option destination is a reference to a hash, the option will take, as value, strings of the form key = value . The value will be stored with the specified key in the hash. GetOptions ("define=s" => \%defines); Alternatively you can use: GetOptions ("define=s%" => \$defines); When used with command line options: --define os=linux --define vendor=redhat the hash %defines (or %$defines ) will contain two keys, "os" with value "linux" and "vendor" with value "redhat" . It is also possible to specify that only integer or floating point numbers are acceptable values. The keys are always taken to be strings. User-defined subroutines to handle options Ultimate control over what should be done when (actually: each time) an option is encountered on the command line can be achieved by designating a reference to a subroutine (or an anonymous subroutine) as the option destination. When GetOptions() encounters the option, it will call the subroutine with two or three arguments. The first argument is the name of the option. (Actually, it is an object that stringifies to the name of the option.) For a scalar or array destination, the second argument is the value to be stored. For a hash destination, the second argument is the key to the hash, and the third argument the value to be stored. It is up to the subroutine to store the value, or do whatever it thinks is appropriate. A trivial application of this mechanism is to implement options that are related to each other. For example: my $verbose = ''; # option variable with default value (false) GetOptions ('verbose' => \$verbose, 'quiet' => sub { $verbose = 0 }); Here --verbose and --quiet control the same variable $verbose , but with opposite values. If the subroutine needs to signal an error, it should call die() with the desired error message as its argument. GetOptions() will catch the die(), issue the error message, and record that an error result must be returned upon completion. If the text of the error message starts with an exclamation mark ! it is interpreted specially by GetOptions(). There is currently one special command implemented: die("!FINISH") will cause GetOptions() to stop processing options, as if it encountered a double dash -- . Here is an example of how to access the option name and value from withi + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-getopt-long --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-getopt-long 2.49 0 +----------------------- +file name : perl-getopt-long-2.49-0.tar.bz2 +name : perl-getopt-long +version : 2.49 +build : 0 +build number: 0 +size : 25 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-getopt-long-2.49-0.tar.bz2 +md5 : ab8a9cabef22d500f4de3af7f5f74d41 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-getopt-long 2.50 pl5.22.0_0 +-------------------------------- +file name : perl-getopt-long-2.50-pl5.22.0_0.tar.bz2 +name : perl-getopt-long +version : 2.50 +build : pl5.22.0_0 +build number: 0 +size : 27 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-getopt-long-2.50-pl5.22.0_0.tar.bz2 +md5 : e32c7ea80c03f6a64ef161d57ec10e2e +dependencies: + - perl 5.22.0* + + +perl-getopt-long 2.50 pl526_1 +----------------------------- +file name : perl-getopt-long-2.50-pl526_1.tar.bz2 +name : perl-getopt-long +version : 2.50 +build : pl526_1 +build number: 1 +size : 27 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-getopt-long-2.50-pl526_1.tar.bz2 +md5 : 3f11f5bb4d7fb82920bf1ffac2e49a0a +timestamp : 2018-06-29 01:15:13 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-getopt-long 2.50 pl5321hdfd78af_2 +-------------------------------------- +file name : perl-getopt-long-2.50-pl5321hdfd78af_2.tar.bz2 +name : perl-getopt-long +version : 2.50 +build : pl5321hdfd78af_2 +build number: 2 +size : 29 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-getopt-long-2.50-pl5321hdfd78af_2.tar.bz2 +md5 : c436e31a16b39bb6eee75d23cc91ea25 +timestamp : 2022-01-17 21:56:32 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-getopt-long 2.52 pl5321hdfd78af_0 +-------------------------------------- +file name : perl-getopt-long-2.52-pl5321hdfd78af_0.tar.bz2 +name : perl-getopt-long +version : 2.52 +build : pl5321hdfd78af_0 +build number: 0 +size : 30 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-getopt-long-2.52-pl5321hdfd78af_0.tar.bz2 +md5 : 99b7930ba6c4424f1bcc55ea2a70d0df +timestamp : 2022-02-10 06:55:45 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-getopt-long 2.53 pl5321hdfd78af_0 +-------------------------------------- +file name : perl-getopt-long-2.53-pl5321hdfd78af_0.tar.bz2 +name : perl-getopt-long +version : 2.53 +build : pl5321hdfd78af_0 +build number: 0 +size : 31 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-getopt-long-2.53-pl5321hdfd78af_0.tar.bz2 +md5 : 5979a0e9a26b8c2056932088fae55ac0 +timestamp : 2022-11-15 14:42:11 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-getopt-long 2.54 pl5321hdfd78af_0 +-------------------------------------- +file name : perl-getopt-long-2.54-pl5321hdfd78af_0.tar.bz2 +name : perl-getopt-long +version : 2.54 +build : pl5321hdfd78af_0 +build number: 0 +size : 31 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-getopt-long-2.54-pl5321hdfd78af_0.tar.bz2 +md5 : 3c301587f1b58f90ecd06aeee46f7cc3 +timestamp : 2022-11-17 18:40:04 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-getopt-long 2.58 pl5321hdfd78af_0 +-------------------------------------- +file name : perl-getopt-long-2.58-pl5321hdfd78af_0.tar.bz2 +name : perl-getopt-long +version : 2.58 +build : pl5321hdfd78af_0 +build number: 0 +size : 33 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-getopt-long-2.58-pl5321hdfd78af_0.tar.bz2 +md5 : 10469a3defbd6dbab17d3d10dd6fd828 +timestamp : 2024-06-11 13:40:56 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-entities-numbered.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-entities-numbered.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..368084d055b1b0e9f95927c2c3587c82a4ad14f3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-entities-numbered.manual_bundle.txt @@ -0,0 +1,111 @@ +# Tool: perl-html-entities-numbered +software_name: perl-html-entities-numbered +tier: T1 +domain: t1_backfill_overall +downloads: 185045 +summary: Conversion of numbered HTML entities +description: Conversion of numbered HTML entities +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-html-entities-numbered --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-html-entities-numbered 0.04 0 +---------------------------------- +file name : perl-html-entities-numbered-0.04-0.tar.bz2 +name : perl-html-entities-numbered +version : 0.04 +build : 0 +build number: 0 +size : 6 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-entities-numbered-0.04-0.tar.bz2 +md5 : fe8b0e89ccb68b47b274d34ab3d28e97 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-html-entities-numbered 0.04 pl526_1 +---------------------------------------- +file name : perl-html-entities-numbered-0.04-pl526_1.tar.bz2 +name : perl-html-entities-numbered +version : 0.04 +build : pl526_1 +build number: 1 +size : 11 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-entities-numbered-0.04-pl526_1.tar.bz2 +md5 : b94f3da1695f22440f7e6cbc3ccfff7a +timestamp : 2018-07-07 00:35:12 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-html-entities-numbered 0.04 pl5321hdfd78af_2 +------------------------------------------------- +file name : perl-html-entities-numbered-0.04-pl5321hdfd78af_2.tar.bz2 +name : perl-html-entities-numbered +version : 0.04 +build : pl5321hdfd78af_2 +build number: 2 +size : 13 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-html-entities-numbered-0.04-pl5321hdfd78af_2.tar.bz2 +md5 : 10ee7d472ae6f205becf84e64f9e591e +timestamp : 2022-01-17 11:35:27 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-tableextract.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-tableextract.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..a79842093bc8979ae0b5964590dbc77411962f54 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-tableextract.manual_bundle.txt @@ -0,0 +1,162 @@ +# Tool: perl-html-tableextract +software_name: perl-html-tableextract +tier: T1 +domain: t1_backfill_overall +downloads: 182896 +summary: Perl module for extracting the content contained in tables within an HTML document, either as text or encoded element trees. +description: Perl module for extracting the content contained in tables within an HTML document, either as text or encoded element trees. +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-html-element-extended, perl-html-parser +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/HTML::TableExtract +doc_url: https://metacpan.org/pod/HTML::TableExtract +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/HTML::TableExtract +HTML::TableExtract - Perl module for extracting the content contained in tables within an HTML document, either as text or encoded element trees. - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution HTML-TableExtract Module version: 2.15 25 May 2017 13:49:56 UTC License: unknown Code Download ( 35.63KB ) Source ( raw ) Browse ( raw ) Changes Project Issues (13) How to Contribute Quality Testers ( 8243 / 488 / 0 ) Testers (Magpie) Kwalitee 69.27% Coverage Bus factor: 0 Activity 24 month Dependencies HTML::ElementTable HTML::Parser and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 2.15 (MSISK on 2017-05-25) 2.14 (MSISK on 2017-05-25) 2.13 (MSISK on 2015-05-21) 2.12 (MSISK on 2015-01-09) 2.11 (MSISK on 2011-08-23) 2.10 (MSISK on 2006-07-16) 2.09 (MSISK on 2006-06-08) 2.08 (MSISK on 2006-05-03) 2.07 (MSISK on 2006-02-19) 2.06 (MSISK on 2005-10-19) 2.05 (MSISK on 2005-10-04) 2.04 (MSISK on 2005-08-03) 2.03 (MSISK on 2005-07-20) 2.02 (MSISK on 2005-06-23) 2.01 (MSISK on 2005-06-22) 2.00 (MSISK on 2005-06-17) 1.10 (MSISK on 2005-03-07) 1.09 (MSISK on 2005-02-25) 1.08 (MSISK on 2002-04-05) 1.07 (MSISK on 2001-08-22) 1.06 (MSISK on 2000-11-02) 1.05 (MSISK on 2000-08-06) 1.04 (MSISK on 2000-07-15) 1.03 (MSISK on 2000-07-07) 1.02 (MSISK on 2000-07-06) 1.01 (MSISK on 2000-07-06) 1.00 (MSISK on 2000-07-04) 0.05 (MSISK on 2000-03-21) 0.04 (MSISK on 2000-03-21) 0.03 (MSISK on 2000-03-09) 0.02 (MSISK on 2000-02-11) 0.01 (MSISK on 2000-02-03) Diff with version 2.15 (MSISK on 2017-05-25) 2.14 (MSISK on 2017-05-25) 2.13 (MSISK on 2015-05-21) 2.12 (MSISK on 2015-01-09) 2.11 (MSISK on 2011-08-23) 2.10 (MSISK on 2006-07-16) 2.09 (MSISK on 2006-06-08) 2.08 (MSISK on 2006-05-03) 2.07 (MSISK on 2006-02-19) 2.06 (MSISK on 2005-10-19) 2.05 (MSISK on 2005-10-04) 2.04 (MSISK on 2005-08-03) 2.03 (MSISK on 2005-07-20) 2.02 (MSISK on 2005-06-23) 2.01 (MSISK on 2005-06-22) 2.00 (MSISK on 2005-06-17) 1.10 (MSISK on 2005-03-07) 1.09 (MSISK on 2005-02-25) 1.08 (MSISK on 2002-04-05) 1.07 (MSISK on 2001-08-22) 1.06 (MSISK on 2000-11-02) 1.05 (MSISK on 2000-08-06) 1.04 (MSISK on 2000-07-15) 1.03 (MSISK on 2000-07-07) 1.02 (MSISK on 2000-07-06) 1.01 (MSISK on 2000-07-06) 1.00 (MSISK on 2000-07-04) 0.05 (MSISK on 2000-03-21) 0.04 (MSISK on 2000-03-21) 0.03 (MSISK on 2000-03-09) 0.02 (MSISK on 2000-02-11) 0.01 (MSISK on 2000-02-03) Permalinks This version Latest version ++ed by: 4 PAUSE users 2 non-PAUSE users Authors: unknown Released by: Matt Sisk Maintainers: MSISK owner Matt Sisk  /  2.15 (MSISK on 2017-05-25) 2.14 (MSISK on 2017-05-25) 2.13 (MSISK on 2015-05-21) 2.12 (MSISK on 2015-01-09) 2.11 (MSISK on 2011-08-23) 2.10 (MSISK on 2006-07-16) 2.09 (MSISK on 2006-06-08) 2.08 (MSISK on 2006-05-03) 2.07 (MSISK on 2006-02-19) 2.06 (MSISK on 2005-10-19) 2.05 (MSISK on 2005-10-04) 2.04 (MSISK on 2005-08-03) 2.03 (MSISK on 2005-07-20) 2.02 (MSISK on 2005-06-23) 2.01 (MSISK on 2005-06-22) 2.00 (MSISK on 2005-06-17) 1.10 (MSISK on 2005-03-07) 1.09 (MSISK on 2005-02-25) 1.08 (MSISK on 2002-04-05) 1.07 (MSISK on 2001-08-22) 1.06 (MSISK on 2000-11-02) 1.05 (MSISK on 2000-08-06) 1.04 (MSISK on 2000-07-15) 1.03 (MSISK on 2000-07-07) 1.02 (MSISK on 2000-07-06) 1.01 (MSISK on 2000-07-06) 1.00 (MSISK on 2000-07-04) 0.05 (MSISK on 2000-03-21) 0.04 (MSISK on 2000-03-21) 0.03 (MSISK on 2000-03-09) 0.02 (MSISK on 2000-02-11) 0.01 (MSISK on 2000-02-03) HTML-TableExtract-2.15 6 ++ 6 ++ / HTML::TableExtract Contents NAME SYNOPSIS DESCRIPTION Extraction Modes Advice METHODS CONSTRUCTOR REGULAR METHODS DEPRECATED METHODS TABLE METHODS NOTES ON TREE EXTRACTION MODE REQUIRES OPTIONALLY REQUIRES AUTHOR COPYRIGHT SEE ALSO NAME HTML::TableExtract - Perl module for extracting the content contained in tables within an HTML document, either as text or encoded element trees. SYNOPSIS # Matched tables are returned as table objects; tables can be matched # using column headers, depth, count within a depth, table tag # attributes, or some combination of the four. # Example: Using column header information. # Assume an HTML document with tables that have "Date", "Price", and # "Cost" somewhere in a row. The columns beneath those headings are # what you want to extract. They will be returned in the same order as # you specified the headers since 'automap' is enabled by default. use HTML::TableExtract; my $te = HTML::TableExtract->new( headers => [qw(Date Price Cost)] ); $te->parse($html_string); # Examine all matching tables foreach my $ts ($te->tables) { print "Table (", join(',', $ts->coords), "):\n"; foreach my $row ($ts->rows) { print join(',', @$row), "\n"; } } # Shorthand...top level rows() method assumes the first table found in # the document if no arguments are supplied. foreach my $row ($te->rows) { print join(',', @$row), "\n"; } # Example: Using depth and count information. # Every table in the document has a unique depth and count tuple, so # when both are specified it is a unique table. Depth and count both # begin with 0, so in this case we are looking for a table (depth 2) # within a table (depth 1) within a table (depth 0, which is the top # level HTML document). In addition, it must be the third (count 2) # such instance of a table at that depth. my $te = HTML::TableExtract->new( depth => 2, count => 2 ); $te->parse_file($html_file); foreach my $ts ($te->tables) { print "Table found at ", join(',', $ts->coords), ":\n"; foreach my $row ($ts->rows) { print " ", join(',', @$row), "\n"; } } # Example: Using table tag attributes. # If multiple attributes are specified, all must be present and equal # for match to occur. my $te = HTML::TableExtract->new( attribs => { border => 1 } ); $te->parse($html_string); foreach my $ts ($te->tables) { print "Table with border=1 found at ", join(',', $ts->coords), ":\n"; foreach my $row ($ts->rows) { print " ", join(',', @$row), "\n"; } } # Example: Extracting as an HTML::Element tree structure # Rather than extracting raw text, the html can be converted into a # tree of element objects. The HTML document is composed of # HTML::Element objects and the tables are HTML::ElementTable # structures. Using this, the contents of tables within a document can # be edited in-place. use HTML::TableExtract qw(tree); my $te = HTML::TableExtract->new( headers => qw(Fee Fie Foe Fum) ); $te->parse_file($html_file); my $table = $te->first_table_found; my $table_tree = $table->tree; $table_tree->cell(4,4)->replace_content('Golden Goose'); my $table_html = $table_tree->as_HTML; my $table_text = $table_tree->as_text; my $document_tree = $te->tree; my $document_html = $document_tree->as_HTML; DESCRIPTION HTML::TableExtract is a subclass of HTML::Parser that serves to extract the information from tables of interest contained within an HTML document. The information from each extracted table is stored in table objects. Tables can be extracted as text, HTML, or HTML::ElementTable structures (for in-place editing or manipulation). There are currently four constraints available to specify which tables you would like to extract from a document: Headers , Depth , Count , and Attributes . Headers , the most flexible and adaptive of the techniques, involves specifying text in an array that you expect to appear above the data in the tables of interest. Once all headers have been located in a row of that table, all further cells beneath the columns that matched your headers are extracted. All other columns are ignored: think of it as vertical slices through a table. In addition, TableExtract automatically rearranges each row in the same order as the headers you provided. If you would like to disable this, set automap to 0 during object creation, and instead rely on the column_map() method to find out the order in which the headers were found. Furthermore, TableExtract will automatically compensate for cell span issues so that columns are really the same columns as you would visually see in a browser. This behavior can be disabled by setting the gridmap parameter to 0. HTML is stripped from the entire textual content of a cell before header matches are attempted -- unless the keep_html parameter was enabled. Depth and Count are more specific ways to specify tables in relation to one another. Depth represents how deeply a table resides in other tables. The depth of a top-level table in the document is 0. A table within a top-level table has a depth of 1, and so on. Each depth can be thought of as a layer; tables sharing the same depth are on the same layer. Within each of these layers, Count represents the order in which a table was seen at that depth, starting with 0. Providing both a depth and a count will uniquely specify a table within a document. Attributes match based on the attributes of the html <table> tag, for example, border widths or background color. Each of the Headers , Depth , Count , and Attributes specifications are cumulative in their effect on the overall extraction. For instance, if you specify only a Depth , then you get all tables at that depth (note that these could very well reside in separate higher- level tables throughout the document since depth extends across tables). If you specify only a Count , then the tables at that Count from all depths are returned (i.e., the n th occurrence of a table at each depth). If you only specify Headers , then you get all tables in the document containing those column headers. If you have specified multiple constraints of Headers , Depth , Count , and Attributes , then each constraint has veto power over whether a particular table is extracted. If no Headers , Depth , Count , or Attributes are specified, then all tables match. When extracting only text from tables, the text is decoded with HTML::Entities by default; this can be disabled by setting the decode parameter to 0. Extraction Modes The default mode of extraction for HTML::TableExtract is raw text or HTML. In this mode, embedded tables are completely decoupled from one another. In this case, HTML::TableExtract is a subclass of HTML::Parser: use HTML::TableExtract; Alternatively, tables can be extracted as HTML::ElementTable structures, which are in turn embedded in an HTML::Element tree representing the entire HTML document. Embedded tables are not decoupled from one another since this tree structure must be maintained. In this case, HTML::TableExtract is a subclass of HTML::TreeBuilder (itself a subclass of HTML:::Parser): use HTML::TableExtract qw(tree); In either case, the basic interface for HTML::TableExtract and the resulting table objects remains the same -- all that changes is what you can do with the resulting data. HTML::TableExtract is a subclass of HTML::Parser, and as such inherits all of its basic methods such as parse() and parse_file() . During scans, start() , end() , and text() are utilized. Feel free to override them, but if you do not eventually invoke them in the SUPER class with some content, results are not guaranteed. Advice The main point of this module was to provide a flexible method of extracting tabular information from HTML documents without relying to heavily on the document layout. For that reason, I suggest using Headers whenever possible -- that way, you are anchoring your extraction on what the document is trying to communicate rather than some feature of the HTML comprising the document (other than the fact that the data is contained in a table). METHODS The following are the top-level methods of the HTML::TableExtract object. Tables that have matched a query are actually returned as separate objects of type HTML::TableExtract::Table. These table objects have their own methods, documented further below. CONSTRUCTOR new() Return a new HTML::TableExtract object. Valid attributes are: headers Passed as an array reference, headers specify strings of interest at the top of columns within targeted tables. They can be either strings or regular expressions (qr//). If they are strings, they will eventually be passed through a non-anchored, case-insensitive regular expression, so regexp special characters are allowed. The table row containing the headers is not returned, unless keep_headers was specified or you are extracting into an element tree. In either case the header row can be accessed via the hrow() method from within the table object. Columns that are not beneath one of the provided headers will be ignored unless slice_columns was set to 0. Columns will, by default, be rearranged into the same order as the headers you provide (see the automap parameter for more information) unless slice_columns is 0. Additionally, by default columns are considered what you would see visually beneath that header when the table is rendered in a browser. See the gridmap parameter for more information. HTML within a header is stripped before the match is attempted, unless the keep_html parameter was specified and strip_html_on_match is false. depth Specify how embedded in other tables your tables of interest should be. Top-level tables in the HTML document have a depth of 0, tables within top-level tables have a depth of 1, and so on. count Specify which table within each depth you are interested in, beginning with 0. attribs Passed as a hash reference, attribs specify attributes of interest within the HTML <table> tag itself. automap Automatically applies the ordering reported by column_map() to the rows returned by rows(). This only makes a difference if you have specified Headers and they turn out to be in a different order in the table than what you specified. Automap will rearrange the columns in the same order as the headers appear. To get the original ordering, you will need to take another slice of each row using column_map(). automap is enabled by default. slice_columns Enabled by default, this option controls whether vertical slices are returned from under headers that match. When disabled, all columns of the matching table are retained, regardles of whether they had a matching header above them. Disabling this also disables automap . keep_headers Disabled by default, and only applicable when header constraints have been specified, keep_headers will retain the matching header row as the first row of table data when enabled. This option has no effect if extracting into an element tree structure. In any case, the header row is accessible from the table method hrow() . gridmap Controls whether the table contents are returned as a grid or a tree. ROWSPAN and COLSPAN issues are compensated for, and columns really are columns. Empty phantom cells are created where they would have been obscured by ROWSPAN or COLSPAN settings. This really becomes an issue when extracting columns beneath headers. Enabled by default. subtables Extract all tables embedded within matched tables. decode Automatically decode retrieved text with HTML::Entities::decode_entities(). Enabled by default. Has no effect if keep_html was specified or if extracting into an element tree structure. br_translate Translate <br> tags into newlines. Sometimes the remaining text can be hard to parse if the <br> tag is simply dropped. Enabled by default. Has no effect if keep_html is enabled or if extracting into an element tree structure. keep_html Return the raw HTML contained in the cell, rather than just the visible text. Embedded tables are not retained in the HTML extracted from a cell. Patterns for header matches must take into account HTML in the string if this option is enabled. This option has no effect if extracting into an elment tree structure. strip_html_on_match When keep_html is enabled, HTML is stripped by default during attempts at matching header strings (so if strip_html_on_match is not enabled and keep_html is, you would have to include potential HTML tags in the regexp for header matches). Stripped header tags are replaced with an empty string, e.g. 'hot d<em>og</em>' would become 'hot dog' before attempting a match. error_handle Filehandle where error messages are printed. STDERR by default. debug Prints some debugging information to STDERR, more for higher values. If error_handle was provided, messages are printed there rather than STDERR. REGULAR METHODS The following methods are invoked directly from an HTML::TableExtract object. depths() Returns all depths that contained matched tables in the document. counts($depth) For a particular depth, returns all counts that contained matched tables. table($depth, $count) For a particular depth and count, return the table object for the table found, if any. tables() Return table objects for all tables that matched. Returns an empty list if no tables matched. first_table_found() Return the table state object for the first table matched in the document. Returns undef if no tables were matched. current_table() Returns the current table object while parsing the HTML. Only useful if you're messing around with overriding HTML::Parser methods. tree() If the module was invoked in tree extraction mode, returns a reference to the top node of the HTML::Element tree structure for the entire document (which includes, ultimately, all tables within the document). tables_report([$show_content, $col_sep]) Return a string summarizing extracted tables, along with their depth and count. Optionally takes a $show_content flag which will dump the extracted contents of each table as well with columns separated by $col_sep . Default $col_sep is ':'. tables_dump([$show_content, $col_sep]) Same as tables_report() except dump the information to STDOUT. start end text These are the hooks into HTML::Parser. If you want to subclass this module and have things work, you must at some point call these with content. DEPRECATED METHODS Tables used to be called 'table states'. Accordingly, the following methods still work but have been deprecated: table_state() Is now table() table_states() Is now tables() first_table_state_found() Is now first_table_found() TABLE METHODS The following methods are invoked from an HTML::TableExtract::Table object, such as those returned from the tables() method. rows() Return all rows within a matched table. Each row returned is a reference to an array containing the text, HTML, or reference to the HTML::Element object of each cell depending the mode of extraction. Tables with rowspan or colspan attributes will have some cells containing undef. Returns a list or a reference to an array depending on context. columns() Return all columns within a matched table. Each column returned is a reference to an array containing the text, HTML, or reference to HTML::Element object of each cell depending on the mode of extraction. Tables with rowspan or colspan attributes will have some cells containing undef. row($row) Return a particular row from within a matched table either as a list or an array reference, depending on context. column($col) Return a particular column from within a matched table as a list or an array reference, depending on context. cell($row,$col) Return a particular item from within a matched table, whether it be the text, HTML, or reference to the HTML::Element object of that cell, depending on the mode of extraction. If the cell was covered due to rowspan or colspan effects, will return undef. space($row,$col) The same as cell(), except in cases where the given coordinates were covered due to rowspan or colspan issues, in which case the content of the covering cell is returned rat + +### https://metacpan.org/pod/HTML::TableExtract +HTML::TableExtract - Perl module for extracting the content contained in tables within an HTML document, either as text or encoded element trees. - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution HTML-TableExtract Module version: 2.15 25 May 2017 13:49:56 UTC License: unknown Code Download ( 35.63KB ) Source ( raw ) Browse ( raw ) Changes Project Issues (13) How to Contribute Quality Testers ( 8243 / 488 / 0 ) Testers (Magpie) Kwalitee 69.27% Coverage Bus factor: 0 Activity 24 month Dependencies HTML::ElementTable HTML::Parser and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 2.15 (MSISK on 2017-05-25) 2.14 (MSISK on 2017-05-25) 2.13 (MSISK on 2015-05-21) 2.12 (MSISK on 2015-01-09) 2.11 (MSISK on 2011-08-23) 2.10 (MSISK on 2006-07-16) 2.09 (MSISK on 2006-06-08) 2.08 (MSISK on 2006-05-03) 2.07 (MSISK on 2006-02-19) 2.06 (MSISK on 2005-10-19) 2.05 (MSISK on 2005-10-04) 2.04 (MSISK on 2005-08-03) 2.03 (MSISK on 2005-07-20) 2.02 (MSISK on 2005-06-23) 2.01 (MSISK on 2005-06-22) 2.00 (MSISK on 2005-06-17) 1.10 (MSISK on 2005-03-07) 1.09 (MSISK on 2005-02-25) 1.08 (MSISK on 2002-04-05) 1.07 (MSISK on 2001-08-22) 1.06 (MSISK on 2000-11-02) 1.05 (MSISK on 2000-08-06) 1.04 (MSISK on 2000-07-15) 1.03 (MSISK on 2000-07-07) 1.02 (MSISK on 2000-07-06) 1.01 (MSISK on 2000-07-06) 1.00 (MSISK on 2000-07-04) 0.05 (MSISK on 2000-03-21) 0.04 (MSISK on 2000-03-21) 0.03 (MSISK on 2000-03-09) 0.02 (MSISK on 2000-02-11) 0.01 (MSISK on 2000-02-03) Diff with version 2.15 (MSISK on 2017-05-25) 2.14 (MSISK on 2017-05-25) 2.13 (MSISK on 2015-05-21) 2.12 (MSISK on 2015-01-09) 2.11 (MSISK on 2011-08-23) 2.10 (MSISK on 2006-07-16) 2.09 (MSISK on 2006-06-08) 2.08 (MSISK on 2006-05-03) 2.07 (MSISK on 2006-02-19) 2.06 (MSISK on 2005-10-19) 2.05 (MSISK on 2005-10-04) 2.04 (MSISK on 2005-08-03) 2.03 (MSISK on 2005-07-20) 2.02 (MSISK on 2005-06-23) 2.01 (MSISK on 2005-06-22) 2.00 (MSISK on 2005-06-17) 1.10 (MSISK on 2005-03-07) 1.09 (MSISK on 2005-02-25) 1.08 (MSISK on 2002-04-05) 1.07 (MSISK on 2001-08-22) 1.06 (MSISK on 2000-11-02) 1.05 (MSISK on 2000-08-06) 1.04 (MSISK on 2000-07-15) 1.03 (MSISK on 2000-07-07) 1.02 (MSISK on 2000-07-06) 1.01 (MSISK on 2000-07-06) 1.00 (MSISK on 2000-07-04) 0.05 (MSISK on 2000-03-21) 0.04 (MSISK on 2000-03-21) 0.03 (MSISK on 2000-03-09) 0.02 (MSISK on 2000-02-11) 0.01 (MSISK on 2000-02-03) Permalinks This version Latest version ++ed by: 4 PAUSE users 2 non-PAUSE users Authors: unknown Released by: Matt Sisk Maintainers: MSISK owner Matt Sisk  /  2.15 (MSISK on 2017-05-25) 2.14 (MSISK on 2017-05-25) 2.13 (MSISK on 2015-05-21) 2.12 (MSISK on 2015-01-09) 2.11 (MSISK on 2011-08-23) 2.10 (MSISK on 2006-07-16) 2.09 (MSISK on 2006-06-08) 2.08 (MSISK on 2006-05-03) 2.07 (MSISK on 2006-02-19) 2.06 (MSISK on 2005-10-19) 2.05 (MSISK on 2005-10-04) 2.04 (MSISK on 2005-08-03) 2.03 (MSISK on 2005-07-20) 2.02 (MSISK on 2005-06-23) 2.01 (MSISK on 2005-06-22) 2.00 (MSISK on 2005-06-17) 1.10 (MSISK on 2005-03-07) 1.09 (MSISK on 2005-02-25) 1.08 (MSISK on 2002-04-05) 1.07 (MSISK on 2001-08-22) 1.06 (MSISK on 2000-11-02) 1.05 (MSISK on 2000-08-06) 1.04 (MSISK on 2000-07-15) 1.03 (MSISK on 2000-07-07) 1.02 (MSISK on 2000-07-06) 1.01 (MSISK on 2000-07-06) 1.00 (MSISK on 2000-07-04) 0.05 (MSISK on 2000-03-21) 0.04 (MSISK on 2000-03-21) 0.03 (MSISK on 2000-03-09) 0.02 (MSISK on 2000-02-11) 0.01 (MSISK on 2000-02-03) HTML-TableExtract-2.15 6 ++ 6 ++ / HTML::TableExtract Contents NAME SYNOPSIS DESCRIPTION Extraction Modes Advice METHODS CONSTRUCTOR REGULAR METHODS DEPRECATED METHODS TABLE METHODS NOTES ON TREE EXTRACTION MODE REQUIRES OPTIONALLY REQUIRES AUTHOR COPYRIGHT SEE ALSO NAME HTML::TableExtract - Perl module for extracting the content contained in tables within an HTML document, either as text or encoded element trees. SYNOPSIS # Matched tables are returned as table objects; tables can be matched # using column headers, depth, count within a depth, table tag # attributes, or some combination of the four. # Example: Using column header information. # Assume an HTML document with tables that have "Date", "Price", and # "Cost" somewhere in a row. The columns beneath those headings are # what you want to extract. They will be returned in the same order as # you specified the headers since 'automap' is enabled by default. use HTML::TableExtract; my $te = HTML::TableExtract->new( headers => [qw(Date Price Cost)] ); $te->parse($html_string); # Examine all matching tables foreach my $ts ($te->tables) { print "Table (", join(',', $ts->coords), "):\n"; foreach my $row ($ts->rows) { print join(',', @$row), "\n"; } } # Shorthand...top level rows() method assumes the first table found in # the document if no arguments are supplied. foreach my $row ($te->rows) { print join(',', @$row), "\n"; } # Example: Using depth and count information. # Every table in the document has a unique depth and count tuple, so # when both are specified it is a unique table. Depth and count both # begin with 0, so in this case we are looking for a table (depth 2) # within a table (depth 1) within a table (depth 0, which is the top # level HTML document). In addition, it must be the third (count 2) # such instance of a table at that depth. my $te = HTML::TableExtract->new( depth => 2, count => 2 ); $te->parse_file($html_file); foreach my $ts ($te->tables) { print "Table found at ", join(',', $ts->coords), ":\n"; foreach my $row ($ts->rows) { print " ", join(',', @$row), "\n"; } } # Example: Using table tag attributes. # If multiple attributes are specified, all must be present and equal # for match to occur. my $te = HTML::TableExtract->new( attribs => { border => 1 } ); $te->parse($html_string); foreach my $ts ($te->tables) { print "Table with border=1 found at ", join(',', $ts->coords), ":\n"; foreach my $row ($ts->rows) { print " ", join(',', @$row), "\n"; } } # Example: Extracting as an HTML::Element tree structure # Rather than extracting raw text, the html can be converted into a # tree of element objects. The HTML document is composed of # HTML::Element objects and the tables are HTML::ElementTable # structures. Using this, the contents of tables within a document can # be edited in-place. use HTML::TableExtract qw(tree); my $te = HTML::TableExtract->new( headers => qw(Fee Fie Foe Fum) ); $te->parse_file($html_file); my $table = $te->first_table_found; my $table_tree = $table->tree; $table_tree->cell(4,4)->replace_content('Golden Goose'); my $table_html = $table_tree->as_HTML; my $table_text = $table_tree->as_text; my $document_tree = $te->tree; my $document_html = $document_tree->as_HTML; DESCRIPTION HTML::TableExtract is a subclass of HTML::Parser that serves to extract the information from tables of interest contained within an HTML document. The information from each extracted table is stored in table objects. Tables can be extracted as text, HTML, or HTML::ElementTable structures (for in-place editing or manipulation). There are currently four constraints available to specify which tables you would like to extract from a document: Headers , Depth , Count , and Attributes . Headers , the most flexible and adaptive of the techniques, involves specifying text in an array that you expect to appear above the data in the tables of interest. Once all headers have been located in a row of that table, all further cells beneath the columns that matched your headers are extracted. All other columns are ignored: think of it as vertical slices through a table. In addition, TableExtract automatically rearranges each row in the same order as the headers you provided. If you would like to disable this, set automap to 0 during object creation, and instead rely on the column_map() method to find out the order in which the headers were found. Furthermore, TableExtract will automatically compensate for cell span issues so that columns are really the same columns as you would visually see in a browser. This behavior can be disabled by setting the gridmap parameter to 0. HTML is stripped from the entire textual content of a cell before header matches are attempted -- unless the keep_html parameter was enabled. Depth and Count are more specific ways to specify tables in relation to one another. Depth represents how deeply a table resides in other tables. The depth of a top-level table in the document is 0. A table within a top-level table has a depth of 1, and so on. Each depth can be thought of as a layer; tables sharing the same depth are on the same layer. Within each of these layers, Count represents the order in which a table was seen at that depth, starting with 0. Providing both a depth and a count will uniquely specify a table within a document. Attributes match based on the attributes of the html <table> tag, for example, border widths or background color. Each of the Headers , Depth , Count , and Attributes specifications are cumulative in their effect on the overall extraction. For instance, if you specify only a Depth , then you get all tables at that depth (note that these could very well reside in separate higher- level tables throughout the document since depth extends across tables). If you specify only a Count , then the tables at that Count from all depths are returned (i.e., the n th occurrence of a table at each depth). If you only specify Headers , then you get all tables in the document containing those column headers. If you have specified multiple constraints of Headers , Depth , Count , and Attributes , then each constraint has veto power over whether a particular table is extracted. If no Headers , Depth , Count , or Attributes are specified, then all tables match. When extracting only text from tables, the text is decoded with HTML::Entities by default; this can be disabled by setting the decode parameter to 0. Extraction Modes The default mode of extraction for HTML::TableExtract is raw text or HTML. In this mode, embedded tables are completely decoupled from one another. In this case, HTML::TableExtract is a subclass of HTML::Parser: use HTML::TableExtract; Alternatively, tables can be extracted as HTML::ElementTable structures, which are in turn embedded in an HTML::Element tree representing the entire HTML document. Embedded tables are not decoupled from one another since this tree structure must be maintained. In this case, HTML::TableExtract is a subclass of HTML::TreeBuilder (itself a subclass of HTML:::Parser): use HTML::TableExtract qw(tree); In either case, the basic interface for HTML::TableExtract and the resulting table objects remains the same -- all that changes is what you can do with the resulting data. HTML::TableExtract is a subclass of HTML::Parser, and as such inherits all of its basic methods such as parse() and parse_file() . During scans, start() , end() , and text() are utilized. Feel free to override them, but if you do not eventually invoke them in the SUPER class with some content, results are not guaranteed. Advice The main point of this module was to provide a flexible method of extracting tabular information from HTML documents without relying to heavily on the document layout. For that reason, I suggest using Headers whenever possible -- that way, you are anchoring your extraction on what the document is trying to communicate rather than some feature of the HTML comprising the document (other than the fact that the data is contained in a table). METHODS The following are the top-level methods of the HTML::TableExtract object. Tables that have matched a query are actually returned as separate objects of type HTML::TableExtract::Table. These table objects have their own methods, documented further below. CONSTRUCTOR new() Return a new HTML::TableExtract object. Valid attributes are: headers Passed as an array reference, headers specify strings of interest at the top of columns within targeted tables. They can be either strings or regular expressions (qr//). If they are strings, they will eventually be passed through a non-anchored, case-insensitive regular expression, so regexp special characters are allowed. The table row containing the headers is not returned, unless keep_headers was specified or you are extracting into an element tree. In either case the header row can be accessed via the hrow() method from within the table object. Columns that are not beneath one of the provided headers will be ignored unless slice_columns was set to 0. Columns will, by default, be rearranged into the same order as the headers you provide (see the automap parameter for more information) unless slice_columns is 0. Additionally, by default columns are considered what you would see visually beneath that header when the table is rendered in a browser. See the gridmap parameter for more information. HTML within a header is stripped before the match is attempted, unless the keep_html parameter was specified and strip_html_on_match is false. depth Specify how embedded in other tables your tables of interest should be. Top-level tables in the HTML document have a depth of 0, tables within top-level tables have a depth of 1, and so on. count Specify which table within each depth you are interested in, beginning with 0. attribs Passed as a hash reference, attribs specify attributes of interest within the HTML <table> tag itself. automap Automatically applies the ordering reported by column_map() to the rows returned by rows(). This only makes a difference if you have specified Headers and they turn out to be in a different order in the table than what you specified. Automap will rearrange the columns in the same order as the headers appear. To get the original ordering, you will need to take another slice of each row using column_map(). automap is enabled by default. slice_columns Enabled by default, this option controls whether vertical slices are returned from under headers that match. When disabled, all columns of the matching table are retained, regardles of whether they had a matching header above them. Disabling this also disables automap . keep_headers Disabled by default, and only applicable when header constraints have been specified, keep_headers will retain the matching header row as the first row of table data when enabled. This option has no effect if extracting into an element tree structure. In any case, the header row is accessible from the table method hrow() . gridmap Controls whether the table contents are returned as a grid or a tree. ROWSPAN and COLSPAN issues are compensated for, and columns really are columns. Empty phantom cells are created where they would have been obscured by ROWSPAN or COLSPAN settings. This really becomes an issue when extracting columns beneath headers. Enabled by default. subtables Extract all tables embedded within matched tables. decode Automatically decode retrieved text with HTML::Entities::decode_entities(). Enabled by default. Has no effect if keep_html was specified or if extracting into an element tree structure. br_translate Translate <br> tags into newlines. Sometimes the remaining text can be hard to parse if the <br> tag is simply dropped. Enabled by default. Has no effect if keep_html is enabled or if extracting into an element tree structure. keep_html Return the raw HTML contained in the cell, rather than just the visible text. Embedded tables are not retained in the HTML extracted from a cell. Patterns for header matches must take into account HTML in the string if this option is enabled. This option has no effect if extracting into an elment tree structure. strip_html_on_match When keep_html is enabled, HTML is stripped by default during attempts at matching header strings (so if strip_html_on_match is not enabled and keep_html is, you would have to include potential HTML tags in the regexp for header matches). Stripped header tags are replaced with an empty string, e.g. 'hot d<em>og</em>' would become 'hot dog' before attempting a match. error_handle Filehandle where error messages are printed. STDERR by default. debug Prints some debugging information to STDERR, more for higher values. If error_handle was provided, messages are printed there rather than STDERR. REGULAR METHODS The following methods are invoked directly from an HTML::TableExtract object. depths() Returns all depths that contained matched tables in the document. counts($depth) For a particular depth, returns all counts that contained matched tables. table($depth, $count) For a particular depth and count, return the table object for the table found, if any. tables() Return table objects for all tables that matched. Returns an empty list if no tables matched. first_table_found() Return the table state object for the first table matched in the document. Returns undef if no tables were matched. current_table() Returns the current table object while parsing the HTML. Only useful if you're messing around with overriding HTML::Parser methods. tree() If the module was invoked in tree extraction mode, returns a reference to the top node of the HTML::Element tree structure for the entire document (which includes, ultimately, all tables within the document). tables_report([$show_content, $col_sep]) Return a string summarizing extracted tables, along with their depth and count. Optionally takes a $show_content flag which will dump the extracted contents of each table as well with columns separated by $col_sep . Default $col_sep is ':'. tables_dump([$show_content, $col_sep]) Same as tables_report() except dump the information to STDOUT. start end text These are the hooks into HTML::Parser. If you want to subclass this module and have things work, you must at some point call these with content. DEPRECATED METHODS Tables used to be called 'table states'. Accordingly, the following methods still work but have been deprecated: table_state() Is now table() table_states() Is now tables() first_table_state_found() Is now first_table_found() TABLE METHODS The following methods are invoked from an HTML::TableExtract::Table object, such as those returned from the tables() method. rows() Return all rows within a matched table. Each row returned is a reference to an array containing the text, HTML, or reference to the HTML::Element object of each cell depending the mode of extraction. Tables with rowspan or colspan attributes will have some cells containing undef. Returns a list or a reference to an array depending on context. columns() Return all columns within a matched table. Each column returned is a reference to an array containing the text, HTML, or reference to HTML::Element object of each cell depending on the mode of extraction. Tables with rowspan or colspan attributes will have some cells containing undef. row($row) Return a particular row from within a matched table either as a list or an array reference, depending on context. column($col) Return a particular column from within a matched table as a list or an array reference, depending on context. cell($row,$col) Return a particular item from within a matched table, whether it be the text, HTML, or reference to the HTML::Element object of that cell, depending on the mode of extraction. If the cell was covered due to rowspan or colspan effects, will return undef. space($row,$col) The same as cell(), except in cases where the given coordinates were covered due to rowspan or colspan issues, in which case the content of the covering cell is returned rat + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-html-tableextract --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-html-tableextract 2.13 0 +----------------------------- +file name : perl-html-tableextract-2.13-0.tar.bz2 +name : perl-html-tableextract +version : 2.13 +build : 0 +build number: 0 +size : 16 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tableextract-2.13-0.tar.bz2 +md5 : 77ad48caae0d0b419bc5e602ae61e401 +dependencies: + - perl-html-element-extended + - perl-html-parser + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-html-tableextract 2.13 pl526_1 +----------------------------------- +file name : perl-html-tableextract-2.13-pl526_1.tar.bz2 +name : perl-html-tableextract +version : 2.13 +build : pl526_1 +build number: 1 +size : 23 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tableextract-2.13-pl526_1.tar.bz2 +md5 : 1dc3ad5cfda75992763062b721436a06 +timestamp : 2018-07-09 06:36:58 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-html-element-extended + - perl-html-parser + + +perl-html-tableextract 2.13 pl526_2 +----------------------------------- +file name : perl-html-tableextract-2.13-pl526_2.tar.bz2 +name : perl-html-tableextract +version : 2.13 +build : pl526_2 +build number: 2 +size : 23 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tableextract-2.13-pl526_2.tar.bz2 +md5 : ce74a864c8e3af76921cb8645372de61 +timestamp : 2018-08-09 06:58:39 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-html-element-extended + - perl-html-parser + + +perl-html-tableextract 2.13 pl5321hdfd78af_3 +-------------------------------------------- +file name : perl-html-tableextract-2.13-pl5321hdfd78af_3.tar.bz2 +name : perl-html-tableextract +version : 2.13 +build : pl5321hdfd78af_3 +build number: 3 +size : 25 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-html-tableextract-2.13-pl5321hdfd78af_3.tar.bz2 +md5 : e884844436fdd2de52d38ba19aeea063 +timestamp : 2022-01-24 20:34:27 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-html-element-extended + - perl-html-parser + + +perl-html-tableextract 2.15 pl5321hdfd78af_0 +-------------------------------------------- +file name : perl-html-tableextract-2.15-pl5321hdfd78af_0.conda +name : perl-html-tableextract +version : 2.15 +build : pl5321hdfd78af_0 +build number: 0 +size : 27 KB +license : Unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-html-tableextract-2.15-pl5321hdfd78af_0.conda +md5 : a6c3090f2e89a9ffa26e296a4b2d1ed4 +timestamp : 2025-08-28 20:15:12 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-html-element-extended + - perl-html-parser diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-tagset.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-tagset.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc5feb16d66aebbdd615444340b0746c2ee6dbb4 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-tagset.manual_bundle.txt @@ -0,0 +1,168 @@ +# Tool: perl-html-tagset +software_name: perl-html-tagset +tier: T1 +domain: t1_backfill_overall +downloads: 542326 +summary: Data tables useful in parsing HTML. +description: Data tables useful in parsing HTML. +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/HTML::Tagset +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/HTML::Tagset +HTML::Tagset - data tables useful in parsing HTML - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution HTML-Tagset Module version: 3.24 11 Mar 2024 17:32:52 UTC License: artistic_2 Perl: v5.10.1 Code Download ( 7.93KB ) Source ( raw ) Browse ( raw ) Changes Project Homepage Repository Issues (7) How to Contribute Quality Testers ( 4613 / 0 / 4 ) Testers (Magpie) Kwalitee 100.00% Coverage Bus factor: 6 Activity 24 month Dependencies unknown Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 3.24 (PETDANCE on 2024-03-11) 3.22 (PETDANCE on 2024-03-10) 3.20 (PETDANCE on 2008-03-01) 3.10 (PETDANCE on 2005-11-08) 3.04 (SBURKE on 2004-12-30) 3.03 (SBURKE on 2000-10-21) 3.02 (SBURKE on 2000-09-04) 3.01 (SBURKE on 2000-08-21) Diff with version 3.24 (PETDANCE on 2024-03-11) 3.22 (PETDANCE on 2024-03-10) 3.20 (PETDANCE on 2008-03-01) 3.10 (PETDANCE on 2005-11-08) 3.04 (SBURKE on 2004-12-30) 3.03 (SBURKE on 2000-10-21) 3.02 (SBURKE on 2000-09-04) 3.01 (SBURKE on 2000-08-21) Permalinks This version Latest version ++ed by: 1 PAUSE user 1 non-PAUSE user Authors: Andy Lester Released by: Andy Lester 6 Maintainers: OALDERS owner CAPOEIRAB ETHER HAARG PETDANCE SKAJI Andy Lester  /  3.24 (PETDANCE on 2024-03-11) 3.22 (PETDANCE on 2024-03-10) 3.20 (PETDANCE on 2008-03-01) 3.10 (PETDANCE on 2005-11-08) 3.04 (SBURKE on 2004-12-30) 3.03 (SBURKE on 2000-10-21) 3.02 (SBURKE on 2000-09-04) 3.01 (SBURKE on 2000-08-21) HTML-Tagset-3.24 2 ++ 2 ++ ⭐ Starred 0 GitHub stars / HTML::Tagset Contents NAME VERSION SYNOPSIS DESCRIPTION VARIABLES hashset %HTML::Tagset::emptyElement hashset %HTML::Tagset::optionalEndTag hash %HTML::Tagset::linkElements hash %HTML::Tagset::boolean_attr hashset %HTML::Tagset::isPhraseMarkup hashset %HTML::Tagset::is_Possible_Strict_P_Content hashset %HTML::Tagset::isHeadElement hashset %HTML::Tagset::isList hashset %HTML::Tagset::isTableElement hashset %HTML::Tagset::isFormElement hashset %HTML::Tagset::isBodyElement hashset %HTML::Tagset::isHeadOrBodyElement hashset %HTML::Tagset::isKnown hashset %HTML::Tagset::canTighten array @HTML::Tagset::p_closure_barriers hashset %isCDATA_Parent CAVEATS SEE ALSO COPYRIGHT & LICENSE ACKNOWLEDGEMENTS AUTHOR BUGS NAME HTML::Tagset - data tables useful in parsing HTML VERSION Version 3.24 SYNOPSIS use HTML::Tagset; # Then use any of the items in the HTML::Tagset package # as need arises DESCRIPTION This module contains several data tables useful in various kinds of HTML parsing operations. Note that all tag names used are lowercase. In the following documentation, a "hashset" is a hash being used as a set -- the hash conveys that its keys are there, and the actual values associated with the keys are not significant. (But what values are there, are always true.) VARIABLES Note that none of these variables are exported. hashset %HTML::Tagset::emptyElement This hashset has as values the tag-names (GIs) of elements that cannot have content. (For example, "base", "br", "hr".) So $HTML::Tagset::emptyElement{'hr'} exists and is true. $HTML::Tagset::emptyElement{'dl'} does not exist, and so is not true. hashset %HTML::Tagset::optionalEndTag This hashset lists tag-names for elements that can have content, but whose end-tags are generally, "safely", omissible. Example: $HTML::Tagset::emptyElement{'li'} exists and is true. hash %HTML::Tagset::linkElements Values in this hash are tagnames for elements that might contain links, and the value for each is a reference to an array of the names of attributes whose values can be links. hash %HTML::Tagset::boolean_attr This hash (not hashset) lists what attributes of what elements can be printed without showing the value (for example, the "noshade" attribute of "hr" elements). For elements with only one such attribute, its value is simply that attribute name. For elements with many such attributes, the value is a reference to a hashset containing all such attributes. hashset %HTML::Tagset::isPhraseMarkup This hashset contains all phrasal-level elements. hashset %HTML::Tagset::is_Possible_Strict_P_Content This hashset contains all phrasal-level elements that be content of a P element, for a strict model of HTML. hashset %HTML::Tagset::isHeadElement This hashset contains all elements that elements that should be present only in the 'head' element of an HTML document. hashset %HTML::Tagset::isList This hashset contains all elements that can contain "li" elements. hashset %HTML::Tagset::isTableElement This hashset contains all elements that are to be found only in/under a "table" element. hashset %HTML::Tagset::isFormElement This hashset contains all elements that are to be found only in/under a "form" element. hashset %HTML::Tagset::isBodyElement This hashset contains all elements that are to be found only in/under the "body" element of an HTML document. hashset %HTML::Tagset::isHeadOrBodyElement This hashset includes all elements that I notice can fall either in the head or in the body. hashset %HTML::Tagset::isKnown This hashset lists all known HTML elements. hashset %HTML::Tagset::canTighten This hashset lists elements that might have ignorable whitespace as children or siblings. array @HTML::Tagset::p_closure_barriers This array has a meaning that I have only seen a need for in HTML::TreeBuilder , but I include it here on the off chance that someone might find it of use: When we see a "<p>" token, we go lookup up the lineage for a p element we might have to minimize. At first sight, we might say that if there's a p anywhere in the lineage of this new p, it should be closed. But that's wrong. Consider this document: <html> <head> <title>foo</title> </head> <body> <p>foo <table> <tr> <td> foo <p>bar </td> </tr> </table> </p> </body> </html> The second p is quite legally inside a much higher p. My formalization of the reason why this is legal, but this: <p>foo<p>bar</p></p> isn't, is that something about the table constitutes a "barrier" to the application of the rule about what p must minimize. So @HTML::Tagset::p_closure_barriers is the list of all such barrier-tags. hashset %isCDATA_Parent This hashset includes all elements whose content is CDATA. CAVEATS You may find it useful to alter the behavior of modules (like HTML::Element or HTML::TreeBuilder ) that use HTML::Tagset 's data tables by altering the data tables themselves. You are welcome to try, but be careful; and be aware that different modules may or may react differently to the data tables being changed. Note that it may be inappropriate to use these tables for producing HTML -- for example, %isHeadOrBodyElement lists the tagnames for all elements that can appear either in the head or in the body, such as "script". That doesn't mean that I am saying your code that produces HTML should feel free to put script elements in either place! If you are producing programs that spit out HTML, you should be intimately familiar with the DTDs for HTML or XHTML (available at http://www.w3.org/ ), and you should slavishly obey them, not the data tables in this document. SEE ALSO HTML::Element , HTML::TreeBuilder , HTML::LinkExtor COPYRIGHT & LICENSE Copyright 1995-2000 Gisle Aas. Copyright 2000-2005 Sean M. Burke. Copyright 2005-2024 Andy Lester. This library is free software; you can redistribute it and/or modify it under the terms of the Artistic License version 2.0. ACKNOWLEDGEMENTS Most of the code/data in this module was adapted from code written by Gisle Aas for HTML::Element , HTML::TreeBuilder , and HTML::LinkExtor . Then it was maintained by Sean M. Burke. AUTHOR Current maintainer: Andy Lester, <andy at petdance.com> BUGS Please report any bugs or feature requests to bug-html-tagset at rt.cpan.org , or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=HTML-Tagset . I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Module Install Instructions To install HTML::Tagset, copy and paste the appropriate command in to your terminal. cpanm cpanm HTML::Tagset CPAN shell perl -MCPAN -e shell install HTML::Tagset For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-html-tagset --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-html-tagset 3.20 0 +----------------------- +file name : perl-html-tagset-3.20-0.tar.bz2 +name : perl-html-tagset +version : 3.20 +build : 0 +build number: 0 +size : 6 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tagset-3.20-0.tar.bz2 +md5 : f29be54e95e8c4b32463e98e70059505 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-html-tagset 3.20 pl5.22.0_1 +-------------------------------- +file name : perl-html-tagset-3.20-pl5.22.0_1.tar.bz2 +name : perl-html-tagset +version : 3.20 +build : pl5.22.0_1 +build number: 1 +size : 9 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tagset-3.20-pl5.22.0_1.tar.bz2 +md5 : c8730cb29b8732d0791d6256b3b15d20 +dependencies: + - perl 5.22.0* + + +perl-html-tagset 3.20 pl526_2 +----------------------------- +file name : perl-html-tagset-3.20-pl526_2.tar.bz2 +name : perl-html-tagset +version : 3.20 +build : pl526_2 +build number: 2 +size : 11 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tagset-3.20-pl526_2.tar.bz2 +md5 : 33c99f32a34c67f7b1a85d5c097cfa61 +timestamp : 2018-07-07 00:28:36 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-html-tagset 3.20 pl526_3 +----------------------------- +file name : perl-html-tagset-3.20-pl526_3.tar.bz2 +name : perl-html-tagset +version : 3.20 +build : pl526_3 +build number: 3 +size : 12 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tagset-3.20-pl526_3.tar.bz2 +md5 : 169010ee892bae283dc8ae4c37ad268b +timestamp : 2018-08-24 03:26:30 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-html-tagset 3.20 pl5321hdfd78af_4 +-------------------------------------- +file name : perl-html-tagset-3.20-pl5321hdfd78af_4.tar.bz2 +name : perl-html-tagset +version : 3.20 +build : pl5321hdfd78af_4 +build number: 4 +size : 14 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-html-tagset-3.20-pl5321hdfd78af_4.tar.bz2 +md5 : 69c71855f076d4e826c1af7b4d197969 +timestamp : 2022-01-17 11:38:42 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-html-tagset 3.24 pl5321hdfd78af_0 +-------------------------------------- +file name : perl-html-tagset-3.24-pl5321hdfd78af_0.tar.bz2 +name : perl-html-tagset +version : 3.24 +build : pl5321hdfd78af_0 +build number: 0 +size : 15 KB +license : Unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-html-tagset-3.24-pl5321hdfd78af_0.tar.bz2 +md5 : 3717890fb544dcd6f16ac07b4ac3b147 +timestamp : 2025-06-11 20:40:29 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-tidy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-tidy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1f062ea952f5cd2aefb50a5218b5ef6d03d9c9d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-html-tidy.manual_bundle.txt @@ -0,0 +1,267 @@ +# Tool: perl-html-tidy +software_name: perl-html-tidy +tier: T1 +domain: t1_backfill_overall +downloads: 192398 +summary: (X)HTML validation in a Perl object +description: (X)HTML validation in a Perl object +dependencies: libgcc >=13, perl >=5.32.1,<5.33.0a0 *_perl5, perl-carp, perl-constant, perl-encode, perl-exporter, perl-getopt-long >=2.58,<3.0a0, tidyp >=1.4,<2.0a0 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://github.com/petdance/html-tidy +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://github.com/petdance/html-tidy +GitHub - petdance/html-tidy: HTML::Tidy is no longer being maintained. Please see the new project https://github.com/petdance/html-tidy5 · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} This repository was archived by the owner on Apr 14, 2019. It is now read-only. petdance / html-tidy Public archive Notifications You must be signed in to change notification settings Fork 19 Star 31 Code Issues 5 Pull requests 1 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights petdance/html-tidy dev Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 129 Commits 129 Commits bin bin lib/ HTML lib/ HTML t t xt xt .gitignore .gitignore Changes Changes MANIFEST MANIFEST Makefile.PL Makefile.PL README.markdown README.markdown Tidy.xs Tidy.xs perlcriticrc perlcriticrc ppport.h ppport.h tags tags View all files Repository files navigation README HTML::Tidy HTML::Tidy is an HTML checker in a handy dandy object. It's meant as a companion to HTML::Lint , which is written in Perl but is not nearly as capable as HTML::Tidy. PREREQUISITES HTML::Tidy does very little work. The real work of HTML::Tidy is done by the tidyp library, which is written in C. To use HTML::Tidy, you must install tidyp. There are two, perhaps three, ways to install tidyp: Get a tarball from the tidyp source distributions from Github and and build it like any other C library. Note that you must get a source tarball, not just clone the source tree via github. Install the Alien::Tidyp Perl module, which automates the tidyp installation process. Your operating system may also have a package for tidyp that you can install. As of this writing, these operating systems are known to provide tidyp library: Fedora contains tidyp-devel package FreeBSD contains tidyp port You need only do one of these steps. INSTALLATION Once you have libtidyp installed via one of the previous methods, install HTML::Tidy like any standard Perl module. perl Makefile.PL make make test make install COPYRIGHT AND LICENSE Copyright (C) 2004-2017 by Andy Lester This library is free software. It may be redistributed and modified under the Artistic License v2.0. About HTML::Tidy is no longer being maintained. Please see the new project https://github.com/petdance/html-tidy5 Resources Readme Uh oh! There was an error while loading. Please reload this page . Activity Stars 31 stars Watchers 10 watching Forks 19 forks Report repository Releases 7 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 62.4% C 29.0% XS 5.8% HTML 2.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-html-tidy --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-html-tidy 1.56 1 +--------------------- +file name : perl-html-tidy-1.56-1.tar.bz2 +name : perl-html-tidy +version : 1.56 +build : 1 +build number: 1 +size : 14 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tidy-1.56-1.tar.bz2 +md5 : e028c0c89e311357ae1ad28f03db2c85 +dependencies: + - perl-threaded + - tidyp + - perl >=5.22.0,<5.23.0 + + +perl-html-tidy 1.56 pl526_2 +--------------------------- +file name : perl-html-tidy-1.56-pl526_2.tar.bz2 +name : perl-html-tidy +version : 1.56 +build : pl526_2 +build number: 2 +size : 19 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tidy-1.56-pl526_2.tar.bz2 +md5 : 510a17f143a431578d44593202e5fdeb +timestamp : 2018-07-07 00:25:27 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - tidyp + + +perl-html-tidy 1.60 pl526_0 +--------------------------- +file name : perl-html-tidy-1.60-pl526_0.tar.bz2 +name : perl-html-tidy +version : 1.60 +build : pl526_0 +build number: 0 +size : 20 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tidy-1.60-pl526_0.tar.bz2 +md5 : 17c81b9261089410fb17206b7998a2af +timestamp : 2018-12-17 16:47:52 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-carp + - perl-constant + - perl-encode + - perl-exporter + - perl-getopt-long + - tidyp + + +perl-html-tidy 1.60 pl5321h031d066_3 +------------------------------------ +file name : perl-html-tidy-1.60-pl5321h031d066_3.tar.bz2 +name : perl-html-tidy +version : 1.60 +build : pl5321h031d066_3 +build number: 3 +size : 23 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tidy-1.60-pl5321h031d066_3.tar.bz2 +md5 : aef60e71576df537c8cb8b0761a2076c +timestamp : 2023-05-15 08:09:15 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-constant + - perl-encode + - perl-exporter + - perl-getopt-long + - tidyp + + +perl-html-tidy 1.60 pl5321h779adbc_1 +------------------------------------ +file name : perl-html-tidy-1.60-pl5321h779adbc_1.tar.bz2 +name : perl-html-tidy +version : 1.60 +build : pl5321h779adbc_1 +build number: 1 +size : 21 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tidy-1.60-pl5321h779adbc_1.tar.bz2 +md5 : 107e24b4ae6998eeb74badaa590a6873 +timestamp : 2022-01-25 17:39:27 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-constant + - perl-encode + - perl-exporter + - perl-getopt-long + - tidyp + + +perl-html-tidy 1.60 pl5321h7b50bb2_5 +------------------------------------ +file name : perl-html-tidy-1.60-pl5321h7b50bb2_5.tar.bz2 +name : perl-html-tidy +version : 1.60 +build : pl5321h7b50bb2_5 +build number: 5 +size : 520 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tidy-1.60-pl5321h7b50bb2_5.tar.bz2 +md5 : c9f46675e1b5f1fa8425a8b78813ac45 +timestamp : 2025-03-18 18:30:59 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-constant + - perl-encode + - perl-exporter + - perl-getopt-long >=2.58,<3.0a0 + - tidyp >=1.4,<2.0a0 + + +perl-html-tidy 1.60 pl5321h7b50bb2_6 +------------------------------------ +file name : perl-html-tidy-1.60-pl5321h7b50bb2_6.tar.bz2 +name : perl-html-tidy +version : 1.60 +build : pl5321h7b50bb2_6 +build number: 6 +size : 521 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tidy-1.60-pl5321h7b50bb2_6.tar.bz2 +md5 : 8236f4e5324ff19f88779d28d66b8dbe +timestamp : 2025-04-27 18:04:41 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-constant + - perl-encode + - perl-exporter + - perl-getopt-long >=2.58,<3.0a0 + - tidyp >=1.4,<2.0a0 + + +perl-html-tidy 1.60 pl5321h7b50bb2_7 +------------------------------------ +file name : perl-html-tidy-1.60-pl5321h7b50bb2_7.tar.bz2 +name : perl-html-tidy +version : 1.60 +build : pl5321h7b50bb2_7 +build number: 7 +size : 518 KB +license : Artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tidy-1.60-pl5321h7b50bb2_7.tar.bz2 +md5 : 96620099696fe9074975cae1a31ef057 +timestamp : 2025-08-01 16:43:42 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-constant + - perl-encode + - perl-exporter + - perl-getopt-long >=2.58,<3.0a0 + - tidyp >=1.4,<2.0a0 + + +perl-html-tidy 1.60 pl5321hec16e2b_2 +------------------------------------ +file name : perl-html-tidy-1.60-pl5321hec16e2b_2.tar.bz2 +name : perl-html-tidy +version : 1.60 +build : pl5321hec16e2b_2 +build number: 2 +size : 21 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-html-tidy-1.60-pl5321hec16e2b_2.tar.bz2 +md5 : c09ae09265c5362cf9717ccd5c62ccee +timestamp : 2022-02-21 22:32:21 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-constant + - perl-encode + - perl-exporter + - perl-getopt-long + - tidyp diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-http-daemon.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-http-daemon.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed210facc544173cb1685c4004419dfab2efd859 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-http-daemon.manual_bundle.txt @@ -0,0 +1,215 @@ +# Tool: perl-http-daemon +software_name: perl-http-daemon +tier: T1 +domain: t1_backfill_overall +downloads: 507600 +summary: a simple http server class +description: a simple http server class +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-carp, perl-http-date, perl-http-message, perl-lwp-mediatypes, perl-socket +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/HTTP-Daemon +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/HTTP-Daemon +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-http-daemon --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-http-daemon 6.01 0 +----------------------- +file name : perl-http-daemon-6.01-0.tar.bz2 +name : perl-http-daemon +version : 6.01 +build : 0 +build number: 0 +size : 9 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-http-daemon-6.01-0.tar.bz2 +md5 : d4d8b57d09f73b62d234a6af1a99851d +dependencies: + - perl-http-date + - perl-http-message + - perl-lwp-mediatypes + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-http-daemon 6.01 pl526_1 +----------------------------- +file name : perl-http-daemon-6.01-pl526_1.tar.bz2 +name : perl-http-daemon +version : 6.01 +build : pl526_1 +build number: 1 +size : 14 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-http-daemon-6.01-pl526_1.tar.bz2 +md5 : b6540672ea97f10b1088ece63b799177 +timestamp : 2018-07-07 22:53:02 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-http-date + - perl-http-message + - perl-lwp-mediatypes + + +perl-http-daemon 6.01 pl5321hdfd78af_2 +-------------------------------------- +file name : perl-http-daemon-6.01-pl5321hdfd78af_2.tar.bz2 +name : perl-http-daemon +version : 6.01 +build : pl5321hdfd78af_2 +build number: 2 +size : 17 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-http-daemon-6.01-pl5321hdfd78af_2.tar.bz2 +md5 : 14261e79c587b2e156ea5fcd3aac1465 +timestamp : 2022-01-26 14:24:53 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-http-date + - perl-http-message + - perl-lwp-mediatypes + + +perl-http-daemon 6.13 pl5321hdfd78af_0 +-------------------------------------- +file name : perl-http-daemon-6.13-pl5321hdfd78af_0.tar.bz2 +name : perl-http-daemon +version : 6.13 +build : pl5321hdfd78af_0 +build number: 0 +size : 20 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-http-daemon-6.13-pl5321hdfd78af_0.tar.bz2 +md5 : a7fec4b066bfb4bf1857c53581347dd3 +timestamp : 2022-02-15 23:12:37 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-http-date + - perl-http-message + - perl-lwp-mediatypes + - perl-socket + + +perl-http-daemon 6.14 pl5321hdfd78af_0 +-------------------------------------- +file name : perl-http-daemon-6.14-pl5321hdfd78af_0.tar.bz2 +name : perl-http-daemon +version : 6.14 +build : pl5321hdfd78af_0 +build number: 0 +size : 20 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-http-daemon-6.14-pl5321hdfd78af_0.tar.bz2 +md5 : ec7208cfb33cb770ec1a2b0fc67a5edf +timestamp : 2022-03-04 01:52:58 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-http-date + - perl-http-message + - perl-lwp-mediatypes + - perl-socket + + +perl-http-daemon 6.15 pl5321hdfd78af_0 +-------------------------------------- +file name : perl-http-daemon-6.15-pl5321hdfd78af_0.tar.bz2 +name : perl-http-daemon +version : 6.15 +build : pl5321hdfd78af_0 +build number: 0 +size : 21 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-http-daemon-6.15-pl5321hdfd78af_0.tar.bz2 +md5 : 28f3694b7bcf7df0571e5222d995bf2d +timestamp : 2023-02-22 23:34:38 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-http-date + - perl-http-message + - perl-lwp-mediatypes + - perl-socket + + +perl-http-daemon 6.16 pl5321hdfd78af_0 +-------------------------------------- +file name : perl-http-daemon-6.16-pl5321hdfd78af_0.tar.bz2 +name : perl-http-daemon +version : 6.16 +build : pl5321hdfd78af_0 +build number: 0 +size : 22 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-http-daemon-6.16-pl5321hdfd78af_0.tar.bz2 +md5 : 55e2a97aa9794010e0f1cedc1abb3f19 +timestamp : 2023-04-13 04:08:29 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-http-date + - perl-http-message + - perl-lwp-mediatypes + - perl-socket diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-image-size.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-image-size.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..59ce1b729f8218c96d342e6bfe8609d46984fb01 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-image-size.manual_bundle.txt @@ -0,0 +1,128 @@ +# Tool: perl-image-size +software_name: perl-image-size +tier: T1 +domain: t1_backfill_overall +downloads: 184063 +summary: A library to extract height/width from images +description: A library to extract height/width from images +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-image-size --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-image-size 3.300 0 +----------------------- +file name : perl-image-size-3.300-0.tar.bz2 +name : perl-image-size +version : 3.300 +build : 0 +build number: 0 +size : 17 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-image-size-3.300-0.tar.bz2 +md5 : 9607a3e14f4aec187bd6ead1ae9b9de2 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-image-size 3.300 pl526_1 +----------------------------- +file name : perl-image-size-3.300-pl526_1.tar.bz2 +name : perl-image-size +version : 3.300 +build : pl526_1 +build number: 1 +size : 25 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-image-size-3.300-pl526_1.tar.bz2 +md5 : 61c6cdc6ff5ae01001895a65bd111443 +timestamp : 2018-07-07 07:33:56 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-image-size 3.300 pl526_2 +----------------------------- +file name : perl-image-size-3.300-pl526_2.tar.bz2 +name : perl-image-size +version : 3.300 +build : pl526_2 +build number: 2 +size : 26 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-image-size-3.300-pl526_2.tar.bz2 +md5 : 4fde2f534700c5db586857c1cb54a7fb +timestamp : 2018-07-29 22:21:59 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-image-size 3.300 pl5321hdfd78af_3 +-------------------------------------- +file name : perl-image-size-3.300-pl5321hdfd78af_3.tar.bz2 +name : perl-image-size +version : 3.300 +build : pl5321hdfd78af_3 +build number: 3 +size : 28 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-image-size-3.300-pl5321hdfd78af_3.tar.bz2 +md5 : e973f8adda73f78fe2ff8138575dc002 +timestamp : 2022-01-24 15:50:08 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-importer.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-importer.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e15eb754415378a7db7adc83584470e5b92bc44f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-importer.manual_bundle.txt @@ -0,0 +1,183 @@ +# Tool: perl-importer +software_name: perl-importer +tier: T1 +domain: t1_backfill_overall +downloads: 123180 +summary: Alternative but compatible interface to modules that export symbols. +description: Alternative but compatible interface to modules that export symbols. +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Importer +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Importer +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-importer --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-importer 0.024 0 +--------------------- +file name : perl-importer-0.024-0.tar.bz2 +name : perl-importer +version : 0.024 +build : 0 +build number: 0 +size : 14 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-importer-0.024-0.tar.bz2 +md5 : e7dac2fadbc2899899e7b218bec9107b +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-importer 0.024 pl526_1 +--------------------------- +file name : perl-importer-0.024-pl526_1.tar.bz2 +name : perl-importer +version : 0.024 +build : pl526_1 +build number: 1 +size : 20 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-importer-0.024-pl526_1.tar.bz2 +md5 : bcaab1fde379423f952360d57731b314 +timestamp : 2018-07-08 12:48:08 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-importer 0.025 pl526_0 +--------------------------- +file name : perl-importer-0.025-pl526_0.tar.bz2 +name : perl-importer +version : 0.025 +build : pl526_0 +build number: 0 +size : 21 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-importer-0.025-pl526_0.tar.bz2 +md5 : adc33fd001447d5e664ac934a6f0852e +timestamp : 2019-01-12 21:29:36 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-importer 0.025 pl526_1 +--------------------------- +file name : perl-importer-0.025-pl526_1.tar.bz2 +name : perl-importer +version : 0.025 +build : pl526_1 +build number: 1 +size : 21 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-importer-0.025-pl526_1.tar.bz2 +md5 : d55b3361ea6a9d86303a8d16cec61be7 +timestamp : 2019-05-02 21:01:15 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-importer 0.025 pl5321hdfd78af_2 +------------------------------------ +file name : perl-importer-0.025-pl5321hdfd78af_2.tar.bz2 +name : perl-importer +version : 0.025 +build : pl5321hdfd78af_2 +build number: 2 +size : 23 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-importer-0.025-pl5321hdfd78af_2.tar.bz2 +md5 : 629bd6ff8952a33e4726fc902bb48bd1 +timestamp : 2022-01-19 14:00:12 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-importer 0.026 pl5321hd8ed1ab_0 +------------------------------------ +file name : perl-importer-0.026-pl5321hd8ed1ab_0.tar.bz2 +name : perl-importer +version : 0.026 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 26 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-importer-0.026-pl5321hd8ed1ab_0.tar.bz2 +md5 : 66e17c342d13c39a12c1059f13f9b72c +timestamp : 2022-08-14 10:02:45 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-importer 0.026 pl5321hdfd78af_0 +------------------------------------ +file name : perl-importer-0.026-pl5321hdfd78af_0.tar.bz2 +name : perl-importer +version : 0.026 +build : pl5321hdfd78af_0 +build number: 0 +size : 23 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-importer-0.026-pl5321hdfd78af_0.tar.bz2 +md5 : 3188368f1c0b76ee2a72447aa63d141f +timestamp : 2022-02-10 17:27:23 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-io-compress.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-io-compress.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..25e5f1d6776ac272df90fd10613707ce17d74514 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-io-compress.manual_bundle.txt @@ -0,0 +1,459 @@ +# Tool: perl-io-compress +software_name: perl-io-compress +tier: T1 +domain: t1_backfill_overall +downloads: 1624078 +summary: IO Interface to compressed data files/buffers. +description: IO Interface to compressed data files/buffers. +dependencies: libgcc >=13, libstdcxx >=13, perl >=5.32.1,<5.33.0a0 *_perl5, perl-compress-raw-bzip2 >=2.214, perl-compress-raw-zlib >=2.214, perl-encode, perl-scalar-list-utils +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/IO::Compress +doc_url: https://metacpan.org/pod/IO::Compress +dev_url: https://github.com/pmqs/IO-Compress + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/IO::Compress +IO::Compress - read/write compressed data in multiple formats - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution IO-Compress Module version: 2.219 09 Mar 2026 13:58:06 UTC License: perl_5 Code Download ( 327KB ) Source ( raw ) Browse ( raw ) Changes Project Homepage Repository Issues (12) How to Contribute Quality Testers Testers (Magpie) Kwalitee 81.88% Coverage Bus factor: 5 Activity 24 month Dependencies Compress::Raw::Bzip2 Compress::Raw::Zlib Encode Scalar::Util Time::Local and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 2.219 (PMQS on 2026-03-09) 2.218 (PMQS on 2026-03-08) 2.217 (PMQS on 2026-02-01) 2.216 (PMQS on 2026-01-30) 2.215 (PMQS on 2026-01-30) 2.214 (PMQS on 2025-10-24) 2.213 (PMQS on 2024-08-28) 2.212 (PMQS on 2024-04-27) 2.211 (PMQS on 2024-04-06) 2.208 (PMQS on 2024-03-31) 2.207 (PMQS on 2024-02-18) 2.206 (PMQS on 2023-07-25) 2.205 (PMQS on 2023-07-16) 2.204 (PMQS on 2023-02-08) 2.201 (PMQS on 2022-06-25) 2.106 (PMQS on 2022-04-12) 2.105 (PMQS on 2022-04-09) 2.103 (PMQS on 2022-04-03) 2.102 (PMQS on 2021-02-28) 2.101 (PMQS on 2021-02-20) 2.100 (PMQS on 2021-01-07) 2.096 (PMQS on 2020-07-31) 2.095 (PMQS on 2020-07-20) 2.094 (PMQS on 2020-07-14) 2.093 (PMQS on 2019-12-07) 2.092 (PMQS on 2019-12-04) 2.091 (PMQS on 2019-11-23) 2.090 (PMQS on 2019-11-09) 2.089 (PMQS on 2019-11-03) 2.088 (PMQS on 2019-11-03) 2.087 (PMQS on 2019-08-10) 2.086 (PMQS on 2019-03-31) 2.084 (PMQS on 2019-01-06) 2.083 (PMQS on 2018-12-30) 2.081 (PMQS on 2018-04-08) 2.080 (PMQS on 2018-04-03) 2.074 (PMQS on 2017-02-19) 2.072 (PMQS on 2017-02-12) 2.070 (PMQS on 2016-12-28) 2.069 (PMQS on 2015-09-26) 2.068 (PMQS on 2014-12-23) 2.067 (PMQS on 2014-12-08) 2.066 (PMQS on 2014-09-21) 2.064 (PMQS on 2014-02-01) 2.063 (PMQS on 2013-11-02) 2.062 (PMQS on 2013-08-12) 2.061 (PMQS on 2013-05-27) 2.060 (PMQS on 2013-01-07) 2.059 (PMQS on 2012-12-15) 2.058 (PMQS on 2012-11-12) 2.057 (PMQS on 2012-11-10) 2.055 (PMQS on 2012-08-05) 2.052 (PMQS on 2012-04-29) 2.049 (PMQS on 2012-02-18) 2.048 (PMQS on 2012-01-29) 2.047 (PMQS on 2012-01-28) 2.046 (PMQS on 2011-12-18) 2.045 (PMQS on 2011-12-04) 2.044 (PMQS on 2011-12-03) 2.043 (PMQS on 2011-11-20) 2.042 (PMQS on 2011-11-17) 2.040 (PMQS on 2011-10-28) 2.039 (PMQS on 2011-10-28) 2.037 (PMQS on 2011-06-22) 2.036 (PMQS on 2011-06-18) 2.035 (PMQS on 2011-05-07) 2.034 (PMQS on 2011-05-02) 2.033 (PMQS on 2011-01-11) 2.032 (PMQS on 2011-01-06) 2.030 (PMQS on 2010-07-24) 2.027 (PMQS on 2010-04-24) 2.026 (PMQS on 2010-04-07) 2.025 (PMQS on 2010-03-28) 2.024 (PMQS on 2010-01-09) 2.023 (PMQS on 2009-11-09) 2.022 (PMQS on 2009-10-09) 2.021 (PMQS on 2009-08-30) 2.020 (PMQS on 2009-06-03) 2.019 (PMQS on 2009-05-04) 2.017 (PMQS on 2009-04-04) 2.104 (PMQS on 2022-04-09) 2.073 (PMQS on 2017-02-19) 2.018 (PMQS on 2009-05-03) Diff with version 2.219 (PMQS on 2026-03-09) 2.218 (PMQS on 2026-03-08) 2.217 (PMQS on 2026-02-01) 2.216 (PMQS on 2026-01-30) 2.215 (PMQS on 2026-01-30) 2.214 (PMQS on 2025-10-24) 2.213 (PMQS on 2024-08-28) 2.212 (PMQS on 2024-04-27) 2.211 (PMQS on 2024-04-06) 2.208 (PMQS on 2024-03-31) 2.207 (PMQS on 2024-02-18) 2.206 (PMQS on 2023-07-25) 2.205 (PMQS on 2023-07-16) 2.204 (PMQS on 2023-02-08) 2.201 (PMQS on 2022-06-25) 2.106 (PMQS on 2022-04-12) 2.105 (PMQS on 2022-04-09) 2.103 (PMQS on 2022-04-03) 2.102 (PMQS on 2021-02-28) 2.101 (PMQS on 2021-02-20) 2.100 (PMQS on 2021-01-07) 2.096 (PMQS on 2020-07-31) 2.095 (PMQS on 2020-07-20) 2.094 (PMQS on 2020-07-14) 2.093 (PMQS on 2019-12-07) 2.092 (PMQS on 2019-12-04) 2.091 (PMQS on 2019-11-23) 2.090 (PMQS on 2019-11-09) 2.089 (PMQS on 2019-11-03) 2.088 (PMQS on 2019-11-03) 2.087 (PMQS on 2019-08-10) 2.086 (PMQS on 2019-03-31) 2.084 (PMQS on 2019-01-06) 2.083 (PMQS on 2018-12-30) 2.081 (PMQS on 2018-04-08) 2.080 (PMQS on 2018-04-03) 2.074 (PMQS on 2017-02-19) 2.072 (PMQS on 2017-02-12) 2.070 (PMQS on 2016-12-28) 2.069 (PMQS on 2015-09-26) 2.068 (PMQS on 2014-12-23) 2.067 (PMQS on 2014-12-08) 2.066 (PMQS on 2014-09-21) 2.064 (PMQS on 2014-02-01) 2.063 (PMQS on 2013-11-02) 2.062 (PMQS on 2013-08-12) 2.061 (PMQS on 2013-05-27) 2.060 (PMQS on 2013-01-07) 2.059 (PMQS on 2012-12-15) 2.058 (PMQS on 2012-11-12) 2.057 (PMQS on 2012-11-10) 2.055 (PMQS on 2012-08-05) 2.052 (PMQS on 2012-04-29) 2.049 (PMQS on 2012-02-18) 2.048 (PMQS on 2012-01-29) 2.047 (PMQS on 2012-01-28) 2.046 (PMQS on 2011-12-18) 2.045 (PMQS on 2011-12-04) 2.044 (PMQS on 2011-12-03) 2.043 (PMQS on 2011-11-20) 2.042 (PMQS on 2011-11-17) 2.040 (PMQS on 2011-10-28) 2.039 (PMQS on 2011-10-28) 2.037 (PMQS on 2011-06-22) 2.036 (PMQS on 2011-06-18) 2.035 (PMQS on 2011-05-07) 2.034 (PMQS on 2011-05-02) 2.033 (PMQS on 2011-01-11) 2.032 (PMQS on 2011-01-06) 2.030 (PMQS on 2010-07-24) 2.027 (PMQS on 2010-04-24) 2.026 (PMQS on 2010-04-07) 2.025 (PMQS on 2010-03-28) 2.024 (PMQS on 2010-01-09) 2.023 (PMQS on 2009-11-09) 2.022 (PMQS on 2009-10-09) 2.021 (PMQS on 2009-08-30) 2.020 (PMQS on 2009-06-03) 2.019 (PMQS on 2009-05-04) 2.017 (PMQS on 2009-04-04) 2.104 (PMQS on 2022-04-09) 2.073 (PMQS on 2017-02-19) 2.018 (PMQS on 2009-05-03) Permalinks This version Latest version ++ed by: 9 PAUSE users 11 non-PAUSE users Authors: Paul Marquess Released by: Paul Marquess Maintainers: PMQS owner Paul Marquess  /  2.219 (PMQS on 2026-03-09) 2.218 (PMQS on 2026-03-08) 2.217 (PMQS on 2026-02-01) 2.216 (PMQS on 2026-01-30) 2.215 (PMQS on 2026-01-30) 2.214 (PMQS on 2025-10-24) 2.213 (PMQS on 2024-08-28) 2.212 (PMQS on 2024-04-27) 2.211 (PMQS on 2024-04-06) 2.208 (PMQS on 2024-03-31) 2.207 (PMQS on 2024-02-18) 2.206 (PMQS on 2023-07-25) 2.205 (PMQS on 2023-07-16) 2.204 (PMQS on 2023-02-08) 2.201 (PMQS on 2022-06-25) 2.106 (PMQS on 2022-04-12) 2.105 (PMQS on 2022-04-09) 2.103 (PMQS on 2022-04-03) 2.102 (PMQS on 2021-02-28) 2.101 (PMQS on 2021-02-20) 2.100 (PMQS on 2021-01-07) 2.096 (PMQS on 2020-07-31) 2.095 (PMQS on 2020-07-20) 2.094 (PMQS on 2020-07-14) 2.093 (PMQS on 2019-12-07) 2.092 (PMQS on 2019-12-04) 2.091 (PMQS on 2019-11-23) 2.090 (PMQS on 2019-11-09) 2.089 (PMQS on 2019-11-03) 2.088 (PMQS on 2019-11-03) 2.087 (PMQS on 2019-08-10) 2.086 (PMQS on 2019-03-31) 2.084 (PMQS on 2019-01-06) 2.083 (PMQS on 2018-12-30) 2.081 (PMQS on 2018-04-08) 2.080 (PMQS on 2018-04-03) 2.074 (PMQS on 2017-02-19) 2.072 (PMQS on 2017-02-12) 2.070 (PMQS on 2016-12-28) 2.069 (PMQS on 2015-09-26) 2.068 (PMQS on 2014-12-23) 2.067 (PMQS on 2014-12-08) 2.066 (PMQS on 2014-09-21) 2.064 (PMQS on 2014-02-01) 2.063 (PMQS on 2013-11-02) 2.062 (PMQS on 2013-08-12) 2.061 (PMQS on 2013-05-27) 2.060 (PMQS on 2013-01-07) 2.059 (PMQS on 2012-12-15) 2.058 (PMQS on 2012-11-12) 2.057 (PMQS on 2012-11-10) 2.055 (PMQS on 2012-08-05) 2.052 (PMQS on 2012-04-29) 2.049 (PMQS on 2012-02-18) 2.048 (PMQS on 2012-01-29) 2.047 (PMQS on 2012-01-28) 2.046 (PMQS on 2011-12-18) 2.045 (PMQS on 2011-12-04) 2.044 (PMQS on 2011-12-03) 2.043 (PMQS on 2011-11-20) 2.042 (PMQS on 2011-11-17) 2.040 (PMQS on 2011-10-28) 2.039 (PMQS on 2011-10-28) 2.037 (PMQS on 2011-06-22) 2.036 (PMQS on 2011-06-18) 2.035 (PMQS on 2011-05-07) 2.034 (PMQS on 2011-05-02) 2.033 (PMQS on 2011-01-11) 2.032 (PMQS on 2011-01-06) 2.030 (PMQS on 2010-07-24) 2.027 (PMQS on 2010-04-24) 2.026 (PMQS on 2010-04-07) 2.025 (PMQS on 2010-03-28) 2.024 (PMQS on 2010-01-09) 2.023 (PMQS on 2009-11-09) 2.022 (PMQS on 2009-10-09) 2.021 (PMQS on 2009-08-30) 2.020 (PMQS on 2009-06-03) 2.019 (PMQS on 2009-05-04) 2.017 (PMQS on 2009-04-04) 2.104 (PMQS on 2022-04-09) 2.073 (PMQS on 2017-02-19) 2.018 (PMQS on 2009-05-03) IO-Compress-2.219 20 ++ 20 ++ ⭐ Starred 14 GitHub stars / IO::Compress Contents NAME DESCRIPTION AUTHOR COPYRIGHT NAME IO::Compress - read/write compressed data in multiple formats DESCRIPTION This is a stub module. It contains no code. AUTHOR Paul Marquess pmqs@cpan.org . COPYRIGHT Copyright (c) 2011-2026 Paul Marquess. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. Module Install Instructions To install IO::Compress, copy and paste the appropriate command in to your terminal. cpanm cpanm IO::Compress CPAN shell perl -MCPAN -e shell install IO::Compress For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +### https://metacpan.org/pod/IO::Compress +IO::Compress - read/write compressed data in multiple formats - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution IO-Compress Module version: 2.219 09 Mar 2026 13:58:06 UTC License: perl_5 Code Download ( 327KB ) Source ( raw ) Browse ( raw ) Changes Project Homepage Repository Issues (12) How to Contribute Quality Testers Testers (Magpie) Kwalitee 81.88% Coverage Bus factor: 5 Activity 24 month Dependencies Compress::Raw::Bzip2 Compress::Raw::Zlib Encode Scalar::Util Time::Local and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 2.219 (PMQS on 2026-03-09) 2.218 (PMQS on 2026-03-08) 2.217 (PMQS on 2026-02-01) 2.216 (PMQS on 2026-01-30) 2.215 (PMQS on 2026-01-30) 2.214 (PMQS on 2025-10-24) 2.213 (PMQS on 2024-08-28) 2.212 (PMQS on 2024-04-27) 2.211 (PMQS on 2024-04-06) 2.208 (PMQS on 2024-03-31) 2.207 (PMQS on 2024-02-18) 2.206 (PMQS on 2023-07-25) 2.205 (PMQS on 2023-07-16) 2.204 (PMQS on 2023-02-08) 2.201 (PMQS on 2022-06-25) 2.106 (PMQS on 2022-04-12) 2.105 (PMQS on 2022-04-09) 2.103 (PMQS on 2022-04-03) 2.102 (PMQS on 2021-02-28) 2.101 (PMQS on 2021-02-20) 2.100 (PMQS on 2021-01-07) 2.096 (PMQS on 2020-07-31) 2.095 (PMQS on 2020-07-20) 2.094 (PMQS on 2020-07-14) 2.093 (PMQS on 2019-12-07) 2.092 (PMQS on 2019-12-04) 2.091 (PMQS on 2019-11-23) 2.090 (PMQS on 2019-11-09) 2.089 (PMQS on 2019-11-03) 2.088 (PMQS on 2019-11-03) 2.087 (PMQS on 2019-08-10) 2.086 (PMQS on 2019-03-31) 2.084 (PMQS on 2019-01-06) 2.083 (PMQS on 2018-12-30) 2.081 (PMQS on 2018-04-08) 2.080 (PMQS on 2018-04-03) 2.074 (PMQS on 2017-02-19) 2.072 (PMQS on 2017-02-12) 2.070 (PMQS on 2016-12-28) 2.069 (PMQS on 2015-09-26) 2.068 (PMQS on 2014-12-23) 2.067 (PMQS on 2014-12-08) 2.066 (PMQS on 2014-09-21) 2.064 (PMQS on 2014-02-01) 2.063 (PMQS on 2013-11-02) 2.062 (PMQS on 2013-08-12) 2.061 (PMQS on 2013-05-27) 2.060 (PMQS on 2013-01-07) 2.059 (PMQS on 2012-12-15) 2.058 (PMQS on 2012-11-12) 2.057 (PMQS on 2012-11-10) 2.055 (PMQS on 2012-08-05) 2.052 (PMQS on 2012-04-29) 2.049 (PMQS on 2012-02-18) 2.048 (PMQS on 2012-01-29) 2.047 (PMQS on 2012-01-28) 2.046 (PMQS on 2011-12-18) 2.045 (PMQS on 2011-12-04) 2.044 (PMQS on 2011-12-03) 2.043 (PMQS on 2011-11-20) 2.042 (PMQS on 2011-11-17) 2.040 (PMQS on 2011-10-28) 2.039 (PMQS on 2011-10-28) 2.037 (PMQS on 2011-06-22) 2.036 (PMQS on 2011-06-18) 2.035 (PMQS on 2011-05-07) 2.034 (PMQS on 2011-05-02) 2.033 (PMQS on 2011-01-11) 2.032 (PMQS on 2011-01-06) 2.030 (PMQS on 2010-07-24) 2.027 (PMQS on 2010-04-24) 2.026 (PMQS on 2010-04-07) 2.025 (PMQS on 2010-03-28) 2.024 (PMQS on 2010-01-09) 2.023 (PMQS on 2009-11-09) 2.022 (PMQS on 2009-10-09) 2.021 (PMQS on 2009-08-30) 2.020 (PMQS on 2009-06-03) 2.019 (PMQS on 2009-05-04) 2.017 (PMQS on 2009-04-04) 2.104 (PMQS on 2022-04-09) 2.073 (PMQS on 2017-02-19) 2.018 (PMQS on 2009-05-03) Diff with version 2.219 (PMQS on 2026-03-09) 2.218 (PMQS on 2026-03-08) 2.217 (PMQS on 2026-02-01) 2.216 (PMQS on 2026-01-30) 2.215 (PMQS on 2026-01-30) 2.214 (PMQS on 2025-10-24) 2.213 (PMQS on 2024-08-28) 2.212 (PMQS on 2024-04-27) 2.211 (PMQS on 2024-04-06) 2.208 (PMQS on 2024-03-31) 2.207 (PMQS on 2024-02-18) 2.206 (PMQS on 2023-07-25) 2.205 (PMQS on 2023-07-16) 2.204 (PMQS on 2023-02-08) 2.201 (PMQS on 2022-06-25) 2.106 (PMQS on 2022-04-12) 2.105 (PMQS on 2022-04-09) 2.103 (PMQS on 2022-04-03) 2.102 (PMQS on 2021-02-28) 2.101 (PMQS on 2021-02-20) 2.100 (PMQS on 2021-01-07) 2.096 (PMQS on 2020-07-31) 2.095 (PMQS on 2020-07-20) 2.094 (PMQS on 2020-07-14) 2.093 (PMQS on 2019-12-07) 2.092 (PMQS on 2019-12-04) 2.091 (PMQS on 2019-11-23) 2.090 (PMQS on 2019-11-09) 2.089 (PMQS on 2019-11-03) 2.088 (PMQS on 2019-11-03) 2.087 (PMQS on 2019-08-10) 2.086 (PMQS on 2019-03-31) 2.084 (PMQS on 2019-01-06) 2.083 (PMQS on 2018-12-30) 2.081 (PMQS on 2018-04-08) 2.080 (PMQS on 2018-04-03) 2.074 (PMQS on 2017-02-19) 2.072 (PMQS on 2017-02-12) 2.070 (PMQS on 2016-12-28) 2.069 (PMQS on 2015-09-26) 2.068 (PMQS on 2014-12-23) 2.067 (PMQS on 2014-12-08) 2.066 (PMQS on 2014-09-21) 2.064 (PMQS on 2014-02-01) 2.063 (PMQS on 2013-11-02) 2.062 (PMQS on 2013-08-12) 2.061 (PMQS on 2013-05-27) 2.060 (PMQS on 2013-01-07) 2.059 (PMQS on 2012-12-15) 2.058 (PMQS on 2012-11-12) 2.057 (PMQS on 2012-11-10) 2.055 (PMQS on 2012-08-05) 2.052 (PMQS on 2012-04-29) 2.049 (PMQS on 2012-02-18) 2.048 (PMQS on 2012-01-29) 2.047 (PMQS on 2012-01-28) 2.046 (PMQS on 2011-12-18) 2.045 (PMQS on 2011-12-04) 2.044 (PMQS on 2011-12-03) 2.043 (PMQS on 2011-11-20) 2.042 (PMQS on 2011-11-17) 2.040 (PMQS on 2011-10-28) 2.039 (PMQS on 2011-10-28) 2.037 (PMQS on 2011-06-22) 2.036 (PMQS on 2011-06-18) 2.035 (PMQS on 2011-05-07) 2.034 (PMQS on 2011-05-02) 2.033 (PMQS on 2011-01-11) 2.032 (PMQS on 2011-01-06) 2.030 (PMQS on 2010-07-24) 2.027 (PMQS on 2010-04-24) 2.026 (PMQS on 2010-04-07) 2.025 (PMQS on 2010-03-28) 2.024 (PMQS on 2010-01-09) 2.023 (PMQS on 2009-11-09) 2.022 (PMQS on 2009-10-09) 2.021 (PMQS on 2009-08-30) 2.020 (PMQS on 2009-06-03) 2.019 (PMQS on 2009-05-04) 2.017 (PMQS on 2009-04-04) 2.104 (PMQS on 2022-04-09) 2.073 (PMQS on 2017-02-19) 2.018 (PMQS on 2009-05-03) Permalinks This version Latest version ++ed by: 9 PAUSE users 11 non-PAUSE users Authors: Paul Marquess Released by: Paul Marquess Maintainers: PMQS owner Paul Marquess  /  2.219 (PMQS on 2026-03-09) 2.218 (PMQS on 2026-03-08) 2.217 (PMQS on 2026-02-01) 2.216 (PMQS on 2026-01-30) 2.215 (PMQS on 2026-01-30) 2.214 (PMQS on 2025-10-24) 2.213 (PMQS on 2024-08-28) 2.212 (PMQS on 2024-04-27) 2.211 (PMQS on 2024-04-06) 2.208 (PMQS on 2024-03-31) 2.207 (PMQS on 2024-02-18) 2.206 (PMQS on 2023-07-25) 2.205 (PMQS on 2023-07-16) 2.204 (PMQS on 2023-02-08) 2.201 (PMQS on 2022-06-25) 2.106 (PMQS on 2022-04-12) 2.105 (PMQS on 2022-04-09) 2.103 (PMQS on 2022-04-03) 2.102 (PMQS on 2021-02-28) 2.101 (PMQS on 2021-02-20) 2.100 (PMQS on 2021-01-07) 2.096 (PMQS on 2020-07-31) 2.095 (PMQS on 2020-07-20) 2.094 (PMQS on 2020-07-14) 2.093 (PMQS on 2019-12-07) 2.092 (PMQS on 2019-12-04) 2.091 (PMQS on 2019-11-23) 2.090 (PMQS on 2019-11-09) 2.089 (PMQS on 2019-11-03) 2.088 (PMQS on 2019-11-03) 2.087 (PMQS on 2019-08-10) 2.086 (PMQS on 2019-03-31) 2.084 (PMQS on 2019-01-06) 2.083 (PMQS on 2018-12-30) 2.081 (PMQS on 2018-04-08) 2.080 (PMQS on 2018-04-03) 2.074 (PMQS on 2017-02-19) 2.072 (PMQS on 2017-02-12) 2.070 (PMQS on 2016-12-28) 2.069 (PMQS on 2015-09-26) 2.068 (PMQS on 2014-12-23) 2.067 (PMQS on 2014-12-08) 2.066 (PMQS on 2014-09-21) 2.064 (PMQS on 2014-02-01) 2.063 (PMQS on 2013-11-02) 2.062 (PMQS on 2013-08-12) 2.061 (PMQS on 2013-05-27) 2.060 (PMQS on 2013-01-07) 2.059 (PMQS on 2012-12-15) 2.058 (PMQS on 2012-11-12) 2.057 (PMQS on 2012-11-10) 2.055 (PMQS on 2012-08-05) 2.052 (PMQS on 2012-04-29) 2.049 (PMQS on 2012-02-18) 2.048 (PMQS on 2012-01-29) 2.047 (PMQS on 2012-01-28) 2.046 (PMQS on 2011-12-18) 2.045 (PMQS on 2011-12-04) 2.044 (PMQS on 2011-12-03) 2.043 (PMQS on 2011-11-20) 2.042 (PMQS on 2011-11-17) 2.040 (PMQS on 2011-10-28) 2.039 (PMQS on 2011-10-28) 2.037 (PMQS on 2011-06-22) 2.036 (PMQS on 2011-06-18) 2.035 (PMQS on 2011-05-07) 2.034 (PMQS on 2011-05-02) 2.033 (PMQS on 2011-01-11) 2.032 (PMQS on 2011-01-06) 2.030 (PMQS on 2010-07-24) 2.027 (PMQS on 2010-04-24) 2.026 (PMQS on 2010-04-07) 2.025 (PMQS on 2010-03-28) 2.024 (PMQS on 2010-01-09) 2.023 (PMQS on 2009-11-09) 2.022 (PMQS on 2009-10-09) 2.021 (PMQS on 2009-08-30) 2.020 (PMQS on 2009-06-03) 2.019 (PMQS on 2009-05-04) 2.017 (PMQS on 2009-04-04) 2.104 (PMQS on 2022-04-09) 2.073 (PMQS on 2017-02-19) 2.018 (PMQS on 2009-05-03) IO-Compress-2.219 20 ++ 20 ++ ⭐ Starred 14 GitHub stars / IO::Compress Contents NAME DESCRIPTION AUTHOR COPYRIGHT NAME IO::Compress - read/write compressed data in multiple formats DESCRIPTION This is a stub module. It contains no code. AUTHOR Paul Marquess pmqs@cpan.org . COPYRIGHT Copyright (c) 2011-2026 Paul Marquess. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. Module Install Instructions To install IO::Compress, copy and paste the appropriate command in to your terminal. cpanm cpanm IO::Compress CPAN shell perl -MCPAN -e shell install IO::Compress For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +### https://github.com/pmqs/IO-Compress +GitHub - pmqs/IO-Compress: IO-Compress - Perl5 module to read/write compressed data in multiple formats · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} pmqs / IO-Compress Public Notifications You must be signed in to change notification settings Fork 15 Star 15 Code Issues 10 Pull requests 1 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights pmqs/IO-Compress master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 508 Commits 508 Commits .github .github bin bin bugs/ 12826 bugs/ 12826 examples examples lib lib private private t t .appveyor.yml .appveyor.yml .cirrus.yml .cirrus.yml .gitignore .gitignore .travis.yml .travis.yml Changes Changes MANIFEST MANIFEST META.json META.json META.yml META.yml Makefile.PL Makefile.PL README README SECURITY.md SECURITY.md View all files Repository files navigation README Security IO-Compress Version 2.219 9 March 2026 Copyright (c) 1995-2026 Paul Marquess. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. DESCRIPTION ----------- This distribution provides a Perl interface to allow reading and writing of compressed data created with the zlib and bzip2. IO-Compress supports reading and writing of the following compressed data formats * bzip2 * RFC 1950 * RFC 1951 * RFC 1952 (i.e. gzip) * zip There are a number of companion modules for IO-Compress that extend the suite of compression formats available. * IO-Compress-Zstd Adds support for zstd (Zstandard). * IO-Compress-Lzma Adds support for lzma, xz and lzip. * IO-Compress-Lzf Adds support for lzf. * IO-Compress-Lzop Adds support for lzop. Note that the following modules used to be distributed separately, but are now included with the IO-Compress distribution. Compress-Zlib IO-Compress-Zlib IO-Compress-Bzip2 IO-Compress-Base PREREQUISITES ------------- Before you can build IO-Compress you need to have the following installed on your system: * Perl 5.006 or better. * Compress::Raw::Zlib * Compress::Raw::Bzip2 BUILDING THE MODULE ------------------- Assuming you have met all the prerequisites, the module can now be built using this sequence of commands: perl Makefile.PL make make test INSTALLATION ------------ To install IO-Compress, run the command below: make install TROUBLESHOOTING --------------- SUPPORT ------- General feedback/questions/bug reports should be sent to https://github.com/pmqs/IO-Compress/issues FEEDBACK -------- How to report a problem with IO-Compress. To help me help you, I need all of the following information: 1. The Versions of everything relevant. This includes: a. The *complete* output from running this perl -V Do not edit the output in any way. Note, I want you to run "perl -V" and NOT "perl -v". If your perl does not understand the "-V" option it is too old. This module needs Perl version 5.004 or better. b. The version of IO-Compress you have. If you have successfully installed IO-Compress, this one-liner will tell you: perl -MIO::Compress::Gzip -e 'print qq[ver $IO::Compress::Gzip::VERSION\n]' If you are running windows use this perl -MIO::Compress::Gzip -e "print qq[ver $IO::Compress::Gzip::VERSION\n]" If you haven't installed IO-Compress then search IO::Compress::Gzip.pm for a line like this: $VERSION = "2.219" ; 2. If you are having problems building IO-Compress, send me a complete log of what happened. Start by unpacking the IO-Compress module into a fresh directory and keep a log of all the steps, including the setting of configuration environment variables (if applicable). [edit config.in or set environment variables, if necessary] perl Makefile.PL make make test TEST_VERBOSE=1 Paul Marquess <pmqs@cpan.org> About IO-Compress - Perl5 module to read/write compressed data in multiple formats Topics streaming compression gzip zip unzip perl bzip2 perl5 inflate zip64 gunzip deflate perl5-module uncompress Resources Readme Security policy Security policy Uh oh! There was an error while loading. Please reload this page . Activity Stars 15 stars Watchers 1 watching Forks 15 forks Report repository Releases 31 IO-Compress 2.219 Latest Mar 9, 2026 + 30 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-io-compress --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-io-compress 2.069 1 +------------------------ +file name : perl-io-compress-2.069-1.tar.bz2 +name : perl-io-compress +version : 2.069 +build : 1 +build number: 1 +size : 75 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.069-1.tar.bz2 +md5 : 3856f2c5a85bf4d0e4b9f378d0fcf3f1 +dependencies: + - perl-compress-raw-bzip2 >=2.069 + - perl-compress-raw-zlib + - perl-scalar-list-utils + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-io-compress 2.069 pl5.22.0_2 +--------------------------------- +file name : perl-io-compress-2.069-pl5.22.0_2.tar.bz2 +name : perl-io-compress +version : 2.069 +build : pl5.22.0_2 +build number: 2 +size : 78 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.069-pl5.22.0_2.tar.bz2 +md5 : 5f8c454ab486d480cd2cdb18b869a3b9 +dependencies: + - perl 5.22.0* + - perl-compress-raw-bzip2 >=2.069 + - perl-compress-raw-zlib + - perl-scalar-list-utils + + +perl-io-compress 2.069 pl526_4 +------------------------------ +file name : perl-io-compress-2.069-pl526_4.tar.bz2 +name : perl-io-compress +version : 2.069 +build : pl526_4 +build number: 4 +size : 79 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.069-pl526_4.tar.bz2 +md5 : fb78b4888e8993674a2bd593833745a8 +timestamp : 2018-07-17 16:16:25 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-compress-raw-bzip2 >=2.069 + - perl-compress-raw-zlib + - perl-scalar-list-utils + + +perl-io-compress 2.069 pl526hfc679d8_5 +-------------------------------------- +file name : perl-io-compress-2.069-pl526hfc679d8_5.tar.bz2 +name : perl-io-compress +version : 2.069 +build : pl526hfc679d8_5 +build number: 5 +size : 79 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.069-pl526hfc679d8_5.tar.bz2 +md5 : 082475a42e38ee57b074ccdc92714ed7 +timestamp : 2018-07-20 16:44:37 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-compress-raw-bzip2 >=2.074 + - perl-compress-raw-zlib + - perl-scalar-list-utils + + +perl-io-compress 2.081 pl526hfc679d8_0 +-------------------------------------- +file name : perl-io-compress-2.081-pl526hfc679d8_0.tar.bz2 +name : perl-io-compress +version : 2.081 +build : pl526hfc679d8_0 +build number: 0 +size : 79 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.081-pl526hfc679d8_0.tar.bz2 +md5 : da43d2a7a3aa8c252c56a7087b8560a6 +timestamp : 2018-11-19 02:44:06 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-compress-raw-bzip2 >=2.074 + - perl-compress-raw-zlib + - perl-scalar-list-utils + + +perl-io-compress 2.083 pl526hfc679d8_0 +-------------------------------------- +file name : perl-io-compress-2.083-pl526hfc679d8_0.tar.bz2 +name : perl-io-compress +version : 2.083 +build : pl526hfc679d8_0 +build number: 0 +size : 80 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.083-pl526hfc679d8_0.tar.bz2 +md5 : 41df934c30496d258c9880da13b6529b +timestamp : 2019-01-03 11:40:00 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-compress-raw-bzip2 >=2.083 + - perl-compress-raw-zlib + - perl-scalar-list-utils + + +perl-io-compress 2.084 pl526hfc679d8_0 +-------------------------------------- +file name : perl-io-compress-2.084-pl526hfc679d8_0.tar.bz2 +name : perl-io-compress +version : 2.084 +build : pl526hfc679d8_0 +build number: 0 +size : 80 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.084-pl526hfc679d8_0.tar.bz2 +md5 : ffe6e51d5ad633c918c8fa91c897e6fe +timestamp : 2019-01-08 16:38:12 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-compress-raw-bzip2 >=2.084 + - perl-compress-raw-zlib >=2.084 + - perl-scalar-list-utils + + +perl-io-compress 2.086 pl526hf484d3e_0 +-------------------------------------- +file name : perl-io-compress-2.086-pl526hf484d3e_0.tar.bz2 +name : perl-io-compress +version : 2.086 +build : pl526hf484d3e_0 +build number: 0 +size : 80 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.086-pl526hf484d3e_0.tar.bz2 +md5 : b0e98686c6726521d6a5173c42d40837 +timestamp : 2019-04-27 15:00:40 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-compress-raw-bzip2 >=2.084 + - perl-compress-raw-zlib >=2.084 + - perl-scalar-list-utils + + +perl-io-compress 2.087 pl526he1b5a44_0 +-------------------------------------- +file name : perl-io-compress-2.087-pl526he1b5a44_0.tar.bz2 +name : perl-io-compress +version : 2.087 +build : pl526he1b5a44_0 +build number: 0 +size : 81 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.087-pl526he1b5a44_0.tar.bz2 +md5 : 67679464cddb80ccc4692c6d76a439d5 +timestamp : 2019-08-10 20:32:03 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-compress-raw-bzip2 >=2.087 + - perl-compress-raw-zlib >=2.087 + - perl-scalar-list-utils + + +perl-io-compress 2.087 pl5321h1b792b2_1 +--------------------------------------- +file name : perl-io-compress-2.087-pl5321h1b792b2_1.tar.bz2 +name : perl-io-compress +version : 2.087 +build : pl5321h1b792b2_1 +build number: 1 +size : 82 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.087-pl5321h1b792b2_1.tar.bz2 +md5 : 57cea2175bf14db0b6fef56760ed9692 +timestamp : 2022-01-19 02:03:19 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-compress-raw-bzip2 >=2.087 + - perl-compress-raw-zlib >=2.087 + - perl-scalar-list-utils + + +perl-io-compress 2.102 pl5321h1b792b2_0 +--------------------------------------- +file name : perl-io-compress-2.102-pl5321h1b792b2_0.tar.bz2 +name : perl-io-compress +version : 2.102 +build : pl5321h1b792b2_0 +build number: 0 +size : 83 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.102-pl5321h1b792b2_0.tar.bz2 +md5 : a4d02dcdcb47c043da2c87a6fef3530d +timestamp : 2022-02-14 19:03:15 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-compress-raw-bzip2 >=2.101 + - perl-compress-raw-zlib >=2.101 + - perl-encode + - perl-scalar-list-utils + + +perl-io-compress 2.102 pl5321h87f3376_1 +--------------------------------------- +file name : perl-io-compress-2.102-pl5321h87f3376_1.tar.bz2 +name : perl-io-compress +version : 2.102 +build : pl5321h87f3376_1 +build number: 1 +size : 83 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.102-pl5321h87f3376_1.tar.bz2 +md5 : 1f40355a2b5ea6089385ed99db5f59e8 +timestamp : 2022-02-22 23:36:02 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-compress-raw-bzip2 >=2.101 + - perl-compress-raw-zlib >=2.101 + - perl-encode + - perl-scalar-list-utils + + +perl-io-compress 2.106 pl5321h87f3376_0 +--------------------------------------- +file name : perl-io-compress-2.106-pl5321h87f3376_0.tar.bz2 +name : perl-io-compress +version : 2.106 +build : pl5321h87f3376_0 +build number: 0 +size : 83 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.106-pl5321h87f3376_0.tar.bz2 +md5 : b2a85e3264debff9cd993acfb412e2c2 +timestamp : 2022-04-18 16:08:51 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-compress-raw-bzip2 >=2.103 + - perl-compress-raw-zlib >=2.103 + - perl-encode + - perl-scalar-list-utils + + +perl-io-compress 2.106 pl5321h87f3376_1 +--------------------------------------- +file name : perl-io-compress-2.106-pl5321h87f3376_1.tar.bz2 +name : perl-io-compress +version : 2.106 +build : pl5321h87f3376_1 +build number: 1 +size : 84 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.106-pl5321h87f3376_1.tar.bz2 +md5 : 4c62c232fda31558e0eba91cc221d00d +timestamp : 2022-08-01 19:52:11 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-compress-raw-bzip2 >=2.103 + - perl-compress-raw-zlib >=2.103 + - perl-encode + - perl-scalar-list-utils + + +perl-io-compress 2.201 pl5321h503566f_4 +--------------------------------------- +file name : perl-io-compress-2.201-pl5321h503566f_4.tar.bz2 +name : perl-io-compress +version : 2.201 +build : pl5321h503566f_4 +build number: 4 +size : 85 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.201-pl5321h503566f_4.tar.bz2 +md5 : 277af80e8084a228351b9833dd8f2896 +timestamp : 2024-12-10 19:06:29 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-compress-raw-bzip2 >=2.103 + - perl-compress-raw-zlib >=2.103 + - perl-encode + - perl-scalar-list-utils + + +perl-io-compress 2.201 pl5321h503566f_5 +--------------------------------------- +file name : perl-io-compress-2.201-pl5321h503566f_5.tar.bz2 +name : perl-io-compress +version : 2.201 +build : pl5321h503566f_5 +build number: 5 +size : 85 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.201-pl5321h503566f_5.tar.bz2 +md5 : 3f56091e7e231ab35f4675460b2d969c +timestamp : 2025-03-13 22:10:35 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-compress-raw-bzip2 >=2.103 + - perl-compress-raw-zlib >=2.103 + - perl-encode + - perl-scalar-list-utils + + +perl-io-compress 2.201 pl5321h87f3376_0 +--------------------------------------- +file name : perl-io-compress-2.201-pl5321h87f3376_0.tar.bz2 +name : perl-io-compress +version : 2.201 +build : pl5321h87f3376_0 +build number: 0 +size : 84 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.201-pl5321h87f3376_0.tar.bz2 +md5 : 63e82cefd14aa01721dcb6c6451c7f56 +timestamp : 2022-09-09 01:32:55 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-compress-raw-bzip2 >=2.103 + - perl-compress-raw-zlib >=2.103 + - perl-encode + - perl-scalar-list-utils + + +perl-io-compress 2.201 pl5321h87f3376_1 +--------------------------------------- +file name : perl-io-compress-2.201-pl5321h87f3376_1.tar.bz2 +name : perl-io-compress +version : 2.201 +build : pl5321h87f3376_1 +build number: 1 +size : 85 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.201-pl5321h87f3376_1.tar.bz2 +md5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-io-zlib.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-io-zlib.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f1faf6307fae1b30819bd25616da14757b43ec5 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-io-zlib.manual_bundle.txt @@ -0,0 +1,202 @@ +# Tool: perl-io-zlib +software_name: perl-io-zlib +tier: T1 +domain: t1_backfill_overall +downloads: 1420391 +summary: IO:: style interface to Compress::Zlib +description: IO:: style interface to Compress::Zlib +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/IO::Zlib +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/IO::Zlib +IO::Zlib - IO:: style interface to Compress::Zlib - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution IO-Zlib Module version: 1.15 29 Feb 2024 20:44:10 UTC License: perl_5 Code Download ( 11.83KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues How to Contribute Quality Testers ( 1523 / 0 / 0 ) Testers (Magpie) Kwalitee 83.18% Coverage Bus factor: 5 Activity 24 month Dependencies Compress::Zlib and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 1.15 (TOMHUGHES on 2024-02-29) 1.14 (TOMHUGHES on 2023-01-10) 1.11 (TOMHUGHES on 2020-09-13) 1.10_01 DEV (RURBAN on 2019-04-16) 1.13 (TOMHUGHES on 2023-01-06) 1.12 (TOMHUGHES on 2022-12-29) 1.10 (TOMHUGHES on 2009-07-14) 1.09 (TOMHUGHES on 2008-01-03) 1.08 (TOMHUGHES on 2007-11-18) 1.07 (TOMHUGHES on 2007-07-27) 1.06 (TOMHUGHES on 2007-07-18) 1.05 (TOMHUGHES on 2007-03-04) 1.04 (TOMHUGHES on 2004-09-05) 1.03 (TOMHUGHES on 2004-08-22) 1.02 (TOMHUGHES on 2004-08-15) 1.01 (TOMHUGHES on 2001-03-24) 1.00 (TOMHUGHES on 2001-01-27) 0.02 (TOMHUGHES on 1998-06-28) 0.01 (TOMHUGHES on 1998-06-25) Diff with version 1.15 (TOMHUGHES on 2024-02-29) 1.14 (TOMHUGHES on 2023-01-10) 1.11 (TOMHUGHES on 2020-09-13) 1.10_01 DEV (RURBAN on 2019-04-16) 1.13 (TOMHUGHES on 2023-01-06) 1.12 (TOMHUGHES on 2022-12-29) 1.10 (TOMHUGHES on 2009-07-14) 1.09 (TOMHUGHES on 2008-01-03) 1.08 (TOMHUGHES on 2007-11-18) 1.07 (TOMHUGHES on 2007-07-27) 1.06 (TOMHUGHES on 2007-07-18) 1.05 (TOMHUGHES on 2007-03-04) 1.04 (TOMHUGHES on 2004-09-05) 1.03 (TOMHUGHES on 2004-08-22) 1.02 (TOMHUGHES on 2004-08-15) 1.01 (TOMHUGHES on 2001-03-24) 1.00 (TOMHUGHES on 2001-01-27) 0.02 (TOMHUGHES on 1998-06-28) 0.01 (TOMHUGHES on 1998-06-25) Permalinks This version Latest version ++ed by: 2 PAUSE users 2 non-PAUSE users Authors: unknown Released by: Tom Hughes Maintainers: TOMHUGHES owner Tom Hughes  /  1.15 (TOMHUGHES on 2024-02-29) 1.14 (TOMHUGHES on 2023-01-10) 1.11 (TOMHUGHES on 2020-09-13) 1.10_01 DEV (RURBAN on 2019-04-16) 1.13 (TOMHUGHES on 2023-01-06) 1.12 (TOMHUGHES on 2022-12-29) 1.10 (TOMHUGHES on 2009-07-14) 1.09 (TOMHUGHES on 2008-01-03) 1.08 (TOMHUGHES on 2007-11-18) 1.07 (TOMHUGHES on 2007-07-27) 1.06 (TOMHUGHES on 2007-07-18) 1.05 (TOMHUGHES on 2007-03-04) 1.04 (TOMHUGHES on 2004-09-05) 1.03 (TOMHUGHES on 2004-08-22) 1.02 (TOMHUGHES on 2004-08-15) 1.01 (TOMHUGHES on 2001-03-24) 1.00 (TOMHUGHES on 2001-01-27) 0.02 (TOMHUGHES on 1998-06-28) 0.01 (TOMHUGHES on 1998-06-25) IO-Zlib-1.15 4 ++ 4 ++ ⭐ Starred 0 GitHub stars / IO::Zlib Contents NAME SYNOPSIS DESCRIPTION CONSTRUCTOR OBJECT METHODS USING THE EXTERNAL GZIP CLASS METHODS DIAGNOSTICS SEE ALSO HISTORY COPYRIGHT NAME IO::Zlib - IO:: style interface to Compress::Zlib SYNOPSIS With any version of Perl 5 you can use the basic OO interface: use IO::Zlib; $fh = new IO::Zlib; if ($fh->open("file.gz", "rb")) { print <$fh>; $fh->close; } $fh = IO::Zlib->new("file.gz", "wb9"); if (defined $fh) { print $fh "bar\n"; $fh->close; } $fh = IO::Zlib->new("file.gz", "rb"); if (defined $fh) { print <$fh>; undef $fh; # automatically closes the file } With Perl 5.004 you can also use the TIEHANDLE interface to access compressed files just like ordinary files: use IO::Zlib; tie *FILE, 'IO::Zlib', "file.gz", "wb"; print FILE "line 1\nline2\n"; tie *FILE, 'IO::Zlib', "file.gz", "rb"; while (<FILE>) { print "LINE: ", $_ }; DESCRIPTION IO::Zlib provides an IO:: style interface to Compress::Zlib and hence to gzip/zlib compressed files. It provides many of the same methods as the IO::Handle interface. Starting from IO::Zlib version 1.02, IO::Zlib can also use an external gzip command. The default behaviour is to try to use an external gzip if no Compress::Zlib can be loaded, unless explicitly disabled by use IO::Zlib qw(:gzip_external 0); If explicitly enabled by use IO::Zlib qw(:gzip_external 1); then the external gzip is used instead of Compress::Zlib . CONSTRUCTOR new ( [ARGS] ) Creates an IO::Zlib object. If it receives any parameters, they are passed to the method open ; if the open fails, the object is destroyed. Otherwise, it is returned to the caller. OBJECT METHODS open ( FILENAME, MODE ) open takes two arguments. The first is the name of the file to open and the second is the open mode. The mode can be anything acceptable to Compress::Zlib and by extension anything acceptable to zlib (that basically means POSIX fopen() style mode strings plus an optional number to indicate the compression level). opened Returns true if the object currently refers to a opened file. close Close the file associated with the object and disassociate the file from the handle. Done automatically on destroy. getc Return the next character from the file, or undef if none remain. getline Return the next line from the file, or undef on end of string. Can safely be called in an array context. Currently ignores $/ ($INPUT_RECORD_SEPARATOR or $RS when English is in use) and treats lines as delimited by "\n". getlines Get all remaining lines from the file. It will croak() if accidentally called in a scalar context. print ( ARGS... ) Print ARGS to the file. read ( BUF, NBYTES, [OFFSET] ) Read some bytes from the file. Returns the number of bytes actually read, 0 on end-of-file, undef on error. eof Returns true if the handle is currently positioned at end of file? seek ( OFFSET, WHENCE ) Seek to a given position in the stream. Not yet supported. tell Return the current position in the stream, as a numeric offset. Not yet supported. setpos ( POS ) Set the current position, using the opaque value returned by getpos() . Not yet supported. getpos ( POS ) Return the current position in the string, as an opaque object. Not yet supported. USING THE EXTERNAL GZIP If the external gzip is used, the following open s are used: open(FH, "gzip -dc $filename |") # for read opens open(FH, " | gzip > $filename") # for write opens You can modify the 'commands' for example to hardwire an absolute path by e.g. use IO::Zlib ':gzip_read_open' => '/some/where/gunzip -c %s |'; use IO::Zlib ':gzip_write_open' => '| /some/where/gzip.exe > %s'; The %s is expanded to be the filename ( sprintf is used, so be careful to escape any other % signs). The 'commands' are checked for sanity - they must contain the %s , and the read open must end with the pipe sign, and the write open must begin with the pipe sign. CLASS METHODS has_Compress_Zlib Returns true if Compress::Zlib is available. Note that this does not mean that Compress::Zlib is being used: see "gzip_external" and gzip_used . gzip_external Undef if an external gzip can be used if Compress::Zlib is not available (see "has_Compress_Zlib" ), true if an external gzip is explicitly used, false if an external gzip must not be used. See "gzip_used" . gzip_used True if an external gzip is being used, false if not. gzip_read_open Return the 'command' being used for opening a file for reading using an external gzip . gzip_write_open Return the 'command' being used for opening a file for writing using an external gzip . DIAGNOSTICS IO::Zlib::getlines: must be called in list context If you want read lines, you must read in list context. IO::Zlib::gzopen_external: mode '...' is illegal Use only modes 'rb' or 'wb' or /wb[1-9]/. IO::Zlib::import: '...' is illegal The known import symbols are the :gzip_external , :gzip_read_open , and :gzip_write_open . Anything else is not recognized. IO::Zlib::import: ':gzip_external' requires an argument The :gzip_external requires one boolean argument. IO::Zlib::import: 'gzip_read_open' requires an argument The :gzip_external requires one string argument. IO::Zlib::import: 'gzip_read' '...' is illegal The :gzip_read_open argument must end with the pipe sign (|) and have the %s for the filename. See "USING THE EXTERNAL GZIP" . IO::Zlib::import: 'gzip_write_open' requires an argument The :gzip_external requires one string argument. IO::Zlib::import: 'gzip_write_open' '...' is illegal The :gzip_write_open argument must begin with the pipe sign (|) and have the %s for the filename. An output redirect (>) is also often a good idea, depending on your operating system shell syntax. See "USING THE EXTERNAL GZIP" . IO::Zlib::import: no Compress::Zlib and no external gzip Given that we failed to load Compress::Zlib and that the use of an external gzip was disabled, IO::Zlib has not much chance of working. IO::Zlib::open: needs a filename No filename, no open. IO::Zlib::READ: NBYTES must be specified We must know how much to read. IO::Zlib::WRITE: too long LENGTH The LENGTH must be less than or equal to the buffer size. SEE ALSO perlfunc , "I/O Operators" in perlop , IO::Handle , Compress::Zlib HISTORY Created by Tom Hughes < tom@compton.nu >. Support for external gzip added by Jarkko Hietaniemi < jhi@iki.fi >. COPYRIGHT Copyright (c) 1998-2004 Tom Hughes < tom@compton.nu >. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. Module Install Instructions To install IO::Zlib, copy and paste the appropriate command in to your terminal. cpanm cpanm IO::Zlib CPAN shell perl -MCPAN -e shell install IO::Zlib For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-io-zlib --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-io-zlib 1.10 1 +------------------- +file name : perl-io-zlib-1.10-1.tar.bz2 +name : perl-io-zlib +version : 1.10 +build : 1 +build number: 1 +size : 7 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-zlib-1.10-1.tar.bz2 +md5 : cf694e509ed05e39671d768b1f5226e7 +dependencies: + - perl-io-compress + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-io-zlib 1.10 pl526_2 +------------------------- +file name : perl-io-zlib-1.10-pl526_2.tar.bz2 +name : perl-io-zlib +version : 1.10 +build : pl526_2 +build number: 2 +size : 9 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-io-zlib-1.10-pl526_2.tar.bz2 +md5 : 14acb0318f4ad06603b5d38706ae043a +timestamp : 2018-07-17 00:04:46 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-io-zlib 1.10 pl5321hdfd78af_3 +---------------------------------- +file name : perl-io-zlib-1.10-pl5321hdfd78af_3.tar.bz2 +name : perl-io-zlib +version : 1.10 +build : pl5321hdfd78af_3 +build number: 3 +size : 11 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-io-zlib-1.10-pl5321hdfd78af_3.tar.bz2 +md5 : a12e04b6c2c106dc7c92fff91b97e76c +timestamp : 2022-01-17 08:33:35 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-io-zlib 1.11 pl5321hdfd78af_0 +---------------------------------- +file name : perl-io-zlib-1.11-pl5321hdfd78af_0.tar.bz2 +name : perl-io-zlib +version : 1.11 +build : pl5321hdfd78af_0 +build number: 0 +size : 11 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-io-zlib-1.11-pl5321hdfd78af_0.tar.bz2 +md5 : 0bc11b066e1ec99fefd5558e87b8e0f0 +timestamp : 2022-02-14 10:12:44 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-io-zlib 1.12 pl5321hdfd78af_0 +---------------------------------- +file name : perl-io-zlib-1.12-pl5321hdfd78af_0.tar.bz2 +name : perl-io-zlib +version : 1.12 +build : pl5321hdfd78af_0 +build number: 0 +size : 12 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-io-zlib-1.12-pl5321hdfd78af_0.tar.bz2 +md5 : 0484e42daf539af75f2848f16a2723d1 +timestamp : 2022-12-29 23:29:17 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-io-zlib 1.14 pl5321hdfd78af_0 +---------------------------------- +file name : perl-io-zlib-1.14-pl5321hdfd78af_0.tar.bz2 +name : perl-io-zlib +version : 1.14 +build : pl5321hdfd78af_0 +build number: 0 +size : 12 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-io-zlib-1.14-pl5321hdfd78af_0.tar.bz2 +md5 : eadd0d684a0e22f08cccd6783c97606e +timestamp : 2023-01-10 21:23:05 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-io-zlib 1.15 pl5321hdfd78af_0 +---------------------------------- +file name : perl-io-zlib-1.15-pl5321hdfd78af_0.tar.bz2 +name : perl-io-zlib +version : 1.15 +build : pl5321hdfd78af_0 +build number: 0 +size : 12 KB +license : Unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-io-zlib-1.15-pl5321hdfd78af_0.tar.bz2 +md5 : fb41948817abc667ba0f261ff2c7dec4 +timestamp : 2025-06-11 20:24:00 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-io-zlib 1.15 pl5321hdfd78af_1 +---------------------------------- +file name : perl-io-zlib-1.15-pl5321hdfd78af_1.tar.bz2 +name : perl-io-zlib +version : 1.15 +build : pl5321hdfd78af_1 +build number: 1 +size : 12 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-io-zlib-1.15-pl5321hdfd78af_1.tar.bz2 +md5 : db92645dabe9467115729e4479841b5d +timestamp : 2025-07-09 14:04:18 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-ipc-cmd.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-ipc-cmd.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..914782d3fad0d26df9b22a1c3be6c28c1ac97923 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-ipc-cmd.manual_bundle.txt @@ -0,0 +1,200 @@ +# Tool: perl-ipc-cmd +software_name: perl-ipc-cmd +tier: T1 +domain: t1_backfill_overall +downloads: 155510 +summary: A cross platform way of running (interactive) commandline programs. +description: A cross platform way of running (interactive) commandline programs. +dependencies: perl >=5.32.1,<6.0a0, perl >=5.32.1,<6.0a0 *_perl5, perl-extutils-makemaker, perl-file-temp, perl-locale-maketext-simple, perl-module-load-conditional, perl-params-check +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/IPC::Cmd +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/IPC::Cmd +IPC::Cmd - finding and running system commands made easy - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution IPC-Cmd Module version: 1.04 13 Jul 2019 09:17:39 UTC License: perl_5 Code Download ( 30.68KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (33) How to Contribute Quality Testers ( 2850 / 4 / 0 ) Testers (Magpie) Kwalitee 50.86% Coverage Bus factor: 5 Activity 24 month 7 Dependencies ExtUtils::MakeMaker File::Spec File::Temp Locale::Maketext::Simple Module::Load::Conditional and 2 more Params::Check Test::More and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 1.04 (BINGOS on 2019-07-13) 1.02 (BINGOS on 2018-05-03) 0.46 (KANE on 2009-06-12) 0.44 (KANE on 2009-05-04) 0.42 (KANE on 2008-10-10) 0.41_07 DEV (KANE on 2008-10-05) 0.41_06 DEV (KANE on 2008-09-24) 0.41_05 DEV (KANE on 2008-09-22) 0.41_04 DEV (KANE on 2008-07-14) 0.41_03 DEV (KANE on 2008-07-13) 0.41_02 DEV (KANE on 2008-06-29) 0.41_01 DEV (KANE on 2008-05-18) 0.40 (KANE on 2007-10-17) 0.38 (KANE on 2007-10-11) 0.36 (KANE on 2006-11-24) 0.34 (KANE on 2006-10-20) 0.32 (KANE on 2006-10-13) 0.29_01 DEV (KANE on 2006-10-05) 0.25 (KANE on 2006-09-06) 0.24 (KANE on 2004-12-09) 0.23 (KANE on 2004-12-03) 0.22 (KANE on 2004-08-16) 0.20 (KANE on 2004-06-18) 0.04 (KANE on 2003-09-25) 0.03 (KANE on 2003-05-11) 0.02 (KANE on 2003-05-10) 1.00 (BINGOS on 2018-02-14) 0.98 (BINGOS on 2017-05-12) 0.96 (BINGOS on 2016-07-28) 0.94 (BINGOS on 2016-02-12) 0.92 (BINGOS on 2014-01-22) 0.90 (BINGOS on 2013-11-18) 0.88 (BINGOS on 2013-11-15) 0.86 (BINGOS on 2013-11-04) 0.85_02 DEV (BINGOS on 2013-10-10) 0.85_01 DEV (BINGOS on 2013-09-05) 0.84 (BINGOS on 2013-08-06) 0.82 (BINGOS on 2013-06-29) 0.80 (BINGOS on 2013-03-02) 0.78 (BINGOS on 2012-04-30) 0.76 (BINGOS on 2012-01-30) 0.74 (BINGOS on 2012-01-30) 0.72 (BINGOS on 2011-06-22) 0.71_03 DEV (BINGOS on 2011-05-26) 0.71_02 DEV (BINGOS on 2011-05-26) 0.71_01 DEV (BINGOS on 2011-05-10) 0.70 (BINGOS on 2011-01-31) 0.68 (BINGOS on 2011-01-07) 0.66 (BINGOS on 2010-11-23) 0.64 (BINGOS on 2010-10-19) 0.62 (BINGOS on 2010-10-19) 0.60 (BINGOS on 2010-07-05) 0.58 (BINGOS on 2010-04-29) 0.56 (BINGOS on 2010-02-03) 0.54 (BINGOS on 2009-11-15) 0.52 (BINGOS on 2009-11-13) 0.51_01 DEV (BINGOS on 2009-11-08) 0.50 (BINGOS on 2009-09-07) 0.48 (BINGOS on 2009-09-07) 0.30 (KANE on 2006-10-11) Diff with version 1.04 (BINGOS on 2019-07-13) 1.02 (BINGOS on 2018-05-03) 0.46 (KANE on 2009-06-12) 0.44 (KANE on 2009-05-04) 0.42 (KANE on 2008-10-10) 0.41_07 DEV (KANE on 2008-10-05) 0.41_06 DEV (KANE on 2008-09-24) 0.41_05 DEV (KANE on 2008-09-22) 0.41_04 DEV (KANE on 2008-07-14) 0.41_03 DEV (KANE on 2008-07-13) 0.41_02 DEV (KANE on 2008-06-29) 0.41_01 DEV (KANE on 2008-05-18) 0.40 (KANE on 2007-10-17) 0.38 (KANE on 2007-10-11) 0.36 (KANE on 2006-11-24) 0.34 (KANE on 2006-10-20) 0.32 (KANE on 2006-10-13) 0.29_01 DEV (KANE on 2006-10-05) 0.25 (KANE on 2006-09-06) 0.24 (KANE on 2004-12-09) 0.23 (KANE on 2004-12-03) 0.22 (KANE on 2004-08-16) 0.20 (KANE on 2004-06-18) 0.04 (KANE on 2003-09-25) 0.03 (KANE on 2003-05-11) 0.02 (KANE on 2003-05-10) 1.00 (BINGOS on 2018-02-14) 0.98 (BINGOS on 2017-05-12) 0.96 (BINGOS on 2016-07-28) 0.94 (BINGOS on 2016-02-12) 0.92 (BINGOS on 2014-01-22) 0.90 (BINGOS on 2013-11-18) 0.88 (BINGOS on 2013-11-15) 0.86 (BINGOS on 2013-11-04) 0.85_02 DEV (BINGOS on 2013-10-10) 0.85_01 DEV (BINGOS on 2013-09-05) 0.84 (BINGOS on 2013-08-06) 0.82 (BINGOS on 2013-06-29) 0.80 (BINGOS on 2013-03-02) 0.78 (BINGOS on 2012-04-30) 0.76 (BINGOS on 2012-01-30) 0.74 (BINGOS on 2012-01-30) 0.72 (BINGOS on 2011-06-22) 0.71_03 DEV (BINGOS on 2011-05-26) 0.71_02 DEV (BINGOS on 2011-05-26) 0.71_01 DEV (BINGOS on 2011-05-10) 0.70 (BINGOS on 2011-01-31) 0.68 (BINGOS on 2011-01-07) 0.66 (BINGOS on 2010-11-23) 0.64 (BINGOS on 2010-10-19) 0.62 (BINGOS on 2010-10-19) 0.60 (BINGOS on 2010-07-05) 0.58 (BINGOS on 2010-04-29) 0.56 (BINGOS on 2010-02-03) 0.54 (BINGOS on 2009-11-15) 0.52 (BINGOS on 2009-11-13) 0.51_01 DEV (BINGOS on 2009-11-08) 0.50 (BINGOS on 2009-09-07) 0.48 (BINGOS on 2009-09-07) 0.30 (KANE on 2006-10-11) Permalinks This version Latest version ++ed by: 16 PAUSE users 4 non-PAUSE users Authors: Jos Boumans Released by: Chris Williams Maintainers: KANE owner BINGOS Contributors: Jos Boumans <kane[at]cpan.org> Chris Williams  /  1.04 (BINGOS on 2019-07-13) 1.02 (BINGOS on 2018-05-03) 0.46 (KANE on 2009-06-12) 0.44 (KANE on 2009-05-04) 0.42 (KANE on 2008-10-10) 0.41_07 DEV (KANE on 2008-10-05) 0.41_06 DEV (KANE on 2008-09-24) 0.41_05 DEV (KANE on 2008-09-22) 0.41_04 DEV (KANE on 2008-07-14) 0.41_03 DEV (KANE on 2008-07-13) 0.41_02 DEV (KANE on 2008-06-29) 0.41_01 DEV (KANE on 2008-05-18) 0.40 (KANE on 2007-10-17) 0.38 (KANE on 2007-10-11) 0.36 (KANE on 2006-11-24) 0.34 (KANE on 2006-10-20) 0.32 (KANE on 2006-10-13) 0.29_01 DEV (KANE on 2006-10-05) 0.25 (KANE on 2006-09-06) 0.24 (KANE on 2004-12-09) 0.23 (KANE on 2004-12-03) 0.22 (KANE on 2004-08-16) 0.20 (KANE on 2004-06-18) 0.04 (KANE on 2003-09-25) 0.03 (KANE on 2003-05-11) 0.02 (KANE on 2003-05-10) 1.00 (BINGOS on 2018-02-14) 0.98 (BINGOS on 2017-05-12) 0.96 (BINGOS on 2016-07-28) 0.94 (BINGOS on 2016-02-12) 0.92 (BINGOS on 2014-01-22) 0.90 (BINGOS on 2013-11-18) 0.88 (BINGOS on 2013-11-15) 0.86 (BINGOS on 2013-11-04) 0.85_02 DEV (BINGOS on 2013-10-10) 0.85_01 DEV (BINGOS on 2013-09-05) 0.84 (BINGOS on 2013-08-06) 0.82 (BINGOS on 2013-06-29) 0.80 (BINGOS on 2013-03-02) 0.78 (BINGOS on 2012-04-30) 0.76 (BINGOS on 2012-01-30) 0.74 (BINGOS on 2012-01-30) 0.72 (BINGOS on 2011-06-22) 0.71_03 DEV (BINGOS on 2011-05-26) 0.71_02 DEV (BINGOS on 2011-05-26) 0.71_01 DEV (BINGOS on 2011-05-10) 0.70 (BINGOS on 2011-01-31) 0.68 (BINGOS on 2011-01-07) 0.66 (BINGOS on 2010-11-23) 0.64 (BINGOS on 2010-10-19) 0.62 (BINGOS on 2010-10-19) 0.60 (BINGOS on 2010-07-05) 0.58 (BINGOS on 2010-04-29) 0.56 (BINGOS on 2010-02-03) 0.54 (BINGOS on 2009-11-15) 0.52 (BINGOS on 2009-11-13) 0.51_01 DEV (BINGOS on 2009-11-08) 0.50 (BINGOS on 2009-09-07) 0.48 (BINGOS on 2009-09-07) 0.30 (KANE on 2006-10-11) IPC-Cmd-1.04 20 ++ 20 ++ / IPC::Cmd Contents NAME SYNOPSIS DESCRIPTION CLASS METHODS $ipc_run_version = IPC::Cmd->can_use_ipc_run( [VERBOSE] ) $ipc_open3_version = IPC::Cmd->can_use_ipc_open3( [VERBOSE] ) $bool = IPC::Cmd->can_capture_buffer $bool = IPC::Cmd->can_use_run_forked FUNCTIONS $path = can_run( PROGRAM ); $ok | ($ok, $err, $full_buf, $stdout_buff, $stderr_buff) = run( command => COMMAND, [verbose => BOOL, buffer => \$SCALAR, timeout => DIGIT] ); $hashref = run_forked( COMMAND, { child_stdin => SCALAR, timeout => DIGIT, stdout_handler => CODEREF, stderr_handler => CODEREF} ); $q = QUOTE HOW IT WORKS Global Variables $IPC::Cmd::VERBOSE $IPC::Cmd::USE_IPC_RUN $IPC::Cmd::USE_IPC_OPEN3 $IPC::Cmd::WARN $IPC::Cmd::INSTANCES $IPC::Cmd::ALLOW_NULL_ARGS Caveats See Also ACKNOWLEDGEMENTS BUG REPORTS AUTHOR COPYRIGHT NAME IPC::Cmd - finding and running system commands made easy SYNOPSIS use IPC::Cmd qw[can_run run run_forked]; my $full_path = can_run('wget') or warn 'wget is not installed!'; ### commands can be arrayrefs or strings ### my $cmd = "$full_path -b theregister.co.uk"; my $cmd = [$full_path, '-b', 'theregister.co.uk']; ### in scalar context ### my $buffer; if( scalar run( command => $cmd, verbose => 0, buffer => \$buffer, timeout => 20 ) ) { print "fetched webpage successfully: $buffer\n"; } ### in list context ### my( $success, $error_message, $full_buf, $stdout_buf, $stderr_buf ) = run( command => $cmd, verbose => 0 ); if( $success ) { print "this is what the command printed:\n"; print join "", @$full_buf; } ### run_forked example ### my $result = run_forked("$full_path -q -O - theregister.co.uk", {'timeout' => 20}); if ($result->{'exit_code'} eq 0 && !$result->{'timeout'}) { print "this is what wget returned:\n"; print $result->{'stdout'}; } ### check for features print "IPC::Open3 available: " . IPC::Cmd->can_use_ipc_open3; print "IPC::Run available: " . IPC::Cmd->can_use_ipc_run; print "Can capture buffer: " . IPC::Cmd->can_capture_buffer; ### don't have IPC::Cmd be verbose, ie don't print to stdout or ### stderr when running commands -- default is '0' $IPC::Cmd::VERBOSE = 0; DESCRIPTION IPC::Cmd allows you to run commands platform independently, interactively if desired, but have them still work. The can_run function can tell you if a certain binary is installed and if so where, whereas the run function can actually execute any of the commands you give it and give you a clear return value, as well as adhere to your verbosity settings. CLASS METHODS $ipc_run_version = IPC::Cmd->can_use_ipc_run( [VERBOSE] ) Utility function that tells you if IPC::Run is available. If the verbose flag is passed, it will print diagnostic messages if IPC::Run can not be found or loaded. $ipc_open3_version = IPC::Cmd->can_use_ipc_open3( [VERBOSE] ) Utility function that tells you if IPC::Open3 is available. If the verbose flag is passed, it will print diagnostic messages if IPC::Open3 can not be found or loaded. $bool = IPC::Cmd->can_capture_buffer Utility function that tells you if IPC::Cmd is capable of capturing buffers in it's current configuration. $bool = IPC::Cmd->can_use_run_forked Utility function that tells you if IPC::Cmd is capable of providing run_forked on the current platform. FUNCTIONS $path = can_run( PROGRAM ); can_run takes only one argument: the name of a binary you wish to locate. can_run works much like the unix binary which or the bash command type , which scans through your path, looking for the requested binary. Unlike which and type , this function is platform independent and will also work on, for example, Win32. If called in a scalar context it will return the full path to the binary you asked for if it was found, or undef if it was not. If called in a list context and the global variable $INSTANCES is a true value, it will return a list of the full paths to instances of the binary where found in PATH , or an empty list if it was not found. $ok | ($ok, $err, $full_buf, $stdout_buff, $stderr_buff) = run( command => COMMAND, [verbose => BOOL, buffer => \$SCALAR, timeout => DIGIT] ); run takes 4 arguments: command This is the command to execute. It may be either a string or an array reference. This is a required argument. See "Caveats" for remarks on how commands are parsed and their limitations. verbose This controls whether all output of a command should also be printed to STDOUT/STDERR or should only be trapped in buffers (NOTE: buffers require IPC::Run to be installed, or your system able to work with IPC::Open3 ). It will default to the global setting of $IPC::Cmd::VERBOSE , which by default is 0. buffer This will hold all the output of a command. It needs to be a reference to a scalar. Note that this will hold both the STDOUT and STDERR messages, and you have no way of telling which is which. If you require this distinction, run the run command in list context and inspect the individual buffers. Of course, this requires that the underlying call supports buffers. See the note on buffers above. timeout Sets the maximum time the command is allowed to run before aborting, using the built-in alarm() call. If the timeout is triggered, the errorcode in the return value will be set to an object of the IPC::Cmd::TimeOut class. See the "error message" section below for details. Defaults to 0 , meaning no timeout is set. run will return a simple true or false when called in scalar context. In list context, you will be returned a list of the following items: success A simple boolean indicating if the command executed without errors or not. error message If the first element of the return value ( success ) was 0, then some error occurred. This second element is the error message the command you requested exited with, if available. This is generally a pretty printed value of $? or $@ . See perldoc perlvar for details on what they can contain. If the error was a timeout, the error message will be prefixed with the string IPC::Cmd::TimeOut , the timeout class. full_buffer This is an array reference containing all the output the command generated. Note that buffers are only available if you have IPC::Run installed, or if your system is able to work with IPC::Open3 -- see below). Otherwise, this element will be undef . out_buffer This is an array reference containing all the output sent to STDOUT the command generated. The notes from "full_buffer" apply. error_buffer This is an arrayreference containing all the output sent to STDERR the command generated. The notes from "full_buffer" apply. See the "HOW IT WORKS" section below to see how IPC::Cmd decides what modules or function calls to use when issuing a command. $hashref = run_forked( COMMAND, { child_stdin => SCALAR, timeout => DIGIT, stdout_handler => CODEREF, stderr_handler => CODEREF} ); run_forked is used to execute some program or a coderef, optionally feed it with some input, get its return code and output (both stdout and stderr into separate buffers). In addition, it allows to terminate the program if it takes too long to finish. The important and distinguishing feature of run_forked is execution timeout which at first seems to be quite a simple task but if you think that the program which you're spawning might spawn some children itself (which in their turn could do the same and so on) it turns out to be not a simple issue. run_forked is designed to survive and successfully terminate almost any long running task, even a fork bomb in case your system has the resources to survive during given timeout. This is achieved by creating separate watchdog process which spawns the specified program in a separate process session and supervises it: optionally feeds it with input, stores its exit code, stdout and stderr, terminates it in case it runs longer than specified. Invocation requires the command to be executed or a coderef and optionally a hashref of options: timeout Specify in seconds how long to run the command before it is killed with SIG_KILL (9), which effectively terminates it and all of its children (direct or indirect). child_stdin Specify some text that will be passed into the STDIN of the executed program. stdout_handler Coderef of a subroutine to call when a portion of data is received on STDOUT from the executing program. stderr_handler Coderef of a subroutine to call when a portion of data is received on STDERR from the executing program. wait_loop_callback Coderef of a subroutine to call inside of the main waiting loop (while run_forked waits for the external to finish or fail). It is useful to stop running external process before it ends by itself, e.g. my $r = run_forked("some external command", { 'wait_loop_callback' => sub { if (condition) { kill(1, $$); } }, 'terminate_on_signal' => 'HUP', }); Combined with stdout_handler and stderr_handler allows terminating external command based on its output. Could also be used as a timer without engaging with alarm (signals). Remember that this code could be called every millisecond (depending on the output which external command generates), so try to make it as lightweight as possible. discard_output Discards the buffering of the standard output and standard errors for return by run_forked(). With this option you have to use the std*_handlers to read what the command outputs. Useful for commands that send a lot of output. terminate_on_parent_sudden_death Enable this option if you wish all spawned processes to be killed if the initially spawned process (the parent) is killed or dies without waiting for child processes. run_forked will return a HASHREF with the following keys: exit_code The exit code of the executed program. timeout The number of seconds the program ran for before being terminated, or 0 if no timeout occurred. stdout Holds the standard output of the executed command (or empty string if there was no STDOUT output or if discard_output was used; it's always defined!) stderr Holds the standard error of the executed command (or empty string if there was no STDERR output or if discard_output was used; it's always defined!) merged Holds the standard output and error of the executed command merged into one stream (or empty string if there was no output at all or if discard_output was used; it's always defined!) err_msg Holds some explanation in the case of an error. $q = QUOTE Returns the character used for quoting strings on this platform. This is usually a ' (single quote) on most systems, but some systems use different quotes. For example, Win32 uses " (double quote). You can use it as follows: use IPC::Cmd qw[run QUOTE]; my $cmd = q[echo ] . QUOTE . q[foo bar] . QUOTE; This makes sure that foo bar is treated as a string, rather than two separate arguments to the echo function. HOW IT WORKS run will try to execute your command using the following logic: If you have IPC::Run installed, and the variable $IPC::Cmd::USE_IPC_RUN is set to true (See the "Global Variables" section) use that to execute the command. You will have the full output available in buffers, interactive commands are sure to work and you are guaranteed to have your verbosity settings honored cleanly. Otherwise, if the variable $IPC::Cmd::USE_IPC_OPEN3 is set to true (See the "Global Variables" section), try to execute the command using IPC::Open3 . Buffers will be available on all platforms, interactive commands will still execute cleanly, and also your verbosity settings will be adhered to nicely; Otherwise, if you have the verbose argument set to true, we fall back to a simple system() call. We cannot capture any buffers, but interactive commands will still work. Otherwise we will try and temporarily redirect STDERR and STDOUT, do a system() call with your command and then re-open STDERR and STDOUT. This is the method of last resort and will still allow you to execute your commands cleanly. However, no buffers will be available. Global Variables The behaviour of IPC::Cmd can be altered by changing the following global variables: $IPC::Cmd::VERBOSE This controls whether IPC::Cmd will print any output from the commands to the screen or not. The default is 0. $IPC::Cmd::USE_IPC_RUN This variable controls whether IPC::Cmd will try to use IPC::Run when available and suitable. $IPC::Cmd::USE_IPC_OPEN3 This variable controls whether IPC::Cmd will try to use IPC::Open3 when available and suitable. Defaults to true. $IPC::Cmd::WARN This variable controls whether run-time warnings should be issued, like the failure to load an IPC::* module you explicitly requested. Defaults to true. Turn this off at your own risk. $IPC::Cmd::INSTANCES This variable controls whether can_run will return all instances of the binary it finds in the PATH when called in a list context. Defaults to false, set to true to enable the described behaviour. $IPC::Cmd::ALLOW_NULL_ARGS This variable controls whether run will remove any empty/null arguments it finds in command arguments. Defaults to false, so it will remove null arguments. Set to true to allow them. Caveats Whitespace and IPC::Open3 / system() When using IPC::Open3 or system , if you provide a string as the command argument, it is assumed to be appropriately escaped. You can use the QUOTE constant to use as a portable quote character (see above). However, if you provide an array reference, special rules apply: If your + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-ipc-cmd --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-ipc-cmd 1.00 0 +------------------- +file name : perl-ipc-cmd-1.00-0.tar.bz2 +name : perl-ipc-cmd +version : 1.00 +build : 0 +build number: 0 +size : 22 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-ipc-cmd-1.00-0.tar.bz2 +md5 : 4d623e63392d93390cc15d867a1c3eeb +dependencies: + - perl >=5.22,<6.0 + - perl-extutils-makemaker + - perl-file-spec + - perl-file-temp + - perl-locale-maketext-simple + - perl-module-load-conditional >=0.66 + - perl-params-check + - perl-test-more + + +perl-ipc-cmd 1.00 pl522_1 +------------------------- +file name : perl-ipc-cmd-1.00-pl522_1.tar.bz2 +name : perl-ipc-cmd +version : 1.00 +build : pl522_1 +build number: 1 +size : 22 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-ipc-cmd-1.00-pl522_1.tar.bz2 +md5 : c8a5d5fce2225671f639f95b50416b86 +timestamp : 2018-07-08 20:46:09 UTC +dependencies: + - perl >=5.22.0.1,<5.23.0a0 + - perl-extutils-makemaker + - perl-file-spec + - perl-file-temp + - perl-locale-maketext-simple + - perl-module-load-conditional >=0.66 + - perl-params-check + - perl-test-more + + +perl-ipc-cmd 1.02 pl526_0 +------------------------- +file name : perl-ipc-cmd-1.02-pl526_0.tar.bz2 +name : perl-ipc-cmd +version : 1.02 +build : pl526_0 +build number: 0 +size : 22 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-ipc-cmd-1.02-pl526_0.tar.bz2 +md5 : a1e40952d5af68c8b36eb32aba7f2632 +timestamp : 2018-07-15 04:49:49 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-extutils-makemaker + - perl-file-temp + - perl-locale-maketext-simple + - perl-module-load-conditional + - perl-params-check + + +perl-ipc-cmd 1.02 pl5321hdfd78af_1 +---------------------------------- +file name : perl-ipc-cmd-1.02-pl5321hdfd78af_1.tar.bz2 +name : perl-ipc-cmd +version : 1.02 +build : pl5321hdfd78af_1 +build number: 1 +size : 24 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-ipc-cmd-1.02-pl5321hdfd78af_1.tar.bz2 +md5 : b81e2a314c0d9364e154c8f3c48de572 +timestamp : 2022-01-20 10:27:35 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-extutils-makemaker + - perl-file-temp + - perl-locale-maketext-simple + - perl-module-load-conditional + - perl-params-check + + +perl-ipc-cmd 1.04 pl5321hdfd78af_0 +---------------------------------- +file name : perl-ipc-cmd-1.04-pl5321hdfd78af_0.tar.bz2 +name : perl-ipc-cmd +version : 1.04 +build : pl5321hdfd78af_0 +build number: 0 +size : 25 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-ipc-cmd-1.04-pl5321hdfd78af_0.tar.bz2 +md5 : 162c5574f37d0837dae8c2120c865f19 +timestamp : 2022-02-15 22:42:49 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-extutils-makemaker + - perl-file-temp + - perl-locale-maketext-simple + - perl-module-load-conditional + - perl-params-check + + +perl-ipc-cmd 1.04 pl5321hdfd78af_1 +---------------------------------- +file name : perl-ipc-cmd-1.04-pl5321hdfd78af_1.tar.bz2 +name : perl-ipc-cmd +version : 1.04 +build : pl5321hdfd78af_1 +build number: 1 +size : 26 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-ipc-cmd-1.04-pl5321hdfd78af_1.tar.bz2 +md5 : eef41f45f0844efff59cda38328c32ae +timestamp : 2025-06-16 07:55:22 UTC +dependencies: + - perl >=5.32.1,<6.0a0 + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-extutils-makemaker + - perl-file-temp + - perl-locale-maketext-simple + - perl-module-load-conditional + - perl-params-check diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-ipc-run.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-ipc-run.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..5513368261138800cca058b06954636f576e3f62 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-ipc-run.manual_bundle.txt @@ -0,0 +1,178 @@ +# Tool: perl-ipc-run +software_name: perl-ipc-run +tier: T1 +domain: t1_backfill_overall +downloads: 351657 +summary: system() and background procs w/ piping, redirs, ptys (Unix, Win32). +description: system() and background procs w/ piping, redirs, ptys (Unix, Win32). +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-io-tty +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/IPC::Run +doc_url: https://metacpan.org/pod/IPC::Run +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/IPC::Run +IPC::Run - system() and background procs w/ piping, redirs, ptys (Unix, Win32) - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution IPC-Run Module version: 20260402.0 02 Apr 2026 18:56:45 UTC License: perl_5 Code Download ( 158.11KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues How to Contribute Quality Testers Testers (Magpie) Kwalitee 75.36% Coverage Bus factor: 2 Activity 24 month Dependencies IO::Pty Test::More and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 20260402.0 (TODDR on 2026-04-02) 20260401.0 (TODDR on 2026-04-01) 20250809.0 (NJM on 2025-08-10) 20250715.0_01 DEV (NJM on 2025-07-15) 0.84 (ADAMK on 2009-07-13) 0.83 (ADAMK on 2009-07-09) 0.82 (ADAMK on 2008-12-18) 0.80 (RSOD on 2006-05-10) 0.80_91 DEV (RSOD on 2006-03-10) 0.79 (RSOD on 2005-01-19) 0.78 (RBS on 2004-03-09) 20260322.0 (TODDR on 2026-03-22) 20231003.0 (TODDR on 2023-10-03) 20220807.0 (TODDR on 2022-08-07) 20200505.0 (TODDR on 2020-05-05) 20180523.0 (TODDR on 2018-05-23) 0.99 (TODDR on 2018-03-30) 0.98 (TODDR on 2018-03-29) 0.97 (TODDR on 2018-03-26) 0.96 (TODDR on 2017-05-12) 0.95 (TODDR on 2017-04-25) 0.94_02 DEV (TODDR on 2016-04-14) 0.94_01 DEV (TODDR on 2016-04-13) 0.94 (TODDR on 2014-12-14) 0.93_01 DEV (TODDR on 2014-12-11) 0.93 (TODDR on 2014-12-11) 0.92 (TODDR on 2012-08-30) 0.92_01 DEV (TODDR on 2012-08-22) 0.91 (TODDR on 2012-02-15) 0.91_01 DEV (TODDR on 2012-01-25) 0.90 (TODDR on 2011-07-03) 0.90_03 DEV (TODDR on 2011-07-01) 0.90_02 DEV (TODDR on 2011-06-29) 0.90_01 DEV (TODDR on 2011-06-03) 0.89 (TODDR on 2010-04-01) 0.88 (TODDR on 2010-03-30) 0.87 (TODDR on 2010-03-29) 0.86 (TODDR on 2010-03-24) 0.85 (TODDR on 2010-03-23) 0.81_01 DEV (ADAMK on 2008-10-15) 0.77 (RBS on 2003-09-26) 0.75 (RBS on 2003-01-28) 0.74 (RBS on 2002-05-23) 0.73 (RBS on 2002-05-22) 0.72 (RBS on 2002-05-09) 0.71 (RBS on 2002-05-06) 0.7 (RBS on 2002-04-26) 0.66 (RBS on 2002-03-27) 0.64 (RBS on 2002-03-14) 0.63 (RBS on 2002-02-27) 0.62 (RBS on 2002-01-01) 0.61 (RBS on 2001-12-07) 0.6 (RBS on 2001-12-06) 0.56 (RBS on 2001-12-02) 0.55 (RBS on 2001-12-01) 0.54 (RBS on 2001-12-01) 0.51 (RBS on 2001-11-12) 0.5 (RBS on 2001-11-11) 0.44 (RBS on 2000-10-02) 0.42 (RBS on 2000-08-17) 0.4 (RBS on 2000-06-15) 0.34 (RBS on 2000-06-08) 0.33 (RBS on 2000-06-08) 0.32 (RBS on 2000-06-06) 0.3 (RBS on 2000-06-03) 0.21 (RBS on 2000-06-02) 0.2 (RBS on 2000-06-01) 0.1 (RBS on 2000-05-22) Diff with version 20260402.0 (TODDR on 2026-04-02) 20260401.0 (TODDR on 2026-04-01) 20250809.0 (NJM on 2025-08-10) 20250715.0_01 DEV (NJM on 2025-07-15) 0.84 (ADAMK on 2009-07-13) 0.83 (ADAMK on 2009-07-09) 0.82 (ADAMK on 2008-12-18) 0.80 (RSOD on 2006-05-10) 0.80_91 DEV (RSOD on 2006-03-10) 0.79 (RSOD on 2005-01-19) 0.78 (RBS on 2004-03-09) 20260322.0 (TODDR on 2026-03-22) 20231003.0 (TODDR on 2023-10-03) 20220807.0 (TODDR on 2022-08-07) 20200505.0 (TODDR on 2020-05-05) 20180523.0 (TODDR on 2018-05-23) 0.99 (TODDR on 2018-03-30) 0.98 (TODDR on 2018-03-29) 0.97 (TODDR on 2018-03-26) 0.96 (TODDR on 2017-05-12) 0.95 (TODDR on 2017-04-25) 0.94_02 DEV (TODDR on 2016-04-14) 0.94_01 DEV (TODDR on 2016-04-13) 0.94 (TODDR on 2014-12-14) 0.93_01 DEV (TODDR on 2014-12-11) 0.93 (TODDR on 2014-12-11) 0.92 (TODDR on 2012-08-30) 0.92_01 DEV (TODDR on 2012-08-22) 0.91 (TODDR on 2012-02-15) 0.91_01 DEV (TODDR on 2012-01-25) 0.90 (TODDR on 2011-07-03) 0.90_03 DEV (TODDR on 2011-07-01) 0.90_02 DEV (TODDR on 2011-06-29) 0.90_01 DEV (TODDR on 2011-06-03) 0.89 (TODDR on 2010-04-01) 0.88 (TODDR on 2010-03-30) 0.87 (TODDR on 2010-03-29) 0.86 (TODDR on 2010-03-24) 0.85 (TODDR on 2010-03-23) 0.81_01 DEV (ADAMK on 2008-10-15) 0.77 (RBS on 2003-09-26) 0.75 (RBS on 2003-01-28) 0.74 (RBS on 2002-05-23) 0.73 (RBS on 2002-05-22) 0.72 (RBS on 2002-05-09) 0.71 (RBS on 2002-05-06) 0.7 (RBS on 2002-04-26) 0.66 (RBS on 2002-03-27) 0.64 (RBS on 2002-03-14) 0.63 (RBS on 2002-02-27) 0.62 (RBS on 2002-01-01) 0.61 (RBS on 2001-12-07) 0.6 (RBS on 2001-12-06) 0.56 (RBS on 2001-12-02) 0.55 (RBS on 2001-12-01) 0.54 (RBS on 2001-12-01) 0.51 (RBS on 2001-11-12) 0.5 (RBS on 2001-11-11) 0.44 (RBS on 2000-10-02) 0.42 (RBS on 2000-08-17) 0.4 (RBS on 2000-06-15) 0.34 (RBS on 2000-06-08) 0.33 (RBS on 2000-06-08) 0.32 (RBS on 2000-06-06) 0.3 (RBS on 2000-06-03) 0.21 (RBS on 2000-06-02) 0.2 (RBS on 2000-06-01) 0.1 (RBS on 2000-05-22) Permalinks This version Latest version ++ed by: 23 PAUSE users 16 non-PAUSE users Authors: Barrie Slaymaker Released by: Todd Rinaldo Maintainers: TODDR owner NJM Contributors: Barrie Slaymaker Todd Rinaldo  /  20260402.0 (TODDR on 2026-04-02) 20260401.0 (TODDR on 2026-04-01) 20250809.0 (NJM on 2025-08-10) 20250715.0_01 DEV (NJM on 2025-07-15) 0.84 (ADAMK on 2009-07-13) 0.83 (ADAMK on 2009-07-09) 0.82 (ADAMK on 2008-12-18) 0.80 (RSOD on 2006-05-10) 0.80_91 DEV (RSOD on 2006-03-10) 0.79 (RSOD on 2005-01-19) 0.78 (RBS on 2004-03-09) 20260322.0 (TODDR on 2026-03-22) 20231003.0 (TODDR on 2023-10-03) 20220807.0 (TODDR on 2022-08-07) 20200505.0 (TODDR on 2020-05-05) 20180523.0 (TODDR on 2018-05-23) 0.99 (TODDR on 2018-03-30) 0.98 (TODDR on 2018-03-29) 0.97 (TODDR on 2018-03-26) 0.96 (TODDR on 2017-05-12) 0.95 (TODDR on 2017-04-25) 0.94_02 DEV (TODDR on 2016-04-14) 0.94_01 DEV (TODDR on 2016-04-13) 0.94 (TODDR on 2014-12-14) 0.93_01 DEV (TODDR on 2014-12-11) 0.93 (TODDR on 2014-12-11) 0.92 (TODDR on 2012-08-30) 0.92_01 DEV (TODDR on 2012-08-22) 0.91 (TODDR on 2012-02-15) 0.91_01 DEV (TODDR on 2012-01-25) 0.90 (TODDR on 2011-07-03) 0.90_03 DEV (TODDR on 2011-07-01) 0.90_02 DEV (TODDR on 2011-06-29) 0.90_01 DEV (TODDR on 2011-06-03) 0.89 (TODDR on 2010-04-01) 0.88 (TODDR on 2010-03-30) 0.87 (TODDR on 2010-03-29) 0.86 (TODDR on 2010-03-24) 0.85 (TODDR on 2010-03-23) 0.81_01 DEV (ADAMK on 2008-10-15) 0.77 (RBS on 2003-09-26) 0.75 (RBS on 2003-01-28) 0.74 (RBS on 2002-05-23) 0.73 (RBS on 2002-05-22) 0.72 (RBS on 2002-05-09) 0.71 (RBS on 2002-05-06) 0.7 (RBS on 2002-04-26) 0.66 (RBS on 2002-03-27) 0.64 (RBS on 2002-03-14) 0.63 (RBS on 2002-02-27) 0.62 (RBS on 2002-01-01) 0.61 (RBS on 2001-12-07) 0.6 (RBS on 2001-12-06) 0.56 (RBS on 2001-12-02) 0.55 (RBS on 2001-12-01) 0.54 (RBS on 2001-12-01) 0.51 (RBS on 2001-11-12) 0.5 (RBS on 2001-11-11) 0.44 (RBS on 2000-10-02) 0.42 (RBS on 2000-08-17) 0.4 (RBS on 2000-06-15) 0.34 (RBS on 2000-06-08) 0.33 (RBS on 2000-06-08) 0.32 (RBS on 2000-06-06) 0.3 (RBS on 2000-06-03) 0.21 (RBS on 2000-06-02) 0.2 (RBS on 2000-06-01) 0.1 (RBS on 2000-05-22) IPC-Run-20260402.0 39 ++ 39 ++ ⭐ Starred 21 GitHub stars / IPC::Run Take me over? The maintainer of this distribution is looking for someone to take over! If you're interested then please contact them via email . Contents NAME SYNOPSIS DESCRIPTION SIMPLE QUICKSTART Capturing output and errors from an external command Passing input to the external program Handling errors And beyond THE DETAILS Harnesses run() vs. start(); pump(); finish(); Using regexps to match output Timeouts and Timers Spawning synchronization, child exception propagation Syntax OBSTINATE CHILDREN PSEUDO TERMINALS CAVEATS Redirection Operators Just doing I/O Options RETURN VALUES ROUTINES FILTERS FILTER IMPLEMENTATION FUNCTIONS TODO Win32 LIMITATIONS LIMITATIONS TODO INSPIRATION SUPPORT AUTHORS COPYRIGHT NAME IPC::Run - system() and background procs w/ piping, redirs, ptys (Unix, Win32) SYNOPSIS ## First,a command to run: my @cat = qw( cat ); ## Using run() instead of system(): use IPC::Run qw( run timeout ); run \@cat, \$in, \$out, \$err, timeout( 10 ) or die "cat: $?"; # Can do I/O to sub refs and filenames, too: run \@cat, '<', "in.txt", \&out, \&err or die "cat: $?"; run \@cat, '<', "in.txt", '>>', "out.txt", '2>>', "err.txt"; # Redirecting using pseudo-terminals instead of pipes. run \@cat, '<pty<', \$in, '>pty>', \$out_and_err; ## Scripting subprocesses (like Expect): use IPC::Run qw( start pump finish timeout ); # Incrementally read from / write to scalars. # $in is drained as it is fed to cat's stdin, # $out accumulates cat's stdout # $err accumulates cat's stderr # $h is for "harness". my $h = start \@cat, \$in, \$out, \$err, timeout( 10 ); $in .= "some input\n"; pump $h until $out =~ /input\n/g; $in .= "some more input\n"; pump $h until $out =~ /\G.*more input\n/; $in .= "some final input\n"; finish $h or die "cat returned $?"; warn $err if $err; print $out; ## All of cat's output # Piping between children run \@cat, '|', \@gzip; # Multiple children simultaneously (run() blocks until all # children exit, use start() for background execution): run \@foo1, '&', \@foo2; # Calling \&set_up_child in the child before it executes the # command (only works on systems with true fork() & exec()) # exceptions thrown in set_up_child() will be propagated back # to the parent and thrown from run(). run \@cat, \$in, \$out, init => \&set_up_child; # Read from / write to file handles you open and close open IN, '<in.txt' or die $!; open OUT, '>out.txt' or die $!; print OUT "preamble\n"; run \@cat, \*IN, \*OUT or die "cat returned $?"; print OUT "postamble\n"; close IN; close OUT; # Create pipes for you to read / write (like IPC::Open2 & 3). $h = start \@cat, '<pipe', \*IN, # may also be a lexical filehandle e.g. \my $infh '>pipe', \*OUT, '2>pipe', \*ERR or die "cat returned $?"; print IN "some input\n"; close IN; print <OUT>, <ERR>; finish $h; # Mixing input and output modes run \@cat, 'in.txt', \&catch_some_out, \*ERR_LOG; # Other redirection constructs run \@cat, '>&', \$out_and_err; run \@cat, '2>&1'; run \@cat, '0<&3'; run \@cat, '<&-'; run \@cat, '3<', \$in3; run \@cat, '4>', \$out4; # etc. # Passing options: run \@cat, 'in.txt', debug => 1; # Call this system's shell, returns TRUE on 0 exit code # THIS IS THE OPPOSITE SENSE OF system()'s RETURN VALUE run "cat a b c" or die "cat returned $?"; # Launch a sub process directly, no shell. Can't do redirection # with this form, it's here to behave like system() with an # inverted result. $r = run "cat a b c"; # Read from a file in to a scalar run io( "filename", 'r', \$recv ); run io( \*HANDLE, 'r', \$recv ); DESCRIPTION IPC::Run allows you to run and interact with child processes using files, pipes, and pseudo-ttys. Both system()-style and scripted usages are supported and may be mixed. Likewise, functional and OO API styles are both supported and may be mixed. Various redirection operators reminiscent of those seen on common Unix and DOS command lines are provided. SIMPLE QUICKSTART Here's a quick guide to basic usage of using IPC::Run's run() function. Capturing output and errors from an external command Say you want to run a command in your shell. We'll use ls for simplicity, although there are far better ways to get a list of files, such as the glob() function or the File::Find module. The basic form of run() has the command and its arguments passed as an arrayref in the first argument. The command cannot be a single string. @cmd = [ 'ls', '-a', '-l', '-r', '-t' ]; # Yes @cmd = ( 'ls -a -l -r -t' ); # No After the command, pass a scalar reference \$in for the input to pass in, and scalar references \$out and \$err to receive the content of stdout and stderr. use IPC::Run qw( run ); @cmd = qw( ls -l -a -r -t ); run( \@cmd, \$in, \$out, \$err ) or die $?; print("\$err is ", length($err), " bytes long\n"); print($err, "\n"); print("\$out is ", length($out), " bytes long\n"); print($out, "\n"); Running this will show something like: $err is 0 bytes long $out is 1410 bytes long total 392 drwxr-xr-x 3 andy staff 96 Mar 17 11:53 .github -rw-r--r-- 1 andy staff 158 Mar 17 11:53 .gitignore ... etc ... Note that $out and $err are always defined after a call to run() , even if they receive no data. Passing input to the external program If you have input to pass in, put it in the $in variables. For example, to use the wc command to count lines, words and characters in a block of text: $in = <<'CARROLL'; 'Twas brillig, and the slithy toves Did gyre and gimble in the wabe: All mimsy were the borogoves, And the mome raths outgrabe. CARROLL @cmd = qw( wc ); run( \@cmd, \$in, \$out, \$err ) or die $?; print "$out"; This gives the output: 4 23 140 Handling errors It's important to check the return code of run() to see if the command ran successfully. run() returns a boolean true on success, and false on failure. Note that this is the opposite of Perl's system() , which returns 0 on success and a non-zero value on failures. For the specific subprocess error code, check $? directly. @cmd = qw( tar xzvf nonexistent.tar ); if ( !run( \@cmd, \$in, \$out, \$err ) ) { print "\$? = $?\n"; print "err = $err\n"; } Running this gives: $? = 256 err = tar: Error opening archive: Failed to open 'nonexistent.tar' If the program does not exist, then run() will die and won't return at all. For example: @cmd = qw( bogus-command ); my $rc = run( \@cmd, \$in, \$out, \$err ); print "run returned ", ($rc ? "true" : "false"), "\n"; Running this doesn't make it to the print statement. Command 'bogus-command' not found in [ list of paths ] at program.pl line N. To handle the possibility of a non-existent program, call run() inside an eval . my $rc; eval { $rc = run( \@cmd, \$in, \$out, \$out ); 1; }; if ( !defined($rc) ) { print "run died: $@\n"; } else { if ( $rc ) { print "run returned true\n"; } else { print "run returned false\n"; print "\$? = $?\n"; } } And beyond That's the basics of using run() as a replacement for system() . If you'd like to do more, such as having subprocesses communicate with each other, setting timeouts on long-running processes, kill running subprocesses, redirecting output, closing file descriptors and much much MUCH more, read on. THE DETAILS Before digging in to the details a few LIMITATIONS are important enough to be mentioned right up front: Win32 Support Win32 support is working but EXPERIMENTAL , but does pass all relevant tests on NT 4.0. See "Win32 LIMITATIONS" . pty Support If you need pty support, IPC::Run should work well enough most of the time, but IO::Pty is being improved, and IPC::Run will be improved to use IO::Pty's new features when it is released. The basic problem is that the pty needs to initialize itself before the parent writes to the master pty, or the data written gets lost. So IPC::Run does a sleep(1) in the parent after forking to (hopefully) give the child a chance to run. This is a kludge that works well on non heavily loaded systems :(. ptys are not supported yet under Win32, but will be emulated... Debugging Tip You may use the environment variable IPCRUNDEBUG to see what's going on under the hood: $ IPCRUNDEBUG=basic myscript # prints minimal debugging $ IPCRUNDEBUG=data myscript # prints all data reads/writes $ IPCRUNDEBUG=details myscript # prints lots of low-level details $ IPCRUNDEBUG=gory myscript # (Win32 only) prints data moving through # the helper processes. Harnesses Child processes and I/O handles are gathered in to a harness, then started and run until the processing is finished or aborted. run() vs. start(); pump(); finish(); There are two modes you can run harnesses in: run() functions as an enhanced system(), and start()/pump()/finish() allow for background processes and scripted interactions with them. When using run(), all data to be sent to the harness is set up in advance (though one can feed subprocesses input from subroutine refs to get around this limitation). The harness is run and all output is collected from it, then any child processes are waited for: run \@cmd, \<<IN, \$out; blah IN ## To precompile harnesses and run them later: my $h = harness \@cmd, \<<IN, \$out; blah IN run $h; The background and scripting API is provided by start(), pump(), and finish(): start() creates a harness if need be (by calling harness()) and launches any subprocesses, pump() allows you to poll them for activity, and finish() then monitors the harnessed activities until they complete. ## Build the harness, open all pipes, and launch the subprocesses my $h = start \@cat, \$in, \$out; $in = "first input\n"; ## Now do I/O. start() does no I/O. pump $h while length $in; ## Wait for all input to go ## Now do some more I/O. $in = "second input\n"; pump $h until $out =~ /second input/; ## Clean up finish $h or die "cat returned $?"; You can optionally compile the harness with harness() prior to start()ing or run()ing, and you may omit start() between harness() and pump(). You might want to do these things if you compile your harnesses ahead of time. Using regexps to match output As shown in most of the scripting examples, the read-to-scalar facility for gathering subcommand's output is often used with regular expressions to detect stopping points. This is because subcommand output often arrives in dribbles and drabs, often only a character or line at a time. This output is input for the main program and piles up in variables like the $out and $err in our examples. Regular expressions can be used to wait for appropriate output in several ways. The cat example in the previous section demonstrates how to pump() until some string appears in the output. Here's an example that uses smb to fetch files from a remote server: $h = harness \@smbclient, \$in, \$out; $in = "cd /src\n"; $h->pump until $out =~ /^smb.*> \Z/m; die "error cding to /src:\n$out" if $out =~ "ERR"; $out = ''; $in = "mget *\n"; $h->pump until $out =~ /^smb.*> \Z/m; die "error retrieving files:\n$out" if $out =~ "ERR"; $in = "quit\n"; $h->finish; Notice that we carefully clear $out after the first command/response cycle? That's because IPC::Run does not delete $out when we continue, and we don't want to trip over the old output in the second command/response cycle. Say you want to accumulate all the output in $out and analyze it afterwards. Perl offers incremental regular expression matching using the m//gc and pattern matching idiom and the \G assertion. IPC::Run is careful not to disturb the current pos() value for scalars it appends data to, so we could modify the above so as not to destroy $out by adding a couple of /gc modifiers. The /g keeps us from tripping over the previous prompt and the /c keeps us from resetting the prior match position if the expected prompt doesn't materialize immediately: $h = harness \@smbclient, \$in, \$out; $in = "cd /src\n"; $h->pump until $out =~ /^smb.*> \Z/mgc; die "error cding to /src:\n$out" if $out =~ "ERR"; $in = "mget *\n"; $h->pump until $out =~ /^smb.*> \Z/mgc; die "error retrieving files:\n$out" if $out =~ "ERR"; $in = "quit\n"; $h->finish; analyze( $out ); When using this technique, you may want to preallocate $out to have plenty of memory or you may find that the act of growing $out each time new input arrives causes an O(length($out)^2) slowdown as $out grows. Say we expect no mor + +### https://metacpan.org/pod/IPC::Run +IPC::Run - system() and background procs w/ piping, redirs, ptys (Unix, Win32) - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution IPC-Run Module version: 20260402.0 02 Apr 2026 18:56:45 UTC License: perl_5 Code Download ( 158.11KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues How to Contribute Quality Testers Testers (Magpie) Kwalitee 75.36% Coverage Bus factor: 2 Activity 24 month Dependencies IO::Pty Test::More and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 20260402.0 (TODDR on 2026-04-02) 20260401.0 (TODDR on 2026-04-01) 20250809.0 (NJM on 2025-08-10) 20250715.0_01 DEV (NJM on 2025-07-15) 0.84 (ADAMK on 2009-07-13) 0.83 (ADAMK on 2009-07-09) 0.82 (ADAMK on 2008-12-18) 0.80 (RSOD on 2006-05-10) 0.80_91 DEV (RSOD on 2006-03-10) 0.79 (RSOD on 2005-01-19) 0.78 (RBS on 2004-03-09) 20260322.0 (TODDR on 2026-03-22) 20231003.0 (TODDR on 2023-10-03) 20220807.0 (TODDR on 2022-08-07) 20200505.0 (TODDR on 2020-05-05) 20180523.0 (TODDR on 2018-05-23) 0.99 (TODDR on 2018-03-30) 0.98 (TODDR on 2018-03-29) 0.97 (TODDR on 2018-03-26) 0.96 (TODDR on 2017-05-12) 0.95 (TODDR on 2017-04-25) 0.94_02 DEV (TODDR on 2016-04-14) 0.94_01 DEV (TODDR on 2016-04-13) 0.94 (TODDR on 2014-12-14) 0.93_01 DEV (TODDR on 2014-12-11) 0.93 (TODDR on 2014-12-11) 0.92 (TODDR on 2012-08-30) 0.92_01 DEV (TODDR on 2012-08-22) 0.91 (TODDR on 2012-02-15) 0.91_01 DEV (TODDR on 2012-01-25) 0.90 (TODDR on 2011-07-03) 0.90_03 DEV (TODDR on 2011-07-01) 0.90_02 DEV (TODDR on 2011-06-29) 0.90_01 DEV (TODDR on 2011-06-03) 0.89 (TODDR on 2010-04-01) 0.88 (TODDR on 2010-03-30) 0.87 (TODDR on 2010-03-29) 0.86 (TODDR on 2010-03-24) 0.85 (TODDR on 2010-03-23) 0.81_01 DEV (ADAMK on 2008-10-15) 0.77 (RBS on 2003-09-26) 0.75 (RBS on 2003-01-28) 0.74 (RBS on 2002-05-23) 0.73 (RBS on 2002-05-22) 0.72 (RBS on 2002-05-09) 0.71 (RBS on 2002-05-06) 0.7 (RBS on 2002-04-26) 0.66 (RBS on 2002-03-27) 0.64 (RBS on 2002-03-14) 0.63 (RBS on 2002-02-27) 0.62 (RBS on 2002-01-01) 0.61 (RBS on 2001-12-07) 0.6 (RBS on 2001-12-06) 0.56 (RBS on 2001-12-02) 0.55 (RBS on 2001-12-01) 0.54 (RBS on 2001-12-01) 0.51 (RBS on 2001-11-12) 0.5 (RBS on 2001-11-11) 0.44 (RBS on 2000-10-02) 0.42 (RBS on 2000-08-17) 0.4 (RBS on 2000-06-15) 0.34 (RBS on 2000-06-08) 0.33 (RBS on 2000-06-08) 0.32 (RBS on 2000-06-06) 0.3 (RBS on 2000-06-03) 0.21 (RBS on 2000-06-02) 0.2 (RBS on 2000-06-01) 0.1 (RBS on 2000-05-22) Diff with version 20260402.0 (TODDR on 2026-04-02) 20260401.0 (TODDR on 2026-04-01) 20250809.0 (NJM on 2025-08-10) 20250715.0_01 DEV (NJM on 2025-07-15) 0.84 (ADAMK on 2009-07-13) 0.83 (ADAMK on 2009-07-09) 0.82 (ADAMK on 2008-12-18) 0.80 (RSOD on 2006-05-10) 0.80_91 DEV (RSOD on 2006-03-10) 0.79 (RSOD on 2005-01-19) 0.78 (RBS on 2004-03-09) 20260322.0 (TODDR on 2026-03-22) 20231003.0 (TODDR on 2023-10-03) 20220807.0 (TODDR on 2022-08-07) 20200505.0 (TODDR on 2020-05-05) 20180523.0 (TODDR on 2018-05-23) 0.99 (TODDR on 2018-03-30) 0.98 (TODDR on 2018-03-29) 0.97 (TODDR on 2018-03-26) 0.96 (TODDR on 2017-05-12) 0.95 (TODDR on 2017-04-25) 0.94_02 DEV (TODDR on 2016-04-14) 0.94_01 DEV (TODDR on 2016-04-13) 0.94 (TODDR on 2014-12-14) 0.93_01 DEV (TODDR on 2014-12-11) 0.93 (TODDR on 2014-12-11) 0.92 (TODDR on 2012-08-30) 0.92_01 DEV (TODDR on 2012-08-22) 0.91 (TODDR on 2012-02-15) 0.91_01 DEV (TODDR on 2012-01-25) 0.90 (TODDR on 2011-07-03) 0.90_03 DEV (TODDR on 2011-07-01) 0.90_02 DEV (TODDR on 2011-06-29) 0.90_01 DEV (TODDR on 2011-06-03) 0.89 (TODDR on 2010-04-01) 0.88 (TODDR on 2010-03-30) 0.87 (TODDR on 2010-03-29) 0.86 (TODDR on 2010-03-24) 0.85 (TODDR on 2010-03-23) 0.81_01 DEV (ADAMK on 2008-10-15) 0.77 (RBS on 2003-09-26) 0.75 (RBS on 2003-01-28) 0.74 (RBS on 2002-05-23) 0.73 (RBS on 2002-05-22) 0.72 (RBS on 2002-05-09) 0.71 (RBS on 2002-05-06) 0.7 (RBS on 2002-04-26) 0.66 (RBS on 2002-03-27) 0.64 (RBS on 2002-03-14) 0.63 (RBS on 2002-02-27) 0.62 (RBS on 2002-01-01) 0.61 (RBS on 2001-12-07) 0.6 (RBS on 2001-12-06) 0.56 (RBS on 2001-12-02) 0.55 (RBS on 2001-12-01) 0.54 (RBS on 2001-12-01) 0.51 (RBS on 2001-11-12) 0.5 (RBS on 2001-11-11) 0.44 (RBS on 2000-10-02) 0.42 (RBS on 2000-08-17) 0.4 (RBS on 2000-06-15) 0.34 (RBS on 2000-06-08) 0.33 (RBS on 2000-06-08) 0.32 (RBS on 2000-06-06) 0.3 (RBS on 2000-06-03) 0.21 (RBS on 2000-06-02) 0.2 (RBS on 2000-06-01) 0.1 (RBS on 2000-05-22) Permalinks This version Latest version ++ed by: 23 PAUSE users 16 non-PAUSE users Authors: Barrie Slaymaker Released by: Todd Rinaldo Maintainers: TODDR owner NJM Contributors: Barrie Slaymaker Todd Rinaldo  /  20260402.0 (TODDR on 2026-04-02) 20260401.0 (TODDR on 2026-04-01) 20250809.0 (NJM on 2025-08-10) 20250715.0_01 DEV (NJM on 2025-07-15) 0.84 (ADAMK on 2009-07-13) 0.83 (ADAMK on 2009-07-09) 0.82 (ADAMK on 2008-12-18) 0.80 (RSOD on 2006-05-10) 0.80_91 DEV (RSOD on 2006-03-10) 0.79 (RSOD on 2005-01-19) 0.78 (RBS on 2004-03-09) 20260322.0 (TODDR on 2026-03-22) 20231003.0 (TODDR on 2023-10-03) 20220807.0 (TODDR on 2022-08-07) 20200505.0 (TODDR on 2020-05-05) 20180523.0 (TODDR on 2018-05-23) 0.99 (TODDR on 2018-03-30) 0.98 (TODDR on 2018-03-29) 0.97 (TODDR on 2018-03-26) 0.96 (TODDR on 2017-05-12) 0.95 (TODDR on 2017-04-25) 0.94_02 DEV (TODDR on 2016-04-14) 0.94_01 DEV (TODDR on 2016-04-13) 0.94 (TODDR on 2014-12-14) 0.93_01 DEV (TODDR on 2014-12-11) 0.93 (TODDR on 2014-12-11) 0.92 (TODDR on 2012-08-30) 0.92_01 DEV (TODDR on 2012-08-22) 0.91 (TODDR on 2012-02-15) 0.91_01 DEV (TODDR on 2012-01-25) 0.90 (TODDR on 2011-07-03) 0.90_03 DEV (TODDR on 2011-07-01) 0.90_02 DEV (TODDR on 2011-06-29) 0.90_01 DEV (TODDR on 2011-06-03) 0.89 (TODDR on 2010-04-01) 0.88 (TODDR on 2010-03-30) 0.87 (TODDR on 2010-03-29) 0.86 (TODDR on 2010-03-24) 0.85 (TODDR on 2010-03-23) 0.81_01 DEV (ADAMK on 2008-10-15) 0.77 (RBS on 2003-09-26) 0.75 (RBS on 2003-01-28) 0.74 (RBS on 2002-05-23) 0.73 (RBS on 2002-05-22) 0.72 (RBS on 2002-05-09) 0.71 (RBS on 2002-05-06) 0.7 (RBS on 2002-04-26) 0.66 (RBS on 2002-03-27) 0.64 (RBS on 2002-03-14) 0.63 (RBS on 2002-02-27) 0.62 (RBS on 2002-01-01) 0.61 (RBS on 2001-12-07) 0.6 (RBS on 2001-12-06) 0.56 (RBS on 2001-12-02) 0.55 (RBS on 2001-12-01) 0.54 (RBS on 2001-12-01) 0.51 (RBS on 2001-11-12) 0.5 (RBS on 2001-11-11) 0.44 (RBS on 2000-10-02) 0.42 (RBS on 2000-08-17) 0.4 (RBS on 2000-06-15) 0.34 (RBS on 2000-06-08) 0.33 (RBS on 2000-06-08) 0.32 (RBS on 2000-06-06) 0.3 (RBS on 2000-06-03) 0.21 (RBS on 2000-06-02) 0.2 (RBS on 2000-06-01) 0.1 (RBS on 2000-05-22) IPC-Run-20260402.0 39 ++ 39 ++ ⭐ Starred 21 GitHub stars / IPC::Run Take me over? The maintainer of this distribution is looking for someone to take over! If you're interested then please contact them via email . Contents NAME SYNOPSIS DESCRIPTION SIMPLE QUICKSTART Capturing output and errors from an external command Passing input to the external program Handling errors And beyond THE DETAILS Harnesses run() vs. start(); pump(); finish(); Using regexps to match output Timeouts and Timers Spawning synchronization, child exception propagation Syntax OBSTINATE CHILDREN PSEUDO TERMINALS CAVEATS Redirection Operators Just doing I/O Options RETURN VALUES ROUTINES FILTERS FILTER IMPLEMENTATION FUNCTIONS TODO Win32 LIMITATIONS LIMITATIONS TODO INSPIRATION SUPPORT AUTHORS COPYRIGHT NAME IPC::Run - system() and background procs w/ piping, redirs, ptys (Unix, Win32) SYNOPSIS ## First,a command to run: my @cat = qw( cat ); ## Using run() instead of system(): use IPC::Run qw( run timeout ); run \@cat, \$in, \$out, \$err, timeout( 10 ) or die "cat: $?"; # Can do I/O to sub refs and filenames, too: run \@cat, '<', "in.txt", \&out, \&err or die "cat: $?"; run \@cat, '<', "in.txt", '>>', "out.txt", '2>>', "err.txt"; # Redirecting using pseudo-terminals instead of pipes. run \@cat, '<pty<', \$in, '>pty>', \$out_and_err; ## Scripting subprocesses (like Expect): use IPC::Run qw( start pump finish timeout ); # Incrementally read from / write to scalars. # $in is drained as it is fed to cat's stdin, # $out accumulates cat's stdout # $err accumulates cat's stderr # $h is for "harness". my $h = start \@cat, \$in, \$out, \$err, timeout( 10 ); $in .= "some input\n"; pump $h until $out =~ /input\n/g; $in .= "some more input\n"; pump $h until $out =~ /\G.*more input\n/; $in .= "some final input\n"; finish $h or die "cat returned $?"; warn $err if $err; print $out; ## All of cat's output # Piping between children run \@cat, '|', \@gzip; # Multiple children simultaneously (run() blocks until all # children exit, use start() for background execution): run \@foo1, '&', \@foo2; # Calling \&set_up_child in the child before it executes the # command (only works on systems with true fork() & exec()) # exceptions thrown in set_up_child() will be propagated back # to the parent and thrown from run(). run \@cat, \$in, \$out, init => \&set_up_child; # Read from / write to file handles you open and close open IN, '<in.txt' or die $!; open OUT, '>out.txt' or die $!; print OUT "preamble\n"; run \@cat, \*IN, \*OUT or die "cat returned $?"; print OUT "postamble\n"; close IN; close OUT; # Create pipes for you to read / write (like IPC::Open2 & 3). $h = start \@cat, '<pipe', \*IN, # may also be a lexical filehandle e.g. \my $infh '>pipe', \*OUT, '2>pipe', \*ERR or die "cat returned $?"; print IN "some input\n"; close IN; print <OUT>, <ERR>; finish $h; # Mixing input and output modes run \@cat, 'in.txt', \&catch_some_out, \*ERR_LOG; # Other redirection constructs run \@cat, '>&', \$out_and_err; run \@cat, '2>&1'; run \@cat, '0<&3'; run \@cat, '<&-'; run \@cat, '3<', \$in3; run \@cat, '4>', \$out4; # etc. # Passing options: run \@cat, 'in.txt', debug => 1; # Call this system's shell, returns TRUE on 0 exit code # THIS IS THE OPPOSITE SENSE OF system()'s RETURN VALUE run "cat a b c" or die "cat returned $?"; # Launch a sub process directly, no shell. Can't do redirection # with this form, it's here to behave like system() with an # inverted result. $r = run "cat a b c"; # Read from a file in to a scalar run io( "filename", 'r', \$recv ); run io( \*HANDLE, 'r', \$recv ); DESCRIPTION IPC::Run allows you to run and interact with child processes using files, pipes, and pseudo-ttys. Both system()-style and scripted usages are supported and may be mixed. Likewise, functional and OO API styles are both supported and may be mixed. Various redirection operators reminiscent of those seen on common Unix and DOS command lines are provided. SIMPLE QUICKSTART Here's a quick guide to basic usage of using IPC::Run's run() function. Capturing output and errors from an external command Say you want to run a command in your shell. We'll use ls for simplicity, although there are far better ways to get a list of files, such as the glob() function or the File::Find module. The basic form of run() has the command and its arguments passed as an arrayref in the first argument. The command cannot be a single string. @cmd = [ 'ls', '-a', '-l', '-r', '-t' ]; # Yes @cmd = ( 'ls -a -l -r -t' ); # No After the command, pass a scalar reference \$in for the input to pass in, and scalar references \$out and \$err to receive the content of stdout and stderr. use IPC::Run qw( run ); @cmd = qw( ls -l -a -r -t ); run( \@cmd, \$in, \$out, \$err ) or die $?; print("\$err is ", length($err), " bytes long\n"); print($err, "\n"); print("\$out is ", length($out), " bytes long\n"); print($out, "\n"); Running this will show something like: $err is 0 bytes long $out is 1410 bytes long total 392 drwxr-xr-x 3 andy staff 96 Mar 17 11:53 .github -rw-r--r-- 1 andy staff 158 Mar 17 11:53 .gitignore ... etc ... Note that $out and $err are always defined after a call to run() , even if they receive no data. Passing input to the external program If you have input to pass in, put it in the $in variables. For example, to use the wc command to count lines, words and characters in a block of text: $in = <<'CARROLL'; 'Twas brillig, and the slithy toves Did gyre and gimble in the wabe: All mimsy were the borogoves, And the mome raths outgrabe. CARROLL @cmd = qw( wc ); run( \@cmd, \$in, \$out, \$err ) or die $?; print "$out"; This gives the output: 4 23 140 Handling errors It's important to check the return code of run() to see if the command ran successfully. run() returns a boolean true on success, and false on failure. Note that this is the opposite of Perl's system() , which returns 0 on success and a non-zero value on failures. For the specific subprocess error code, check $? directly. @cmd = qw( tar xzvf nonexistent.tar ); if ( !run( \@cmd, \$in, \$out, \$err ) ) { print "\$? = $?\n"; print "err = $err\n"; } Running this gives: $? = 256 err = tar: Error opening archive: Failed to open 'nonexistent.tar' If the program does not exist, then run() will die and won't return at all. For example: @cmd = qw( bogus-command ); my $rc = run( \@cmd, \$in, \$out, \$err ); print "run returned ", ($rc ? "true" : "false"), "\n"; Running this doesn't make it to the print statement. Command 'bogus-command' not found in [ list of paths ] at program.pl line N. To handle the possibility of a non-existent program, call run() inside an eval . my $rc; eval { $rc = run( \@cmd, \$in, \$out, \$out ); 1; }; if ( !defined($rc) ) { print "run died: $@\n"; } else { if ( $rc ) { print "run returned true\n"; } else { print "run returned false\n"; print "\$? = $?\n"; } } And beyond That's the basics of using run() as a replacement for system() . If you'd like to do more, such as having subprocesses communicate with each other, setting timeouts on long-running processes, kill running subprocesses, redirecting output, closing file descriptors and much much MUCH more, read on. THE DETAILS Before digging in to the details a few LIMITATIONS are important enough to be mentioned right up front: Win32 Support Win32 support is working but EXPERIMENTAL , but does pass all relevant tests on NT 4.0. See "Win32 LIMITATIONS" . pty Support If you need pty support, IPC::Run should work well enough most of the time, but IO::Pty is being improved, and IPC::Run will be improved to use IO::Pty's new features when it is released. The basic problem is that the pty needs to initialize itself before the parent writes to the master pty, or the data written gets lost. So IPC::Run does a sleep(1) in the parent after forking to (hopefully) give the child a chance to run. This is a kludge that works well on non heavily loaded systems :(. ptys are not supported yet under Win32, but will be emulated... Debugging Tip You may use the environment variable IPCRUNDEBUG to see what's going on under the hood: $ IPCRUNDEBUG=basic myscript # prints minimal debugging $ IPCRUNDEBUG=data myscript # prints all data reads/writes $ IPCRUNDEBUG=details myscript # prints lots of low-level details $ IPCRUNDEBUG=gory myscript # (Win32 only) prints data moving through # the helper processes. Harnesses Child processes and I/O handles are gathered in to a harness, then started and run until the processing is finished or aborted. run() vs. start(); pump(); finish(); There are two modes you can run harnesses in: run() functions as an enhanced system(), and start()/pump()/finish() allow for background processes and scripted interactions with them. When using run(), all data to be sent to the harness is set up in advance (though one can feed subprocesses input from subroutine refs to get around this limitation). The harness is run and all output is collected from it, then any child processes are waited for: run \@cmd, \<<IN, \$out; blah IN ## To precompile harnesses and run them later: my $h = harness \@cmd, \<<IN, \$out; blah IN run $h; The background and scripting API is provided by start(), pump(), and finish(): start() creates a harness if need be (by calling harness()) and launches any subprocesses, pump() allows you to poll them for activity, and finish() then monitors the harnessed activities until they complete. ## Build the harness, open all pipes, and launch the subprocesses my $h = start \@cat, \$in, \$out; $in = "first input\n"; ## Now do I/O. start() does no I/O. pump $h while length $in; ## Wait for all input to go ## Now do some more I/O. $in = "second input\n"; pump $h until $out =~ /second input/; ## Clean up finish $h or die "cat returned $?"; You can optionally compile the harness with harness() prior to start()ing or run()ing, and you may omit start() between harness() and pump(). You might want to do these things if you compile your harnesses ahead of time. Using regexps to match output As shown in most of the scripting examples, the read-to-scalar facility for gathering subcommand's output is often used with regular expressions to detect stopping points. This is because subcommand output often arrives in dribbles and drabs, often only a character or line at a time. This output is input for the main program and piles up in variables like the $out and $err in our examples. Regular expressions can be used to wait for appropriate output in several ways. The cat example in the previous section demonstrates how to pump() until some string appears in the output. Here's an example that uses smb to fetch files from a remote server: $h = harness \@smbclient, \$in, \$out; $in = "cd /src\n"; $h->pump until $out =~ /^smb.*> \Z/m; die "error cding to /src:\n$out" if $out =~ "ERR"; $out = ''; $in = "mget *\n"; $h->pump until $out =~ /^smb.*> \Z/m; die "error retrieving files:\n$out" if $out =~ "ERR"; $in = "quit\n"; $h->finish; Notice that we carefully clear $out after the first command/response cycle? That's because IPC::Run does not delete $out when we continue, and we don't want to trip over the old output in the second command/response cycle. Say you want to accumulate all the output in $out and analyze it afterwards. Perl offers incremental regular expression matching using the m//gc and pattern matching idiom and the \G assertion. IPC::Run is careful not to disturb the current pos() value for scalars it appends data to, so we could modify the above so as not to destroy $out by adding a couple of /gc modifiers. The /g keeps us from tripping over the previous prompt and the /c keeps us from resetting the prior match position if the expected prompt doesn't materialize immediately: $h = harness \@smbclient, \$in, \$out; $in = "cd /src\n"; $h->pump until $out =~ /^smb.*> \Z/mgc; die "error cding to /src:\n$out" if $out =~ "ERR"; $in = "mget *\n"; $h->pump until $out =~ /^smb.*> \Z/mgc; die "error retrieving files:\n$out" if $out =~ "ERR"; $in = "quit\n"; $h->finish; analyze( $out ); When using this technique, you may want to preallocate $out to have plenty of memory or you may find that the act of growing $out each time new input arrives causes an O(length($out)^2) slowdown as $out grows. Say we expect no mor + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-ipc-run --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-ipc-run 0.94 0 +------------------- +file name : perl-ipc-run-0.94-0.tar.bz2 +name : perl-ipc-run +version : 0.94 +build : 0 +build number: 0 +size : 54 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-ipc-run-0.94-0.tar.bz2 +md5 : 89c6874033534291677404559da1a42e +dependencies: + - perl-io-tty + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-ipc-run 0.94 pl526_1 +------------------------- +file name : perl-ipc-run-0.94-pl526_1.tar.bz2 +name : perl-ipc-run +version : 0.94 +build : pl526_1 +build number: 1 +size : 73 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-ipc-run-0.94-pl526_1.tar.bz2 +md5 : 584e390f8a96220b350ed7c8fa4abdfe +timestamp : 2018-07-07 00:00:08 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-io-tty + + +perl-ipc-run 20180523.0 pl526_0 +------------------------------- +file name : perl-ipc-run-20180523.0-pl526_0.tar.bz2 +name : perl-ipc-run +version : 20180523.0 +build : pl526_0 +build number: 0 +size : 74 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-ipc-run-20180523.0-pl526_0.tar.bz2 +md5 : 8c4578f521fdeb854012141a98295526 +timestamp : 2018-11-11 06:20:38 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-io-tty + + +perl-ipc-run 20180523.0 pl5321hdfd78af_1 +---------------------------------------- +file name : perl-ipc-run-20180523.0-pl5321hdfd78af_1.tar.bz2 +name : perl-ipc-run +version : 20180523.0 +build : pl5321hdfd78af_1 +build number: 1 +size : 76 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-ipc-run-20180523.0-pl5321hdfd78af_1.tar.bz2 +md5 : f03d2c4590c360a449727038a29ccde6 +timestamp : 2022-01-18 07:07:48 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-io-tty + + +perl-ipc-run 20200505.0 pl5321hdfd78af_0 +---------------------------------------- +file name : perl-ipc-run-20200505.0-pl5321hdfd78af_0.tar.bz2 +name : perl-ipc-run +version : 20200505.0 +build : pl5321hdfd78af_0 +build number: 0 +size : 76 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-ipc-run-20200505.0-pl5321hdfd78af_0.tar.bz2 +md5 : b0234081e5c5fd205c900dd9bc920da6 +timestamp : 2022-02-09 18:31:26 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-io-tty + + +perl-ipc-run 20250809.0 pl5321hdfd78af_0 +---------------------------------------- +file name : perl-ipc-run-20250809.0-pl5321hdfd78af_0.conda +name : perl-ipc-run +version : 20250809.0 +build : pl5321hdfd78af_0 +build number: 0 +size : 83 KB +license : Perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-ipc-run-20250809.0-pl5321hdfd78af_0.conda +md5 : f1092c32b516388b31320d3136a905f3 +timestamp : 2025-08-15 07:43:29 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-io-tty diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-lib.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-lib.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..88711fd17201d4eb6479ef5754195a24d951bc8d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-lib.manual_bundle.txt @@ -0,0 +1,127 @@ +# Tool: perl-lib +software_name: perl-lib +tier: T1 +domain: t1_backfill_overall +downloads: 167467 +summary: +description: +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-lib --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-lib 0.63 pl5.22.0_0 +------------------------ +file name : perl-lib-0.63-pl5.22.0_0.tar.bz2 +name : perl-lib +version : 0.63 +build : pl5.22.0_0 +build number: 0 +size : 5 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lib-0.63-pl5.22.0_0.tar.bz2 +md5 : f9623e15769591919967ca0842efe841 +dependencies: + - perl 5.22.0* + + +perl-lib 0.63 pl526_1 +--------------------- +file name : perl-lib-0.63-pl526_1.tar.bz2 +name : perl-lib +version : 0.63 +build : pl526_1 +build number: 1 +size : 6 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lib-0.63-pl526_1.tar.bz2 +md5 : 03381abd528ca5beab93d60bc93106d0 +timestamp : 2018-07-08 13:07:20 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-lib 0.63 pl5321hd8ed1ab_0 +------------------------------ +file name : perl-lib-0.63-pl5321hd8ed1ab_0.tar.bz2 +name : perl-lib +version : 0.63 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 15 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-lib-0.63-pl5321hd8ed1ab_0.tar.bz2 +md5 : 15490ba86c0d931f19f477eb612c12c2 +timestamp : 2022-09-23 15:25:44 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-lib 0.63 pl5321hdfd78af_2 +------------------------------ +file name : perl-lib-0.63-pl5321hdfd78af_2.tar.bz2 +name : perl-lib +version : 0.63 +build : pl5321hdfd78af_2 +build number: 2 +size : 9 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-lib-0.63-pl5321hdfd78af_2.tar.bz2 +md5 : fa7b3ceba90bf02ef23133f5774bb812 +timestamp : 2022-01-18 12:34:32 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-lwp-mediatypes.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-lwp-mediatypes.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed7c555d2d554493a2f0579f7b53188372c07bb4 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-lwp-mediatypes.manual_bundle.txt @@ -0,0 +1,172 @@ +# Tool: perl-lwp-mediatypes +software_name: perl-lwp-mediatypes +tier: T1 +domain: t1_backfill_overall +downloads: 522697 +summary: guess media type for a file or a URL +description: guess media type for a file or a URL +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-carp, perl-exporter +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/LWP::MediaTypes +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/LWP::MediaTypes +LWP::MediaTypes - guess media type for a file or a URL - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution LWP-MediaTypes Module version: 6.04 20 Mar 2019 13:01:30 UTC License: perl_5 Perl: v5.6.2 Code Download ( 39.06KB ) Source ( raw ) Browse ( raw ) Changes Project Homepage Repository Issues (0) How to Contribute Chat Quality Testers ( 14560 / 1 / 0 ) Testers (Magpie) Kwalitee 87.50% Coverage Bus factor: 6 Activity 24 month Dependencies Carp Exporter File::Basename Scalar::Util strict Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 6.04 (OALDERS on 2019-03-20) 6.03-TRIAL DEV (OALDERS on 2019-03-19) 6.02 (GAAS on 2012-02-16) 6.01 (GAAS on 2011-02-27) 6.00 (GAAS on 2011-02-25) Diff with version 6.04 (OALDERS on 2019-03-20) 6.03-TRIAL DEV (OALDERS on 2019-03-19) 6.02 (GAAS on 2012-02-16) 6.01 (GAAS on 2011-02-27) 6.00 (GAAS on 2011-02-25) Permalinks This version Latest version ++ed by: 1 PAUSE user 2 non-PAUSE users Authors: Gisle Aas Released by: Olaf Alders 8 Maintainers: OALDERS owner CAPOEIRAB ETHER GAAS LWWWP MSCHILLI SIMBABQUE SKAJI 47 Contributors: Adam Kennedy Adam Sjogren Alex Kapranoff Alexey Tourbin amire80 Andreas J. Koenig Bill Mann Bron Gondwana Daniel Hedlund David E. Wheeler DAVIDRW Father Chrysostomos FWILES Gavin Peters Gisle Aas Graeme Thompson Hans-H. Froehlich Ian Kilgore Jacob J jefflee john9art Karen Etheridge Mark Stosberg Mike Schilli mschilli murphy Olaf Alders Ondrej Hanak Peter Rabbitson phrstbrn Robert Stone Rolf Grossmann ruff sasao Sean M. Burke Slaven Rezic Spiros Denaxas Steve Hay Todd Lipcon Tom Hukins Tony Finch Toru Yamaguchi uid39246 <uid39246> Ville Skytta Wesley Schwengle Yuri Karaban Zefram Olaf Alders  /  6.04 (OALDERS on 2019-03-20) 6.03-TRIAL DEV (OALDERS on 2019-03-19) 6.02 (GAAS on 2012-02-16) 6.01 (GAAS on 2011-02-27) 6.00 (GAAS on 2011-02-25) LWP-MediaTypes-6.04 3 ++ 3 ++ ⭐ Starred 1 GitHub stars / LWP::MediaTypes Contents NAME SYNOPSIS DESCRIPTION COPYRIGHT NAME LWP::MediaTypes - guess media type for a file or a URL SYNOPSIS use LWP::MediaTypes qw(guess_media_type); $type = guess_media_type("/tmp/foo.gif"); DESCRIPTION This module provides functions for handling media (also known as MIME) types and encodings. The mapping from file extensions to media types is defined by the media.types file. If the ~/.media.types file exists it is used instead. For backwards compatibility we will also look for ~/.mime.types . The following functions are exported by default: guess_media_type( $filename ) guess_media_type( $uri ) guess_media_type( $filename_or_object, $header_to_modify ) This function tries to guess media type and encoding for a file or objects that support the a path or filename method, eg, URI or File::Temp objects. When an object does not support either method, it will be stringified to determine the filename. It returns the content type, which is a string like "text/html" . In array context it also returns any content encodings applied (in the order used to encode the file). You can pass a URI object reference, instead of the file name. If the type can not be deduced from looking at the file name, then guess_media_type() will let the -T Perl operator take a look. If this works (and -T returns a TRUE value) then we return text/plain as the type, otherwise we return application/octet-stream as the type. The optional second argument should be a reference to a HTTP::Headers object or any object that implements the $obj->header method in a similar way. When it is present the values of the 'Content-Type' and 'Content-Encoding' will be set for this header. media_suffix( $type, ... ) This function will return all suffixes that can be used to denote the specified media type(s). Wildcard types can be used. In a scalar context it will return the first suffix found. Examples: @suffixes = media_suffix('image/*', 'audio/basic'); $suffix = media_suffix('text/html'); The following functions are only exported by explicit request: add_type( $type, @exts ) Associate a list of file extensions with the given media type. Example: add_type("x-world/x-vrml" => qw(wrl vrml)); add_encoding( $type, @ext ) Associate a list of file extensions with an encoding type. Example: add_encoding("x-gzip" => "gz"); read_media_types( @files ) Parse media types files and add the type mappings found there. Example: read_media_types("conf/mime.types"); COPYRIGHT Copyright 1995-1999 Gisle Aas. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. Module Install Instructions To install LWP::MediaTypes, copy and paste the appropriate command in to your terminal. cpanm cpanm LWP::MediaTypes CPAN shell perl -MCPAN -e shell install LWP::MediaTypes For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-lwp-mediatypes --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-lwp-mediatypes 6.02 0 +-------------------------- +file name : perl-lwp-mediatypes-6.02-0.tar.bz2 +name : perl-lwp-mediatypes +version : 6.02 +build : 0 +build number: 0 +size : 17 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-mediatypes-6.02-0.tar.bz2 +md5 : 66217d408b8cd0d2a96c4dddae929e40 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-lwp-mediatypes 6.02 pl5.22.0_1 +----------------------------------- +file name : perl-lwp-mediatypes-6.02-pl5.22.0_1.tar.bz2 +name : perl-lwp-mediatypes +version : 6.02 +build : pl5.22.0_1 +build number: 1 +size : 19 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-mediatypes-6.02-pl5.22.0_1.tar.bz2 +md5 : c5efc299c333e7b76340d4bb79893534 +dependencies: + - perl 5.22.0* + + +perl-lwp-mediatypes 6.02 pl526_2 +-------------------------------- +file name : perl-lwp-mediatypes-6.02-pl526_2.tar.bz2 +name : perl-lwp-mediatypes +version : 6.02 +build : pl526_2 +build number: 2 +size : 21 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-mediatypes-6.02-pl526_2.tar.bz2 +md5 : f27f962f3edb554dc04adf21bbdb526d +timestamp : 2018-07-06 23:45:21 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-lwp-mediatypes 6.02 pl526_3 +-------------------------------- +file name : perl-lwp-mediatypes-6.02-pl526_3.tar.bz2 +name : perl-lwp-mediatypes +version : 6.02 +build : pl526_3 +build number: 3 +size : 21 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-mediatypes-6.02-pl526_3.tar.bz2 +md5 : 54f77b3c56608790c017d018278b0dc4 +timestamp : 2018-08-27 15:24:30 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-lwp-mediatypes 6.04 pl526_0 +-------------------------------- +file name : perl-lwp-mediatypes-6.04-pl526_0.tar.bz2 +name : perl-lwp-mediatypes +version : 6.04 +build : pl526_0 +build number: 0 +size : 22 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-mediatypes-6.04-pl526_0.tar.bz2 +md5 : 39688aa6f280b77af17f539350fe1744 +timestamp : 2019-05-06 10:46:16 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-carp + - perl-exporter + + +perl-lwp-mediatypes 6.04 pl5321hdfd78af_1 +----------------------------------------- +file name : perl-lwp-mediatypes-6.04-pl5321hdfd78af_1.tar.bz2 +name : perl-lwp-mediatypes +version : 6.04 +build : pl5321hdfd78af_1 +build number: 1 +size : 24 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-lwp-mediatypes-6.04-pl5321hdfd78af_1.tar.bz2 +md5 : 386b035f45e9389e6e9b1a367fdd19bb +timestamp : 2022-01-20 20:37:03 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-exporter diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-lwp-simple.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-lwp-simple.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6f32e87f40432a3c43d5343c695d7553962fef4e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-lwp-simple.manual_bundle.txt @@ -0,0 +1,195 @@ +# Tool: perl-lwp-simple +software_name: perl-lwp-simple +tier: T1 +domain: t1_backfill_overall +downloads: 250306 +summary: simple procedural interface to LWP +description: simple procedural interface to LWP +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-libwww-perl 6.67.* +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/LWP::Simple +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/LWP::Simple +LWP::Simple - simple procedural interface to LWP - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution libwww-perl Module version: 6.82 29 Mar 2026 17:03:41 UTC License: perl_5 Perl: v5.8.1 Code Download ( 183.1KB ) Source ( raw ) Browse ( raw ) Changes Project Homepage Repository Issues (135) How to Contribute Chat Quality Testers Testers (Magpie) Kwalitee % Coverage Bus factor: 6 Activity 24 month 32 Dependencies Digest::MD5 Encode Encode::Locale File::Copy File::Listing and 27 more File::Temp Getopt::Long HTML::Entities HTML::HeadParser HTTP::Cookies HTTP::Date HTTP::Message HTTP::Negotiate HTTP::Request HTTP::Request::Common HTTP::Response HTTP::Status IO::Select IO::Socket LWP::MediaTypes MIME::Base64 Module::Load Net::FTP Net::HTTP Scalar::Util Try::Tiny URI URI::Escape WWW::RobotRules parent strict warnings Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 6.82 (OALDERS on 2026-03-29) 6.81 (OALDERS on 2025-10-22) 6.80 (OALDERS on 2025-09-11) 6.79 (OALDERS on 2025-06-27) 6.78 (OALDERS on 2025-02-20) 6.77 (OALDERS on 2024-03-11) 6.76 (OALDERS on 2024-01-25) 6.75 (OALDERS on 2024-01-24) 6.74 (OALDERS on 2024-01-22) 6.73 (OALDERS on 2024-01-13) 6.72 (OALDERS on 2023-07-17) 6.71 (OALDERS on 2023-06-20) 6.70 (SIMBABQUE on 2023-04-30) 6.69 (SIMBABQUE on 2023-04-29) 6.68 (OALDERS on 2023-02-27) 6.67 (OALDERS on 2022-06-14) 6.66 (OALDERS on 2022-05-18) 6.65 (OALDERS on 2022-05-09) 6.64 (OALDERS on 2022-04-26) 6.63 (OALDERS on 2022-04-25) 6.62 (OALDERS on 2022-04-05) 6.61 (OALDERS on 2022-01-21) 6.60 (OALDERS on 2021-12-17) 6.59 (OALDERS on 2021-12-02) 6.58 (OALDERS on 2021-10-25) 6.57 (OALDERS on 2021-09-20) 6.56 (OALDERS on 2021-08-17) 6.55 (OALDERS on 2021-06-17) 6.54 (OALDERS on 2021-05-06) 6.53 (OALDERS on 2021-03-07) 6.52 (OALDERS on 2021-01-07) 6.51 (OALDERS on 2020-12-29) 6.50 (OALDERS on 2020-12-16) 6.49 (OALDERS on 2020-09-24) 6.48 (OALDERS on 2020-09-20) 6.47 (OALDERS on 2020-08-18) 6.46 (OALDERS on 2020-06-23) 6.45 (OALDERS on 2020-06-08) 6.44 (OALDERS on 2020-04-14) 6.43 (OALDERS on 2019-11-26) 6.42 (OALDERS on 2019-11-20) 6.41 (OALDERS on 2019-10-28) 6.40 (OALDERS on 2019-10-24) 6.39 (OALDERS on 2019-05-06) 6.38 (OALDERS on 2019-03-25) 6.37 (OALDERS on 2019-03-06) 6.36 (ETHER on 2018-10-10) 6.33 (OALDERS on 2018-02-27) 6.32 (OALDERS on 2018-02-20) 6.29 (OALDERS on 2017-11-06) 6.28 (OALDERS on 2017-11-06) 6.27 (OALDERS on 2017-09-21) 6.25 (OALDERS on 2017-04-03) 6.24 (OALDERS on 2017-03-14) 6.23 (OALDERS on 2017-03-07) 6.22 (OALDERS on 2017-03-01) 6.21 (OALDERS on 2017-02-21) 6.20 (OALDERS on 2017-02-21) 6.19 (OALDERS on 2017-02-14) 6.18 (OALDERS on 2017-02-03) 6.08 (MSCHILLI on 2014-07-25) 6.07 (MSCHILLI on 2014-07-02) 6.06 (MSCHILLI on 2014-04-16) 6.05 (GAAS on 2013-03-11) 5.837 (GAAS on 2010-09-20) 6.35 (ETHER on 2018-07-16) 6.34 (ETHER on 2018-06-05) 6.31 (ETHER on 2017-12-11) 6.30 (OALDERS on 2017-12-08) 6.26 (OALDERS on 2017-04-12) 6.17 (OALDERS on 2017-01-31) 6.16 (OALDERS on 2017-01-18) 6.15_004 DEV (CAPOEIRAB on 2016-02-13) 6.15_003 DEV (CAPOEIRAB on 2016-01-14) 6.15_002 DEV (CAPOEIRAB on 2016-01-14) 6.15_001 DEV (CAPOEIRAB on 2016-01-05) 6.15 (ETHER on 2015-12-05) 6.14_001 DEV (CAPOEIRAB on 2015-11-25) 6.13 (ETHER on 2015-02-14) 6.12 (ETHER on 2015-02-14) 6.11 (ETHER on 2015-02-13) 6.10 (ETHER on 2015-02-12) 6.09 (ETHER on 2015-02-10) 6.04 (GAAS on 2012-02-18) 6.03 (GAAS on 2011-10-15) 6.02 (GAAS on 2011-03-27) 6.01 (GAAS on 2011-03-09) 6.00 (GAAS on 2011-03-08) 5.837 (OLEG on 2010-11-04) 5.836 (GAAS on 2010-05-13) 5.835 (GAAS on 2010-05-05) 5.834 (GAAS on 2009-11-21) 5.833 (GAAS on 2009-10-06) 5.832 (GAAS on 2009-09-21) 5.831 (GAAS on 2009-08-13) 5.830 (GAAS on 2009-07-26) 5.829 (GAAS on 2009-07-08) 5.828 (GAAS on 2009-06-25) 5.827 (GAAS on 2009-06-15) 5.826 (GAAS on 2009-04-24) 5.825 (GAAS on 2009-02-16) 5.824 (GAAS on 2009-02-13) 5.823 (GAAS on 2009-01-12) 5.822 (GAAS on 2008-12-05) 5.821 (GAAS on 2008-11-25) 5.820 (GAAS on 2008-11-05) 5.819 (GAAS on 2008-10-20) 5.818 (GAAS on 2008-10-16) 5.817 (GAAS on 2008-10-10) 5.816 (GAAS on 2008-09-29) 5.815 (GAAS on 2008-09-24) 5.814 (GAAS on 2008-07-25) 5.813 (GAAS on 2008-06-17) 5.812 (GAAS on 2008-04-16) 5.811 (GAAS on 2008-04-14) 5.810 (GAAS on 2008-04-08) 5.808 (GAAS on 2007-08-05) 5.807 (GAAS on 2007-07-31) 5.806 (GAAS on 2007-07-19) 5.805 (GAAS on 2005-12-08) 5.804 (GAAS on 2005-12-06) 5.803 (GAAS on 2004-12-11) 5.802 (GAAS on 2004-11-30) 5.801 (GAAS on 2004-11-12) 5.800 (GAAS on 2004-06-16) 5.79 (GAAS on 2004-04-13) 5.78 (GAAS on 2004-04-07) 5.77 (GAAS on 2004-04-06) 5.76 (GAAS on 2003-11-21) 5.75 (GAAS on 2003-10-26) 5.74 (GAAS on 2003-10-23) 5.73 (GAAS on 2003-10-19) 5.72 (GAAS on 2003-10-15) 5.71 (GAAS on 2003-10-14) 5.70 (GAAS on 2003-10-13) 5.69 (GAAS on 2003-01-24) 5.68 (GAAS on 2003-01-03) 5.67 (GAAS on 2003-01-01) 5.66 (GAAS on 2002-12-20) 5.65 (GAAS on 2002-05-31) 5.64 (GAAS on 2002-02-09) 5.63 (GAAS on 2001-12-14) 5.62 (GAAS on 2001-11-21) 5.61 (GAAS on 2001-11-17) 5.60 (GAAS on 2001-10-26) 5.53_97 DEV (GAAS on 2001-09-20) 5.53_96 DEV (GAAS on 2001-08-28) 5.53_95 DEV (GAAS on 2001-08-07) 5.53_94 DEV (GAAS on 2001-05-05) 5.53_93 DEV (GAAS on 2001-04-29) 5.53_92 DEV (GAAS on 2001-04-25) 5.53_91 DEV (GAAS on 2001-04-21) 5.53_90 DEV (GAAS on 2001-04-19) 5.53 (GAAS on 2001-04-10) 5.52 (GAAS on 2001-03-29) 5.51 (GAAS on 2001-03-14) 5.50 (GAAS on 2001-01-12) 5.49 (GAAS on 2001-01-01) 5.48 (GAAS on 2000-04-09) 5.47 (GAAS on 1999-11-16) 5.46 (GAAS on 1999-10-28) 5.45 (GAAS on 1999-09-20) 5.44 (GAAS on 1999-06-25) 5.43 (GAAS on 1999-05-09) 5.42 (GAAS on 1999-03-20) 5.41 (GAAS on 1998-11-19) 5.40_01 DEV (GAAS on 1998-10-12) 5.36 (GAAS on 1998-08-04) 5.35 (GAAS on 1998-07-09) 5.34 (GAAS on 1998-07-07) 5.33 (GAAS on 1998-05-07) 5.32 (GAAS on 1998-04-17) 5.31 (GAAS on 1998-04-10) 5.30 (GAAS on 1998-03-31) 5.22 (GAAS on 1998-03-24) 5.21 (GAAS on 1998-03-12) 5.20 (GAAS on 1998-02-12) 5.19 (GAAS on 1998-01-26) 5.18_05 DEV (GAAS on 1998-01-20) 5.18_04 DEV (GAAS on 1997-12-17) 5.18_03 DEV (GAAS on 1997-12-16) 5.18 (GAAS on 1997-12-12) 5.15 (GAAS on 1997-11-06) 5.14 (GAAS on 1997-10-12) 5.13 (GAAS on 1997-09-20) 5.12 (GAAS on 1997-09-05) 5.11 (GAAS on 1997-08-06) 5.10 (GAAS on 1997-06-20) 5.09 (GAAS on 1997-06-10) 5.08 (GAAS on 1997-04-05) 5.07 (GAAS on 1997-02-11) 5.06 (GAAS on 1997-01-27) 5.05 (GAAS on 1996-12-04) 5.04 (GAAS on 1996-10-22) 5.03 (GAAS on 1996-09-30) 5.02 (GAAS on 1996-09-11) 5.01 (GAAS on 1996-08-02) 5.00 (GAAS on 1996-05-26) 5b13 (GAAS on 1996-05-09) 5b6 (GAAS on 1995-11-06) 5b5 (GAAS on 1995-09-16) Diff with version 6.82 (OALDERS on 2026-03-29) 6.81 (OALDERS on 2025-10-22) 6.80 (OALDERS on 2025-09-11) 6.79 (OALDERS on 2025-06-27) 6.78 (OALDERS on 2025-02-20) 6.77 (OALDERS on 2024-03-11) 6.76 (OALDERS on 2024-01-25) 6.75 (OALDERS on 2024-01-24) 6.74 (OALDERS on 2024-01-22) 6.73 (OALDERS on 2024-01-13) 6.72 (OALDERS on 2023-07-17) 6.71 (OALDERS on 2023-06-20) 6.70 (SIMBABQUE on 2023-04-30) 6.69 (SIMBABQUE on 2023-04-29) 6.68 (OALDERS on 2023-02-27) 6.67 (OALDERS on 2022-06-14) 6.66 (OALDERS on 2022-05-18) 6.65 (OALDERS on 2022-05-09) 6.64 (OALDERS on 2022-04-26) 6.63 (OALDERS on 2022-04-25) 6.62 (OALDERS on 2022-04-05) 6.61 (OALDERS on 2022-01-21) 6.60 (OALDERS on 2021-12-17) 6.59 (OALDERS on 2021-12-02) 6.58 (OALDERS on 2021-10-25) 6.57 (OALDERS on 2021-09-20) 6.56 (OALDERS on 2021-08-17) 6.55 (OALDERS on 2021-06-17) 6.54 (OALDERS on 2021-05-06) 6.53 (OALDERS on 2021-03-07) 6.52 (OALDERS on 2021-01-07) 6.51 (OALDERS on 2020-12-29) 6.50 (OALDERS on 2020-12-16) 6.49 (OALDERS on 2020-09-24) 6.48 (OALDERS on 2020-09-20) 6.47 (OALDERS on 2020-08-18) 6.46 (OALDERS on 2020-06-23) 6.45 (OALDERS on 2020-06-08) 6.44 (OALDERS on 2020-04-14) 6.43 (OALDERS on 2019-11-26) 6.42 (OALDERS on 2019-11-20) 6.41 (OALDERS on 2019-10-28) 6.40 (OALDERS on 2019-10-24) 6.39 (OALDERS on 2019-05-06) 6.38 (OALDERS on 2019-03-25) 6.37 (OALDERS on 2019-03-06) 6.36 (ETHER on 2018-10-10) 6.33 (OALDERS on 2018-02-27) 6.32 (OALDERS on 2018-02-20) 6.29 (OALDERS on 2017-11-06) 6.28 (OALDERS on 2017-11-06) 6.27 (OALDERS on 2017-09-21) 6.25 (OALDERS on 2017-04-03) 6.24 (OALDERS on 2017-03-14) 6.23 (OALDERS on 2017-03-07) 6.22 (OALDERS on 2017-03-01) 6.21 (OALDERS on 2017-02-21) 6.20 (OALDERS on 2017-02-21) 6.19 (OALDERS on 2017-02-14) 6.18 (OALDERS on 2017-02-03) 6.08 (MSCHILLI on 2014-07-25) 6.07 (MSCHILLI on 2014-07-02) 6.06 (MSCHILLI on 2014-04-16) 6.05 (GAAS on 2013-03-11) 5.837 (GAAS on 2010-09-20) 6.35 (ETHER on 2018-07-16) 6.34 (ETHER on 2018-06-05) 6.31 (ETHER on 2017-12-11) 6.30 (OALDERS on 2017-12-08) 6.26 (OALDERS on 2017-04-12) 6.17 (OALDERS on 2017-01-31) 6.16 (OALDERS on 2017-01-18) 6.15_004 DEV (CAPOEIRAB on 2016-02-13) 6.15_003 DEV (CAPOEIRAB on 2016-01-14) 6.15_002 DEV (CAPOEIRAB on 2016-01-14) 6.15_001 DEV (CAPOEIRAB on 2016-01-05) 6.15 (ETHER on 2015-12-05) 6.14_001 DEV (CAPOEIRAB on 2015-11-25) 6.13 (ETHER on 2015-02-14) 6.12 (ETHER on 2015-02-14) 6.11 (ETHER on 2015-02-13) 6.10 (ETHER on 2015-02-12) 6.09 (ETHER on 2015-02-10) 6.04 (GAAS on 2012-02-18) 6.03 (GAAS on 2011-10-15) 6.02 (GAAS on 2011-03-27) 6.01 (GAAS on 2011-03-09) 6.00 (GAAS on 2011-03-08) 5.837 (OLEG on 2010-11-04) 5.836 (GAAS on 2010-05-13) 5.835 (GAAS on 2010-05-05) 5.834 (GAAS on 2009-11-21) 5.833 (GAAS on 2009-10-06) 5.832 (GAAS on 2009-09-21) 5.831 (GAAS on 2009-08-13) 5.830 (GAAS on 2009-07-26) 5.829 (GAAS on 2009-07-08) 5.828 (GAAS on 2009-06-25) 5.827 (GAAS on 2009-06-15) 5.826 (GAAS on 2009-04-24) 5.825 (GAAS on 2009-02-16) 5.824 (GAAS on 2009-02-13) 5.823 (GAAS on 2009-01-12) 5.822 (GAAS on 2008-12-05) 5.821 (GAAS on 2008-11-25) 5.820 (GAAS on 2008-11-05) 5.819 (GAAS on 2008-10-20) 5.818 (GAAS on 2008-10-16) 5.817 (GAAS on 2008-10-10) 5.816 (GAAS on 2008-09-29) 5.815 (GAAS on 2008-09-24) 5.814 (GAAS on 2008-07-25) 5.813 (GAAS on 2008-06-17) 5.812 (GAAS on 2008-04-16) 5.811 (GAAS on 2008-04-14) 5.810 (GAAS on 2008-04-08) 5.808 (GAAS on 2007-08-05) 5.807 (GAAS on 2007-07-31) 5.806 (GAAS on 2007-07-19) 5.805 (GAAS on 2005-12-08) 5.804 (GAAS on 2005-12-06) 5.803 (GAAS on 2004-12-11) 5.802 (GAAS on 2004-11-30) 5.801 (GAAS on 2004-11-12) 5.800 (GAAS on 2004-06-16) 5.79 (GAAS on 2004-04-13) 5.78 (GAAS on 2004-04-07) 5.77 (GAAS on 2004-04-06) 5.76 (GAAS on 2003-11-21) 5.75 (GAAS on 2003-10-26) 5.74 (GAAS on 2003-10-23) 5.73 (GAAS on 2003-10-19) 5.72 (GAAS on 2003-10-15) 5.71 (GAAS on 2003-10-14) 5.70 (GAAS on 2003-10-13) 5.69 (GAAS on 2003-01-24) 5.68 (GAAS on 2003-01-03) 5.67 (GAAS on 2003-01-01) 5.66 (GAAS on 2002-12-20) 5.65 (GAAS on 2002-05-31) 5.64 (GAAS on 2002-02-09) 5.63 (GAAS on 2001-12-14) 5.62 (GAAS on 2001-11-21) 5.61 (GAAS on 2001-11-17) 5.60 (GAAS on 2001-10-26) 5.53_97 DEV (GAAS on 2001-09-20) 5.53_96 DEV (GAAS on 2001-08-28) 5.53_95 DEV (GAAS on 2001-08-07) 5.53_94 DEV (GAAS on 2001-05-05) 5.53_93 DEV (GAAS on 2001-04-29) 5.53_92 DEV (GAAS on 2001-04-25) 5.53_91 DEV (GAAS on 2001-04-21) 5.53_90 DEV (GAAS on 2001-04-19) 5.53 (GAAS on 2001-04-10) 5.52 (GAAS on 2001-03-29) 5.51 (GAAS on 2001-03-14) 5.50 (GAAS on 2001-01-12) 5.49 (GAAS on 2001-01-01) 5.48 (GAAS on 2000-04-09) 5.47 (GAAS on 1999-11-16) 5.46 (GAAS on 1999-10-28) 5.45 (GAAS on 1999-09-20) 5.44 (GAAS on 1999-06-25) 5.43 (GAAS on 1999-05-09) 5.42 (GAAS on 1999-03-20) 5.41 (GAAS on 1998-11-19) 5.40_01 DEV (GAAS on 1998-10-12) 5.36 (GAAS on 1998-08-04) 5.35 (GAAS on 1998-07-09) 5.34 (GAAS on 1998-07-07) 5.33 (GAAS on 1998-05-07) 5.32 (GAAS on 1998-04-17) 5.31 (GAAS on 1998-04-10) 5.30 (GAAS on 1998-03-31) 5.22 (GAAS on 1998-03-24) 5.21 (GAAS on 1998-03-12) 5.20 (GAAS on 1998-02-12) 5.19 (GAAS on 1998-01-26) 5.18_05 DEV (GAAS on 1998-01-20) 5.18_04 DEV (GAAS on 1997-12-17) 5.18_03 DEV (GAAS on 1997-12-16) 5.18 (GAAS on 1997-12-12) 5.15 (GAAS on 1997-11-06) 5.14 (GAAS on 1997-10-12) 5.13 (GAAS on 1997-09-20) 5.12 (GAAS on 1997-09-05) 5.11 (GAAS on 1997-08-06) 5.10 (GAAS on 1997-06-20) 5.09 (GAAS on 1997-06-10) 5.08 (GAAS on 1997-04-05) 5.07 (GAAS on 1997-02-11) 5.06 (GAAS on 1997-01-27) 5.05 (GAAS on 1996-12-04) 5.04 (GAAS on 1996-10-22) 5.03 (GAAS on 1996-09-30) 5.02 (GAAS on 1996-09-11) 5.01 (GAAS on 1996-08-02) 5.00 (GAAS on 1996-05-26) 5b13 (GAAS on 1996-05-09) 5b6 (GAAS on 1995-11-06) 5b5 (GAAS on 1995-09-16) Permalinks This version Latest version ++ed by: 88 PAUSE users 86 non-PAUSE users Authors: Gisle Aas Released by: Olaf Alders 8 Maintainers: OALDERS owner CAPOEIRAB ETHER GAAS LWWWP MSCHILLI SIMBABQUE SKAJI 119 Contributors: Adam Kennedy Adam Sjogren Alex Kapranoff Alexey Tourbin amire80 Andreas J. Koenig Andrew Grangaard Andrew Hewus Fresh Anirvan Chatterjee Arne Johannessen Austin Hill Axel Burri BGMNT Bill Mann Bron Gondwana Bryan Cardillo Burak Gursoy Chase Whitener Christopher J. Madsen Colin Newell copilot-swe-agent[bot] Daina Pettit Dan Church Daniel Hedlund David E. Wheeler David Standish David Steinbrunner DAVIDRW dependabot[bot] Desmond Daignault Devin Dooley Dmitriy Shamatrin Doug Bell Eric Johnson Fabian Zeindler Father Chrysostomos Frank Maas FWILES Galen Huntington Gavin Peters Gerhard Poul Gianni Ceccarelli Gisle Aas Graeme Thompson Graham Knop Gregory Oschwald grr Hans-H. Froehlich Ian Kilgore Jacob J Jakub Wilk James Raspass Jason A Fesler Javier Puche jefflee Jeremy Mates Joe Atzberger John Wittkoski john9art Jonathan Dahan Julien Fiegehenn Kacper Gutowski Karen Etheridge Katarina Durechova leedo Mark Fowler Mark Stosberg Martin H. Sluka Matthew Horsfall Max Maischein Michael G. Schwern michael gong Michal Josef Špaček Michiel Beijen Mike Schilli Mikko Johannes Koivunalho Moritz Onken murphy Naveed Massjouni Nigel Gregoire Nik LaBelle Niko Tyni Olaf Alders Ondrej Hanak Patrik Lundin Peter Rabbitson phrstbrn Piotr Roszatycki Robert Stone Rolf Grossmann Roman Galeev ruff Russell Shingleton sasao Sean M. Burke Sebastian Paaske Tørholm Sergey Romanov Shoichi Kaji Slaven Rezic Spiros Denaxas Steffen Ullrich Steve Hay Takumi Akiyama Theo van Hoesel Theodore Robert Campbell Jr Tim Couzins Todd Lipcon Tom Hukins Tomasz Konojacki Tony Finch Toru Yamaguchi turugina uid39246 <uid39246> Ville Skyttä Vyacheslav Matyukhin Yuri Karaban Yury Zavarin Yves Orton Zefram Olaf Alders  /  6.82 (OALDERS on 2026-03-29) 6.81 (OALDERS on 2025-10-22) 6.80 (OALDERS on 2025-09-11) 6.79 (OALDERS on 2025-06-27) 6.78 (OALDERS on 2025-02-20) 6.77 (OALDERS on 2024-03-11) 6.76 (OALDERS on 2024-01-25) 6.75 (OALDERS on 2024-01-24) 6.74 (OALDERS on 2024-01-22) 6.73 (OALDERS on 2024-01-13) 6.72 (OALDERS on 2023-07-17) 6.71 (OALDERS on 2023-06-20) 6.70 (SIMBABQUE on 2023-04-30) 6.69 (SIMBABQUE on 2023-04-29) 6.68 (OALDERS on 2023-02-27) 6.67 (OALDERS on 2022-06-14) 6.66 (OALDERS on 2022-05-18) 6.65 (OALDERS on 2022-05-09) 6.64 (OALDERS on 2022-04-26) 6.63 (OALDERS on 2022-04-25) 6.62 (OALDERS on 2022-04-05) 6.61 (OALDERS on 2022-01-21) 6.60 (OALDERS on 2021-12-17) 6.59 (OALDERS on 2021-12-02) 6.58 (OALDERS on 2021-10-25) 6.57 (OALDERS on 2021-09-20) 6.56 (OALDERS on 2021-08-17) 6.55 (OALDERS on 2021-06-17) 6.54 (OALDERS on 2021-05-06) 6.53 (OALDERS on 2021-03-07) 6.52 (OALDERS on 2021-01-07) 6.51 (OALDERS on 2020-12-29) 6.50 (OALDERS on 2020-12-16) 6.49 (OALDERS on 2020-09-24) 6.48 (OALDERS on 2020-09-20) 6.47 (OALDERS on 2020-08-18) 6.46 (OALDERS on 2020-06-23) 6.45 (OALDERS on 2020-06-08) 6.44 (OALDERS on 2020-04-14) 6.43 (OALDERS on 2019-11-26) 6.42 (OALDERS on 2019-11-20) 6.41 (OALDERS on 2019-10-28) 6.40 (OALDERS on 2019-10-24) 6.39 (OALDERS on 2019-05-06) 6.38 (OALDERS on 2019-03-25) 6.37 (OALDERS on 2019-03-06) 6.36 (ETHER on 2018-10-10) 6.33 (OALDERS on 2018-02-27) 6.32 (OALDERS on 2018-02-20) 6.29 (OALDERS on 2017-11-06) 6.28 (OALDERS on 2017-11-06) 6.27 (OALDERS on 2017-09-21) 6.25 (OALDERS on 2017-04-03) 6.24 (OALDERS on 2017-03-14) 6.23 (OALDERS on 2017-03-07) 6.22 (OALDERS on 2017-03-01) 6.21 (OALDERS on 2017-02-21) 6.20 (OALDERS on 2017-02-21) 6.19 (OALDERS on 2017-02-14) 6.18 (OALDERS on 2017-02-03) 6.08 (MSCHILLI on 2014-07-25) 6.07 (MSCHILLI on 2014-07-02) 6.06 (MSCHILLI on 2014-04-16) 6.05 (GAAS on 2013-03-11) 5.837 (GAAS on 2010-09-20) 6.35 (ETHER on 2018-07-16) 6.34 (ETHER on 2018-06-05) 6.31 (ETHER on 2017-12-11) 6.30 (OALDERS on 2017-12-08) 6.26 (OALDERS on 2017-04-12) 6.17 (OALDERS on 2017-01-31) 6.16 (OALDERS on 2017-01-18) 6.15_004 DEV (CAPOEIRAB on 2016-02-13) 6.15_003 DEV (CAPOEIRAB on 2016-01-14) 6.15_002 DEV (CAPOEIRAB on 2016-01-14) 6.15_001 DEV (CAPOEIRAB on 2016-01-05) 6.15 (ETHER on 2015-12-05) 6.14_001 DEV (CAPOEIRAB on 2015-11-25) 6.13 (ETHER on 2015-02-14) 6.12 (ETHER on 2015-02-14) 6.11 (ETHER on 2015-02-13) 6.10 (ETHER on 2015-02-12) 6.09 (ETHER on 2015-02-10) 6.04 (GAAS on 2012-02-18) 6.03 (GAAS on 2011-10-15) 6.02 (GAAS on 2011-03-27) 6.01 (GAAS on 2011-03-09) 6.00 (GAAS on 2011-03-08) 5.837 (OLEG on 2010-11-04) 5.836 (GAAS on 2010-05-13) 5.835 (GAAS on 2010-05-05) 5.834 (GAAS on 2009-11-21) 5.833 (GAAS on 2009-10-06) 5.832 (GAAS on 2009-09-21) 5.831 (GAAS on 2009-08-13) 5.830 (GAAS on 2009-07-26) 5.829 (GAAS on 2009-07-08) 5.828 (GAAS on 2009-06-25) 5.827 (GAAS on 2009-06-15) 5.826 (GAAS on 2009-04-24) 5.825 (GAAS on 2009-02-16) 5.824 (GAAS on 2009-02-13) 5.823 (GAAS on 2009-01-12) 5.822 (GAAS on 2008-12-05) 5.821 (GAAS on 2008-11-25) 5.820 (GAAS on 2008-11-05) 5.819 (GAAS on 2008-10-20) 5.818 (GAAS on 2008-10-16) 5.817 (GAAS on 2008-10-10) 5.816 (GAAS on 2008-09-29) 5.815 (GAAS on 2008-09-24) 5.814 (GAAS on 2008-07-25) 5.813 (GAAS on 2008-06-17) 5.812 (GAAS on 2008-04-16) 5.811 (GAAS on 2008-04-14) 5.810 (GAAS on 2008-04-08) 5.808 (GAAS on 2007-08-05) 5.807 (GAAS on 2007-07-31) 5.806 (GAAS on 2007-07-19) 5.805 (GAAS on 2005-12-08) 5.804 (GAAS on 2005-12-06) 5.803 (GAAS on 2004-12-11) 5.802 (GAAS on 2004-11-30) 5.801 (GAAS on 2004-11-12) 5.800 (GAAS on 2004-06-16) 5.79 (GAAS on 2004-04-13) 5.78 (GAAS on 2004-04-07) 5.77 (GAAS on 2004-04-06) 5.76 (GAAS on 2003-11-21) 5.75 (GAAS on 2003-10-26) 5.74 (GAAS on 2003-10-23) 5.73 (GAAS on 2003-10-19) 5.72 (GAAS on 2003-10-15) 5.71 (GAAS on 2003-10-14) 5.70 (GAAS on 2003-10-13) 5.69 (GAAS on 2003-01-24) 5.68 (GAAS on 2003-01-03) 5.67 (GAAS on 2003-01-01) 5.66 (GAAS on 2002-12-20) 5.65 (GAAS on 2002-05-31) 5.64 (GAAS on 2002-02-09) 5.63 (GAAS on 2001-12-14) 5.62 (GAAS on 2001-11-21) 5.61 (GAAS on 2001-11-17) 5.60 (GAAS on 2001-10-26) 5.53_97 DEV (GAAS on 2001-09-20) 5.53_96 DEV (GAAS on 2001-08-28) 5.53_95 DEV (GAAS on 2001-08-07) 5.53_94 DEV (GAAS on 2001-05-05) 5.53_93 DEV (GAAS on 2001-04-29) 5.53_92 DEV (GAAS on 2001-04-25) 5.53_91 DEV (GAAS on 2001-04-21) 5.53_90 DEV (GAAS on 2001-04-19) 5.53 (GAAS on 2001-04-10) 5.52 (GAAS on 2001-03-29) 5.51 (GAAS on 2001-03-14) 5.50 (GAAS on 2001-01-12) 5.49 (GAAS on 2001-01-01) 5.48 (GAAS on 2000-04-09) 5.47 (GAAS on 1999-11-16) 5.46 (GAAS on 1999-10-28) 5.45 (GAAS on 1999-09-20) 5.44 (GAAS on 1999-06-25) 5.43 (GAAS on 1999-05-09) 5.42 (GAAS on 1999-03-20) 5.41 (GAAS on 1998-11-19) 5.40_01 DEV (GAAS on 1998-10-12) 5.36 (GAAS on 1998-08-04) 5.35 (GAAS on 1998-07-09) 5.34 (GAAS on 1998-07-07) 5.33 (GAAS on 1998-05-07) 5.32 (GAAS on 1998-04-17) 5.31 (GAAS on 1998-04-10) 5.30 (GAAS on 1998-03-31) 5.22 (GAAS on 1998-03-24) 5.21 (GAAS on 1998-03-12) 5.20 (GAAS on 1998-02-12) 5.19 (GAAS on 1998-01-26) 5.18_05 DEV (GAAS on 1998-01-20) 5.18_04 DEV (GAAS on 1997-12-17) 5.18_03 DEV (GAAS on 1997-12-16) 5.18 (GAAS on 1997-12-12) 5.15 (GAAS on 1997-11-06) 5.14 (GAAS on 1997-10-12) 5.13 (GAAS on 1997-09-20) 5.12 (GAAS on 1997-09-05) 5.11 (GAAS on 1997-08-06) 5.10 (GAAS on 1997-06-20) 5.09 (GAAS on 1997-06-10) 5.08 (GAAS on 1997-04-05) 5.07 (GAAS on 1997-02-11) 5.06 (GAAS on 1997-01-27) 5.05 (GAAS on 1996-12-04) 5.04 (GAAS on 1996-10-22) 5.03 (GAAS on 1996-09-30) 5.02 (GAAS on 1996-09-11) 5.01 (GAAS on 1996-08-02) 5.00 (GAAS on 1996-05-26) 5b13 (GAAS on 1996-05-09) 5b6 (GAAS on 1995-11-06) 5b5 (GAAS on 1995-09-16) libwww-perl-6.82 174 ++ 174 ++ ⭐ Starred 204 GitHub stars / LWP::Simple Conte + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-lwp-simple --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-lwp-simple 6.15 1 +---------------------- +file name : perl-lwp-simple-6.15-1.tar.bz2 +name : perl-lwp-simple +version : 6.15 +build : 1 +build number: 1 +size : 228 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-simple-6.15-1.tar.bz2 +md5 : 2bdcaf7d922336bda66c0c015c44c75e +dependencies: + - perl-encode-locale + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-lwp-simple 6.15 2 +---------------------- +file name : perl-lwp-simple-6.15-2.tar.bz2 +name : perl-lwp-simple +version : 6.15 +build : 2 +build number: 2 +size : 228 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-simple-6.15-2.tar.bz2 +md5 : 1d668bcc0542538277a539a22e6f5ab1 +dependencies: + - libgcc + - perl-encode-locale + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-lwp-simple 6.15 3 +---------------------- +file name : perl-lwp-simple-6.15-3.tar.bz2 +name : perl-lwp-simple +version : 6.15 +build : 3 +build number: 3 +size : 228 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-simple-6.15-3.tar.bz2 +md5 : 91f907443767d28fb9056bcb3d5c34e6 +dependencies: + - libgcc + - perl-encode-locale + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-lwp-simple 6.15 pl5.22.0_0 +------------------------------- +file name : perl-lwp-simple-6.15-pl5.22.0_0.tar.bz2 +name : perl-lwp-simple +version : 6.15 +build : pl5.22.0_0 +build number: 0 +size : 227 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-simple-6.15-pl5.22.0_0.tar.bz2 +md5 : e45422c243419907218fbb60b263ed34 +dependencies: + - perl 5.22.0* + - perl-encode-locale + + +perl-lwp-simple 6.15 pl526h470a237_4 +------------------------------------ +file name : perl-lwp-simple-6.15-pl526h470a237_4.tar.bz2 +name : perl-lwp-simple +version : 6.15 +build : pl526h470a237_4 +build number: 4 +size : 348 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-simple-6.15-pl526h470a237_4.tar.bz2 +md5 : 317554602ab7c16820944e7d75b36dd0 +timestamp : 2018-07-07 23:00:16 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.27.0a0 + - perl-encode-locale + + +perl-lwp-simple 6.39 pl5321h9ee0642_5 +------------------------------------- +file name : perl-lwp-simple-6.39-pl5321h9ee0642_5.tar.bz2 +name : perl-lwp-simple +version : 6.39 +build : pl5321h9ee0642_5 +build number: 5 +size : 6 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-lwp-simple-6.39-pl5321h9ee0642_5.tar.bz2 +md5 : 6094d97adf4a3db8736c337c3406a590 +timestamp : 2022-01-28 08:35:41 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-libwww-perl 6.39.* + + +perl-lwp-simple 6.67 pl5321hdfd78af_0 +------------------------------------- +file name : perl-lwp-simple-6.67-pl5321hdfd78af_0.tar.bz2 +name : perl-lwp-simple +version : 6.67 +build : pl5321hdfd78af_0 +build number: 0 +size : 7 KB +license : Perl +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-lwp-simple-6.67-pl5321hdfd78af_0.tar.bz2 +md5 : 7225adfef5c964b72ca1db26bba27d23 +timestamp : 2025-01-29 14:37:00 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-libwww-perl 6.67.* diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-math-cdf.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-math-cdf.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e346d3da0866f44a6b969693ccf09b3472c5f1cd --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-math-cdf.manual_bundle.txt @@ -0,0 +1,291 @@ +# Tool: perl-math-cdf +software_name: perl-math-cdf +tier: T1 +domain: t1_backfill_overall +downloads: 232641 +summary: Generate probabilities and quantiles from several statistical probability functions +description: Generate probabilities and quantiles from several statistical probability functions +dependencies: libgcc >=13, perl >=5.32.1,<5.33.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-math-cdf --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-math-cdf 0.1 1 +------------------- +file name : perl-math-cdf-0.1-1.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : 1 +build number: 1 +size : 64 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-1.tar.bz2 +md5 : 4e144ebacc2b0ff40c712b0f894be398 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-math-cdf 0.1 2 +------------------- +file name : perl-math-cdf-0.1-2.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : 2 +build number: 2 +size : 64 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-2.tar.bz2 +md5 : a520ba68bab9653baca9f802fcbac9a5 +dependencies: + - libgcc + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-math-cdf 0.1 3 +------------------- +file name : perl-math-cdf-0.1-3.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : 3 +build number: 3 +size : 64 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-3.tar.bz2 +md5 : 06a6b720091d72fc68088c1cdad51d54 +dependencies: + - libgcc + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-math-cdf 0.1 pl5.22.0_0 +---------------------------- +file name : perl-math-cdf-0.1-pl5.22.0_0.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : pl5.22.0_0 +build number: 0 +size : 63 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl5.22.0_0.tar.bz2 +md5 : e5c5066a7e34fa72640097bb26de55b9 +dependencies: + - perl 5.22.0* + + +perl-math-cdf 0.1 pl526h14c3975_5 +--------------------------------- +file name : perl-math-cdf-0.1-pl526h14c3975_5.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : pl526h14c3975_5 +build number: 5 +size : 69 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl526h14c3975_5.tar.bz2 +md5 : 0f96fd4f8528a673b2b7acf152745f39 +timestamp : 2019-04-22 22:03:35 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + + +perl-math-cdf 0.1 pl526h470a237_4 +--------------------------------- +file name : perl-math-cdf-0.1-pl526h470a237_4.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : pl526h470a237_4 +build number: 4 +size : 70 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl526h470a237_4.tar.bz2 +md5 : ee67e17ca0e2838d699b1105b4531bb3 +timestamp : 2018-07-07 07:22:42 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.27.0a0 + + +perl-math-cdf 0.1 pl5321h031d066_10 +----------------------------------- +file name : perl-math-cdf-0.1-pl5321h031d066_10.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : pl5321h031d066_10 +build number: 10 +size : 69 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl5321h031d066_10.tar.bz2 +md5 : c3ed5a7d9dd5551cd01bdd1b8ccbf673 +timestamp : 2024-11-04 19:17:49 UTC +dependencies: + - libgcc >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-math-cdf 0.1 pl5321h031d066_8 +---------------------------------- +file name : perl-math-cdf-0.1-pl5321h031d066_8.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : pl5321h031d066_8 +build number: 8 +size : 69 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl5321h031d066_8.tar.bz2 +md5 : a8ab5d20e22e03103a06bc16b132d9c3 +timestamp : 2023-05-15 00:03:34 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-math-cdf 0.1 pl5321h031d066_9 +---------------------------------- +file name : perl-math-cdf-0.1-pl5321h031d066_9.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : pl5321h031d066_9 +build number: 9 +size : 69 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl5321h031d066_9.tar.bz2 +md5 : 6c48e698ee97ff46bbb7d947bab7df3b +timestamp : 2023-05-16 06:55:55 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-math-cdf 0.1 pl5321h779adbc_6 +---------------------------------- +file name : perl-math-cdf-0.1-pl5321h779adbc_6.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : pl5321h779adbc_6 +build number: 6 +size : 69 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl5321h779adbc_6.tar.bz2 +md5 : ead148beedce6553965ff7d99f95da8d +timestamp : 2022-01-17 08:52:38 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-math-cdf 0.1 pl5321h7b50bb2_11 +----------------------------------- +file name : perl-math-cdf-0.1-pl5321h7b50bb2_11.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : pl5321h7b50bb2_11 +build number: 11 +size : 69 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl5321h7b50bb2_11.tar.bz2 +md5 : 94a822b01fe8663289b7a852120915b6 +timestamp : 2024-12-13 23:01:03 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-math-cdf 0.1 pl5321hec16e2b_7 +---------------------------------- +file name : perl-math-cdf-0.1-pl5321hec16e2b_7.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : pl5321hec16e2b_7 +build number: 7 +size : 69 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl5321hec16e2b_7.tar.bz2 +md5 : ee852db29ab49961cad4e7e0e3847380 +timestamp : 2022-02-21 22:45:29 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-math-cdf 0.1 pl5321hec16e2b_8 +---------------------------------- +file name : perl-math-cdf-0.1-pl5321hec16e2b_8.tar.bz2 +name : perl-math-cdf +version : 0.1 +build : pl5321hec16e2b_8 +build number: 8 +size : 70 KB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl5321hec16e2b_8.tar.bz2 +md5 : aad38da09ddd5edca0b96a4eec38a1ba +timestamp : 2023-05-11 17:10:13 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-math-round.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-math-round.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a40c5bffaa2f065b7c9b2f91853831154889508 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-math-round.manual_bundle.txt @@ -0,0 +1,128 @@ +# Tool: perl-math-round +software_name: perl-math-round +tier: T1 +domain: t1_backfill_overall +downloads: 129855 +summary: Perl extension for rounding numbers +description: Perl extension for rounding numbers +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-math-round --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-math-round 0.07 0 +---------------------- +file name : perl-math-round-0.07-0.tar.bz2 +name : perl-math-round +version : 0.07 +build : 0 +build number: 0 +size : 5 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-round-0.07-0.tar.bz2 +md5 : 5ebc786a400d3a29289b917fac5008cf +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-math-round 0.07 pl526_1 +---------------------------- +file name : perl-math-round-0.07-pl526_1.tar.bz2 +name : perl-math-round +version : 0.07 +build : pl526_1 +build number: 1 +size : 9 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-math-round-0.07-pl526_1.tar.bz2 +md5 : e83e315d32b7d9c06d276495482a7728 +timestamp : 2018-06-29 01:29:56 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-math-round 0.07 pl5321ha770c72_0 +------------------------------------- +file name : perl-math-round-0.07-pl5321ha770c72_0.tar.bz2 +name : perl-math-round +version : 0.07 +build : pl5321ha770c72_0 +build number: 0 +size : 18 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-math-round-0.07-pl5321ha770c72_0.tar.bz2 +md5 : 5d287f877cdb21b81d78aefd98b0e0db +timestamp : 2022-11-03 20:45:22 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-math-round 0.07 pl5321hdfd78af_2 +------------------------------------- +file name : perl-math-round-0.07-pl5321hdfd78af_2.tar.bz2 +name : perl-math-round +version : 0.07 +build : pl5321hdfd78af_2 +build number: 2 +size : 11 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-math-round-0.07-pl5321hdfd78af_2.tar.bz2 +md5 : 5a21a8b74912c3f089f31142f925ac4d +timestamp : 2022-01-20 08:53:07 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mime-lite.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mime-lite.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..460b648f74ddc9d76a31a86854c697ae2c29ea51 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mime-lite.manual_bundle.txt @@ -0,0 +1,120 @@ +# Tool: perl-mime-lite +software_name: perl-mime-lite +tier: T1 +domain: t1_backfill_overall +downloads: 189752 +summary: Handy-dandy MIME mailing class +description: Handy-dandy MIME mailing class +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-email-date-format, perl-mailtools, perl-mime-types +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-mime-lite --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-mime-lite 3.030 0 +---------------------- +file name : perl-mime-lite-3.030-0.tar.bz2 +name : perl-mime-lite +version : 3.030 +build : 0 +build number: 0 +size : 35 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mime-lite-3.030-0.tar.bz2 +md5 : c2143bdd35f101cb2897f6fe1fcc724b +dependencies: + - perl-email-date-format + - perl-mailtools + - perl-mime-types + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-mime-lite 3.030 pl526_1 +---------------------------- +file name : perl-mime-lite-3.030-pl526_1.tar.bz2 +name : perl-mime-lite +version : 3.030 +build : pl526_1 +build number: 1 +size : 51 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mime-lite-3.030-pl526_1.tar.bz2 +md5 : 4496ad7bf37b103f30e600e9d263e4b1 +timestamp : 2018-07-07 16:41:50 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-email-date-format + - perl-mailtools + - perl-mime-types + + +perl-mime-lite 3.030 pl5321hdfd78af_2 +------------------------------------- +file name : perl-mime-lite-3.030-pl5321hdfd78af_2.tar.bz2 +name : perl-mime-lite +version : 3.030 +build : pl5321hdfd78af_2 +build number: 2 +size : 54 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mime-lite-3.030-pl5321hdfd78af_2.tar.bz2 +md5 : f578b22e5e4f1beda527d667a190852a +timestamp : 2022-01-29 09:44:44 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-email-date-format + - perl-mailtools + - perl-mime-types diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mime-types.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mime-types.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a0ee97615f07b72c5385b8494805c62b20499c8 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mime-types.manual_bundle.txt @@ -0,0 +1,251 @@ +# Tool: perl-mime-types +software_name: perl-mime-types +tier: T1 +domain: t1_backfill_overall +downloads: 199648 +summary: Definition of MIME types +description: Definition of MIME types +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/MIME-Types +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/MIME-Types +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-mime-types --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-mime-types 2.12 0 +---------------------- +file name : perl-mime-types-2.12-0.tar.bz2 +name : perl-mime-types +version : 2.12 +build : 0 +build number: 0 +size : 41 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mime-types-2.12-0.tar.bz2 +md5 : f648c613d36568dca46c92694e16600e +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-mime-types 2.12 pl526_1 +---------------------------- +file name : perl-mime-types-2.12-pl526_1.tar.bz2 +name : perl-mime-types +version : 2.12 +build : pl526_1 +build number: 1 +size : 50 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mime-types-2.12-pl526_1.tar.bz2 +md5 : 0c4223efdf4a254a361edbad01389aa6 +timestamp : 2018-07-06 23:25:50 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-mime-types 2.17 pl526_0 +---------------------------- +file name : perl-mime-types-2.17-pl526_0.tar.bz2 +name : perl-mime-types +version : 2.17 +build : pl526_0 +build number: 0 +size : 56 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mime-types-2.17-pl526_0.tar.bz2 +md5 : a2b8a924ddd48c80098dcbc31f3fd789 +timestamp : 2018-11-11 05:52:37 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-mime-types 2.17 pl5321hdfd78af_1 +------------------------------------- +file name : perl-mime-types-2.17-pl5321hdfd78af_1.tar.bz2 +name : perl-mime-types +version : 2.17 +build : pl5321hdfd78af_1 +build number: 1 +size : 58 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mime-types-2.17-pl5321hdfd78af_1.tar.bz2 +md5 : f733e6cfaf3ec062a21878d4d1fd4883 +timestamp : 2022-01-17 11:48:57 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-mime-types 2.22 pl5321hdfd78af_0 +------------------------------------- +file name : perl-mime-types-2.22-pl5321hdfd78af_0.tar.bz2 +name : perl-mime-types +version : 2.22 +build : pl5321hdfd78af_0 +build number: 0 +size : 61 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mime-types-2.22-pl5321hdfd78af_0.tar.bz2 +md5 : f8fed58e32d8e9e05e5103335635cc29 +timestamp : 2022-02-09 22:02:37 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-mime-types 2.23 pl5321hdfd78af_0 +------------------------------------- +file name : perl-mime-types-2.23-pl5321hdfd78af_0.tar.bz2 +name : perl-mime-types +version : 2.23 +build : pl5321hdfd78af_0 +build number: 0 +size : 62 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mime-types-2.23-pl5321hdfd78af_0.tar.bz2 +md5 : 8f70c0fa83f9e17527522956c3d0d1ca +timestamp : 2022-12-22 17:29:56 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-mime-types 2.24 pl5321hdfd78af_0 +------------------------------------- +file name : perl-mime-types-2.24-pl5321hdfd78af_0.tar.bz2 +name : perl-mime-types +version : 2.24 +build : pl5321hdfd78af_0 +build number: 0 +size : 62 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mime-types-2.24-pl5321hdfd78af_0.tar.bz2 +md5 : df2bbe852961a4ba751532a28bc06ad8 +timestamp : 2022-12-28 13:24:27 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-mime-types 2.27 pl5321hdfd78af_0 +------------------------------------- +file name : perl-mime-types-2.27-pl5321hdfd78af_0.tar.bz2 +name : perl-mime-types +version : 2.27 +build : pl5321hdfd78af_0 +build number: 0 +size : 64 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mime-types-2.27-pl5321hdfd78af_0.tar.bz2 +md5 : 63f39e9d9e534942bcb1501a1b876757 +timestamp : 2025-02-07 12:57:52 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-mime-types 2.28 pl5321hdfd78af_0 +------------------------------------- +file name : perl-mime-types-2.28-pl5321hdfd78af_0.tar.bz2 +name : perl-mime-types +version : 2.28 +build : pl5321hdfd78af_0 +build number: 0 +size : 65 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mime-types-2.28-pl5321hdfd78af_0.tar.bz2 +md5 : 047c4cb267e57b8e4be3e45fcd7f25b3 +timestamp : 2025-04-19 10:18:53 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-mime-types 2.29 pl5321hdfd78af_0 +------------------------------------- +file name : perl-mime-types-2.29-pl5321hdfd78af_0.conda +name : perl-mime-types +version : 2.29 +build : pl5321hdfd78af_0 +build number: 0 +size : 62 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mime-types-2.29-pl5321hdfd78af_0.conda +md5 : e7472a6be120065f3065440f3a3770e4 +timestamp : 2025-09-15 12:16:06 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-mime-types 2.30 pl5321hdfd78af_0 +------------------------------------- +file name : perl-mime-types-2.30-pl5321hdfd78af_0.conda +name : perl-mime-types +version : 2.30 +build : pl5321hdfd78af_0 +build number: 0 +size : 62 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mime-types-2.30-pl5321hdfd78af_0.conda +md5 : 05107f86c240d3f2e18172b91a693d9c +timestamp : 2025-12-08 20:19:05 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mldbm.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mldbm.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..30df605d53951c263c7e6c00f0605ad277b14789 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mldbm.manual_bundle.txt @@ -0,0 +1,111 @@ +# Tool: perl-mldbm +software_name: perl-mldbm +tier: T1 +domain: t1_backfill_overall +downloads: 186095 +summary: store multi-level Perl hash structure in single level tied hash +description: store multi-level Perl hash structure in single level tied hash +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-mldbm --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-mldbm 2.05 0 +----------------- +file name : perl-mldbm-2.05-0.tar.bz2 +name : perl-mldbm +version : 2.05 +build : 0 +build number: 0 +size : 8 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mldbm-2.05-0.tar.bz2 +md5 : e70835075dba947312e8ddb779e5ba47 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-mldbm 2.05 pl526_1 +----------------------- +file name : perl-mldbm-2.05-pl526_1.tar.bz2 +name : perl-mldbm +version : 2.05 +build : pl526_1 +build number: 1 +size : 15 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mldbm-2.05-pl526_1.tar.bz2 +md5 : 57b7a95f18db31d9a14be8821d78fb1c +timestamp : 2018-07-19 03:36:43 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-mldbm 2.05 pl5321hdfd78af_2 +-------------------------------- +file name : perl-mldbm-2.05-pl5321hdfd78af_2.tar.bz2 +name : perl-mldbm +version : 2.05 +build : pl5321hdfd78af_2 +build number: 2 +size : 17 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mldbm-2.05-pl5321hdfd78af_2.tar.bz2 +md5 : f2a1441fb07bdd9e99834d210827e771 +timestamp : 2022-01-24 09:31:54 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-build.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-build.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab8db162bd22bcd03a775f2f0021008c2ace0145 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-build.manual_bundle.txt @@ -0,0 +1,355 @@ +# Tool: perl-module-build +software_name: perl-module-build +tier: T1 +domain: t1_backfill_overall +downloads: 145261 +summary: Build and install Perl modules +description: Build and install Perl modules +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-cpan-meta, perl-data-dumper, perl-extutils-cbuilder, perl-extutils-manifest, perl-extutils-parsexs, perl-file-path, perl-getopt-long, perl-module-metadata, perl-perl-ostype, perl-text-abbrev, perl-text-parsewords, perl-version +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Module-Build +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Module-Build +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-module-build --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-module-build 0.4214 0 +-------------------------- +file name : perl-module-build-0.4214-0.tar.bz2 +name : perl-module-build +version : 0.4214 +build : 0 +build number: 0 +size : 92 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-build-0.4214-0.tar.bz2 +md5 : d1985ead8048f1bb26c3ac78c573b437 +dependencies: + - perl >=5.22.0 + + +perl-module-build 0.4214 1 +-------------------------- +file name : perl-module-build-0.4214-1.tar.bz2 +name : perl-module-build +version : 0.4214 +build : 1 +build number: 1 +size : 92 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-build-0.4214-1.tar.bz2 +md5 : 6a8f9f78ffab5dcf1843fb55bceb56c3 +dependencies: + - perl-threaded >=5.22.0 + - perl >=5.22.0,<5.23.0 + + +perl-module-build 0.4214 2 +-------------------------- +file name : perl-module-build-0.4214-2.tar.bz2 +name : perl-module-build +version : 0.4214 +build : 2 +build number: 2 +size : 92 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-build-0.4214-2.tar.bz2 +md5 : bfcdfae93a3645da7d8be90c581b43ea +dependencies: + - libgcc + - perl-threaded >=5.22.0 + - perl >=5.22.0,<5.23.0 + + +perl-module-build 0.4214 pl5.22.0_3 +----------------------------------- +file name : perl-module-build-0.4214-pl5.22.0_3.tar.bz2 +name : perl-module-build +version : 0.4214 +build : pl5.22.0_3 +build number: 3 +size : 121 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-build-0.4214-pl5.22.0_3.tar.bz2 +md5 : cef23e604240038d196f739875a4c2d4 +dependencies: + - libgcc + - perl 5.22.0* + + +perl-module-build 0.4224 pl5.22.0_0 +----------------------------------- +file name : perl-module-build-0.4224-pl5.22.0_0.tar.bz2 +name : perl-module-build +version : 0.4224 +build : pl5.22.0_0 +build number: 0 +size : 124 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-build-0.4224-pl5.22.0_0.tar.bz2 +md5 : c76d31823fa38eae167e49090e27eaee +dependencies: + - libgcc + - perl 5.22.0* + + +perl-module-build 0.4224 pl526_2 +-------------------------------- +file name : perl-module-build-0.4224-pl526_2.tar.bz2 +name : perl-module-build +version : 0.4224 +build : pl526_2 +build number: 2 +size : 126 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-build-0.4224-pl526_2.tar.bz2 +md5 : 86e41c40d5dc0c5757be97263b79c359 +timestamp : 2018-07-17 04:54:34 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-cpan-meta + - perl-data-dumper + - perl-extutils-cbuilder + - perl-extutils-manifest + - perl-extutils-parsexs + - perl-file-path + - perl-getopt-long + - perl-module-metadata + - perl-perl-ostype + - perl-text-abbrev + - perl-text-parsewords + - perl-version + + +perl-module-build 0.4224 pl526_3 +-------------------------------- +file name : perl-module-build-0.4224-pl526_3.tar.bz2 +name : perl-module-build +version : 0.4224 +build : pl526_3 +build number: 3 +size : 126 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-build-0.4224-pl526_3.tar.bz2 +md5 : 3d0ec58cb31ae53380e0cfe5dd68d3b6 +timestamp : 2018-08-06 21:51:01 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-cpan-meta + - perl-data-dumper + - perl-extutils-cbuilder + - perl-extutils-manifest + - perl-extutils-parsexs + - perl-file-path + - perl-getopt-long + - perl-module-metadata + - perl-perl-ostype + - perl-text-abbrev + - perl-text-parsewords + - perl-version + + +perl-module-build 0.4224 pl526h470a237_1 +---------------------------------------- +file name : perl-module-build-0.4224-pl526h470a237_1.tar.bz2 +name : perl-module-build +version : 0.4224 +build : pl526h470a237_1 +build number: 1 +size : 125 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-build-0.4224-pl526h470a237_1.tar.bz2 +md5 : 077e50dc90ad6a347ed613a94fa57e08 +timestamp : 2018-07-07 05:55:19 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.27.0a0 + + +perl-module-build 0.4224 pl5321hdfd78af_4 +----------------------------------------- +file name : perl-module-build-0.4224-pl5321hdfd78af_4.tar.bz2 +name : perl-module-build +version : 0.4224 +build : pl5321hdfd78af_4 +build number: 4 +size : 129 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-module-build-0.4224-pl5321hdfd78af_4.tar.bz2 +md5 : cb965acf0be0e905ca8af4e5b88ceab0 +timestamp : 2022-01-23 22:47:19 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-cpan-meta + - perl-data-dumper + - perl-extutils-cbuilder + - perl-extutils-manifest + - perl-extutils-parsexs + - perl-file-path + - perl-getopt-long + - perl-module-metadata + - perl-perl-ostype + - perl-text-abbrev + - perl-text-parsewords + - perl-version + + +perl-module-build 0.4231 pl5321ha770c72_0 +----------------------------------------- +file name : perl-module-build-0.4231-pl5321ha770c72_0.conda +name : perl-module-build +version : 0.4231 +build : pl5321ha770c72_0 +build number: 0 +size : 131 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-module-build-0.4231-pl5321ha770c72_0.conda +md5 : dd04c27baf4985045f35f9e6d56e8b26 +timestamp : 2022-11-24 09:32:24 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-inc-latest 0.500.* + + +perl-module-build 0.4231 pl5321hdfd78af_0 +----------------------------------------- +file name : perl-module-build-0.4231-pl5321hdfd78af_0.tar.bz2 +name : perl-module-build +version : 0.4231 +build : pl5321hdfd78af_0 +build number: 0 +size : 128 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-module-build-0.4231-pl5321hdfd78af_0.tar.bz2 +md5 : 3991991c2b317f1110468d34ecf95d85 +timestamp : 2022-02-14 08:52:59 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-cpan-meta + - perl-data-dumper + - perl-extutils-cbuilder + - perl-extutils-manifest + - perl-extutils-parsexs + - perl-file-path + - perl-getopt-long + - perl-module-metadata + - perl-perl-ostype + - perl-text-abbrev + - perl-text-parsewords + - perl-version + + +perl-module-build 0.4232 pl5321ha770c72_0 +----------------------------------------- +file name : perl-module-build-0.4232-pl5321ha770c72_0.conda +name : perl-module-build +version : 0.4232 +build : pl5321ha770c72_0 +build number: 0 +size : 133 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-module-build-0.4232-pl5321ha770c72_0.conda +md5 : 2382d3e326cbd2ddd4b2a4095e0a5d44 +timestamp : 2022-12-09 07:13:33 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-inc-latest 0.500.* + + +perl-module-build 0.4234 pl5321ha770c72_0 +----------------------------------------- +file name : perl-module-build-0.4234-pl5321ha770c72_0.conda +name : perl-module-build +version : 0.4234 +build : pl5321ha770c72_0 +build number: 0 +size : 134 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-module-build-0.4234-pl5321ha770c72_0.conda +md5 : af01774fb685212da8e42be8f4a136cc +timestamp : 2023-04-28 10:19:09 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-inc-latest 0.500.* + + +perl-module-build 0.4234 pl5321ha770c72_1 +----------------------------------------- +file name : perl-module-build-0.4234-pl5321ha770c72_1.conda +name : perl-module-build +version : 0.4234 +build : pl5321ha770c72_1 +build number: 1 +size : 134 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-module-build-0.4234-pl5321ha770c72_1.conda +md5 : 358d42e9f08dd917b649089526e2ae1f +timestamp : 2025-01-30 12:43:55 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-inc-latest 0.500.* diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-implementation.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-implementation.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e14b38eb23f8d3d9198c39372ecb14a4a2f5292 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-implementation.manual_bundle.txt @@ -0,0 +1,162 @@ +# Tool: perl-module-implementation +software_name: perl-module-implementation +tier: T1 +domain: t1_backfill_overall +downloads: 346904 +summary: Loads one of several alternate underlying implementations for a module +description: Loads one of several alternate underlying implementations for a module +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-carp, perl-module-runtime, perl-try-tiny +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-module-implementation --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-module-implementation 0.09 0 +--------------------------------- +file name : perl-module-implementation-0.09-0.tar.bz2 +name : perl-module-implementation +version : 0.09 +build : 0 +build number: 0 +size : 4 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-implementation-0.09-0.tar.bz2 +md5 : a5fe351f0033ea470db1ef331f70bb6d +dependencies: + - perl-module-runtime + - perl-threaded + - perl-try-tiny + - perl >=5.22.0,<5.23.0 + + +perl-module-implementation 0.09 pl526_2 +--------------------------------------- +file name : perl-module-implementation-0.09-pl526_2.tar.bz2 +name : perl-module-implementation +version : 0.09 +build : pl526_2 +build number: 2 +size : 9 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-implementation-0.09-pl526_2.tar.bz2 +md5 : 97f9a0c37978d25299f4f1434c7a12e9 +timestamp : 2018-07-17 22:50:57 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-carp + - perl-module-runtime + - perl-try-tiny + + +perl-module-implementation 0.09 pl5321ha770c72_0 +------------------------------------------------ +file name : perl-module-implementation-0.09-pl5321ha770c72_0.conda +name : perl-module-implementation +version : 0.09 +build : pl5321ha770c72_0 +build number: 0 +size : 14 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-module-implementation-0.09-pl5321ha770c72_0.conda +md5 : 643428b6d6040d6030e20bae64d652eb +timestamp : 2022-12-12 15:22:35 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-module-runtime 0.016.* + - perl-test-fatal 0.016.* + - perl-try-tiny 0.31.* + + +perl-module-implementation 0.09 pl5321ha770c72_1 +------------------------------------------------ +file name : perl-module-implementation-0.09-pl5321ha770c72_1.conda +name : perl-module-implementation +version : 0.09 +build : pl5321ha770c72_1 +build number: 1 +size : 14 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-module-implementation-0.09-pl5321ha770c72_1.conda +md5 : 1fc9b09c7194da078842ac3f8502ed57 +timestamp : 2025-02-28 01:30:59 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-module-runtime 0.016.* + - perl-test-fatal 0.016.* + - perl-try-tiny 0.31.* + + +perl-module-implementation 0.09 pl5321hdfd78af_3 +------------------------------------------------ +file name : perl-module-implementation-0.09-pl5321hdfd78af_3.tar.bz2 +name : perl-module-implementation +version : 0.09 +build : pl5321hdfd78af_3 +build number: 3 +size : 11 KB +license : artistic_2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-module-implementation-0.09-pl5321hdfd78af_3.tar.bz2 +md5 : 637e4d02c336d89f356090017ee86ba9 +timestamp : 2022-01-24 11:58:05 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-module-runtime + - perl-try-tiny diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-load-conditional.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-load-conditional.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa85cffcc13ba773122e133efa80e0ad4e498ffd --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-load-conditional.manual_bundle.txt @@ -0,0 +1,186 @@ +# Tool: perl-module-load-conditional +software_name: perl-module-load-conditional +tier: T1 +domain: t1_backfill_overall +downloads: 157625 +summary: Looking up module information / loading at runtime +description: Looking up module information / loading at runtime +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-locale-maketext-simple, perl-module-corelist, perl-module-load, perl-module-metadata >=1.000005, perl-params-check, perl-version +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Module::Load::Conditional +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Module::Load::Conditional +Module::Load::Conditional - Looking up module information / loading at runtime - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Module-Load-Conditional Module version: 0.74 21 Aug 2020 08:09:10 UTC License: perl_5 Code Download ( 13.35KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (1) How to Contribute Quality Testers ( 3067 / 0 / 0 ) Testers (Magpie) Kwalitee 68.90% Coverage Bus factor: 5 Activity 24 month 6 Dependencies Locale::Maketext::Simple Module::CoreList Module::Load Module::Metadata Params::Check and 1 more version and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 0.74 (BINGOS on 2020-08-21) 0.72 (BINGOS on 2020-06-25) 0.70 (BINGOS on 2019-11-10) 0.68 (BINGOS on 2016-07-29) 0.66 (BINGOS on 2016-07-27) 0.64 (BINGOS on 2015-01-17) 0.30 (KANE on 2009-01-19) 0.28 (KANE on 2008-12-17) 0.26 (KANE on 2008-02-29) 0.24 (KANE on 2008-01-02) 0.22 (KANE on 2007-10-15) 0.20 (KANE on 2007-10-03) 0.18 (KANE on 2007-09-15) 0.16 (KANE on 2007-01-25) 0.14 (KANE on 2007-01-03) 0.12 (KANE on 2006-08-13) 0.10 (KANE on 2006-08-01) 0.08 (KANE on 2005-01-14) 0.07 (KANE on 2005-01-13) 0.06 (KANE on 2004-12-03) 0.05 (KANE on 2004-05-22) 0.04 (KANE on 2003-10-05) 0.03 (KANE on 2003-05-31) 0.02 (KANE on 2003-05-10) 0.62 (BINGOS on 2014-01-24) 0.60 (BINGOS on 2014-01-16) 0.58 (BINGOS on 2013-09-01) 0.56 (BINGOS on 2013-08-29) 0.54 (BINGOS on 2012-08-12) 0.52 (BINGOS on 2012-07-29) 0.50 (BINGOS on 2012-04-27) 0.48 (BINGOS on 2012-03-15) 0.46 (BINGOS on 2011-09-07) 0.44 (BINGOS on 2011-02-09) 0.42 (BINGOS on 2011-02-09) 0.40 (BINGOS on 2011-01-07) 0.38 (BINGOS on 2010-04-23) 0.36 (BINGOS on 2010-02-09) 0.34 (BINGOS on 2009-10-29) 0.32 (BINGOS on 2009-10-23) 0.31_01 DEV (BINGOS on 2009-10-23) Diff with version 0.74 (BINGOS on 2020-08-21) 0.72 (BINGOS on 2020-06-25) 0.70 (BINGOS on 2019-11-10) 0.68 (BINGOS on 2016-07-29) 0.66 (BINGOS on 2016-07-27) 0.64 (BINGOS on 2015-01-17) 0.30 (KANE on 2009-01-19) 0.28 (KANE on 2008-12-17) 0.26 (KANE on 2008-02-29) 0.24 (KANE on 2008-01-02) 0.22 (KANE on 2007-10-15) 0.20 (KANE on 2007-10-03) 0.18 (KANE on 2007-09-15) 0.16 (KANE on 2007-01-25) 0.14 (KANE on 2007-01-03) 0.12 (KANE on 2006-08-13) 0.10 (KANE on 2006-08-01) 0.08 (KANE on 2005-01-14) 0.07 (KANE on 2005-01-13) 0.06 (KANE on 2004-12-03) 0.05 (KANE on 2004-05-22) 0.04 (KANE on 2003-10-05) 0.03 (KANE on 2003-05-31) 0.02 (KANE on 2003-05-10) 0.62 (BINGOS on 2014-01-24) 0.60 (BINGOS on 2014-01-16) 0.58 (BINGOS on 2013-09-01) 0.56 (BINGOS on 2013-08-29) 0.54 (BINGOS on 2012-08-12) 0.52 (BINGOS on 2012-07-29) 0.50 (BINGOS on 2012-04-27) 0.48 (BINGOS on 2012-03-15) 0.46 (BINGOS on 2011-09-07) 0.44 (BINGOS on 2011-02-09) 0.42 (BINGOS on 2011-02-09) 0.40 (BINGOS on 2011-01-07) 0.38 (BINGOS on 2010-04-23) 0.36 (BINGOS on 2010-02-09) 0.34 (BINGOS on 2009-10-29) 0.32 (BINGOS on 2009-10-23) 0.31_01 DEV (BINGOS on 2009-10-23) Permalinks This version Latest version ++ed by: 3 PAUSE users 5 non-PAUSE users Authors: Jos Boumans Released by: Chris Williams Maintainers: KANE owner BINGOS Contributors: Jos Boumans <kane[at]cpan.org> Chris Williams  /  0.74 (BINGOS on 2020-08-21) 0.72 (BINGOS on 2020-06-25) 0.70 (BINGOS on 2019-11-10) 0.68 (BINGOS on 2016-07-29) 0.66 (BINGOS on 2016-07-27) 0.64 (BINGOS on 2015-01-17) 0.30 (KANE on 2009-01-19) 0.28 (KANE on 2008-12-17) 0.26 (KANE on 2008-02-29) 0.24 (KANE on 2008-01-02) 0.22 (KANE on 2007-10-15) 0.20 (KANE on 2007-10-03) 0.18 (KANE on 2007-09-15) 0.16 (KANE on 2007-01-25) 0.14 (KANE on 2007-01-03) 0.12 (KANE on 2006-08-13) 0.10 (KANE on 2006-08-01) 0.08 (KANE on 2005-01-14) 0.07 (KANE on 2005-01-13) 0.06 (KANE on 2004-12-03) 0.05 (KANE on 2004-05-22) 0.04 (KANE on 2003-10-05) 0.03 (KANE on 2003-05-31) 0.02 (KANE on 2003-05-10) 0.62 (BINGOS on 2014-01-24) 0.60 (BINGOS on 2014-01-16) 0.58 (BINGOS on 2013-09-01) 0.56 (BINGOS on 2013-08-29) 0.54 (BINGOS on 2012-08-12) 0.52 (BINGOS on 2012-07-29) 0.50 (BINGOS on 2012-04-27) 0.48 (BINGOS on 2012-03-15) 0.46 (BINGOS on 2011-09-07) 0.44 (BINGOS on 2011-02-09) 0.42 (BINGOS on 2011-02-09) 0.40 (BINGOS on 2011-01-07) 0.38 (BINGOS on 2010-04-23) 0.36 (BINGOS on 2010-02-09) 0.34 (BINGOS on 2009-10-29) 0.32 (BINGOS on 2009-10-23) 0.31_01 DEV (BINGOS on 2009-10-23) Module-Load-Conditional-0.74 8 ++ 8 ++ / Module::Load::Conditional Contents NAME SYNOPSIS DESCRIPTION Methods $href = check_install( module => NAME [, version => VERSION, verbose => BOOL ] ); $bool = can_load( modules => { NAME => VERSION [,NAME => VERSION] }, [verbose => BOOL, nocache => BOOL, autoload => BOOL] ) @list = requires( MODULE ); Global Variables $Module::Load::Conditional::VERBOSE $Module::Load::Conditional::FIND_VERSION $Module::Load::Conditional::CHECK_INC_HASH $Module::Load::Conditional::FORCE_SAFE_INC $Module::Load::Conditional::CACHE $Module::Load::Conditional::ERROR $Module::Load::Conditional::DEPRECATED See Also BUG REPORTS AUTHOR COPYRIGHT NAME Module::Load::Conditional - Looking up module information / loading at runtime SYNOPSIS use Module::Load::Conditional qw[can_load check_install requires]; my $use_list = { CPANPLUS => 0.05, LWP => 5.60, 'Test::More' => undef, }; print can_load( modules => $use_list ) ? 'all modules loaded successfully' : 'failed to load required modules'; my $rv = check_install( module => 'LWP', version => 5.60 ) or print 'LWP is not installed!'; print 'LWP up to date' if $rv->{uptodate}; print "LWP version is $rv->{version}\n"; print "LWP is installed as file $rv->{file}\n"; print "LWP requires the following modules to be installed:\n"; print join "\n", requires('LWP'); ### allow M::L::C to peek in your %INC rather than just ### scanning @INC $Module::Load::Conditional::CHECK_INC_HASH = 1; ### reset the 'can_load' cache undef $Module::Load::Conditional::CACHE; ### don't have Module::Load::Conditional issue warnings -- ### default is '1' $Module::Load::Conditional::VERBOSE = 0; ### The last error that happened during a call to 'can_load' my $err = $Module::Load::Conditional::ERROR; DESCRIPTION Module::Load::Conditional provides simple ways to query and possibly load any of the modules you have installed on your system during runtime. It is able to load multiple modules at once or none at all if one of them was not able to load. It also takes care of any error checking and so forth. Methods $href = check_install( module => NAME [, version => VERSION, verbose => BOOL ] ); check_install allows you to verify if a certain module is installed or not. You may call it with the following arguments: module The name of the module you wish to verify -- this is a required key version The version this module needs to be -- this is optional verbose Whether or not to be verbose about what it is doing -- it will default to $Module::Load::Conditional::VERBOSE It will return undef if it was not able to find where the module was installed, or a hash reference with the following keys if it was able to find the file: file Full path to the file that contains the module dir Directory, or more exact the @INC entry, where the module was loaded from. version The version number of the installed module - this will be undef if the module had no (or unparsable) version number, or if the variable $Module::Load::Conditional::FIND_VERSION was set to true. (See the GLOBAL VARIABLES section below for details) uptodate A boolean value indicating whether or not the module was found to be at least the version you specified. If you did not specify a version, uptodate will always be true if the module was found. If no parsable version was found in the module, uptodate will also be true, since check_install had no way to verify clearly. See also $Module::Load::Conditional::DEPRECATED , which affects the outcome of this value. $bool = can_load( modules => { NAME => VERSION [,NAME => VERSION] }, [verbose => BOOL, nocache => BOOL, autoload => BOOL] ) can_load will take a list of modules, optionally with version numbers and determine if it is able to load them. If it can load *ALL* of them, it will. If one or more are unloadable, none will be loaded. This is particularly useful if you have More Than One Way (tm) to solve a problem in a program, and only wish to continue down a path if all modules could be loaded, and not load them if they couldn't. This function uses the load function or the autoload_remote function from Module::Load under the hood. can_load takes the following arguments: modules This is a hashref of module/version pairs. The version indicates the minimum version to load. If no version is provided, any version is assumed to be good enough. verbose This controls whether warnings should be printed if a module failed to load. The default is to use the value of $Module::Load::Conditional::VERBOSE. nocache can_load keeps its results in a cache, so it will not load the same module twice, nor will it attempt to load a module that has already failed to load before. By default, can_load will check its cache, but you can override that by setting nocache to true. autoload This controls whether imports the functions of a loaded modules to the caller package. The default is no importing any functions. See the autoload function and the autoload_remote function from Module::Load for details. @list = requires( MODULE ); requires can tell you what other modules a particular module requires. This is particularly useful when you're intending to write a module for public release and are listing its prerequisites. requires takes but one argument: the name of a module. It will then first check if it can actually load this module, and return undef if it can't. Otherwise, it will return a list of modules and pragmas that would have been loaded on the module's behalf. Note: The list require returns has originated from your current perl and your current install. Global Variables The behaviour of Module::Load::Conditional can be altered by changing the following global variables: $Module::Load::Conditional::VERBOSE This controls whether Module::Load::Conditional will issue warnings and explanations as to why certain things may have failed. If you set it to 0, Module::Load::Conditional will not output any warnings. The default is 0; $Module::Load::Conditional::FIND_VERSION This controls whether Module::Load::Conditional will try to parse (and eval) the version from the module you're trying to load. If you don't wish to do this, set this variable to false . Understand then that version comparisons are not possible, and Module::Load::Conditional can not tell you what module version you have installed. This may be desirable from a security or performance point of view. Note that $FIND_VERSION code runs safely under taint mode . The default is 1; $Module::Load::Conditional::CHECK_INC_HASH This controls whether Module::Load::Conditional checks your %INC hash to see if a module is available. By default, only @INC is scanned to see if a module is physically on your filesystem, or available via an @INC-hook . Setting this variable to true will trust any entries in %INC and return them for you. The default is 0; $Module::Load::Conditional::FORCE_SAFE_INC This controls whether Module::Load::Conditional sanitises @INC by removing " . ". The current default setting is 0 , but this may change in a future release. $Module::Load::Conditional::CACHE This holds the cache of the can_load function. If you explicitly want to remove the current cache, you can set this variable to undef $Module::Load::Conditional::ERROR This holds a string of the last error that happened during a call to can_load . It is useful to inspect this when can_load returns undef . $Module::Load::Conditional::DEPRECATED This controls whether Module::Load::Conditional checks if a dual-life core module has been deprecated. If this is set to true check_install will return false to uptodate , if a dual-life module is found to be loaded from $Config{privlibexp} The default is 0; See Also Module::Load BUG REPORTS Please report bugs or other issues to <bug-module-load-conditional@rt.cpan.org>. AUTHOR This module by Jos Boumans <kane@cpan.org>. COPYRIGHT This library is free software; you may redistribute and/or modify it under the same terms as Perl itself. Module Install Instructions To install Module::Load::Conditional, copy and paste the appropriate command in to your terminal. cpanm cpanm Module::Load::Conditional CPAN shell perl -MCPAN -e shell install Module::Load::Conditional For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-module-load-conditional --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-module-load-conditional 0.62 pl5.22.0_0 +-------------------------------------------- +file name : perl-module-load-conditional-0.62-pl5.22.0_0.tar.bz2 +name : perl-module-load-conditional +version : 0.62 +build : pl5.22.0_0 +build number: 0 +size : 2 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-load-conditional-0.62-pl5.22.0_0.tar.bz2 +md5 : 57b512cf09698e28228c9ca026ce3a48 +dependencies: + - perl 5.22.0* + + +perl-module-load-conditional 0.62 pl526_1 +----------------------------------------- +file name : perl-module-load-conditional-0.62-pl526_1.tar.bz2 +name : perl-module-load-conditional +version : 0.62 +build : pl526_1 +build number: 1 +size : 3 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-load-conditional-0.62-pl526_1.tar.bz2 +md5 : a8949b904ac48efd2c01d0d9f788d8a2 +timestamp : 2018-07-08 13:34:31 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-module-load-conditional 0.68 0 +----------------------------------- +file name : perl-module-load-conditional-0.68-0.tar.bz2 +name : perl-module-load-conditional +version : 0.68 +build : 0 +build number: 0 +size : 10 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-load-conditional-0.68-0.tar.bz2 +md5 : 389aafdf77c72ddc93f6456b87e3f416 +dependencies: + - perl >=5.22,<6.0 + - perl-locale-maketext-simple + - perl-module-corelist + - perl-module-load + - perl-module-metadata >=1.000005 + - perl-params-check + + +perl-module-load-conditional 0.68 pl522_1 +----------------------------------------- +file name : perl-module-load-conditional-0.68-pl522_1.tar.bz2 +name : perl-module-load-conditional +version : 0.68 +build : pl522_1 +build number: 1 +size : 10 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-load-conditional-0.68-pl522_1.tar.bz2 +md5 : 83f635a657eefbf682b31735a3f22730 +timestamp : 2018-07-08 13:31:27 UTC +dependencies: + - perl >=5.22.0.1,<5.23.0a0 + - perl-locale-maketext-simple + - perl-module-corelist + - perl-module-load + - perl-module-metadata >=1.000005 + - perl-params-check + + +perl-module-load-conditional 0.68 pl526_2 +----------------------------------------- +file name : perl-module-load-conditional-0.68-pl526_2.tar.bz2 +name : perl-module-load-conditional +version : 0.68 +build : pl526_2 +build number: 2 +size : 10 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-load-conditional-0.68-pl526_2.tar.bz2 +md5 : 7e3d417a0c4d52b688a6a8e3a36bc341 +timestamp : 2018-07-15 04:46:33 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-locale-maketext-simple + - perl-module-corelist + - perl-module-load + - perl-module-metadata >=1.000005 + - perl-params-check + - perl-version + + +perl-module-load-conditional 0.68 pl5321hdfd78af_3 +-------------------------------------------------- +file name : perl-module-load-conditional-0.68-pl5321hdfd78af_3.tar.bz2 +name : perl-module-load-conditional +version : 0.68 +build : pl5321hdfd78af_3 +build number: 3 +size : 12 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-module-load-conditional-0.68-pl5321hdfd78af_3.tar.bz2 +md5 : 62958e9c2abac17674a8fc7234422e89 +timestamp : 2022-01-20 10:05:37 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-locale-maketext-simple + - perl-module-corelist + - perl-module-load + - perl-module-metadata >=1.000005 + - perl-params-check + - perl-version diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-runtime-conflicts.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-runtime-conflicts.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2e0b51620161351e352e2cd0c662acf3738079c8 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-module-runtime-conflicts.manual_bundle.txt @@ -0,0 +1,80 @@ +# Tool: perl-module-runtime-conflicts +software_name: perl-module-runtime-conflicts +tier: T1 +domain: t1_backfill_overall +downloads: 241230 +summary: Provide information on conflicts for Module::Runtime +description: Provide information on conflicts for Module::Runtime +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-dist-checkconflicts, perl-module-runtime +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/karenetheridge/Module-Runtime-Conflicts +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/karenetheridge/Module-Runtime-Conflicts +GitHub - karenetheridge/Module-Runtime-Conflicts: Provide information on conflicts for Module::Runtime · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} karenetheridge / Module-Runtime-Conflicts Public Notifications You must be signed in to change notification settings Fork 0 Star 0 Code Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Pull requests Actions Projects Wiki Security and quality Insights karenetheridge/Module-Runtime-Conflicts master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 26 Commits 26 Commits lib/ Module/ Runtime lib/ Module/ Runtime t t .gitignore .gitignore .mailmap .mailmap .travis.yml .travis.yml CONTRIBUTING CONTRIBUTING Changes Changes INSTALL INSTALL LICENCE LICENCE README.pod README.pod dist.ini dist.ini View all files Repository files navigation README Contributing License NAME Module::Runtime::Conflicts - Provide information on conflicts for Module::Runtime VERSION version 0.003 SYNOPSIS `moose-outdated` or use Module::Runtime::Conflicts; Module::Runtime::Conflicts->check_conflicts; DESCRIPTION This module provides conflicts checking for Module::Runtime , which had a recent release that broke some versions of Moose . It is called from Moose::Conflicts and moose-outdated . SEE ALSO Dist::CheckConflicts Moose::Conflicts Dist::Zilla::Plugin::Breaks Dist::Zilla::Plugin::Test::CheckBreaks SUPPORT Bugs may be submitted through the RT bug tracker (or bug-Module-Runtime-Conflicts@rt.cpan.org ). There is also a mailing list available for users of this distribution, at http://lists.perl.org/list/cpan-workers.html . There is also an irc channel available for users of this distribution, at #toolchain on irc.perl.org . I am also usually active on irc, as 'ether' at irc.perl.org . AUTHOR Karen Etheridge <ether@cpan.org> COPYRIGHT AND LICENCE This software is copyright (c) 2014 by Karen Etheridge. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. About Provide information on conflicts for Module::Runtime metacpan.org/release/Module-Runtime-Conflicts/ Resources Readme License View license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 0 stars Watchers 2 watching Forks 0 forks Report repository Releases 3 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-module-runtime-conflicts --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-module-runtime-conflicts 0.003 pl526_0 +------------------------------------------- +file name : perl-module-runtime-conflicts-0.003-pl526_0.tar.bz2 +name : perl-module-runtime-conflicts +version : 0.003 +build : pl526_0 +build number: 0 +size : 7 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-module-runtime-conflicts-0.003-pl526_0.tar.bz2 +md5 : b8eb3619137af69458c36fdc79b6a129 +timestamp : 2018-08-17 21:25:27 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-dist-checkconflicts + - perl-module-runtime + + +perl-module-runtime-conflicts 0.003 pl5321ha770c72_0 +---------------------------------------------------- +file name : perl-module-runtime-conflicts-0.003-pl5321ha770c72_0.conda +name : perl-module-runtime-conflicts +version : 0.003 +build : pl5321ha770c72_0 +build number: 0 +size : 16 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-module-runtime-conflicts-0.003-pl5321ha770c72_0.conda +md5 : 861010a9e8e33bb83717724e59fa1dcf +timestamp : 2023-01-23 13:18:19 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-dist-checkconflicts 0.11.* + - perl-module-runtime 0.016.* + + +perl-module-runtime-conflicts 0.003 pl5321hdfd78af_1 +---------------------------------------------------- +file name : perl-module-runtime-conflicts-0.003-pl5321hdfd78af_1.tar.bz2 +name : perl-module-runtime-conflicts +version : 0.003 +build : pl5321hdfd78af_1 +build number: 1 +size : 9 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-module-runtime-conflicts-0.003-pl5321hdfd78af_1.tar.bz2 +md5 : 0aeb5e85a3fb4354d24e7448c937107e +timestamp : 2022-01-24 15:49:11 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-dist-checkconflicts + - perl-module-runtime diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mozilla-ca.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mozilla-ca.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..da3b05437858f6da8d1f74e0ba681baf7ec3e2fd --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mozilla-ca.manual_bundle.txt @@ -0,0 +1,206 @@ +# Tool: perl-mozilla-ca +software_name: perl-mozilla-ca +tier: T1 +domain: t1_backfill_overall +downloads: 389029 +summary: Mozilla's CA cert bundle in PEM format. +description: Mozilla's CA cert bundle in PEM format. +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/Mozilla::CA +doc_url: https://metacpan.org/pod/Mozilla::CA +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/Mozilla::CA +Mozilla::CA - Mozilla's CA cert bundle in PEM format - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Mozilla-CA Module version: 20250602 02 Jun 2025 17:39:28 UTC License: open_source Code Download ( 142.82KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (0) How to Contribute Chat Quality Testers ( 1880 / 0 / 0 ) Testers (Magpie) Kwalitee 100.00% Coverage Bus factor: 7 Activity 24 month Dependencies none Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 20250602 (LWP on 2025-06-02) 20250202 (LWP on 2025-02-02) 20240924 (LWP on 2024-09-24) 20240730 (LWP on 2024-07-30) 20240313 (LWP on 2024-03-13) 20231213 (LWP on 2023-12-13) 20230821 (LWP on 2023-08-21) 20230807 (LWP on 2023-08-07) 20230801 (LWP on 2023-08-01) 20221114 (HAARG on 2022-11-14) 20211001 (ABH on 2021-10-01) 20200520 (ABH on 2020-05-20) 20180117 (ABH on 2018-03-01) 20160104 (ABH on 2016-01-04) 20150826 (ABH on 2015-08-26) 20141217 (ABH on 2014-12-22) 20130114 (ABH on 2013-01-14) 20120823 (ABH on 2012-08-22) 20120309 (ABH on 2012-03-09) 20120118 (ABH on 2012-01-18) 20110209 (GAAS on 2011-02-11) 20120822 (ABH on 2012-08-22) 20111025 (ABH on 2011-10-25) 20110914 (ABH on 2011-09-15) 20110904 (ABH on 2011-09-04) 20110409 (ABH on 2011-04-09) 20110301 (ABH on 2011-03-01) 20110126 (GAAS on 2011-01-26) 20110122 (GAAS on 2011-01-22) Diff with version 20250602 (LWP on 2025-06-02) 20250202 (LWP on 2025-02-02) 20240924 (LWP on 2024-09-24) 20240730 (LWP on 2024-07-30) 20240313 (LWP on 2024-03-13) 20231213 (LWP on 2023-12-13) 20230821 (LWP on 2023-08-21) 20230807 (LWP on 2023-08-07) 20230801 (LWP on 2023-08-01) 20221114 (HAARG on 2022-11-14) 20211001 (ABH on 2021-10-01) 20200520 (ABH on 2020-05-20) 20180117 (ABH on 2018-03-01) 20160104 (ABH on 2016-01-04) 20150826 (ABH on 2015-08-26) 20141217 (ABH on 2014-12-22) 20130114 (ABH on 2013-01-14) 20120823 (ABH on 2012-08-22) 20120309 (ABH on 2012-03-09) 20120118 (ABH on 2012-01-18) 20110209 (GAAS on 2011-02-11) 20120822 (ABH on 2012-08-22) 20111025 (ABH on 2011-10-25) 20110914 (ABH on 2011-09-15) 20110904 (ABH on 2011-09-04) 20110409 (ABH on 2011-04-09) 20110301 (ABH on 2011-03-01) 20110126 (GAAS on 2011-01-26) 20110122 (GAAS on 2011-01-22) Permalinks This version Latest version ++ed by: 10 PAUSE users 9 non-PAUSE users Authors: Gisle Aas Released by: libwww-perl 8 Maintainers: OALDERS owner ABH ETHER GAAS HAARG LWP SIMBABQUE STIGTSP Contributors: Gisle Aas libwww-perl  /  20250602 (LWP on 2025-06-02) 20250202 (LWP on 2025-02-02) 20240924 (LWP on 2024-09-24) 20240730 (LWP on 2024-07-30) 20240313 (LWP on 2024-03-13) 20231213 (LWP on 2023-12-13) 20230821 (LWP on 2023-08-21) 20230807 (LWP on 2023-08-07) 20230801 (LWP on 2023-08-01) 20221114 (HAARG on 2022-11-14) 20211001 (ABH on 2021-10-01) 20200520 (ABH on 2020-05-20) 20180117 (ABH on 2018-03-01) 20160104 (ABH on 2016-01-04) 20150826 (ABH on 2015-08-26) 20141217 (ABH on 2014-12-22) 20130114 (ABH on 2013-01-14) 20120823 (ABH on 2012-08-22) 20120309 (ABH on 2012-03-09) 20120118 (ABH on 2012-01-18) 20110209 (GAAS on 2011-02-11) 20120822 (ABH on 2012-08-22) 20111025 (ABH on 2011-10-25) 20110914 (ABH on 2011-09-15) 20110904 (ABH on 2011-09-04) 20110409 (ABH on 2011-04-09) 20110301 (ABH on 2011-03-01) 20110126 (GAAS on 2011-01-26) 20110122 (GAAS on 2011-01-22) Mozilla-CA-20250602 19 ++ 19 ++ ⭐ Starred 1 GitHub stars / Mozilla::CA Contents NAME SYNOPSIS DESCRIPTION SEE ALSO LICENSE NAME Mozilla::CA - Mozilla's CA cert bundle in PEM format SYNOPSIS use IO::Socket::SSL; use Mozilla::CA; my $host = "www.paypal.com"; my $client = IO::Socket::SSL->new( PeerHost => "$host:443", SSL_verify_mode => 0x02, SSL_ca_file => Mozilla::CA::SSL_ca_file(), ) || die "Can't connect: $@"; $client->verify_hostname($host, "http") || die "hostname verification failure"; DESCRIPTION Mozilla::CA provides a copy of Mozilla's bundle of Certificate Authority certificates in a form that can be consumed by modules and libraries based on OpenSSL. The module provide a single function: SSL_ca_file() Returns the absolute path to the Mozilla's CA cert bundle PEM file. SEE ALSO http://curl.haxx.se/docs/caextract.html LICENSE For the bundled Mozilla CA PEM file the following applies: This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/. The Mozilla::CA distribution itself is available under the same license. Module Install Instructions To install Mozilla::CA, copy and paste the appropriate command in to your terminal. cpanm cpanm Mozilla::CA CPAN shell perl -MCPAN -e shell install Mozilla::CA For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +### https://metacpan.org/pod/Mozilla::CA +Mozilla::CA - Mozilla's CA cert bundle in PEM format - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Mozilla-CA Module version: 20250602 02 Jun 2025 17:39:28 UTC License: open_source Code Download ( 142.82KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (0) How to Contribute Chat Quality Testers ( 1880 / 0 / 0 ) Testers (Magpie) Kwalitee 100.00% Coverage Bus factor: 7 Activity 24 month Dependencies none Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 20250602 (LWP on 2025-06-02) 20250202 (LWP on 2025-02-02) 20240924 (LWP on 2024-09-24) 20240730 (LWP on 2024-07-30) 20240313 (LWP on 2024-03-13) 20231213 (LWP on 2023-12-13) 20230821 (LWP on 2023-08-21) 20230807 (LWP on 2023-08-07) 20230801 (LWP on 2023-08-01) 20221114 (HAARG on 2022-11-14) 20211001 (ABH on 2021-10-01) 20200520 (ABH on 2020-05-20) 20180117 (ABH on 2018-03-01) 20160104 (ABH on 2016-01-04) 20150826 (ABH on 2015-08-26) 20141217 (ABH on 2014-12-22) 20130114 (ABH on 2013-01-14) 20120823 (ABH on 2012-08-22) 20120309 (ABH on 2012-03-09) 20120118 (ABH on 2012-01-18) 20110209 (GAAS on 2011-02-11) 20120822 (ABH on 2012-08-22) 20111025 (ABH on 2011-10-25) 20110914 (ABH on 2011-09-15) 20110904 (ABH on 2011-09-04) 20110409 (ABH on 2011-04-09) 20110301 (ABH on 2011-03-01) 20110126 (GAAS on 2011-01-26) 20110122 (GAAS on 2011-01-22) Diff with version 20250602 (LWP on 2025-06-02) 20250202 (LWP on 2025-02-02) 20240924 (LWP on 2024-09-24) 20240730 (LWP on 2024-07-30) 20240313 (LWP on 2024-03-13) 20231213 (LWP on 2023-12-13) 20230821 (LWP on 2023-08-21) 20230807 (LWP on 2023-08-07) 20230801 (LWP on 2023-08-01) 20221114 (HAARG on 2022-11-14) 20211001 (ABH on 2021-10-01) 20200520 (ABH on 2020-05-20) 20180117 (ABH on 2018-03-01) 20160104 (ABH on 2016-01-04) 20150826 (ABH on 2015-08-26) 20141217 (ABH on 2014-12-22) 20130114 (ABH on 2013-01-14) 20120823 (ABH on 2012-08-22) 20120309 (ABH on 2012-03-09) 20120118 (ABH on 2012-01-18) 20110209 (GAAS on 2011-02-11) 20120822 (ABH on 2012-08-22) 20111025 (ABH on 2011-10-25) 20110914 (ABH on 2011-09-15) 20110904 (ABH on 2011-09-04) 20110409 (ABH on 2011-04-09) 20110301 (ABH on 2011-03-01) 20110126 (GAAS on 2011-01-26) 20110122 (GAAS on 2011-01-22) Permalinks This version Latest version ++ed by: 10 PAUSE users 9 non-PAUSE users Authors: Gisle Aas Released by: libwww-perl 8 Maintainers: OALDERS owner ABH ETHER GAAS HAARG LWP SIMBABQUE STIGTSP Contributors: Gisle Aas libwww-perl  /  20250602 (LWP on 2025-06-02) 20250202 (LWP on 2025-02-02) 20240924 (LWP on 2024-09-24) 20240730 (LWP on 2024-07-30) 20240313 (LWP on 2024-03-13) 20231213 (LWP on 2023-12-13) 20230821 (LWP on 2023-08-21) 20230807 (LWP on 2023-08-07) 20230801 (LWP on 2023-08-01) 20221114 (HAARG on 2022-11-14) 20211001 (ABH on 2021-10-01) 20200520 (ABH on 2020-05-20) 20180117 (ABH on 2018-03-01) 20160104 (ABH on 2016-01-04) 20150826 (ABH on 2015-08-26) 20141217 (ABH on 2014-12-22) 20130114 (ABH on 2013-01-14) 20120823 (ABH on 2012-08-22) 20120309 (ABH on 2012-03-09) 20120118 (ABH on 2012-01-18) 20110209 (GAAS on 2011-02-11) 20120822 (ABH on 2012-08-22) 20111025 (ABH on 2011-10-25) 20110914 (ABH on 2011-09-15) 20110904 (ABH on 2011-09-04) 20110409 (ABH on 2011-04-09) 20110301 (ABH on 2011-03-01) 20110126 (GAAS on 2011-01-26) 20110122 (GAAS on 2011-01-22) Mozilla-CA-20250602 19 ++ 19 ++ ⭐ Starred 1 GitHub stars / Mozilla::CA Contents NAME SYNOPSIS DESCRIPTION SEE ALSO LICENSE NAME Mozilla::CA - Mozilla's CA cert bundle in PEM format SYNOPSIS use IO::Socket::SSL; use Mozilla::CA; my $host = "www.paypal.com"; my $client = IO::Socket::SSL->new( PeerHost => "$host:443", SSL_verify_mode => 0x02, SSL_ca_file => Mozilla::CA::SSL_ca_file(), ) || die "Can't connect: $@"; $client->verify_hostname($host, "http") || die "hostname verification failure"; DESCRIPTION Mozilla::CA provides a copy of Mozilla's bundle of Certificate Authority certificates in a form that can be consumed by modules and libraries based on OpenSSL. The module provide a single function: SSL_ca_file() Returns the absolute path to the Mozilla's CA cert bundle PEM file. SEE ALSO http://curl.haxx.se/docs/caextract.html LICENSE For the bundled Mozilla CA PEM file the following applies: This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/. The Mozilla::CA distribution itself is available under the same license. Module Install Instructions To install Mozilla::CA, copy and paste the appropriate command in to your terminal. cpanm cpanm Mozilla::CA CPAN shell perl -MCPAN -e shell install Mozilla::CA For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-mozilla-ca --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-mozilla-ca 20160104 0 +-------------------------- +file name : perl-mozilla-ca-20160104-0.tar.bz2 +name : perl-mozilla-ca +version : 20160104 +build : 0 +build number: 0 +size : 150 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mozilla-ca-20160104-0.tar.bz2 +md5 : 018517fc1b5b9f8879c22ca6d034c8b1 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-mozilla-ca 20160104 pl526_1 +-------------------------------- +file name : perl-mozilla-ca-20160104-pl526_1.tar.bz2 +name : perl-mozilla-ca +version : 20160104 +build : pl526_1 +build number: 1 +size : 155 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mozilla-ca-20160104-pl526_1.tar.bz2 +md5 : 56a706853e673e2f649c50f77c937271 +timestamp : 2018-07-06 23:14:47 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-mozilla-ca 20160104 pl526_2 +-------------------------------- +file name : perl-mozilla-ca-20160104-pl526_2.tar.bz2 +name : perl-mozilla-ca +version : 20160104 +build : pl526_2 +build number: 2 +size : 155 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mozilla-ca-20160104-pl526_2.tar.bz2 +md5 : 673934fc4baea13874c093d176312936 +timestamp : 2018-08-07 19:30:57 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-mozilla-ca 20180117 pl526_0 +-------------------------------- +file name : perl-mozilla-ca-20180117-pl526_0.tar.bz2 +name : perl-mozilla-ca +version : 20180117 +build : pl526_0 +build number: 0 +size : 139 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mozilla-ca-20180117-pl526_0.tar.bz2 +md5 : e708699f1d7efc64f6b24ada77208574 +timestamp : 2018-08-24 03:32:16 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-mozilla-ca 20180117 pl526_1 +-------------------------------- +file name : perl-mozilla-ca-20180117-pl526_1.tar.bz2 +name : perl-mozilla-ca +version : 20180117 +build : pl526_1 +build number: 1 +size : 140 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mozilla-ca-20180117-pl526_1.tar.bz2 +md5 : 33c797816376ee2a58fd4187848ced82 +timestamp : 2019-05-07 10:59:46 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-mozilla-ca 20180117 pl5321hdfd78af_2 +----------------------------------------- +file name : perl-mozilla-ca-20180117-pl5321hdfd78af_2.tar.bz2 +name : perl-mozilla-ca +version : 20180117 +build : pl5321hdfd78af_2 +build number: 2 +size : 142 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mozilla-ca-20180117-pl5321hdfd78af_2.tar.bz2 +md5 : 8941f01d165ee105a3b8ea64ae652bd4 +timestamp : 2022-01-20 08:21:40 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-mozilla-ca 20211001 pl5321hdfd78af_0 +----------------------------------------- +file name : perl-mozilla-ca-20211001-pl5321hdfd78af_0.tar.bz2 +name : perl-mozilla-ca +version : 20211001 +build : pl5321hdfd78af_0 +build number: 0 +size : 133 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mozilla-ca-20211001-pl5321hdfd78af_0.tar.bz2 +md5 : 3143471a42244ba6dd52fb8f156a3915 +timestamp : 2022-02-10 17:35:40 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-mozilla-ca 20250602 pl5321hdfd78af_0 +----------------------------------------- +file name : perl-mozilla-ca-20250602-pl5321hdfd78af_0.conda +name : perl-mozilla-ca +version : 20250602 +build : pl5321hdfd78af_0 +build number: 0 +size : 130 KB +license : Unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mozilla-ca-20250602-pl5321hdfd78af_0.conda +md5 : bfda873e9a298e1d51ba2eaa45be279c +timestamp : 2025-08-19 02:42:41 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mro-compat.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mro-compat.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..91aa3381bc989cb25fcadc434550b59c8d965423 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-mro-compat.manual_bundle.txt @@ -0,0 +1,94 @@ +# Tool: perl-mro-compat +software_name: perl-mro-compat +tier: T1 +domain: t1_backfill_overall +downloads: 244840 +summary: mro::* interface compatibility for Perls < 5.9.5 +description: mro::* interface compatibility for Perls < 5.9.5 +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/release/MRO-Compat +doc_url: +dev_url: + +## URL Docs Extract +### https://metacpan.org/release/MRO-Compat +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-mro-compat --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-mro-compat 0.13 pl526_0 +---------------------------- +file name : perl-mro-compat-0.13-pl526_0.tar.bz2 +name : perl-mro-compat +version : 0.13 +build : pl526_0 +build number: 0 +size : 10 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-mro-compat-0.13-pl526_0.tar.bz2 +md5 : 1a374860fe4735444128341b386b0661 +timestamp : 2018-08-17 21:28:20 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-mro-compat 0.13 pl5321hdfd78af_1 +------------------------------------- +file name : perl-mro-compat-0.13-pl5321hdfd78af_1.tar.bz2 +name : perl-mro-compat +version : 0.13 +build : pl5321hdfd78af_1 +build number: 1 +size : 12 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mro-compat-0.13-pl5321hdfd78af_1.tar.bz2 +md5 : 5adf5accf1a6d77a38a95250514e08f5 +timestamp : 2022-01-19 02:30:58 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-mro-compat 0.15 pl5321ha770c72_0 +------------------------------------- +file name : perl-mro-compat-0.15-pl5321ha770c72_0.conda +name : perl-mro-compat +version : 0.15 +build : pl5321ha770c72_0 +build number: 0 +size : 19 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-mro-compat-0.15-pl5321ha770c72_0.conda +md5 : cf20bcb8f8177bd2058988fe44216642 +timestamp : 2022-11-23 21:41:22 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-mro-compat 0.15 pl5321hdfd78af_0 +------------------------------------- +file name : perl-mro-compat-0.15-pl5321hdfd78af_0.tar.bz2 +name : perl-mro-compat +version : 0.15 +build : pl5321hdfd78af_0 +build number: 0 +size : 12 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-mro-compat-0.15-pl5321hdfd78af_0.tar.bz2 +md5 : b435974ea02a59f280e48b44f93091cb +timestamp : 2022-02-09 14:07:11 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-net-http.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-net-http.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0369b11ff2a2fda666d64084e2e0d08435af8671 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-net-http.manual_bundle.txt @@ -0,0 +1,243 @@ +# Tool: perl-net-http +software_name: perl-net-http +tier: T1 +domain: t1_backfill_overall +downloads: 506844 +summary: Low-level HTTP connection (client). +description: Low-level HTTP connection (client). +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-base, perl-carp, perl-compress-raw-zlib, perl-io-socket-ssl, perl-uri +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/libwww-perl/Net-HTTP +doc_url: https://metacpan.org/pod/Net::HTTP +dev_url: https://github.com/libwww-perl/Net-HTTP + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/Net::HTTP +Net::HTTP - Low-level HTTP connection (client) - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Net-HTTP Module version: 6.24 29 Aug 2025 11:23:03 UTC License: perl_5 Perl: v5.6.2 Code Download ( 42.69KB ) Source ( raw ) Browse ( raw ) Changes Project Homepage Repository Issues (29) How to Contribute Chat Quality Testers ( 779 / 7 / 0 ) Testers (Magpie) Kwalitee 65.93% Coverage Bus factor: 6 Activity 24 month 8 Dependencies Carp Compress::Raw::Zlib IO::Socket::INET IO::Uncompress::Gunzip URI and 3 more base strict warnings Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 6.24 (OALDERS on 2025-08-29) 6.23 (OALDERS on 2023-06-16) 6.22 (OALDERS on 2022-01-21) 6.21 (OALDERS on 2021-03-18) 6.20 (OALDERS on 2021-01-08) 6.19 (OALDERS on 2019-05-16) 6.18 (OALDERS on 2018-05-09) 6.17 (OALDERS on 2017-09-01) 6.16 (OALDERS on 2017-05-29) 6.15 (OALDERS on 2017-05-12) 6.14 (OALDERS on 2017-04-24) 6.13 (OALDERS on 2017-02-20) 6.12 (OALDERS on 2017-01-05) 6.11 (OALDERS on 2017-01-04) 6.10-TRIAL DEV (OALDERS on 2016-12-30) 6.09 (ETHER on 2015-05-20) 6.07 (MSCHILLI on 2014-07-24) 6.06 (GAAS on 2013-03-10) 6.08_002 DEV (ETHER on 2015-05-02) 6.08_001 DEV (ETHER on 2015-05-01) 6.05 (GAAS on 2012-11-10) 6.04 (GAAS on 2012-11-08) 6.03 (GAAS on 2012-02-16) 6.02 (GAAS on 2011-11-21) 6.01 (GAAS on 2011-04-17) 6.00 (GAAS on 2011-02-27) Diff with version 6.24 (OALDERS on 2025-08-29) 6.23 (OALDERS on 2023-06-16) 6.22 (OALDERS on 2022-01-21) 6.21 (OALDERS on 2021-03-18) 6.20 (OALDERS on 2021-01-08) 6.19 (OALDERS on 2019-05-16) 6.18 (OALDERS on 2018-05-09) 6.17 (OALDERS on 2017-09-01) 6.16 (OALDERS on 2017-05-29) 6.15 (OALDERS on 2017-05-12) 6.14 (OALDERS on 2017-04-24) 6.13 (OALDERS on 2017-02-20) 6.12 (OALDERS on 2017-01-05) 6.11 (OALDERS on 2017-01-04) 6.10-TRIAL DEV (OALDERS on 2016-12-30) 6.09 (ETHER on 2015-05-20) 6.07 (MSCHILLI on 2014-07-24) 6.06 (GAAS on 2013-03-10) 6.08_002 DEV (ETHER on 2015-05-02) 6.08_001 DEV (ETHER on 2015-05-01) 6.05 (GAAS on 2012-11-10) 6.04 (GAAS on 2012-11-08) 6.03 (GAAS on 2012-02-16) 6.02 (GAAS on 2011-11-21) 6.01 (GAAS on 2011-04-17) 6.00 (GAAS on 2011-02-27) Permalinks This version Latest version ++ed by: 4 PAUSE users 8 non-PAUSE users Authors: Gisle Aas Released by: Olaf Alders 7 Maintainers: OALDERS owner CAPOEIRAB ETHER GAAS MSCHILLI SIMBABQUE SKAJI 67 Contributors: Adam Kennedy Adam Sjogren Alex Kapranoff Alexey Tourbin amire80 Andreas J. Koenig Andy Grundman Bill Mann Bron Gondwana Chase Whitener copilot-swe-agent[bot] Dagfinn Ilmari Mannsåker Daniel Hedlund Dave Rolsky David E. Wheeler David Steinbrunner DAVIDRW Eric Wong Father Chrysostomos FWILES Gavin Peters Gisle Aas Graeme Thompson Hans-H. Froehlich Ian Kilgore Jacob J James Raspass Jason A Fesler Jay Hannah Jean-Louis Martineau jefflee Jesse Luehrs john9art Julien Fiegehenn Karen Etheridge Kent Fredric Lasse Makholm Marinos Yannikos Mark Overmeer Mark Stosberg Mohammad S Anwar mschilli murphy Olaf Alders Ondrej Hanak Paul Cochrane Peter Rabbitson phrstbrn Robert Stone Rolf Grossmann ruff sasao Sean M. Burke Shoichi Kaji Slaven Rezic Spiros Denaxas Steffen Ullrich Steve Hay Todd Lipcon Tom Hukins Tom Wyant Tony Finch Toru Yamaguchi uid39246 <uid39246> Ville Skyttä Yuri Karaban Zefram Olaf Alders  /  6.24 (OALDERS on 2025-08-29) 6.23 (OALDERS on 2023-06-16) 6.22 (OALDERS on 2022-01-21) 6.21 (OALDERS on 2021-03-18) 6.20 (OALDERS on 2021-01-08) 6.19 (OALDERS on 2019-05-16) 6.18 (OALDERS on 2018-05-09) 6.17 (OALDERS on 2017-09-01) 6.16 (OALDERS on 2017-05-29) 6.15 (OALDERS on 2017-05-12) 6.14 (OALDERS on 2017-04-24) 6.13 (OALDERS on 2017-02-20) 6.12 (OALDERS on 2017-01-05) 6.11 (OALDERS on 2017-01-04) 6.10-TRIAL DEV (OALDERS on 2016-12-30) 6.09 (ETHER on 2015-05-20) 6.07 (MSCHILLI on 2014-07-24) 6.06 (GAAS on 2013-03-10) 6.08_002 DEV (ETHER on 2015-05-02) 6.08_001 DEV (ETHER on 2015-05-01) 6.05 (GAAS on 2012-11-10) 6.04 (GAAS on 2012-11-08) 6.03 (GAAS on 2012-02-16) 6.02 (GAAS on 2011-11-21) 6.01 (GAAS on 2011-04-17) 6.00 (GAAS on 2011-02-27) Net-HTTP-6.24 12 ++ 12 ++ ⭐ Starred 19 GitHub stars / Net::HTTP Contents NAME VERSION SYNOPSIS DESCRIPTION SUBCLASSING SEE ALSO AUTHOR COPYRIGHT AND LICENSE NAME Net::HTTP - Low-level HTTP connection (client) VERSION version 6.24 SYNOPSIS use Net::HTTP; my $s = Net::HTTP->new(Host => "www.perl.com") || die $@; $s->write_request(GET => "/", 'User-Agent' => "Mozilla/5.0"); my($code, $mess, %h) = $s->read_response_headers; while (1) { my $buf; my $n = $s->read_entity_body($buf, 1024); die "read failed: $!" unless defined $n; last unless $n; print $buf; } DESCRIPTION The Net::HTTP class is a low-level HTTP client. An instance of the Net::HTTP class represents a connection to an HTTP server. The HTTP protocol is described in RFC 2616. The Net::HTTP class supports HTTP/1.0 and HTTP/1.1 . Net::HTTP is a sub-class of one of IO::Socket::IP (IPv6+IPv4), IO::Socket::INET6 (IPv6+IPv4), or IO::Socket::INET (IPv4 only). You can mix the methods described below with reading and writing from the socket directly. This is not necessary a good idea, unless you know what you are doing. The following methods are provided (in addition to those of IO::Socket::INET ): $s = Net::HTTP->new( %options ) The Net::HTTP constructor method takes the same options as IO::Socket::INET 's as well as these: Host: Initial host attribute value KeepAlive: Initial keep_alive attribute value SendTE: Initial send_te attribute_value HTTPVersion: Initial http_version attribute value PeerHTTPVersion: Initial peer_http_version attribute value MaxLineLength: Initial max_line_length attribute value MaxHeaderLines: Initial max_header_lines attribute value The Host option is also the default for IO::Socket::INET 's PeerAddr . The PeerPort defaults to 80 if not provided. The PeerPort specification can also be embedded in the PeerAddr by preceding it with a ":", and closing the IPv6 address on brackets "[]" if necessary: "192.0.2.1:80","[2001:db8::1]:80","any.example.com:80". The Listen option provided by IO::Socket::INET 's constructor method is not allowed. If unable to connect to the given HTTP server then the constructor returns undef and $@ contains the reason. After a successful connect, a Net:HTTP object is returned. $s->host Get/set the default value of the Host header to send. The $host must not be set to an empty string (or undef ) for HTTP/1.1. $s->keep_alive Get/set the keep-alive value. If this value is TRUE then the request will be sent with headers indicating that the server should try to keep the connection open so that multiple requests can be sent. The actual headers set will depend on the value of the http_version and peer_http_version attributes. $s->send_te Get/set the a value indicating if the request will be sent with a "TE" header to indicate the transfer encodings that the server can choose to use. The list of encodings announced as accepted by this client depends on availability of the following modules: Compress::Raw::Zlib for deflate , and IO::Compress::Gunzip for gzip . $s->http_version Get/set the HTTP version number that this client should announce. This value can only be set to "1.0" or "1.1". The default is "1.1". $s->peer_http_version Get/set the protocol version number of our peer. This value will initially be "1.0", but will be updated by a successful read_response_headers() method call. $s->max_line_length Get/set a limit on the length of response line and response header lines. The default is 8192. A value of 0 means no limit. $s->max_header_length Get/set a limit on the number of header lines that a response can have. The default is 128. A value of 0 means no limit. $s->format_request($method, $uri, %headers, [$content]) Format a request message and return it as a string. If the headers do not include a Host header, then a header is inserted with the value of the host attribute. Headers like Connection and Keep-Alive might also be added depending on the status of the keep_alive attribute. If $content is given (and it is non-empty), then a Content-Length header is automatically added unless it was already present. $s->write_request($method, $uri, %headers, [$content]) Format and send a request message. Arguments are the same as for format_request(). Returns true if successful. $s->format_chunk( $data ) Returns the string to be written for the given chunk of data. $s->write_chunk($data) Will write a new chunk of request entity body data. This method should only be used if the Transfer-Encoding header with a value of chunked was sent in the request. Note, writing zero-length data is a no-op. Use the write_chunk_eof() method to signal end of entity body data. Returns true if successful. $s->format_chunk_eof( %trailers ) Returns the string to be written for signaling EOF when a Transfer-Encoding of chunked is used. $s->write_chunk_eof( %trailers ) Will write eof marker for chunked data and optional trailers. Note that trailers should not really be used unless is was signaled with a Trailer header. Returns true if successful. ($code, $mess, %headers) = $s->read_response_headers( %opts ) Read response headers from server and return it. The $code is the 3 digit HTTP status code (see HTTP::Status ) and $mess is the textual message that came with it. Headers are then returned as key/value pairs. Since key letter casing is not normalized and the same key can even occur multiple times, assigning these values directly to a hash is not wise. Only the $code is returned if this method is called in scalar context. As a side effect this method updates the 'peer_http_version' attribute. Options might be passed in as key/value pairs. There are currently only two options supported; laxed and junk_out . The laxed option will make read_response_headers() more forgiving towards servers that have not learned how to speak HTTP properly. The laxed option is a boolean flag, and is enabled by passing in a TRUE value. The junk_out option can be used to capture bad header lines when laxed is enabled. The value should be an array reference. Bad header lines will be pushed onto the array. The laxed option must be specified in order to communicate with pre-HTTP/1.0 servers that don't describe the response outcome or the data they send back with a header block. For these servers peer_http_version is set to "0.9" and this method returns (200, "Assumed OK"). The method will raise an exception (die) if the server does not speak proper HTTP or if the max_line_length or max_header_length limits are reached. If the laxed option is turned on and max_line_length and max_header_length checks are turned off, then no exception will be raised and this method will always return a response code. $n = $s->read_entity_body($buf, $size); Reads chunks of the entity body content. Basically the same interface as for read() and sysread(), but the buffer offset argument is not supported yet. This method should only be called after a successful read_response_headers() call. The return value will be undef on read errors, 0 on EOF, -1 if no data could be returned this time, otherwise the number of bytes assigned to $buf. The $buf is set to "" when the return value is -1. You normally want to retry this call if this function returns either -1 or undef with $! as EINTR or EAGAIN (see Errno ). EINTR can happen if the application catches signals and EAGAIN can happen if you made the socket non-blocking. This method will raise exceptions (die) if the server does not speak proper HTTP. This can only happen when reading chunked data. %headers = $s->get_trailers After read_entity_body() has returned 0 to indicate end of the entity body, you might call this method to pick up any trailers. $s->_rbuf Get/set the read buffer content. The read_response_headers() and read_entity_body() methods use an internal buffer which they will look for data before they actually sysread more from the socket itself. If they read too much, the remaining data will be left in this buffer. $s->_rbuf_length Returns the number of bytes in the read buffer. This should always be the same as: length($s->_rbuf) but might be more efficient. SUBCLASSING The read_response_headers() and read_entity_body() will invoke the sysread() method when they need more data. Subclasses might want to override this method to control how reading takes place. The object itself is a glob. Subclasses should avoid using hash key names prefixed with http_ and io_ . SEE ALSO LWP , IO::Socket::INET , Net::HTTP::NB AUTHOR Gisle Aas <gisle@activestate.com> COPYRIGHT AND LICENSE This software is copyright (c) 2001 by Gisle Aas. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. Module Install Instructions To install Net::HTTP, copy and paste the appropriate command in to your terminal. cpanm cpanm Net::HTTP CPAN shell perl -MCPAN -e shell install Net::HTTP For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +### https://github.com/libwww-perl/Net-HTTP +GitHub - libwww-perl/Net-HTTP: Low-level HTTP client · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} libwww-perl / Net-HTTP Public Notifications You must be signed in to change notification settings Fork 27 Star 20 Code Issues 29 Pull requests 2 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights libwww-perl/Net-HTTP master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 2,782 Commits 2,782 Commits .github/ workflows .github/ workflows lib/ Net lib/ Net t t xt xt .gitignore .gitignore .mailmap .mailmap Changes Changes Install Install LICENSE LICENSE META.json META.json Makefile.PL Makefile.PL README.md README.md cpanfile cpanfile dist.ini dist.ini perlcriticrc perlcriticrc perltidyrc perltidyrc tidyall.ini tidyall.ini View all files Repository files navigation README License NAME Net::HTTP - Low-level HTTP connection (client) VERSION version 6.24 SYNOPSIS use Net::HTTP; my $s = Net::HTTP->new(Host => "www.perl.com") || die $@; $s->write_request(GET => "/", 'User-Agent' => "Mozilla/5.0"); my($code, $mess, %h) = $s->read_response_headers; while (1) { my $buf; my $n = $s->read_entity_body($buf, 1024); die "read failed: $!" unless defined $n; last unless $n; print $buf; } DESCRIPTION The Net::HTTP class is a low-level HTTP client. An instance of the Net::HTTP class represents a connection to an HTTP server. The HTTP protocol is described in RFC 2616. The Net::HTTP class supports HTTP/1.0 and HTTP/1.1 . Net::HTTP is a sub-class of one of IO::Socket::IP (IPv6+IPv4), IO::Socket::INET6 (IPv6+IPv4), or IO::Socket::INET (IPv4 only). You can mix the methods described below with reading and writing from the socket directly. This is not necessary a good idea, unless you know what you are doing. The following methods are provided (in addition to those of IO::Socket::INET ): $s = Net::HTTP->new( %options ) The Net::HTTP constructor method takes the same options as IO::Socket::INET 's as well as these: Host: Initial host attribute value KeepAlive: Initial keep_alive attribute value SendTE: Initial send_te attribute_value HTTPVersion: Initial http_version attribute value PeerHTTPVersion: Initial peer_http_version attribute value MaxLineLength: Initial max_line_length attribute value MaxHeaderLines: Initial max_header_lines attribute value The Host option is also the default for IO::Socket::INET 's PeerAddr . The PeerPort defaults to 80 if not provided. The PeerPort specification can also be embedded in the PeerAddr by preceding it with a ":", and closing the IPv6 address on brackets "[]" if necessary: "192.0.2.1:80","[2001:db8::1]:80","any.example.com:80". The Listen option provided by IO::Socket::INET 's constructor method is not allowed. If unable to connect to the given HTTP server then the constructor returns undef and $@ contains the reason. After a successful connect, a Net:HTTP object is returned. $s->host Get/set the default value of the Host header to send. The $host must not be set to an empty string (or undef ) for HTTP/1.1. $s->keep_alive Get/set the keep-alive value. If this value is TRUE then the request will be sent with headers indicating that the server should try to keep the connection open so that multiple requests can be sent. The actual headers set will depend on the value of the http_version and peer_http_version attributes. $s->send_te Get/set the a value indicating if the request will be sent with a "TE" header to indicate the transfer encodings that the server can choose to use. The list of encodings announced as accepted by this client depends on availability of the following modules: Compress::Raw::Zlib for deflate , and IO::Compress::Gunzip for gzip . $s->http_version Get/set the HTTP version number that this client should announce. This value can only be set to "1.0" or "1.1". The default is "1.1". $s->peer_http_version Get/set the protocol version number of our peer. This value will initially be "1.0", but will be updated by a successful read_response_headers() method call. $s->max_line_length Get/set a limit on the length of response line and response header lines. The default is 8192. A value of 0 means no limit. $s->max_header_length Get/set a limit on the number of header lines that a response can have. The default is 128. A value of 0 means no limit. $s->format_request($method, $uri, %headers, [$content]) Format a request message and return it as a string. If the headers do not include a Host header, then a header is inserted with the value of the host attribute. Headers like Connection and Keep-Alive might also be added depending on the status of the keep_alive attribute. If $content is given (and it is non-empty), then a Content-Length header is automatically added unless it was already present. $s->write_request($method, $uri, %headers, [$content]) Format and send a request message. Arguments are the same as for format_request(). Returns true if successful. $s->format_chunk( $data ) Returns the string to be written for the given chunk of data. $s->write_chunk($data) Will write a new chunk of request entity body data. This method should only be used if the Transfer-Encoding header with a value of chunked was sent in the request. Note, writing zero-length data is a no-op. Use the write_chunk_eof() method to signal end of entity body data. Returns true if successful. $s->format_chunk_eof( %trailers ) Returns the string to be written for signaling EOF when a Transfer-Encoding of chunked is used. $s->write_chunk_eof( %trailers ) Will write eof marker for chunked data and optional trailers. Note that trailers should not really be used unless is was signaled with a Trailer header. Returns true if successful. ($code, $mess, %headers) = $s->read_response_headers( %opts ) Read response headers from server and return it. The $code is the 3 digit HTTP status code (see HTTP::Status ) and $mess is the textual message that came with it. Headers are then returned as key/value pairs. Since key letter casing is not normalized and the same key can even occur multiple times, assigning these values directly to a hash is not wise. Only the $code is returned if this method is called in scalar context. As a side effect this method updates the 'peer_http_version' attribute. Options might be passed in as key/value pairs. There are currently only two options supported; laxed and junk_out . The laxed option will make read_response_headers() more forgiving towards servers that have not learned how to speak HTTP properly. The laxed option is a boolean flag, and is enabled by passing in a TRUE value. The junk_out option can be used to capture bad header lines when laxed is enabled. The value should be an array reference. Bad header lines will be pushed onto the array. The laxed option must be specified in order to communicate with pre-HTTP/1.0 servers that don't describe the response outcome or the data they send back with a header block. For these servers peer_http_version is set to "0.9" and this method returns (200, "Assumed OK"). The method will raise an exception (die) if the server does not speak proper HTTP or if the max_line_length or max_header_length limits are reached. If the laxed option is turned on and max_line_length and max_header_length checks are turned off, then no exception will be raised and this method will always return a response code. $n = $s->read_entity_body($buf, $size); Reads chunks of the entity body content. Basically the same interface as for read() and sysread(), but the buffer offset argument is not supported yet. This method should only be called after a successful read_response_headers() call. The return value will be undef on read errors, 0 on EOF, -1 if no data could be returned this time, otherwise the number of bytes assigned to $buf. The $buf is set to "" when the return value is -1. You normally want to retry this call if this function returns either -1 or undef with $! as EINTR or EAGAIN (see Errno ). EINTR can happen if the application catches signals and EAGAIN can happen if you made the socket non-blocking. This method will raise exceptions (die) if the server does not speak proper HTTP. This can only happen when reading chunked data. %headers = $s->get_trailers After read_entity_body() has returned 0 to indicate end of the entity body, you might call this method to pick up any trailers. $s->_rbuf Get/set the read buffer content. The read_response_headers() and read_entity_body() methods use an internal buffer which they will look for data before they actually sysread more from the socket itself. If they read too much, the remaining data will be left in this buffer. $s->_rbuf_length Returns the number of bytes in the read buffer. This should always be the same as: length($s->_rbuf) but might be more efficient. SUBCLASSING The read_response_headers() and read_entity_body() will invoke the sysread() method when they need more data. Subclasses might want to override this method to control how reading takes place. The object itself is a glob. Subclasses should avoid using hash key names prefixed with http_ and io_ . SEE ALSO LWP , IO::Socket::INET , Net::HTTP::NB AUTHOR Gisle Aas gisle@activestate.com COPYRIGHT AND LICENSE This software is copyright (c) 2001 by Gisle Aas. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. About Low-level HTTP client metacpan.org/pod/Net::HTTP Topics hacktoberfest Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 20 stars Watchers 11 watching Forks 27 forks Report repository Releases 26 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/libwww-perl/Net-HTTP +GitHub - libwww-perl/Net-HTTP: Low-level HTTP client · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} libwww-perl / Net-HTTP Public Notifications You must be signed in to change notification settings Fork 27 Star 20 Code Issues 29 Pull requests 2 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights libwww-perl/Net-HTTP master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 2,782 Commits 2,782 Commits .github/ workflows .github/ workflows lib/ Net lib/ Net t t xt xt .gitignore .gitignore .mailmap .mailmap Changes Changes Install Install LICENSE LICENSE META.json META.json Makefile.PL Makefile.PL README.md README.md cpanfile cpanfile dist.ini dist.ini perlcriticrc perlcriticrc perltidyrc perltidyrc tidyall.ini tidyall.ini View all files Repository files navigation README License NAME Net::HTTP - Low-level HTTP connection (client) VERSION version 6.24 SYNOPSIS use Net::HTTP; my $s = Net::HTTP->new(Host => "www.perl.com") || die $@; $s->write_request(GET => "/", 'User-Agent' => "Mozilla/5.0"); my($code, $mess, %h) = $s->read_response_headers; while (1) { my $buf; my $n = $s->read_entity_body($buf, 1024); die "read failed: $!" unless defined $n; last unless $n; print $buf; } DESCRIPTION The Net::HTTP class is a low-level HTTP client. An instance of the Net::HTTP class represents a connection to an HTTP server. The HTTP protocol is described in RFC 2616. The Net::HTTP class supports HTTP/1.0 and HTTP/1.1 . Net::HTTP is a sub-class of one of IO::Socket::IP (IPv6+IPv4), IO::Socket::INET6 (IPv6+IPv4), or IO::Socket::INET (IPv4 only). You can mix the methods described below with reading and writing from the socket directly. This is not necessary a good idea, unless you know what you are doing. The following methods are provided (in addition to those of IO::Socket::INET ): $s = Net::HTTP->new( %options ) The Net::HTTP constructor method takes the same options as IO::Socket::INET 's as well as these: Host: Initial host attribute value KeepAlive: Initial keep_alive attribute value SendTE: Initial send_te attribute_value HTTPVersion: Initial http_version attribute value PeerHTTPVersion: Initial peer_http_version attribute value MaxLineLength: Initial max_line_length attribute value MaxHeaderLines: Initial max_header_lines attribute value The Host option is also the default for IO::Socket::INET 's PeerAddr . The PeerPort defaults to 80 if not provided. The PeerPort specification can also be embedded in the PeerAddr by preceding it with a ":", and closing the IPv6 address on brackets "[]" if necessary: "192.0.2.1:80","[2001:db8::1]:80","any.example.com:80". The Listen option provided by IO::Socket::INET 's constructor method is not allowed. If unable to connect to the given HTTP server then the constructor returns undef and $@ contains the reason. After a successful connect, a Net:HTTP object is returned. $s->host Get/set the default value of the Host header to send. The $host must not be set to an empty string (or undef ) for HTTP/1.1. $s->keep_alive Get/set the keep-alive value. If this value is TRUE then the request will be sent with headers indicating that the server should try to keep the connection open so that multiple requests can be sent. The actual headers set will depend on the value of the http_version and peer_http_version attributes. $s->send_te Get/set the a value indicating if the request will be sent with a "TE" header to indicate the transfer encodings that the server can choose to use. The list of encodings announced as accepted by this client depends on availability of the following modules: Compress::Raw::Zlib for deflate , and IO::Compress::Gunzip for gzip . $s->http_version Get/set the HTTP version number that this client should announce. This value can only be set to "1.0" or "1.1". The default is "1.1". $s->peer_http_version Get/set the protocol version number of our peer. This value will initially be "1.0", but will be updated by a successful read_response_headers() method call. $s->max_line_length Get/set a limit on the length of response line and response header lines. The default is 8192. A value of 0 means no limit. $s->max_header_length Get/set a limit on the number of header lines that a response can have. The default is 128. A value of 0 means no limit. $s->format_request($method, $uri, %headers, [$content]) Format a request message and return it as a string. If the headers do not include a Host header, then a header is inserted with the value of the host attribute. Headers like Connection and Keep-Alive might also be added depending on the status of the keep_alive attribute. If $content is given (and it is non-empty), then a Content-Length header is automatically added unless it was already present. $s->write_request($method, $uri, %headers, [$content]) Format and send a request message. Arguments are the same as for format_request(). Returns true if successful. $s->format_chunk( $data ) Returns the string to be written for the given chunk of data. $s->write_chunk($data) Will write a new chunk of request entity body data. This method should only be used if the Transfer-Encoding header with a value of chunked was sent in the request. Note, writing zero-length data is a no-op. Use the write_chunk_eof() method to signal end of entity body data. Returns true if successful. $s->format_chunk_eof( %trailers ) Returns the string to be written for signaling EOF when a Transfer-Encoding of chunked is used. $s->write_chunk_eof( %trailers ) Will write eof marker for chunked data and optional trailers. Note that trailers should not really be used unless is was signaled with a Trailer header. Returns true if successful. ($code, $mess, %headers) = $s->read_response_headers( %opts ) Read response headers from server and return it. The $code is the 3 digit HTTP status code (see HTTP::Status ) and $mess is the textual message that came with it. Headers are then returned as key/value pairs. Since key letter casing is not normalized and the same key can even occur multiple times, assigning these values directly to a hash is not wise. Only the $code is returned if this method is called in scalar context. As a side effect this method updates the 'peer_http_version' attribute. Options might be passed in as key/value pairs. There are currently only two options supported; laxed and junk_out . The laxed option will make read_response_headers() more forgiving towards servers that have not learned how to speak HTTP properly. The laxed option is a boolean flag, and is enabled by passing in a TRUE value. The junk_out option can be used to capture bad header lines when laxed is enabled. The value should be an array reference. Bad header lines will be pushed onto the array. The laxed option must be specified in order to communicate with pre-HTTP/1.0 servers that don't describe the response outcome or the data they send back with a header block. For these servers peer_http_version is set to "0.9" and this method returns (200, "Assumed OK"). The method will raise an exception (die) if the server does not speak proper HTTP or if the max_line_length or max_header_length limits are reached. If the laxed option is turned on and max_line_length and max_header_length checks are turned off, then no exception will be raised and this method will always return a response code. $n = $s->read_entity_body($buf, $size); Reads chunks of the entity body content. Basically the same interface as for read() and sysread(), but the buffer offset argument is not supported yet. This method should only be called after a successful read_response_headers() call. The return value will be undef on read errors, 0 on EOF, -1 if no data could be returned this time, otherwise the number of bytes assigned to $buf. The $buf is set to "" when the return value is -1. You normally want to retry this call if this function returns either -1 or undef with $! as EINTR or EAGAIN (see Errno ). EINTR can happen if the application catches signals and EAGAIN can happen if you made the socket non-blocking. This method will raise exceptions (die) if the server does not speak proper HTTP. This can only happen when reading chunked data. %headers = $s->get_trailers After read_entity_body() has returned 0 to indicate end of the entity body, you might call this method to pick up any trailers. $s->_rbuf Get/set the read buffer content. The read_response_headers() and read_entity_body() methods use an internal buffer which they will look for data before they actually sysread more from the socket itself. If they read too much, the remaining data will be left in this buffer. $s->_rbuf_length Returns the number of bytes in the read buffer. This should always be the same as: length($s->_rbuf) but might be more efficient. SUBCLASSING The read_response_headers() and read_entity_body() will invoke the sysread() method when they need more data. Subclasses might want to override this method to control how reading takes place. The object itself is a glob. Subclasses should avoid using hash key names prefixed with http_ and io_ . SEE ALSO LWP , IO::Socket::INET , Net::HTTP::NB AUTHOR Gisle Aas gisle@activestate.com COPYRIGHT AND LICENSE This software is copyright (c) 2001 by Gisle Aas. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. About Low-level HTTP client metacpan.org/pod/Net::HTTP Topics hacktoberfest Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 20 stars Watchers 11 watching Forks 27 forks Report repository Releases 26 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-net-http --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-net-http 6.09 0 +-------------------- +file name : perl-net-http-6.09-0.tar.bz2 +name : perl-net-http +version : 6.09 +build : 0 +build number: 0 +size : 11 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-net-http-6.09-0.tar.bz2 +md5 : 6a207c72e56d1783c1fdef728681b6ba +dependencies: + - perl-io-socket-ssl + - perl-threaded + - perl-uri + - perl >=5.22.0,<5.23.0 + + +perl-net-http 6.09 pl526_1 +-------------------------- +file name : perl-net-http-6.09-pl526_1.tar.bz2 +name : perl-net-http +version : 6.09 +build : pl526_1 +build number: 1 +size : 18 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-net-http-6.09-pl526_1.tar.bz2 +md5 : fff0634200544e37fad805b64541e414 +timestamp : 2018-07-08 17:02:29 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-io-socket-ssl + - perl-uri + + +perl-net-http 6.18 pl526_0 +-------------------------- +file name : perl-net-http-6.18-pl526_0.tar.bz2 +name : perl-net-http +version : 6.18 +build : pl526_0 +build number: 0 +size : 19 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-net-http-6.18-pl526_0.tar.bz2 +md5 : ed8ac92fb657b0161e9cdbe303712229 +timestamp : 2018-08-24 03:20:45 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-carp + - perl-compress-raw-zlib + - perl-io-socket-ssl + - perl-uri + + +perl-net-http 6.19 pl526_0 +-------------------------- +file name : perl-net-http-6.19-pl526_0.tar.bz2 +name : perl-net-http +version : 6.19 +build : pl526_0 +build number: 0 +size : 19 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-net-http-6.19-pl526_0.tar.bz2 +md5 : 160f8e846ea37406d973acbf83b5a26b +timestamp : 2019-05-21 11:05:48 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-base + - perl-carp + - perl-compress-raw-zlib + - perl-io-socket-ssl + - perl-uri + + +perl-net-http 6.19 pl5321hdfd78af_1 +----------------------------------- +file name : perl-net-http-6.19-pl5321hdfd78af_1.tar.bz2 +name : perl-net-http +version : 6.19 +build : pl5321hdfd78af_1 +build number: 1 +size : 21 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-net-http-6.19-pl5321hdfd78af_1.tar.bz2 +md5 : 6f6dcf2fa0d08c2f49ebaa232b652c00 +timestamp : 2022-01-26 13:36:03 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-base + - perl-carp + - perl-compress-raw-zlib + - perl-io-socket-ssl + - perl-uri + + +perl-net-http 6.22 pl5321hdfd78af_0 +----------------------------------- +file name : perl-net-http-6.22-pl5321hdfd78af_0.tar.bz2 +name : perl-net-http +version : 6.22 +build : pl5321hdfd78af_0 +build number: 0 +size : 21 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-net-http-6.22-pl5321hdfd78af_0.tar.bz2 +md5 : f3b44f2b9932c3def346e6ad9aabe43d +timestamp : 2022-02-15 07:21:50 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-base + - perl-carp + - perl-compress-raw-zlib + - perl-io-socket-ssl + - perl-uri + + +perl-net-http 6.23 pl5321hdfd78af_0 +----------------------------------- +file name : perl-net-http-6.23-pl5321hdfd78af_0.conda +name : perl-net-http +version : 6.23 +build : pl5321hdfd78af_0 +build number: 0 +size : 22 KB +license : Perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-net-http-6.23-pl5321hdfd78af_0.conda +md5 : adef500cebc1f616ff4a2cdb3ba62dca +timestamp : 2025-08-19 00:53:19 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-base + - perl-carp + - perl-compress-raw-zlib + - perl-io-socket-ssl + - perl-uri + + +perl-net-http 6.24 pl5321hdfd78af_0 +----------------------------------- +file name : perl-net-http-6.24-pl5321hdfd78af_0.conda +name : perl-net-http +version : 6.24 +build : pl5321hdfd78af_0 +build number: 0 +size : 22 KB +license : Perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-net-http-6.24-pl5321hdfd78af_0.conda +md5 : b52c57918e321baa0b44040086d1ca8c +timestamp : 2025-08-29 12:26:26 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-base + - perl-carp + - perl-compress-raw-zlib + - perl-io-socket-ssl + - perl-uri diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-ntlm.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-ntlm.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..a2ab57df8d2a5111b3049773acbb9f9be59d03af --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-ntlm.manual_bundle.txt @@ -0,0 +1,153 @@ +# Tool: perl-ntlm +software_name: perl-ntlm +tier: T1 +domain: t1_backfill_overall +downloads: 491115 +summary: An NTLM authentication module +description: An NTLM authentication module +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-digest-hmac +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-ntlm --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-ntlm 1.09 1 +---------------- +file name : perl-ntlm-1.09-1.tar.bz2 +name : perl-ntlm +version : 1.09 +build : 1 +build number: 1 +size : 9 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-ntlm-1.09-1.tar.bz2 +md5 : c8e13cd462596010a2b5477cd91ad78e +dependencies: + - perl-digest-hmac + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-ntlm 1.09 pl526_2 +---------------------- +file name : perl-ntlm-1.09-pl526_2.tar.bz2 +name : perl-ntlm +version : 1.09 +build : pl526_2 +build number: 2 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-ntlm-1.09-pl526_2.tar.bz2 +md5 : 086fb4ae540823fd9f0904801690b2e4 +timestamp : 2018-07-07 16:54:06 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-digest-hmac + + +perl-ntlm 1.09 pl526_3 +---------------------- +file name : perl-ntlm-1.09-pl526_3.tar.bz2 +name : perl-ntlm +version : 1.09 +build : pl526_3 +build number: 3 +size : 14 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-ntlm-1.09-pl526_3.tar.bz2 +md5 : 29a236cfc9a9285ec8910ce7139d1ad9 +timestamp : 2018-08-01 23:37:46 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-digest-hmac + + +perl-ntlm 1.09 pl526_4 +---------------------- +file name : perl-ntlm-1.09-pl526_4.tar.bz2 +name : perl-ntlm +version : 1.09 +build : pl526_4 +build number: 4 +size : 15 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-ntlm-1.09-pl526_4.tar.bz2 +md5 : 7863718bc88444211e686dc91dbf4292 +timestamp : 2019-03-09 11:53:52 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-digest-hmac + + +perl-ntlm 1.09 pl5321hdfd78af_5 +------------------------------- +file name : perl-ntlm-1.09-pl5321hdfd78af_5.tar.bz2 +name : perl-ntlm +version : 1.09 +build : pl5321hdfd78af_5 +build number: 5 +size : 16 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-ntlm-1.09-pl5321hdfd78af_5.tar.bz2 +md5 : dac95634eb35296b62569c77e2ceef5c +timestamp : 2022-01-17 23:27:43 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-digest-hmac diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-number-format.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-number-format.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dd49a49c008adc05d8a64115f0b82d1cd11975f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-number-format.manual_bundle.txt @@ -0,0 +1,185 @@ +# Tool: perl-number-format +software_name: perl-number-format +tier: T1 +domain: t1_backfill_overall +downloads: 184685 +summary: Perl extension for formatting numbers +description: Perl extension for formatting numbers +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-carp +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Number::Format +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Number::Format +Number::Format - Perl extension for formatting numbers - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Number-Format Module version: 1.76 26 May 2023 01:00:16 UTC License: perl_5 Code Download ( 24.36KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (22) How to Contribute Quality Testers ( 4416 / 383 / 20 ) Testers (Magpie) Kwalitee 87.89% Coverage Bus factor: 1 Activity 24 month Dependencies Carp POSIX and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 1.77-TRIAL DEV (RJBS on 2026-02-22) 0.001-TRIAL DEV (RJBS on 2026-02-22) 1.76 (RJBS on 2023-05-26) 1.75 (WRW on 2015-06-25) 1.73 (WRW on 2009-09-26) 1.72a (WRW on 2009-05-05) 1.72 (WRW on 2009-05-05) 1.71 (WRW on 2009-05-03) 1.70 (WRW on 2009-02-13) 1.63 (WRW on 2009-02-10) 1.62 (WRW on 2009-02-09) 1.61a (WRW on 2008-12-30) 1.61 (WRW on 2008-12-30) 1.60 (WRW on 2008-07-03) 1.52 (WRW on 2006-09-21) 1.51 (WRW on 2006-04-26) 1.45 (WRW on 2002-08-28) 1.44 (WRW on 2001-12-11) 1.43 (WRW on 2001-12-11) 1.42 (WRW on 2000-05-24) 1.41 (WRW on 1999-03-09) 1.30 (WRW on 1998-11-17) 1.12 (WRW on 1998-03-02) 1.10 (WRW on 1998-02-13) Diff with version 1.77-TRIAL DEV (RJBS on 2026-02-22) 0.001-TRIAL DEV (RJBS on 2026-02-22) 1.76 (RJBS on 2023-05-26) 1.75 (WRW on 2015-06-25) 1.73 (WRW on 2009-09-26) 1.72a (WRW on 2009-05-05) 1.72 (WRW on 2009-05-05) 1.71 (WRW on 2009-05-03) 1.70 (WRW on 2009-02-13) 1.63 (WRW on 2009-02-10) 1.62 (WRW on 2009-02-09) 1.61a (WRW on 2008-12-30) 1.61 (WRW on 2008-12-30) 1.60 (WRW on 2008-07-03) 1.52 (WRW on 2006-09-21) 1.51 (WRW on 2006-04-26) 1.45 (WRW on 2002-08-28) 1.44 (WRW on 2001-12-11) 1.43 (WRW on 2001-12-11) 1.42 (WRW on 2000-05-24) 1.41 (WRW on 1999-03-09) 1.30 (WRW on 1998-11-17) 1.12 (WRW on 1998-03-02) 1.10 (WRW on 1998-02-13) Permalinks This version Latest version ++ed by: 12 PAUSE users 3 non-PAUSE users Authors: William R. Ward Released by: Ricardo SIGNES 🙂 Maintainers: WRW owner RJBS Contributors: William R. Ward Ricardo SIGNES 🙂  /  1.77-TRIAL DEV (RJBS on 2026-02-22) 0.001-TRIAL DEV (RJBS on 2026-02-22) 1.76 (RJBS on 2023-05-26) 1.75 (WRW on 2015-06-25) 1.73 (WRW on 2009-09-26) 1.72a (WRW on 2009-05-05) 1.72 (WRW on 2009-05-05) 1.71 (WRW on 2009-05-03) 1.70 (WRW on 2009-02-13) 1.63 (WRW on 2009-02-10) 1.62 (WRW on 2009-02-09) 1.61a (WRW on 2008-12-30) 1.61 (WRW on 2008-12-30) 1.60 (WRW on 2008-07-03) 1.52 (WRW on 2006-09-21) 1.51 (WRW on 2006-04-26) 1.45 (WRW on 2002-08-28) 1.44 (WRW on 2001-12-11) 1.43 (WRW on 2001-12-11) 1.42 (WRW on 2000-05-24) 1.41 (WRW on 1999-03-09) 1.30 (WRW on 1998-11-17) 1.12 (WRW on 1998-03-02) 1.10 (WRW on 1998-02-13) Number-Format-1.76 15 ++ 15 ++ / Number::Format Contents NAME SYNOPSIS REQUIRES DESCRIPTION EXPORTS METHODS CAVEATS BUGS AUTHOR SEE ALSO NAME Number::Format - Perl extension for formatting numbers SYNOPSIS use Number::Format; my $x = new Number::Format %args; $formatted = $x->round($number, $precision); $formatted = $x->format_number($number, $precision, $trailing_zeroes); $formatted = $x->format_negative($number, $picture); $formatted = $x->format_picture($number, $picture); $formatted = $x->format_price($number, $precision, $symbol); $formatted = $x->format_bytes($number, $precision); $number = $x->unformat_number($formatted); use Number::Format qw(:subs); $formatted = round($number, $precision); $formatted = format_number($number, $precision, $trailing_zeroes); $formatted = format_negative($number, $picture); $formatted = format_picture($number, $picture); $formatted = format_price($number, $precision, $symbol); $formatted = format_bytes($number, $precision); $number = unformat_number($formatted); REQUIRES Perl, version 5.8 or higher. POSIX.pm to determine locale settings. Carp.pm is used for some error reporting. DESCRIPTION These functions provide an easy means of formatting numbers in a manner suitable for displaying to the user. There are two ways to use this package. One is to declare an object of type Number::Format, which you can think of as a formatting engine. The various functions defined here are provided as object methods. The constructor new() can be used to set the parameters of the formatting engine. Valid parameters are: THOUSANDS_SEP - character inserted between groups of 3 digits DECIMAL_POINT - character separating integer and fractional parts MON_THOUSANDS_SEP - like THOUSANDS_SEP, but used for format_price MON_DECIMAL_POINT - like DECIMAL_POINT, but used for format_price INT_CURR_SYMBOL - character(s) denoting currency (see format_price()) DECIMAL_DIGITS - number of digits to the right of dec point (def 2) DECIMAL_FILL - boolean; whether to add zeroes to fill out decimal NEG_FORMAT - format to display negative numbers (def ``-x'') KILO_SUFFIX - suffix to add when format_bytes formats kilobytes (trad) MEGA_SUFFIX - " " " " " " megabytes (trad) GIGA_SUFFIX - " " " " " " gigabytes (trad) KIBI_SUFFIX - suffix to add when format_bytes formats kibibytes (iec) MEBI_SUFFIX - " " " " " " mebibytes (iec) GIBI_SUFFIX - " " " " " " gibibytes (iec) They may be specified in upper or lower case, with or without a leading hyphen ( - ). If THOUSANDS_SEP is set to the empty string, format_number will not insert any separators. The defaults for THOUSANDS_SEP , DECIMAL_POINT , MON_THOUSANDS_SEP , MON_DECIMAL_POINT , and INT_CURR_SYMBOL come from the POSIX locale information (see perllocale ). If your POSIX locale does not provide MON_THOUSANDS_SEP and/or MON_DECIMAL_POINT fields, then the THOUSANDS_SEP and/or DECIMAL_POINT values are used for those parameters. Formerly, POSIX was optional but this caused problems in some cases, so it is now required. If this causes you hardship, please contact the author of this package at <SwPrAwM@cpan.org> (remove "SPAM" to get correct email address) for help. If any of the above parameters are not specified when you invoke new() , then the values are taken from package global variables of the same name (e.g. $DECIMAL_POINT is the default for the DECIMAL_POINT parameter). If you use the :vars keyword on your use Number::Format line (see non-object-oriented example below) you will import those variables into your namesapce and can assign values as if they were your own local variables. The default values for all the parameters are: THOUSANDS_SEP = ',' DECIMAL_POINT = '.' MON_THOUSANDS_SEP = ',' MON_DECIMAL_POINT = '.' INT_CURR_SYMBOL = 'USD' DECIMAL_DIGITS = 2 DECIMAL_FILL = 0 NEG_FORMAT = '-x' KILO_SUFFIX = 'K' MEGA_SUFFIX = 'M' GIGA_SUFFIX = 'G' KIBI_SUFFIX = 'KiB' MEBI_SUFFIX = 'MiB' GIBI_SUFFIX = 'GiB' Note however that when you first call one of the functions in this module without using the object-oriented interface, further setting of those global variables will have no effect on non-OO calls. It is recommended that you use the object-oriented interface instead for fewer headaches and a cleaner design. The DECIMAL_FILL and DECIMAL_DIGITS values are not set by the Locale system, but are definable by the user. They affect the output of format_number() . Setting DECIMAL_DIGITS is like giving that value as the $precision argument to that function. Setting DECIMAL_FILL to a true value causes format_number() to append zeroes to the right of the decimal digits until the length is the specified number of digits. NEG_FORMAT is only used by format_negative() and is a string containing the letter 'x', where that letter will be replaced by a positive representation of the number being passed to that function. format_number() and format_price() utilize this feature by calling format_negative() if the number was less than 0. KILO_SUFFIX , MEGA_SUFFIX , and GIGA_SUFFIX are used by format_bytes() when the value is over 1024, 1024*1024, or 1024*1024*1024, respectively. The default values are "K", "M", and "G". These apply in the default "traditional" mode only. Note: TERA or higher are not implemented because of integer overflows on 32-bit systems. KIBI_SUFFIX , MEBI_SUFFIX , and GIBI_SUFFIX are used by format_bytes() when the value is over 1024, 1024*1024, or 1024*1024*1024, respectively. The default values are "KiB", "MiB", and "GiB". These apply in the "iso60027"" mode only. Note: TEBI or higher are not implemented because of integer overflows on 32-bit systems. The only restrictions on DECIMAL_POINT and THOUSANDS_SEP are that they must not be digits and must not be identical. There are no restrictions on INT_CURR_SYMBOL . For example, a German user might include this in their code: use Number::Format; my $de = new Number::Format(-thousands_sep => '.', -decimal_point => ',', -int_curr_symbol => 'DEM'); my $formatted = $de->format_number($number); Or, if you prefer not to use the object oriented interface, you can do this instead: use Number::Format qw(:subs :vars); $THOUSANDS_SEP = '.'; $DECIMAL_POINT = ','; $INT_CURR_SYMBOL = 'DEM'; my $formatted = format_number($number); EXPORTS Nothing is exported by default. To export the functions or the global variables defined herein, specify the function name(s) on the import list of the use Number::Format statement. To export all functions defined herein, use the special tag :subs . To export the variables, use the special tag :vars ; to export both subs and vars you can use the tag :all . METHODS new( %args ) Creates a new Number::Format object. Valid keys for %args are any of the parameters described above. Keys may be in all uppercase or all lowercase, and may optionally be preceded by a hyphen (-) character. Example: my $de = new Number::Format(-thousands_sep => '.', -decimal_point => ',', -int_curr_symbol => 'DEM'); round($number, $precision) Rounds the number to the specified precision. If $precision is omitted, the value of the DECIMAL_DIGITS parameter is used (default value 2). Both input and output are numeric (the function uses math operators rather than string manipulation to do its job), The value of $precision may be any integer, positive or negative. Examples: round(3.14159) yields 3.14 round(3.14159, 4) yields 3.1416 round(42.00, 4) yields 42 round(1234, -2) yields 1200 Since this is a mathematical rather than string oriented function, there will be no trailing zeroes to the right of the decimal point, and the DECIMAL_POINT and THOUSANDS_SEP variables are ignored. To format your number using the DECIMAL_POINT and THOUSANDS_SEP variables, use format_number() instead. format_number($number, $precision, $trailing_zeroes) Formats a number by adding THOUSANDS_SEP between each set of 3 digits to the left of the decimal point, substituting DECIMAL_POINT for the decimal point, and rounding to the specified precision using round() . Note that $precision is a maximum precision specifier; trailing zeroes will only appear in the output if $trailing_zeroes is provided, or the parameter DECIMAL_FILL is set, with a value that is true (not zero, undef, or the empty string). If $precision is omitted, the value of the DECIMAL_DIGITS parameter (default value of 2) is used. If the value is too large or great to work with as a regular number, but instead must be shown in scientific notation, returns that number in scientific notation without further formatting. Examples: format_number(12345.6789) yields '12,345.68' format_number(123456.789, 2) yields '123,456.79' format_number(1234567.89, 2) yields '1,234,567.89' format_number(1234567.8, 2) yields '1,234,567.8' format_number(1234567.8, 2, 1) yields '1,234,567.80' format_number(1.23456789, 6) yields '1.234568' format_number("0.000020000E+00", 7);' yields '2e-05' Of course the output would have your values of THOUSANDS_SEP and DECIMAL_POINT instead of ',' and '.' respectively. format_negative($number, $picture) Formats a negative number. Picture should be a string that contains the letter x where the number should be inserted. For example, for standard negative numbers you might use `` -x '', while for accounting purposes you might use `` (x) ''. If the specified number begins with a ``-'' character, that will be removed before formatting, but formatting will occur whether or not the number is negative. format_picture($number, $picture) Returns a string based on $picture with the # characters replaced by digits from $number . If the length of the integer part of $number is too large to fit, the # characters are replaced with asterisks ( * ) instead. Examples: format_picture(100.023, 'USD ##,###.##') yields 'USD 100.02' format_picture(1000.23, 'USD ##,###.##') yields 'USD 1,000.23' format_picture(10002.3, 'USD ##,###.##') yields 'USD 10,002.30' format_picture(100023, 'USD ##,###.##') yields 'USD **,***.**' format_picture(1.00023, 'USD #.###,###') yields 'USD 1.002,300' The comma (,) and period (.) you see in the picture examples should match the values of THOUSANDS_SEP and DECIMAL_POINT , respectively, for proper operation. However, the THOUSANDS_SEP characters in $picture need not occur every three digits; the only use of that variable by this function is to remove leading commas (see the first example above). There may not be more than one instance of DECIMAL_POINT in $picture . The value of NEG_FORMAT is used to determine how negative numbers are displayed. The result of this is that the output of this function my have unexpected spaces before and/or after the number. This is necessary so that positive and negative numbers are formatted into a space the same size. If you are only using positive numbers and want to avoid this problem, set NEG_FORMAT to "x". format_price($number, $precision, $symbol) Returns a string containing $number formatted similarly to format_number() , except that the decimal portion may have trailing zeroes added to make it be exactly $precision characters long, and the currency string will be prefixed. The $symbol attribute may be one of "INT_CURR_SYMBOL" or "CURRENCY_SYMBOL" (case insensitive) to use the value of that attribute of the object, or a string containing the symbol to be used. The default is "INT_CURR_SYMBOL" if this argument is undefined or not given; if set to the empty string, or if set to undef and the INT_CURR_SYMBOL attribute of the object is the empty string, no currency will be added. If $precision is not provided, the default of 2 will be used. Examples: format_price(12.95) yields 'USD 12.95' format_price(12) yields 'USD 12.00' format_price(12, 3) yields '12.000' The third example assumes that INT_CURR_SYMBOL is the empty string. format_bytes($number, %options) format_bytes($number, $precision) # deprecated Returns a string containing $number formatted similarly to format_number() , except that large numbers may be abbreviated by adding a suffix to indicate 1024, 1,048,576, or 1,073,741,824 bytes. Suffix may be the traditional K, M, or G (default); or the IEC standard 60027 "KiB," "MiB," or "GiB" depending on the "mode" option. Negative values will result in an error. The second parameter can be either a hash that sets options, or a number. Using a number here is deprecated and will generate a warning; early versions of Number::Format only allowed a numeric value. A future release of Number::Format will change this warning to an error. New code should use a hash instead to set options. If it is a number this sets the value of the "precision" option. Valid options are: precision Set the precision for displaying numbers. If not provided, a default of 2 will be used. Examples: format_bytes(12.95) yields '12.95' format_bytes(12.95, precision => 0) yields '13' format_bytes(2048) yields '2K' format_bytes(2048, mode => "iec") yields '2KiB' format_bytes(9999999) yields '9.54M' format_bytes(9999999, precision => 1) yields '9.5M' unit Sets the default units used for the results. The default is to determine this automatically in order to minimize the length of the string. In other words, numbers greater than or equal to 1024 (or other number given by the 'base' option, q.v.) will be divided by 1024 and $KILO_SUFFIX or $KIBI_SUFFIX added; if greater than or equal to 1048576 (1024*1024), it will be divided by 1048576 and $MEGA_SUFFIX or $MEBI_SUFFIX appended to the end; etc. However if a value is given for unit it will use that value instead. The first letter (case-insensitive) of the value given indicates the threshhold for conversion; acceptable values are G (for giga/gibi), M (for mega/mebi), K (for kilo/kibi), or A (for automatic, the default). For example: format_bytes(1048576, unit => 'K') yields '1,024K' instead of '1M' Note that the valid values to this option do not vary even when the suffix configuration variables have been changed. base Sets the number at which the $KILO_SUFFIX is added. Default is 1024. Set to any value; the only other useful value is probably 1000, as hard disk manufacturers use that number to make their disks sound bigger than they really are. If the mode (see below) is set to "iec" or "iec60027" then setting the base option results in an error. mode Traditionally, bytes have been given in SI (metric) units such as "kilo" and "mega" even though they represent powers of 2 (1024, etc.) rather than powers of 10 (1000, etc.) This "binary prefix" causes much confusion in consumer products where "GB" may mean either 1,048,576 or 1,000,000, for example. The International Electrotechnical Commission has created standard IEC 60027 to introduce prefixes Ki, Mi, Gi, etc. ("kibibytes," "mebibytes," "gibibytes," etc.) to remove this confusion. Specify a mode option with either "traditional" or "iec60027" (or abbreviate as "trad" or "iec") to indicate which type of binary prefix you want format_bytes to use. For backward compatibility, "traditional" is the default. See http://en.wikipedia.org/wiki/Binary_prefix for more information. unformat_number($formatted) Converts a string as returned by format_number() , format_price() , or format_picture() , and returns the corresponding value as a numeric scalar. Returns undef if the number does not contain any digits. Examples: unformat_number('USD 12.95') yields 12.95 unformat_number('USD 12.00') yields 12 unformat_number('foobar') yields undef unformat_number('1234-567@.8') yields 1234567.8 The value of DECIMAL_POINT is used to determine where to separate the integer and decimal portions of the input. All other non-digit characters, including but not limited to INT_CURR_SYMBOL and THOUSANDS_SEP , are removed. If the number matches the pattern of NEG_FORMAT or there is a ``-'' character before any of the digits, then a negative number is returned. If the number ends with the KILO_SUFFIX , KIBI_SUFFIX , MEGA_SUFFIX , MEBI_SUFFIX , GIGA_SUFFIX , or GIBI_SUFFIX characters, then the number returned will be multiplied by the appropriate multiple of 1024 (or if the base option is given, by the multiple of that value) as appropriate. Examples: unformat_number("4K", base => 1024) yields 4096 unformat_n + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-number-format --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-number-format 1.75 1 +------------------------- +file name : perl-number-format-1.75-1.tar.bz2 +name : perl-number-format +version : 1.75 +build : 1 +build number: 1 +size : 14 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-number-format-1.75-1.tar.bz2 +md5 : 6d89a5ef06aedebdf0fe7f3b4faeea38 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-number-format 1.75 pl5.22.0_0 +---------------------------------- +file name : perl-number-format-1.75-pl5.22.0_0.tar.bz2 +name : perl-number-format +version : 1.75 +build : pl5.22.0_0 +build number: 0 +size : 14 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-number-format-1.75-pl5.22.0_0.tar.bz2 +md5 : 9d13a5ff1a8558edb5f2f106a2a4a10d +dependencies: + - perl 5.22.0* + + +perl-number-format 1.75 pl526_2 +------------------------------- +file name : perl-number-format-1.75-pl526_2.tar.bz2 +name : perl-number-format +version : 1.75 +build : pl526_2 +build number: 2 +size : 20 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-number-format-1.75-pl526_2.tar.bz2 +md5 : e01897224e04d900295b5df8b88e59fe +timestamp : 2018-07-08 13:40:46 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-number-format 1.75 pl526_3 +------------------------------- +file name : perl-number-format-1.75-pl526_3.tar.bz2 +name : perl-number-format +version : 1.75 +build : pl526_3 +build number: 3 +size : 20 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-number-format-1.75-pl526_3.tar.bz2 +md5 : 9c71056389596bcea214fbadd7f72eb7 +timestamp : 2018-08-27 22:36:03 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-carp + + +perl-number-format 1.75 pl5321hdfd78af_4 +---------------------------------------- +file name : perl-number-format-1.75-pl5321hdfd78af_4.tar.bz2 +name : perl-number-format +version : 1.75 +build : pl5321hdfd78af_4 +build number: 4 +size : 23 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-number-format-1.75-pl5321hdfd78af_4.tar.bz2 +md5 : 7432a95c0f962cfa5412419905035a09 +timestamp : 2022-01-20 00:41:40 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + + +perl-number-format 1.76 pl5321hd8ed1ab_0 +---------------------------------------- +file name : perl-number-format-1.76-pl5321hd8ed1ab_0.conda +name : perl-number-format +version : 1.76 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 34 KB +license : Artistic-1.0-Perl OR GPL-1.0-or-later +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-number-format-1.76-pl5321hd8ed1ab_0.conda +md5 : 9eeca3397a5a51a7ff35ca30be3c44e0 +timestamp : 2024-02-07 04:00:28 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-number-format 1.76 pl5321hdfd78af_0 +---------------------------------------- +file name : perl-number-format-1.76-pl5321hdfd78af_0.tar.bz2 +name : perl-number-format +version : 1.76 +build : pl5321hdfd78af_0 +build number: 0 +size : 24 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-number-format-1.76-pl5321hdfd78af_0.tar.bz2 +md5 : 8989a9122b03e99f613877fb18cb30c5 +timestamp : 2023-05-29 02:21:57 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-package-stash.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-package-stash.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f1b05a7f210f74eb20ec554578ff1256d04cdd5 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-package-stash.manual_bundle.txt @@ -0,0 +1,356 @@ +# Tool: perl-package-stash +software_name: perl-package-stash +tier: T1 +domain: t1_backfill_overall +downloads: 269514 +summary: routines for manipulating stashes +description: routines for manipulating stashes +dependencies: libgcc-ng >=10.3.0, libstdcxx-ng >=10.3.0, perl >=5.32.1,<5.33.0a0 *_perl5, perl-apache-test, perl-app-cpanminus, perl-dist-checkconflicts, perl-getopt-long, perl-module-implementation, perl-package-stash-xs, perl-scalar-list-utils +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/release/Package-Stash +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/release/Package-Stash +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-package-stash --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-package-stash 0.37 pl5.22.0_0 +---------------------------------- +file name : perl-package-stash-0.37-pl5.22.0_0.tar.bz2 +name : perl-package-stash +version : 0.37 +build : pl5.22.0_0 +build number: 0 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-0.37-pl5.22.0_0.tar.bz2 +md5 : 9ec2844508bb76f038c8f25bd5902a5a +dependencies: + - perl 5.22.0* + - perl-apache-test + - perl-dist-checkconflicts + - perl-getopt-long + - perl-module-implementation + - perl-scalar-list-utils + + +perl-package-stash 0.37 pl526hfc679d8_2 +--------------------------------------- +file name : perl-package-stash-0.37-pl526hfc679d8_2.tar.bz2 +name : perl-package-stash +version : 0.37 +build : pl526hfc679d8_2 +build number: 2 +size : 70 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-0.37-pl526hfc679d8_2.tar.bz2 +md5 : 48330a4654daafc23eeaa9cfbd1ed991 +timestamp : 2018-07-19 11:03:44 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.27.0a0 + - perl-apache-test + - perl-app-cpanminus + - perl-dist-checkconflicts + - perl-getopt-long + - perl-module-implementation + - perl-package-stash-xs + - perl-scalar-list-utils + + +perl-package-stash 0.38 pl526hf484d3e_1 +--------------------------------------- +file name : perl-package-stash-0.38-pl526hf484d3e_1.tar.bz2 +name : perl-package-stash +version : 0.38 +build : pl526hf484d3e_1 +build number: 1 +size : 66 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-0.38-pl526hf484d3e_1.tar.bz2 +md5 : cfceef3c9c95da229cccb715ddd11c18 +timestamp : 2019-05-07 20:48:47 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-apache-test + - perl-app-cpanminus + - perl-dist-checkconflicts + - perl-getopt-long + - perl-module-implementation + - perl-package-stash-xs + - perl-scalar-list-utils + + +perl-package-stash 0.38 pl526hfc679d8_0 +--------------------------------------- +file name : perl-package-stash-0.38-pl526hfc679d8_0.tar.bz2 +name : perl-package-stash +version : 0.38 +build : pl526hfc679d8_0 +build number: 0 +size : 71 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-0.38-pl526hfc679d8_0.tar.bz2 +md5 : c640553283711378561e27a6482458b0 +timestamp : 2018-12-31 21:39:14 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-apache-test + - perl-app-cpanminus + - perl-dist-checkconflicts + - perl-getopt-long + - perl-module-implementation + - perl-package-stash-xs + - perl-scalar-list-utils + + +perl-package-stash 0.38 pl5321h1b792b2_2 +---------------------------------------- +file name : perl-package-stash-0.38-pl5321h1b792b2_2.tar.bz2 +name : perl-package-stash +version : 0.38 +build : pl5321h1b792b2_2 +build number: 2 +size : 96 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-0.38-pl5321h1b792b2_2.tar.bz2 +md5 : 480d994790fbc3dc439985defae4c3e8 +timestamp : 2022-01-24 13:03:12 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-apache-test + - perl-app-cpanminus + - perl-dist-checkconflicts + - perl-getopt-long + - perl-module-implementation + - perl-package-stash-xs + - perl-scalar-list-utils + + +perl-package-stash 0.38 pl5321h1b792b2_3 +---------------------------------------- +file name : perl-package-stash-0.38-pl5321h1b792b2_3.tar.bz2 +name : perl-package-stash +version : 0.38 +build : pl5321h1b792b2_3 +build number: 3 +size : 91 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-0.38-pl5321h1b792b2_3.tar.bz2 +md5 : e5662eb62818a2c52b380e6139f94143 +timestamp : 2022-02-11 01:08:55 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-apache-test + - perl-app-cpanminus + - perl-dist-checkconflicts + - perl-getopt-long + - perl-module-implementation + - perl-package-stash-xs + - perl-scalar-list-utils + + +perl-package-stash 0.39 pl5321h1b792b2_0 +---------------------------------------- +file name : perl-package-stash-0.39-pl5321h1b792b2_0.tar.bz2 +name : perl-package-stash +version : 0.39 +build : pl5321h1b792b2_0 +build number: 0 +size : 121 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-0.39-pl5321h1b792b2_0.tar.bz2 +md5 : 7edfee216ad4142c211798bcb3e3020c +timestamp : 2022-02-14 15:10:33 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-apache-test + - perl-app-cpanminus + - perl-dist-checkconflicts + - perl-getopt-long + - perl-module-implementation + - perl-package-stash-xs + - perl-scalar-list-utils + + +perl-package-stash 0.40 pl5321h87f3376_0 +---------------------------------------- +file name : perl-package-stash-0.40-pl5321h87f3376_0.tar.bz2 +name : perl-package-stash +version : 0.40 +build : pl5321h87f3376_0 +build number: 0 +size : 121 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-0.40-pl5321h87f3376_0.tar.bz2 +md5 : eac84679bcbbd26d70d05d6bdf5aed12 +timestamp : 2022-02-22 13:44:17 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-apache-test + - perl-app-cpanminus + - perl-dist-checkconflicts + - perl-getopt-long + - perl-module-implementation + - perl-package-stash-xs + - perl-scalar-list-utils + + +perl-package-stash 0.40 pl5321h87f3376_1 +---------------------------------------- +file name : perl-package-stash-0.40-pl5321h87f3376_1.tar.bz2 +name : perl-package-stash +version : 0.40 +build : pl5321h87f3376_1 +build number: 1 +size : 121 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-0.40-pl5321h87f3376_1.tar.bz2 +md5 : bc9e29e8c6022f04dc34e9be0377bec1 +timestamp : 2022-03-02 18:02:30 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-apache-test + - perl-app-cpanminus + - perl-dist-checkconflicts + - perl-getopt-long + - perl-module-implementation + - perl-package-stash-xs + - perl-scalar-list-utils + + +perl-package-stash 0.40 pl5321ha770c72_0 +---------------------------------------- +file name : perl-package-stash-0.40-pl5321ha770c72_0.conda +name : perl-package-stash +version : 0.40 +build : pl5321ha770c72_0 +build number: 0 +size : 24 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-package-stash-0.40-pl5321ha770c72_0.conda +md5 : 33df8eff696d40df0801289c9018dc31 +timestamp : 2022-12-12 16:44:29 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-cpan-meta-check 0.014.* + - perl-dist-checkconflicts 0.11.* + - perl-module-implementation 0.09.* + - perl-package-stash-xs 0.30.* + + +perl-package-stash 0.40 pl5321ha770c72_1 +---------------------------------------- +file name : perl-package-stash-0.40-pl5321ha770c72_1.conda +name : perl-package-stash +version : 0.40 +build : pl5321ha770c72_1 +build number: 1 +size : 24 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-package-stash-0.40-pl5321ha770c72_1.conda +md5 : b7809c3203c945367c37aa64b8b9563b +timestamp : 2025-02-28 08:13:21 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-cpan-meta-check 0.014.* + - perl-dist-checkconflicts 0.11.* + - perl-module-implementation 0.09.* + - perl-package-stash-xs 0.30.* + + +perl-package-stash 0.40 pl5321ha770c72_2 +---------------------------------------- +file name : perl-package-stash-0.40-pl5321ha770c72_2.conda +name : perl-package-stash +version : 0.40 +build : pl5321ha770c72_2 +build number: 2 +size : 24 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-package-stash-0.40-pl5321ha770c72_2.conda +md5 : 4a5b2fcfca8712948b62bb045dbeeca4 +timestamp : 2025-04-25 16:25:30 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-cpan-meta-check 0.014.* + - perl-dist-checkconflicts 0.11.* + - perl-module-implementation 0.09.* + - perl-package-stash-xs 0.30.* diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-params-check.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-params-check.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..73616f65f62279ced454d2c7ec348ee722799f76 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-params-check.manual_bundle.txt @@ -0,0 +1,110 @@ +# Tool: perl-params-check +software_name: perl-params-check +tier: T1 +domain: t1_backfill_overall +downloads: 154281 +summary: +description: +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-params-check --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-params-check 0.38 pl5.22.0_0 +--------------------------------- +file name : perl-params-check-0.38-pl5.22.0_0.tar.bz2 +name : perl-params-check +version : 0.38 +build : pl5.22.0_0 +build number: 0 +size : 2 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-check-0.38-pl5.22.0_0.tar.bz2 +md5 : b6c1eaa1b93f085607ac22becbf9e459 +dependencies: + - perl 5.22.0* + + +perl-params-check 0.38 pl526_1 +------------------------------ +file name : perl-params-check-0.38-pl526_1.tar.bz2 +name : perl-params-check +version : 0.38 +build : pl526_1 +build number: 1 +size : 4 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-check-0.38-pl526_1.tar.bz2 +md5 : 2895ed33ead5b5c4ea7276fd5c38e6f0 +timestamp : 2018-07-06 23:08:38 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-params-check 0.38 pl5321hdfd78af_2 +--------------------------------------- +file name : perl-params-check-0.38-pl5321hdfd78af_2.tar.bz2 +name : perl-params-check +version : 0.38 +build : pl5321hdfd78af_2 +build number: 2 +size : 6 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-params-check-0.38-pl5321hdfd78af_2.tar.bz2 +md5 : aecdb2a88d7c5695902d7b130e928f79 +timestamp : 2022-01-17 00:12:53 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-params-validate.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-params-validate.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a136aedc51ca28929368d97ae623e5734023ff8 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-params-validate.manual_bundle.txt @@ -0,0 +1,408 @@ +# Tool: perl-params-validate +software_name: perl-params-validate +tier: T1 +domain: t1_backfill_overall +downloads: 268439 +summary: Validate method/function parameters +description: Validate method/function parameters +dependencies: libgcc >=13, perl >=5.32.1,<5.33.0a0 *_perl5, perl-carp, perl-exporter, perl-module-build 0.4234.*, perl-module-implementation 0.09.*, perl-test-fatal 0.016.* +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Params-Validate +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Params-Validate +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-params-validate --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-params-validate 1.08 0 +--------------------------- +file name : perl-params-validate-1.08-0.tar.bz2 +name : perl-params-validate +version : 1.08 +build : 0 +build number: 0 +size : 35 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.08-0.tar.bz2 +md5 : 092f66366e7c8983ef4424617083b85c +dependencies: + - perl-module-implementation + - perl-scalar-list-utils + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-params-validate 1.08 pl526h470a237_2 +----------------------------------------- +file name : perl-params-validate-1.08-pl526h470a237_2.tar.bz2 +name : perl-params-validate +version : 1.08 +build : pl526h470a237_2 +build number: 2 +size : 46 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.08-pl526h470a237_2.tar.bz2 +md5 : 92e74e01a995e9ad881b8e76e0ae3861 +timestamp : 2018-07-24 21:16:27 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-module-implementation + - perl-scalar-list-utils + + +perl-params-validate 1.26 pl5.22.0_0 +------------------------------------ +file name : perl-params-validate-1.26-pl5.22.0_0.tar.bz2 +name : perl-params-validate +version : 1.26 +build : pl5.22.0_0 +build number: 0 +size : 42 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.26-pl5.22.0_0.tar.bz2 +md5 : 22d9540d71a287b41e94e4907cd76c67 +dependencies: + - libgcc + - perl 5.22.0* + - perl-module-implementation + - perl-xsloader + + +perl-params-validate 1.26 pl526_1 +--------------------------------- +file name : perl-params-validate-1.26-pl526_1.tar.bz2 +name : perl-params-validate +version : 1.26 +build : pl526_1 +build number: 1 +size : 44 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.26-pl526_1.tar.bz2 +md5 : eb1dedd4471f1f7ef3c93cfe1739fe8b +timestamp : 2018-07-24 21:13:19 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-module-implementation + - perl-xsloader + + +perl-params-validate 1.29 pl526h14c3975_1 +----------------------------------------- +file name : perl-params-validate-1.29-pl526h14c3975_1.tar.bz2 +name : perl-params-validate +version : 1.29 +build : pl526h14c3975_1 +build number: 1 +size : 25 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.29-pl526h14c3975_1.tar.bz2 +md5 : 519c57ffec490207bbbbb983e8849fb1 +timestamp : 2019-05-17 11:56:05 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-carp + - perl-exporter + - perl-module-implementation + - perl-xsloader + + +perl-params-validate 1.29 pl526h470a237_0 +----------------------------------------- +file name : perl-params-validate-1.29-pl526h470a237_0.tar.bz2 +name : perl-params-validate +version : 1.29 +build : pl526h470a237_0 +build number: 0 +size : 46 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.29-pl526h470a237_0.tar.bz2 +md5 : 9d9efa3f1bddc20b13bdb41168711c63 +timestamp : 2018-11-16 05:59:08 UTC +dependencies: + - libgcc-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + - perl-carp + - perl-exporter + - perl-module-implementation + - perl-xsloader + + +perl-params-validate 1.29 pl5321h779adbc_3 +------------------------------------------ +file name : perl-params-validate-1.29-pl5321h779adbc_3.tar.bz2 +name : perl-params-validate +version : 1.29 +build : pl5321h779adbc_3 +build number: 3 +size : 26 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.29-pl5321h779adbc_3.tar.bz2 +md5 : 834bf14ffa0931d752295d9d469ad301 +timestamp : 2022-02-10 20:09:08 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-exporter + - perl-module-implementation + + +perl-params-validate 1.30 pl5321h779adbc_0 +------------------------------------------ +file name : perl-params-validate-1.30-pl5321h779adbc_0.tar.bz2 +name : perl-params-validate +version : 1.30 +build : pl5321h779adbc_0 +build number: 0 +size : 49 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.30-pl5321h779adbc_0.tar.bz2 +md5 : 48e5bb3e7a8aac05b69696deeb632b4b +timestamp : 2022-02-14 14:11:17 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-exporter + - perl-module-implementation + + +perl-params-validate 1.30 pl5321hec16e2b_1 +------------------------------------------ +file name : perl-params-validate-1.30-pl5321hec16e2b_1.tar.bz2 +name : perl-params-validate +version : 1.30 +build : pl5321hec16e2b_1 +build number: 1 +size : 48 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.30-pl5321hec16e2b_1.tar.bz2 +md5 : 4bbd7947789d55746c44c746dfa1ddb8 +timestamp : 2022-02-24 23:29:10 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-exporter + - perl-module-implementation + + +perl-params-validate 1.31 pl5321h031d066_1 +------------------------------------------ +file name : perl-params-validate-1.31-pl5321h031d066_1.tar.bz2 +name : perl-params-validate +version : 1.31 +build : pl5321h031d066_1 +build number: 1 +size : 49 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.31-pl5321h031d066_1.tar.bz2 +md5 : 0d88538c07986817766961dc0a471d4f +timestamp : 2023-05-14 23:35:18 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-exporter + - perl-module-build 0.4234.* + - perl-module-implementation 0.09.* + - perl-test-fatal 0.016.* + + +perl-params-validate 1.31 pl5321h031d066_2 +------------------------------------------ +file name : perl-params-validate-1.31-pl5321h031d066_2.tar.bz2 +name : perl-params-validate +version : 1.31 +build : pl5321h031d066_2 +build number: 2 +size : 49 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.31-pl5321h031d066_2.tar.bz2 +md5 : 6083e6722b58a73ebdcc572450ac0669 +timestamp : 2023-05-16 16:00:15 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-exporter + - perl-module-build 0.4234.* + - perl-module-implementation 0.09.* + - perl-test-fatal 0.016.* + + +perl-params-validate 1.31 pl5321h7b50bb2_3 +------------------------------------------ +file name : perl-params-validate-1.31-pl5321h7b50bb2_3.tar.bz2 +name : perl-params-validate +version : 1.31 +build : pl5321h7b50bb2_3 +build number: 3 +size : 49 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.31-pl5321h7b50bb2_3.tar.bz2 +md5 : ab17b2903c90355f61169400506c0c07 +timestamp : 2024-12-11 21:58:03 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-exporter + - perl-module-build 0.4232.* + - perl-module-implementation 0.09.* + - perl-test-fatal 0.016.* + + +perl-params-validate 1.31 pl5321h7b50bb2_4 +------------------------------------------ +file name : perl-params-validate-1.31-pl5321h7b50bb2_4.tar.bz2 +name : perl-params-validate +version : 1.31 +build : pl5321h7b50bb2_4 +build number: 4 +size : 49 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.31-pl5321h7b50bb2_4.tar.bz2 +md5 : 6e5a6a4b1cc873ce16f49aa6a9cd9a55 +timestamp : 2025-02-05 09:34:24 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-exporter + - perl-module-build 0.4234.* + - perl-module-implementation 0.09.* + - perl-test-fatal 0.016.* + + +perl-params-validate 1.31 pl5321h7b50bb2_5 +------------------------------------------ +file name : perl-params-validate-1.31-pl5321h7b50bb2_5.tar.bz2 +name : perl-params-validate +version : 1.31 +build : pl5321h7b50bb2_5 +build number: 5 +size : 49 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.31-pl5321h7b50bb2_5.tar.bz2 +md5 : 352e598f9be93b471aa08b8bb26589ec +timestamp : 2025-04-21 21:17:27 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-exporter + - perl-module-build 0.4234.* + - perl-module-implementation 0.09.* + - perl-test-fatal 0.016.* + + +perl-params-validate 1.31 pl5321hec16e2b_0 +------------------------------------------ +file name : perl-params-validate-1.31-pl5321hec16e2b_0.tar.bz2 +name : perl-params-validate +version : 1.31 +build : pl5321hec16e2b_0 +build number: 0 +size : 49 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.31-pl5321hec16e2b_0.tar.bz2 +md5 : 875cb10f33da3c7fa7e6ff4662ab5c15 +timestamp : 2022-10-30 08:11:33 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-exporter + - perl-module-implementation + - perl-test-fatal 0.016.* + + +perl-params-validate 1.31 pl5321hec16e2b_1 +------------------------------------------ +file name : perl-params-validate-1.31-pl5321hec16e2b_1.tar.bz2 +name : perl-params-validate +version : 1.31 +build : pl5321hec16e2b_1 +build number: 1 +size : 49 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.31-pl5321hec16e2b_1.tar.bz2 +md5 : 4cc2825509741a5c256438c65a1f5e4a +timestamp : 2023-05-11 16:39:04 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-carp + - perl-exporter + - perl-module-build 0.4234.* + - perl-module-implementation 0.09.* + - perl-test-fatal 0.016.* diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-parent.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-parent.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba427ac975af178125f7ed1e29e96abb0c6b2e50 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-parent.manual_bundle.txt @@ -0,0 +1,232 @@ +# Tool: perl-parent +software_name: perl-parent +tier: T1 +domain: t1_backfill_overall +downloads: 683005 +summary: +description: +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-parent --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-parent 0.236 pl5.22.0_0 +---------------------------- +file name : perl-parent-0.236-pl5.22.0_0.tar.bz2 +name : perl-parent +version : 0.236 +build : pl5.22.0_0 +build number: 0 +size : 4 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-parent-0.236-pl5.22.0_0.tar.bz2 +md5 : b05f37ab2caf153f0f31bece2585af73 +dependencies: + - perl 5.22.0* + + +perl-parent 0.236 pl526_1 +------------------------- +file name : perl-parent-0.236-pl526_1.tar.bz2 +name : perl-parent +version : 0.236 +build : pl526_1 +build number: 1 +size : 5 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-parent-0.236-pl526_1.tar.bz2 +md5 : 389bb45e15d386db8e32613a2eb2e949 +timestamp : 2018-07-08 13:43:52 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-parent 0.236 pl5321hd8ed1ab_0 +---------------------------------- +file name : perl-parent-0.236-pl5321hd8ed1ab_0.tar.bz2 +name : perl-parent +version : 0.236 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 11 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-parent-0.236-pl5321hd8ed1ab_0.tar.bz2 +md5 : cb7fddefd8478897533a23b7fc61d486 +timestamp : 2021-11-11 15:58:02 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-parent 0.236 pl5321hdfd78af_2 +---------------------------------- +file name : perl-parent-0.236-pl5321hdfd78af_2.tar.bz2 +name : perl-parent +version : 0.236 +build : pl5321hdfd78af_2 +build number: 2 +size : 8 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-parent-0.236-pl5321hdfd78af_2.tar.bz2 +md5 : 39654d6adccb863ac8973da0f745dd52 +timestamp : 2022-01-17 22:49:43 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-parent 0.238 pl5321hd8ed1ab_0 +---------------------------------- +file name : perl-parent-0.238-pl5321hd8ed1ab_0.tar.bz2 +name : perl-parent +version : 0.238 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 11 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-parent-0.238-pl5321hd8ed1ab_0.tar.bz2 +md5 : 62eee5798cac901f449678c93cfa6277 +timestamp : 2021-11-12 05:46:50 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-parent 0.239 pl5321hd8ed1ab_0 +---------------------------------- +file name : perl-parent-0.239-pl5321hd8ed1ab_0.conda +name : perl-parent +version : 0.239 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 13 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-parent-0.239-pl5321hd8ed1ab_0.conda +md5 : 50606a6bd9fe2375b3a0e8f4cdae19f7 +timestamp : 2022-12-07 06:26:52 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-parent 0.240 pl5321hd8ed1ab_0 +---------------------------------- +file name : perl-parent-0.240-pl5321hd8ed1ab_0.conda +name : perl-parent +version : 0.240 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 13 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-parent-0.240-pl5321hd8ed1ab_0.conda +md5 : 2a3282e266565a11a953b9ebb43d850d +timestamp : 2023-02-14 06:26:36 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-parent 0.241 pl5321hd8ed1ab_0 +---------------------------------- +file name : perl-parent-0.241-pl5321hd8ed1ab_0.conda +name : perl-parent +version : 0.241 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 13 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-parent-0.241-pl5321hd8ed1ab_0.conda +md5 : 44ab631ed23c25c224ed4c849d713aac +timestamp : 2023-02-15 06:21:17 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-parent 0.242 pl5321hd8ed1ab_0 +---------------------------------- +file name : perl-parent-0.242-pl5321hd8ed1ab_0.conda +name : perl-parent +version : 0.242 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 14 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-parent-0.242-pl5321hd8ed1ab_0.conda +md5 : 82dc4aa56b13cba07513f8e27cb0fbe7 +timestamp : 2024-10-24 15:26:29 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-parent 0.243 pl5321hd8ed1ab_0 +---------------------------------- +file name : perl-parent-0.243-pl5321hd8ed1ab_0.conda +name : perl-parent +version : 0.243 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 14 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-parent-0.243-pl5321hd8ed1ab_0.conda +md5 : 314caa3b72d65f8078d426c6721dcacc +timestamp : 2024-12-05 20:15:36 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-perlio-gzip.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-perlio-gzip.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..730dc68da93ddc42940e3f198c09f7bb81bd2a3c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-perlio-gzip.manual_bundle.txt @@ -0,0 +1,291 @@ +# Tool: perl-perlio-gzip +software_name: perl-perlio-gzip +tier: T1 +domain: t1_backfill_overall +downloads: 173964 +summary: PerlIO interface to gzip/gunzip +description: PerlIO interface to gzip/gunzip +dependencies: libgcc >=13, libzlib >=1.3.1,<2.0a0, perl >=5.32.1,<5.33.0a0 *_perl5, zlib +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/PerlIO-gzip +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/PerlIO-gzip +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-perlio-gzip --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-perlio-gzip 0.19 0 +----------------------- +file name : perl-perlio-gzip-0.19-0.tar.bz2 +name : perl-perlio-gzip +version : 0.19 +build : 0 +build number: 0 +size : 12 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.19-0.tar.bz2 +md5 : 43b0367b16898e5acdf7d826ec6c2eab +dependencies: + - perl-threaded + - zlib + - perl >=5.22.0,<5.23.0 + + +perl-perlio-gzip 0.19 pl5.22.0_1 +-------------------------------- +file name : perl-perlio-gzip-0.19-pl5.22.0_1.tar.bz2 +name : perl-perlio-gzip +version : 0.19 +build : pl5.22.0_1 +build number: 1 +size : 16 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.19-pl5.22.0_1.tar.bz2 +md5 : d4e37a928f6d830f5afe47badb142d00 +dependencies: + - perl 5.22.0* + - zlib + + +perl-perlio-gzip 0.19 pl5.22.0_2 +-------------------------------- +file name : perl-perlio-gzip-0.19-pl5.22.0_2.tar.bz2 +name : perl-perlio-gzip +version : 0.19 +build : pl5.22.0_2 +build number: 2 +size : 16 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.19-pl5.22.0_2.tar.bz2 +md5 : 1f51ac70b6fd4b5589716170c6a01d53 +dependencies: + - perl 5.22.0* + - zlib 1.2.11* + + +perl-perlio-gzip 0.19 pl526h1341992_3 +------------------------------------- +file name : perl-perlio-gzip-0.19-pl526h1341992_3.tar.bz2 +name : perl-perlio-gzip +version : 0.19 +build : pl526h1341992_3 +build number: 3 +size : 16 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.19-pl526h1341992_3.tar.bz2 +md5 : 785d6477ee00df49355db84cecfbd6ca +timestamp : 2018-07-06 22:54:11 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +perl-perlio-gzip 0.20 pl526h1341992_0 +------------------------------------- +file name : perl-perlio-gzip-0.20-pl526h1341992_0.tar.bz2 +name : perl-perlio-gzip +version : 0.20 +build : pl526h1341992_0 +build number: 0 +size : 16 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.20-pl526h1341992_0.tar.bz2 +md5 : 80059d432043f4af5df07c2cc027e99e +timestamp : 2018-11-11 06:14:32 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +perl-perlio-gzip 0.20 pl526h84994c4_1 +------------------------------------- +file name : perl-perlio-gzip-0.20-pl526h84994c4_1.tar.bz2 +name : perl-perlio-gzip +version : 0.20 +build : pl526h84994c4_1 +build number: 1 +size : 17 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.20-pl526h84994c4_1.tar.bz2 +md5 : 7dd59002b832b5ca1406ada7991334eb +timestamp : 2019-04-19 17:05:22 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +perl-perlio-gzip 0.20 pl5321h577a1d6_7 +-------------------------------------- +file name : perl-perlio-gzip-0.20-pl5321h577a1d6_7.tar.bz2 +name : perl-perlio-gzip +version : 0.20 +build : pl5321h577a1d6_7 +build number: 7 +size : 19 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.20-pl5321h577a1d6_7.tar.bz2 +md5 : 81f556e71d07c5c3db8b845dfaf875e9 +timestamp : 2024-12-12 17:02:42 UTC +dependencies: + - libgcc >=13 + - libzlib >=1.3.1,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - zlib + + +perl-perlio-gzip 0.20 pl5321h5bf99c6_2 +-------------------------------------- +file name : perl-perlio-gzip-0.20-pl5321h5bf99c6_2.tar.bz2 +name : perl-perlio-gzip +version : 0.20 +build : pl5321h5bf99c6_2 +build number: 2 +size : 18 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.20-pl5321h5bf99c6_2.tar.bz2 +md5 : 47a53f9d618e55885c14ad38dffd2b1d +timestamp : 2022-01-17 08:03:45 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libzlib >=1.2.11,<1.3.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - zlib >=1.2.11,<1.3.0a0 + + +perl-perlio-gzip 0.20 pl5321h7132678_3 +-------------------------------------- +file name : perl-perlio-gzip-0.20-pl5321h7132678_3.tar.bz2 +name : perl-perlio-gzip +version : 0.20 +build : pl5321h7132678_3 +build number: 3 +size : 18 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.20-pl5321h7132678_3.tar.bz2 +md5 : b9bb53e5abae4d15cc9aed1e47080eea +timestamp : 2022-02-22 23:03:09 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - zlib >=1.2.11,<1.3.0a0 + + +perl-perlio-gzip 0.20 pl5321h7132678_4 +-------------------------------------- +file name : perl-perlio-gzip-0.20-pl5321h7132678_4.tar.bz2 +name : perl-perlio-gzip +version : 0.20 +build : pl5321h7132678_4 +build number: 4 +size : 19 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.20-pl5321h7132678_4.tar.bz2 +md5 : 631874ec7ffff164e7d82213f81fbd99 +timestamp : 2023-05-11 15:08:06 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - zlib >=1.2.13,<1.3.0a0 + + +perl-perlio-gzip 0.20 pl5321he4a0461_5 +-------------------------------------- +file name : perl-perlio-gzip-0.20-pl5321he4a0461_5.tar.bz2 +name : perl-perlio-gzip +version : 0.20 +build : pl5321he4a0461_5 +build number: 5 +size : 19 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.20-pl5321he4a0461_5.tar.bz2 +md5 : a7382c92569cfc4e43d9c95dd46f6070 +timestamp : 2023-05-16 01:48:49 UTC +dependencies: + - libgcc-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - zlib + + +perl-perlio-gzip 0.20 pl5321he4a0461_6 +-------------------------------------- +file name : perl-perlio-gzip-0.20-pl5321he4a0461_6.tar.bz2 +name : perl-perlio-gzip +version : 0.20 +build : pl5321he4a0461_6 +build number: 6 +size : 19 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-perlio-gzip-0.20-pl5321he4a0461_6.tar.bz2 +md5 : 0d31e1fcce11003a1a52328648c13297 +timestamp : 2024-11-05 10:13:24 UTC +dependencies: + - libgcc >=12 + - libzlib >=1.2.13,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - zlib diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-pod-escapes.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-pod-escapes.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f31b4d65f7c3a949fa8825d6abcd7574d40615f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-pod-escapes.manual_bundle.txt @@ -0,0 +1,113 @@ +# Tool: perl-pod-escapes +software_name: perl-pod-escapes +tier: T1 +domain: t1_backfill_overall +downloads: 179594 +summary: +description: +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-exporter +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-pod-escapes --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-pod-escapes 1.07 pl5.22.0_0 +-------------------------------- +file name : perl-pod-escapes-1.07-pl5.22.0_0.tar.bz2 +name : perl-pod-escapes +version : 1.07 +build : pl5.22.0_0 +build number: 0 +size : 9 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-pod-escapes-1.07-pl5.22.0_0.tar.bz2 +md5 : f6385529e4798afbab99e36fb41241cf +dependencies: + - perl 5.22.0* + - perl-exporter + + +perl-pod-escapes 1.07 pl526_1 +----------------------------- +file name : perl-pod-escapes-1.07-pl526_1.tar.bz2 +name : perl-pod-escapes +version : 1.07 +build : pl526_1 +build number: 1 +size : 10 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-pod-escapes-1.07-pl526_1.tar.bz2 +md5 : e742de28b39935198dd942aae04335ea +timestamp : 2018-07-08 17:35:21 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-exporter + + +perl-pod-escapes 1.07 pl5321hdfd78af_2 +-------------------------------------- +file name : perl-pod-escapes-1.07-pl5321hdfd78af_2.tar.bz2 +name : perl-pod-escapes +version : 1.07 +build : pl5321hdfd78af_2 +build number: 2 +size : 13 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-pod-escapes-1.07-pl5321hdfd78af_2.tar.bz2 +md5 : 74a0d5297d6771288ffd05bd596244bb +timestamp : 2022-01-19 01:24:23 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-exporter diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-pod-usage.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-pod-usage.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8455761224c80904fb4a19be2116981968818cf8 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-pod-usage.manual_bundle.txt @@ -0,0 +1,189 @@ +# Tool: perl-pod-usage +software_name: perl-pod-usage +tier: T1 +domain: t1_backfill_overall +downloads: 167219 +summary: Print a usage message from embedded pod documentation. +description: Print a usage message from embedded pod documentation. +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-carp, perl-getopt-long, perl-pod-escapes, perl-test +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://search.cpan.org/~marekr/Pod-Usage-1.69/ +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://search.cpan.org/~marekr/Pod-Usage-1.69/ +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-pod-usage --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-pod-usage 1.69 pl5.22.0_0 +------------------------------ +file name : perl-pod-usage-1.69-pl5.22.0_0.tar.bz2 +name : perl-pod-usage +version : 1.69 +build : pl5.22.0_0 +build number: 0 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-pod-usage-1.69-pl5.22.0_0.tar.bz2 +md5 : a63aa914fb09d3bcfaafe6dac75adf68 +dependencies: + - perl 5.22.0* + - perl-carp + - perl-getopt-long + - perl-pod-escapes + - perl-test + + +perl-pod-usage 1.69 pl526_1 +--------------------------- +file name : perl-pod-usage-1.69-pl526_1.tar.bz2 +name : perl-pod-usage +version : 1.69 +build : pl526_1 +build number: 1 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-pod-usage-1.69-pl526_1.tar.bz2 +md5 : 7b9be57b2eb879efe65d7672d35d630c +timestamp : 2018-07-08 20:40:17 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-carp + - perl-getopt-long + - perl-pod-escapes + - perl-test + + +perl-pod-usage 1.69 pl5321hdfd78af_2 +------------------------------------ +file name : perl-pod-usage-1.69-pl5321hdfd78af_2.tar.bz2 +name : perl-pod-usage +version : 1.69 +build : pl5321hdfd78af_2 +build number: 2 +size : 16 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-pod-usage-1.69-pl5321hdfd78af_2.tar.bz2 +md5 : 6be03d520512cbbe150d75d8749b3d11 +timestamp : 2022-01-20 19:34:15 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-getopt-long + - perl-pod-escapes + - perl-test + + +perl-pod-usage 2.01 pl5321hdfd78af_0 +------------------------------------ +file name : perl-pod-usage-2.01-pl5321hdfd78af_0.tar.bz2 +name : perl-pod-usage +version : 2.01 +build : pl5321hdfd78af_0 +build number: 0 +size : 16 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-pod-usage-2.01-pl5321hdfd78af_0.tar.bz2 +md5 : 64538dc25c21b32009cb5c28b3178af0 +timestamp : 2022-02-09 17:48:57 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-getopt-long + - perl-pod-escapes + - perl-test + + +perl-pod-usage 2.03 pl5321hdfd78af_0 +------------------------------------ +file name : perl-pod-usage-2.03-pl5321hdfd78af_0.tar.bz2 +name : perl-pod-usage +version : 2.03 +build : pl5321hdfd78af_0 +build number: 0 +size : 16 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-pod-usage-2.03-pl5321hdfd78af_0.tar.bz2 +md5 : 0d3854eabc8c6c4865f10b4800dad4b5 +timestamp : 2022-05-21 19:28:16 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-getopt-long + - perl-pod-escapes + - perl-test + + +perl-pod-usage 2.05 pl5321hdfd78af_0 +------------------------------------ +file name : perl-pod-usage-2.05-pl5321hdfd78af_0.tar.bz2 +name : perl-pod-usage +version : 2.05 +build : pl5321hdfd78af_0 +build number: 0 +size : 17 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-pod-usage-2.05-pl5321hdfd78af_0.tar.bz2 +md5 : a402402b231695a65821a7c22a362038 +timestamp : 2025-04-04 21:23:52 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-getopt-long + - perl-pod-escapes + - perl-test diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-readonly.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-readonly.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e3ab7d7cac542a3eebf9e0887cc4face54b83d6 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-readonly.manual_bundle.txt @@ -0,0 +1,166 @@ +# Tool: perl-readonly +software_name: perl-readonly +tier: T1 +domain: t1_backfill_overall +downloads: 134656 +summary: Facility for creating read-only scalars, arrays, hashes +description: Facility for creating read-only scalars, arrays, hashes +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/sanko/readonly +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/sanko/readonly +GitHub - sanko/readonly: Facility for creating read-only scalars, arrays, hashes · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} sanko / readonly Public Uh oh! There was an error while loading. Please reload this page . Notifications You must be signed in to change notification settings Fork 8 Star 17 Code Issues 19 Pull requests 3 Discussions Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Wiki Security and quality Insights sanko/readonly master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 64 Commits 64 Commits .github .github eg eg lib lib t t .gitignore .gitignore Build.PL Build.PL Changes Changes LICENSE LICENSE MANIFEST.SKIP MANIFEST.SKIP META.json META.json README.md README.md cpanfile cpanfile minil.toml minil.toml View all files Repository files navigation README License NAME Readonly - Facility for creating read-only scalars, arrays, hashes Synopsis use Readonly; # Deep Read-only scalar Readonly::Scalar $sca => $initial_value; Readonly::Scalar my $sca => $initial_value; # Deep Read-only array Readonly::Array @arr => @values; Readonly::Array my @arr => @values; # Deep Read-only hash Readonly::Hash %has => (key => value, key => value, ...); Readonly::Hash my %has => (key => value, key => value, ...); # or: Readonly::Hash %has => {key => value, key => value, ...}; # You can use the read-only variables like any regular variables: print $sca; $something = $sca + $arr[2]; next if $has{$some_key}; # But if you try to modify a value, your program will die: $sca = 7; push @arr, 'seven'; delete $has{key}; # The error message is "Modification of a read-only value attempted" # Alternate form (Perl 5.8 and later) Readonly $sca => $initial_value; Readonly my $sca => $initial_value; Readonly @arr => @values; Readonly my @arr => @values; Readonly %has => (key => value, key => value, ...); Readonly my %has => (key => value, key => value, ...); Readonly my $sca; # Implicit undef, readonly value # Alternate form (for Perls earlier than v5.8) Readonly \$sca => $initial_value; Readonly \my $sca => $initial_value; Readonly \@arr => @values; Readonly \my @arr => @values; Readonly \%has => (key => value, key => value, ...); Readonly \my %has => (key => value, key => value, ...); Description This is a facility for creating non-modifiable variables. This is useful for configuration files, headers, etc. It can also be useful as a development and debugging tool for catching updates to variables that should not be changed. Variable Depth Readonly has the ability to create both deep and shallow readonly variables. If you pass a $ref , an @array or a %hash to corresponding functions ::Scalar() , ::Array() and ::Hash() , then those functions recurse over the data structure, marking everything as readonly. The entire structure is then non-modifiable. This is normally what you want. If you want only the top level to be readonly, use the alternate (and poorly named) ::Scalar1() , ::Array1() , and ::Hash1() functions. Plain Readonly() creates what the original author calls a "shallow" readonly variable, which is great if you don't plan to use it on anything but only one dimensional scalar values. Readonly::Scalar() makes the variable 'deeply' readonly, so the following snippet kills over as you expect: use Readonly; Readonly::Scalar my $ref => { 1 => 'a' }; $ref->{1} = 'b'; $ref->{2} = 'b'; While the following snippet does not make your structure 'deeply' readonly: use Readonly; Readonly my $ref => { 1 => 'a' }; $ref->{1} = 'b'; $ref->{2} = 'b'; The Past The following sections are updated versions of the previous authors documentation. Comparison with "use constant" Perl provides a facility for creating constant values, via the constant pragma. There are several problems with this pragma. The constants created have no leading sigils. These constants cannot be interpolated into strings. Syntax can get dicey sometimes. For example: use constant CARRAY => (2, 3, 5, 7, 11, 13); $a_prime = CARRAY[2]; # wrong! $a_prime = (CARRAY)[2]; # right -- MUST use parentheses You have to be very careful in places where barewords are allowed. For example: use constant SOME_KEY => 'key'; %hash = (key => 'value', other_key => 'other_value'); $some_value = $hash{SOME_KEY}; # wrong! $some_value = $hash{+SOME_KEY}; # right (who thinks to use a unary plus when using a hash to scalarize the key?) use constant works for scalars and arrays, not hashes. These constants are global to the package in which they're declared; cannot be lexically scoped. Works only at compile time. Can be overridden: use constant PI => 3.14159; ... use constant PI => 2.71828; (this does generate a warning, however, if you have warnings enabled). It is very difficult to make and use deep structures (complex data structures) with use constant . Comparison with typeglob constants Another popular way to create read-only scalars is to modify the symbol table entry for the variable by using a typeglob: *a = \'value'; This works fine, but it only works for global variables ("my" variables have no symbol table entry). Also, the following similar constructs do not work: *a = [1, 2, 3]; # Does NOT create a read-only array *a = { a => 'A'}; # Does NOT create a read-only hash Pros Readonly.pm, on the other hand, will work with global variables and with lexical ("my") variables. It will create scalars, arrays, or hashes, all of which look and work like normal, read-write Perl variables. You can use them in scalar context, in list context; you can take references to them, pass them to functions, anything. Readonly.pm also works well with complex data structures, allowing you to tag the whole structure as nonmodifiable, or just the top level. Also, Readonly variables may not be reassigned. The following code will die: Readonly::Scalar $pi => 3.14159; ... Readonly::Scalar $pi => 2.71828; Cons Readonly.pm used to impose a performance penalty. It was pretty slow. How slow? Run the eg/benchmark.pl script that comes with Readonly. On my test system, "use constant" (const), typeglob constants (tglob), regular read/write Perl variables (normal/literal), and the new Readonly (ro/ro_simple) are all about the same speed, the old, tie based Readonly.pm constants were about 1/22 the speed. However, there is relief. There is a companion module available, Readonly::XS. You won't need this if you're using Perl 5.8.x or higher. I repeat, you do not need Readonly::XS if your environment has perl 5.8.x or higher. Please see section entitled Internals for more. Functions Readonly::Scalar $var => $value; Creates a nonmodifiable scalar, $var , and assigns a value of $value to it. Thereafter, its value may not be changed. Any attempt to modify the value will cause your program to die. A value must be supplied. If you want the variable to have undef as its value, you must specify undef . If $value is a reference to a scalar, array, or hash, then this function will mark the scalar, array, or hash it points to as being Readonly as well, and it will recursively traverse the structure, marking the whole thing as Readonly. Usually, this is what you want. However, if you want only the $value marked as Readonly, use Scalar1 . If $var is already a Readonly variable, the program will die with an error about reassigning Readonly variables. Readonly::Array @arr => (value, value, ...); Creates a nonmodifiable array, @arr , and assigns the specified list of values to it. Thereafter, none of its values may be changed; the array may not be lengthened or shortened or spliced. Any attempt to do so will cause your program to die. If any of the values passed is a reference to a scalar, array, or hash, then this function will mark the scalar, array, or hash it points to as being Readonly as well, and it will recursively traverse the structure, marking the whole thing as Readonly. Usually, this is what you want. However, if you want only the hash %@arr itself marked as Readonly, use Array1 . If @arr is already a Readonly variable, the program will die with an error about reassigning Readonly variables. Readonly::Hash %h => (key => value, key => value, ...); Readonly::Hash %h => {key => value, key => value, ...}; Creates a nonmodifiable hash, %h , and assigns the specified keys and values to it. Thereafter, its keys or values may not be changed. Any attempt to do so will cause your program to die. A list of keys and values may be specified (with parentheses in the synopsis above), or a hash reference may be specified (curly braces in the synopsis above). If a list is specified, it must have an even number of elements, or the function will die. If any of the values is a reference to a scalar, array, or hash, then this function will mark the scalar, array, or hash it points to as being Readonly as well, and it will recursively traverse the structure, marking the whole thing as Readonly. Usually, this is what you want. However, if you want only the hash %h itself marked as Readonly, use Hash1 . If %h is already a Readonly variable, the program will die with an error about reassigning Readonly variables. Readonly $var => $value; Readonly @arr => (value, value, ...); Readonly %h => (key => value, ...); Readonly %h => {key => value, ...}; Readonly $var; The Readonly function is an alternate to the Scalar , Array , and Hash functions. It has the advantage (if you consider it an advantage) of being one function. That may make your program look neater, if you're initializing a whole bunch of constants at once. You may or may not prefer this uniform style. It has the disadvantage of having a slightly different syntax for versions of Perl prior to 5.8. For earlier versions, you must supply a backslash, because it requires a reference as the first parameter. Readonly \$var => $value; Readonly \@arr => (value, value, ...); Readonly \%h => (key => value, ...); Readonly \%h => {key => value, ...}; You may or may not consider this ugly. Note that you can create implicit undefined variables with this function like so Readonly my $var; while a verbose undefined value must be passed to the standard Scalar , Array , and Hash functions. Readonly::Scalar1 $var => $value; Readonly::Array1 @arr => (value, value, ...); Readonly::Hash1 %h => (key => value, key => value, ...); Readonly::Hash1 %h => {key => value, key => value, ...}; These alternate functions create shallow Readonly variables, instead of deep ones. For example: Readonly::Array1 @shal => (1, 2, {perl=>'Rules', java=>'Bites'}, 4, 5); Readonly::Array @deep => (1, 2, {perl=>'Rules', java=>'Bites'}, 4, 5); $shal[1] = 7; # error $shal[2]{APL}='Weird'; # Allowed! since the hash isn't Readonly $deep[1] = 7; # error $deep[2]{APL}='Weird'; # error, since the hash is Readonly Cloning When cloning using Storable or Clone you will notice that the value stays readonly, which is correct. If you want to clone the value without copying the readonly flag, use the Clone function: Readonly::Scalar my $scalar => {qw[this that]}; # $scalar->{'eh'} = 'foo'; # Modification of a read-only value attempted my $scalar_clone = Readonly::Clone $scalar; $scalar_clone->{'eh'} = 'foo'; # $scalar_clone is now {this => 'that', eh => 'foo'}; The new variable ( $scalar_clone ) is a mutable clone of the original $scalar . Examples These are a few very simple examples: Scalars A plain old read-only value Readonly::Scalar $a => "A string value"; The value need not be a compile-time constant: Readonly::Scalar $a => $computed_value; Arrays/Lists A read-only array: Readonly::Array @a => (1, 2, 3, 4); The parentheses are optional: Readonly::Array @a => 1, 2, 3, 4; You can use Perl's built-in array quoting syntax: Readonly::Array @a => qw/1 2 3 4/; You can initialize a read-only array from a variable one: Readonly::Array @a => @computed_values; A read-only array can be empty, too: Readonly::Array @a => (); Readonly::Array @a; # equivalent Hashes Typical usage: Readonly::Hash %a => (key1 => 'value1', key2 => 'value2'); A read-only hash can be initialized from a variable one: Readonly::Hash %a => %computed_values; A read-only hash can be empty: Readonly::Hash %a => (); Readonly::Hash %a; # equivalent If you pass an odd number of values, the program will die: Readonly::Hash %a => (key1 => 'value1', "value2"); # This dies with "May not store an odd number of values in a hash" Exports Historically, this module exports the Readonly symbol into the calling program's namespace by default. The following symbols are also available for import into your program, if you like: Scalar , Scalar1 , Array , Array1 , Hash , and Hash1 . Internals Some people simply do not understand the relationship between this module and Readonly::XS so I'm adding this section. Odds are, they still won't understand but I like to write so... In the past, Readonly's "magic" was performed by tie() -ing variables to the Readonly::Scalar , Readonly::Array , and Readonly::Hash packages (not to be confused with the functions of the same names) and acting on WRITE , READ , et. al. While this worked well, it was slow. Very slow. Like 20-30 times slower than accessing variables directly or using one of the other const-related modules that have cropped up since Readonly was released in 2003. To 'fix' this, Readonly::XS was written. If installed, Readonly::XS used the internal methods SvREADONLY and SvREADONLY_on to lock simple scalars. On the surface, everything was peachy but things weren't the same behind the scenes. In edge cases, code performed very differently if Readonly::XS was installed and because it wasn't a required dependency in most code, it made downstream bugs very hard to track. In the years since Readonly::XS was released, the then private internal methods have been exposed and can be used in pure perl. Similar modules were written to take advantage of this and a patch to Readonly was created. We no longer need to build and install another module to make Readonly useful on modern builds of perl. You do not need to install Readonly::XS. You should stop listing Readonly::XS as a dependency or expect it to be installed. Stop testing the $Readonly::XSokay variable! Requirements Please note that most users of Readonly no longer need to install the companion module Readonly::XS which is recommended but not required for perl 5.6.x and under. Please do not force it as a requirement in new code and do not use the package variable $Readonly::XSokay in code/tests. For more, see "Internals" in the section on Readonly's new internals . There are no non-core requirements. Bug Reports If email is better for you, my address is mentioned below but I would rather have bugs sent through the issue tracker found at http://github.com/sanko/readonly/issues . Acknowledgements Thanks to Slaven Rezic for the idea of one common function (Readonly) for all three types of variables (13 April 2002). Thanks to Ernest Lergon for the idea (and initial code) for deeply-Readonly data structures (21 May 2002). Thanks to Damian Conway for the idea (and code) for making the Readonly function work a lot smoother under perl 5.8+. Author Sanko Robinson sanko@cpan.org - http://sankorobinson.com/ CPAN ID: SANKO Original author: Eric J. Roode, roode@cpan.org License and Legal Copyright (C) 2013-2016 by Sanko Robinson sanko@cpan.org Copyright (c) 2001-2004 by Eric J. Roode. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. About Facility for creating read-only scalars, arrays, hashes metacpan.org/release/Readonly Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Stars 17 stars Watchers 3 watching Forks 8 forks Report repository Releases 22 tags Sponsor this project   Sponsor Uh oh! There was an error while loading. Please reload this page . Learn more about GitHub Sponsors Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-readonly --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-readonly 1.04 pl5.22.0_0 +----------------------------- +file name : perl-readonly-1.04-pl5.22.0_0.tar.bz2 +name : perl-readonly +version : 1.04 +build : pl5.22.0_0 +build number: 0 +size : 8 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-readonly-1.04-pl5.22.0_0.tar.bz2 +md5 : 9526a4040adf5546267f99f19469a540 +dependencies: + - perl 5.22.0* + + +perl-readonly 1.04 pl526_1 +-------------------------- +file name : perl-readonly-1.04-pl526_1.tar.bz2 +name : perl-readonly +version : 1.04 +build : pl526_1 +build number: 1 +size : 15 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-readonly-1.04-pl526_1.tar.bz2 +md5 : 3cbd4f6ad704d2802b5c579719dac62f +timestamp : 2018-07-19 03:42:47 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-readonly 1.04 pl526_2 +-------------------------- +file name : perl-readonly-1.04-pl526_2.tar.bz2 +name : perl-readonly +version : 1.04 +build : pl526_2 +build number: 2 +size : 15 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-readonly-1.04-pl526_2.tar.bz2 +md5 : 9cbc09c5c85f6d055270d6e338bfc914 +timestamp : 2018-07-19 22:48:18 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-readonly 2.05 pl526_0 +-------------------------- +file name : perl-readonly-2.05-pl526_0.tar.bz2 +name : perl-readonly +version : 2.05 +build : pl526_0 +build number: 0 +size : 17 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-readonly-2.05-pl526_0.tar.bz2 +md5 : bccc10364be7bdde1b6a6126f8feaa97 +timestamp : 2018-12-17 16:45:30 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-readonly 2.05 pl5321ha770c72_0 +----------------------------------- +file name : perl-readonly-2.05-pl5321ha770c72_0.tar.bz2 +name : perl-readonly +version : 2.05 +build : pl5321ha770c72_0 +build number: 0 +size : 25 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-readonly-2.05-pl5321ha770c72_0.tar.bz2 +md5 : 4a5fedeb429a9cb12b528ac60a5b5009 +timestamp : 2022-11-10 14:31:12 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-module-build-tiny 0.039.* + + +perl-readonly 2.05 pl5321hdfd78af_1 +----------------------------------- +file name : perl-readonly-2.05-pl5321hdfd78af_1.tar.bz2 +name : perl-readonly +version : 2.05 +build : pl5321hdfd78af_1 +build number: 1 +size : 19 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-readonly-2.05-pl5321hdfd78af_1.tar.bz2 +md5 : 01f730cbd9d7fcafef36364b75200a9e +timestamp : 2022-01-21 04:39:23 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-regexp-common.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-regexp-common.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2d9b30d670f82108990ab8bcc1f8a87ccb5306eb --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-regexp-common.manual_bundle.txt @@ -0,0 +1,151 @@ +# Tool: perl-regexp-common +software_name: perl-regexp-common +tier: T1 +domain: t1_backfill_overall +downloads: 135177 +summary: Provide commonly requested regular expressions +description: Provide commonly requested regular expressions +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Regexp::Common +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Regexp::Common +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-regexp-common --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-regexp-common 2016060801 0 +------------------------------- +file name : perl-regexp-common-2016060801-0.tar.bz2 +name : perl-regexp-common +version : 2016060801 +build : 0 +build number: 0 +size : 69 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-regexp-common-2016060801-0.tar.bz2 +md5 : 078d4e68f4f54f7a1dca41d3de8911a2 +dependencies: + - perl-extutils-makemaker + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-regexp-common 2016060801 pl526_1 +------------------------------------- +file name : perl-regexp-common-2016060801-pl526_1.tar.bz2 +name : perl-regexp-common +version : 2016060801 +build : pl526_1 +build number: 1 +size : 93 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-regexp-common-2016060801-pl526_1.tar.bz2 +md5 : 23eb8f41450ed7c77c89fe67b501961d +timestamp : 2018-07-08 13:53:45 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-extutils-makemaker + + +perl-regexp-common 2017060201 pl526_0 +------------------------------------- +file name : perl-regexp-common-2017060201-pl526_0.tar.bz2 +name : perl-regexp-common +version : 2017060201 +build : pl526_0 +build number: 0 +size : 93 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-regexp-common-2017060201-pl526_0.tar.bz2 +md5 : 7b6a10fecd71fddc1ef37f8af8fb97b1 +timestamp : 2018-08-21 14:10:38 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-regexp-common 2017060201 pl5321hd8ed1ab_0 +---------------------------------------------- +file name : perl-regexp-common-2017060201-pl5321hd8ed1ab_0.tar.bz2 +name : perl-regexp-common +version : 2017060201 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 98 KB +license : MIT OR BSD-3-Clause OR Artistic-1.0-Perl OR Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-regexp-common-2017060201-pl5321hd8ed1ab_0.tar.bz2 +md5 : a5f770daa07a2075ac13e17e0bcb42e3 +timestamp : 2022-10-11 15:53:59 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-regexp-common 2017060201 pl5321hdfd78af_1 +---------------------------------------------- +file name : perl-regexp-common-2017060201-pl5321hdfd78af_1.tar.bz2 +name : perl-regexp-common +version : 2017060201 +build : pl5321hdfd78af_1 +build number: 1 +size : 96 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-regexp-common-2017060201-pl5321hdfd78af_1.tar.bz2 +md5 : 305070916169eec81f5d5a6461e0973d +timestamp : 2022-01-19 09:01:22 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sereal-decoder.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sereal-decoder.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..144ff4977260f2f7da3f9dd5d9e0adb9ff0bef4f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sereal-decoder.manual_bundle.txt @@ -0,0 +1,300 @@ +# Tool: perl-sereal-decoder +software_name: perl-sereal-decoder +tier: T1 +domain: t1_backfill_overall +downloads: 141262 +summary: Fast, compact, powerful binary deserialization. +description: Fast, compact, powerful binary deserialization. +dependencies: libgcc >=13, perl >=5.32.1,<5.33.0a0 *_perl5, perl-devel-checklib >=1.16,<2.0a0, perl-extutils-parsexs >=3.58,<4.0a0 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/Sereal::Decoder +doc_url: https://metacpan.org/pod/Sereal::Decoder +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/Sereal::Decoder +Sereal::Decoder - Fast, compact, powerful binary deserialization - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Sereal-Decoder Module version: 5.004 19 Apr 2023 13:20:25 UTC License: perl_5 Perl: v5.8.0 Code Download ( 819.04KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues How to Contribute Quality Testers ( 5334 / 5 / 0 ) Testers (Magpie) Kwalitee % Coverage Bus factor: 1 Activity 24 month Dependencies XSLoader and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 5.004 (YVES on 2023-04-19) 5.003 (YVES on 2023-02-08) 5.002_002 DEV (YVES on 2023-02-07) 5.002_001 DEV (YVES on 2023-02-06) 5.002 (YVES on 2023-02-01) 5.001_003 DEV (YVES on 2023-02-01) 5.001_002 DEV (YVES on 2023-02-01) 5.001_001 DEV (YVES on 2023-01-31) 5.001 (YVES on 2022-09-03) 5.000_002 DEV (YVES on 2022-09-02) 5.000_001 DEV (YVES on 2022-09-01) 4.025 (YVES on 2022-07-28) 4.024 (YVES on 2022-07-28) 4.023 (YVES on 2022-02-20) 4.022 (YVES on 2022-02-19) 4.021 (YVES on 2022-02-18) 4.020 (YVES on 2022-02-17) 4.019 (YVES on 2022-02-07) 4.018 (YVES on 2020-08-03) 4.017_001 DEV (YVES on 2020-07-29) 4.017 (YVES on 2020-07-09) 4.016 (YVES on 2020-07-09) 4.015 (YVES on 2020-07-08) 4.014 (YVES on 2020-06-11) 4.012 (YVES on 2020-06-10) 4.011 (YVES on 2020-02-04) 4.010 (YVES on 2020-02-04) 4.009_003 DEV (YVES on 2020-02-02) 4.009_002 DEV (YVES on 2020-02-02) 4.009_001 DEV (YVES on 2020-02-02) 4.009 (YVES on 2020-01-31) 4.008 (YVES on 2020-01-30) 4.007_001 DEV (YVES on 2020-01-29) 4.007 (YVES on 2019-04-09) 4.006 (YVES on 2019-04-08) 4.005 (YVES on 2018-01-23) 4.004 (YVES on 2017-11-12) 4.003 (YVES on 2017-11-12) 4.002 (YVES on 2017-11-11) 4.001_003 DEV (IKRUGLOV on 2017-04-23) 4.001_002 DEV (IKRUGLOV on 2017-04-22) 4.001_001 DEV (IKRUGLOV on 2017-02-06) 3.015 (YVES on 2016-09-01) 3.014_002 DEV (YVES on 2016-08-30) 3.014 (YVES on 2015-12-07) 3.012 (YVES on 2015-12-06) 3.011 (YVES on 2015-12-06) 3.009 (YVES on 2015-11-30) 3.008 (YVES on 2015-11-27) 3.007 (YVES on 2015-11-26) 3.006_007 DEV (YVES on 2015-11-25) 3.006_006 DEV (YVES on 2015-11-21) 3.006_005 DEV (YVES on 2015-11-20) 3.006_004 DEV (YVES on 2015-11-18) 3.006_003 DEV (YVES on 2015-11-18) 3.006_002 DEV (YVES on 2015-11-16) 3.006_001 DEV (YVES on 2015-11-16) 3.006 (YVES on 2015-11-14) 3.005_005 DEV (YVES on 2015-11-13) 3.005_004 DEV (YVES on 2015-11-13) 3.005_003 DEV (YVES on 2015-11-12) 3.005_002 DEV (YVES on 2015-11-09) 3.005_001 DEV (YVES on 2015-01-27) 3.005 (YVES on 2015-01-05) 3.004 (YVES on 2014-12-27) 3.003_004 DEV (YVES on 2014-12-26) 3.003_003 DEV (YVES on 2014-12-26) 3.003_002 DEV (YVES on 2014-12-21) 3.003_001 DEV (YVES on 2014-11-23) 3.003 (YVES on 2014-10-19) 3.002_002 DEV (YVES on 2014-10-18) 3.002_001 DEV (YVES on 2014-09-26) 3.002 (YVES on 2014-08-20) 3.001_012 DEV (YVES on 2014-08-15) 3.001_011 DEV (YVES on 2014-08-12) 3.001_010 DEV (YVES on 2014-08-12) 3.001_009 DEV (YVES on 2014-08-05) 3.001_008 DEV (YVES on 2014-08-05) 3.001_007 DEV (YVES on 2014-08-04) 3.001_006 DEV (YVES on 2014-08-03) 3.001_005 DEV (YVES on 2014-07-28) 3.001_004 DEV (YVES on 2014-07-27) 3.001_003 DEV (YVES on 2014-07-15) 3.001_002 DEV (YVES on 2014-06-27) 3.001_001 DEV (YVES on 2014-06-12) 3.001 (YVES on 2014-06-04) 3.000_004 DEV (YVES on 2014-06-03) 3.000_003 DEV (YVES on 2014-06-01) 3.000_002 DEV (YVES on 2014-06-01) 3.000_001 DEV (YVES on 2014-05-29) 2.12 (YVES on 2014-05-11) 2.11 (YVES on 2014-04-13) 2.10 (YVES on 2014-04-13) 2.09 (YVES on 2014-04-13) 2.08 (YVES on 2014-04-10) 2.070_103 DEV (YVES on 2014-04-08) 2.070_102 DEV (YVES on 2014-04-06) 2.070_101 DEV (YVES on 2014-04-06) 2.06 (SMUELLER on 2014-03-09) 0.36 (YVES on 2013-05-07) 0.35 (YVES on 2013-04-01) 0.34 (YVES on 2013-03-23) 0.33 (YVES on 2013-03-23) 0.32 (YVES on 2013-03-23) 0.31 (YVES on 2013-02-17) 0.30 (YVES on 2013-02-13) 0.29 (YVES on 2013-02-09) 0.28 (YVES on 2013-02-09) 0.27 (YVES on 2013-02-09) 2.07_01 DEV (SMUELLER on 2014-03-26) 2.04 (SMUELLER on 2014-03-05) 2.03 (SMUELLER on 2014-01-07) 2.02 (SMUELLER on 2014-01-06) 2.01 (SMUELLER on 2013-12-31) 2.00_03 DEV (SMUELLER on 2013-12-29) 2.00_02 DEV (SMUELLER on 2013-10-28) 2.00_01 DEV (SMUELLER on 2013-10-01) 0.37 (SMUELLER on 2013-09-02) 0.25 (SMUELLER on 2013-01-22) 0.24 (SMUELLER on 2013-01-10) 0.23 (SMUELLER on 2013-01-08) 0.21 (SMUELLER on 2013-01-02) 0.19 (SMUELLER on 2012-11-23) 0.15 (SMUELLER on 2012-10-17) 0.13 (SMUELLER on 2012-10-02) 0.11 (SMUELLER on 2012-09-18) 0.10 (SMUELLER on 2012-09-17) 0.09 (SMUELLER on 2012-09-14) 0.08 (SMUELLER on 2012-09-13) 0.07 (SMUELLER on 2012-09-11) 0.06 (SMUELLER on 2012-09-10) Diff with version 5.004 (YVES on 2023-04-19) 5.003 (YVES on 2023-02-08) 5.002_002 DEV (YVES on 2023-02-07) 5.002_001 DEV (YVES on 2023-02-06) 5.002 (YVES on 2023-02-01) 5.001_003 DEV (YVES on 2023-02-01) 5.001_002 DEV (YVES on 2023-02-01) 5.001_001 DEV (YVES on 2023-01-31) 5.001 (YVES on 2022-09-03) 5.000_002 DEV (YVES on 2022-09-02) 5.000_001 DEV (YVES on 2022-09-01) 4.025 (YVES on 2022-07-28) 4.024 (YVES on 2022-07-28) 4.023 (YVES on 2022-02-20) 4.022 (YVES on 2022-02-19) 4.021 (YVES on 2022-02-18) 4.020 (YVES on 2022-02-17) 4.019 (YVES on 2022-02-07) 4.018 (YVES on 2020-08-03) 4.017_001 DEV (YVES on 2020-07-29) 4.017 (YVES on 2020-07-09) 4.016 (YVES on 2020-07-09) 4.015 (YVES on 2020-07-08) 4.014 (YVES on 2020-06-11) 4.012 (YVES on 2020-06-10) 4.011 (YVES on 2020-02-04) 4.010 (YVES on 2020-02-04) 4.009_003 DEV (YVES on 2020-02-02) 4.009_002 DEV (YVES on 2020-02-02) 4.009_001 DEV (YVES on 2020-02-02) 4.009 (YVES on 2020-01-31) 4.008 (YVES on 2020-01-30) 4.007_001 DEV (YVES on 2020-01-29) 4.007 (YVES on 2019-04-09) 4.006 (YVES on 2019-04-08) 4.005 (YVES on 2018-01-23) 4.004 (YVES on 2017-11-12) 4.003 (YVES on 2017-11-12) 4.002 (YVES on 2017-11-11) 4.001_003 DEV (IKRUGLOV on 2017-04-23) 4.001_002 DEV (IKRUGLOV on 2017-04-22) 4.001_001 DEV (IKRUGLOV on 2017-02-06) 3.015 (YVES on 2016-09-01) 3.014_002 DEV (YVES on 2016-08-30) 3.014 (YVES on 2015-12-07) 3.012 (YVES on 2015-12-06) 3.011 (YVES on 2015-12-06) 3.009 (YVES on 2015-11-30) 3.008 (YVES on 2015-11-27) 3.007 (YVES on 2015-11-26) 3.006_007 DEV (YVES on 2015-11-25) 3.006_006 DEV (YVES on 2015-11-21) 3.006_005 DEV (YVES on 2015-11-20) 3.006_004 DEV (YVES on 2015-11-18) 3.006_003 DEV (YVES on 2015-11-18) 3.006_002 DEV (YVES on 2015-11-16) 3.006_001 DEV (YVES on 2015-11-16) 3.006 (YVES on 2015-11-14) 3.005_005 DEV (YVES on 2015-11-13) 3.005_004 DEV (YVES on 2015-11-13) 3.005_003 DEV (YVES on 2015-11-12) 3.005_002 DEV (YVES on 2015-11-09) 3.005_001 DEV (YVES on 2015-01-27) 3.005 (YVES on 2015-01-05) 3.004 (YVES on 2014-12-27) 3.003_004 DEV (YVES on 2014-12-26) 3.003_003 DEV (YVES on 2014-12-26) 3.003_002 DEV (YVES on 2014-12-21) 3.003_001 DEV (YVES on 2014-11-23) 3.003 (YVES on 2014-10-19) 3.002_002 DEV (YVES on 2014-10-18) 3.002_001 DEV (YVES on 2014-09-26) 3.002 (YVES on 2014-08-20) 3.001_012 DEV (YVES on 2014-08-15) 3.001_011 DEV (YVES on 2014-08-12) 3.001_010 DEV (YVES on 2014-08-12) 3.001_009 DEV (YVES on 2014-08-05) 3.001_008 DEV (YVES on 2014-08-05) 3.001_007 DEV (YVES on 2014-08-04) 3.001_006 DEV (YVES on 2014-08-03) 3.001_005 DEV (YVES on 2014-07-28) 3.001_004 DEV (YVES on 2014-07-27) 3.001_003 DEV (YVES on 2014-07-15) 3.001_002 DEV (YVES on 2014-06-27) 3.001_001 DEV (YVES on 2014-06-12) 3.001 (YVES on 2014-06-04) 3.000_004 DEV (YVES on 2014-06-03) 3.000_003 DEV (YVES on 2014-06-01) 3.000_002 DEV (YVES on 2014-06-01) 3.000_001 DEV (YVES on 2014-05-29) 2.12 (YVES on 2014-05-11) 2.11 (YVES on 2014-04-13) 2.10 (YVES on 2014-04-13) 2.09 (YVES on 2014-04-13) 2.08 (YVES on 2014-04-10) 2.070_103 DEV (YVES on 2014-04-08) 2.070_102 DEV (YVES on 2014-04-06) 2.070_101 DEV (YVES on 2014-04-06) 2.06 (SMUELLER on 2014-03-09) 0.36 (YVES on 2013-05-07) 0.35 (YVES on 2013-04-01) 0.34 (YVES on 2013-03-23) 0.33 (YVES on 2013-03-23) 0.32 (YVES on 2013-03-23) 0.31 (YVES on 2013-02-17) 0.30 (YVES on 2013-02-13) 0.29 (YVES on 2013-02-09) 0.28 (YVES on 2013-02-09) 0.27 (YVES on 2013-02-09) 2.07_01 DEV (SMUELLER on 2014-03-26) 2.04 (SMUELLER on 2014-03-05) 2.03 (SMUELLER on 2014-01-07) 2.02 (SMUELLER on 2014-01-06) 2.01 (SMUELLER on 2013-12-31) 2.00_03 DEV (SMUELLER on 2013-12-29) 2.00_02 DEV (SMUELLER on 2013-10-28) 2.00_01 DEV (SMUELLER on 2013-10-01) 0.37 (SMUELLER on 2013-09-02) 0.25 (SMUELLER on 2013-01-22) 0.24 (SMUELLER on 2013-01-10) 0.23 (SMUELLER on 2013-01-08) 0.21 (SMUELLER on 2013-01-02) 0.19 (SMUELLER on 2012-11-23) 0.15 (SMUELLER on 2012-10-17) 0.13 (SMUELLER on 2012-10-02) 0.11 (SMUELLER on 2012-09-18) 0.10 (SMUELLER on 2012-09-17) 0.09 (SMUELLER on 2012-09-14) 0.08 (SMUELLER on 2012-09-13) 0.07 (SMUELLER on 2012-09-11) 0.06 (SMUELLER on 2012-09-10) Permalinks This version Latest version ++ed by: 14 PAUSE users 12 non-PAUSE users Authors: Steffen Mueller <smueller@cpan.org>, Yves Orton Released by: Yves Maintainers: YVES owner AVAR DGRYSKI RGARCIA SMUELLER Contributors: Steffen Mueller, Yves Orton <yves@cpan.org> Yves  /  5.004 (YVES on 2023-04-19) 5.003 (YVES on 2023-02-08) 5.002_002 DEV (YVES on 2023-02-07) 5.002_001 DEV (YVES on 2023-02-06) 5.002 (YVES on 2023-02-01) 5.001_003 DEV (YVES on 2023-02-01) 5.001_002 DEV (YVES on 2023-02-01) 5.001_001 DEV (YVES on 2023-01-31) 5.001 (YVES on 2022-09-03) 5.000_002 DEV (YVES on 2022-09-02) 5.000_001 DEV (YVES on 2022-09-01) 4.025 (YVES on 2022-07-28) 4.024 (YVES on 2022-07-28) 4.023 (YVES on 2022-02-20) 4.022 (YVES on 2022-02-19) 4.021 (YVES on 2022-02-18) 4.020 (YVES on 2022-02-17) 4.019 (YVES on 2022-02-07) 4.018 (YVES on 2020-08-03) 4.017_001 DEV (YVES on 2020-07-29) 4.017 (YVES on 2020-07-09) 4.016 (YVES on 2020-07-09) 4.015 (YVES on 2020-07-08) 4.014 (YVES on 2020-06-11) 4.012 (YVES on 2020-06-10) 4.011 (YVES on 2020-02-04) 4.010 (YVES on 2020-02-04) 4.009_003 DEV (YVES on 2020-02-02) 4.009_002 DEV (YVES on 2020-02-02) 4.009_001 DEV (YVES on 2020-02-02) 4.009 (YVES on 2020-01-31) 4.008 (YVES on 2020-01-30) 4.007_001 DEV (YVES on 2020-01-29) 4.007 (YVES on 2019-04-09) 4.006 (YVES on 2019-04-08) 4.005 (YVES on 2018-01-23) 4.004 (YVES on 2017-11-12) 4.003 (YVES on 2017-11-12) 4.002 (YVES on 2017-11-11) 4.001_003 DEV (IKRUGLOV on 2017-04-23) 4.001_002 DEV (IKRUGLOV on 2017-04-22) 4.001_001 DEV (IKRUGLOV on 2017-02-06) 3.015 (YVES on 2016-09-01) 3.014_002 DEV (YVES on 2016-08-30) 3.014 (YVES on 2015-12-07) 3.012 (YVES on 2015-12-06) 3.011 (YVES on 2015-12-06) 3.009 (YVES on 2015-11-30) 3.008 (YVES on 2015-11-27) 3.007 (YVES on 2015-11-26) 3.006_007 DEV (YVES on 2015-11-25) 3.006_006 DEV (YVES on 2015-11-21) 3.006_005 DEV (YVES on 2015-11-20) 3.006_004 DEV (YVES on 2015-11-18) 3.006_003 DEV (YVES on 2015-11-18) 3.006_002 DEV (YVES on 2015-11-16) 3.006_001 DEV (YVES on 2015-11-16) 3.006 (YVES on 2015-11-14) 3.005_005 DEV (YVES on 2015-11-13) 3.005_004 DEV (YVES on 2015-11-13) 3.005_003 DEV (YVES on 2015-11-12) 3.005_002 DEV (YVES on 2015-11-09) 3.005_001 DEV (YVES on 2015-01-27) 3.005 (YVES on 2015-01-05) 3.004 (YVES on 2014-12-27) 3.003_004 DEV (YVES on 2014-12-26) 3.003_003 DEV (YVES on 2014-12-26) 3.003_002 DEV (YVES on 2014-12-21) 3.003_001 DEV (YVES on 2014-11-23) 3.003 (YVES on 2014-10-19) 3.002_002 DEV (YVES on 2014-10-18) 3.002_001 DEV (YVES on 2014-09-26) 3.002 (YVES on 2014-08-20) 3.001_012 DEV (YVES on 2014-08-15) 3.001_011 DEV (YVES on 2014-08-12) 3.001_010 DEV (YVES on 2014-08-12) 3.001_009 DEV (YVES on 2014-08-05) 3.001_008 DEV (YVES on 2014-08-05) 3.001_007 DEV (YVES on 2014-08-04) 3.001_006 DEV (YVES on 2014-08-03) 3.001_005 DEV (YVES on 2014-07-28) 3.001_004 DEV (YVES on 2014-07-27) 3.001_003 DEV (YVES on 2014-07-15) 3.001_002 DEV (YVES on 2014-06-27) 3.001_001 DEV (YVES on 2014-06-12) 3.001 (YVES on 2014-06-04) 3.000_004 DEV (YVES on 2014-06-03) 3.000_003 DEV (YVES on 2014-06-01) 3.000_002 DEV (YVES on 2014-06-01) 3.000_001 DEV (YVES on 2014-05-29) 2.12 (YVES on 2014-05-11) 2.11 (YVES on 2014-04-13) 2.10 (YVES on 2014-04-13) 2.09 (YVES on 2014-04-13) 2.08 (YVES on 2014-04-10) 2.070_103 DEV (YVES on 2014-04-08) 2.070_102 DEV (YVES on 2014-04-06) 2.070_101 DEV (YVES on 2014-04-06) 2.06 (SMUELLER on 2014-03-09) 0.36 (YVES on 2013-05-07) 0.35 (YVES on 2013-04-01) 0.34 (YVES on 2013-03-23) 0.33 (YVES on 2013-03-23) 0.32 (YVES on 2013-03-23) 0.31 (YVES on 2013-02-17) 0.30 (YVES on 2013-02-13) 0.29 (YVES on 2013-02-09) 0.28 (YVES on 2013-02-09) 0.27 (YVES on 2013-02-09) 2.07_01 DEV (SMUELLER on 2014-03-26) 2.04 (SMUELLER on 2014-03-05) 2.03 (SMUELLER on 2014-01-07) 2.02 (SMUELLER on 2014-01-06) 2.01 (SMUELLER on 2013-12-31) 2.00_03 DEV (SMUELLER on 2013-12-29) 2.00_02 DEV (SMUELLER on 2013-10-28) 2.00_01 DEV (SMUELLER on 2013-10-01) 0.37 (SMUELLER on 2013-09-02) 0.25 (SMUELLER on 2013-01-22) 0.24 (SMUELLER on 2013-01-10) 0.23 (SMUELLER on 2013-01-08) 0.21 (SMUELLER on 2013-01-02) 0.19 (SMUELLER on 2012-11-23) 0.15 (SMUELLER on 2012-10-17) 0.13 (SMUELLER on 2012-10-02) 0.11 (SMUELLER on 2012-09-18) 0.10 (SMUELLER on 2012-09-17) 0.09 (SMUELLER on 2012-09-14) 0.08 (SMUELLER on 2012-09-13) 0.07 (SMUELLER on 2012-09-11) 0.06 (SMUELLER on 2012-09-10) Sereal-Decoder-5.004 26 ++ 26 ++ ⭐ Starred 413 GitHub stars / Sereal::Decoder Security Advisories (1) CVE-2018-12913 (2018-06-27) In Miniz 2.0.7, tinfl_decompress in miniz_tinfl.c has an infinite loop because sym2 and counter can both remain equal to zero. https://github.com/richgel999/miniz/issues/90 Contents NAME SYNOPSIS DESCRIPTION CLASS METHODS new refuse_snappy refuse_objects no_bless_objects no_thaw_objects validate_utf8 max_recursion_depth max_num_hash_entries max_num_array_entries max_string_length max_uncompressed_size incremental alias_smallint alias_varint_under use_undef set_readonly set_readonly_scalars INSTANCE METHODS decode decode_with_header decode_only_header decode_with_offset decode_only_header_with_offset decode_with_header_and_offset bytes_consumed decode_from_file looks_like_sereal EXPORTABLE FUNCTIONS sereal_decode_with_object sereal_decode_with_header_with_object sereal_decode_only_header_with_object sereal_decode_only_header_with_offset_with_object sereal_decode_with_header_and_offset_with_object sereal_decode_with_offset_with_object decode_sereal decode_sereal_with_header_data scalar_looks_like_sereal ROBUSTNESS FREEZE/THAW CALLBACK MECHANISM PERFORMANCE THREAD-SAFETY BUGS, CONTACT AND SUPPORT AUTHORS AND CONTRIBUTORS ACKNOWLEDGMENT COPYRIGHT AND LICENSE NAME Sereal::Decoder - Fast, compact, powerful binary deserialization SYNOPSIS use Sereal::Decoder qw(decode_sereal sereal_decode_with_object scalar_looks_like_sereal); my $decoder = Sereal::Decoder->new({...options...}); my $structure; $decoder->decode($blob, $structure); # deserializes into $structure # or if you don't have references to the top level structure, this works, too: $structure = $decoder->decode($blob); # alternatively functional interface: (See Sereal::Performance) sereal_decode_with_object($decoder, $blob, $structure); $structure = sereal_decode_with_object($decoder, $blob); # much slower functional interface with no persistent objects: decode_sereal($blob, {... options ...}, $structure); $structure = decode_sereal($blob, {... options ...}); # Not a full validation, but just a quick check for a reasonable header: my $is_likely_sereal = scalar_looks_like_sereal($some_string); # or: $is_likely_sereal = $decoder->looks_like_sereal($some_string); DESCRIPTION This library implements a deserializer for an efficient, compact-output, and feature-rich binary protocol called Sereal . Its sister module Sereal::Encoder implements an encoder for this format. The two are released separately to allow for independent and safer upgrading. The Sereal protocol versions that are compatible with this decoder implementation are currently protocol versions 1, 2, 3 and 4. As it stands, it will refuse to attempt to decode future versions of the protocol, but if necessary there is likely going to be an option to decode the parts of the input that are compatible with version 4 of the protocol. The protocol was designed to allow for this. The protocol specification and many other bits of documentation can be found in the github repository. Right now, the specification is at https://github.com/Sereal/Sereal/blob/master/sereal_spec.pod , there is a discussion of the design objectives in https://github.com/Sereal/Sereal/blob/master/README.pod , and the output of our benchmarks can be seen at https://github.com/Sereal/Sereal/wiki/Sereal-Comparison-Graphs . CLASS METHODS new Constructor. Optionally takes a hash reference as first parameter. This hash reference may contain any number of options that influence the behaviour of the encoder. Currently, the following options are recognized, none of them are on by default. refuse_snappy If set, the decoder will refuse Snappy-compressed input data. This can be desirable for robustness. See the section ROBUSTNESS below. refuse_objects If set, the decoder will refuse deserializing any objects in the input stream and instead throw an exception. Defaults to off. See the section ROBUSTNESS below. no_bless_objects If set, the decoder will deserialize any objects in the input stream but without blessing them. Defaults to off. See the section ROBUSTNESS below. no_thaw_objects If set, the decoder will deserialize frozen objects in the objects stream as an array ref of arguments that would be passed into the THAW subroutine instead of calling THAW itself. validate_utf8 If set, the decoder will refuse invalid UTF-8 byte sequences. This is off by default, but it's strongly encouraged to be turned on if you're dealing with any data that has been encoded by an external source (e.g. http cookies). max_recursion_depth Sereal::Decoder is recursive. If you pass it a Sereal document that is deeply nested, it will eventually exhaust the C stack. Therefore, there is a limit on the depth of recursion that is accepted. It defaults to 10000 nested calls. You may choose to override this value with the max_recursion_depth option. Beware that setting it too high can cause hard crashes. Do note that the setting is somewhat approximate. Setting it to 10000 may break at somewhere between 9997 and 10003 nested structures depending on their types. max_num_hash_entries If set to a non-zero value (default: 0), then Sereal::Decoder will refuse to deserialize any hash/dictionary (or hash-based object) with more than that number of entries. This is to be able to respond quickly to any future hash-collision attacks on Perl's hash function, and also the memory exhaustion attacks on Sereal itself. For a gentle introduction to the topic from the cryptographic point of view, see http://en.wikipedia.org/wiki/Collision_attack . max_num_array_entries If set to a non-zero value (default: 0), then Sereal::Decoder will refuse to deserialize any array with more than that number of entries. This is to be able to respond quickly to any future memory exhaustion attacks on Sereal. max_string_length If set to a non-zero value (default: 0), then Sereal::Decoder will refuse to deserialize any string with more than that number of characters. This is to be able to respond quickly to any future memory exhaustion attacks on Sereal. max_uncompressed_size If set to a non-zero value (default: 0), then Sereal::Decoder will refuse to deserialize any blob with a size that exceds the value when uncompressed. This is to be able to respond quickly to any future memory exhaustion attacks on Sereal. incremental If set to a non-zero value (default: 0), then Sereal::Decoder will destructively parse Sereal documents out of a variable. Every time a Sereal document is successfully parsed it is removed from the front of the string it is parsed from. This means you can do this: while (length $buffer) { my $data= decode_sereal($buffer,{incremental=>1}); } alias_smallint If set to a true value then Ser + +### https://metacpan.org/pod/Sereal::Decoder +Sereal::Decoder - Fast, compact, powerful binary deserialization - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Sereal-Decoder Module version: 5.004 19 Apr 2023 13:20:25 UTC License: perl_5 Perl: v5.8.0 Code Download ( 819.04KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues How to Contribute Quality Testers ( 5334 / 5 / 0 ) Testers (Magpie) Kwalitee % Coverage Bus factor: 1 Activity 24 month Dependencies XSLoader and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 5.004 (YVES on 2023-04-19) 5.003 (YVES on 2023-02-08) 5.002_002 DEV (YVES on 2023-02-07) 5.002_001 DEV (YVES on 2023-02-06) 5.002 (YVES on 2023-02-01) 5.001_003 DEV (YVES on 2023-02-01) 5.001_002 DEV (YVES on 2023-02-01) 5.001_001 DEV (YVES on 2023-01-31) 5.001 (YVES on 2022-09-03) 5.000_002 DEV (YVES on 2022-09-02) 5.000_001 DEV (YVES on 2022-09-01) 4.025 (YVES on 2022-07-28) 4.024 (YVES on 2022-07-28) 4.023 (YVES on 2022-02-20) 4.022 (YVES on 2022-02-19) 4.021 (YVES on 2022-02-18) 4.020 (YVES on 2022-02-17) 4.019 (YVES on 2022-02-07) 4.018 (YVES on 2020-08-03) 4.017_001 DEV (YVES on 2020-07-29) 4.017 (YVES on 2020-07-09) 4.016 (YVES on 2020-07-09) 4.015 (YVES on 2020-07-08) 4.014 (YVES on 2020-06-11) 4.012 (YVES on 2020-06-10) 4.011 (YVES on 2020-02-04) 4.010 (YVES on 2020-02-04) 4.009_003 DEV (YVES on 2020-02-02) 4.009_002 DEV (YVES on 2020-02-02) 4.009_001 DEV (YVES on 2020-02-02) 4.009 (YVES on 2020-01-31) 4.008 (YVES on 2020-01-30) 4.007_001 DEV (YVES on 2020-01-29) 4.007 (YVES on 2019-04-09) 4.006 (YVES on 2019-04-08) 4.005 (YVES on 2018-01-23) 4.004 (YVES on 2017-11-12) 4.003 (YVES on 2017-11-12) 4.002 (YVES on 2017-11-11) 4.001_003 DEV (IKRUGLOV on 2017-04-23) 4.001_002 DEV (IKRUGLOV on 2017-04-22) 4.001_001 DEV (IKRUGLOV on 2017-02-06) 3.015 (YVES on 2016-09-01) 3.014_002 DEV (YVES on 2016-08-30) 3.014 (YVES on 2015-12-07) 3.012 (YVES on 2015-12-06) 3.011 (YVES on 2015-12-06) 3.009 (YVES on 2015-11-30) 3.008 (YVES on 2015-11-27) 3.007 (YVES on 2015-11-26) 3.006_007 DEV (YVES on 2015-11-25) 3.006_006 DEV (YVES on 2015-11-21) 3.006_005 DEV (YVES on 2015-11-20) 3.006_004 DEV (YVES on 2015-11-18) 3.006_003 DEV (YVES on 2015-11-18) 3.006_002 DEV (YVES on 2015-11-16) 3.006_001 DEV (YVES on 2015-11-16) 3.006 (YVES on 2015-11-14) 3.005_005 DEV (YVES on 2015-11-13) 3.005_004 DEV (YVES on 2015-11-13) 3.005_003 DEV (YVES on 2015-11-12) 3.005_002 DEV (YVES on 2015-11-09) 3.005_001 DEV (YVES on 2015-01-27) 3.005 (YVES on 2015-01-05) 3.004 (YVES on 2014-12-27) 3.003_004 DEV (YVES on 2014-12-26) 3.003_003 DEV (YVES on 2014-12-26) 3.003_002 DEV (YVES on 2014-12-21) 3.003_001 DEV (YVES on 2014-11-23) 3.003 (YVES on 2014-10-19) 3.002_002 DEV (YVES on 2014-10-18) 3.002_001 DEV (YVES on 2014-09-26) 3.002 (YVES on 2014-08-20) 3.001_012 DEV (YVES on 2014-08-15) 3.001_011 DEV (YVES on 2014-08-12) 3.001_010 DEV (YVES on 2014-08-12) 3.001_009 DEV (YVES on 2014-08-05) 3.001_008 DEV (YVES on 2014-08-05) 3.001_007 DEV (YVES on 2014-08-04) 3.001_006 DEV (YVES on 2014-08-03) 3.001_005 DEV (YVES on 2014-07-28) 3.001_004 DEV (YVES on 2014-07-27) 3.001_003 DEV (YVES on 2014-07-15) 3.001_002 DEV (YVES on 2014-06-27) 3.001_001 DEV (YVES on 2014-06-12) 3.001 (YVES on 2014-06-04) 3.000_004 DEV (YVES on 2014-06-03) 3.000_003 DEV (YVES on 2014-06-01) 3.000_002 DEV (YVES on 2014-06-01) 3.000_001 DEV (YVES on 2014-05-29) 2.12 (YVES on 2014-05-11) 2.11 (YVES on 2014-04-13) 2.10 (YVES on 2014-04-13) 2.09 (YVES on 2014-04-13) 2.08 (YVES on 2014-04-10) 2.070_103 DEV (YVES on 2014-04-08) 2.070_102 DEV (YVES on 2014-04-06) 2.070_101 DEV (YVES on 2014-04-06) 2.06 (SMUELLER on 2014-03-09) 0.36 (YVES on 2013-05-07) 0.35 (YVES on 2013-04-01) 0.34 (YVES on 2013-03-23) 0.33 (YVES on 2013-03-23) 0.32 (YVES on 2013-03-23) 0.31 (YVES on 2013-02-17) 0.30 (YVES on 2013-02-13) 0.29 (YVES on 2013-02-09) 0.28 (YVES on 2013-02-09) 0.27 (YVES on 2013-02-09) 2.07_01 DEV (SMUELLER on 2014-03-26) 2.04 (SMUELLER on 2014-03-05) 2.03 (SMUELLER on 2014-01-07) 2.02 (SMUELLER on 2014-01-06) 2.01 (SMUELLER on 2013-12-31) 2.00_03 DEV (SMUELLER on 2013-12-29) 2.00_02 DEV (SMUELLER on 2013-10-28) 2.00_01 DEV (SMUELLER on 2013-10-01) 0.37 (SMUELLER on 2013-09-02) 0.25 (SMUELLER on 2013-01-22) 0.24 (SMUELLER on 2013-01-10) 0.23 (SMUELLER on 2013-01-08) 0.21 (SMUELLER on 2013-01-02) 0.19 (SMUELLER on 2012-11-23) 0.15 (SMUELLER on 2012-10-17) 0.13 (SMUELLER on 2012-10-02) 0.11 (SMUELLER on 2012-09-18) 0.10 (SMUELLER on 2012-09-17) 0.09 (SMUELLER on 2012-09-14) 0.08 (SMUELLER on 2012-09-13) 0.07 (SMUELLER on 2012-09-11) 0.06 (SMUELLER on 2012-09-10) Diff with version 5.004 (YVES on 2023-04-19) 5.003 (YVES on 2023-02-08) 5.002_002 DEV (YVES on 2023-02-07) 5.002_001 DEV (YVES on 2023-02-06) 5.002 (YVES on 2023-02-01) 5.001_003 DEV (YVES on 2023-02-01) 5.001_002 DEV (YVES on 2023-02-01) 5.001_001 DEV (YVES on 2023-01-31) 5.001 (YVES on 2022-09-03) 5.000_002 DEV (YVES on 2022-09-02) 5.000_001 DEV (YVES on 2022-09-01) 4.025 (YVES on 2022-07-28) 4.024 (YVES on 2022-07-28) 4.023 (YVES on 2022-02-20) 4.022 (YVES on 2022-02-19) 4.021 (YVES on 2022-02-18) 4.020 (YVES on 2022-02-17) 4.019 (YVES on 2022-02-07) 4.018 (YVES on 2020-08-03) 4.017_001 DEV (YVES on 2020-07-29) 4.017 (YVES on 2020-07-09) 4.016 (YVES on 2020-07-09) 4.015 (YVES on 2020-07-08) 4.014 (YVES on 2020-06-11) 4.012 (YVES on 2020-06-10) 4.011 (YVES on 2020-02-04) 4.010 (YVES on 2020-02-04) 4.009_003 DEV (YVES on 2020-02-02) 4.009_002 DEV (YVES on 2020-02-02) 4.009_001 DEV (YVES on 2020-02-02) 4.009 (YVES on 2020-01-31) 4.008 (YVES on 2020-01-30) 4.007_001 DEV (YVES on 2020-01-29) 4.007 (YVES on 2019-04-09) 4.006 (YVES on 2019-04-08) 4.005 (YVES on 2018-01-23) 4.004 (YVES on 2017-11-12) 4.003 (YVES on 2017-11-12) 4.002 (YVES on 2017-11-11) 4.001_003 DEV (IKRUGLOV on 2017-04-23) 4.001_002 DEV (IKRUGLOV on 2017-04-22) 4.001_001 DEV (IKRUGLOV on 2017-02-06) 3.015 (YVES on 2016-09-01) 3.014_002 DEV (YVES on 2016-08-30) 3.014 (YVES on 2015-12-07) 3.012 (YVES on 2015-12-06) 3.011 (YVES on 2015-12-06) 3.009 (YVES on 2015-11-30) 3.008 (YVES on 2015-11-27) 3.007 (YVES on 2015-11-26) 3.006_007 DEV (YVES on 2015-11-25) 3.006_006 DEV (YVES on 2015-11-21) 3.006_005 DEV (YVES on 2015-11-20) 3.006_004 DEV (YVES on 2015-11-18) 3.006_003 DEV (YVES on 2015-11-18) 3.006_002 DEV (YVES on 2015-11-16) 3.006_001 DEV (YVES on 2015-11-16) 3.006 (YVES on 2015-11-14) 3.005_005 DEV (YVES on 2015-11-13) 3.005_004 DEV (YVES on 2015-11-13) 3.005_003 DEV (YVES on 2015-11-12) 3.005_002 DEV (YVES on 2015-11-09) 3.005_001 DEV (YVES on 2015-01-27) 3.005 (YVES on 2015-01-05) 3.004 (YVES on 2014-12-27) 3.003_004 DEV (YVES on 2014-12-26) 3.003_003 DEV (YVES on 2014-12-26) 3.003_002 DEV (YVES on 2014-12-21) 3.003_001 DEV (YVES on 2014-11-23) 3.003 (YVES on 2014-10-19) 3.002_002 DEV (YVES on 2014-10-18) 3.002_001 DEV (YVES on 2014-09-26) 3.002 (YVES on 2014-08-20) 3.001_012 DEV (YVES on 2014-08-15) 3.001_011 DEV (YVES on 2014-08-12) 3.001_010 DEV (YVES on 2014-08-12) 3.001_009 DEV (YVES on 2014-08-05) 3.001_008 DEV (YVES on 2014-08-05) 3.001_007 DEV (YVES on 2014-08-04) 3.001_006 DEV (YVES on 2014-08-03) 3.001_005 DEV (YVES on 2014-07-28) 3.001_004 DEV (YVES on 2014-07-27) 3.001_003 DEV (YVES on 2014-07-15) 3.001_002 DEV (YVES on 2014-06-27) 3.001_001 DEV (YVES on 2014-06-12) 3.001 (YVES on 2014-06-04) 3.000_004 DEV (YVES on 2014-06-03) 3.000_003 DEV (YVES on 2014-06-01) 3.000_002 DEV (YVES on 2014-06-01) 3.000_001 DEV (YVES on 2014-05-29) 2.12 (YVES on 2014-05-11) 2.11 (YVES on 2014-04-13) 2.10 (YVES on 2014-04-13) 2.09 (YVES on 2014-04-13) 2.08 (YVES on 2014-04-10) 2.070_103 DEV (YVES on 2014-04-08) 2.070_102 DEV (YVES on 2014-04-06) 2.070_101 DEV (YVES on 2014-04-06) 2.06 (SMUELLER on 2014-03-09) 0.36 (YVES on 2013-05-07) 0.35 (YVES on 2013-04-01) 0.34 (YVES on 2013-03-23) 0.33 (YVES on 2013-03-23) 0.32 (YVES on 2013-03-23) 0.31 (YVES on 2013-02-17) 0.30 (YVES on 2013-02-13) 0.29 (YVES on 2013-02-09) 0.28 (YVES on 2013-02-09) 0.27 (YVES on 2013-02-09) 2.07_01 DEV (SMUELLER on 2014-03-26) 2.04 (SMUELLER on 2014-03-05) 2.03 (SMUELLER on 2014-01-07) 2.02 (SMUELLER on 2014-01-06) 2.01 (SMUELLER on 2013-12-31) 2.00_03 DEV (SMUELLER on 2013-12-29) 2.00_02 DEV (SMUELLER on 2013-10-28) 2.00_01 DEV (SMUELLER on 2013-10-01) 0.37 (SMUELLER on 2013-09-02) 0.25 (SMUELLER on 2013-01-22) 0.24 (SMUELLER on 2013-01-10) 0.23 (SMUELLER on 2013-01-08) 0.21 (SMUELLER on 2013-01-02) 0.19 (SMUELLER on 2012-11-23) 0.15 (SMUELLER on 2012-10-17) 0.13 (SMUELLER on 2012-10-02) 0.11 (SMUELLER on 2012-09-18) 0.10 (SMUELLER on 2012-09-17) 0.09 (SMUELLER on 2012-09-14) 0.08 (SMUELLER on 2012-09-13) 0.07 (SMUELLER on 2012-09-11) 0.06 (SMUELLER on 2012-09-10) Permalinks This version Latest version ++ed by: 14 PAUSE users 12 non-PAUSE users Authors: Steffen Mueller <smueller@cpan.org>, Yves Orton Released by: Yves Maintainers: YVES owner AVAR DGRYSKI RGARCIA SMUELLER Contributors: Steffen Mueller, Yves Orton <yves@cpan.org> Yves  /  5.004 (YVES on 2023-04-19) 5.003 (YVES on 2023-02-08) 5.002_002 DEV (YVES on 2023-02-07) 5.002_001 DEV (YVES on 2023-02-06) 5.002 (YVES on 2023-02-01) 5.001_003 DEV (YVES on 2023-02-01) 5.001_002 DEV (YVES on 2023-02-01) 5.001_001 DEV (YVES on 2023-01-31) 5.001 (YVES on 2022-09-03) 5.000_002 DEV (YVES on 2022-09-02) 5.000_001 DEV (YVES on 2022-09-01) 4.025 (YVES on 2022-07-28) 4.024 (YVES on 2022-07-28) 4.023 (YVES on 2022-02-20) 4.022 (YVES on 2022-02-19) 4.021 (YVES on 2022-02-18) 4.020 (YVES on 2022-02-17) 4.019 (YVES on 2022-02-07) 4.018 (YVES on 2020-08-03) 4.017_001 DEV (YVES on 2020-07-29) 4.017 (YVES on 2020-07-09) 4.016 (YVES on 2020-07-09) 4.015 (YVES on 2020-07-08) 4.014 (YVES on 2020-06-11) 4.012 (YVES on 2020-06-10) 4.011 (YVES on 2020-02-04) 4.010 (YVES on 2020-02-04) 4.009_003 DEV (YVES on 2020-02-02) 4.009_002 DEV (YVES on 2020-02-02) 4.009_001 DEV (YVES on 2020-02-02) 4.009 (YVES on 2020-01-31) 4.008 (YVES on 2020-01-30) 4.007_001 DEV (YVES on 2020-01-29) 4.007 (YVES on 2019-04-09) 4.006 (YVES on 2019-04-08) 4.005 (YVES on 2018-01-23) 4.004 (YVES on 2017-11-12) 4.003 (YVES on 2017-11-12) 4.002 (YVES on 2017-11-11) 4.001_003 DEV (IKRUGLOV on 2017-04-23) 4.001_002 DEV (IKRUGLOV on 2017-04-22) 4.001_001 DEV (IKRUGLOV on 2017-02-06) 3.015 (YVES on 2016-09-01) 3.014_002 DEV (YVES on 2016-08-30) 3.014 (YVES on 2015-12-07) 3.012 (YVES on 2015-12-06) 3.011 (YVES on 2015-12-06) 3.009 (YVES on 2015-11-30) 3.008 (YVES on 2015-11-27) 3.007 (YVES on 2015-11-26) 3.006_007 DEV (YVES on 2015-11-25) 3.006_006 DEV (YVES on 2015-11-21) 3.006_005 DEV (YVES on 2015-11-20) 3.006_004 DEV (YVES on 2015-11-18) 3.006_003 DEV (YVES on 2015-11-18) 3.006_002 DEV (YVES on 2015-11-16) 3.006_001 DEV (YVES on 2015-11-16) 3.006 (YVES on 2015-11-14) 3.005_005 DEV (YVES on 2015-11-13) 3.005_004 DEV (YVES on 2015-11-13) 3.005_003 DEV (YVES on 2015-11-12) 3.005_002 DEV (YVES on 2015-11-09) 3.005_001 DEV (YVES on 2015-01-27) 3.005 (YVES on 2015-01-05) 3.004 (YVES on 2014-12-27) 3.003_004 DEV (YVES on 2014-12-26) 3.003_003 DEV (YVES on 2014-12-26) 3.003_002 DEV (YVES on 2014-12-21) 3.003_001 DEV (YVES on 2014-11-23) 3.003 (YVES on 2014-10-19) 3.002_002 DEV (YVES on 2014-10-18) 3.002_001 DEV (YVES on 2014-09-26) 3.002 (YVES on 2014-08-20) 3.001_012 DEV (YVES on 2014-08-15) 3.001_011 DEV (YVES on 2014-08-12) 3.001_010 DEV (YVES on 2014-08-12) 3.001_009 DEV (YVES on 2014-08-05) 3.001_008 DEV (YVES on 2014-08-05) 3.001_007 DEV (YVES on 2014-08-04) 3.001_006 DEV (YVES on 2014-08-03) 3.001_005 DEV (YVES on 2014-07-28) 3.001_004 DEV (YVES on 2014-07-27) 3.001_003 DEV (YVES on 2014-07-15) 3.001_002 DEV (YVES on 2014-06-27) 3.001_001 DEV (YVES on 2014-06-12) 3.001 (YVES on 2014-06-04) 3.000_004 DEV (YVES on 2014-06-03) 3.000_003 DEV (YVES on 2014-06-01) 3.000_002 DEV (YVES on 2014-06-01) 3.000_001 DEV (YVES on 2014-05-29) 2.12 (YVES on 2014-05-11) 2.11 (YVES on 2014-04-13) 2.10 (YVES on 2014-04-13) 2.09 (YVES on 2014-04-13) 2.08 (YVES on 2014-04-10) 2.070_103 DEV (YVES on 2014-04-08) 2.070_102 DEV (YVES on 2014-04-06) 2.070_101 DEV (YVES on 2014-04-06) 2.06 (SMUELLER on 2014-03-09) 0.36 (YVES on 2013-05-07) 0.35 (YVES on 2013-04-01) 0.34 (YVES on 2013-03-23) 0.33 (YVES on 2013-03-23) 0.32 (YVES on 2013-03-23) 0.31 (YVES on 2013-02-17) 0.30 (YVES on 2013-02-13) 0.29 (YVES on 2013-02-09) 0.28 (YVES on 2013-02-09) 0.27 (YVES on 2013-02-09) 2.07_01 DEV (SMUELLER on 2014-03-26) 2.04 (SMUELLER on 2014-03-05) 2.03 (SMUELLER on 2014-01-07) 2.02 (SMUELLER on 2014-01-06) 2.01 (SMUELLER on 2013-12-31) 2.00_03 DEV (SMUELLER on 2013-12-29) 2.00_02 DEV (SMUELLER on 2013-10-28) 2.00_01 DEV (SMUELLER on 2013-10-01) 0.37 (SMUELLER on 2013-09-02) 0.25 (SMUELLER on 2013-01-22) 0.24 (SMUELLER on 2013-01-10) 0.23 (SMUELLER on 2013-01-08) 0.21 (SMUELLER on 2013-01-02) 0.19 (SMUELLER on 2012-11-23) 0.15 (SMUELLER on 2012-10-17) 0.13 (SMUELLER on 2012-10-02) 0.11 (SMUELLER on 2012-09-18) 0.10 (SMUELLER on 2012-09-17) 0.09 (SMUELLER on 2012-09-14) 0.08 (SMUELLER on 2012-09-13) 0.07 (SMUELLER on 2012-09-11) 0.06 (SMUELLER on 2012-09-10) Sereal-Decoder-5.004 26 ++ 26 ++ ⭐ Starred 413 GitHub stars / Sereal::Decoder Security Advisories (1) CVE-2018-12913 (2018-06-27) In Miniz 2.0.7, tinfl_decompress in miniz_tinfl.c has an infinite loop because sym2 and counter can both remain equal to zero. https://github.com/richgel999/miniz/issues/90 Contents NAME SYNOPSIS DESCRIPTION CLASS METHODS new refuse_snappy refuse_objects no_bless_objects no_thaw_objects validate_utf8 max_recursion_depth max_num_hash_entries max_num_array_entries max_string_length max_uncompressed_size incremental alias_smallint alias_varint_under use_undef set_readonly set_readonly_scalars INSTANCE METHODS decode decode_with_header decode_only_header decode_with_offset decode_only_header_with_offset decode_with_header_and_offset bytes_consumed decode_from_file looks_like_sereal EXPORTABLE FUNCTIONS sereal_decode_with_object sereal_decode_with_header_with_object sereal_decode_only_header_with_object sereal_decode_only_header_with_offset_with_object sereal_decode_with_header_and_offset_with_object sereal_decode_with_offset_with_object decode_sereal decode_sereal_with_header_data scalar_looks_like_sereal ROBUSTNESS FREEZE/THAW CALLBACK MECHANISM PERFORMANCE THREAD-SAFETY BUGS, CONTACT AND SUPPORT AUTHORS AND CONTRIBUTORS ACKNOWLEDGMENT COPYRIGHT AND LICENSE NAME Sereal::Decoder - Fast, compact, powerful binary deserialization SYNOPSIS use Sereal::Decoder qw(decode_sereal sereal_decode_with_object scalar_looks_like_sereal); my $decoder = Sereal::Decoder->new({...options...}); my $structure; $decoder->decode($blob, $structure); # deserializes into $structure # or if you don't have references to the top level structure, this works, too: $structure = $decoder->decode($blob); # alternatively functional interface: (See Sereal::Performance) sereal_decode_with_object($decoder, $blob, $structure); $structure = sereal_decode_with_object($decoder, $blob); # much slower functional interface with no persistent objects: decode_sereal($blob, {... options ...}, $structure); $structure = decode_sereal($blob, {... options ...}); # Not a full validation, but just a quick check for a reasonable header: my $is_likely_sereal = scalar_looks_like_sereal($some_string); # or: $is_likely_sereal = $decoder->looks_like_sereal($some_string); DESCRIPTION This library implements a deserializer for an efficient, compact-output, and feature-rich binary protocol called Sereal . Its sister module Sereal::Encoder implements an encoder for this format. The two are released separately to allow for independent and safer upgrading. The Sereal protocol versions that are compatible with this decoder implementation are currently protocol versions 1, 2, 3 and 4. As it stands, it will refuse to attempt to decode future versions of the protocol, but if necessary there is likely going to be an option to decode the parts of the input that are compatible with version 4 of the protocol. The protocol was designed to allow for this. The protocol specification and many other bits of documentation can be found in the github repository. Right now, the specification is at https://github.com/Sereal/Sereal/blob/master/sereal_spec.pod , there is a discussion of the design objectives in https://github.com/Sereal/Sereal/blob/master/README.pod , and the output of our benchmarks can be seen at https://github.com/Sereal/Sereal/wiki/Sereal-Comparison-Graphs . CLASS METHODS new Constructor. Optionally takes a hash reference as first parameter. This hash reference may contain any number of options that influence the behaviour of the encoder. Currently, the following options are recognized, none of them are on by default. refuse_snappy If set, the decoder will refuse Snappy-compressed input data. This can be desirable for robustness. See the section ROBUSTNESS below. refuse_objects If set, the decoder will refuse deserializing any objects in the input stream and instead throw an exception. Defaults to off. See the section ROBUSTNESS below. no_bless_objects If set, the decoder will deserialize any objects in the input stream but without blessing them. Defaults to off. See the section ROBUSTNESS below. no_thaw_objects If set, the decoder will deserialize frozen objects in the objects stream as an array ref of arguments that would be passed into the THAW subroutine instead of calling THAW itself. validate_utf8 If set, the decoder will refuse invalid UTF-8 byte sequences. This is off by default, but it's strongly encouraged to be turned on if you're dealing with any data that has been encoded by an external source (e.g. http cookies). max_recursion_depth Sereal::Decoder is recursive. If you pass it a Sereal document that is deeply nested, it will eventually exhaust the C stack. Therefore, there is a limit on the depth of recursion that is accepted. It defaults to 10000 nested calls. You may choose to override this value with the max_recursion_depth option. Beware that setting it too high can cause hard crashes. Do note that the setting is somewhat approximate. Setting it to 10000 may break at somewhere between 9997 and 10003 nested structures depending on their types. max_num_hash_entries If set to a non-zero value (default: 0), then Sereal::Decoder will refuse to deserialize any hash/dictionary (or hash-based object) with more than that number of entries. This is to be able to respond quickly to any future hash-collision attacks on Perl's hash function, and also the memory exhaustion attacks on Sereal itself. For a gentle introduction to the topic from the cryptographic point of view, see http://en.wikipedia.org/wiki/Collision_attack . max_num_array_entries If set to a non-zero value (default: 0), then Sereal::Decoder will refuse to deserialize any array with more than that number of entries. This is to be able to respond quickly to any future memory exhaustion attacks on Sereal. max_string_length If set to a non-zero value (default: 0), then Sereal::Decoder will refuse to deserialize any string with more than that number of characters. This is to be able to respond quickly to any future memory exhaustion attacks on Sereal. max_uncompressed_size If set to a non-zero value (default: 0), then Sereal::Decoder will refuse to deserialize any blob with a size that exceds the value when uncompressed. This is to be able to respond quickly to any future memory exhaustion attacks on Sereal. incremental If set to a non-zero value (default: 0), then Sereal::Decoder will destructively parse Sereal documents out of a variable. Every time a Sereal document is successfully parsed it is removed from the front of the string it is parsed from. This means you can do this: while (length $buffer) { my $data= decode_sereal($buffer,{incremental=>1}); } alias_smallint If set to a true value then Ser + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-sereal-decoder --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-sereal-decoder 3.015 0 +--------------------------- +file name : perl-sereal-decoder-3.015-0.tar.bz2 +name : perl-sereal-decoder +version : 3.015 +build : 0 +build number: 0 +size : 92 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-3.015-0.tar.bz2 +md5 : 2faf5c0288fb90c7afc610659d59effe +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-sereal-decoder 3.015 pl526_1 +--------------------------------- +file name : perl-sereal-decoder-3.015-pl526_1.tar.bz2 +name : perl-sereal-decoder +version : 3.015 +build : pl526_1 +build number: 1 +size : 101 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-3.015-pl526_1.tar.bz2 +md5 : ee5cbbea9b3971805604d9efe0b97fed +timestamp : 2018-07-08 20:55:46 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-sereal-decoder 4.005 pl526_0 +--------------------------------- +file name : perl-sereal-decoder-4.005-pl526_0.tar.bz2 +name : perl-sereal-decoder +version : 4.005 +build : pl526_0 +build number: 0 +size : 140 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-4.005-pl526_0.tar.bz2 +md5 : 78ff3cd64eae4136edebb7de56f03c10 +timestamp : 2019-01-12 21:41:30 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-sereal-decoder 4.007 pl526h14c3975_0 +----------------------------------------- +file name : perl-sereal-decoder-4.007-pl526h14c3975_0.tar.bz2 +name : perl-sereal-decoder +version : 4.007 +build : pl526h14c3975_0 +build number: 0 +size : 139 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-4.007-pl526h14c3975_0.tar.bz2 +md5 : d4b97726c7ecff0774896aba2b92d619 +timestamp : 2019-05-13 22:13:02 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + + +perl-sereal-decoder 4.007 pl5321h779adbc_1 +------------------------------------------ +file name : perl-sereal-decoder-4.007-pl5321h779adbc_1.tar.bz2 +name : perl-sereal-decoder +version : 4.007 +build : pl5321h779adbc_1 +build number: 1 +size : 142 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-4.007-pl5321h779adbc_1.tar.bz2 +md5 : c04733a526cf6753391fa4c4e214732d +timestamp : 2022-01-20 21:09:36 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-decoder 4.019 pl5321h779adbc_0 +------------------------------------------ +file name : perl-sereal-decoder-4.019-pl5321h779adbc_0.tar.bz2 +name : perl-sereal-decoder +version : 4.019 +build : pl5321h779adbc_0 +build number: 0 +size : 176 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-4.019-pl5321h779adbc_0.tar.bz2 +md5 : 85e2b6f6d0d3fc01b9a2a09d78b22ef8 +timestamp : 2022-02-09 17:29:36 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-decoder 4.020 pl5321h779adbc_0 +------------------------------------------ +file name : perl-sereal-decoder-4.020-pl5321h779adbc_0.tar.bz2 +name : perl-sereal-decoder +version : 4.020 +build : pl5321h779adbc_0 +build number: 0 +size : 176 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-4.020-pl5321h779adbc_0.tar.bz2 +md5 : 0c8def28d2d7f815c532c0369cbf868a +timestamp : 2022-02-17 16:37:14 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-decoder 4.023 pl5321h779adbc_0 +------------------------------------------ +file name : perl-sereal-decoder-4.023-pl5321h779adbc_0.tar.bz2 +name : perl-sereal-decoder +version : 4.023 +build : pl5321h779adbc_0 +build number: 0 +size : 176 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-4.023-pl5321h779adbc_0.tar.bz2 +md5 : 97f33c179d4759abc9080bb87cf10056 +timestamp : 2022-02-20 22:14:56 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-decoder 4.023 pl5321hec16e2b_1 +------------------------------------------ +file name : perl-sereal-decoder-4.023-pl5321hec16e2b_1.tar.bz2 +name : perl-sereal-decoder +version : 4.023 +build : pl5321hec16e2b_1 +build number: 1 +size : 169 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-4.023-pl5321hec16e2b_1.tar.bz2 +md5 : 3fe58619e9ce76739cdefbb5e1788bc6 +timestamp : 2022-02-24 13:58:08 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-decoder 4.025 pl5321h7b50bb2_2 +------------------------------------------ +file name : perl-sereal-decoder-4.025-pl5321h7b50bb2_2.tar.bz2 +name : perl-sereal-decoder +version : 4.025 +build : pl5321h7b50bb2_2 +build number: 2 +size : 174 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-4.025-pl5321h7b50bb2_2.tar.bz2 +md5 : 19e3afbf3eee81350a4e44ccf2a187ad +timestamp : 2025-02-24 12:54:19 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-decoder 4.025 pl5321hec16e2b_0 +------------------------------------------ +file name : perl-sereal-decoder-4.025-pl5321hec16e2b_0.tar.bz2 +name : perl-sereal-decoder +version : 4.025 +build : pl5321hec16e2b_0 +build number: 0 +size : 170 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-4.025-pl5321hec16e2b_0.tar.bz2 +md5 : b7613ee97c0d27cfbd0ed78647123cbf +timestamp : 2022-07-28 13:28:09 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-decoder 4.025 pl5321hec16e2b_1 +------------------------------------------ +file name : perl-sereal-decoder-4.025-pl5321hec16e2b_1.tar.bz2 +name : perl-sereal-decoder +version : 4.025 +build : pl5321hec16e2b_1 +build number: 1 +size : 171 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-4.025-pl5321hec16e2b_1.tar.bz2 +md5 : ffd38890f6136dbbd1594f21f4f52dce +timestamp : 2022-08-01 15:30:14 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-decoder 5.004 pl5321h7b50bb2_0 +------------------------------------------ +file name : perl-sereal-decoder-5.004-pl5321h7b50bb2_0.conda +name : perl-sereal-decoder +version : 5.004 +build : pl5321h7b50bb2_0 +build number: 0 +size : 173 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-decoder-5.004-pl5321h7b50bb2_0.conda +md5 : e531378d644e24e6142f0c187c2ad521 +timestamp : 2025-08-15 04:10:41 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-devel-checklib >=1.16,<2.0a0 + - perl-extutils-parsexs >=3.58,<4.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sereal-encoder.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sereal-encoder.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ecefd6451d948b2782b55b7f0d1d3306f78e6b3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sereal-encoder.manual_bundle.txt @@ -0,0 +1,340 @@ +# Tool: perl-sereal-encoder +software_name: perl-sereal-encoder +tier: T1 +domain: t1_backfill_overall +downloads: 140619 +summary: Fast, compact, powerful binary serialization. +description: Fast, compact, powerful binary serialization. +dependencies: libgcc >=13, perl >=5.32.1,<5.33.0a0 *_perl5, perl-devel-checklib >=1.16,<2.0a0, perl-extutils-parsexs >=3.58,<4.0a0, perl-sereal-decoder >=5.004, perl-sereal-decoder >=5.4,<6.0a0 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/Sereal::Encoder +doc_url: https://metacpan.org/pod/Sereal::Encoder +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/Sereal::Encoder +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +### https://metacpan.org/pod/Sereal::Encoder +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-sereal-encoder --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-sereal-encoder 3.015 0 +--------------------------- +file name : perl-sereal-encoder-3.015-0.tar.bz2 +name : perl-sereal-encoder +version : 3.015 +build : 0 +build number: 0 +size : 88 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-3.015-0.tar.bz2 +md5 : a8324383db4dbd73029a8ae7162a8c5e +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-sereal-encoder 3.015 pl526_1 +--------------------------------- +file name : perl-sereal-encoder-3.015-pl526_1.tar.bz2 +name : perl-sereal-encoder +version : 3.015 +build : pl526_1 +build number: 1 +size : 98 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-3.015-pl526_1.tar.bz2 +md5 : 482ffaaefc138cf5b56b3af79bcdb3b5 +timestamp : 2018-07-08 20:59:17 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-sereal-encoder 4.005 pl526_0 +--------------------------------- +file name : perl-sereal-encoder-4.005-pl526_0.tar.bz2 +name : perl-sereal-encoder +version : 4.005 +build : pl526_0 +build number: 0 +size : 160 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.005-pl526_0.tar.bz2 +md5 : 5397834250665f8b37b5c8912c79784a +timestamp : 2019-01-13 19:29:11 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-sereal-encoder 4.007 pl526h14c3975_0 +----------------------------------------- +file name : perl-sereal-encoder-4.007-pl526h14c3975_0.tar.bz2 +name : perl-sereal-encoder +version : 4.007 +build : pl526h14c3975_0 +build number: 0 +size : 174 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.007-pl526h14c3975_0.tar.bz2 +md5 : 1b08ae8995416c682a5f70e23f32e48b +timestamp : 2019-05-21 11:06:06 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + + +perl-sereal-encoder 4.007 pl5321h779adbc_1 +------------------------------------------ +file name : perl-sereal-encoder-4.007-pl5321h779adbc_1.tar.bz2 +name : perl-sereal-encoder +version : 4.007 +build : pl5321h779adbc_1 +build number: 1 +size : 174 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.007-pl5321h779adbc_1.tar.bz2 +md5 : 960527cfe06b0c21c9264fb690aa6ed2 +timestamp : 2022-01-21 13:38:07 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-encoder 4.019 pl5321h779adbc_0 +------------------------------------------ +file name : perl-sereal-encoder-4.019-pl5321h779adbc_0.tar.bz2 +name : perl-sereal-encoder +version : 4.019 +build : pl5321h779adbc_0 +build number: 0 +size : 290 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.019-pl5321h779adbc_0.tar.bz2 +md5 : 1cba291577cc3d07c98b7187833332af +timestamp : 2022-02-10 08:37:55 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-encoder 4.020 pl5321h779adbc_0 +------------------------------------------ +file name : perl-sereal-encoder-4.020-pl5321h779adbc_0.tar.bz2 +name : perl-sereal-encoder +version : 4.020 +build : pl5321h779adbc_0 +build number: 0 +size : 290 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.020-pl5321h779adbc_0.tar.bz2 +md5 : f1d407c77cad311966ee4f1168258213 +timestamp : 2022-02-17 15:24:37 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-encoder 4.021 pl5321h779adbc_0 +------------------------------------------ +file name : perl-sereal-encoder-4.021-pl5321h779adbc_0.tar.bz2 +name : perl-sereal-encoder +version : 4.021 +build : pl5321h779adbc_0 +build number: 0 +size : 290 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.021-pl5321h779adbc_0.tar.bz2 +md5 : 6120cee97a32c9bf3faae17913ba5fe3 +timestamp : 2022-02-18 07:57:37 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-encoder 4.021 pl5321hec16e2b_1 +------------------------------------------ +file name : perl-sereal-encoder-4.021-pl5321hec16e2b_1.tar.bz2 +name : perl-sereal-encoder +version : 4.021 +build : pl5321hec16e2b_1 +build number: 1 +size : 282 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.021-pl5321hec16e2b_1.tar.bz2 +md5 : c09bdde02ccc1b5bf747637e8e90dce5 +timestamp : 2022-02-24 14:21:39 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-encoder 4.023 pl5321hec16e2b_0 +------------------------------------------ +file name : perl-sereal-encoder-4.023-pl5321hec16e2b_0.tar.bz2 +name : perl-sereal-encoder +version : 4.023 +build : pl5321hec16e2b_0 +build number: 0 +size : 282 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.023-pl5321hec16e2b_0.tar.bz2 +md5 : f0f5a0c4ae9febc0b7583f48473ae1eb +timestamp : 2022-03-13 13:38:46 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-encoder 4.025 pl5321h7b50bb2_2 +------------------------------------------ +file name : perl-sereal-encoder-4.025-pl5321h7b50bb2_2.tar.bz2 +name : perl-sereal-encoder +version : 4.025 +build : pl5321h7b50bb2_2 +build number: 2 +size : 290 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.025-pl5321h7b50bb2_2.tar.bz2 +md5 : 668c95994a463170f88beaf8d2cb4d3d +timestamp : 2025-02-24 14:15:08 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-sereal-decoder >=4.25,<5.0a0 + + +perl-sereal-encoder 4.025 pl5321h7b50bb2_3 +------------------------------------------ +file name : perl-sereal-encoder-4.025-pl5321h7b50bb2_3.tar.bz2 +name : perl-sereal-encoder +version : 4.025 +build : pl5321h7b50bb2_3 +build number: 3 +size : 291 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.025-pl5321h7b50bb2_3.tar.bz2 +md5 : c68887ab3526fd378ad2bfc975236fc2 +timestamp : 2025-04-25 11:33:01 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-sereal-decoder >=4.25,<5.0a0 + + +perl-sereal-encoder 4.025 pl5321hec16e2b_0 +------------------------------------------ +file name : perl-sereal-encoder-4.025-pl5321hec16e2b_0.tar.bz2 +name : perl-sereal-encoder +version : 4.025 +build : pl5321hec16e2b_0 +build number: 0 +size : 283 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.025-pl5321hec16e2b_0.tar.bz2 +md5 : 6b1010a58250d747a046e4a88c0939b0 +timestamp : 2022-07-28 13:30:38 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-encoder 4.025 pl5321hec16e2b_1 +------------------------------------------ +file name : perl-sereal-encoder-4.025-pl5321hec16e2b_1.tar.bz2 +name : perl-sereal-encoder +version : 4.025 +build : pl5321hec16e2b_1 +build number: 1 +size : 283 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-4.025-pl5321hec16e2b_1.tar.bz2 +md5 : 5eba4ab6f505a40c2d531d3ef6debd3d +timestamp : 2022-08-01 15:36:30 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sereal-encoder 5.004 pl5321h7b50bb2_0 +------------------------------------------ +file name : perl-sereal-encoder-5.004-pl5321h7b50bb2_0.conda +name : perl-sereal-encoder +version : 5.004 +build : pl5321h7b50bb2_0 +build number: 0 +size : 300 KB +license : Perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sereal-encoder-5.004-pl5321h7b50bb2_0.conda +md5 : 00d0c3e5337ccc5d7f7512159f1fb4b5 +timestamp : 2025-08-15 05:05:46 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-devel-checklib >=1.16,<2.0a0 + - perl-extutils-parsexs >=3.58,<4.0a0 + - perl-sereal-decoder >=5.004 + - perl-sereal-decoder >=5.4,<6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-soap-lite.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-soap-lite.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b247e22c255c6489277c1a5ef83078bed1acac3c --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-soap-lite.manual_bundle.txt @@ -0,0 +1,172 @@ +# Tool: perl-soap-lite +software_name: perl-soap-lite +tier: T1 +domain: t1_backfill_overall +downloads: 193310 +summary: Perl's Web Services Toolkit +description: Perl's Web Services Toolkit +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-class-inspector, perl-io-sessiondata, perl-io-socket-ssl, perl-libwww-perl, perl-lwp-protocol-https, perl-mime-lite, perl-mime-tools, perl-task-weaken, perl-uri, perl-xml-parser +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/SOAP-Lite +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/SOAP-Lite +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-soap-lite --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-soap-lite 1.19 0 +--------------------- +file name : perl-soap-lite-1.19-0.tar.bz2 +name : perl-soap-lite +version : 1.19 +build : 0 +build number: 0 +size : 86 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-soap-lite-1.19-0.tar.bz2 +md5 : 5aa92af1b448cf8487efde053b045774 +dependencies: + - perl-class-inspector + - perl-io-sessiondata + - perl-io-socket-ssl + - perl-libwww-perl + - perl-lwp-protocol-https + - perl-mime-lite + - perl-mime-tools + - perl-task-weaken + - perl-threaded + - perl-uri + - perl-xml-parser + - perl >=5.22.0,<5.23.0 + + +perl-soap-lite 1.19 pl526_1 +--------------------------- +file name : perl-soap-lite-1.19-pl526_1.tar.bz2 +name : perl-soap-lite +version : 1.19 +build : pl526_1 +build number: 1 +size : 117 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-soap-lite-1.19-pl526_1.tar.bz2 +md5 : 5eff39fd516c8c8fbe1fe911150f38b2 +timestamp : 2018-08-08 13:07:47 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-class-inspector + - perl-io-sessiondata + - perl-io-socket-ssl + - perl-libwww-perl + - perl-lwp-protocol-https + - perl-mime-lite + - perl-mime-tools + - perl-task-weaken + - perl-uri + - perl-xml-parser + + +perl-soap-lite 1.19 pl5321hdfd78af_2 +------------------------------------ +file name : perl-soap-lite-1.19-pl5321hdfd78af_2.tar.bz2 +name : perl-soap-lite +version : 1.19 +build : pl5321hdfd78af_2 +build number: 2 +size : 120 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-soap-lite-1.19-pl5321hdfd78af_2.tar.bz2 +md5 : adc248b1b8cccd99a9f38842a3979f67 +timestamp : 2022-01-29 22:45:22 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-class-inspector + - perl-io-sessiondata + - perl-io-socket-ssl + - perl-libwww-perl + - perl-lwp-protocol-https + - perl-mime-lite + - perl-mime-tools + - perl-task-weaken + - perl-uri + - perl-xml-parser + + +perl-soap-lite 1.27 pl5321hdfd78af_0 +------------------------------------ +file name : perl-soap-lite-1.27-pl5321hdfd78af_0.tar.bz2 +name : perl-soap-lite +version : 1.27 +build : pl5321hdfd78af_0 +build number: 0 +size : 120 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-soap-lite-1.27-pl5321hdfd78af_0.tar.bz2 +md5 : 84e9b73f98ab49f7521827f0ee31026b +timestamp : 2022-02-15 07:25:58 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-class-inspector + - perl-io-sessiondata + - perl-io-socket-ssl + - perl-libwww-perl + - perl-lwp-protocol-https + - perl-mime-lite + - perl-mime-tools + - perl-task-weaken + - perl-uri + - perl-xml-parser diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-statistics-descriptive.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-statistics-descriptive.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c027c38d4949e2bcd08df748ee129fdaec6dc21f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-statistics-descriptive.manual_bundle.txt @@ -0,0 +1,273 @@ +# Tool: perl-statistics-descriptive +software_name: perl-statistics-descriptive +tier: T1 +domain: t1_backfill_overall +downloads: 217434 +summary: Module of basic descriptive statistical functions. +description: Module of basic descriptive statistical functions. +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-list-moreutils +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://web-cpan.shlomifish.org/modules/Statistics-Descriptive/ +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-statistics-descriptive --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-statistics-descriptive 3.0609 1 +------------------------------------ +file name : perl-statistics-descriptive-3.0609-1.tar.bz2 +name : perl-statistics-descriptive +version : 3.0609 +build : 1 +build number: 1 +size : 77 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-statistics-descriptive-3.0609-1.tar.bz2 +md5 : 8d901b0ce47683cc6a79c47c7c7d39c1 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-statistics-descriptive 3.0609 2 +------------------------------------ +file name : perl-statistics-descriptive-3.0609-2.tar.bz2 +name : perl-statistics-descriptive +version : 3.0609 +build : 2 +build number: 2 +size : 76 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-statistics-descriptive-3.0609-2.tar.bz2 +md5 : c8cee742929829f5197d5d4763211e1c +dependencies: + - libgcc + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-statistics-descriptive 3.0609 3 +------------------------------------ +file name : perl-statistics-descriptive-3.0609-3.tar.bz2 +name : perl-statistics-descriptive +version : 3.0609 +build : 3 +build number: 3 +size : 76 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-statistics-descriptive-3.0609-3.tar.bz2 +md5 : 2783e44340e861410f28e29adb35fcb8 +dependencies: + - libgcc + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-statistics-descriptive 3.0609 pl5.22.0_0 +--------------------------------------------- +file name : perl-statistics-descriptive-3.0609-pl5.22.0_0.tar.bz2 +name : perl-statistics-descriptive +version : 3.0609 +build : pl5.22.0_0 +build number: 0 +size : 69 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-statistics-descriptive-3.0609-pl5.22.0_0.tar.bz2 +md5 : 39f81de8772056ed236aad242d8fb415 +dependencies: + - perl 5.22.0* + + +perl-statistics-descriptive 3.0609 pl526_4 +------------------------------------------ +file name : perl-statistics-descriptive-3.0609-pl526_4.tar.bz2 +name : perl-statistics-descriptive +version : 3.0609 +build : pl526_4 +build number: 4 +size : 24 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-statistics-descriptive-3.0609-pl526_4.tar.bz2 +md5 : a3cb360229f2ee3d01f3cc00961a59df +timestamp : 2018-07-19 03:48:53 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-list-moreutils + + +perl-statistics-descriptive 3.0609 pl5321hdfd78af_5 +--------------------------------------------------- +file name : perl-statistics-descriptive-3.0609-pl5321hdfd78af_5.tar.bz2 +name : perl-statistics-descriptive +version : 3.0609 +build : pl5321hdfd78af_5 +build number: 5 +size : 27 KB +license : Perl +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-statistics-descriptive-3.0609-pl5321hdfd78af_5.tar.bz2 +md5 : d00339d5108218a08a9e315e1e7c5ed4 +timestamp : 2022-01-25 14:13:07 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-list-moreutils + + +perl-statistics-descriptive 3.0612 0 +------------------------------------ +file name : perl-statistics-descriptive-3.0612-0.tar.bz2 +name : perl-statistics-descriptive +version : 3.0612 +build : 0 +build number: 0 +size : 15 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-statistics-descriptive-3.0612-0.tar.bz2 +md5 : dc4a0bac154d829ffeca789b10e1683a +dependencies: + - perl-list-moreutils + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-statistics-descriptive 3.0612 pl526_2 +------------------------------------------ +file name : perl-statistics-descriptive-3.0612-pl526_2.tar.bz2 +name : perl-statistics-descriptive +version : 3.0612 +build : pl526_2 +build number: 2 +size : 25 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-statistics-descriptive-3.0612-pl526_2.tar.bz2 +md5 : 2697640df2d2d7793a40434160edf6cb +timestamp : 2018-07-19 03:45:50 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-list-moreutils + + +perl-statistics-descriptive 3.0702 pl526_0 +------------------------------------------ +file name : perl-statistics-descriptive-3.0702-pl526_0.tar.bz2 +name : perl-statistics-descriptive +version : 3.0702 +build : pl526_0 +build number: 0 +size : 32 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-statistics-descriptive-3.0702-pl526_0.tar.bz2 +md5 : d30fe55f90cc24a85fa9a89a0a94c7b0 +timestamp : 2018-11-11 21:19:04 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-list-moreutils + + +perl-statistics-descriptive 3.0702 pl5321hdfd78af_1 +--------------------------------------------------- +file name : perl-statistics-descriptive-3.0702-pl5321hdfd78af_1.tar.bz2 +name : perl-statistics-descriptive +version : 3.0702 +build : pl5321hdfd78af_1 +build number: 1 +size : 34 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-statistics-descriptive-3.0702-pl5321hdfd78af_1.tar.bz2 +md5 : 5e9b6f1837c5742782566ae55527062c +timestamp : 2022-01-25 14:04:53 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-list-moreutils + + +perl-statistics-descriptive 3.0800 pl5321hdfd78af_0 +--------------------------------------------------- +file name : perl-statistics-descriptive-3.0800-pl5321hdfd78af_0.tar.bz2 +name : perl-statistics-descriptive +version : 3.0800 +build : pl5321hdfd78af_0 +build number: 0 +size : 33 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-statistics-descriptive-3.0800-pl5321hdfd78af_0.tar.bz2 +md5 : 9d5c9fc2856726234e7cae2c2817e524 +timestamp : 2022-02-10 22:21:53 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-list-moreutils + + +perl-statistics-descriptive 3.0801 pl5321hdfd78af_0 +--------------------------------------------------- +file name : perl-statistics-descriptive-3.0801-pl5321hdfd78af_0.tar.bz2 +name : perl-statistics-descriptive +version : 3.0801 +build : pl5321hdfd78af_0 +build number: 0 +size : 35 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-statistics-descriptive-3.0801-pl5321hdfd78af_0.tar.bz2 +md5 : 2bcfb0e07836962525c6127882134825 +timestamp : 2023-07-02 10:28:30 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-list-moreutils diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sub-exporter.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sub-exporter.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc23f9c6391a17c29b1cceba04a5517b2b0b6276 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sub-exporter.manual_bundle.txt @@ -0,0 +1,289 @@ +# Tool: perl-sub-exporter +software_name: perl-sub-exporter +tier: T1 +domain: t1_backfill_overall +downloads: 255603 +summary: a sophisticated exporter for custom-built routines +description: a sophisticated exporter for custom-built routines +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-carp, perl-data-optlist, perl-params-util, perl-sub-install +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/rjbs/Sub-Exporter +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/rjbs/Sub-Exporter +GitHub - rjbs/Sub-Exporter: a sophisticated, customizable code exporter for Perl · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} rjbs / Sub-Exporter Public Notifications You must be signed in to change notification settings Fork 12 Star 10 Code Issues 4 Pull requests 2 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights rjbs/Sub-Exporter main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 235 Commits 235 Commits .github/ workflows .github/ workflows lib/ Sub lib/ Sub t t .gitignore .gitignore .mailmap .mailmap Changes Changes dist.ini dist.ini View all files About a sophisticated, customizable code exporter for Perl Uh oh! There was an error while loading. Please reload this page . Activity Stars 10 stars Watchers 1 watching Forks 12 forks Report repository Releases 23 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-sub-exporter --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-sub-exporter 0.987 0 +------------------------- +file name : perl-sub-exporter-0.987-0.tar.bz2 +name : perl-sub-exporter +version : 0.987 +build : 0 +build number: 0 +size : 20 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sub-exporter-0.987-0.tar.bz2 +md5 : eb96eb0fa992ad9da8d7b9707900ebf9 +dependencies: + - perl-apache-test + - perl-data-optlist + - perl-params-util + - perl-sub-install + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-sub-exporter 0.987 pl526_1 +------------------------------- +file name : perl-sub-exporter-0.987-pl526_1.tar.bz2 +name : perl-sub-exporter +version : 0.987 +build : pl526_1 +build number: 1 +size : 30 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sub-exporter-0.987-pl526_1.tar.bz2 +md5 : c662382c83be8d69050c6502c5a55245 +timestamp : 2018-07-08 23:11:05 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-apache-test + - perl-data-optlist + - perl-params-util + - perl-sub-install + + +perl-sub-exporter 0.987 pl526_2 +------------------------------- +file name : perl-sub-exporter-0.987-pl526_2.tar.bz2 +name : perl-sub-exporter +version : 0.987 +build : pl526_2 +build number: 2 +size : 30 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sub-exporter-0.987-pl526_2.tar.bz2 +md5 : 5c47be06a5776fa6f3b6fb4e799bc5a1 +timestamp : 2018-08-20 13:22:00 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-carp + - perl-data-optlist + - perl-params-util + - perl-sub-install + + +perl-sub-exporter 0.987 pl5321hdfd78af_3 +---------------------------------------- +file name : perl-sub-exporter-0.987-pl5321hdfd78af_3.tar.bz2 +name : perl-sub-exporter +version : 0.987 +build : pl5321hdfd78af_3 +build number: 3 +size : 33 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-sub-exporter-0.987-pl5321hdfd78af_3.tar.bz2 +md5 : 7eb6ce83616b71e50cccefecefde9913 +timestamp : 2022-01-20 23:16:56 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-data-optlist + - perl-params-util + - perl-sub-install + + +perl-sub-exporter 0.988 pl5321ha770c72_0 +---------------------------------------- +file name : perl-sub-exporter-0.988-pl5321ha770c72_0.conda +name : perl-sub-exporter +version : 0.988 +build : pl5321ha770c72_0 +build number: 0 +size : 43 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-sub-exporter-0.988-pl5321ha770c72_0.conda +md5 : 225f0a615a1a9e916c2584857e8a6505 +timestamp : 2022-12-12 15:44:35 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-data-optlist 0.112.* + - perl-params-util 1.102.* + - perl-sub-install + + +perl-sub-exporter 0.988 pl5321hdfd78af_0 +---------------------------------------- +file name : perl-sub-exporter-0.988-pl5321hdfd78af_0.tar.bz2 +name : perl-sub-exporter +version : 0.988 +build : pl5321hdfd78af_0 +build number: 0 +size : 37 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-sub-exporter-0.988-pl5321hdfd78af_0.tar.bz2 +md5 : 0940b3a8d422b87b77e7706a631ac23a +timestamp : 2022-02-09 21:56:20 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-carp + - perl-data-optlist + - perl-params-util + - perl-sub-install + + +perl-sub-exporter 0.989 pl5321ha770c72_0 +---------------------------------------- +file name : perl-sub-exporter-0.989-pl5321ha770c72_0.conda +name : perl-sub-exporter +version : 0.989 +build : pl5321ha770c72_0 +build number: 0 +size : 43 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-sub-exporter-0.989-pl5321ha770c72_0.conda +md5 : 0bce2a1c8716345588f4f1bb82d25419 +timestamp : 2023-01-03 11:47:44 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-data-optlist 0.112.* + - perl-params-util 1.102.* + - perl-sub-install + + +perl-sub-exporter 0.989 pl5321ha770c72_1 +---------------------------------------- +file name : perl-sub-exporter-0.989-pl5321ha770c72_1.conda +name : perl-sub-exporter +version : 0.989 +build : pl5321ha770c72_1 +build number: 1 +size : 43 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-sub-exporter-0.989-pl5321ha770c72_1.conda +md5 : b78db10c07a7e75df30fe331464c360e +timestamp : 2023-01-24 10:49:58 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-data-optlist 0.113.* + - perl-params-util 1.102.* + - perl-sub-install + + +perl-sub-exporter 0.990 pl5321ha770c72_0 +---------------------------------------- +file name : perl-sub-exporter-0.990-pl5321ha770c72_0.conda +name : perl-sub-exporter +version : 0.990 +build : pl5321ha770c72_0 +build number: 0 +size : 43 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-sub-exporter-0.990-pl5321ha770c72_0.conda +md5 : 6bba4a4f1cc435d08356484b0eabdb61 +timestamp : 2023-07-22 07:13:16 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-data-optlist 0.114.* + - perl-params-util 1.102.* + - perl-sub-install + + +perl-sub-exporter 0.991 pl5321ha770c72_0 +---------------------------------------- +file name : perl-sub-exporter-0.991-pl5321ha770c72_0.conda +name : perl-sub-exporter +version : 0.991 +build : pl5321ha770c72_0 +build number: 0 +size : 43 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-sub-exporter-0.991-pl5321ha770c72_0.conda +md5 : e96211ecd6575a4c00f17282a0d5d350 +timestamp : 2023-11-24 02:10:52 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-data-optlist 0.114.* + - perl-params-util 1.102.* + - perl-sub-install + + +perl-sub-exporter 0.991 pl5321ha770c72_1 +---------------------------------------- +file name : perl-sub-exporter-0.991-pl5321ha770c72_1.conda +name : perl-sub-exporter +version : 0.991 +build : pl5321ha770c72_1 +build number: 1 +size : 43 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-sub-exporter-0.991-pl5321ha770c72_1.conda +md5 : 7639c6421eb53c1413a60eef3c95e728 +timestamp : 2025-04-23 20:04:52 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-data-optlist 0.114.* + - perl-params-util 1.102.* + - perl-sub-install diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sub-identify.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sub-identify.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..9065fa2c83f069fe975e5bf660fc0d14f1bf8e84 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-sub-identify.manual_bundle.txt @@ -0,0 +1,207 @@ +# Tool: perl-sub-identify +software_name: perl-sub-identify +tier: T1 +domain: t1_backfill_overall +downloads: 259700 +summary: Retrieve names of code references +description: Retrieve names of code references +dependencies: libgcc-ng >=10.3.0, perl >=5.32.1,<5.33.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Sub::Identify +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Sub::Identify +Sub::Identify - Retrieve names of code references - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Sub-Identify Module version: 0.14 11 Apr 2017 07:18:17 UTC License: perl_5 Code Download ( 51.89KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (2) How to Contribute Quality Testers ( 20800 / 6 / 3 ) Testers (Magpie) Kwalitee 80.00% Coverage Bus factor: 0 Activity 24 month Dependencies Test::More and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 0.14 (RGARCIA on 2017-04-11) 0.13 (RGARCIA on 2017-04-02) 0.12 (RGARCIA on 2015-09-08) 0.11 (RGARCIA on 2015-09-04) 0.10 (RGARCIA on 2015-01-02) 0.09 (RGARCIA on 2014-12-31) 0.08 (RGARCIA on 2014-09-17) 0.07 (RGARCIA on 2014-09-11) 0.06 (RGARCIA on 2014-09-10) 0.05 (RGARCIA on 2014-09-10) 0.04 (RGARCIA on 2008-12-15) 0.03 (RGARCIA on 2008-05-19) 0.02 (RGARCIA on 2005-05-13) 0.01 (RGARCIA on 2005-05-13) Diff with version 0.14 (RGARCIA on 2017-04-11) 0.13 (RGARCIA on 2017-04-02) 0.12 (RGARCIA on 2015-09-08) 0.11 (RGARCIA on 2015-09-04) 0.10 (RGARCIA on 2015-01-02) 0.09 (RGARCIA on 2014-12-31) 0.08 (RGARCIA on 2014-09-17) 0.07 (RGARCIA on 2014-09-11) 0.06 (RGARCIA on 2014-09-10) 0.05 (RGARCIA on 2014-09-10) 0.04 (RGARCIA on 2008-12-15) 0.03 (RGARCIA on 2008-05-19) 0.02 (RGARCIA on 2005-05-13) 0.01 (RGARCIA on 2005-05-13) Permalinks This version Latest version ++ed by: 7 PAUSE users 3 non-PAUSE users Authors: unknown Released by: Rafaël Garcia-Suarez Maintainers: RGARCIA owner Rafaël Garcia-Suarez  /  0.14 (RGARCIA on 2017-04-11) 0.13 (RGARCIA on 2017-04-02) 0.12 (RGARCIA on 2015-09-08) 0.11 (RGARCIA on 2015-09-04) 0.10 (RGARCIA on 2015-01-02) 0.09 (RGARCIA on 2014-12-31) 0.08 (RGARCIA on 2014-09-17) 0.07 (RGARCIA on 2014-09-11) 0.06 (RGARCIA on 2014-09-10) 0.05 (RGARCIA on 2014-09-10) 0.04 (RGARCIA on 2008-12-15) 0.03 (RGARCIA on 2008-05-19) 0.02 (RGARCIA on 2005-05-13) 0.01 (RGARCIA on 2005-05-13) Sub-Identify-0.14 10 ++ 10 ++ / Sub::Identify Contents NAME SYNOPSIS DESCRIPTION Pure-Perl version SEE ALSO SOURCE LICENSE NAME Sub::Identify - Retrieve names of code references SYNOPSIS use Sub::Identify ':all'; my $subname = sub_name( $some_coderef ); my $packagename = stash_name( $some_coderef ); # or, to get all at once... my $fully_qualified_name = sub_fullname( $some_coderef ); defined $subname and say "this coderef points to sub $subname in package $packagename"; my ($file, $line) = get_code_location( $some_coderef ); $file and say "this coderef is defined at line $line in file $file"; is_sub_constant( $some_coderef ) and say "this coderef points to a constant subroutine"; DESCRIPTION Sub::Identify allows you to retrieve the real name of code references. It provides six functions, all of them taking a code reference. sub_name returns the name of the code reference passed as an argument (or __ANON__ if it's an anonymous code reference), stash_name returns its package, and sub_fullname returns the concatenation of the two. get_code_info returns a list of two elements, the package and the subroutine name (in case of you want both and are worried by the speed.) In case of subroutine aliasing, those functions always return the original name. get_code_location returns a two-element list containing the file name and the line number where the subroutine has been defined. is_sub_constant returns a boolean value indicating whether the subroutine is a constant or not. Pure-Perl version By default Sub::Identify tries to load an XS implementation of the get_code_info , get_code_location and (on perl versions 5.16.0 and later) is_sub_constant functions, for speed; if that fails, or if the environment variable PERL_SUB_IDENTIFY_PP is defined to a true value, it will fall back to a pure perl implementation, that uses perl's introspection mechanism, provided by the B module. SEE ALSO Sub::Util , part of the module distribution Scalar::List::Utils since version 1.40. Since this will be a core module starting with perl 5.22.0, it is encouraged to migrate to Sub::Util when possible. Sub::Name SOURCE A git repository for the sources is at https://github.com/rgs/Sub-Identify . LICENSE (c) Rafael Garcia-Suarez (rgs at consttype dot org) 2005, 2008, 2012, 2014, 2015 This program is free software; you may redistribute it and/or modify it under the same terms as Perl itself. Module Install Instructions To install Sub::Identify, copy and paste the appropriate command in to your terminal. cpanm cpanm Sub::Identify CPAN shell perl -MCPAN -e shell install Sub::Identify For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-sub-identify --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-sub-identify 0.12 pl5.22.0_0 +--------------------------------- +file name : perl-sub-identify-0.12-pl5.22.0_0.tar.bz2 +name : perl-sub-identify +version : 0.12 +build : pl5.22.0_0 +build number: 0 +size : 10 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sub-identify-0.12-pl5.22.0_0.tar.bz2 +md5 : 5878661da0613a399dc211122d1b7ca9 +dependencies: + - perl 5.22.0* + + +perl-sub-identify 0.12 pl526_1 +------------------------------ +file name : perl-sub-identify-0.12-pl526_1.tar.bz2 +name : perl-sub-identify +version : 0.12 +build : pl526_1 +build number: 1 +size : 12 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sub-identify-0.12-pl526_1.tar.bz2 +md5 : 37dacb9fa5fb36cabac08a0f24e46254 +timestamp : 2018-07-06 22:20:34 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-sub-identify 0.14 pl526h14c3975_0 +-------------------------------------- +file name : perl-sub-identify-0.14-pl526h14c3975_0.tar.bz2 +name : perl-sub-identify +version : 0.14 +build : pl526h14c3975_0 +build number: 0 +size : 12 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sub-identify-0.14-pl526h14c3975_0.tar.bz2 +md5 : 17126c427ca6c885ce4836d69f3f4825 +timestamp : 2019-05-15 21:52:08 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + + +perl-sub-identify 0.14 pl5321h166bdaf_0 +--------------------------------------- +file name : perl-sub-identify-0.14-pl5321h166bdaf_0.tar.bz2 +name : perl-sub-identify +version : 0.14 +build : pl5321h166bdaf_0 +build number: 0 +size : 20 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-sub-identify-0.14-pl5321h166bdaf_0.tar.bz2 +md5 : 042f949ae52549119535b544714df51b +timestamp : 2022-10-10 20:59:02 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sub-identify 0.14 pl5321h779adbc_1 +--------------------------------------- +file name : perl-sub-identify-0.14-pl5321h779adbc_1.tar.bz2 +name : perl-sub-identify +version : 0.14 +build : pl5321h779adbc_1 +build number: 1 +size : 14 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sub-identify-0.14-pl5321h779adbc_1.tar.bz2 +md5 : 3ced5413fa1d1bbef586ed46c83f3fd1 +timestamp : 2022-01-19 00:53:18 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sub-identify 0.14 pl5321hb9d3cd8_1 +--------------------------------------- +file name : perl-sub-identify-0.14-pl5321hb9d3cd8_1.conda +name : perl-sub-identify +version : 0.14 +build : pl5321hb9d3cd8_1 +build number: 1 +size : 20 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-sub-identify-0.14-pl5321hb9d3cd8_1.conda +md5 : c9e357e0328b1f759976c89f5ab2d1e7 +timestamp : 2025-01-28 14:40:02 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sub-identify 0.14 pl5321hb9d3cd8_2 +--------------------------------------- +file name : perl-sub-identify-0.14-pl5321hb9d3cd8_2.conda +name : perl-sub-identify +version : 0.14 +build : pl5321hb9d3cd8_2 +build number: 2 +size : 21 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-sub-identify-0.14-pl5321hb9d3cd8_2.conda +md5 : dad8c17ee696b3fb6a44760083a83e92 +timestamp : 2025-03-03 14:46:51 UTC +dependencies: + - __glibc >=2.17,<3.0.a0 + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-sub-identify 0.14 pl5321hec16e2b_2 +--------------------------------------- +file name : perl-sub-identify-0.14-pl5321hec16e2b_2.tar.bz2 +name : perl-sub-identify +version : 0.14 +build : pl5321hec16e2b_2 +build number: 2 +size : 14 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-sub-identify-0.14-pl5321hec16e2b_2.tar.bz2 +md5 : f36c9c3c5c57865ed7107286403fb35c +timestamp : 2022-02-22 06:55:05 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-template-toolkit.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-template-toolkit.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..d484eabe6ce72492e9dde7e307f1864f078c9463 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-template-toolkit.manual_bundle.txt @@ -0,0 +1,308 @@ +# Tool: perl-template-toolkit +software_name: perl-template-toolkit +tier: T1 +domain: t1_backfill_overall +downloads: 194178 +summary: Comprehensive template processing system. +description: Comprehensive template processing system. +dependencies: libgcc >=13, perl >=5.32.1,<5.33.0a0 *_perl5, perl-appconfig, perl-image-info, perl-image-size, perl-test-leaktrace 0.17.* +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/Template::Toolkit +doc_url: https://metacpan.org/pod/Template::Toolkit +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/Template::Toolkit +Template::Toolkit - Template Processing System - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Template-Toolkit Module version: 3.100 21 Jun 2024 21:58:51 UTC License: perl_5 Code Download ( 510.56KB ) Source ( raw ) Browse ( raw ) Changes Project Homepage Repository Issues How to Contribute Quality Testers ( 4547 / 64 / 0 ) Testers (Magpie) Kwalitee % Coverage Bus factor: 2 Activity 24 month Dependencies AppConfig File::Spec File::Temp Scalar::Util and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 3.102 (TODDR on 2024-06-21) 3.101 (ABW on 2022-08-16) 3.100 (TODDR on 2022-04-26) 3.009 (ATOOMIC on 2020-07-13) 3.008 (ATOOMIC on 2020-03-30) 3.007 (ATOOMIC on 2020-01-27) 3.006 (ATOOMIC on 2020-01-16) 3.005 (ATOOMIC on 2020-01-15) 3.004 (ATOOMIC on 2020-01-13) 3.003 (ATOOMIC on 2019-12-27) 3.002 (ATOOMIC on 2019-12-23) 3.001 (ATOOMIC on 2019-12-23) 3.000 (ATOOMIC on 2019-12-23) 2.29 (ATOOMIC on 2019-04-29) 2.28 (ATOOMIC on 2018-10-11) 2.27 (ABW on 2017-04-15) 2.26 (ABW on 2014-09-17) 2.25 (ABW on 2013-07-24) 2.24 (ABW on 2012-02-08) 2.23 (ABW on 2012-01-21) 2.22 (ABW on 2009-07-21) 2.21_02 DEV (ABW on 2009-07-04) 2.21_01 DEV (ABW on 2009-07-04) 2.21 (ABW on 2009-06-30) 2.20_4 DEV (ABW on 2009-05-21) 2.20_3 DEV (ABW on 2009-05-20) 2.20_2 DEV (ABW on 2009-05-17) 2.20_1 DEV (ABW on 2009-04-07) 2.20 (ABW on 2008-08-13) 2.00 (ABW on 2000-12-06) 1.07 (ABW on 2000-06-16) 3.010 (ATOOMIC on 2021-12-13) 2.19_03 DEV (ABW on 2008-08-12) 2.19_02 DEV (ABW on 2008-08-08) 2.19_01 DEV (ABW on 2008-08-07) 2.19 (ABW on 2007-04-30) 2.18 (ABW on 2007-02-09) 2.17 (ADAMK on 2007-02-08) 2.16 (ADAMK on 2007-01-23) 2.15 (ABW on 2006-05-26) 2.14 (ABW on 2004-10-04) 2.13 (ABW on 2004-01-30) 2.12 (ABW on 2004-01-12) 2.11 (ABW on 2004-01-06) 2.10 (ABW on 2003-07-24) 2.09 (ABW on 2003-04-23) 2.08 (ABW on 2002-07-30) 2.07 (ABW on 2002-04-17) 2.06d (ABW on 2002-01-22) 2.06 (ABW on 2001-11-07) 2.04 (ABW on 2001-06-29) 2.03 (ABW on 2001-06-15) 2.01 (ABW on 2001-03-30) 2.00-beta5 (ABW on 2000-09-14) 2.00-beta4 (ABW on 2000-09-12) 1.06 (ABW on 2000-03-28) 1.05 (ABW on 2000-03-20) 1.04 (ABW on 2000-03-02) 1.03 (ABW on 2000-02-01) 1.02 (ABW on 1999-12-21) 1.00 (ABW on 1999-12-02) 0.28 (ABW on 1999-11-05) 0.27 (ABW on 1999-10-01) 0.26 (ABW on 1999-09-15) 0.25 (ABW on 1999-08-16) 0.24 (ABW on 1999-08-12) 0.23 (ABW on 1999-08-10) 0.22 (ABW on 1999-08-06) Diff with version 3.102 (TODDR on 2024-06-21) 3.101 (ABW on 2022-08-16) 3.100 (TODDR on 2022-04-26) 3.009 (ATOOMIC on 2020-07-13) 3.008 (ATOOMIC on 2020-03-30) 3.007 (ATOOMIC on 2020-01-27) 3.006 (ATOOMIC on 2020-01-16) 3.005 (ATOOMIC on 2020-01-15) 3.004 (ATOOMIC on 2020-01-13) 3.003 (ATOOMIC on 2019-12-27) 3.002 (ATOOMIC on 2019-12-23) 3.001 (ATOOMIC on 2019-12-23) 3.000 (ATOOMIC on 2019-12-23) 2.29 (ATOOMIC on 2019-04-29) 2.28 (ATOOMIC on 2018-10-11) 2.27 (ABW on 2017-04-15) 2.26 (ABW on 2014-09-17) 2.25 (ABW on 2013-07-24) 2.24 (ABW on 2012-02-08) 2.23 (ABW on 2012-01-21) 2.22 (ABW on 2009-07-21) 2.21_02 DEV (ABW on 2009-07-04) 2.21_01 DEV (ABW on 2009-07-04) 2.21 (ABW on 2009-06-30) 2.20_4 DEV (ABW on 2009-05-21) 2.20_3 DEV (ABW on 2009-05-20) 2.20_2 DEV (ABW on 2009-05-17) 2.20_1 DEV (ABW on 2009-04-07) 2.20 (ABW on 2008-08-13) 2.00 (ABW on 2000-12-06) 1.07 (ABW on 2000-06-16) 3.010 (ATOOMIC on 2021-12-13) 2.19_03 DEV (ABW on 2008-08-12) 2.19_02 DEV (ABW on 2008-08-08) 2.19_01 DEV (ABW on 2008-08-07) 2.19 (ABW on 2007-04-30) 2.18 (ABW on 2007-02-09) 2.17 (ADAMK on 2007-02-08) 2.16 (ADAMK on 2007-01-23) 2.15 (ABW on 2006-05-26) 2.14 (ABW on 2004-10-04) 2.13 (ABW on 2004-01-30) 2.12 (ABW on 2004-01-12) 2.11 (ABW on 2004-01-06) 2.10 (ABW on 2003-07-24) 2.09 (ABW on 2003-04-23) 2.08 (ABW on 2002-07-30) 2.07 (ABW on 2002-04-17) 2.06d (ABW on 2002-01-22) 2.06 (ABW on 2001-11-07) 2.04 (ABW on 2001-06-29) 2.03 (ABW on 2001-06-15) 2.01 (ABW on 2001-03-30) 2.00-beta5 (ABW on 2000-09-14) 2.00-beta4 (ABW on 2000-09-12) 1.06 (ABW on 2000-03-28) 1.05 (ABW on 2000-03-20) 1.04 (ABW on 2000-03-02) 1.03 (ABW on 2000-02-01) 1.02 (ABW on 1999-12-21) 1.00 (ABW on 1999-12-02) 0.28 (ABW on 1999-11-05) 0.27 (ABW on 1999-10-01) 0.26 (ABW on 1999-09-15) 0.25 (ABW on 1999-08-16) 0.24 (ABW on 1999-08-12) 0.23 (ABW on 1999-08-10) 0.22 (ABW on 1999-08-06) Permalinks This version Latest version ++ed by: 73 PAUSE users 76 non-PAUSE users Authors: Andy Wardley Released by: Todd Rinaldo Maintainers: ABW owner ATOOMIC TODDR Contributors: Andy Wardley Todd Rinaldo  /  3.102 (TODDR on 2024-06-21) 3.101 (ABW on 2022-08-16) 3.100 (TODDR on 2022-04-26) 3.009 (ATOOMIC on 2020-07-13) 3.008 (ATOOMIC on 2020-03-30) 3.007 (ATOOMIC on 2020-01-27) 3.006 (ATOOMIC on 2020-01-16) 3.005 (ATOOMIC on 2020-01-15) 3.004 (ATOOMIC on 2020-01-13) 3.003 (ATOOMIC on 2019-12-27) 3.002 (ATOOMIC on 2019-12-23) 3.001 (ATOOMIC on 2019-12-23) 3.000 (ATOOMIC on 2019-12-23) 2.29 (ATOOMIC on 2019-04-29) 2.28 (ATOOMIC on 2018-10-11) 2.27 (ABW on 2017-04-15) 2.26 (ABW on 2014-09-17) 2.25 (ABW on 2013-07-24) 2.24 (ABW on 2012-02-08) 2.23 (ABW on 2012-01-21) 2.22 (ABW on 2009-07-21) 2.21_02 DEV (ABW on 2009-07-04) 2.21_01 DEV (ABW on 2009-07-04) 2.21 (ABW on 2009-06-30) 2.20_4 DEV (ABW on 2009-05-21) 2.20_3 DEV (ABW on 2009-05-20) 2.20_2 DEV (ABW on 2009-05-17) 2.20_1 DEV (ABW on 2009-04-07) 2.20 (ABW on 2008-08-13) 2.00 (ABW on 2000-12-06) 1.07 (ABW on 2000-06-16) 3.010 (ATOOMIC on 2021-12-13) 2.19_03 DEV (ABW on 2008-08-12) 2.19_02 DEV (ABW on 2008-08-08) 2.19_01 DEV (ABW on 2008-08-07) 2.19 (ABW on 2007-04-30) 2.18 (ABW on 2007-02-09) 2.17 (ADAMK on 2007-02-08) 2.16 (ADAMK on 2007-01-23) 2.15 (ABW on 2006-05-26) 2.14 (ABW on 2004-10-04) 2.13 (ABW on 2004-01-30) 2.12 (ABW on 2004-01-12) 2.11 (ABW on 2004-01-06) 2.10 (ABW on 2003-07-24) 2.09 (ABW on 2003-04-23) 2.08 (ABW on 2002-07-30) 2.07 (ABW on 2002-04-17) 2.06d (ABW on 2002-01-22) 2.06 (ABW on 2001-11-07) 2.04 (ABW on 2001-06-29) 2.03 (ABW on 2001-06-15) 2.01 (ABW on 2001-03-30) 2.00-beta5 (ABW on 2000-09-14) 2.00-beta4 (ABW on 2000-09-12) 1.06 (ABW on 2000-03-28) 1.05 (ABW on 2000-03-20) 1.04 (ABW on 2000-03-02) 1.03 (ABW on 2000-02-01) 1.02 (ABW on 1999-12-21) 1.00 (ABW on 1999-12-02) 0.28 (ABW on 1999-11-05) 0.27 (ABW on 1999-10-01) 0.26 (ABW on 1999-09-15) 0.25 (ABW on 1999-08-16) 0.24 (ABW on 1999-08-12) 0.23 (ABW on 1999-08-10) 0.22 (ABW on 1999-08-06) Template-Toolkit-3.102 149 ++ 149 ++ ⭐ Starred 148 GitHub stars / Template::Toolkit Contents NAME Introduction Documentation Author Copyright See Also NAME Template::Toolkit - Template Processing System Introduction The Template Toolkit is a collection of Perl modules which implement a fast, flexible, powerful and extensible template processing system. It is "input-agnostic" and can be used equally well for processing any kind of text documents: HTML, XML, CSS, Javascript, Perl code, plain text, and so on. However, it is most often used for generating static and dynamic web content, so that's what we'll focus on here. Although the Template Toolkit is written in Perl, you don't need to be a Perl programmer to use it. It was designed to allow non-programmers to easily create and maintain template-based web sites without having to mess around writing Perl code or going crazy with cut-n-paste. However, the Template Toolkit is also designed to be extremely flexible and extensible. If you are a Perl programmer, or know someone who is, then you can easily hook the Template Toolkit into your existing code, data, databases and web applications. Furthermore, you can easily extend the Template Toolkit through the use of its plugin mechanism and other developer APIs. Whatever context you use it in, the primary purpose of the Template Toolkit is to allow you to create a clear separation between the presentation elements of your web site and everything else. If you're generating static web pages, then you can use it to separate the commonly repeated user interface elements on each page (headers, menus, footers, etc.) from the core content. If you're generating dynamic web pages for the front end of a web application, then you'll also be using it to keep the back-end Perl code entirely separate from the front-end HTML templates. Either way, a clear separation of concerns is what allow you to concentrate on one thing at a time without the other things getting in your way. And that's what the Template Toolkit is all about. Documentation The documentation for the Template Toolkit is organised into five sections. The Template::Manual contains detailed information about using the Template Toolkit. It gives examples of its use and includes a full reference of the template language, configuration options, filters, plugins and other component parts. The Template::Modules page lists the Perl modules that comprise the Template Toolkit. It gives a brief explanation of what each of them does, and provides a link to the complete documentation for each module for further information. If you're a Perl programmer looking to use the Template Toolkit from your Perl programs then this section is likely to be of interest. Most, if not all of the information you need to call the Template Toolkit from Perl is in the documentation for the Template module. You only really need to start thinking about the other modules if you want to extend or modify the Template Toolkit in some way, or if you're interested in looking under the hood to see how it all works. The documentation for each module is embedded as POD in each module, so you can always use perldoc from the command line to read a module's documentation. e.g. $ perldoc Template $ perldoc Template::Context ...etc... It's worth noting that all the other documentation, including the user manual is available as POD. e.g. $ perldoc Template::Manual $ perldoc Template::Manual::Config ...etc... The Template::Tools section contains the documentation for Template::Tools::tpage and Template::Tools::ttree . These are two command line programs that are distributed with the Template Toolkit. tpage is used to process a single template file, ttree for processing entire directories of template files. The Template::Tutorial section contains two introductory tutorials on using the Template Toolkit. The first is Template::Tutorial::Web on generating web content. The second is Template::Tutorial::Datafile on using the Template Toolkit to generate other data formats including XML. The final section of the manual is Template::FAQ which contains answers to some of the Frequently Asked Questions about the Template Toolkit. You can read the documentation in HTML format either online at the Template Toolkit web site, http://template-toolkit.org/ , or by downloading the HTML version of the documentation from http://template-toolkit.org/download/index.html#html_docs and unpacking it on your local machine. Author The Template Toolkit was written by Andy Wardley ( http://wardley.org/ mailto:abw@wardley.org ) with assistance and contributions from a great number of people. Please see Template::Manual::Credits for a full list. Copyright Copyright (C) 1996-2022 Andy Wardley. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See Also Template , Template::Manual , Template::Modules , Template::Tools , Template::Tutorial Module Install Instructions To install Template::Toolkit, copy and paste the appropriate command in to your terminal. cpanm cpanm Template::Toolkit CPAN shell perl -MCPAN -e shell install Template::Toolkit For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +### https://metacpan.org/pod/Template::Toolkit +Template::Toolkit - Template Processing System - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Template-Toolkit Module version: 3.100 21 Jun 2024 21:58:51 UTC License: perl_5 Code Download ( 510.56KB ) Source ( raw ) Browse ( raw ) Changes Project Homepage Repository Issues How to Contribute Quality Testers ( 4547 / 64 / 0 ) Testers (Magpie) Kwalitee % Coverage Bus factor: 2 Activity 24 month Dependencies AppConfig File::Spec File::Temp Scalar::Util and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 3.102 (TODDR on 2024-06-21) 3.101 (ABW on 2022-08-16) 3.100 (TODDR on 2022-04-26) 3.009 (ATOOMIC on 2020-07-13) 3.008 (ATOOMIC on 2020-03-30) 3.007 (ATOOMIC on 2020-01-27) 3.006 (ATOOMIC on 2020-01-16) 3.005 (ATOOMIC on 2020-01-15) 3.004 (ATOOMIC on 2020-01-13) 3.003 (ATOOMIC on 2019-12-27) 3.002 (ATOOMIC on 2019-12-23) 3.001 (ATOOMIC on 2019-12-23) 3.000 (ATOOMIC on 2019-12-23) 2.29 (ATOOMIC on 2019-04-29) 2.28 (ATOOMIC on 2018-10-11) 2.27 (ABW on 2017-04-15) 2.26 (ABW on 2014-09-17) 2.25 (ABW on 2013-07-24) 2.24 (ABW on 2012-02-08) 2.23 (ABW on 2012-01-21) 2.22 (ABW on 2009-07-21) 2.21_02 DEV (ABW on 2009-07-04) 2.21_01 DEV (ABW on 2009-07-04) 2.21 (ABW on 2009-06-30) 2.20_4 DEV (ABW on 2009-05-21) 2.20_3 DEV (ABW on 2009-05-20) 2.20_2 DEV (ABW on 2009-05-17) 2.20_1 DEV (ABW on 2009-04-07) 2.20 (ABW on 2008-08-13) 2.00 (ABW on 2000-12-06) 1.07 (ABW on 2000-06-16) 3.010 (ATOOMIC on 2021-12-13) 2.19_03 DEV (ABW on 2008-08-12) 2.19_02 DEV (ABW on 2008-08-08) 2.19_01 DEV (ABW on 2008-08-07) 2.19 (ABW on 2007-04-30) 2.18 (ABW on 2007-02-09) 2.17 (ADAMK on 2007-02-08) 2.16 (ADAMK on 2007-01-23) 2.15 (ABW on 2006-05-26) 2.14 (ABW on 2004-10-04) 2.13 (ABW on 2004-01-30) 2.12 (ABW on 2004-01-12) 2.11 (ABW on 2004-01-06) 2.10 (ABW on 2003-07-24) 2.09 (ABW on 2003-04-23) 2.08 (ABW on 2002-07-30) 2.07 (ABW on 2002-04-17) 2.06d (ABW on 2002-01-22) 2.06 (ABW on 2001-11-07) 2.04 (ABW on 2001-06-29) 2.03 (ABW on 2001-06-15) 2.01 (ABW on 2001-03-30) 2.00-beta5 (ABW on 2000-09-14) 2.00-beta4 (ABW on 2000-09-12) 1.06 (ABW on 2000-03-28) 1.05 (ABW on 2000-03-20) 1.04 (ABW on 2000-03-02) 1.03 (ABW on 2000-02-01) 1.02 (ABW on 1999-12-21) 1.00 (ABW on 1999-12-02) 0.28 (ABW on 1999-11-05) 0.27 (ABW on 1999-10-01) 0.26 (ABW on 1999-09-15) 0.25 (ABW on 1999-08-16) 0.24 (ABW on 1999-08-12) 0.23 (ABW on 1999-08-10) 0.22 (ABW on 1999-08-06) Diff with version 3.102 (TODDR on 2024-06-21) 3.101 (ABW on 2022-08-16) 3.100 (TODDR on 2022-04-26) 3.009 (ATOOMIC on 2020-07-13) 3.008 (ATOOMIC on 2020-03-30) 3.007 (ATOOMIC on 2020-01-27) 3.006 (ATOOMIC on 2020-01-16) 3.005 (ATOOMIC on 2020-01-15) 3.004 (ATOOMIC on 2020-01-13) 3.003 (ATOOMIC on 2019-12-27) 3.002 (ATOOMIC on 2019-12-23) 3.001 (ATOOMIC on 2019-12-23) 3.000 (ATOOMIC on 2019-12-23) 2.29 (ATOOMIC on 2019-04-29) 2.28 (ATOOMIC on 2018-10-11) 2.27 (ABW on 2017-04-15) 2.26 (ABW on 2014-09-17) 2.25 (ABW on 2013-07-24) 2.24 (ABW on 2012-02-08) 2.23 (ABW on 2012-01-21) 2.22 (ABW on 2009-07-21) 2.21_02 DEV (ABW on 2009-07-04) 2.21_01 DEV (ABW on 2009-07-04) 2.21 (ABW on 2009-06-30) 2.20_4 DEV (ABW on 2009-05-21) 2.20_3 DEV (ABW on 2009-05-20) 2.20_2 DEV (ABW on 2009-05-17) 2.20_1 DEV (ABW on 2009-04-07) 2.20 (ABW on 2008-08-13) 2.00 (ABW on 2000-12-06) 1.07 (ABW on 2000-06-16) 3.010 (ATOOMIC on 2021-12-13) 2.19_03 DEV (ABW on 2008-08-12) 2.19_02 DEV (ABW on 2008-08-08) 2.19_01 DEV (ABW on 2008-08-07) 2.19 (ABW on 2007-04-30) 2.18 (ABW on 2007-02-09) 2.17 (ADAMK on 2007-02-08) 2.16 (ADAMK on 2007-01-23) 2.15 (ABW on 2006-05-26) 2.14 (ABW on 2004-10-04) 2.13 (ABW on 2004-01-30) 2.12 (ABW on 2004-01-12) 2.11 (ABW on 2004-01-06) 2.10 (ABW on 2003-07-24) 2.09 (ABW on 2003-04-23) 2.08 (ABW on 2002-07-30) 2.07 (ABW on 2002-04-17) 2.06d (ABW on 2002-01-22) 2.06 (ABW on 2001-11-07) 2.04 (ABW on 2001-06-29) 2.03 (ABW on 2001-06-15) 2.01 (ABW on 2001-03-30) 2.00-beta5 (ABW on 2000-09-14) 2.00-beta4 (ABW on 2000-09-12) 1.06 (ABW on 2000-03-28) 1.05 (ABW on 2000-03-20) 1.04 (ABW on 2000-03-02) 1.03 (ABW on 2000-02-01) 1.02 (ABW on 1999-12-21) 1.00 (ABW on 1999-12-02) 0.28 (ABW on 1999-11-05) 0.27 (ABW on 1999-10-01) 0.26 (ABW on 1999-09-15) 0.25 (ABW on 1999-08-16) 0.24 (ABW on 1999-08-12) 0.23 (ABW on 1999-08-10) 0.22 (ABW on 1999-08-06) Permalinks This version Latest version ++ed by: 73 PAUSE users 76 non-PAUSE users Authors: Andy Wardley Released by: Todd Rinaldo Maintainers: ABW owner ATOOMIC TODDR Contributors: Andy Wardley Todd Rinaldo  /  3.102 (TODDR on 2024-06-21) 3.101 (ABW on 2022-08-16) 3.100 (TODDR on 2022-04-26) 3.009 (ATOOMIC on 2020-07-13) 3.008 (ATOOMIC on 2020-03-30) 3.007 (ATOOMIC on 2020-01-27) 3.006 (ATOOMIC on 2020-01-16) 3.005 (ATOOMIC on 2020-01-15) 3.004 (ATOOMIC on 2020-01-13) 3.003 (ATOOMIC on 2019-12-27) 3.002 (ATOOMIC on 2019-12-23) 3.001 (ATOOMIC on 2019-12-23) 3.000 (ATOOMIC on 2019-12-23) 2.29 (ATOOMIC on 2019-04-29) 2.28 (ATOOMIC on 2018-10-11) 2.27 (ABW on 2017-04-15) 2.26 (ABW on 2014-09-17) 2.25 (ABW on 2013-07-24) 2.24 (ABW on 2012-02-08) 2.23 (ABW on 2012-01-21) 2.22 (ABW on 2009-07-21) 2.21_02 DEV (ABW on 2009-07-04) 2.21_01 DEV (ABW on 2009-07-04) 2.21 (ABW on 2009-06-30) 2.20_4 DEV (ABW on 2009-05-21) 2.20_3 DEV (ABW on 2009-05-20) 2.20_2 DEV (ABW on 2009-05-17) 2.20_1 DEV (ABW on 2009-04-07) 2.20 (ABW on 2008-08-13) 2.00 (ABW on 2000-12-06) 1.07 (ABW on 2000-06-16) 3.010 (ATOOMIC on 2021-12-13) 2.19_03 DEV (ABW on 2008-08-12) 2.19_02 DEV (ABW on 2008-08-08) 2.19_01 DEV (ABW on 2008-08-07) 2.19 (ABW on 2007-04-30) 2.18 (ABW on 2007-02-09) 2.17 (ADAMK on 2007-02-08) 2.16 (ADAMK on 2007-01-23) 2.15 (ABW on 2006-05-26) 2.14 (ABW on 2004-10-04) 2.13 (ABW on 2004-01-30) 2.12 (ABW on 2004-01-12) 2.11 (ABW on 2004-01-06) 2.10 (ABW on 2003-07-24) 2.09 (ABW on 2003-04-23) 2.08 (ABW on 2002-07-30) 2.07 (ABW on 2002-04-17) 2.06d (ABW on 2002-01-22) 2.06 (ABW on 2001-11-07) 2.04 (ABW on 2001-06-29) 2.03 (ABW on 2001-06-15) 2.01 (ABW on 2001-03-30) 2.00-beta5 (ABW on 2000-09-14) 2.00-beta4 (ABW on 2000-09-12) 1.06 (ABW on 2000-03-28) 1.05 (ABW on 2000-03-20) 1.04 (ABW on 2000-03-02) 1.03 (ABW on 2000-02-01) 1.02 (ABW on 1999-12-21) 1.00 (ABW on 1999-12-02) 0.28 (ABW on 1999-11-05) 0.27 (ABW on 1999-10-01) 0.26 (ABW on 1999-09-15) 0.25 (ABW on 1999-08-16) 0.24 (ABW on 1999-08-12) 0.23 (ABW on 1999-08-10) 0.22 (ABW on 1999-08-06) Template-Toolkit-3.102 149 ++ 149 ++ ⭐ Starred 148 GitHub stars / Template::Toolkit Contents NAME Introduction Documentation Author Copyright See Also NAME Template::Toolkit - Template Processing System Introduction The Template Toolkit is a collection of Perl modules which implement a fast, flexible, powerful and extensible template processing system. It is "input-agnostic" and can be used equally well for processing any kind of text documents: HTML, XML, CSS, Javascript, Perl code, plain text, and so on. However, it is most often used for generating static and dynamic web content, so that's what we'll focus on here. Although the Template Toolkit is written in Perl, you don't need to be a Perl programmer to use it. It was designed to allow non-programmers to easily create and maintain template-based web sites without having to mess around writing Perl code or going crazy with cut-n-paste. However, the Template Toolkit is also designed to be extremely flexible and extensible. If you are a Perl programmer, or know someone who is, then you can easily hook the Template Toolkit into your existing code, data, databases and web applications. Furthermore, you can easily extend the Template Toolkit through the use of its plugin mechanism and other developer APIs. Whatever context you use it in, the primary purpose of the Template Toolkit is to allow you to create a clear separation between the presentation elements of your web site and everything else. If you're generating static web pages, then you can use it to separate the commonly repeated user interface elements on each page (headers, menus, footers, etc.) from the core content. If you're generating dynamic web pages for the front end of a web application, then you'll also be using it to keep the back-end Perl code entirely separate from the front-end HTML templates. Either way, a clear separation of concerns is what allow you to concentrate on one thing at a time without the other things getting in your way. And that's what the Template Toolkit is all about. Documentation The documentation for the Template Toolkit is organised into five sections. The Template::Manual contains detailed information about using the Template Toolkit. It gives examples of its use and includes a full reference of the template language, configuration options, filters, plugins and other component parts. The Template::Modules page lists the Perl modules that comprise the Template Toolkit. It gives a brief explanation of what each of them does, and provides a link to the complete documentation for each module for further information. If you're a Perl programmer looking to use the Template Toolkit from your Perl programs then this section is likely to be of interest. Most, if not all of the information you need to call the Template Toolkit from Perl is in the documentation for the Template module. You only really need to start thinking about the other modules if you want to extend or modify the Template Toolkit in some way, or if you're interested in looking under the hood to see how it all works. The documentation for each module is embedded as POD in each module, so you can always use perldoc from the command line to read a module's documentation. e.g. $ perldoc Template $ perldoc Template::Context ...etc... It's worth noting that all the other documentation, including the user manual is available as POD. e.g. $ perldoc Template::Manual $ perldoc Template::Manual::Config ...etc... The Template::Tools section contains the documentation for Template::Tools::tpage and Template::Tools::ttree . These are two command line programs that are distributed with the Template Toolkit. tpage is used to process a single template file, ttree for processing entire directories of template files. The Template::Tutorial section contains two introductory tutorials on using the Template Toolkit. The first is Template::Tutorial::Web on generating web content. The second is Template::Tutorial::Datafile on using the Template Toolkit to generate other data formats including XML. The final section of the manual is Template::FAQ which contains answers to some of the Frequently Asked Questions about the Template Toolkit. You can read the documentation in HTML format either online at the Template Toolkit web site, http://template-toolkit.org/ , or by downloading the HTML version of the documentation from http://template-toolkit.org/download/index.html#html_docs and unpacking it on your local machine. Author The Template Toolkit was written by Andy Wardley ( http://wardley.org/ mailto:abw@wardley.org ) with assistance and contributions from a great number of people. Please see Template::Manual::Credits for a full list. Copyright Copyright (C) 1996-2022 Andy Wardley. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See Also Template , Template::Manual , Template::Modules , Template::Tools , Template::Tutorial Module Install Instructions To install Template::Toolkit, copy and paste the appropriate command in to your terminal. cpanm cpanm Template::Toolkit CPAN shell perl -MCPAN -e shell install Template::Toolkit For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-template-toolkit --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-template-toolkit 2.26 0 +---------------------------- +file name : perl-template-toolkit-2.26-0.tar.bz2 +name : perl-template-toolkit +version : 2.26 +build : 0 +build number: 0 +size : 217 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-2.26-0.tar.bz2 +md5 : 4cb4a78989c3a919070b71fc13459606 +dependencies: + - perl-appconfig + - perl-cgi + - perl-image-info + - perl-image-size + - perl-test-leaktrace + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-template-toolkit 2.26 pl526_1 +---------------------------------- +file name : perl-template-toolkit-2.26-pl526_1.tar.bz2 +name : perl-template-toolkit +version : 2.26 +build : pl526_1 +build number: 1 +size : 319 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-2.26-pl526_1.tar.bz2 +md5 : fa89ace236f54f558e7569b276338968 +timestamp : 2018-07-08 22:36:47 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-appconfig + - perl-cgi + - perl-image-info + - perl-image-size + - perl-test-leaktrace + + +perl-template-toolkit 2.26 pl5321h779adbc_2 +------------------------------------------- +file name : perl-template-toolkit-2.26-pl5321h779adbc_2.tar.bz2 +name : perl-template-toolkit +version : 2.26 +build : pl5321h779adbc_2 +build number: 2 +size : 345 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-2.26-pl5321h779adbc_2.tar.bz2 +md5 : 839adad183e27cf44bfb2dd5542da6f5 +timestamp : 2022-01-24 06:28:05 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-appconfig + - perl-cgi + - perl-image-info + - perl-image-size + - perl-test-leaktrace + + +perl-template-toolkit 3.010 pl5321h779adbc_0 +-------------------------------------------- +file name : perl-template-toolkit-3.010-pl5321h779adbc_0.tar.bz2 +name : perl-template-toolkit +version : 3.010 +build : pl5321h779adbc_0 +build number: 0 +size : 330 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-3.010-pl5321h779adbc_0.tar.bz2 +md5 : 5d7c5d8ef1f9f2e3c9170f9d22e0120d +timestamp : 2022-02-14 22:14:03 UTC +dependencies: + - libgcc-ng >=9.4.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-appconfig + - perl-cgi + - perl-image-info + - perl-image-size + + +perl-template-toolkit 3.010 pl5321hec16e2b_1 +-------------------------------------------- +file name : perl-template-toolkit-3.010-pl5321hec16e2b_1.tar.bz2 +name : perl-template-toolkit +version : 3.010 +build : pl5321hec16e2b_1 +build number: 1 +size : 353 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-3.010-pl5321hec16e2b_1.tar.bz2 +md5 : 73e4a61b76a2bb6e8379196a73a13d67 +timestamp : 2022-02-26 08:17:59 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-appconfig + - perl-cgi + - perl-image-info + - perl-image-size + + +perl-template-toolkit 3.100 pl5321h031d066_2 +-------------------------------------------- +file name : perl-template-toolkit-3.100-pl5321h031d066_2.tar.bz2 +name : perl-template-toolkit +version : 3.100 +build : pl5321h031d066_2 +build number: 2 +size : 351 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-3.100-pl5321h031d066_2.tar.bz2 +md5 : 033887867e1cccf5ab40e3a1f02ca1aa +timestamp : 2023-05-15 07:24:37 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-appconfig + - perl-image-info + - perl-image-size + - perl-test-leaktrace 0.17.* + + +perl-template-toolkit 3.100 pl5321h7b50bb2_3 +-------------------------------------------- +file name : perl-template-toolkit-3.100-pl5321h7b50bb2_3.tar.bz2 +name : perl-template-toolkit +version : 3.100 +build : pl5321h7b50bb2_3 +build number: 3 +size : 354 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-3.100-pl5321h7b50bb2_3.tar.bz2 +md5 : 834f90d37f78b8f18e70ee2c21679845 +timestamp : 2024-12-15 17:35:09 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-appconfig + - perl-image-info + - perl-image-size + - perl-test-leaktrace 0.17.* + + +perl-template-toolkit 3.100 pl5321hec16e2b_0 +-------------------------------------------- +file name : perl-template-toolkit-3.100-pl5321hec16e2b_0.tar.bz2 +name : perl-template-toolkit +version : 3.100 +build : pl5321hec16e2b_0 +build number: 0 +size : 359 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-3.100-pl5321hec16e2b_0.tar.bz2 +md5 : ba109a43dd85763547ee43a4b07123c2 +timestamp : 2022-05-29 16:11:38 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-appconfig + - perl-image-info + - perl-image-size + + +perl-template-toolkit 3.100 pl5321hec16e2b_1 +-------------------------------------------- +file name : perl-template-toolkit-3.100-pl5321hec16e2b_1.tar.bz2 +name : perl-template-toolkit +version : 3.100 +build : pl5321hec16e2b_1 +build number: 1 +size : 356 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-3.100-pl5321hec16e2b_1.tar.bz2 +md5 : fcbe128a8a30a42508fe30ff0d688f8d +timestamp : 2022-08-01 15:45:32 UTC +dependencies: + - libgcc-ng >=12 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-appconfig + - perl-image-info + - perl-image-size + + +perl-template-toolkit 3.102 pl5321h7b50bb2_0 +-------------------------------------------- +file name : perl-template-toolkit-3.102-pl5321h7b50bb2_0.tar.bz2 +name : perl-template-toolkit +version : 3.102 +build : pl5321h7b50bb2_0 +build number: 0 +size : 353 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-3.102-pl5321h7b50bb2_0.tar.bz2 +md5 : da089419927ee84ea6037dc06b6766d7 +timestamp : 2025-02-05 06:59:38 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-appconfig + - perl-image-info + - perl-image-size + - perl-test-leaktrace 0.17.* + + +perl-template-toolkit 3.102 pl5321h7b50bb2_1 +-------------------------------------------- +file name : perl-template-toolkit-3.102-pl5321h7b50bb2_1.tar.bz2 +name : perl-template-toolkit +version : 3.102 +build : pl5321h7b50bb2_1 +build number: 1 +size : 351 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-3.102-pl5321h7b50bb2_1.tar.bz2 +md5 : 3fd1cc8733a751013890bbd16dcda5a6 +timestamp : 2025-02-19 11:07:51 UTC +dependencies: + - libgcc >=13 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-appconfig + - perl-image-info + - perl-image-size + - perl-test-leaktrace 0.17.* diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-differences.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-differences.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba88bfab208bd7ee0b9b98e809a43c8bc0fea92f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-differences.manual_bundle.txt @@ -0,0 +1,250 @@ +# Tool: perl-test-differences +software_name: perl-test-differences +tier: T1 +domain: t1_backfill_overall +downloads: 219192 +summary: Test strings and data structures and show differences if not ok +description: Test strings and data structures and show differences if not ok +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-capture-tiny, perl-text-diff +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Test-Differences +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Test-Differences +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-test-differences --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-test-differences 0.64 0 +---------------------------- +file name : perl-test-differences-0.64-0.tar.bz2 +name : perl-test-differences +version : 0.64 +build : 0 +build number: 0 +size : 7 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-differences-0.64-0.tar.bz2 +md5 : 3ed4cc2b499d458bbe9241f9d5c5a798 +dependencies: + - perl-capture-tiny + - perl-text-diff + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-test-differences 0.64 pl526_1 +---------------------------------- +file name : perl-test-differences-0.64-pl526_1.tar.bz2 +name : perl-test-differences +version : 0.64 +build : pl526_1 +build number: 1 +size : 14 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-differences-0.64-pl526_1.tar.bz2 +md5 : 08c175afffa1f08cd6d95265579db9c8 +timestamp : 2018-07-19 03:51:59 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-capture-tiny + - perl-text-diff + + +perl-test-differences 0.64 pl526_2 +---------------------------------- +file name : perl-test-differences-0.64-pl526_2.tar.bz2 +name : perl-test-differences +version : 0.64 +build : pl526_2 +build number: 2 +size : 14 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-differences-0.64-pl526_2.tar.bz2 +md5 : 4bbc4b5aadc12543faa42909c4bd7414 +timestamp : 2018-07-19 22:51:24 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-capture-tiny + - perl-text-diff + + +perl-test-differences 0.67 pl526_0 +---------------------------------- +file name : perl-test-differences-0.67-pl526_0.tar.bz2 +name : perl-test-differences +version : 0.67 +build : pl526_0 +build number: 0 +size : 15 KB +license : Perl +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-test-differences-0.67-pl526_0.tar.bz2 +md5 : 256f0110145fa69a7c0ccf41a993fae5 +timestamp : 2019-06-18 21:24:16 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-capture-tiny + - perl-text-diff + + +perl-test-differences 0.67 pl5321hdfd78af_1 +------------------------------------------- +file name : perl-test-differences-0.67-pl5321hdfd78af_1.tar.bz2 +name : perl-test-differences +version : 0.67 +build : pl5321hdfd78af_1 +build number: 1 +size : 15 KB +license : Perl +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-test-differences-0.67-pl5321hdfd78af_1.tar.bz2 +md5 : ca5971a8a30a154eec2c67806315ae33 +timestamp : 2022-01-21 12:11:38 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-capture-tiny + - perl-text-diff + + +perl-test-differences 0.69 pl5321ha770c72_0 +------------------------------------------- +file name : perl-test-differences-0.69-pl5321ha770c72_0.tar.bz2 +name : perl-test-differences +version : 0.69 +build : pl5321ha770c72_0 +build number: 0 +size : 22 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-test-differences-0.69-pl5321ha770c72_0.tar.bz2 +md5 : 6950cdcd0cb61e908cc4aae658f825c8 +timestamp : 2022-10-31 16:21:42 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-text-diff + + +perl-test-differences 0.69 pl5321hdfd78af_0 +------------------------------------------- +file name : perl-test-differences-0.69-pl5321hdfd78af_0.tar.bz2 +name : perl-test-differences +version : 0.69 +build : pl5321hdfd78af_0 +build number: 0 +size : 19 KB +license : Perl +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-test-differences-0.69-pl5321hdfd78af_0.tar.bz2 +md5 : 1f7a9aa718798b8f9544d0a80dea3673 +timestamp : 2022-02-15 22:40:33 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-capture-tiny + - perl-text-diff + + +perl-test-differences 0.70 pl5321ha770c72_0 +------------------------------------------- +file name : perl-test-differences-0.70-pl5321ha770c72_0.conda +name : perl-test-differences +version : 0.70 +build : pl5321ha770c72_0 +build number: 0 +size : 23 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-test-differences-0.70-pl5321ha770c72_0.conda +md5 : ecbe29ea9f2d808fb49a3c7e5a0af769 +timestamp : 2023-07-08 05:57:25 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-text-diff + + +perl-test-differences 0.71 pl5321ha770c72_0 +------------------------------------------- +file name : perl-test-differences-0.71-pl5321ha770c72_0.conda +name : perl-test-differences +version : 0.71 +build : pl5321ha770c72_0 +build number: 0 +size : 23 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-test-differences-0.71-pl5321ha770c72_0.conda +md5 : f8d63311ef6aac0220fc3d490ccff6bd +timestamp : 2023-10-13 08:33:15 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-text-diff + + +perl-test-differences 0.72 pl5321ha770c72_0 +------------------------------------------- +file name : perl-test-differences-0.72-pl5321ha770c72_0.conda +name : perl-test-differences +version : 0.72 +build : pl5321ha770c72_0 +build number: 0 +size : 24 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-test-differences-0.72-pl5321ha770c72_0.conda +md5 : d079d274039b439b6388a450e36b7dc7 +timestamp : 2025-07-07 18:51:01 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-text-diff diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-harness.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-harness.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3fdc866fcf0588ebec9a1639745c755f3d5cf1e7 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-harness.manual_bundle.txt @@ -0,0 +1,215 @@ +# Tool: perl-test-harness +software_name: perl-test-harness +tier: T1 +domain: t1_backfill_overall +downloads: 264432 +summary: contributing to TAP::Harness +description: contributing to TAP::Harness +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://testanything.org/ +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://testanything.org/ +Home - Test Anything Protocol Home Testing with TAP Producers Consumers Specification Test Anything Protocol TAP, the Test Anything Protocol, is a simple text-based interface between testing modules in a test harness. It decouples the reporting of errors from the presentation of the reports. One of its major uses is for noise reduction; when you have a suite of many tests, making them TAP producers and using a TAP consumer to view them helps ensures that you will see everything you need to notice and diagnose breakage without being distracted by a flood of irrelevant success messages. It can assist other forms of analysis and statistics-gathering as well. TAP started life as part of the test harness for Perl but now has implementations in C, C++, Python, PHP, Perl, Java, JavaScript, Go, Rust, and others. Consumers and producers do not have to be written in the same language to interoperate. Here’s what a TAP test stream looks like: 1..4 ok 1 - Input file opened not ok 2 - First line of the input valid ok 3 - Read the rest of the file not ok 4 - Summarized correctly # TODO Not written yet Testing with TAP Testing with TAP - How to run TAP based tests in your language of choice TAP Development TAP Producers - Testing tools that generate TAP output TAP Consumers - Test harnesses that read TAP TAP Philosophy - The Tao of TAP TAP History - The story of TAP Specifications TAP version 14 specification (Current) TAP version 13 specification TAP specification External Resources Wikipedia article on TAP The TAP subreddit github.com/testanything + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-test-harness --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-test-harness 3.30 1 +------------------------ +file name : perl-test-harness-3.30-1.tar.bz2 +name : perl-test-harness +version : 3.30 +build : 1 +build number: 1 +size : 73 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-harness-3.30-1.tar.bz2 +md5 : b4d438b0ab8381a42314ae7bf62f81e3 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-test-harness 3.30 pl5.22.0_2 +--------------------------------- +file name : perl-test-harness-3.30-pl5.22.0_2.tar.bz2 +name : perl-test-harness +version : 3.30 +build : pl5.22.0_2 +build number: 2 +size : 76 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-harness-3.30-pl5.22.0_2.tar.bz2 +md5 : 0242706e045f2fa62eac72f470e22486 +dependencies: + - perl 5.22.0* + + +perl-test-harness 3.30 pl526_3 +------------------------------ +file name : perl-test-harness-3.30-pl526_3.tar.bz2 +name : perl-test-harness +version : 3.30 +build : pl526_3 +build number: 3 +size : 81 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-harness-3.30-pl526_3.tar.bz2 +md5 : a65c4d65c1efa1b2dbe9b15ec50bf152 +timestamp : 2018-06-29 01:46:23 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-test-harness 3.36 pl5.22.0_0 +--------------------------------- +file name : perl-test-harness-3.36-pl5.22.0_0.tar.bz2 +name : perl-test-harness +version : 3.36 +build : pl5.22.0_0 +build number: 0 +size : 77 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-harness-3.36-pl5.22.0_0.tar.bz2 +md5 : b6188d43e484a775d3c97ed5d86d8fa5 +dependencies: + - perl 5.22.0* + + +perl-test-harness 3.36 pl526_1 +------------------------------ +file name : perl-test-harness-3.36-pl526_1.tar.bz2 +name : perl-test-harness +version : 3.36 +build : pl526_1 +build number: 1 +size : 82 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-harness-3.36-pl526_1.tar.bz2 +md5 : 8ed3e4632f219626c6a76b7e3c94d59a +timestamp : 2018-06-29 01:49:35 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-test-harness 3.42 pl526_0 +------------------------------ +file name : perl-test-harness-3.42-pl526_0.tar.bz2 +name : perl-test-harness +version : 3.42 +build : pl526_0 +build number: 0 +size : 82 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-harness-3.42-pl526_0.tar.bz2 +md5 : 5a82f26d026ea1dec91ceb9d0ab55b21 +timestamp : 2018-08-21 20:37:00 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-test-harness 3.42 pl5321hdfd78af_1 +--------------------------------------- +file name : perl-test-harness-3.42-pl5321hdfd78af_1.tar.bz2 +name : perl-test-harness +version : 3.42 +build : pl5321hdfd78af_1 +build number: 1 +size : 84 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-test-harness-3.42-pl5321hdfd78af_1.tar.bz2 +md5 : 25b801ae40e7c4c522609a8f223f2505 +timestamp : 2022-01-19 12:17:14 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-test-harness 3.44 pl5321hd8ed1ab_0 +--------------------------------------- +file name : perl-test-harness-3.44-pl5321hd8ed1ab_0.tar.bz2 +name : perl-test-harness +version : 3.44 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 90 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-test-harness-3.44-pl5321hd8ed1ab_0.tar.bz2 +md5 : 8a4acd1dda1520b3f7903dbe1ccb376a +timestamp : 2022-09-05 17:41:53 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-test-harness 3.44 pl5321hdfd78af_0 +--------------------------------------- +file name : perl-test-harness-3.44-pl5321hdfd78af_0.tar.bz2 +name : perl-test-harness +version : 3.44 +build : pl5321hdfd78af_0 +build number: 0 +size : 85 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-test-harness-3.44-pl5321hdfd78af_0.tar.bz2 +md5 : f6a9c19b95737821062fbe49c4fcd4e1 +timestamp : 2022-04-17 16:22:41 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-most.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-most.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e82af4395a8e4e393ccb145dbe35340a18f84f7 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-most.manual_bundle.txt @@ -0,0 +1,199 @@ +# Tool: perl-test-most +software_name: perl-test-most +tier: T1 +domain: t1_backfill_overall +downloads: 310738 +summary: Most commonly needed test functions and features +description: Most commonly needed test functions and features +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-exception-class, perl-test-deep, perl-test-differences, perl-test-exception, perl-test-warn +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Test-Most +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Test-Most +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-test-most --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-test-most 0.34 1 +--------------------- +file name : perl-test-most-0.34-1.tar.bz2 +name : perl-test-most +version : 0.34 +build : 1 +build number: 1 +size : 10 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-most-0.34-1.tar.bz2 +md5 : 88139be953d787f9b2802d200a900863 +dependencies: + - perl-exception-class + - perl-test-deep + - perl-test-differences + - perl-test-exception + - perl-test-warn + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-test-most 0.34 pl526_2 +--------------------------- +file name : perl-test-most-0.34-pl526_2.tar.bz2 +name : perl-test-most +version : 0.34 +build : pl526_2 +build number: 2 +size : 17 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-most-0.34-pl526_2.tar.bz2 +md5 : 3f7d9ed31095f4bb964f272cfc466f0d +timestamp : 2018-07-31 23:21:15 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-exception-class + - perl-test-deep + - perl-test-differences + - perl-test-exception + - perl-test-warn + + +perl-test-most 0.35 pl526_0 +--------------------------- +file name : perl-test-most-0.35-pl526_0.tar.bz2 +name : perl-test-most +version : 0.35 +build : pl526_0 +build number: 0 +size : 18 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-most-0.35-pl526_0.tar.bz2 +md5 : 19ec7be21e08029005c2ff33b67c483f +timestamp : 2018-11-11 03:20:59 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-exception-class + - perl-test-deep + - perl-test-differences + - perl-test-exception + - perl-test-warn + + +perl-test-most 0.35 pl5321hdfd78af_1 +------------------------------------ +file name : perl-test-most-0.35-pl5321hdfd78af_1.tar.bz2 +name : perl-test-most +version : 0.35 +build : pl5321hdfd78af_1 +build number: 1 +size : 19 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-test-most-0.35-pl5321hdfd78af_1.tar.bz2 +md5 : ce47c02da67799de9a46e79cdf3ffbbb +timestamp : 2022-01-21 12:20:56 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-exception-class + - perl-test-deep + - perl-test-differences + - perl-test-exception + - perl-test-warn + + +perl-test-most 0.37 pl5321hdfd78af_0 +------------------------------------ +file name : perl-test-most-0.37-pl5321hdfd78af_0.tar.bz2 +name : perl-test-most +version : 0.37 +build : pl5321hdfd78af_0 +build number: 0 +size : 20 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-test-most-0.37-pl5321hdfd78af_0.tar.bz2 +md5 : fba1e55e28fc0530b94db9db5288cc1a +timestamp : 2022-02-14 23:02:44 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-exception-class + - perl-test-deep + - perl-test-differences + - perl-test-exception + - perl-test-warn + + +perl-test-most 0.38 pl5321hdfd78af_0 +------------------------------------ +file name : perl-test-most-0.38-pl5321hdfd78af_0.tar.bz2 +name : perl-test-most +version : 0.38 +build : pl5321hdfd78af_0 +build number: 0 +size : 20 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-test-most-0.38-pl5321hdfd78af_0.tar.bz2 +md5 : af484f1f44bf33bb0a6ab33e109ab8cb +timestamp : 2022-09-24 14:36:13 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-exception-class + - perl-test-deep + - perl-test-differences + - perl-test-exception + - perl-test-warn diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-requiresinternet.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-requiresinternet.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..586765c997f2ee655d1f9ffa91566b9338744528 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-test-requiresinternet.manual_bundle.txt @@ -0,0 +1,62 @@ +# Tool: perl-test-requiresinternet +software_name: perl-test-requiresinternet +tier: T1 +domain: t1_backfill_overall +downloads: 363605 +summary: Easily test network connectivity +description: Easily test network connectivity +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-socket +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/dist/Test-RequiresInternet +doc_url: +dev_url: + +## URL Docs Extract +### https://metacpan.org/dist/Test-RequiresInternet +Test-RequiresInternet-0.05 - Easily test network connectivity - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution Test-RequiresInternet 26 May 2015 01:38:59 UTC License: perl_5 Code Download ( 10.77KB ) Browse ( raw ) Changes Project Homepage Repository Issues (2) How to Contribute Quality Testers ( 23960 / 3 / 0 ) Testers (Magpie) Kwalitee 88.89% Coverage Bus factor: 0 Activity 24 month Dependencies Socket strict warnings Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 0.05 (MALLEN on 2015-05-26) 0.04 (MALLEN on 2015-01-29) 0.03 (MALLEN on 2014-09-07) 0.02 (MALLEN on 2014-07-03) 0.01 (MALLEN on 2014-06-24) Diff with version 0.05 (MALLEN on 2015-05-26) 0.04 (MALLEN on 2015-01-29) 0.03 (MALLEN on 2014-09-07) 0.02 (MALLEN on 2014-07-03) 0.01 (MALLEN on 2014-06-24) Permalinks This version Latest version ++ed by: 15 PAUSE users 6 non-PAUSE users Authors: Mark Allen Released by: Jade Allen Maintainers: MALLEN owner Jade Allen  /  0.05 (MALLEN on 2015-05-26) 0.04 (MALLEN on 2015-01-29) 0.03 (MALLEN on 2014-09-07) 0.02 (MALLEN on 2014-07-03) 0.01 (MALLEN on 2014-06-24) Test-RequiresInternet-0.05 21 ++ 21 ++ Changes for version 0.05 - 2015-05-25 Fix test error when NO_NETWORK_TESTING is set (Karen Etheridge, RT#101996 , GH#3 ) [ Show less Show more ] Modules Test::RequiresInternet Easily test network connectivity Other files Changes LICENSE MANIFEST META.json META.yml Makefile.PL README dist.ini Module Install Instructions To install Test::RequiresInternet, copy and paste the appropriate command in to your terminal. cpanm cpanm Test::RequiresInternet CPAN shell perl -MCPAN -e shell install Test::RequiresInternet For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-test-requiresinternet --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-test-requiresinternet 0.05 pl526_0 +--------------------------------------- +file name : perl-test-requiresinternet-0.05-pl526_0.tar.bz2 +name : perl-test-requiresinternet +version : 0.05 +build : pl526_0 +build number: 0 +size : 7 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-test-requiresinternet-0.05-pl526_0.tar.bz2 +md5 : 47a9cfbedd72952aa493625692404a4e +timestamp : 2018-08-08 09:19:48 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-socket + + +perl-test-requiresinternet 0.05 pl5321hdfd78af_1 +------------------------------------------------ +file name : perl-test-requiresinternet-0.05-pl5321hdfd78af_1.tar.bz2 +name : perl-test-requiresinternet +version : 0.05 +build : pl5321hdfd78af_1 +build number: 1 +size : 9 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-test-requiresinternet-0.05-pl5321hdfd78af_1.tar.bz2 +md5 : 715b1cf617730df28080c5c3981212e4 +timestamp : 2022-01-21 10:13:40 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-socket diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-text-diff.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-text-diff.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..5163a9efa616c68b124109cadc75ca201c426c02 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-text-diff.manual_bundle.txt @@ -0,0 +1,189 @@ +# Tool: perl-text-diff +software_name: perl-text-diff +tier: T1 +domain: t1_backfill_overall +downloads: 219531 +summary: Perform diffs on files and record sets +description: Perform diffs on files and record sets +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-algorithm-diff +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/Text-Diff +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/Text-Diff +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-text-diff --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-text-diff 1.44 0 +--------------------- +file name : perl-text-diff-1.44-0.tar.bz2 +name : perl-text-diff +version : 1.44 +build : 0 +build number: 0 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-text-diff-1.44-0.tar.bz2 +md5 : 4b44af269e69444071a91c7bdacc9bf9 +dependencies: + - perl-algorithm-diff + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-text-diff 1.44 pl5.22.0_0 +------------------------------ +file name : perl-text-diff-1.44-pl5.22.0_0.tar.bz2 +name : perl-text-diff +version : 1.44 +build : pl5.22.0_0 +build number: 0 +size : 20 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-text-diff-1.44-pl5.22.0_0.tar.bz2 +md5 : e941d41b4ec8744bc82334b44bb1ff5e +dependencies: + - perl 5.22.0* + - perl-algorithm-diff + + +perl-text-diff 1.44 pl526_1 +--------------------------- +file name : perl-text-diff-1.44-pl526_1.tar.bz2 +name : perl-text-diff +version : 1.44 +build : pl526_1 +build number: 1 +size : 20 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-text-diff-1.44-pl526_1.tar.bz2 +md5 : c2c0c73f07584c0ebc19b62a63da7d75 +timestamp : 2018-07-07 23:51:10 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-algorithm-diff + + +perl-text-diff 1.44 pl526_2 +--------------------------- +file name : perl-text-diff-1.44-pl526_2.tar.bz2 +name : perl-text-diff +version : 1.44 +build : pl526_2 +build number: 2 +size : 20 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-text-diff-1.44-pl526_2.tar.bz2 +md5 : 48e70941c6a7516a8d9ea3e0ee9e0a0d +timestamp : 2018-07-19 22:06:20 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-algorithm-diff + + +perl-text-diff 1.45 pl526_0 +--------------------------- +file name : perl-text-diff-1.45-pl526_0.tar.bz2 +name : perl-text-diff +version : 1.45 +build : pl526_0 +build number: 0 +size : 20 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-text-diff-1.45-pl526_0.tar.bz2 +md5 : 98e32f19827755284e6d6e4c100b4108 +timestamp : 2018-11-11 06:05:22 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-algorithm-diff + + +perl-text-diff 1.45 pl5321hd8ed1ab_0 +------------------------------------ +file name : perl-text-diff-1.45-pl5321hd8ed1ab_0.tar.bz2 +name : perl-text-diff +version : 1.45 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 32 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-text-diff-1.45-pl5321hd8ed1ab_0.tar.bz2 +md5 : 7c91b422ca8ccb679449d1e3cdd3b7d7 +timestamp : 2022-09-23 14:09:13 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-algorithm-diff + + +perl-text-diff 1.45 pl5321hdfd78af_1 +------------------------------------ +file name : perl-text-diff-1.45-pl5321hdfd78af_1.tar.bz2 +name : perl-text-diff +version : 1.45 +build : pl5321hdfd78af_1 +build number: 1 +size : 23 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-text-diff-1.45-pl5321hdfd78af_1.tar.bz2 +md5 : e9b9f91c7e44a671faa8fbf20cbdd6f6 +timestamp : 2022-01-18 06:02:47 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-algorithm-diff diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-try-tiny.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-try-tiny.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1a50f458856645d3d3fe7055e5e5e2a261f766b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-try-tiny.manual_bundle.txt @@ -0,0 +1,270 @@ +# Tool: perl-try-tiny +software_name: perl-try-tiny +tier: T1 +domain: t1_backfill_overall +downloads: 476030 +summary: minimal try/catch with proper preservation of $@ +description: minimal try/catch with proper preservation of $@ +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/karenetheridge/Try-Tiny +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/karenetheridge/Try-Tiny +GitHub - p5sagit/Try-Tiny: minimal try/catch with proper preservation of $@ · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} p5sagit / Try-Tiny Public forked from doy/try-tiny Notifications You must be signed in to change notification settings Fork 6 Star 10 Code Pull requests 4 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Pull requests Actions Projects Wiki Security and quality Insights p5sagit/Try-Tiny master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 221 Commits 221 Commits lib/ Try lib/ Try maint maint t t .gitignore .gitignore .mailmap .mailmap .travis.yml .travis.yml CONTRIBUTING CONTRIBUTING Changes Changes INSTALL INSTALL LICENCE LICENCE README.pod README.pod dist.ini dist.ini View all files Repository files navigation README Contributing License NAME Try::Tiny - Minimal try/catch with proper preservation of $@ VERSION version 0.32 SYNOPSIS You can use Try::Tiny's try and catch to expect and handle exceptional conditions, avoiding quirks in Perl and common mistakes: # handle errors with a catch handler try { die "foo"; } catch { warn "caught error: $_"; # not $@ }; You can also use it like a standalone eval to catch and ignore any error conditions. Obviously, this is an extreme measure not to be undertaken lightly: # just silence errors try { die "foo"; }; DESCRIPTION This module provides bare bones try / catch / finally statements that are designed to minimize common mistakes with eval blocks, and NOTHING else. This is unlike TryCatch which provides a nice syntax and avoids adding another call stack layer, and supports calling return from the try block to return from the parent subroutine. These extra features come at a cost of a few dependencies, namely Devel::Declare and Scope::Upper which are occasionally problematic, and the additional catch filtering uses Moose type constraints which may not be desirable either. The main focus of this module is to provide simple and reliable error handling for those having a hard time installing TryCatch , but who still want to write correct eval blocks without 5 lines of boilerplate each time. It's designed to work as correctly as possible in light of the various pathological edge cases (see "BACKGROUND" ) and to be compatible with any style of error values (simple strings, references, objects, overloaded objects, etc). If the try block dies, it returns the value of the last statement executed in the catch block, if there is one. Otherwise, it returns undef in scalar context or the empty list in list context. The following examples all assign "bar" to $x : my $x = try { die "foo" } catch { "bar" }; my $x = try { die "foo" } || "bar"; my $x = (try { die "foo" }) // "bar"; my $x = eval { die "foo" } || "bar"; You can add finally blocks, yielding the following: my $x; try { die 'foo' } finally { $x = 'bar' }; try { die 'foo' } catch { warn "Got a die: $_" } finally { $x = 'bar' }; finally blocks are always executed making them suitable for cleanup code which cannot be handled using local. You can add as many finally blocks to a given try block as you like. Note that adding a finally block without a preceding catch block suppresses any errors. This behaviour is consistent with using a standalone eval , but it is not consistent with try / finally patterns found in other programming languages, such as Java, Python, Javascript or C#. If you learned the try / finally pattern from one of these languages, watch out for this. EXPORTS All functions are exported by default using Exporter . If you need to rename the try , catch or finally keyword consider using Sub::Import to get Sub::Exporter 's flexibility. try (&;@) Takes one mandatory try subroutine, an optional catch subroutine and finally subroutine. The mandatory subroutine is evaluated in the context of an eval block. If no error occurred the value from the first block is returned, preserving list/scalar context. If there was an error and the second subroutine was given it will be invoked with the error in $_ (localized) and as that block's first and only argument. $@ does not contain the error. Inside the catch block it has the same value it had before the try block was executed. Note that the error may be false, but if that happens the catch block will still be invoked. Once all execution is finished then the finally block, if given, will execute. catch (&;@) Intended to be used in the second argument position of try . Returns a reference to the subroutine it was given but blessed as Try::Tiny::Catch which allows try to decode correctly what to do with this code reference. catch { ... } Inside the catch block the caught error is stored in $_ , while previous value of $@ is still available for use. This value may or may not be meaningful depending on what happened before the try , but it might be a good idea to preserve it in an error stack. For code that captures $@ when throwing new errors (i.e. Class::Throwable ), you'll need to do: local $@ = $_; finally (&;@) try { ... } catch { ... } finally { ... }; Or try { ... } finally { ... }; Or even try { ... } finally { ... } catch { ... }; Intended to be the second or third element of try . finally blocks are always executed in the event of a successful try or if catch is run. This allows you to locate cleanup code which cannot be done via local() e.g. closing a file handle. When invoked, the finally block is passed the error that was caught. If no error was caught, it is passed nothing. (Note that the finally block does not localize $_ with the error, since unlike in a catch block, there is no way to know if $_ == undef implies that there were no errors.) In other words, the following code does just what you would expect: try { die_sometimes(); } catch { # ...code run in case of error } finally { if (@_) { print "The try block died with: @_\n"; } else { print "The try block ran without error.\n"; } }; You must always do your own error handling in the finally block . Try::Tiny will not do anything about handling possible errors coming from code located in these blocks. Furthermore exceptions in finally blocks are not trappable and are unable to influence the execution of your program . This is due to limitation of DESTROY -based scope guards, which finally is implemented on top of. This may change in a future version of Try::Tiny. In the same way catch() blesses the code reference this subroutine does the same except it bless them as Try::Tiny::Finally . BACKGROUND There are a number of issues with eval . Clobbering $@ When you run an eval block and it succeeds, $@ will be cleared, potentially clobbering an error that is currently being caught. This causes action at a distance, clearing previous errors your caller may have not yet handled. $@ must be properly localized before invoking eval in order to avoid this issue. More specifically, before Perl version 5.14.0 $@ was clobbered at the beginning of the eval , which also made it impossible to capture the previous error before you die (for instance when making exception objects with error stacks). For this reason try will actually set $@ to its previous value (the one available before entering the try block) in the beginning of the eval block. Localizing $@ silently masks errors Inside an eval block, die behaves sort of like: sub die { $@ = $_[0]; return_undef_from_eval(); } This means that if you were polite and localized $@ you can't die in that scope, or your error will be discarded (printing "Something's wrong" instead). The workaround is very ugly: my $error = do { local $@; eval { ... }; $@; }; ... die $error; $@ might not be a true value This code is wrong: if ( $@ ) { ... } because due to the previous caveats it may have been unset. $@ could also be an overloaded error object that evaluates to false, but that's asking for trouble anyway. The classic failure mode (fixed in Perl 5.14.0 ) is: sub Object::DESTROY { eval { ... } } eval { my $obj = Object->new; die "foo"; }; if ( $@ ) { } In this case since Object::DESTROY is not localizing $@ but still uses eval , it will set $@ to "" . The destructor is called when the stack is unwound, after die sets $@ to "foo at Foo.pm line 42\n" , so by the time if ( $@ ) is evaluated it has been cleared by eval in the destructor. The workaround for this is even uglier than the previous ones. Even though we can't save the value of $@ from code that doesn't localize, we can at least be sure the eval was aborted due to an error: my $failed = not eval { ... return 1; }; This is because an eval that caught a die will always return a false value. ALTERNATE SYNTAX Using Perl 5.10 you can use "Switch statements" in perlsyn (but please don't, because that syntax has since been deprecated because there was too much unexpected magical behaviour). The catch block is invoked in a topicalizer context (like a given block), but note that you can't return a useful value from catch using the when blocks without an explicit return . This is somewhat similar to Perl 6's CATCH blocks. You can use it to concisely match errors: try { require Foo; } catch { when (/^Can't locate .*?\.pm in \@INC/) { } # ignore default { die $_ } }; CAVEATS @_ is not available within the try block, so you need to copy your argument list. In case you want to work with argument values directly via @_ aliasing (i.e. allow $_[1] = "foo" ), you need to pass @_ by reference: sub foo { my ( $self, @args ) = @_; try { $self->bar(@args) } } or sub bar_in_place { my $self = shift; my $args = \@_; try { $_ = $self->bar($_) for @$args } } return returns from the try block, not from the parent sub (note that this is also how eval works, but not how TryCatch works): sub parent_sub { try { die; } catch { return; }; say "this text WILL be displayed, even though an exception is thrown"; } Instead, you should capture the return value: sub parent_sub { my $success = try { die; 1; }; return unless $success; say "This text WILL NEVER appear!"; } # OR sub parent_sub_with_catch { my $success = try { die; 1; } catch { # do something with $_ return undef; #see note }; return unless $success; say "This text WILL NEVER appear!"; } Note that if you have a catch block, it must return undef for this to work, since if a catch block exists, its return value is returned in place of undef when an exception is thrown. try introduces another caller stack frame. Sub::Uplevel is not used. Carp will not report this when using full stack traces, though, because %Carp::Internal is used. This lack of magic is considered a feature. The value of $_ in the catch block is not guaranteed to be the value of the exception thrown ( $@ ) in the try block. There is no safe way to ensure this, since eval may be used unhygienically in destructors. The only guarantee is that the catch will be called if an exception is thrown. The return value of the catch block is not ignored, so if testing the result of the expression for truth on success, be sure to return a false value from the catch block: my $obj = try { MightFail->new; } catch { ... return; # avoid returning a true value; }; return unless $obj; $SIG{__DIE__} is still in effect. Though it can be argued that $SIG{__DIE__} should be disabled inside of eval blocks, since it isn't people have grown to rely on it. Therefore in the interests of compatibility, try does not disable $SIG{__DIE__} for the scope of the error throwing code. Lexical $_ may override the one set by catch . For example Perl 5.10's given form uses a lexical $_ , creating some confusing behavior: given ($foo) { when (...) { try { ... } catch { warn $_; # will print $foo, not the error warn $_[0]; # instead, get the error like this } } } Note that this behavior was changed once again in Perl5 version 18 . However, since the entirety of lexical $_ is now considered experimental , it is unclear whether the new version 18 behavior is final. SEE ALSO Syntax::Keyword::Try Only available on perls >= 5.14, with a slightly different syntax (e.g. no trailing ; because it's actually a keyword, not a sub, but this means you can return and next within it). Use Feature::Compat::Try to automatically switch to the native try syntax in newer perls (when available). See also Try Catch Exception Handling . TryCatch Much more feature complete, more convenient semantics, but at the cost of implementation complexity. autodie Automatic error throwing for builtin functions and more. Also designed to work well with given / when . Throwable A lightweight role for rolling your own exception classes. Error Exception object implementation with a try statement. Does not localize $@ . Exception::Class::TryCatch Provides a catch statement, but properly calling eval is your responsibility. The try keyword pushes $@ onto an error stack, avoiding some of the issues with $@ , but you still need to localize to prevent clobbering. LIGHTNING TALK I gave a lightning talk about this module, you can see the slides (Firefox only): http://web.archive.org/web/20100628040134/http://nothingmuch.woobling.org/talks/takahashi.xul Or read the source: http://web.archive.org/web/20100305133605/http://nothingmuch.woobling.org/talks/yapc_asia_2009/try_tiny.yml SUPPORT Bugs may be submitted through the RT bug tracker (or bug-Try-Tiny@rt.cpan.org ). AUTHORS ×�×�×�×� ק×�×�'×�×� (Yuval Kogman) <nothingmuch@woobling.org> Jesse Luehrs <doy@tozt.net> CONTRIBUTORS Karen Etheridge <ether@cpan.org> Peter Rabbitson <ribasushi@cpan.org> Ricardo Signes <rjbs@cpan.org> Mark Fowler <mark@twoshortplanks.com> Graham Knop <haarg@haarg.org> Aristotle Pagaltzis <pagaltzis@gmx.de> Dagfinn Ilmari Mannsåker <ilmari@ilmari.org> Lukas Mai <l.mai@web.de> Alex <alex@koban.(none)> anaxagoras <walkeraj@gmail.com> Andrew Yates <ayates@haddock.local> awalker <awalker@sourcefire.com> chromatic <chromatic@wgz.org> cm-perl <cm-perl@users.noreply.github.com> David Lowe <davidl@lokku.com> Glenn Fowler <cebjyre@cpan.org> Hans Dieter Pearcey <hdp@weftsoar.net> Jens Berthold <jens@jebecs.de> Jonathan Yu <JAWNSY@cpan.org> Marc Mims <marc@questright.com> Mark Stosberg <mark@stosberg.com> Pali <pali@cpan.org> Paul Howarth <paul@city-fan.org> Rudolf Leermakers <rudolf@hatsuseno.org> COPYRIGHT AND LICENCE This software is Copyright (c) 2009 by ×�×�×�×� ק×�×�'×�×� (Yuval Kogman). This is free software, licensed under: The MIT (X11) License About minimal try/catch with proper preservation of $@ metacpan.org/release/Try-Tiny/ Resources Readme License View license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 10 stars Watchers 3 watching Forks 6 forks Report repository Releases 32 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-try-tiny --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-try-tiny 0.24 0 +-------------------- +file name : perl-try-tiny-0.24-0.tar.bz2 +name : perl-try-tiny +version : 0.24 +build : 0 +build number: 0 +size : 9 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-try-tiny-0.24-0.tar.bz2 +md5 : c2a349da07a14043866c88310d4597f9 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-try-tiny 0.24 1 +-------------------- +file name : perl-try-tiny-0.24-1.tar.bz2 +name : perl-try-tiny +version : 0.24 +build : 1 +build number: 1 +size : 9 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-try-tiny-0.24-1.tar.bz2 +md5 : 558f43869f8f2a248b0bd34e0cb7180f +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-try-tiny 0.24 pl5.22.0_2 +----------------------------- +file name : perl-try-tiny-0.24-pl5.22.0_2.tar.bz2 +name : perl-try-tiny +version : 0.24 +build : pl5.22.0_2 +build number: 2 +size : 14 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-try-tiny-0.24-pl5.22.0_2.tar.bz2 +md5 : 9da7bacae169835cab5fd5bd2b44d953 +dependencies: + - perl 5.22.0* + + +perl-try-tiny 0.24 pl526_3 +-------------------------- +file name : perl-try-tiny-0.24-pl526_3.tar.bz2 +name : perl-try-tiny +version : 0.24 +build : pl526_3 +build number: 3 +size : 15 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-try-tiny-0.24-pl526_3.tar.bz2 +md5 : 363e22437d6ed95eba77302c2b3e6c84 +timestamp : 2018-07-07 18:19:01 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-try-tiny 0.30 pl526_0 +-------------------------- +file name : perl-try-tiny-0.30-pl526_0.tar.bz2 +name : perl-try-tiny +version : 0.30 +build : pl526_0 +build number: 0 +size : 16 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-try-tiny-0.30-pl526_0.tar.bz2 +md5 : cd166bb492ad47a94272e477fdd2fec3 +timestamp : 2018-11-11 06:28:16 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-try-tiny 0.30 pl526_1 +-------------------------- +file name : perl-try-tiny-0.30-pl526_1.tar.bz2 +name : perl-try-tiny +version : 0.30 +build : pl526_1 +build number: 1 +size : 17 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-try-tiny-0.30-pl526_1.tar.bz2 +md5 : cf04b17e5804be0615363036e37b9ca7 +timestamp : 2019-03-09 12:23:31 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-try-tiny 0.30 pl5321hdfd78af_2 +----------------------------------- +file name : perl-try-tiny-0.30-pl5321hdfd78af_2.tar.bz2 +name : perl-try-tiny +version : 0.30 +build : pl5321hdfd78af_2 +build number: 2 +size : 18 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-try-tiny-0.30-pl5321hdfd78af_2.tar.bz2 +md5 : 7a3d56a0b75ec07087060740055dcbbc +timestamp : 2022-01-19 10:20:39 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-try-tiny 0.31 pl5321ha770c72_0 +----------------------------------- +file name : perl-try-tiny-0.31-pl5321ha770c72_0.tar.bz2 +name : perl-try-tiny +version : 0.31 +build : pl5321ha770c72_0 +build number: 0 +size : 17 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-try-tiny-0.31-pl5321ha770c72_0.tar.bz2 +md5 : cc23b14ed56bf51d84832d98ebd156af +timestamp : 2022-08-05 10:32:50 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-try-tiny 0.31 pl5321hdfd78af_0 +----------------------------------- +file name : perl-try-tiny-0.31-pl5321hdfd78af_0.tar.bz2 +name : perl-try-tiny +version : 0.31 +build : pl5321hdfd78af_0 +build number: 0 +size : 18 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-try-tiny-0.31-pl5321hdfd78af_0.tar.bz2 +md5 : 1a1fe1aa9ed92450774d8bb7900fe268 +timestamp : 2022-02-10 17:15:15 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-try-tiny 0.31 pl5321hdfd78af_1 +----------------------------------- +file name : perl-try-tiny-0.31-pl5321hdfd78af_1.tar.bz2 +name : perl-try-tiny +version : 0.31 +build : pl5321hdfd78af_1 +build number: 1 +size : 19 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-try-tiny-0.31-pl5321hdfd78af_1.tar.bz2 +md5 : 392bfccbd3a8c498b6b9c72bef1a2f21 +timestamp : 2022-08-06 12:33:19 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + + +perl-try-tiny 0.32 pl5321ha770c72_0 +----------------------------------- +file name : perl-try-tiny-0.32-pl5321ha770c72_0.conda +name : perl-try-tiny +version : 0.32 +build : pl5321ha770c72_0 +build number: 0 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-try-tiny-0.32-pl5321ha770c72_0.conda +md5 : 8f28ac455f0c8d1bea7f7649da08b748 +timestamp : 2024-08-17 04:57:23 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-try-tiny 0.32 pl5321ha770c72_1 +----------------------------------- +file name : perl-try-tiny-0.32-pl5321ha770c72_1.conda +name : perl-try-tiny +version : 0.32 +build : pl5321ha770c72_1 +build number: 1 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-try-tiny-0.32-pl5321ha770c72_1.conda +md5 : 991a399e90945d848c0cf5707c3ffca3 +timestamp : 2025-02-27 12:53:44 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-uri.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-uri.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..20cf50b1639db1b5db7b068e2c4242fa8dab77ce --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-uri.manual_bundle.txt @@ -0,0 +1,514 @@ +# Tool: perl-uri +software_name: perl-uri +tier: T1 +domain: t1_backfill_overall +downloads: 656596 +summary: Uniform Resource Identifiers (absolute and relative) +description: Uniform Resource Identifiers (absolute and relative) +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-business-isbn, perl-carp, perl-constant, perl-data-dumper, perl-encode, perl-exporter, perl-mime-base64, perl-parent +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/libwww-perl/URI +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/libwww-perl/URI +GitHub - libwww-perl/URI: The Perl URI module · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} libwww-perl / URI Public Notifications You must be signed in to change notification settings Fork 50 Star 59 Code Issues 29 Pull requests 8 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights libwww-perl/URI master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 825 Commits 825 Commits .github .github lib lib t t xt xt .gitignore .gitignore .mailmap .mailmap .perltidyrc .perltidyrc CONTRIBUTING.md CONTRIBUTING.md Changes Changes LICENSE LICENSE README.md README.md cpanfile cpanfile dist.ini dist.ini draft-duerst-iri-bis.txt draft-duerst-iri-bis.txt perlimports.toml perlimports.toml rfc2396.txt rfc2396.txt rfc3986.txt rfc3986.txt rfc3987.txt rfc3987.txt uri-test uri-test View all files Repository files navigation README Contributing License NAME URI - Uniform Resource Identifiers (absolute and relative) SYNOPSIS use URI (); $u1 = URI->new("http://www.example.com"); $u2 = URI->new("foo", "http"); $u3 = $u2->abs($u1); $u4 = $u3->clone; $u5 = URI->new("HTTP://WWW.example.com:80")->canonical; $str = $u->as_string; $str = "$u"; $scheme = $u->scheme; $opaque = $u->opaque; $path = $u->path; $frag = $u->fragment; $u->scheme("ftp"); $u->host("ftp.example.com"); $u->path("cpan/"); DESCRIPTION This module implements the URI class. Objects of this class represent "Uniform Resource Identifier references" as specified in RFC 2396 (and updated by RFC 2732). A Uniform Resource Identifier is a compact string of characters that identifies an abstract or physical resource. A Uniform Resource Identifier can be further classified as either a Uniform Resource Locator (URL) or a Uniform Resource Name (URN). The distinction between URL and URN does not matter to the URI class interface. A "URI-reference" is a URI that may have additional information attached in the form of a fragment identifier. An absolute URI reference consists of three parts: a scheme , a scheme-specific part and a fragment identifier. A subset of URI references share a common syntax for hierarchical namespaces. For these, the scheme-specific part is further broken down into authority , path and query components. These URIs can also take the form of relative URI references, where the scheme (and usually also the authority) component is missing, but implied by the context of the URI reference. The three forms of URI reference syntax are summarized as follows: <scheme>:<scheme-specific-part>#<fragment> <scheme>://<authority><path>?<query>#<fragment> <path>?<query>#<fragment> The components into which a URI reference can be divided depend on the scheme . The URI class provides methods to get and set the individual components. The methods available for a specific URI object depend on the scheme. CONSTRUCTORS The following methods construct new URI objects: $uri = URI->new( $str ) $uri = URI->new( $str, $scheme ) Constructs a new URI object. The string representation of a URI is given as argument, together with an optional scheme specification. Common URI wrappers like "" and <>, as well as leading and trailing white space, are automatically removed from the $str argument before it is processed further. The constructor determines the scheme, maps this to an appropriate URI subclass, constructs a new object of that class and returns it. If the scheme isn't one of those that URI recognizes, you still get an URI object back that you can access the generic methods on. The $uri->has_recognized_scheme method can be used to test for this. The $scheme argument is only used when $str is a relative URI. It can be either a simple string that denotes the scheme, a string containing an absolute URI reference, or an absolute URI object. If no $scheme is specified for a relative URI $str, then $str is simply treated as a generic URI (no scheme-specific methods available). The set of characters available for building URI references is restricted (see URI::Escape ). Characters outside this set are automatically escaped by the URI constructor. $uri = URI->new_abs( $str, $base_uri ) Constructs a new absolute URI object. The $str argument can denote a relative or absolute URI. If relative, then it is absolutized using $base_uri as base. The $base_uri must be an absolute URI. $uri = URI::file->new( $filename ) $uri = URI::file->new( $filename, $os ) Constructs a new file URI from a file name. See URI::file . $uri = URI::file->new_abs( $filename ) $uri = URI::file->new_abs( $filename, $os ) Constructs a new absolute file URI from a file name. See URI::file . $uri = URI::file->cwd Returns the current working directory as a file URI. See URI::file . $uri->clone Returns a copy of the $uri. COMMON METHODS The methods described in this section are available for all URI objects. Methods that give access to components of a URI always return the old value of the component. The value returned is undef if the component was not present. There is generally a difference between a component that is empty (represented as "" ) and a component that is missing (represented as undef ). If an accessor method is given an argument, it updates the corresponding component in addition to returning the old value of the component. Passing an undefined argument removes the component (if possible). The description of each accessor method indicates whether the component is passed as an escaped (percent-encoded) or an unescaped string. A component that can be further divided into sub-parts are usually passed escaped, as unescaping might change its semantics. The common methods available for all URI are: $uri->scheme $uri->scheme( $new_scheme ) Sets and returns the scheme part of the $uri. If the $uri is relative, then $uri->scheme returns undef . If called with an argument, it updates the scheme of $uri, possibly changing the class of $uri, and returns the old scheme value. The method croaks if the new scheme name is illegal; a scheme name must begin with a letter and must consist of only US-ASCII letters, numbers, and a few special marks: ".", "+", "-". This restriction effectively means that the scheme must be passed unescaped. Passing an undefined argument to the scheme method makes the URI relative (if possible). Letter case does not matter for scheme names. The string returned by $uri->scheme is always lowercase. If you want the scheme just as it was written in the URI in its original case, you can use the $uri->_scheme method instead. $uri->has_recognized_scheme Returns TRUE if the URI scheme is one that URI recognizes. It will also be TRUE for relative URLs where a recognized scheme was provided to the constructor, even if $uri->scheme returns undef for these. $uri->opaque $uri->opaque( $new_opaque ) Sets and returns the scheme-specific part of the $uri (everything between the scheme and the fragment) as an escaped string. $uri->path $uri->path( $new_path ) Sets and returns the same value as $uri->opaque unless the URI supports the generic syntax for hierarchical namespaces. In that case the generic method is overridden to set and return the part of the URI between the host name and the fragment . $uri->fragment $uri->fragment( $new_frag ) Returns the fragment identifier of a URI reference as an escaped string. $uri->as_string Returns a URI object to a plain ASCII string. URI objects are also converted to plain strings automatically by overloading. This means that $uri objects can be used as plain strings in most Perl constructs. $uri->as_iri Returns a Unicode string representing the URI. Escaped UTF-8 sequences representing non-ASCII characters are turned into their corresponding Unicode code point. $uri->canonical Returns a normalized version of the URI. The rules for normalization are scheme-dependent. They usually involve lowercasing the scheme and Internet host name components, removing the explicit port specification if it matches the default port, uppercasing all escape sequences, and unescaping octets that can be better represented as plain characters. For efficiency reasons, if the $uri is already in normalized form, then a reference to it is returned instead of a copy. $uri->eq( $other_uri ) URI::eq( $first_uri, $other_uri ) Tests whether two URI references are equal. URI references that normalize to the same string are considered equal. The method can also be used as a plain function which can also test two string arguments. If you need to test whether two URI object references denote the same object, use the '==' operator. $uri->abs( $base_uri ) Returns an absolute URI reference. If $uri is already absolute, then a reference to it is simply returned. If the $uri is relative, then a new absolute URI is constructed by combining the $uri and the $base_uri, and returned. $uri->rel( $base_uri ) Returns a relative URI reference if it is possible to make one that denotes the same resource relative to $base_uri. If not, then $uri is simply returned. $uri->secure Returns a TRUE value if the URI is considered to point to a resource on a secure channel, such as an SSL or TLS encrypted one. GENERIC METHODS The following methods are available to schemes that use the common/generic syntax for hierarchical namespaces. The descriptions of schemes below indicate which these are. Unrecognized schemes are assumed to support the generic syntax, and therefore the following methods: $uri->authority $uri->authority( $new_authority ) Sets and returns the escaped authority component of the $uri. $uri->path $uri->path( $new_path ) Sets and returns the escaped path component of the $uri (the part between the host name and the query or fragment). The path can never be undefined, but it can be the empty string. $uri->path_query $uri->path_query( $new_path_query ) Sets and returns the escaped path and query components as a single entity. The path and the query are separated by a "?" character, but the query can itself contain "?". $uri->path_segments $uri->path_segments( $segment, ... ) Sets and returns the path. In a scalar context, it returns the same value as $uri->path. In a list context, it returns the unescaped path segments that make up the path. Path segments that have parameters are returned as an anonymous array. The first element is the unescaped path segment proper; subsequent elements are escaped parameter strings. Such an anonymous array uses overloading so it can be treated as a string too, but this string does not include the parameters. Note that absolute paths have the empty string as their first path_segment , i.e. the path /foo/bar have 3 path_segments ; "", "foo" and "bar". $uri->query $uri->query( $new_query ) Sets and returns the escaped query component of the $uri. $uri->query_form $uri->query_form( $key1 => $val1, $key2 => $val2, ... ) $uri->query_form( $key1 => $val1, $key2 => $val2, ..., $delim ) $uri->query_form( \@key_value_pairs ) $uri->query_form( \@key_value_pairs, $delim ) $uri->query_form( \%hash ) $uri->query_form( \%hash, $delim ) Sets and returns query components that use the application/x-www-form-urlencoded format. Key/value pairs are separated by "&", and the key is separated from the value by a "=" character. The form can be set either by passing separate key/value pairs, or via an array or hash reference. Passing an empty array or an empty hash removes the query component, whereas passing no arguments at all leaves the component unchanged. The order of keys is undefined if a hash reference is passed. The old value is always returned as a list of separate key/value pairs. Assigning this list to a hash is unwise as the keys returned might repeat. The values passed when setting the form can be plain strings or references to arrays of strings. Passing an array of values has the same effect as passing the key repeatedly with one value at a time. All the following statements have the same effect: $uri->query_form(foo => 1, foo => 2); $uri->query_form(foo => [1, 2]); $uri->query_form([ foo => 1, foo => 2 ]); $uri->query_form([ foo => [1, 2] ]); $uri->query_form({ foo => [1, 2] }); The $delim parameter can be passed as ";" to force the key/value pairs to be delimited by ";" instead of "&" in the query string. This practice is often recommended for URLs embedded in HTML or XML documents as this avoids the trouble of escaping the "&" character. You might also set the $URI::DEFAULT_QUERY_FORM_DELIMITER variable to ";" for the same global effect. @keys = $u->query_param @values = $u->query_param( $key ) $first_value = $u->query_param( $key ) $u->query_param( $key, $value,... ) If $u->query_param is called with no arguments, it returns all the distinct parameter keys of the URI. In a scalar context it returns the number of distinct keys. When a $key argument is given, the method returns the parameter values with the given key. In a scalar context, only the first parameter value is returned. If additional arguments are given, they are used to update successive parameters with the given key. If any of the values provided are array references, then the array is dereferenced to get the actual values. Please note that you can supply multiple values to this method, but you cannot supply multiple keys. Do this: $uri->query_param( widget_id => 1, 5, 9 ); Do NOT do this: $uri->query_param( widget_id => 1, frobnicator_id => 99 ); $u->query_param_append($key, $value,...) Adds new parameters with the given key without touching any old parameters with the same key. It can be explained as a more efficient version of: $u->query_param($key, $u->query_param($key), $value,...); One difference is that this expression would return the old values of $key, whereas the query_param_append() method does not. @values = $u->query_param_delete($key) $first_value = $u->query_param_delete($key) Deletes all key/value pairs with the given key. The old values are returned. In a scalar context, only the first value is returned. Using the query_param_delete() method is slightly more efficient than the equivalent: $u->query_param($key, []); $hashref = $u->query_form_hash $u->query_form_hash( \%new_form ) Returns a reference to a hash that represents the query form's key/value pairs. If a key occurs multiple times, then the hash value becomes an array reference. Note that sequence information is lost. This means that: $u->query_form_hash($u->query_form_hash); is not necessarily a no-op, as it may reorder the key/value pairs. The values returned by the query_param() method should stay the same though. $uri->query_keywords $uri->query_keywords( $keywords, ... ) $uri->query_keywords( \@keywords ) Sets and returns query components that use the keywords separated by "+" format. The keywords can be set either by passing separate keywords directly or by passing a reference to an array of keywords. Passing an empty array removes the query component, whereas passing no arguments at all leaves the component unchanged. The old value is always returned as a list of separate words. SERVER METHODS For schemes where the authority component denotes an Internet host, the following methods are available in addition to the generic methods. $uri->userinfo $uri->userinfo( $new_userinfo ) Sets and returns the escaped userinfo part of the authority component. For some schemes this is a user name and a password separated by a colon. This practice is not recommended. Embedding passwords in clear text (such as URI) has proven to be a security risk in almost every case where it has been used. $uri->host $uri->host( $new_host ) Sets and returns the unescaped hostname. If the $new_host string ends with a colon and a number, then this number also sets the port. For IPv6 addresses the brackets around the raw address is removed in the return value from $uri->host. When setting the host attribute to an IPv6 address you can use a raw address or one enclosed in brackets. The address needs to be enclosed in brackets if you want to pass in a new port value as well. my $uri = URI->new("http://www.\xC3\xBCri-sample/foo/bar.html"); print $u->host; # www.xn--ri-sample-fra0f $uri->ihost Returns the host in Unicode form. Any IDNA A-labels (encoded unicode chars with xn-- prefix) are turned into U-labels (unicode chars). my $uri = URI->new("http://www.\xC3\xBCri-sample/foo/bar.html"); print $u->ihost; # www.\xC3\xBCri-sample $uri->port $uri->port( $new_port ) Sets and returns the port. The port is a simple integer that should be greater than 0. If a port is not specified explicitly in the URI, then the URI scheme's default port is returned. If you don't want the default port substituted, then you can use the $uri->_port method instead. $uri->host_port $uri->host_port( $new_host_port ) Sets and returns the host and port as a single unit. The returned value includes a port, even if it matches the default port. The host part and the port part are separated by a colon: ":". For IPv6 addresses the bracketing is preserved; thus URI->new("http://[::1]/")->host_port returns "[::1]:80". Contrast this with $uri->host which w + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-uri --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-uri 1.69 1 +--------------- +file name : perl-uri-1.69-1.tar.bz2 +name : perl-uri +version : 1.69 +build : 1 +build number: 1 +size : 36 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.69-1.tar.bz2 +md5 : 71a40a36d68795c60a26785ee89e2713 +dependencies: + - perl-scalar-list-utils + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-uri 1.69 2 +--------------- +file name : perl-uri-1.69-2.tar.bz2 +name : perl-uri +version : 1.69 +build : 2 +build number: 2 +size : 36 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.69-2.tar.bz2 +md5 : e0a22a4f57243376c86ee0460f6433ec +dependencies: + - libgcc + - perl-scalar-list-utils + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-uri 1.69 3 +--------------- +file name : perl-uri-1.69-3.tar.bz2 +name : perl-uri +version : 1.69 +build : 3 +build number: 3 +size : 36 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.69-3.tar.bz2 +md5 : 69cadd9c1828689173276b84e701e171 +dependencies: + - libgcc + - perl-scalar-list-utils + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-uri 1.69 pl5.22.0_0 +------------------------ +file name : perl-uri-1.69-pl5.22.0_0.tar.bz2 +name : perl-uri +version : 1.69 +build : pl5.22.0_0 +build number: 0 +size : 36 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.69-pl5.22.0_0.tar.bz2 +md5 : 0bd5612d5bd66b53a32049c23e7f83b8 +dependencies: + - perl 5.22.0* + - perl-scalar-list-utils + + +perl-uri 1.69 pl5.22.0_4 +------------------------ +file name : perl-uri-1.69-pl5.22.0_4.tar.bz2 +name : perl-uri +version : 1.69 +build : pl5.22.0_4 +build number: 4 +size : 54 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.69-pl5.22.0_4.tar.bz2 +md5 : ed0c2b3e65de49a26c8f471f8e6cfe11 +dependencies: + - perl 5.22.0* + + +perl-uri 1.69 pl526_5 +--------------------- +file name : perl-uri-1.69-pl526_5.tar.bz2 +name : perl-uri +version : 1.69 +build : pl526_5 +build number: 5 +size : 54 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.69-pl526_5.tar.bz2 +md5 : ded8aae4f8f2702a4fa56ebdda36333d +timestamp : 2018-07-06 20:58:21 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-uri 1.69 pl526_6 +--------------------- +file name : perl-uri-1.69-pl526_6.tar.bz2 +name : perl-uri +version : 1.69 +build : pl526_6 +build number: 6 +size : 55 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.69-pl526_6.tar.bz2 +md5 : 8b54d75cce0f1bee0b8567b34d8669b2 +timestamp : 2018-07-20 21:15:09 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-uri 1.69 pl526_7 +--------------------- +file name : perl-uri-1.69-pl526_7.tar.bz2 +name : perl-uri +version : 1.69 +build : pl526_7 +build number: 7 +size : 55 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.69-pl526_7.tar.bz2 +md5 : a7a09c207be9c94224efcecfa4e24a07 +timestamp : 2018-08-07 19:43:08 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-uri 1.71 0 +--------------- +file name : perl-uri-1.71-0.tar.bz2 +name : perl-uri +version : 1.71 +build : 0 +build number: 0 +size : 37 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.71-0.tar.bz2 +md5 : 7113c657f7d85e919dce5e7b74f6d285 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-uri 1.71 pl5.22.0_1 +------------------------ +file name : perl-uri-1.71-pl5.22.0_1.tar.bz2 +name : perl-uri +version : 1.71 +build : pl5.22.0_1 +build number: 1 +size : 54 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.71-pl5.22.0_1.tar.bz2 +md5 : e64d9c46e744c3a1a49a5a7a5e55e271 +dependencies: + - perl 5.22.0* + + +perl-uri 1.71 pl526_2 +--------------------- +file name : perl-uri-1.71-pl526_2.tar.bz2 +name : perl-uri +version : 1.71 +build : pl526_2 +build number: 2 +size : 54 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.71-pl526_2.tar.bz2 +md5 : e7a248c7771226706dc1ed7abf366695 +timestamp : 2018-07-06 21:01:37 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-uri 1.71 pl526_3 +--------------------- +file name : perl-uri-1.71-pl526_3.tar.bz2 +name : perl-uri +version : 1.71 +build : pl526_3 +build number: 3 +size : 54 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.71-pl526_3.tar.bz2 +md5 : d03ce9600ef8fdad9a788829a0362b72 +timestamp : 2018-07-20 23:06:01 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-uri 1.74 pl526_0 +--------------------- +file name : perl-uri-1.74-pl526_0.tar.bz2 +name : perl-uri +version : 1.74 +build : pl526_0 +build number: 0 +size : 54 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.74-pl526_0.tar.bz2 +md5 : adec266a62200aa354be76461913b6f3 +timestamp : 2018-08-24 03:17:45 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-business-isbn + - perl-carp + - perl-constant + - perl-data-dumper + - perl-encode + - perl-exporter + - perl-mime-base64 + - perl-parent + + +perl-uri 1.76 pl526_0 +--------------------- +file name : perl-uri-1.76-pl526_0.tar.bz2 +name : perl-uri +version : 1.76 +build : pl526_0 +build number: 0 +size : 55 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.76-pl526_0.tar.bz2 +md5 : 30afcde2552ea47cdb5420e5319f66ad +timestamp : 2019-01-10 21:57:12 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-business-isbn + - perl-carp + - perl-constant + - perl-data-dumper + - perl-encode + - perl-exporter + - perl-mime-base64 + - perl-parent + + +perl-uri 1.76 pl5321hdfd78af_1 +------------------------------ +file name : perl-uri-1.76-pl5321hdfd78af_1.tar.bz2 +name : perl-uri +version : 1.76 +build : pl5321hdfd78af_1 +build number: 1 +size : 56 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-uri-1.76-pl5321hdfd78af_1.tar.bz2 +md5 : 4f40cf5e3200a47ebceaf916e494ca1c +timestamp : 2022-01-20 08:09:48 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-business-isbn + - perl-carp + - perl-constant + - perl-data-dumper + - perl-encode + - perl-exporter + - perl-mime-base64 + - perl-parent + + +perl-uri 5.10 pl5321hdfd78af_0 +------------------------------ +file name : perl-uri-5.10-pl5321hdfd78af_0.tar.bz2 +name : perl-uri +version : 5.10 +build : pl5321hdfd78af_0 +build number: 0 +size : 57 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-uri-5.10-pl5321hdfd78af_0.tar.bz2 +md5 : 1062162df2c0d8904de295bac419e68d +timestamp : 2022-02-14 10:12:59 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-business-isbn + - perl-carp + - perl-constant + - perl-data-dumper + - perl-encode + - perl-exporter + - perl-mime-base64 + - perl-parent + + +perl-uri 5.11 pl5321hdfd78af_0 +------------------------------ +file name : perl-uri-5.11-pl5321hdfd78af_0.tar.bz2 +name : perl-uri +version : 5.11 +build : pl5321hdfd78af_0 +build number: 0 +size : 59 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-uri-5.11-pl5321hdfd78af_0.tar.bz2 +md5 : 688b3211773dcf1029ebbf01a4b6e757 +timestamp : 2022-07-04 22:39:58 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-business-isbn + - perl-carp + - perl-constant + - perl-data-dumper + - perl-encode + - perl-exporter + - perl-mime-base64 + - perl-parent + + +perl-uri 5.12 pl5321hdfd78af_0 +------------------------------ +file name : perl-uri-5.12-pl5321hdfd78af_0.tar.bz2 +name : perl-uri +version : 5.12 +build : pl5321hdfd78af_0 +build number: 0 +size : 59 KB +license : perl_5 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-uri-5.12-pl5321hdfd78af_0.tar.bz2 +md5 : 6b571eaa643024a4bdaa12704928375f +timestamp : 2022-07-11 00:34:09 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-business-isbn + - perl-carp + - perl-constant + - perl-data-dumper + - perl-encode + - perl-exporter + - perl-mime-base64 + - perl-parent + + +perl-uri 5.17 pl5321ha770c72_0 +------------------------------ +file name : perl-uri-5.17-pl5321ha770c72_0.conda +name : perl-uri +version : 5.17 +build : pl5321ha770c72_0 +build number: 0 +size : 66 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-uri-5.17-pl5321ha770c72_0.conda +md5 : 847c007d5f4a59b356a9cd577010b89c +timestamp : 2023-05-22 21:09:28 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-business-isbn + - perl-test-fatal 0.016.* + - perl-test-warnings 0.031.* + + +perl-uri 5.32 pl5321ha770c72_0 +------------------------------ +file name : perl-uri-5.32-pl5321ha770c72_0.conda +name : perl-uri +version : 5.32 +build : pl5321ha770c72_0 +build number: 0 +size : 76 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-uri-5.32-pl5321ha770c72_0.conda +md5 : 4a1303be5829ef32c17940dda55942de +timestamp : 2025-08-19 18:23:00 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-business-isbn + - perl-test-fatal 0.016.* + - perl-test-warnings 0.031.* + + +perl-uri 5.32 pl5321ha770c72_1 +------------------------------ +file name : perl-uri-5.32-pl5321ha770c72_1.conda +name : perl-uri +version : 5.32 +build : pl5321ha770c72_1 +build number: 1 +size : 76 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-uri-5.32-pl5321ha770c72_1.conda +md5 : d64b7c896f2e47305fd97bb8fca09fb8 +timestamp : 2025-08-19 18:52:39 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-business-isbn + - perl-test-fatal 0.016.* + - perl-test-warnings 0.031.* + + +perl-uri 5.33 pl5321ha770c72_0 +------------------------------ +file name : perl-uri-5.33-pl5321ha770c72_0.conda +name : perl-uri +version : 5.33 +build : pl5321ha770c72_0 +build number: 0 +size : 76 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/perl-uri-5.33-pl5321ha770c72_0.conda +md5 : 9322cb8935ec226fe522e5a1465b3eef +timestamp : 2025-09-17 09:53:54 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-business-isbn + - perl-test-fatal 0.016.* + - perl-test-warnings 0.031.* + + +perl-uri 5.34 pl5321ha770c72_0 +------------------------------ +file name : perl-uri-5.34-pl5321ha770c72_0.conda +name : perl-uri +version : 5.34 +build : pl5321ha770c72_0 +build number: 0 +si diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-url-encode.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-url-encode.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6392fb252de496de2827a271b8aa1513cee5f617 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-url-encode.manual_bundle.txt @@ -0,0 +1,57 @@ +# Tool: perl-url-encode +software_name: perl-url-encode +tier: T1 +domain: t1_backfill_overall +downloads: 214689 +summary: Encoding and decoding of application/x-www-form-urlencoded encoding. +description: Encoding and decoding of application/x-www-form-urlencoded encoding. +dependencies: perl >=5.32.1,<5.33.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/URL-Encode +doc_url: +dev_url: + +## URL Docs Extract +### http://metacpan.org/pod/URL-Encode +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-url-encode --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-url-encode 0.03 pl5321h9ee0642_0 +------------------------------------- +file name : perl-url-encode-0.03-pl5321h9ee0642_0.tar.bz2 +name : perl-url-encode +version : 0.03 +build : pl5321h9ee0642_0 +build number: 0 +size : 15 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-url-encode-0.03-pl5321h9ee0642_0.tar.bz2 +md5 : ae808218ba4a3eb830f03e4277ba4625 +timestamp : 2022-01-27 21:42:52 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 + + +perl-url-encode 0.03 pl5321h9ee0642_1 +------------------------------------- +file name : perl-url-encode-0.03-pl5321h9ee0642_1.tar.bz2 +name : perl-url-encode +version : 0.03 +build : pl5321h9ee0642_1 +build number: 1 +size : 13 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-url-encode-0.03-pl5321h9ee0642_1.tar.bz2 +md5 : dc4d3ec16f80c73207ea86de42a62b51 +timestamp : 2024-11-05 10:21:32 UTC +dependencies: + - perl >=5.32.1,<5.33.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-dom.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-dom.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..e909fe9779a4610df0675f35b537100738cc7b75 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-dom.manual_bundle.txt @@ -0,0 +1,152 @@ +# Tool: perl-xml-dom +software_name: perl-xml-dom +tier: T1 +domain: t1_backfill_overall +downloads: 328050 +summary: A perl module for building DOM Level 1 compliant document structures +description: A perl module for building DOM Level 1 compliant document structures +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-http-message >=6.18, perl-libwww-perl, perl-libxml-perl, perl-xml-parser, perl-xml-regexp +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/XML-DOM +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/XML-DOM +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-xml-dom --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +perl-xml-dom 1.45 0 +------------------- +file name : perl-xml-dom-1.45-0.tar.bz2 +name : perl-xml-dom +version : 1.45 +build : 0 +build number: 0 +size : 38 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-dom-1.45-0.tar.bz2 +md5 : 3334b907ef1a18132d7a42ae1da04b88 +dependencies: + - perl-libwww-perl + - perl-libxml-perl + - perl-threaded + - perl-xml-parser + - perl-xml-regexp + - perl >=5.22.0,<5.23.0 + + +perl-xml-dom 1.45 pl526_1 +------------------------- +file name : perl-xml-dom-1.45-pl526_1.tar.bz2 +name : perl-xml-dom +version : 1.45 +build : pl526_1 +build number: 1 +size : 56 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-dom-1.45-pl526_1.tar.bz2 +md5 : ab310b5d2c2ea7a1401edb3e402f29bf +timestamp : 2018-08-07 19:11:53 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-libwww-perl + - perl-libxml-perl + - perl-xml-parser + - perl-xml-regexp + + +perl-xml-dom 1.46 pl526_0 +------------------------- +file name : perl-xml-dom-1.46-pl526_0.tar.bz2 +name : perl-xml-dom +version : 1.46 +build : pl526_0 +build number: 0 +size : 56 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-dom-1.46-pl526_0.tar.bz2 +md5 : 0be82b3d737f4412d9a11481f5e74e8b +timestamp : 2018-11-11 06:23:56 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-libwww-perl + - perl-libxml-perl + - perl-xml-parser + - perl-xml-regexp + + +perl-xml-dom 1.46 pl5321hdfd78af_1 +---------------------------------- +file name : perl-xml-dom-1.46-pl5321hdfd78af_1.tar.bz2 +name : perl-xml-dom +version : 1.46 +build : pl5321hdfd78af_1 +build number: 1 +size : 59 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-xml-dom-1.46-pl5321hdfd78af_1.tar.bz2 +md5 : 45b7ce435727456727f45b3e2121b23b +timestamp : 2022-01-28 00:31:28 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-http-message >=6.18 + - perl-libwww-perl + - perl-libxml-perl + - perl-xml-parser + - perl-xml-regexp diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-filter-buffertext.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-filter-buffertext.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2317f878742e47f7b24fc395e99dbdfaae1a1ff3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-filter-buffertext.manual_bundle.txt @@ -0,0 +1,150 @@ +# Tool: perl-xml-filter-buffertext +software_name: perl-xml-filter-buffertext +tier: T1 +domain: t1_backfill_overall +downloads: 182034 +summary: Filter to put all characters() in one event +description: Filter to put all characters() in one event +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-xml-sax-base +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-xml-filter-buffertext --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-xml-filter-buffertext 1.01 0 +--------------------------------- +file name : perl-xml-filter-buffertext-1.01-0.tar.bz2 +name : perl-xml-filter-buffertext +version : 1.01 +build : 0 +build number: 0 +size : 3 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-filter-buffertext-1.01-0.tar.bz2 +md5 : 56e89663b96e30e6e083ceb0a1eab16c +dependencies: + - perl-threaded + - perl-xml-sax-base + - perl >=5.22.0,<5.23.0 + + +perl-xml-filter-buffertext 1.01 pl526_1 +--------------------------------------- +file name : perl-xml-filter-buffertext-1.01-pl526_1.tar.bz2 +name : perl-xml-filter-buffertext +version : 1.01 +build : pl526_1 +build number: 1 +size : 7 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-filter-buffertext-1.01-pl526_1.tar.bz2 +md5 : aedc1cf4368903485969eed1dbceeffc +timestamp : 2018-07-06 20:48:41 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-xml-sax-base + + +perl-xml-filter-buffertext 1.01 pl526_2 +--------------------------------------- +file name : perl-xml-filter-buffertext-1.01-pl526_2.tar.bz2 +name : perl-xml-filter-buffertext +version : 1.01 +build : pl526_2 +build number: 2 +size : 7 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-filter-buffertext-1.01-pl526_2.tar.bz2 +md5 : b24d93bb57d72099dbaae9b7d442f932 +timestamp : 2018-08-08 11:08:19 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-xml-sax-base + + +perl-xml-filter-buffertext 1.01 pl5321hd8ed1ab_0 +------------------------------------------------ +file name : perl-xml-filter-buffertext-1.01-pl5321hd8ed1ab_0.tar.bz2 +name : perl-xml-filter-buffertext +version : 1.01 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 15 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-xml-filter-buffertext-1.01-pl5321hd8ed1ab_0.tar.bz2 +md5 : dff60f1089285f06f11bdab687e956c0 +timestamp : 2022-10-03 22:24:32 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-xml-sax-base + + +perl-xml-filter-buffertext 1.01 pl5321hdfd78af_3 +------------------------------------------------ +file name : perl-xml-filter-buffertext-1.01-pl5321hdfd78af_3.tar.bz2 +name : perl-xml-filter-buffertext +version : 1.01 +build : pl5321hdfd78af_3 +build number: 3 +size : 9 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-xml-filter-buffertext-1.01-pl5321hdfd78af_3.tar.bz2 +md5 : 0e5c77d9a021560c2624bc9b8f6e9e0e +timestamp : 2022-01-19 14:40:33 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-xml-sax-base diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-libxml.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-libxml.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e0c140daec1b1290581ebf4dd51ba0b380df413 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-libxml.manual_bundle.txt @@ -0,0 +1,246 @@ +# Tool: perl-xml-libxml +software_name: perl-xml-libxml +tier: T1 +domain: t1_backfill_overall +downloads: 579133 +summary: Interface to Gnome libxml2 xml parsing and DOM library +description: Interface to Gnome libxml2 xml parsing and DOM library +dependencies: libgcc >=13, libiconv >=1.18,<2.0a0, liblzma >=5.8.1,<6.0a0, libxml2 >=2.14.4,<2.15.0a0, libzlib >=1.3.1,<2.0a0, perl >=5.32.1,<5.33.0a0 *_perl5, perl-alien-build >=2.84,<3.0a0, perl-alien-libxml2 >=0.20,<0.21.0a0, perl-xml-namespacesupport, perl-xml-sax +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://bitbucket.org/shlomif/perl-xml-libxml +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-xml-libxml --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-xml-libxml 2.0124 0 +------------------------ +file name : perl-xml-libxml-2.0124-0.tar.bz2 +name : perl-xml-libxml +version : 2.0124 +build : 0 +build number: 0 +size : 214 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0124-0.tar.bz2 +md5 : d8af92caf48906d6ea082fcd1af4e905 +dependencies: + - libxml2 + - perl-threaded + - perl-xml-namespacesupport + - perl-xml-sax + - perl >=5.22.0,<5.23.0 + + +perl-xml-libxml 2.0132 pl526h7ec2d77_1 +-------------------------------------- +file name : perl-xml-libxml-2.0132-pl526h7ec2d77_1.tar.bz2 +name : perl-xml-libxml +version : 2.0132 +build : pl526h7ec2d77_1 +build number: 1 +size : 260 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0132-pl526h7ec2d77_1.tar.bz2 +md5 : a9501a6119c0b10f7d20e6d3c15f9714 +timestamp : 2019-08-08 21:08:17 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libxml2 >=2.9.9,<2.10.0a0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-xml-namespacesupport + - perl-xml-sax + + +perl-xml-libxml 2.0132 pl526hbc14f71_0 +-------------------------------------- +file name : perl-xml-libxml-2.0132-pl526hbc14f71_0.tar.bz2 +name : perl-xml-libxml +version : 2.0132 +build : pl526hbc14f71_0 +build number: 0 +size : 258 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0132-pl526hbc14f71_0.tar.bz2 +md5 : 4dca07116df02f179fffeb47ce93fe60 +timestamp : 2018-08-06 22:09:34 UTC +dependencies: + - libxml2 >=2.9.8,<2.10.0a0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-xml-namespacesupport + - perl-xml-sax + + +perl-xml-libxml 2.0132 pl5321h661654b_3 +--------------------------------------- +file name : perl-xml-libxml-2.0132-pl5321h661654b_3.tar.bz2 +name : perl-xml-libxml +version : 2.0132 +build : pl5321h661654b_3 +build number: 3 +size : 270 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0132-pl5321h661654b_3.tar.bz2 +md5 : 168a99f2f17c6a5137387f58dc387ca9 +timestamp : 2022-02-21 21:08:21 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libxml2 >=2.9.12,<2.10.0a0 + - libzlib >=1.2.11,<1.3.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-namespacesupport + - perl-xml-sax + - zlib >=1.2.11,<1.3.0a0 + + +perl-xml-libxml 2.0132 pl5321h8cb1974_2 +--------------------------------------- +file name : perl-xml-libxml-2.0132-pl5321h8cb1974_2.tar.bz2 +name : perl-xml-libxml +version : 2.0132 +build : pl5321h8cb1974_2 +build number: 2 +size : 269 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0132-pl5321h8cb1974_2.tar.bz2 +md5 : 29e52de96f4be6824b475382282c11e1 +timestamp : 2022-01-23 14:05:52 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libxml2 >=2.9.12,<2.10.0a0 + - libzlib >=1.2.11,<1.3.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-namespacesupport + - perl-xml-sax + - zlib >=1.2.11,<1.3.0a0 + + +perl-xml-libxml 2.0207 pl5321h661654b_0 +--------------------------------------- +file name : perl-xml-libxml-2.0207-pl5321h661654b_0.tar.bz2 +name : perl-xml-libxml +version : 2.0207 +build : pl5321h661654b_0 +build number: 0 +size : 252 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0207-pl5321h661654b_0.tar.bz2 +md5 : 1ce8ba66c656dbe547110201b1456797 +timestamp : 2022-03-28 21:09:34 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libxml2 >=2.9.12,<2.10.0a0 + - libzlib >=1.2.11,<1.3.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-alien-build 2.48.* + - perl-alien-libxml2 0.17.* + - perl-xml-namespacesupport + - perl-xml-sax + - zlib >=1.2.11,<1.3.0a0 + + +perl-xml-libxml 2.0210 pl5321hd2ab53c_1 +--------------------------------------- +file name : perl-xml-libxml-2.0210-pl5321hd2ab53c_1.tar.bz2 +name : perl-xml-libxml +version : 2.0210 +build : pl5321hd2ab53c_1 +build number: 1 +size : 265 KB +license : Perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0210-pl5321hd2ab53c_1.tar.bz2 +md5 : d130de1f7ab29fb034f4a3884f00bebf +timestamp : 2025-06-18 08:47:43 UTC +dependencies: + - libgcc >=13 + - libiconv >=1.18,<2.0a0 + - liblzma >=5.8.1,<6.0a0 + - libxml2 >=2.14.4,<2.15.0a0 + - libzlib >=1.3.1,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-alien-build >=2.84,<3.0a0 + - perl-alien-libxml2 >=0.20,<0.21.0a0 + - perl-xml-namespacesupport + - perl-xml-sax + + +perl-xml-libxml 2.0210 pl5321hf886d80_0 +--------------------------------------- +file name : perl-xml-libxml-2.0210-pl5321hf886d80_0.tar.bz2 +name : perl-xml-libxml +version : 2.0210 +build : pl5321hf886d80_0 +build number: 0 +size : 271 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0210-pl5321hf886d80_0.tar.bz2 +md5 : ee29e9d7e2f57fa48b6da8ea82ab9e61 +timestamp : 2025-01-03 14:23:38 UTC +dependencies: + - libgcc >=13 + - libxml2 >=2.13.5,<3.0a0 + - libzlib >=1.3.1,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-alien-build >=2.84,<3.0a0 + - perl-alien-libxml2 >=0.17,<0.18.0a0 + - perl-xml-namespacesupport + - perl-xml-sax + - zlib diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-libxslt.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-libxslt.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..b6479e43754d002d7e015eadb24243576c0e1d90 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-libxslt.manual_bundle.txt @@ -0,0 +1,342 @@ +# Tool: perl-xml-libxslt +software_name: perl-xml-libxslt +tier: T1 +domain: t1_backfill_overall +downloads: 199772 +summary: Interface to GNOME libxslt library +description: Interface to GNOME libxslt library +dependencies: libgcc >=13, libxslt >=1.1.39,<2.0a0, perl >=5.32.1,<5.33.0a0 *_perl5, perl-xml-libxml >=2.210,<3.0a0 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/XML::LibXSLT +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/XML::LibXSLT +XML::LibXSLT - Interface to the GNOME libxslt library - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution XML-LibXSLT Module version: 2.003000 11 Jun 2024 11:15:35 UTC License: perl_5 Perl: v5.14.0 Code Download ( 116.04KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (17) How to Contribute Quality Testers ( 691 / 52 / 6 ) Testers (Magpie) Kwalitee % Coverage Bus factor: 3 Activity 24 month Dependencies Encode File::Path XML::LibXML strict warnings and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 2.003000 (SHLOMIF on 2024-06-11) 2.002001 (SHLOMIF on 2023-02-10) 2.002000 (SHLOMIF on 2022-05-17) 2.001000 (SHLOMIF on 2022-05-16) 2.000000 (SHLOMIF on 2022-04-09) 1.99 (SHLOMIF on 2020-01-16) 1.98 (SHLOMIF on 2020-01-16) 1.97 (SHLOMIF on 2020-01-14) 1.96 (SHLOMIF on 2018-02-21) 1.70 (PAJAS on 2009-10-07) 1.68 (PAJAS on 2008-11-05) 1.67 (PAJAS on 2008-11-04) 1.66 (PAJAS on 2008-01-29) 1.63 (PAJAS on 2007-09-09) 1.62 (PAJAS on 2006-11-18) 1.61 (PAJAS on 2006-09-24) 1.60 (PAJAS on 2006-08-26) 1.59 (PAJAS on 2006-08-02) 1.58 (MSERGEANT on 2005-08-05) 1.95 (SHLOMIF on 2016-07-30) 1.94 (SHLOMIF on 2015-01-19) 1.93 (SHLOMIF on 2015-01-17) 1.92 (SHLOMIF on 2014-04-12) 1.91 (SHLOMIF on 2014-04-12) 1.90 (SHLOMIF on 2014-04-10) 1.89 (SHLOMIF on 2014-03-05) 1.88 (SHLOMIF on 2014-02-17) 1.87 (SHLOMIF on 2014-02-03) 1.86 (SHLOMIF on 2014-02-02) 1.85 (SHLOMIF on 2014-02-01) 1.84 (SHLOMIF on 2013-12-26) 1.83 (SHLOMIF on 2013-12-22) 1.82 (SHLOMIF on 2013-11-06) 1.81 (SHLOMIF on 2013-07-05) 1.80 (SHLOMIF on 2013-01-23) 1.79 (SHLOMIF on 2012-11-26) 1.78 (SHLOMIF on 2012-09-06) 1.77 (SHLOMIF on 2012-02-25) 1.76 (SHLOMIF on 2012-01-12) 1.75 (SHLOMIF on 2011-10-28) 1.74 (SHLOMIF on 2011-10-25) 1.73 (SHLOMIF on 2011-10-09) 1.72 (SHLOMIF on 2011-10-06) 1.71 (SHLOMIF on 2011-09-10) 1.57 (MSERGEANT on 2004-03-01) 1.53 (MSERGEANT on 2003-02-13) 1.52 (MSERGEANT on 2002-09-04) 1.51 (MSERGEANT on 2002-08-14) 1.50 (MSERGEANT on 2002-05-23) 1.49 (MSERGEANT on 2002-05-12) 1.31 (MSERGEANT on 2001-11-25) 1.30 (MSERGEANT on 2001-11-14) 1.09 (MSERGEANT on 2001-07-20) 1.08 (MSERGEANT on 2001-07-17) 1.07 (MSERGEANT on 2001-06-10) 1.06 (MSERGEANT on 2001-06-09) 1.05 (MSERGEANT on 2001-06-07) 1.04 (MSERGEANT on 2001-06-03) 1.03 (MSERGEANT on 2001-05-29) 1.02 (MSERGEANT on 2001-05-20) 1.01 (MSERGEANT on 2001-05-18) 1.00 (MSERGEANT on 2001-05-07) 0.99_01 DEV (MSERGEANT on 2001-04-17) 0.99 (MSERGEANT on 2001-04-17) 0.98 (MSERGEANT on 2001-04-14) 0.97 (MSERGEANT on 2001-04-12) 0.96 (MSERGEANT on 2001-03-15) 0.95 (MSERGEANT on 2001-03-14) 0.94 (MSERGEANT on 2001-03-12) Diff with version 2.003000 (SHLOMIF on 2024-06-11) 2.002001 (SHLOMIF on 2023-02-10) 2.002000 (SHLOMIF on 2022-05-17) 2.001000 (SHLOMIF on 2022-05-16) 2.000000 (SHLOMIF on 2022-04-09) 1.99 (SHLOMIF on 2020-01-16) 1.98 (SHLOMIF on 2020-01-16) 1.97 (SHLOMIF on 2020-01-14) 1.96 (SHLOMIF on 2018-02-21) 1.70 (PAJAS on 2009-10-07) 1.68 (PAJAS on 2008-11-05) 1.67 (PAJAS on 2008-11-04) 1.66 (PAJAS on 2008-01-29) 1.63 (PAJAS on 2007-09-09) 1.62 (PAJAS on 2006-11-18) 1.61 (PAJAS on 2006-09-24) 1.60 (PAJAS on 2006-08-26) 1.59 (PAJAS on 2006-08-02) 1.58 (MSERGEANT on 2005-08-05) 1.95 (SHLOMIF on 2016-07-30) 1.94 (SHLOMIF on 2015-01-19) 1.93 (SHLOMIF on 2015-01-17) 1.92 (SHLOMIF on 2014-04-12) 1.91 (SHLOMIF on 2014-04-12) 1.90 (SHLOMIF on 2014-04-10) 1.89 (SHLOMIF on 2014-03-05) 1.88 (SHLOMIF on 2014-02-17) 1.87 (SHLOMIF on 2014-02-03) 1.86 (SHLOMIF on 2014-02-02) 1.85 (SHLOMIF on 2014-02-01) 1.84 (SHLOMIF on 2013-12-26) 1.83 (SHLOMIF on 2013-12-22) 1.82 (SHLOMIF on 2013-11-06) 1.81 (SHLOMIF on 2013-07-05) 1.80 (SHLOMIF on 2013-01-23) 1.79 (SHLOMIF on 2012-11-26) 1.78 (SHLOMIF on 2012-09-06) 1.77 (SHLOMIF on 2012-02-25) 1.76 (SHLOMIF on 2012-01-12) 1.75 (SHLOMIF on 2011-10-28) 1.74 (SHLOMIF on 2011-10-25) 1.73 (SHLOMIF on 2011-10-09) 1.72 (SHLOMIF on 2011-10-06) 1.71 (SHLOMIF on 2011-09-10) 1.57 (MSERGEANT on 2004-03-01) 1.53 (MSERGEANT on 2003-02-13) 1.52 (MSERGEANT on 2002-09-04) 1.51 (MSERGEANT on 2002-08-14) 1.50 (MSERGEANT on 2002-05-23) 1.49 (MSERGEANT on 2002-05-12) 1.31 (MSERGEANT on 2001-11-25) 1.30 (MSERGEANT on 2001-11-14) 1.09 (MSERGEANT on 2001-07-20) 1.08 (MSERGEANT on 2001-07-17) 1.07 (MSERGEANT on 2001-06-10) 1.06 (MSERGEANT on 2001-06-09) 1.05 (MSERGEANT on 2001-06-07) 1.04 (MSERGEANT on 2001-06-03) 1.03 (MSERGEANT on 2001-05-29) 1.02 (MSERGEANT on 2001-05-20) 1.01 (MSERGEANT on 2001-05-18) 1.00 (MSERGEANT on 2001-05-07) 0.99_01 DEV (MSERGEANT on 2001-04-17) 0.99 (MSERGEANT on 2001-04-17) 0.98 (MSERGEANT on 2001-04-14) 0.97 (MSERGEANT on 2001-04-12) 0.96 (MSERGEANT on 2001-03-15) 0.95 (MSERGEANT on 2001-03-14) 0.94 (MSERGEANT on 2001-03-12) Permalinks This version Latest version ++ed by: 7 PAUSE users 4 non-PAUSE users Authors: Matt Sergeant Released by: Shlomi Fish 6 Maintainers: PERIGRIN owner MSERGEANT PAJAS SHLOMIF SREZIC TIMBRODY Contributors: Matt Sergeant Shlomi Fish  /  2.003000 (SHLOMIF on 2024-06-11) 2.002001 (SHLOMIF on 2023-02-10) 2.002000 (SHLOMIF on 2022-05-17) 2.001000 (SHLOMIF on 2022-05-16) 2.000000 (SHLOMIF on 2022-04-09) 1.99 (SHLOMIF on 2020-01-16) 1.98 (SHLOMIF on 2020-01-16) 1.97 (SHLOMIF on 2020-01-14) 1.96 (SHLOMIF on 2018-02-21) 1.70 (PAJAS on 2009-10-07) 1.68 (PAJAS on 2008-11-05) 1.67 (PAJAS on 2008-11-04) 1.66 (PAJAS on 2008-01-29) 1.63 (PAJAS on 2007-09-09) 1.62 (PAJAS on 2006-11-18) 1.61 (PAJAS on 2006-09-24) 1.60 (PAJAS on 2006-08-26) 1.59 (PAJAS on 2006-08-02) 1.58 (MSERGEANT on 2005-08-05) 1.95 (SHLOMIF on 2016-07-30) 1.94 (SHLOMIF on 2015-01-19) 1.93 (SHLOMIF on 2015-01-17) 1.92 (SHLOMIF on 2014-04-12) 1.91 (SHLOMIF on 2014-04-12) 1.90 (SHLOMIF on 2014-04-10) 1.89 (SHLOMIF on 2014-03-05) 1.88 (SHLOMIF on 2014-02-17) 1.87 (SHLOMIF on 2014-02-03) 1.86 (SHLOMIF on 2014-02-02) 1.85 (SHLOMIF on 2014-02-01) 1.84 (SHLOMIF on 2013-12-26) 1.83 (SHLOMIF on 2013-12-22) 1.82 (SHLOMIF on 2013-11-06) 1.81 (SHLOMIF on 2013-07-05) 1.80 (SHLOMIF on 2013-01-23) 1.79 (SHLOMIF on 2012-11-26) 1.78 (SHLOMIF on 2012-09-06) 1.77 (SHLOMIF on 2012-02-25) 1.76 (SHLOMIF on 2012-01-12) 1.75 (SHLOMIF on 2011-10-28) 1.74 (SHLOMIF on 2011-10-25) 1.73 (SHLOMIF on 2011-10-09) 1.72 (SHLOMIF on 2011-10-06) 1.71 (SHLOMIF on 2011-09-10) 1.57 (MSERGEANT on 2004-03-01) 1.53 (MSERGEANT on 2003-02-13) 1.52 (MSERGEANT on 2002-09-04) 1.51 (MSERGEANT on 2002-08-14) 1.50 (MSERGEANT on 2002-05-23) 1.49 (MSERGEANT on 2002-05-12) 1.31 (MSERGEANT on 2001-11-25) 1.30 (MSERGEANT on 2001-11-14) 1.09 (MSERGEANT on 2001-07-20) 1.08 (MSERGEANT on 2001-07-17) 1.07 (MSERGEANT on 2001-06-10) 1.06 (MSERGEANT on 2001-06-09) 1.05 (MSERGEANT on 2001-06-07) 1.04 (MSERGEANT on 2001-06-03) 1.03 (MSERGEANT on 2001-05-29) 1.02 (MSERGEANT on 2001-05-20) 1.01 (MSERGEANT on 2001-05-18) 1.00 (MSERGEANT on 2001-05-07) 0.99_01 DEV (MSERGEANT on 2001-04-17) 0.99 (MSERGEANT on 2001-04-17) 0.98 (MSERGEANT on 2001-04-14) 0.97 (MSERGEANT on 2001-04-12) 0.96 (MSERGEANT on 2001-03-15) 0.95 (MSERGEANT on 2001-03-14) 0.94 (MSERGEANT on 2001-03-12) XML-LibXSLT-2.003000 11 ++ 11 ++ / XML::LibXSLT Contents NAME SYNOPSIS DESCRIPTION OPTIONS API Input Callbacks Security Callbacks XML::LibXSLT::Stylesheet Parameters XML::LibXSLT::Security Using XML::LibXSLT::Security Interface BENCHMARK LIBRARY VERSIONS LICENSE AUTHOR MAINTAINER BUGS SEE ALSO NAME XML::LibXSLT - Interface to the GNOME libxslt library SYNOPSIS use XML::LibXSLT; use XML::LibXML; my $xslt = XML::LibXSLT->new(); my $source = XML::LibXML->load_xml(location => 'foo.xml'); my $style_doc = XML::LibXML->load_xml(location=>'bar.xsl', no_cdata=>1); my $stylesheet = $xslt->parse_stylesheet($style_doc); my $results = $stylesheet->transform($source); print $stylesheet->output_as_bytes($results); DESCRIPTION This module is an interface to the GNOME project's libxslt. This is an extremely good XSLT engine, highly compliant and also very fast. I have tests showing this to be more than twice as fast as Sablotron. OPTIONS XML::LibXSLT has some global options. Note that these are probably not thread or even fork safe - so only set them once per process. Each one of these options can be called either as class methods, or as instance methods. However either way you call them, it still sets global options. Each of the option methods returns its previous value, and can be called without a parameter to retrieve the current value. max_depth XML::LibXSLT->max_depth(1000); This option sets the maximum recursion depth for a stylesheet. See the very end of section 5.4 of the XSLT specification for more details on recursion and detecting it. If your stylesheet or XML file requires seriously deep recursion, this is the way to set it. Default value is 250. max_vars XML::LibXSLT->max_vars(100_000); This option sets the maximum number of variables for a stylesheet. If your stylesheet or XML file requires many variables, this is the way to increase their limit. Default value is system-specific and may vary. debug_callback XML::LibXSLT->debug_callback($subref); Sets a callback to be used for debug messages. If you don't set this, debug messages will be ignored. register_function XML::LibXSLT->register_function($uri, $name, $subref); $stylesheet->register_function($uri, $name, $subref); Registers an XSLT extension function mapped to the given URI. For example: XML::LibXSLT->register_function("urn:foo", "bar", sub { scalar localtime }); Will register a bar function in the urn:foo namespace (which you have to define in your XSLT using xmlns:... ) that will return the current date and time as a string: <xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:foo="urn:foo"> <xsl:template match="/"> The time is: <xsl:value-of select="foo:bar()"/> </xsl:template> </xsl:stylesheet> Parameters can be in whatever format you like. If you pass in a nodelist it will be a XML::LibXML::NodeList object in your perl code, but ordinary values (strings, numbers and booleans) will be ordinary perl scalars. If you wish them to be XML::LibXML::Literal , XML::LibXML::Number and XML::LibXML::Number values respectively then set the variable $XML::LibXSLT::USE_LIBXML_DATA_TYPES to a true value. Return values can be a nodelist or a plain value - the code will just do the right thing. But only a single return value is supported (a list is not converted to a nodelist). register_element $stylesheet->register_element($uri, $name, $subref) Registers an XSLT extension element $name mapped to the given URI. For example: $stylesheet->register_element("urn:foo", "hello", sub { my $name = $_[2]->getAttribute( "name" ); return XML::LibXML::Text->new( "Hello, $name!" ); }); Will register a hello element in the urn:foo namespace that returns a "Hello, X!" text node. You must define this namespace in your XSLT and include its prefix in the extension-element-prefixes list: <xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:foo="urn:foo" extension-element-prefixes="foo"> <xsl:template match="/"> <foo:hello name="bob"/> </xsl:template> </xsl:stylesheet> The callback is passed the input document node as $_[1] and the stylesheet node as $_[2]. $_[0] is reserved for future use. API The following methods are available on the new XML::LibXSLT object: parse_stylesheet($stylesheet_doc) $stylesheet_doc here is an XML::LibXML::Document object (see XML::LibXML ) representing an XSLT file. This method will return a XML::LibXSLT::Stylesheet object, or undef on failure. If the XSLT is invalid, an exception will be thrown, so wrap the call to parse_stylesheet in an eval{} block to trap this. IMPORTANT: $stylesheet_doc should not contain CDATA sections, otherwise libxslt may misbehave. The best way to assure this is to load the stylesheet with no_cdata flag, e.g. my $stylesheet_doc = XML::LibXML->load_xml(location=>"some.xsl", no_cdata=>1); parse_stylesheet_file($filename) Exactly the same as the above, but parses the given filename directly. Input Callbacks To define XML::LibXSLT or XML::LibXSLT::Stylesheet specific input callbacks, reuse the XML::LibXML input callback API as described in XML::LibXML::InputCallback(3) . input_callbacks($icb) Enable the callbacks in $icb only for this XML::LibXSLT object. $icb should be a XML::LibXML::InputCallback object. This will call init_callbacks and cleanup_callbacks automatically during parsing or transformation. Security Callbacks To create security preferences for the transformation see XML::LibXSLT::Security . Once the security preferences have been defined you can apply them to an XML::LibXSLT or XML::LibXSLT::Stylesheet instance using the security_callbacks() method. XML::LibXSLT::Stylesheet The main API is on the stylesheet, though it is fairly minimal. One of the main advantages of XML::LibXSLT is that you have a generic stylesheet object which you call the transform() method passing in a document to transform. This allows you to have multiple transformations happen with one stylesheet without requiring a reparse. transform(doc, %params) my $results = $stylesheet->transform($doc, foo => "'bar'"); print $stylesheet->output_as_bytes($results); Transforms the passed in XML::LibXML::Document object, and returns a new XML::LibXML::Document. Extra hash entries are used as parameters. Be sure to keep in mind the caveat with regard to quotes explained in the section on "Parameters" below. transform_file(filename, %params) my $results = $stylesheet->transform_file($filename, bar => "'baz'"); Note the string parameter caveat, detailed in the section on "Parameters" below. output_as_bytes(result) Returns a scalar that is the XSLT rendering of the XML::LibXML::Document object using the desired output format (specified in the xsl:output tag in the stylesheet). Note that you can also call $result->toString, but that will *always* output the document in XML format which may not be what you asked for in the xsl:output tag. The scalar is a byte string encoded in the output encoding specified in the stylesheet. output_as_chars(result) Like output_as_bytes(result) , but always return the output as (UTF-8 encoded) string of characters. output_string(result) DEPRECATED: This method is something between output_as_bytes(result) and output_as_bytes(result) : The scalar returned by this function appears to Perl as characters (UTF8 flag is on) if the output encoding specified in the XSLT stylesheet was UTF-8 and as bytes if no output encoding was specified or if the output encoding was other than UTF-8. Since the behavior of this function depends on the particular stylesheet, it is deprecated in favor of output_as_bytes(result) and output_as_chars(result) . output_fh(result, fh) Outputs the result to the filehandle given in $fh . output_file(result, filename) Outputs the result to the file named in $filename . output_encoding() Returns the output encoding of the results. Defaults to "UTF-8". output_method() Returns the value of the method attribute from xsl:output (usually xml , html or text ). If this attribute is unspecified, the default value is initially xml . If the transform method is used to produce an HTML document, as per the XSLT spec , the default value will change to html . To override this behavior completely, supply an xsl:output element in the stylesheet source document. media_type() Returns the value of the media-type attribute from xsl:output . If this attribute is unspecified, the default media type is initially text/xml . This default changes to text/html under the same conditions as output_method . input_callbacks($icb) Enable the callbacks in $icb only for this stylesheet. $icb should be a XML::LibXML::InputCallback object. This will call init_callbacks and cleanup_callbacks automatically during transformation. transform_into_chars(doc, %params) Combines transform() and output_as_chars() . (Added in version 2.0000 .) Parameters LibXSLT expects parameters in XPath format. That is, if you wish to pass a string to the XSLT engine, you actually have to pass it as a quoted string: $stylesheet->transform($doc, param => "'string'"); Note the quotes within quotes there! Obviously this isn't much fun, so you can make it easy on yourself: $stylesheet->transform($doc, XML::LibXSLT::xpath_to_string( param => "string" )); The utility function does the right thing with respect to strings in XPath, including when you have quotes already embedded within your string. XML::LibXSLT::Security Provides an interface to the libxslt security framework by allowing callbacks to be defined that can restrict access to various resources (files or URLs) during a transformation. The libxslt security framework allows callbacks to be defined for certain actions that a stylesheet may attempt during a transformation. It may be desirable to restrict some of these actions (for example, writing a new file using exsl:document). The actions that may be restricted are: read_file Called when the stylesheet attempts to open a local file (ie: when using the document() function). write_file Called when an attempt is made to write a local file (ie: when using the exsl:document element). create_dir Called when a directory needs to be created in order to write a file. NOTE: By default, create_dir is not allowed. To enable it a callback must be registered. read_net Called when the stylesheet attempts to read from the network. write_net Called when the stylesheet attempts to write to the network. Using XML::LibXSLT::Security The interface for this module is similar to XML::LibXML::InputCallback. After creating a new instance you may register callbacks for each of the security options listed above. Then you apply the security preferences to the XML::LibXSLT or XML::LibXSLT::Stylesheet object using security_callbacks() . my $security = XML::LibXSLT::Security->new(); $security->register_callback( read_file => $read_cb ); $security->register_callback( write_file => $write_cb ); $security->register_callback( create_dir => $create_cb ); $security->register_callback( read_net => $read_net_cb ); $security->register_callback( write_net => $write_net_cb ); $xslt->security_callbacks( $security ); -OR- $stylesheet->security_callbacks( $security ); The registered callback functions are called when access to a resource is requested. If the access should be allowed the callback should return 1, if not it should return 0. The callback functions should accept the following arguments: $tctxt This is the transform context (XML::LibXSLT::TransformContext). You can use this to get the current XML::LibXSLT::Stylesheet object by calling stylesheet() . my $stylesheet = $tctxt->stylesheet(); The stylesheet object can then be used to share contextual information between different calls to the security callbacks. $value This is the name of the resource (file or URI) that has been requested. If a particular option (except for create_dir ) doesn't have a registered callback, then the stylesheet will have full access for that action. Interface new() Creates a new XML::LibXSLT::Security object. register_callback( $option, $callback ) Registers a callback function for the given security option (listed above). unregister_callback( $option ) Removes the callback for the given option. This has the effect of allowing all access for the given option (except for create_dir ). BENCHMARK Inclu + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-xml-libxslt --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-xml-libxslt 1.94 0 +----------------------- +file name : perl-xml-libxslt-1.94-0.tar.bz2 +name : perl-xml-libxslt +version : 1.94 +build : 0 +build number: 0 +size : 33 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-1.94-0.tar.bz2 +md5 : d27ac7d464b1b18f4477c54fa71798de +dependencies: + - libxslt + - perl-threaded + - perl-xml-libxml + - perl >=5.22.0,<5.23.0 + + +perl-xml-libxslt 1.94 pl526_1 +----------------------------- +file name : perl-xml-libxslt-1.94-pl526_1.tar.bz2 +name : perl-xml-libxslt +version : 1.94 +build : pl526_1 +build number: 1 +size : 40 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-1.94-pl526_1.tar.bz2 +md5 : d9e8421667819f405cba79dab4723bab +timestamp : 2018-08-07 19:46:22 UTC +dependencies: + - libxslt >=1.1.32,<2.0a0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-xml-libxml + + +perl-xml-libxslt 1.94 pl5321h779adbc_2 +-------------------------------------- +file name : perl-xml-libxslt-1.94-pl5321h779adbc_2.tar.bz2 +name : perl-xml-libxslt +version : 1.94 +build : pl5321h779adbc_2 +build number: 2 +size : 41 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-1.94-pl5321h779adbc_2.tar.bz2 +md5 : 782d9ecb77246b6fcda1d15229e5e80b +timestamp : 2022-01-26 00:09:33 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libxslt >=1.1.33,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 1.99 pl5321h779adbc_0 +-------------------------------------- +file name : perl-xml-libxslt-1.99-pl5321h779adbc_0.tar.bz2 +name : perl-xml-libxslt +version : 1.99 +build : pl5321h779adbc_0 +build number: 0 +size : 41 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-1.99-pl5321h779adbc_0.tar.bz2 +md5 : 191c90dfc58e16742b5b8c8c03773011 +timestamp : 2022-02-09 19:03:30 UTC +dependencies: + - libgcc-ng >=9.4.0 + - libxslt >=1.1.33,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 1.99 pl5321hec16e2b_1 +-------------------------------------- +file name : perl-xml-libxslt-1.99-pl5321hec16e2b_1.tar.bz2 +name : perl-xml-libxslt +version : 1.99 +build : pl5321hec16e2b_1 +build number: 1 +size : 41 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-1.99-pl5321hec16e2b_1.tar.bz2 +md5 : 5fea89ed65851a29272a0abd5a837bdb +timestamp : 2022-02-21 21:39:33 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libxslt >=1.1.33,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 2.000000 pl5321hec16e2b_0 +------------------------------------------ +file name : perl-xml-libxslt-2.000000-pl5321hec16e2b_0.tar.bz2 +name : perl-xml-libxslt +version : 2.000000 +build : pl5321hec16e2b_0 +build number: 0 +size : 43 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-2.000000-pl5321hec16e2b_0.tar.bz2 +md5 : 6ce341f63b53e55614b2c5eb878b9b01 +timestamp : 2022-04-09 07:28:50 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libxslt >=1.1.33,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 2.002000 pl5321hec16e2b_0 +------------------------------------------ +file name : perl-xml-libxslt-2.002000-pl5321hec16e2b_0.tar.bz2 +name : perl-xml-libxslt +version : 2.002000 +build : pl5321hec16e2b_0 +build number: 0 +size : 45 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-2.002000-pl5321hec16e2b_0.tar.bz2 +md5 : 3cf54d4ddd1b67f09e33b081250df9f1 +timestamp : 2022-05-21 10:47:21 UTC +dependencies: + - libgcc-ng >=12 + - libxslt >=1.1.33,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 2.002000 pl5321hec16e2b_1 +------------------------------------------ +file name : perl-xml-libxslt-2.002000-pl5321hec16e2b_1.tar.bz2 +name : perl-xml-libxslt +version : 2.002000 +build : pl5321hec16e2b_1 +build number: 1 +size : 46 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-2.002000-pl5321hec16e2b_1.tar.bz2 +md5 : 3fed81f23a64e08d3f0ce6e4c2718c31 +timestamp : 2022-08-01 15:52:34 UTC +dependencies: + - libgcc-ng >=12 + - libxslt >=1.1.35,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 2.002001 pl5321h031d066_2 +------------------------------------------ +file name : perl-xml-libxslt-2.002001-pl5321h031d066_2.tar.bz2 +name : perl-xml-libxslt +version : 2.002001 +build : pl5321h031d066_2 +build number: 2 +size : 46 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-2.002001-pl5321h031d066_2.tar.bz2 +md5 : 3ac86bceb73afa177b495003ffd7e3d2 +timestamp : 2023-05-15 21:41:47 UTC +dependencies: + - libgcc-ng >=12 + - libxslt >=1.1.35,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 2.002001 pl5321hec16e2b_0 +------------------------------------------ +file name : perl-xml-libxslt-2.002001-pl5321hec16e2b_0.tar.bz2 +name : perl-xml-libxslt +version : 2.002001 +build : pl5321hec16e2b_0 +build number: 0 +size : 46 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-2.002001-pl5321hec16e2b_0.tar.bz2 +md5 : e8422a132b06c83417372c7ed47f65c2 +timestamp : 2023-04-13 03:33:45 UTC +dependencies: + - libgcc-ng >=12 + - libxslt >=1.1.35,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 2.002001 pl5321hec16e2b_1 +------------------------------------------ +file name : perl-xml-libxslt-2.002001-pl5321hec16e2b_1.tar.bz2 +name : perl-xml-libxslt +version : 2.002001 +build : pl5321hec16e2b_1 +build number: 1 +size : 46 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-2.002001-pl5321hec16e2b_1.tar.bz2 +md5 : e49dd333fd62531ac820cf8d64a0da9a +timestamp : 2023-05-13 16:11:45 UTC +dependencies: + - libgcc-ng >=12 + - libxslt >=1.1.35,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 2.003000 pl5321h031d066_0 +------------------------------------------ +file name : perl-xml-libxslt-2.003000-pl5321h031d066_0.tar.bz2 +name : perl-xml-libxslt +version : 2.003000 +build : pl5321h031d066_0 +build number: 0 +size : 46 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-2.003000-pl5321h031d066_0.tar.bz2 +md5 : 841aba1900f8b5c82c0572b579db792f +timestamp : 2024-06-12 07:45:26 UTC +dependencies: + - libgcc-ng >=12 + - libxslt >=1.1.35,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 2.003000 pl5321h7b50bb2_1 +------------------------------------------ +file name : perl-xml-libxslt-2.003000-pl5321h7b50bb2_1.tar.bz2 +name : perl-xml-libxslt +version : 2.003000 +build : pl5321h7b50bb2_1 +build number: 1 +size : 47 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-2.003000-pl5321h7b50bb2_1.tar.bz2 +md5 : a5787bf92e9966a8411c500aac7bec85 +timestamp : 2024-12-12 03:55:41 UTC +dependencies: + - libgcc >=13 + - libxslt >=1.1.35,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml + + +perl-xml-libxslt 2.003000 pl5321h7b50bb2_2 +------------------------------------------ +file name : perl-xml-libxslt-2.003000-pl5321h7b50bb2_2.tar.bz2 +name : perl-xml-libxslt +version : 2.003000 +build : pl5321h7b50bb2_2 +build number: 2 +size : 47 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-2.003000-pl5321h7b50bb2_2.tar.bz2 +md5 : c3170401c167629735a923975c083abb +timestamp : 2025-03-17 18:01:42 UTC +dependencies: + - libgcc >=13 + - libxslt >=1.1.39,<2.0a0 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-xml-libxml >=2.210,<3.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-sax.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-sax.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..bfa93a961f6fd9a14d36306f9025e4bd9a43df12 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-sax.manual_bundle.txt @@ -0,0 +1,185 @@ +# Tool: perl-xml-sax +software_name: perl-xml-sax +tier: T1 +domain: t1_backfill_overall +downloads: 535211 +summary: Simple API for XML +description: Simple API for XML +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-file-temp, perl-xml-namespacesupport, perl-xml-sax-base +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://metacpan.org/pod/XML::SAX +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://metacpan.org/pod/XML::SAX +XML::SAX - Simple API for XML - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution XML-SAX Module version: 1.02 14 Jun 2019 02:18:34 UTC License: unknown Code Download ( 46.21KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues (42) How to Contribute Quality Testers ( 14553 / 3 / 0 ) Testers (Magpie) Kwalitee 50.38% Coverage Bus factor: 0 Activity 24 month Dependencies File::Temp XML::NamespaceSupport XML::SAX::Base and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 1.02 (GRANTM on 2019-06-14) 1.00 (GRANTM on 2018-02-15) 0.99 (GRANTM on 2011-09-04) 0.96 (GRANTM on 2008-08-05) 0.14 (MSERGEANT on 2006-04-24) 0.95 (GRANTM on 2008-08-04) 0.16 (GRANTM on 2007-06-27) 0.15 (GRANTM on 2007-02-08) 0.13 (MSERGEANT on 2005-10-24) 0.12 (MSERGEANT on 2002-11-20) 0.11 (MSERGEANT on 2002-09-03) 0.10 (MSERGEANT on 2002-02-14) 0.09 (MSERGEANT on 2002-02-06) 0.08 (MSERGEANT on 2002-01-30) 0.07 (MSERGEANT on 2002-01-29) 0.06 (MSERGEANT on 2002-01-28) 0.05 (MSERGEANT on 2002-01-21) 0.04 (MSERGEANT on 2002-01-21) 0.03 (MSERGEANT on 2001-11-25) 0.02 (MSERGEANT on 2001-11-14) 0.01 (MSERGEANT on 2001-11-13) Diff with version 1.02 (GRANTM on 2019-06-14) 1.00 (GRANTM on 2018-02-15) 0.99 (GRANTM on 2011-09-04) 0.96 (GRANTM on 2008-08-05) 0.14 (MSERGEANT on 2006-04-24) 0.95 (GRANTM on 2008-08-04) 0.16 (GRANTM on 2007-06-27) 0.15 (GRANTM on 2007-02-08) 0.13 (MSERGEANT on 2005-10-24) 0.12 (MSERGEANT on 2002-11-20) 0.11 (MSERGEANT on 2002-09-03) 0.10 (MSERGEANT on 2002-02-14) 0.09 (MSERGEANT on 2002-02-06) 0.08 (MSERGEANT on 2002-01-30) 0.07 (MSERGEANT on 2002-01-29) 0.06 (MSERGEANT on 2002-01-28) 0.05 (MSERGEANT on 2002-01-21) 0.04 (MSERGEANT on 2002-01-21) 0.03 (MSERGEANT on 2001-11-25) 0.02 (MSERGEANT on 2001-11-14) 0.01 (MSERGEANT on 2001-11-13) Permalinks This version Latest version ++ed by: 5 PAUSE users 5 non-PAUSE users Authors: unknown Released by: Grant McLean Maintainers: GRANTM owner ISABELLF Grant McLean  /  1.02 (GRANTM on 2019-06-14) 1.00 (GRANTM on 2018-02-15) 0.99 (GRANTM on 2011-09-04) 0.96 (GRANTM on 2008-08-05) 0.14 (MSERGEANT on 2006-04-24) 0.95 (GRANTM on 2008-08-04) 0.16 (GRANTM on 2007-06-27) 0.15 (GRANTM on 2007-02-08) 0.13 (MSERGEANT on 2005-10-24) 0.12 (MSERGEANT on 2002-11-20) 0.11 (MSERGEANT on 2002-09-03) 0.10 (MSERGEANT on 2002-02-14) 0.09 (MSERGEANT on 2002-02-06) 0.08 (MSERGEANT on 2002-01-30) 0.07 (MSERGEANT on 2002-01-29) 0.06 (MSERGEANT on 2002-01-28) 0.05 (MSERGEANT on 2002-01-21) 0.04 (MSERGEANT on 2002-01-21) 0.03 (MSERGEANT on 2001-11-25) 0.02 (MSERGEANT on 2001-11-14) 0.01 (MSERGEANT on 2001-11-13) XML-SAX-1.02 10 ++ 10 ++ / XML::SAX Take me over? The maintainer of this distribution is looking for someone to take over! If you're interested then please contact them via email . Contents NAME SYNOPSIS DESCRIPTION USING A SAX2 PARSER WRITING A SAX2 PARSER EXPORTS AUTHOR LICENSE SEE ALSO NAME XML::SAX - Simple API for XML SYNOPSIS use XML::SAX; # get a list of known parsers my $parsers = XML::SAX->parsers(); # add/update a parser XML::SAX->add_parser(q(XML::SAX::PurePerl)); # remove parser XML::SAX->remove_parser(q(XML::SAX::Foodelberry)); # save parsers XML::SAX->save_parsers(); DESCRIPTION XML::SAX is a SAX parser access API for Perl. It includes classes and APIs required for implementing SAX drivers, along with a factory class for returning any SAX parser installed on the user's system. USING A SAX2 PARSER The factory class is XML::SAX::ParserFactory. Please see the documentation of that module for how to instantiate a SAX parser: XML::SAX::ParserFactory . However if you don't want to load up another manual page, here's a short synopsis: use XML::SAX::ParserFactory; use XML::SAX::XYZHandler; my $handler = XML::SAX::XYZHandler->new(); my $p = XML::SAX::ParserFactory->parser(Handler => $handler); $p->parse_uri("foo.xml"); # or $p->parse_string("<foo/>") or $p->parse_file($fh); This will automatically load a SAX2 parser (defaulting to XML::SAX::PurePerl if no others are found) and return it to you. In order to learn how to use SAX to parse XML, you will need to read XML::SAX::Intro and for reference, XML::SAX::Specification . WRITING A SAX2 PARSER The first thing to remember in writing a SAX2 parser is to subclass XML::SAX::Base. This will make your life infinitely easier, by providing a number of methods automagically for you. See XML::SAX::Base for more details. When writing a SAX2 parser that is compatible with XML::SAX, you need to inform XML::SAX of the presence of that driver when you install it. In order to do that, XML::SAX contains methods for saving the fact that the parser exists on your system to a "INI" file, which is then loaded to determine which parsers are installed. The best way to do this is to follow these rules: Add XML::SAX as a prerequisite in Makefile.PL: WriteMakefile( ... PREREQ_PM => { 'XML::SAX' => 0 }, ... ); Alternatively you may wish to check for it in other ways that will cause more than just a warning. Add the following code snippet to your Makefile.PL: sub MY::install { package MY; my $script = shift->SUPER::install(@_); if (ExtUtils::MakeMaker::prompt( "Do you want to modify ParserDetails.ini?", 'Y') =~ /^y/i) { $script =~ s/install :: (.*)$/install :: $1 install_sax_driver/m; $script .= <<"INSTALL"; install_sax_driver : \t\@\$(PERL) -MXML::SAX -e "XML::SAX->add_parser(q(\$(NAME)))->save_parsers()" INSTALL } return $script; } Note that you should check the output of this - \$(NAME) will use the name of your distribution, which may not be exactly what you want. For example XML::LibXML has a driver called XML::LibXML::SAX::Generator, which is used in place of \$(NAME) in the above. Add an XML::SAX test: A test file should be added to your t/ directory containing something like the following: use Test; BEGIN { plan tests => 3 } use XML::SAX; use XML::SAX::PurePerl::DebugHandler; XML::SAX->add_parser(q(XML::SAX::MyDriver)); local $XML::SAX::ParserPackage = 'XML::SAX::MyDriver'; eval { my $handler = XML::SAX::PurePerl::DebugHandler->new(); ok($handler); my $parser = XML::SAX::ParserFactory->parser(Handler => $handler); ok($parser); ok($parser->isa('XML::SAX::MyDriver'); $parser->parse_string("<tag/>"); ok($handler->{seen}{start_element}); }; EXPORTS By default, XML::SAX exports nothing into the caller's namespace. However you can request the symbols Namespaces and Validation which are the URIs for those features, allowing an easier way to request those features via ParserFactory: use XML::SAX qw(Namespaces Validation); my $factory = XML::SAX::ParserFactory->new(); $factory->require_feature(Namespaces); $factory->require_feature(Validation); my $parser = $factory->parser(); AUTHOR Current maintainer: Grant McLean, grantm@cpan.org Originally written by: Matt Sergeant, matt@sergeant.org Kip Hampton, khampton@totalcinema.com Robin Berjon, robin@knowscape.com LICENSE This is free software, you may use it and distribute it under the same terms as Perl itself. SEE ALSO XML::SAX::Base for writing SAX Filters and Parsers XML::SAX::PurePerl for an XML parser written in 100% pure perl. XML::SAX::Exception for details on exception handling Module Install Instructions To install XML::SAX, copy and paste the appropriate command in to your terminal. cpanm cpanm XML::SAX CPAN shell perl -MCPAN -e shell install XML::SAX For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-xml-sax --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +perl-xml-sax 0.99 0 +------------------- +file name : perl-xml-sax-0.99-0.tar.bz2 +name : perl-xml-sax +version : 0.99 +build : 0 +build number: 0 +size : 24 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-sax-0.99-0.tar.bz2 +md5 : da103af523835e838e8f4c2bb552768b +dependencies: + - perl-threaded + - perl-xml-namespacesupport + - perl-xml-sax-base + - perl >=5.22.0,<5.23.0 + + +perl-xml-sax 0.99 pl526_1 +------------------------- +file name : perl-xml-sax-0.99-pl526_1.tar.bz2 +name : perl-xml-sax +version : 0.99 +build : pl526_1 +build number: 1 +size : 34 KB +license : Perl +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-sax-0.99-pl526_1.tar.bz2 +md5 : 6559135f993ece823a483de08c08a87a +timestamp : 2018-07-06 20:43:08 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-xml-namespacesupport + - perl-xml-sax-base + + +perl-xml-sax 1.00 pl526_0 +------------------------- +file name : perl-xml-sax-1.00-pl526_0.tar.bz2 +name : perl-xml-sax +version : 1.00 +build : pl526_0 +build number: 0 +size : 35 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-sax-1.00-pl526_0.tar.bz2 +md5 : 28c7879a96db2a54213a45498cdc8c05 +timestamp : 2018-07-21 18:20:48 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-file-temp + - perl-xml-namespacesupport + - perl-xml-sax-base + + +perl-xml-sax 1.02 pl526_0 +------------------------- +file name : perl-xml-sax-1.02-pl526_0.tar.bz2 +name : perl-xml-sax +version : 1.02 +build : pl526_0 +build number: 0 +size : 36 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-xml-sax-1.02-pl526_0.tar.bz2 +md5 : b4fda7e83376806d5eedbef2c3a3b356 +timestamp : 2019-06-18 21:45:02 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-file-temp + - perl-xml-namespacesupport + - perl-xml-sax-base + + +perl-xml-sax 1.02 pl5321hd8ed1ab_0 +---------------------------------- +file name : perl-xml-sax-1.02-pl5321hd8ed1ab_0.tar.bz2 +name : perl-xml-sax +version : 1.02 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 43 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-xml-sax-1.02-pl5321hd8ed1ab_0.tar.bz2 +md5 : 3e3fac6ffef3fcda271b5511aecacaa8 +timestamp : 2022-10-02 16:37:26 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-file-temp + - perl-xml-namespacesupport + - perl-xml-sax-base + + +perl-xml-sax 1.02 pl5321hdfd78af_1 +---------------------------------- +file name : perl-xml-sax-1.02-pl5321hdfd78af_1.tar.bz2 +name : perl-xml-sax +version : 1.02 +build : pl5321hdfd78af_1 +build number: 1 +size : 37 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-xml-sax-1.02-pl5321hdfd78af_1.tar.bz2 +md5 : 2402f3f7aab47052aa38e00fe6a2de3d +timestamp : 2022-01-19 14:00:03 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-file-temp + - perl-xml-namespacesupport + - perl-xml-sax-base diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-xpath.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-xpath.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3340a3ed003329f1d183d7e7c9c2adee3552fedb --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-xpath.manual_bundle.txt @@ -0,0 +1,172 @@ +# Tool: perl-xml-xpath +software_name: perl-xml-xpath +tier: T1 +domain: t1_backfill_overall +downloads: 190315 +summary: Parse and evaluate XPath statements. +description: Parse and evaluate XPath statements. +dependencies: perl >=5.32.1,<6.0a0 *_perl5, perl-xml-parser +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/pod/XML::XPath +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/pod/XML::XPath +XML::XPath - Parse and evaluate XPath statements. - metacpan.org About Sponsor grep::cpan Recent FAQ Tools API Identities Profile Favorites Logout GitHub Google Distribution XML-XPath Module version: 1.49 29 Mar 2026 00:51:32 UTC License: artistic_2 Perl: v5.10.1 Code Download ( 56.12KB ) Source ( raw ) Browse ( raw ) Changes Project Repository Issues How to Contribute Quality Testers Testers (Magpie) Kwalitee % Coverage Bus factor: 2 Activity 24 month Dependencies Scalar::Util XML::Parser and possibly others Reverse dependencies CPAN Testers List Dependency graph Tools MetaCPAN Explorer Permissions Subscribe to distribution Install Instructions Find in Distribution search grep Versions Jump to version 1.49 (MANWAR on 2026-03-29) 1.48 (MANWAR on 2022-08-09) 1.47 (MANWAR on 2022-05-13) 1.46 (MANWAR on 2022-05-12) 1.45 (MANWAR on 2022-05-12) 1.44 (MANWAR on 2018-10-11) 1.43 (MANWAR on 2018-10-10) 1.42 (MANWAR on 2017-07-30) 1.41 (MANWAR on 2017-07-28) 1.40 (MANWAR on 2016-11-13) 1.39 (MANWAR on 2016-11-08) 1.38 (MANWAR on 2016-10-31) 1.37 (MANWAR on 2016-06-02) 1.36 (MANWAR on 2016-04-14) 1.35 (MANWAR on 2016-04-06) 1.34 (MANWAR on 2016-03-08) 1.33 (MANWAR on 2016-03-02) 1.32 (MANWAR on 2016-02-23) 1.31 (MANWAR on 2016-02-22) 1.30 (MANWAR on 2016-02-04) 1.29 (MANWAR on 2016-02-03) 1.28 (MANWAR on 2016-01-31) 1.27 (MANWAR on 2016-01-30) 1.26 (MANWAR on 2016-01-25) 1.25 (MANWAR on 2016-01-20) 1.24 (MANWAR on 2016-01-19) 1.23 (MANWAR on 2016-01-18) 1.22 (MANWAR on 2016-01-13) 1.21 (MANWAR on 2016-01-12) 1.20 (MANWAR on 2016-01-10) 1.19 (MANWAR on 2016-01-05) 1.18 (MANWAR on 2016-01-04) 1.17 (MANWAR on 2016-01-01) 1.16 (MANWAR on 2015-12-28) 1.15 (MANWAR on 2015-12-27) 1.14 (MANWAR on 2015-12-26) 1.13 (MSERGEANT on 2003-01-26) 1.12 (MSERGEANT on 2001-11-26) 1.11 (MSERGEANT on 2001-11-16) 1.10 (MSERGEANT on 2001-06-12) 1.09 (MSERGEANT on 2001-04-23) 1.08 (MSERGEANT on 2001-04-01) 1.07 (MSERGEANT on 2001-03-16) 1.06 (MSERGEANT on 2001-03-09) 1.05 (MSERGEANT on 2001-02-26) 1.04 (MSERGEANT on 2001-01-19) 1.03 (MSERGEANT on 2000-12-06) 1.02 (MSERGEANT on 2000-10-02) 1.01 (MSERGEANT on 2000-09-26) 1.00 (MSERGEANT on 2000-09-11) 0.99 (MSERGEANT on 2000-08-28) 0.98 (MSERGEANT on 2000-08-24) 0.57 (MSERGEANT on 2000-08-16) 0.55 (MSERGEANT on 2000-06-15) 0.54 (MSERGEANT on 2000-06-09) 0.53 (MSERGEANT on 2000-06-08) 0.52 (MSERGEANT on 2000-05-28) 0.51 (MSERGEANT on 2000-05-11) 0.50 (MSERGEANT on 2000-05-10) 0.24 (MSERGEANT on 2000-04-25) 0.23 (MSERGEANT on 2000-04-22) 0.22 (MSERGEANT on 2000-04-18) 0.21 (MSERGEANT on 2000-04-17) 0.20 (MSERGEANT on 2000-03-20) 0.19 (MSERGEANT on 2000-03-20) 0.18 (MSERGEANT on 2000-03-07) 0.17 (MSERGEANT on 2000-03-07) 0.16 (MSERGEANT on 2000-02-28) 0.15 (MSERGEANT on 2000-02-24) 0.14 (MSERGEANT on 2000-02-24) 0.13 (MSERGEANT on 2000-02-19) 0.11 (MSERGEANT on 2000-02-10) 0.10 (MSERGEANT on 2000-01-26) Diff with version 1.49 (MANWAR on 2026-03-29) 1.48 (MANWAR on 2022-08-09) 1.47 (MANWAR on 2022-05-13) 1.46 (MANWAR on 2022-05-12) 1.45 (MANWAR on 2022-05-12) 1.44 (MANWAR on 2018-10-11) 1.43 (MANWAR on 2018-10-10) 1.42 (MANWAR on 2017-07-30) 1.41 (MANWAR on 2017-07-28) 1.40 (MANWAR on 2016-11-13) 1.39 (MANWAR on 2016-11-08) 1.38 (MANWAR on 2016-10-31) 1.37 (MANWAR on 2016-06-02) 1.36 (MANWAR on 2016-04-14) 1.35 (MANWAR on 2016-04-06) 1.34 (MANWAR on 2016-03-08) 1.33 (MANWAR on 2016-03-02) 1.32 (MANWAR on 2016-02-23) 1.31 (MANWAR on 2016-02-22) 1.30 (MANWAR on 2016-02-04) 1.29 (MANWAR on 2016-02-03) 1.28 (MANWAR on 2016-01-31) 1.27 (MANWAR on 2016-01-30) 1.26 (MANWAR on 2016-01-25) 1.25 (MANWAR on 2016-01-20) 1.24 (MANWAR on 2016-01-19) 1.23 (MANWAR on 2016-01-18) 1.22 (MANWAR on 2016-01-13) 1.21 (MANWAR on 2016-01-12) 1.20 (MANWAR on 2016-01-10) 1.19 (MANWAR on 2016-01-05) 1.18 (MANWAR on 2016-01-04) 1.17 (MANWAR on 2016-01-01) 1.16 (MANWAR on 2015-12-28) 1.15 (MANWAR on 2015-12-27) 1.14 (MANWAR on 2015-12-26) 1.13 (MSERGEANT on 2003-01-26) 1.12 (MSERGEANT on 2001-11-26) 1.11 (MSERGEANT on 2001-11-16) 1.10 (MSERGEANT on 2001-06-12) 1.09 (MSERGEANT on 2001-04-23) 1.08 (MSERGEANT on 2001-04-01) 1.07 (MSERGEANT on 2001-03-16) 1.06 (MSERGEANT on 2001-03-09) 1.05 (MSERGEANT on 2001-02-26) 1.04 (MSERGEANT on 2001-01-19) 1.03 (MSERGEANT on 2000-12-06) 1.02 (MSERGEANT on 2000-10-02) 1.01 (MSERGEANT on 2000-09-26) 1.00 (MSERGEANT on 2000-09-11) 0.99 (MSERGEANT on 2000-08-28) 0.98 (MSERGEANT on 2000-08-24) 0.57 (MSERGEANT on 2000-08-16) 0.55 (MSERGEANT on 2000-06-15) 0.54 (MSERGEANT on 2000-06-09) 0.53 (MSERGEANT on 2000-06-08) 0.52 (MSERGEANT on 2000-05-28) 0.51 (MSERGEANT on 2000-05-11) 0.50 (MSERGEANT on 2000-05-10) 0.24 (MSERGEANT on 2000-04-25) 0.23 (MSERGEANT on 2000-04-22) 0.22 (MSERGEANT on 2000-04-18) 0.21 (MSERGEANT on 2000-04-17) 0.20 (MSERGEANT on 2000-03-20) 0.19 (MSERGEANT on 2000-03-20) 0.18 (MSERGEANT on 2000-03-07) 0.17 (MSERGEANT on 2000-03-07) 0.16 (MSERGEANT on 2000-02-28) 0.15 (MSERGEANT on 2000-02-24) 0.14 (MSERGEANT on 2000-02-24) 0.13 (MSERGEANT on 2000-02-19) 0.11 (MSERGEANT on 2000-02-10) 0.10 (MSERGEANT on 2000-01-26) Permalinks This version Latest version ++ed by: 5 PAUSE users 4 non-PAUSE users Authors: Matt Sergeant, AxKit.com Ltd Released by: Mohammad Sajid Anwar Maintainers: PERIGRIN owner MANWAR MSERGEANT Contributors: Matt Sergeant, AxKit.com Ltd Mohammad Sajid Anwar  /  1.49 (MANWAR on 2026-03-29) 1.48 (MANWAR on 2022-08-09) 1.47 (MANWAR on 2022-05-13) 1.46 (MANWAR on 2022-05-12) 1.45 (MANWAR on 2022-05-12) 1.44 (MANWAR on 2018-10-11) 1.43 (MANWAR on 2018-10-10) 1.42 (MANWAR on 2017-07-30) 1.41 (MANWAR on 2017-07-28) 1.40 (MANWAR on 2016-11-13) 1.39 (MANWAR on 2016-11-08) 1.38 (MANWAR on 2016-10-31) 1.37 (MANWAR on 2016-06-02) 1.36 (MANWAR on 2016-04-14) 1.35 (MANWAR on 2016-04-06) 1.34 (MANWAR on 2016-03-08) 1.33 (MANWAR on 2016-03-02) 1.32 (MANWAR on 2016-02-23) 1.31 (MANWAR on 2016-02-22) 1.30 (MANWAR on 2016-02-04) 1.29 (MANWAR on 2016-02-03) 1.28 (MANWAR on 2016-01-31) 1.27 (MANWAR on 2016-01-30) 1.26 (MANWAR on 2016-01-25) 1.25 (MANWAR on 2016-01-20) 1.24 (MANWAR on 2016-01-19) 1.23 (MANWAR on 2016-01-18) 1.22 (MANWAR on 2016-01-13) 1.21 (MANWAR on 2016-01-12) 1.20 (MANWAR on 2016-01-10) 1.19 (MANWAR on 2016-01-05) 1.18 (MANWAR on 2016-01-04) 1.17 (MANWAR on 2016-01-01) 1.16 (MANWAR on 2015-12-28) 1.15 (MANWAR on 2015-12-27) 1.14 (MANWAR on 2015-12-26) 1.13 (MSERGEANT on 2003-01-26) 1.12 (MSERGEANT on 2001-11-26) 1.11 (MSERGEANT on 2001-11-16) 1.10 (MSERGEANT on 2001-06-12) 1.09 (MSERGEANT on 2001-04-23) 1.08 (MSERGEANT on 2001-04-01) 1.07 (MSERGEANT on 2001-03-16) 1.06 (MSERGEANT on 2001-03-09) 1.05 (MSERGEANT on 2001-02-26) 1.04 (MSERGEANT on 2001-01-19) 1.03 (MSERGEANT on 2000-12-06) 1.02 (MSERGEANT on 2000-10-02) 1.01 (MSERGEANT on 2000-09-26) 1.00 (MSERGEANT on 2000-09-11) 0.99 (MSERGEANT on 2000-08-28) 0.98 (MSERGEANT on 2000-08-24) 0.57 (MSERGEANT on 2000-08-16) 0.55 (MSERGEANT on 2000-06-15) 0.54 (MSERGEANT on 2000-06-09) 0.53 (MSERGEANT on 2000-06-08) 0.52 (MSERGEANT on 2000-05-28) 0.51 (MSERGEANT on 2000-05-11) 0.50 (MSERGEANT on 2000-05-10) 0.24 (MSERGEANT on 2000-04-25) 0.23 (MSERGEANT on 2000-04-22) 0.22 (MSERGEANT on 2000-04-18) 0.21 (MSERGEANT on 2000-04-17) 0.20 (MSERGEANT on 2000-03-20) 0.19 (MSERGEANT on 2000-03-20) 0.18 (MSERGEANT on 2000-03-07) 0.17 (MSERGEANT on 2000-03-07) 0.16 (MSERGEANT on 2000-02-28) 0.15 (MSERGEANT on 2000-02-24) 0.14 (MSERGEANT on 2000-02-24) 0.13 (MSERGEANT on 2000-02-19) 0.11 (MSERGEANT on 2000-02-10) 0.10 (MSERGEANT on 2000-01-26) XML-XPath-1.49 9 ++ 9 ++ / XML::XPath Contents NAME VERSION DESCRIPTION SYNOPSIS DETAILS METHODS new() find($path, [$context]) findnodes($path, [$context]) matches($node, $path, [$context]) findnodes_as_string($path, [$context]) findvalue($path, [$context]) exists($path, [$context]) getNodeText($path) setNodeText($path, $text) createNode($path) set_namespace($prefix, $uri) clear_namespaces() $XML::XPath::Namespaces Node Object Model On Garbage Collection Example AUTHOR SEE ALSO LICENSE AND COPYRIGHT NAME XML::XPath - Parse and evaluate XPath statements. VERSION Version 1.49 DESCRIPTION This module aims to comply exactly to the XPath specification at http://www.w3.org/TR/xpath and yet allow extensions to be added in the form of functions.Modules such as XSLT and XPointer may need to do this as they support functionality beyond XPath. SYNOPSIS use XML::XPath; use XML::XPath::XMLParser; my $xp = XML::XPath->new(filename => 'test.xhtml'); my $nodeset = $xp->find('/html/body/p'); # find all paragraphs foreach my $node ($nodeset->get_nodelist) { print "FOUND\n\n", XML::XPath::XMLParser::as_string($node), "\n\n"; } DETAILS There is an awful lot to all of this, so bear with it - if you stick it out it should be worth it. Please get a good understanding of XPath by reading the spec before asking me questions. All of the classes and parts herein are named to be synonymous with the names in the specification, so consult that if you don't understand why I'm doing something in the code. Currently, it supports XPath 1.0 with a small number of XPath 2.0 functions. See XML::XPath::Function for the complete list of predefined functions. METHODS The API of XML::XPath itself is extremely simple to allow you to get going almost immediately. The deeper API's are more complex, but you shouldn't have to touch most of that. new() This constructor follows the often seen named parameter method call. Parameters you can use are: filename, parser, xml, ioref and context. The filename parameter specifies an XML file to parse. The xml parameter specifies a string to parse, and the ioref parameter specifies an ioref to parse. The context option allows you to specify a context node. The context node has to be in the format of a node as specified in XML::XPath::XMLParser . The 4 parameters filename, xml, ioref and context are mutually exclusive - you should only specify one (if you specify anything other than context, the context node is the root of your document). The parser option allows you to pass in an already prepared XML::Parser object, to save you having to create more than one in your application (if, for example, you are doing more than just XPath). my $xp = XML::XPath->new( context => $node ); It is very much recommended that you use only 1 XPath object throughout the life of your application. This is because the object (and it's sub-objects) maintain certain bits of state information that will be useful (such as XPath variables) to later calls to find(). It's also a good idea because you'll use less memory this way. find($path, [$context]) The find function takes an XPath expression (a string) and returns either an XML::XPath::NodeSet object containing the nodes it found (or empty if no nodes matched the path), or one of XML::XPath::Literal (a string), XML::XPath::Number or XML::XPath::Boolean . It should always return something - and you can use ->isa() to find out what it returned. If you need to check how many nodes it found you should check $nodeset->size. See XML::XPath::NodeSet . An optional second parameter of a context node allows you to use this method repeatedly, for example XSLT needs to do this. findnodes($path, [$context]) Returns a list of nodes found by $path, optionally in context $context. In scalar context returns an XML::XPath::NodeSet object. matches($node, $path, [$context]) Returns true if the node matches the path (optionally in context $context). findnodes_as_string($path, [$context]) Returns the nodes found reproduced as XML.The result isn't guaranteed to be valid XML though. findvalue($path, [$context]) Returns either a XML::XPath::Literal , a XML::XPath::Boolean or a XML::XPath::Number object.If the path returns a NodeSet,$nodeset->to_literal is called automatically for you (and thus a XML::XPath::Literal is returned).Note that for each of the objects stringification is overloaded, so you can just print the value found, or manipulate it in the ways you would a normal perl value (e.g. using regular expressions). exists($path, [$context]) Returns true if the given path exists. getNodeText($path) Returns the XML::XPath::Literal for a particular XML node. Returns a string if exists or '' (empty string) if the node doesn't exist. setNodeText($path, $text) Sets the text string for a particular XML node. The node can be an element or an attribute. If the node to be set is an attribute, and the attribute node does not exist, it will be created automatically. createNode($path) Creates the node matching the $path given. If part of the path given or all of the path do not exist, the necessary nodes will be created automatically. set_namespace($prefix, $uri) Sets the namespace prefix mapping to the uri. Normally in XML::XPath the prefixes in XPath node test take their context from the current node. This means that foo:bar will always match an element <foo:bar> regardless of the namespace that the prefix foo is mapped to (which might even change within the document, resulting in unexpected results). In order to make prefixes in XPath node tests actually map to a real URI, you need to enable that via a call to the set_namespace method of your XML::XPath object. clear_namespaces() Clears all previously set namespace mappings. $XML::XPath::Namespaces Set this to 0 if you don't want namespace processing to occur. This will make everything a little (tiny) bit faster, but you'll suffer for it, probably. Node Object Model See XML::XPath::Node , XML::XPath::Node::Element , XML::XPath::Node::Text , XML::XPath::Node::Comment , XML::XPath::Node::Attribute , XML::XPath::Node::Namespace , and XML::XPath::Node::PI . On Garbage Collection XPath nodes work in a special way that allows circular references, and yet still lets Perl's reference counting garbage collector to clean up the nodes after use. This should be totally transparent to the user, with one caveat: If you free your tree before letting go of a sub-tree,consider that playing with fire and you may get burned . What does this mean to the average user? Not much. Provided you don't free (or let go out of scope) either the tree you passed to XML::XPath->new, or if you didn't pass a tree, and passed a filename or IO-ref, then provided you don't let the XML::XPath object go out of scope before you let results of find() and its friends go out of scope, then you'll be fine. Even if you do let the tree go out of scope before results, you'll probably still be fine. The only case where you may get stung is when the last part of your path/query is either an ancestor or parent axis. In that case the worst that will happen is you'll end up with a circular reference that won't get cleared until interpreter destruction time.You can get around that by explicitly calling $node->DESTROY on each of your result nodes, if you really need to do that. Mail me direct if that's not clear. Note that it's not doom and gloom. It's by no means perfect,but the worst that will happen is a long running process could leak memory. Most long running processes will therefore be able to explicitly be careful not to free the tree (or XML::XPath object) before freeing results.AxKit, an application that uses XML::XPath, does this and I didn't have to make any changes to the code - it's already sensible programming. If you really don't want all this to happen, then set the variable $XML::XPath::SafeMode, and call $xp->cleanup() on the XML::XPath object when you're finished, or $tree->dispose() if you have a tree instead. Example Please see the test files in t/ for examples on how to use XPath. AUTHOR Original author Matt Sergeant, <matt at sergeant.org> Currently maintained by Mohammad S Anwar, <mohammad.anwar at yahoo.com> SEE ALSO XML::XPath::Function , XML::XPath::Literal , XML::XPath::Boolean , XML::XPath::Number , XML::XPath::XMLParser , XML::XPath::NodeSet , XML::XPath::PerlSAX , XML::XPath::Builder . LICENSE AND COPYRIGHT This module is copyright 2000 AxKit.com Ltd. This is free software, and as such comes with NO WARRANTY. No dates are used in this module. You may distribute this module under the terms of either the Gnu GPL, or the Artistic License (the same terms as Perl itself). For support, please subscribe to the Perl-XML mailing list at the URL Module Install Instructions To install XML::XPath, copy and paste the appropriate command in to your terminal. cpanm cpanm XML::XPath CPAN shell perl -MCPAN -e shell install XML::XPath For more information on module installation, please visit the detailed CPAN module installation guide . Close About Sponsor grep::cpan Recent FAQ Tools API Perl.org Keyboard Shortcuts Global s Focus search bar ? Bring up this help dialog GitHub g p Go to pull requests g i Go to GitHub issues (only if GitHub is preferred repository) POD g a Go to author g c Go to changes g i Go to issues g d Go to dist g r Go to repository/SCM g s Go to source g b Go to file browse Search terms module: (e.g. module:Plugin ) distribution: (e.g. distribution:Dancer auth ) author: (e.g. author:SONGMU Redis ) version: (e.g. version:1.00 ) + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-xml-xpath --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-xml-xpath 1.33 0 +--------------------- +file name : perl-xml-xpath-1.33-0.tar.bz2 +name : perl-xml-xpath +version : 1.33 +build : 0 +build number: 0 +size : 29 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-xpath-1.33-0.tar.bz2 +md5 : 4dedafd47e15c1ceba7a1293190b0699 +dependencies: + - perl-threaded + - perl-xml-parser + - perl >=5.22.0,<5.23.0 + + +perl-xml-xpath 1.33 pl526_1 +--------------------------- +file name : perl-xml-xpath-1.33-pl526_1.tar.bz2 +name : perl-xml-xpath +version : 1.33 +build : pl526_1 +build number: 1 +size : 41 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-xpath-1.33-pl526_1.tar.bz2 +md5 : f4694d224754c81a3306574e3845df64 +timestamp : 2018-08-06 21:38:02 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-xml-parser + + +perl-xml-xpath 1.44 pl526_0 +--------------------------- +file name : perl-xml-xpath-1.44-pl526_0.tar.bz2 +name : perl-xml-xpath +version : 1.44 +build : pl526_0 +build number: 0 +size : 42 KB +license : artistic_2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-xpath-1.44-pl526_0.tar.bz2 +md5 : 166779d5aaca0eaf3074430e1afc4ebe +timestamp : 2018-11-11 03:16:41 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + - perl-xml-parser + + +perl-xml-xpath 1.44 pl5321hdfd78af_1 +------------------------------------ +file name : perl-xml-xpath-1.44-pl5321hdfd78af_1.tar.bz2 +name : perl-xml-xpath +version : 1.44 +build : pl5321hdfd78af_1 +build number: 1 +size : 44 KB +license : artistic_2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-xml-xpath-1.44-pl5321hdfd78af_1.tar.bz2 +md5 : e28c5fb6a09293a2fbc0f857091bad36 +timestamp : 2022-01-19 14:06:35 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-xml-parser + + +perl-xml-xpath 1.47 pl5321hdfd78af_0 +------------------------------------ +file name : perl-xml-xpath-1.47-pl5321hdfd78af_0.tar.bz2 +name : perl-xml-xpath +version : 1.47 +build : pl5321hdfd78af_0 +build number: 0 +size : 45 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-xml-xpath-1.47-pl5321hdfd78af_0.tar.bz2 +md5 : 3e496dbd4fbe933863764156b8fa54d1 +timestamp : 2022-05-21 11:44:31 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-xml-parser + + +perl-xml-xpath 1.48 pl5321hd8ed1ab_0 +------------------------------------ +file name : perl-xml-xpath-1.48-pl5321hd8ed1ab_0.tar.bz2 +name : perl-xml-xpath +version : 1.48 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 46 KB +license : Artistic-2.0 +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-xml-xpath-1.48-pl5321hd8ed1ab_0.tar.bz2 +md5 : 02fc6f065f126c6c37efa3a1636837d0 +timestamp : 2022-08-13 23:35:49 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 + - perl-xml-parser diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-xpathengine.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-xpathengine.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c1739e5e362408479c0534969debf4832da5849 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xml-xpathengine.manual_bundle.txt @@ -0,0 +1,131 @@ +# Tool: perl-xml-xpathengine +software_name: perl-xml-xpathengine +tier: T1 +domain: t1_backfill_overall +downloads: 324798 +summary: a re-usable XPath engine for DOM-like trees +description: a re-usable XPath engine for DOM-like trees +dependencies: perl >=5.32.1,<6.0a0 *_perl5 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-xml-xpathengine --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +perl-xml-xpathengine 0.14 0 +--------------------------- +file name : perl-xml-xpathengine-0.14-0.tar.bz2 +name : perl-xml-xpathengine +version : 0.14 +build : 0 +build number: 0 +size : 18 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-xpathengine-0.14-0.tar.bz2 +md5 : 069f86f7900cca0f3b79dcb756015b84 +dependencies: + - perl-threaded + - perl >=5.22.0,<5.23.0 + + +perl-xml-xpathengine 0.14 pl526_1 +--------------------------------- +file name : perl-xml-xpathengine-0.14-pl526_1.tar.bz2 +name : perl-xml-xpathengine +version : 0.14 +build : pl526_1 +build number: 1 +size : 26 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-xpathengine-0.14-pl526_1.tar.bz2 +md5 : bd98d0692ed15d85486f28aacb94daa4 +timestamp : 2018-07-06 20:27:44 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-xml-xpathengine 0.14 pl526_2 +--------------------------------- +file name : perl-xml-xpathengine-0.14-pl526_2.tar.bz2 +name : perl-xml-xpathengine +version : 0.14 +build : pl526_2 +build number: 2 +size : 26 KB +license : unknown +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xml-xpathengine-0.14-pl526_2.tar.bz2 +md5 : d268cc26d463321abc01f107beaf2553 +timestamp : 2018-08-06 21:31:51 UTC +dependencies: + - perl >=5.26.2,<5.26.3.0a0 + + +perl-xml-xpathengine 0.14 pl5321hdfd78af_3 +------------------------------------------ +file name : perl-xml-xpathengine-0.14-pl5321hdfd78af_3.tar.bz2 +name : perl-xml-xpathengine +version : 0.14 +build : pl5321hdfd78af_3 +build number: 3 +size : 28 KB +license : unknown +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/perl-xml-xpathengine-0.14-pl5321hdfd78af_3.tar.bz2 +md5 : 4af616066d02762108e88cf5413d3ded +timestamp : 2022-01-17 12:45:41 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xsloader.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xsloader.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c059768ed33f550145aa0c95a4e8d4f225510e18 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/perl-xsloader.manual_bundle.txt @@ -0,0 +1,152 @@ +# Tool: perl-xsloader +software_name: perl-xsloader +tier: T1 +domain: t1_backfill_overall +downloads: 624790 +summary: Dynamically load C libraries into Perl code +description: Dynamically load C libraries into Perl code +dependencies: perl >=5.26.2,<5.27.0a0 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://metacpan.org/module/XSLoader +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://metacpan.org/module/XSLoader +Client Challenge JavaScript is disabled in your browser. Please enable JavaScript to proceed. A required part of this site couldn’t load. This may be due to a browser extension, network issues, or browser settings. Please check your connection, disable any ad blockers, or try using a different browser. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge perl-xsloader --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +perl-xsloader 0.16 pl5.22.0_0 +----------------------------- +file name : perl-xsloader-0.16-pl5.22.0_0.tar.bz2 +name : perl-xsloader +version : 0.16 +build : pl5.22.0_0 +build number: 0 +size : 2 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xsloader-0.16-pl5.22.0_0.tar.bz2 +md5 : 049f945c643a160631babcc7c833b92f +dependencies: + - perl 5.22.0* + + +perl-xsloader 0.22 pl5.22.0_0 +----------------------------- +file name : perl-xsloader-0.22-pl5.22.0_0.tar.bz2 +name : perl-xsloader +version : 0.22 +build : pl5.22.0_0 +build number: 0 +size : 7 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xsloader-0.22-pl5.22.0_0.tar.bz2 +md5 : 85561859c28a1f5b9e832712eadcb74b +dependencies: + - perl 5.22.0* + - perl-test-more + + +perl-xsloader 0.22 pl526_1 +-------------------------- +file name : perl-xsloader-0.22-pl526_1.tar.bz2 +name : perl-xsloader +version : 0.22 +build : pl526_1 +build number: 1 +size : 8 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xsloader-0.22-pl526_1.tar.bz2 +md5 : f94754e77f342143845e38a469af0fcf +timestamp : 2018-07-08 16:48:15 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + - perl-test-more + + +perl-xsloader 0.24 pl526_0 +-------------------------- +file name : perl-xsloader-0.24-pl526_0.tar.bz2 +name : perl-xsloader +version : 0.24 +build : pl526_0 +build number: 0 +size : 8 KB +license : perl_5 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/perl-xsloader-0.24-pl526_0.tar.bz2 +md5 : 878d48f2a6bdff58c7b9589e3b25ff6b +timestamp : 2018-07-10 05:18:51 UTC +dependencies: + - perl >=5.26.2,<5.27.0a0 + + +perl-xsloader 0.24 pl5321hd8ed1ab_0 +----------------------------------- +file name : perl-xsloader-0.24-pl5321hd8ed1ab_0.tar.bz2 +name : perl-xsloader +version : 0.24 +build : pl5321hd8ed1ab_0 +build number: 0 +size : 14 KB +license : GPL-1.0-or-later OR Artistic-1.0-Perl +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/perl-xsloader-0.24-pl5321hd8ed1ab_0.tar.bz2 +md5 : 0f34739daf8b7063716d75669ca1992d +timestamp : 2021-11-11 15:38:36 UTC +dependencies: + - perl >=5.32.1,<6.0a0 *_perl5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/piaso.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/piaso.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ee76e9218658e866ccd7c12739127fb3cc6bebd3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/piaso.manual_bundle.txt @@ -0,0 +1,58 @@ +# Tool: piaso +software_name: piaso +tier: T1 +domain: single_cell +downloads: 46 +summary: PIASO: Precise Integrative Analysis of Single-cell Omics +description: PIASO is a Python toolkit for precise integrative analysis of single-cell omics data. +It provides methods for single-cell RNA-seq and ATAC-seq data analysis, including +batch integration, clustering, and visualization. +dependencies: anndata >=0.8, cosg >=1.0.3, matplotlib-base >=3.5.2, numpy >=1.21.6, pandas >=1.4.4, python >=3.9, requests, scanpy >=1.9.1, scikit-learn >=1.1, scipy >=1.7.3, seaborn >=0.11.2, statsmodels >=0.13.2, tqdm, typing_extensions +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://piaso.org +doc_url: https://piaso.org +dev_url: https://github.com/genecell/PIASO + +## URL Docs Extract +### https://piaso.org +PIASO - Precise Integrative Analysis of Single-cell Omics Installation Tutorials API About References Release Notes Get Started Installation Tutorials API About References Release Notes GitHub Install PIASO Install from PyPI (stable release) pip install piaso-tools Install from GitHub (latest development version) pip install git+https://github.com/genecell/PIASO.git Full Installation Guide Done Python Toolkit for Single-cell Omics The toolkit for P recise I ntegrative A nalysis of S ingle-cell O mics Data analysis support, for your biological insight. Get started Tutorials Modules INFOG GDR COSG Emergene SCALAR LARIS stitchSpace PIASOmarkerDB Explore PIASO Modules An efficient and versatile toolkit for analysis of single-cell omics All Modules scRNA-seq scATAC-seq Spatial Integration Annotation Visualization Coming Soon Citation If PIASO is useful for your research, please consider citing: Wu, S.J., Dai, M. et al. Pyramidal neurons proportionately alter cortical interneuron subtypes. Nature (2026). DOI: 10.1038/s41586-025-09996-8 PIASO is developed and maintained by the Gord Fishell Laboratory at Harvard Medical School and Broad Institute of MIT and Harvard. Contact: Min Dai - dai@broadinstitute.org Developed at Harvard Medical School • Broad Institute of MIT and Harvard About Privacy Policy Terms of Use License (BSD-3-Clause) © 2025 PIASO. Built for the single-cell community. Version 1.0.3 + +### https://github.com/genecell/PIASO +GitHub - genecell/PIASO: PIASO: Precise Integrative Analysis of Single-cell Omics · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} genecell / PIASO Public Notifications You must be signed in to change notification settings Fork 2 Star 6 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights genecell/PIASO master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 133 Commits 133 Commits .github/ workflows .github/ workflows docs docs piaso piaso src src .gitignore .gitignore .nojekyll .nojekyll Cargo.toml Cargo.toml LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml View all files Repository files navigation README BSD-3-Clause license PIASO Precise Integrative Analysis of Single-cell Omics Documentation piaso.org Installation Install from PyPI (stable release): pip install piaso-tools Install from bioconda (stable release): conda install -c conda-forge -c bioconda piaso Install from GitHub (latest development version): pip install git+https://github.com/genecell/PIASO.git Citation If PIASO is useful for your research, please consider citing Wu, S.J., Dai, M. et al . Pyramidal neurons proportionately alter cortical interneuron subtypes. Nature (2026). https://doi.org/10.1038/s41586-025-09996-8 Contact Min Dai dai@broadinstitute.org About PIASO: Precise Integrative Analysis of Single-cell Omics piaso.org Topics data-science bioinformatics bioinformatics-pipeline transcriptomics single-cell marker-genes single-cell-genomics single-cell-rna-seq single-cell-analysis single-cell-atac-seq spatial-transcriptomics piaso Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Stars 6 stars Watchers 1 watching Forks 2 forks Report repository Releases 5 PIASO v1.1.0: Rust-Accelerated Scoring & Multi-Batch GDR Parallelism Latest Apr 1, 2026 + 4 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 95.5% Rust 4.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge piaso --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +piaso 1.0.3 pyhdfd78af_0 +------------------------ +file name : piaso-1.0.3-pyhdfd78af_0.conda +name : piaso +version : 1.0.3 +build : pyhdfd78af_0 +build number: 0 +size : 86 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/piaso-1.0.3-pyhdfd78af_0.conda +md5 : 7613d9a5814dc56a5e58a5ac19ff4cdf +timestamp : 2026-01-21 19:52:45 UTC +dependencies: + - anndata >=0.8 + - cosg >=1.0.3 + - matplotlib-base >=3.5.2 + - numpy >=1.21.6 + - pandas >=1.4.4 + - python >=3.9 + - requests + - scanpy >=1.9.1 + - scikit-learn >=1.1 + - scipy >=1.7.3 + - seaborn >=0.11.2 + - statsmodels >=0.13.2 + - tqdm + - typing_extensions diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/picard-slim.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/picard-slim.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c4df6084dbe0f5f1236cc2c9b457376dfb220344 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/picard-slim.manual_bundle.txt @@ -0,0 +1,556 @@ +# Tool: picard-slim +software_name: picard-slim +tier: T1 +domain: t1_backfill_overall +downloads: 203485 +summary: Java tools for working with NGS data in the BAM format. +description: Java tools for working with NGS data in the BAM format. This package lacks the R dependency that is only required for some metrics tasks. This keeps the size of the package smaller, at the cost of breaking some of Picards's commands. The 'picard' package contains all the necessary dependencies. +dependencies: openjdk >=17, zlib +execution_environment: Java +execution_environment_reason: inferred from Java runtime dependencies + +## URLs +home_url: http://broadinstitute.github.io/picard/ +doc_url: +dev_url: https://github.com/broadinstitute/picard + +## CLI Help Source +java:-help +## CLI Help Content +$ conda run -n bioenv_java java -help +[rc=0] + +Usage: java [-options] class [args...] + (to execute a class) + or java [-options] -jar jarfile [args...] + (to execute a jar file) +where options include: + -d32 use a 32-bit data model if available + -d64 use a 64-bit data model if available + -server to select the "server" VM + The default VM is server, + because you are running on a server-class machine. + + + -cp + -classpath + A : separated list of directories, JAR archives, + and ZIP archives to search for class files. + -D= + set a system property + -verbose:[class|gc|jni] + enable verbose output + -version print product version and exit + -version: + Warning: this feature is deprecated and will be removed + in a future release. + require the specified version to run + -showversion print product version and continue + -jre-restrict-search | -no-jre-restrict-search + Warning: this feature is deprecated and will be removed + in a future release. + include/exclude user private JREs in the version search + -? -help print this help message + -X print help on non-standard options + -ea[:...|:] + -enableassertions[:...|:] + enable assertions with specified granularity + -da[:...|:] + -disableassertions[:...|:] + disable assertions with specified granularity + -esa | -enablesystemassertions + enable system assertions + -dsa | -disablesystemassertions + disable system assertions + -agentlib:[=] + load native agent library , e.g. -agentlib:hprof + see also, -agentlib:jdwp=help and -agentlib:hprof=help + -agentpath:[=] + load native agent library by full pathname + -javaagent:[=] + load Java programming language agent, see java.lang.instrument + -splash: + show splash screen with specified image +See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details. + + + +## URL Docs Extract +### http://broadinstitute.github.io/picard/ +Picard Tools - By Broad Institute Picard A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. View the Project on GitHub broadinstitute/picard Latest Jar Release Source Code ZIP File Source Code TAR Ball View On GitHub Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification . Note that the information on this page is targeted at end-users. For developers, the source code, building instructions and implementation/development resources are available on GitHub . The Picard toolkit is open-source under the MIT license and free for all uses. Enjoy! Quick Start Download Software The Picard command-line tools are provided as a single executable jar file. You can download the jar file from the Latest Release project page on Github. The file name will be picard.jar . Install Open the downloaded package and place the folder containing the jar file in a convenient directory on your hard drive (or server). Unlike C-compiled programs such as Samtools, Picard cannot simply be added to your PATH, so we recommend setting up an environment variable to act as a shortcut. For the tools to run properly, you must have Java 1.8 installed. To check your java version by open your terminal application and run the following command: java -version If the output looks something like java version "1.8.x" , you are good to go. If not, you may need to update your version; see the Oracle Java website to download the latest JDK. Test Installation To test that you can run Picard tools, run the following command in your terminal application, providing either the full path to the picard.jar file: java -jar /path/to/picard.jar -h or the environment variable that you set up as a shortcut (here we are using $PICARD ): java -jar $PICARD -h You should see a complete list of all the tools in the Picard toolkit. If you don't, read on to the section on Getting Help. Use Picard Tools The tools, which are all listed further below, are invoked as follows: java jvm-args -jar picard.jar PicardToolName OPTION1=value1 OPTION2=value2... See the Tool Documentation for details on the Picard command syntax and standard options as well as a complete list of tools with usage recommendations, options, and example commands. Getting Help Picard is supported through the GATK Forums . Register now and you can ask questions and report problems that you might encounter while using Picard and related tools such as GATK (for source code-related questions, post an issue on Github instead), with the following guidelines: Before Asking For Help Before posting to the Forum, please do the following: Try the latest version of Picard . See if your problem is covered discussed in the Frequently Asked Questions . Search the GATK Forums to see if a similar problem has previously been discussed there. Run Picard ValidateSamFile with MODE=SUMMARY on your input SAM or BAM file (if applicable). Attempt to resolve or at least understand any problems reported. When Asking For Help When asking a question about a problem, please include the following: Command line(s) you ran Program console output and metrics files. Repetitive console output may be abbreviated Entire stack trace if one was produced Version of JVM you are using (obtained by running 'java -version') Additional Resources Detailed tool documentation Description of output of metrics programs SAM differences in Picard Explain SAM flags Explain Base Qualities Javadoc Full list of Picard tools AddCommentsToBam AddOrReplaceReadGroups BaitDesigner BamToBfq BamIndexStats BedToIntervalList BuildBamIndex CalculateReadGroupChecksum CleanSam CollectAlignmentSummaryMetrics CollectBaseDistributionByCycle CollectGcBiasMetrics CollectHiSeqXPfFailMetrics CollectHsMetrics CollectIlluminaBasecallingMetrics CollectIlluminaLaneMetrics CollectInsertSizeMetrics CollectJumpingLibraryMetrics CollectMultipleMetrics CollectOxoGMetrics CollectQualityYieldMetrics CollectRawWgsMetrics CollectTargetedPcrMetrics CollectRnaSeqMetrics CollectRrbsMetrics CollectSequencingArtifactMetrics CollectVariantCallingMetrics CollectWgsMetrics CollectWgsMetricsWithNonZeroCoverage CompareMetrics CompareSAMs ConvertSequencingArtifactToOxoG CreateSequenceDictionary DownsampleSam ExtractIlluminaBarcodes EstimateLibraryComplexity FastqToSam FifoBuffer FindMendelianViolations CrosscheckFingerprints ClusterCrosscheckMetrics CheckFingerprint FilterSamReads FilterVcf FixMateInformation GatherBamFiles GatherVcfs GenotypeConcordance IlluminaBasecallsToFastq IlluminaBasecallsToSam CheckIlluminaDirectory CheckTerminatorBlock IntervalListTools LiftOverIntervalList LiftoverVcf MakeSitesOnlyVcf MarkDuplicates MarkDuplicatesWithMateCigar MeanQualityByCycle MergeBamAlignment MergeSamFiles MergeVcfs NormalizeFasta PositionBasedDownsampleSam ExtractSequences QualityScoreDistribution RenameSampleInVcf ReorderSam ReplaceSamHeader RevertSam RevertOriginalBaseQualitiesAndAddMateCigar SamFormatConverter SamToFastq ScatterIntervalsByNs SetNmMdAndUqTags SortSam SortVcf SplitSamByLibrary UmiAwareMarkDuplicatesWithMateCigar UpdateVcfSequenceDictionary VcfFormatConverter MarkIlluminaAdapters SplitVcfs ValidateSamFile ViewSam VcfToIntervalList Project maintained by broadinstitute Hosted on GitHub Pages — Theme by orderedlist + +### https://github.com/broadinstitute/picard +GitHub - broadinstitute/picard: A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} broadinstitute / picard Public Notifications You must be signed in to change notification settings Fork 382 Star 1.1k Code Issues 214 Pull requests 24 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights broadinstitute/picard master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 3,072 Commits 3,072 Commits .github .github docs/ fingerprinting docs/ fingerprinting etc/ test etc/ test gradle/ wrapper gradle/ wrapper scripts/ travis scripts/ travis src src testdata/ picard testdata/ picard .dockerignore .dockerignore .gitattributes .gitattributes .gitignore .gitignore Dockerfile Dockerfile LICENSE.txt LICENSE.txt README.md README.md build.gradle build.gradle build.xml build.xml build_push_docker.sh build_push_docker.sh gradlew gradlew settings.gradle settings.gradle View all files Repository files navigation README Code of conduct MIT license User Support: For user questions please look for answers and ask first in the GATK forum . A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library HTSJDK to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM and VCF . As of version 3.0, Picard requires Java 1.17. Building Picard First, clone the repo: git clone https://github.com/broadinstitute/picard.git cd picard/ Picard is now built using gradle . A wrapper script ( gradlew ) is included which will download the appropriate version of gradle on the first invocation. To build a fully-packaged, runnable Picard jar with all dependencies included, run: ./gradlew shadowJar The resulting jar will be in build/libs . To run it, the command is: java -jar build/libs/picard.jar or java -jar build/libs/picard-<VERSION>-all.jar To build a jar containing only Picard classes (without its dependencies), run: ./gradlew jar To clean the build directory, run: ./gradlew clean Running Tests To run all tests, the command is: ./gradlew test To run a specific test, the command is: ./gradlew legacyTest --tests "*TestClassName*" or ./gradlew barclayTest --tests "*TestClassName*" Running legacyTest uses the legacy commandline parser while barclayTest uses the new parser. Changing the released version of HTSJDK that Picard depends on To switch Picard's HTSJDK dependency to a different released version: Open build.gradle Edit VERSION in the following line to be a different released version of HTSJDK. HTSJDK releases are listed here final htsjdkVersion = System.getProperty('htsjdk.version', 'VERSION')` Open a pull request with this change Building Picard with a Custom Version of HTSJDK During development in Picard, it is sometimes necessary to build locally against an unreleased version or branch of HTSJDK. To build against an unreleased version of HTSJDK's master branch: Go to the Broad artifactory , where continuous snapshots of HTSJDK's master branch are published, and select the version you want to use. For example, 2.5.1-9-g5740ca1-SNAPSHOT . You can search by tag or short git commit hash. In your Picard clone, run ./gradlew shadowJar -Dhtsjdk.version=VERSION , where VERSION is the version of the HTSJDK master branch snapshot you want to use. To build against a version of HTSJDK that has not yet been merged into HTSJDK's master branch: Clone HTSJDK , and in your clone check out the tag or branch you want to build Picard with. Run ./gradlew install printVersion in your htsjdk clone to install that version to your local maven repository. Take note of the version number that gets printed at the end. Switch back to your Picard clone, and run ./gradlew shadowJar -Dhtsjdk.version=VERSION , where VERSION is the version of HTSJDK you installed to your local maven repository. Releasing Picard Full instructions on how to create a new release of Picard are here Path providers Picard has limited support for reading from Path providers. Currently only google's api is supported, and only a few tools support this. To run with this support you need to compile the cloudJar target with gradle: ./gradlew cloudJar then run picard as follows: java -jar build/lib/picardcloud.jar < Picard arguments starting from program > For example: java -jar build/lib/picardcloud.jar CrosscheckFingerprints \ I=gs://sample1.vcf \ I=gs://sample2.vcf \ CROSSCHECK_BY=FILE \ H=Haplotype_db.txt \ O=crosscheck.out Alternatively, you can run the tool via the GATK which bundles the Google-Cloud jar, and should thus "Just Work". Citing Please cite this repository when using Picard tools for your publications. “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/ ; Broad Institute @misc{Picard2019toolkit, title = {Picard toolkit}, year = {2019}, publisher = {Broad Institute}, journal = {Broad Institute, GitHub repository}, howpublished = {\url{https://broadinstitute.github.io/picard/}} } Identifiers from software registries are increasingly accepted by journals, as in (biotools:picard_tools) or (RRID:SCR_006525). Picard is migrating to semantic versioning . We will eventually adhere to it strictly and bump our major version whenever there are breaking changes to our API, but until we more clearly define what constitutes our official API, clients should assume that every release potentially contains at least minor changes to public methods. Please see the Picard Documentation for more information. About A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. broadinstitute.github.io/picard/ Resources Readme License MIT license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1.1k stars Watchers 149 watching Forks 382 forks Report repository Releases 186 3.4.0 Latest Apr 13, 2025 + 185 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Java 98.5% R 0.4% XSLT 0.3% Python 0.3% HTML 0.2% Shell 0.2% Other 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge picard-slim --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +picard-slim 2.20.4 0 +-------------------- +file name : picard-slim-2.20.4-0.tar.bz2 +name : picard-slim +version : 2.20.4 +build : 0 +build number: 0 +size : 14.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.20.4-0.tar.bz2 +md5 : b02697f1bdd59a91de7127fbbc713648 +timestamp : 2019-08-05 12:45:26 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.20.5 0 +-------------------- +file name : picard-slim-2.20.5-0.tar.bz2 +name : picard-slim +version : 2.20.5 +build : 0 +build number: 0 +size : 14.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.20.5-0.tar.bz2 +md5 : 5af5bcd002cbf8ba3b5bc0c0ee090428 +timestamp : 2019-08-06 08:48:43 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.20.6 0 +-------------------- +file name : picard-slim-2.20.6-0.tar.bz2 +name : picard-slim +version : 2.20.6 +build : 0 +build number: 0 +size : 14.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.20.6-0.tar.bz2 +md5 : 6e6ae05d8e2568e1303f0bd3d96094ec +timestamp : 2019-08-20 14:24:55 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.20.7 0 +-------------------- +file name : picard-slim-2.20.7-0.tar.bz2 +name : picard-slim +version : 2.20.7 +build : 0 +build number: 0 +size : 14.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.20.7-0.tar.bz2 +md5 : b40eb2d5ab794f8ea0029f3bdc088c62 +timestamp : 2019-09-04 21:32:31 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.20.8 0 +-------------------- +file name : picard-slim-2.20.8-0.tar.bz2 +name : picard-slim +version : 2.20.8 +build : 0 +build number: 0 +size : 14.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.20.8-0.tar.bz2 +md5 : 52bdebde704531a89987363533278edf +timestamp : 2019-09-16 20:17:53 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.21.1 0 +-------------------- +file name : picard-slim-2.21.1-0.tar.bz2 +name : picard-slim +version : 2.21.1 +build : 0 +build number: 0 +size : 14.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.21.1-0.tar.bz2 +md5 : bf99f78452f0c4ae787f2a6062aa7a71 +timestamp : 2019-10-03 16:57:14 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.21.2 0 +-------------------- +file name : picard-slim-2.21.2-0.tar.bz2 +name : picard-slim +version : 2.21.2 +build : 0 +build number: 0 +size : 14.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.21.2-0.tar.bz2 +md5 : f14d1ac1c42010bd4a4dfa39bf973e00 +timestamp : 2019-10-29 19:29:21 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.21.3 0 +-------------------- +file name : picard-slim-2.21.3-0.tar.bz2 +name : picard-slim +version : 2.21.3 +build : 0 +build number: 0 +size : 14.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.21.3-0.tar.bz2 +md5 : 46018587312a04beb227116118dd1bf2 +timestamp : 2019-11-12 21:29:59 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.21.4 0 +-------------------- +file name : picard-slim-2.21.4-0.tar.bz2 +name : picard-slim +version : 2.21.4 +build : 0 +build number: 0 +size : 14.7 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.21.4-0.tar.bz2 +md5 : 364438d0e47d06c5796b412411d81d0e +timestamp : 2019-11-26 15:08:35 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.21.5 0 +-------------------- +file name : picard-slim-2.21.5-0.tar.bz2 +name : picard-slim +version : 2.21.5 +build : 0 +build number: 0 +size : 14.7 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.21.5-0.tar.bz2 +md5 : 4d6151314338a48d25b30dc3a05686aa +timestamp : 2019-12-19 05:13:05 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.21.6 0 +-------------------- +file name : picard-slim-2.21.6-0.tar.bz2 +name : picard-slim +version : 2.21.6 +build : 0 +build number: 0 +size : 14.7 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.21.6-0.tar.bz2 +md5 : 04cb5e58b500b357b13fc27b35cd90d3 +timestamp : 2019-12-19 21:11:20 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.21.7 0 +-------------------- +file name : picard-slim-2.21.7-0.tar.bz2 +name : picard-slim +version : 2.21.7 +build : 0 +build number: 0 +size : 14.7 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.21.7-0.tar.bz2 +md5 : 49a03f430147f2a174c47d1082ea45d6 +timestamp : 2020-01-21 17:08:53 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.21.8 0 +-------------------- +file name : picard-slim-2.21.8-0.tar.bz2 +name : picard-slim +version : 2.21.8 +build : 0 +build number: 0 +size : 14.7 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.21.8-0.tar.bz2 +md5 : f0a8f63145104e218ac34afe429a552c +timestamp : 2020-02-05 16:11:36 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.21.9 0 +-------------------- +file name : picard-slim-2.21.9-0.tar.bz2 +name : picard-slim +version : 2.21.9 +build : 0 +build number: 0 +size : 14.7 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.21.9-0.tar.bz2 +md5 : f414ce5174fbe2cad86a3c2ed9e6e6cf +timestamp : 2020-02-19 15:09:56 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.22.0 0 +-------------------- +file name : picard-slim-2.22.0-0.tar.bz2 +name : picard-slim +version : 2.22.0 +build : 0 +build number: 0 +size : 14.7 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.22.0-0.tar.bz2 +md5 : a5bf52145ce3760a7173cfd1bb8441b4 +timestamp : 2020-02-27 19:13:48 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.22.1 0 +-------------------- +file name : picard-slim-2.22.1-0.tar.bz2 +name : picard-slim +version : 2.22.1 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.22.1-0.tar.bz2 +md5 : d97e18e0d3aa08eddaf65b89fc3c98b5 +timestamp : 2020-03-16 20:13:40 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.22.2 0 +-------------------- +file name : picard-slim-2.22.2-0.tar.bz2 +name : picard-slim +version : 2.22.2 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.22.2-0.tar.bz2 +md5 : 86b80dd374190907a574c886b31e9c61 +timestamp : 2020-03-30 18:38:42 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.22.3 0 +-------------------- +file name : picard-slim-2.22.3-0.tar.bz2 +name : picard-slim +version : 2.22.3 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.22.3-0.tar.bz2 +md5 : dfe1f7b7935105874af9aa035769c8e2 +timestamp : 2020-04-08 20:14:15 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.22.4 0 +-------------------- +file name : picard-slim-2.22.4-0.tar.bz2 +name : picard-slim +version : 2.22.4 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.22.4-0.tar.bz2 +md5 : 24c98fd579e0da465f956d9773c16ad8 +timestamp : 2020-04-28 14:13:56 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.22.5 0 +-------------------- +file name : picard-slim-2.22.5-0.tar.bz2 +name : picard-slim +version : 2.22.5 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.22.5-0.tar.bz2 +md5 : 4302f25e1a2e99dc0831cc1da4a84cd9 +timestamp : 2020-05-11 23:48:53 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.22.6 0 +-------------------- +file name : picard-slim-2.22.6-0.tar.bz2 +name : picard-slim +version : 2.22.6 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.22.6-0.tar.bz2 +md5 : b4ef76e680bb1bb025edf4220fbd9f35 +timestamp : 2020-05-14 14:53:23 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.22.7 0 +-------------------- +file name : picard-slim-2.22.7-0.tar.bz2 +name : picard-slim +version : 2.22.7 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.22.7-0.tar.bz2 +md5 : 429f67939caefbb2824f425ae391d2cb +timestamp : 2020-05-18 19:22:05 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.22.8 0 +-------------------- +file name : picard-slim-2.22.8-0.tar.bz2 +name : picard-slim +version : 2.22.8 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.22.8-0.tar.bz2 +md5 : f372b96f1a0f670374fd7cc7fecd39c2 +timestamp : 2020-05-21 21:57:14 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.22.9 0 +-------------------- +file name : picard-slim-2.22.9-0.tar.bz2 +name : picard-slim +version : 2.22.9 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.22.9-0.tar.bz2 +md5 : f87211deb6fb8c1fea962a14f0ed07b8 +timestamp : 2020-06-02 20:22:39 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.23.0 0 +-------------------- +file name : picard-slim-2.23.0-0.tar.bz2 +name : picard-slim +version : 2.23.0 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.23.0-0.tar.bz2 +md5 : 03916b12397d518d2b55f5c7eb8fdc77 +timestamp : 2020-06-09 19:09:16 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.23.1 0 +-------------------- +file name : picard-slim-2.23.1-0.tar.bz2 +name : picard-slim +version : 2.23.1 +build : 0 +build number: 0 +size : 15.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.23.1-0.tar.bz2 +md5 : 993b5576070b1729d20ff11900b132bf +timestamp : 2020-06-23 15:54:13 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.23.2 0 +-------------------- +file name : picard-slim-2.23.2-0.tar.bz2 +name : picard-slim +version : 2.23.2 +build : 0 +build number: 0 +size : 15.9 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-slim-2.23.2-0.tar.bz2 +md5 : 73468bb50a51c2b1eaa010bb0adb8349 +timestamp : 2020-07-09 20:17:34 UTC +dependencies: + - openjdk >=8 + + +picard-slim 2.23.3 0 +-------------------- +file name : picard-slim-2.23.3-0.tar.bz2 +name : picard-slim +version : 2.23.3 +build : 0 +build number: 0 +size diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/picard.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/picard.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..fffb280147b90c6ef8af4bc22d5a30a34053684f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/picard.manual_bundle.txt @@ -0,0 +1,639 @@ +# Tool: picard +software_name: picard +tier: T1 +domain: t1_backfill_overall +downloads: 2866281 +summary: Java tools for working with NGS data in the BAM format +description: Java tools for working with NGS data in the BAM format. This package depends on 'r-base' because Picard requires R to run some of its metrics commands. The 'picard-slim' package offers an installation of Picard without the 'r-base' dependency. +dependencies: openjdk >=17, r-base +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: http://broadinstitute.github.io/picard/ +doc_url: +dev_url: https://github.com/broadinstitute/picard + +## CLI Help Source +cli:picard +## CLI Help Content +$ conda run -n bioenv_r_bioc picard --help +[rc=1] + +/225040511/miniconda3/envs/bioenv_r_bioc/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory +USAGE: PicardCommandLine  [-h] + +Available Programs: +-------------------------------------------------------------------------------------- +Base Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters + CheckIlluminaDirectory Asserts the validity for specified Illumina basecalling data.  + CollectIlluminaBasecallingMetrics Collects Illumina Basecalling metrics for a sequencing run.  + CollectIlluminaLaneMetrics Collects Illumina lane metrics for the given BaseCalling analysis directory.  + ExtractIlluminaBarcodes Tool determines the barcode for each read in an Illumina lane.  + IlluminaBasecallsToFastq Generate FASTQ file(s) from Illumina basecall read data.  + IlluminaBasecallsToSam Transforms raw Illumina sequencing data into an unmapped SAM or BAM file. + MarkIlluminaAdapters Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.  + +-------------------------------------------------------------------------------------- +Diagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics + AccumulateVariantCallingMetrics Combines multiple Variant Calling Metrics files into a single file + BamIndexStats Generate index statistics from a BAM file + CalculateFingerprintMetrics Calculate statistics on fingerprints, checking their viability + CalculateReadGroupChecksum Creates a hash code based on the read groups (RG).  + CheckFingerprint Computes a fingerprint from the supplied input (SAM/BAM or VCF) file and compares it to the provided genotypes + CheckTerminatorBlock Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise + ClusterCrosscheckMetrics Clusters the results of a CrosscheckFingerprints run by LOD score + CollectAlignmentSummaryMetrics Produces a summary of alignment metrics from a SAM or BAM file.  + CollectBaseDistributionByCycle Chart the nucleotide distribution per cycle in a SAM or BAM file + CollectGcBiasMetrics Collect metrics regarding GC bias.  + CollectHiSeqXPfFailMetrics Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories. + CollectHsMetrics Collects hybrid-selection (HS) metrics for a SAM or BAM file.  + CollectIndependentReplicateMetrics **EXPERIMENTAL - USE AT YOUR OWN RISK** Estimates the rate of independent replication of reads within a bam. + CollectInsertSizeMetrics Collect metrics about the insert size distribution of a paired-end library. + CollectJumpingLibraryMetrics Collect jumping library metrics.  + CollectMultipleMetrics Collect multiple classes of metrics. + CollectOxoGMetrics Collect metrics to assess oxidative artifacts. + CollectQualityYieldMetrics Collect metrics about reads that pass quality thresholds and Illumina-specific filters.  + CollectRawWgsMetrics Collect whole genome sequencing-related metrics.  + CollectRnaSeqMetrics Produces RNA alignment metrics for a SAM or BAM file.  + CollectRrbsMetrics Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.  + CollectSamErrorMetrics Program to collect error metrics on bases stratified in various ways. + CollectSequencingArtifactMetrics Collect metrics to quantify single-base sequencing artifacts.  + CollectTargetedPcrMetrics Calculate PCR-related metrics from targeted sequencing data.  + CollectVariantCallingMetrics Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file + CollectWgsMetrics Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. + CollectWgsMetricsWithNonZeroCoverage **EXPERIMENTAL - USE AT YOUR OWN RISK** Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  + CompareMetrics Compare two metrics files. + CompareSAMs Compare two input ".sam" or ".bam" files.  + ConvertSequencingArtifactToOxoG Extract OxoG metrics from generalized artifacts metrics.  + CrosscheckFingerprints Checks that all data in the input files appear to have come from the same individual + CrosscheckReadGroupFingerprints DEPRECATED: USE CrosscheckFingerprints.  + EstimateLibraryComplexity Estimates the numbers of unique molecules in a sequencing library.  + IdentifyContaminant Computes a fingerprint from the supplied SAM/BAM file, given a contamination estimate. + MeanQualityByCycle Collect mean quality by cycle. + QualityScoreDistribution Chart the distribution of quality scores.  + ValidateSamFile Validates a SAM or BAM file. + ViewSam Prints a SAM or BAM file to the screen + +-------------------------------------------------------------------------------------- +Genotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays + GtcToVcf Program to convert a GTC file to a VCF + MergePedIntoVcf Program to merge a single-sample ped file from zCall into a single-sample VCF. + VcfToAdpc Program to convert an Arrays VCF to an ADPC file. + +-------------------------------------------------------------------------------------- +Intervals Manipulation: Tools that process genomic intervals in various formats + BedToIntervalList Converts a BED file to a Picard Interval List.  + IntervalListToBed Converts an Picard IntervalList file to a BED file. + IntervalListTools A tool for performing various IntervalList manipulations + LiftOverIntervalList Lifts over an interval list from one reference build to another.  + +-------------------------------------------------------------------------------------- +Other: Miscellaneous tools, e.g. those that aid in data streaming + FifoBuffer Provides a large, FIFO buffer that can be used to buffer input and output streams between programs. + +-------------------------------------------------------------------------------------- +Read Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format + AddCommentsToBam Adds comments to the header of a BAM file. + AddOATag Record current alignment information to OA tag. + AddOrReplaceReadGroups Assigns all the reads in a file to a single new read-group. + BamToBfq Converts a BAM file into a BFQ (binary fastq formatted) file + BuildBamIndex Generates a BAM index ".bai" file.  + CleanSam Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads + DownsampleSam Downsample a SAM or BAM file. + FastqToSam Converts a FASTQ file to an unaligned BAM or SAM file + FilterSamReads Subsets reads from a SAM or BAM file by applying one of several filters. + FixMateInformation Verify mate-pair information between mates and fix if needed. + GatherBamFiles Concatenate efficiently BAM files that resulted from a scattered parallel analysis + MarkDuplicates Identifies duplicate reads.  + MarkDuplicatesWithMateCigar Identifies duplicate reads, accounting for mate CIGAR.  + MergeBamAlignment Merge alignment data from a SAM or BAM with data in an unmapped BAM file.  + MergeSamFiles Merges multiple SAM and/or BAM files into a single file.  + PositionBasedDownsampleSam Downsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell. + ReorderSam Reorders reads in a SAM or BAM file to match ordering in a second reference file. + ReplaceSamHeader Replaces the SAMFileHeader in a SAM or BAM file.  + RevertOriginalBaseQualitiesAndAddMateCigar Reverts the original base qualities and adds the mate cigar tag to read-group BAMs + RevertSam Reverts SAM or BAM files to a previous state.  + SamFormatConverter Convert a BAM file to a SAM file, or a SAM to a BAM + SamToFastq Converts a SAM or BAM file to FASTQ. + SamToFastqWithTags Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags. + SetNmAndUqTags DEPRECATED: Use SetNmMdAndUqTags instead. + SetNmMdAndUqTags Fixes the NM, MD, and UQ tags in a SAM file  + SimpleMarkDuplicatesWithMateCigar **EXPERIMENTAL - USE AT YOUR OWN RISK** Exami + +## URL Docs Extract +### http://broadinstitute.github.io/picard/ +Picard Tools - By Broad Institute Picard A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. View the Project on GitHub broadinstitute/picard Latest Jar Release Source Code ZIP File Source Code TAR Ball View On GitHub Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification . Note that the information on this page is targeted at end-users. For developers, the source code, building instructions and implementation/development resources are available on GitHub . The Picard toolkit is open-source under the MIT license and free for all uses. Enjoy! Quick Start Download Software The Picard command-line tools are provided as a single executable jar file. You can download the jar file from the Latest Release project page on Github. The file name will be picard.jar . Install Open the downloaded package and place the folder containing the jar file in a convenient directory on your hard drive (or server). Unlike C-compiled programs such as Samtools, Picard cannot simply be added to your PATH, so we recommend setting up an environment variable to act as a shortcut. For the tools to run properly, you must have Java 1.8 installed. To check your java version by open your terminal application and run the following command: java -version If the output looks something like java version "1.8.x" , you are good to go. If not, you may need to update your version; see the Oracle Java website to download the latest JDK. Test Installation To test that you can run Picard tools, run the following command in your terminal application, providing either the full path to the picard.jar file: java -jar /path/to/picard.jar -h or the environment variable that you set up as a shortcut (here we are using $PICARD ): java -jar $PICARD -h You should see a complete list of all the tools in the Picard toolkit. If you don't, read on to the section on Getting Help. Use Picard Tools The tools, which are all listed further below, are invoked as follows: java jvm-args -jar picard.jar PicardToolName OPTION1=value1 OPTION2=value2... See the Tool Documentation for details on the Picard command syntax and standard options as well as a complete list of tools with usage recommendations, options, and example commands. Getting Help Picard is supported through the GATK Forums . Register now and you can ask questions and report problems that you might encounter while using Picard and related tools such as GATK (for source code-related questions, post an issue on Github instead), with the following guidelines: Before Asking For Help Before posting to the Forum, please do the following: Try the latest version of Picard . See if your problem is covered discussed in the Frequently Asked Questions . Search the GATK Forums to see if a similar problem has previously been discussed there. Run Picard ValidateSamFile with MODE=SUMMARY on your input SAM or BAM file (if applicable). Attempt to resolve or at least understand any problems reported. When Asking For Help When asking a question about a problem, please include the following: Command line(s) you ran Program console output and metrics files. Repetitive console output may be abbreviated Entire stack trace if one was produced Version of JVM you are using (obtained by running 'java -version') Additional Resources Detailed tool documentation Description of output of metrics programs SAM differences in Picard Explain SAM flags Explain Base Qualities Javadoc Full list of Picard tools AddCommentsToBam AddOrReplaceReadGroups BaitDesigner BamToBfq BamIndexStats BedToIntervalList BuildBamIndex CalculateReadGroupChecksum CleanSam CollectAlignmentSummaryMetrics CollectBaseDistributionByCycle CollectGcBiasMetrics CollectHiSeqXPfFailMetrics CollectHsMetrics CollectIlluminaBasecallingMetrics CollectIlluminaLaneMetrics CollectInsertSizeMetrics CollectJumpingLibraryMetrics CollectMultipleMetrics CollectOxoGMetrics CollectQualityYieldMetrics CollectRawWgsMetrics CollectTargetedPcrMetrics CollectRnaSeqMetrics CollectRrbsMetrics CollectSequencingArtifactMetrics CollectVariantCallingMetrics CollectWgsMetrics CollectWgsMetricsWithNonZeroCoverage CompareMetrics CompareSAMs ConvertSequencingArtifactToOxoG CreateSequenceDictionary DownsampleSam ExtractIlluminaBarcodes EstimateLibraryComplexity FastqToSam FifoBuffer FindMendelianViolations CrosscheckFingerprints ClusterCrosscheckMetrics CheckFingerprint FilterSamReads FilterVcf FixMateInformation GatherBamFiles GatherVcfs GenotypeConcordance IlluminaBasecallsToFastq IlluminaBasecallsToSam CheckIlluminaDirectory CheckTerminatorBlock IntervalListTools LiftOverIntervalList LiftoverVcf MakeSitesOnlyVcf MarkDuplicates MarkDuplicatesWithMateCigar MeanQualityByCycle MergeBamAlignment MergeSamFiles MergeVcfs NormalizeFasta PositionBasedDownsampleSam ExtractSequences QualityScoreDistribution RenameSampleInVcf ReorderSam ReplaceSamHeader RevertSam RevertOriginalBaseQualitiesAndAddMateCigar SamFormatConverter SamToFastq ScatterIntervalsByNs SetNmMdAndUqTags SortSam SortVcf SplitSamByLibrary UmiAwareMarkDuplicatesWithMateCigar UpdateVcfSequenceDictionary VcfFormatConverter MarkIlluminaAdapters SplitVcfs ValidateSamFile ViewSam VcfToIntervalList Project maintained by broadinstitute Hosted on GitHub Pages — Theme by orderedlist + +### https://github.com/broadinstitute/picard +GitHub - broadinstitute/picard: A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} broadinstitute / picard Public Notifications You must be signed in to change notification settings Fork 382 Star 1.1k Code Issues 214 Pull requests 24 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights broadinstitute/picard master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 3,072 Commits 3,072 Commits .github .github docs/ fingerprinting docs/ fingerprinting etc/ test etc/ test gradle/ wrapper gradle/ wrapper scripts/ travis scripts/ travis src src testdata/ picard testdata/ picard .dockerignore .dockerignore .gitattributes .gitattributes .gitignore .gitignore Dockerfile Dockerfile LICENSE.txt LICENSE.txt README.md README.md build.gradle build.gradle build.xml build.xml build_push_docker.sh build_push_docker.sh gradlew gradlew settings.gradle settings.gradle View all files Repository files navigation README Code of conduct MIT license User Support: For user questions please look for answers and ask first in the GATK forum . A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library HTSJDK to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM and VCF . As of version 3.0, Picard requires Java 1.17. Building Picard First, clone the repo: git clone https://github.com/broadinstitute/picard.git cd picard/ Picard is now built using gradle . A wrapper script ( gradlew ) is included which will download the appropriate version of gradle on the first invocation. To build a fully-packaged, runnable Picard jar with all dependencies included, run: ./gradlew shadowJar The resulting jar will be in build/libs . To run it, the command is: java -jar build/libs/picard.jar or java -jar build/libs/picard-<VERSION>-all.jar To build a jar containing only Picard classes (without its dependencies), run: ./gradlew jar To clean the build directory, run: ./gradlew clean Running Tests To run all tests, the command is: ./gradlew test To run a specific test, the command is: ./gradlew legacyTest --tests "*TestClassName*" or ./gradlew barclayTest --tests "*TestClassName*" Running legacyTest uses the legacy commandline parser while barclayTest uses the new parser. Changing the released version of HTSJDK that Picard depends on To switch Picard's HTSJDK dependency to a different released version: Open build.gradle Edit VERSION in the following line to be a different released version of HTSJDK. HTSJDK releases are listed here final htsjdkVersion = System.getProperty('htsjdk.version', 'VERSION')` Open a pull request with this change Building Picard with a Custom Version of HTSJDK During development in Picard, it is sometimes necessary to build locally against an unreleased version or branch of HTSJDK. To build against an unreleased version of HTSJDK's master branch: Go to the Broad artifactory , where continuous snapshots of HTSJDK's master branch are published, and select the version you want to use. For example, 2.5.1-9-g5740ca1-SNAPSHOT . You can search by tag or short git commit hash. In your Picard clone, run ./gradlew shadowJar -Dhtsjdk.version=VERSION , where VERSION is the version of the HTSJDK master branch snapshot you want to use. To build against a version of HTSJDK that has not yet been merged into HTSJDK's master branch: Clone HTSJDK , and in your clone check out the tag or branch you want to build Picard with. Run ./gradlew install printVersion in your htsjdk clone to install that version to your local maven repository. Take note of the version number that gets printed at the end. Switch back to your Picard clone, and run ./gradlew shadowJar -Dhtsjdk.version=VERSION , where VERSION is the version of HTSJDK you installed to your local maven repository. Releasing Picard Full instructions on how to create a new release of Picard are here Path providers Picard has limited support for reading from Path providers. Currently only google's api is supported, and only a few tools support this. To run with this support you need to compile the cloudJar target with gradle: ./gradlew cloudJar then run picard as follows: java -jar build/lib/picardcloud.jar < Picard arguments starting from program > For example: java -jar build/lib/picardcloud.jar CrosscheckFingerprints \ I=gs://sample1.vcf \ I=gs://sample2.vcf \ CROSSCHECK_BY=FILE \ H=Haplotype_db.txt \ O=crosscheck.out Alternatively, you can run the tool via the GATK which bundles the Google-Cloud jar, and should thus "Just Work". Citing Please cite this repository when using Picard tools for your publications. “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/ ; Broad Institute @misc{Picard2019toolkit, title = {Picard toolkit}, year = {2019}, publisher = {Broad Institute}, journal = {Broad Institute, GitHub repository}, howpublished = {\url{https://broadinstitute.github.io/picard/}} } Identifiers from software registries are increasingly accepted by journals, as in (biotools:picard_tools) or (RRID:SCR_006525). Picard is migrating to semantic versioning . We will eventually adhere to it strictly and bump our major version whenever there are breaking changes to our API, but until we more clearly define what constitutes our official API, clients should assume that every release potentially contains at least minor changes to public methods. Please see the Picard Documentation for more information. About A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. broadinstitute.github.io/picard/ Resources Readme License MIT license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1.1k stars Watchers 149 watching Forks 382 forks Report repository Releases 186 3.4.0 Latest Apr 13, 2025 + 185 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Java 98.5% R 0.4% XSLT 0.3% Python 0.3% HTML 0.2% Shell 0.2% Other 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge picard --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +picard 1.56 0 +------------- +file name : picard-1.56-0.tar.bz2 +name : picard +version : 1.56 +build : 0 +build number: 0 +size : 29.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.56-0.tar.bz2 +md5 : 21575134c20a72c932a7b212178c267a +dependencies: + - openjdk >=6 + + +picard 1.56 1 +------------- +file name : picard-1.56-1.tar.bz2 +name : picard +version : 1.56 +build : 1 +build number: 1 +size : 29.4 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-1.56-1.tar.bz2 +md5 : 60e68d1e1d6cfe579e8ca49c1c048b03 +timestamp : 2018-07-05 21:33:24 UTC +dependencies: + - openjdk >=6 + + +picard 1.97 0 +------------- +file name : picard-1.97-0.tar.bz2 +name : picard +version : 1.97 +build : 0 +build number: 0 +size : 42.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.97-0.tar.bz2 +md5 : 8f190d92b3c763813b692ff18af94900 +dependencies: + - java-jdk 6.* + + +picard 1.126 2 +-------------- +file name : picard-1.126-2.tar.bz2 +name : picard +version : 1.126 +build : 2 +build number: 2 +size : 6.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.126-2.tar.bz2 +md5 : b4b2b2cf8e1a2256680b765c8a734915 +dependencies: [] + + +picard 1.126 3 +-------------- +file name : picard-1.126-3.tar.bz2 +name : picard +version : 1.126 +build : 3 +build number: 3 +size : 6.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.126-3.tar.bz2 +md5 : fc69b876a33edbd4fa0508f87c6805a8 +dependencies: + - java-jdk + + +picard 1.126 4 +-------------- +file name : picard-1.126-4.tar.bz2 +name : picard +version : 1.126 +build : 4 +build number: 4 +size : 6.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.126-4.tar.bz2 +md5 : 0cbfd4bbf4b4d375455cbfdee095f0a2 +dependencies: + - java-jdk >=8 + + +picard 1.126 5 +-------------- +file name : picard-1.126-5.tar.bz2 +name : picard +version : 1.126 +build : 5 +build number: 5 +size : 6.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.126-5.tar.bz2 +md5 : 6712218c1ff11facde67e81ddc27a6e6 +timestamp : 2018-07-05 21:40:23 UTC +dependencies: + - java-jdk >=8 + + +picard 1.139 0 +-------------- +file name : picard-1.139-0.tar.bz2 +name : picard +version : 1.139 +build : 0 +build number: 0 +size : 4.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.139-0.tar.bz2 +md5 : fe1af5e5845b370102a5a125ff1653f1 +dependencies: [] + + +picard 1.141 0 +-------------- +file name : picard-1.141-0.tar.bz2 +name : picard +version : 1.141 +build : 0 +build number: 0 +size : 6.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.141-0.tar.bz2 +md5 : 9d55d5027aae591edcacf5fae404018a +dependencies: [] + + +picard 1.141 1 +-------------- +file name : picard-1.141-1.tar.bz2 +name : picard +version : 1.141 +build : 1 +build number: 1 +size : 6.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.141-1.tar.bz2 +md5 : 443a160ee90d5f88f6345ccd805f214f +dependencies: [] + + +picard 1.141 3 +-------------- +file name : picard-1.141-3.tar.bz2 +name : picard +version : 1.141 +build : 3 +build number: 3 +size : 6.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.141-3.tar.bz2 +md5 : 85065e36ebc1d881edced6e2dc03875f +dependencies: + - java-jdk + + +picard 1.141 4 +-------------- +file name : picard-1.141-4.tar.bz2 +name : picard +version : 1.141 +build : 4 +build number: 4 +size : 6.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-1.141-4.tar.bz2 +md5 : 5fd933c6d60146957f5eca1b2793fa01 +timestamp : 2018-07-05 21:29:31 UTC +dependencies: + - java-jdk + + +picard 1.141 5 +-------------- +file name : picard-1.141-5.tar.bz2 +name : picard +version : 1.141 +build : 5 +build number: 5 +size : 6.0 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-1.141-5.tar.bz2 +md5 : 038a116968e4cde51a03f2f291f0062c +timestamp : 2019-10-18 06:10:37 UTC +dependencies: + - openjdk >=8 + + +picard 1.141 hdfd78af_6 +----------------------- +file name : picard-1.141-hdfd78af_6.tar.bz2 +name : picard +version : 1.141 +build : hdfd78af_6 +build number: 6 +size : 6.0 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/picard-1.141-hdfd78af_6.tar.bz2 +md5 : ae2bc9f1c320495db3a73f8267898992 +timestamp : 2021-03-25 19:33:19 UTC +dependencies: + - openjdk >=8 + + +picard 2.0.1 0 +-------------- +file name : picard-2.0.1-0.tar.bz2 +name : picard +version : 2.0.1 +build : 0 +build number: 0 +size : 6.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.0.1-0.tar.bz2 +md5 : 6d70a605a3bc49deae57488c00db9359 +dependencies: + - java-jdk >=8 + + +picard 2.0.1 1 +-------------- +file name : picard-2.0.1-1.tar.bz2 +name : picard +version : 2.0.1 +build : 1 +build number: 1 +size : 6.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.0.1-1.tar.bz2 +md5 : 91bfabfd3e9fe1271b212226d3f338dd +timestamp : 2018-07-05 21:26:18 UTC +dependencies: + - java-jdk >=8 + + +picard 2.3.0 0 +-------------- +file name : picard-2.3.0-0.tar.bz2 +name : picard +version : 2.3.0 +build : 0 +build number: 0 +size : 6.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.3.0-0.tar.bz2 +md5 : 78920c8cb2f9c7fdc98d3c9689d1cef8 +dependencies: + - java-jdk >=8 + + +picard 2.5.0 0 +-------------- +file name : picard-2.5.0-0.tar.bz2 +name : picard +version : 2.5.0 +build : 0 +build number: 0 +size : 8.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.5.0-0.tar.bz2 +md5 : 4af76554ca75e32489715e554eaab4db +dependencies: + - java-jdk >=8 + + +picard 2.5.0 1 +-------------- +file name : picard-2.5.0-1.tar.bz2 +name : picard +version : 2.5.0 +build : 1 +build number: 1 +size : 8.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.5.0-1.tar.bz2 +md5 : 84300681fb9d3f5d5705f2ab1d944917 +dependencies: + - java-jdk >=8 + + +picard 2.5.0 2 +-------------- +file name : picard-2.5.0-2.tar.bz2 +name : picard +version : 2.5.0 +build : 2 +build number: 2 +size : 8.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.5.0-2.tar.bz2 +md5 : a63cbe74b8b941c918f8f89164258317 +timestamp : 2018-07-05 21:37:08 UTC +dependencies: + - java-jdk >=8 + + +picard 2.7.1 py27_0 +------------------- +file name : picard-2.7.1-py27_0.tar.bz2 +name : picard +version : 2.7.1 +build : py27_0 +build number: 0 +size : 26.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.7.1-py27_0.tar.bz2 +md5 : dfde4238cc97157bfb283169e673a896 +dependencies: + - java-jdk >=8 + - python 2.7* + + +picard 2.7.1 py27_1 +------------------- +file name : picard-2.7.1-py27_1.tar.bz2 +name : picard +version : 2.7.1 +build : py27_1 +build number: 1 +size : 26.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.7.1-py27_1.tar.bz2 +md5 : 2d8f95d9de3812dc0b8e39bab5bad6f4 +dependencies: + - java-jdk >=8 + - python 2.7* + + +picard 2.7.1 py27_2 +------------------- +file name : picard-2.7.1-py27_2.tar.bz2 +name : picard +version : 2.7.1 +build : py27_2 +build number: 2 +size : 26.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.7.1-py27_2.tar.bz2 +md5 : d6bad13397ee47a970eb0719ab95fc3e +dependencies: + - java-jdk >=8 + - python 2.7* + + +picard 2.7.1 py34_0 +------------------- +file name : picard-2.7.1-py34_0.tar.bz2 +name : picard +version : 2.7.1 +build : py34_0 +build number: 0 +size : 26.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.7.1-py34_0.tar.bz2 +md5 : b3365d562249fc0a3f9dcd2bbb2cab78 +dependencies: + - java-jdk >=8 + - python 3.4* + + +picard 2.7.1 py34_1 +------------------- +file name : picard-2.7.1-py34_1.tar.bz2 +name : picard +version : 2.7.1 +build : py34_1 +build number: 1 +size : 26.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.7.1-py34_1.tar.bz2 +md5 : f9e81c2fdcaf9ea92944e05b396c3db5 +dependencies: + - java-jdk >=8 + - python 3.4* + + +picard 2.7.1 py34_2 +------------------- +file name : picard-2.7.1-py34_2.tar.bz2 +name : picard +version : 2.7.1 +build : py34_2 +build number: 2 +size : 26.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.7.1-py34_2.tar.bz2 +md5 : 657bb3fe947c1f0eebae611abd7642bb +dependencies: + - java-jdk >=8 + - python 3.4* + + +picard 2.7.1 py35_0 +------------------- +file name : picard-2.7.1-py35_0.tar.bz2 +name : picard +version : 2.7.1 +build : py35_0 +build number: 0 +size : 26.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.7.1-py35_0.tar.bz2 +md5 : b4efd2ec5ba9d73c180b5016524573eb +dependencies: + - java-jdk >=8 + - python 3.5* + + +picard 2.7.1 py35_1 +------------------- +file name : picard-2.7.1-py35_1.tar.bz2 +name : picard +version : 2.7.1 +build : py35_1 +build number: 1 +size : 26.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.7.1-py35_1.tar.bz2 +md5 : 7cf78c1b7b403bbe5bb8939c492e776d +dependencies: + - java-jdk >=8 + - python 3.5* + + +picard 2.7.1 py35_2 +------------------- +file name : picard-2.7.1-py35_2.tar.bz2 +name : picard +version : 2.7.1 +build : py35_2 +build number: 2 +size : 26.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.7.1-py35_2.tar.bz2 +md5 : c4ca718dfcad2e94cddf8b16ee685a8d +dependencies: + - java-jdk >=8 + - python 3.5* + + +picard 2.7.1 py36_2 +------------------- +file name : picard-2.7.1-py36_2.tar.bz2 +name : picard +version : 2.7.1 +build : py36_2 +build number: 2 +size : 26.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/picard-2.7.1-py36_2.tar.bz2 +md5 : d4cdbcf8089019ade048aa27af198fb2 +dependencies: + - java-jdk >=8 + - python 3.6* + + +picard 2.9.0 py27_0 +------------------- +file name : picard-2.9.0-py27_0.tar.bz2 +name : picard +version : 2.9.0 +build : py27_0 +build number: 0 +size : 19.5 MB +license : MIT +subdir diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pilon.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pilon.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..04d3f3eefbaedf7c32539454b7ab1d8919a2b73d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pilon.manual_bundle.txt @@ -0,0 +1,461 @@ +# Tool: pilon +software_name: pilon +tier: T1 +domain: t1_backfill_overall +downloads: 133301 +summary: Pilon is an automated genome assembly improvement and variant detection tool. +description: Pilon is an automated genome assembly improvement and variant detection tool. +dependencies: openjdk, python +execution_environment: Java +execution_environment_reason: inferred from Java runtime dependencies + +## URLs +home_url: https://github.com/broadinstitute/pilon/ +doc_url: +dev_url: + +## CLI Help Source +java:-help +## CLI Help Content +$ conda run -n bioenv_java java -help +[rc=0] + +Usage: java [-options] class [args...] + (to execute a class) + or java [-options] -jar jarfile [args...] + (to execute a jar file) +where options include: + -d32 use a 32-bit data model if available + -d64 use a 64-bit data model if available + -server to select the "server" VM + The default VM is server, + because you are running on a server-class machine. + + + -cp + -classpath + A : separated list of directories, JAR archives, + and ZIP archives to search for class files. + -D= + set a system property + -verbose:[class|gc|jni] + enable verbose output + -version print product version and exit + -version: + Warning: this feature is deprecated and will be removed + in a future release. + require the specified version to run + -showversion print product version and continue + -jre-restrict-search | -no-jre-restrict-search + Warning: this feature is deprecated and will be removed + in a future release. + include/exclude user private JREs in the version search + -? -help print this help message + -X print help on non-standard options + -ea[:...|:] + -enableassertions[:...|:] + enable assertions with specified granularity + -da[:...|:] + -disableassertions[:...|:] + disable assertions with specified granularity + -esa | -enablesystemassertions + enable system assertions + -dsa | -disablesystemassertions + disable system assertions + -agentlib:[=] + load native agent library , e.g. -agentlib:hprof + see also, -agentlib:jdwp=help and -agentlib:hprof=help + -agentpath:[=] + load native agent library by full pathname + -javaagent:[=] + load Java programming language agent, see java.lang.instrument + -splash: + show splash screen with specified image +See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details. + + + +## URL Docs Extract +### https://github.com/broadinstitute/pilon/ +GitHub - broadinstitute/pilon: Pilon is an automated genome assembly improvement and variant detection tool · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} broadinstitute / pilon Public Notifications You must be signed in to change notification settings Fork 60 Star 380 Code Issues 83 Pull requests 3 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights broadinstitute/pilon master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 319 Commits 319 Commits .settings .settings project project src/ main/ scala/ org/ broadinstitute/ pilon src/ main/ scala/ org/ broadinstitute/ pilon .classpath .classpath .gitignore .gitignore .project .project COPYRIGHT COPYRIGHT LICENSE LICENSE README.md README.md build.sbt build.sbt build.sh build.sh View all files Repository files navigation README Code of conduct GPL-2.0 license Pilon For further information, please visit the Wiki About Pilon is an automated genome assembly improvement and variant detection tool Resources Readme License GPL-2.0 license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 380 stars Watchers 27 watching Forks 60 forks Report repository Releases 26 Pilon version 1.24 Latest Jan 28, 2021 + 25 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Scala 99.6% Shell 0.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge pilon --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +pilon 1.16 0 +------------ +file name : pilon-1.16-0.tar.bz2 +name : pilon +version : 1.16 +build : 0 +build number: 0 +size : 6.3 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.16-0.tar.bz2 +md5 : a36eced08403a090408b569e9d0e33d7 +dependencies: + - java-jdk + + +pilon 1.17 0 +------------ +file name : pilon-1.17-0.tar.bz2 +name : pilon +version : 1.17 +build : 0 +build number: 0 +size : 6.3 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.17-0.tar.bz2 +md5 : 5bc194dbb808959f6dffb2996faeb99e +dependencies: + - java-jdk + + +pilon 1.18 0 +------------ +file name : pilon-1.18-0.tar.bz2 +name : pilon +version : 1.18 +build : 0 +build number: 0 +size : 6.5 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.18-0.tar.bz2 +md5 : 4d1c2080b967b4619855032305edb1f7 +dependencies: + - java-jdk + + +pilon 1.19 py27_0 +----------------- +file name : pilon-1.19-py27_0.tar.bz2 +name : pilon +version : 1.19 +build : py27_0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.19-py27_0.tar.bz2 +md5 : 17097b7e999550218dd47780e86103ec +dependencies: + - java-jdk + - python 2.7* + + +pilon 1.19 py34_0 +----------------- +file name : pilon-1.19-py34_0.tar.bz2 +name : pilon +version : 1.19 +build : py34_0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.19-py34_0.tar.bz2 +md5 : 8f7f1255cd6b3551699f12b0c820a663 +dependencies: + - java-jdk + - python 3.4* + + +pilon 1.19 py35_0 +----------------- +file name : pilon-1.19-py35_0.tar.bz2 +name : pilon +version : 1.19 +build : py35_0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.19-py35_0.tar.bz2 +md5 : 2d42639c29aab4b8876c93131c66503c +dependencies: + - java-jdk + - python 3.5* + + +pilon 1.20 py27_0 +----------------- +file name : pilon-1.20-py27_0.tar.bz2 +name : pilon +version : 1.20 +build : py27_0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.20-py27_0.tar.bz2 +md5 : bba2c8ed6c9bc3f464bc3da91caf7915 +dependencies: + - java-jdk + - python 2.7* + + +pilon 1.20 py27_1 +----------------- +file name : pilon-1.20-py27_1.tar.bz2 +name : pilon +version : 1.20 +build : py27_1 +build number: 1 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.20-py27_1.tar.bz2 +md5 : c148238b0af3fadfc7687c9fc2583c4b +dependencies: + - java-jdk + - python 2.7* + + +pilon 1.20 py34_0 +----------------- +file name : pilon-1.20-py34_0.tar.bz2 +name : pilon +version : 1.20 +build : py34_0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.20-py34_0.tar.bz2 +md5 : 2c3303a7c4fcea5bcb15c6ecd5a0b6c4 +dependencies: + - java-jdk + - python 3.4* + + +pilon 1.20 py34_1 +----------------- +file name : pilon-1.20-py34_1.tar.bz2 +name : pilon +version : 1.20 +build : py34_1 +build number: 1 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.20-py34_1.tar.bz2 +md5 : 48e3a0d2322cf2c3a113f8d68e354d4d +dependencies: + - java-jdk + - python 3.4* + + +pilon 1.20 py35_0 +----------------- +file name : pilon-1.20-py35_0.tar.bz2 +name : pilon +version : 1.20 +build : py35_0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.20-py35_0.tar.bz2 +md5 : ba6c719810329f9410f58e3fbeef8570 +dependencies: + - java-jdk + - python 3.5* + + +pilon 1.20 py35_1 +----------------- +file name : pilon-1.20-py35_1.tar.bz2 +name : pilon +version : 1.20 +build : py35_1 +build number: 1 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.20-py35_1.tar.bz2 +md5 : 1f4384124a5ba4c38dfb8b22b1588655 +dependencies: + - java-jdk + - python 3.5* + + +pilon 1.22 1 +------------ +file name : pilon-1.22-1.tar.bz2 +name : pilon +version : 1.22 +build : 1 +build number: 1 +size : 6.6 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pilon-1.22-1.tar.bz2 +md5 : 4fa28141228fed38e0e36e463aef6b0c +timestamp : 2018-07-05 21:21:40 UTC +dependencies: + - openjdk + - python + + +pilon 1.22 py27_0 +----------------- +file name : pilon-1.22-py27_0.tar.bz2 +name : pilon +version : 1.22 +build : py27_0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.22-py27_0.tar.bz2 +md5 : a639ebe2299463abf4521f08414f3096 +dependencies: + - openjdk + - python 2.7* + + +pilon 1.22 py34_0 +----------------- +file name : pilon-1.22-py34_0.tar.bz2 +name : pilon +version : 1.22 +build : py34_0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.22-py34_0.tar.bz2 +md5 : e84b71d5c41b4d2b8d62570575b6b833 +dependencies: + - openjdk + - python 3.4* + + +pilon 1.22 py35_0 +----------------- +file name : pilon-1.22-py35_0.tar.bz2 +name : pilon +version : 1.22 +build : py35_0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.22-py35_0.tar.bz2 +md5 : 4359487cf81d360853853882a75022b8 +dependencies: + - openjdk + - python 3.5* + + +pilon 1.22 py36_0 +----------------- +file name : pilon-1.22-py36_0.tar.bz2 +name : pilon +version : 1.22 +build : py36_0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pilon-1.22-py36_0.tar.bz2 +md5 : 67b8afafd22852612129fd99d74b4337 +dependencies: + - openjdk + - python 3.6* + + +pilon 1.23 0 +------------ +file name : pilon-1.23-0.tar.bz2 +name : pilon +version : 1.23 +build : 0 +build number: 0 +size : 6.6 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pilon-1.23-0.tar.bz2 +md5 : 6e7130e343d8f024aeb2c4a62479af9c +timestamp : 2018-11-27 21:49:38 UTC +dependencies: + - openjdk + - python + + +pilon 1.23 1 +------------ +file name : pilon-1.23-1.tar.bz2 +name : pilon +version : 1.23 +build : 1 +build number: 1 +size : 6.6 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pilon-1.23-1.tar.bz2 +md5 : f5febf0925b391e239136236851c02d8 +timestamp : 2019-07-31 15:35:11 UTC +dependencies: + - openjdk + - python + + +pilon 1.23 2 +------------ +file name : pilon-1.23-2.tar.bz2 +name : pilon +version : 1.23 +build : 2 +build number: 2 +size : 6.6 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pilon-1.23-2.tar.bz2 +md5 : 966dc33966cc41293188423968f6d6d2 +timestamp : 2019-10-26 12:47:30 UTC +dependencies: + - openjdk + - python + + +pilon 1.23 hdfd78af_3 +--------------------- +file name : pilon-1.23-hdfd78af_3.tar.bz2 +name : pilon +version : 1.23 +build : hdfd78af_3 +build number: 3 +size : 6.6 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pilon-1.23-hdfd78af_3.tar.bz2 +md5 : c4df8c1dde3da1a80217955e94c51e2b +timestamp : 2021-03-25 00:02:53 UTC +dependencies: + - openjdk + - python + + +pilon 1.24 hdfd78af_0 +--------------------- +file name : pilon-1.24-hdfd78af_0.tar.bz2 +name : pilon +version : 1.24 +build : hdfd78af_0 +build number: 0 +size : 9.9 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/pilon-1.24-hdfd78af_0.tar.bz2 +md5 : 4eef0c771dd3f81effb0d21ba8bb6734 +timestamp : 2021-04-05 10:13:33 UTC +dependencies: + - openjdk + - python diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/plink.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/plink.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..eca787966b182532de627322fbfd320d894a609f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/plink.manual_bundle.txt @@ -0,0 +1,665 @@ +# Tool: plink +software_name: plink +tier: T1 +domain: t1_backfill_overall +downloads: 156704 +summary: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. +description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. +dependencies: libgcc-ng >=7.3.0, libgfortran-ng >=7,<8.0a0, libstdcxx-ng >=7.3.0, openblas >=0.3.6,<0.3.7.0a0, zlib >=1.2.11,<1.3.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://www.cog-genomics.org/plink +doc_url: +dev_url: + +## CLI Help Source +cli:plink +## CLI Help Content +$ conda run -n bioenv_cli plink --help +[rc=0] +PLINK v1.9.0-b.7.7 64-bit (22 Oct 2024) cog-genomics.org/plink/1.9/ +(C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3 + +In the command line flag definitions that follow, + * denote a required parameter, where the text between the + angle brackets describes its nature. + * ['square brackets + single-quotes'] denotes an optional modifier. Use the + EXACT text in the quotes. + * [{bar|separated|braced|bracketed|values}] denotes a collection of mutually + exclusive optional modifiers (again, the exact text must be used). When + there are no outer square brackets, one of the choices must be selected. + * ['quoted_text='] denotes an optional modifier that + must begin with the quoted text, and be followed by a value with no + whitespace in between. '|' may also be used here to indicate mutually + exclusive options. + * [square brackets without quotes or braces] denote an optional parameter, + where the text between the brackets describes its nature. + * An ellipsis (...) indicates that you may enter multiple parameters of the + specified type. + + plink [command flag(s)...] [other flag(s)...] + plink --help [flag name(s)...] + +Most PLINK runs require exactly one main input fileset. The following flags +are available for defining its form and location: + + --bfile [prefix] : Specify .bed + .bim + .fam prefix (default 'plink'). + --bed : Specify full name of .bed file. + --bim : Specify full name of .bim file. + --fam : Specify full name of .fam file. + + --keep-autoconv : With --file/--tfile/--lfile/--vcf/--bcf/--data/--23file, + don't delete autogenerated binary fileset at end of run. + + --file [prefix] : Specify .ped + .map filename prefix (default 'plink'). + --ped : Specify full name of .ped file. + --map : Specify full name of .map file. + + --no-fid : .fam/.ped file does not contain column 1 (family ID). + --no-parents : .fam/.ped file does not contain columns 3-4 (parents). + --no-sex : .fam/.ped file does not contain column 5 (sex). + --no-pheno : .fam/.ped file does not contain column 6 (phenotype). + + --tfile [prefix] : Specify .tped + .tfam filename prefix (default 'plink'). + --tped : Specify full name of .tped file. + --tfam : Specify full name of .tfam file. + + --lfile [prefix] : Specify .lgen + .map + .fam (long-format fileset) prefix. + --lgen : Specify full name of .lgen file. + --reference : Specify default allele file accompanying .lgen input. + --allele-count : When used with --lfile/--lgen + --reference, specifies + that the .lgen file contains reference allele counts. + + --vcf : Specify full name of .vcf or .vcf.gz file. + --bcf : Specify full name of BCF2 file. + + --data [prefix] : Specify Oxford .gen + .sample prefix (default 'plink'). + --gen : Specify full name of .gen or .gen.gz file. + --bgen ['snpid-chr'] : Specify full name of .bgen file. + --sample : Specify full name of .sample file. + + --23file [FID] [IID] [sex] [pheno] [pat. ID] [mat. ID] : + Specify 23andMe input file. + + --grm-gz [prfx] : Specify .grm.gz + .grm.id (GCTA rel. matrix) prefix. + --grm-bin [prfx] : Specify .grm.bin + .grm.N.bin + .grm.id (GCTA triangular + binary relationship matrix) filename prefix. + + --dummy [missing geno freq] [missing pheno freq] + [{acgt | 1234 | 12}] ['scalar-pheno'] + This generates a fake input dataset with the specified number of samples + and SNPs. By default, the missing genotype and phenotype frequencies are + zero, and genotypes are As and Bs (change the latter with + 'acgt'/'1234'/'12'). The 'scalar-pheno' modifier causes a normally + distributed scalar phenotype to be generated instead of a binary one. + + --simulate [{tags | haps}] [{acgt | 1234 | 12}] + --simulate-qt [{tags | haps}] [{acgt | 1234 | 12}] + --simulate generates a fake input dataset with disease-associated SNPs, + while --simulate-qt generates a dataset with quantitative trait loci. + +Output files have names of the form 'plink.' by default. You can +change the 'plink' prefix with + + --out : Specify prefix for output files. + +Most runs also require at least one of the following commands: + + --make-bed + Create a new binary fileset. Unlike the automatic text-to-binary + converters (which only heed chromosome filters), this supports all of + PLINK's filtering flags. + --make-just-bim + --make-just-fam + Variants of --make-bed which only write a new .bim or .fam file. Can be + used with only .bim/.fam input. + USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary + genotype data and your .bim/.fam indexes if you use these commands + improperly. If you have any doubt, stick with --make-bed. + + --recode [{01 | 12}] [{tab | tabx | spacex | bgz | gen-gz}] + ['include-alt'] ['omit-nonmale-y'] + Create a new text fileset with all filters applied. The following output + formats are supported: + * '23': 23andMe 4-column format. This can only be used on a single + sample's data (--keep may be handy), and does not support multicharacter + allele codes. + * 'A': Sample-major additive (0/1/2) coding, suitable for loading from R. + If you need uncounted alleles to be named in the header line, add the + 'include-alt' modifier. + * 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding. + Also supports 'include-alt'. + * 'A-transpose': Variant-major 0/1/2. + * 'beagle': Unphased per-autosome .dat and .map files, readable by early + BEAGLE versions. + * 'beagle-nomap': Single .beagle.dat file. + * 'bimbam': Regular BIMBAM format. + * 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file. Does not + support multiple chromosomes. + * 'fastphase': Per-chromosome fastPHASE files, with + .chr-.recode.phase.inp filename extensions. + * 'fastphase-1chr': Single .recode.phase.inp file. Does not support + multiple chromosomes. + * 'HV': Per-chromosome Haploview files, with .chr-{.ped,.info} + filename extensions. + * 'HV-1chr': Single Haploview .ped + .info file pair. Does not support + multiple chromosomes. + * 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile. + * 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile + + --reference. + * 'list': Single genotype-based list, up to 4 lines per variant. To omit + nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y' modifier. + * 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a + genotype-based list which omits the most common genotype for each + variant. Also supports 'omit-nonmale-y'. + * 'oxford': Oxford-format .gen + .sample. With the 'gen-gz' modifier, the + .gen file is gzipped. + * 'ped': PLINK 1 sample-major (.ped + .map), loadable with --file. + * 'compound-genotypes': Same as 'ped', except that the space between each + pair of same-variant allele codes is removed. + * 'structure': Structure-format. + * 'transpose': PLINK 1 variant-major (.tped + .tfam), loadable with + --tfile. + * 'vcf', 'vcf-fid', 'vcf-iid': VCFv4.2. 'vcf-fid' and 'vcf-iid' cause + family IDs or within-family IDs respectively to be used for the sample + IDs in the last header row, while 'vcf' merges both IDs and puts an + underscore between them. If the 'bgz' modifier is added, the VCF file is + block-gzipped. + The A2 allele is saved as the reference and normally flagged as not based + on a real reference genome (INFO:PR). When it is important for reference + alleles to be correct, you'll also want to include --a2-allele and + --real-ref-alleles in your command. + In addition, + * The '12' modifier causes A1 (usually minor) alleles to be coded as '1' + and A2 alleles to be coded as '2', while '01' maps A1 -> 0 and A2 -> 1. + * The 'tab' modifier makes the output mostly tab-delimited instead of + mostly space-delimited. 'tabx' and 'spacex' force all tabs and all + spaces, respectively. + + --flip-scan ['verbose'] + (alias: --flipscan) + LD-based scan for case/control strand inconsistency. + + --write-covar + If a --covar file is loaded, --make-bed/--make-just-fam and --recode + automatically generate an updated version (with all filters applied). + However, if you do not wish to simultaneously generate a new genotype file, + you can use --write-covar to just produce a pruned covariate file. + + --write-cluster ['omit-unassigned'] + If clusters are specified with --within/--family, this generates a new + cluster file (with all filters applied). The 'omit-unassigned' modifier + causes unclustered samples to be omitted from the file; otherwise their + cluster is 'NA'. + + --write-set + --set-table + If sets have been defined, --write-set dumps 'END'-terminated set + membership lists to .set, while --set-table writes a + variant-by-set membership table to .set.table. + + --merge <.ped filename> <.map filename> + --merge + --bmerge <.bed filename> <.bim filename> <.fam filename> + --bmerge + Merge the given fileset with the initially loaded fileset, writing the + result to .bed + .bim + .fam. (It is no longer necessary to + simultaneously specify --make-bed.) + --merge-list + Merge all filesets named in the text file with the reference fileset, if + one was specified. (However, this can also be used *without* a reference; + in that case, the newly created fileset is then treated as the reference by + most other PLINK operations.) The text file is interpreted as follows: + * If a line contains only one name, it is assumed to be the prefix for a + binary fileset. + * If a line contains exactly two names, they are assumed to be the full + filenames for a text fileset (.ped first, then .map). + * If a line contains exactly three names, they are assumed to be the full + filenames for a binary fileset (.bed, then .bim, then .fam). + + --write-snplist + --list-23-indels + --write-snplist writes a .snplist file listing the names of all variants + which pass the filters and inclusion thresholds you've specified, while + --list-23-indels writes the subset with 23andMe-style indel calls (D/I + allele codes). + + --list-duplicate-vars ['require-same-ref'] ['ids-only'] ['suppress-first'] + --list-duplicate-vars writes a .dupvar file describing all groups of + variants with matching positions and allele codes. + * By default, A1/A2 allele assignments are ignored; use 'require-same-ref' + to override this. + * Normally, the report contains position and allele codes. To remove them + (and produce a file directly usable with e.g. --extract/--exclude), use + 'ids-only'. Note that this command will fail in 'ids-only' mode if any + of the reported IDs are not unique. + * 'suppress-first' causes the first variant ID in each group to be omitted + from the report. + + --freq [{counts | case-control}] ['gz'] + --freqx ['gz'] + --freq generates a basic allele frequency (or count, if the 'counts' + modifier is present) report. This can be combined with --within/--family + to produce a cluster-stratified allele frequency/count report instead, or + the 'case-control' modifier to report case and control allele frequencies + separately. + --freqx generates a more detailed genotype count report, designed for use + with --read-freq. + + --missing ['gz'] + Generate sample- and variant-based missing data reports. If clusters are + + +## URL Docs Extract +### https://www.cog-genomics.org/plink +PLINK 1.9 This website does not support Internet Explorer 6. Please upgrade to a newer version of IE, or a different browser. PLINK 1.9 home plink2-users ... GitHub ... File formats ... PLINK 1.9 index ... PLINK 2.0  >> Introduction, downloads S: 19 Aug 2025 (b.7.11) D: 19 Aug 2025 Recent version history What's new? Future development Limitations Note to testers [Jump to search box] General usage Getting started Citation instructions Standard data input PLINK 1 binary (.bed) Autoconversion behavior PLINK text (.ped, .tped...) VCF (.vcf[.gz], .bcf) Oxford (.gen[.gz], .bgen) 23andMe text Generate random Unusual chromosome IDs Recombination map Allele frequencies Phenotypes Covariates Clusters of samples Variant sets Binary distance matrix IBD report (.genome) Input filtering Sample ID file Variant ID file Positional ranges file Cluster membership Set membership Attribute-based Chromosomes SNPs only Simple variant window Multiple variant ranges Sample/variant thinning Covariates (--filter) Missing genotypes Missing phenotypes Minor allele frequencies Hardy-Weinberg Mendel errors Quality scores Relationships Main functions Data management --make-bed --recode --output-chr --zero-cluster --split-x/--merge-x --set-me-missing --fill-missing-a2 --set-missing-var-ids --update-map... --update-ids... --flip --flip-scan --keep-allele-order... --indiv-sort --write-covar... --[b]merge... Merge failures VCF reference merge --merge-list --write-snplist --list-duplicate-vars Basic statistics --freq[x] --missing --test-mishap --hardy --mendel --het/--ibc --check-sex/--impute-sex --fst Linkage disequilibrium --indep... --r/--r2 --show-tags --blocks Distance matrices Identity-by-state/Hamming   (--distance...) Relationship/covariance   (--make-grm-bin...) --rel-cutoff Distance-pheno. analysis   (--ibs-test...) Identity-by-descent --genome --homozyg... Population stratification --cluster --pca --mds-plot --neighbour Association analysis Basic case/control   (--assoc, --model) Stratified case/control   (--mh, --mh2, --homog) Quantitative trait   (--assoc, --gxe) Regression w/ covariates   (--linear, --logistic) --dosage --lasso --test-missing Monte Carlo permutation Set-based tests REML additive heritability Family-based association --tdt --dfam --qfam... --tucc Report postprocessing --annotate --clump --gene-report --meta-analysis Epistasis --fast-epistasis --epistasis --twolocus Allelic scoring (--score) R plugins (--R) Secondary input Copy number (.cnv, .gvar) --> GCTA matrix (.grm.bin...) Secondary functions Copy number analysis --cnv-del/--cnv-dup --cnv-kb... --cnv-intersect... --cnv-overlap... --cnv-freq-exclude-above... --cnv-write --cnv-indiv-perm --cnv-test[-region] --cnv-enrichment-test --> Distributed computation Command-line help Miscellaneous Tabs vs. spaces Flag/parameter reuse System resource usage Pseudorandom numbers Resources 1000 Genomes Teaching materials Gene range lists Functional SNP attributes PLINK 1.0 PDF copy Errors and warnings Output file list Order of operations For developers GitHub repository Compilation Core algorithms Partial sum lookup Bit population count Ternary dot product Vertical population count Exact statistical tests Multithreaded gzip Adding new functionality Discussion forums plink2-users Credits File formats Quick index search PLINK 1.9 beta PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. PLINK 1.9 is a comprehensive update to the original version developed by Shaun Purcell . It was developed by Christopher Chang with support from the NIH-NIDDK 's Laboratory of Biological Modeling, the Purcell Lab , and others. ( What's new? ) ( Credits. ) ( Methods paper. ) (Usage questions should be sent to the plink2-users Google group , not Christopher's email.) Binary downloads Build Operating system 1 Stable (beta 7.11, 19 Aug 2025) Development (19 Aug 2025)   Old 2 (v1.07)   Linux 64-bit download download download Linux 32-bit download download download macOS (64-bit) download download download (32-bit) Windows 64-bit download download download Windows 32-bit download download 1: Solaris is no longer explicitly supported, but it should be able to run the Linux binaries. 2: These are just mirrors of the binaries posted at https://zzz.bwh.harvard.edu/plink/download.shtml . Source code, compilation instructions, and the like are on the developer page . The following documented PLINK 1.07 flags are not supported by 1.9.0 beta 7: --qual-geno-scores 3 --segment 4 --p2 , --genedrop --hap, --hap-window, --hap-snps 5 --proxy-assoc, --proxy-impute 5 --cnv-list, --cfile, --gfile --id-dict, --id-match 6 --compress, --decompress 7 Continue using PLINK 1.07 for most of these operations. However, be aware that red flags will not be supported by the final 1.9.0 release. We recommend migrating away from PLINK 1 here, but if that's not practical, keep a permanent copy of the PLINK 1.07 binary around and modify the relevant lines of your scripts to explicitly refer to it. --> green flags are supported by the latest development build. You're more than welcome to try the new implementations; just make sure to check some of your results against PLINK 1.07 if you do so. red flags will not be supported by the final 1.9.0 release. We recommend migrating away from PLINK 1 here, but if that's not practical, keep a permanent copy of the PLINK 1.07 binary around and modify the relevant lines of your scripts to explicitly refer to it. 3: We believe this now has almost no practical value, since the file format it expects is too different from VCF. 4: This was not fully developed in PLINK 1.07, and has been superseded by other IBD analysis packages. 5: PLINK's haplotype phasing and imputation algorithms are obsolete. Future PLINK versions will be able to import phase and dosage information emitted by other programs; the haplotype association commands will be reintroduced when that functionality is in place. Until then, BEAGLE 3.3 should be more accurate than PLINK for case/control haplotype association. 6: Free database software handles these operations in a more flexible and powerful manner. 7: Just use gzip / gunzip for this. Or better, pigz / unpigz . Recent version history 19 Aug 2025: --chr-set no-x/no-y/no-xy modifiers should now work as documented (i.e. PLINK now consistently errors out when encountering the forbidden chromosome). 6 Aug: --me-exclude-one should now work properly. 31 Jul: Fixed " --me var-first" bug that could result in overcounting of trio Mendel errors. 15 Jun 2025: Fixed --cm-map bug that could occur with a nonstandard 4-column input file. These Linux binaries were built with a newer glibc version (2.31 for 64-bit, 2.28 for 32-bit) than earlier precompiled Linux binaries, so if you are using a >5 year old Linux kernel, you may encounter a "Kernel too old" error. You will need to either compile from source or used older precompiled binaries (e.g. replace the datestamp in the download URL with "20241022") to run PLINK 1.9 in this case. 22 Oct 2024: Fixed VCF-export bug (extra null character in header line) in 11 and 13 Oct builds. 13 Oct: --annotate subset= and --gene-subset should work properly now. 11 Oct: Fixed --r[2] dprime bug that affected runs covering both chrX/chrY and autosomal data. Main part of version string has been reformatted to adhere to Semantic Versioning 2.0.0 spec . 18 Aug: --r[2] now explicitly reports active filters when generating tabular output. 4 Aug 2024: .ped and .map lines starting with '#' are now consistently treated as comments, following hint #2 in the original PED documentation . We have updated the respective PLINK 1.9 and 2.0 "File formats" entries, and apologize for overlooking this earlier. 11 Dec 2023: --ld-window-cm should work properly now. 18 Oct: Fixed --clump bug that, when multiple input files were provided, could cause it to fail to open the first file. 16 Jan 2023 (beta 7): .bim reader now defaults to treating '.' as a missing allele code; without this, merge could fail with a spurious "variants with 3+ alleles present" error when given .bim files generated by PLINK 2.0 that didn't have all allele codes filled in. This can be controlled with the --missing-genotype2 flag. 10 Dec 2022: --r/--r2 triangle + --parallel bugfix. 2 Apr: --make-set and similar flags no longer error out when --allow-extra-chr is specified and a contig is present in its input file but absent from the main dataset. 5 Mar 2022: --recode recognizes 'Av' and 'tped' as aliases for the 'A-transpose' and 'transpose' formats, respectively. --pedmap is now recognized as an alias for --file. 6 Jun 2021: --clump results should now be consistent across operating systems. (Previously, minor variations were possible when there were p-value ties.) 28 May: Genotyping rate is explicitly logged when equal to, or very close to, 1. These two cases are distinguished ("in [0.9999995, 1)" vs. "exactly 1"). 16 Apr 2021: --data/--gen now supports .gen files with 6 leading columns. 19 Oct 2020: Linux binaries no longer default to allowing Intel MKL to use processor-specific code paths, since this behavior made some results more difficult to reproduce across different machines. (This may make some commands a bit slower. You can remove this restriction with --native .) 21 Sep: Fixed --logistic bug that could cause the entire analysis to be skipped with an inaccurate "Skipping --linear/--logistic since phenotype is constant" warning. 16 Sep: Fixed --qfam bug that occurred when a variant filter (--extract, --maf, etc.) was applied simultaneously, and the remaining variant set was not contiguous (so if your only variant filter was --chr on a single chromosome, this bug did not trigger). The bug was pretty obvious if you were affected by it (the .within and .within.perm output files had mismatched variant IDs), but if you're unsure you should rerun --qfam with the latest build. 16 Jun: Fixed --het bug that caused the wrong variants to be skipped when chrM was present but not at the end of the file. 28 Apr: Fixed --allow-extra-chr + --autosome-num/--cow/... segfault that could occur when the chromosome-set flag prohibited X/Y/XY/MT but that chromosome code was in the dataset anyway; an appropriate error message is now printed instead. --ld-window-r2 can now be used with --r. 19 Feb: --bcf now parses header line IDX fields; previously, if e.g. a FILTER key and an INFO key were identical in a BCFv2.2 file, --bcf may have computed the wrong string index for FORMAT:GT, in which case import would fail. 21 Jan: "--extract range" and "--exclude range" no longer error out when their input files contain a chromosome code absent from the current dataset. 7 Jan 2020: Fixed --meta-analysis-se-field bug. --meta-analysis-chr-field and --meta-analysis-bp-field flags added. In the development build, --dfam consistently errors out with an appropriate message, instead of possibly segfaulting, when no valid cases are present. 30 Nov 2019: "--recode rlist" no longer forgets to generate a .map file. 28 Oct: --meta-analysis-se-field flag added, for interoperation with recent PLINK 2.0 logistic regression output (which uses a 'LOG(OR)_SE' field name to disambiguate the standard error's units). (more...) 24 Oct: Fixed uninitialized-variable bug in --dosage + --q-score-range. "--indep-pairwise 500kb ..." works properly again (the previous build required a space before the 'kb'). 17 Jun: --loop-assoc now works properly when the original .fam file has missing phenotype values. 4 Mar: Brackets in command-line help text are now used in a manner more similar to other tools. --tests now works properly when a numeric argument is 1 past the end. 15 Feb 2019: Logistic regression no longer reports intercept beta values when it's supposed to report odds ratios. Scientific notation can now be used for command-line integer parameters. 2 Dec 2018: --set bugfix. 10 Oct: Fixed --tdt parent-of-origin-analysis handling of chrX. 13 Sep: Improved logistic regression convergence-failure detection (affects case/control --epistasis as well as --logistic). Fixed --R memory leak. 7 Aug: --assoc set-test bugfix. 17 Jul: Fixed uninitialized --make-set-border value bug. 12 Jun: "--assoc fisher"'s multiple testing corrections no longer treat zero-MAF variants as valid tests. 28 May: Fixed --file triallelic-variant handling bug which occurred when the .map was unsorted. 26 May (beta 6): --merge-equal-pos bugfixes. If you used --merge-equal-pos with .bed+.bim+.fam filesets where allele order may have differed between .bim files, or with any .ped+.map fileset at all, we recommend redoing that run. 10 Apr: --zero-cluster command-line parsing bugfix. --mendel-multigen bugfix. 21 Feb: "--indiv-sort file" no longer scrambles the phenotypes when used with --[b]merge or --merge-list. 9 Jan 2018: --all-pheno no longer gets into an infinite loop when one phenotype is all-missing. 20 Dec 2017: --meta-analysis 'report-all' now reports original stats instead of 'NA' when N=1. Fixed an inaccuracy in --adjust's handling of very small p-values. --make-just-fam works properly with just .fam input again. 14 Nov (beta 5): --file + --merge[-list] bugfix. This bug was much more likely to trigger if the first .map file was unsorted, but if you have the chance we recommend redoing any --file + --merge and --file + --merge-list multi-.ped merges performed with earlier plink 1.9 builds. (.bed merging was unaffected, and --merge-list without --file was practically never affected.) 3 Nov: --meta-analysis-snp-field and --meta-analysis-ess-field bugfixes. 15 Oct: A2 allele is now consistently reference on chr3 in our 1000 Genomes phase 1 downloads . As a general rule, you shouldn't expect to keep REF/ALT alleles straight with PLINK 1.x, but we tried to make A2 consistently reference in these files and still didn't quite succeed; sorry about that. (Why was this discovered now, more than 2.5 years after the fact? Because PLINK 2.0 now has a --ref-from-fa flag which can easily check for this type of error.) 13 Oct: "--freq counts" no longer gives reversed results when alleles have been flipped from the initial .bim/.bed order. Fixed --logistic bug that could cause spurious NA results. 12 Oct: --snps/--exclude-snps no longer always includes other variants at the same positions as the variant(s) you named. 7 Oct: Fixed corner-case (two of the four haplotypes have no known observations) bug in --ld/--r2/--blocks/--clump's statistical phasing procedure. 32-bit build can now sort >2GB .bed files without crashing. --annotate and --gene-report now work with --allow-extra-chr. 15 Aug: --lasso should now work properly when there are samples with all covariates present but the main phenotype missing. 25 Jul: --lfile now works properly when the .map file has three columns. 21 May: "--linear interaction sex" and "--logistic interaction sex" now work properly when no covariates are present. --tucc added to development build. 9 May: --tests now works properly on MT and haploid chromosomes. Improved --score compatibility with v1.07 and v2.0. 7 May: --r/--r2 + variant filter bugfix. 30 March: --ld-snps bugfix. 20 March (beta 4): --pca var-wts now reports allele codes. Minor statistical phasing bugfix. --[max-]mac, --R, and --thin-indiv[-count] no longer classified as unstable. PLINK 2.0 alpha builds are now available. 13 February: --R now works properly with missing covariate entries. --epistasis + variant filter bugfix. 13 January 2017: --ld-snps now works properly with other variant filters. --set-mixed-mt-missing flag added. 17 November 2016: chrX and chrY are no longer mishandled with --chr-set. 13 November: --geno/--missing now treat heterozygous haploid calls as nonmissing; this is consistent with --mind, and PLINK 1.07's behavior with --recode/--make-bed active. They're now inconsistent with what PLINK 1.07 did without --recode/--make-bed ; use --make-bed + --set-hh-missing first if you want the old behavior. "--ci 0.95" no longer produces 'L94'/'U94' column names when plink gets unlucky with rounding. Minor --exclude/--extract/--flip bugfix for input files with no newline at the end. --qfam[-within] bugfix. --dosage 'sex' modifier now works properly when some samples have been filtered out (e.g. because some phenotypes were missing). 20 September: VCF export no longer erases an alt allele absent from the immediate dataset, due to a retroactive revision to the VCF specification . Fixed "--model gen" permutation testing bug. 10 September: --remove-cluster-names + --family bugfix. --indep-pairwise/--indep-pairphase consistency improvements (MAF comparison now takes floating point imprecision into account; a few pairwise comparisons are no longer improperly skipped when the window is kb-based). 16 August: --merge-x 'no-fail' modifier works properly again. "--hard-call-threshold random" bugfix for probabilities with less than 4-digit precision. 5 August: --silent Windows bugfix. --r/--r2 'd' and 'dprime-signed' modes added. --ld-window-cm flag added. --output-missing-genotype now works properly with --make-bed. --genome + --read-freq bugfix. 7 June: --23file X/Y/MT chromosome conversion bugfix. --pheno bugfix (if phenotype was quantitative, but first value was nonnumeric, it was treated as '0' instead of missing in recent builds). 16 May: Set test bugfix. "--R debug" bugfix. 31 March: "--split-x b38" now works properly. 32-bit set-test bugfix. --cluster + --within bugfix. 25 March: --recode beagle bugfix. --gene bugfix. "--vcf-half-call reference" mode added. 15 March: Fixed --update-alleles bug introduced in 24 Feb build. 13 March: Fixed .lgen loading bug introduced in 24 Feb build. Fixed use-after-free bug in extra chromosome name cleanup code. --allow-no-{samples,vars,covars} added to stable build. 24 February: Contig limit raised to ~65000. --annotate/--gene-report bugfix for 3-4 column case. --flip-scan bugfix. 3 February: Number-to-string encoding bugfix (occasionally affected numbers ≥ 10 6 saved in the .bim centimorgan column). 27 January 2016: Speed improvement for operating on a subset of samples. Fix minor --1 backward compatibility break. 24 December 2015: Fix --dosage + --extract/--exclude bug introduced in 4 November build. Minor --test-missing permutation bugfix. --vcf-min-qual bugfix for .bcf files. 16 December: "--meta-analysis + study qt" now reports regression betas instead of odds ratios in the study-specific columns. "--score header" no longer forgets to append .nopred to the problem list filename. 13 December: --allow-no-samples and --allow-no-vars flags added. --dosage now suppresses regression results for very-low-MAF variants in the same same manner as it does in PLINK 1.07. --lgen flag now supported. --gxe works properly again (it was inadvertently disabled a few months ago). --hardy now produces 'nan' results for chrY/chrM variants (like PLINK 1.07) instead of entirely omitting them. --hwe "observation counts" warning is no longer triggered by chrY variants, and is now more informative when only triggered by chrX variants. 26 November: --logistic can now report intercepts. --logistic adaptive permutation bugfix. If you used adaptive permutation with --logistic in the past, we recommend that you redo the run with the latest build. 22 November: --indep{,-pairwise,-pairphase} kb-based windows now work properly with sample/variant filters. Several --indep-pairphase bugfixes. --all-pheno no longer causes exit code 127 to be returned on successful runs. --recode-allele segfault bugfix. --meta-analysis now only considers the first appearance when a variant appears multiple times in the same file. --no-const-covar and --meta-analysis-report-dups flags added. 4 November: Fixed "--r[2] square0" bug which occasionally caused a line break to be missing in the middle of the output file. Fixed --genome + --parallel missing- + +## Conda Search Info +$ conda search -c bioconda -c conda-forge plink --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +plink 1.9.0b.7.7 h7b50bb2_0 +--------------------------- +file name : plink-1.9.0b.7.7-h7b50bb2_0.tar.bz2 +name : plink +version : 1.9.0b.7.7 +build : h7b50bb2_0 +build number: 0 +size : 6.9 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.9.0b.7.7-h7b50bb2_0.tar.bz2 +md5 : 07a045bbba3b77e59f05a9602ec8c151 +timestamp : 2025-02-22 21:53:20 UTC +dependencies: + - libgcc >=13 + + +plink 1.90b4 0 +-------------- +file name : plink-1.90b4-0.tar.bz2 +name : plink +version : 1.90b4 +build : 0 +build number: 0 +size : 947 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b4-0.tar.bz2 +md5 : 84241b8c60973d68c84f30c9037f3f63 +dependencies: + - libgcc + - openblas + - zlib + + +plink 1.90b4 1 +-------------- +file name : plink-1.90b4-1.tar.bz2 +name : plink +version : 1.90b4 +build : 1 +build number: 1 +size : 948 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b4-1.tar.bz2 +md5 : e2bcbbe127933477939828750446db6d +dependencies: + - libgcc + - openblas + - zlib 1.2.11* + + +plink 1.90b4 h0a6d026_2 +----------------------- +file name : plink-1.90b4-h0a6d026_2.tar.bz2 +name : plink +version : 1.90b4 +build : h0a6d026_2 +build number: 2 +size : 945 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b4-h0a6d026_2.tar.bz2 +md5 : 4140f78ce0d800e06f20b648c1e02509 +timestamp : 2018-07-15 21:58:25 UTC +dependencies: + - libstdcxx-ng >=4.9 + - openblas >=0.2.20,<0.2.21.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +plink 1.90b4 h5b829b9_3 +----------------------- +file name : plink-1.90b4-h5b829b9_3.tar.bz2 +name : plink +version : 1.90b4 +build : h5b829b9_3 +build number: 3 +size : 948 KB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b4-h5b829b9_3.tar.bz2 +md5 : c7477584a7422d801e2541f2eef71b59 +timestamp : 2019-03-13 17:19:21 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.3,<0.3.4.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +plink 1.90b5 heea4ae3_0 +----------------------- +file name : plink-1.90b5-heea4ae3_0.tar.bz2 +name : plink +version : 1.90b5 +build : heea4ae3_0 +build number: 0 +size : 4.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b5-heea4ae3_0.tar.bz2 +md5 : e13daed2ead6270f2c93feebbdc7cbf7 +timestamp : 2019-10-25 20:20:39 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.6,<0.3.7.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +plink 1.90b5 heea4ae3_1 +----------------------- +file name : plink-1.90b5-heea4ae3_1.tar.bz2 +name : plink +version : 1.90b5 +build : heea4ae3_1 +build number: 1 +size : 4.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b5-heea4ae3_1.tar.bz2 +md5 : fee07de4487b2d9b9016e3ef4c8ae15e +timestamp : 2019-10-28 10:58:56 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.6,<0.3.7.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +plink 1.90b6.12 h47f1b9f_2 +-------------------------- +file name : plink-1.90b6.12-h47f1b9f_2.tar.bz2 +name : plink +version : 1.90b6.12 +build : h47f1b9f_2 +build number: 2 +size : 911 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.12-h47f1b9f_2.tar.bz2 +md5 : 0bacbe56ed71ac71d36fe1d7027b3516 +timestamp : 2020-08-31 10:27:17 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.5.0 + - openblas + - zlib >=1.2.11,<1.3.0a0 + + +plink 1.90b6.12 heea4ae3_0 +-------------------------- +file name : plink-1.90b6.12-heea4ae3_0.tar.bz2 +name : plink +version : 1.90b6.12 +build : heea4ae3_0 +build number: 0 +size : 4.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.12-heea4ae3_0.tar.bz2 +md5 : 37673c7caef46cbc023f8fccb3ed9ca9 +timestamp : 2019-11-19 16:13:03 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.6,<0.3.7.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +plink 1.90b6.12 heea4ae3_1 +-------------------------- +file name : plink-1.90b6.12-heea4ae3_1.tar.bz2 +name : plink +version : 1.90b6.12 +build : heea4ae3_1 +build number: 1 +size : 4.3 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.12-heea4ae3_1.tar.bz2 +md5 : 4b90c524e8b0d6852ed9d7e37ff38d45 +timestamp : 2020-05-16 12:29:41 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.5.0 + - openblas >=0.3.6,<0.3.7.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +plink 1.90b6.18 h516909a_0 +-------------------------- +file name : plink-1.90b6.18-h516909a_0.tar.bz2 +name : plink +version : 1.90b6.18 +build : h516909a_0 +build number: 0 +size : 6.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.18-h516909a_0.tar.bz2 +md5 : 944b37170702c59c4a1211542b8bbc80 +timestamp : 2020-09-10 19:59:01 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +plink 1.90b6.18 h779adbc_1 +-------------------------- +file name : plink-1.90b6.18-h779adbc_1.tar.bz2 +name : plink +version : 1.90b6.18 +build : h779adbc_1 +build number: 1 +size : 6.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.18-h779adbc_1.tar.bz2 +md5 : ef7f4542c0ac5697016b4b6b80bd89dd +timestamp : 2021-03-27 13:38:07 UTC +dependencies: + - libgcc-ng >=9.3.0 + + +plink 1.90b6.21 h031d066_5 +-------------------------- +file name : plink-1.90b6.21-h031d066_5.tar.bz2 +name : plink +version : 1.90b6.21 +build : h031d066_5 +build number: 5 +size : 6.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.21-h031d066_5.tar.bz2 +md5 : 289460cbdaed264df10a936dc45de3e9 +timestamp : 2023-05-16 01:26:31 UTC +dependencies: + - libgcc-ng >=12 + + +plink 1.90b6.21 h516909a_0 +-------------------------- +file name : plink-1.90b6.21-h516909a_0.tar.bz2 +name : plink +version : 1.90b6.21 +build : h516909a_0 +build number: 0 +size : 6.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.21-h516909a_0.tar.bz2 +md5 : de636b310feaa8a33f0cca25e64cd90b +timestamp : 2021-03-24 19:57:46 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +plink 1.90b6.21 h779adbc_1 +-------------------------- +file name : plink-1.90b6.21-h779adbc_1.tar.bz2 +name : plink +version : 1.90b6.21 +build : h779adbc_1 +build number: 1 +size : 6.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.21-h779adbc_1.tar.bz2 +md5 : af30e3779c71245c1ff88e37324487fb +timestamp : 2021-04-01 00:04:18 UTC +dependencies: + - libgcc-ng >=9.3.0 + + +plink 1.90b6.21 h7b50bb2_6 +-------------------------- +file name : plink-1.90b6.21-h7b50bb2_6.tar.bz2 +name : plink +version : 1.90b6.21 +build : h7b50bb2_6 +build number: 6 +size : 6.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.21-h7b50bb2_6.tar.bz2 +md5 : e1de9767214f3cb355fcfba9ad4e610a +timestamp : 2024-12-11 16:37:25 UTC +dependencies: + - libgcc >=13 + + +plink 1.90b6.21 h7b50bb2_7 +-------------------------- +file name : plink-1.90b6.21-h7b50bb2_7.tar.bz2 +name : plink +version : 1.90b6.21 +build : h7b50bb2_7 +build number: 7 +size : 6.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.21-h7b50bb2_7.tar.bz2 +md5 : 2d5b79387aa060e838078e034fbb6849 +timestamp : 2025-02-21 10:05:05 UTC +dependencies: + - libgcc >=13 + + +plink 1.90b6.21 hec16e2b_2 +-------------------------- +file name : plink-1.90b6.21-hec16e2b_2.tar.bz2 +name : plink +version : 1.90b6.21 +build : hec16e2b_2 +build number: 2 +size : 6.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.21-hec16e2b_2.tar.bz2 +md5 : b9f4562ba5cd3e337c89f6d236a5d18f +timestamp : 2022-02-22 00:07:44 UTC +dependencies: + - libgcc-ng >=10.3.0 + + +plink 1.90b6.21 hec16e2b_3 +-------------------------- +file name : plink-1.90b6.21-hec16e2b_3.tar.bz2 +name : plink +version : 1.90b6.21 +build : hec16e2b_3 +build number: 3 +size : 6.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.21-hec16e2b_3.tar.bz2 +md5 : 280afab84ddafdabe65f3d2887970355 +timestamp : 2023-03-06 17:00:49 UTC +dependencies: + - libgcc-ng >=12 + + +plink 1.90b6.21 hec16e2b_4 +-------------------------- +file name : plink-1.90b6.21-hec16e2b_4.tar.bz2 +name : plink +version : 1.90b6.21 +build : hec16e2b_4 +build number: 4 +size : 6.8 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b6.21-hec16e2b_4.tar.bz2 +md5 : 7faa4c9c990d3e5b3855453473797e67 +timestamp : 2023-05-11 14:12:44 UTC +dependencies: + - libgcc-ng >=12 + + +plink 1.90b7.7 h18e278d_1 +------------------------- +file name : plink-1.90b7.7-h18e278d_1.tar.bz2 +name : plink +version : 1.90b7.7 +build : h18e278d_1 +build number: 1 +size : 941 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b7.7-h18e278d_1.tar.bz2 +md5 : 1ab1ae7b594fcb5b98cd1a5b96137aa8 +timestamp : 2025-03-18 11:44:30 UTC +dependencies: + - libgcc >=13 + - libopenblas + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + + +plink 1.90b7.7 h7b50bb2_0 +------------------------- +file name : plink-1.90b7.7-h7b50bb2_0.tar.bz2 +name : plink +version : 1.90b7.7 +build : h7b50bb2_0 +build number: 0 +size : 6.9 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/plink-1.90b7.7-h7b50bb2_0.tar.bz2 +md5 : 2f380a683699ee7c2c1f234f5746b81f +timestamp : 2025-03-04 19:42:39 UTC +dependencies: + - libgcc >=13 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pplacer.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pplacer.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..a3ce4fef2f181b517723e4af177fa6f93e20a4f5 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pplacer.manual_bundle.txt @@ -0,0 +1,199 @@ +# Tool: pplacer +software_name: pplacer +tier: T1 +domain: t1_backfill_overall +downloads: 116692 +summary: Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. +description: Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. +dependencies: gsl >=2.8,<2.9.0a0, libgcc >=13, libsqlite >=3.51.2,<4.0a0, libzlib >=1.3.1,<2.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://matsen.fredhutch.org/pplacer/ +doc_url: +dev_url: https://github.com/matsen/pplacer/ + +## CLI Help Source +cli:pplacer +## CLI Help Content +$ conda run -n bioenv_cli pplacer --help +[rc=0] +pplacer [options] [alignment] + -c Specify the path to the reference package. + -t Specify the reference tree filename. + -r Specify the reference alignment filename. + -s Supply a phyml stats.txt or a RAxML info file giving the model parameters. + -d Specify the directory containing the reference information. + -p Calculate posterior probabilities. + -m Substitution model. Protein: LG, WAG, or JTT. Nucleotides: GTR. + --model-freqs Use model frequencies instead of reference alignment frequencies. + --gamma-cats Number of categories for discrete gamma model. + --gamma-alpha Specify the shape parameter for a discrete gamma model. + --ml-tolerance 1st stage branch len optimization tolerance (2nd stage to 1e-5). Default: 0.01. + --pp-rel-err Relative error for the posterior probability calculation. Default is 0.01. + --unif-prior Use a uniform prior rather than exponential. + --inform-prior Use an informative exponential prior based on rooted distance to leaves. + --prior-lower Lower bound for the informative prior mean. Default is 0. + --start-pend Starting pendant branch length. Default is 0.1. + --max-pend Set the maximum ML pendant branch length. Default is 2. + --fig-cutoff The cutoff for determining figs. Default is 0; specify 0 to disable. + --fig-eval-all Evaluate all likelihoods to ensure that the best location was selected. + --fig-eval-discrepancy-tree Write out a tree showing the discrepancies between the best complete and observed locations. + --fig-tree Write out a tree showing the figs on the tree. + --max-strikes Maximum number of strikes for baseball. 0 -> no ball playing. Default is 6. + --strike-box Set the size of the strike box in log likelihood units. Default is 3. + --max-pitches Set the maximum number of pitches for baseball. Default is 40. + --fantasy Desired likelihood cutoff for fantasy baseball mode. 0 -> no fantasy. + --fantasy-frac Fraction of fragments to use when running fantasy baseball. Default is 0.1. + --write-masked Write alignment masked to the region without gaps in the query. + --verbosity Set verbosity level. 0 is silent, and 2 is quite a lot. Default is 1. + --out-dir Specify the directory to write place files to. + -o Specify the output file name + --pretend Only check out the files then report. Do not run the analysis. + --check-like Write out the likelihood of the reference tree, calculated two ways. + -j The number of child processes to spawn when doing placements. Default is 2. + --timing Display timing information after the pplacer run finishes. + --no-pre-mask Don't pre-mask sequences before placement. + --write-pre-masked Write out the pre-masked sequences to the specified fasta file before placement. + --map-mrca Specify a file to write out MAP sequences for MRCAs and corresponding placements. + --map-mrca-min Specify cutoff for inclusion in MAP sequence file. Default is 0.8. + --map-identity Add the percent identity of the query sequence to the nearest MAP sequence to each placement. + --keep-at-most The maximum number of placements we keep. Default is 7. + --keep-factor Throw away anything that has ml_ratio below keep_factor times (best ml_ratio). Default is 0.01. + --mrca-class Classify with MRCAs instead of a painted tree. + --groups Split query alignment into the specified number of groups. + --always-refine Always refine the model before placing. + --mmap-file Instead of doing large allocations, mmap the given file. It will be created if it doesn't exist. + --discard-nonoverlapped When pre-masking, silently discard sequences which don't overlap the mask. + --version Write out the version number and exit. + -help Display this list of options + --help Display this list of options + + + +## URL Docs Extract +### https://github.com/matsen/pplacer/ +GitHub - matsen/pplacer: Phylogenetic placement and downstream analysis · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} matsen / pplacer Public Notifications You must be signed in to change notification settings Fork 20 Star 91 Code Issues 30 Pull requests 2 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights matsen/pplacer master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 2,773 Commits 2,773 Commits .github/ workflows .github/ workflows cdd_src cdd_src common_src common_src docs docs donovan-test/ ar53_pplacer_testset donovan-test/ ar53_pplacer_testset json_src json_src mcl @ 1f1932b mcl @ 1f1932b pam_src pam_src pdprune_src pdprune_src pplacer_src pplacer_src scripts scripts tests tests .dockerignore .dockerignore .gitignore .gitignore .gitmodules .gitmodules BUILD.md BUILD.md CHANGELOG CHANGELOG COPYING COPYING Dockerfile Dockerfile INSTALL.md INSTALL.md Makefile Makefile README.md README.md _tags _tags build-macos-native-ci.sh build-macos-native-ci.sh dune dune dune-project dune-project myocamlbuild.ml myocamlbuild.ml opam-requirements.txt opam-requirements.txt static-binaries-issue.md static-binaries-issue.md version.ml version.ml wercker.yml wercker.yml View all files Repository files navigation README GPL-3.0 license pplacer suite of programs pplacer places reads on a phylogenetic tree. guppy (Grand Unified Phylogenetic Placement Yanalyzer) yanalyzes them. rppr is a helpful tool for working with reference packages. Download compiled binaries (Linux x86_64, ARM64, macOS ARM64) project webpage documentation tutorial compilation instructions pplacer , guppy , and rppr are free software under the GPL v3. Related tools Several other tools have used pplacer as one of their main components. Some of these include: SEPP ( Mirarab, Nguyen, Warnow, PSB, 2012 ) aims to improve the scalability of phylogenetic placement using divide-and-conquer. It uses Ensembles of Hidden Markov Models (implemented by HMMER) to both align sequnces and to find a (small) subtree for placement using pplacer. SEPP can place on the GreenGenes dataset with 200,000 sequences. A standalone version for the GreenGenes reference is available here . paprica ( Bowman and Ducklow, PLOS One, 2015 ) uses Infernal and pplacer to place reads on a reference tree of 16S rRNA genes from all completed genomes in Genbank. The domains Bacteria, Archaea, and Eukarya are all supported. paprica normalizes for 16S rRNA gene copy number and provides and estimate of the enzymes, metabolic contents, and genomic character (e.g. GC content, genome length) of the community. It is available as an Amazon Machine Instance or VirtualBox appliance, however, we recommend that you install the dependencies and run locally. A basic tutorial can be found here . Thank yous Thank you to the Matsen research group, as well as to the OCaml community for their support throughout the years. We are especially grateful to Nicolás Ojeda Bär (@nojb) for helping update our legacy code to modern OCaml. About Phylogenetic placement and downstream analysis matsen.fredhutch.org/pplacer/ Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 91 stars Watchers 10 watching Forks 20 forks Report repository Releases 7 v1.1.alpha22 Latest Jan 28, 2026 + 6 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages OCaml 65.1% C 26.0% Python 6.2% Shell 2.0% Dockerfile 0.3% Standard ML 0.2% Other 0.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge pplacer --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +pplacer 1.1.alpha17 0 +--------------------- +file name : pplacer-1.1.alpha17-0.tar.bz2 +name : pplacer +version : 1.1.alpha17 +build : 0 +build number: 0 +size : 8.6 MB +license : GNU General Public License v3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pplacer-1.1.alpha17-0.tar.bz2 +md5 : 6b91879d7e2bb7953dcbcd7af797e49b +dependencies: [] + + +pplacer 1.1.alpha17 h9ee0642_3 +------------------------------ +file name : pplacer-1.1.alpha17-h9ee0642_3.tar.bz2 +name : pplacer +version : 1.1.alpha17 +build : h9ee0642_3 +build number: 3 +size : 8.6 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pplacer-1.1.alpha17-h9ee0642_3.tar.bz2 +md5 : d3085f4b73e295d3db63cfbd719df52b +timestamp : 2024-11-28 06:56:35 UTC +dependencies: [] + + +pplacer 1.1.alpha19 0 +--------------------- +file name : pplacer-1.1.alpha19-0.tar.bz2 +name : pplacer +version : 1.1.alpha19 +build : 0 +build number: 0 +size : 8.6 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pplacer-1.1.alpha19-0.tar.bz2 +md5 : c636033eb7b90fd13b52ecdc30fbfc8d +dependencies: [] + + +pplacer 1.1.alpha19 1 +--------------------- +file name : pplacer-1.1.alpha19-1.tar.bz2 +name : pplacer +version : 1.1.alpha19 +build : 1 +build number: 1 +size : 8.6 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pplacer-1.1.alpha19-1.tar.bz2 +md5 : 0f47674328078a8dac6e621a3085cbe0 +timestamp : 2018-07-05 21:02:57 UTC +dependencies: [] + + +pplacer 1.1.alpha19 h9ee0642_2 +------------------------------ +file name : pplacer-1.1.alpha19-h9ee0642_2.tar.bz2 +name : pplacer +version : 1.1.alpha19 +build : h9ee0642_2 +build number: 2 +size : 8.6 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pplacer-1.1.alpha19-h9ee0642_2.tar.bz2 +md5 : 9c132838ff736fc8c11edfe81699a4c1 +timestamp : 2021-03-24 18:09:16 UTC +dependencies: [] + + +pplacer 1.1.alpha20 hd563303_0 +------------------------------ +file name : pplacer-1.1.alpha20-hd563303_0.tar.bz2 +name : pplacer +version : 1.1.alpha20 +build : hd563303_0 +build number: 0 +size : 10.3 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pplacer-1.1.alpha20-hd563303_0.tar.bz2 +md5 : 32025af31b15a77c5c64657bef4d1944 +timestamp : 2025-08-05 00:45:42 UTC +dependencies: + - gsl >=2.8,<2.9.0a0 + - libgcc >=13 + - libsqlite >=3.50.4,<4.0a0 + - libzlib >=1.3.1,<2.0a0 + + +pplacer 1.1.alpha22 hd563303_0 +------------------------------ +file name : pplacer-1.1.alpha22-hd563303_0.conda +name : pplacer +version : 1.1.alpha22 +build : hd563303_0 +build number: 0 +size : 8.7 MB +license : GPL-3.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pplacer-1.1.alpha22-hd563303_0.conda +md5 : 79e225b92a37d12be6f2357b093f20fc +timestamp : 2026-01-28 22:47:13 UTC +dependencies: + - gsl >=2.8,<2.9.0a0 + - libgcc >=13 + - libsqlite >=3.51.2,<4.0a0 + - libzlib >=1.3.1,<2.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/prank.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/prank.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f90743271f721023fd2e759a2800fedc3fed8ff --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/prank.manual_bundle.txt @@ -0,0 +1,303 @@ +# Tool: prank +software_name: prank +tier: T1 +domain: t1_backfill_overall +downloads: 183476 +summary: PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. +description: PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. +dependencies: libgcc >=14, libstdcxx >=14 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +cli:prank +## CLI Help Content +$ conda run -n bioenv_cli prank --help +[rc=0] +Unknown option: --help + + +prank v.250331. Minimal usage: 'prank sequence_file' + +Advanced usage: 'prank [optional parameters] -d=sequence_file [optional parameters]' + + input/output parameters: + -d=sequence_file (in FASTA format) + -t=tree_file [default: no tree, generate approximate NJ tree] + -o=output_file [default: 'output'] + -f=output_format ['fasta' (default), 'phylipi', 'phylips', 'paml', 'nexus'] + -showxml [output xml-files] + -showtree [output dnd-files] + -showanc [output ancestral sequences] + -showevents [output evolutioanry events] + -showall [output all of these] + -support [compute posterior support] + -njtree [estimate tree from input alignment (and realign)] + -treeonly [estimate tree only] + -quiet + + model parameters: + +F or -F [force insertions to be always skipped] + -gaprate=# [gap opening rate; default: dna 0.025 / prot 0.005] + -gapext=# [gap extension probability; default: dna 0.75 / prot 0.5] + -codon [for coding DNA: use empirical codon model] + -DNA / -protein [no autodetection: use dna or protein model] + -termgap [penalise terminal gaps normally] + -nomissing [no missing data, use -F for terminal gaps ] + + other parameters: + -keep [keep alignment "as is" (e.g. for ancestor inference)] + -iterate=# [rounds of re-alignment iteration] + -once [run only once; same as -iterate=1] + -prunetree [prune guide tree branches with no sequence data] + -prunedata [prune sequence data with no guide tree leaves] + -uselogs [slower but should work for a greater number of sequences] + -translate [translate to protein] + -mttranslate [translate to protein using mt table] + + other: + -convert [no alignment, just convert to another format] + -version [check for updates] + + -help [show more options] + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge prank --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +prank v.150803 0 +---------------- +file name : prank-v.150803-0.tar.bz2 +name : prank +version : v.150803 +build : 0 +build number: 0 +size : 398 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-v.150803-0.tar.bz2 +md5 : 8e301cd00687a312e6c14353a0328f9a +dependencies: + - libgcc + + +prank v.170427 0 +---------------- +file name : prank-v.170427-0.tar.bz2 +name : prank +version : v.170427 +build : 0 +build number: 0 +size : 397 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-v.170427-0.tar.bz2 +md5 : 2eb84579dcf3403559c47ce34c5e7775 +dependencies: + - libgcc + + +prank v.170427 h2d50403_1 +------------------------- +file name : prank-v.170427-h2d50403_1.tar.bz2 +name : prank +version : v.170427 +build : h2d50403_1 +build number: 1 +size : 409 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-v.170427-h2d50403_1.tar.bz2 +md5 : 98b4ca4d87fbe978d6a78930eb586e8f +timestamp : 2018-06-29 00:54:32 UTC +dependencies: + - libstdcxx-ng >=4.9 + + +prank v.170427 h4ac6f70_6 +------------------------- +file name : prank-v.170427-h4ac6f70_6.tar.bz2 +name : prank +version : v.170427 +build : h4ac6f70_6 +build number: 6 +size : 381 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-v.170427-h4ac6f70_6.tar.bz2 +md5 : 73b22246aae74a7ed7420d97356815c2 +timestamp : 2023-05-14 22:46:18 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +prank v.170427 h4ac6f70_7 +------------------------- +file name : prank-v.170427-h4ac6f70_7.tar.bz2 +name : prank +version : v.170427 +build : h4ac6f70_7 +build number: 7 +size : 381 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-v.170427-h4ac6f70_7.tar.bz2 +md5 : d3e916c19c458ea5129105de6c1f483d +timestamp : 2023-05-15 20:35:43 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +prank v.170427 h6bb024c_2 +------------------------- +file name : prank-v.170427-h6bb024c_2.tar.bz2 +name : prank +version : v.170427 +build : h6bb024c_2 +build number: 2 +size : 409 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-v.170427-h6bb024c_2.tar.bz2 +md5 : f312350e3a0bc24e6371f38c06d944b4 +timestamp : 2019-03-13 17:14:56 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +prank v.170427 h7d875b9_4 +------------------------- +file name : prank-v.170427-h7d875b9_4.tar.bz2 +name : prank +version : v.170427 +build : h7d875b9_4 +build number: 4 +size : 444 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-v.170427-h7d875b9_4.tar.bz2 +md5 : ea30fecc92215f78d49d2d88d715cec4 +timestamp : 2021-03-25 03:11:30 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + + +prank v.170427 h9f5acd7_5 +------------------------- +file name : prank-v.170427-h9f5acd7_5.tar.bz2 +name : prank +version : v.170427 +build : h9f5acd7_5 +build number: 5 +size : 377 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-v.170427-h9f5acd7_5.tar.bz2 +md5 : aea43532dd04620f1abaf08146c89892 +timestamp : 2022-02-23 18:23:01 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + + +prank v.170427 h9f5acd7_6 +------------------------- +file name : prank-v.170427-h9f5acd7_6.tar.bz2 +name : prank +version : v.170427 +build : h9f5acd7_6 +build number: 6 +size : 378 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-v.170427-h9f5acd7_6.tar.bz2 +md5 : 580d8a125f057af388919f61b0117c2a +timestamp : 2023-05-14 10:06:38 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +prank v.170427 hc9558a2_3 +------------------------- +file name : prank-v.170427-hc9558a2_3.tar.bz2 +name : prank +version : v.170427 +build : hc9558a2_3 +build number: 3 +size : 402 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-v.170427-hc9558a2_3.tar.bz2 +md5 : 7ca92ee64ae0b9a5d135a8573c94fa79 +timestamp : 2020-07-13 01:16:36 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + + +prank 170427 h4ac6f70_0 +----------------------- +file name : prank-170427-h4ac6f70_0.tar.bz2 +name : prank +version : 170427 +build : h4ac6f70_0 +build number: 0 +size : 405 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-170427-h4ac6f70_0.tar.bz2 +md5 : 42e251b6b23b3f8a3071d185eff4bb35 +timestamp : 2024-03-26 13:03:49 UTC +dependencies: + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +prank 170427 h9948957_1 +----------------------- +file name : prank-170427-h9948957_1.tar.bz2 +name : prank +version : 170427 +build : h9948957_1 +build number: 1 +size : 401 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-170427-h9948957_1.tar.bz2 +md5 : b42e651a06117c624a977b6a24b1006d +timestamp : 2024-12-10 03:58:58 UTC +dependencies: + - libgcc >=13 + - libstdcxx >=13 + + +prank 251117 hd63eeec_0 +----------------------- +file name : prank-251117-hd63eeec_0.conda +name : prank +version : 251117 +build : hd63eeec_0 +build number: 0 +size : 443 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prank-251117-hd63eeec_0.conda +md5 : 62e656e8faac6f46598cfdda62215869 +timestamp : 2026-04-09 01:49:46 UTC +dependencies: + - libgcc >=14 + - libstdcxx >=14 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/primer3.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/primer3.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..acabfa175a42c2241888a1085ad54d88c4d46617 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/primer3.manual_bundle.txt @@ -0,0 +1,473 @@ +# Tool: primer3 +software_name: primer3 +tier: T1 +domain: t1_backfill_overall +downloads: 449197 +summary: Design PCR primers from DNA sequence. From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. +description: Design PCR primers from DNA sequence. From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. +dependencies: libgcc >=13, libstdcxx >=13, perl >=5.32.1,<5.33.0a0 *_perl5 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/primer3-org/primer3 +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/primer3-org/primer3 +GitHub - primer3-org/primer3: Primer3 is a command line tool to select primers for polymerase chain reaction (PCR). · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} primer3-org / primer3 Public Notifications You must be signed in to change notification settings Fork 69 Star 285 Code Issues 7 Pull requests 3 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights primer3-org/primer3 main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,252 Commits 1,252 Commits .github/ workflows .github/ workflows kmer_lists kmer_lists settings_files settings_files src src test test .gitignore .gitignore LICENSE LICENSE README.md README.md cmp_settings.pl cmp_settings.pl create_test_folders.pl create_test_folders.pl example example View all files Repository files navigation README GPL-2.0 license Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Installing sudo apt-get install -y build-essential g++ cmake git-all git clone https://github.com/primer3-org/primer3.git primer3 cd primer3/src make make test Run Primer3 ./primer3_core ../example Read the complete Primer3 manual Primer3 Manual or see /src/primer3_manual.htm About Primer3 is a command line tool to select primers for polymerase chain reaction (PCR). Resources Readme License GPL-2.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 285 stars Watchers 10 watching Forks 69 forks Report repository Releases 3 Release version 2.6.1 Latest Jan 26, 2022 + 2 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C 45.4% C++ 25.4% HTML 17.6% Perl 8.5% Makefile 1.3% Python 1.3% Other 0.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge primer3 --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +primer3 v2.5.0 pl526he1b5a44_0 +------------------------------ +file name : primer3-v2.5.0-pl526he1b5a44_0.tar.bz2 +name : primer3 +version : v2.5.0 +build : pl526he1b5a44_0 +build number: 0 +size : 787 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-v2.5.0-pl526he1b5a44_0.tar.bz2 +md5 : d3876e81770f4be89c4bb8c430db1555 +timestamp : 2019-11-08 15:18:02 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + + +primer3 1.1.4 0 +--------------- +file name : primer3-1.1.4-0.tar.bz2 +name : primer3 +version : 1.1.4 +build : 0 +build number: 0 +size : 169 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-1.1.4-0.tar.bz2 +md5 : fe8f1f8268d0e841cefd02c9d2f6beaa +dependencies: + - libgcc + - perl-threaded + + +primer3 1.1.4 h031d066_6 +------------------------ +file name : primer3-1.1.4-h031d066_6.tar.bz2 +name : primer3 +version : 1.1.4 +build : h031d066_6 +build number: 6 +size : 208 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-1.1.4-h031d066_6.tar.bz2 +md5 : 73db99dad435788aa2557c1350f9db01 +timestamp : 2023-05-16 06:37:35 UTC +dependencies: + - libgcc-ng >=12 + - perl + + +primer3 1.1.4 h470a237_1 +------------------------ +file name : primer3-1.1.4-h470a237_1.tar.bz2 +name : primer3 +version : 1.1.4 +build : h470a237_1 +build number: 1 +size : 171 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-1.1.4-h470a237_1.tar.bz2 +md5 : 490c63f7fbc41139ed660c206fc54c3a +timestamp : 2018-06-28 21:32:10 UTC +dependencies: + - libgcc-ng >=4.9 + - perl + + +primer3 1.1.4 h516909a_2 +------------------------ +file name : primer3-1.1.4-h516909a_2.tar.bz2 +name : primer3 +version : 1.1.4 +build : h516909a_2 +build number: 2 +size : 183 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-1.1.4-h516909a_2.tar.bz2 +md5 : b32f746d09f53ecd13bfc2686ca44f74 +timestamp : 2020-07-13 22:03:09 UTC +dependencies: + - libgcc-ng >=7.5.0 + - perl + + +primer3 1.1.4 h779adbc_3 +------------------------ +file name : primer3-1.1.4-h779adbc_3.tar.bz2 +name : primer3 +version : 1.1.4 +build : h779adbc_3 +build number: 3 +size : 206 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-1.1.4-h779adbc_3.tar.bz2 +md5 : f5a4ef1c5427b1c6ec8a4465907cefa7 +timestamp : 2021-03-26 03:52:26 UTC +dependencies: + - libgcc-ng >=9.3.0 + - perl + + +primer3 1.1.4 h7b50bb2_7 +------------------------ +file name : primer3-1.1.4-h7b50bb2_7.tar.bz2 +name : primer3 +version : 1.1.4 +build : h7b50bb2_7 +build number: 7 +size : 208 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-1.1.4-h7b50bb2_7.tar.bz2 +md5 : 0c55be372ddc0e8c99987c73b2bf5d77 +timestamp : 2024-12-13 04:18:36 UTC +dependencies: + - libgcc >=13 + - perl + + +primer3 1.1.4 hec16e2b_4 +------------------------ +file name : primer3-1.1.4-hec16e2b_4.tar.bz2 +name : primer3 +version : 1.1.4 +build : hec16e2b_4 +build number: 4 +size : 207 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-1.1.4-hec16e2b_4.tar.bz2 +md5 : 8a5f577287ab8e0abdf0fc104ca09cab +timestamp : 2022-02-22 07:20:08 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl + + +primer3 1.1.4 hec16e2b_5 +------------------------ +file name : primer3-1.1.4-hec16e2b_5.tar.bz2 +name : primer3 +version : 1.1.4 +build : hec16e2b_5 +build number: 5 +size : 208 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-1.1.4-hec16e2b_5.tar.bz2 +md5 : 90dee0f7f7297d11a31f752c9221f6bf +timestamp : 2023-05-13 09:09:10 UTC +dependencies: + - libgcc-ng >=12 + - perl + + +primer3 2.0.0a h031d066_7 +------------------------- +file name : primer3-2.0.0a-h031d066_7.tar.bz2 +name : primer3 +version : 2.0.0a +build : h031d066_7 +build number: 7 +size : 287 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.0.0a-h031d066_7.tar.bz2 +md5 : 4bb74d5e45805c34fd01abcacc09ceb6 +timestamp : 2023-05-16 06:50:01 UTC +dependencies: + - libgcc-ng >=12 + - perl + + +primer3 2.0.0a h14c3975_2 +------------------------- +file name : primer3-2.0.0a-h14c3975_2.tar.bz2 +name : primer3 +version : 2.0.0a +build : h14c3975_2 +build number: 2 +size : 238 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.0.0a-h14c3975_2.tar.bz2 +md5 : 09efa8413f760112ebb4edd3975b537b +timestamp : 2019-03-09 11:13:35 UTC +dependencies: + - libgcc-ng >=7.3.0 + - perl + + +primer3 2.0.0a h470a237_1 +------------------------- +file name : primer3-2.0.0a-h470a237_1.tar.bz2 +name : primer3 +version : 2.0.0a +build : h470a237_1 +build number: 1 +size : 236 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.0.0a-h470a237_1.tar.bz2 +md5 : 4eef81af0b50d99e494a9ad866a4a0c9 +timestamp : 2018-06-28 21:37:28 UTC +dependencies: + - libgcc-ng >=4.9 + - perl + + +primer3 2.0.0a h516909a_3 +------------------------- +file name : primer3-2.0.0a-h516909a_3.tar.bz2 +name : primer3 +version : 2.0.0a +build : h516909a_3 +build number: 3 +size : 260 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.0.0a-h516909a_3.tar.bz2 +md5 : 6979ab7d134a62047cbdef2a86e817f9 +timestamp : 2020-07-13 21:57:05 UTC +dependencies: + - libgcc-ng >=7.5.0 + - perl + + +primer3 2.0.0a h779adbc_4 +------------------------- +file name : primer3-2.0.0a-h779adbc_4.tar.bz2 +name : primer3 +version : 2.0.0a +build : h779adbc_4 +build number: 4 +size : 286 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.0.0a-h779adbc_4.tar.bz2 +md5 : 05bbdf9ac1c1449b936d127e329fed81 +timestamp : 2021-03-26 04:00:09 UTC +dependencies: + - libgcc-ng >=9.3.0 + - perl + + +primer3 2.0.0a h7b50bb2_8 +------------------------- +file name : primer3-2.0.0a-h7b50bb2_8.tar.bz2 +name : primer3 +version : 2.0.0a +build : h7b50bb2_8 +build number: 8 +size : 288 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.0.0a-h7b50bb2_8.tar.bz2 +md5 : 3342b58ee292a63516d24a7f5bd053f3 +timestamp : 2024-12-13 04:12:15 UTC +dependencies: + - libgcc >=13 + - perl + + +primer3 2.0.0a hec16e2b_5 +------------------------- +file name : primer3-2.0.0a-hec16e2b_5.tar.bz2 +name : primer3 +version : 2.0.0a +build : hec16e2b_5 +build number: 5 +size : 289 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.0.0a-hec16e2b_5.tar.bz2 +md5 : 42f63d6968292c9b92a43291dc86fb08 +timestamp : 2022-02-22 07:31:46 UTC +dependencies: + - libgcc-ng >=10.3.0 + - perl + + +primer3 2.0.0a hec16e2b_6 +------------------------- +file name : primer3-2.0.0a-hec16e2b_6.tar.bz2 +name : primer3 +version : 2.0.0a +build : hec16e2b_6 +build number: 6 +size : 291 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.0.0a-hec16e2b_6.tar.bz2 +md5 : 76470ca7b6b38779e2de79d46ed1aa13 +timestamp : 2023-05-13 09:00:55 UTC +dependencies: + - libgcc-ng >=12 + - perl + + +primer3 2.0.0a pl5.22.0_0 +------------------------- +file name : primer3-2.0.0a-pl5.22.0_0.tar.bz2 +name : primer3 +version : 2.0.0a +build : pl5.22.0_0 +build number: 0 +size : 235 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.0.0a-pl5.22.0_0.tar.bz2 +md5 : 33d236aaf726b8b39ec1027826939888 +dependencies: + - libgcc + - perl 5.22.0* + + +primer3 2.3.7 0 +--------------- +file name : primer3-2.3.7-0.tar.bz2 +name : primer3 +version : 2.3.7 +build : 0 +build number: 0 +size : 418 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.3.7-0.tar.bz2 +md5 : 7e11e09d8d3df6b721a1a802a28540ac +dependencies: + - libgcc + - perl-threaded + + +primer3 2.3.7 pl526hfc679d8_1 +----------------------------- +file name : primer3-2.3.7-pl526hfc679d8_1.tar.bz2 +name : primer3 +version : 2.3.7 +build : pl526hfc679d8_1 +build number: 1 +size : 423 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.3.7-pl526hfc679d8_1.tar.bz2 +md5 : 3e8e5e0d6595866aab2683e37644fea5 +timestamp : 2018-06-29 00:57:43 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.27.0a0 + + +primer3 2.4.0 pl526hfc679d8_0 +----------------------------- +file name : primer3-2.4.0-pl526hfc679d8_0.tar.bz2 +name : primer3 +version : 2.4.0 +build : pl526hfc679d8_0 +build number: 0 +size : 752 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.4.0-pl526hfc679d8_0.tar.bz2 +md5 : cc33a103345f8932a682119338a953e3 +timestamp : 2018-07-29 06:26:17 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + + +primer3 2.4.1a pl526he1b5a44_2 +------------------------------ +file name : primer3-2.4.1a-pl526he1b5a44_2.tar.bz2 +name : primer3 +version : 2.4.1a +build : pl526he1b5a44_2 +build number: 2 +size : 753 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.4.1a-pl526he1b5a44_2.tar.bz2 +md5 : 8ec7551b596458a299f3fb10f614536e +timestamp : 2019-10-26 22:44:00 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + + +primer3 2.4.1a pl526hf484d3e_1 +------------------------------ +file name : primer3-2.4.1a-pl526hf484d3e_1.tar.bz2 +name : primer3 +version : 2.4.1a +build : pl526hf484d3e_1 +build number: 1 +size : 738 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.4.1a-pl526hf484d3e_1.tar.bz2 +md5 : e06230af06e3916513bfb24420d644e2 +timestamp : 2019-03-09 11:09:47 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl >=5.26.2,<5.26.3.0a0 + + +primer3 2.4.1a pl526hfc679d8_0 +------------------------------ +file name : primer3-2.4.1a-pl526hfc679d8_0.tar.bz2 +name : primer3 +version : 2.4.1a +build : pl526hfc679d8_0 +build number: 0 +size : 737 KB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/primer3-2.4.1a-pl526hfc679d8_0.tar.bz2 +md5 : 9603bc991a7c9401b181e3467ee49eab +timestamp : 2018-08-29 08:39:26 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - perl >=5.26.2,<5.26.3.0a0 + + +primer3 2.5.0 pl5262h1b792b2_1 +------------------------------ +file name : primer3-2.5.0-pl5262h1b792b2_1.tar.bz2 +name : primer3 +version : 2.5.0 +build : pl5262h1b792b2_1 +build number: 1 +size : 919 KB +license : GPLv2 +subdir : diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/prodigal.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/prodigal.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab674dc47232e8cd33a4f2e0c0104d47fc7c1bea --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/prodigal.manual_bundle.txt @@ -0,0 +1,305 @@ +# Tool: prodigal +software_name: prodigal +tier: T1 +domain: t1_backfill_overall +downloads: 466192 +summary: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program +description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program +dependencies: libgcc >=13, libzlib >=1.3.1,<2.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: +doc_url: +dev_url: + +## CLI Help Source +cli:prodigal +## CLI Help Content +$ conda run -n bioenv_cli prodigal --help +[rc=15] + + +Unknown option. + +Usage: prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type] + [-g tr_table] [-h] [-i input_file] [-m] [-n] [-o output_file] + [-p mode] [-q] [-s start_file] [-t training_file] [-v] + +Do 'prodigal -h' for more information. + + +ERROR conda.cli.main_run:execute(127): `conda run prodigal --help` failed. (See above for error) + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge prodigal --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +prodigal 2.6.2 1 +---------------- +file name : prodigal-2.6.2-1.tar.bz2 +name : prodigal +version : 2.6.2 +build : 1 +build number: 1 +size : 992 B +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.2-1.tar.bz2 +md5 : e2dad59082b2c1ffdf7fd3c659cff760 +dependencies: [] + + +prodigal 2.6.2 2 +---------------- +file name : prodigal-2.6.2-2.tar.bz2 +name : prodigal +version : 2.6.2 +build : 2 +build number: 2 +size : 903 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.2-2.tar.bz2 +md5 : 2f2ccf8725f06d9929d2d39ebd87fd21 +dependencies: [] + + +prodigal 2.6.2 3 +---------------- +file name : prodigal-2.6.2-3.tar.bz2 +name : prodigal +version : 2.6.2 +build : 3 +build number: 3 +size : 904 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.2-3.tar.bz2 +md5 : 04dd2ee4f0dea7659c2c35e880c4f1f2 +dependencies: [] + + +prodigal 2.6.3 0 +---------------- +file name : prodigal-2.6.3-0.tar.bz2 +name : prodigal +version : 2.6.3 +build : 0 +build number: 0 +size : 902 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-0.tar.bz2 +md5 : fa7329cbaebc30948378fd2fab9a27d7 +dependencies: [] + + +prodigal 2.6.3 1 +---------------- +file name : prodigal-2.6.3-1.tar.bz2 +name : prodigal +version : 2.6.3 +build : 1 +build number: 1 +size : 904 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-1.tar.bz2 +md5 : 4255165f81d949ca4a4b986a4959641b +timestamp : 2018-06-28 22:04:21 UTC +dependencies: [] + + +prodigal 2.6.3 h031d066_5 +------------------------- +file name : prodigal-2.6.3-h031d066_5.tar.bz2 +name : prodigal +version : 2.6.3 +build : h031d066_5 +build number: 5 +size : 560 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h031d066_5.tar.bz2 +md5 : c63c310f12a95622cff300f3c9cd9f92 +timestamp : 2023-05-15 02:25:39 UTC +dependencies: + - libgcc-ng >=12 + + +prodigal 2.6.3 h031d066_6 +------------------------- +file name : prodigal-2.6.3-h031d066_6.tar.bz2 +name : prodigal +version : 2.6.3 +build : h031d066_6 +build number: 6 +size : 559 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h031d066_6.tar.bz2 +md5 : 05eb05a68e41b289530c1f434a63fc73 +timestamp : 2023-05-16 07:46:47 UTC +dependencies: + - libgcc-ng >=12 + + +prodigal 2.6.3 h031d066_7 +------------------------- +file name : prodigal-2.6.3-h031d066_7.tar.bz2 +name : prodigal +version : 2.6.3 +build : h031d066_7 +build number: 7 +size : 561 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h031d066_7.tar.bz2 +md5 : c1d1bd1417074d8fa6d6f213b7ee51e2 +timestamp : 2024-01-05 20:47:41 UTC +dependencies: + - libgcc-ng >=12 + + +prodigal 2.6.3 h031d066_8 +------------------------- +file name : prodigal-2.6.3-h031d066_8.tar.bz2 +name : prodigal +version : 2.6.3 +build : h031d066_8 +build number: 8 +size : 562 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h031d066_8.tar.bz2 +md5 : 593c6c69156c71a5c6d12a86df6fc743 +timestamp : 2024-03-26 14:19:49 UTC +dependencies: + - libgcc-ng >=12 + + +prodigal 2.6.3 h031d066_9 +------------------------- +file name : prodigal-2.6.3-h031d066_9.tar.bz2 +name : prodigal +version : 2.6.3 +build : h031d066_9 +build number: 9 +size : 562 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h031d066_9.tar.bz2 +md5 : fca8ee966b536b3f767dee56d3256e1f +timestamp : 2024-06-05 13:20:09 UTC +dependencies: + - libgcc-ng >=12 + + +prodigal 2.6.3 h516909a_2 +------------------------- +file name : prodigal-2.6.3-h516909a_2.tar.bz2 +name : prodigal +version : 2.6.3 +build : h516909a_2 +build number: 2 +size : 777 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h516909a_2.tar.bz2 +md5 : 96d5aa2d9910bf82f7b5dcf335c6eac2 +timestamp : 2019-10-27 23:38:28 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +prodigal 2.6.3 h577a1d6_11 +-------------------------- +file name : prodigal-2.6.3-h577a1d6_11.tar.bz2 +name : prodigal +version : 2.6.3 +build : h577a1d6_11 +build number: 11 +size : 588 KB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h577a1d6_11.tar.bz2 +md5 : 7b083f573760cbd88a206e05f73f5e9d +timestamp : 2025-07-17 00:38:51 UTC +dependencies: + - libgcc >=13 + - libzlib >=1.3.1,<2.0a0 + + +prodigal 2.6.3 h779adbc_3 +------------------------- +file name : prodigal-2.6.3-h779adbc_3.tar.bz2 +name : prodigal +version : 2.6.3 +build : h779adbc_3 +build number: 3 +size : 776 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h779adbc_3.tar.bz2 +md5 : abfa08335024f62b2aa5d7aacef138b8 +timestamp : 2021-03-25 00:12:03 UTC +dependencies: + - libgcc-ng >=9.3.0 + + +prodigal 2.6.3 h7b50bb2_10 +-------------------------- +file name : prodigal-2.6.3-h7b50bb2_10.tar.bz2 +name : prodigal +version : 2.6.3 +build : h7b50bb2_10 +build number: 10 +size : 568 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h7b50bb2_10.tar.bz2 +md5 : 66cc94ede7d4cd483a0412adaf9532ce +timestamp : 2024-12-13 10:42:43 UTC +dependencies: + - libgcc >=13 + + +prodigal 2.6.3 hec16e2b_4 +------------------------- +file name : prodigal-2.6.3-hec16e2b_4.tar.bz2 +name : prodigal +version : 2.6.3 +build : hec16e2b_4 +build number: 4 +size : 777 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-hec16e2b_4.tar.bz2 +md5 : 0f8b880d727df321ac70a224c18690cb +timestamp : 2022-02-22 04:24:39 UTC +dependencies: + - libgcc-ng >=10.3.0 + + +prodigal 2.6.3 hec16e2b_5 +------------------------- +file name : prodigal-2.6.3-hec16e2b_5.tar.bz2 +name : prodigal +version : 2.6.3 +build : hec16e2b_5 +build number: 5 +size : 778 KB +license : GPL v3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-hec16e2b_5.tar.bz2 +md5 : 62369aad3bd564248fac8b44bf393c2c +timestamp : 2023-05-11 15:22:56 UTC +dependencies: + - libgcc-ng >=12 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/prokka.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/prokka.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d7da204ca3cec050533e5a5491165c49e72382b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/prokka.manual_bundle.txt @@ -0,0 +1,577 @@ +# Tool: prokka +software_name: prokka +tier: T1 +domain: t1_backfill_overall +downloads: 241438 +summary: Rapid annotation of prokaryotic genomes +description: Rapid annotation of prokaryotic genomes +dependencies: aragorn >=1.2, barrnap >=0.7, blast >=2.7.1, hmmer >=3.1b2, infernal >=1.1.2, minced >=0.3, parallel >=20180522, perl >=5.32.1,<6.0a0 *_perl5, perl-bioperl >=1.7.2, perl-xml-simple, prodigal >=2.6, tbl2asn-forever >=25.7 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/tseemann/prokka +doc_url: +dev_url: https://github.com/tseemann/prokka + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/tseemann/prokka +GitHub - tseemann/prokka: :zap: Rapid prokaryotic genome annotation · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} tseemann / prokka Public Notifications You must be signed in to change notification settings Fork 235 Star 976 Code Issues 226 Pull requests 17 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights tseemann/prokka master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 350 Commits 350 Commits .github/ workflows .github/ workflows bin bin db db doc doc test test update-dbs update-dbs .gitignore .gitignore CITATION.cff CITATION.cff CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md LICENSE LICENSE README.md README.md environment.yml environment.yml View all files Repository files navigation README Code of conduct GPL-3.0 license Prokka: rapid prokaryotic genome annotation Introduction Whole genome annotation is the process of identifying features of interest in a set of genomic DNA sequences, and labelling them with useful information. Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Bakta is the next generation of Prokka Prokka has served the community well for over a decade. I can no longer maintain it, so, with my blessing and gratitude, Oliver Schwengers has taken the bacterial annotation toruch and developed Bakta which is a modern version of Prokka with better tooling and maintained databases, including db-light which is in the spirit of Prokka's "fast and lean" approach. I recommend replacing Prokka with Bakta in your analysis pipelines going forward. Installation Bioconda The best way to install Prokka is using Conda ( miniforge ). conda create -n prokka bioconda::prokka conda activate prokka prokka --version Docker Maintained by STAPHB : docker pull staphb/prokka:latest docker run staphb/prokka:latest prokka --version Singularity singularity build prokka.sif docker://staphb/prokka:latest singularity exec prokka.sif prokka -h Test Type prokka and it should output its help screen. Type prokka --version and you should see an output like prokka 1.x Type prokka --listdb and it will show you what databases it has installed to use. Invoking Prokka Beginner # Vanilla (but with free toppings) % prokka contigs.fa # Look for a folder called PROKKA_yyyymmdd (today's date) and look at stats % cat PROKKA_yyyymmdd/*.txt Moderate # Choose the names of the output files % prokka --outdir mydir --prefix mygenome contigs.fa # Visualize it in Artemis % art mydir/mygenome.gff Specialist # Have curated genomes I want to use to annotate from % prokka --proteins MG1655.gbk --outdir mutant --prefix K12_mut contigs.fa # Look at tabular features % less -S mutant/K12_mut.tsv Expert # It's not just for bacteria, people % prokka --kingdom Archaea --outdir mydir --genus Pyrococcus --locustag PYCC # Search for your favourite gene % exonerate --bestn 1 zetatoxin.fasta mydir/PYCC_06072012.faa | less Wizard # Watch and learn % prokka --outdir mydir --locustag EHEC --proteins NewToxins.faa --evalue 0.001 --gram neg --addgenes contigs.fa # Check to see if anything went really wrong % less mydir/EHEC_06072012.err # Add final details using Sequin % sequin mydir/EHEC_0607201.sqn NCBI Genbank submitter # Register your BioProject (e.g. PRJNA123456) and your locus_tag prefix (e.g. EHEC) first! % prokka --compliant --centre UoN --outdir PRJNA123456 --locustag EHEC --prefix EHEC-Chr1 contigs.fa # Check to see if anything went really wrong % less PRJNA123456/EHEC-Chr1.err # Add final details using Sequin % sequin PRJNA123456/EHEC-Chr1.sqn European Nucleotide Archive (ENA) submitter # Register your BioProject (e.g. PRJEB12345) and your locus_tag (e.g. EHEC) prefix first! % prokka --compliant --centre UoN --outdir PRJEB12345 --locustag EHEC --prefix EHEC-Chr1 contigs.fa # Check to see if anything went really wrong % less PRJNA123456/EHEC-Chr1.err # Install and run Sanger Pathogen group's Prokka GFF3 to EMBL converter # available from https://github.com/sanger-pathogens/gff3toembl # Find the closest NCBI taxonomy id (e.g. 562 for Escherichia coli) % gff3_to_embl -i "Submitter, A." \ -m "Escherichia coli EHEC annotated using Prokka." \ -g linear -c PROK -n 11 -f PRJEB12345/EHEC-Chr1.embl \ "Escherichia coli" 562 PRJEB12345 "Escherichia coli strain EHEC" PRJEB12345/EHEC-Chr1.gff # Download and run the latest EMBL validator prior to submitting the EMBL flat file # from http://central.maven.org/maven2/uk/ac/ebi/ena/sequence/embl-api-validator/ # which at the time of writing is v1.1.129 % curl -L -O http://central.maven.org/maven2/uk/ac/ebi/ena/sequence/embl-api-validator/1.1.129/embl-api-validator-1.1.129.jar % java -jar embl-api-validator-1.1.129.jar -r PRJEB12345/EHEC-Chr1.embl # Compress the file ready to upload to ENA, and calculate MD5 checksum % gzip PRJEB12345/EHEC-Chr1.embl % md5sum PRJEB12345/EHEC-Chr1.embl.gz Crazy Person # No stinking Perl script is going to control me % prokka \ --outdir $HOME/genomes/Ec_POO247 --force \ --prefix Ec_POO247 --addgenes --locustag ECPOOp \ --increment 10 --gffver 2 --centre CDC --compliant \ --genus Escherichia --species coli --strain POO247 --plasmid pECPOO247 \ --kingdom Bacteria --gcode 11 --usegenus \ --proteins /opt/prokka/db/trusted/Ecocyc-17.6 \ --evalue 1e-9 --rfam \ plasmid-closed.fna Output Files Extension Description .gff This is the master annotation in GFF3 format, containing both sequences and annotations. It can be viewed directly in Artemis or IGV. .gbk This is a standard Genbank file derived from the master .gff. If the input to prokka was a multi-FASTA, then this will be a multi-Genbank, with one record for each sequence. .fna Nucleotide FASTA file of the input contig sequences. .faa Protein FASTA file of the translated CDS sequences. .ffn Nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) .sqn An ASN1 format "Sequin" file for submission to Genbank. It needs to be edited to set the correct taxonomy, authors, related publication etc. .fsa Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines. .tbl Feature Table file, used by "tbl2asn" to create the .sqn file. .err Unacceptable annotations - the NCBI discrepancy report. .log Contains all the output that Prokka produced during its run. This is a record of what settings you used, even if the --quiet option was enabled. .txt Statistics relating to the annotated features found. .tsv Tab-separated file of all features: locus_tag,ftype,len_bp,gene,EC_number,COG,product Command line options General: --help This help --version Print version and exit --citation Print citation for referencing Prokka --quiet No screen output (default OFF) --debug Debug mode: keep all temporary files (default OFF) Setup: --listdb List all configured databases --setupdb Index all installed databases --cleandb Remove all database indices --depends List all software dependencies Outputs: --outdir [X] Output folder [auto] (default '') --force Force overwriting existing output folder (default OFF) --prefix [X] Filename output prefix [auto] (default '') --addgenes Add 'gene' features for each 'CDS' feature (default OFF) --locustag [X] Locus tag prefix (default 'PROKKA') --increment [N] Locus tag counter increment (default '1') --gffver [N] GFF version (default '3') --compliant Force Genbank/ENA/DDJB compliance: --genes --mincontiglen 200 --centre XXX (default OFF) --centre [X] Sequencing centre ID. (default '') Organism details: --genus [X] Genus name (default 'Genus') --species [X] Species name (default 'species') --strain [X] Strain name (default 'strain') --plasmid [X] Plasmid name or identifier (default '') Annotations: --kingdom [X] Annotation mode: Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria') --gcode [N] Genetic code / Translation table (set if --kingdom is set) (default '0') --prodigaltf [X] Prodigal training file (default '') --gram [X] Gram: -/neg +/pos (default '') --usegenus Use genus-specific BLAST databases (needs --genus) (default OFF) --proteins [X] Fasta file of trusted proteins to first annotate from (default '') --hmms [X] Trusted HMM to first annotate from (default '') --metagenome Improve gene predictions for highly fragmented genomes (default OFF) --rawproduct Do not clean up /product annotation (default OFF) Computation: --fast Fast mode - skip CDS /product searching (default OFF) --cpus [N] Number of CPUs to use [0=all] (default '8') --mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1') --evalue [n.n] Similarity e-value cut-off (default '1e-06') --rfam Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0') --norrna Don't run rRNA search (default OFF) --notrna Don't run tRNA search (default OFF) --rnammer Prefer RNAmmer over Barrnap for rRNA prediction (default OFF) Option: --proteins The --proteins option is recommended when you have good quality reference genomes and want to ensure gene naming is consistent. Some species use specific terminology which will be often lost if you rely on the default Swiss-Prot database included with Prokka. If you have Genbank or Protein FASTA file(s) that you want to annotate genes from as the first priority, use the --proteins myfile.gbk . Please make sure it has a recognisable file extension like .gb or .gbk or auto-detect will fail. The use of Genbank is recommended over FASTA, because it will provide /gene and /EC_number annotations that a typical .faa file will not provide, unless you have specially formatted it for Prokka . Option: --prodigaltf Instead of letting prodigal train its gene model on the contigs you provide, you can pre-train it on some good closed reference genomes first using the prodigal -t option. Once you've done that, provide prokka the training file using the --prodgialtf option. Option: --rawproduct Prokka annotates proteins by using sequence similarity to other proteins in its database, or the databases the user provides via --proteins . By default, Prokka tries to "cleans" the /product names to ensure they are compliant with Genbank/ENA conventions. Some of the main things it does is: set vague names to hypothetical protein consistifies terms like possible , probable , predicted , ... to putative removes EC, COG and locus_tag identifiers Full details can be found in the cleanup_product() function in the prokka script. If you feel your annotations are being ruined, try using the --rawproduct option, and please file an issue if you find an example of where it is "behaving badly" and I will fix it. Databases The Core (BLAST+) Databases Prokka uses a variety of databases when trying to assign function to the predicted CDS features. It takes a hierarchical approach to make it fast. A small, core set of well characterized proteins are first searched using BLAST+. This combination of small database and fast search typically completes about 70% of the workload. Then a series of slower but more sensitive HMM databases are searched using HMMER3. The three core databases, applied in order, are: ISfinder : Only the tranposase (protein) sequences; the whole transposon is not annotated. NCBI Bacterial Antimicrobial Resistance Reference Gene Database : Antimicrobial resistance genes curated by NCBI. UniProtKB (SwissProt) : For each --kingdom we include curated proteins with evidence that (i) from Bacteria (or Archaea or Viruses); (ii) not be "Fragment" entries; and (iii) have an evidence level ("PE") of 2 or lower, which corresponds to experimental mRNA or proteomics evidence. Making a Core Databases If you want to modify these core databases, the included script prokka-uniprot_to_fasta_db , along with the official uniprot_sprot.dat , can be used to generate a new database to put in /opt/prokka/db/kingdom/ . If you add new ones, the command prokka --listdb will show you whether it has been detected properly. The Genus Databases ⚠️ This is no longer recommended. Please use --proteins instead. If you enable --usegenus and also provide a Genus via --genus then it will first use a BLAST database which is Genus specific. Prokka comes with a set of databases for the most common Bacterial genera; type prokka --listdb to see what they are. Adding a Genus Databases If you have a set of Genbank files and want to create a new Genus database, Prokka comes with a tool called prokka-genbank_to_fasta_db to help. For example, if you had four annotated "Coccus" genomes, you could do the following: % prokka-genbank_to_fasta_db Coccus1.gbk Coccus2.gbk Coccus3.gbk Coccus4.gbk > Coccus.faa % cd-hit -i Coccus.faa -o Coccus -T 0 -M 0 -g 1 -s 0.8 -c 0.9 % rm -fv Coccus.faa Coccus.bak.clstr Coccus.clstr % makeblastdb -dbtype prot -in Coccus % mv Coccus.p* /path/to/prokka/db/genus/ The HMM Databases Prokka comes with a bunch of HMM libraries for HMMER3. They are mostly Bacteria-specific. They are searched after the core and genus databases. You can add more simply by putting them in /opt/prokka/db/hmm . Type prokka --listdb to confirm they are recognised. FASTA database format Prokka understands two annotation tag formats, a plain one and a detailed one. The plain one is a standard FASTA-like line with the ID after the > sign, and the protein /product after the ID (the "description" part of the line): >SeqID product The detailed one consists of a special encoded three-part description line. The parts are the /EC_number , the /gene code, then the /product - and they are separated by a special "~~~" sequence: >SeqID EC_number~~~gene~~~product~~~COG Here are some examples. Note that not all parts need to be present, but the "~~~" should still be there: >YP_492693.1 2.1.1.48~~~ermC~~~rRNA adenine N-6-methyltransferase~~~COG1234 MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEI DHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVF* >YP_492697.1 ~~~traB~~~transfer complex protein TraB~~~ MIKKFSLTTVYVAFLSIVLSNITLGAENPGPKIEQGLQQVQTFLTGLIVAVGICAGVWIV LKKLPGIDDPMVKNEMFRGVGMVLAGVAVGAALVWLVPWVYNLFQ* >YP_492694.1 ~~~~~~transposase~~~ MNYFRYKQFNKDVITVAVGYYLRYALSYRDISEILRGRGVNVHHSTVYRWVQEYAPILYQ QSINTAKNTLKGIECIYALYKKNRRSLQIYGFSPCHEISIMLAS* The same description lines apply to HMM models, except the "NAME" and "DESC" fields are used: NAME PRK00001 ACC PRK00001 DESC 2.1.1.48~~~ermC~~~rRNA adenine N-6-methyltransferase~~~COG1234 LENG 284 FAQ Where does the name "Prokka" come from? Prokka is a contraction of "prokaryotic annotation". It's also relatively unique within Google, and also rhymes with a native Australian marsupial called the quokka. Can I annotate by eukaryote genome with Prokka? No. Prokka is specifically designed for Bacteria, Archaea and Viruses. It can't handle multi-exon gene models; I would recommend using MAKER 2 for that purpose. Why does Prokka keeps on crashing when it gets to the "tbl2asn" stage? It seems that the tbl2asn program from NCBI "expires" after 6-12 months, and refuses to run. Unfortunately you need to install a newer version which you can download from here . The hmmscan step seems to hang and do nothing? The problem here is GNU Parallel. It seems the Debian package for hmmer has modified it to require the --gnu option to behave in the 'default' way. There is no clear reason for this. The only way to restore normal behaviour is to edit the prokka script and change parallel to parallel --gnu . Why does prokka fail when it gets to hmmscan? Unfortunately HMMER keeps changing its database format, and they aren't upward compatible. If you upgraded HMMER (from 3.0 to 3.1 say) then you need to "re-press" the files. This can be done as follows: cd /path/to/prokka/db/hmm mkdir new for D in *.hmm ; do hmmconvert $D > new/$D ; done cd new for D in *.hmm ; do hmmpress $D ; done mv * .. rmdir new Why can't I load Prokka .GBK files into Mauve? Mauve uses BioJava to parse GenBank files, and it is very picky about Genbank files. It does not like long contig names, like those from Velvet or Spades. One solution is to use --centre XXX in Prokka and it will rename all your contigs to be NCBI (and Mauve) compliant. It does not like the ACCESSION and VERSION strings that Prokka produces via the "tbl2asn" tool. The following Unix command will fix them: egrep -v '^(ACCESSION|VERSION)' prokka.gbk > mauve.gbk How can I make my GFF not have the contig sequences in it? sed '/^##FASTA/Q' prokka.gff > nosequence.gff Dependencies Mandatory BioPerl Used for input/output of various file formats Stajich et al, The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002 Oct;12(10):1611-8. GNU Parallel A shell tool for executing jobs in parallel using one or more computers O. Tange, GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, Feb 2011:42-47. BLAST+ Used for similarity searching against protein sequence libraries Camacho C et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421. Prodigal Finds protein-coding features (CDS) Hyatt D et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11:119. TBL2ASN Prepare sequence records for Genbank submission Tbl2asn home page Recommended Aragorn Finds transfer RNA features (tRNA) Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Re + +### https://github.com/tseemann/prokka +GitHub - tseemann/prokka: :zap: Rapid prokaryotic genome annotation · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} tseemann / prokka Public Notifications You must be signed in to change notification settings Fork 235 Star 976 Code Issues 226 Pull requests 17 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights tseemann/prokka master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 350 Commits 350 Commits .github/ workflows .github/ workflows bin bin db db doc doc test test update-dbs update-dbs .gitignore .gitignore CITATION.cff CITATION.cff CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md LICENSE LICENSE README.md README.md environment.yml environment.yml View all files Repository files navigation README Code of conduct GPL-3.0 license Prokka: rapid prokaryotic genome annotation Introduction Whole genome annotation is the process of identifying features of interest in a set of genomic DNA sequences, and labelling them with useful information. Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Bakta is the next generation of Prokka Prokka has served the community well for over a decade. I can no longer maintain it, so, with my blessing and gratitude, Oliver Schwengers has taken the bacterial annotation toruch and developed Bakta which is a modern version of Prokka with better tooling and maintained databases, including db-light which is in the spirit of Prokka's "fast and lean" approach. I recommend replacing Prokka with Bakta in your analysis pipelines going forward. Installation Bioconda The best way to install Prokka is using Conda ( miniforge ). conda create -n prokka bioconda::prokka conda activate prokka prokka --version Docker Maintained by STAPHB : docker pull staphb/prokka:latest docker run staphb/prokka:latest prokka --version Singularity singularity build prokka.sif docker://staphb/prokka:latest singularity exec prokka.sif prokka -h Test Type prokka and it should output its help screen. Type prokka --version and you should see an output like prokka 1.x Type prokka --listdb and it will show you what databases it has installed to use. Invoking Prokka Beginner # Vanilla (but with free toppings) % prokka contigs.fa # Look for a folder called PROKKA_yyyymmdd (today's date) and look at stats % cat PROKKA_yyyymmdd/*.txt Moderate # Choose the names of the output files % prokka --outdir mydir --prefix mygenome contigs.fa # Visualize it in Artemis % art mydir/mygenome.gff Specialist # Have curated genomes I want to use to annotate from % prokka --proteins MG1655.gbk --outdir mutant --prefix K12_mut contigs.fa # Look at tabular features % less -S mutant/K12_mut.tsv Expert # It's not just for bacteria, people % prokka --kingdom Archaea --outdir mydir --genus Pyrococcus --locustag PYCC # Search for your favourite gene % exonerate --bestn 1 zetatoxin.fasta mydir/PYCC_06072012.faa | less Wizard # Watch and learn % prokka --outdir mydir --locustag EHEC --proteins NewToxins.faa --evalue 0.001 --gram neg --addgenes contigs.fa # Check to see if anything went really wrong % less mydir/EHEC_06072012.err # Add final details using Sequin % sequin mydir/EHEC_0607201.sqn NCBI Genbank submitter # Register your BioProject (e.g. PRJNA123456) and your locus_tag prefix (e.g. EHEC) first! % prokka --compliant --centre UoN --outdir PRJNA123456 --locustag EHEC --prefix EHEC-Chr1 contigs.fa # Check to see if anything went really wrong % less PRJNA123456/EHEC-Chr1.err # Add final details using Sequin % sequin PRJNA123456/EHEC-Chr1.sqn European Nucleotide Archive (ENA) submitter # Register your BioProject (e.g. PRJEB12345) and your locus_tag (e.g. EHEC) prefix first! % prokka --compliant --centre UoN --outdir PRJEB12345 --locustag EHEC --prefix EHEC-Chr1 contigs.fa # Check to see if anything went really wrong % less PRJNA123456/EHEC-Chr1.err # Install and run Sanger Pathogen group's Prokka GFF3 to EMBL converter # available from https://github.com/sanger-pathogens/gff3toembl # Find the closest NCBI taxonomy id (e.g. 562 for Escherichia coli) % gff3_to_embl -i "Submitter, A." \ -m "Escherichia coli EHEC annotated using Prokka." \ -g linear -c PROK -n 11 -f PRJEB12345/EHEC-Chr1.embl \ "Escherichia coli" 562 PRJEB12345 "Escherichia coli strain EHEC" PRJEB12345/EHEC-Chr1.gff # Download and run the latest EMBL validator prior to submitting the EMBL flat file # from http://central.maven.org/maven2/uk/ac/ebi/ena/sequence/embl-api-validator/ # which at the time of writing is v1.1.129 % curl -L -O http://central.maven.org/maven2/uk/ac/ebi/ena/sequence/embl-api-validator/1.1.129/embl-api-validator-1.1.129.jar % java -jar embl-api-validator-1.1.129.jar -r PRJEB12345/EHEC-Chr1.embl # Compress the file ready to upload to ENA, and calculate MD5 checksum % gzip PRJEB12345/EHEC-Chr1.embl % md5sum PRJEB12345/EHEC-Chr1.embl.gz Crazy Person # No stinking Perl script is going to control me % prokka \ --outdir $HOME/genomes/Ec_POO247 --force \ --prefix Ec_POO247 --addgenes --locustag ECPOOp \ --increment 10 --gffver 2 --centre CDC --compliant \ --genus Escherichia --species coli --strain POO247 --plasmid pECPOO247 \ --kingdom Bacteria --gcode 11 --usegenus \ --proteins /opt/prokka/db/trusted/Ecocyc-17.6 \ --evalue 1e-9 --rfam \ plasmid-closed.fna Output Files Extension Description .gff This is the master annotation in GFF3 format, containing both sequences and annotations. It can be viewed directly in Artemis or IGV. .gbk This is a standard Genbank file derived from the master .gff. If the input to prokka was a multi-FASTA, then this will be a multi-Genbank, with one record for each sequence. .fna Nucleotide FASTA file of the input contig sequences. .faa Protein FASTA file of the translated CDS sequences. .ffn Nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) .sqn An ASN1 format "Sequin" file for submission to Genbank. It needs to be edited to set the correct taxonomy, authors, related publication etc. .fsa Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines. .tbl Feature Table file, used by "tbl2asn" to create the .sqn file. .err Unacceptable annotations - the NCBI discrepancy report. .log Contains all the output that Prokka produced during its run. This is a record of what settings you used, even if the --quiet option was enabled. .txt Statistics relating to the annotated features found. .tsv Tab-separated file of all features: locus_tag,ftype,len_bp,gene,EC_number,COG,product Command line options General: --help This help --version Print version and exit --citation Print citation for referencing Prokka --quiet No screen output (default OFF) --debug Debug mode: keep all temporary files (default OFF) Setup: --listdb List all configured databases --setupdb Index all installed databases --cleandb Remove all database indices --depends List all software dependencies Outputs: --outdir [X] Output folder [auto] (default '') --force Force overwriting existing output folder (default OFF) --prefix [X] Filename output prefix [auto] (default '') --addgenes Add 'gene' features for each 'CDS' feature (default OFF) --locustag [X] Locus tag prefix (default 'PROKKA') --increment [N] Locus tag counter increment (default '1') --gffver [N] GFF version (default '3') --compliant Force Genbank/ENA/DDJB compliance: --genes --mincontiglen 200 --centre XXX (default OFF) --centre [X] Sequencing centre ID. (default '') Organism details: --genus [X] Genus name (default 'Genus') --species [X] Species name (default 'species') --strain [X] Strain name (default 'strain') --plasmid [X] Plasmid name or identifier (default '') Annotations: --kingdom [X] Annotation mode: Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria') --gcode [N] Genetic code / Translation table (set if --kingdom is set) (default '0') --prodigaltf [X] Prodigal training file (default '') --gram [X] Gram: -/neg +/pos (default '') --usegenus Use genus-specific BLAST databases (needs --genus) (default OFF) --proteins [X] Fasta file of trusted proteins to first annotate from (default '') --hmms [X] Trusted HMM to first annotate from (default '') --metagenome Improve gene predictions for highly fragmented genomes (default OFF) --rawproduct Do not clean up /product annotation (default OFF) Computation: --fast Fast mode - skip CDS /product searching (default OFF) --cpus [N] Number of CPUs to use [0=all] (default '8') --mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1') --evalue [n.n] Similarity e-value cut-off (default '1e-06') --rfam Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0') --norrna Don't run rRNA search (default OFF) --notrna Don't run tRNA search (default OFF) --rnammer Prefer RNAmmer over Barrnap for rRNA prediction (default OFF) Option: --proteins The --proteins option is recommended when you have good quality reference genomes and want to ensure gene naming is consistent. Some species use specific terminology which will be often lost if you rely on the default Swiss-Prot database included with Prokka. If you have Genbank or Protein FASTA file(s) that you want to annotate genes from as the first priority, use the --proteins myfile.gbk . Please make sure it has a recognisable file extension like .gb or .gbk or auto-detect will fail. The use of Genbank is recommended over FASTA, because it will provide /gene and /EC_number annotations that a typical .faa file will not provide, unless you have specially formatted it for Prokka . Option: --prodigaltf Instead of letting prodigal train its gene model on the contigs you provide, you can pre-train it on some good closed reference genomes first using the prodigal -t option. Once you've done that, provide prokka the training file using the --prodgialtf option. Option: --rawproduct Prokka annotates proteins by using sequence similarity to other proteins in its database, or the databases the user provides via --proteins . By default, Prokka tries to "cleans" the /product names to ensure they are compliant with Genbank/ENA conventions. Some of the main things it does is: set vague names to hypothetical protein consistifies terms like possible , probable , predicted , ... to putative removes EC, COG and locus_tag identifiers Full details can be found in the cleanup_product() function in the prokka script. If you feel your annotations are being ruined, try using the --rawproduct option, and please file an issue if you find an example of where it is "behaving badly" and I will fix it. Databases The Core (BLAST+) Databases Prokka uses a variety of databases when trying to assign function to the predicted CDS features. It takes a hierarchical approach to make it fast. A small, core set of well characterized proteins are first searched using BLAST+. This combination of small database and fast search typically completes about 70% of the workload. Then a series of slower but more sensitive HMM databases are searched using HMMER3. The three core databases, applied in order, are: ISfinder : Only the tranposase (protein) sequences; the whole transposon is not annotated. NCBI Bacterial Antimicrobial Resistance Reference Gene Database : Antimicrobial resistance genes curated by NCBI. UniProtKB (SwissProt) : For each --kingdom we include curated proteins with evidence that (i) from Bacteria (or Archaea or Viruses); (ii) not be "Fragment" entries; and (iii) have an evidence level ("PE") of 2 or lower, which corresponds to experimental mRNA or proteomics evidence. Making a Core Databases If you want to modify these core databases, the included script prokka-uniprot_to_fasta_db , along with the official uniprot_sprot.dat , can be used to generate a new database to put in /opt/prokka/db/kingdom/ . If you add new ones, the command prokka --listdb will show you whether it has been detected properly. The Genus Databases ⚠️ This is no longer recommended. Please use --proteins instead. If you enable --usegenus and also provide a Genus via --genus then it will first use a BLAST database which is Genus specific. Prokka comes with a set of databases for the most common Bacterial genera; type prokka --listdb to see what they are. Adding a Genus Databases If you have a set of Genbank files and want to create a new Genus database, Prokka comes with a tool called prokka-genbank_to_fasta_db to help. For example, if you had four annotated "Coccus" genomes, you could do the following: % prokka-genbank_to_fasta_db Coccus1.gbk Coccus2.gbk Coccus3.gbk Coccus4.gbk > Coccus.faa % cd-hit -i Coccus.faa -o Coccus -T 0 -M 0 -g 1 -s 0.8 -c 0.9 % rm -fv Coccus.faa Coccus.bak.clstr Coccus.clstr % makeblastdb -dbtype prot -in Coccus % mv Coccus.p* /path/to/prokka/db/genus/ The HMM Databases Prokka comes with a bunch of HMM libraries for HMMER3. They are mostly Bacteria-specific. They are searched after the core and genus databases. You can add more simply by putting them in /opt/prokka/db/hmm . Type prokka --listdb to confirm they are recognised. FASTA database format Prokka understands two annotation tag formats, a plain one and a detailed one. The plain one is a standard FASTA-like line with the ID after the > sign, and the protein /product after the ID (the "description" part of the line): >SeqID product The detailed one consists of a special encoded three-part description line. The parts are the /EC_number , the /gene code, then the /product - and they are separated by a special "~~~" sequence: >SeqID EC_number~~~gene~~~product~~~COG Here are some examples. Note that not all parts need to be present, but the "~~~" should still be there: >YP_492693.1 2.1.1.48~~~ermC~~~rRNA adenine N-6-methyltransferase~~~COG1234 MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEI DHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVF* >YP_492697.1 ~~~traB~~~transfer complex protein TraB~~~ MIKKFSLTTVYVAFLSIVLSNITLGAENPGPKIEQGLQQVQTFLTGLIVAVGICAGVWIV LKKLPGIDDPMVKNEMFRGVGMVLAGVAVGAALVWLVPWVYNLFQ* >YP_492694.1 ~~~~~~transposase~~~ MNYFRYKQFNKDVITVAVGYYLRYALSYRDISEILRGRGVNVHHSTVYRWVQEYAPILYQ QSINTAKNTLKGIECIYALYKKNRRSLQIYGFSPCHEISIMLAS* The same description lines apply to HMM models, except the "NAME" and "DESC" fields are used: NAME PRK00001 ACC PRK00001 DESC 2.1.1.48~~~ermC~~~rRNA adenine N-6-methyltransferase~~~COG1234 LENG 284 FAQ Where does the name "Prokka" come from? Prokka is a contraction of "prokaryotic annotation". It's also relatively unique within Google, and also rhymes with a native Australian marsupial called the quokka. Can I annotate by eukaryote genome with Prokka? No. Prokka is specifically designed for Bacteria, Archaea and Viruses. It can't handle multi-exon gene models; I would recommend using MAKER 2 for that purpose. Why does Prokka keeps on crashing when it gets to the "tbl2asn" stage? It seems that the tbl2asn program from NCBI "expires" after 6-12 months, and refuses to run. Unfortunately you need to install a newer version which you can download from here . The hmmscan step seems to hang and do nothing? The problem here is GNU Parallel. It seems the Debian package for hmmer has modified it to require the --gnu option to behave in the 'default' way. There is no clear reason for this. The only way to restore normal behaviour is to edit the prokka script and change parallel to parallel --gnu . Why does prokka fail when it gets to hmmscan? Unfortunately HMMER keeps changing its database format, and they aren't upward compatible. If you upgraded HMMER (from 3.0 to 3.1 say) then you need to "re-press" the files. This can be done as follows: cd /path/to/prokka/db/hmm mkdir new for D in *.hmm ; do hmmconvert $D > new/$D ; done cd new for D in *.hmm ; do hmmpress $D ; done mv * .. rmdir new Why can't I load Prokka .GBK files into Mauve? Mauve uses BioJava to parse GenBank files, and it is very picky about Genbank files. It does not like long contig names, like those from Velvet or Spades. One solution is to use --centre XXX in Prokka and it will rename all your contigs to be NCBI (and Mauve) compliant. It does not like the ACCESSION and VERSION strings that Prokka produces via the "tbl2asn" tool. The following Unix command will fix them: egrep -v '^(ACCESSION|VERSION)' prokka.gbk > mauve.gbk How can I make my GFF not have the contig sequences in it? sed '/^##FASTA/Q' prokka.gff > nosequence.gff Dependencies Mandatory BioPerl Used for input/output of various file formats Stajich et al, The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002 Oct;12(10):1611-8. GNU Parallel A shell tool for executing jobs in parallel using one or more computers O. Tange, GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, Feb 2011:42-47. BLAST+ Used for similarity searching against protein sequence libraries Camacho C et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421. Prodigal Finds protein-coding features (CDS) Hyatt D et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11:119. TBL2ASN Prepare sequence records for Genbank submission Tbl2asn home page Recommended Aragorn Finds transfer RNA features (tRNA) Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Re + +## Conda Search Info +$ conda search -c bioconda -c conda-forge prokka --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +prokka 1.11 0 +------------- +file name : prokka-1.11-0.tar.bz2 +name : prokka +version : 1.11 +build : 0 +build number: 0 +size : 172.5 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.11-0.tar.bz2 +md5 : 04185c6824bcc2f2190ed622eb862963 +dependencies: + - aragorn + - barrnap >=0.7 + - blast + - hmmer >=3.1b2 + - infernal >=1.1.1 + - minced + - parallel + - perl-bioperl + - perl-xml-simple + - prodigal + - tbl2asn + + +prokka 1.12 1 +------------- +file name : prokka-1.12-1.tar.bz2 +name : prokka +version : 1.12 +build : 1 +build number: 1 +size : 187.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.12-1.tar.bz2 +md5 : 4c38f970faf2c6c6c98f80d320045091 +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.2 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.2 + - parallel >=20130422 + - perl-bioperl ==1.6.924 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.3 + + +prokka 1.12 2 +------------- +file name : prokka-1.12-2.tar.bz2 +name : prokka +version : 1.12 +build : 2 +build number: 2 +size : 187.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.12-2.tar.bz2 +md5 : abf262d4a1650c1d6ec88c65331188f0 +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.6 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.2 + - parallel >=20130422 + - perl-bioperl ==1.6.924 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.3 + + +prokka 1.12 3 +------------- +file name : prokka-1.12-3.tar.bz2 +name : prokka +version : 1.12 +build : 3 +build number: 3 +size : 187.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.12-3.tar.bz2 +md5 : 97c9a25c48797ad98cdcbf240c669bad +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.6 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - libidn + - minced >=0.2 + - parallel >=20130422 + - perl-bioperl ==1.6.924 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.3 + + +prokka 1.12 4 +------------- +file name : prokka-1.12-4.tar.bz2 +name : prokka +version : 1.12 +build : 4 +build number: 4 +size : 187.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.12-4.tar.bz2 +md5 : b7cfe1860d81c089e6440dc35ee345dc +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.6 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.2 + - parallel >=20130422 + - perl-bioperl ==1.6.924 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.6 + + +prokka 1.12 pl526_0 +------------------- +file name : prokka-1.12-pl526_0.tar.bz2 +name : prokka +version : 1.12 +build : pl526_0 +build number: 0 +size : 187.7 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.12-pl526_0.tar.bz2 +md5 : 916c0a5d969a7658f24a28743f2cbe5c +timestamp : 2018-12-27 22:49:17 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.3 + - parallel >=20180522 + - perl >=5.26.2,<5.26.3.0a0 + - perl-bioperl >=1.7.2 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.6 + + +prokka 1.13 0 +------------- +file name : prokka-1.13-0.tar.bz2 +name : prokka +version : 1.13 +build : 0 +build number: 0 +size : 188.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.13-0.tar.bz2 +md5 : 6b20b2590340554fa2a3c8a216bef8cf +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.6 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.2 + - parallel >=20130422 + - perl-bioperl ==1.6.924 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.6 + + +prokka 1.13 1 +------------- +file name : prokka-1.13-1.tar.bz2 +name : prokka +version : 1.13 +build : 1 +build number: 1 +size : 188.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.13-1.tar.bz2 +md5 : 053e96374d15776f0b6c27136bae8bd5 +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.2 + - parallel >=20130422 + - perl-bioperl ==1.6.924 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.6 + + +prokka 1.13 2 +------------- +file name : prokka-1.13-2.tar.bz2 +name : prokka +version : 1.13 +build : 2 +build number: 2 +size : 188.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.13-2.tar.bz2 +md5 : 88caba01cc05b565973ebc8464a58da7 +timestamp : 2018-07-16 12:43:28 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.2 + - parallel >=20130422 + - perl-bioperl 1.6.924 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.6 + + +prokka 1.13 3 +------------- +file name : prokka-1.13-3.tar.bz2 +name : prokka +version : 1.13 +build : 3 +build number: 3 +size : 188.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.13-3.tar.bz2 +md5 : 048d50e78811ac9f152b5fd054587c68 +timestamp : 2018-08-16 19:46:58 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.2 + - parallel >=20130422 + - perl-bioperl >=1.7.2 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.6 + + +prokka 1.13 pl526_4 +------------------- +file name : prokka-1.13-pl526_4.tar.bz2 +name : prokka +version : 1.13 +build : pl526_4 +build number: 4 +size : 188.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.13-pl526_4.tar.bz2 +md5 : 60e18968d21c2c305dfb9672526ca1d9 +timestamp : 2018-08-23 11:36:57 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.3 + - parallel >=20180522 + - perl >=5.26.2,<5.26.3.0a0 + - perl-bioperl >=1.7.2 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.6 + + +prokka 1.13.3 pl526_0 +--------------------- +file name : prokka-1.13.3-pl526_0.tar.bz2 +name : prokka +version : 1.13.3 +build : pl526_0 +build number: 0 +size : 191.0 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.13.3-pl526_0.tar.bz2 +md5 : b64a6288561d610fc374ee55d0019054 +timestamp : 2018-09-05 23:42:13 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.3 + - parallel >=20180522 + - perl >=5.26.2,<5.26.3.0a0 + - perl-bioperl >=1.7.2 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.6 + + +prokka 1.13.4 pl526_0 +--------------------- +file name : prokka-1.13.4-pl526_0.tar.bz2 +name : prokka +version : 1.13.4 +build : pl526_0 +build number: 0 +size : 191.0 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/prokka-1.13.4-pl526_0.tar.bz2 +md5 : f13216a1314a0006efdc8fde861ec0d1 +timestamp : 2018-12-18 04:04:34 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.3 + - parallel >=20180522 + - perl >=5.26.2,<5.26.3.0a0 + - perl-bioperl >=1.7.2 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.6 + + +prokka 1.13.7 pl526_0 +--------------------- +file name : prokka-1.13.7-pl526_0.tar.bz2 +name : prokka +version : 1.13.7 +build : pl526_0 +build number: 0 +size : 191.0 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/prokka-1.13.7-pl526_0.tar.bz2 +md5 : 9f654ec11da32e245bd6b21f4663834b +timestamp : 2019-06-18 21:30:04 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.3 + - parallel >=20180522 + - perl >=5.26.2,<5.26.3.0a0 + - perl-bioperl >=1.7.2 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.6 + + +prokka 1.14.0 pl526_0 +--------------------- +file name : prokka-1.14.0-pl526_0.tar.bz2 +name : prokka +version : 1.14.0 +build : pl526_0 +build number: 0 +size : 191.0 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/prokka-1.14.0-pl526_0.tar.bz2 +md5 : 2232598a94a209f8dddc6b3157301add +timestamp : 2019-08-09 08:23:09 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.3 + - parallel >=20180522 + - perl >=5.26.2,<5.26.3.0a0 + - perl-bioperl >=1.7.2 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.7 + + +prokka 1.14.0 pl526_1 +--------------------- +file name : prokka-1.14.0-pl526_1.tar.bz2 +name : prokka +version : 1.14.0 +build : pl526_1 +build number: 1 +size : 191.0 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/prokka-1.14.0-pl526_1.tar.bz2 +md5 : 90ecab3fe78a8f75b63061e55bfe2759 +timestamp : 2019-10-27 16:21:29 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.3 + - parallel >=20180522 + - perl >=5.26.2,<5.26.3.0a0 + - perl-bioperl >=1.7.2 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.7 + + +prokka 1.14.5 pl526_0 +--------------------- +file name : prokka-1.14.5-pl526_0.tar.bz2 +name : prokka +version : 1.14.5 +build : pl526_0 +build number: 0 +size : 212.7 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/prokka-1.14.5-pl526_0.tar.bz2 +md5 : 32b1e482c35b772137488ea39d436a4b +timestamp : 2019-11-11 19:41:52 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.3 + - parallel >=20180522 + - perl >=5.26.2,<5.26.3.0a0 + - perl-bioperl >=1.7.2 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn >=25.7 + + +prokka 1.14.5 pl526_1 +--------------------- +file name : prokka-1.14.5-pl526_1.tar.bz2 +name : prokka +version : 1.14.5 +build : pl526_1 +build number: 1 +size : 212.7 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/prokka-1.14.5-pl526_1.tar.bz2 +md5 : 5b750c0568a04061f03fbe04b211394c +timestamp : 2020-02-17 21:21:23 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 + - minced >=0.3 + - parallel >=20180522 + - perl >=5.26.2,<5.26.3.0a0 + - perl-bioperl >=1.7.2 + - perl-xml-simple + - prodigal >=2.6 + - tbl2asn-forever >=25.7 + + +prokka 1.14.6 pl5262hdfd78af_1 +------------------------------ +file name : prokka-1.14.6-pl5262hdfd78af_1.tar.bz2 +name : prokka +version : 1.14.6 +build : pl5262hdfd78af_1 +build number: 1 +size : 212.7 MB +license : GPLv2 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/prokka-1.14.6-pl5262hdfd78af_1.tar.bz2 +md5 : d1f48b941fb8379e4582647ac046fbf6 +timestamp : 2021-03-26 18:37:23 UTC +dependencies: + - aragorn >=1.2 + - barrnap >=0.7 + - blast >=2.7.1 + - hmmer >=3.1b2 + - infernal >=1.1.2 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/proteinortho.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/proteinortho.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..88b9cee1745a53c84439f920dbbf58f830b9a931 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/proteinortho.manual_bundle.txt @@ -0,0 +1,506 @@ +# Tool: proteinortho +software_name: proteinortho +tier: T1 +domain: t1_backfill_overall +downloads: 190698 +summary: Proteinortho is a tool to detect orthologous genes within different species. +description: Proteinortho is a tool to detect orthologous genes within different species. +dependencies: _openmp_mutex >=4.5, diamond >=0.9.29, libblas >=3.9.0,<4.0a0, libgcc >=13, libgfortran, libgfortran5 >=13.3.0, libgomp, liblapacke >=3.9.0,<4.0a0, libstdcxx >=13, perl, python +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://gitlab.com/paulklemm_PHD/proteinortho/ +doc_url: https://gitlab.com/paulklemm_PHD/proteinortho/-/blob/master/README.md +dev_url: https://gitlab.com/paulklemm_PHD/proteinortho + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://gitlab.com/paulklemm_PHD/proteinortho/ +PHD / proteinortho · GitLab proteinortho Project information Proteinortho is a tool to detect orthologous genes within different species. (Download) Read more orthology in... orthology bioinformatics 812 Commits 1 Branch 60 Tags 57 Releases README GNU General Public License v3.0 or later CHANGELOG Created on June 28, 2018 Loading + +### https://gitlab.com/paulklemm_PHD/proteinortho +PHD / proteinortho · GitLab proteinortho Project information Proteinortho is a tool to detect orthologous genes within different species. (Download) Read more orthology in... orthology bioinformatics 812 Commits 1 Branch 60 Tags 57 Releases README GNU General Public License v3.0 or later CHANGELOG Created on June 28, 2018 Loading + +## Conda Search Info +$ conda search -c bioconda -c conda-forge proteinortho --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +proteinortho 6.0b py27pl526h9ad8f1e_0 +------------------------------------- +file name : proteinortho-6.0b-py27pl526h9ad8f1e_0.tar.bz2 +name : proteinortho +version : 6.0b +build : py27pl526h9ad8f1e_0 +build number: 0 +size : 8.3 MB +license : GNU-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0b-py27pl526h9ad8f1e_0.tar.bz2 +md5 : 94d55ad172a482363172bf99082091c4 +timestamp : 2019-04-29 12:53:31 UTC +dependencies: + - diamond + - lapack + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl >=5.26.2,<5.26.3.0a0 + - python >=2.7,<2.8.0a0 + + +proteinortho 6.0b py36pl526h9ad8f1e_0 +------------------------------------- +file name : proteinortho-6.0b-py36pl526h9ad8f1e_0.tar.bz2 +name : proteinortho +version : 6.0b +build : py36pl526h9ad8f1e_0 +build number: 0 +size : 8.3 MB +license : GNU-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0b-py36pl526h9ad8f1e_0.tar.bz2 +md5 : 7494670663c3b2cf9ef8f135c4cacf4f +timestamp : 2019-04-29 12:51:44 UTC +dependencies: + - diamond + - lapack + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl >=5.26.2,<5.26.3.0a0 + - python >=3.6,<3.7.0a0 + + +proteinortho 6.0b py37pl526h9ad8f1e_0 +------------------------------------- +file name : proteinortho-6.0b-py37pl526h9ad8f1e_0.tar.bz2 +name : proteinortho +version : 6.0b +build : py37pl526h9ad8f1e_0 +build number: 0 +size : 8.3 MB +license : GNU-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0b-py37pl526h9ad8f1e_0.tar.bz2 +md5 : 8eaff4115c4672aec811fffd5dc172a9 +timestamp : 2019-04-29 12:55:29 UTC +dependencies: + - diamond + - lapack + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl >=5.26.2,<5.26.3.0a0 + - python >=3.7,<3.8.0a0 + + +proteinortho 6.0 py27pl526h9ad8f1e_0 +------------------------------------ +file name : proteinortho-6.0-py27pl526h9ad8f1e_0.tar.bz2 +name : proteinortho +version : 6.0 +build : py27pl526h9ad8f1e_0 +build number: 0 +size : 8.3 MB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0-py27pl526h9ad8f1e_0.tar.bz2 +md5 : fc3068fedde6ae1c815b80bfabc0bab2 +timestamp : 2019-05-08 18:26:09 UTC +dependencies: + - diamond + - lapack + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl >=5.26.2,<5.26.3.0a0 + - python >=2.7,<2.8.0a0 + + +proteinortho 6.0 py36pl526h9ad8f1e_0 +------------------------------------ +file name : proteinortho-6.0-py36pl526h9ad8f1e_0.tar.bz2 +name : proteinortho +version : 6.0 +build : py36pl526h9ad8f1e_0 +build number: 0 +size : 8.3 MB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0-py36pl526h9ad8f1e_0.tar.bz2 +md5 : 93584532ecc33f196440a9b2000cdeb7 +timestamp : 2019-05-08 18:28:02 UTC +dependencies: + - diamond + - lapack + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl >=5.26.2,<5.26.3.0a0 + - python >=3.6,<3.7.0a0 + + +proteinortho 6.0 py37pl526h9ad8f1e_0 +------------------------------------ +file name : proteinortho-6.0-py37pl526h9ad8f1e_0.tar.bz2 +name : proteinortho +version : 6.0 +build : py37pl526h9ad8f1e_0 +build number: 0 +size : 8.3 MB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0-py37pl526h9ad8f1e_0.tar.bz2 +md5 : db4c3de8f7e71dcd95a2eebd97653749 +timestamp : 2019-05-08 18:29:58 UTC +dependencies: + - diamond + - lapack + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl >=5.26.2,<5.26.3.0a0 + - python >=3.7,<3.8.0a0 + + +proteinortho 6.0.1 h9428810_0 +----------------------------- +file name : proteinortho-6.0.1-h9428810_0.tar.bz2 +name : proteinortho +version : 6.0.1 +build : h9428810_0 +build number: 0 +size : 7.8 MB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.1-h9428810_0.tar.bz2 +md5 : 05a1c605d32af454adae468dc6f5d767 +timestamp : 2019-05-12 12:39:33 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.3,<0.3.4.0a0 + - openmp + - perl + - python + + +proteinortho 6.0.2c h9428810_0 +------------------------------ +file name : proteinortho-6.0.2c-h9428810_0.tar.bz2 +name : proteinortho +version : 6.0.2c +build : h9428810_0 +build number: 0 +size : 164 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.2c-h9428810_0.tar.bz2 +md5 : d3708bdb8676112e12425cbb06fe12aa +timestamp : 2019-05-29 10:52:44 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.3,<0.3.4.0a0 + - openmp + - perl + - python + + +proteinortho 6.0.3 h9428810_0 +----------------------------- +file name : proteinortho-6.0.3-h9428810_0.tar.bz2 +name : proteinortho +version : 6.0.3 +build : h9428810_0 +build number: 0 +size : 164 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.3-h9428810_0.tar.bz2 +md5 : 3efc3a0b8014a8c24b00a29ca5900ca4 +timestamp : 2019-06-06 12:30:30 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.3,<0.3.4.0a0 + - openmp + - perl + - python + + +proteinortho 6.0.4 h9428810_0 +----------------------------- +file name : proteinortho-6.0.4-h9428810_0.tar.bz2 +name : proteinortho +version : 6.0.4 +build : h9428810_0 +build number: 0 +size : 165 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.4-h9428810_0.tar.bz2 +md5 : 1c512f8c1544a5c3d573c432e8d847db +timestamp : 2019-06-30 11:19:30 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.3,<0.3.4.0a0 + - openmp + - perl + - python + + +proteinortho 6.0.5 h9428810_0 +----------------------------- +file name : proteinortho-6.0.5-h9428810_0.tar.bz2 +name : proteinortho +version : 6.0.5 +build : h9428810_0 +build number: 0 +size : 165 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.5-h9428810_0.tar.bz2 +md5 : 67f9a55ac1fe5980e8cca314f0e856f9 +timestamp : 2019-07-01 08:41:32 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.3,<0.3.4.0a0 + - openmp + - perl + - python + + +proteinortho 6.0.6 h9428810_0 +----------------------------- +file name : proteinortho-6.0.6-h9428810_0.tar.bz2 +name : proteinortho +version : 6.0.6 +build : h9428810_0 +build number: 0 +size : 167 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.6-h9428810_0.tar.bz2 +md5 : dc1f986f1cd9b55fecc0a26183542b4d +timestamp : 2019-07-12 11:27:53 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.3,<0.3.4.0a0 + - openmp + - perl + - python + + +proteinortho 6.0.7 hfd40d39_0 +----------------------------- +file name : proteinortho-6.0.7-hfd40d39_0.tar.bz2 +name : proteinortho +version : 6.0.7 +build : hfd40d39_0 +build number: 0 +size : 167 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.7-hfd40d39_0.tar.bz2 +md5 : 23fd14be20502526b75bf0cab3607efd +timestamp : 2019-09-16 13:18:40 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - liblapacke >=3.8.0,<3.9.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl + - python + + +proteinortho 6.0.8 hfd40d39_0 +----------------------------- +file name : proteinortho-6.0.8-hfd40d39_0.tar.bz2 +name : proteinortho +version : 6.0.8 +build : hfd40d39_0 +build number: 0 +size : 167 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.8-hfd40d39_0.tar.bz2 +md5 : bb4b4e0fb99b3c3cab5cfe9898526a10 +timestamp : 2019-09-25 14:01:09 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - liblapacke >=3.8.0,<3.9.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl + - python + + +proteinortho 6.0.9 hfd40d39_0 +----------------------------- +file name : proteinortho-6.0.9-hfd40d39_0.tar.bz2 +name : proteinortho +version : 6.0.9 +build : hfd40d39_0 +build number: 0 +size : 167 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.9-hfd40d39_0.tar.bz2 +md5 : 2f7002a55d5d8f06f9bb03871e470612 +timestamp : 2019-10-25 10:43:25 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - liblapacke >=3.8.0,<3.9.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl + - python + + +proteinortho 6.0.10 hfd40d39_0 +------------------------------ +file name : proteinortho-6.0.10-hfd40d39_0.tar.bz2 +name : proteinortho +version : 6.0.10 +build : hfd40d39_0 +build number: 0 +size : 167 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.10-hfd40d39_0.tar.bz2 +md5 : 1b996e410edba9d05c318fb4d552a658 +timestamp : 2019-11-05 12:24:19 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - liblapacke >=3.8.0,<3.9.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl + - python + + +proteinortho 6.0.11 hfd40d39_0 +------------------------------ +file name : proteinortho-6.0.11-hfd40d39_0.tar.bz2 +name : proteinortho +version : 6.0.11 +build : hfd40d39_0 +build number: 0 +size : 170 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.11-hfd40d39_0.tar.bz2 +md5 : cef7b4f947767266f88edf676384772a +timestamp : 2019-11-27 09:28:42 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - liblapacke >=3.8.0,<3.9.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl + - python + + +proteinortho 6.0.12 hfd40d39_0 +------------------------------ +file name : proteinortho-6.0.12-hfd40d39_0.tar.bz2 +name : proteinortho +version : 6.0.12 +build : hfd40d39_0 +build number: 0 +size : 173 KB +license : GNU GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/proteinortho-6.0.12-hfd40d39_0.tar.bz2 +md5 : f46ff34475adcb72a1cf8ed215fc8ec9 +timestamp : 2019-12-13 07:16:34 UTC +dependencies: + - diamond + - libgcc-ng >=7.3.0 + - libgfortran-ng >=7,<8.0a0 + - liblapacke >=3.8.0,<3.9.0a0 + - libstdcxx-ng >=7.3.0 + - openmp + - perl + - python + + +proteinortho 6.0.13 hfd40d39_0 +------------------------------ +file name : proteinortho-6.0.13-hfd40d39_0.tar.bz2 +name : proteinortho +version diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/proteomiqon-peptidespectrummatching.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/proteomiqon-peptidespectrummatching.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8017459b8ca0ae2cb92fb97c29a51d50a3b9a1e0 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/proteomiqon-peptidespectrummatching.manual_bundle.txt @@ -0,0 +1,161 @@ +# Tool: proteomiqon-peptidespectrummatching +software_name: proteomiqon-peptidespectrummatching +tier: T1 +domain: proteomics +downloads: 14550 +summary: Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST, Andromeda and XTandem. +description: Given raw a MS run in the mzLite or mzml format, this tool iterates accross all recorded MS/MS scans and determines the charge state of precursor +ions which were selected for fragmentation. With this it is possible to query the peptide data base for every precursor ion mass +/- a +tolerance (which defines the so called 'search space') and retrieve peptides that are theoretical candidates for a match. For each of the peptide +candidates we create an theoretical spectrum in silico and compare it to the measured MS/MS scan. +dependencies: dotnet-runtime 5.0.*, openssl 1.1.* +execution_environment: Other +execution_environment_reason: fallback runtime classification + +## URLs +home_url: https://csbiology.github.io/ProteomIQon/ +doc_url: https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html +dev_url: https://github.com/CSBiology/ProteomIQon + +## CLI Help Source +cli:proteomiqon-peptidespectrummatching +## CLI Help Content +$ conda run -n bioenv_cli proteomiqon-peptidespectrummatching --help +[rc=150] + +You must install or update .NET to run this application. + +App: /225040511/miniconda3/envs/bioenv_cli/bin/proteomiqon-peptidespectrummatching +Architecture: x64 +Framework: 'Microsoft.NETCore.App', version '5.0.0' (x64) +.NET location: /225040511/miniconda3/envs/bioenv_cli/lib/dotnet + +The following frameworks were found: + 10.0.0 at [/225040511/miniconda3/envs/bioenv_cli/lib/dotnet/shared/Microsoft.NETCore.App] + +Learn more: +https://aka.ms/dotnet/app-launch-failed + +To install missing framework, download: +https://aka.ms/dotnet-core-applaunch?framework=Microsoft.NETCore.App&framework_version=5.0.0&arch=x64&rid=linux-x64&os=ubuntu.22.04 + +ERROR conda.cli.main_run:execute(127): `conda run proteomiqon-peptidespectrummatching --help` failed. (See above for error) + + +## URL Docs Extract +### https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html +PeptideSpectrumMatching ProteomIQon General Home Tools MzMLToMzLite PeptideDB PeptideSpectrumMatching PSMStatistics PSMBasedQuantification ProteinInference QuantBasedAlignment AlignmentbasedQuantification AddDeducedPeptides JoinQuantPepIonsWithProteins LabelFreeProteinQuantification LabeledProteinQuantification Developer Notes How to create your own tool How to document your work How to build binaries or packages Powered By MzIO BioFSharp BioFSharp.Mz FSharp.Stats Deedle FSharp     Peptide Spectrum Matching Disclaimer this tool needs a peptide database to query against, if you did not create one yet you can do so by using the PeptideDB tool. An established method to identify acquired MS/MS spectra is the comparison of each spectrum with peptides in a reference database . Given raw a MS run in the mzLite or mzml format, this tool iterates accross all recorded MS/MS scans and determines the charge state of precursor ions which were selected for fragmentation. With this it is possible to query the peptide data base for every precursor ion mass +/- a tolerance (which defines the so called 'search space') and retrieve peptides that are theoretical candidates for a match. For each of the peptide candidates we create an theoretical spectrum in silico and compare it to the measured MS/MS scan. To measure similarity we use our own implementations of three established search enginge scores: SEQUEST, Andromeda and XTandem. The search space is extended by so called decoys. Decoys are reversed counterparts of peptides within the search space and allow us to assign a false discovery rate to each scored peptide using the PSMStatistics tool . Parameters The following table gives an overview of the parameter set: Parameter Default Value Description ChargeStateDeterminationParams {ExpectedMinimalCharge = 2; ExpectedMaximumCharge = 5; Width = 1.1; MinIntensity = 0.15; DeltaMinIntensity = 0.3; NrOfRndSpectra = 10000} Parameters used for the charge state determination of the peptides LookUpPPM 30 Mass range in Da in which potential peptides are selected MS2ScanRange 100.,2000. m/z range for MS2 spectra nTerminalSeries NTerminalSeries.B Considered ions starting from the N-Terminus cTerminalSeries CTerminalSeries.Y Considered ions starting from the C-Terminus Andromeda {PMinPMax = 4,10; MatchingIonTolerancePPM = 100.} Andromeda scoring parameters Parameter Generation Parameters are handed to the cli tool as a .json file. you can download the default file here , or use an F# script, which can be downloaded or run in Binder at the top of the page, to write your own parameter file: #r "nuget: BioFSharp.Mz, 0.1.5-beta" #r "nuget: Newtonsoft.Json, 12.0.3" #r "nuget: ProteomIQon, 0.0.5" open BioFSharp . Mz . SearchDB open Newtonsoft . Json open ProteomIQon open ProteomIQon . Domain open BioFSharp . Mz let chargeDetermParams : ChargeState . ChargeDetermParams = { ExpectedMinimalCharge = 2 ExpectedMaximumCharge = 5 Width = 1.1 MinIntensity = 0.15 DeltaMinIntensity = 0.3 NrOfRndSpectra = 10000 } let andromedaParams : AndromedaParams = { PMinPMax = 4 , 10 MatchingIonTolerancePPM = 100. } let peptideSpectrumMatchingParams : Dto . PeptideSpectrumMatchingParams = { ChargeStateDeterminationParams = chargeDetermParams LookUpPPM = 30. nTerminalSeries = NTerminalSeries . B cTerminalSeries = CTerminalSeries . Y Andromeda = andromedaParams } let serialized = peptideSpectrumMatchingParams |> JsonConvert . SerializeObject Executing the Tool Disclaimer this tool needs a peptide database to query against, if you did not create one yet you can do so by using the PeptideDB tool. To score all MS/MS of an MS run simply call: proteomiqon - peptidespectrummatching - i "path/to/your/run.mzml" - d "path/to/your/database.sqlite" - o "path/to/your/outDirectory" - p "path/to/your/params.json" It is also possible to call the tool on a list of MS files. If you have a mulitcore cpu it is possible to score multiple runs in parallel using the -c flag: proteomiqon - peptidespectrummatching - i "path/to/your/run1.mzml" "path/to/your/run2.mzml" "path/to/your/run3.mzml" - d "path/to/your/database.sqlite" - o "path/to/your/outDirectory" - p "path/to/your/params.json" - c 3 A detailed description of the CLI arguments the tool expects can be obtained by calling the tool: proteomiqon - peptidespectrummatching -- help namespace BioFSharp namespace BioFSharp.Mz module SearchDB from BioFSharp.Mz namespace Newtonsoft namespace Newtonsoft.Json namespace ProteomIQon module Domain from ProteomIQon val chargeDetermParams : ChargeState.ChargeDetermParams module ChargeState from BioFSharp.Mz type ChargeDetermParams =   { ExpectedMinimalCharge: int     ExpectedMaximumCharge: int     Width: float     MinIntensity: float     DeltaMinIntensity: float     NrOfRndSpectra: int } val andromedaParams : AndromedaParams type AndromedaParams =   { PMinPMax: int * int     MatchingIonTolerancePPM: float } val peptideSpectrumMatchingParams : Dto.PeptideSpectrumMatchingParams module Dto from ProteomIQon Multiple items module PeptideSpectrumMatchingParams from ProteomIQon.Dto -------------------- type PeptideSpectrumMatchingParams =   { ChargeStateDeterminationParams: ChargeDetermParams     LookUpPPM: float     nTerminalSeries: NTerminalSeries     cTerminalSeries: CTerminalSeries     Andromeda: AndromedaParams } Multiple items module NTerminalSeries from ProteomIQon.Common -------------------- type NTerminalSeries = (BioFSharp.IBioItem -> float) -> BioFSharp.AminoAcids.AminoAcid list -> PeakFamily<TaggedMass.TaggedMass> list union case NTerminalSeries.B: NTerminalSeries Multiple items module CTerminalSeries from ProteomIQon.Common -------------------- type CTerminalSeries = (BioFSharp.IBioItem -> float) -> BioFSharp.AminoAcids.AminoAcid list -> PeakFamily<TaggedMass.TaggedMass> list union case CTerminalSeries.Y: CTerminalSeries val serialized : string type JsonConvert =   static member DeserializeAnonymousType<'T> : value: string * anonymousTypeObject: 'T -> 'T + 1 overload   static member DeserializeObject : value: string -> obj + 7 overloads   static member DeserializeXNode : value: string -> XDocument + 3 overloads   static member DeserializeXmlNode : value: string -> XmlDocument + 3 overloads   static member EnsureDecimalPlace : value: float * text: string -> string + 1 overload   static member EnsureFloatFormat : value: float * text: string * floatFormatHandling: FloatFormatHandling * quoteChar: char * nullable: bool -> string   static member PopulateObject : value: string * target: obj -> unit + 1 overload   static member SerializeObject : value: obj -> string + 7 overloads   static member SerializeObjectInternal : value: obj * type: Type * jsonSerializer: JsonSerializer -> string   static member SerializeXNode : node: XObject -> string + 2 overloads   ... JsonConvert.SerializeObject(value: obj) : string JsonConvert.SerializeObject(value: obj, settings: JsonSerializerSettings) : string JsonConvert.SerializeObject(value: obj, [<System.ParamArray>] converters: JsonConverter []) : string JsonConvert.SerializeObject(value: obj, formatting: Formatting) : string JsonConvert.SerializeObject(value: obj, formatting: Formatting, settings: JsonSerializerSettings) : string JsonConvert.SerializeObject(value: obj, type: System.Type, settings: JsonSerializerSettings) : string JsonConvert.SerializeObject(value: obj, formatting: Formatting, [<System.ParamArray>] converters: JsonConverter []) : string JsonConvert.SerializeObject(value: obj, type: System.Type, formatting: Formatting, settings: JsonSerializerSettings) : string + +### https://csbiology.github.io/ProteomIQon/ +index ProteomIQon General Home Tools MzMLToMzLite PeptideDB PeptideSpectrumMatching PSMStatistics PSMBasedQuantification ProteinInference QuantBasedAlignment AlignmentbasedQuantification AddDeducedPeptides JoinQuantPepIonsWithProteins LabelFreeProteinQuantification LabeledProteinQuantification Developer Notes How to create your own tool How to document your work How to build binaries or packages Powered By MzIO BioFSharp BioFSharp.Mz FSharp.Stats Deedle FSharp The ProteomIQon The ProteomIQon is a collection of open source computational proteomics tools to build pipelines for the evaluation of MS derived proteomics data written in F#. The current state of the tool chain allows handle tasks like signal detection, peptide identification, quantification and protein inference. Each ProteomIQon tool is concerned with a specific task. This makes the tool-chain flexibel and easily extendable. An example of a prototypical chaining of tools to identify and quantify a mix of 14N and 15N labeled proteins can be found in the here . We are currently working on the cwl tool and workflow descriptions , so you can expect a to see more workflow graphs in the near future! All tools are available using nuget and soon via BioConda. Each tool is described in detail on its corresponding documentation page, accessible via the navigation pane, if you think a functionality is missing, feel free to contact us or to join us as a contributor! The Core Project The ProteomIQon core is referenced by all tools. It contains mainly serializable data transfer objects such as tool results and tool parameters, as well as their mapping to domain specific types. This is also the place for any kind of code reusable across tools such as thin wrappers around data readers, logging or CLI formatting. Documentation The documentation and tutorials for this library are automatically generated (using the F# Formatting) from .fsx and .md files in the docs folder. If you find a typo, please submit a pull request! Contributing Please refer to the CSB Contribution guidelines Community/Social Want to get in touch with us? We recently joined the twitter crowd: + +### https://github.com/CSBiology/ProteomIQon +GitHub - CSBiology/ProteomIQon · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} CSBiology / ProteomIQon Public Notifications You must be signed in to change notification settings Fork 6 Star 14 Code Issues 1 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights CSBiology/ProteomIQon dev Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 818 Commits 818 Commits .config .config .github .github ConsoleTemplate ConsoleTemplate build build docs docs docs_WIP docs_WIP lib lib src src tests tests testsOld testsOld .gitattributes .gitattributes .gitignore .gitignore .travis.yml .travis.yml CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md LICENSE.txt LICENSE.txt PULL_REQUEST_TEMPLATE.md PULL_REQUEST_TEMPLATE.md ProteomIQon.sln ProteomIQon.sln README.md README.md appveyor.yml appveyor.yml build.cmd build.cmd global.json global.json install tool.txt install tool.txt nuget.config nuget.config View all files Repository files navigation README Code of conduct Contributing MIT license The ProteomIQon The ProteomIQon is a collection of open source computational proteomics tools to build pipelines for the evaluation of MS derived proteomics data written in F#. Each tool is described in detail on its corresponding documentation page . The Core Project The ProteomIQon core is referenced by all tools. It contains mainly serializable data transfer objects such as tool results and tool parameters, as well as their mapping to domain specific types. This is also the place for any kind of code reusable across tools such as thin wrappers around data readers, logging or CLI formatting. Documentation The documentation and tutorials for this library are automatically generated (using the F# Formatting) from *.fsx and *.md files in the docs folder. If you find a typo, please submit a pull request! Contributing Please refer to the CSB Contribution guidelines Community/Social Want to get in touch with us? We recently joined the twitter crowd: Citation When using ProteomIQon in scientifc or commercial releases, please cite us using the following DOI: 10.5281/zenodo.6335068 About csbiology.github.io/ProteomIQon/ Resources Readme License MIT license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 14 stars Watchers 4 watching Forks 6 forks Report repository Releases 3 ProteomIQon_v0.0.7 Latest Dec 10, 2024 + 2 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages F# 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge proteomiqon-peptidespectrummatching --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +proteomiqon-peptidespectrummatching 0.0.3 hdfd78af_0 +---------------------------------------------------- +file name : proteomiqon-peptidespectrummatching-0.0.3-hdfd78af_0.tar.bz2 +name : proteomiqon-peptidespectrummatching +version : 0.0.3 +build : hdfd78af_0 +build number: 0 +size : 16.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/proteomiqon-peptidespectrummatching-0.0.3-hdfd78af_0.tar.bz2 +md5 : 3f3ef776b43ed5d36cbc9583a525b2ba +timestamp : 2021-05-12 17:35:22 UTC +dependencies: + - dotnet-runtime + + +proteomiqon-peptidespectrummatching 0.0.4 hdfd78af_0 +---------------------------------------------------- +file name : proteomiqon-peptidespectrummatching-0.0.4-hdfd78af_0.tar.bz2 +name : proteomiqon-peptidespectrummatching +version : 0.0.4 +build : hdfd78af_0 +build number: 0 +size : 16.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/proteomiqon-peptidespectrummatching-0.0.4-hdfd78af_0.tar.bz2 +md5 : fe411d04bfa748a3209d82ff00731597 +timestamp : 2021-05-25 13:38:20 UTC +dependencies: + - dotnet-runtime + + +proteomiqon-peptidespectrummatching 0.0.5 hdfd78af_0 +---------------------------------------------------- +file name : proteomiqon-peptidespectrummatching-0.0.5-hdfd78af_0.tar.bz2 +name : proteomiqon-peptidespectrummatching +version : 0.0.5 +build : hdfd78af_0 +build number: 0 +size : 16.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/proteomiqon-peptidespectrummatching-0.0.5-hdfd78af_0.tar.bz2 +md5 : 37e668d345c8b4da5c0e8642f036daee +timestamp : 2021-06-21 22:20:34 UTC +dependencies: + - dotnet-runtime + + +proteomiqon-peptidespectrummatching 0.0.6 hdfd78af_0 +---------------------------------------------------- +file name : proteomiqon-peptidespectrummatching-0.0.6-hdfd78af_0.tar.bz2 +name : proteomiqon-peptidespectrummatching +version : 0.0.6 +build : hdfd78af_0 +build number: 0 +size : 16.5 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/proteomiqon-peptidespectrummatching-0.0.6-hdfd78af_0.tar.bz2 +md5 : 777dfc4821e7b567cb6a9f4ca647d348 +timestamp : 2021-07-09 22:45:33 UTC +dependencies: + - dotnet-runtime + + +proteomiqon-peptidespectrummatching 0.0.7 hdfd78af_0 +---------------------------------------------------- +file name : proteomiqon-peptidespectrummatching-0.0.7-hdfd78af_0.tar.bz2 +name : proteomiqon-peptidespectrummatching +version : 0.0.7 +build : hdfd78af_0 +build number: 0 +size : 16.6 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/proteomiqon-peptidespectrummatching-0.0.7-hdfd78af_0.tar.bz2 +md5 : a4686bb4dcd93cdf0ec3d39b50c93a69 +timestamp : 2021-07-13 14:52:13 UTC +dependencies: + - dotnet-runtime + + +proteomiqon-peptidespectrummatching 0.0.7 hdfd78af_1 +---------------------------------------------------- +file name : proteomiqon-peptidespectrummatching-0.0.7-hdfd78af_1.tar.bz2 +name : proteomiqon-peptidespectrummatching +version : 0.0.7 +build : hdfd78af_1 +build number: 1 +size : 8.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/proteomiqon-peptidespectrummatching-0.0.7-hdfd78af_1.tar.bz2 +md5 : 831f0c996412b15c879ca3b015017784 +timestamp : 2022-04-27 08:20:05 UTC +dependencies: + - dotnet-runtime 5.0.* + - openssl 1.1.* diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pybedtools.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pybedtools.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ec32140a96c4ec261aec9c93699eaccccb89527 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pybedtools.manual_bundle.txt @@ -0,0 +1,525 @@ +# Tool: pybedtools +software_name: pybedtools +tier: T1 +domain: t1_backfill_overall +downloads: 1223103 +summary: Wraps BEDTools for use in Python and adds many additional features. +description: Wraps BEDTools for use in Python and adds many additional features. +dependencies: bedtools, libgcc >=13, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, numpy, pysam, python >=3.10,<3.11.0a0, python_abi 3.10.* *_cp310 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/daler/pybedtools +doc_url: https://daler.github.io/pybedtools +dev_url: https://github.com/daler/pybedtools + +## URL Docs Extract +### https://daler.github.io/pybedtools +pybedtools documentation — pybedtools 0.12.0 documentation pybedtools documentation ¶ Overview ¶ The BEDTools suite of programs is widely used for genomic interval manipulation or “genome algebra”. pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. See full online documentation, including installation instructions, at https://daler.github.io/pybedtools/ . The GitHub repo is at https://github.com/daler/pybedtools . Why pybedtools ? ¶ Here is an example to get the names of genes that are <5 kb away from intergenic SNPs: from pybedtools import BedTool snps = BedTool ( 'snps.bed.gz' ) # [1] genes = BedTool ( 'hg19.gff' ) # [1] intergenic_snps = snps . subtract ( genes ) # [2] nearby = genes . closest ( intergenic_snps , d = True , stream = True ) # [2, 3] for gene in nearby : # [4] if int ( gene [ - 1 ]) < 5000 : # [4] print gene . name # [4] Useful features shown here include: [1] support for all BEDTools-supported formats (here gzipped BED and GFF) [2] wrapping of all BEDTools programs and arguments (here, subtract and closest and passing the -d flag to closest ); [3] streaming results (like Unix pipes, here specified by stream=True ) [4] iterating over results while accessing feature data by index or by attribute access (here [-1] and .name ). In contrast, here is the same analysis using shell scripting. Note that this requires knowledge in Perl, bash, and awk. The run time is identical to the pybedtools version above: snps = snps.bed.gz genes = hg19.gff intergenic_snps = /tmp/intergenic_snps snp_fields = ` zcat $snps | awk '(NR == 2){print NF; exit;}' ` gene_fields = 9 distance_field = $(( $gene_fields + $snp_fields + 1 )) intersectBed -a $snps -b $genes -v > $intergenic_snps closestBed -a $genes -b $intergenic_snps -d \ | awk '($' $distance_field ' < 5000){print $9;}' \ | perl -ne 'm/[ID|Name|gene_id]=(.*?);/; print "$1\n"' rm $intergenic_snps See the Shell script comparison in the docs for more details on this comparison, or keep reading the full documentation at http://daler.github.io/pybedtools . As of 2022, pybedtools is released under the MIT license; see LICENSE.txt for more info. Note If you use pybedtools in your work, please cite the pybedtools manuscript and the BEDTools manuscript : Dale RK, Pedersen BS, and Quinlan AR. 2011. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations . Bioinformatics 27(24):3423-3424. Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features . Bioinformatics 26(6):841–842. Getting started ¶ The documentation is separated into 4 main parts, depending on the depth you’d like to cover: Lazy, or just want to jump in? Check out Three brief examples to get a feel for the package. Want a guided tour? Give the Tutorial Contents a shot. More advanced features are described in the Topical Documentation section. Finally, doctested module documentation can be found in pybedtools Reference . Contents: ¶ Installation Install via conda Installing pybedtools Quick test Running tests, compiling docs Test current installation Test within isolated conda environments Compile docs Contributing Three brief examples Example 1: Save a BED file of intersections, with track line Example 2: Intersections for a 3-way Venn diagram Example 3: Count reads in introns and exons, in parallel Tutorial Contents Intro Create a BedTool Intersections Saving the results Default arguments Chaining methods together (pipe) Operator overloading Intervals Filtering Each Using the history and tags Deleting temp files specific to a single BedTool Topical Documentation Design principles Creating a BedTool Saving BedTool results Using BedTool objects as iterators/generators Low-level operations Working with BAM files Notes on BAM file semantics Specifying genomes Randomization Wrapping new tools Comparisons Shell script comparison pybedtools development model Under the hood FAQs “Does pybedtools have a simple reader/writer for BED files?” “Can I create a BedTool object from an existing list?” “I’m getting an empty BedTool” “I’m getting a MalformedBedLineError” “I get a segfault when iterating over a BedTool object” “Can I add extra information to FASTA headers when using BedTool.sequence()?” “Too many files open” error Scripts pybedtools Reference BedTool creation BEDTools wrappers Other BedTool methods Module-level functions pybedtools.contrib Changelog Changes in v0.12.0 Changes in v0.11.0 Changes in v0.10.1 Changes in v0.9.1 Changes in v0.9 Changes in v0.8.2 Changes in v0.8.1 Changes in v0.8.0 Changes in v0.7.10 Changes in v0.7.9 Changes in v0.7.8 Changes in v0.7.7 Changes in v0.7.6 Changes in v0.7.5 Changes in v0.7.4 Changes in v0.7.1 Changes in v0.7.0 Changes in v0.6.9 Changes in v0.6.8 Changes in v0.6.7 Changes in v0.6.6 Changes in v0.6.5 Changes in v0.6.4 Changes in v0.6.3 Changes in v0.6.2 Changes in v0.6.1 Changes in v0.6 Changes in v0.5.5 Changes in v0.5 Indices and tables ¶ Index Module Index Search Page pybedtools Navigation Installation Running tests, compiling docs Three brief examples Tutorial Contents Topical Documentation FAQs Scripts pybedtools Reference Changelog Related Topics Documentation overview Next: Installation Navigation index modules | next | pybedtools 0.12.0 documentation » pybedtools documentation ©2010-2015, Ryan Dale. | Powered by Sphinx 8.1.3 & Alabaster 1.0.0 | Page source + +### https://github.com/daler/pybedtools +GitHub - daler/pybedtools: Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic") · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} daler / pybedtools Public Notifications You must be signed in to change notification settings Fork 106 Star 330 Code Issues 16 Pull requests 4 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights daler/pybedtools master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,878 Commits 1,878 Commits .github/ workflows .github/ workflows docker docker docs docs pybedtools pybedtools tools tools .gitignore .gitignore LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in README.rst README.rst build-docs.sh build-docs.sh dev-requirements.txt dev-requirements.txt ez_setup.py ez_setup.py optional-requirements.txt optional-requirements.txt pyproject.toml pyproject.toml requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py test-requirements.txt test-requirements.txt View all files Repository files navigation README License Overview The BEDTools suite of programs is widely used for genomic interval manipulation or "genome algebra". pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. See full online documentation, including installation instructions, at https://daler.github.io/pybedtools/ . The GitHub repo is at https://github.com/daler/pybedtools . Why pybedtools? Here is an example to get the names of genes that are <5 kb away from intergenic SNPs: from pybedtools import BedTool snps = BedTool ( 'snps.bed.gz' ) # [1] genes = BedTool ( 'hg19.gff' ) # [1] intergenic_snps = snps . subtract ( genes ) # [2] nearby = genes . closest ( intergenic_snps , d = True , stream = True ) # [2, 3] for gene in nearby : # [4] if int ( gene [ - 1 ]) < 5000 : # [4] print gene . name # [4] Useful features shown here include: [1] support for all BEDTools-supported formats (here gzipped BED and GFF) [2] wrapping of all BEDTools programs and arguments (here, subtract and closest and passing the -d flag to closest); [3] streaming results (like Unix pipes, here specified by stream=True) [4] iterating over results while accessing feature data by index or by attribute access (here [-1] and .name). In contrast, here is the same analysis using shell scripting. Note that this requires knowledge in Perl, bash, and awk. The run time is identical to the pybedtools version above: snps=snps.bed.gz genes=hg19.gff intergenic_snps=/tmp/intergenic_snps snp_fields= ` zcat $snps | awk ' (NR == 2){print NF; exit;} ' ` gene_fields=9 distance_field= $(( $gene_fields + $snp_fields + 1 )) intersectBed -a $snps -b $genes -v > $intergenic_snps closestBed -a $genes -b $intergenic_snps -d \ | awk ' ($ ' $distance_field ' < 5000){print $9;} ' \ | perl -ne ' m/[ID|Name|gene_id]=(.*?);/; print "$1\n" ' rm $intergenic_snps See the Shell script comparison in the docs for more details on this comparison, or keep reading the full documentation at http://daler.github.io/pybedtools . About Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic") daler.github.io/pybedtools Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Stars 330 stars Watchers 16 watching Forks 106 forks Report repository Releases 6 v0.12.0 Latest Mar 16, 2025 + 5 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 82.9% Cython 8.2% C++ 7.5% Other 1.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/daler/pybedtools +GitHub - daler/pybedtools: Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic") · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} daler / pybedtools Public Notifications You must be signed in to change notification settings Fork 106 Star 330 Code Issues 16 Pull requests 4 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights daler/pybedtools master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,878 Commits 1,878 Commits .github/ workflows .github/ workflows docker docker docs docs pybedtools pybedtools tools tools .gitignore .gitignore LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in README.rst README.rst build-docs.sh build-docs.sh dev-requirements.txt dev-requirements.txt ez_setup.py ez_setup.py optional-requirements.txt optional-requirements.txt pyproject.toml pyproject.toml requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py test-requirements.txt test-requirements.txt View all files Repository files navigation README License Overview The BEDTools suite of programs is widely used for genomic interval manipulation or "genome algebra". pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. See full online documentation, including installation instructions, at https://daler.github.io/pybedtools/ . The GitHub repo is at https://github.com/daler/pybedtools . Why pybedtools? Here is an example to get the names of genes that are <5 kb away from intergenic SNPs: from pybedtools import BedTool snps = BedTool ( 'snps.bed.gz' ) # [1] genes = BedTool ( 'hg19.gff' ) # [1] intergenic_snps = snps . subtract ( genes ) # [2] nearby = genes . closest ( intergenic_snps , d = True , stream = True ) # [2, 3] for gene in nearby : # [4] if int ( gene [ - 1 ]) < 5000 : # [4] print gene . name # [4] Useful features shown here include: [1] support for all BEDTools-supported formats (here gzipped BED and GFF) [2] wrapping of all BEDTools programs and arguments (here, subtract and closest and passing the -d flag to closest); [3] streaming results (like Unix pipes, here specified by stream=True) [4] iterating over results while accessing feature data by index or by attribute access (here [-1] and .name). In contrast, here is the same analysis using shell scripting. Note that this requires knowledge in Perl, bash, and awk. The run time is identical to the pybedtools version above: snps=snps.bed.gz genes=hg19.gff intergenic_snps=/tmp/intergenic_snps snp_fields= ` zcat $snps | awk ' (NR == 2){print NF; exit;} ' ` gene_fields=9 distance_field= $(( $gene_fields + $snp_fields + 1 )) intersectBed -a $snps -b $genes -v > $intergenic_snps closestBed -a $genes -b $intergenic_snps -d \ | awk ' ($ ' $distance_field ' < 5000){print $9;} ' \ | perl -ne ' m/[ID|Name|gene_id]=(.*?);/; print "$1\n" ' rm $intergenic_snps See the Shell script comparison in the docs for more details on this comparison, or keep reading the full documentation at http://daler.github.io/pybedtools . About Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic") daler.github.io/pybedtools Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Stars 330 stars Watchers 16 watching Forks 106 forks Report repository Releases 6 v0.12.0 Latest Mar 16, 2025 + 5 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 82.9% Cython 8.2% C++ 7.5% Other 1.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge pybedtools --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +pybedtools 0.6.9 py27_0 +----------------------- +file name : pybedtools-0.6.9-py27_0.tar.bz2 +name : pybedtools +version : 0.6.9 +build : py27_0 +build number: 0 +size : 18.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.6.9-py27_0.tar.bz2 +md5 : ef658a88c3a1383a877ddb9098ec85e9 +dependencies: + - bedtools + - libgcc + - pandas + - python 2.7* + - samtools + - six + - zlib 1.2.8* + + +pybedtools 0.6.9 py27_1 +----------------------- +file name : pybedtools-0.6.9-py27_1.tar.bz2 +name : pybedtools +version : 0.6.9 +build : py27_1 +build number: 1 +size : 18.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.6.9-py27_1.tar.bz2 +md5 : a4ea4f841803fa31040343e591e8fc7e +dependencies: + - bedtools + - libgcc + - pandas + - python 2.7* + - samtools + - six + - zlib 1.2.11* + + +pybedtools 0.6.9 py27h8eb80aa_5 +------------------------------- +file name : pybedtools-0.6.9-py27h8eb80aa_5.tar.bz2 +name : pybedtools +version : 0.6.9 +build : py27h8eb80aa_5 +build number: 5 +size : 17.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.6.9-py27h8eb80aa_5.tar.bz2 +md5 : 699eff2ffc61f3441c16e93797c38c83 +timestamp : 2021-03-28 11:54:21 UTC +dependencies: + - bedtools + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - pandas + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + - samtools + - six + - zlib >=1.2.11,<1.3.0a0 + + +pybedtools 0.6.9 py27h8f2a353_6 +------------------------------- +file name : pybedtools-0.6.9-py27h8f2a353_6.tar.bz2 +name : pybedtools +version : 0.6.9 +build : py27h8f2a353_6 +build number: 6 +size : 17.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.6.9-py27h8f2a353_6.tar.bz2 +md5 : 7077f7b8f08b9e7d19ec675a369aba2c +timestamp : 2022-02-24 04:20:57 UTC +dependencies: + - bedtools + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - pandas + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + - samtools + - six + - zlib >=1.2.11,<1.3.0a0 + + +pybedtools 0.6.9 py27ha92aebf_2 +------------------------------- +file name : pybedtools-0.6.9-py27ha92aebf_2.tar.bz2 +name : pybedtools +version : 0.6.9 +build : py27ha92aebf_2 +build number: 2 +size : 18.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.6.9-py27ha92aebf_2.tar.bz2 +md5 : 402d74de16b3acca17a4010b465a2880 +timestamp : 2018-06-28 23:28:27 UTC +dependencies: + - bedtools + - libgcc-ng >=4.9 + - pandas + - python >=2.7,<2.8.0a0 + - samtools + - six + - zlib >=1.2.11,<1.3.0a0 + + +pybedtools 0.6.9 py27he860b03_3 +------------------------------- +file name : pybedtools-0.6.9-py27he860b03_3.tar.bz2 +name : pybedtools +version : 0.6.9 +build : py27he860b03_3 +build number: 3 +size : 17.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.6.9-py27he860b03_3.tar.bz2 +md5 : b015f240e12fed11e4c7baa38394b1af +timestamp : 2019-02-04 11:08:05 UTC +dependencies: + - bedtools + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - pandas + - python >=2.7,<2.8.0a0 + - samtools + - six + - zlib >=1.2.11,<1.3.0a0 + + +pybedtools 0.6.9 py27heb12742_4 +------------------------------- +file name : pybedtools-0.6.9-py27heb12742_4.tar.bz2 +name : pybedtools +version : 0.6.9 +build : py27heb12742_4 +build number: 4 +size : 17.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.6.9-py27heb12742_4.tar.bz2 +md5 : ff2f9a890b1b5ef010ffed60498887a3 +timestamp : 2020-07-11 02:08:41 UTC +dependencies: + - bedtools + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - pandas + - python >=2.7,<2.8.0a0 + - python_abi 2.7.* *_cp27mu + - samtools + - six + - zlib >=1.2.11,<1.3.0a0 + + +pybedtools 0.7.0 py34_1 +----------------------- +file name : pybedtools-0.7.0-py34_1.tar.bz2 +name : pybedtools +version : 0.7.0 +build : py34_1 +build number: 1 +size : 12.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.0-py34_1.tar.bz2 +md5 : 953c8cd4f3df9fbc848966cf7b0a37a3 +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.4* + - six + + +pybedtools 0.7.2 py27_1 +----------------------- +file name : pybedtools-0.7.2-py27_1.tar.bz2 +name : pybedtools +version : 0.7.2 +build : py27_1 +build number: 1 +size : 12.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.2-py27_1.tar.bz2 +md5 : 449d74757d3be04aa35b045dc4729e8f +dependencies: + - pandas + - pysam >=0.8.1 + - python 2.7* + - six + + +pybedtools 0.7.2 py34_1 +----------------------- +file name : pybedtools-0.7.2-py34_1.tar.bz2 +name : pybedtools +version : 0.7.2 +build : py34_1 +build number: 1 +size : 12.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.2-py34_1.tar.bz2 +md5 : e7743b0175b0172b8aa9fd0693b80309 +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.4* + - six + + +pybedtools 0.7.4 py27_0 +----------------------- +file name : pybedtools-0.7.4-py27_0.tar.bz2 +name : pybedtools +version : 0.7.4 +build : py27_0 +build number: 0 +size : 12.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.4-py27_0.tar.bz2 +md5 : 4fe5107189221b4ce8189dcc7c36429e +dependencies: + - pandas + - pysam >=0.8.1 + - python 2.7* + - six + + +pybedtools 0.7.4 py34_0 +----------------------- +file name : pybedtools-0.7.4-py34_0.tar.bz2 +name : pybedtools +version : 0.7.4 +build : py34_0 +build number: 0 +size : 12.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.4-py34_0.tar.bz2 +md5 : 18e9e6832501d708ef7fa1c1a0c0271b +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.4* + - six + + +pybedtools 0.7.4 py35_0 +----------------------- +file name : pybedtools-0.7.4-py35_0.tar.bz2 +name : pybedtools +version : 0.7.4 +build : py35_0 +build number: 0 +size : 12.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.4-py35_0.tar.bz2 +md5 : 95963c20d23add040a0c9a7b0211e9f3 +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.5* + - six + + +pybedtools 0.7.5 py27_0 +----------------------- +file name : pybedtools-0.7.5-py27_0.tar.bz2 +name : pybedtools +version : 0.7.5 +build : py27_0 +build number: 0 +size : 12.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.5-py27_0.tar.bz2 +md5 : 0f6b68bab7c16936d369575f2f38ada8 +dependencies: + - pandas + - pysam >=0.8.1 + - python 2.7* + - six + + +pybedtools 0.7.5 py34_0 +----------------------- +file name : pybedtools-0.7.5-py34_0.tar.bz2 +name : pybedtools +version : 0.7.5 +build : py34_0 +build number: 0 +size : 12.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.5-py34_0.tar.bz2 +md5 : f4b6fe216efb8340bd31f433eab2a44a +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.4* + - six + + +pybedtools 0.7.5 py35_0 +----------------------- +file name : pybedtools-0.7.5-py35_0.tar.bz2 +name : pybedtools +version : 0.7.5 +build : py35_0 +build number: 0 +size : 12.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.5-py35_0.tar.bz2 +md5 : 4ab50100ac19ba2fab7340d332039847 +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.5* + - six + + +pybedtools 0.7.6 py27_1 +----------------------- +file name : pybedtools-0.7.6-py27_1.tar.bz2 +name : pybedtools +version : 0.7.6 +build : py27_1 +build number: 1 +size : 12.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.6-py27_1.tar.bz2 +md5 : 1f44446037e2af7430a0509d4d27bd2d +dependencies: + - pandas + - pysam >=0.8.1 + - python 2.7* + - six + + +pybedtools 0.7.6 py34_1 +----------------------- +file name : pybedtools-0.7.6-py34_1.tar.bz2 +name : pybedtools +version : 0.7.6 +build : py34_1 +build number: 1 +size : 12.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.6-py34_1.tar.bz2 +md5 : 7b38fd4f36be1714f79e27409a0e2aac +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.4* + - six + + +pybedtools 0.7.6 py35_1 +----------------------- +file name : pybedtools-0.7.6-py35_1.tar.bz2 +name : pybedtools +version : 0.7.6 +build : py35_1 +build number: 1 +size : 12.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.6-py35_1.tar.bz2 +md5 : f414000b4d0f4800dac9339b81cdaa08 +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.5* + - six + + +pybedtools 0.7.7 py27_1 +----------------------- +file name : pybedtools-0.7.7-py27_1.tar.bz2 +name : pybedtools +version : 0.7.7 +build : py27_1 +build number: 1 +size : 12.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.7-py27_1.tar.bz2 +md5 : 524cc4cdc9bcb1a7ace5d12736c0cbd7 +dependencies: + - pandas + - pysam >=0.8.1 + - python 2.7* + - six + + +pybedtools 0.7.7 py34_1 +----------------------- +file name : pybedtools-0.7.7-py34_1.tar.bz2 +name : pybedtools +version : 0.7.7 +build : py34_1 +build number: 1 +size : 13.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.7-py34_1.tar.bz2 +md5 : 8a08d8c6dcc7d0ce64255bcf837cabc9 +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.4* + - six + + +pybedtools 0.7.7 py35_1 +----------------------- +file name : pybedtools-0.7.7-py35_1.tar.bz2 +name : pybedtools +version : 0.7.7 +build : py35_1 +build number: 1 +size : 13.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.7-py35_1.tar.bz2 +md5 : d0a622d927c6ba4af191a6e1059dedf5 +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.5* + - six + + +pybedtools 0.7.8 py27_1 +----------------------- +file name : pybedtools-0.7.8-py27_1.tar.bz2 +name : pybedtools +version : 0.7.8 +build : py27_1 +build number: 1 +size : 12.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.8-py27_1.tar.bz2 +md5 : ff8914d0e5a1285bc64a937966179a9d +dependencies: + - pandas + - pysam >=0.8.1 + - python 2.7* + - six + + +pybedtools 0.7.8 py34_1 +----------------------- +file name : pybedtools-0.7.8-py34_1.tar.bz2 +name : pybedtools +version : 0.7.8 +build : py34_1 +build number: 1 +size : 12.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.7.8-py34_1.tar.bz2 +md5 : 71cbbb431e0dfa917a989ac0cdc29fe8 +dependencies: + - pandas + - pysam >=0.8.1 + - python 3.4* + - six + + +pybedtools 0.7.8 py35_ diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pyfastx.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pyfastx.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..09412f4441fbd13867bb999062881272098a48f0 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pyfastx.manual_bundle.txt @@ -0,0 +1,465 @@ +# Tool: pyfastx +software_name: pyfastx +tier: T1 +domain: t1_backfill_overall +downloads: 219881 +summary: pyfastx is a python module for fast random access to sequences from plain and gzipped FASTA/Q file. +description: pyfastx is a python module for fast random access to sequences from plain and gzipped FASTA/Q file. +dependencies: libgcc >=14, libzlib >=1.3.1,<2.0a0, python >=3.12,<3.13.0a0, python_abi 3.12.* *_cp312 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/lmdu/pyfastx +doc_url: https://pyfastx.readthedocs.io/en/latest +dev_url: https://github.com/lmdu/pyfastx + +## CLI Help Source +cli:pyfastx +## CLI Help Content +$ conda run -n bioenv_cli pyfastx --help +[rc=0] +usage: pyfastx COMMAND [OPTIONS] + +A command line tool for FASTA/Q file manipulation + +options: + -h, --help show this help message and exit + -v, --version show program's version number and exit + +Commands: + + index build index for fasta/q file + stat show detailed statistics information of fasta/q file + split split fasta/q file into multiple files + fq2fa convert fastq file to fasta file + subseq get subsequences from fasta file by region + sample randomly sample sequences from fasta or fastq file + extract extract full sequences or reads from fasta/q file + + + +## URL Docs Extract +### https://pyfastx.readthedocs.io/en/latest +Welcome to pyfastx’s documentation! — pyfastx 2.3.0 documentation pyfastx Contents: Installation FASTX FASTA Sequence FASTQ Read FastaKeys FastqKeys Command line interface Multiple processes Drawbacks Changelog API Reference Acknowledgements pyfastx Welcome to pyfastx’s documentation! View page source Welcome to pyfastx’s documentation!  The pyfastx is a lightweight Python C extension that enables users to randomly access to sequences from plain and gzipped FASTA/Q files. This module aims to provide simple APIs for users to extract sequence from FASTA and reads from FASTQ by identifier and index number. The pyfastx will build indexes stored in a sqlite3 database file for random access to avoid consuming excessive amount of memory. In addition, the pyfastx can parse standard ( sequence is spread into multiple lines with same length ) and nonstandard ( sequence is spread into one or more lines with different length ) FASTA format. This module used kseq.h written by @attractivechaos in klib project to parse plain FASTA/Q file and zran.c written by @pauldmccarthy in project indexed_gzip to index gzipped file for random access. This project was heavily inspired by @mdshw5 ’s project pyfaidx and @brentp ’s project pyfasta . Features Single file for the Python extension Lightweight, memory efficient for parsing FASTA file Fast random access to sequences from gzipped FASTA file Read sequences from FASTA file line by line Calculate assembly N50 and L50 Calculate GC content and nucleotides composition Extract reverse, complement and antisense sequence Excellent compatibility, support for parsing nonstandard FASTA file Support for random access reads from FASTQ file Contents: Installation Install from PyPI Install from source FASTX Iterate over sequences in FASTA Iterate over reads in FASTQ FASTA Read FASTA file FASTA records iteration Get FASTA information Get longest and shortest sequence Calculate N50 and L50 Get sequence mean and median length Get sequence counts Get subsequences Get flank sequences Key function Sequence Get a sequence from FASTA Get sequence information Sequence slice Reverse and complement sequence Read sequence line by line Search for subsequence FASTQ Read FASTQ file FASTQ records iteration Get FASTQ information Read Get read from FASTQ Get read information FastaKeys Get fasta keys Sort keys Filter keys Clear filter and sort order FastqKeys Get fastq keys Command line interface Build index Show statistics information Split FASTA/Q file Convert FASTQ to FASTA file Get subsequence with region Sample sequences Extract sequences Multiple processes Example one Drawbacks Changelog Version 2.1.0 (2024-02-28) Version 2.0.2 (2023-11-25) Version 2.0.1 (2023-09-18) Version 2.0.0 (2023-09-05) Version 1.1.0 (2023-04-19) Version 1.0.1 (2023-03-28) Version 1.0.0 (2023-03-24) Version 0.9.1 (2022-12-31) Version 0.9.0 (2022-12-30) Older versions API Reference pyfastx.version pyfastx.Fasta pyfastx.Sequence pyfastx.Fastq pyfastx.Read pyfastx.Fastx pyfastx.FastaKeys pyfastx.FastqKeys Acknowledgements Indices and tables  Index Module Index Search Page Next © Copyright 2023, Lianming Du. Built with Sphinx using a theme provided by Read the Docs . + +### https://github.com/lmdu/pyfastx +GitHub - lmdu/pyfastx: a python package for fast random access to sequences from plain and gzipped FASTA/Q files · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} lmdu / pyfastx Public Notifications You must be signed in to change notification settings Fork 24 Star 294 Code Issues 24 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights lmdu/pyfastx master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 626 Commits 626 Commits .github/ workflows .github/ workflows benchmark benchmark docs docs src src tests tests .gitignore .gitignore .readthedocs.yaml .readthedocs.yaml LICENSE LICENSE MANIFEST.in MANIFEST.in README.rst README.rst pyfastxcli.py pyfastxcli.py setup.py setup.py View all files Repository files navigation README MIT license pyfastx Citation: Lianming Du, Qin Liu, Zhenxin Fan, Jie Tang, Xiuyue Zhang, Megan Price, Bisong Yue, Kelei Zhao. Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files. Briefings in Bioinformatics, 2021, 22(4):bbaa368 . Table of Contents Introduction Features Installation FASTX FASTA sequences iteration FASTQ reads iteration FASTA Read FASTA file FASTA records iteration Get FASTA information Get longest and shortest sequence Calculate N50 and L50 Get sequence mean and median length Get sequence counts Get subsequences Key function Sequence Get a sequence from FASTA Get sequence information Sequence slice Reverse and complement sequence Read sequence line by line Search for subsequence FastaKeys Get keys Sort keys Filter keys FASTQ Read FASTQ file FASTQ records iteration Get FASTQ information Read Get read from FASTQ Get read information FastqKeys Get fastq keys Command line interface Build index Show statistics information Split FASTA/Q file Convert FASTQ to FASTA file Get subsequence with region Sample sequences Extract sequences Drawbacks Testing Acknowledgements Introduction The pyfastx is a lightweight Python C extension that enables users to randomly access to sequences from plain and gzipped FASTA/Q files. This module aims to provide simple APIs for users to extract seqeunce from FASTA and reads from FASTQ by identifier and index number. The pyfastx will build indexes stored in a sqlite3 database file for random access to avoid consuming excessive amount of memory. In addition, the pyfastx can parse standard ( sequence is spread into multiple lines with same length ) and nonstandard ( sequence is spread into one or more lines with different length ) FASTA format. This module used kseq.h written by @attractivechaos in klib project to parse plain FASTA/Q file and zran.c written by @pauldmccarthy in project indexed_gzip to index gzipped file for random access. This project was heavily inspired by @mdshw5 's project pyfaidx and @brentp 's project pyfasta . Features Single file for the Python extension Lightweight, memory efficient for parsing FASTA/Q file Fast random access to sequences from gzipped FASTA/Q file Read sequences from FASTA file line by line Calculate N50 and L50 of sequences in FASTA file Calculate GC content and nucleotides composition Extract reverse, complement and antisense sequences Excellent compatibility, support for parsing nonstandard FASTA file Support for FASTQ quality score conversion Provide command line interface for splitting FASTA/Q file Installation Currently, pyfastx supports Python 3.8, 3.9, 3.10, 3.11, 3.12, 3.13, 3.14. Make sure you have installed both pip and Python before starting. You can install pyfastx via the Python Package Index (PyPI) pip install pyfastx Update pyfastx module pip install -U pyfastx FASTX New in pyfastx 0.8.0. Pyfastx provide a simple and fast python binding for kseq.h to iterate over sequences or reads in fasta/q file. The FASTX object will automatically detect the input sequence format (fasta or fastq) to return different tuple. FASTA sequences iteration When iterating over sequences on FASTX object, a tuple (name, seq) will be returned. > >> fa = pyfastx . Fastx ( 'tests/data/test.fa.gz' ) > >> for name , seq in fa : > >> print ( name ) > >> print ( seq ) > >> #always output uppercase sequence >> > for item in pyfastx . Fastx ( 'tests/data/test.fa' , uppercase = True ): > >> print ( item ) > >> #Manually specify sequence format >> > for item in pyfastx . Fastx ( 'tests/data/test.fa' , format = "fasta" ): > >> print ( item ) If you want the sequence comment, you can set comment to True, New in pyfastx 0.9.0. > >> fa = pyfastx . Fastx ( 'tests/data/test.fa.gz' , comment = True ) > >> for name , seq , comment in fa : > >> print ( name ) > >> print ( seq ) > >> print ( comment ) The comment is the content of header line after the first white space or tab character. FASTQ reads iteration When iterating over reads on FASTX object, a tuple (name, seq, qual) will be returned. > >> fq = pyfastx . Fastx ( 'tests/data/test.fq.gz' ) > >> for name , seq , qual in fq : > >> print ( name ) > >> print ( seq ) > >> print ( qual ) If you want the read comment, you can set comment to True, New in pyfastx 0.9.0. > >> fq = pyfastx . Fastx ( 'tests/data/test.fq.gz' , comment = True ) > >> for name , seq , qual , comment in fq : > >> print ( name ) > >> print ( seq ) > >> print ( qual ) > >> print ( comment ) The comment is the content of header line after the first white space or tab character. FASTA Read FASTA file Read plain or gzipped FASTA file and build index, support for random access to FASTA. > >> import pyfastx > >> fa = pyfastx . Fasta ( 'test/data/test.fa.gz' ) > >> fa < Fasta > test / data / test . fa . gz contains 211 seqs Note Building index may take some times. The time required to build index depends on the size of FASTA file. If index built, you can randomly access to any sequences in FASTA file. The index file can be reused to save time when you read seqeunces from FASTA file next time. FASTA records iteration The fastest way to iterate plain or gzipped FASTA file without building index, the iteration will return a tuple contains name and sequence. > >> import pyfastx > >> for name , seq in pyfastx . Fasta ( 'test/data/test.fa.gz' , build_index = False ): > >> print ( name , seq ) You can also iterate sequence object from FASTA object like this: > >> import pyfastx > >> for seq in pyfastx . Fasta ( 'test/data/test.fa.gz' ): > >> print ( seq . name ) > >> print ( seq . seq ) > >> print ( seq . description ) Iteration with build_index=True (default) return sequence object which allows you to access attributions of sequence. New in pyfastx 0.6.3. Get FASTA information > >> # get sequence counts in FASTA >> > len ( fa ) 211 > >> # get total sequence length of FASTA >> > fa . size 86262 > >> # get GC content of DNA sequence of FASTA >> > fa . gc_content 43.529014587402344 > >> # get GC skew of DNA sequences in FASTA >> > # New in pyfastx 0.3.8 >> > fa . gc_skew 0.004287730902433395 > >> # get composition of nucleotides in FASTA >> > fa . composition { 'A' : 24534 , 'C' : 18694 , 'G' : 18855 , 'T' : 24179 } > >> # get fasta type (DNA, RNA, or protein) >> > fa . type 'DNA' > >> # check fasta file is gzip compressed >> > fa . is_gzip True Get longest and shortest sequence New in pyfastx 0.3.0 > >> # get longest sequence >> > s = fa . longest > >> s < Sequence > JZ822609 . 1 with length of 821 >> > s . name 'JZ822609.1' >> > len ( s ) 821 >> > # get shortest sequence >> > s = fa . shortest >> > s < Sequence > JZ822617 . 1 with length of 118 >> > s . name 'JZ822617.1' >> > len ( s ) 118 Calculate N50 and L50 New in pyfastx 0.3.0 Calculate assembly N50 and L50, return (N50, L50), learn more about N50,L50 > >> # get FASTA N50 and L50 >> > fa . nl ( 50 ) ( 516 , 66 ) > >> # get FASTA N90 and L90 >> > fa . nl ( 90 ) ( 231 , 161 ) > >> # get FASTA N75 and L75 >> > fa . nl ( 75 ) ( 365 , 117 ) Get sequence mean and median length New in pyfastx 0.3.0 > >> # get sequence average length >> > fa . mean 408 > >> # get seqeunce median length >> > fa . median 430 Get sequence counts New in pyfastx 0.3.0 Get counts of sequences whose length >= specified length > >> # get counts of sequences with length >= 200 bp >> > fa . count ( 200 ) 173 > >> # get counts of sequences with length >= 500 bp >> > fa . count ( 500 ) 70 Get subsequences Subsequences can be retrieved from FASTA file by using a list of [start, end] coordinates > >> # get subsequence with start and end position >> > interval = ( 1 , 10 ) > >> fa . fetch ( 'JZ822577.1' , interval ) 'CTCTAGAGAT' > >> # get subsequences with a list of start and end position >> > intervals = [( 1 , 10 ), ( 50 , 60 )] > >> fa . fetch ( 'JZ822577.1' , intervals ) 'CTCTAGAGATTTTAGTTTGAC' > >> # get subsequences with reverse strand >> > fa . fetch ( 'JZ822577.1' , ( 1 , 10 ), strand = '-' ) 'ATCTCTAGAG' Key function New in pyfastx 0.5.1 Sometimes your fasta will have a long header which contains multiple identifiers and description, for example, ">JZ822577.1 contig1 cDNA library of flower petals in tree peony by suppression subtractive hybridization Paeonia suffruticosa cDNA, mRNA sequence". In this case, both "JZ822577.1" and "contig1" can be used as identifer. you can specify the key function to select one as identifier. > >> #default use JZ822577.1 as identifier >> > #specify key_func to select contig1 as identifer >> > fa = pyfastx . Fasta ( 'tests/data/test.fa.gz' , key_func = lambda x : x . split ()[ 1 ]) > >> fa < Fasta > tests / data / test . fa . gz contains 211 seqs Sequence Get a sequence from FASTA > >> # get sequence like a dictionary by identifier >> > s1 = fa [ 'JZ822577.1' ] > >> s1 < Sequence > JZ822577 . 1 with length of 333 >> > # get sequence like a list by index >> > s2 = fa [ 2 ] >> > s2 < Sequence > JZ822579 . 1 with length of 176 >> > # get last sequence > >> s3 = fa [ - 1 ] >> > s3 < Sequence > JZ840318 . 1 with length of 134 >> > # check a sequence name weather in FASTA file > >> 'JZ822577.1' in fa True Get sequence information > >> s = fa [ - 1 ] > >> s < Sequence > JZ840318 . 1 with length of 134 >> > # get sequence order number in FASTA file >> > # New in pyfastx 0.3.7 >> > s . id 211 >> > # get sequence name >> > s . name 'JZ840318.1' >> > # get sequence description >> > # New in pyfastx 0.3.1 >> > s . description 'R283 cDNA library of flower petals in tree peony by suppression subtractive hybridization Paeonia suffruticosa cDNA, mRNA sequence' >> > # get sequence string >> > s . seq 'ACTGGAGGTTCTTCTTCCTGTGGAAAGTAACTTGTTTTGCCTTCACCTGCCTGTTCTTCACATCAACCTTGTTCCCACACAAAACAATGGGAATGTTCTCACACACCCTGCAGAGATCACGATGCCATGTTGGT' >> > # get sequence raw string, New in pyfastx 0.6.3 >> > print ( s . raw ) > JZ840318 . 1 R283 cDNA library of flower petals in tree peony by suppression subtractive hybridization Paeonia suffruticosa cDNA , mRNA sequence ACTGGAGGTTCTTCTTCCTGTGGAAAGTAACTTGTTTTGCCTTCACCTGCCTGTTCTTCACATCAACCTT GTTCCCACACAAAACAATGGGAATGTTCTCACACACCCTGCAGAGATCACGATGCCATGTTGGT >> > # get sequence length >> > len ( s ) 134 >> > # get GC content if dna sequence >> > s . gc_content 46.26865768432617 >> > # get nucleotide composition if dna sequence >> > s . composition { 'A' : 31 , 'C' : 37 , 'G' : 25 , 'T' : 41 , 'N' : 0 } Sequence slice Sequence object can be sliced like a python string > >> # get a sub seq from sequence >> > s = fa [ - 1 ] > >> ss = s [ 10 : 30 ] > >> ss < Sequence > JZ840318 . 1 from 11 to 30 >> > ss . name 'JZ840318.1:11-30' > >> ss . seq 'CTTCTTCCTGTGGAAAGTAA' > >> ss = s [ - 10 :] > >> ss < Sequence > JZ840318 . 1 from 125 to 134 >> > ss . name 'JZ840318.1:125-134' > >> ss . seq 'CCATGTTGGT' Note Slicing start and end coordinates are 0-based. Currently, pyfastx does not support an optional third step or stride argument. For example ss[::-1] Reverse and complement sequence > >> # get sliced sequence >> > fa [ 0 ][ 10 : 20 ]. seq 'GTCAATTTCC' > >> # get reverse of sliced sequence >> > fa [ 0 ][ 10 : 20 ]. reverse 'CCTTTAACTG' > >> # get complement of sliced sequence >> > fa [ 0 ][ 10 : 20 ]. complement 'CAGTTAAAGG' > >> # get reversed complement sequence, corresponding to sequence in antisense strand >> > fa [ 0 ][ 10 : 20 ]. antisense 'GGAAATTGAC' Read sequence line by line New in pyfastx 0.3.0 The sequence object can be iterated line by line as they appear in FASTA file. > >> for line in fa [ 0 ]: ... print ( line ) ... CTCTAGAGATTACTTCTTCACATTCCAGATCACTCAGGCTCTTTGTCATTTTAGTTTGACTAGGATATCG AGTATTCAAGCTCATCGCTTTTGGTAATCTTTGCGGTGCATGCCTTTGCATGCTGTATTGCTGCTTCATC ATCCCCTTTGACTTGTGTGGCGGTGGCAAGACATCCGAAGAGTTAAGCGATGCTTGTCTAGTCAATTTCC CCATGTACAGAATCATTGTTGTCAATTGGTTGTTTCCTTGATGGTGAAGGGGCTTCAATACATGAGTTCC AAACTAACATTTCTTGACTAACACTTGAGGAAGAAGGACAAGGGTCCCCATGT Note Sliced sequence (e.g. fa[0][10:50]) cannot be read line by line Search for subsequence New in pyfastx 0.3.6 Search for subsequence from given sequence and get one-based start position of the first occurrence > >> # search subsequence in sense strand >> > fa [ 0 ]. search ( 'GCTTCAATACA' ) 262 > >> # check subsequence weather in sequence >> > 'GCTTCAATACA' in fa [ 0 ] True > >> # search subsequence in antisense strand >> > fa [ 0 ]. search ( 'CCTCAAGT' , '-' ) 301 FastaKeys New in pyfastx 0.8.0. We have changed Identifier object to FastaKeys object. Get keys Get all names of sequence as a list-like object. > >> ids = fa . keys () > >> ids < FastaKeys > contains 211 keys >> > # get count of sequence > >> len ( ids ) 211 > >> # get key by index >> > ids [ 0 ] 'JZ822577.1' > >> # check key whether in fasta >> > 'JZ822577.1' in ids True > >> # iterate over keys >> > for name in ids : > >> print ( name ) > >> # convert to a list >> > list ( ids ) Sort keys Sort keys by sequence id, name, or length for iteration New in pyfastx 0.5.0 > >> # sort keys by length with descending order >> > for name in ids . sort ( by = 'length' , reverse = True ): > >> print ( name ) > >> # sort keys by name with ascending order >> > for name in ids . sort ( by = 'name' ): > >> print ( name ) > >> # sort keys by id with descending order >> > for name in ids . sort ( by = 'id' , reverse = True ) >> > print ( name ) Filter keys Filter keys by sequence length and name New in pyfastx 0.5.10 > >> # get keys with length > 600 >> > ids . filter ( ids > 600 ) < FastaKeys > contains 48 keys >> > # get keys with length >= 500 and <= 700 > >> ids . filter ( ids >= 500 , ids <= 700 ) < FastaKeys > contains 48 keys >> > # get keys with length > 500 and < 600 > >> ids . filter ( 500 < ids < 600 ) < FastaKeys > contains 22 keys >> > # get keys contain JZ8226 > >> ids . filter ( ids % 'JZ8226' ) < FastaKeys > contains 90 keys >> > # get keys contain JZ8226 with length > 550 > >> ids . filter ( ids % 'JZ8226' , ids > 550 ) < FastaKeys > contains 17 keys >> > # clear sort order and filters > >> ids . reset () < FastaKeys > contains 211 keys >> > # list a filtered result > >> ids . filter ( ids % 'JZ8226' , ids > 730 ) > >> list ( ids ) [ 'JZ822609.1' , 'JZ822650.1' , 'JZ822664.1' , 'JZ822699.1' ] > >> # list a filtered result with sort order >> > ids . filter ( ids % 'JZ8226' , ids > 730 ). sort ( 'length' , reverse = True ) > >> list ( ids ) [ 'JZ822609.1' , 'JZ822699.1' , 'JZ822664.1' , 'JZ822650.1' ] > >> ids . filter ( ids % 'JZ8226' , ids > 730 ). sort ( 'name' , reverse = True ) > >> list ( ids ) [ 'JZ822699.1' , 'JZ822664.1' , 'JZ822650.1' , 'JZ822609.1' ] FASTQ New in pyfastx 0.4.0 Read FASTQ file Read plain or gzipped file and build index, support for random access to reads from FASTQ. > >> import pyfastx > >> fq = pyfastx . Fastq ( 'tests/data/test.fq.gz' ) > >> fq < Fastq > tests / data / test . fq . gz contains 100 + +### https://github.com/lmdu/pyfastx +GitHub - lmdu/pyfastx: a python package for fast random access to sequences from plain and gzipped FASTA/Q files · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} lmdu / pyfastx Public Notifications You must be signed in to change notification settings Fork 24 Star 294 Code Issues 24 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights lmdu/pyfastx master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 626 Commits 626 Commits .github/ workflows .github/ workflows benchmark benchmark docs docs src src tests tests .gitignore .gitignore .readthedocs.yaml .readthedocs.yaml LICENSE LICENSE MANIFEST.in MANIFEST.in README.rst README.rst pyfastxcli.py pyfastxcli.py setup.py setup.py View all files Repository files navigation README MIT license pyfastx Citation: Lianming Du, Qin Liu, Zhenxin Fan, Jie Tang, Xiuyue Zhang, Megan Price, Bisong Yue, Kelei Zhao. Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files. Briefings in Bioinformatics, 2021, 22(4):bbaa368 . Table of Contents Introduction Features Installation FASTX FASTA sequences iteration FASTQ reads iteration FASTA Read FASTA file FASTA records iteration Get FASTA information Get longest and shortest sequence Calculate N50 and L50 Get sequence mean and median length Get sequence counts Get subsequences Key function Sequence Get a sequence from FASTA Get sequence information Sequence slice Reverse and complement sequence Read sequence line by line Search for subsequence FastaKeys Get keys Sort keys Filter keys FASTQ Read FASTQ file FASTQ records iteration Get FASTQ information Read Get read from FASTQ Get read information FastqKeys Get fastq keys Command line interface Build index Show statistics information Split FASTA/Q file Convert FASTQ to FASTA file Get subsequence with region Sample sequences Extract sequences Drawbacks Testing Acknowledgements Introduction The pyfastx is a lightweight Python C extension that enables users to randomly access to sequences from plain and gzipped FASTA/Q files. This module aims to provide simple APIs for users to extract seqeunce from FASTA and reads from FASTQ by identifier and index number. The pyfastx will build indexes stored in a sqlite3 database file for random access to avoid consuming excessive amount of memory. In addition, the pyfastx can parse standard ( sequence is spread into multiple lines with same length ) and nonstandard ( sequence is spread into one or more lines with different length ) FASTA format. This module used kseq.h written by @attractivechaos in klib project to parse plain FASTA/Q file and zran.c written by @pauldmccarthy in project indexed_gzip to index gzipped file for random access. This project was heavily inspired by @mdshw5 's project pyfaidx and @brentp 's project pyfasta . Features Single file for the Python extension Lightweight, memory efficient for parsing FASTA/Q file Fast random access to sequences from gzipped FASTA/Q file Read sequences from FASTA file line by line Calculate N50 and L50 of sequences in FASTA file Calculate GC content and nucleotides composition Extract reverse, complement and antisense sequences Excellent compatibility, support for parsing nonstandard FASTA file Support for FASTQ quality score conversion Provide command line interface for splitting FASTA/Q file Installation Currently, pyfastx supports Python 3.8, 3.9, 3.10, 3.11, 3.12, 3.13, 3.14. Make sure you have installed both pip and Python before starting. You can install pyfastx via the Python Package Index (PyPI) pip install pyfastx Update pyfastx module pip install -U pyfastx FASTX New in pyfastx 0.8.0. Pyfastx provide a simple and fast python binding for kseq.h to iterate over sequences or reads in fasta/q file. The FASTX object will automatically detect the input sequence format (fasta or fastq) to return different tuple. FASTA sequences iteration When iterating over sequences on FASTX object, a tuple (name, seq) will be returned. > >> fa = pyfastx . Fastx ( 'tests/data/test.fa.gz' ) > >> for name , seq in fa : > >> print ( name ) > >> print ( seq ) > >> #always output uppercase sequence >> > for item in pyfastx . Fastx ( 'tests/data/test.fa' , uppercase = True ): > >> print ( item ) > >> #Manually specify sequence format >> > for item in pyfastx . Fastx ( 'tests/data/test.fa' , format = "fasta" ): > >> print ( item ) If you want the sequence comment, you can set comment to True, New in pyfastx 0.9.0. > >> fa = pyfastx . Fastx ( 'tests/data/test.fa.gz' , comment = True ) > >> for name , seq , comment in fa : > >> print ( name ) > >> print ( seq ) > >> print ( comment ) The comment is the content of header line after the first white space or tab character. FASTQ reads iteration When iterating over reads on FASTX object, a tuple (name, seq, qual) will be returned. > >> fq = pyfastx . Fastx ( 'tests/data/test.fq.gz' ) > >> for name , seq , qual in fq : > >> print ( name ) > >> print ( seq ) > >> print ( qual ) If you want the read comment, you can set comment to True, New in pyfastx 0.9.0. > >> fq = pyfastx . Fastx ( 'tests/data/test.fq.gz' , comment = True ) > >> for name , seq , qual , comment in fq : > >> print ( name ) > >> print ( seq ) > >> print ( qual ) > >> print ( comment ) The comment is the content of header line after the first white space or tab character. FASTA Read FASTA file Read plain or gzipped FASTA file and build index, support for random access to FASTA. > >> import pyfastx > >> fa = pyfastx . Fasta ( 'test/data/test.fa.gz' ) > >> fa < Fasta > test / data / test . fa . gz contains 211 seqs Note Building index may take some times. The time required to build index depends on the size of FASTA file. If index built, you can randomly access to any sequences in FASTA file. The index file can be reused to save time when you read seqeunces from FASTA file next time. FASTA records iteration The fastest way to iterate plain or gzipped FASTA file without building index, the iteration will return a tuple contains name and sequence. > >> import pyfastx > >> for name , seq in pyfastx . Fasta ( 'test/data/test.fa.gz' , build_index = False ): > >> print ( name , seq ) You can also iterate sequence object from FASTA object like this: > >> import pyfastx > >> for seq in pyfastx . Fasta ( 'test/data/test.fa.gz' ): > >> print ( seq . name ) > >> print ( seq . seq ) > >> print ( seq . description ) Iteration with build_index=True (default) return sequence object which allows you to access attributions of sequence. New in pyfastx 0.6.3. Get FASTA information > >> # get sequence counts in FASTA >> > len ( fa ) 211 > >> # get total sequence length of FASTA >> > fa . size 86262 > >> # get GC content of DNA sequence of FASTA >> > fa . gc_content 43.529014587402344 > >> # get GC skew of DNA sequences in FASTA >> > # New in pyfastx 0.3.8 >> > fa . gc_skew 0.004287730902433395 > >> # get composition of nucleotides in FASTA >> > fa . composition { 'A' : 24534 , 'C' : 18694 , 'G' : 18855 , 'T' : 24179 } > >> # get fasta type (DNA, RNA, or protein) >> > fa . type 'DNA' > >> # check fasta file is gzip compressed >> > fa . is_gzip True Get longest and shortest sequence New in pyfastx 0.3.0 > >> # get longest sequence >> > s = fa . longest > >> s < Sequence > JZ822609 . 1 with length of 821 >> > s . name 'JZ822609.1' >> > len ( s ) 821 >> > # get shortest sequence >> > s = fa . shortest >> > s < Sequence > JZ822617 . 1 with length of 118 >> > s . name 'JZ822617.1' >> > len ( s ) 118 Calculate N50 and L50 New in pyfastx 0.3.0 Calculate assembly N50 and L50, return (N50, L50), learn more about N50,L50 > >> # get FASTA N50 and L50 >> > fa . nl ( 50 ) ( 516 , 66 ) > >> # get FASTA N90 and L90 >> > fa . nl ( 90 ) ( 231 , 161 ) > >> # get FASTA N75 and L75 >> > fa . nl ( 75 ) ( 365 , 117 ) Get sequence mean and median length New in pyfastx 0.3.0 > >> # get sequence average length >> > fa . mean 408 > >> # get seqeunce median length >> > fa . median 430 Get sequence counts New in pyfastx 0.3.0 Get counts of sequences whose length >= specified length > >> # get counts of sequences with length >= 200 bp >> > fa . count ( 200 ) 173 > >> # get counts of sequences with length >= 500 bp >> > fa . count ( 500 ) 70 Get subsequences Subsequences can be retrieved from FASTA file by using a list of [start, end] coordinates > >> # get subsequence with start and end position >> > interval = ( 1 , 10 ) > >> fa . fetch ( 'JZ822577.1' , interval ) 'CTCTAGAGAT' > >> # get subsequences with a list of start and end position >> > intervals = [( 1 , 10 ), ( 50 , 60 )] > >> fa . fetch ( 'JZ822577.1' , intervals ) 'CTCTAGAGATTTTAGTTTGAC' > >> # get subsequences with reverse strand >> > fa . fetch ( 'JZ822577.1' , ( 1 , 10 ), strand = '-' ) 'ATCTCTAGAG' Key function New in pyfastx 0.5.1 Sometimes your fasta will have a long header which contains multiple identifiers and description, for example, ">JZ822577.1 contig1 cDNA library of flower petals in tree peony by suppression subtractive hybridization Paeonia suffruticosa cDNA, mRNA sequence". In this case, both "JZ822577.1" and "contig1" can be used as identifer. you can specify the key function to select one as identifier. > >> #default use JZ822577.1 as identifier >> > #specify key_func to select contig1 as identifer >> > fa = pyfastx . Fasta ( 'tests/data/test.fa.gz' , key_func = lambda x : x . split ()[ 1 ]) > >> fa < Fasta > tests / data / test . fa . gz contains 211 seqs Sequence Get a sequence from FASTA > >> # get sequence like a dictionary by identifier >> > s1 = fa [ 'JZ822577.1' ] > >> s1 < Sequence > JZ822577 . 1 with length of 333 >> > # get sequence like a list by index >> > s2 = fa [ 2 ] >> > s2 < Sequence > JZ822579 . 1 with length of 176 >> > # get last sequence > >> s3 = fa [ - 1 ] >> > s3 < Sequence > JZ840318 . 1 with length of 134 >> > # check a sequence name weather in FASTA file > >> 'JZ822577.1' in fa True Get sequence information > >> s = fa [ - 1 ] > >> s < Sequence > JZ840318 . 1 with length of 134 >> > # get sequence order number in FASTA file >> > # New in pyfastx 0.3.7 >> > s . id 211 >> > # get sequence name >> > s . name 'JZ840318.1' >> > # get sequence description >> > # New in pyfastx 0.3.1 >> > s . description 'R283 cDNA library of flower petals in tree peony by suppression subtractive hybridization Paeonia suffruticosa cDNA, mRNA sequence' >> > # get sequence string >> > s . seq 'ACTGGAGGTTCTTCTTCCTGTGGAAAGTAACTTGTTTTGCCTTCACCTGCCTGTTCTTCACATCAACCTTGTTCCCACACAAAACAATGGGAATGTTCTCACACACCCTGCAGAGATCACGATGCCATGTTGGT' >> > # get sequence raw string, New in pyfastx 0.6.3 >> > print ( s . raw ) > JZ840318 . 1 R283 cDNA library of flower petals in tree peony by suppression subtractive hybridization Paeonia suffruticosa cDNA , mRNA sequence ACTGGAGGTTCTTCTTCCTGTGGAAAGTAACTTGTTTTGCCTTCACCTGCCTGTTCTTCACATCAACCTT GTTCCCACACAAAACAATGGGAATGTTCTCACACACCCTGCAGAGATCACGATGCCATGTTGGT >> > # get sequence length >> > len ( s ) 134 >> > # get GC content if dna sequence >> > s . gc_content 46.26865768432617 >> > # get nucleotide composition if dna sequence >> > s . composition { 'A' : 31 , 'C' : 37 , 'G' : 25 , 'T' : 41 , 'N' : 0 } Sequence slice Sequence object can be sliced like a python string > >> # get a sub seq from sequence >> > s = fa [ - 1 ] > >> ss = s [ 10 : 30 ] > >> ss < Sequence > JZ840318 . 1 from 11 to 30 >> > ss . name 'JZ840318.1:11-30' > >> ss . seq 'CTTCTTCCTGTGGAAAGTAA' > >> ss = s [ - 10 :] > >> ss < Sequence > JZ840318 . 1 from 125 to 134 >> > ss . name 'JZ840318.1:125-134' > >> ss . seq 'CCATGTTGGT' Note Slicing start and end coordinates are 0-based. Currently, pyfastx does not support an optional third step or stride argument. For example ss[::-1] Reverse and complement sequence > >> # get sliced sequence >> > fa [ 0 ][ 10 : 20 ]. seq 'GTCAATTTCC' > >> # get reverse of sliced sequence >> > fa [ 0 ][ 10 : 20 ]. reverse 'CCTTTAACTG' > >> # get complement of sliced sequence >> > fa [ 0 ][ 10 : 20 ]. complement 'CAGTTAAAGG' > >> # get reversed complement sequence, corresponding to sequence in antisense strand >> > fa [ 0 ][ 10 : 20 ]. antisense 'GGAAATTGAC' Read sequence line by line New in pyfastx 0.3.0 The sequence object can be iterated line by line as they appear in FASTA file. > >> for line in fa [ 0 ]: ... print ( line ) ... CTCTAGAGATTACTTCTTCACATTCCAGATCACTCAGGCTCTTTGTCATTTTAGTTTGACTAGGATATCG AGTATTCAAGCTCATCGCTTTTGGTAATCTTTGCGGTGCATGCCTTTGCATGCTGTATTGCTGCTTCATC ATCCCCTTTGACTTGTGTGGCGGTGGCAAGACATCCGAAGAGTTAAGCGATGCTTGTCTAGTCAATTTCC CCATGTACAGAATCATTGTTGTCAATTGGTTGTTTCCTTGATGGTGAAGGGGCTTCAATACATGAGTTCC AAACTAACATTTCTTGACTAACACTTGAGGAAGAAGGACAAGGGTCCCCATGT Note Sliced sequence (e.g. fa[0][10:50]) cannot be read line by line Search for subsequence New in pyfastx 0.3.6 Search for subsequence from given sequence and get one-based start position of the first occurrence > >> # search subsequence in sense strand >> > fa [ 0 ]. search ( 'GCTTCAATACA' ) 262 > >> # check subsequence weather in sequence >> > 'GCTTCAATACA' in fa [ 0 ] True > >> # search subsequence in antisense strand >> > fa [ 0 ]. search ( 'CCTCAAGT' , '-' ) 301 FastaKeys New in pyfastx 0.8.0. We have changed Identifier object to FastaKeys object. Get keys Get all names of sequence as a list-like object. > >> ids = fa . keys () > >> ids < FastaKeys > contains 211 keys >> > # get count of sequence > >> len ( ids ) 211 > >> # get key by index >> > ids [ 0 ] 'JZ822577.1' > >> # check key whether in fasta >> > 'JZ822577.1' in ids True > >> # iterate over keys >> > for name in ids : > >> print ( name ) > >> # convert to a list >> > list ( ids ) Sort keys Sort keys by sequence id, name, or length for iteration New in pyfastx 0.5.0 > >> # sort keys by length with descending order >> > for name in ids . sort ( by = 'length' , reverse = True ): > >> print ( name ) > >> # sort keys by name with ascending order >> > for name in ids . sort ( by = 'name' ): > >> print ( name ) > >> # sort keys by id with descending order >> > for name in ids . sort ( by = 'id' , reverse = True ) >> > print ( name ) Filter keys Filter keys by sequence length and name New in pyfastx 0.5.10 > >> # get keys with length > 600 >> > ids . filter ( ids > 600 ) < FastaKeys > contains 48 keys >> > # get keys with length >= 500 and <= 700 > >> ids . filter ( ids >= 500 , ids <= 700 ) < FastaKeys > contains 48 keys >> > # get keys with length > 500 and < 600 > >> ids . filter ( 500 < ids < 600 ) < FastaKeys > contains 22 keys >> > # get keys contain JZ8226 > >> ids . filter ( ids % 'JZ8226' ) < FastaKeys > contains 90 keys >> > # get keys contain JZ8226 with length > 550 > >> ids . filter ( ids % 'JZ8226' , ids > 550 ) < FastaKeys > contains 17 keys >> > # clear sort order and filters > >> ids . reset () < FastaKeys > contains 211 keys >> > # list a filtered result > >> ids . filter ( ids % 'JZ8226' , ids > 730 ) > >> list ( ids ) [ 'JZ822609.1' , 'JZ822650.1' , 'JZ822664.1' , 'JZ822699.1' ] > >> # list a filtered result with sort order >> > ids . filter ( ids % 'JZ8226' , ids > 730 ). sort ( 'length' , reverse = True ) > >> list ( ids ) [ 'JZ822609.1' , 'JZ822699.1' , 'JZ822664.1' , 'JZ822650.1' ] > >> ids . filter ( ids % 'JZ8226' , ids > 730 ). sort ( 'name' , reverse = True ) > >> list ( ids ) [ 'JZ822699.1' , 'JZ822664.1' , 'JZ822650.1' , 'JZ822609.1' ] FASTQ New in pyfastx 0.4.0 Read FASTQ file Read plain or gzipped file and build index, support for random access to reads from FASTQ. > >> import pyfastx > >> fq = pyfastx . Fastq ( 'tests/data/test.fq.gz' ) > >> fq < Fastq > tests / data / test . fq . gz contains 100 + +## Conda Search Info +$ conda search -c bioconda -c conda-forge pyfastx --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +pyfastx 0.6.4 py36hed695b0_0 +---------------------------- +file name : pyfastx-0.6.4-py36hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.4 +build : py36hed695b0_0 +build number: 0 +size : 56 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.4-py36hed695b0_0.tar.bz2 +md5 : 00405665a465e0d8f68db21436e5a23d +timestamp : 2020-01-28 12:55:27 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.4 py37hed695b0_0 +---------------------------- +file name : pyfastx-0.6.4-py37hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.4 +build : py37hed695b0_0 +build number: 0 +size : 56 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.4-py37hed695b0_0.tar.bz2 +md5 : bf11147f4b88cf72f85b789847052380 +timestamp : 2020-01-28 12:53:56 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.5 py36hed695b0_0 +---------------------------- +file name : pyfastx-0.6.5-py36hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.5 +build : py36hed695b0_0 +build number: 0 +size : 58 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.5-py36hed695b0_0.tar.bz2 +md5 : 3d8492ab44f9556739affc116d5bfdf6 +timestamp : 2020-01-31 09:25:52 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.5 py37hed695b0_0 +---------------------------- +file name : pyfastx-0.6.5-py37hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.5 +build : py37hed695b0_0 +build number: 0 +size : 58 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.5-py37hed695b0_0.tar.bz2 +md5 : d3681c89686b5e04cf5d436401301a69 +timestamp : 2020-01-31 09:26:49 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.6 py36hed695b0_0 +---------------------------- +file name : pyfastx-0.6.6-py36hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.6 +build : py36hed695b0_0 +build number: 0 +size : 58 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.6-py36hed695b0_0.tar.bz2 +md5 : 67029802a65eeb125402b91d348cf3d4 +timestamp : 2020-02-15 16:12:11 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.6 py37hed695b0_0 +---------------------------- +file name : pyfastx-0.6.6-py37hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.6 +build : py37hed695b0_0 +build number: 0 +size : 58 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.6-py37hed695b0_0.tar.bz2 +md5 : 54b6a16c4dcd01d2b206695d905059b2 +timestamp : 2020-02-15 16:13:11 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.7 py36hed695b0_0 +---------------------------- +file name : pyfastx-0.6.7-py36hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.7 +build : py36hed695b0_0 +build number: 0 +size : 58 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.7-py36hed695b0_0.tar.bz2 +md5 : 7fbe63a52f740354f7a5ceef85646a07 +timestamp : 2020-03-03 16:13:43 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.7 py37hed695b0_0 +---------------------------- +file name : pyfastx-0.6.7-py37hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.7 +build : py37hed695b0_0 +build number: 0 +size : 59 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.7-py37hed695b0_0.tar.bz2 +md5 : dc7f8622cad1775dbb9763c3e53a5af5 +timestamp : 2020-03-03 16:12:09 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.8 py36hed695b0_0 +---------------------------- +file name : pyfastx-0.6.8-py36hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.8 +build : py36hed695b0_0 +build number: 0 +size : 59 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.8-py36hed695b0_0.tar.bz2 +md5 : 746cbb132901f6c700c2dc249176ffab +timestamp : 2020-03-14 16:11:02 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.8 py37hed695b0_0 +---------------------------- +file name : pyfastx-0.6.8-py37hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.8 +build : py37hed695b0_0 +build number: 0 +size : 59 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.8-py37hed695b0_0.tar.bz2 +md5 : e1aa600c2b3026c78340f0b1aed79a4c +timestamp : 2020-03-14 16:09:49 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.9 py36hed695b0_0 +---------------------------- +file name : pyfastx-0.6.9-py36hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.9 +build : py36hed695b0_0 +build number: 0 +size : 61 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.9-py36hed695b0_0.tar.bz2 +md5 : 1f75a8288a584e380f56d069285b5a23 +timestamp : 2020-04-13 12:14:18 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.9 py37hed695b0_0 +---------------------------- +file name : pyfastx-0.6.9-py37hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.9 +build : py37hed695b0_0 +build number: 0 +size : 61 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.9-py37hed695b0_0.tar.bz2 +md5 : 06bb540cb671bfa31c143d63b03558c0 +timestamp : 2020-04-13 12:13:03 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.10 py36hed695b0_0 +----------------------------- +file name : pyfastx-0.6.10-py36hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.10 +build : py36hed695b0_0 +build number: 0 +size : 62 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.10-py36hed695b0_0.tar.bz2 +md5 : c9cfab282307114fd5582a495f3ec540 +timestamp : 2020-04-22 03:20:49 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.10 py37hed695b0_0 +----------------------------- +file name : pyfastx-0.6.10-py37hed695b0_0.tar.bz2 +name : pyfastx +version : 0.6.10 +build : py37hed695b0_0 +build number: 0 +size : 62 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.10-py37hed695b0_0.tar.bz2 +md5 : 8787e6016c197329721267abdb146823 +timestamp : 2020-04-22 03:21:52 UTC +dependencies: + - libgcc-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.11 py36hde715ba_0 +----------------------------- +file name : pyfastx-0.6.11-py36hde715ba_0.tar.bz2 +name : pyfastx +version : 0.6.11 +build : py36hde715ba_0 +build number: 0 +size : 63 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.11-py36hde715ba_0.tar.bz2 +md5 : 08af789056f7dd8ec5e33ebdba23f2e0 +timestamp : 2020-05-18 11:24:57 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.11 py37h6cf0177_0 +----------------------------- +file name : pyfastx-0.6.11-py37h6cf0177_0.tar.bz2 +name : pyfastx +version : 0.6.11 +build : py37h6cf0177_0 +build number: 0 +size : 63 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.11-py37h6cf0177_0.tar.bz2 +md5 : 43af6dd6f81a0c3eb7bfe5d094d6d8ec +timestamp : 2020-05-18 11:26:06 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.12 py36hde715ba_0 +----------------------------- +file name : pyfastx-0.6.12-py36hde715ba_0.tar.bz2 +name : pyfastx +version : 0.6.12 +build : py36hde715ba_0 +build number: 0 +size : 64 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.12-py36hde715ba_0.tar.bz2 +md5 : d4358cd869e06e0f9c78d7df39e4eb9a +timestamp : 2020-06-14 04:13:43 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.12 py37h6cf0177_0 +----------------------------- +file name : pyfastx-0.6.12-py37h6cf0177_0.tar.bz2 +name : pyfastx +version : 0.6.12 +build : py37h6cf0177_0 +build number: 0 +size : 64 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.12-py37h6cf0177_0.tar.bz2 +md5 : 3b997590a3e0b974c659dcb0f9e99543 +timestamp : 2020-06-14 04:15:10 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.13 py36h955c1b8_0 +----------------------------- +file name : pyfastx-0.6.13-py36h955c1b8_0.tar.bz2 +name : pyfastx +version : 0.6.13 +build : py36h955c1b8_0 +build number: 0 +size : 64 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.13-py36h955c1b8_0.tar.bz2 +md5 : db44b39b28cf16caf02c11c9ad1ba272 +timestamp : 2020-07-09 16:25:47 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.13 py37hb5aa323_0 +----------------------------- +file name : pyfastx-0.6.13-py37hb5aa323_0.tar.bz2 +name : pyfastx +version : 0.6.13 +build : py37hb5aa323_0 +build number: 0 +size : 65 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.13-py37hb5aa323_0.tar.bz2 +md5 : e43fa21f5c01af173fab139abf7960c5 +timestamp : 2020-07-09 16:24:03 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - zlib >=1.2.11,<1.3.0a0 + + +pyfastx 0.6.14 py36h955c1b8_0 +----------------------------- +file name : pyfastx-0.6.14-py36h955c1b8_0.tar.bz2 +name : pyfastx +version : 0.6.14 +build : py36h955c1b8_0 +build number: 0 +size : 65 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyfastx-0.6.14-py36h955c1b8_0.tar.bz2 +md5 : 687b4b8e9dd4895312f2c75e4a2b0e96 +timestamp : 2020-07-31 06:21:36 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.6,<3.7.0a0 + - python_ diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pyrodigal.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pyrodigal.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..d53b343114c0160e326b137b1c78d86390fb589f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pyrodigal.manual_bundle.txt @@ -0,0 +1,496 @@ +# Tool: pyrodigal +software_name: pyrodigal +tier: T1 +domain: t1_backfill_overall +downloads: 221316 +summary: Python bindings to Prodigal, an ORF finder for microbial sequences. +description: Python bindings to Prodigal, an ORF finder for microbial sequences. +dependencies: archspec >=0.2.0, libgcc >=14, python >=3.13,<3.14.0a0, python_abi 3.13.* *_cp313 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/althonos/pyrodigal +doc_url: https://pyrodigal.readthedocs.org +dev_url: https://github.com/althonos/pyrodigal + +## CLI Help Source +cli:pyrodigal +## CLI Help Content +$ conda run -n bioenv_cli pyrodigal --help +[rc=0] +usage: pyrodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type] + [-g tr_table] [-i input_file] [-m] [-n] [-o output_file] + [-p mode] [-s start_file] [-t training_file] [-j jobs] [-h] + [-V] [--min-gene MIN_GENE] [--min-edge-gene MIN_EDGE_GENE] + [--max-overlap MAX_OVERLAP] [--no-stop-codon] + [--pool {thread,process}] + +options: + -a trans_file Write protein translations to the selected file. + (default: None) + -c Closed ends. Do not allow genes to run off edges. + (default: False) + -d nuc_file Write nucleotide sequences of genes to the selected + file. (default: None) + -f output_type Select output format. (default: gff) + -g tr_table Specify a translation table to use. (default: 11) + -i input_file Specify FASTA input file. (default: None) + -m Treat runs of N as masked sequence; don't build genes + across them. (default: False) + -n Bypass Shine-Dalgarno trainer and force a full motif + scan. (default: False) + -o output_file Specify output file. (default: None) + -p mode Select procedure. (default: single) + -s start_file Write all potential genes (with scores) to the + selected file. (default: None) + -t training_file Write a training file (if none exists); otherwise, + read and use the specified training file. (default: + None) + -j jobs, --jobs jobs The number of threads to use if input contains + multiple sequences. (default: 1) + -h, --help Show this help message and exit. + -V, --version Show version number and exit. + --min-gene MIN_GENE The minimum gene length. (default: 90) + --min-edge-gene MIN_EDGE_GENE + The minimum edge gene length. (default: 60) + --max-overlap MAX_OVERLAP + The maximum number of nucleotides that can overlap + between two genes on the same strand. This must be + lower or equal to the minimum gene length. (default: + 60) + --no-stop-codon Disables translation of stop codons into star + characters (*) for complete genes. (default: False) + --pool {thread,process} + The sort of pool to use to process genomes in + parallel. Processes may be faster than threads on some + machines, refer to documentation. (default: thread) + + + +## URL Docs Extract +### https://pyrodigal.readthedocs.org +Pyrodigal — pyrodigal 3.7.1 documentation Skip to main content Back to top Ctrl + K Pyrodigal Choose version User Guide API Reference Paper Search Ctrl + K GitHub PyPI Search Ctrl + K User Guide API Reference Paper GitHub PyPI Pyrodigal # Cython bindings and Python interface to Prodigal , an ORF finder for genomes and metagenomes . Now with SIMD! Overview # Pyrodigal is a Python module that provides bindings to Prodigal using Cython . It directly interacts with the Prodigal internals, which has the following advantages: Batteries-included Just add pyrodigal as a pip or conda dependency, no need for the Prodigal binary or any external dependency. Flexible I/O Directly pass sequences to process as Python str objects, no need for intermediate files. Memory-efficient Benefit from conservative memory allocation and a reworked data layout for candidate nodes. Faster computation Use the full power of your CPU with SIMD instructions to filter out candidate genes prior to the scoring stage. Consistent results Get the same results as Prodigal v2.6.3+31b300a , with additional bug fixes compared to the latest stable Prodigal version. Feature-complete Access all the features of the original CLI through the Python API or a drop-in CLI replacement . Features # The library now features everything from the original Prodigal CLI: run mode selection : Choose between single mode, using a training sequence to count nucleotide hexamers, or metagenomic mode, using pre-trained data from different organisms ( prodigal -p ). region masking : Prevent genes from being predicted across regions containing unknown nucleotides ( prodigal -m ). closed ends : Genes will be identified as running over edges if they are larger than a certain size, but this can be disabled ( prodigal -c ). training configuration : During the training process, a custom translation table can be given ( prodigal -g ), and the Shine-Dalgarno motif search can be forcefully bypassed ( prodigal -n ) output files : Output files can be written in a format mostly compatible with the Prodigal binary, including the protein translations in FASTA format ( prodigal -a ), the gene sequences in FASTA format ( prodigal -d ), or the potential gene scores in tabular format ( prodigal -s ). See the Output Formats section for supported formats. training data persistence : Getting training data from a sequence and using it for other sequences is supported; in addition, a training data file can be saved and loaded transparently ( prodigal -t ). In addition, the new features are available: custom gene size threshold : While Prodigal uses a minimum gene size of 90 nucleotides (60 if on edge), Pyrodigal allows to customize this threshold, allowing for smaller ORFs to be identified if needed. Several changes were done regarding memory management : digitized sequences : Sequences are stored as raw bytes instead of compressed bitmaps. This means that the sequence itself takes 3/8th more space, but since the memory used for storing the sequence is often negligible compared to the memory used to store dynamic programming nodes, this is an acceptable trade-off for better performance when extracting said nodes. node buffer growth : Node arrays are dynamically allocated and grow exponentially instead of being pre-allocated with a large size. On small sequences, this leads to Pyrodigal using about 30% less memory. lightweight genes : Genes are stored in a more compact data structure than in Prodigal (which reserves a buffer to store string data), saving around 1KiB per gene. Setup # Run pip install pyrodigal in a shell to download the latest release and all its dependencies from PyPi, or have a look at the Installation page to find other ways to install pyrodigal . Citation # Pyrodigal is scientific software, with a published paper in the Journal of Open-Source Software . Check the Publications page to see how to cite Pyrodigal properly. Library # Check the following pages of the user guide or the API reference for more in-depth reference about library setup, usage, and rationale: User Guide Installation Output Formats Command Line Interface Parallelism Publications Benchmarks Contribution Guide Changelog Copyright Notice API Reference Gene Finder Training Info Metagenomic Bin Genes Nodes Sequence Masks Related Projects # The following Python libraries may be of interest for bioinformaticians. PyHMMER Profile Hidden Markov Models (with HMMER). https://pyhmmer.readthedocs.io PyInfernal RNA covariance models (with Infernal). https://pyinfernal.readthedocs.io Pyrodigal Prokaryotic Gene Finding (with Prodigal). https://pyrodigal.readthedocs.io Pyrodigal-gv Pyrodigal for Giant Viruses. https://pypi.org/project/pyrodigal-gv/ PyFAMSA Multiple Sequence Alignment (with FAMSA). https://pyfamsa.readthedocs.io PytrimAl Alignment Trimming (with trimAl). https://pytrimal.readthedocs.io LightMotif Platform-accelerated motif scoring. https://lightmotif.readthedocs.io Diced CRISPR Detection (with MinCED). https://diced.readthedocs.io Scoring Matrices Scoring matrices for Cython. https://scoring-matrices.readthedocs.io Pyskani Average Nucleotide Identity (with skani). https://pyskani.readthedocs.io PySylph ANI containment and taxonomic profiling (with sylph). https://pysylph.readthedocs.io PyFastANI Average Nucleotide Identity (with FastANI). https://pyfastani.readthedocs.io PyJess Geometric Template Matching (with Jess). https://pyjess.readthedocs.io PyTantan Tandem Repeat Masking (with Tantan). https://pytantan.readthedocs.io PyOpal Query/Database Aligner (with Opal). https://pyopal.readthedocs.io PySWRD Database Heuristic Filtering (with SWORD). https://pyswrd.readthedocs.io Mini3di Protein structure to 3di with NumPy. https://pypi.org/project/mini3di/ MiniNEAR Protein sequence to NEAR embedding with NumPy. https://pypi.org/project/mininear/ peptides.py Peptide descriptors for Python. https://peptides.readthedocs.io Pronto Open Biomedical Ontologies for Python. https://pronto.readthedocs.io NAFcodec Nucleotide Archival Format for Python (and Rust). https://pypi.org/project/nafcodec/ gb-io.py Fast GenBank parser for Python (with gb-io ). https://gb-io.readthedocs.io PyOrthoANI OrthoAni re-implementation in Python. https://pypi.org/project/pyorthoani/ PyCoMSA Multiple Sequence Alignment compression (with CoMSA). https://pycomsa.readthedocs.io PyARAGORN tRNA, tmRNA and mtRNA gene prediction (with ARAGORN). https://pyaragorn.readthedocs.io License # This library is provided under the GNU General Public License v3.0 . The Prodigal code was written by Doug Hyatt and is distributed under the terms of the GPLv3 as well. See the Copyright Notice section for the full GPLv3 license. This project is in no way not affiliated, sponsored, or otherwise endorsed by the original Prodigal authors. It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team . The project icon was derived from UXWing and is re-used under their permissive license . next User Guide On this page Overview Features Setup Citation Library Related Projects License Edit on GitHub This Page Show Source so the DOM is not blocked --> © Copyright 2020-2026, Martin Larralde. Created using Sphinx 9.0.4. Built with the PyData Sphinx Theme 0.16.1. + +### https://github.com/althonos/pyrodigal +GitHub - althonos/pyrodigal: Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD! · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} althonos / pyrodigal Public Notifications You must be signed in to change notification settings Fork 10 Star 183 Code Issues 12 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights althonos/pyrodigal main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 879 Commits 879 Commits .github/ workflows .github/ workflows benches benches docs docs paper paper pkg/ aur pkg/ aur src src vendor vendor .gitignore .gitignore .gitmodules .gitmodules .readthedocs.yaml .readthedocs.yaml CHANGELOG.md CHANGELOG.md CITATION.cff CITATION.cff CMakeLists.txt CMakeLists.txt CONTRIBUTING.md CONTRIBUTING.md COPYING COPYING README.md README.md pyproject.toml pyproject.toml View all files Repository files navigation README Contributing GPL-3.0 license 🔥 Pyrodigal Cython bindings and Python interface to Prodigal , an ORF finder for genomes and metagenomes. Now with SIMD! 🗺️ Overview Pyrodigal is a Python module that provides bindings to Prodigal using Cython . It directly interacts with the Prodigal internals, which has the following advantages: single dependency : Pyrodigal is distributed as a Python package, so you can add it as a dependency to your project, and stop worrying about the Prodigal binary being present on the end-user machine. no intermediate files : Everything happens in memory, in a Python object you fully control, so you don't have to invoke the Prodigal CLI using a sub-process and temporary files. Sequences can be passed directly as strings or bytes, which avoids the overhead of formatting your input to FASTA for Prodigal. better memory usage : Pyrodigal uses more compact data structures compared to the original Prodigal implementation, allowing to save memory to store the same information. A heuristic is used to estimate the number of nodes to allocate based on the sequence GC% in order to minimize reallocations. better performance : Pyrodigal uses SIMD instructions to compute which dynamic programming nodes can be ignored when scoring connections. This can save from a third to half the runtime depending on the sequence. The Benchmarks page of the documentation contains comprehensive comparisons. See the JOSS paper for details about how this is achieved. same results : Pyrodigal is tested to make sure it produces exactly the same results as Prodigal v2.6.3+31b300a . This was verified extensively by Julian Hahnfeld and can be checked with his comparison repository . 📋 Features The library now features everything from the original Prodigal CLI: run mode selection : Choose between single mode, using a training sequence to count nucleotide hexamers, or metagenomic mode, using pre-trained data from different organisms ( prodigal -p ). region masking : Prevent genes from being predicted across regions containing unknown nucleotides ( prodigal -m ). closed ends : Genes will be identified as running over edges if they are larger than a certain size, but this can be disabled ( prodigal -c ). training configuration : During the training process, a custom translation table can be given ( prodigal -g ), and the Shine-Dalgarno motif search can be forcefully bypassed ( prodigal -n ) output files : Output files can be written in a format mostly compatible with the Prodigal binary, including the protein translations in FASTA format ( prodigal -a ), the gene sequences in FASTA format ( prodigal -d ), or the potential gene scores in tabular format ( prodigal -s ). training data persistence : Getting training data from a sequence and using it for other sequences is supported; in addition, a training data file can be saved and loaded transparently ( prodigal -t ). In addition, the new features are available: custom gene size threshold : While Prodigal uses a minimum gene size of 90 nucleotides (60 if on edge), Pyrodigal allows to customize this threshold, allowing for smaller ORFs to be identified if needed. custom metagenomic models : Since v3.0.0 , you can use your own metagenomic models to run Pyrodigal in meta -mode. Check for instance pyrodigal-gv by Antônio Camargo , which provides additional models for giant viruses and gut phages, or pyrodigal-rv by Lander De Coninck which provides additional models for RNA viruses. 🐏 Memory Pyrodigal makes several changes compared to the original Prodigal binary regarding memory management: Sequences are stored as raw bytes instead of compressed bitmaps. This means that the sequence itself takes 3/8th more space, but since the memory used for storing the sequence is often negligible compared to the memory used to store dynamic programming nodes, this is an acceptable trade-off for better performance when extracting said nodes. Node fields use smaller data types to fit into 128 bytes, compared to the 176 bytes of the original Prodigal data structure. Node arrays are pre-allocated based on the sequence GC% to extrapolate the probability to find a start or stop codon. Genes are stored in a more compact data structure than in Prodigal (which reserves a buffer to store string data), saving around 1KiB per gene. 🧶 Thread-safety pyrodigal.GeneFinder instances are thread-safe. In addition, the find_genes method is re-entrant. This means you can train an GeneFinder instance once, and then use a pool to process sequences in parallel: import multiprocessing . pool import pyrodigal gene_finder = pyrodigal . GeneFinder () gene_finder . train ( training_sequence ) with multiprocessing . pool . ThreadPool () as pool : predictions = pool . map ( gene_finder . find_genes , sequences ) 🔧 Installing This project is supported on Python 3.7 and later. Pyrodigal can be installed directly from PyPI , which hosts some pre-built wheels for the x86-64 architecture (Linux/MacOS/Windows) and the Aarch64 architecture (Linux/MacOS), as well as the code required to compile from source with Cython: $ pip install pyrodigal Otherwise, Pyrodigal is also available as a Bioconda package: $ conda install -c bioconda pyrodigal Check the install page of the documentation for other ways to install Pyrodigal on your machine. 💡 Example Let's load a sequence from a GenBank file, use a GeneFinder to find all the genes it contains, and print the proteins in two-line FASTA format. 🔬 Biopython To use the GeneFinder in single mode (corresponding to prodigal -p single , the default operation mode of Prodigal), you must explicitly call the train method with the sequence you want to use for training before trying to find genes, or you will get a RuntimeError : import Bio . SeqIO import pyrodigal record = Bio . SeqIO . read ( "sequence.gbk" , "genbank" ) gene_finder = pyrodigal . GeneFinder () gene_finder . train ( bytes ( record . seq )) genes = gene_finder . find_genes ( bytes ( record . seq )) However, in meta mode (corresponding to prodigal -p meta ), you can find genes directly: import Bio . SeqIO import pyrodigal record = Bio . SeqIO . read ( "sequence.gbk" , "genbank" ) gene_finder = pyrodigal . GeneFinder ( meta = True ) for i , pred in enumerate ( gene_finder . find_genes ( bytes ( record . seq ))): print ( f"> { record . id } _ { i + 1 } " ) print ( pred . translate ()) On older versions of Biopython (before 1.79) you will need to use record.seq.encode() instead of bytes(record.seq) . 🧪 Scikit-bio import skbio . io import pyrodigal seq = next ( skbio . io . read ( "sequence.gbk" , "genbank" )) gene_finder = pyrodigal . GeneFinder ( meta = True ) for i , pred in enumerate ( gene_finder . find_genes ( seq . values . view ( 'B' ))): print ( f"> { record . id } _ { i + 1 } " ) print ( pred . translate ()) We need to use the view method to get the sequence viewable by Cython as an array of unsigned char . 🔖 Citation Pyrodigal is scientific software, with a published paper in the Journal of Open-Source Software . Please cite both Pyrodigal and Prodigal if you are using it in an academic work, for instance as: Pyrodigal (Larralde, 2022), a Python library binding to Prodigal (Hyatt et al. , 2010). Detailed references are available on the Publications page of the online documentation . 💭 Feedback ⚠️ Issue Tracker Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation. 🏗️ Contributing Contributions are more than welcome! See CONTRIBUTING.md for more details. 📋 Changelog This project adheres to Semantic Versioning and provides a changelog in the Keep a Changelog format. ⚖️ License This library is provided under the GNU General Public License v3.0 . The Prodigal code was written by Doug Hyatt and is distributed under the terms of the GPLv3 as well. See vendor/Prodigal/LICENSE for more information. This project is in no way not affiliated, sponsored, or otherwise endorsed by the original Prodigal authors . It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team . About Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD! pyrodigal.readthedocs.org Topics python bioinformatics genome python-library simd bioconda python-interface metagenomes cython-wrapper prodigal gene-finding orf-finder Resources Readme License GPL-3.0 license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 183 stars Watchers 5 watching Forks 10 forks Report repository Releases 73 v3.7.1 Latest Mar 7, 2026 + 72 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Cython 59.6% Python 22.3% C 11.7% CMake 4.6% TeX 1.3% Shell 0.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/althonos/pyrodigal +GitHub - althonos/pyrodigal: Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD! · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} althonos / pyrodigal Public Notifications You must be signed in to change notification settings Fork 10 Star 183 Code Issues 12 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights althonos/pyrodigal main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 879 Commits 879 Commits .github/ workflows .github/ workflows benches benches docs docs paper paper pkg/ aur pkg/ aur src src vendor vendor .gitignore .gitignore .gitmodules .gitmodules .readthedocs.yaml .readthedocs.yaml CHANGELOG.md CHANGELOG.md CITATION.cff CITATION.cff CMakeLists.txt CMakeLists.txt CONTRIBUTING.md CONTRIBUTING.md COPYING COPYING README.md README.md pyproject.toml pyproject.toml View all files Repository files navigation README Contributing GPL-3.0 license 🔥 Pyrodigal Cython bindings and Python interface to Prodigal , an ORF finder for genomes and metagenomes. Now with SIMD! 🗺️ Overview Pyrodigal is a Python module that provides bindings to Prodigal using Cython . It directly interacts with the Prodigal internals, which has the following advantages: single dependency : Pyrodigal is distributed as a Python package, so you can add it as a dependency to your project, and stop worrying about the Prodigal binary being present on the end-user machine. no intermediate files : Everything happens in memory, in a Python object you fully control, so you don't have to invoke the Prodigal CLI using a sub-process and temporary files. Sequences can be passed directly as strings or bytes, which avoids the overhead of formatting your input to FASTA for Prodigal. better memory usage : Pyrodigal uses more compact data structures compared to the original Prodigal implementation, allowing to save memory to store the same information. A heuristic is used to estimate the number of nodes to allocate based on the sequence GC% in order to minimize reallocations. better performance : Pyrodigal uses SIMD instructions to compute which dynamic programming nodes can be ignored when scoring connections. This can save from a third to half the runtime depending on the sequence. The Benchmarks page of the documentation contains comprehensive comparisons. See the JOSS paper for details about how this is achieved. same results : Pyrodigal is tested to make sure it produces exactly the same results as Prodigal v2.6.3+31b300a . This was verified extensively by Julian Hahnfeld and can be checked with his comparison repository . 📋 Features The library now features everything from the original Prodigal CLI: run mode selection : Choose between single mode, using a training sequence to count nucleotide hexamers, or metagenomic mode, using pre-trained data from different organisms ( prodigal -p ). region masking : Prevent genes from being predicted across regions containing unknown nucleotides ( prodigal -m ). closed ends : Genes will be identified as running over edges if they are larger than a certain size, but this can be disabled ( prodigal -c ). training configuration : During the training process, a custom translation table can be given ( prodigal -g ), and the Shine-Dalgarno motif search can be forcefully bypassed ( prodigal -n ) output files : Output files can be written in a format mostly compatible with the Prodigal binary, including the protein translations in FASTA format ( prodigal -a ), the gene sequences in FASTA format ( prodigal -d ), or the potential gene scores in tabular format ( prodigal -s ). training data persistence : Getting training data from a sequence and using it for other sequences is supported; in addition, a training data file can be saved and loaded transparently ( prodigal -t ). In addition, the new features are available: custom gene size threshold : While Prodigal uses a minimum gene size of 90 nucleotides (60 if on edge), Pyrodigal allows to customize this threshold, allowing for smaller ORFs to be identified if needed. custom metagenomic models : Since v3.0.0 , you can use your own metagenomic models to run Pyrodigal in meta -mode. Check for instance pyrodigal-gv by Antônio Camargo , which provides additional models for giant viruses and gut phages, or pyrodigal-rv by Lander De Coninck which provides additional models for RNA viruses. 🐏 Memory Pyrodigal makes several changes compared to the original Prodigal binary regarding memory management: Sequences are stored as raw bytes instead of compressed bitmaps. This means that the sequence itself takes 3/8th more space, but since the memory used for storing the sequence is often negligible compared to the memory used to store dynamic programming nodes, this is an acceptable trade-off for better performance when extracting said nodes. Node fields use smaller data types to fit into 128 bytes, compared to the 176 bytes of the original Prodigal data structure. Node arrays are pre-allocated based on the sequence GC% to extrapolate the probability to find a start or stop codon. Genes are stored in a more compact data structure than in Prodigal (which reserves a buffer to store string data), saving around 1KiB per gene. 🧶 Thread-safety pyrodigal.GeneFinder instances are thread-safe. In addition, the find_genes method is re-entrant. This means you can train an GeneFinder instance once, and then use a pool to process sequences in parallel: import multiprocessing . pool import pyrodigal gene_finder = pyrodigal . GeneFinder () gene_finder . train ( training_sequence ) with multiprocessing . pool . ThreadPool () as pool : predictions = pool . map ( gene_finder . find_genes , sequences ) 🔧 Installing This project is supported on Python 3.7 and later. Pyrodigal can be installed directly from PyPI , which hosts some pre-built wheels for the x86-64 architecture (Linux/MacOS/Windows) and the Aarch64 architecture (Linux/MacOS), as well as the code required to compile from source with Cython: $ pip install pyrodigal Otherwise, Pyrodigal is also available as a Bioconda package: $ conda install -c bioconda pyrodigal Check the install page of the documentation for other ways to install Pyrodigal on your machine. 💡 Example Let's load a sequence from a GenBank file, use a GeneFinder to find all the genes it contains, and print the proteins in two-line FASTA format. 🔬 Biopython To use the GeneFinder in single mode (corresponding to prodigal -p single , the default operation mode of Prodigal), you must explicitly call the train method with the sequence you want to use for training before trying to find genes, or you will get a RuntimeError : import Bio . SeqIO import pyrodigal record = Bio . SeqIO . read ( "sequence.gbk" , "genbank" ) gene_finder = pyrodigal . GeneFinder () gene_finder . train ( bytes ( record . seq )) genes = gene_finder . find_genes ( bytes ( record . seq )) However, in meta mode (corresponding to prodigal -p meta ), you can find genes directly: import Bio . SeqIO import pyrodigal record = Bio . SeqIO . read ( "sequence.gbk" , "genbank" ) gene_finder = pyrodigal . GeneFinder ( meta = True ) for i , pred in enumerate ( gene_finder . find_genes ( bytes ( record . seq ))): print ( f"> { record . id } _ { i + 1 } " ) print ( pred . translate ()) On older versions of Biopython (before 1.79) you will need to use record.seq.encode() instead of bytes(record.seq) . 🧪 Scikit-bio import skbio . io import pyrodigal seq = next ( skbio . io . read ( "sequence.gbk" , "genbank" )) gene_finder = pyrodigal . GeneFinder ( meta = True ) for i , pred in enumerate ( gene_finder . find_genes ( seq . values . view ( 'B' ))): print ( f"> { record . id } _ { i + 1 } " ) print ( pred . translate ()) We need to use the view method to get the sequence viewable by Cython as an array of unsigned char . 🔖 Citation Pyrodigal is scientific software, with a published paper in the Journal of Open-Source Software . Please cite both Pyrodigal and Prodigal if you are using it in an academic work, for instance as: Pyrodigal (Larralde, 2022), a Python library binding to Prodigal (Hyatt et al. , 2010). Detailed references are available on the Publications page of the online documentation . 💭 Feedback ⚠️ Issue Tracker Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation. 🏗️ Contributing Contributions are more than welcome! See CONTRIBUTING.md for more details. 📋 Changelog This project adheres to Semantic Versioning and provides a changelog in the Keep a Changelog format. ⚖️ License This library is provided under the GNU General Public License v3.0 . The Prodigal code was written by Doug Hyatt and is distributed under the terms of the GPLv3 as well. See vendor/Prodigal/LICENSE for more information. This project is in no way not affiliated, sponsored, or otherwise endorsed by the original Prodigal authors . It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team . About Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD! pyrodigal.readthedocs.org Topics python bioinformatics genome python-library simd bioconda python-interface metagenomes cython-wrapper prodigal gene-finding orf-finder Resources Readme License GPL-3.0 license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 183 stars Watchers 5 watching Forks 10 forks Report repository Releases 73 v3.7.1 Latest Mar 7, 2026 + 72 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Cython 59.6% Python 22.3% C 11.7% CMake 4.6% TeX 1.3% Shell 0.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge pyrodigal --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +pyrodigal 0.2.1 py36h4c5857e_1 +------------------------------ +file name : pyrodigal-0.2.1-py36h4c5857e_1.tar.bz2 +name : pyrodigal +version : 0.2.1 +build : py36h4c5857e_1 +build number: 1 +size : 850 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.2.1-py36h4c5857e_1.tar.bz2 +md5 : 36b9d4816a33f3e4697c00c038dcc664 +timestamp : 2020-08-13 09:08:49 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - setuptools + + +pyrodigal 0.2.1 py36h70b2009_0 +------------------------------ +file name : pyrodigal-0.2.1-py36h70b2009_0.tar.bz2 +name : pyrodigal +version : 0.2.1 +build : py36h70b2009_0 +build number: 0 +size : 861 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.2.1-py36h70b2009_0.tar.bz2 +md5 : f06205152abd59993e94a0cde5a5f170 +timestamp : 2020-06-29 21:40:52 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - setuptools + + +pyrodigal 0.2.1 py37he7d4d9d_0 +------------------------------ +file name : pyrodigal-0.2.1-py37he7d4d9d_0.tar.bz2 +name : pyrodigal +version : 0.2.1 +build : py37he7d4d9d_0 +build number: 0 +size : 850 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.2.1-py37he7d4d9d_0.tar.bz2 +md5 : 5e4e100f152196a2c2ef57030551037d +timestamp : 2020-06-29 21:46:12 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - setuptools + + +pyrodigal 0.2.1 py37hf01694f_1 +------------------------------ +file name : pyrodigal-0.2.1-py37hf01694f_1.tar.bz2 +name : pyrodigal +version : 0.2.1 +build : py37hf01694f_1 +build number: 1 +size : 849 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.2.1-py37hf01694f_1.tar.bz2 +md5 : 932a7136c3229b59bb5fbad39b72c2f7 +timestamp : 2020-08-13 09:15:15 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - setuptools + + +pyrodigal 0.2.1 py38h0213d0e_1 +------------------------------ +file name : pyrodigal-0.2.1-py38h0213d0e_1.tar.bz2 +name : pyrodigal +version : 0.2.1 +build : py38h0213d0e_1 +build number: 1 +size : 860 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.2.1-py38h0213d0e_1.tar.bz2 +md5 : 4843c40b3c6440b092188133de1a1e43 +timestamp : 2020-08-30 14:44:58 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - setuptools + + +pyrodigal 0.3.0 py36h4c5857e_0 +------------------------------ +file name : pyrodigal-0.3.0-py36h4c5857e_0.tar.bz2 +name : pyrodigal +version : 0.3.0 +build : py36h4c5857e_0 +build number: 0 +size : 476 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.3.0-py36h4c5857e_0.tar.bz2 +md5 : c4b616500792cfa228429aed3708e823 +timestamp : 2020-10-23 09:42:42 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - setuptools + + +pyrodigal 0.3.0 py37hf01694f_0 +------------------------------ +file name : pyrodigal-0.3.0-py37hf01694f_0.tar.bz2 +name : pyrodigal +version : 0.3.0 +build : py37hf01694f_0 +build number: 0 +size : 476 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.3.0-py37hf01694f_0.tar.bz2 +md5 : 51e5ca0cd98f62d3b164a02282e16ed5 +timestamp : 2020-10-23 09:44:57 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - setuptools + + +pyrodigal 0.3.0 py38h0213d0e_0 +------------------------------ +file name : pyrodigal-0.3.0-py38h0213d0e_0.tar.bz2 +name : pyrodigal +version : 0.3.0 +build : py38h0213d0e_0 +build number: 0 +size : 478 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.3.0-py38h0213d0e_0.tar.bz2 +md5 : 70d8b224342a8ea1802ea02db10b1c6f +timestamp : 2020-10-23 09:40:24 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - setuptools + + +pyrodigal 0.4.5 py36h4c5857e_0 +------------------------------ +file name : pyrodigal-0.4.5-py36h4c5857e_0.tar.bz2 +name : pyrodigal +version : 0.4.5 +build : py36h4c5857e_0 +build number: 0 +size : 487 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.5-py36h4c5857e_0.tar.bz2 +md5 : 66ebd78a42bd7ddb1167e2ff9905085e +timestamp : 2021-03-03 20:25:14 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - setuptools + + +pyrodigal 0.4.5 py37hf01694f_0 +------------------------------ +file name : pyrodigal-0.4.5-py37hf01694f_0.tar.bz2 +name : pyrodigal +version : 0.4.5 +build : py37hf01694f_0 +build number: 0 +size : 487 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.5-py37hf01694f_0.tar.bz2 +md5 : 4554cf5d86c59470d5370bc044dc0306 +timestamp : 2021-03-03 20:31:03 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - setuptools + + +pyrodigal 0.4.5 py38h0213d0e_0 +------------------------------ +file name : pyrodigal-0.4.5-py38h0213d0e_0.tar.bz2 +name : pyrodigal +version : 0.4.5 +build : py38h0213d0e_0 +build number: 0 +size : 481 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.5-py38h0213d0e_0.tar.bz2 +md5 : a9e7fa9f5f71c4d66a8b4c91e7364778 +timestamp : 2021-03-03 20:28:07 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - setuptools + + +pyrodigal 0.4.6 py36h4c5857e_0 +------------------------------ +file name : pyrodigal-0.4.6-py36h4c5857e_0.tar.bz2 +name : pyrodigal +version : 0.4.6 +build : py36h4c5857e_0 +build number: 0 +size : 600 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.6-py36h4c5857e_0.tar.bz2 +md5 : 8ae118044a75fb1ac93526e3a62bb892 +timestamp : 2021-03-05 16:11:18 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - setuptools + + +pyrodigal 0.4.6 py36hc5360cc_1 +------------------------------ +file name : pyrodigal-0.4.6-py36hc5360cc_1.tar.bz2 +name : pyrodigal +version : 0.4.6 +build : py36hc5360cc_1 +build number: 1 +size : 613 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.6-py36hc5360cc_1.tar.bz2 +md5 : f5e36f6fa8b8d51e6c34418432251526 +timestamp : 2021-03-25 18:02:00 UTC +dependencies: + - libgcc-ng >=9.3.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - setuptools + + +pyrodigal 0.4.6 py37h73a75cf_1 +------------------------------ +file name : pyrodigal-0.4.6-py37h73a75cf_1.tar.bz2 +name : pyrodigal +version : 0.4.6 +build : py37h73a75cf_1 +build number: 1 +size : 607 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.6-py37h73a75cf_1.tar.bz2 +md5 : a1a8dfdbfe92ae3bdd66cf0f28aa417e +timestamp : 2021-03-25 18:04:38 UTC +dependencies: + - libgcc-ng >=9.3.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - setuptools + + +pyrodigal 0.4.6 py37hf01694f_0 +------------------------------ +file name : pyrodigal-0.4.6-py37hf01694f_0.tar.bz2 +name : pyrodigal +version : 0.4.6 +build : py37hf01694f_0 +build number: 0 +size : 600 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.6-py37hf01694f_0.tar.bz2 +md5 : 380cdf67bbea960843cb710476ee05be +timestamp : 2021-03-05 16:14:11 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - setuptools + + +pyrodigal 0.4.6 py38h0213d0e_0 +------------------------------ +file name : pyrodigal-0.4.6-py38h0213d0e_0.tar.bz2 +name : pyrodigal +version : 0.4.6 +build : py38h0213d0e_0 +build number: 0 +size : 601 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.6-py38h0213d0e_0.tar.bz2 +md5 : f8a7588f1fc70795d56622546c711a23 +timestamp : 2021-03-05 16:08:32 UTC +dependencies: + - libgcc-ng >=7.5.0 + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - setuptools + + +pyrodigal 0.4.6 py38h4a8c8d9_1 +------------------------------ +file name : pyrodigal-0.4.6-py38h4a8c8d9_1.tar.bz2 +name : pyrodigal +version : 0.4.6 +build : py38h4a8c8d9_1 +build number: 1 +size : 609 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.6-py38h4a8c8d9_1.tar.bz2 +md5 : d08868961339187bbaf763655af45079 +timestamp : 2021-03-25 17:57:00 UTC +dependencies: + - libgcc-ng >=9.3.0 + - python >=3.8,<3.9.0a0 + - python_abi 3.8.* *_cp38 + - setuptools + + +pyrodigal 0.4.6 py39h38f01e4_1 +------------------------------ +file name : pyrodigal-0.4.6-py39h38f01e4_1.tar.bz2 +name : pyrodigal +version : 0.4.6 +build : py39h38f01e4_1 +build number: 1 +size : 607 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.6-py39h38f01e4_1.tar.bz2 +md5 : 2a0b65ed5a244362d70a8fb7ae082411 +timestamp : 2021-03-25 17:59:28 UTC +dependencies: + - libgcc-ng >=9.3.0 + - python >=3.9,<3.10.0a0 + - python_abi 3.9.* *_cp39 + - setuptools + + +pyrodigal 0.4.7 py36hc5360cc_0 +------------------------------ +file name : pyrodigal-0.4.7-py36hc5360cc_0.tar.bz2 +name : pyrodigal +version : 0.4.7 +build : py36hc5360cc_0 +build number: 0 +size : 611 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.7-py36hc5360cc_0.tar.bz2 +md5 : 70182e8a642becd17fc907c12bb2ef0e +timestamp : 2021-04-09 02:30:27 UTC +dependencies: + - libgcc-ng >=9.3.0 + - python >=3.6,<3.7.0a0 + - python_abi 3.6.* *_cp36m + - setuptools + + +pyrodigal 0.4.7 py37h73a75cf_0 +------------------------------ +file name : pyrodigal-0.4.7-py37h73a75cf_0.tar.bz2 +name : pyrodigal +version : 0.4.7 +build : py37h73a75cf_0 +build number: 0 +size : 605 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pyrodigal-0.4.7-py37h73a75cf_0.tar.bz2 +md5 : cd5fc34a85189628e683bd48f305c34b +timestamp : 2021-04-09 02:33:40 UTC +dependencies: + - libgcc-ng >=9.3.0 + - python >=3.7,<3.8.0a0 + - python_abi 3.7.* *_cp37m + - setuptools + + +pyrodigal 0.4.7 py38h4a8c8d9_0 +------------------------------ +file name : pyrodigal-0.4.7-py38h4a8c8d9_0.tar.bz2 +name : pyrodigal +version : 0.4.7 +build : py38h4a8c8d9_0 +build number: 0 +size : 607 KB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pysftp.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pysftp.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b6bc59d673780f86de4f51e0d8910abe9d98fa3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/pysftp.manual_bundle.txt @@ -0,0 +1,249 @@ +# Tool: pysftp +software_name: pysftp +tier: T1 +domain: t1_backfill_overall +downloads: 133838 +summary: A friendly face on SFTP +description: A friendly face on SFTP +dependencies: paramiko >=1.7.7, python 2.7* +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: +doc_url: +dev_url: + +## Conda Search Info +$ conda search -c bioconda -c conda-forge pysftp --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +pysftp 0.2.8 py27_0 +------------------- +file name : pysftp-0.2.8-py27_0.tar.bz2 +name : pysftp +version : 0.2.8 +build : py27_0 +build number: 0 +size : 23 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pysftp-0.2.8-py27_0.tar.bz2 +md5 : faa0bbb6243331ea8708223b8cabecb2 +dependencies: + - paramiko >=1.7.7 + - python 2.7* + + +pysftp 0.2.8 py34_0 +------------------- +file name : pysftp-0.2.8-py34_0.tar.bz2 +name : pysftp +version : 0.2.8 +build : py34_0 +build number: 0 +size : 24 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pysftp-0.2.8-py34_0.tar.bz2 +md5 : f59b25061f62383ea4b241368a9f552b +dependencies: + - paramiko >=1.7.7 + - python 3.4* + + +pysftp 0.2.8 py35_0 +------------------- +file name : pysftp-0.2.8-py35_0.tar.bz2 +name : pysftp +version : 0.2.8 +build : py35_0 +build number: 0 +size : 24 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pysftp-0.2.8-py35_0.tar.bz2 +md5 : f359a425e4241b817b7332eca7ef1f27 +dependencies: + - paramiko >=1.7.7 + - python 3.5* + + +pysftp 0.2.9 py27_0 +------------------- +file name : pysftp-0.2.9-py27_0.tar.bz2 +name : pysftp +version : 0.2.9 +build : py27_0 +build number: 0 +size : 31 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pysftp-0.2.9-py27_0.tar.bz2 +md5 : 6eff4199ac1df90eb950c22797b07bd2 +dependencies: + - paramiko >=1.7.7 + - python 2.7* + + +pysftp 0.2.9 py27_0 +------------------- +file name : pysftp-0.2.9-py27_0.tar.bz2 +name : pysftp +version : 0.2.9 +build : py27_0 +build number: 0 +size : 24 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/pysftp-0.2.9-py27_0.tar.bz2 +md5 : cc64255ba516787f43a8d73791cecee3 +constraints : + - python_abi * *_cp27mu +dependencies: + - paramiko >=1.17.0 + - python 2.7* + + +pysftp 0.2.9 py34_0 +------------------- +file name : pysftp-0.2.9-py34_0.tar.bz2 +name : pysftp +version : 0.2.9 +build : py34_0 +build number: 0 +size : 32 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pysftp-0.2.9-py34_0.tar.bz2 +md5 : 90c634e837a5a76a21f91b02edeae76b +dependencies: + - paramiko >=1.7.7 + - python 3.4* + + +pysftp 0.2.9 py35_0 +------------------- +file name : pysftp-0.2.9-py35_0.tar.bz2 +name : pysftp +version : 0.2.9 +build : py35_0 +build number: 0 +size : 31 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pysftp-0.2.9-py35_0.tar.bz2 +md5 : 06dfc4ce30f9d47acf813893bcab2004 +dependencies: + - paramiko >=1.7.7 + - python 3.5* + + +pysftp 0.2.9 py35_0 +------------------- +file name : pysftp-0.2.9-py35_0.tar.bz2 +name : pysftp +version : 0.2.9 +build : py35_0 +build number: 0 +size : 24 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/pysftp-0.2.9-py35_0.tar.bz2 +md5 : 52e23f86aa8b43fccd98ca95b9ead60d +constraints : + - python_abi * *_cp35m +dependencies: + - paramiko >=1.17.0 + - python 3.5* + + +pysftp 0.2.9 py36_0 +------------------- +file name : pysftp-0.2.9-py36_0.tar.bz2 +name : pysftp +version : 0.2.9 +build : py36_0 +build number: 0 +size : 31 KB +license : BSD License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/pysftp-0.2.9-py36_0.tar.bz2 +md5 : 02aeb1325ad2ed4579a1fe6282cc136d +dependencies: + - paramiko >=1.7.7 + - python 3.6* + + +pysftp 0.2.9 py36_0 +------------------- +file name : pysftp-0.2.9-py36_0.tar.bz2 +name : pysftp +version : 0.2.9 +build : py36_0 +build number: 0 +size : 24 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/conda-forge/linux-64/pysftp-0.2.9-py36_0.tar.bz2 +md5 : 06ba476544f5664a547c38c8fd6a5c22 +constraints : + - python_abi * *_cp36m +dependencies: + - paramiko >=1.17.0 + - python 3.6* + + +pysftp 0.2.9 py_1 +----------------- +file name : pysftp-0.2.9-py_1.tar.bz2 +name : pysftp +version : 0.2.9 +build : py_1 +build number: 1 +size : 15 KB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/conda-forge/noarch/pysftp-0.2.9-py_1.tar.bz2 +md5 : 3172621a36e00ef8711a393784d8fa7f +timestamp : 2018-07-09 14:55:33 UTC +dependencies: + - paramiko >=1.17.0 + - python + + +pysftp 0.2.9 py_1 +----------------- +file name : pysftp-0.2.9-py_1.conda +name : pysftp +version : 0.2.9 +build : py_1 +build number: 1 +size : 18 KB +license : BSD-3-Clause +subdir : noarch +url : https://repo.anaconda.com/pkgs/main/noarch/pysftp-0.2.9-py_1.conda +md5 : 51ac80a527220282edced5fe6efa5bdd +timestamp : 2020-06-18 20:59:22 UTC +dependencies: + - paramiko >=1.17.0 + - python + + +pysftp 0.2.9 pyhd3eb1b0_1 +------------------------- +file name : pysftp-0.2.9-pyhd3eb1b0_1.conda +name : pysftp +version : 0.2.9 +build : pyhd3eb1b0_1 +build number: 1 +size : 18 KB +license : BSD-3-Clause +subdir : noarch +url : https://repo.anaconda.com/pkgs/main/noarch/pysftp-0.2.9-pyhd3eb1b0_1.conda +md5 : e1f2085b184e58f0581a968bfcffa45f +timestamp : 2021-08-23 11:09:01 UTC +dependencies: + - paramiko >=1.17.0 + - python diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/python-edlib.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/python-edlib.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2e0a36288bbc9c8f62b79f5c0c53d9cf9c6684ea --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/python-edlib.manual_bundle.txt @@ -0,0 +1,432 @@ +# Tool: python-edlib +software_name: python-edlib +tier: T1 +domain: t1_backfill_overall +downloads: 270767 +summary: Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance. +description: Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance. +dependencies: libgcc >=14, libstdcxx >=14, python >=3.10,<3.11.0a0, python_abi 3.10.* *_cp310 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/Martinsos/edlib +doc_url: https://martinsos.github.io/edlib +dev_url: https://github.com/Martinsos/edlib + +## URL Docs Extract +### https://martinsos.github.io/edlib +Edlib: Edlib Edlib   1.1.2. Lightweight, super fast C/C++ library for sequence alignment using edit distance. Edlib A lightweight and super fast C/C++ library for sequence alignment using edit distance . Calculating edit distance of two strings is as simple as: edlibAlign ( "hello" , 5, "world!" , 6, edlibDefaultAlignConfig ()). editDistance ; Features Calculates edit distance (Levehnstein distance) . It can find optimal alignment path (instructions how to transform first sequence into the second sequence). It can find just the start and/or end locations of alignment path - can be useful when speed is more important than having exact alignment path. Supports multiple alignment methods : global( NW ), prefix( SHW ) and infix( HW ), each of them useful for different scenarios. It can easily handle small or very large sequences, even when finding alignment path, while consuming very little memory. Super fast thanks to Myers's bit-vector algorithm. Edlib is also available for Python and Node.js . Building Edlib uses CMAKE to build libraries (static and shared) and binaries (apps and tests). Execute following commands to build Edlib using CMAKE: cd build cmake -D CMAKE_BUILD_TYPE=Release .. make This will create binaries in bin/ directory and libraries (static and shared) in lib/ directory. You can run ./bin/runTests to confirm that it works! Optionally, you can run sudo make install to install edlib library on your machine (on Linux, this will usually install it to usr/local/lib and usr/local/include ). You may also install edlib using Conda : conda install edlib . Using Edlib in your project You can use Edlib in you project by either directly copying header and source files from edlib/ , or by linking Edlib library (see Building for instructions how to build Edlib libraries). In any case, only thing that you have to do in your source files is to include edlib.h . To get you started quickly, let's take a look at a few ways to get simple Hello World project working. Our Hello World project has just one source file, helloWorld.c file, and it looks like this: #include <stdio.h> #include " edlib.h " int main() { EdlibAlignResult result = edlibAlign ( "hello" , 5, "world!" , 6, edlibDefaultAlignConfig ()); printf( "edit_distance('hello', 'world!') = %d\n" , result. editDistance ); edlibFreeAlignResult (result); } Running it should output `edit_distance('hello', 'world!') = 5`. Approach #1: Directly copying edlib source and header files. Here we directly copied edlib/ directory to our project, to get following project structure: edlib/ -> copied from edlib/ include/ edlib.h src/ edlib.cpp helloWorld.c -> your program Compile it with g++ helloWorld.c edlib/src/edlib.cpp -o helloWorld -I edlib/include and that is it! Approach #2: Copying edlib header file and static library. Instead of copying edlib source files, you could copy static library (check Building on how to create static library). We also need to copy edlib header files. We get following project structure: edlib/ -> copied from edlib include/ edlib.h edlib.a helloWorld.c -> your program Now you can compile it with g++ helloWorld.c -o helloWorld -I edlib/include -L edlib -ledlib_static . Approach #3: Install edlib library on machine. Alternatively, you could avoid copying any Edlib files and instead install libraries by running sudo make install (check Building ). Now, all you have to do to compile your project is g++ helloWorld.c -o helloWorld -ledlib . If you get error message like cannot open shared object file: No such file or directory , make sure that your linker includes path where edlib was installed. For more example projects take a look at applications in apps/ . Usage and examples Main function in edlib is edlibAlign . Given two sequences (and their lengths), it will find edit distance, alignment path or its end and start locations. char * query = "ACCTCTG" ; char * target = "ACTCTGAAA" EdlibAlignResult result = edlibAlign (query, 7, target, 9, edlibDefaultAlignConfig ()); printf( "%d" , result. editDistance ); edlibFreeAlignResult (result); Configuring edlibAlign() edlibAlign takes configuration object (it is a struct EdlibAlignConfig ), which allows you to further customize how alignment will be done. You can choose alignment method , tell edlib what to calculate (just edit distance or also path and locations) and set upper limit for edit distance. For example, if you want to use infix(HW) alignment method, want to find alignment path (and edit distance), and are interested in result only if edit distance is not larger than 42, you would call it like this: edlibAlign (seq1, seq1Length, seq2, seq2Length, edlibNewAlignConfig (42, EDLIB_MODE_HW , EDLIB_TASK_PATH )); Or, if you want to use suffix(SHW) alignment method, want to find only edit distance, and do not have any limits on edit distance, you would call it like this: edlibAlign (seq1, seq1Length, seq2, seq2Length, edlibNewAlignConfig (-1, EDLIB_MODE_SHW , EDLIB_TASK_DISTANCE )); We used edlibNewAlignConfig helper function to easily create config, however we could have also just created an instance of it and set its members accordingly. Handling result of edlibAlign() edlibAlign function returns a result object ( EdlibAlignResult ), which will contain results of alignment (corresponding to the task that you passed in config). EdlibAlignResult result = edlibAlign (seq1, seq1Length, seq2, seq2Length, edlibNewAlignConfig (-1, EDLIB_MODE_HW , EDLIB_TASK_PATH )); printf( "%d\n" , result. editDistance ); printf( "%d\n" , result. alignmentLength ); printf( "%d\n" , result. endLocations [0]); edlibFreeAlignResult (result); It is important to remember to free the result object using edlibFreeAlignResult function, since Edlib allocates memory on heap for certain members. If you decide to do the cleaning manually and not use edlibFreeAlignResult , do not forget to manually free() required members. Turning alignment to cigar Cigar is a standard way to represent alignment path. Edlib has helper function that transforms alignment path into cigar. char * cigar = edlibAlignmentToCigar (result. alignment , result. alignmentLength , EDLIB_CIGAR_STANDARD ); printf( "%s" , cigar); free(cigar); API documentation For complete documentation of Edlib library API, visit http://martinsos.github.io/edlib (should be updated to the latest release). To generate the latest API documentation yourself from the source, you need to have doxygen installed. Position yourself in the root directory and run doxygen , this will generate docs/ directory. Then open docs/html/index.html file with you favorite browser. Alignment methods Edlib supports 3 alignment methods: global (NW) - This is the standard method, when we say "edit distance" this is the method that is assumed. It tells us the smallest number of operations needed to transform first sequence into second sequence. This method is appropriate when you want to find out how similar is first sequence to second sequence. prefix (SHW) - Similar to global method, but with a small twist - gap at query end is not penalized. What that means is that deleting elements from the end of second sequence is "free"! For example, if we had AACT and AACTGGC , edit distance would be 0, because removing GGC from the end of second sequence is "free" and does not count into total edit distance. This method is appropriate when you want to find out how well first sequence fits at the beginning of second sequence. infix (HW) : Similar as prefix method, but with one more twist - gaps at query end and start are not penalized. What that means is that deleting elements from the start and end of second sequence is "free"! For example, if we had ACT and CGACTGAC , edit distance would be 0, because removing CG from the start and GAC from the end of second sequence is "free" and does not count into total edit distance. This method is appropriate when you want to find out how well first sequence fits at any part of second sequence. For example, if your second sequence was a long text and your first sequence was a sentence from that text, but slightly scrambled, you could use this method to discover how scrambled it is and where it fits in that text. In bioinformatics, this method is appropriate for aligning read to a sequence. Aligner Edlib comes with a standalone aligner cli app, which can be found at apps/aligner/ . Aligner reads sequences from fasta files, and it can display alignment path in graphical manner or as a cigar. It also measures calculation time, so it can be useful for testing speed and comparing Edlib with other tools. Check Building to see how to build binaries (including edlib-aligner ). Run ./build/bin/edlib-aligner with no params for help and detailed instructions. Example of usage: ./build/bin/edlib-aligner -p apps/aligner/test_data/query.fasta apps/aligner/test_data/target.fasta NOTE : Aligner currently does not work on Windows, because it uses getopt to parse command line arguments, which is not supported on Windows. Running tests Check Building to see how to build binaries (including binary runTests ). To run tests, just run ./runTests . This will run random tests for each alignment method, and also some specific unit tests. Time and space complexity Edlib is based on Myers's bit-vector algorithm and extends from it. It calculates a dynamic programming matrix of dimensions Q x T , where Q is the length of the first sequence (query), and T is the length of the second sequence (target). It uses Ukkonen's banded algorithm to reduce the space of search, and there is also parallelization from Myers's algorithm, however time complexity is still quadratic. Edlib uses Hirschberg's algorithm to find alignment path, therefore space complexity is linear. Time complexity: O(T * Q) . Space complexity: O(T + Q) . It is worth noting that Edlib works best for large, similar sequences, since such sequences get the highest speedup from banded approach and bit-vector parallelization. Test data In [test_data/](test_data) directory there are different genome sequences, ranging from 10 kbp to 5 Mbp in length. They are ranging in length and similarity, so they can be useful for testing and measuring speed in different scenarios. Development and contributing Feel free to send pull requests and raise issues. When developing, you may want to use -D CMAKE_BUILD_TYPE=Debug flag when calling cmake in order to get debugging flags passed to compiler. This should also happen if you just run cmake .. with no flags, but I think I have noticed it does not always works as expected (probably has something to do with cmake cache). To check which flags is compiler using, run make with VERBOSE=1 : make VERBOSE=1 . Publication Martin Šošić, Mile Šikić; Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance. Bioinformatics 2017 btw753. doi: 10.1093/bioinformatics/btw753 Acknowledgements Mile Šikić () - Mentoring and guidance through whole project. Ivan Sović () - Help with testing and prioritizing features, valuable comments on the manuscript. Generated by   1.8.12 + +### https://github.com/Martinsos/edlib +GitHub - Martinsos/edlib: Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Martinsos / edlib Public Notifications You must be signed in to change notification settings Fork 172 Star 590 Code Issues 60 Pull requests 7 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights Martinsos/edlib master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 262 Commits 262 Commits .github .github apps apps bindings/ python bindings/ python build build edlib edlib images images test test test_data test_data .gitignore .gitignore CMakeLists.txt CMakeLists.txt Dockerfile Dockerfile Doxyfile Doxyfile LICENSE LICENSE Makefile Makefile README.md README.md edlib-config.cmake.in edlib-config.cmake.in edlib.pc.in edlib.pc.in meson.build meson.build View all files Repository files navigation README MIT license Edlib · A lightweight and super fast C/C++ library for sequence alignment using edit distance . Calculating edit distance of two strings is as simple as: edlibAlign ( "hello" , 5 , "world!" , 6 , edlibDefaultAlignConfig ()). editDistance ; Edlib is also available for Python (Click here for Python README) , with code residing at bindings/python . There are third-party bindings to edlib in other languages as well: Edlib.jl , a Julia package created and supported by Christopher Rowley ( @cjdoris ) edlibR , an R package created and supported by Evan Biederstedt ( @evanbiederstedt ) ruby-edlib , a Ruby package created and supported by @kojix2 Text::Levenshtein::Edlib , a Perl wrapper created and supported by Marius Gavrilescu Features Calculates edit distance (Levenshtein distance) . It can find optimal alignment path (instructions how to transform first sequence into the second sequence). It can find just the start and/or end locations of alignment path - can be useful when speed is more important than having exact alignment path. Supports multiple alignment methods : global( NW ), prefix( SHW ) and infix( HW ), each of them useful for different scenarios. You can extend character equality definition , enabling you to e.g. have wildcard characters, to have case insensitive alignment or to work with degenerate nucleotides. It can easily handle small or very large sequences , even when finding alignment path, while consuming very little memory. Super fast thanks to Myers's bit-vector algorithm. Contents Features Building Using Edlib in your project Usage and examples API documentation Alignment methods Aligner Running tests Time and space complexity Test data Development and contributing Publication Acknowledgements Using Edlib in your project You can use Edlib in you project by either directly copying header and source files from edlib/ , or by linking Edlib library (see Building for instructions how to build Edlib libraries). In any case, only thing that you have to do in your source files is to include edlib.h . To get you started quickly, let's take a look at a few ways to get simple Hello World project working. Our Hello World project has just one source file, helloWorld.cpp file, and it looks like this: # include < cstdio > # include " edlib.h " int main () { EdlibAlignResult result = edlibAlign ( " hello " , 5 , " world! " , 6 , edlibDefaultAlignConfig ()); if (result. status == EDLIB_STATUS_OK) { printf ( " edit_distance('hello', 'world!') = %d \n " , result. editDistance ); } edlibFreeAlignResult (result); } Running it should output edit_distance('hello', 'world!') = 5 . Approach #1: Directly copying edlib source and header files. Here we directly copied edlib/ directory to our project, to get following project structure: edlib/ -> copied from edlib/ include/ edlib.h src/ edlib.cpp helloWorld.cpp -> your program Since helloWorld is a c++ program, we can compile it with just one line: c++ helloWorld.cpp edlib/src/edlib.cpp -o helloWorld -I edlib/include . If hello world was a C program, we would compile it like this: c++ -c edlib/src/edlib.cpp -o edlib.o -I edlib/include cc -c helloWorld.c -o helloWorld.o -I edlib/include c++ helloWorld.o edlib.o -o helloWorld Approach #2: Copying edlib header file and static library. Instead of copying edlib source files, you could copy static library (check Building on how to create static library). We also need to copy edlib header files. We get following project structure: edlib/ -> copied from edlib include/ edlib.h edlib.a helloWorld.cpp -> your program Now you can compile it with c++ helloWorld.cpp -o helloWorld -I edlib/include -L edlib -ledlib . Approach #3: Install edlib library on machine. Alternatively, you could avoid copying any Edlib files and instead install libraries by running sudo make install (check Building for exact instructions depending on approach you used for building). Now, all you have to do to compile your project is c++ helloWorld.cpp -o helloWorld -ledlib . If you get error message like cannot open shared object file: No such file or directory , make sure that your linker includes path where edlib was installed. Approach #4: Use edlib in your project via CMake. Using git submodule If you are using CMake for compilation, we suggest adding edlib as a git submodule with the command git submodule add https://github.com/martinsos/edlib vendor/edlib . Afterwards, modify your top level CMakeLists.txt file accordingly: add_subdirectory(vendor/edlib EXCLUDE_FROM_ALL) target_link_libraries(your_exe edlib) # or target_link_libraries(your_exe edlib) The add_subdirectory command adds a folder to the build tree, meaning it will run CMakeLists.txt from the included folder as well. Flag EXCLUDE_FROM_ALL disables building (and instalment) of targets in the added folder which are not needed in your project. In the above example only the (static) library edlib will be build, while edlib-aligner , hello_world and the rest won't. In order to access the edlib API, add #include "edlib.h" in your source file (CMake will automatically update your include path). For more example projects take a look at applications in apps/ . Using VCPKG Edlib is available on VCPKG package manager. With VCPKG on your system, Edlib can be downloaded using the VCPKG install command vcpkg install edlib . Once the library has been downloaded, add the following instructions to your CMakeLists.txt file: find_package(edlib CONFIG REQUIRED) target_link_libraries(MyProject PRIVATE edlib::edlib) then you should be able to include the library header in your project ( #include "edlib.h ) Building Meson Primary way of building Edlib is via Meson build tool. Requirements: make sure that you have meson installed on your system. Execute make to build static library and binaries (apps and tests) and also run tests. To build shared library and binaries, do make LIBRARY_TYPE=shared . Library and binaries will be created in meson-build directory. You can choose alternate build directory like this: make BUILD_DIR=some-other-dir . Optionally, you can run sudo make install to install edlib library on your machine (on Linux, this will usually install it to usr/local/lib and usr/local/include ). Check Makefile if you want to run individual steps on your own (building, tests, ...). NOTE: If you need more control, use meson command directly, Makefile is here only to help with common commands. CMake Edlib can alternatively be built with CMake. Execute following command to build Edlib using CMAKE: cd build && cmake -D CMAKE_BUILD_TYPE=Release .. && make This will create binaries in bin/ directory and libraries (static and shared) in lib/ directory. ./bin/runTests to run tests. Optionally, you can run sudo make install to install edlib library on your machine. Conda Edlib can also be installed via Conda: : conda install edlib . Usage and examples Main function in edlib is edlibAlign . Given two sequences (and their lengths), it will find edit distance, alignment path or its end and start locations. char * query = "ACCTCTG" ; char * target = "ACTCTGAAA" EdlibAlignResult result = edlibAlign ( query , 7 , target , 9 , edlibDefaultAlignConfig ()); if ( result . status == EDLIB_STATUS_OK ) { printf ( "%d" , result . editDistance ); } edlibFreeAlignResult ( result ); NOTE: One character is expected to occupy one char/byte, meaning that characters spanning multiple chars/bytes are not supported. As long as your alphabet size is <= 256 you can manually map it to numbers/chars from 0 to 255 and solve this that way, but if its size is > 256 then you will not be able to use Edlib. Configuring edlibAlign() edlibAlign takes configuration object (it is a struct EdlibAlignConfig ), which allows you to further customize how alignment will be done. You can choose alignment method , tell edlib what to calculate (just edit distance or also path and locations) and set upper limit for edit distance. For example, if you want to use infix(HW) alignment method, want to find alignment path (and edit distance), are interested in result only if edit distance is not larger than 42 and do not want to extend character equality definition, you would call it like this: edlibAlign ( seq1 , seq1Length , seq2 , seq2Length , edlibNewAlignConfig ( 42 , EDLIB_MODE_HW , EDLIB_TASK_PATH , NULL , 0 )); Or, if you want to use suffix(SHW) alignment method, want to find only edit distance, do not have any limits on edit distance and want character '?' to match both itself and characters 'X' and 'Y', you would call it like this: EdlibEqualityPair additionalEqualities [ 2 ] = {{ '?' , 'X' }, { '?' , 'Y' }}; edlibAlign ( seq1 , seq1Length , seq2 , seq2Length , edlibNewAlignConfig ( -1 , EDLIB_MODE_SHW , EDLIB_TASK_DISTANCE , additionalEqualities , 2 )); We used edlibNewAlignConfig helper function to easily create config, however we could have also just created an instance of it and set its members accordingly. Handling result of edlibAlign() edlibAlign function returns a result object ( EdlibAlignResult ), which will contain results of alignment (corresponding to the task that you passed in config). EdlibAlignResult result = edlibAlign ( seq1 , seq1Length , seq2 , seq2Length , edlibNewAlignConfig ( -1 , EDLIB_MODE_HW , EDLIB_TASK_PATH , NULL , 0 )); if ( result . status == EDLIB_STATUS_OK ) { printf ( "%d\n" , result . editDistance ); printf ( "%d\n" , result . alignmentLength ); printf ( "%d\n" , result . endLocations [ 0 ]); } edlibFreeAlignResult ( result ); It is important to remember to free the result object using edlibFreeAlignResult function, since Edlib allocates memory on heap for certain members. If you decide to do the cleaning manually and not use edlibFreeAlignResult , do not forget to manually free() required members. Turning alignment to cigar Cigar is a standard way to represent alignment path. Edlib has helper function that transforms alignment path into cigar. char * cigar = edlibAlignmentToCigar ( result . alignment , result . alignmentLength , EDLIB_CIGAR_STANDARD ); printf ( "%s" , cigar ); free ( cigar ); API documentation For complete documentation of Edlib library API, visit http://martinsos.github.io/edlib (should be updated to the latest release). To generate the latest API documentation yourself from the source, you need to have doxygen installed. Position yourself in the root directory and run doxygen , this will generate docs/ directory. Then open docs/html/index.html file with you favorite browser. Alternatively, you can directly check edlib.h . Alignment methods Edlib supports 3 alignment methods: global (NW) - This is the standard method, when we say "edit distance" this is the method that is assumed. It tells us the smallest number of operations needed to transform first sequence into second sequence. This method is appropriate when you want to find out how similar is first sequence to second sequence. prefix (SHW) - Similar to global method, but with a small twist - gap at query end is not penalized. What that means is that deleting elements from the end of second sequence is "free"! For example, if we had AACT and AACTGGC , edit distance would be 0, because removing GGC from the end of second sequence is "free" and does not count into total edit distance. This method is appropriate when you want to find out how well first sequence fits at the beginning of second sequence. infix (HW) : Similar as prefix method, but with one more twist - gaps at query end and start are not penalized. What that means is that deleting elements from the start and end of second sequence is "free"! For example, if we had ACT and CGACTGAC , edit distance would be 0, because removing CG from the start and GAC from the end of second sequence is "free" and does not count into total edit distance. This method is appropriate when you want to find out how well first sequence fits at any part of second sequence. For example, if your second sequence was a long text and your first sequence was a sentence from that text, but slightly scrambled, you could use this method to discover how scrambled it is and where it fits in that text. In bioinformatics, this method is appropriate for aligning read to a sequence. Aligner Edlib comes with a standalone aligner cli app, which can be found at apps/aligner/ . Aligner reads sequences from fasta files, and it can display alignment path in graphical manner or as a cigar. It also measures calculation time, so it can be useful for testing speed and comparing Edlib with other tools. Check Building to see how to build binaries (including edlib-aligner ). Run ./build/bin/edlib-aligner with no params for help and detailed instructions. Example of usage: ./build/bin/edlib-aligner -p apps/aligner/test_data/query.fasta apps/aligner/test_data/target.fasta NOTE : Aligner currently does not work on Windows, because it uses getopt to parse command line arguments, which is not supported on Windows. Running tests Check Building to see how to build binaries (including binary runTests ). To run tests, just run ./runTests . This will run random tests for each alignment method, and also some specific unit tests. Time and space complexity Edlib is based on Myers's bit-vector algorithm and extends from it. It calculates a dynamic programming matrix of dimensions Q x T , where Q is the length of the first sequence (query), and T is the length of the second sequence (target). It uses Ukkonen's banded algorithm to reduce the space of search, and there is also parallelization from Myers's algorithm, however time complexity is still quadratic. Edlib uses Hirschberg's algorithm to find alignment path, therefore space complexity is linear. Time complexity: O(T * Q) . Space complexity: O(T + Q) . It is worth noting that Edlib works best for large, similar sequences, since such sequences get the highest speedup from banded approach and bit-vector parallelization. Test data In test_data/ directory there are different genome sequences, ranging from 10 kbp to 5 Mbp in length. They are ranging in length and similarity, so they can be useful for testing and measuring speed in different scenarios. Development and contributing Feel free to send pull requests and raise issues. When developing, you may want to use -D CMAKE_BUILD_TYPE=Debug flag when calling cmake in order to get debugging flags passed to compiler. This should also happen if you just run cmake .. with no flags, but I think I have noticed it does not always works as expected (probably has something to do with cmake cache). To check which flags is compiler using, run make with VERBOSE=1 : make VERBOSE=1 . Publication Martin Šošić, Mile Šikić; Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance. Bioinformatics 2017 btw753. doi: 10.1093/bioinformatics/btw753 Acknowledgements Mile Šikić (@msikic) - Mentoring and guidance through whole project. Ivan Sović (@isovic) - Help with testing and prioritizing features, valuable comments on the manuscript. FAQ What do terms NW, HW and SHW stand for? NW stands for Needleman-Wunsch, HW for Hybrid Wunsch, and SHW for Semi Hybrid Wunsch. While NW is a common abbreviation, HW and SHW abbreviations were made up at the very start of this project to describe additional modes of alignment. Later we started using terms "global", "infix" and "prefix" more, as they describe the modes better, but terms NW, HW and SHW are still very present in the project. About Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance. martinsos.github.io/edlib Topics python c-plus-plus library bioinformatics edit-distance sequence-alignment levehnstein-distance alignment-path Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 590 stars Watchers 21 watching Forks 172 forks Report repository Releases 11 v1.2.7 Latest Aug 20, 2021 + 10 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 66.8% Cython 7.6% Shell 6.7% C 6.7% Python 4.2% CMake 3.0% Other 5.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/Martinsos/edlib +GitHub - Martinsos/edlib: Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Martinsos / edlib Public Notifications You must be signed in to change notification settings Fork 172 Star 590 Code Issues 60 Pull requests 7 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights Martinsos/edlib master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 262 Commits 262 Commits .github .github apps apps bindings/ python bindings/ python build build edlib edlib images images test test test_data test_data .gitignore .gitignore CMakeLists.txt CMakeLists.txt Dockerfile Dockerfile Doxyfile Doxyfile LICENSE LICENSE Makefile Makefile README.md README.md edlib-config.cmake.in edlib-config.cmake.in edlib.pc.in edlib.pc.in meson.build meson.build View all files Repository files navigation README MIT license Edlib · A lightweight and super fast C/C++ library for sequence alignment using edit distance . Calculating edit distance of two strings is as simple as: edlibAlign ( "hello" , 5 , "world!" , 6 , edlibDefaultAlignConfig ()). editDistance ; Edlib is also available for Python (Click here for Python README) , with code residing at bindings/python . There are third-party bindings to edlib in other languages as well: Edlib.jl , a Julia package created and supported by Christopher Rowley ( @cjdoris ) edlibR , an R package created and supported by Evan Biederstedt ( @evanbiederstedt ) ruby-edlib , a Ruby package created and supported by @kojix2 Text::Levenshtein::Edlib , a Perl wrapper created and supported by Marius Gavrilescu Features Calculates edit distance (Levenshtein distance) . It can find optimal alignment path (instructions how to transform first sequence into the second sequence). It can find just the start and/or end locations of alignment path - can be useful when speed is more important than having exact alignment path. Supports multiple alignment methods : global( NW ), prefix( SHW ) and infix( HW ), each of them useful for different scenarios. You can extend character equality definition , enabling you to e.g. have wildcard characters, to have case insensitive alignment or to work with degenerate nucleotides. It can easily handle small or very large sequences , even when finding alignment path, while consuming very little memory. Super fast thanks to Myers's bit-vector algorithm. Contents Features Building Using Edlib in your project Usage and examples API documentation Alignment methods Aligner Running tests Time and space complexity Test data Development and contributing Publication Acknowledgements Using Edlib in your project You can use Edlib in you project by either directly copying header and source files from edlib/ , or by linking Edlib library (see Building for instructions how to build Edlib libraries). In any case, only thing that you have to do in your source files is to include edlib.h . To get you started quickly, let's take a look at a few ways to get simple Hello World project working. Our Hello World project has just one source file, helloWorld.cpp file, and it looks like this: # include < cstdio > # include " edlib.h " int main () { EdlibAlignResult result = edlibAlign ( " hello " , 5 , " world! " , 6 , edlibDefaultAlignConfig ()); if (result. status == EDLIB_STATUS_OK) { printf ( " edit_distance('hello', 'world!') = %d \n " , result. editDistance ); } edlibFreeAlignResult (result); } Running it should output edit_distance('hello', 'world!') = 5 . Approach #1: Directly copying edlib source and header files. Here we directly copied edlib/ directory to our project, to get following project structure: edlib/ -> copied from edlib/ include/ edlib.h src/ edlib.cpp helloWorld.cpp -> your program Since helloWorld is a c++ program, we can compile it with just one line: c++ helloWorld.cpp edlib/src/edlib.cpp -o helloWorld -I edlib/include . If hello world was a C program, we would compile it like this: c++ -c edlib/src/edlib.cpp -o edlib.o -I edlib/include cc -c helloWorld.c -o helloWorld.o -I edlib/include c++ helloWorld.o edlib.o -o helloWorld Approach #2: Copying edlib header file and static library. Instead of copying edlib source files, you could copy static library (check Building on how to create static library). We also need to copy edlib header files. We get following project structure: edlib/ -> copied from edlib include/ edlib.h edlib.a helloWorld.cpp -> your program Now you can compile it with c++ helloWorld.cpp -o helloWorld -I edlib/include -L edlib -ledlib . Approach #3: Install edlib library on machine. Alternatively, you could avoid copying any Edlib files and instead install libraries by running sudo make install (check Building for exact instructions depending on approach you used for building). Now, all you have to do to compile your project is c++ helloWorld.cpp -o helloWorld -ledlib . If you get error message like cannot open shared object file: No such file or directory , make sure that your linker includes path where edlib was installed. Approach #4: Use edlib in your project via CMake. Using git submodule If you are using CMake for compilation, we suggest adding edlib as a git submodule with the command git submodule add https://github.com/martinsos/edlib vendor/edlib . Afterwards, modify your top level CMakeLists.txt file accordingly: add_subdirectory(vendor/edlib EXCLUDE_FROM_ALL) target_link_libraries(your_exe edlib) # or target_link_libraries(your_exe edlib) The add_subdirectory command adds a folder to the build tree, meaning it will run CMakeLists.txt from the included folder as well. Flag EXCLUDE_FROM_ALL disables building (and instalment) of targets in the added folder which are not needed in your project. In the above example only the (static) library edlib will be build, while edlib-aligner , hello_world and the rest won't. In order to access the edlib API, add #include "edlib.h" in your source file (CMake will automatically update your include path). For more example projects take a look at applications in apps/ . Using VCPKG Edlib is available on VCPKG package manager. With VCPKG on your system, Edlib can be downloaded using the VCPKG install command vcpkg install edlib . Once the library has been downloaded, add the following instructions to your CMakeLists.txt file: find_package(edlib CONFIG REQUIRED) target_link_libraries(MyProject PRIVATE edlib::edlib) then you should be able to include the library header in your project ( #include "edlib.h ) Building Meson Primary way of building Edlib is via Meson build tool. Requirements: make sure that you have meson installed on your system. Execute make to build static library and binaries (apps and tests) and also run tests. To build shared library and binaries, do make LIBRARY_TYPE=shared . Library and binaries will be created in meson-build directory. You can choose alternate build directory like this: make BUILD_DIR=some-other-dir . Optionally, you can run sudo make install to install edlib library on your machine (on Linux, this will usually install it to usr/local/lib and usr/local/include ). Check Makefile if you want to run individual steps on your own (building, tests, ...). NOTE: If you need more control, use meson command directly, Makefile is here only to help with common commands. CMake Edlib can alternatively be built with CMake. Execute following command to build Edlib using CMAKE: cd build && cmake -D CMAKE_BUILD_TYPE=Release .. && make This will create binaries in bin/ directory and libraries (static and shared) in lib/ directory. ./bin/runTests to run tests. Optionally, you can run sudo make install to install edlib library on your machine. Conda Edlib can also be installed via Conda: : conda install edlib . Usage and examples Main function in edlib is edlibAlign . Given two sequences (and their lengths), it will find edit distance, alignment path or its end and start locations. char * query = "ACCTCTG" ; char * target = "ACTCTGAAA" EdlibAlignResult result = edlibAlign ( query , 7 , target , 9 , edlibDefaultAlignConfig ()); if ( result . status == EDLIB_STATUS_OK ) { printf ( "%d" , result . editDistance ); } edlibFreeAlignResult ( result ); NOTE: One character is expected to occupy one char/byte, meaning that characters spanning multiple chars/bytes are not supported. As long as your alphabet size is <= 256 you can manually map it to numbers/chars from 0 to 255 and solve this that way, but if its size is > 256 then you will not be able to use Edlib. Configuring edlibAlign() edlibAlign takes configuration object (it is a struct EdlibAlignConfig ), which allows you to further customize how alignment will be done. You can choose alignment method , tell edlib what to calculate (just edit distance or also path and locations) and set upper limit for edit distance. For example, if you want to use infix(HW) alignment method, want to find alignment path (and edit distance), are interested in result only if edit distance is not larger than 42 and do not want to extend character equality definition, you would call it like this: edlibAlign ( seq1 , seq1Length , seq2 , seq2Length , edlibNewAlignConfig ( 42 , EDLIB_MODE_HW , EDLIB_TASK_PATH , NULL , 0 )); Or, if you want to use suffix(SHW) alignment method, want to find only edit distance, do not have any limits on edit distance and want character '?' to match both itself and characters 'X' and 'Y', you would call it like this: EdlibEqualityPair additionalEqualities [ 2 ] = {{ '?' , 'X' }, { '?' , 'Y' }}; edlibAlign ( seq1 , seq1Length , seq2 , seq2Length , edlibNewAlignConfig ( -1 , EDLIB_MODE_SHW , EDLIB_TASK_DISTANCE , additionalEqualities , 2 )); We used edlibNewAlignConfig helper function to easily create config, however we could have also just created an instance of it and set its members accordingly. Handling result of edlibAlign() edlibAlign function returns a result object ( EdlibAlignResult ), which will contain results of alignment (corresponding to the task that you passed in config). EdlibAlignResult result = edlibAlign ( seq1 , seq1Length , seq2 , seq2Length , edlibNewAlignConfig ( -1 , EDLIB_MODE_HW , EDLIB_TASK_PATH , NULL , 0 )); if ( result . status == EDLIB_STATUS_OK ) { printf ( "%d\n" , result . editDistance ); printf ( "%d\n" , result . alignmentLength ); printf ( "%d\n" , result . endLocations [ 0 ]); } edlibFreeAlignResult ( result ); It is important to remember to free the result object using edlibFreeAlignResult function, since Edlib allocates memory on heap for certain members. If you decide to do the cleaning manually and not use edlibFreeAlignResult , do not forget to manually free() required members. Turning alignment to cigar Cigar is a standard way to represent alignment path. Edlib has helper function that transforms alignment path into cigar. char * cigar = edlibAlignmentToCigar ( result . alignment , result . alignmentLength , EDLIB_CIGAR_STANDARD ); printf ( "%s" , cigar ); free ( cigar ); API documentation For complete documentation of Edlib library API, visit http://martinsos.github.io/edlib (should be updated to the latest release). To generate the latest API documentation yourself from the source, you need to have doxygen installed. Position yourself in the root directory and run doxygen , this will generate docs/ directory. Then open docs/html/index.html file with you favorite browser. Alternatively, you can directly check edlib.h . Alignment methods Edlib supports 3 alignment methods: global (NW) - This is the standard method, when we say "edit distance" this is the method that is assumed. It tells us the smallest number of operations needed to transform first sequence into second sequence. This method is appropriate when you want to find out how similar is first sequence to second sequence. prefix (SHW) - Similar to global method, but with a small twist - gap at query end is not penalized. What that means is that deleting elements from the end of second sequence is "free"! For example, if we had AACT and AACTGGC , edit distance would be 0, because removing GGC from the end of second sequence is "free" and does not count into total edit distance. This method is appropriate when you want to find out how well first sequence fits at the beginning of second sequence. infix (HW) : Similar as prefix method, but with one more twist - gaps at query end and start are not penalized. What that means is that deleting elements from the start and end of second sequence is "free"! For example, if we had ACT and CGACTGAC , edit distance would be 0, because removing CG from the start and GAC from the end of second sequence is "free" and does not count into total edit distance. This method is appropriate when you want to find out how well first sequence fits at any part of second sequence. For example, if your second sequence was a long text and your first sequence was a sentence from that text, but slightly scrambled, you could use this method to discover how scrambled it is and where it fits in that text. In bioinformatics, this method is appropriate for aligning read to a sequence. Aligner Edlib comes with a standalone aligner cli app, which can be found at apps/aligner/ . Aligner reads sequences from fasta files, and it can display alignment path in graphical manner or as a cigar. It also measures calculation time, so it can be useful for testing speed and comparing Edlib with other tools. Check Building to see how to build binaries (including edlib-aligner ). Run ./build/bin/edlib-aligner with no params for help and detailed instructions. Example of usage: ./build/bin/edlib-aligner -p apps/aligner/test_data/query.fasta apps/aligner/test_data/target.fasta NOTE : Aligner currently does not work on Windows, because it uses getopt to parse command line arguments, which is not supported on Windows. Running tests Check Building to see how to build binaries (including binary runTests ). To run tests, just run ./runTests . This will run random tests for each alignment method, and also some specific unit tests. Time and space complexity Edlib is based on Myers's bit-vector algorithm and extends from it. It calculates a dynamic programming matrix of dimensions Q x T , where Q is the length of the first sequence (query), and T is the length of the second sequence (target). It uses Ukkonen's banded algorithm to reduce the space of search, and there is also parallelization from Myers's algorithm, however time complexity is still quadratic. Edlib uses Hirschberg's algorithm to find alignment path, therefore space complexity is linear. Time complexity: O(T * Q) . Space complexity: O(T + Q) . It is worth noting that Edlib works best for large, similar sequences, since such sequences get the highest speedup from banded approach and bit-vector parallelization. Test data In test_data/ directory there are different genome sequences, ranging from 10 kbp to 5 Mbp in length. They are ranging in length and similarity, so they can be useful for testing and measuring speed in different scenarios. Development and contributing Feel free to send pull requests and raise issues. When developing, you may want to use -D CMAKE_BUILD_TYPE=Debug flag when calling cmake in order to get debugging flags passed to compiler. This should also happen if you just run cmake .. with no flags, but I think I have noticed it does not always works as expected (probably has something to do with cmake cache). To check which flags is compiler using, run make with VERBOSE=1 : make VERBOSE=1 . Publication Martin Šošić, Mile Šikić; Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance. Bioinformatics 2017 btw753. doi: 10.1093/bioinformatics/btw753 Acknowledgements Mile Šikić (@msikic) - Mentoring and guidance through whole project. Ivan Sović (@isovic) - Help with testing and prioritizing features, valuable comments on the manuscript. FAQ What do terms NW, HW and SHW stand for? NW stands for Needleman-Wunsch, HW for Hybrid Wunsch, and SHW for Semi Hybrid Wunsch. While NW is a common abbreviation, HW and SHW abbreviations were made up at the very start of this project to describe additional modes of alignment. Later we started using terms "global", "infix" and "prefix" more, as they describe the modes better, but terms NW, HW and SHW are still very present in the project. About Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance. martinsos.github.io/edlib Topics python c-plus-plus library bioinformatics edit-distance sequence-alignment levehnstein-distance alignment-path Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 590 stars Watchers 21 watching Forks 172 forks Report repository Releases 11 v1.2.7 Latest Aug 20, 2021 + 10 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 66.8% Cython 7.6% Shell 6.7% C 6.7% Python 4.2% CMake 3.0% Other 5.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge python-edlib --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +python-edlib 1.2.3 py27_0 +------------------------- +file name : python-edlib-1.2.3-py27_0.tar.bz2 +name : python-edlib +version : 1.2.3 +build : py27_0 +build number: 0 +size : 139 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.3-py27_0.tar.bz2 +md5 : 355c8f6860b49284740b1c6f098a9220 +dependencies: + - libgcc + - python 2.7* + + +python-edlib 1.2.3 py27h470a237_1 +--------------------------------- +file name : python-edlib-1.2.3-py27h470a237_1.tar.bz2 +name : python-edlib +version : 1.2.3 +build : py27h470a237_1 +build number: 1 +size : 139 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.3-py27h470a237_1.tar.bz2 +md5 : b5f2079623f1fb9de9ed8eb0cb6e8fdd +timestamp : 2018-07-15 20:15:53 UTC +dependencies: + - libgcc-ng >=4.9 + - python >=2.7,<2.8.0a0 + + +python-edlib 1.2.3 py35_0 +------------------------- +file name : python-edlib-1.2.3-py35_0.tar.bz2 +name : python-edlib +version : 1.2.3 +build : py35_0 +build number: 0 +size : 144 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.3-py35_0.tar.bz2 +md5 : 17f9a919bea9733abb78f0845164ad1f +dependencies: + - libgcc + - python 3.5* + + +python-edlib 1.2.3 py35h470a237_1 +--------------------------------- +file name : python-edlib-1.2.3-py35h470a237_1.tar.bz2 +name : python-edlib +version : 1.2.3 +build : py35h470a237_1 +build number: 1 +size : 143 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.3-py35h470a237_1.tar.bz2 +md5 : 25be06d9033d3930866e8255f845fb40 +timestamp : 2018-07-15 20:15:23 UTC +dependencies: + - libgcc-ng >=4.9 + - python >=3.5,<3.6.0a0 + + +python-edlib 1.2.3 py36_0 +------------------------- +file name : python-edlib-1.2.3-py36_0.tar.bz2 +name : python-edlib +version : 1.2.3 +build : py36_0 +build number: 0 +size : 144 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.3-py36_0.tar.bz2 +md5 : e4b1055c1735946165f941abacf2f44a +dependencies: + - libgcc + - python 3.6* + + +python-edlib 1.2.3 py36h470a237_1 +--------------------------------- +file name : python-edlib-1.2.3-py36h470a237_1.tar.bz2 +name : python-edlib +version : 1.2.3 +build : py36h470a237_1 +build number: 1 +size : 143 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.3-py36h470a237_1.tar.bz2 +md5 : d9dc83dc679716d81b5a9ed3b47f5713 +timestamp : 2018-07-15 20:14:51 UTC +dependencies: + - libgcc-ng >=4.9 + - python >=3.6,<3.7.0a0 + + +python-edlib 1.2.3.post1 py27h470a237_0 +--------------------------------------- +file name : python-edlib-1.2.3.post1-py27h470a237_0.tar.bz2 +name : python-edlib +version : 1.2.3.post1 +build : py27h470a237_0 +build number: 0 +size : 135 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.3.post1-py27h470a237_0.tar.bz2 +md5 : 9987eadbf1dbdff1e768903826595b3d +timestamp : 2018-10-29 01:42:04 UTC +dependencies: + - libgcc-ng >=4.9 + - python >=2.7,<2.8.0a0 + + +python-edlib 1.2.3.post1 py35h470a237_0 +--------------------------------------- +file name : python-edlib-1.2.3.post1-py35h470a237_0.tar.bz2 +name : python-edlib +version : 1.2.3.post1 +build : py35h470a237_0 +build number: 0 +size : 140 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.3.post1-py35h470a237_0.tar.bz2 +md5 : eadc0084a6d4d0fc8e803004e56a4b2b +timestamp : 2018-10-29 01:41:26 UTC +dependencies: + - libgcc-ng >=4.9 + - python >=3.5,<3.6.0a0 + + +python-edlib 1.2.3.post1 py36h470a237_0 +--------------------------------------- +file name : python-edlib-1.2.3.post1-py36h470a237_0.tar.bz2 +name : python-edlib +version : 1.2.3.post1 +build : py36h470a237_0 +build number: 0 +size : 140 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.3.post1-py36h470a237_0.tar.bz2 +md5 : ecd2b97eacbe4cc55c34b2a6e0308a2c +timestamp : 2018-10-29 01:42:46 UTC +dependencies: + - libgcc-ng >=4.9 + - python >=3.6,<3.7.0a0 + + +python-edlib 1.2.4 py27h6bb024c_0 +--------------------------------- +file name : python-edlib-1.2.4-py27h6bb024c_0.tar.bz2 +name : python-edlib +version : 1.2.4 +build : py27h6bb024c_0 +build number: 0 +size : 39 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.4-py27h6bb024c_0.tar.bz2 +md5 : 5babcb8d2e08d4d6ea75640555da6cba +timestamp : 2019-05-03 19:52:21 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=2.7,<2.8.0a0 + + +python-edlib 1.2.4 py36h6bb024c_0 +--------------------------------- +file name : python-edlib-1.2.4-py36h6bb024c_0.tar.bz2 +name : python-edlib +version : 1.2.4 +build : py36h6bb024c_0 +build number: 0 +size : 40 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.4-py36h6bb024c_0.tar.bz2 +md5 : 8874e9d48715519565598f03217ebe3c +timestamp : 2019-05-03 19:51:10 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + + +python-edlib 1.2.4 py37h6bb024c_0 +--------------------------------- +file name : python-edlib-1.2.4-py37h6bb024c_0.tar.bz2 +name : python-edlib +version : 1.2.4 +build : py37h6bb024c_0 +build number: 0 +size : 40 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.4-py37h6bb024c_0.tar.bz2 +md5 : 6d1d86f14d24a5f860c6a130cb9cb608 +timestamp : 2019-05-03 19:53:28 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + + +python-edlib 1.2.4.post1 py27h6bb024c_0 +--------------------------------------- +file name : python-edlib-1.2.4.post1-py27h6bb024c_0.tar.bz2 +name : python-edlib +version : 1.2.4.post1 +build : py27h6bb024c_0 +build number: 0 +size : 61 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.4.post1-py27h6bb024c_0.tar.bz2 +md5 : ce9fe85e1f83a9dc4b7f0a5a2920131e +timestamp : 2019-05-26 17:51:31 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=2.7,<2.8.0a0 + + +python-edlib 1.2.4.post1 py36h6bb024c_0 +--------------------------------------- +file name : python-edlib-1.2.4.post1-py36h6bb024c_0.tar.bz2 +name : python-edlib +version : 1.2.4.post1 +build : py36h6bb024c_0 +build number: 0 +size : 63 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.4.post1-py36h6bb024c_0.tar.bz2 +md5 : ada7f0b8e1120d09542de1e6d3c455fa +timestamp : 2019-05-26 17:50:32 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + + +python-edlib 1.2.4.post1 py37h6bb024c_0 +--------------------------------------- +file name : python-edlib-1.2.4.post1-py37h6bb024c_0.tar.bz2 +name : python-edlib +version : 1.2.4.post1 +build : py37h6bb024c_0 +build number: 0 +size : 63 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.2.4.post1-py37h6bb024c_0.tar.bz2 +md5 : c6977bbe1b51733dffc7a875fa9d42f5 +timestamp : 2019-05-26 17:49:19 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + + +python-edlib 1.3.4 py27hc9558a2_0 +--------------------------------- +file name : python-edlib-1.3.4-py27hc9558a2_0.tar.bz2 +name : python-edlib +version : 1.3.4 +build : py27hc9558a2_0 +build number: 0 +size : 69 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.3.4-py27hc9558a2_0.tar.bz2 +md5 : af39a198d986a8995e338916c2a9548b +timestamp : 2019-08-21 21:21:28 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=2.7,<2.8.0a0 + + +python-edlib 1.3.4 py36hc9558a2_0 +--------------------------------- +file name : python-edlib-1.3.4-py36hc9558a2_0.tar.bz2 +name : python-edlib +version : 1.3.4 +build : py36hc9558a2_0 +build number: 0 +size : 72 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.3.4-py36hc9558a2_0.tar.bz2 +md5 : 0c9dc34034b2547855c8364a115eabce +timestamp : 2019-08-21 21:20:25 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + + +python-edlib 1.3.4 py37hc9558a2_0 +--------------------------------- +file name : python-edlib-1.3.4-py37hc9558a2_0.tar.bz2 +name : python-edlib +version : 1.3.4 +build : py37hc9558a2_0 +build number: 0 +size : 72 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.3.4-py37hc9558a2_0.tar.bz2 +md5 : 10388181d06d13227fff79f08ec527a1 +timestamp : 2019-08-21 21:22:22 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + + +python-edlib 1.3.5 py27hc9558a2_0 +--------------------------------- +file name : python-edlib-1.3.5-py27hc9558a2_0.tar.bz2 +name : python-edlib +version : 1.3.5 +build : py27hc9558a2_0 +build number: 0 +size : 68 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.3.5-py27hc9558a2_0.tar.bz2 +md5 : 4c0fa3fb83f0122f9f9cc8a30095556c +timestamp : 2019-11-07 02:43:58 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=2.7,<2.8.0a0 + + +python-edlib 1.3.5 py36hc9558a2_0 +--------------------------------- +file name : python-edlib-1.3.5-py36hc9558a2_0.tar.bz2 +name : python-edlib +version : 1.3.5 +build : py36hc9558a2_0 +build number: 0 +size : 71 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.3.5-py36hc9558a2_0.tar.bz2 +md5 : 06c2bac1a2aec2a7414ea40f715b8852 +timestamp : 2019-11-07 02:42:55 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=3.6,<3.7.0a0 + + +python-edlib 1.3.5 py37hc9558a2_0 +--------------------------------- +file name : python-edlib-1.3.5-py37hc9558a2_0.tar.bz2 +name : python-edlib +version : 1.3.5 +build : py37hc9558a2_0 +build number: 0 +size : 71 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.3.5-py37hc9558a2_0.tar.bz2 +md5 : 4b6e41052080f889114e4fbbf950de11 +timestamp : 2019-11-07 02:44:55 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - python >=3.7,<3.8.0a0 + + +python-edlib 1.3.6 py27hc9558a2_0 +--------------------------------- +file name : python-edlib-1.3.6-py27hc9558a2_0.tar.bz2 +name : python-edlib +version : 1.3.6 +build : py27hc9558a2_0 +build number: 0 +size : 68 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioc diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-basejump.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-basejump.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b4ffe7ce1d31e73a3ae20b5dfcf0ce2be190bc9 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-basejump.manual_bundle.txt @@ -0,0 +1,536 @@ +# Tool: r-basejump +software_name: r-basejump +tier: T1 +domain: t1_backfill_overall +downloads: 180214 +summary: Base functions for bioinformatics and R package development. +description: Base functions for bioinformatics and R package development. +dependencies: bioconductor-singlecellexperiment >=1.22.0, bioconductor-summarizedexperiment >=1.30.0, r-acidbase >=0.7.0, r-acidexperiment >=0.5.0, r-acidgenomes >=0.6.0, r-acidmarkdown >=0.3.0, r-acidplots >=0.7.0, r-acidplyr >=0.5.0, r-acidsinglecell >=0.4.0, r-base >=4.4,<4.5.0a0, r-pipette >=0.14.0, r-syntactic >=0.7.0 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://github.com/steinbaugh/basejump +doc_url: +dev_url: https://github.com/acidgenomics/r-basejump + +## URL Docs Extract +### https://github.com/steinbaugh/basejump +GitHub - acidgenomics/r-basejump: Base functions for bioinformatics and R package development. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} acidgenomics / r-basejump Public Notifications You must be signed in to change notification settings Fork 3 Star 5 Code Issues 0 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights acidgenomics/r-basejump main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 8,093 Commits 8,093 Commits R R man man pkgdown pkgdown .Rbuildignore .Rbuildignore .gitignore .gitignore .lintr .lintr DESCRIPTION DESCRIPTION LICENSE LICENSE NAMESPACE NAMESPACE NEWS.md NEWS.md README.md README.md _pkgdown.yml _pkgdown.yml package.Rproj package.Rproj todo.org todo.org View all files Repository files navigation README AGPL-3.0 license basejump Base functions for bioinformatics and R package development. Installation This is an R package. if ( ! requireNamespace( " BiocManager " , quietly = TRUE )) { install.packages( " BiocManager " ) } install.packages( pkgs = " basejump " , repos = c( " https://r.acidgenomics.com " , BiocManager :: repositories() ), dependencies = TRUE ) Conda method Configure Conda to use the Bioconda channels. # Don't install recipe into base environment. name= ' r-basejump ' conda create --name= " $name " " $name " conda activate " $name " R About Base functions for bioinformatics and R package development. r.acidgenomics.com/packages/basejump/ Resources Readme License AGPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 5 stars Watchers 2 watching Forks 3 forks Report repository Releases 177 tags Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 95.6% CSS 4.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/acidgenomics/r-basejump +GitHub - acidgenomics/r-basejump: Base functions for bioinformatics and R package development. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} acidgenomics / r-basejump Public Notifications You must be signed in to change notification settings Fork 3 Star 5 Code Issues 0 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights acidgenomics/r-basejump main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 8,093 Commits 8,093 Commits R R man man pkgdown pkgdown .Rbuildignore .Rbuildignore .gitignore .gitignore .lintr .lintr DESCRIPTION DESCRIPTION LICENSE LICENSE NAMESPACE NAMESPACE NEWS.md NEWS.md README.md README.md _pkgdown.yml _pkgdown.yml package.Rproj package.Rproj todo.org todo.org View all files Repository files navigation README AGPL-3.0 license basejump Base functions for bioinformatics and R package development. Installation This is an R package. if ( ! requireNamespace( " BiocManager " , quietly = TRUE )) { install.packages( " BiocManager " ) } install.packages( pkgs = " basejump " , repos = c( " https://r.acidgenomics.com " , BiocManager :: repositories() ), dependencies = TRUE ) Conda method Configure Conda to use the Bioconda channels. # Don't install recipe into base environment. name= ' r-basejump ' conda create --name= " $name " " $name " conda activate " $name " R About Base functions for bioinformatics and R package development. r.acidgenomics.com/packages/basejump/ Resources Readme License AGPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 5 stars Watchers 2 watching Forks 3 forks Report repository Releases 177 tags Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 95.6% CSS 4.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge r-basejump --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +r-basejump 0.1.1 0 +------------------ +file name : r-basejump-0.1.1-0.tar.bz2 +name : r-basejump +version : 0.1.1 +build : 0 +build number: 0 +size : 3.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-basejump-0.1.1-0.tar.bz2 +md5 : 67f51797fa3e393bddef666f090eb093 +dependencies: + - bioconductor-annotationhub + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-ensembldb + - bioconductor-s4vectors + - r-base >=3.4,<3.5 + - r-cowplot + - r-dendsort + - r-devtools + - r-dplyr + - r-ggplot2 + - r-knitr + - r-magrittr + - r-matrix + - r-matrix.utils + - r-pheatmap + - r-r.utils + - r-rcolorbrewer + - r-rcurl + - r-readr + - r-readxl + - r-rlang + - r-scales + - r-stringr + - r-tibble + - r-tidyr + - r-viridis + - r-yaml + + +r-basejump 0.5.3 0 +------------------ +file name : r-basejump-0.5.3-0.tar.bz2 +name : r-basejump +version : 0.5.3 +build : 0 +build number: 0 +size : 1.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-basejump-0.5.3-0.tar.bz2 +md5 : 4c842f575807bf4926b20dd4e0b25a87 +dependencies: + - bioconductor-annotationhub + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-ensembldb + - bioconductor-s4vectors + - r-assertive + - r-base >=3.4,<3.5 + - r-cowplot + - r-dendsort + - r-devtools + - r-dplyr + - r-ggplot2 + - r-knitr + - r-magrittr + - r-matrix + - r-matrix.utils + - r-pbapply + - r-pheatmap + - r-r.utils + - r-rcolorbrewer + - r-rcurl + - r-readr + - r-readxl + - r-rlang + - r-scales + - r-stringr + - r-tibble + - r-tidyr + - r-viridis + - r-yaml + + +r-basejump 0.5.9 0 +------------------ +file name : r-basejump-0.5.9-0.tar.bz2 +name : r-basejump +version : 0.5.9 +build : 0 +build number: 0 +size : 1.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-basejump-0.5.9-0.tar.bz2 +md5 : 8a10175ed52f1eab4b694b0b9b55c36a +dependencies: + - bioconductor-annotationhub + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-ensembldb + - bioconductor-genomeinfodb + - bioconductor-s4vectors + - r-assertive + - r-base >=3.4,<3.5 + - r-cowplot >=0.9 + - r-dendsort + - r-devtools + - r-dplyr >=0.7 + - r-ggplot2 >=2.2.1 + - r-knitr >=1.2.0 + - r-magrittr >=1.5 + - r-matrix >=1.2 + - r-matrix.utils >=0.9 + - r-pbapply + - r-pheatmap + - r-r.utils + - r-rcolorbrewer + - r-rcurl >=1.95 + - r-readr >=1.1 + - r-readxl >=1.0 + - r-rlang >=0.2 + - r-scales + - r-stringr >=1.3 + - r-tibble >=1.4 + - r-tidyr >=0.8 + - r-viridis + - r-yaml + + +r-basejump 0.7.2 r341_0 +----------------------- +file name : r-basejump-0.7.2-r341_0.tar.bz2 +name : r-basejump +version : 0.7.2 +build : r341_0 +build number: 0 +size : 921 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-basejump-0.7.2-r341_0.tar.bz2 +md5 : 5f7b64549d25ea793cbf4e5d7cab2772 +timestamp : 2018-09-28 04:22:09 UTC +dependencies: + - bioconductor-annotationhub + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-ensembldb + - bioconductor-genomeinfodb + - bioconductor-s4vectors + - r-assertive + - r-base >=3.4.1,<3.4.2.0a0 + - r-cowplot >=0.9 + - r-dendsort + - r-devtools + - r-dplyr >=0.7 + - r-ggplot2 >=2.2.1 + - r-knitr >=1.2.0 + - r-magrittr >=1.5 + - r-matrix >=1.2 + - r-matrix.utils >=0.9 + - r-pbapply + - r-pheatmap + - r-r.utils + - r-rcolorbrewer + - r-rcurl >=1.95 + - r-readr >=1.1 + - r-readxl >=1.0 + - r-rio + - r-rlang >=0.2 + - r-scales + - r-sessioninfo + - r-stringr >=1.3 + - r-tibble >=1.4 + - r-tidyr >=0.8 + - r-viridis + - r-yaml + + +r-basejump 0.7.2 r351_1 +----------------------- +file name : r-basejump-0.7.2-r351_1.tar.bz2 +name : r-basejump +version : 0.7.2 +build : r351_1 +build number: 1 +size : 1.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-basejump-0.7.2-r351_1.tar.bz2 +md5 : 5bda27c8666cc2b0801cf8c26ba007e0 +timestamp : 2019-01-29 16:27:09 UTC +dependencies: + - bioconductor-annotationhub + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-ensembldb + - bioconductor-genomeinfodb + - bioconductor-s4vectors + - r-assertive + - r-base >=3.5.1,<3.5.2.0a0 + - r-cowplot >=0.9 + - r-dendsort + - r-devtools + - r-dplyr >=0.7 + - r-ggplot2 >=2.2.1 + - r-knitr >=1.2.0 + - r-magrittr >=1.5 + - r-matrix >=1.2 + - r-matrix.utils >=0.9 + - r-pbapply + - r-pheatmap + - r-r.utils + - r-rcolorbrewer + - r-rcurl >=1.95 + - r-readr >=1.1 + - r-readxl >=1.0 + - r-rio + - r-rlang >=0.2 + - r-scales + - r-sessioninfo + - r-stringr >=1.3 + - r-tibble >=1.4 + - r-tidyr >=0.8 + - r-viridis + - r-yaml + + +r-basejump 0.9.9 r351_0 +----------------------- +file name : r-basejump-0.9.9-r351_0.tar.bz2 +name : r-basejump +version : 0.9.9 +build : r351_0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-basejump-0.9.9-r351_0.tar.bz2 +md5 : c9ddd0dc9ee548c03360b9deeeabe7d7 +timestamp : 2019-02-14 13:01:25 UTC +dependencies: + - bioconductor-annotationhub + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-ensembldb + - bioconductor-genomeinfodb + - bioconductor-s4vectors + - r-assertive + - r-base >=3.5.1,<3.5.2.0a0 + - r-bioverbs >=0.1.6 + - r-brio >=0.1.5 + - r-cowplot >=0.9 + - r-dendsort + - r-devtools + - r-dplyr >=0.7 + - r-ggplot2 >=3.0 + - r-ggrepel >=0.8 + - r-goalie >=0.2.8 + - r-knitr >=1.2.1 + - r-magrittr >=1.5 + - r-matrix >=1.2 + - r-matrix.utils >=0.9 + - r-matrixstats >=0.54 + - r-pbapply + - r-pheatmap >=1.0 + - r-purrr >=0.2 + - r-r.utils + - r-rcolorbrewer + - r-rcurl >=1.95 + - r-readr >=1.3 + - r-readxl >=1.0 + - r-reshape2 >=1.4 + - r-rio + - r-rlang >=0.3 + - r-scales + - r-sessioninfo >=1.1 + - r-stringr >=1.3 + - r-syntactic >=0.1.4 + - r-tibble >=2.0 + - r-tidyr >=0.8 + - r-tidyselect >=0.2 + - r-transformer >=0.1.4 + - r-viridis + - r-yaml + + +r-basejump 0.9.11 r351_0 +------------------------ +file name : r-basejump-0.9.11-r351_0.tar.bz2 +name : r-basejump +version : 0.9.11 +build : r351_0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-basejump-0.9.11-r351_0.tar.bz2 +md5 : 70fd67001e71035e77abac2898813786 +timestamp : 2019-02-26 17:30:05 UTC +dependencies: + - bioconductor-annotationhub + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-ensembldb + - bioconductor-genomeinfodb + - bioconductor-s4vectors + - r-assertive + - r-base >=3.5.1,<3.5.2.0a0 + - r-bioverbs >=0.1.8 + - r-brio >=0.1.8 + - r-cowplot >=0.9 + - r-dendsort + - r-devtools + - r-dplyr >=0.7 + - r-ggplot2 >=3.0 + - r-ggrepel >=0.8 + - r-goalie >=0.2.9 + - r-knitr >=1.2.1 + - r-magrittr >=1.5 + - r-matrix >=1.2 + - r-matrix.utils >=0.9 + - r-matrixstats >=0.54 + - r-pbapply + - r-pheatmap >=1.0 + - r-purrr >=0.2 + - r-r.utils + - r-rcolorbrewer + - r-rcurl >=1.95 + - r-readr >=1.3 + - r-readxl >=1.0 + - r-reshape2 >=1.4 + - r-rio + - r-rlang >=0.3 + - r-scales + - r-sessioninfo >=1.1 + - r-stringr >=1.3 + - r-syntactic >=0.1.5 + - r-tibble >=2.0 + - r-tidyr >=0.8 + - r-tidyselect >=0.2 + - r-transformer >=0.1.6 + - r-viridis + - r-yaml + + +r-basejump 0.10.9 r351_0 +------------------------ +file name : r-basejump-0.10.9-r351_0.tar.bz2 +name : r-basejump +version : 0.10.9 +build : r351_0 +build number: 0 +size : 1010 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-basejump-0.10.9-r351_0.tar.bz2 +md5 : 14486cdef98f31d0d3ce6b50d69e2833 +timestamp : 2019-05-30 10:39:35 UTC +dependencies: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-base >=3.5.1,<3.5.2.0a0 + - r-bioverbs >=0.1.19 + - r-brio >=0.2.1 + - r-dplyr >=0.8 + - r-freerange >=0.1.6 + - r-goalie >=0.2.16 + - r-knitr >=1.22 + - r-magrittr >=1.5 + - r-matrix >=1.2 + - r-matrix.utils >=0.9 + - r-matrixstats >=0.54 + - r-purrr >=0.2 + - r-readr >=1.3 + - r-reshape2 >=1.4 + - r-rlang >=0.3 + - r-sessioninfo >=1.1 + - r-stringr >=1.3 + - r-syntactic >=0.1.9 + - r-tibble >=2.0 + - r-tidyr >=0.8 + - r-tidyselect >=0.2 + - r-transformer >=0.1.11 + + +r-basejump 0.10.9 r351_1 +------------------------ +file name : r-basejump-0.10.9-r351_1.tar.bz2 +name : r-basejump +version : 0.10.9 +build : r351_1 +build number: 1 +size : 1007 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-basejump-0.10.9-r351_1.tar.bz2 +md5 : 10c2b5928faa677feb7be4a2d1c690cf +timestamp : 2019-05-30 19:11:25 UTC +dependencies: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-assertthat >=0.2.1 + - r-base >=3.5.1,<3.5.2.0a0 + - r-bioverbs >=0.1.19 + - r-brio >=0.2.1 + - r-dplyr >=0.8 + - r-freerange >=0.1.6 + - r-glue >=1.3.0 + - r-goalie >=0.2.16 + - r-knitr >=1.22 + - r-magrittr >=1.5 + - r-matrix >=1.2 + - r-matrix.utils >=0.9 + - r-matrixstats >=0.54 + - r-purrr >=0.2 + - r-rcpp >=1.0.1 + - r-readr >=1.3 + - r-reshape2 >=1.4 + - r-rlang >=0.3.4 + - r-sessioninfo >=1.1 + - r-stringr >=1.3 + - r-syntactic >=0.1.9 + - r-tibble >=2.1.1 + - r-tidyr >=0.8 + - r-tidyselect >=0.2 + - r-transformer >=0.1.11 + + +r-basejump 0.11.5 r36_0 +----------------------- +file name : r-basejump-0.11.5-r36_0.tar.bz2 +name : r-basejump +version : 0.11.5 +build : r36_0 +build number: 0 +size : 1.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-basejump-0.11.5-r36_0.tar.bz2 +md5 : 1afe3b0f97d767cda3a13b4ff6c156e5 +timestamp : 2019-08-12 13:31:14 UTC +dependencies: + - bioconductor-biobase >=2.44 + - bioconductor-biocgenerics >=0.30 + - bioconductor-delayedarray >=0.10 + - bioconductor-delayedmatrixstats >=1.6 + - bioconductor-genomeinfodb >=1.20 + - bioconductor-genomicranges >=1.36 + - bioconductor-iranges >=2.18 + - bioconductor-s4vectors >=0.22 + - bioconductor-singlecellexperiment >=1.6 + - bioconductor-summarizedexperiment >=1.14 + - r-assertthat >=0.2.1 + - r-base >=3.6,<3.7.0a0 + - r-bioverbs >=0.2.4 + - r-brio >=0.3.2 + - r-dplyr >=0.8 + - r-freerange >=0.2.1 + - r-glue >=1.3.1 + - r-goalie >=0.3.3 + - r-knitr >=1.22 + - r-magrittr >=1.5 + - r-matrix >=1.2 + - r-matrix.utils >=0.9 + - r-matrixstats >=0.54 + - r-purrr >=0.3 + - r-rcpp >=1.0.2 + - r-readr >=1.3 + - r-reshape2 >=1.4 + - r-rlang >=0.4 + - r-scales >=1.0 + - r-sessioninfo >=1.1 + - r-stringr >=1.4 + - r-syntactic >=0.2.3 + - r-tibble >=2.1.1 + - r-tidyr >=0.8 + - r-tidyselect >=0.2 + - r-transformer >=0.2.2 + + +r-basejump 0.11.7 r36_0 +----------------------- +file name : r-basejump-0.11.7-r36_0.tar.bz2 +name : r-basejump +version : 0.11.7 +build : r36_0 +build number: 0 +size : 1.1 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-basejump-0.11.7-r36_0.ta diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-cdseq.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-cdseq.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..461c6505f4401edc85e3cf664ab18aa0f9298712 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-cdseq.manual_bundle.txt @@ -0,0 +1,263 @@ +# Tool: r-cdseq +software_name: r-cdseq +tier: T1 +domain: single_cell +downloads: 4065 +summary: Estimate cell-type-specific gene expression profiles and sample-specific cell-type proportions simultaneously using bulk sequencing data. Kang et al. (2019) . +description: Estimate cell-type-specific gene expression profiles and sample-specific cell-type proportions simultaneously using bulk sequencing data. Kang et al. (2019) . +dependencies: bioconductor-biobase >=2.66.0,<2.67.0a0, libgcc >=13, libstdcxx >=13, r-base >=4.4,<4.5.0a0, r-clue, r-dirmult, r-doparallel, r-dplyr, r-foreach, r-ggplot2, r-ggpubr, r-gplots, r-harmony, r-iterators, r-magrittr, r-mass, r-matrix, r-matrixstats, r-pheatmap, r-qlcmatrix, r-rcpp >=1.0.3, r-rcppthread, r-rlang, r-seurat +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://github.com/kkang7/CDSeq_R_Package +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/kkang7/CDSeq_R_Package +GitHub - kkang7/CDSeq_R_Package: CDSeq R Package · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} kkang7 / CDSeq_R_Package Public Notifications You must be signed in to change notification settings Fork 10 Star 21 Code Issues 15 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights kkang7/CDSeq_R_Package master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 57 Commits 57 Commits .github .github R R data data docs docs inst inst man man src src tests tests vignettes vignettes .DS_Store .DS_Store .Rbuildignore .Rbuildignore .Rhistory .Rhistory .gitignore .gitignore .travis.yml .travis.yml CDSeq.Rproj CDSeq.Rproj CRAN-RELEASE CRAN-RELEASE DESCRIPTION DESCRIPTION NAMESPACE NAMESPACE NEWS.md NEWS.md README.Rmd README.Rmd README.md README.md _pkgdown.yml _pkgdown.yml cran-comments.md cran-comments.md View all files Repository files navigation README CDSeq CDSeq is a complete deconvolution method for dissecting bulk RNA-Seq data. The input of CDSeq is, ideally, bulk RNA-Seq read counts (similar to the input format required by DESeq2), and CDSeq will estimate, simultaneously, the cell-type-specific gene expression profiles and the sample-specific cell-type proportions, no reference of pure cell line GEPs or scRNAseq reference is needed for running CDSeq. For example, if you have a bulk RNA-Seq data, a G by M matrix A , which is a G by M matrix. G denotes the number of genes and M is the sample size, then CDSeq will output B (a G by T matrix) and C (a T by M matrix), where T is the number of cell types, B is the estimate of cell-type-specific GEPs and C is the estimate of sample-specific cell-type proportions. Importantly, you can ask CDSeq to estimate the number of cell types, i.e. T, by providing a vector of possible integer values for T. For example, if the user input for T is a vector, i.e. (T={2,3,4,5,6}), then CDSeq will estimate the most likely number for T. Installation You can install the released version of CDSeq from CRAN with: install.packages( " CDSeq " ) And the development version from GitHub with: # install.packages("devtools") devtools :: install_github( " kkang7/CDSeq_R_Package " ) build the vignette with # install.packages("devtools") devtools :: install_github( " kkang7/CDSeq_R_Package " , build_vignettes = TRUE ) Known issue about MacOS installation It is possible for Mac users to run into some errors when install from source due to problems of Rcpp compiler tools. Follow the instruction here may help: https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/ Example Load package library( CDSeq ) When the number of cell types is a scalar # # basic example code result1 <- CDSeq( bulk_data = mixtureGEP , cell_type_number = 6 , mcmc_iterations = 5 , # increase the mcmc_iterations to 700 or above gene_length = as.vector( gene_length ), reference_gep = refGEP , # gene expression profile of pure cell lines cpu_number = 1 ) When the number of cell types is a vector The cell_type_number can also be a vector which contains different integer values. CDSeq will perform estimation for each integer in the vector and estimate the number of cell types in the mixtures. For example, one can set cell_type_number = 2:10 as follows, and CDSeq will estimate the most likely number of cell types from 2 to 10. result2 <- CDSeq( bulk_data = mixtureGEP , cell_type_number = 2 : 10 , mcmc_iterations = 5 , dilution_factor = 1 , block_number = 1 , gene_length = as.vector( gene_length ), reference_gep = refGEP , # gene expression profile of pure cell lines cpu_number = 1 , # use multiple cores to save time. Set the cpu_number = length(cell_type_number) if there is enough cores. print_progress_msg_to_file = 0 ) Use single cell to annotate CDSeq-estimated cell types cdseq.result <- CDSeq :: CDSeq( bulk_data = pbmc_mix , cell_type_number = seq( 3 , 12 , 3 ), beta = 0.5 , alpha = 5 , mcmc_iterations = 700 , cpu_number = 4 , dilution_factor = 10 ) cdseq.result.celltypeassign <- cellTypeAssignSCRNA( cdseq_gep = cdseq.result $ estGEP , # CDSeq-estimated cell-type-specific GEPs cdseq_prop = cdseq.result $ estProp , # CDSeq-estimated cell type proportions sc_gep = sc_gep , # PBMC single cell data sc_annotation = sc_annotation , # PBMC single data annotations sc_pt_size = 3 , cdseq_pt_size = 6 , seurat_nfeatures = 100 , seurat_npcs = 50 , seurat_dims = 1 : 5 , plot_umap = 1 , plot_tsne = 0 ) Setting recommendations We provide recommendations for parameter settings. Note that these recommendations are merely emperical and there is no theoretical justifications yet. User can tune the parameters based on specific applications and domain knowledges. Parameters Recommended setting beta 0.5 alpha 5 mcmc_iteration 700-2000 dilution_factor 2-10 gene_subset_size 200-500 block_number >5 Check vignette for more details and examples: browseVignettes(“CDSeq”) . Contact email: kangkai0714@gmail.com About CDSeq R Package Resources Readme Uh oh! There was an error while loading. Please reload this page . Activity Stars 21 stars Watchers 2 watching Forks 10 forks Report repository Releases No releases published Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 78.1% C++ 21.8% C 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge r-cdseq --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +r-cdseq 0 r41h7d875b9_0 +----------------------- +file name : r-cdseq-0-r41h7d875b9_0.tar.bz2 +name : r-cdseq +version : 0 +build : r41h7d875b9_0 +build number: 0 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-cdseq-0-r41h7d875b9_0.tar.bz2 +md5 : 8a0e14bd12ac018e0fbd003bc5747233 +timestamp : 2021-11-17 03:31:00 UTC +dependencies: + - bioconductor-biobase + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - r-base >=4.1,<4.2.0a0 + - r-clue + - r-dirmult + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-ggpubr + - r-gplots + - r-harmony + - r-iterators + - r-magrittr + - r-mass + - r-matrix + - r-matrixstats + - r-pheatmap + - r-qlcmatrix + - r-rcpp >=1.0.3 + - r-rcppthread + - r-rlang + - r-seurat + + +r-cdseq 0 r41h9f5acd7_1 +----------------------- +file name : r-cdseq-0-r41h9f5acd7_1.tar.bz2 +name : r-cdseq +version : 0 +build : r41h9f5acd7_1 +build number: 1 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-cdseq-0-r41h9f5acd7_1.tar.bz2 +md5 : b8deb9d74af529a09c69a275db330082 +timestamp : 2022-02-28 04:41:30 UTC +dependencies: + - bioconductor-biobase + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - r-base >=4.1,<4.2.0a0 + - r-clue + - r-dirmult + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-ggpubr + - r-gplots + - r-harmony + - r-iterators + - r-magrittr + - r-mass + - r-matrix + - r-matrixstats + - r-pheatmap + - r-qlcmatrix + - r-rcpp >=1.0.3 + - r-rcppthread + - r-rlang + - r-seurat + + +r-cdseq 0 r41h9f5acd7_2 +----------------------- +file name : r-cdseq-0-r41h9f5acd7_2.tar.bz2 +name : r-cdseq +version : 0 +build : r41h9f5acd7_2 +build number: 2 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-cdseq-0-r41h9f5acd7_2.tar.bz2 +md5 : 98463d07e94d7363fdb1a1dd50f32068 +timestamp : 2022-07-19 09:52:22 UTC +dependencies: + - bioconductor-biobase + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - r-base >=4.1,<4.2.0a0 + - r-clue + - r-dirmult + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-ggpubr + - r-gplots + - r-harmony + - r-iterators + - r-magrittr + - r-mass + - r-matrix + - r-matrixstats + - r-pheatmap + - r-qlcmatrix + - r-rcpp >=1.0.3 + - r-rcppthread + - r-rlang + - r-seurat + + +r-cdseq 0 r42h9f5acd7_3 +----------------------- +file name : r-cdseq-0-r42h9f5acd7_3.tar.bz2 +name : r-cdseq +version : 0 +build : r42h9f5acd7_3 +build number: 3 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-cdseq-0-r42h9f5acd7_3.tar.bz2 +md5 : 483329804b7f32a59fcc0217a9d5618f +timestamp : 2022-11-06 05:22:20 UTC +dependencies: + - bioconductor-biobase + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-clue + - r-dirmult + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-ggpubr + - r-gplots + - r-harmony + - r-iterators + - r-magrittr + - r-mass + - r-matrix + - r-matrixstats + - r-pheatmap + - r-qlcmatrix + - r-rcpp >=1.0.3 + - r-rcppthread + - r-rlang + - r-seurat + + +r-cdseq 0 r43h4ac6f70_5 +----------------------- +file name : r-cdseq-0-r43h4ac6f70_5.tar.bz2 +name : r-cdseq +version : 0 +build : r43h4ac6f70_5 +build number: 5 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-cdseq-0-r43h4ac6f70_5.tar.bz2 +md5 : cfca54bb8205395b435f9ecde331c183 +timestamp : 2023-07-16 20:51:48 UTC +dependencies: + - bioconductor-biobase + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + - r-clue + - r-dirmult + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-ggpubr + - r-gplots + - r-harmony + - r-iterators + - r-magrittr + - r-mass + - r-matrix + - r-matrixstats + - r-pheatmap + - r-qlcmatrix + - r-rcpp >=1.0.3 + - r-rcppthread + - r-rlang + - r-seurat + + +r-cdseq 0 r44h9948957_6 +----------------------- +file name : r-cdseq-0-r44h9948957_6.tar.bz2 +name : r-cdseq +version : 0 +build : r44h9948957_6 +build number: 6 +size : 1.3 MB +license : GPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-cdseq-0-r44h9948957_6.tar.bz2 +md5 : 248ac5a71b1391be17338fab267a084a +timestamp : 2024-12-16 18:03:31 UTC +dependencies: + - bioconductor-biobase >=2.66.0,<2.67.0a0 + - libgcc >=13 + - libstdcxx >=13 + - r-base >=4.4,<4.5.0a0 + - r-clue + - r-dirmult + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-ggpubr + - r-gplots + - r-harmony + - r-iterators + - r-magrittr + - r-mass + - r-matrix + - r-matrixstats + - r-pheatmap + - r-qlcmatrix + - r-rcpp >=1.0.3 + - r-rcppthread + - r-rlang + - r-seurat diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-restfulr.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-restfulr.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbe12c484059f13c9645a21ed582c88cd3a4ec06 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-restfulr.manual_bundle.txt @@ -0,0 +1,330 @@ +# Tool: r-restfulr +software_name: r-restfulr +tier: T1 +domain: t1_backfill_overall +downloads: 282914 +summary: Models a RESTful service as if it were a nested R list. +description: Models a RESTful service as if it were a nested R list. +dependencies: bioconductor-s4vectors >=0.13.15, bioconductor-s4vectors >=0.48.0,<0.49.0a0, libgcc >=14, r-base >=4.5,<4.6.0a0, r-rcurl, r-rjson, r-xml, r-yaml +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://CRAN.R-project.org/package=restfulr +doc_url: +dev_url: + +## URL Docs Extract +### https://CRAN.R-project.org/package=restfulr +CRAN: Package restfulr restfulr: R Interface to RESTful Web Services Models a RESTful service as if it were a nested R list. Version: 0.0.16 Depends: R (≥ 3.4.0), methods Imports: XML , RCurl , rjson , S4Vectors (≥ 0.13.15), yaml Suggests: getPass , rsolr , RUnit Published: 2025-06-27 DOI: 10.32614/CRAN.package.restfulr Author: Michael Lawrence [aut, cre] Maintainer: Michael Lawrence <michafla at gene.com> License: Artistic-2.0 NeedsCompilation: yes In views: WebTechnologies CRAN checks: restfulr results Documentation: Reference manual: restfulr.html , restfulr.pdf Downloads: Package source: restfulr_0.0.16.tar.gz Windows binaries: r-devel: restfulr_0.0.16.zip , r-release: restfulr_0.0.16.zip , r-oldrel: restfulr_0.0.16.zip macOS binaries: r-release (arm64): restfulr_0.0.16.tgz , r-oldrel (arm64): restfulr_0.0.16.tgz , r-release (x86_64): restfulr_0.0.16.tgz , r-oldrel (x86_64): restfulr_0.0.16.tgz Old sources: restfulr archive Reverse dependencies: Reverse imports: rsolr , rtracklayer Linking: Please use the canonical form https://CRAN.R-project.org/package=restfulr to link to this page. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge r-restfulr --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +r-restfulr 0.0.13 r41h73dbb54_2 +------------------------------- +file name : r-restfulr-0.0.13-r41h73dbb54_2.tar.bz2 +name : r-restfulr +version : 0.0.13 +build : r41h73dbb54_2 +build number: 2 +size : 386 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.13-r41h73dbb54_2.tar.bz2 +md5 : fa7cd7a3e4cfbf2639677c12d0d08fb5 +timestamp : 2022-02-25 07:10:25 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - libgcc-ng >=10.3.0 + - r-base >=4.1,<4.2.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.13 r41hdf9a8c9_0 +------------------------------- +file name : r-restfulr-0.0.13-r41hdf9a8c9_0.tar.bz2 +name : r-restfulr +version : 0.0.13 +build : r41hdf9a8c9_0 +build number: 0 +size : 387 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.13-r41hdf9a8c9_0.tar.bz2 +md5 : bc6e71652b7d419eb89aaac90451ca32 +timestamp : 2021-05-31 22:47:47 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - libgcc-ng >=9.3.0 + - r-base >=4.1,<4.2.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.13 r41hdf9a8c9_1 +------------------------------- +file name : r-restfulr-0.0.13-r41hdf9a8c9_1.tar.bz2 +name : r-restfulr +version : 0.0.13 +build : r41hdf9a8c9_1 +build number: 1 +size : 387 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.13-r41hdf9a8c9_1.tar.bz2 +md5 : b62a27fc5bc904ef5a4c3db90519adb2 +timestamp : 2021-06-07 13:38:02 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - libgcc-ng >=9.3.0 + - r-base >=4.1,<4.2.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.14 r41h73dbb54_0 +------------------------------- +file name : r-restfulr-0.0.14-r41h73dbb54_0.tar.bz2 +name : r-restfulr +version : 0.0.14 +build : r41h73dbb54_0 +build number: 0 +size : 388 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.14-r41h73dbb54_0.tar.bz2 +md5 : 2df4ea5874294428ceda9548a09e1adf +timestamp : 2022-06-05 18:24:27 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - libgcc-ng >=12 + - r-base >=4.1,<4.2.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.15 r41h73dbb54_0 +------------------------------- +file name : r-restfulr-0.0.15-r41h73dbb54_0.tar.bz2 +name : r-restfulr +version : 0.0.15 +build : r41h73dbb54_0 +build number: 0 +size : 388 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.15-r41h73dbb54_0.tar.bz2 +md5 : be982d5db1378e1c30e906897ba0f9d5 +timestamp : 2022-06-23 10:07:07 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - libgcc-ng >=12 + - r-base >=4.1,<4.2.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.15 r42h56115f1_2 +------------------------------- +file name : r-restfulr-0.0.15-r42h56115f1_2.tar.bz2 +name : r-restfulr +version : 0.0.15 +build : r42h56115f1_2 +build number: 2 +size : 391 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.15-r42h56115f1_2.tar.bz2 +md5 : 1227c0f387373a10a7fee6c5153611fc +timestamp : 2023-05-18 18:19:34 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - libgcc-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.15 r42h73dbb54_1 +------------------------------- +file name : r-restfulr-0.0.15-r42h73dbb54_1.tar.bz2 +name : r-restfulr +version : 0.0.15 +build : r42h73dbb54_1 +build number: 1 +size : 391 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.15-r42h73dbb54_1.tar.bz2 +md5 : a1efd39130ec7fc5058a3d25c9c4cbed +timestamp : 2022-11-04 00:35:39 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - libgcc-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.15 r43h56115f1_3 +------------------------------- +file name : r-restfulr-0.0.15-r43h56115f1_3.tar.bz2 +name : r-restfulr +version : 0.0.15 +build : r43h56115f1_3 +build number: 3 +size : 431 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.15-r43h56115f1_3.tar.bz2 +md5 : ea161a74aa5ca7ad7164cca80b607d33 +timestamp : 2023-07-12 08:12:31 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - libgcc-ng >=12 + - r-base >=4.3,<4.4.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.15 r43h56115f1_4 +------------------------------- +file name : r-restfulr-0.0.15-r43h56115f1_4.tar.bz2 +name : r-restfulr +version : 0.0.15 +build : r43h56115f1_4 +build number: 4 +size : 428 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.15-r43h56115f1_4.tar.bz2 +md5 : 98d1b64d34553c9cafe9ad01bd956844 +timestamp : 2024-05-24 10:22:55 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - bioconductor-s4vectors >=0.40.2,<0.41.0a0 + - libgcc-ng >=12 + - r-base >=4.3,<4.4.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.15 r44h5ef9028_5 +------------------------------- +file name : r-restfulr-0.0.15-r44h5ef9028_5.tar.bz2 +name : r-restfulr +version : 0.0.15 +build : r44h5ef9028_5 +build number: 5 +size : 440 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.15-r44h5ef9028_5.tar.bz2 +md5 : 8bcd6ed06a66b6dcc870b2726c883e37 +timestamp : 2024-12-18 02:12:05 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - bioconductor-s4vectors >=0.44.0,<0.45.0a0 + - libgcc >=13 + - r-base >=4.4,<4.5.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.15 r44h5ef9028_6 +------------------------------- +file name : r-restfulr-0.0.15-r44h5ef9028_6.tar.bz2 +name : r-restfulr +version : 0.0.15 +build : r44h5ef9028_6 +build number: 6 +size : 438 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.15-r44h5ef9028_6.tar.bz2 +md5 : efffdc2f16b96b1c360f467690b13735 +timestamp : 2025-04-15 00:23:08 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - bioconductor-s4vectors >=0.44.0,<0.45.0a0 + - libgcc >=13 + - r-base >=4.4,<4.5.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.16 r44h5ef9028_0 +------------------------------- +file name : r-restfulr-0.0.16-r44h5ef9028_0.tar.bz2 +name : r-restfulr +version : 0.0.16 +build : r44h5ef9028_0 +build number: 0 +size : 438 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.16-r44h5ef9028_0.tar.bz2 +md5 : 5a366eab5e0c57f1660798e6b1f601d5 +timestamp : 2025-06-27 20:22:18 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - bioconductor-s4vectors >=0.44.0,<0.45.0a0 + - libgcc >=13 + - r-base >=4.4,<4.5.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml + + +r-restfulr 0.0.16 r45hf7ecca6_1 +------------------------------- +file name : r-restfulr-0.0.16-r45hf7ecca6_1.conda +name : r-restfulr +version : 0.0.16 +build : r45hf7ecca6_1 +build number: 1 +size : 389 KB +license : Artistic-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-restfulr-0.0.16-r45hf7ecca6_1.conda +md5 : 2a679393cf368e756d2b16d4c9f25c49 +timestamp : 2026-03-02 07:01:52 UTC +dependencies: + - bioconductor-s4vectors >=0.13.15 + - bioconductor-s4vectors >=0.48.0,<0.49.0a0 + - libgcc >=14 + - r-base >=4.5,<4.6.0a0 + - r-rcurl + - r-rjson + - r-xml + - r-yaml diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-sceasy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-sceasy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..690800304358be9ac8121b2054aaa2e82ea6681d --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-sceasy.manual_bundle.txt @@ -0,0 +1,282 @@ +# Tool: r-sceasy +software_name: r-sceasy +tier: T1 +domain: single_cell +downloads: 20209 +summary: A package providing functions to convert between different single-cell data formats. +description: A package providing functions to convert between different single-cell data formats. +dependencies: anndata, bioconductor-loomexperiment >=1.1.5, bioconductor-singlecellexperiment >=1.4.0, r-base >=4.4,<4.5.0a0, r-monocle3 >=1.0.0, r-reticulate, r-seurat >=3.0.1, scipy +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://github.com/cellgeni/sceasy +doc_url: +dev_url: https://github.com/cellgeni/sceasy + +## URL Docs Extract +### https://github.com/cellgeni/sceasy +GitHub - cellgeni/sceasy: A package to help convert different single-cell data formats to each other · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} cellgeni / sceasy Public Notifications You must be signed in to change notification settings Fork 67 Star 465 Code Issues 44 Pull requests 5 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights cellgeni/sceasy master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 72 Commits 72 Commits R R .gitattributes .gitattributes .gitignore .gitignore .travis.yml .travis.yml DESCRIPTION DESCRIPTION LICENSE LICENSE NAMESPACE NAMESPACE README.md README.md View all files Repository files navigation README GPL-3.0 license sceasy sceasy is a package that helps easy conversion of different single-cell data formats to each other. Converting to AnnData creates a file that can be directly used in cellxgene which is an interactive explorer for single-cell transcriptomics datasets. 💡 for h5da to rds conversion also see https://github.com/cellgeni/schard 💡 for rds to h5ad conversion also see https://github.com/cellgeni/py8rds Warning Before installing the conda packages below please first create a new conda environment EnvironmentName and activate it. Everything else can be installed in R. Installation sceasy is installable either as a bioconda package: conda install -c bioconda r-sceasy or as an R package: devtools::install_github("cellgeni/sceasy") which will require the biconductor packages BiocManager and LoomExperiment: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(c("LoomExperiment", "SingleCellExperiment")) To use sceasy ensure the anndata package is installed: conda install anndata -c bioconda Optionally, if you plan to convert between loom and anndata, please also ensure that the loompy package is installed: conda install loompy -c bioconda You will also need to install reticulate package: install.packages('reticulate') Usage Before converting your data please load the following libraries in your R session: library(sceasy) library(reticulate) use_condaenv('EnvironmentName') loompy <- reticulate::import('loompy') Seurat to AnnData sceasy::convertFormat(seurat_object, from="seurat", to="anndata", outFile='filename.h5ad') AnnData to Seurat sceasy::convertFormat(h5ad_file, from="anndata", to="seurat", outFile='filename.rds') Seurat to SingleCellExperiment sceasy::convertFormat(seurat_object, from="seurat", to="sce", outFile='filename.rds') SingleCellExperiment to AnnData sceasy::convertFormat(sce_object, from="sce", to="anndata", outFile='filename.h5ad') SingleCellExperiment to Loom sceasy::convertFormat(sce_object, from="sce", to="loom", outFile='filename.loom') Loom to AnnData sceasy::convertFormat('filename.loom', from="loom", to="anndata", outFile='filename.h5ad') Loom to SingleCellExperiment sceasy::convertFormat('filename.loom', from="loom", to="sce", outFile='filename.rds') About A package to help convert different single-cell data formats to each other Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 465 stars Watchers 8 watching Forks 67 forks Report repository Releases 7 v0.0.7 Latest Sep 1, 2022 + 6 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/cellgeni/sceasy +GitHub - cellgeni/sceasy: A package to help convert different single-cell data formats to each other · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} cellgeni / sceasy Public Notifications You must be signed in to change notification settings Fork 67 Star 465 Code Issues 44 Pull requests 5 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights cellgeni/sceasy master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 72 Commits 72 Commits R R .gitattributes .gitattributes .gitignore .gitignore .travis.yml .travis.yml DESCRIPTION DESCRIPTION LICENSE LICENSE NAMESPACE NAMESPACE README.md README.md View all files Repository files navigation README GPL-3.0 license sceasy sceasy is a package that helps easy conversion of different single-cell data formats to each other. Converting to AnnData creates a file that can be directly used in cellxgene which is an interactive explorer for single-cell transcriptomics datasets. 💡 for h5da to rds conversion also see https://github.com/cellgeni/schard 💡 for rds to h5ad conversion also see https://github.com/cellgeni/py8rds Warning Before installing the conda packages below please first create a new conda environment EnvironmentName and activate it. Everything else can be installed in R. Installation sceasy is installable either as a bioconda package: conda install -c bioconda r-sceasy or as an R package: devtools::install_github("cellgeni/sceasy") which will require the biconductor packages BiocManager and LoomExperiment: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(c("LoomExperiment", "SingleCellExperiment")) To use sceasy ensure the anndata package is installed: conda install anndata -c bioconda Optionally, if you plan to convert between loom and anndata, please also ensure that the loompy package is installed: conda install loompy -c bioconda You will also need to install reticulate package: install.packages('reticulate') Usage Before converting your data please load the following libraries in your R session: library(sceasy) library(reticulate) use_condaenv('EnvironmentName') loompy <- reticulate::import('loompy') Seurat to AnnData sceasy::convertFormat(seurat_object, from="seurat", to="anndata", outFile='filename.h5ad') AnnData to Seurat sceasy::convertFormat(h5ad_file, from="anndata", to="seurat", outFile='filename.rds') Seurat to SingleCellExperiment sceasy::convertFormat(seurat_object, from="seurat", to="sce", outFile='filename.rds') SingleCellExperiment to AnnData sceasy::convertFormat(sce_object, from="sce", to="anndata", outFile='filename.h5ad') SingleCellExperiment to Loom sceasy::convertFormat(sce_object, from="sce", to="loom", outFile='filename.loom') Loom to AnnData sceasy::convertFormat('filename.loom', from="loom", to="anndata", outFile='filename.h5ad') Loom to SingleCellExperiment sceasy::convertFormat('filename.loom', from="loom", to="sce", outFile='filename.rds') About A package to help convert different single-cell data formats to each other Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 465 stars Watchers 8 watching Forks 67 forks Report repository Releases 7 v0.0.7 Latest Sep 1, 2022 + 6 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge r-sceasy --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +r-sceasy 0.0.3 r36_0 +-------------------- +file name : r-sceasy-0.0.3-r36_0.tar.bz2 +name : r-sceasy +version : 0.0.3 +build : r36_0 +build number: 0 +size : 54 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.3-r36_0.tar.bz2 +md5 : df99740c98cd2b5129524c8627178914 +timestamp : 2019-09-25 20:18:29 UTC +dependencies: + - anndata <=0.6.19 + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=3.6,<3.7.0a0 + - r-reticulate + - r-seurat >=3.0.1 + + +r-sceasy 0.0.4 r36_0 +-------------------- +file name : r-sceasy-0.0.4-r36_0.tar.bz2 +name : r-sceasy +version : 0.0.4 +build : r36_0 +build number: 0 +size : 55 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.4-r36_0.tar.bz2 +md5 : 74607d4b51bdff3e050dbb34ca8c6694 +timestamp : 2019-10-03 01:30:10 UTC +dependencies: + - anndata <=0.6.19 + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=3.6,<3.7.0a0 + - r-reticulate + - r-seurat >=3.0.1 + - scipy <1.3.0 + + +r-sceasy 0.0.5 r36_0 +-------------------- +file name : r-sceasy-0.0.5-r36_0.tar.bz2 +name : r-sceasy +version : 0.0.5 +build : r36_0 +build number: 0 +size : 59 KB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.5-r36_0.tar.bz2 +md5 : 19d1c4b30e06bb70afa97fb14ebea05e +timestamp : 2019-10-14 12:22:06 UTC +dependencies: + - anndata <=0.6.19 + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=3.6,<3.7.0a0 + - r-reticulate + - r-seurat >=3.0.1 + - scipy <1.3.0 + + +r-sceasy 0.0.5 r40_1 +-------------------- +file name : r-sceasy-0.0.5-r40_1.tar.bz2 +name : r-sceasy +version : 0.0.5 +build : r40_1 +build number: 1 +size : 60 KB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.5-r40_1.tar.bz2 +md5 : 7313262d79ef3ec1360be8109cdb0ffe +timestamp : 2020-05-14 14:18:47 UTC +dependencies: + - anndata <=0.6.19 + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=4.0,<4.1.0a0 + - r-reticulate + - r-seurat >=3.0.1 + - scipy <1.3.0 + + +r-sceasy 0.0.6 r40_0 +-------------------- +file name : r-sceasy-0.0.6-r40_0.tar.bz2 +name : r-sceasy +version : 0.0.6 +build : r40_0 +build number: 0 +size : 69 KB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.6-r40_0.tar.bz2 +md5 : 982f88b42fa96465d7604684e274627b +timestamp : 2020-11-06 09:29:39 UTC +dependencies: + - anndata <=0.6.19 + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=4.0,<4.1.0a0 + - r-reticulate + - r-seurat >=3.0.1 + - scipy <1.3.0 + + +r-sceasy 0.0.6 r40hdfd78af_1 +---------------------------- +file name : r-sceasy-0.0.6-r40hdfd78af_1.tar.bz2 +name : r-sceasy +version : 0.0.6 +build : r40hdfd78af_1 +build number: 1 +size : 69 KB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.6-r40hdfd78af_1.tar.bz2 +md5 : c89f9aa741eaf4ccb1456803b27d0088 +timestamp : 2021-04-01 17:02:56 UTC +dependencies: + - anndata <=0.6.19 + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=4.0,<4.1.0a0 + - r-reticulate + - r-seurat >=3.0.1 + - scipy <1.3.0 + + +r-sceasy 0.0.6 r41hdfd78af_2 +---------------------------- +file name : r-sceasy-0.0.6-r41hdfd78af_2.tar.bz2 +name : r-sceasy +version : 0.0.6 +build : r41hdfd78af_2 +build number: 2 +size : 69 KB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.6-r41hdfd78af_2.tar.bz2 +md5 : 8dabf0d82b3c68267dffe553e234b19c +timestamp : 2021-06-02 16:35:19 UTC +dependencies: + - anndata <=0.6.19 + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=4.1,<4.2.0a0 + - r-reticulate + - r-seurat >=3.0.1 + - scipy <1.3.0 + + +r-sceasy 0.0.7 r41hdfd78af_0 +---------------------------- +file name : r-sceasy-0.0.7-r41hdfd78af_0.tar.bz2 +name : r-sceasy +version : 0.0.7 +build : r41hdfd78af_0 +build number: 0 +size : 80 KB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.7-r41hdfd78af_0.tar.bz2 +md5 : 0910c20197224ec0a25c0c38a6ed0f4f +timestamp : 2022-09-03 20:34:01 UTC +dependencies: + - anndata + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=4.1,<4.2.0a0 + - r-monocle3 >=1.0.0 + - r-reticulate + - r-seurat >=3.0.1 + - scipy + + +r-sceasy 0.0.7 r42hdfd78af_1 +---------------------------- +file name : r-sceasy-0.0.7-r42hdfd78af_1.tar.bz2 +name : r-sceasy +version : 0.0.7 +build : r42hdfd78af_1 +build number: 1 +size : 81 KB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.7-r42hdfd78af_1.tar.bz2 +md5 : 0bffe98c6e2596552230eeb9857916b1 +timestamp : 2022-11-06 12:33:51 UTC +dependencies: + - anndata + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=4.2,<4.3.0a0 + - r-monocle3 >=1.0.0 + - r-reticulate + - r-seurat >=3.0.1 + - scipy + + +r-sceasy 0.0.7 r43hdfd78af_2 +---------------------------- +file name : r-sceasy-0.0.7-r43hdfd78af_2.tar.bz2 +name : r-sceasy +version : 0.0.7 +build : r43hdfd78af_2 +build number: 2 +size : 82 KB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.7-r43hdfd78af_2.tar.bz2 +md5 : e195720df36f749a21d31d49ac6d26ba +timestamp : 2023-07-19 11:48:42 UTC +dependencies: + - anndata + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=4.3,<4.4.0a0 + - r-monocle3 >=1.0.0 + - r-reticulate + - r-seurat >=3.0.1 + - scipy + + +r-sceasy 0.0.7 r44hdfd78af_3 +---------------------------- +file name : r-sceasy-0.0.7-r44hdfd78af_3.tar.bz2 +name : r-sceasy +version : 0.0.7 +build : r44hdfd78af_3 +build number: 3 +size : 82 KB +license : GPL3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-sceasy-0.0.7-r44hdfd78af_3.tar.bz2 +md5 : 7a080fa3a7aafb107960008de0cb6325 +timestamp : 2024-12-25 07:29:01 UTC +dependencies: + - anndata + - bioconductor-loomexperiment >=1.1.5 + - bioconductor-singlecellexperiment >=1.4.0 + - r-base >=4.4,<4.5.0a0 + - r-monocle3 >=1.0.0 + - r-reticulate + - r-seurat >=3.0.1 + - scipy diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-scopfunctions.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-scopfunctions.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a74eece994a5b8c7a65029da1db31bd07f263d9 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-scopfunctions.manual_bundle.txt @@ -0,0 +1,158 @@ +# Tool: r-scopfunctions +software_name: r-scopfunctions +tier: T1 +domain: single_cell +downloads: 3471 +summary: An R package of functions for single cell -omics analysis. +description: An R package of functions for single cell -omics analysis. +dependencies: bioconductor-mast >=1.32.0,<1.33.0a0, libgcc >=13, libstdcxx >=13, r-base >=4.4,<4.5.0a0, r-data.table, r-ggplot2, r-magrittr, r-patchwork, r-r.utils, r-sessioninfo, r-seurat +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://github.com/CBMR-Single-Cell-Omics-Platform/SCOPfunctions +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/CBMR-Single-Cell-Omics-Platform/SCOPfunctions +GitHub - CBMR-Single-Cell-Omics-Platform/SCOPfunctions: An R package of functions for single cell -omics analysis. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} CBMR-Single-Cell-Omics-Platform / SCOPfunctions Public Notifications You must be signed in to change notification settings Fork 7 Star 9 Code Issues 3 Pull requests 2 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights CBMR-Single-Cell-Omics-Platform/SCOPfunctions main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 26 Commits 26 Commits .github/ ISSUE_TEMPLATE .github/ ISSUE_TEMPLATE R R assets assets man man tests tests DESCRIPTION DESCRIPTION LICENSE.md LICENSE.md NAMESPACE NAMESPACE README.Rmd README.Rmd README.md README.md SCOPfunctions.Rproj SCOPfunctions.Rproj tmp_testDE.R tmp_testDE.R View all files Repository files navigation README AGPL-3.0 license SCOPfunctions An R package of functions for single cell -omics analysis. Fits into Seurat workflow. Install Install using devtools: devtools::install_github("CBMR-Single-Cell-Omics-Platform/SCOPfunctions") install manually git clone https://www.github.com/CBMR-Single-Cell-Omics-Platform/SCOPfunctions.git then from R: install.packages("./SCOPfunctions", type="source", repos=NULL) Usage library("SCOPfunctions") library("Seurat") Download the example data used in the Seurat hashing vignette at https://satijalab.org/seurat/archive/v3.1/hashing_vignette.html Follow the initial steps of the hashing vignette up till and including the HTO normalization Preprocess Generate an area plot showing how proportions of singlets, doublets and negatives vary with the positive quantile p_quantile = SCOPfunctions::prep_HTO_q_area_plot( seurat_obj=pbmc.hashtag, vec_range_quantile=seq(0.8,0.99,0.01), n_cores_max=Inf ) infer intra-hash doublets # First demultiplex hashtags q = 0.98 pbmc.hashtag = Seurat::HTOdemux(pbmc.hashtag,assay = "HTO", positive.quantile = q) # use inter-hash doublets to infer intra-hash doublets pbmc.hashtag = SCOPfunctions::prep_intrahash_doub( seurat_obj=pbmc.hashtag, assay = "RNA", npcs=20, randomSeed = 12345 ) Do QC on RNA assay pbmc.hashtag = prep_qc_rna( seurat_obj=pbmc.hashtag, assay = "RNA" ) Differential expression # first find clusters (after normalizing the RNA, finding variable features and scaling the data - not shown) pbmc.hashtag <- FindNeighbors(pbmc.hashtag, reduction = "pca", dims = 1:20) pbmc.hashtag <- FindClusters(pbmc.hashtag, resolution = 10, verbose = FALSE) # find DE genes for cluster 0 df_DE = SCOPfunctions::DE_MAST_RE_seurat( object=pbmc.hashtag, random_effect.vars="hash.ID", test.use = "MAST", ident.1 = "0", group.by = "seurat_clusters" ) find the activity values for a geneset # as an example, just use the top DE genes for cluster 0 vec_geneWeights <- seq(from = 1, to = 0.1, by = -0.1) vec_geneWeights <- vec_geneWeights/sum(vec_geneWeights) names(vec_geneWeights) = head(rownames(df_DE), 10) pbmc.hashtag$my_geneset_embeddings <- geneset_embed( mat_datExpr = as.matrix(GetAssayData(pbmc.hashtag, slot="scale.data", assay="SCT")), vec_geneWeights=vec_geneWeights, min_feats_present = 5) find the activity values for a list of genesets pbmc.hashtag <- geneset_embed_list_seurat( seurat_obj = pbmc.hashtag, list_vec_geneWeights=list_vec_geneWeights, slot="scale.data", assay="SCT", min_feats_present = 5, n_cores_max = Inf) Plot results plot the distribution of cell clusters in different samples plot_barIdentGroup(seurat_obj=pbmc.hashtag, var_ident="sample_ID", var_group="cluster", vec_group_colors=NULL, f_color=colorRampPalette(brewer.pal(n=11, name="RdYlBu")), do_plot = F) plot a cluster * feature grid of gene expression violin plots # Here we just use the top variable genes, but normally we would use cluster marker genes plot_vlnGrid(seurat_obj, slot="data", var_group="cluster", vec_features=head(VariableFeatures(seurat_obj),n=15), vec_group_colors=NULL, f_color = colorRampPalette(brewer.pal(n=11, name="RdYlBu"))) make a network plot of a set of co-expressed features SCOPfunctions::plot_network( mat_datExpr=as.matrix(GetAssayData(seurat_obj, slot="data")), vec_geneImportance=vec_geneImportance, vec_genes_highlight=c(), n_max_genes=50, igraph_algorithm = "drl", fontface_labels="bold.italic", color_edge = "grey70", edge_thickness = 1) Contribute Issues and pull requests are welcome! All contributions should be in line with the usethis code of conduct . This package uses the methods and R tools set out in R packages . All Pull Requests should follow the tidyverse style guide . About An R package of functions for single cell -omics analysis. Resources Readme License AGPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 9 stars Watchers 0 watching Forks 7 forks Report repository Releases No releases published Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge r-scopfunctions --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +r-scopfunctions 0 r41h9f5acd7_0 +------------------------------- +file name : r-scopfunctions-0-r41h9f5acd7_0.tar.bz2 +name : r-scopfunctions +version : 0 +build : r41h9f5acd7_0 +build number: 0 +size : 116 KB +license : AGPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-scopfunctions-0-r41h9f5acd7_0.tar.bz2 +md5 : ff009b48b4a7c616f389fd3a47addfc5 +timestamp : 2022-07-19 16:59:46 UTC +dependencies: + - bioconductor-mast + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - r-base >=4.1,<4.2.0a0 + - r-data.table + - r-ggplot2 + - r-magrittr + - r-patchwork + - r-r.utils + - r-sessioninfo + - r-seurat + + +r-scopfunctions 0 r42h4ac6f70_2 +------------------------------- +file name : r-scopfunctions-0-r42h4ac6f70_2.tar.bz2 +name : r-scopfunctions +version : 0 +build : r42h4ac6f70_2 +build number: 2 +size : 117 KB +license : AGPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-scopfunctions-0-r42h4ac6f70_2.tar.bz2 +md5 : 8c665b3ae5bc9f4a104ba71e33ce5eb8 +timestamp : 2023-05-29 22:15:02 UTC +dependencies: + - bioconductor-mast + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-data.table + - r-ggplot2 + - r-magrittr + - r-patchwork + - r-r.utils + - r-sessioninfo + - r-seurat + + +r-scopfunctions 0 r42h9f5acd7_1 +------------------------------- +file name : r-scopfunctions-0-r42h9f5acd7_1.tar.bz2 +name : r-scopfunctions +version : 0 +build : r42h9f5acd7_1 +build number: 1 +size : 117 KB +license : AGPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-scopfunctions-0-r42h9f5acd7_1.tar.bz2 +md5 : 77f69c34726247bb96000ad3f261c113 +timestamp : 2022-11-11 22:43:25 UTC +dependencies: + - bioconductor-mast + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - r-base >=4.2,<4.3.0a0 + - r-data.table + - r-ggplot2 + - r-magrittr + - r-patchwork + - r-r.utils + - r-sessioninfo + - r-seurat + + +r-scopfunctions 0 r43h4ac6f70_3 +------------------------------- +file name : r-scopfunctions-0-r43h4ac6f70_3.tar.bz2 +name : r-scopfunctions +version : 0 +build : r43h4ac6f70_3 +build number: 3 +size : 117 KB +license : AGPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-scopfunctions-0-r43h4ac6f70_3.tar.bz2 +md5 : 0506c944a1cb88ba98faeefb8d7a4327 +timestamp : 2023-07-15 12:02:33 UTC +dependencies: + - bioconductor-mast + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - r-base >=4.3,<4.4.0a0 + - r-data.table + - r-ggplot2 + - r-magrittr + - r-patchwork + - r-r.utils + - r-sessioninfo + - r-seurat + + +r-scopfunctions 0 r44h9948957_4 +------------------------------- +file name : r-scopfunctions-0-r44h9948957_4.tar.bz2 +name : r-scopfunctions +version : 0 +build : r44h9948957_4 +build number: 4 +size : 121 KB +license : AGPL-3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-scopfunctions-0-r44h9948957_4.tar.bz2 +md5 : cf3a05428d8ff2c0f96c81f14092d6e6 +timestamp : 2024-12-27 05:58:45 UTC +dependencies: + - bioconductor-mast >=1.32.0,<1.33.0a0 + - libgcc >=13 + - libstdcxx >=13 + - r-base >=4.4,<4.5.0a0 + - r-data.table + - r-ggplot2 + - r-magrittr + - r-patchwork + - r-r.utils + - r-sessioninfo + - r-seurat diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-seurat-data.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-seurat-data.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..3d4d2d0bf4b159d435cb14768ee1330a0a4ba905 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-seurat-data.manual_bundle.txt @@ -0,0 +1,111 @@ +# Tool: r-seurat-data +software_name: r-seurat-data +tier: T1 +domain: single_cell +downloads: 3783 +summary: Single cell RNA sequencing datasets can be large, consisting of matrices that contain expression data for several thousand features across several thousand cells. This package is designed to easily install, manage, and learn about various single-cell datasets, provided Seurat objects and distributed as independent packages. +description: Single cell RNA sequencing datasets can be large, consisting of matrices that contain expression data for several thousand features across several thousand cells. This package is designed to easily install, manage, and learn about various single-cell datasets, provided Seurat objects and distributed as independent packages. +dependencies: r-base >=4.4,<4.5.0a0, r-cli, r-crayon, r-rappdirs, r-seurat >=5, r-seuratobject >=5 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: http://www.satijalab.org/seurat +doc_url: https://github.com/satijalab/seurat-data/blob/main/README.md +dev_url: https://github.com/satijalab/seurat-data + +## URL Docs Extract +### https://github.com/satijalab/seurat-data/blob/main/README.md +seurat-data/README.md at main · satijalab/seurat-data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} satijalab / seurat-data Public Notifications You must be signed in to change notification settings Fork 46 Star 153 Code Issues 38 Pull requests 1 Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Wiki Security and quality Insights Files Expand file tree main Breadcrumbs seurat-data / README.md Copy path Blame More file actions Blame More file actions Latest commit History History History 95 lines (67 loc) · 6.55 KB main Breadcrumbs seurat-data / README.md Top File metadata and controls Preview Code Blame 95 lines (67 loc) · 6.55 KB Raw Copy raw file Download raw file Outline Edit and raw actions SeuratData SeuratData is a mechanism for distributing datasets in the form of Seurat objects using R's internal package and data management systems. It represents an easy way for users to get access to datasets that are used in the Seurat vignettes. Installation Installation of SeuratData can be accomplished through devtools devtools :: install_github( ' satijalab/seurat-data ' ) Getting Started When loading SeuratData, a list of all available datasets will be displayed (this is similar to other metapackages like tidyverse along with the version of Seurat used to create each dataset). This message can be suppressed with suppressPackageStartupMessages > library( SeuratData ) ── Installed datasets ───────────────────────────────────────────────────────────── SeuratData v0.1.0 ── ✔ cbmc 3.0.0 ✔ panc8 3.0.0 ✔ ifnb 3.0.0 ✔ pbmc3k 3.0.0 ───────────────────────────────────────────────── Key ────────────────────────────────────────────────── ✔ Dataset loaded successfully To see a manifest of all available datasets, use AvailableData ; this manifest will update as new datasets are uploaded to our data repository. > AvailableData() Dataset Version Summary species system ncells tech notes Installed InstalledVersion cbmc.SeuratData cbmc 3.0.0 scRNAseq and 13 - antibody sequencing of CBMCs human CBMC ( cord blood ) 8617 CITE - seq < NA > TRUE 3.0.0 hcabm40k.SeuratData hcabm40k 3.0.0 40 , 000 Cells From the Human Cell Atlas ICA Bone Marrow Dataset human bone marrow 40000 10x v2 < NA > FALSE 3.0.0 ifnb.SeuratData ifnb 3.0.0 IFNB - Stimulated and Control PBMCs human PBMC 13999 10x v1 < NA > TRUE 3.0.0 panc8.SeuratData panc8 3.0.0 Eight Pancreas Datasets Across Five Technologies human Pancreatic Islets 14892 SMARTSeq2 , Fluidigm C1 , CelSeq , CelSeq2 , inDrops < NA > TRUE 3.0.0 pbmc3k.SeuratData pbmc3k 3.0.0 3k PBMCs from 10X Genomics human PBMC 2700 10x v1 < NA > TRUE 3.0.0 pbmcsca.SeuratData pbmcsca 3.0.0 Broad Institute PBMC Systematic Comparative Analysis human PBMC 31021 10x v2 , 10x v3 , SMARTSeq2 , Seq - Well , inDrops , Drop - seq , CelSeq2 HCA benchmark FALSE 3.0.0 Installation of datasets can be done with InstallData ; this function will accept either a dataset name (eg. pbmc3k ) or the corresponding package name (eg. pbmc3k.SeuratData ). InstallData will automatically attach the installed dataset package so one can immediately load and use the dataset. > InstallData( " pbmc3k " ) Loading a dataset is done using the data function > data( " pbmc3k " ) > pbmc3k An object of class Seurat 13714 features across 2700 samples within 1 assay Active assay : RNA ( 13714 features ) Dataset documentation and information All datasets provided have help pages built for them. These pages are accessed using the standard help function > ? pbmc3k > ? ifnb A full command list for the steps taken to generate each dataset is present in the examples section of these help pages. Packages will also often have citation information bundled with the package. Citation information can be accessed by passing the package name , not the dataset name, to the citation function > citation( ' cbmc.SeuratData ' ) To cite the CBMC dataset , please use : Stoeckius et al. Simultaneous epitope and transcriptome measurement in single cells. Nature Methods ( 2017 ) A BibTeX entry for LaTeX users is @ Article {, author = { Marlon Stoeckius and Christoph Hafemeister and William Stephenson and Brian Houck - Loomis and Pratip K Chattopadhyay and Harold Swerdlow and Rahul Satija and Peter Smibert }, title = { Simultaneous epitope and transcriptome measurement in single cells }, journal = { Nature Methods }, year = { 2017 }, doi = { 10.1038 / nmeth.4380 }, url = { https : // www.nature.com / articles / nmeth.4380 }, } Rationale and Implementation We created SeuratData in order to distribute datasets for Seurat vignettes in as painless and reproducible a way as possible. We also wanted to give users the flexibility to selectively install and load datasets of interest, to minimize disk storage and memory use. To accomplish this, we opted to distribute datasets through individual R packages. Under the hood, SeuratData uses and extends standard R functions, such as install.packages for dataset installation, available.packages for dataset listing, and data for dataset loading. SeuratData therefore serves as a more specific package manager (similar to a metapackage) for R. We provide wrappers around R's package management functions, extend them to provide relevant metadata about each dataset, and set default settings (for example, the repository where data is stored) to facilitate easy installation. Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### http://www.satijalab.org/seurat +Tools for Single Cell Genomics • Seurat Toggle navigation Seurat 5.4.0 Install Get started Vignettes Introductory vignettes PBMC 3K guided tutorial Data visualization vignette SCTransform, v2 regularization Using Seurat with multi-modal data Seurat v5 Command Cheat Sheet Data integration Introduction to scRNA-seq integration Integrative analysis in Seurat v5 Mapping and annotating query datasets Multi-assay data Dictionary Learning for cross-modality integration Weighted Nearest Neighbor Analysis Integrating scRNA-seq and scATAC-seq data Multimodal reference mapping Mixscape Vignette Massively scalable analysis Sketch-based analysis in Seurat v5 Sketch integration using a 1 million cell dataset from Parse Biosciences Map COVID PBMC datasets to a healthy reference BPCells Interaction Spatial analysis Analysis of spatial datasets (Imaging-based) Analysis of spatial datasets (Sequencing-based) Analysis of Visium HD spatial datasets Analysis of Visium HD with cell segmentations Other Cell-cycle scoring and regression Differential expression testing Demultiplexing with hashtag oligos (HTOs) Extensions FAQ News Reference Archive Seurat v5 We are excited to release Seurat v5! To install, please follow the instructions in our install page . This update brings the following new features and functionality: Integrative multimodal analysis: The cellular transcriptome is just one aspect of cellular identity, and recent technologies enable routine profiling of chromatin accessibility, histone modifications, and protein levels from single cells. In Seurat v5, we introduce ‘bridge integration’, a statistical method to integrate experiments measuring different modalities (i.e. separate scRNA-seq and scATAC-seq datasets), using a separate multiomic dataset as a molecular ‘bridge’. For example, we demonstrate how to map scATAC-seq datasets onto scRNA-seq datasets, to assist users in interpreting and annotating data from new modalities. We recognize that while the goal of matching shared cell types across datasets may be important for many problems, users may also be concerned about which method to use, or that integration could result in a loss of biological resolution. In Seurat v5, we also introduce flexible and streamlined workflows for the integration of multiple scRNA-seq datasets. This makes it easier to explore the results of different integration methods, and to compare these results to a workflow that excludes integration steps. Paper: Dictionary learning for integrative, multimodal, and scalable single-cell analysis Vignette: Streamlined integration of scRNA-seq data Vignette: Cross-modality bridge integration Website: Azimuth-ATAC, reference-mapping for scATAC-seq datasets Flexible, interactive, and highly scalable analsyis: The size and scale of single-cell sequencing datasets is rapidly increasing, outpacing even Moore’s law. In Seurat v5, we introduce new infrastructure and methods to analyze, interpret, and explore exciting datasets spanning millions of cells, even if they cannot be fully loaded into memory. We introduce support for ‘sketch’-based analysis, where representative subsamples of a large dataset are stored in-memory to enable rapid and iterative analysis - while the full dataset remains accessible via on-disk storage. We enable high-performance via the BPCells package, developed by Ben Parks in the Greenleaf Lab. The BPCells package enables high-performance analysis via innovative bit-packing compression techniques, optimized C++ code, and use of streamlined and lazy operations. Vignette: Sketch-based clustering of 1.3M brain cells (10x Genomics) Vignette: Sketch-based integration of 1M healthy and diabetic PBMC (Parse Biosciences) Vignette: Mapping 1.5M cells from multiple studies to an Azimuth reference Vignette: Interacting with BPCell matrices in Seurat v5 BPCells R Package: Scaling Single Cell Analysis to Millions of Cells Analysis of sequencing and imaging-based spatial datasets: Spatially resolved datasets are redefining our understanding of cellular interactions and the organization of human tissues. Both sequencing-based(i.e. Visium, SLIDE-seq, etc.), and imaging-based (MERFISH/Vizgen, Xenium, CosMX, etc.) technologies have unique advantages, and require tailored analytical methods and software infrastructure. In Seurat v5, we introduce flexible and diverse support for a wide variety of spatially resolved data types, and support for analytical techniqiues for scRNA-seq integration, deconvolution, and niche identification. Vignette: Analysis of spatial datasets (Sequencing-based) Vignette: Analysis of spatial datasets (Imaging-based) Backwards compatibility: While Seurat v5 introduces new functionality, we have ensured that the software is backwards-compatible with previous versions, so that users will continue to be able to re-run existing workflows. Previous versions of Seurat, such as Seurat v4, can also be installed following the instructions in our install page . Changes between v4 and v5 We have documented major changes between Seurat v4 and v5 in our News page for reference. About Seurat Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. If you use Seurat in your research, please considering citing: Hao, et al., Nature Biotechnology 2023 [Seurat v5] Hao*, Hao*, et al., Cell 2021 [Seurat v4] Stuart*, Butler*, et al., Cell 2019 [Seurat v3] Butler, et al., Nat Biotechnol 2018 [Seurat v2] Satija*, Farrell*, et al., Nat Biotechnol 2015 [Seurat v1] All methods emphasize clear, attractive, and interpretable visualizations, and were designed to be easily used by both dry-lab and wet-lab researchers. Seurat is developed and maintained by the Satija lab and is released under the MIT license. Links View on CRAN Browse source code Report a bug License Full license MIT + file LICENSE Community Code of conduct Citation Citing Seurat Developers Rahul Satija Author, maintainer Satija Lab and Collaborators Funder More about authors... Developed by Rahul Satija, Satija Lab and Collaborators. Site built with pkgdown 2.0.7. + +### https://github.com/satijalab/seurat-data +GitHub - satijalab/seurat-data: Dataset distribution for Seurat · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} satijalab / seurat-data Public Notifications You must be signed in to change notification settings Fork 46 Star 153 Code Issues 38 Pull requests 1 Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Wiki Security and quality Insights satijalab/seurat-data main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 109 Commits 109 Commits .github .github R R exec exec inst/ extdata inst/ extdata man man .Rbuildignore .Rbuildignore .gitignore .gitignore DESCRIPTION DESCRIPTION LICENSE LICENSE NAMESPACE NAMESPACE README.md README.md seurat-data.Rproj seurat-data.Rproj View all files Repository files navigation README GPL-3.0 license SeuratData SeuratData is a mechanism for distributing datasets in the form of Seurat objects using R's internal package and data management systems. It represents an easy way for users to get access to datasets that are used in the Seurat vignettes. Installation Installation of SeuratData can be accomplished through devtools devtools :: install_github( ' satijalab/seurat-data ' ) Getting Started When loading SeuratData, a list of all available datasets will be displayed (this is similar to other metapackages like tidyverse along with the version of Seurat used to create each dataset). This message can be suppressed with suppressPackageStartupMessages > library( SeuratData ) ── Installed datasets ───────────────────────────────────────────────────────────── SeuratData v0.1.0 ── ✔ cbmc 3.0.0 ✔ panc8 3.0.0 ✔ ifnb 3.0.0 ✔ pbmc3k 3.0.0 ───────────────────────────────────────────────── Key ────────────────────────────────────────────────── ✔ Dataset loaded successfully To see a manifest of all available datasets, use AvailableData ; this manifest will update as new datasets are uploaded to our data repository. > AvailableData() Dataset Version Summary species system ncells tech notes Installed InstalledVersion cbmc.SeuratData cbmc 3.0.0 scRNAseq and 13 - antibody sequencing of CBMCs human CBMC ( cord blood ) 8617 CITE - seq < NA > TRUE 3.0.0 hcabm40k.SeuratData hcabm40k 3.0.0 40 , 000 Cells From the Human Cell Atlas ICA Bone Marrow Dataset human bone marrow 40000 10x v2 < NA > FALSE 3.0.0 ifnb.SeuratData ifnb 3.0.0 IFNB - Stimulated and Control PBMCs human PBMC 13999 10x v1 < NA > TRUE 3.0.0 panc8.SeuratData panc8 3.0.0 Eight Pancreas Datasets Across Five Technologies human Pancreatic Islets 14892 SMARTSeq2 , Fluidigm C1 , CelSeq , CelSeq2 , inDrops < NA > TRUE 3.0.0 pbmc3k.SeuratData pbmc3k 3.0.0 3k PBMCs from 10X Genomics human PBMC 2700 10x v1 < NA > TRUE 3.0.0 pbmcsca.SeuratData pbmcsca 3.0.0 Broad Institute PBMC Systematic Comparative Analysis human PBMC 31021 10x v2 , 10x v3 , SMARTSeq2 , Seq - Well , inDrops , Drop - seq , CelSeq2 HCA benchmark FALSE 3.0.0 Installation of datasets can be done with InstallData ; this function will accept either a dataset name (eg. pbmc3k ) or the corresponding package name (eg. pbmc3k.SeuratData ). InstallData will automatically attach the installed dataset package so one can immediately load and use the dataset. > InstallData( " pbmc3k " ) Loading a dataset is done using the data function > data( " pbmc3k " ) > pbmc3k An object of class Seurat 13714 features across 2700 samples within 1 assay Active assay : RNA ( 13714 features ) Dataset documentation and information All datasets provided have help pages built for them. These pages are accessed using the standard help function > ? pbmc3k > ? ifnb A full command list for the steps taken to generate each dataset is present in the examples section of these help pages. Packages will also often have citation information bundled with the package. Citation information can be accessed by passing the package name , not the dataset name, to the citation function > citation( ' cbmc.SeuratData ' ) To cite the CBMC dataset , please use : Stoeckius et al. Simultaneous epitope and transcriptome measurement in single cells. Nature Methods ( 2017 ) A BibTeX entry for LaTeX users is @ Article {, author = { Marlon Stoeckius and Christoph Hafemeister and William Stephenson and Brian Houck - Loomis and Pratip K Chattopadhyay and Harold Swerdlow and Rahul Satija and Peter Smibert }, title = { Simultaneous epitope and transcriptome measurement in single cells }, journal = { Nature Methods }, year = { 2017 }, doi = { 10.1038 / nmeth.4380 }, url = { https : // www.nature.com / articles / nmeth.4380 }, } Rationale and Implementation We created SeuratData in order to distribute datasets for Seurat vignettes in as painless and reproducible a way as possible. We also wanted to give users the flexibility to selectively install and load datasets of interest, to minimize disk storage and memory use. To accomplish this, we opted to distribute datasets through individual R packages. Under the hood, SeuratData uses and extends standard R functions, such as install.packages for dataset installation, available.packages for dataset listing, and data for dataset loading. SeuratData therefore serves as a more specific package manager (similar to a metapackage) for R. We provide wrappers around R's package management functions, extend them to provide relevant metadata about each dataset, and set default settings (for example, the repository where data is stored) to facilitate easy installation. About Dataset distribution for Seurat Topics datasets single-cell single-cell-genomics Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 153 stars Watchers 8 watching Forks 46 forks Report repository Releases 2 tags Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge r-seurat-data --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +r-seurat-data 0.2.1 r43h9ee0642_0 +--------------------------------- +file name : r-seurat-data-0.2.1-r43h9ee0642_0.tar.bz2 +name : r-seurat-data +version : 0.2.1 +build : r43h9ee0642_0 +build number: 0 +size : 82 KB +license : GPL-3.0-only +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-seurat-data-0.2.1-r43h9ee0642_0.tar.bz2 +md5 : 3618bdc28aaed13168dd6f971ef1a78c +timestamp : 2024-03-15 15:55:27 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + - r-cli + - r-crayon + - r-rappdirs + + +r-seurat-data 0.2.1 r44h9ee0642_1 +--------------------------------- +file name : r-seurat-data-0.2.1-r44h9ee0642_1.tar.bz2 +name : r-seurat-data +version : 0.2.1 +build : r44h9ee0642_1 +build number: 1 +size : 83 KB +license : GPL-3.0-only +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-seurat-data-0.2.1-r44h9ee0642_1.tar.bz2 +md5 : 50cfa8ca001f7a9d2633f5cfa2f837e6 +timestamp : 2024-12-14 03:15:14 UTC +dependencies: + - r-base >=4.4,<4.5.0a0 + - r-cli + - r-crayon + - r-rappdirs + + +r-seurat-data 0.2.1 r44hdfd78af_2 +--------------------------------- +file name : r-seurat-data-0.2.1-r44hdfd78af_2.conda +name : r-seurat-data +version : 0.2.1 +build : r44hdfd78af_2 +build number: 2 +size : 77 KB +license : GPL-3.0-only +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-seurat-data-0.2.1-r44hdfd78af_2.conda +md5 : 0404b6f5e23915f1a8ed562bc9760978 +timestamp : 2025-08-22 03:04:57 UTC +dependencies: + - r-base >=4.4,<4.5.0a0 + - r-cli + - r-crayon + - r-rappdirs + + +r-seurat-data 0.2.2.9002 r44hdfd78af_0 +-------------------------------------- +file name : r-seurat-data-0.2.2.9002-r44hdfd78af_0.conda +name : r-seurat-data +version : 0.2.2.9002 +build : r44hdfd78af_0 +build number: 0 +size : 86 KB +license : GPL-3.0-only +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-seurat-data-0.2.2.9002-r44hdfd78af_0.conda +md5 : d15809d0217a318c55e82a9050d2b598 +timestamp : 2025-08-22 04:19:22 UTC +dependencies: + - r-base >=4.4,<4.5.0a0 + - r-cli + - r-crayon + - r-rappdirs + - r-seurat >=5 + - r-seuratobject >=5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-seurat-disk.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-seurat-disk.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa8812552b87b304b6a6e5300e07ed642e9d9a0f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/r-seurat-disk.manual_bundle.txt @@ -0,0 +1,107 @@ +# Tool: r-seurat-disk +software_name: r-seurat-disk +tier: T1 +domain: single_cell +downloads: 3392 +summary: The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. We also support rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy. +description: The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. We also support rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy. +dependencies: r-base >=4.4,<4.5.0a0, r-cli >=2.0.1, r-crayon >=1.3.4, r-hdf5r >=1.3.0, r-matrix >=1.2.18, r-r6 >=2.4.1, r-rlang >=0.4.4, r-seurat >=3.2.0, r-seuratobject >=4.0.0, r-stringi >=1.4.6, r-withr >=2.1.2 +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://mojaveazure.github.io/seurat-disk/ +doc_url: +dev_url: https://github.com/mojaveazure/seurat-disk + +## URL Docs Extract +### https://mojaveazure.github.io/seurat-disk/ +Interfaces for HDF5-Based Single Cell File Formats • SeuratDisk Toggle navigation SeuratDisk 0.0.0.9011 Reference Articles Conversions: h5Seurat and AnnData Saving and Loading Data from an h5Seurat File h5Seurat File Format Specification SeuratDisk v0.0.0.9011 The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. We also support rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy. Installation SeuratDisk is not currently available on CRAN. You can install it from GitHub with: if (! requireNamespace ( "remotes" , quietly = TRUE )) { install.packages ( "remotes" ) } remotes :: install_github ( "mojaveazure/seurat-disk" ) Dependencies SeuratDisk depends on the following non-standard packages: Package CRAN Webpage Source Website cli CRAN GitHub – crayon CRAN GitHub – hdf5r CRAN GitHub Website Matrix CRAN – Website R6 CRAN GitHub Website rlang CRAN GitHub Website Seurat CRAN GitHub Website withr CRAN – Website Links Browse source code at https://​github.com/​mojaveazure/​seurat-disk/​ Report a bug at https://​github.com/​mojaveazure/​seurat-disk/​issues License GPL-3 | file LICENSE Developers Paul Hoffman Author, maintainer All authors... Dev status Developed by Paul Hoffman. Site built with pkgdown 1.5.1. + +### https://github.com/mojaveazure/seurat-disk +GitHub - mojaveazure/seurat-disk: Interfaces for HDF5-based Single Cell File Formats · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} mojaveazure / seurat-disk Public Notifications You must be signed in to change notification settings Fork 60 Star 176 Code Issues 152 Pull requests 4 Security and quality 0 Insights Additional navigation options Code Issues Pull requests Security and quality Insights mojaveazure/seurat-disk master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 176 Commits 176 Commits .github .github R R docs docs man man vignettes vignettes .Rbuildignore .Rbuildignore .gitignore .gitignore DESCRIPTION DESCRIPTION LICENSE LICENSE NAMESPACE NAMESPACE README.Rmd README.Rmd README.md README.md _pkgdown.yml _pkgdown.yml View all files Repository files navigation README GPL-3.0 license SeuratDisk v0.0.0.9015 The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. We also support rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy. Installation SeuratDisk is not currently available on CRAN. You can install it from GitHub with: if ( ! requireNamespace( " remotes " , quietly = TRUE )) { install.packages( " remotes " ) } remotes :: install_github( " mojaveazure/seurat-disk " ) Dependencies SeuratDisk depends on the following non-standard packages: Package CRAN Webpage Source Website cli CRAN GitHub – crayon CRAN GitHub – hdf5r CRAN GitHub Website Matrix CRAN – Website R6 CRAN GitHub Website rlang CRAN GitHub Website Seurat CRAN GitHub Website SeuratObject CRAN GitHub Website stringi CRAN – [Website]( https://stringi.gagolewski.com/ http://site.icu-project.org/ https://www.unicode.org/ ) withr CRAN GitHub Website About Interfaces for HDF5-based Single Cell File Formats mojaveazure.github.io/seurat-disk Topics hdf5-format single-cell-genomics single-cell-rna-seq Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 176 stars Watchers 12 watching Forks 60 forks Report repository Releases No releases published Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge r-seurat-disk --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +r-seurat-disk 0.0.0.9021 r43h9ee0642_0 +-------------------------------------- +file name : r-seurat-disk-0.0.0.9021-r43h9ee0642_0.tar.bz2 +name : r-seurat-disk +version : 0.0.0.9021 +build : r43h9ee0642_0 +build number: 0 +size : 535 KB +license : GPL-3.0-only +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-seurat-disk-0.0.0.9021-r43h9ee0642_0.tar.bz2 +md5 : 227e726f63476df7571f330b843aead9 +timestamp : 2024-03-15 15:46:12 UTC +dependencies: + - r-base >=4.3,<4.4.0a0 + - r-cli >=2.0.1 + - r-crayon >=1.3.4 + - r-hdf5r >=1.3.0 + - r-matrix >=1.2.18 + - r-r6 >=2.4.1 + - r-rlang >=0.4.4 + - r-seurat >=3.2.0 + - r-seuratobject >=4.0.0 + - r-stringi >=1.4.6 + - r-withr >=2.1.2 + + +r-seurat-disk 0.0.0.9021 r44h9ee0642_1 +-------------------------------------- +file name : r-seurat-disk-0.0.0.9021-r44h9ee0642_1.tar.bz2 +name : r-seurat-disk +version : 0.0.0.9021 +build : r44h9ee0642_1 +build number: 1 +size : 543 KB +license : GPL-3.0-only +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/r-seurat-disk-0.0.0.9021-r44h9ee0642_1.tar.bz2 +md5 : fe9d4fdc96b931307feafc8686715d30 +timestamp : 2024-12-11 16:19:24 UTC +dependencies: + - r-base >=4.4,<4.5.0a0 + - r-cli >=2.0.1 + - r-crayon >=1.3.4 + - r-hdf5r >=1.3.0 + - r-matrix >=1.2.18 + - r-r6 >=2.4.1 + - r-rlang >=0.4.4 + - r-seurat >=3.2.0 + - r-seuratobject >=4.0.0 + - r-stringi >=1.4.6 + - r-withr >=2.1.2 + + +r-seurat-disk 0.0.0.9021 r44hdfd78af_2 +-------------------------------------- +file name : r-seurat-disk-0.0.0.9021-r44hdfd78af_2.conda +name : r-seurat-disk +version : 0.0.0.9021 +build : r44hdfd78af_2 +build number: 2 +size : 506 KB +license : GPL-3.0-only +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/r-seurat-disk-0.0.0.9021-r44hdfd78af_2.conda +md5 : c71e62c8fd1d274a68f98498ef912393 +timestamp : 2025-08-22 03:09:50 UTC +dependencies: + - r-base >=4.4,<4.5.0a0 + - r-cli >=2.0.1 + - r-crayon >=1.3.4 + - r-hdf5r >=1.3.0 + - r-matrix >=1.2.18 + - r-r6 >=2.4.1 + - r-rlang >=0.4.4 + - r-seurat >=3.2.0 + - r-seuratobject >=4.0.0 + - r-stringi >=1.4.6 + - r-withr >=2.1.2 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/raxml.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/raxml.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..87991602a256f688dd41ea6144b0d6b9c3795758 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/raxml.manual_bundle.txt @@ -0,0 +1,489 @@ +# Tool: raxml +software_name: raxml +tier: T1 +domain: t1_backfill_overall +downloads: 1298846 +summary: Phylogenetics - Randomized Axelerated Maximum Likelihood. +description: Phylogenetics - Randomized Axelerated Maximum Likelihood. +dependencies: libgcc >=13 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://sco.h-its.org/exelixis/web/software/raxml/index.html +doc_url: +dev_url: + +## URL Docs Extract +### http://sco.h-its.org/exelixis/web/software/raxml/index.html +The Exelixis Lab --> The Exelixis Lab --> The Exelixis Lab News Research Publications Software Teaching Talks Outreach People Jobs Contact Us The Exelixis Lab Enabling Research in Evolutionary Biology --> Download Source code Links Publication Documentation Google group GUI Web services Helper scripts RAxML - Randomized Axelerated Maximum Likelihood New RAxML citation When using RAxML please cite the following paper: A. Stamatakis: "RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies". In Bioinformatics , 2014, open access . Latest code download Get the most up-to-date RAxML version from github . Documentation new RAxML version 8.0.0 manual PDF copy of the old v704 manual: PDF For a basic step by step tutorial using some more recent features see RAxML step-by-step tutorial For a basic step by step tutorial by Pavlos Pavlidis on how to install and run RAxML on a Linux cluster see RAxML on cluster step-by-step tutorial For a video explaining the evolutionary placement algorithm for short reads see Alexis talking about evolutionary placement of short reads Video of Alexis talking about evolutionary placement of short reads at the Joint Genome Institute Some nice slides by Wayne Pfeiffer (SDSC) on the hybrid MPI/Pthreads version of RAxML and the hybrid MPI/OpenMP version of MrBayes some useful slides by Nick Pattengale explaining the bootstrap convergence criteria implemented in RAxML Antonis Rokas has written a nice chapter about hands-on phylogeny reconstruction that uses RAxML as example program A tutorial on how to install and run RAxML on a MAC in less than a minute by Dave Carmean User Support Please send all your questions and feature request to the RAxML google group . Before posting, keep in mind that a google group actually has a search function! Emails to Exelixis lab members regarding RAxML will not be answered. Messages posted via github will also not be answered. RAxML memory requirements Since datasets are getting larger here is a formula to estimate RAxML memory requirements: Given an alignment of n taxa and m distinct patterns the memory consumption is approximately: MEM(AA+GAMMA) = (n-2) * m * (80 * 8) bytes MEM(AA+CAT) = (n-2) * m * (20 * 8) bytes MEM(DNA+GAMMA) = (n-2) * m * (16 * 8) bytes MEM(DNA+CAT) = (n-2) * m * (4 * 8) bytes To convert bytes to MB or GB you can use this on-line converter You may also use th on-line calculator below: taxa (n): pattern (m): AA+GAMMA AA+CAT DNA+GAMMA DNA+CAT Required size: (n-2) * m * (x * 8) bytes = MEM Web-Servers for evolutionary placement of short reads Web-Servers for phylogenetic placement of short sequence reads (including alignment and visualization tools): advanced Swiss Server with pre-computed trees, please cite this paper when using it basic German Server without pre-computed trees, please cite this paper when using it Web-Servers for tree building co-maintaned by Exelixis Lab: Vital IT unit of the Swiss Institute of Bioinformatics CIPRES portal at San Diego Supercomputer Center New beta-versio n of the CIPRES portal that provides a full workbench. I recently found this youtube video (in Spanish) with a nice tutorial on how to use the CIPRES portal: not maintained by the Exelixis Lab: Bioportal in Norway (University of Oslo) Trex on-line Web-Server at  Université du Québec à Montréal Graphical User Interfaces (GUIs) Daniele Silvestro and Ingo Michalak at the Senckenberg Museum and Research Center have started developing a GUI for RAxML that runs under MACs, Windows, and Linux. The code for the GUI is available here . Please send suggestions and comments to Daniele Silvestro at senckenberg de Jacek Kominek from the University of Gdansk in Poland has developed this nice GUI here Helper Scripts and Tools Phylogenetic Binning tool Phylogenetic binning tool for paper on "Morphology-based phylogenetic binning of the lichen genera Allographa and Graphis via molecular site wieght calibration" by Simon Berger available for download  here tech report PDF and paper File Conversion scripts shell script by Andre Aberer for fasta to phylip conversion matlab programs by Lowie Li for fasta to phylip and phylip to fasta conversion Wrapper Scripts Apurva Narechania at the American Museum of Natural history has kindly put togetehr a couple of wrapper scripts for RAxML :-) raxml_launch_serially.sh : A simple shell script that launches one job after the other awaiting for completion of each job. raxml_nexusPartConvert.pl: A Perl script that parses a partitioned alignment in Nexus format with charsets and produces a partition guide file to be fed to RAxML with -q. Preliminary - works with DNA or AA, but not the two together yet, so not suitable for mixed-molecule data. Unless the output gets redirected to a file with ">", it will appear on screen. raxml_wrapper.pl : A Perl script that reads a raxml.config file with common run parameters and executes a directory of Phylip alignment files in batch, then outputs the results in another directory. See the documentation with "perldoc ./raxml_wrapper.pl". Guy Leonard at Exeter has updated his wrapper environment called easyRax Alexis has developed a couple of perls scripts A  perl script for computing bootstrap branch lengths with RAxML. This script can be used to perform the following task with RAxML: Given a best-known ML tree, generate a number of Bootstrap replicates and just re-estimate the branch lengths for that given fixed tree topology on each Bootstrap replicate. To invoke the script call it as follows: "perl bsBranchLengths.pl alignmentFileName treeFileName numberOfReplicates".   The script assumes that the RAxML executable is located in the directory where you execute it. Otherwise, if RAxML is located in your Linux/Unix path just replace every occurence of "./raxmlHPC" by "raxmlHPC" in the script. The bootstrapped trees with branch lengths will be written into a file called "bsTrees" .  This script is intended for use with programs that infer divergence time estimates. A perl script for finding the best protein substitution model Here is a little perl-script that will automatically determine the best-scoring AA substitution model on a fixed starting tree.  Note that raxmlHPC must be in your $PATH for this to work. For unpartitioned datasets execute it like this: perl ProteinModelSelection.pl alignmentFile.phylip > outfile The outfile will then contain the best-scoring AA model to use with RAxML. For partitioned datasets execute it like this: perl ProteinModelSelection.pl alignmentFile.phylip partitionData.txt > outfile The outfile will then contain the best-scoring AA model for every partition. James Munro has written a  Guide to install RAxML on MACs Olaf Bininda-Emonds has written  batchRAxML.pl . This nice script by my good colleague from Munich times Olaf Bininda-Emonds provides a wrapper around RAxML to easily analyze a set of data files according to a common set of the search criteria. Also organizes the RAxML output into a set of subdirectories. Frank Kauff has written  PYRAXML2 . Frank Kauff at University of Kaiserslautern (formerly at Duke University) has written this cool script that reads NEXUS-style data files and prepares the necessary input files and command-line options for RAxML-VI-HPC. You can download the BETA-version here: PYRAXML2 It requires PYTHON and BIOPYTHON to be installed on your computer. Old RAxML code versions RAxML v7.2.8 alpha release source code available here RAxML v7.2.7 (alpha) available for download here RAxML v7.2.6 available for download here and here is a windows executable RAxML v7.2.5 (alpha) available for download here and here is a windows executable RAxML v7.2.4(alpha) available for download here RAxML v7.2.3 (alpha) available for download here RAxML v7.2.2 available for download here and download windows executable RAxML v7.2.1 (alpha) available for download here windows executable here RAxML v7.2.0 (alpha) available for download here RAxML v7.1.0 (alpha) available for download here RAxML v7.0.4 available for download here RAxML v7.0.3 available for download here Windows executable. Graham Jones has provided a nice PDF on How to run RAxML under XP and Vista. Mac executable (iMAC) Mac executable (iMAC Pthreads-version) Mac executable (PowerMac G5) Mac executable (PowerMac G5 Pthreads-version) RAxML-VI-HPC (version 2.2.3) and a comprehensive Manual (v2.2.3) RAxML-VI-HPC (version 2.0.2) and a comprehensive Manual (v2.0) RAxML-VI-HPC (version 1.0) and a comprehensive Manual (v1.0) RAxML-VI: Sequential program with significantly accelerated hill-climbing search algorithm for huge alignment data. RAxML-III: Sequential program, includes more models of nucleotide substitution than RAxML-II. RAxML-II: Sequential, Parallel, and Distributed implementation of RAxML with less model functionality. On-line material for some old RAxML papers Material (alignments) for 2008 Systematic Biology paper on the rapid bootstrap algorithm test datasets available here Material (test datasets) for 2007 Supercomputing paper on parallelizing RAxML on the IBM BlueGene/L test datasets available here Material for HICOMB2006 paper: "Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective" Click here for a table with the experimental raw data Material for HPCC05 paper: “Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood” Initial and final optimization phase of RAxML for an alignment with 150 sequences Program Flow of P-Rec-I-DCM-3(RAxML) Speedup value: Time to complete one iteration of P-Rec-I-DCM3 for datasets 1-5 and 1 up to 16 processors Material on RAxML-VI performance: 1,000 taxa plot alignment Alignment of 1,000 sequences from the ARB database containing Eucarya, Bacteria, Archaea by Harald Meier, TU München 1,497 taxa plot Alignment of 1,497 Bacteria by Josh Wilcox, Pace Lab, University of Colorado at Boulder, for more information on this alignment please contact the Pace Lab 1,663 taxa plot alignment Alignment of 1,663 sequences from the ARB database containing Eucarya, Bacteria, Archaea by Harald Meier, TU München 1,728 taxa plot alignment  Alignment of 1,728 Archaea by Chuck Robertson, Pace Lab, University of Colorado at Boulder 2,000 taxa plot alignment  Ribosomal RNA sequences by Gutell Lab, University of Texas at Austin, for more information on this alignment please contact Robin Gutell 2,560 taxa plot alignment upon request via email Kallersjo, M., et al., Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants. Pl. Syst. Evol., 1998. 213: p. 259-287. 4,114 taxa plot alignment  16S ribosomal Actinobacteria RNA sequences, by Usman Roshan, New Jersey Institute of Technology 6,722 taxa plot alignment Ribosomal RNA sequences by Gutell Lab, University of Texas at Austin, for more information on this alignment please contact Robin Gutell 7,769 taxa plot alignment  Ribosomal RNA sequences by Gutell Lab, University of Texas at Austin, for more information on this alignment please contact Robin Gutell 8,780 taxa plot alignment  Alignment of 8,780 sequences from the ARB database containing Eucarya, Bacteria, Archaea . Original alignment by Harald Meier, TU München, modified by Usman Roshan, New Jersey Institute of Technology 25,057 taxa plot alignment  Alignment of 25,057 Protobacteria, by Usman Roshan, New Jersey Institute of Technology Old Alignment Benchmark Set The old Alignment Benchmark set : includes some large real-world alignments and best-known trees for those alignments © The Exelixis Lab 2013 | Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg Privacy Imprint + +## Conda Search Info +$ conda search -c bioconda -c conda-forge raxml --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +raxml 7.3.0 0 +------------- +file name : raxml-7.3.0-0.tar.bz2 +name : raxml +version : 7.3.0 +build : 0 +build number: 0 +size : 444 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-7.3.0-0.tar.bz2 +md5 : 1b895af793826268930ed36cc3d40bd0 +dependencies: [] + + +raxml 7.3.0 1 +------------- +file name : raxml-7.3.0-1.tar.bz2 +name : raxml +version : 7.3.0 +build : 1 +build number: 1 +size : 447 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-7.3.0-1.tar.bz2 +md5 : fe7855f14d14b8bfc11027817da18e35 +timestamp : 2018-06-22 16:10:05 UTC +dependencies: [] + + +raxml 8.2.4 0 +------------- +file name : raxml-8.2.4-0.tar.bz2 +name : raxml +version : 8.2.4 +build : 0 +build number: 0 +size : 531 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.4-0.tar.bz2 +md5 : a28159fc9c4a1470dd11e0c33da0eaed +dependencies: [] + + +raxml 8.2.4 1 +------------- +file name : raxml-8.2.4-1.tar.bz2 +name : raxml +version : 8.2.4 +build : 1 +build number: 1 +size : 1.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.4-1.tar.bz2 +md5 : 2ce9ad4ff11bb7d1d9ae3f642ad89e2f +dependencies: [] + + +raxml 8.2.4 h031d066_7 +---------------------- +file name : raxml-8.2.4-h031d066_7.tar.bz2 +name : raxml +version : 8.2.4 +build : h031d066_7 +build number: 7 +size : 3.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.4-h031d066_7.tar.bz2 +md5 : 49f790ac4c63de535eadbe70e36c7fb9 +timestamp : 2023-05-15 21:27:22 UTC +dependencies: + - libgcc-ng >=12 + + +raxml 8.2.4 h470a237_2 +---------------------- +file name : raxml-8.2.4-h470a237_2.tar.bz2 +name : raxml +version : 8.2.4 +build : h470a237_2 +build number: 2 +size : 3.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.4-h470a237_2.tar.bz2 +md5 : d675daffca360e04c0d8b30e1b15a0f7 +timestamp : 2018-06-22 16:14:51 UTC +dependencies: + - libgcc-ng >=4.9 + + +raxml 8.2.4 h516909a_3 +---------------------- +file name : raxml-8.2.4-h516909a_3.tar.bz2 +name : raxml +version : 8.2.4 +build : h516909a_3 +build number: 3 +size : 3.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.4-h516909a_3.tar.bz2 +md5 : 1caab7e2de1261e0e85967a0081b388e +timestamp : 2020-07-13 21:49:01 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +raxml 8.2.4 h779adbc_4 +---------------------- +file name : raxml-8.2.4-h779adbc_4.tar.bz2 +name : raxml +version : 8.2.4 +build : h779adbc_4 +build number: 4 +size : 3.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.4-h779adbc_4.tar.bz2 +md5 : 01fbda62eeed6386b5679d6a5520cec7 +timestamp : 2021-03-25 11:11:54 UTC +dependencies: + - libgcc-ng >=9.3.0 + + +raxml 8.2.4 h7b50bb2_8 +---------------------- +file name : raxml-8.2.4-h7b50bb2_8.tar.bz2 +name : raxml +version : 8.2.4 +build : h7b50bb2_8 +build number: 8 +size : 3.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.4-h7b50bb2_8.tar.bz2 +md5 : a6020c5c88ea286271ddc9913fcd4ea7 +timestamp : 2024-12-11 17:15:30 UTC +dependencies: + - libgcc >=13 + + +raxml 8.2.4 hec16e2b_5 +---------------------- +file name : raxml-8.2.4-hec16e2b_5.tar.bz2 +name : raxml +version : 8.2.4 +build : hec16e2b_5 +build number: 5 +size : 3.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.4-hec16e2b_5.tar.bz2 +md5 : b950b352be31adc278515dd8eba6f2b7 +timestamp : 2022-02-23 01:43:33 UTC +dependencies: + - libgcc-ng >=10.3.0 + + +raxml 8.2.4 hec16e2b_6 +---------------------- +file name : raxml-8.2.4-hec16e2b_6.tar.bz2 +name : raxml +version : 8.2.4 +build : hec16e2b_6 +build number: 6 +size : 3.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.4-hec16e2b_6.tar.bz2 +md5 : 5c73c4492b8821344204c13fe72e1275 +timestamp : 2023-05-11 13:11:42 UTC +dependencies: + - libgcc-ng >=12 + + +raxml 8.2.9 0 +------------- +file name : raxml-8.2.9-0.tar.bz2 +name : raxml +version : 8.2.9 +build : 0 +build number: 0 +size : 2.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.9-0.tar.bz2 +md5 : 0374f882845d46e4cd75c0ce52d4019e +dependencies: + - libgcc + + +raxml 8.2.9 1 +------------- +file name : raxml-8.2.9-1.tar.bz2 +name : raxml +version : 8.2.9 +build : 1 +build number: 1 +size : 2.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.9-1.tar.bz2 +md5 : 31153e6329193edd0fa494364cf5f6b1 +dependencies: + - libgcc + + +raxml 8.2.9 h031d066_7 +---------------------- +file name : raxml-8.2.9-h031d066_7.tar.bz2 +name : raxml +version : 8.2.9 +build : h031d066_7 +build number: 7 +size : 2.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.9-h031d066_7.tar.bz2 +md5 : 8dfa0633c2beea0d0b3b058846b353b1 +timestamp : 2023-05-15 21:35:07 UTC +dependencies: + - libgcc-ng >=12 + + +raxml 8.2.9 h470a237_2 +---------------------- +file name : raxml-8.2.9-h470a237_2.tar.bz2 +name : raxml +version : 8.2.9 +build : h470a237_2 +build number: 2 +size : 2.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.9-h470a237_2.tar.bz2 +md5 : a6194052e4e4e690c280196580f4388f +timestamp : 2018-06-22 16:06:51 UTC +dependencies: + - libgcc-ng >=4.9 + + +raxml 8.2.9 h516909a_3 +---------------------- +file name : raxml-8.2.9-h516909a_3.tar.bz2 +name : raxml +version : 8.2.9 +build : h516909a_3 +build number: 3 +size : 2.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.9-h516909a_3.tar.bz2 +md5 : 9734fcfe7b4bbf05894141b3d67f3327 +timestamp : 2020-07-13 21:55:19 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +raxml 8.2.9 h779adbc_4 +---------------------- +file name : raxml-8.2.9-h779adbc_4.tar.bz2 +name : raxml +version : 8.2.9 +build : h779adbc_4 +build number: 4 +size : 2.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.9-h779adbc_4.tar.bz2 +md5 : ce7973a8a07943a19231d91f52fd236b +timestamp : 2021-03-25 11:02:31 UTC +dependencies: + - libgcc-ng >=9.3.0 + + +raxml 8.2.9 h7b50bb2_8 +---------------------- +file name : raxml-8.2.9-h7b50bb2_8.tar.bz2 +name : raxml +version : 8.2.9 +build : h7b50bb2_8 +build number: 8 +size : 2.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.9-h7b50bb2_8.tar.bz2 +md5 : f8c3e0374555471ab0607434225cf929 +timestamp : 2024-12-11 17:19:45 UTC +dependencies: + - libgcc >=13 + + +raxml 8.2.9 hec16e2b_5 +---------------------- +file name : raxml-8.2.9-hec16e2b_5.tar.bz2 +name : raxml +version : 8.2.9 +build : hec16e2b_5 +build number: 5 +size : 2.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.9-hec16e2b_5.tar.bz2 +md5 : b0b250a0d534fe0373971d03a0cbaaee +timestamp : 2022-02-23 13:49:23 UTC +dependencies: + - libgcc-ng >=10.3.0 + + +raxml 8.2.9 hec16e2b_6 +---------------------- +file name : raxml-8.2.9-hec16e2b_6.tar.bz2 +name : raxml +version : 8.2.9 +build : hec16e2b_6 +build number: 6 +size : 2.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.9-hec16e2b_6.tar.bz2 +md5 : c7e4081d1afdb0a07df2b229f80e6c01 +timestamp : 2023-05-11 12:52:29 UTC +dependencies: + - libgcc-ng >=12 + + +raxml 8.2.10 0 +-------------- +file name : raxml-8.2.10-0.tar.bz2 +name : raxml +version : 8.2.10 +build : 0 +build number: 0 +size : 3.2 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.10-0.tar.bz2 +md5 : 70e6208c15a0167b0db5679e0f33729a +dependencies: + - libgcc + + +raxml 8.2.10 h470a237_1 +----------------------- +file name : raxml-8.2.10-h470a237_1.tar.bz2 +name : raxml +version : 8.2.10 +build : h470a237_1 +build number: 1 +size : 3.2 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.10-h470a237_1.tar.bz2 +md5 : ae6db3b7d22934be329db914c390b2c6 +timestamp : 2018-06-22 16:19:49 UTC +dependencies: + - libgcc-ng >=4.9 + + +raxml 8.2.12 h031d066_6 +----------------------- +file name : raxml-8.2.12-h031d066_6.tar.bz2 +name : raxml +version : 8.2.12 +build : h031d066_6 +build number: 6 +size : 3.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.12-h031d066_6.tar.bz2 +md5 : ca41d971127e5d6fce1bd1ff4a8fde63 +timestamp : 2023-05-15 21:43:38 UTC +dependencies: + - libgcc-ng >=12 + + +raxml 8.2.12 h14c3975_1 +----------------------- +file name : raxml-8.2.12-h14c3975_1.tar.bz2 +name : raxml +version : 8.2.12 +build : h14c3975_1 +build number: 1 +size : 3.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.12-h14c3975_1.tar.bz2 +md5 : 2a6dd9242c1b644dbe4a977c96a58840 +timestamp : 2019-04-24 03:02:29 UTC +dependencies: + - libgcc-ng >=7.3.0 + + +raxml 8.2.12 h470a237_0 +----------------------- +file name : raxml-8.2.12-h470a237_0.tar.bz2 +name : raxml +version : 8.2.12 +build : h470a237_0 +build number: 0 +size : 3.2 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.12-h470a237_0.tar.bz2 +md5 : bc2029694866d6411082f72f0a32f4bc +timestamp : 2018-10-24 23:26:38 UTC +dependencies: + - libgcc-ng >=4.9 + + +raxml 8.2.12 h516909a_2 +----------------------- +file name : raxml-8.2.12-h516909a_2.tar.bz2 +name : raxml +version : 8.2.12 +build : h516909a_2 +build number: 2 +size : 3.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.12-h516909a_2.tar.bz2 +md5 : 88daa254ffd3e01d09aa7120e1846b26 +timestamp : 2020-07-03 04:06:53 UTC +dependencies: + - libgcc-ng >=7.5.0 + + +raxml 8.2.12 h779adbc_3 +----------------------- +file name : raxml-8.2.12-h779adbc_3.tar.bz2 +name : raxml +version : 8.2.12 +build : h779adbc_3 +build number: 3 +size : 3.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.12-h779adbc_3.tar.bz2 +md5 : 91eb90712fc90103a79abd08ff65d054 +timestamp : 2021-03-25 10:54:02 UTC +dependencies: + - libgcc-ng >=9.3.0 + + +raxml 8.2.12 hec16e2b_4 +----------------------- +file name : raxml-8.2.12-hec16e2b_4.tar.bz2 +name : raxml +version : 8.2.12 +build : hec16e2b_4 +build number: 4 +size : 3.1 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/raxml-8.2.12-hec16e2b_4.tar.bz2 +md5 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/repeatmasker.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/repeatmasker.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..36db8fc1355c8b12ef1dcc3a8597090229b7cef8 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/repeatmasker.manual_bundle.txt @@ -0,0 +1,471 @@ +# Tool: repeatmasker +software_name: repeatmasker +tier: T1 +domain: t1_backfill_overall +downloads: 130928 +summary: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. +description: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. +dependencies: h5py, hmmer, perl >=5.32.1,<6.0a0 *_perl5, rmblast, trf, wget +execution_environment: Other +execution_environment_reason: fallback runtime classification + +## URLs +home_url: https://www.repeatmasker.org/RepeatMasker +doc_url: https://www.repeatmasker.org/RepeatMasker +dev_url: https://github.com/Dfam-consortium/RepeatMasker + +## URL Docs Extract +### https://www.repeatmasker.org/RepeatMasker +Download Page RepeatMasker Download Prerequisites Unix system with perl 5.8.0 or higher installed Python 3 and the h5py python library. See https://docs.h5py.org/en/latest/build.html for installation instructions. Sequence Search Engine RepeatMasker uses a sequence search engine to perform it's search for repeats. Currently Cross_Match, RMBlast and WUBlast/ABBlast are supported. You will need to obtain one or the other of these and install them on your system. For Cross_Match go to http://www.phrap.org You will want to select "Phred/Phrap/Consed" as Cross_Match is part of the Phrap package. For RMBlast ( NCBI Blast modified for use with RepeatMasker/RepeatModeler ) please go to our download page: http://www.repeatmasker.org/rmblast . It is highly recommended to use 2.13.0 or higher. For HMMER please download the v3.2.1 version here: http://hmmer.org/ For ABBlast/WUBlast go to [ NOTE: Rights to BLAST 2.0 (WU-BLAST) have been acquired by Advanced Biocomputing, LLC. http://blast.advbiocomp.com/licensing/ RepeatMasker 3.2.8 and above fully support both variants ] TRF - Tandem Repeat Finder, G. Benson et al. You can obtain a free copy at http://tandem.bu.edu/trf/trf.html or https://github.com/Benson-Genomics-Lab/TRF . RepeatMasker was developed using TRF version 4.0.9 Repeat Database RepeatMasker can be used with custom libraries, or with Dfam out of the box. Dfam is an open database of transposable element (TE) profile HMM models and consensus sequences. The current release of RepeatMasker is shipped without a TE database, however libraries in FamDB H5 format may be downloaded from Dfam at: https://www.dfam.org/releases/current/families/FamDB and installed in the Libraries/famdb directory. The files are divided by taxa groups and numbered starting from '0' ( aka the root partition ) which contains required information for RepeatMasker/FamDB. In addition the last Repbase RepeatMasker Edition may be downloaded and combined with Dfam. The RepBase RepeatMasker Library can be obtained at: http://www.girinst.org . Installation Download RepeatMasker Latest Released Version: 12/17/25: RepeatMasker-4.2.3.tar.gz Previous Released Version: 10/3/25: RepeatMasker-4.2.2.tar.gz Unpack Distribution Unpack the distribution in your home directory or in a location where it may be shared with other users of your system ( ie. /usr/local/ ). Make sure you do not extract in a directory already containing a pre-existing directory called "RepeatMasker" as it will attempt to overwrite files contained within. cp RepeatMasker-open-4-#-#.tar.gz /usr/local cd /usr/local gunzip RepeatMasker-open-4-#-#.tar.gz tar xvf RepeatMasker-open-4-#-#.tar Install RepeatMasker Libraries RepeatMasker is currently not distributed with a database. The program may be used immediately with custom databases ("-lib mylib.fa" option) or you may download TE libraries and configure them for use with RepeatMasker. There are three options for supplementing/updating the main RepeatMasker library: The Dfam database may be downloaded from www.dfam.org in famdb HDF5 format partitioned by taxa . The root ("dfam##_full.0.h5") partition is required if you plan to use Dfam, however any combination of additional partitions may also be downloaded and configured. For example: wget https://www.dfam.org/releases/Dfam_3.9/families/FamDB/dfam39_full.1.h5.gz gunzip dfam39_full.1.h5.gz mv dfam39_full.1.h5 /usr/local/RepeatMasker/Libraries/famdb NOTE: Only partitions from the same Dfam release should be in this directory. Repeat for any additional partitions you wish to use. A list of partions and the taxa they contain can be found here . and/or: The RepBase RepeatMasker Edition ( final version 10/26/2018 ) may be downloaded from www.girinst.org and unpaked in the RepeatMasker directory. For example: cp RepBaseRepeatMaskerEdition-20181026.tar.gz /usr/local/RepeatMasker/ cd /usr/local/RepeatMasker gunzip RepBaseRepeatMaskerEdition-20181026.tar.gz tar xvf RepBaseRepeatMaskerEdition-20181026.tar rm RepBaseRepeatMaskerEdition-20181026.tar Run Configure Script The program requires some initial configuration. This should also be re-run after updates to the library files. cd /usr/local/RepeatMasker perl ./configure RepeatMasker "open-3.0/4.0" is licensed under the Open Source License v2.1 . Release Notes RepeatMasker-4.2.3 BUGFIX: Since the 4.1.1 release the staged approach to searching TE families has not been applied species in the 'rodentia' order due to a flag being set incorrectly. While this doesn't prohibit families from being annotated, it does decrease the sensitivity of the search. This release fixes this issue. This problem did not impact any other orders. Feature Request: Added support for BGZIP files by changing the method used to process compressed files. Instead of uncompressing input files in-place, the program now leaves the original compressed file intact. RepeatMasker-4.2.2 BUGFIX: In the 4.2.1 release a bug was introduced that impacted the handling of poly-A tails and the naming of LINE annotations. While the overall masking level remained the same, the change caused some previously hidden and overlapping annotations to appear with invalid query ranges ( query start > query end ). (github #362) Added support for '+' symbol in input filenames. (github #365) RepeatMasker-4.2.1 BUGFIX: An infinite loop was possible in rare circumstances involoving interleaved satellite consensi while using the "-a" option. This caused the alignment file to keep growing and eventually ProcessRepeats to crash. BUGFIX: Fix a one-off issue in alignment range calculations induced by the clipping mechanism in RepeatMasker. BUGFIX: The configure script was crashing while attempting to import Repbase in the previous version. Updated to the latest famdb version (2.0.5) Crossmatch alignment format parser hardening. While not proper, negative coordinates can appear in the alignment file due to incorrect range calculations. This change allows for the parser to handle these cases and not mis-align the data columns. Updated the length of the Charlie7 family in RepeatAnnotationData.pm RepeatMasker-4.2.0 BUGFIX: For mammalian genomes searched using the "-species" option, newer Dfam families without search stages, or with the "-uncurated" flag Dfam DR families were not being included in the search. BUGFIX: RepeatMasker exits with an error code if no repetitive sequences were found in the input file. BUGFIX: famdb.py was not reporting the correct counts for families ancestral to the query term. RepeatMasker uses this count and therefore was also reporting an incorrect value. Remove duplicate families when attempting to merge Repbase RepeatMaskerEdition into FamDB. The configure utility was not using the -libdir path when creating the RepeatMasker.lib file. (github #344) RepeatMasker-4.1.9 BUGFIX: When the RepeatMasker adjudicator (ProcessRepeats) is faced with a huge number of overlapping and redundant alignments the joining can go awry, creating a infinite loop. The effect is that ProcessRepeats never completes. BUGFIX: When using nhmmer/pHMMs and a non-species-level "-species" parameters (e.g. "-species mammals"), RepeatMasker was using an exteremly permissive per-family score cutoff. This overwhelmed ProcessRepeats with many low-scoring alignments. BUGFIX: ProcessRepeats dies around line 8190 with a "Division by zero" error. BUGFIX: Fixed call to famdb for buildSummary.pl in the -species option. Updated documentation. Updated repeatmasker.help. RepeatMasker-4.1.8 Fixed table format for non-mammals. The "Retroelements" heading didn't include Penelope elements ( "PLE/" ) in it's tabulation. ProcessRepeats - A major change in how annotations are processed to reduce PR's memory footprint. Instead of loading all anntations in memory, they are now streamed and processed a sequence at a time. For chromosomal assemblies this reduced the memory footprint to the size of the largest chromosome, instead of the whole genome. Fixed a bug that caused general/is.lib to be left in a unfrozen state for rmblastn. Updated to FamDB 2.0.0 RepeatMasker-4.1.7-p1 This is a critical fix to the 4.1.7 release. The -species option was not being interpreted correctly by RepeatMasker/ProcessRepeats. The most obvious change for mammals/primates was that the output format (*.tbl file) looked different than it had before. Under the hood this also changed the way some species were handled in the library searches. RepeatMasker-4.1.7 Handle the case were the default search engine is not configured and require the user to provide it using -e/-engine. Use the global alignment bandwidth simulation for the refinement step. Allow for minimal database install and warn when used with -species. Fixed a bug on configure with setting the default search engine when only one search engine is configured. RepeatProteinMask wasn't obtaining the correct search engine if configure didn't set it up correctly. FamDB wasn't exporting RepeatMasker.lib with class-name suffixes. This had an impact on the RepeatModeler/RepeatClassifier package but not on RepeatMasker itself. Upgraded to FamDB 1.0.5 Fixed an issue with parsing RepBase. Some records were not being parsed correctly for records that do not include the keyword "repbase" following the identifier. New semantantics for NCBIBlastSearchEngine bandwidth interpretation. Fixed a divide-by-zero error in ProcessRepeat's merging of DNA tranpsoson overlapping fragments. FamDB fixed inconsistency between curated/uncurated counts vs exports. RepeatMasker-4.1.6 Upgraded to FamDB 1.0.2 to support Dfam 3.8 and the new partitioned database format. Added Libraries/RMRB_spec_to_tax.json to project. This maps the RepBase taxanames to current NCBI tax_ids and needs to be refreshed with each new Dfam release. Added softmasking support to NCBIBlastSearchEngine.pm. Added new '--uncurated' flag to handle single export Dfam format. If this flag is used the CONS/HMM cached directories will be suffixed with "_wunc". Fixed sunk error messages from famdb.py. Now they will be displayed and cause RepeatMasker to quit. Additional library setup steps and error checking for configure utility. CAF documentation in SearchResult. calcDivergenceFromAlign clarified use of "-a" in documentation. RepeatMasker-4.1.5 Updated codebase for Dfam 3.7 compatibility (famdb format 4.3). Penelope classification change caused *.tbl file accounting to place them in the Unknown category. Also fixed landscape generation tool. Added a new utility to merge *.out *.align files generated by running RepeatMasker serially. Repbase metadata was out-of-date, updated species names so that they match the current NCBI Taxonomy names. Fixed an issue with the HMM parser. It wasn't recognizing negative values for Tau with models that do not have GA thresholds. RepeatMasker-4.1.4 Added support for RMBlast 2.13.0. Release of the TE genome browser visualization (UCSC) and trackhub generation tool. New CpGSites and unadjusted Kimura stats in the *.align file. Fixed a bug that caused the read-only state of the input fasta file to propogate to the intermediate files and cause the program to exit. Removed DateRepeats as it's based on old library formats - this functionality will return with the refactored version of RM in the works. RepeatMasker-4.1.3-p1 A recent change in 4.1.3 to correct blank fragment ID fields can in rare cases causing the error message: 'Can't call method "setLeftLinkedHit"'. The RepeatAnnotationData.pm file containing necessary information for recognizing equivalent fragments of DNA transposons was missing data. The MULE-MuDR class was added to the *.tbl file for "-lib" searches. RepeatMasker-4.1.3 A new utility for generating trackHubs for our new UCSC TE visualization Fix a bug where killing RM while starting up can leave the cached libraries in an inconsistent state. Fixed a bug where in rare cases the joined fragment ID field is blank Merged in changes to Dupmasker supporting multi-threaded use Fixed legacy RepBase taxonomic labels Added support for GFF v3 output and fixed the utility/rmOutToGFF3.pl RepeatMasker-4.1.2-p1 Releases 4.1.1-4.1.2 contained a bug with the processing of Alu sequences in primates. The step where an initial annotation is refined into a particular Alu subfamily was not performed and the annotations remained labeled with the initial capture sequence ( AluJb, AluSx, or AluY ). This patch release fixes this one issue. RepeatMasker-4.1.2 Fixed 21 protein family classifications in RepeatProteinLib. Fixed a problem with the generation of the RepeatMasker.lib file for use by RepeatModeler. In release 4.1.1 it did not add the classification info to this auxilary file. Fixed a "log(0)" error that can cause the program to fault in rare circumstances. buildSummary now supports FamDB and has improved documentation. Bugfixes and improvements to FamDB. RepeatMasker-4.1.1 Dfam (starting with version 3.2) is now distributed in the FamDB file format based on HDF5, which has improved support for large datasets compared to the EMBL and HMM formats that were previously used. RepeatMasker therefore includes a copy of famdb.py, and depends on the python package h5py . The 'configure' script and other parts of RepeatMasker have been updated to accomodate these changes. The utilities 'queryTaxonomyDatabase.pl' and 'queryRepeatDatabase.pl' are no longer included, since that data is now included in FamDB. The 'famdb.py' tool can be used to make many of the same queries as the removed utilies, and even more. RepeatMasker-4.1.0 RepeatMasker now has a refactored configuration system making it easier to distribute RepeatMasker via package managers and/or bundle RepeatMasker into containers. RepeatMasker-open-4-0-9-p1 Input files containing multiple FASTA sequences caused RepeatMasker to error out with a message like: "WARNING: TRF returned an error (Return code = ### ) TRF parameters: 2.7.7.80.10.50.10 A search phase could not complete on this batch. The batch file will be re-run and if possible the program will resume. WARNING: Retrying batch ( 1 ) [ 255,, 195]..." This bug was introduced when we attempted to improve TRF error catching. Unfortunatly the return codes are not documented for TRF and the assumption that 256 is the only successful return code is wrong. The "success" code appears to change depending on the number of sequences in the file. The workaround is to fail only if there is a message in the error output file. RepeatMasker-open-4-0-9 General compatibility update for Dfam 3.0. Dfam and Dfam_consensus have merged into one combined database. RepeatMasker can use Dfam using any of it search engines and will automatically switch to using consensus sequences or profile HMMs based on the engine used. It is important to note that, by default RepeatMasker will use Dfam consensus sequences when library duplicates are detected. Bugfix: The -dir option no longer assumes that the directory already exists. Feature: The configure script now accepts command-line parameters to change configuration settings. Configure also re-reads existing configuration options to use as prompt defaults. Archived Releases RepeatMasker-4.2.1.tar.gz RepeatMasker-4.2.0.tar.gz RepeatMasker-4.1.9.tar.gz RepeatMasker-4.1.8.tar.gz RepeatMasker-4.1.7-p1.tar.gz RepeatMasker-4.1.6.tar.gz RepeatMasker-4.1.5.tar.gz Institute for Systems Biology This server is made possible by funding from the National Human Genome Research Institute (NIGRI grant # RO1 HG002939). + +### https://www.repeatmasker.org/RepeatMasker +Download Page RepeatMasker Download Prerequisites Unix system with perl 5.8.0 or higher installed Python 3 and the h5py python library. See https://docs.h5py.org/en/latest/build.html for installation instructions. Sequence Search Engine RepeatMasker uses a sequence search engine to perform it's search for repeats. Currently Cross_Match, RMBlast and WUBlast/ABBlast are supported. You will need to obtain one or the other of these and install them on your system. For Cross_Match go to http://www.phrap.org You will want to select "Phred/Phrap/Consed" as Cross_Match is part of the Phrap package. For RMBlast ( NCBI Blast modified for use with RepeatMasker/RepeatModeler ) please go to our download page: http://www.repeatmasker.org/rmblast . It is highly recommended to use 2.13.0 or higher. For HMMER please download the v3.2.1 version here: http://hmmer.org/ For ABBlast/WUBlast go to [ NOTE: Rights to BLAST 2.0 (WU-BLAST) have been acquired by Advanced Biocomputing, LLC. http://blast.advbiocomp.com/licensing/ RepeatMasker 3.2.8 and above fully support both variants ] TRF - Tandem Repeat Finder, G. Benson et al. You can obtain a free copy at http://tandem.bu.edu/trf/trf.html or https://github.com/Benson-Genomics-Lab/TRF . RepeatMasker was developed using TRF version 4.0.9 Repeat Database RepeatMasker can be used with custom libraries, or with Dfam out of the box. Dfam is an open database of transposable element (TE) profile HMM models and consensus sequences. The current release of RepeatMasker is shipped without a TE database, however libraries in FamDB H5 format may be downloaded from Dfam at: https://www.dfam.org/releases/current/families/FamDB and installed in the Libraries/famdb directory. The files are divided by taxa groups and numbered starting from '0' ( aka the root partition ) which contains required information for RepeatMasker/FamDB. In addition the last Repbase RepeatMasker Edition may be downloaded and combined with Dfam. The RepBase RepeatMasker Library can be obtained at: http://www.girinst.org . Installation Download RepeatMasker Latest Released Version: 12/17/25: RepeatMasker-4.2.3.tar.gz Previous Released Version: 10/3/25: RepeatMasker-4.2.2.tar.gz Unpack Distribution Unpack the distribution in your home directory or in a location where it may be shared with other users of your system ( ie. /usr/local/ ). Make sure you do not extract in a directory already containing a pre-existing directory called "RepeatMasker" as it will attempt to overwrite files contained within. cp RepeatMasker-open-4-#-#.tar.gz /usr/local cd /usr/local gunzip RepeatMasker-open-4-#-#.tar.gz tar xvf RepeatMasker-open-4-#-#.tar Install RepeatMasker Libraries RepeatMasker is currently not distributed with a database. The program may be used immediately with custom databases ("-lib mylib.fa" option) or you may download TE libraries and configure them for use with RepeatMasker. There are three options for supplementing/updating the main RepeatMasker library: The Dfam database may be downloaded from www.dfam.org in famdb HDF5 format partitioned by taxa . The root ("dfam##_full.0.h5") partition is required if you plan to use Dfam, however any combination of additional partitions may also be downloaded and configured. For example: wget https://www.dfam.org/releases/Dfam_3.9/families/FamDB/dfam39_full.1.h5.gz gunzip dfam39_full.1.h5.gz mv dfam39_full.1.h5 /usr/local/RepeatMasker/Libraries/famdb NOTE: Only partitions from the same Dfam release should be in this directory. Repeat for any additional partitions you wish to use. A list of partions and the taxa they contain can be found here . and/or: The RepBase RepeatMasker Edition ( final version 10/26/2018 ) may be downloaded from www.girinst.org and unpaked in the RepeatMasker directory. For example: cp RepBaseRepeatMaskerEdition-20181026.tar.gz /usr/local/RepeatMasker/ cd /usr/local/RepeatMasker gunzip RepBaseRepeatMaskerEdition-20181026.tar.gz tar xvf RepBaseRepeatMaskerEdition-20181026.tar rm RepBaseRepeatMaskerEdition-20181026.tar Run Configure Script The program requires some initial configuration. This should also be re-run after updates to the library files. cd /usr/local/RepeatMasker perl ./configure RepeatMasker "open-3.0/4.0" is licensed under the Open Source License v2.1 . Release Notes RepeatMasker-4.2.3 BUGFIX: Since the 4.1.1 release the staged approach to searching TE families has not been applied species in the 'rodentia' order due to a flag being set incorrectly. While this doesn't prohibit families from being annotated, it does decrease the sensitivity of the search. This release fixes this issue. This problem did not impact any other orders. Feature Request: Added support for BGZIP files by changing the method used to process compressed files. Instead of uncompressing input files in-place, the program now leaves the original compressed file intact. RepeatMasker-4.2.2 BUGFIX: In the 4.2.1 release a bug was introduced that impacted the handling of poly-A tails and the naming of LINE annotations. While the overall masking level remained the same, the change caused some previously hidden and overlapping annotations to appear with invalid query ranges ( query start > query end ). (github #362) Added support for '+' symbol in input filenames. (github #365) RepeatMasker-4.2.1 BUGFIX: An infinite loop was possible in rare circumstances involoving interleaved satellite consensi while using the "-a" option. This caused the alignment file to keep growing and eventually ProcessRepeats to crash. BUGFIX: Fix a one-off issue in alignment range calculations induced by the clipping mechanism in RepeatMasker. BUGFIX: The configure script was crashing while attempting to import Repbase in the previous version. Updated to the latest famdb version (2.0.5) Crossmatch alignment format parser hardening. While not proper, negative coordinates can appear in the alignment file due to incorrect range calculations. This change allows for the parser to handle these cases and not mis-align the data columns. Updated the length of the Charlie7 family in RepeatAnnotationData.pm RepeatMasker-4.2.0 BUGFIX: For mammalian genomes searched using the "-species" option, newer Dfam families without search stages, or with the "-uncurated" flag Dfam DR families were not being included in the search. BUGFIX: RepeatMasker exits with an error code if no repetitive sequences were found in the input file. BUGFIX: famdb.py was not reporting the correct counts for families ancestral to the query term. RepeatMasker uses this count and therefore was also reporting an incorrect value. Remove duplicate families when attempting to merge Repbase RepeatMaskerEdition into FamDB. The configure utility was not using the -libdir path when creating the RepeatMasker.lib file. (github #344) RepeatMasker-4.1.9 BUGFIX: When the RepeatMasker adjudicator (ProcessRepeats) is faced with a huge number of overlapping and redundant alignments the joining can go awry, creating a infinite loop. The effect is that ProcessRepeats never completes. BUGFIX: When using nhmmer/pHMMs and a non-species-level "-species" parameters (e.g. "-species mammals"), RepeatMasker was using an exteremly permissive per-family score cutoff. This overwhelmed ProcessRepeats with many low-scoring alignments. BUGFIX: ProcessRepeats dies around line 8190 with a "Division by zero" error. BUGFIX: Fixed call to famdb for buildSummary.pl in the -species option. Updated documentation. Updated repeatmasker.help. RepeatMasker-4.1.8 Fixed table format for non-mammals. The "Retroelements" heading didn't include Penelope elements ( "PLE/" ) in it's tabulation. ProcessRepeats - A major change in how annotations are processed to reduce PR's memory footprint. Instead of loading all anntations in memory, they are now streamed and processed a sequence at a time. For chromosomal assemblies this reduced the memory footprint to the size of the largest chromosome, instead of the whole genome. Fixed a bug that caused general/is.lib to be left in a unfrozen state for rmblastn. Updated to FamDB 2.0.0 RepeatMasker-4.1.7-p1 This is a critical fix to the 4.1.7 release. The -species option was not being interpreted correctly by RepeatMasker/ProcessRepeats. The most obvious change for mammals/primates was that the output format (*.tbl file) looked different than it had before. Under the hood this also changed the way some species were handled in the library searches. RepeatMasker-4.1.7 Handle the case were the default search engine is not configured and require the user to provide it using -e/-engine. Use the global alignment bandwidth simulation for the refinement step. Allow for minimal database install and warn when used with -species. Fixed a bug on configure with setting the default search engine when only one search engine is configured. RepeatProteinMask wasn't obtaining the correct search engine if configure didn't set it up correctly. FamDB wasn't exporting RepeatMasker.lib with class-name suffixes. This had an impact on the RepeatModeler/RepeatClassifier package but not on RepeatMasker itself. Upgraded to FamDB 1.0.5 Fixed an issue with parsing RepBase. Some records were not being parsed correctly for records that do not include the keyword "repbase" following the identifier. New semantantics for NCBIBlastSearchEngine bandwidth interpretation. Fixed a divide-by-zero error in ProcessRepeat's merging of DNA tranpsoson overlapping fragments. FamDB fixed inconsistency between curated/uncurated counts vs exports. RepeatMasker-4.1.6 Upgraded to FamDB 1.0.2 to support Dfam 3.8 and the new partitioned database format. Added Libraries/RMRB_spec_to_tax.json to project. This maps the RepBase taxanames to current NCBI tax_ids and needs to be refreshed with each new Dfam release. Added softmasking support to NCBIBlastSearchEngine.pm. Added new '--uncurated' flag to handle single export Dfam format. If this flag is used the CONS/HMM cached directories will be suffixed with "_wunc". Fixed sunk error messages from famdb.py. Now they will be displayed and cause RepeatMasker to quit. Additional library setup steps and error checking for configure utility. CAF documentation in SearchResult. calcDivergenceFromAlign clarified use of "-a" in documentation. RepeatMasker-4.1.5 Updated codebase for Dfam 3.7 compatibility (famdb format 4.3). Penelope classification change caused *.tbl file accounting to place them in the Unknown category. Also fixed landscape generation tool. Added a new utility to merge *.out *.align files generated by running RepeatMasker serially. Repbase metadata was out-of-date, updated species names so that they match the current NCBI Taxonomy names. Fixed an issue with the HMM parser. It wasn't recognizing negative values for Tau with models that do not have GA thresholds. RepeatMasker-4.1.4 Added support for RMBlast 2.13.0. Release of the TE genome browser visualization (UCSC) and trackhub generation tool. New CpGSites and unadjusted Kimura stats in the *.align file. Fixed a bug that caused the read-only state of the input fasta file to propogate to the intermediate files and cause the program to exit. Removed DateRepeats as it's based on old library formats - this functionality will return with the refactored version of RM in the works. RepeatMasker-4.1.3-p1 A recent change in 4.1.3 to correct blank fragment ID fields can in rare cases causing the error message: 'Can't call method "setLeftLinkedHit"'. The RepeatAnnotationData.pm file containing necessary information for recognizing equivalent fragments of DNA transposons was missing data. The MULE-MuDR class was added to the *.tbl file for "-lib" searches. RepeatMasker-4.1.3 A new utility for generating trackHubs for our new UCSC TE visualization Fix a bug where killing RM while starting up can leave the cached libraries in an inconsistent state. Fixed a bug where in rare cases the joined fragment ID field is blank Merged in changes to Dupmasker supporting multi-threaded use Fixed legacy RepBase taxonomic labels Added support for GFF v3 output and fixed the utility/rmOutToGFF3.pl RepeatMasker-4.1.2-p1 Releases 4.1.1-4.1.2 contained a bug with the processing of Alu sequences in primates. The step where an initial annotation is refined into a particular Alu subfamily was not performed and the annotations remained labeled with the initial capture sequence ( AluJb, AluSx, or AluY ). This patch release fixes this one issue. RepeatMasker-4.1.2 Fixed 21 protein family classifications in RepeatProteinLib. Fixed a problem with the generation of the RepeatMasker.lib file for use by RepeatModeler. In release 4.1.1 it did not add the classification info to this auxilary file. Fixed a "log(0)" error that can cause the program to fault in rare circumstances. buildSummary now supports FamDB and has improved documentation. Bugfixes and improvements to FamDB. RepeatMasker-4.1.1 Dfam (starting with version 3.2) is now distributed in the FamDB file format based on HDF5, which has improved support for large datasets compared to the EMBL and HMM formats that were previously used. RepeatMasker therefore includes a copy of famdb.py, and depends on the python package h5py . The 'configure' script and other parts of RepeatMasker have been updated to accomodate these changes. The utilities 'queryTaxonomyDatabase.pl' and 'queryRepeatDatabase.pl' are no longer included, since that data is now included in FamDB. The 'famdb.py' tool can be used to make many of the same queries as the removed utilies, and even more. RepeatMasker-4.1.0 RepeatMasker now has a refactored configuration system making it easier to distribute RepeatMasker via package managers and/or bundle RepeatMasker into containers. RepeatMasker-open-4-0-9-p1 Input files containing multiple FASTA sequences caused RepeatMasker to error out with a message like: "WARNING: TRF returned an error (Return code = ### ) TRF parameters: 2.7.7.80.10.50.10 A search phase could not complete on this batch. The batch file will be re-run and if possible the program will resume. WARNING: Retrying batch ( 1 ) [ 255,, 195]..." This bug was introduced when we attempted to improve TRF error catching. Unfortunatly the return codes are not documented for TRF and the assumption that 256 is the only successful return code is wrong. The "success" code appears to change depending on the number of sequences in the file. The workaround is to fail only if there is a message in the error output file. RepeatMasker-open-4-0-9 General compatibility update for Dfam 3.0. Dfam and Dfam_consensus have merged into one combined database. RepeatMasker can use Dfam using any of it search engines and will automatically switch to using consensus sequences or profile HMMs based on the engine used. It is important to note that, by default RepeatMasker will use Dfam consensus sequences when library duplicates are detected. Bugfix: The -dir option no longer assumes that the directory already exists. Feature: The configure script now accepts command-line parameters to change configuration settings. Configure also re-reads existing configuration options to use as prompt defaults. Archived Releases RepeatMasker-4.2.1.tar.gz RepeatMasker-4.2.0.tar.gz RepeatMasker-4.1.9.tar.gz RepeatMasker-4.1.8.tar.gz RepeatMasker-4.1.7-p1.tar.gz RepeatMasker-4.1.6.tar.gz RepeatMasker-4.1.5.tar.gz Institute for Systems Biology This server is made possible by funding from the National Human Genome Research Institute (NIGRI grant # RO1 HG002939). + +### https://github.com/Dfam-consortium/RepeatMasker +GitHub - Dfam-consortium/RepeatMasker: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Dfam-consortium / RepeatMasker Public Notifications You must be signed in to change notification settings Fork 50 Star 301 Code Issues 26 Pull requests 3 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Dfam-consortium/RepeatMasker master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 265 Commits 265 Commits .github/ ISSUE_TEMPLATE .github/ ISSUE_TEMPLATE Libraries Libraries Matrices Matrices t t util util .gitattributes .gitattributes ArrayList.pm ArrayList.pm ArrayListIterator.pm ArrayListIterator.pm CHANGELOG.md CHANGELOG.md CITATION.cff CITATION.cff CrossmatchSearchEngine.pm CrossmatchSearchEngine.pm DFAM.pm DFAM.pm DFAMRecord.pm DFAMRecord.pm DateRepeats DateRepeats DupMasker DupMasker EMBL.pm EMBL.pm FastaDB.pm FastaDB.pm HMMERSearchEngine.pm HMMERSearchEngine.pm HTMLAnnotHeader.html HTMLAnnotHeader.html INSTALL INSTALL LICENSE LICENSE LibraryUtils.pm LibraryUtils.pm Matrix.pm Matrix.pm NCBIBlastSearchEngine.pm NCBIBlastSearchEngine.pm NCBIBlastXSearchEngine.pm NCBIBlastXSearchEngine.pm PRSearchResult.pm PRSearchResult.pm ProcessRepeats ProcessRepeats PubRef.pm PubRef.pm README.md README.md RepbaseEMBL.pm RepbaseEMBL.pm RepbaseRecord.pm RepbaseRecord.pm RepeatMasker RepeatMasker RepeatMaskerConfig.pm RepeatMaskerConfig.pm RepeatProteinMask RepeatProteinMask RepeatRecord.pm RepeatRecord.pm SearchEngineI.pm SearchEngineI.pm SearchResult.pm SearchResult.pm SearchResultCollection.pm SearchResultCollection.pm SeqDBI.pm SeqDBI.pm SimpleBatcher.pm SimpleBatcher.pm TRF.pm TRF.pm TRFResult.pm TRFResult.pm TRFSearchResult.pm TRFSearchResult.pm Taxonomy.pm Taxonomy.pm WUBlastSearchEngine.pm WUBlastSearchEngine.pm WUBlastXSearchEngine.pm WUBlastXSearchEngine.pm addRepBase.pl addRepBase.pl bluegrad.jpg bluegrad.jpg configure configure daterepeats.help daterepeats.help famdb.py famdb.py famdb_classes.py famdb_classes.py famdb_globals.py famdb_globals.py famdb_helper_classes.py famdb_helper_classes.py famdb_helper_methods.py famdb_helper_methods.py repeatmasker.help repeatmasker.help View all files Repository files navigation README License RepeatMasker Developed by Arian Smit and Robert Hubley Please refer to: Smit, AFA, Hubley, R. & Green, P "RepeatMasker" at http://www.repeatmasker.org IMPORTANT: The github 'master' branch does not contain any TE libraries. As of 4.1.7, you may use the release as-is for custom library searches (e.g "-lib mylib.fasta"). For searches against community developed TE libraries, you will need to download and install one or more of the Dfam database FamDB partition. See the RepeatMasker website for more information: http://www.repeatmasker.org/RepeatMasker/ RepeatMasker RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Sequence comparisons in RepeatMasker are performed by one of several available alignment programs: RMBlast, a variant of NCBI blastn that supports substitution matrices, complexity adjusted scoring and masklevel filtering. crossmatch, an efficient implementation of the Smith-Waterman-Gotoh algorithm developed by Phil Green. NHMMER, a profile Hidden Markov Model aligner written by Travis Wheeler and Sean Eddy. ABBLAST, A blast variant developed by Warren Gish. See "INSTALL" for instructions on how to install RepeatMasker. See "repeatmasker.help" for a detailed program manual. Libraries Overview Updates of the RepeatMasker program are distributed with a copy of the Dfam database ( www.dfam.org ). Dfam is an "open" databases of Transposable Element seed alignments, profile Hidden Markov Models and consensus sequences. RepeatMasker is also compatible with the RepBase database managed by the Genetic Information Research Institute and requires a license to use. Up until 2019 we maintained the "Repbase RepeatMasker Edition" libraries as co-editor of RepBase Update. For newer versions of RepBase users will need to use the sequences in FASTA format with RepeatMasker's "-lib" option. RepeatMasker "open-4.0" and later versions are distributed under the Open Source License. Please read LICENSE file for more information. About RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 301 stars Watchers 6 watching Forks 50 forks Report repository Releases No releases published Packages 0       Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 99.4% Other 0.6% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge repeatmasker --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +repeatmasker 4.0.6 4 +-------------------- +file name : repeatmasker-4.0.6-4.tar.bz2 +name : repeatmasker +version : 4.0.6 +build : 4 +build number: 4 +size : 206.5 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.6-4.tar.bz2 +md5 : 1bb0b86ca9757cc3abd8f798c208f57f +dependencies: + - hmmer + - perl-text-soundex + - perl-threaded + - rmblast + - trf + + +repeatmasker 4.0.6 5 +-------------------- +file name : repeatmasker-4.0.6-5.tar.bz2 +name : repeatmasker +version : 4.0.6 +build : 5 +build number: 5 +size : 206.5 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.6-5.tar.bz2 +md5 : b1651cbe84db18e8dbf96c18b4c8e7b8 +dependencies: + - hmmer + - perl-text-soundex + - perl-threaded + - rmblast + - trf + + +repeatmasker 4.0.6 6 +-------------------- +file name : repeatmasker-4.0.6-6.tar.bz2 +name : repeatmasker +version : 4.0.6 +build : 6 +build number: 6 +size : 206.5 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.6-6.tar.bz2 +md5 : 067b3b8608e0352da5a36407b4e992db +dependencies: + - hmmer + - perl-text-soundex + - perl-threaded + - rmblast + - trf + + +repeatmasker 4.0.6 pl5.22.0_10 +------------------------------ +file name : repeatmasker-4.0.6-pl5.22.0_10.tar.bz2 +name : repeatmasker +version : 4.0.6 +build : pl5.22.0_10 +build number: 10 +size : 206.5 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.6-pl5.22.0_10.tar.bz2 +md5 : 66b7923b93ac32b19bcb5b03daec7930 +dependencies: + - hmmer + - perl 5.22.0* + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.6 pl5.22.0_7 +----------------------------- +file name : repeatmasker-4.0.6-pl5.22.0_7.tar.bz2 +name : repeatmasker +version : 4.0.6 +build : pl5.22.0_7 +build number: 7 +size : 206.5 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.6-pl5.22.0_7.tar.bz2 +md5 : 9827cb5ec0414dca26a3d38fb6f7af29 +dependencies: + - hmmer + - perl 5.22.0* + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.6 pl5.22.0_8 +----------------------------- +file name : repeatmasker-4.0.6-pl5.22.0_8.tar.bz2 +name : repeatmasker +version : 4.0.6 +build : pl5.22.0_8 +build number: 8 +size : 206.5 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.6-pl5.22.0_8.tar.bz2 +md5 : c5e571ef0e22f24d22818aa915c9eb6b +dependencies: + - hmmer + - perl 5.22.0* + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.6 pl5.22.0_9 +----------------------------- +file name : repeatmasker-4.0.6-pl5.22.0_9.tar.bz2 +name : repeatmasker +version : 4.0.6 +build : pl5.22.0_9 +build number: 9 +size : 206.5 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.6-pl5.22.0_9.tar.bz2 +md5 : 2d28e584e7be7d8fdea774a550f74316 +dependencies: + - hmmer + - perl 5.22.0* + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.7 pl5.22.0_10 +------------------------------ +file name : repeatmasker-4.0.7-pl5.22.0_10.tar.bz2 +name : repeatmasker +version : 4.0.7 +build : pl5.22.0_10 +build number: 10 +size : 202.3 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.7-pl5.22.0_10.tar.bz2 +md5 : 45206f0bb5428a22e2acce601d2b48ce +dependencies: + - hmmer + - perl 5.22.0* + - perl-text-soundex + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.7 pl5.22.0_11 +------------------------------ +file name : repeatmasker-4.0.7-pl5.22.0_11.tar.bz2 +name : repeatmasker +version : 4.0.7 +build : pl5.22.0_11 +build number: 11 +size : 202.4 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.7-pl5.22.0_11.tar.bz2 +md5 : 681e454c074266a9bbbe2e78de0fb05d +dependencies: + - hmmer + - perl 5.22.0* + - perl-text-soundex + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.7 pl526_13 +--------------------------- +file name : repeatmasker-4.0.7-pl526_13.tar.bz2 +name : repeatmasker +version : 4.0.7 +build : pl526_13 +build number: 13 +size : 202.3 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.7-pl526_13.tar.bz2 +md5 : 3c7b5f59c3445dfd5df206a5455a256e +timestamp : 2018-09-11 17:56:47 UTC +dependencies: + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.8 pl526_13 +--------------------------- +file name : repeatmasker-4.0.8-pl526_13.tar.bz2 +name : repeatmasker +version : 4.0.8 +build : pl526_13 +build number: 13 +size : 223.2 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.8-pl526_13.tar.bz2 +md5 : 00221e7e7556a333e2f54e6659a24d51 +timestamp : 2019-01-23 08:27:47 UTC +dependencies: + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.8 pl526_14 +--------------------------- +file name : repeatmasker-4.0.8-pl526_14.tar.bz2 +name : repeatmasker +version : 4.0.8 +build : pl526_14 +build number: 14 +size : 214.9 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.8-pl526_14.tar.bz2 +md5 : 50ef8bf515592a990fcf6374032117f2 +timestamp : 2019-05-02 23:15:46 UTC +dependencies: + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.9_p2 pl526_0 +----------------------------- +file name : repeatmasker-4.0.9_p2-pl526_0.tar.bz2 +name : repeatmasker +version : 4.0.9_p2 +build : pl526_0 +build number: 0 +size : 243.4 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.9_p2-pl526_0.tar.bz2 +md5 : dafc39f37c858d4315852b03980fff51 +timestamp : 2019-05-10 13:10:28 UTC +dependencies: + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.9_p2 pl526_1 +----------------------------- +file name : repeatmasker-4.0.9_p2-pl526_1.tar.bz2 +name : repeatmasker +version : 4.0.9_p2 +build : pl526_1 +build number: 1 +size : 251.8 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.9_p2-pl526_1.tar.bz2 +md5 : 0042b840bc03651dedd1f0965f0c45f8 +timestamp : 2019-12-09 14:46:41 UTC +dependencies: + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.0.9_p2 pl526_2 +----------------------------- +file name : repeatmasker-4.0.9_p2-pl526_2.tar.bz2 +name : repeatmasker +version : 4.0.9_p2 +build : pl526_2 +build number: 2 +size : 251.8 MB +license : Open Software License v2.1 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/repeatmasker-4.0.9_p2-pl526_2.tar.bz2 +md5 : 6c368f434baab42521b37aeb96e39572 +timestamp : 2020-04-23 11:02:06 UTC +dependencies: + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.1.0 pl526_0 +-------------------------- +file name : repeatmasker-4.1.0-pl526_0.tar.bz2 +name : repeatmasker +version : 4.1.0 +build : pl526_0 +build number: 0 +size : 270.2 MB +license : Open Software License v2.1 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/repeatmasker-4.1.0-pl526_0.tar.bz2 +md5 : 4feb2a282e50791ef4c82ce924f171a6 +timestamp : 2020-09-15 19:16:58 UTC +dependencies: + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.1.1 pl5262hdfd78af_2 +----------------------------------- +file name : repeatmasker-4.1.1-pl5262hdfd78af_2.tar.bz2 +name : repeatmasker +version : 4.1.1 +build : pl5262hdfd78af_2 +build number: 2 +size : 279.0 MB +license : Open Software License v2.1 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/repeatmasker-4.1.1-pl5262hdfd78af_2.tar.bz2 +md5 : db4b72455455affd58197dde9805cb2b +timestamp : 2021-03-27 10:47:06 UTC +dependencies: + - h5py + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.1.1 pl526_0 +-------------------------- +file name : repeatmasker-4.1.1-pl526_0.tar.bz2 +name : repeatmasker +version : 4.1.1 +build : pl526_0 +build number: 0 +size : 279.0 MB +license : Open Software License v2.1 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/repeatmasker-4.1.1-pl526_0.tar.bz2 +md5 : ab0ba202e3dae964de6400a204fb3938 +timestamp : 2020-11-04 07:16:57 UTC +dependencies: + - h5py + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.1.1 pl526_1 +-------------------------- +file name : repeatmasker-4.1.1-pl526_1.tar.bz2 +name : repeatmasker +version : 4.1.1 +build : pl526_1 +build number: 1 +size : 279.0 MB +license : Open Software License v2.1 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/repeatmasker-4.1.1-pl526_1.tar.bz2 +md5 : 48df25726a3e39888b1723871103afa9 +timestamp : 2020-11-23 19:28:40 UTC +dependencies: + - h5py + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - perl-text-soundex + - rmblast + - trf + + +repeatmasker 4.1.2.p1 pl5262hdfd78af_0 +-------------------------------------- +file name : repeatmasker-4.1.2.p1-pl5262hdfd78af_0.tar.bz2 +name : repeatmasker +version : 4.1.2.p1 +build : pl5262hdfd78af_0 +build number: 0 +size : 279.0 MB +license : Open Software License v2.1 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/repeatmasker-4.1.2.p1-pl5262hdfd78af_0.tar.bz2 +md5 : 287bd99f63cc15cca04512982238e918 +timestamp : 2021-05-06 21:32:15 UTC +dependencies: + - h5py + - hmmer + - perl >=5.26.2,<5.26.3.0a0 + - rmblast + - trf + + +repeatmasker 4.1.2.p1 pl5321hdfd78af_1 +-------------------------------------- +file name : repeatmasker-4.1.2.p1-pl5321hdfd78af_1.tar.bz2 +name : repeatmasker +version : 4.1.2.p1 +build : pl5321hdfd78af_1 +build number: 1 +size : 279.1 MB +license : Open Software License v2.1 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/repeatmasker-4.1.2.p1-pl5321hdfd78af_1.tar.bz2 +md5 : ed062e0f3a40daa86595c787491cb1df +timestamp : 2022-01-14 23:27:08 UTC +dependencies: + - h5py + - hmmer + - perl >=5.32.1,<6.0a0 *_perl5 + - rmblast + - trf + + +repeatmasker 4.1.5 pl5321hdfd78af_0 +----------------------------------- +fi diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/rnastructure.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/rnastructure.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..ec55e96ffaa650bc5b0f3dfe38e048d08edbfbbd --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/rnastructure.manual_bundle.txt @@ -0,0 +1,367 @@ +# Tool: rnastructure +software_name: rnastructure +tier: T1 +domain: t1_backfill_overall +downloads: 117006 +summary: RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data. +description: RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data. +dependencies: _openmp_mutex >=4.5, libgcc >=14, libgomp, libstdcxx >=14 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://rna.urmc.rochester.edu/RNAstructure.html +doc_url: https://rna.urmc.rochester.edu/Overview/index.html +dev_url: + +## URL Docs Extract +### https://rna.urmc.rochester.edu/Overview/index.html +RNAstructure Installation and Overview RNAstructure Installation and Overview Version 6.6 Contents Index RNAstructure is a product of the Mathews Lab , University of Rochester Medical Center , Department of Biochemistry and Biophysics . Continued development of RNAstructure is made possible by the support of NIH grant R35GM145283. How to Install the Pre-Built Packages: Installation Instructions for Linux Systems Step-by-step instructions detailing how to install theRNAstructure package on Linux systems. Installation Instructions for Macintosh Systems Step-by-step instructions detailing how to install the RNAstructure package on Macintosh systems. Installation Instructions for Windows Systems Step-by-step instructions detailing how to install the RNAstructure package on Windows systems. Other Help Instructions: Building Instructions Guide to building the programs in the RNAstructure repository. Building Requirements Guide to external programs or variables necessary to build the RNAstructure repository tools. Cleaning the Repository Important information about how the RNAstructure repository conducts cleaning operations. Components A complete list of components of the RNAstructure software package, including references to the literature. Contributors A list of people who contributed to the code base of RNAstructure. Interfaces Summary A detailed summary of each interface in the RNAstructure repository, including name, location, and building commands. Libraries Descriptions of the libraries that are built by the RNAstructure repository. Makefiles Detailed descriptions about how each of the Makefiles in the RNAstructure repository work. Object Files Important information about object file creation when building the text interfaces and Java GUI in the RNAstructure repository. Python Library A guide to using RNAstructure in Python. Repository Organization Details on how the RNAstructure repository is organized. Running the RNAstructure JAVA GUI Special considerations to be aware of when attempting to run the JAVA GUI. Thermodynamic Parameter Tables Information about the thermodynamic parameter tables. Update History History of changes and updates to the RNAstructure repository. Visit The Mathews Lab RNAstructure Page for updates and latest information. + +### https://rna.urmc.rochester.edu/RNAstructure.html +RNAstructure Mathews lab Computational Biology of RNA Home Research Publications RNAstructure Software RNAstructure Web Servers Group tags that contain these fields. However, it's fine to edit any of the text around the tags and the styles applied to #release-version and #release-date can be changed. --> RNAstructure, Version 6.6 : Updated April 2, 2026 ( change log ) RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data. RNAstructure is available as a graphical user interface for Windows; a JAVA graphical user interface for Mac OS-X or Linux; command line interfaces for Max OS-X, Linux, or Windows; and source code for local compilation. The source code includes a set of C++ classes for convenient inclusion of the methods into new programs. List of All Package Components List of Package Versions, Changes, and Bugfixes Online Help & Documentation Download/Use: Download RNAstructure to run software locally. We ask you to register before downloading so that we may occasionally notify you of significant updates and to track the number of users to make a case for continued support by funding agencies. RNAstructure is free of charge and provided under the GNU public license. or Use the Online Tools (RNAstructure Webservers) Most RNAstructure features can be accessed using these online tools, however some parameters are limited (e.g. sequence length, calculation time, etc). If you need to perform long-running calculations or these limits are not sufficient for your application, please consider downloading the full package to run the software locally. Grant Support: RNAstructure is made possible by the support of the National Institutes of Health grant R35GM145283. © 2012-2026 Mathews group Contributors | Contact Us + +## Conda Search Info +$ conda search -c bioconda -c conda-forge rnastructure --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +rnastructure 5.7 0 +------------------ +file name : rnastructure-5.7-0.tar.bz2 +name : rnastructure +version : 5.7 +build : 0 +build number: 0 +size : 59.0 MB +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-5.7-0.tar.bz2 +md5 : 9f376eefdb9f26d34d985ee5fd2034d2 +dependencies: [] + + +rnastructure 5.7 1 +------------------ +file name : rnastructure-5.7-1.tar.bz2 +name : rnastructure +version : 5.7 +build : 1 +build number: 1 +size : 15.8 MB +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-5.7-1.tar.bz2 +md5 : 8e4bf592f2998e395a4981d9ef24565e +dependencies: + - libgcc + + +rnastructure 5.7 h2d50403_2 +--------------------------- +file name : rnastructure-5.7-h2d50403_2.tar.bz2 +name : rnastructure +version : 5.7 +build : h2d50403_2 +build number: 2 +size : 15.8 MB +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-5.7-h2d50403_2.tar.bz2 +md5 : 21acc08cd944987d2e036270b416a637 +timestamp : 2018-06-30 06:53:01 UTC +dependencies: + - libstdcxx-ng >=4.9 + + +rnastructure 6.0 0 +------------------ +file name : rnastructure-6.0-0.tar.bz2 +name : rnastructure +version : 6.0 +build : 0 +build number: 0 +size : 26.9 MB +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.0-0.tar.bz2 +md5 : 5936d5c4799cf8bb004543f13904f809 +dependencies: + - libgcc + + +rnastructure 6.0 hfc679d8_1 +--------------------------- +file name : rnastructure-6.0-hfc679d8_1.tar.bz2 +name : rnastructure +version : 6.0 +build : hfc679d8_1 +build number: 1 +size : 26.8 MB +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.0-hfc679d8_1.tar.bz2 +md5 : 001e6c7fcc3bf7d51749e772b536b55e +timestamp : 2018-06-30 07:00:04 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + + +rnastructure 6.1 h1b792b2_2 +--------------------------- +file name : rnastructure-6.1-h1b792b2_2.tar.bz2 +name : rnastructure +version : 6.1 +build : h1b792b2_2 +build number: 2 +size : 26.8 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.1-h1b792b2_2.tar.bz2 +md5 : ca5b2b6e1c548caa02bbaae876a0eb68 +timestamp : 2021-03-24 22:34:10 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + + +rnastructure 6.1 he1b5a44_1 +--------------------------- +file name : rnastructure-6.1-he1b5a44_1.tar.bz2 +name : rnastructure +version : 6.1 +build : he1b5a44_1 +build number: 1 +size : 26.3 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.1-he1b5a44_1.tar.bz2 +md5 : eefb56fa4fe301d7ccb9fbe78afbeb45 +timestamp : 2020-07-13 01:07:51 UTC +dependencies: + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + + +rnastructure 6.1 hfc679d8_0 +--------------------------- +file name : rnastructure-6.1-hfc679d8_0.tar.bz2 +name : rnastructure +version : 6.1 +build : hfc679d8_0 +build number: 0 +size : 27.4 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.1-hfc679d8_0.tar.bz2 +md5 : 7a67fd65dd97e98a71728f071bcd3a7b +timestamp : 2018-10-18 18:55:34 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + + +rnastructure 6.3 h1b792b2_0 +--------------------------- +file name : rnastructure-6.3-h1b792b2_0.tar.bz2 +name : rnastructure +version : 6.3 +build : h1b792b2_0 +build number: 0 +size : 321.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.3-h1b792b2_0.tar.bz2 +md5 : 41f17e770e293b0cc746367aeb2e0768 +timestamp : 2021-08-06 19:19:38 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + + +rnastructure 6.3 h87f3376_1 +--------------------------- +file name : rnastructure-6.3-h87f3376_1.tar.bz2 +name : rnastructure +version : 6.3 +build : h87f3376_1 +build number: 1 +size : 307.2 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.3-h87f3376_1.tar.bz2 +md5 : 272ecc8f87a4352c172a4fed0937d30a +timestamp : 2022-02-23 16:46:40 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + + +rnastructure 6.3 h87f3376_2 +--------------------------- +file name : rnastructure-6.3-h87f3376_2.tar.bz2 +name : rnastructure +version : 6.3 +build : h87f3376_2 +build number: 2 +size : 307.3 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.3-h87f3376_2.tar.bz2 +md5 : f01232ccd285fa407595c8f1198fe705 +timestamp : 2023-05-12 13:39:17 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +rnastructure 6.3 hdbdd923_2 +--------------------------- +file name : rnastructure-6.3-hdbdd923_2.tar.bz2 +name : rnastructure +version : 6.3 +build : hdbdd923_2 +build number: 2 +size : 314.6 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.3-hdbdd923_2.tar.bz2 +md5 : 3a606b3682473d0128162000e0b3d3ad +timestamp : 2023-05-14 22:19:23 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +rnastructure 6.3 hdbdd923_3 +--------------------------- +file name : rnastructure-6.3-hdbdd923_3.tar.bz2 +name : rnastructure +version : 6.3 +build : hdbdd923_3 +build number: 3 +size : 314.8 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.3-hdbdd923_3.tar.bz2 +md5 : da5ca66923fd2859ecca3ef719404c99 +timestamp : 2023-05-16 06:46:51 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +rnastructure 6.4 h503566f_1 +--------------------------- +file name : rnastructure-6.4-h503566f_1.tar.bz2 +name : rnastructure +version : 6.4 +build : h503566f_1 +build number: 1 +size : 312.0 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.4-h503566f_1.tar.bz2 +md5 : 8ea6c539711f5a54738747b3fb49f3b3 +timestamp : 2024-12-14 05:46:17 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc >=13 + - libstdcxx >=13 + + +rnastructure 6.4 h503566f_2 +--------------------------- +file name : rnastructure-6.4-h503566f_2.tar.bz2 +name : rnastructure +version : 6.4 +build : h503566f_2 +build number: 2 +size : 312.0 MB +license : GPL-2.0-only +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.4-h503566f_2.tar.bz2 +md5 : bce33944339f89c25b6cd0e7bb05adf0 +timestamp : 2025-01-23 12:34:58 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc >=13 + - libstdcxx >=13 + + +rnastructure 6.4 hdbdd923_0 +--------------------------- +file name : rnastructure-6.4-hdbdd923_0.tar.bz2 +name : rnastructure +version : 6.4 +build : hdbdd923_0 +build number: 0 +size : 314.0 MB +license : GPLv2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.4-hdbdd923_0.tar.bz2 +md5 : 89141d85446539cb20a549fc4e4f32bd +timestamp : 2024-02-03 01:49:16 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +rnastructure 6.5 hde5307d_0 +--------------------------- +file name : rnastructure-6.5-hde5307d_0.conda +name : rnastructure +version : 6.5 +build : hde5307d_0 +build number: 0 +size : 285.5 MB +license : GPL-2.0-only +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.5-hde5307d_0.conda +md5 : de5f85b16603c28057ac8685563ed81e +timestamp : 2026-02-12 10:45:26 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc >=14 + - libstdcxx >=14 + + +rnastructure 6.5 hde5307d_1 +--------------------------- +file name : rnastructure-6.5-hde5307d_1.conda +name : rnastructure +version : 6.5 +build : hde5307d_1 +build number: 1 +size : 285.5 MB +license : GPL-2.0-only +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.5-hde5307d_1.conda +md5 : 65d3b8b85dee24620e0b55354df70f34 +timestamp : 2026-03-04 11:42:07 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc >=14 + - libstdcxx >=14 + + +rnastructure 6.6 hde5307d_0 +--------------------------- +file name : rnastructure-6.6-hde5307d_0.conda +name : rnastructure +version : 6.6 +build : hde5307d_0 +build number: 0 +size : 284.9 MB +license : GPL-2.0-only +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rnastructure-6.6-hde5307d_0.conda +md5 : ff0c8822fd98776a9c0dc456bdcf463b +timestamp : 2026-04-12 21:27:50 UTC +dependencies: + - _openmp_mutex >=4.5 + - libgcc >=14 + - libgomp + - libstdcxx >=14 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/rscape.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/rscape.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a16008daa7e4d6824f96c9957047ae3b5970ebd --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/rscape.manual_bundle.txt @@ -0,0 +1,528 @@ +# Tool: rscape +software_name: rscape +tier: T1 +domain: t1_backfill_overall +downloads: 154608 +summary: R-scape (RNA Structural Covariation Above Phylogenetic Expectation) looks for evidence of a conserved RNA secondary structure by measuring pairwise covariations observed in an input multiple sequence alignment. +description: R-scape (RNA Structural Covariation Above Phylogenetic Expectation) looks for evidence of a conserved RNA secondary structure by measuring pairwise covariations observed in an input multiple sequence alignment. +dependencies: gnuplot, libgcc >=13, libstdcxx >=13, perl +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: http://eddylab.org/R-scape/ +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### http://eddylab.org/R-scape/ +R-scape Toggle navigation R-scape RNA Structural Covariation Above Phylogenetic Expectation R-scape looks for evidence of a conserved RNA structure by measuring pairwise covariations observed in an input multiple sequence alignment. It analyzes all possible pairs, including those in your proposed structure (if you provide one). R-scape uses a null hypothesis that takes phylogenetic correlations and base composition biases into account, which can be sources of apparent pairwise covariation that are not due to conserved RNA structure. The input is an RNA multiple sequence alignment in Stockholm format , optionally (usually) with an annotated consensus secondary structure. The structure may include pseudoknots. Only the first alignment in the file is analyzed; if you submit a Stockholm file containing more than one alignment, the others are ignored. The output is a list of covarying pairs that are statistically significant at a given E-value. The E-value (or threshold for the number of false positives expected). For each covarying pair, the output also reports the inferred number of substitutions that occurred at these two positions in the phylogenetic tree, and the estimated statistical power for R-scape to detect a significantly covarying base pair when that much variation is present. R-scape has two different modes of operation which determine how it calculates E-values. One mode analyses all possible pairs equally. The other mode requires a given consensus structure and performs two independent covariation tests: one on the set of proposed base pairs, the other on all other possible pairs. For either mode, R-scape can calculate a structure based on the observed covariations using the CaCoFold algorithm. To see an example , you can download the Rfam seed alignment for the purine riboswitch (RF00167) - or any other Rfam RNA alignment - and upload that file to R-scape. Analyze an RNA alignment Find base pairs with statistically significant covariation support. Optionally, propose a structure compatible with all significantly covarying base pairs. Choose a Stockholm alignment file to upload: E-value Choose a mode Evaluate region for conserved structure Predict new structure Evaluate given structure Improve given structure Upload and run R-scape analysis Evaluate region for conserved structure All possible pairs are analyzed equally in one single test. If a consensus structure is provided, that structure is ignored in the covariation test, but it is visualized with the significant covarying pairs highlighted in green. preferred use: This option is most appropriate if you're trying to determine if a conserved structure exists. Predict new structure All possible pairs are analyzed equally in one single test. A structure is predicted and visualized with the significant covarying pairs highlighted in green. preferred use: This option is most appropriate for obtaining a new consensus structure prediction based on covariation analysis. Evaluate given structure Requires that your Stockholm file has a proposed consensus structure annotation. Two independent covariation tests are performed, one on the set of proposed base pairs, the other on all other possible pairs. The given structure is visualized with the significant covarying pairs highlighted in green. preferred use: This option is most appropriate for evaluating how well an independently proposed consensus structure is supported by covariation analysis. Improve given structure Requires that your Stockholm file has a proposed consensus structure annotation. Two independent covariation tests are performed, one on the set of proposed base pairs, the other on all other possible pairs. A new consensus structure is predicted and visualized with the significant covarying pairs highlighted in green. preferred use: This option is most appropriate for using covariation analysis to improve your current consensus structure. Download Current source code distribution: rscape.tar.gz Documentation R-scape manual: R-scape_userguide.pdf Publications A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs. E Rivas, J Clements, and SR Eddy. Nature Methods 14:45-48, 2017. Estimating the power of sequence covariation for detecting conserved RNA structure. E Rivas, J Clements, and SR Eddy. Bioinformatics 36:3072-3076, 2020. RNA structure prediction using positive and negative evolutionary information. E Rivas. PLOS Computational Biology 16:e100838, 2020. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge rscape --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +rscape 0.2.1 0 +-------------- +file name : rscape-0.2.1-0.tar.bz2 +name : rscape +version : 0.2.1 +build : 0 +build number: 0 +size : 5.6 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.2.1-0.tar.bz2 +md5 : d392485a1588bd6c7cdcb5dd45882eb8 +dependencies: + - gnuplot + - libgcc + + +rscape 0.3.1 0 +-------------- +file name : rscape-0.3.1-0.tar.bz2 +name : rscape +version : 0.3.1 +build : 0 +build number: 0 +size : 6.5 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.3.1-0.tar.bz2 +md5 : bb97c8878c7f8187301aef0cbf7f0d83 +dependencies: + - gnuplot + - libgcc + + +rscape 0.6.1 0 +-------------- +file name : rscape-0.6.1-0.tar.bz2 +name : rscape +version : 0.6.1 +build : 0 +build number: 0 +size : 8.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.6.1-0.tar.bz2 +md5 : 09fcfc4e461800a0dff9e236584cb40d +dependencies: + - gnuplot + - libgcc + + +rscape 0.6.1 2 +-------------- +file name : rscape-0.6.1-2.tar.bz2 +name : rscape +version : 0.6.1 +build : 2 +build number: 2 +size : 8.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.6.1-2.tar.bz2 +md5 : 64c38c4c5c36992dfa190c62d0b79de5 +dependencies: + - gnuplot ==5.0.4 + - libgcc + + +rscape 0.6.1 3 +-------------- +file name : rscape-0.6.1-3.tar.bz2 +name : rscape +version : 0.6.1 +build : 3 +build number: 3 +size : 8.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.6.1-3.tar.bz2 +md5 : 13b95022ebce0be51870d9d197a92f3c +dependencies: + - gnuplot ==5.0.6 + - libgcc + + +rscape 0.6.1 h470a237_4 +----------------------- +file name : rscape-0.6.1-h470a237_4.tar.bz2 +name : rscape +version : 0.6.1 +build : h470a237_4 +build number: 4 +size : 7.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.6.1-h470a237_4.tar.bz2 +md5 : 7a76f9c178b4416700853daf1056dd03 +timestamp : 2018-06-22 03:11:48 UTC +dependencies: + - gnuplot 5.0.6 + - libgcc-ng >=4.9 + + +rscape 0.8.3 h1b792b2_4 +----------------------- +file name : rscape-0.8.3-h1b792b2_4.tar.bz2 +name : rscape +version : 0.8.3 +build : h1b792b2_4 +build number: 4 +size : 9.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.8.3-h1b792b2_4.tar.bz2 +md5 : d3393ca3268a80fd243492091f338284 +timestamp : 2021-03-27 00:04:54 UTC +dependencies: + - gnuplot + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + + +rscape 0.8.3 h503566f_8 +----------------------- +file name : rscape-0.8.3-h503566f_8.tar.bz2 +name : rscape +version : 0.8.3 +build : h503566f_8 +build number: 8 +size : 8.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.8.3-h503566f_8.tar.bz2 +md5 : 12148d3143bf3305c64d9aeb9e705374 +timestamp : 2024-12-13 21:01:32 UTC +dependencies: + - gnuplot + - libgcc >=13 + - libstdcxx >=13 + + +rscape 0.8.3 h87f3376_5 +----------------------- +file name : rscape-0.8.3-h87f3376_5.tar.bz2 +name : rscape +version : 0.8.3 +build : h87f3376_5 +build number: 5 +size : 9.0 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.8.3-h87f3376_5.tar.bz2 +md5 : 212d09a256039da1bb2f37fda7625019 +timestamp : 2022-02-23 22:13:08 UTC +dependencies: + - gnuplot + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + + +rscape 0.8.3 h87f3376_6 +----------------------- +file name : rscape-0.8.3-h87f3376_6.tar.bz2 +name : rscape +version : 0.8.3 +build : h87f3376_6 +build number: 6 +size : 9.1 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.8.3-h87f3376_6.tar.bz2 +md5 : 937a85edd0cc82e7a02b7180625256d2 +timestamp : 2023-05-13 16:36:46 UTC +dependencies: + - gnuplot + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +rscape 0.8.3 hdbdd923_6 +----------------------- +file name : rscape-0.8.3-hdbdd923_6.tar.bz2 +name : rscape +version : 0.8.3 +build : hdbdd923_6 +build number: 6 +size : 9.0 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.8.3-hdbdd923_6.tar.bz2 +md5 : a0fc38c921ebd4fd5b75124fde270004 +timestamp : 2023-05-14 22:32:45 UTC +dependencies: + - gnuplot + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +rscape 0.8.3 hdbdd923_7 +----------------------- +file name : rscape-0.8.3-hdbdd923_7.tar.bz2 +name : rscape +version : 0.8.3 +build : hdbdd923_7 +build number: 7 +size : 9.0 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.8.3-hdbdd923_7.tar.bz2 +md5 : edda13e99ace019c177ff3bb83faac14 +timestamp : 2023-05-15 20:53:32 UTC +dependencies: + - gnuplot + - libgcc-ng >=12 + - libstdcxx-ng >=12 + + +rscape 0.8.3 he1b5a44_3 +----------------------- +file name : rscape-0.8.3-he1b5a44_3.tar.bz2 +name : rscape +version : 0.8.3 +build : he1b5a44_3 +build number: 3 +size : 7.5 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.8.3-he1b5a44_3.tar.bz2 +md5 : 6b22f00b1c716032f7072859ea8d121f +timestamp : 2019-10-26 17:31:46 UTC +dependencies: + - gnuplot + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +rscape 0.8.3 hf484d3e_0 +----------------------- +file name : rscape-0.8.3-hf484d3e_0.tar.bz2 +name : rscape +version : 0.8.3 +build : hf484d3e_0 +build number: 0 +size : 7.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.8.3-hf484d3e_0.tar.bz2 +md5 : f57e448fba851615e8af7b0d890010d6 +timestamp : 2018-08-06 15:12:51 UTC +dependencies: + - gnuplot + - libgcc-ng >=7.2.0 + - libstdcxx-ng >=7.2.0 + + +rscape 0.8.3 hf484d3e_1 +----------------------- +file name : rscape-0.8.3-hf484d3e_1.tar.bz2 +name : rscape +version : 0.8.3 +build : hf484d3e_1 +build number: 1 +size : 7.5 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.8.3-hf484d3e_1.tar.bz2 +md5 : 1b5a7bfb672f864c4b8f77593cd3b5ea +timestamp : 2018-12-19 16:11:48 UTC +dependencies: + - gnuplot + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +rscape 0.8.3 hf484d3e_2 +----------------------- +file name : rscape-0.8.3-hf484d3e_2.tar.bz2 +name : rscape +version : 0.8.3 +build : hf484d3e_2 +build number: 2 +size : 7.5 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-0.8.3-hf484d3e_2.tar.bz2 +md5 : e70e2d8b5153c08859122c8a22f2192a +timestamp : 2018-12-20 19:17:55 UTC +dependencies: + - gnuplot + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +rscape 1.0.4 hf484d3e_1 +----------------------- +file name : rscape-1.0.4-hf484d3e_1.tar.bz2 +name : rscape +version : 1.0.4 +build : hf484d3e_1 +build number: 1 +size : 6.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-1.0.4-hf484d3e_1.tar.bz2 +md5 : 2d705e84263362db939e4d2545f09583 +timestamp : 2018-12-19 16:02:57 UTC +dependencies: + - gnuplot + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +rscape 1.0.4 hf484d3e_2 +----------------------- +file name : rscape-1.0.4-hf484d3e_2.tar.bz2 +name : rscape +version : 1.0.4 +build : hf484d3e_2 +build number: 2 +size : 6.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-1.0.4-hf484d3e_2.tar.bz2 +md5 : cc3ac2dca93a9a64c072e00e5c73492e +timestamp : 2018-12-20 19:09:13 UTC +dependencies: + - gnuplot + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +rscape 1.2.2 he1b5a44_2 +----------------------- +file name : rscape-1.2.2-he1b5a44_2.tar.bz2 +name : rscape +version : 1.2.2 +build : he1b5a44_2 +build number: 2 +size : 4.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-1.2.2-he1b5a44_2.tar.bz2 +md5 : 01907a672494fce9c1581904bdbfbf09 +timestamp : 2019-09-27 20:38:04 UTC +dependencies: + - gnuplot + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + + +rscape 1.2.2 hf484d3e_0 +----------------------- +file name : rscape-1.2.2-hf484d3e_0.tar.bz2 +name : rscape +version : 1.2.2 +build : hf484d3e_0 +build number: 0 +size : 4.6 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-1.2.2-hf484d3e_0.tar.bz2 +md5 : bcc48e3a03f17a0a32300c9d6be71df4 +timestamp : 2019-01-03 20:58:35 UTC +dependencies: + - gnuplot + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +rscape 1.2.2 hf484d3e_1 +----------------------- +file name : rscape-1.2.2-hf484d3e_1.tar.bz2 +name : rscape +version : 1.2.2 +build : hf484d3e_1 +build number: 1 +size : 4.6 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-1.2.2-hf484d3e_1.tar.bz2 +md5 : 60907a99e0485a5804d4eb8476038ddf +timestamp : 2019-01-04 11:00:58 UTC +dependencies: + - gnuplot + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +rscape 1.4.0 h1b792b2_1 +----------------------- +file name : rscape-1.4.0-h1b792b2_1.tar.bz2 +name : rscape +version : 1.4.0 +build : h1b792b2_1 +build number: 1 +size : 4.5 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-1.4.0-h1b792b2_1.tar.bz2 +md5 : 9fdad0d59a5a15397ceab323435e7fd2 +timestamp : 2021-03-27 00:24:21 UTC +dependencies: + - gnuplot + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + + +rscape 1.4.0 h503566f_5 +----------------------- +file name : rscape-1.4.0-h503566f_5.tar.bz2 +name : rscape +version : 1.4.0 +build : h503566f_5 +build number: 5 +size : 4.6 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-1.4.0-h503566f_5.tar.bz2 +md5 : b305b92da16df27543b6a161dff99ab1 +timestamp : 2024-12-13 21:09:01 UTC +dependencies: + - gnuplot + - libgcc >=13 + - libstdcxx >=13 + - perl + + +rscape 1.4.0 h87f3376_2 +----------------------- +file name : rscape-1.4.0-h87f3376_2.tar.bz2 +name : rscape +version : 1.4.0 +build : h87f3376_2 +build number: 2 +size : 4.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-1.4.0-h87f3376_2.tar.bz2 +md5 : e3cda70230648754973edbea3d4fb797 +timestamp : 2022-02-23 22:33:40 UTC +dependencies: + - gnuplot + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - perl + + +rscape 1.4.0 h87f3376_3 +----------------------- +file name : rscape-1.4.0-h87f3376_3.tar.bz2 +name : rscape +version : 1.4.0 +build : h87f3376_3 +build number: 3 +size : 4.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rscape-1.4.0-h87f3376_3.tar.bz2 +md5 : 60147be725b04b5e56daafc6300ba3b2 +times diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/rust-bio-tools.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/rust-bio-tools.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..540a7a4c99359c0ac27a6f8faf53b85ab151ce57 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/rust-bio-tools.manual_bundle.txt @@ -0,0 +1,455 @@ +# Tool: rust-bio-tools +software_name: rust-bio-tools +tier: T1 +domain: t1_backfill_overall +downloads: 318270 +summary: A growing collection of fast and secure command line utilities for dealing with NGS data +implemented on top of Rust-Bio. +description: A growing collection of fast and secure command line utilities for dealing with NGS data +implemented on top of Rust-Bio. +dependencies: gsl >=2.7,<2.8.0a0, libcblas >=3.9.0,<4.0a0, libgcc >=13, libstdcxx >=13, openssl >=3.5.3,<4.0a0, starcode +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/rust-bio/rust-bio-tools +doc_url: +dev_url: https://github.com/rust-bio/rust-bio-tools + +## URL Docs Extract +### https://github.com/rust-bio/rust-bio-tools +GitHub - rust-bio/rust-bio-tools: A set of command line utilities based on Rust-Bio. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} rust-bio / rust-bio-tools Public Notifications You must be signed in to change notification settings Fork 20 Star 205 Code Issues 9 Pull requests 6 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights rust-bio/rust-bio-tools master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 610 Commits 610 Commits .cargo .cargo .github .github src src tests tests .gitignore .gitignore .gitpod.yml .gitpod.yml .pre-commit-config.yaml .pre-commit-config.yaml CHANGELOG.md CHANGELOG.md Cargo.toml Cargo.toml Dockerfile Dockerfile LICENSE.md LICENSE.md README.md README.md View all files Repository files navigation README MIT license Rust-Bio-Tools A set of ultra fast and robust command line utilities for bioinformatics tasks based on Rust-Bio. Rust-Bio-Tools provides a command rbt , which currently supports the following operations: a linear time implementation for fuzzy matching of two vcf/bcf files ( rbt vcf-match ) a vcf/bcf to txt converter, that flexibly allows to select tags and properly handles multiallelic sites ( rbt vcf-to-txt ) a linear time round-robin FASTQ splitter that splits a given FASTQ files into a given number of chunks ( rbt fastq-split ) a linear time extraction of depth information from BAMs at given loci ( rbt bam-depth ) a utility to quickly filter records from a FASTQ file ( rbt fastq-filter ) a tool to merge BAM or FASTQ reads using marked duplicates respectively unique molecular identifiers (UMIs) ( rbt collapse-reads-to-fragments bam|fastq ) a tool to generate interactive HTML based reports that offer multiple plots visualizing the provided genomics data in VCF and BAM format ( rbt vcf-report ) a tool to generate an interactive HTML based report from a csv file including visualizations ( rbt csv-report ) a tool for splitting VCF/BCF files into N equal chunks, including BND support ( rbt vcf-split ) a tool to generate visualizations for a specific region of one or multiple BAM files with a given reference contained in a single HTML file ( rbt plot-bam ) Further functionality is added as it is needed by the authors. Check out the Contributing section if you want contribute anything yourself. For a list of changes, take a look at the CHANGELOG . Installation Requirements Rust-Bio-Tools depends rgsl which needs GSL to be installed: Ubuntu: sudo apt-get install libgsl-dev Arch: sudo pacman -S gsl OSX: brew install gsl Bioconda Rust-Bio-Tools is available via Bioconda . With Bioconda set up, installation is as easy as conda install rust-bio-tools Cargo If the Rust compiler and associated Cargo are installed, Rust-Bio-Tools may be installed via cargo install rust-bio-tools Source Download the source code and within the root directory of source run cargo install Usage and Documentation Rust-Bio-Tools installs a command line utility rbt . Issue rbt --help for a summary of all options and tools. Contributing Any contributions are highly welcome. If you plan to contribute we suggest installing pre-commit hooks. To do so: Install pre-commit as explained here Run pre-commit install in the rust-bio-tools base directory This should format, check and lint your code when committing. Authors Johannes Köster ( https://koesterlab.github.io ) Felix Mölder Henning Timm Felix Wiegand About A set of command line utilities based on Rust-Bio. Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 205 stars Watchers 22 watching Forks 20 forks Report repository Releases 81 rust-bio-tools v0.42.2 Latest Apr 10, 2024 + 80 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Rust 77.0% HTML 19.3% JavaScript 3.4% Other 0.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/rust-bio/rust-bio-tools +GitHub - rust-bio/rust-bio-tools: A set of command line utilities based on Rust-Bio. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} rust-bio / rust-bio-tools Public Notifications You must be signed in to change notification settings Fork 20 Star 205 Code Issues 9 Pull requests 6 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights rust-bio/rust-bio-tools master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 610 Commits 610 Commits .cargo .cargo .github .github src src tests tests .gitignore .gitignore .gitpod.yml .gitpod.yml .pre-commit-config.yaml .pre-commit-config.yaml CHANGELOG.md CHANGELOG.md Cargo.toml Cargo.toml Dockerfile Dockerfile LICENSE.md LICENSE.md README.md README.md View all files Repository files navigation README MIT license Rust-Bio-Tools A set of ultra fast and robust command line utilities for bioinformatics tasks based on Rust-Bio. Rust-Bio-Tools provides a command rbt , which currently supports the following operations: a linear time implementation for fuzzy matching of two vcf/bcf files ( rbt vcf-match ) a vcf/bcf to txt converter, that flexibly allows to select tags and properly handles multiallelic sites ( rbt vcf-to-txt ) a linear time round-robin FASTQ splitter that splits a given FASTQ files into a given number of chunks ( rbt fastq-split ) a linear time extraction of depth information from BAMs at given loci ( rbt bam-depth ) a utility to quickly filter records from a FASTQ file ( rbt fastq-filter ) a tool to merge BAM or FASTQ reads using marked duplicates respectively unique molecular identifiers (UMIs) ( rbt collapse-reads-to-fragments bam|fastq ) a tool to generate interactive HTML based reports that offer multiple plots visualizing the provided genomics data in VCF and BAM format ( rbt vcf-report ) a tool to generate an interactive HTML based report from a csv file including visualizations ( rbt csv-report ) a tool for splitting VCF/BCF files into N equal chunks, including BND support ( rbt vcf-split ) a tool to generate visualizations for a specific region of one or multiple BAM files with a given reference contained in a single HTML file ( rbt plot-bam ) Further functionality is added as it is needed by the authors. Check out the Contributing section if you want contribute anything yourself. For a list of changes, take a look at the CHANGELOG . Installation Requirements Rust-Bio-Tools depends rgsl which needs GSL to be installed: Ubuntu: sudo apt-get install libgsl-dev Arch: sudo pacman -S gsl OSX: brew install gsl Bioconda Rust-Bio-Tools is available via Bioconda . With Bioconda set up, installation is as easy as conda install rust-bio-tools Cargo If the Rust compiler and associated Cargo are installed, Rust-Bio-Tools may be installed via cargo install rust-bio-tools Source Download the source code and within the root directory of source run cargo install Usage and Documentation Rust-Bio-Tools installs a command line utility rbt . Issue rbt --help for a summary of all options and tools. Contributing Any contributions are highly welcome. If you plan to contribute we suggest installing pre-commit hooks. To do so: Install pre-commit as explained here Run pre-commit install in the rust-bio-tools base directory This should format, check and lint your code when committing. Authors Johannes Köster ( https://koesterlab.github.io ) Felix Mölder Henning Timm Felix Wiegand About A set of command line utilities based on Rust-Bio. Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 205 stars Watchers 22 watching Forks 20 forks Report repository Releases 81 rust-bio-tools v0.42.2 Latest Apr 10, 2024 + 80 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Rust 77.0% HTML 19.3% JavaScript 3.4% Other 0.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge rust-bio-tools --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +rust-bio-tools 0.1.1 0 +---------------------- +file name : rust-bio-tools-0.1.1-0.tar.bz2 +name : rust-bio-tools +version : 0.1.1 +build : 0 +build number: 0 +size : 1.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.1.1-0.tar.bz2 +md5 : 4b722946012434e76d33efd18893454f +dependencies: + - libgcc + - zlib + + +rust-bio-tools 0.1.2 0 +---------------------- +file name : rust-bio-tools-0.1.2-0.tar.bz2 +name : rust-bio-tools +version : 0.1.2 +build : 0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.1.2-0.tar.bz2 +md5 : c27437c7e2ddbab033ddba8a5a4372b2 +dependencies: + - libgcc + - zlib + + +rust-bio-tools 0.1.3 0 +---------------------- +file name : rust-bio-tools-0.1.3-0.tar.bz2 +name : rust-bio-tools +version : 0.1.3 +build : 0 +build number: 0 +size : 2.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.1.3-0.tar.bz2 +md5 : 45964524136bce600ef0c595f51ea64d +dependencies: + - libgcc + - zlib 1.2.8* + + +rust-bio-tools 0.2.1 0 +---------------------- +file name : rust-bio-tools-0.2.1-0.tar.bz2 +name : rust-bio-tools +version : 0.2.1 +build : 0 +build number: 0 +size : 2.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.2.1-0.tar.bz2 +md5 : 7ef8a20c31b013a506b7adf98bddfd67 +dependencies: + - libgcc + - zlib 1.2.11* + + +rust-bio-tools 0.2.2 0 +---------------------- +file name : rust-bio-tools-0.2.2-0.tar.bz2 +name : rust-bio-tools +version : 0.2.2 +build : 0 +build number: 0 +size : 2.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.2.2-0.tar.bz2 +md5 : 4ea56179fae10a23300511da57462746 +dependencies: + - libgcc + - zlib 1.2.11* + + +rust-bio-tools 0.2.3 0 +---------------------- +file name : rust-bio-tools-0.2.3-0.tar.bz2 +name : rust-bio-tools +version : 0.2.3 +build : 0 +build number: 0 +size : 2.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.2.3-0.tar.bz2 +md5 : 5beef87c4d9f3ed8b664d10ae0b92e99 +dependencies: + - libgcc + - zlib 1.2.11* + + +rust-bio-tools 0.2.4 0 +---------------------- +file name : rust-bio-tools-0.2.4-0.tar.bz2 +name : rust-bio-tools +version : 0.2.4 +build : 0 +build number: 0 +size : 2.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.2.4-0.tar.bz2 +md5 : e743e52760ed6d067b05621e8650d06d +dependencies: + - libgcc + - zlib 1.2.11* + + +rust-bio-tools 0.2.5 0 +---------------------- +file name : rust-bio-tools-0.2.5-0.tar.bz2 +name : rust-bio-tools +version : 0.2.5 +build : 0 +build number: 0 +size : 2.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.2.5-0.tar.bz2 +md5 : 7927cda32d6cac1b1e9b97f7b00d9b43 +dependencies: + - libgcc + - zlib 1.2.11* + + +rust-bio-tools 0.2.5 ha92aebf_1 +------------------------------- +file name : rust-bio-tools-0.2.5-ha92aebf_1.tar.bz2 +name : rust-bio-tools +version : 0.2.5 +build : ha92aebf_1 +build number: 1 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.2.5-ha92aebf_1.tar.bz2 +md5 : 9f86410520e581a62fd7bc4639afa618 +timestamp : 2018-06-22 02:57:14 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.2.6 ha92aebf_1 +------------------------------- +file name : rust-bio-tools-0.2.6-ha92aebf_1.tar.bz2 +name : rust-bio-tools +version : 0.2.6 +build : ha92aebf_1 +build number: 1 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.2.6-ha92aebf_1.tar.bz2 +md5 : d22ff3d96bb6ff769b59d43cdcc792cf +timestamp : 2018-07-04 20:20:22 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.2.7 ha92aebf_0 +------------------------------- +file name : rust-bio-tools-0.2.7-ha92aebf_0.tar.bz2 +name : rust-bio-tools +version : 0.2.7 +build : ha92aebf_0 +build number: 0 +size : 2.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.2.7-ha92aebf_0.tar.bz2 +md5 : f7f62231d4202a2cae4b2aad6eb70788 +timestamp : 2018-12-28 23:04:35 UTC +dependencies: + - libgcc-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.2.8 hd28b015_0 +------------------------------- +file name : rust-bio-tools-0.2.8-hd28b015_0.tar.bz2 +name : rust-bio-tools +version : 0.2.8 +build : hd28b015_0 +build number: 0 +size : 3.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.2.8-hd28b015_0.tar.bz2 +md5 : 478096f359c894b2a25db3fdd976de16 +timestamp : 2019-01-31 07:13:31 UTC +dependencies: + - libgcc-ng >=4.9 + - libstdcxx-ng >=4.9 + - starcode + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.2.9 hdbcaa40_0 +------------------------------- +file name : rust-bio-tools-0.2.9-hdbcaa40_0.tar.bz2 +name : rust-bio-tools +version : 0.2.9 +build : hdbcaa40_0 +build number: 0 +size : 3.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.2.9-hdbcaa40_0.tar.bz2 +md5 : 1361e00228da0ec0972b4ef64b1092c0 +timestamp : 2019-02-24 23:01:39 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - starcode + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.3.0 hbbd2374_0 +------------------------------- +file name : rust-bio-tools-0.3.0-hbbd2374_0.tar.bz2 +name : rust-bio-tools +version : 0.3.0 +build : hbbd2374_0 +build number: 0 +size : 4.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.3.0-hbbd2374_0.tar.bz2 +md5 : 459958e5476d424b2c7bc2dc17c5f4db +timestamp : 2019-04-01 12:54:19 UTC +dependencies: + - gsl >=2.4,<2.5.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - starcode + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.4.0 hbbd2374_0 +------------------------------- +file name : rust-bio-tools-0.4.0-hbbd2374_0.tar.bz2 +name : rust-bio-tools +version : 0.4.0 +build : hbbd2374_0 +build number: 0 +size : 4.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.4.0-hbbd2374_0.tar.bz2 +md5 : 474357f9466538d6addf0d2251fc9072 +timestamp : 2019-04-11 11:57:29 UTC +dependencies: + - gsl >=2.4,<2.5.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - starcode + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.4.1 h34b176d_0 +------------------------------- +file name : rust-bio-tools-0.4.1-h34b176d_0.tar.bz2 +name : rust-bio-tools +version : 0.4.1 +build : h34b176d_0 +build number: 0 +size : 3.3 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.4.1-h34b176d_0.tar.bz2 +md5 : 7923f218b09c99adb894502b559e70d1 +timestamp : 2019-05-02 15:42:20 UTC +dependencies: + - gsl >=2.4,<2.5.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.3,<0.3.4.0a0 + - starcode + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.5.0 h34b176d_0 +------------------------------- +file name : rust-bio-tools-0.5.0-h34b176d_0.tar.bz2 +name : rust-bio-tools +version : 0.5.0 +build : h34b176d_0 +build number: 0 +size : 3.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.5.0-h34b176d_0.tar.bz2 +md5 : d78f8faeb3c4e976df597255209adf3f +timestamp : 2019-05-08 15:42:50 UTC +dependencies: + - gsl >=2.4,<2.5.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.3,<0.3.4.0a0 + - starcode + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.6.0 hf53bd2b_0 +------------------------------- +file name : rust-bio-tools-0.6.0-hf53bd2b_0.tar.bz2 +name : rust-bio-tools +version : 0.6.0 +build : hf53bd2b_0 +build number: 0 +size : 3.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.6.0-hf53bd2b_0.tar.bz2 +md5 : 97fd0b82b6434833747ae465c939af66 +timestamp : 2019-08-28 20:39:31 UTC +dependencies: + - gsl >=2.5,<2.6.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.6,<0.3.7.0a0 + - starcode + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.8.0 h80d5dcc_0 +------------------------------- +file name : rust-bio-tools-0.8.0-h80d5dcc_0.tar.bz2 +name : rust-bio-tools +version : 0.8.0 +build : h80d5dcc_0 +build number: 0 +size : 4.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.8.0-h80d5dcc_0.tar.bz2 +md5 : 0a7d094063881dfa0449bf34ad7c6886 +timestamp : 2019-10-16 10:44:24 UTC +dependencies: + - gsl >=2.5,<2.6.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.6,<0.3.7.0a0 + - openssl >=1.1.1a,<1.1.2a + - starcode + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.8.0 h80d5dcc_1 +------------------------------- +file name : rust-bio-tools-0.8.0-h80d5dcc_1.tar.bz2 +name : rust-bio-tools +version : 0.8.0 +build : h80d5dcc_1 +build number: 1 +size : 4.7 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.8.0-h80d5dcc_1.tar.bz2 +md5 : bce3e0c832924a6202d9d5a1a365b9e9 +timestamp : 2019-10-26 13:21:25 UTC +dependencies: + - gsl >=2.5,<2.6.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.6,<0.3.7.0a0 + - openssl >=1.1.1a,<1.1.2a + - starcode + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.8.1 h80d5dcc_0 +------------------------------- +file name : rust-bio-tools-0.8.1-h80d5dcc_0.tar.bz2 +name : rust-bio-tools +version : 0.8.1 +build : h80d5dcc_0 +build number: 0 +size : 4.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.8.1-h80d5dcc_0.tar.bz2 +md5 : 3191560ef3aa5cdae77ada8241e7cc44 +timestamp : 2019-11-08 20:54:28 UTC +dependencies: + - gsl >=2.5,<2.6.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - openblas >=0.3.6,<0.3.7.0a0 + - openssl >=1.1.1a,<1.1.2a + - starcode + - zlib >=1.2.11,<1.3.0a0 + + +rust-bio-tools 0.8.2 h80d5dcc_0 +------------------------------- +file name : rust-bio-tools-0.8.2-h80d5dcc_0.tar.bz2 +name : rust-bio-tools +version : 0.8.2 +build : h80d5dcc_0 +build number: 0 +size : 4.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/rust-bio-tools-0.8.2-h80d5dcc_0.tar.bz2 +md5 : 3ed5934286529fe61bf9beb83277b836 +timestamp : 2019-11-22 09:26:58 UTC +dependencies: + - gsl >=2.5,<2.6.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/samsift.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/samsift.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1efeae8e6264883f31b2d62a4234bfd7d4cad910 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/samsift.manual_bundle.txt @@ -0,0 +1,499 @@ +# Tool: samsift +software_name: samsift +tier: T1 +domain: t1_backfill_overall +downloads: 262008 +summary: Advanced filtering and tagging of SAM/BAM alignments using Python expressions. +description: Advanced filtering and tagging of SAM/BAM alignments using Python expressions. +dependencies: curl, pysam, python >=3.8, python-dateutil +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/karel-brinda/samsift +doc_url: +dev_url: https://github.com/karel-brinda/samsift + +## URL Docs Extract +### https://github.com/karel-brinda/samsift +GitHub - karel-brinda/samsift: SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} karel-brinda / samsift Public Notifications You must be signed in to change notification settings Fork 2 Star 23 Code Issues 8 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights karel-brinda/samsift master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 156 Commits 156 Commits .github/ workflows .github/ workflows samsift samsift tests tests .editorconfig .editorconfig .gitignore .gitignore .style.yapf .style.yapf LICENSE LICENSE Makefile Makefile README.rst README.rst pyproject.toml pyproject.toml requirements.txt requirements.txt setup.cfg setup.cfg View all files Repository files navigation README MIT license SAMsift SAMsift is a program for advanced filtering and tagging of SAM/BAM alignments using Python expressions. Getting started # clone this repo and add it to PATH git clone http://github.com/karel-brinda/samsift cd samsift export PATH= $( pwd ) /samsift: $PATH # filtering: keep only alignments with score >94, save them as filtered.bam samsift -i tests/test.bam -o filtered.bam -f ' AS>94 ' # filtering: keep only unaligned reads samsift -i tests/test.bam -f ' FLAG & 0x04 ' # filtering: keep only aligned reads samsift -i tests/test.bam -f ' not(FLAG & 0x04) ' # filtering: keep only sequences containing ACCAGAGGAT samsift -i tests/test.bam -f ' SEQ.find("ACCAGAGGAT")!=-1 ' # filtering: keep only sequences containing A and T only (defined using regular expressions) samsift -i tests/test.bam -f ' re.match(r"^[AT]*$", SEQ) ' # filtering: sample alignments with 25% rate samsift -i tests/test.bam -f ' random.random()<0.25 ' # filtering: sample alignments with 25% rate with a fixed RNG seed samsift -i tests/test.bam -f ' random.random()<0.25 ' -0 ' random.seed(42) ' # filtering: keep only alignments of reads specified in tests/qnames.txt samsift -i tests/test.bam -0 ' q=open("tests/qnames.txt").read().splitlines() ' -f ' QNAME in q ' # filtering: keep only first 5000 reads from chr1 and 5000 reads from chr2 samsift -i tests/test.bam -0 ' c={"chr1":5000,"chr2":5000} ' -f ' c[RNAME]>0 ' -c ' c[RNAME]-=1 ' -m nonstop-remove # tagging: add tags 'ln' with sequence length and 'ab' with average base quality samsift -i tests/test.bam -c ' ln=len(SEQ);ab=1.0*sum(QUALa)/ln ' # tagging: add a tag 'ii' with the number of the current alignment samsift -i tests/test.bam -0 ' i=0 ' -c ' i+=1;ii=i ' # updating: removing sequences and base qualities samsift -i tests/test.bam -c ' a.query_sequence="" ' # updating: switching all reads to unaligned samsift -i tests/test.bam -c ' a.flag|=0x4;a.reference_start=-1;a.cigarstring="";a.reference_id=-1;a.mapping_quality=0 ' Installation Using Bioconda: # add all necessary Bioconda channels conda config --add channels defaults conda config --add channels conda-forge conda config --add channels bioconda # install samsift conda install samsift Using PIP from PyPI: pip install --upgrade samsift Using PIP from Github: pip install --upgrade git+https://github.com/karel-brinda/samsift Command-line parameters Program: samsift (advanced filtering and tagging of SAM/BAM alignments using Python expressions) Version: 0.3.1 Author: Karel Brinda <karel.brinda@inria.fr> Usage: samsift.py [-i FILE] [-o FILE] [-f [PY_EXPR ...]] [-c [PY_CODE ...]] [-m STR] [-0 [PY_CODE ...]] [-d [PY_EXPR ...]] [-t [PY_EXPR ...]] Basic options: -h, --help show this help message and exit -v, --version show program's version number and exit -i FILE input SAM/BAM file [-] -o FILE output SAM/BAM file [-] -f [PY_EXPR ...] filtering expression [True] -c [PY_CODE ...] code to be executed (e.g., assigning new tags) [None] -m STR mode: strict (stop on first error) nonstop-keep (keep alignments causing errors) nonstop-remove (remove alignments causing errors) [strict] Advanced options: -0 [PY_CODE ...] initialization [None] -d [PY_EXPR ...] debugging expression to print [None] -t [PY_EXPR ...] debugging trigger [True] Algorithm exec ( INITIALIZATION ) for ALIGNMENT in ALIGNMENTS : if eval ( DEBUG_TRIGER ): print ( eval ( DEBUG_EXPR )) if eval ( FILTER ): exec ( CODE ) print ( ALIGNMENT ) Python expressions and code. All expressions and code should be valid with respect to Python 3 . Expressions are evaluated using the eval function and code is executed using the exec function. Initialization can be used for importing Python modules, setting global variables (e.g., counters) or loading data from disk. Some modules (namely datetime , math , random , and re ) are loaded without an explicit request, and the internal RNG seed is set to 42. Example (printing all alignments): samsift -i tests/test.bam -f ' True ' SAM fields. Expressions and code can access variables mirroring the fields from the alignment section of the SAM specification , i.e., QNAME , FLAG , RNAME , POS (1-based), MAPQ , CIGAR , RNEXT , PNEXT , TLEN , SEQ , and QUAL . Several additional variables are defined to simply accessing some useful information: QUALa stores the base qualities as an integer array; SEQs , QUALs , QUALsa skip soft-clipped bases; and RNAMEi and RNEXTi store the reference ids as integers. Example (keeping only the alignments with leftmost position <= 10000): samsift -i tests/test.bam -f ' POS<=10000 ' SAMsift internally uses the PySam library and the representation of the current alignment (an instance of the class pysam.AlignedSegment ) is available as a variable a . Therefore, the previous example is equivalent to samsift -i tests/test.bam -f ' a.reference_start+1<=10000 ' The a variable can also be used for modifying the current alignment record. Example (removing the sequence and the bases from every record): samsift -i tests/test.bam -c ' a.query_sequence="" ' SAM tags. Every SAM tag is translated to a variable with the same name. Example (removing alignments with a score smaller or equal to the sequence length): samsift -i tests/test.bam -f ' AS>len(SEQ) ' If CODE is provided, all two-letter variables except re (the Python regex module) are back-translated to tags after the code execution. Example (adding a tag ab carrying the average base quality): samsift -i tests/test.bam -c ' ab=1.0*sum(QUALa)/len(QUALa) ' Errors. If an error occurs during an evalution of an expression or an execution of a code (e.g., due to accessing an undefined tag), then SAMsift behavior depends on the specified mode ( -m ). With the strict mode ( -m strict , default), SAMsift will immediately interrupt the computation and report an error. With the -m nonstop-keep option, SAMsift will continue processing the alignments while keeping the error-causing alignments in the output. With the -m nonstop-remove option, all error-causing alignments are skipped and ommited from the output. Similar programs samtools view can filter alignments based on FLAGS, read group tags, and CIGAR strings. sambamba view supports, in addition to SAMtools, a filtration using simple Perl-like expressions . However, it is not possible to use floats or compare different tags. BamQL provides a simple query language for filtering SAM/BAM files. bamPals adds tags XB, XE, XP and XL. SamJavascript can filter alignments using JavaScript expressions. Picard FilterSamReads can also filter alignments using JavaScript expressions. Issues Please use Github issues . Changelog See Releases . Licence MIT Author Karel Brinda < karel.brinda@inria.fr > About SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions. Topics ngs alignment Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 23 stars Watchers 2 watching Forks 2 forks Report repository Releases 8 SAMsift 0.3.1 Latest Sep 18, 2025 + 7 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 80.4% Makefile 19.1% Shell 0.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/karel-brinda/samsift +GitHub - karel-brinda/samsift: SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} karel-brinda / samsift Public Notifications You must be signed in to change notification settings Fork 2 Star 23 Code Issues 8 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights karel-brinda/samsift master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 156 Commits 156 Commits .github/ workflows .github/ workflows samsift samsift tests tests .editorconfig .editorconfig .gitignore .gitignore .style.yapf .style.yapf LICENSE LICENSE Makefile Makefile README.rst README.rst pyproject.toml pyproject.toml requirements.txt requirements.txt setup.cfg setup.cfg View all files Repository files navigation README MIT license SAMsift SAMsift is a program for advanced filtering and tagging of SAM/BAM alignments using Python expressions. Getting started # clone this repo and add it to PATH git clone http://github.com/karel-brinda/samsift cd samsift export PATH= $( pwd ) /samsift: $PATH # filtering: keep only alignments with score >94, save them as filtered.bam samsift -i tests/test.bam -o filtered.bam -f ' AS>94 ' # filtering: keep only unaligned reads samsift -i tests/test.bam -f ' FLAG & 0x04 ' # filtering: keep only aligned reads samsift -i tests/test.bam -f ' not(FLAG & 0x04) ' # filtering: keep only sequences containing ACCAGAGGAT samsift -i tests/test.bam -f ' SEQ.find("ACCAGAGGAT")!=-1 ' # filtering: keep only sequences containing A and T only (defined using regular expressions) samsift -i tests/test.bam -f ' re.match(r"^[AT]*$", SEQ) ' # filtering: sample alignments with 25% rate samsift -i tests/test.bam -f ' random.random()<0.25 ' # filtering: sample alignments with 25% rate with a fixed RNG seed samsift -i tests/test.bam -f ' random.random()<0.25 ' -0 ' random.seed(42) ' # filtering: keep only alignments of reads specified in tests/qnames.txt samsift -i tests/test.bam -0 ' q=open("tests/qnames.txt").read().splitlines() ' -f ' QNAME in q ' # filtering: keep only first 5000 reads from chr1 and 5000 reads from chr2 samsift -i tests/test.bam -0 ' c={"chr1":5000,"chr2":5000} ' -f ' c[RNAME]>0 ' -c ' c[RNAME]-=1 ' -m nonstop-remove # tagging: add tags 'ln' with sequence length and 'ab' with average base quality samsift -i tests/test.bam -c ' ln=len(SEQ);ab=1.0*sum(QUALa)/ln ' # tagging: add a tag 'ii' with the number of the current alignment samsift -i tests/test.bam -0 ' i=0 ' -c ' i+=1;ii=i ' # updating: removing sequences and base qualities samsift -i tests/test.bam -c ' a.query_sequence="" ' # updating: switching all reads to unaligned samsift -i tests/test.bam -c ' a.flag|=0x4;a.reference_start=-1;a.cigarstring="";a.reference_id=-1;a.mapping_quality=0 ' Installation Using Bioconda: # add all necessary Bioconda channels conda config --add channels defaults conda config --add channels conda-forge conda config --add channels bioconda # install samsift conda install samsift Using PIP from PyPI: pip install --upgrade samsift Using PIP from Github: pip install --upgrade git+https://github.com/karel-brinda/samsift Command-line parameters Program: samsift (advanced filtering and tagging of SAM/BAM alignments using Python expressions) Version: 0.3.1 Author: Karel Brinda <karel.brinda@inria.fr> Usage: samsift.py [-i FILE] [-o FILE] [-f [PY_EXPR ...]] [-c [PY_CODE ...]] [-m STR] [-0 [PY_CODE ...]] [-d [PY_EXPR ...]] [-t [PY_EXPR ...]] Basic options: -h, --help show this help message and exit -v, --version show program's version number and exit -i FILE input SAM/BAM file [-] -o FILE output SAM/BAM file [-] -f [PY_EXPR ...] filtering expression [True] -c [PY_CODE ...] code to be executed (e.g., assigning new tags) [None] -m STR mode: strict (stop on first error) nonstop-keep (keep alignments causing errors) nonstop-remove (remove alignments causing errors) [strict] Advanced options: -0 [PY_CODE ...] initialization [None] -d [PY_EXPR ...] debugging expression to print [None] -t [PY_EXPR ...] debugging trigger [True] Algorithm exec ( INITIALIZATION ) for ALIGNMENT in ALIGNMENTS : if eval ( DEBUG_TRIGER ): print ( eval ( DEBUG_EXPR )) if eval ( FILTER ): exec ( CODE ) print ( ALIGNMENT ) Python expressions and code. All expressions and code should be valid with respect to Python 3 . Expressions are evaluated using the eval function and code is executed using the exec function. Initialization can be used for importing Python modules, setting global variables (e.g., counters) or loading data from disk. Some modules (namely datetime , math , random , and re ) are loaded without an explicit request, and the internal RNG seed is set to 42. Example (printing all alignments): samsift -i tests/test.bam -f ' True ' SAM fields. Expressions and code can access variables mirroring the fields from the alignment section of the SAM specification , i.e., QNAME , FLAG , RNAME , POS (1-based), MAPQ , CIGAR , RNEXT , PNEXT , TLEN , SEQ , and QUAL . Several additional variables are defined to simply accessing some useful information: QUALa stores the base qualities as an integer array; SEQs , QUALs , QUALsa skip soft-clipped bases; and RNAMEi and RNEXTi store the reference ids as integers. Example (keeping only the alignments with leftmost position <= 10000): samsift -i tests/test.bam -f ' POS<=10000 ' SAMsift internally uses the PySam library and the representation of the current alignment (an instance of the class pysam.AlignedSegment ) is available as a variable a . Therefore, the previous example is equivalent to samsift -i tests/test.bam -f ' a.reference_start+1<=10000 ' The a variable can also be used for modifying the current alignment record. Example (removing the sequence and the bases from every record): samsift -i tests/test.bam -c ' a.query_sequence="" ' SAM tags. Every SAM tag is translated to a variable with the same name. Example (removing alignments with a score smaller or equal to the sequence length): samsift -i tests/test.bam -f ' AS>len(SEQ) ' If CODE is provided, all two-letter variables except re (the Python regex module) are back-translated to tags after the code execution. Example (adding a tag ab carrying the average base quality): samsift -i tests/test.bam -c ' ab=1.0*sum(QUALa)/len(QUALa) ' Errors. If an error occurs during an evalution of an expression or an execution of a code (e.g., due to accessing an undefined tag), then SAMsift behavior depends on the specified mode ( -m ). With the strict mode ( -m strict , default), SAMsift will immediately interrupt the computation and report an error. With the -m nonstop-keep option, SAMsift will continue processing the alignments while keeping the error-causing alignments in the output. With the -m nonstop-remove option, all error-causing alignments are skipped and ommited from the output. Similar programs samtools view can filter alignments based on FLAGS, read group tags, and CIGAR strings. sambamba view supports, in addition to SAMtools, a filtration using simple Perl-like expressions . However, it is not possible to use floats or compare different tags. BamQL provides a simple query language for filtering SAM/BAM files. bamPals adds tags XB, XE, XP and XL. SamJavascript can filter alignments using JavaScript expressions. Picard FilterSamReads can also filter alignments using JavaScript expressions. Issues Please use Github issues . Changelog See Releases . Licence MIT Author Karel Brinda < karel.brinda@inria.fr > About SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions. Topics ngs alignment Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 23 stars Watchers 2 watching Forks 2 forks Report repository Releases 8 SAMsift 0.3.1 Latest Sep 18, 2025 + 7 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 80.4% Makefile 19.1% Shell 0.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge samsift --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +samsift 0.1.0 py35_0 +-------------------- +file name : samsift-0.1.0-py35_0.tar.bz2 +name : samsift +version : 0.1.0 +build : py35_0 +build number: 0 +size : 10 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.1.0-py35_0.tar.bz2 +md5 : 4054135b36f0b6aaadef278fff79cc40 +dependencies: + - pysam + - python 3.5* + + +samsift 0.1.0 py35_1 +-------------------- +file name : samsift-0.1.0-py35_1.tar.bz2 +name : samsift +version : 0.1.0 +build : py35_1 +build number: 1 +size : 10 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.1.0-py35_1.tar.bz2 +md5 : 1aca7e306d58233eca2a7ae068b0f381 +timestamp : 2018-06-29 13:22:36 UTC +dependencies: + - pysam + - python >=3.5,<3.6.0a0 + + +samsift 0.1.0 py36_0 +-------------------- +file name : samsift-0.1.0-py36_0.tar.bz2 +name : samsift +version : 0.1.0 +build : py36_0 +build number: 0 +size : 10 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.1.0-py36_0.tar.bz2 +md5 : 30ff2d9879ac59b7204dcbeb3ddcf505 +dependencies: + - pysam + - python 3.6* + + +samsift 0.1.0 py36_1 +-------------------- +file name : samsift-0.1.0-py36_1.tar.bz2 +name : samsift +version : 0.1.0 +build : py36_1 +build number: 1 +size : 10 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.1.0-py36_1.tar.bz2 +md5 : d4ba83ce8a38bd99e9baa87a755861a1 +timestamp : 2018-06-29 13:21:41 UTC +dependencies: + - pysam + - python >=3.6,<3.7.0a0 + + +samsift 0.2.0 py35_0 +-------------------- +file name : samsift-0.2.0-py35_0.tar.bz2 +name : samsift +version : 0.2.0 +build : py35_0 +build number: 0 +size : 14 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.0-py35_0.tar.bz2 +md5 : 21015ffe76264061c1581fa470e682bd +dependencies: + - pysam + - python 3.5* + + +samsift 0.2.0 py35_1 +-------------------- +file name : samsift-0.2.0-py35_1.tar.bz2 +name : samsift +version : 0.2.0 +build : py35_1 +build number: 1 +size : 15 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.0-py35_1.tar.bz2 +md5 : eca080110193c599c946ccae9f5137cf +timestamp : 2018-06-29 17:04:48 UTC +dependencies: + - pysam + - python >=3.5,<3.6.0a0 + + +samsift 0.2.0 py36_0 +-------------------- +file name : samsift-0.2.0-py36_0.tar.bz2 +name : samsift +version : 0.2.0 +build : py36_0 +build number: 0 +size : 14 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.0-py36_0.tar.bz2 +md5 : 1fc7c22deeab25176721a3c5f29d3852 +dependencies: + - pysam + - python 3.6* + + +samsift 0.2.0 py36_1 +-------------------- +file name : samsift-0.2.0-py36_1.tar.bz2 +name : samsift +version : 0.2.0 +build : py36_1 +build number: 1 +size : 15 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.0-py36_1.tar.bz2 +md5 : 27010b2212625318b80d3e2a55bb9766 +timestamp : 2018-06-29 17:05:30 UTC +dependencies: + - pysam + - python >=3.6,<3.7.0a0 + + +samsift 0.2.1 py35_0 +-------------------- +file name : samsift-0.2.1-py35_0.tar.bz2 +name : samsift +version : 0.2.1 +build : py35_0 +build number: 0 +size : 16 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.1-py35_0.tar.bz2 +md5 : 54e732e2c4a23318cf0563dccef10f77 +dependencies: + - pysam + - python 3.5* + + +samsift 0.2.1 py35_1 +-------------------- +file name : samsift-0.2.1-py35_1.tar.bz2 +name : samsift +version : 0.2.1 +build : py35_1 +build number: 1 +size : 16 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.1-py35_1.tar.bz2 +md5 : 9b72878a1929462163c5f9ea5a470af2 +timestamp : 2018-06-29 17:28:57 UTC +dependencies: + - pysam + - python >=3.5,<3.6.0a0 + + +samsift 0.2.1 py36_0 +-------------------- +file name : samsift-0.2.1-py36_0.tar.bz2 +name : samsift +version : 0.2.1 +build : py36_0 +build number: 0 +size : 16 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.1-py36_0.tar.bz2 +md5 : 22a5e1fc4f4c3b14ee4e1daaf312e9a7 +dependencies: + - pysam + - python 3.6* + + +samsift 0.2.1 py36_1 +-------------------- +file name : samsift-0.2.1-py36_1.tar.bz2 +name : samsift +version : 0.2.1 +build : py36_1 +build number: 1 +size : 16 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.1-py36_1.tar.bz2 +md5 : a610b4bc60c545dd6232abb6f0d91986 +timestamp : 2018-06-29 17:29:39 UTC +dependencies: + - pysam + - python >=3.6,<3.7.0a0 + + +samsift 0.2.2 py35_0 +-------------------- +file name : samsift-0.2.2-py35_0.tar.bz2 +name : samsift +version : 0.2.2 +build : py35_0 +build number: 0 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.2-py35_0.tar.bz2 +md5 : 3b423607bbb648ff2f97175ec8535261 +dependencies: + - pysam + - python 3.5* + + +samsift 0.2.2 py35_1 +-------------------- +file name : samsift-0.2.2-py35_1.tar.bz2 +name : samsift +version : 0.2.2 +build : py35_1 +build number: 1 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.2-py35_1.tar.bz2 +md5 : ef570cb1a441b27d3b4c85c8c3851f8e +timestamp : 2018-06-29 17:13:19 UTC +dependencies: + - pysam + - python >=3.5,<3.6.0a0 + + +samsift 0.2.2 py36_0 +-------------------- +file name : samsift-0.2.2-py36_0.tar.bz2 +name : samsift +version : 0.2.2 +build : py36_0 +build number: 0 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.2-py36_0.tar.bz2 +md5 : 57e4f22f2b5812b714aaec2714a64f3f +dependencies: + - pysam + - python 3.6* + + +samsift 0.2.2 py36_1 +-------------------- +file name : samsift-0.2.2-py36_1.tar.bz2 +name : samsift +version : 0.2.2 +build : py36_1 +build number: 1 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.2-py36_1.tar.bz2 +md5 : 76f8f3f5d33ab2edd1d4e7c93b58eb28 +timestamp : 2018-06-29 17:14:06 UTC +dependencies: + - pysam + - python >=3.6,<3.7.0a0 + + +samsift 0.2.3 py35_0 +-------------------- +file name : samsift-0.2.3-py35_0.tar.bz2 +name : samsift +version : 0.2.3 +build : py35_0 +build number: 0 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.3-py35_0.tar.bz2 +md5 : 81840a183bf6bb9f1226b2ec3a0bd9d3 +dependencies: + - pysam + - python 3.5* + + +samsift 0.2.3 py35_1 +-------------------- +file name : samsift-0.2.3-py35_1.tar.bz2 +name : samsift +version : 0.2.3 +build : py35_1 +build number: 1 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.3-py35_1.tar.bz2 +md5 : f0f965409ac9df022764b94e205e6f60 +timestamp : 2018-06-29 17:22:22 UTC +dependencies: + - pysam + - python >=3.5,<3.6.0a0 + + +samsift 0.2.3 py36_0 +-------------------- +file name : samsift-0.2.3-py36_0.tar.bz2 +name : samsift +version : 0.2.3 +build : py36_0 +build number: 0 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.3-py36_0.tar.bz2 +md5 : 0ff2885e62cbec0e7f3431086dfa5fa7 +dependencies: + - pysam + - python 3.6* + + +samsift 0.2.3 py36_1 +-------------------- +file name : samsift-0.2.3-py36_1.tar.bz2 +name : samsift +version : 0.2.3 +build : py36_1 +build number: 1 +size : 18 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.3-py36_1.tar.bz2 +md5 : 8d83722eca99c6ad2f80365cb46269db +timestamp : 2018-06-29 17:21:27 UTC +dependencies: + - pysam + - python >=3.6,<3.7.0a0 + + +samsift 0.2.5 py35_0 +-------------------- +file name : samsift-0.2.5-py35_0.tar.bz2 +name : samsift +version : 0.2.5 +build : py35_0 +build number: 0 +size : 19 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.5-py35_0.tar.bz2 +md5 : 6565edc812a89e7de348d034da1aaf6b +dependencies: + - pysam + - python 3.5* + + +samsift 0.2.5 py35_1 +-------------------- +file name : samsift-0.2.5-py35_1.tar.bz2 +name : samsift +version : 0.2.5 +build : py35_1 +build number: 1 +size : 19 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.5-py35_1.tar.bz2 +md5 : 5ff8112dbdce43761756caebecdf44ee +timestamp : 2018-06-29 13:15:20 UTC +dependencies: + - pysam + - python >=3.5,<3.6.0a0 + - python-dateutil + + +samsift 0.2.5 py36_0 +-------------------- +file name : samsift-0.2.5-py36_0.tar.bz2 +name : samsift +version : 0.2.5 +build : py36_0 +build number: 0 +size : 19 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.5-py36_0.tar.bz2 +md5 : f4293be056874909c93c1b17f2223e2a +dependencies: + - pysam + - python 3.6* + + +samsift 0.2.5 py36_1 +-------------------- +file name : samsift-0.2.5-py36_1.tar.bz2 +name : samsift +version : 0.2.5 +build : py36_1 +build number: 1 +size : 19 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.5-py36_1.tar.bz2 +md5 : 7e33180462ad386eaa16f99ac78221b4 +timestamp : 2018-06-29 13:14:23 UTC +dependencies: + - pysam + - python >=3.6,<3.7.0a0 + - python-dateutil + + +samsift 0.2.5 py36_2 +-------------------- +file name : samsift-0.2.5-py36_2.tar.bz2 +name : samsift +version : 0.2.5 +build : py36_2 +build number: 2 +size : 20 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.5-py36_2.tar.bz2 +md5 : 661f29b687c82370fe53a807934dd6d2 +timestamp : 2019-03-13 05:24:18 UTC +dependencies: + - pysam + - python >=3.6,<3.7.0a0 + - python-dateutil + + +samsift 0.2.5 py37_2 +-------------------- +file name : samsift-0.2.5-py37_2.tar.bz2 +name : samsift +version : 0.2.5 +build : py37_2 +build number: 2 +size : 20 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/samsift-0.2.5-py37_2.tar.bz2 +md5 : c5e4587096f448c621228ea6c0a4e1bb +timestamp : 2019-03-13 05:25:19 UTC +dependencies: + - pysam + - python >=3.7,<3.8.0a0 + - python-dateutil + + +samsift 0.2.5 py_3 +------------------ +file name : samsift-0.2.5-py_3.tar.bz2 +name : samsift +version : 0.2.5 +build : py_3 +build number: 3 +size : 14 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/samsift-0.2 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sc-musketeers.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sc-musketeers.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0b300b1cb9cca335cd54a7cc92351c2fb3a6b31a --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sc-musketeers.manual_bundle.txt @@ -0,0 +1,112 @@ +# Tool: sc-musketeers +software_name: sc-musketeers +tier: T1 +domain: single_cell +downloads: 1460 +summary: A tri-partite modular autoencoder for addressing imbalanced cell type annotation and batch effect reduction +description: A tri-partite modular autoencoder for addressing imbalanced cell type annotation and batch effect reduction +dependencies: keras >=3.3.3,<4.0.0, matplotlib-base >=3.9.3,<4.0.0, neptune >=1.10.4,<2.0.0, numpy >=1.23.0,<2.0.0, pandas >=2.2.3,<3.0.0, pillow >=11.0.0,<12.0.0, poetry >=1.8.1,<2.0.0, pympler >=1.0.1,<2.0.0, python >=3.10.0,<4.0.0, scanpy >=1.10.1,<2.0.0, scikit-learn >=1.5.2,<2.0.0, seaborn >=0.13.2,<0.14.0, tensorflow >=2.10.0,<3.0.0 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://sc-musketeers.readthedocs.io/ +doc_url: +dev_url: + +## URL Docs Extract +### https://sc-musketeers.readthedocs.io/ +scMusketeers scMusketeers Home Summary Tutorial Install Examples Contributing scMusketeers Home Edit on GitHub scMusketeers : A tri-partite modular autoencoder for addressing imbalanced cell type annotation and batch effect reduction Summary We developed scMusketeer, a modular deep learning model producing an optimal dimension-reduced representation with a focus on imbalanced cell type annotation and batch effect reduction. The architecture of scMusketeers is made of three modules. The first module is an autoencoder which provides a reduced latent representation, while removing noise, thus resulting in a better data reconstruction. The second module, is a classifier with a focal loss providing higher prediction for smaller populations of cell types. The third module is an adversarial domain adaptation (DANN) module that corrects batch effect. scMusketeers performance was optimized after conducting a precise ablation study to assess model's hyperparameters. The model was compared to reference tools for single-cell integration and annotation. It was at least on par with state-of-the-art models, often outperforming most of them. It showed increased performance on the identification of rare cell types. Despite the rather simple structure of its deep learning model, it demonstrated equivalent performance to UCE foundation model. Finally, scMusketeers was able to transfer the cell label from single-cell RNA-Seq to spatial transcriptomics. Our tripartite modular autoencoder demonstrates versatile capabilities while addressing key challenges in single-cell atlas reconstruction. We noticed in particular that the generic modular framework of scMusketeers should be easily generalized to other large-scale biology projects that require deep learning models. Tutorial Access to the tutorial on Google collab We will see in this tutorial two use-cases: - Transfer cell annotation to unlabeled cells - Transfer cell annotation and reduce batch from a query atlas to a reference atlas Install You can install sc_musketeers with Pypi: $ pip install sc-musketeers with conda $ conda -c bioconda sc-musketeers with docker Examples sc-musketeers can be used for different task in integration and annotation of single-cell atlas. Here are 2 different examples: Transfer cell annotation to unlabeled cells $ sc-musketeers transfer my_atlas --class_key celltype --batch_key donor --unlabeled_category=Unknown Transfer cell annotation and reduce batch from a query atlas to a reference atlas $ sc-musketeers transfer ref_dataset --query_path query_dataset --class_key=celltype --batch_key donor --unlabeled_category=Unknown Read the CONTRIBUTING.md file. Next Built with MkDocs using a theme provided by Read the Docs . + +## Conda Search Info +$ conda search -c bioconda -c conda-forge sc-musketeers --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +sc-musketeers 0.3.7 pyhdfd78af_0 +-------------------------------- +file name : sc-musketeers-0.3.7-pyhdfd78af_0.tar.bz2 +name : sc-musketeers +version : 0.3.7 +build : pyhdfd78af_0 +build number: 0 +size : 77 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sc-musketeers-0.3.7-pyhdfd78af_0.tar.bz2 +md5 : cc93a3660cece0b3cb50c480bb12f36a +timestamp : 2024-12-04 14:06:40 UTC +dependencies: + - ax-platform >=0.4.0,<0.5.0 + - keras >=3.3.3,<4.0.0 + - matplotlib-base >=3.9.3,<4.0.0 + - neptune >=1.10.4,<2.0.0 + - numpy >=1.23.0,<2.0.0 + - pandas >=2.2.3,<3.0.0 + - pillow >=11.0.0,<12.0.0 + - poetry >=1.8.1,<2.0.0 + - pympler >=1.0.1,<2.0.0 + - python >=3.10.0,<4.0.0 + - pytorch >=2.3.1,<3.0.0 + - scanpy >=1.10.1,<2.0.0 + - scikit-learn >=1.5.2,<2.0.0 + - seaborn >=0.13.2,<0.14.0 + - tensorflow >=2.10.0,<3.0.0 + + +sc-musketeers 0.4.1 pyhdfd78af_0 +-------------------------------- +file name : sc-musketeers-0.4.1-pyhdfd78af_0.tar.bz2 +name : sc-musketeers +version : 0.4.1 +build : pyhdfd78af_0 +build number: 0 +size : 77 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sc-musketeers-0.4.1-pyhdfd78af_0.tar.bz2 +md5 : fc2f7323fcf1417ade1293308572b794 +timestamp : 2024-12-23 11:57:41 UTC +dependencies: + - keras >=3.3.3,<4.0.0 + - matplotlib-base >=3.9.3,<4.0.0 + - neptune >=1.10.4,<2.0.0 + - numpy >=1.23.0,<2.0.0 + - pandas >=2.2.3,<3.0.0 + - pillow >=11.0.0,<12.0.0 + - poetry >=1.8.1,<2.0.0 + - pympler >=1.0.1,<2.0.0 + - python >=3.10.0,<4.0.0 + - scanpy >=1.10.1,<2.0.0 + - scikit-learn >=1.5.2,<2.0.0 + - seaborn >=0.13.2,<0.14.0 + - tensorflow >=2.10.0,<3.0.0 + + +sc-musketeers 0.4.2 pyhdfd78af_0 +-------------------------------- +file name : sc-musketeers-0.4.2-pyhdfd78af_0.tar.bz2 +name : sc-musketeers +version : 0.4.2 +build : pyhdfd78af_0 +build number: 0 +size : 77 KB +license : GPL-3.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sc-musketeers-0.4.2-pyhdfd78af_0.tar.bz2 +md5 : 85f024749b34a7f7c16983e0e6c2fbfa +timestamp : 2025-03-27 19:13:22 UTC +dependencies: + - keras >=3.3.3,<4.0.0 + - matplotlib-base >=3.9.3,<4.0.0 + - neptune >=1.10.4,<2.0.0 + - numpy >=1.23.0,<2.0.0 + - pandas >=2.2.3,<3.0.0 + - pillow >=11.0.0,<12.0.0 + - poetry >=1.8.1,<2.0.0 + - pympler >=1.0.1,<2.0.0 + - python >=3.10.0,<4.0.0 + - scanpy >=1.10.1,<2.0.0 + - scikit-learn >=1.5.2,<2.0.0 + - seaborn >=0.13.2,<0.14.0 + - tensorflow >=2.10.0,<3.0.0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scepia.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scepia.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8c47ed0ccdce67d2a13b429857117176948548c1 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scepia.manual_bundle.txt @@ -0,0 +1,120 @@ +# Tool: scepia +software_name: scepia +tier: T1 +domain: single_cell +downloads: 8785 +summary: Single Cell Epigenome-based Inference of Activity +description: Single Cell Epigenome-based Inference of Activity +dependencies: adjusttext, geosketch, gimmemotifs >=0.15.2,<=0.17.1, leidenalg, loguru, louvain, python >=3.7, scanpy +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/vanheeringen-lab/scepia +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/vanheeringen-lab/scepia +GitHub - vanheeringen-lab/scepia: Single Cell Epigenome-based Inference of Activity · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} vanheeringen-lab / scepia Public Notifications You must be signed in to change notification settings Fork 2 Star 19 Code Issues 6 Pull requests 4 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights vanheeringen-lab/scepia master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 144 Commits 144 Commits data data scepia scepia scripts scripts tests tests tutorials tutorials .gitattributes .gitattributes .gitignore .gitignore .travis.yml .travis.yml LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md environment.txt environment.txt setup.cfg setup.cfg setup.py setup.py versioneer.py versioneer.py View all files Repository files navigation README MIT license Please note: at the moment this package is being actively developed and might not always be stable. SCEPIA - Single Cell Epigenome-based Inference of Activity SCEPIA predicts transcription factor motif activity from single cell RNA-seq data. It uses computationally inferred epigenomes of single cells to identify transcription factors that determine cellular states. The regulatory inference is based on a two-step process: Single cells are matched to a combination of (bulk) reference H3K27ac ChIP-seq or ATAC-seq profiles. Using the H3K27ac ChIP-seq or ATAC-seq signal in enhancers associated with hypervariable genes the TF motif activity is inferred. Currently five different references are available, three for human and two for mouse. Different data sets may give different results, based on a) the type of data (H3K27ac ChIP-seq or ATAC-seq) and b) the different cell types being represented. While SCEPIA does not require exact matching cell types to give good results, it does work best when relatively similar cell types are in the reference. The following references can be used: ENCODE.H3K27ac.human - All H3K27ac experiments from ENCODE. Includes cell lines, tissues BLUEPRINT.H3K27ac.human - All H3K27ac cell types from BLUEPRINT (mostly hematopoietic cell types) Domcke.ATAC.fetal.human - Fetal single cell-based ATAC-seq clusters from 15 different organs ( Domcke et al 2020 ). Cusanovich.ATAC.adult.mouse - ATAC-seq data of single cell-based clusters from 13 adult mouse tissues ( Cusanovich et al, 2018 ). ENCODE.H3K27ac.mouse - All H3K27ac experiments from mouse ENCODE. So sorry, but only human and mouse are supported for now. However, if you have data from other species you can try it if gene names tend to match. Make sure you use gene names as identifiers, and scepia will run fine. In our (very limited) experience this can yield good results, but there are a lot of assumptions on conservation of regulatory interactions. If you have a large collection of ATAC-seq or ChIP-seq reference experiments available you can also create your own reference with ScepiaDataset.create() . This is not well-documented at the moment, let us know if you need help to do so. Requirements and installation You will need conda using the bioconda channel. Make sure you have conda installed. If you have not used bioconda before, first set up the necessary channels (in this order!). You only have to do this once. $ conda config --add channels defaults $ conda config --add channels bioconda $ conda config --add channels conda-forge Now you can create an environment for scepia: conda create -n scepia "scepia>=0.5.0" # Note: if you want to use scepia in a Jupyter notebook, you also have to install the following packages: `ipywidgets nb_conda`. conda activate scepia Usage Before using SCEPIA You have to install genomes that scepia uses through genomepy . The genomes that are used include hg38 , hg19 , mm10 and mm9 , depending on the reference. For example, to install hg38 : $ conda activate scepia $ genomepy install hg38 You only need to do this once for each genome. Note: this is independent of which genome / annotation you used for your single cell RNA-seq! Command line Remember to activate the environment before using it conda activate scepia The command line script scepia infer_motifs works on any file that is supported by scanpy.read() . We recommend to process your data, including QC, filtering, normalization and clustering, using scanpy. If you save the results to an .h5ad file, scepia can continue from your analysis to infer motif activity. However, the command line tool also works on formats such as CSV files or tab-separated files. In that case, scepia will run some basic pre-processing steps. To run scepia : scepia infer_motifs <input_file> <output_dir> Jupyter notebook tutorial A tutorial on how to use scepia interactively in Jupyter can be found here . Single cell data should be loaded in an AnnData object. Make sure of the following: Gene names are used in adata.var_names , not Ensembl identifiers or any other gene identifiers. adata.raw stores the raw, log-transformed single cell expression data. The main adata object is filtered to contain only hypervariable genes. Louvain or Leiden clustering has been run. Once these preprocessing steps are met, infer_motifs() can be run to infer the TF motif activity. The first time the reference data will be downloaded, so this will take somewhat longer. from scepia.sc import infer_motifs # load and preprocess single-cell data using scanpy infer_motifs(adata, dataset="ENCODE.H3K27ac.human") The resulting AnnData object can be saved and loaded as normal. Determine enhancer-based regulatory potential The approach to determine the enhancer-based regulatory potential (ERP) score per gene is based on the approach developed by Wang et al., 2016 . There is one difference, in this approach the score is calculates based only on H3K27ac signal in enhancers. We use log-transformed, z-score normalized H3K27ac read counts in 2kb windows centered at enhancer locations. The ERP score is used to match single cell RNA-seq data to the reference H3K27ac profiles. To use, an H3K27ac BAM file is needed (mapped to hg38). The -N argument specifies the number of threads to use. scepia area27 <bamfile> <outfile> -N 12 About Single Cell Epigenome-based Inference of Activity Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 19 stars Watchers 3 watching Forks 2 forks Report repository Releases 9 Version 0.5.1 Latest Jun 2, 2021 + 8 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 97.2% Python 2.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge scepia --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +scepia 0.4.0 py_0 +----------------- +file name : scepia-0.4.0-py_0.tar.bz2 +name : scepia +version : 0.4.0 +build : py_0 +build number: 0 +size : 22.2 MB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scepia-0.4.0-py_0.tar.bz2 +md5 : 3a5abc909a16e405f76c966e90e75e36 +timestamp : 2020-10-14 06:55:34 UTC +dependencies: + - adjusttext + - biofluff + - geosketch + - gimmemotifs >=0.15.1 + - leidenalg + - loguru + - louvain + - python >=3.7 + - scanpy + + +scepia 0.5.0 py_0 +----------------- +file name : scepia-0.5.0-py_0.tar.bz2 +name : scepia +version : 0.5.0 +build : py_0 +build number: 0 +size : 27 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scepia-0.5.0-py_0.tar.bz2 +md5 : 0c8b632ddeb49ab2ade3232f6635cf2c +timestamp : 2020-11-27 10:50:19 UTC +dependencies: + - adjusttext + - geosketch + - gimmemotifs >=0.15.2 + - leidenalg + - loguru + - louvain + - python >=3.7 + - scanpy + + +scepia 0.5.1 pyhdfd78af_0 +------------------------- +file name : scepia-0.5.1-pyhdfd78af_0.tar.bz2 +name : scepia +version : 0.5.1 +build : pyhdfd78af_0 +build number: 0 +size : 27 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scepia-0.5.1-pyhdfd78af_0.tar.bz2 +md5 : 02e6342f84adb048769f51197f56139a +timestamp : 2021-06-02 13:11:06 UTC +dependencies: + - adjusttext + - geosketch + - gimmemotifs >=0.15.2 + - leidenalg + - loguru + - louvain + - python >=3.7 + - scanpy + + +scepia 0.5.1 pyhdfd78af_1 +------------------------- +file name : scepia-0.5.1-pyhdfd78af_1.tar.bz2 +name : scepia +version : 0.5.1 +build : pyhdfd78af_1 +build number: 1 +size : 29 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scepia-0.5.1-pyhdfd78af_1.tar.bz2 +md5 : 02ead9d52e86ceaba3693116a1dfb15b +timestamp : 2023-08-08 18:06:04 UTC +dependencies: + - adjusttext + - geosketch + - gimmemotifs >=0.15.2,<=0.17.1 + - leidenalg + - loguru + - louvain + - python >=3.7 + - scanpy diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scirpy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scirpy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b6167bd1e349ca65303186ae030dbd76254cf01 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scirpy.manual_bundle.txt @@ -0,0 +1,555 @@ +# Tool: scirpy +software_name: scirpy +tier: T1 +domain: single_cell +downloads: 76995 +summary: A Scanpy extension for analyzing single-cell T-cell and B-cell receptor (TCR/BCR) sequencing data. +description: A Scanpy extension for analyzing single-cell T-cell and B-cell receptor (TCR/BCR) sequencing data. +dependencies: adjusttext >=0.7, airr >=1.4.1, anndata >=0.9, awkward >=2.1.0, joblib >=1.3.1, logomaker !=0.8.5, mudata >=0.2.3, networkx >=2.5, numba >=0.41.0, numpy >=1.17.0, pandas >=2.3, pooch >=1.7.0, python >=3.12, python-igraph >0.10.1|<0.10.0, python-levenshtein, scanpy >=1.9.3, scikit-learn, scipy, setuptools <82, squarify, tqdm >=4.63 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://icbi-lab.github.io/scirpy +doc_url: +dev_url: https://github.com/icbi-lab/scirpy + +## URL Docs Extract +### https://icbi-lab.github.io/scirpy +Redirecting... If you're not automatically redirected, click here . + +### https://github.com/icbi-lab/scirpy +GitHub - scverse/scirpy: A scanpy extension to analyse single-cell TCR and BCR data. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} scverse / scirpy Public Notifications You must be signed in to change notification settings Fork 46 Star 250 Code Issues 38 Pull requests 5 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights scverse/scirpy main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,273 Commits 1,273 Commits .conda .conda .github .github .vscode .vscode docs docs src/ scirpy src/ scirpy .cirun.yml .cirun.yml .codecov.yaml .codecov.yaml .cruft.json .cruft.json .editorconfig .editorconfig .gitattributes .gitattributes .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml .readthedocs.yaml .readthedocs.yaml CHANGELOG.md CHANGELOG.md CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE README.md README.md biome.jsonc biome.jsonc pyproject.toml pyproject.toml View all files Repository files navigation README Code of conduct Contributing BSD-3-Clause license Scirpy: single-cell immune receptor analysis in Python Scirpy is a package to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data in Python. It seamlessly integrates with scanpy and mudata and provides various modules for data import, analysis and visualization. scirpy is part of the scverse® project ( website , governance ) and is fiscally sponsored by NumFOCUS . If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs. Getting started Please refer to the documentation . In particular, the Tutorial , and the API documentation . Installation You need to have Python 3.11 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge . There are several alternative options to install scirpy: Install the latest release of scirpy from PyPI : pip install scirpy Get it from Bioconda : First setup conda channels as described here . Then install scirpy: conda install scirpy Install the latest development version: pip install git+https://github.com/scverse/scirpy.git@main Run it in a container using Docker or Podman : docker pull quay.io/biocontainers/scirpy: < tag > where tag is one of these tags . Release notes See the changelog . Support and Contact We are happy to assist with problems when using scirpy. If you need help with scirpy or have questions regarding single-cell immune-cell receptor analysis in general, please join us in the scverse discourse . For bug report or feature requests, please use the issue tracker . We try to respond within two working days, however fixing bugs or implementing new features can take substantially longer, depending on the availability of our developers. Citation If you use scirpy in your work, please cite the scirpy publication as follows: Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data Gregor Sturm, Tamas Szabo, Georgios Fotakis, Marlene Haider, Dietmar Rieder, Zlatko Trajanoski, Francesca Finotello Bioinformatics 2020 Sep 15. doi: 10.1093/bioinformatics/btaa611 . You can cite the scverse publication as follows: The scverse project provides a computational ecosystem for single-cell omics data analysis Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle & Fabian J. Theis Nat Biotechnol. 2023 Apr 10. doi: 10.1038/s41587-023-01733-8 . About A scanpy extension to analyse single-cell TCR and BCR data. scirpy.scverse.org/en/latest/ Resources Readme License BSD-3-Clause license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 250 stars Watchers 10 watching Forks 46 forks Report repository Releases 47 v0.23.0 Latest Feb 10, 2026 + 46 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge scirpy --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +scirpy 0.1.1 py_0 +----------------- +file name : scirpy-0.1.1-py_0.tar.bz2 +name : scirpy +version : 0.1.1 +build : py_0 +build number: 0 +size : 50 KB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.1.1-py_0.tar.bz2 +md5 : 093a053a5257414a9a0ebb7e0f44dc30 +timestamp : 2020-04-14 19:14:51 UTC +dependencies: + - anndata >=0.7.1 + - get_version + - networkx + - numpy + - pandas >=0.21 + - parasail-python + - python >=3.6 + - python-igraph + - python-levenshtein + - scanpy >=1.4.6 + - scikit-learn + - scipy + - squarify + + +scirpy 0.1.2 py_0 +----------------- +file name : scirpy-0.1.2-py_0.tar.bz2 +name : scirpy +version : 0.1.2 +build : py_0 +build number: 0 +size : 51 KB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.1.2-py_0.tar.bz2 +md5 : bb60b5b7080dcff77ff06ace178cc9ba +timestamp : 2020-04-15 20:21:05 UTC +dependencies: + - anndata >=0.7.1 + - get_version + - networkx + - numpy + - pandas >=0.21 + - parasail-python + - python >=3.6 + - python-igraph + - python-levenshtein + - scanpy >=1.4.6 + - scikit-learn + - scipy + - squarify + + +scirpy 0.2 py_0 +--------------- +file name : scirpy-0.2-py_0.tar.bz2 +name : scirpy +version : 0.2 +build : py_0 +build number: 0 +size : 56 KB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.2-py_0.tar.bz2 +md5 : 3432a6af37afb0b253f85d9dcaf93f4f +timestamp : 2020-05-22 12:12:17 UTC +dependencies: + - anndata >=0.7.3 + - get_version + - networkx + - numpy + - pandas >=0.21 + - parasail-python + - python >=3.6 + - python-igraph + - python-levenshtein + - scanpy >=1.5.1 + - scikit-learn + - scipy + - squarify + - tqdm >=4.29.1 + + +scirpy 0.3 py_0 +--------------- +file name : scirpy-0.3-py_0.tar.bz2 +name : scirpy +version : 0.3 +build : py_0 +build number: 0 +size : 58 KB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.3-py_0.tar.bz2 +md5 : 8b39dd502758cd26711f12758582bdfa +timestamp : 2020-06-05 07:40:03 UTC +dependencies: + - airr >=1.2 + - anndata >=0.7.3 + - get_version + - networkx + - numpy + - pandas >=0.21 + - parasail-python + - python >=3.6 + - python-igraph + - python-levenshtein + - scanpy >=1.5.1 + - scikit-learn + - scipy + - squarify + - tqdm >=4.29.1 + + +scirpy 0.4 py_0 +--------------- +file name : scirpy-0.4-py_0.tar.bz2 +name : scirpy +version : 0.4 +build : py_0 +build number: 0 +size : 60 KB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.4-py_0.tar.bz2 +md5 : e380e3d9ab053a97a95af8935eef8b81 +timestamp : 2020-08-26 16:11:23 UTC +dependencies: + - airr >=1.2 + - anndata >=0.7.3 + - networkx + - numpy + - pandas >=0.21 + - parasail-python + - python >=3.6 + - python-igraph + - python-levenshtein + - scanpy >=1.5.1 + - scikit-learn + - scipy + - squarify + - tqdm >=4.29.1 + + +scirpy 0.4.1 py_0 +----------------- +file name : scirpy-0.4.1-py_0.tar.bz2 +name : scirpy +version : 0.4.1 +build : py_0 +build number: 0 +size : 60 KB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.4.1-py_0.tar.bz2 +md5 : 4ff1bb7a13cba42bbc585d1347b1f77d +timestamp : 2020-10-01 09:40:10 UTC +dependencies: + - airr >=1.2 + - anndata >=0.7.3 + - networkx + - numpy + - pandas >=0.21 + - parasail-python + - python >=3.6 + - python-igraph + - python-levenshtein + - scanpy >=1.5.1 + - scikit-learn + - scipy + - squarify + - tqdm >=4.29.1 + + +scirpy 0.4.2 py_0 +----------------- +file name : scirpy-0.4.2-py_0.tar.bz2 +name : scirpy +version : 0.4.2 +build : py_0 +build number: 0 +size : 315 KB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.4.2-py_0.tar.bz2 +md5 : 9988c32fdf2cf9eb29c52b30ccbcb624 +timestamp : 2020-10-01 11:13:41 UTC +dependencies: + - airr >=1.2 + - anndata >=0.7.3 + - networkx + - numpy + - pandas >=0.21 + - parasail-python + - python >=3.6 + - python-igraph + - python-levenshtein + - scanpy >=1.5.1 + - scikit-learn + - scipy + - squarify + - tqdm >=4.29.1 + + +scirpy 0.5.0 py_0 +----------------- +file name : scirpy-0.5.0-py_0.tar.bz2 +name : scirpy +version : 0.5.0 +build : py_0 +build number: 0 +size : 903 KB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.5.0-py_0.tar.bz2 +md5 : 0059b43e5ec50bc2b62bd9f1b3caf0a2 +timestamp : 2020-10-20 18:31:08 UTC +dependencies: + - airr >=1.2 + - anndata >=0.7.3 + - networkx + - numpy + - pandas >=0.21 + - parasail-python + - python >=3.6 + - python-igraph + - python-levenshtein + - scanpy >=1.6.0 + - scikit-learn + - scipy + - squarify + - tqdm >=4.29.1 + + +scirpy 0.6.0 py_0 +----------------- +file name : scirpy-0.6.0-py_0.tar.bz2 +name : scirpy +version : 0.6.0 +build : py_0 +build number: 0 +size : 894 KB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.6.0-py_0.tar.bz2 +md5 : 05facd055e43adfcc7d502770d904cb8 +timestamp : 2020-12-10 15:41:35 UTC +dependencies: + - airr >=1.2 + - anndata >=0.7.3 + - networkx + - numpy + - pandas >=0.21 + - parasail-python + - python >=3.6 + - python-igraph + - python-levenshtein + - scanpy >=1.6.0 + - scikit-learn + - scipy + - squarify + - tqdm >=4.29.1 + + +scirpy 0.6.1 py_0 +----------------- +file name : scirpy-0.6.1-py_0.tar.bz2 +name : scirpy +version : 0.6.1 +build : py_0 +build number: 0 +size : 903 KB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.6.1-py_0.tar.bz2 +md5 : 5dc88401ed2b7367f79fbba7c632af19 +timestamp : 2021-01-30 17:24:10 UTC +dependencies: + - airr >=1.2 + - anndata >=0.7.3 + - networkx + - numpy + - pandas >=0.21 + - parasail-python + - python >=3.6 + - python-igraph + - python-levenshtein + - scanpy >=1.6.0 + - scikit-learn + - scipy + - squarify + - tqdm >=4.29.1 + + +scirpy 0.7.0 pyhdfd78af_0 +------------------------- +file name : scirpy-0.7.0-pyhdfd78af_0.tar.bz2 +name : scirpy +version : 0.7.0 +build : pyhdfd78af_0 +build number: 0 +size : 1.2 MB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.7.0-pyhdfd78af_0.tar.bz2 +md5 : 2b8d0dd90e73f035a60b8b741ac1bb9a +timestamp : 2021-04-28 14:26:16 UTC +dependencies: + - airr >=1.2 + - anndata >=0.7.6 + - networkx + - numpy + - pandas >=1.0 + - parasail-python + - python >=3.7 + - python-igraph + - python-levenshtein + - scanpy >=1.6.0 + - scikit-learn + - scipy + - squarify + - tqdm >=4.42.0 + + +scirpy 0.7.1 pyhdfd78af_0 +------------------------- +file name : scirpy-0.7.1-pyhdfd78af_0.tar.bz2 +name : scirpy +version : 0.7.1 +build : pyhdfd78af_0 +build number: 0 +size : 1.2 MB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.7.1-pyhdfd78af_0.tar.bz2 +md5 : 5570b78614713a65bd34443331fd9b7b +timestamp : 2021-07-02 08:23:18 UTC +dependencies: + - airr >=1.2 + - anndata >=0.7.6 + - networkx + - numpy + - pandas >=1.0 + - parasail-python + - python >=3.7 + - python-igraph + - python-levenshtein + - scanpy >=1.6.0 + - scikit-learn + - scipy + - squarify + - tqdm >=4.42.0 + + +scirpy 0.8.0 pyhdfd78af_0 +------------------------- +file name : scirpy-0.8.0-pyhdfd78af_0.tar.bz2 +name : scirpy +version : 0.8.0 +build : pyhdfd78af_0 +build number: 0 +size : 1.2 MB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.8.0-pyhdfd78af_0.tar.bz2 +md5 : 382429c7c253d4bc387e4c76cad12105 +timestamp : 2021-07-22 08:29:37 UTC +dependencies: + - airr >=1.2 + - anndata >=0.7.6 + - networkx + - numpy + - pandas >=1.0 + - parasail-python + - python >=3.7 + - python-igraph + - python-levenshtein + - scanpy >=1.6.0 + - scikit-learn + - scipy + - squarify + - tqdm >=4.42.0 + + +scirpy 0.9.0 pyhdfd78af_0 +------------------------- +file name : scirpy-0.9.0-pyhdfd78af_0.tar.bz2 +name : scirpy +version : 0.9.0 +build : pyhdfd78af_0 +build number: 0 +size : 1.2 MB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.9.0-pyhdfd78af_0.tar.bz2 +md5 : 7f6bee76ba14d111698c0a66494bd1f7 +timestamp : 2021-09-07 17:22:59 UTC +dependencies: + - adjusttext + - airr >=1.2 + - anndata >=0.7.6 + - networkx + - numpy + - pandas >=1.0 + - parasail-python + - python >=3.7 + - python-igraph + - python-levenshtein + - scanpy >=1.6.0 + - scikit-learn + - scipy + - squarify + - tqdm >=4.42.0 + + +scirpy 0.9.1 pyhdfd78af_0 +------------------------- +file name : scirpy-0.9.1-pyhdfd78af_0.tar.bz2 +name : scirpy +version : 0.9.1 +build : pyhdfd78af_0 +build number: 0 +size : 1.2 MB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.9.1-pyhdfd78af_0.tar.bz2 +md5 : 54fbe3e99452dabaa46c86ba970a4fea +timestamp : 2021-09-24 07:27:13 UTC +dependencies: + - adjusttext + - airr >=1.2 + - anndata >=0.7.6 + - networkx + - numpy + - pandas >=1.0 + - parasail-python + - python >=3.7 + - python-igraph + - python-levenshtein + - scanpy >=1.6.0 + - scikit-learn + - scipy + - squarify + - tqdm >=4.42.0 + + +scirpy 0.10.0 pyhdfd78af_0 +-------------------------- +file name : scirpy-0.10.0-pyhdfd78af_0.tar.bz2 +name : scirpy +version : 0.10.0 +build : pyhdfd78af_0 +build number: 0 +size : 1.2 MB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.10.0-pyhdfd78af_0.tar.bz2 +md5 : aa953e31f6e681dd20ca748bd4a4f57e +timestamp : 2021-11-15 20:35:50 UTC +dependencies: + - adjusttext + - airr >=1.2 + - anndata >=0.7.6 + - networkx >=2.5 + - numba >=0.41.0 + - numpy + - pandas >=1.0 + - parasail-python + - python >=3.7 + - python-igraph + - python-levenshtein + - scanpy >=1.6.0 + - scikit-learn + - scipy + - squarify + - tqdm >=4.44.1 + + +scirpy 0.10.1 pyhdfd78af_0 +-------------------------- +file name : scirpy-0.10.1-pyhdfd78af_0.tar.bz2 +name : scirpy +version : 0.10.1 +build : pyhdfd78af_0 +build number: 0 +size : 1.2 MB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.10.1-pyhdfd78af_0.tar.bz2 +md5 : 9ebced6cdd684e5f6366c7170e8d869f +timestamp : 2021-11-22 10:34:56 UTC +dependencies: + - adjusttext + - airr >=1.2 + - anndata >=0.7.6 + - networkx >=2.5 + - numba >=0.41.0 + - numpy + - pandas >=1.0 + - parasail-python + - python >=3.7 + - python-igraph + - python-levenshtein + - scanpy >=1.6.0 + - scikit-learn + - scipy + - squarify + - tqdm >=4.44.1 + + +scirpy 0.11.0 pyhdfd78af_0 +-------------------------- +file name : scirpy-0.11.0-pyhdfd78af_0.tar.bz2 +name : scirpy +version : 0.11.0 +build : pyhdfd78af_0 +build number: 0 +size : 2.1 MB +license : BSD-3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scirpy-0.11.0-pyhdfd78af_0.tar.bz2 +md5 : d8a0c19e5b8f29a diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sctriangulate.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sctriangulate.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..91f15c0980c6998689b95108dadd2844b58735bc --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sctriangulate.manual_bundle.txt @@ -0,0 +1,49 @@ +# Tool: sctriangulate +software_name: sctriangulate +tier: T1 +domain: spatial_transcriptomics +downloads: 1155 +summary: A Python package to mix-and-match conflicting clustering results in single cell analysis, and generate reconciled clustering solutions. +description: A Python package to mix-and-match conflicting clustering results in single cell analysis, and generate reconciled clustering solutions. +dependencies: anytree, gseapy 0.10.4, mygene 3.2.2, python >=3.7, scrublet 0.2.3, squidpy, yattag +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/frankligy/scTriangulate +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/frankligy/scTriangulate +GitHub - frankligy/scTriangulate: scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled clustering solutions · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} frankligy / scTriangulate Public Notifications You must be signed in to change notification settings Fork 6 Star 38 Code Issues 10 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights frankligy/scTriangulate main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 303 Commits 303 Commits docker docker docs docs image image reproduce reproduce sctriangulate sctriangulate test test .gitignore .gitignore .readthedocs.yaml .readthedocs.yaml LICENSE LICENSE README.md README.md setup.py setup.py View all files Repository files navigation README MIT license scTriangulate scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis, and generate reconciled clustering solutions. scTriangulate leverages cooperative game theory (Shapley Value) in conjunction with complimentary stability metrics (i.e. reassign score, TFIDF score and SCCAF score) to intelligently integrate clustering solutions from nearly unlimited sources. Applied to multimodal datasets, this approach highlights new cell populations and mechanisms underlying lineage diversity. Please don't hesitate to reach out to me if you have any questions (contact down the page), I will be responsive. Overview It can be used in an array of settings: Integrate results from the same or multiple unsupervised clustering algorithms (i.e. Leiden, Seurat, SnapATAC) using different resolutions. Integrate results from both unsupervised and supervised (i.e. cellHarmony, Seurat label transfer) clustering algorithms. Integrate results from different reference atlases. Integrate labels from multi-modality single cell datasets (CITE-Seq, Multiome, TEA-Seq, ASAP-Seq, etc.). Installation # get a copy of original yml file from /reproduce/sctri_new_env_py37_linux.yml conda env create -f sctri_new_env_py37_linux.yml -p ./py37_new_linux_env ./py37_new_linux_env/bin/python3.7 -m pip install --no-cache-dir git+https://github.com/frankligy/sctriangulate.git ./py37_new_linux_env/bin/python3.7 -m pip install --no-cache-dir pyarrow Tutorials Check out our full documentation and step-by-step tutorials . But let's get a quick sense for a minimum example, it has been tested in python>=3.7 on MacOS, Linux and Windows PC import scanpy as sc from sctriangulate import * from sctriangulate . preprocessing import * from sctriangulate . colors import * # If you are using Mac or PC, set Matplotlib backend as Agg sctriangulate_setting ( backend = 'Agg' ) # If you are using Linux server, make sure you have internet connections # Your adata should have: # (a) adata.X, properly normalized (i.e. log CPTT for RNA, CLR for ADT, etc), check sctriangulate.preprocessing.Normalization for various choices # (b) at least two columns representing conflicting annotations in adata.obs, passed to query argument # (c) adata.obsm['X_umap'] for automatically generate visualization, check sctriangulate.preprocessing.scanpy_recipe to generate umap # (d) don't have adata.raw attribute, if have, del adata.raw, this will interfere how scanpy calculate marker genes adata = sc . read ( './test/input.h5ad' ) sctri = ScTriangulate ( dir = './output' , adata = adata , query = [ 'sctri_rna_leiden_1' , 'sctri_rna_leiden_2' , 'sctri_rna_leiden_3' ]) sctri . lazy_run () # All the results will be saved in the dir you specified Docker You can run the main functionalities using a docker container: docker pull frankligy123/sctriangulate:0.12.0.1 # imagine you are in the folder where your input.h5ad file sits, and you want to save your results to a new folder in the # same directory as ./output, here is how you run the docker docker run -v $PWD :/usr/src/app/run -t frankligy123/sctriangulate:0.12.0.1 --adata_path ./run/input.h5ad \ --dir_path ./run/output --query sctri_rna_leiden_1 sctri_rna_leiden_2 sctri_rna_leiden_3 # access help page docker run -v $PWD :/usr/src/app/run -t frankligy123/sctriangulate:0.12.0.1 --help Citation Li, G., Song, B., Singh, H. et al. Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nat Commun 14, 406 (2023). https://doi.org/10.1038/s41467-023-36016-y Reproducibility All scripts for reproducing the analyses in the preprint are available in the reproduce folder , along with all the necessary input files and intermediate outputs which are avaiable in Synapse storage . Contact Guangyuan(Frank) Li Email: li2g2@mail.uc.edu PhD student, Biomedical Informatics Cincinnati Children’s Hospital Medical Center(CCHMC) University of Cincinnati, College of Medicine About scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled clustering solutions Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 38 stars Watchers 3 watching Forks 6 forks Report repository Releases 16 Version 0.13.0 Latest Jul 21, 2023 + 15 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 95.9% R 2.3% Other 1.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge sctriangulate --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +sctriangulate 0.13.0 pyhdfd78af_0 +--------------------------------- +file name : sctriangulate-0.13.0-pyhdfd78af_0.tar.bz2 +name : sctriangulate +version : 0.13.0 +build : pyhdfd78af_0 +build number: 0 +size : 136 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sctriangulate-0.13.0-pyhdfd78af_0.tar.bz2 +md5 : 6e72bd3a4eb145685e31601929d5fcf2 +timestamp : 2024-02-19 20:31:10 UTC +dependencies: + - anytree + - gseapy 0.10.4 + - mygene 3.2.2 + - python >=3.7 + - scrublet 0.2.3 + - squidpy + - yattag diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scvi.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scvi.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..0cc09a93791b2c2f55e12f902369459a894ceb5e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scvi.manual_bundle.txt @@ -0,0 +1,562 @@ +# Tool: scvi +software_name: scvi +tier: T1 +domain: single_cell +downloads: 66341 +summary: Single-cell Variational Inference +description: Single-cell Variational Inference +dependencies: anndata >=0.7, h5py >=2.9.0, hyperopt 0.1.2, matplotlib-base >=3.0.3, numpy >=1.16.2, pandas >=0.25, python >=3.6, pytorch >=1.1, scanpy >=1.4.6, scikit-learn >=0.20.3, tqdm >=4.31.1, xlrd >=1.2.0 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/YosefLab/scVI +doc_url: https://scvi.readthedocs.io +dev_url: https://github.com/YosefLab/scVI + +## URL Docs Extract +### https://scvi.readthedocs.io +Documentation — scvi-tools Skip to main content Back to top Ctrl + K Installation Tutorials Quick start Introduction to scvi-tools Data loading and preparation scRNA-seq Atlas-level integration of lung data MrVI Quick Start Tutorial Benchmarking the scANVI fix Seed labeling with scANVI Integration and label transfer with Tabula Muris Differential expression on C. elegans data Annotation with CellAssign Isolating perturbation-induced variations with contrastiveVI Linearly decoded VAE Topic Modeling with Amortized LDA Identification of zero-inflated genes Integration of scRNA-seq data with substantial batch effects using sysVI Decipher Quick Start Tutorial Variational inference for RNA velocity with VeloVI MrVI analysis over Tahoe100M cells dataset ATAC-seq PeakVI: Analyzing scATACseq data PoissonVI: Analyzing quantitative scATAC-seq fragment counts ScBasset: Analyzing scATACseq data scBasset: Batch correction of scATACseq data Cytometry Quick start tutorial for CytoVI Advanced Tutorial: Multi-Panel Integration and Downstream Analysis with CytoVI scBS-seq Integrating single-cell methylation data from different scBS-seq experiments with methylVI Multimodal CITE-seq analysis with totalVI Reference mapping with SCVI-Tools CITE-seq reference mapping with totalVI Integration of CITE-seq and scRNA-seq data Joint analysis of paired and unpaired multiomic data with MultiVI Spatial transcriptomics ResolVI to address noise and biases in spatial transcriptomics scVIVA for representing cells and their environment in spatial transcriptomics Multi-resolution deconvolution of spatial transcriptomics Introduction to gimVI Spatial mapping with Tangram Stereoscope applied to left ventricule data Mapping human lymph node cell types to 10X Visium with Cell2location Model hub Using scvi-hub to download pretrained scvi-tools models Using scvi-hub to upload pretrained scvi-tools models Use pretrained models of scVI-hub for CELLxGENE Querying the Human Lung Cell Atlas Use pretrained models of scVI-hub for Tahoe100M Common Modelling Use Cases Preprocessing datasets for analysis with scvi-tools Model hyperparameter tuning with scVI Minification Using SHAP values and IntegratedGradients for cell type classification interpretability Train a scVI model using multiGPU Custom Data Loaders Train a scVI model using Census data Train a scVI model using Lamin Train a scVI model using Anncollection dataloader wrapper MrVI analysis over Tahoe100M cells dataset using LaminDB Custom Dataloader R Tutorials Using Python in R with reticulate Introduction to scvi-tools in R Integrating datasets with scVI in R CITE-seq analysis in R ATAC-seq analysis in R Multi-resolution deconvolution of spatial transcriptomics in R Development Data handling in scvi-tools Constructing a probabilistic module Constructing a high-level model User guide Background Overview of the scvi-tools codebase Counterfactual prediction Differential Expression Transfer learning Variational Inference Use Cases Train SCVI model with custom dataloaders Perform downstream analysis tasks of SCVI models Optimize SCVI model with hyperparameter tuning Train SCVI model with multi-GPU support Saving and loading SCVI models SCVI Criticism Training configuration Train SCVI model with callbacks Models Amortized LDA AUTOZI CellAssign contrastiveVI CytoVI Decipher DestVI gimVI LDVAE MethylANVI MethylVI MrVI MultiVI PeakVI PoissonVI ResolVI scANVI scAR scBasset scVI scVIVA Solo Stereoscope SysVI Tangram TotalANVI totalVI VeloVI API User scvi.model.AUTOZI scvi.model.CondSCVI scvi.model.DestVI scvi.model.LinearSCVI scvi.model.PEAKVI scvi.model.SCANVI scvi.model.SCVI scvi.model.TOTALVI scvi.model.MULTIVI scvi.model.AmortizedLDA scvi.model.JaxSCVI scvi.model.mlxSCVI scvi.external.CellAssign scvi.external.CYTOVI scvi.external.GIMVI scvi.external.RNAStereoscope scvi.external.SpatialStereoscope scvi.external.SOLO scvi.external.SCAR scvi.external.Tangram scvi.external.SCBASSET scvi.external.ContrastiveVI scvi.external.POISSONVI scvi.external.VELOVI scvi.external.MRVI scvi.external.TorchMRVI scvi.external.JaxMRVI scvi.external.METHYLVI scvi.external.METHYLANVI scvi.external.Decipher scvi.external.TOTALANVI scvi.external.RESOLVI scvi.external.SysVI scvi.external.SCVIVA scvi.data.read_h5ad scvi.data.read_csv scvi.data.read_loom scvi.data.read_text scvi.data.read_10x_atac scvi.data.read_10x_multiome scvi.data.poisson_gene_selection scvi.data.organize_cite_seq_10x scvi.data.organize_multiome_anndatas scvi.data.add_dna_sequence scvi.data.reads_to_fragments scvi.autotune.run_autotune scvi.autotune.AutotuneExperiment scvi.train.TrainingPlanConfig scvi.train.AdversarialTrainingPlanConfig scvi.train.SemiSupervisedTrainingPlanConfig scvi.train.SemiSupervisedAdversarialTrainingPlanConfig scvi.train.PyroTrainingPlanConfig scvi.train.LowLevelPyroTrainingPlanConfig scvi.train.ClassifierTrainingPlanConfig scvi.train.JaxTrainingPlanConfig scvi.train.TrainerConfig scvi.hub.HubMetadata scvi.hub.HubModelCardHelper scvi.hub.HubModel scvi.criticism.PosteriorPredictiveCheck scvi.model.utils.get_minified_adata_scrna scvi._settings.ScviConfig Developer scvi.data.AnnDataManager scvi.data.AnnDataManagerValidationCheck scvi.data.fields.BaseAnnDataField scvi.data.fields.LayerField scvi.data.fields.CategoricalObsField scvi.data.fields.CategoricalVarField scvi.data.fields.NumericalJointObsField scvi.data.fields.NumericalJointVarField scvi.data.fields.CategoricalJointObsField scvi.data.fields.CategoricalJointVarField scvi.data.fields.ObsmField scvi.data.fields.VarmField scvi.data.fields.ProteinObsmField scvi.data.fields.StringUnsField scvi.data.fields.LabelsWithUnlabeledObsField scvi.data.fields.BaseMuDataWrapperClass scvi.data.fields.MuDataWrapper scvi.data.fields.MuDataLayerField scvi.data.fields.MuDataProteinLayerField scvi.data.fields.MuDataNumericalObsField scvi.data.fields.MuDataNumericalVarField scvi.data.fields.MuDataCategoricalObsField scvi.data.fields.MuDataCategoricalVarField scvi.data.fields.MuDataObsmField scvi.data.fields.MuDataVarmField scvi.data.fields.MuDataNumericalJointObsField scvi.data.fields.MuDataNumericalJointVarField scvi.data.fields.MuDataCategoricalJointObsField scvi.data.fields.MuDataCategoricalJointVarField scvi.data.AnnTorchDataset scvi.dataloaders.AnnDataLoader scvi.dataloaders.AnnTorchDataset scvi.dataloaders.CollectionAdapter scvi.dataloaders.ConcatDataLoader scvi.dataloaders.DataSplitter scvi.dataloaders.SemiSupervisedDataLoader scvi.dataloaders.SemiSupervisedDataSplitter scvi.dataloaders.BatchDistributedSampler scvi.dataloaders.MappedCollectionDataModule scvi.dataloaders.TileDBDataModule scvi.distributions.Poisson scvi.distributions.NegativeBinomial scvi.distributions.NegativeBinomialMixture scvi.distributions.ZeroInflatedNegativeBinomial scvi.distributions.JaxNegativeBinomialMeanDisp scvi.distributions.BetaBinomial scvi.model.base.BaseModelClass scvi.model.base.BaseMinifiedModeModelClass scvi.model.base.VAEMixin scvi.model.base.RNASeqMixin scvi.model.base.ArchesMixin scvi.model.base.UnsupervisedTrainingMixin scvi.model.base.SemisupervisedTrainingMixin scvi.model.base.PyroSviTrainMixin scvi.model.base.PyroSampleMixin scvi.model.base.PyroJitGuideWarmup scvi.model.base.PyroModelGuideWarmup scvi.model.base.DifferentialComputation scvi.model.base.EmbeddingMixin scvi.module.AutoZIVAE scvi.module.Classifier scvi.module.LDVAE scvi.module.MRDeconv scvi.module.PEAKVAE scvi.module.MULTIVAE scvi.module.SCANVAE scvi.module.TOTALVAE scvi.module.VAE scvi.module.VAEC scvi.module.AmortizedLDAPyroModule scvi.module.JaxVAE scvi.external.gimvi.JVAE scvi.external.cytovi.CytoVAE scvi.external.cellassign.CellAssignModule scvi.external.contrastivevi.ContrastiveDataSplitter scvi.external.stereoscope.RNADeconv scvi.external.stereoscope.SpatialDeconv scvi.external.tangram.TangramMapper scvi.external.scbasset.ScBassetModule scvi.external.contrastivevi.ContrastiveVAE scvi.external.velovi.VELOVAE scvi.external.mrvi_jax.JaxMRVAE scvi.external.mrvi_torch.TorchMRVAE scvi.external.methylvi.METHYLVAE scvi.external.methylvi.METHYLANVAE scvi.external.decipher.DecipherPyroModule scvi.external.resolvi.RESOLVAE scvi.external.scviva.nicheVAE scvi.external.scviva.NicheLossOutput scvi.external.sysvi.SysVAE scvi.module.base.BaseModuleClass scvi.module.base.BaseMinifiedModeModuleClass scvi.module.base.SupervisedModuleClass scvi.module.base.PyroBaseModuleClass scvi.module.base.JaxBaseModuleClass scvi.module.base.EmbeddingModuleMixin scvi.module.base.LossOutput scvi.module.base.auto_move_data scvi.nn.FCLayers scvi.nn.Encoder scvi.nn.Decoder scvi.nn.DecoderSCVI scvi.nn.LinearDecoderSCVI scvi.nn.Embedding scvi.nn.DecoderTOTALVI scvi.nn.EncoderTOTALVI scvi.train.AdversarialTrainingPlan scvi.train.ClassifierTrainingPlan scvi.train.SemiSupervisedTrainingPlan scvi.train.SemiSupervisedAdversarialTrainingPlan scvi.train.LowLevelPyroTrainingPlan scvi.train.PyroTrainingPlan scvi.train.JaxTrainingPlan scvi.train.Trainer scvi.train.TrainingPlan scvi.train.TrainRunner scvi.train.ScibCallback scvi.train.SaveCheckpoint scvi.train.LoudEarlyStopping scvi.utils.track scvi.utils.setup_anndata_dsp scvi.utils.attrdict scvi.external.decipher.utils.Trajectory Datasets scvi.data.cellxgene scvi.data.pbmc_seurat_v4_cite_seq scvi.data.spleen_lymph_cite_seq scvi.data.heart_cell_atlas_subsampled scvi.data.pbmcs_10x_cite_seq scvi.data.purified_pbmc_dataset scvi.data.dataset_10x scvi.data.brainlarge_dataset scvi.data.pbmc_dataset scvi.data.cortex scvi.data.smfish scvi.data.synthetic_iid scvi.data.breast_cancer_dataset scvi.data.mouse_ob_dataset scvi.data.retina scvi.data.prefrontalcortex_starmap scvi.data.frontalcortex_dropseq Developer documentation Contributing code Maintenance guide Frequently asked questions Release notes References Discussion GitHub Model hub .md .pdf Documentation Documentation # scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data primarily developed and maintained by the Yosef Lab at the Weizmann Institute of Science. scvi-tools has two components: Interface for easy use of a range of probabilistic models for single-cell omics (e.g., scVI, scANVI, totalVI). Tools to build new probabilistic models, which are powered by PyTorch, PyTorch Lightning, and Pyro. If you find a model useful for your research, please consider citing the scvi-tools manuscript as well as the publication describing the model, which can be found in the corresponding documentation. scvi-tools is part of the scverse® project ( website , governance ) and is fiscally sponsored by NumFOCUS . If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs. Installation New to scvi-tools ? Check out the installation guide. Installation User guide The user guide provides distilled mathematical descriptions of the models implemented in scvi-tools and connects the math with the code. User guide API reference The API reference contains a detailed description of the scvi-tools API. API Tutorials The tutorials walk you through real-world applications of scvi-tools models. Developer tutorials help you build new probabilistic models. Tutorials Discussion Need help? Reach out on our forum to get your questions answered! https://discourse.scverse.org/ GitHub Find a bug? Interested in improving scvi-tools? Check out our GitHub for the latest developments. https://github.com/scverse/scvi-tools next Installation By The scvi-tools development team © Copyright 2026, The scvi-tools development team.. so the DOM is not blocked --> + +### https://github.com/YosefLab/scVI +GitHub - scverse/scvi-tools: Deep probabilistic analysis of single-cell and spatial omics data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} scverse / scvi-tools Public Notifications You must be signed in to change notification settings Fork 447 Star 1.6k Code Issues 14 Pull requests 11 Discussions Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Security and quality Insights scverse/scvi-tools main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 4,426 Commits 4,426 Commits .github .github docs docs src/ scvi src/ scvi tests tests .codecov.yaml .codecov.yaml .editorconfig .editorconfig .gitignore .gitignore .gitmodules .gitmodules .markdownlint.yaml .markdownlint.yaml .pre-commit-config.yaml .pre-commit-config.yaml .readthedocs.yaml .readthedocs.yaml CHANGELOG.md CHANGELOG.md Dockerfile Dockerfile LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml View all files Repository files navigation README Code of conduct BSD-3-Clause license scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData . Analysis of single-cell omics data scvi-tools is composed of models that perform many analysis tasks across single-cell, multi, and spatial omics data: Dimensionality reduction Data integration Automated annotation Factor analysis Doublet detection Spatial deconvolution and more! In the user guide , we provide an overview of each model. All model implementations have a high-level API that interacts with Scanpy and includes standard save/load functions, GPU acceleration, etc. Rapid development of novel probabilistic models scvi-tools contains the building blocks to develop and deploy novel probabilistic models. These building blocks are powered by popular probabilistic and machine learning frameworks such as PyTorch Lightning and Pyro . For an overview of how the scvi-tools package is structured, you may refer to the codebase overview page. We recommend checking out the skeleton repository as a starting point for developing and deploying new models with scvi-tools. Basic installation For conda, conda install scvi-tools -c conda-forge and for pip, pip install scvi-tools Please be sure to install a version of PyTorch that is compatible with your GPU (if applicable). Resources Tutorials, API reference, and installation guides are available in the documentation . For discussion of usage, check out our forum . Please use the issues to submit bug reports. If you'd like to contribute, check out our contributing guide . If you find a model useful for your research, please consider citing the corresponding publication. Reference If you use scvi-tools in your work, please cite A Python library for probabilistic analysis of single-cell omics data Adam Gayoso, Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong, Katherine Wu, Michael Jayasuriya, Edouard Mehlman, Maxime Langevin, Yining Liu, Jules Samaran, Gabriel Misrachi, Achille Nazaret, Oscar Clivio, Chenling Xu, Tal Ashuach, Mariano Gabitto, Mohammad Lotfollahi, Valentine Svensson, Eduardo da Veiga Beltrame, Vitalii Kleshchevnikov, Carlos Talavera-López, Lior Pachter, Fabian J. Theis, Aaron Streets, Michael I. Jordan, Jeffrey Regier & Nir Yosef Nature Biotechnology 2022 Feb 07. doi: 10.1038/s41587-021-01206-w . along with the publication describing the model used. You can cite the scverse publication as follows: The scverse project provides a computational ecosystem for single-cell omics data analysis Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle & Fabian J. Theis Nature Biotechnology 2023 Apr 10. doi: 10.1038/s41587-023-01733-8 . scvi-tools is part of the scverse® project ( website , governance ) and is fiscally sponsored by NumFOCUS . If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs. Copyright (c) 2026, Yosef Lab, Weizmann Institute of Science About Deep probabilistic analysis of single-cell and spatial omics data scvi-tools.org/ Topics deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse Resources Readme License BSD-3-Clause license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1.6k stars Watchers 26 watching Forks 447 forks Report repository Releases 93 scvi-tools 1.4.2 Latest Feb 26, 2026 + 92 releases Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/YosefLab/scVI +GitHub - scverse/scvi-tools: Deep probabilistic analysis of single-cell and spatial omics data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} scverse / scvi-tools Public Notifications You must be signed in to change notification settings Fork 447 Star 1.6k Code Issues 14 Pull requests 11 Discussions Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Security and quality Insights scverse/scvi-tools main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 4,426 Commits 4,426 Commits .github .github docs docs src/ scvi src/ scvi tests tests .codecov.yaml .codecov.yaml .editorconfig .editorconfig .gitignore .gitignore .gitmodules .gitmodules .markdownlint.yaml .markdownlint.yaml .pre-commit-config.yaml .pre-commit-config.yaml .readthedocs.yaml .readthedocs.yaml CHANGELOG.md CHANGELOG.md Dockerfile Dockerfile LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml View all files Repository files navigation README Code of conduct BSD-3-Clause license scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData . Analysis of single-cell omics data scvi-tools is composed of models that perform many analysis tasks across single-cell, multi, and spatial omics data: Dimensionality reduction Data integration Automated annotation Factor analysis Doublet detection Spatial deconvolution and more! In the user guide , we provide an overview of each model. All model implementations have a high-level API that interacts with Scanpy and includes standard save/load functions, GPU acceleration, etc. Rapid development of novel probabilistic models scvi-tools contains the building blocks to develop and deploy novel probabilistic models. These building blocks are powered by popular probabilistic and machine learning frameworks such as PyTorch Lightning and Pyro . For an overview of how the scvi-tools package is structured, you may refer to the codebase overview page. We recommend checking out the skeleton repository as a starting point for developing and deploying new models with scvi-tools. Basic installation For conda, conda install scvi-tools -c conda-forge and for pip, pip install scvi-tools Please be sure to install a version of PyTorch that is compatible with your GPU (if applicable). Resources Tutorials, API reference, and installation guides are available in the documentation . For discussion of usage, check out our forum . Please use the issues to submit bug reports. If you'd like to contribute, check out our contributing guide . If you find a model useful for your research, please consider citing the corresponding publication. Reference If you use scvi-tools in your work, please cite A Python library for probabilistic analysis of single-cell omics data Adam Gayoso, Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong, Katherine Wu, Michael Jayasuriya, Edouard Mehlman, Maxime Langevin, Yining Liu, Jules Samaran, Gabriel Misrachi, Achille Nazaret, Oscar Clivio, Chenling Xu, Tal Ashuach, Mariano Gabitto, Mohammad Lotfollahi, Valentine Svensson, Eduardo da Veiga Beltrame, Vitalii Kleshchevnikov, Carlos Talavera-López, Lior Pachter, Fabian J. Theis, Aaron Streets, Michael I. Jordan, Jeffrey Regier & Nir Yosef Nature Biotechnology 2022 Feb 07. doi: 10.1038/s41587-021-01206-w . along with the publication describing the model used. You can cite the scverse publication as follows: The scverse project provides a computational ecosystem for single-cell omics data analysis Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle & Fabian J. Theis Nature Biotechnology 2023 Apr 10. doi: 10.1038/s41587-023-01733-8 . scvi-tools is part of the scverse® project ( website , governance ) and is fiscally sponsored by NumFOCUS . If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs. Copyright (c) 2026, Yosef Lab, Weizmann Institute of Science About Deep probabilistic analysis of single-cell and spatial omics data scvi-tools.org/ Topics deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse Resources Readme License BSD-3-Clause license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1.6k stars Watchers 26 watching Forks 447 forks Report repository Releases 93 scvi-tools 1.4.2 Latest Feb 26, 2026 + 92 releases Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge scvi --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +scvi 0.1.2 py_0 +--------------- +file name : scvi-0.1.2-py_0.tar.bz2 +name : scvi +version : 0.1.2 +build : py_0 +build number: 0 +size : 27 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.1.2-py_0.tar.bz2 +md5 : 97c877dea638cf1cfcd174b9f7358dab +timestamp : 2018-06-20 19:25:53 UTC +dependencies: + - loompy >=2.0 + - matplotlib >=2.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - pytorch >=0.4 + - scikit-learn >=0.18 + - scipy >=1.0 + + +scvi 0.1.3 py_0 +--------------- +file name : scvi-0.1.3-py_0.tar.bz2 +name : scvi +version : 0.1.3 +build : py_0 +build number: 0 +size : 26 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.1.3-py_0.tar.bz2 +md5 : dddf0e8c6d6fe10e816176dbd54c9f30 +timestamp : 2018-06-23 12:06:48 UTC +dependencies: + - h5py >=2.8 + - loompy >=2.0 + - matplotlib >=2.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - pytorch >=0.4 + - scikit-learn >=0.18 + - scipy >=1.0 + - tqdm >=4 + + +scvi 0.1.4 py_0 +--------------- +file name : scvi-0.1.4-py_0.tar.bz2 +name : scvi +version : 0.1.4 +build : py_0 +build number: 0 +size : 29 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.1.4-py_0.tar.bz2 +md5 : 4fdb9ed5a35d61583c134585587fdbe4 +timestamp : 2018-07-02 23:58:17 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.8 + - loompy >=2.0 + - matplotlib >=2.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - pytorch >=0.4 + - scikit-learn >=0.18 + - scipy >=1.0 + - tqdm >=4 + + +scvi 0.1.5 py_0 +--------------- +file name : scvi-0.1.5-py_0.tar.bz2 +name : scvi +version : 0.1.5 +build : py_0 +build number: 0 +size : 35 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.1.5-py_0.tar.bz2 +md5 : fffa508317d44eafa847b1aa07800807 +timestamp : 2018-07-24 11:06:43 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.8 + - loompy >=2.0 + - matplotlib >=2.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - pytorch >=0.4 + - scikit-learn >=0.18 + - scipy >=1.0 + - tqdm >=4 + - xlrd >=1.0 + + +scvi 0.1.6 py_0 +--------------- +file name : scvi-0.1.6-py_0.tar.bz2 +name : scvi +version : 0.1.6 +build : py_0 +build number: 0 +size : 42 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.1.6-py_0.tar.bz2 +md5 : 16d21402f5faeacb681d6cc90852f58b +timestamp : 2018-08-09 12:21:35 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.8 + - loompy >=2.0 + - matplotlib >=2.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - pytorch >=0.4 + - scikit-learn >=0.18 + - scipy >=1.0 + - tqdm >=4 + - xlrd >=1.0 + + +scvi 0.2.0 py_0 +--------------- +file name : scvi-0.2.0-py_0.tar.bz2 +name : scvi +version : 0.2.0 +build : py_0 +build number: 0 +size : 44 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.2.0-py_0.tar.bz2 +md5 : 530f3ecdec66b34ff577b8f8628326f3 +timestamp : 2018-09-05 14:01:15 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.8 + - loompy >=2.0 + - matplotlib >=2.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - pytorch >=0.4.1 + - scikit-learn >=0.18 + - scipy >=1.0 + - tqdm >=4 + - xlrd >=1.0 + + +scvi 0.2.1 py_0 +--------------- +file name : scvi-0.2.1-py_0.tar.bz2 +name : scvi +version : 0.2.1 +build : py_0 +build number: 0 +size : 45 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.2.1-py_0.tar.bz2 +md5 : e3f84a44c7a82c1c3ec39b4ee536a781 +timestamp : 2018-09-14 14:11:48 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.8 + - loompy >=2.0 + - matplotlib >=2.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - pytorch >=0.4.1 + - scikit-learn >=0.18 + - scipy >=1.0 + - tqdm >=4 + - xlrd >=1.0 + + +scvi 0.2.2 py_0 +--------------- +file name : scvi-0.2.2-py_0.tar.bz2 +name : scvi +version : 0.2.2 +build : py_0 +build number: 0 +size : 47 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.2.2-py_0.tar.bz2 +md5 : 3ffe96af2b0d8441a6af7d54371d0756 +timestamp : 2018-11-09 18:09:00 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.8 + - loompy >=2.0 + - matplotlib >=2.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - pytorch >=0.4.1 + - scikit-learn >=0.18 + - scipy >=1.0 + - tqdm >=4 + - xlrd >=1.0 + + +scvi 0.2.3 py_0 +--------------- +file name : scvi-0.2.3-py_0.tar.bz2 +name : scvi +version : 0.2.3 +build : py_0 +build number: 0 +size : 48 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.2.3-py_0.tar.bz2 +md5 : f253da29cea571c803101ab58ac58a48 +timestamp : 2018-11-30 12:00:03 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.8 + - ipython >=7 + - jupyter >=1.0.0 + - loompy 2.0.9 + - matplotlib >=2.0 + - nbconvert >=5.4.0 + - nbformat >=4.4.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - pytorch >=0.4.1 + - scikit-learn >=0.18 + - scipy >=1.1 + - tqdm >=4 + - xlrd >=1.0 + + +scvi 0.2.4 py_0 +--------------- +file name : scvi-0.2.4-py_0.tar.bz2 +name : scvi +version : 0.2.4 +build : py_0 +build number: 0 +size : 48 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.2.4-py_0.tar.bz2 +md5 : 96699d20f5ef792f9c0b8c45b4e8bbaa +timestamp : 2018-12-20 21:34:07 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.8 + - ipython >=7 + - jupyter >=1.0.0 + - loompy 2.0.9 + - matplotlib >=2.0 + - nbconvert >=5.4.0 + - nbformat >=4.4.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - pytorch >=0.4.1 + - scikit-learn >=0.18 + - scipy >=1.1 + - tqdm >=4 + - xlrd >=1.0 + + +scvi 0.3.0 py_0 +--------------- +file name : scvi-0.3.0-py_0.tar.bz2 +name : scvi +version : 0.3.0 +build : py_0 +build number: 0 +size : 50 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.3.0-py_0.tar.bz2 +md5 : b5164795f9d6aa7aab2b060099e03095 +timestamp : 2019-03-30 16:53:43 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.8 + - ipython >=7 + - jupyter >=1.0.0 + - leidenalg >=0.7.0 + - loompy 2.0.9 + - matplotlib >=2.0 + - nbconvert >=5.4.0 + - nbformat >=4.4.0 + - numpy >=1.0 + - pandas >=0.2 + - python >=3.6 + - python-igraph >=0.7.1 + - pytorch 0.4.1 + - scikit-learn >=0.18 + - scipy >=1.1 + - seaborn >=0.9.0 + - tqdm >=4 + - umap-learn >=0.3.7 + - xlrd >=1.0 + + +scvi 0.3.0 py_1 +--------------- +file name : scvi-0.3.0-py_1.tar.bz2 +name : scvi +version : 0.3.0 +build : py_1 +build number: 1 +size : 50 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.3.0-py_1.tar.bz2 +md5 : d20f19c5762b68981145acc9b8771e52 +timestamp : 2019-05-10 16:08:27 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.9 + - ipython >=7.5 + - jupyter >=1.0.0 + - leidenalg >=0.7.0 + - loompy >=2.0.17 + - matplotlib >=3.0 + - nbconvert >=5.5.0 + - nbformat >=4.4.0 + - numpy >=1.16 + - pandas >=0.24 + - python >=3.6 + - python-igraph >=0.7.1 + - scikit-learn >=0.20 + - scipy >=1.2 + - seaborn >=0.9.0 + - tqdm >=4 + - umap-learn >=0.3.7 + - xlrd >=1.2 + + +scvi 0.4.1 py_0 +--------------- +file name : scvi-0.4.1-py_0.tar.bz2 +name : scvi +version : 0.4.1 +build : py_0 +build number: 0 +size : 76 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.4.1-py_0.tar.bz2 +md5 : d795df68d555022222f4b414182e2a02 +timestamp : 2019-08-05 08:38:59 UTC +dependencies: + - anndata >=0.6 + - h5py >=2.9 + - ipython >=7.5 + - jupyter >=1.0.0 + - leidenalg >=0.7.0 + - loompy >=2.0.17 + - matplotlib >=3.0 + - nbconvert >=5.5.0 + - nbformat >=4.4.0 + - numpy >=1.16 + - pandas >=0.24 + - python >=3.6 + - python-igraph >=0.7.1 + - scikit-learn >=0.20 + - scipy >=1.2 + - seaborn >=0.9.0 + - tqdm >=4 + - umap-learn >=0.3.7 + - xlrd >=1.2 + + +scvi 0.4.1 py_1 +--------------- +file name : scvi-0.4.1-py_1.tar.bz2 +name : scvi +version : 0.4.1 +build : py_1 +build number: 1 +size : 76 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.4.1-py_1.tar.bz2 +md5 : 812f70d11e67cace14e582287cebd335 +timestamp : 2019-08-19 21:41:38 UTC +dependencies: + - anndata >=0.6 + - colour >=0.1 + - h5py >=2.9 + - hyperopt >=0.1.2 + - ipython >=7.5 + - jupyter >=1.0.0 + - leidenalg >=0.7.0 + - loompy >=2.0.17 + - matplotlib >=3.0 + - mongodb >=4 + - nbconvert >=5.5.0 + - nbformat >=4.4.0 + - numpy >=1.16 + - pandas >=0.24 + - python >=3.6 + - python-igraph >=0.7.1 + - scanpy >=1.4 + - scikit-learn >=0.20 + - scipy >=1.2 + - seaborn >=0.9.0 + - tqdm >=4 + - umap-learn >=0.3.7 + - xlrd >=1.2 + + +scvi 0.5.0 py_0 +--------------- +file name : scvi-0.5.0-py_0.tar.bz2 +name : scvi +version : 0.5.0 +build : py_0 +build number: 0 +size : 85 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.5.0-py_0.tar.bz2 +md5 : e2fb7b179324b223b3bf3a4c82985c1e +timestamp : 2019-10-17 11:56:38 UTC +dependencies: + - anndata >=0.6 + - colour >=0.1 + - h5py >=2.9 + - hyperopt >=0.1.2 + - ipython >=7.5 + - jupyter >=1.0.0 + - leidenalg >=0.7.0 + - loompy >=2.0.17 + - matplotlib >=3.0 + - mongodb >=4 + - nbconvert >=5.5.0 + - nbformat >=4.4.0 + - numpy >=1.16 + - pandas >=0.24 + - python >=3.7 + - python-igraph >=0.7.1 + - scanpy >=1.4 + - scikit-learn >=0.20 + - scipy >=1.2 + - seaborn >=0.9.0 + - tqdm >=4 + - umap-learn >=0.3.7 + - xlrd >=1.2 + + +scvi 0.6.0 py_0 +--------------- +file name : scvi-0.6.0-py_0.tar.bz2 +name : scvi +version : 0.6.0 +build : py_0 +build number: 0 +size : 98 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.6.0-py_0.tar.bz2 +md5 : 3463d7940d9c0291c885ad8f2cb6ab55 +timestamp : 2020-02-29 10:30:35 UTC +dependencies: + - anndata >=0.6.22rc1 + - h5py >=2.9.0 + - hyperopt 0.1.2 + - loompy >=2.0.16 + - matplotlib >=3.0.3 + - numpy >=1.16.2 + - pandas >=0.24.2 + - python >=3.7 + - pytorch >=1.1 + - scanpy >=1.4 + - scikit-learn >=0.20.3 + - statsmodels + - tqdm >=4.31.1 + - xlrd >=1.2.0 + + +scvi 0.6.1 py_0 +--------------- +file name : scvi-0.6.1-py_0.tar.bz2 +name : scvi +version : 0.6.1 +build : py_0 +build number: 0 +size : 99 KB +license : MIT License +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scvi-0.6.1-py_0.tar.bz2 +md5 : dad69e9942752275a5fd1e66f5854afe +timestamp : 2020-03-14 00:48:44 UTC +dependencies: + - anndata >=0.6.22rc1 + - h5py >=2.9.0 + - hyperopt 0.1.2 + - loompy >=2.0.16 + - matplotlib >=3.0.3 + - numpy >=1.16.2 + - pandas >=0.24.2 + - python >=3.7 + - pytorch >=1.1 + - scanpy >=1.4 + - scikit-learn >=0.20.3 + - statsmodels + - tqdm >=4.31.1 + - xlrd >=1.2.0 + + +scvi 0.6.3 py_0 +--------------- +file name : scvi-0.6.3-py_0.tar.bz2 +name : scvi +version : 0.6.3 +build : py diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scxmatch.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scxmatch.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..a159dcce04b8e7d10d8534cfad766a9c0b9ad78e --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/scxmatch.manual_bundle.txt @@ -0,0 +1,107 @@ +# Tool: scxmatch +software_name: scxmatch +tier: T1 +domain: single_cell +downloads: 1020 +summary: Python implementation for single-cell cross match test, an efficient implementation of Rosenbaum's test. +description: Python implementation for single-cell cross match test, an efficient implementation of Rosenbaum's test. +dependencies: anndata >=0.10.9, graph-tool >=2.92,<3, python >=3.9, scanpy >=1.10.3,<2, scipy >=1.13.1,<2 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/bionetslab/scxmatch +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/bionetslab/scxmatch +GitHub - bionetslab/scxmatch · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bionetslab / scxmatch Public Notifications You must be signed in to change notification settings Fork 1 Star 1 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights bionetslab/scxmatch master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 56 Commits 56 Commits .github/ workflows .github/ workflows scxmatch scxmatch tests tests LICENSE LICENSE README.md README.md logo.svg logo.svg pyproject.toml pyproject.toml View all files Repository files navigation README MIT license scXMatch (single-cell cross match) is a Python package that implements Rosenbaum's cross-match test using distance-based matching to assess statistical dependence between two groups of high-dimensional data. This is particularly useful in analyzing multivariate distributions in structured data, such as single-cell RNA-seq. This package provides a Python implementation inspired by the methodology described in Rosenbaum (2005) . Installation Due to its dependence on graph-tool, this package can only be installed from conda, not from PyPI. The channels need to be specified. conda install scxmatch -c conda-forge -c bioconda Requirements Python ≥ 3.9 anndata scanpy scipy graph-tool $\geq$ 2.92 API Documentation scxmatch.test scxmatch . test ( adata , group_by , test_group , reference = None , metric = "sqeuclidean" , rank = False , k = 100 , total_RAM_available_gb = None ) Description Performs Rosenbaum’s matching-based test to determine if there is a statistically significant difference between two groups of samples using a distance-based graph matching approach. Parameters adata ( anndata.AnnData ): The input data matrix. Features should be in adata.X , and group labels in adata.obs[group_by] . group_by ( str ): Column in adata.obs indicating group labels. test_group ( str or list of str ): The group(s) to be tested. reference ( str or list of str , optional): The reference group(s). If None , all non-test samples are used as reference. metric ( str , default "sqeuclidean" ): Distance metric for matching. Follows scipy.spatial.distance.cdist standards. rank ( bool , default False ): If True , features are rank-transformed before distance computation. k ( int , "auto" , or "full" , default 100 ): Number of nearest neighbors to use for graph construction. If full , a full distance matrix will be calculated. total_RAM_available_gb ( float , optional): Required if k="auto" . Returns p_value ( float ): P-value from the Rosenbaum crossmatch test. z_score ( float ): Standardized test statistic. relative_support ( float ): Proportion of samples included in the matching. Raises TypeError : If the input adata is not an AnnData object. ValueError : If test_group or reference contains values not present in adata.obs[group_by] . ValueError : If k="auto" and total_RAM_available_gb is not provided. ValueError : If k is not an integer, "auto" , or "full" . Modifies: Modifies adata.obs in-place by adding the following columns: XMatch_partner_<test_group>_vs_<reference> : The index of each sample’s matched partner in the MWMCM. Example Usage import anndata as ad import scxmatch # Load your AnnData object or load scanpy dataset # adata = ad.read_h5ad("your_data.h5ad") adata = sc . datasets . krumsiek11 () # Run test p_val , z , support = scxmatch . test ( adata = adata , group_by = "condition" , test_group = "treated" , reference = "control" , metric = "sqeuclidean" , rank = False , k = 100 ) print ( f"P-value: { p_val :.4f } , Z-score: { z :.2f } , Support: { support :.2% } " ) Citation If you use scXMatch in your research, please cite the original paper and our publication: Rosenbaum, P. R. (2005). An exact distribution-free test comparing two multivariate distributions based on adjacency. Journal of the Royal Statistical Society: Series B , 67(4), 515–530. Anna Moeller, Miriam Schnitzerlein, Eric Greto, Vasily Zaburdaev, Stefan Uderhardt, David B. Blumenthal. Quantifying distribution shifts in single-cell data with scXMatch. bioRxiv 2025.06.25.661473; doi: https://doi.org/10.1101/2025.06.25.661473 License MIT License About No description, website, or topics provided. Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1 star Watchers 2 watching Forks 1 fork Report repository Releases 4 scxmatch-0.1.1 Latest Jan 29, 2026 + 3 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge scxmatch --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +scxmatch 0.0.2 pyhdfd78af_0 +--------------------------- +file name : scxmatch-0.0.2-pyhdfd78af_0.tar.bz2 +name : scxmatch +version : 0.0.2 +build : pyhdfd78af_0 +build number: 0 +size : 14 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scxmatch-0.0.2-pyhdfd78af_0.tar.bz2 +md5 : 75f4e422e5305e07921bfe982f458049 +timestamp : 2025-05-19 16:16:31 UTC +dependencies: + - anndata >=0.10.9 + - graph-tool >=2.92,<3 + - python >=3.9 + - scanpy >=1.10.3,<2 + - scipy >=1.13.1,<2 + + +scxmatch 0.0.3 pyhdfd78af_0 +--------------------------- +file name : scxmatch-0.0.3-pyhdfd78af_0.tar.bz2 +name : scxmatch +version : 0.0.3 +build : pyhdfd78af_0 +build number: 0 +size : 16 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scxmatch-0.0.3-pyhdfd78af_0.tar.bz2 +md5 : 50d998bae9dfdeb3019f464c7e3d5f2c +timestamp : 2025-06-02 11:58:01 UTC +dependencies: + - anndata >=0.10.9 + - graph-tool >=2.92,<3 + - python >=3.9 + - scanpy >=1.10.3,<2 + - scipy >=1.13.1,<2 + + +scxmatch 0.1.0 pyhdfd78af_0 +--------------------------- +file name : scxmatch-0.1.0-pyhdfd78af_0.tar.bz2 +name : scxmatch +version : 0.1.0 +build : pyhdfd78af_0 +build number: 0 +size : 16 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scxmatch-0.1.0-pyhdfd78af_0.tar.bz2 +md5 : bace99b79b18937c8c307e5af12a668d +timestamp : 2025-08-04 13:13:29 UTC +dependencies: + - anndata >=0.10.9 + - graph-tool >=2.92,<3 + - python >=3.9 + - scanpy >=1.10.3,<2 + - scipy >=1.13.1,<2 + + +scxmatch 0.1.1 pyhdfd78af_0 +--------------------------- +file name : scxmatch-0.1.1-pyhdfd78af_0.conda +name : scxmatch +version : 0.1.1 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/scxmatch-0.1.1-pyhdfd78af_0.conda +md5 : 19d7ba90353201deee4d586a63f4db41 +timestamp : 2026-01-29 14:52:07 UTC +dependencies: + - anndata >=0.10.9 + - graph-tool >=2.92,<3 + - python >=3.9 + - scanpy >=1.10.3,<2 + - scipy >=1.13.1,<2 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sdeper.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sdeper.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..7456191da40db15dbe11b517462fcf043b0ac86b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sdeper.manual_bundle.txt @@ -0,0 +1,522 @@ +# Tool: sdeper +software_name: sdeper +tier: T1 +domain: single_cell +downloads: 11077 +summary: Spatial Deconvolution method with Platform Effect Removal +description: SDePER (Spatial Deconvolution method with Platform Effect Removal) is a hybrid machine learning and regression method to deconvolve Spatial barcoding-based transcriptomic data using reference single-cell RNA sequencing data, considering platform effects removal, sparsity of cell types per capture spot and across-spots spatial correlation in cell type compositions. SDePER is also able to impute cell type compositions and gene expression at unmeasured locations in a tissue map with enhanced resolution. +dependencies: distinctipy 1.2.2, libopencv 4.9.0 headless_*, matplotlib-base 3.5.2, numba 0.59.1, numpy 1.26.4, opencv 4.9.0, openpyxl 3.0.10, pandas 1.4.3, py-opencv 4.9.0, python >=3.9,<=3.10, reportlab 4.1.0, scanpy 1.9.1, scikit-learn 1.1.1, scikit-misc 0.1.4, scipy 1.11.4, seaborn 0.13.2, tensorflow-base 2.15.0 cpu_*, umap-learn 0.5.3 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://az7jh2.github.io/SDePER/ +doc_url: https://sdeper.readthedocs.io/en/latest/ +dev_url: https://github.com/az7jh2/SDePER + +## URL Docs Extract +### https://sdeper.readthedocs.io/en/latest/ +Welcome to SDePER’s documentation! — SDePER 2.0.0 documentation SDePER Table of Contents Installation Usage CLI Options Vignettes Best Practice Changelog Python API Modules SDePER Welcome to SDePER’s documentation! View page source Welcome to SDePER’s documentation!  SDePER ( S patial De convolution method with P latform E ffect R emoval) is a hybrid machine learning and regression method to deconvolve Spatial barcoding-based transcriptomic data using reference single-cell RNA sequencing data, considering platform effects removal , sparsity of cell types per capture spot and across-spots spatial correlation in cell type compositions. SDePER is also able to impute cell type compositions and gene expression at unmeasured locations in a tissue map with enhanced resolution .. Quick Start  SDePER currently supports only Linux operating systems such as Ubuntu, and is compatible with Python 3.9.x and 3.10.x releases (3.11+ not yet supported). SDePER can be installed using conda conda create -n sdeper-env -c bioconda -c conda-forge python = 3 .9.12 sdeper or pip conda create -n sdeper-env python = 3 .9.12 conda activate sdeper-env pip install sdeper SDePER supports an out-of-the-box feature, meaning that users only need to provide the required four input files for cell type deconvolution. The package manages all aspects of file reading, preprocessing, cell type-specific marker gene identification, and more internally. The required files are: raw nUMI counts of spatial transcriptomics data (spots × genes): spatial.csv raw nUMI counts of reference scRNA-seq data (cells × genes): scrna_ref.csv cell type annotations for all cells in scRNA-seq data (cells × 1): scrna_anno.csv adjacency matrix of spots in spatial transcriptomics data (spots × spots; optional ): adjacency.csv To start cell type deconvolution using all default settings, run: runDeconvolution -q spatial.csv -r scrna_ref.csv -c scrna_anno.csv -a adjacency.csv Check out Installation page for detailed installation instructions, and Usage page for commands for cell type deconvolution and imputation. The detailed descriptions of all options in commands are in CLI Options page, and a guidance on setting the options is in Best Practice page. If you use SDePER, please cite: Yunqing Liu, Ningshan Li, Ji Qi et al. SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data. Genome Biology 25 , 271 (2024). https://doi.org/10.1186/s13059-024-03416-2 Next © Copyright 2023, Ningshan Li. Built with Sphinx using a theme provided by Read the Docs . + +### https://az7jh2.github.io/SDePER/ +SDePER SDePER | Spatial Deconvolution method with Platform Effect Removal Skip to the content. SDePER S patial De convolution method with P latform E ffect R emoval View on GitHub Documentation Analysis Repo SDePER SDePER ( S patial De convolution method with P latform E ffect R emoval) is a hybrid machine learning and regression method to deconvolve Spatial barcoding-based transcriptomic data using reference single-cell RNA sequencing data, considering platform effects removal , sparsity of cell types per capture spot and across-spots spatial correlation in cell type compositions. SDePER is also able to impute cell type compositions and gene expression at unmeasured locations in a tissue map with enhanced resolution . Quick Start SDePER currently supports only Linux operating systems such as Ubuntu, and is compatible with Python 3.9.x and 3.10.x releases (3.11+ not yet supported). SDePER can be installed via conda conda create -n sdeper-env -c bioconda -c conda-forge python = 3.9.12 sdeper or pip conda create -n sdeper-env python = 3.9.12 conda activate sdeper-env pip install sdeper SDePER supports an out-of-the-box feature, meaning that users only need to provide the required four input files for cell type deconvolution. The package manages all aspects of file reading, preprocessing, cell type-specific marker gene identification, and more internally. The required files are: raw nUMI counts of spatial transcriptomics data (spots × genes): spatial.csv raw nUMI counts of reference scRNA-seq data (cells × genes): scrna_ref.csv cell type annotations for all cells in scRNA-seq data (cells × 1): scrna_anno.csv adjacency matrix of spots in spatial transcriptomics data (spots × spots; optional ): adjacency.csv To start cell type deconvolution using all default settings by running runDeconvolution -q spatial.csv -r scrna_ref.csv -c scrna_anno.csv -a adjacency.csv Homepage : https://az7jh2.github.io/SDePER/ . Full Documentation for SDePER is available here . Example data and Analysis using SDePER are summarized in this page . All related materials can be found in the Analysis repository . Citation If you use SDePER, please cite: Yunqing Liu, Ningshan Li, Ji Qi et al. SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data. Genome Biology 25 , 271 (2024). https://doi.org/10.1186/s13059-024-03416-2 SDePER is maintained by az7jh2 . This page was generated by GitHub Pages . + +### https://github.com/az7jh2/SDePER +GitHub - az7jh2/SDePER: Spatial Deconvolution method with Platform Effect Removal · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} az7jh2 / SDePER Public Notifications You must be signed in to change notification settings Fork 1 Star 5 Code Issues 0 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights az7jh2/SDePER main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 33 Commits 33 Commits .github/ workflows .github/ workflows docs docs src src .readthedocs.yaml .readthedocs.yaml Dockerfile Dockerfile LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md STRUCTURE.md STRUCTURE.md meta.yaml meta.yaml pyproject.toml pyproject.toml requirements.txt requirements.txt setup.py setup.py View all files Repository files navigation README MIT license SDePER SDePER ( S patial De convolution method with P latform E ffect R emoval) is a hybrid machine learning and regression method to deconvolve Spatial barcoding-based transcriptomic data using reference single-cell RNA sequencing data, considering platform effects removal , sparsity of cell types per capture spot and across-spots spatial correlation in cell type compositions. SDePER is also able to impute cell type compositions and gene expression at unmeasured locations in a tissue map with enhanced resolution . Quick Start SDePER currently supports only Linux operating systems such as Ubuntu, and is compatible with Python 3.9.x and 3.10.x releases (3.11+ not yet supported). SDePER can be installed via conda conda create -n sdeper-env -c bioconda -c conda-forge python=3.9.12 sdeper or pip conda create -n sdeper-env python=3.9.12 conda activate sdeper-env pip install sdeper SDePER supports an out-of-the-box feature, meaning that users only need to provide the required four input files for cell type deconvolution. The package manages all aspects of file reading, preprocessing, cell type-specific marker gene identification, and more internally. The required files are: raw nUMI counts of spatial transcriptomics data (spots × genes): spatial.csv raw nUMI counts of reference scRNA-seq data (cells × genes): scrna_ref.csv cell type annotations for all cells in scRNA-seq data (cells × 1): scrna_anno.csv adjacency matrix of spots in spatial transcriptomics data (spots × spots; optional ): adjacency.csv To start cell type deconvolution using all default settings by running runDeconvolution -q spatial.csv -r scrna_ref.csv -c scrna_anno.csv -a adjacency.csv Homepage : https://az7jh2.github.io/SDePER/ . Full Documentation for SDePER is available here . Example data and Analysis using SDePER are summarized in this page . All related materials can be found in the Analysis repository . Citation If you use SDePER, please cite: Yunqing Liu, Ningshan Li, Ji Qi et al. SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data. Genome Biology 25 , 271 (2024). https://doi.org/10.1186/s13059-024-03416-2 About Spatial Deconvolution method with Platform Effect Removal az7jh2.github.io/SDePER/ Topics spatial-transcriptomics cell-type-deconvolution Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 5 stars Watchers 2 watching Forks 1 fork Report repository Releases 19 SDePER v2.0.0 Latest Jan 28, 2026 + 18 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.9% Dockerfile 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge sdeper --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +sdeper 1.0.0 pyhdfd78af_0 +------------------------- +file name : sdeper-1.0.0-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.0.0 +build : pyhdfd78af_0 +build number: 0 +size : 54 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.0.0-pyhdfd78af_0.tar.bz2 +md5 : 3f3b88a03f8bac8cee36ad8ff92476a5 +timestamp : 2023-08-15 08:54:06 UTC +dependencies: + - distinctipy 1.2.2 + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.55.2 + - numpy 1.22.4 + - openpyxl 3.0.10 + - pandas 1.4.3 + - python >=3.9.12 + - reportlab 3.6.12 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.8.1 + - seaborn 0.11.2 + - tensorflow 2.9.1 + - umap-learn 0.5.3 + + +sdeper 1.1.0 pyhdfd78af_0 +------------------------- +file name : sdeper-1.1.0-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.1.0 +build : pyhdfd78af_0 +build number: 0 +size : 57 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.1.0-pyhdfd78af_0.tar.bz2 +md5 : 834904d792e474e2fc12157f9c8c882d +timestamp : 2024-04-20 15:49:44 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv 4.6.0 + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.55.2 + - numpy 1.22.4 + - opencv 4.6.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.6.0 + - python >=3.9.12,<=3.11 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.8.1 + - seaborn 0.11.2 + - tensorflow-base 2.9.1 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.2.0 pyhdfd78af_0 +------------------------- +file name : sdeper-1.2.0-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.2.0 +build : pyhdfd78af_0 +build number: 0 +size : 62 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.2.0-pyhdfd78af_0.tar.bz2 +md5 : ffd1d5f65827aebfca4be2ddfc920059 +timestamp : 2024-04-28 06:37:25 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv 4.6.0 + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.55.2 + - numpy 1.22.4 + - opencv 4.6.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.6.0 + - python >=3.9.12,<=3.11 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.8.1 + - seaborn 0.11.2 + - tensorflow-base 2.9.1 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.2.1 pyhdfd78af_0 +------------------------- +file name : sdeper-1.2.1-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.2.1 +build : pyhdfd78af_0 +build number: 0 +size : 64 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.2.1-pyhdfd78af_0.tar.bz2 +md5 : bcb5380f1343636435e903da649d7ec5 +timestamp : 2024-05-03 18:16:09 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv 4.6.0 + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.55.2 + - numpy 1.22.4 + - opencv 4.6.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.6.0 + - python >=3.9.12,<3.11 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.8.1 + - seaborn 0.11.2 + - tensorflow-base 2.9.1 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.3.0 pyhdfd78af_0 +------------------------- +file name : sdeper-1.3.0-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.3.0 +build : pyhdfd78af_0 +build number: 0 +size : 65 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.3.0-pyhdfd78af_0.tar.bz2 +md5 : 94ab37fc3f4d05dab39424251d65f1db +timestamp : 2024-05-09 04:30:00 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv 4.6.0 + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.55.2 + - numpy 1.22.4 + - opencv 4.6.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.6.0 + - python >=3.9.12,<3.11 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.8.1 + - seaborn 0.11.2 + - tensorflow-base 2.9.1 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.3.1 pyhdfd78af_0 +------------------------- +file name : sdeper-1.3.1-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.3.1 +build : pyhdfd78af_0 +build number: 0 +size : 66 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.3.1-pyhdfd78af_0.tar.bz2 +md5 : 9f561b8617cbd98ddd6f71dd08800b68 +timestamp : 2024-06-06 15:25:56 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv 4.6.0 + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.55.2 + - numpy 1.22.4 + - opencv 4.6.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.6.0 + - python >=3.9.12,<3.11 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.8.1 + - seaborn 0.11.2 + - tensorflow-base 2.9.1 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.4.0 pyhdfd78af_0 +------------------------- +file name : sdeper-1.4.0-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.4.0 +build : pyhdfd78af_0 +build number: 0 +size : 68 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.4.0-pyhdfd78af_0.tar.bz2 +md5 : 57988f4b248d32ed38294f38c4acfbb0 +timestamp : 2024-06-26 03:21:14 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv 4.6.0 + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.55.2 + - numpy 1.22.4 + - opencv 4.6.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.6.0 + - python >=3.9.12,<3.11 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.8.1 + - seaborn 0.11.2 + - tensorflow-base 2.9.1 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.5.0 pyhdfd78af_0 +------------------------- +file name : sdeper-1.5.0-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.5.0 +build : pyhdfd78af_0 +build number: 0 +size : 68 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.5.0-pyhdfd78af_0.tar.bz2 +md5 : 88b04bb60153b45bec0fad1a5ad96217 +timestamp : 2024-07-12 09:28:29 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv 4.6.0 + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.55.2 + - numpy 1.22.4 + - opencv 4.6.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.6.0 + - python >=3.9.12,<3.11 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.8.1 + - seaborn 0.11.2 + - tensorflow-base 2.9.1 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.6.1 pyhdfd78af_0 +------------------------- +file name : sdeper-1.6.1-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.6.1 +build : pyhdfd78af_0 +build number: 0 +size : 73 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.6.1-pyhdfd78af_0.tar.bz2 +md5 : 2f1bed18673384bc771495f853e74245 +timestamp : 2024-08-05 06:09:22 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv 4.6.0 + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.55.2 + - numpy 1.22.4 + - opencv 4.6.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.6.0 + - python >=3.9.12,<3.11 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.8.1 + - seaborn-base 0.11.2 + - tensorflow-base 2.9.1 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.6.2 pyhdfd78af_0 +------------------------- +file name : sdeper-1.6.2-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.6.2 +build : pyhdfd78af_0 +build number: 0 +size : 72 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.6.2-pyhdfd78af_0.tar.bz2 +md5 : 2ef1a770aae11dba8544326eaad3740a +timestamp : 2024-08-05 11:49:55 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv ==4.9.0 headless_* + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.59.1 + - numpy 1.26.4 + - opencv 4.9.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.9.0 + - python >=3.9,<=3.10 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.11.4 + - seaborn 0.13.2 + - tensorflow-base 2.15.0 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.6.3 pyhdfd78af_0 +------------------------- +file name : sdeper-1.6.3-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.6.3 +build : pyhdfd78af_0 +build number: 0 +size : 72 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.6.3-pyhdfd78af_0.tar.bz2 +md5 : 508e412ee2e6a698d62e4b450e5634e7 +timestamp : 2024-10-20 10:29:49 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv ==4.9.0 headless_* + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.59.1 + - numpy 1.26.4 + - opencv 4.9.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.9.0 + - python >=3.9,<=3.10 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.11.4 + - seaborn 0.13.2 + - tensorflow-base 2.15.0 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.6.4 pyhdfd78af_0 +------------------------- +file name : sdeper-1.6.4-pyhdfd78af_0.tar.bz2 +name : sdeper +version : 1.6.4 +build : pyhdfd78af_0 +build number: 0 +size : 73 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.6.4-pyhdfd78af_0.tar.bz2 +md5 : a19b336885de12ff13ef437260f709fb +timestamp : 2025-06-01 14:15:40 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv ==4.9.0 headless_* + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.59.1 + - numpy 1.26.4 + - opencv 4.9.0 + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv 4.9.0 + - python >=3.9,<=3.10 + - reportlab 4.1.0 + - scanpy 1.9.1 + - scikit-learn 1.1.1 + - scikit-misc 0.1.4 + - scipy 1.11.4 + - seaborn 0.13.2 + - tensorflow-base 2.15.0 cpu_* + - umap-learn 0.5.3 + + +sdeper 1.6.4 pyhdfd78af_1 +------------------------- +file name : sdeper-1.6.4-pyhdfd78af_1.conda +name : sdeper +version : 1.6.4 +build : pyhdfd78af_1 +build number: 1 +size : 72 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.6.4-pyhdfd78af_1.conda +md5 : 55c9c96f29498a58efc55ca29cc04fa8 +timestamp : 2025-09-15 21:20:32 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv + - libprotobuf + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.59.1 + - numpy 1.26.4 + - opencv + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv + - python >=3.9,<=3.10 + - reportlab + - scanpy 1.9.1 + - scikit-learn + - scikit-misc + - scipy + - seaborn-base 0.13.2 + - tensorflow + - umap-learn + + +sdeper 1.7.0 pyhdfd78af_0 +------------------------- +file name : sdeper-1.7.0-pyhdfd78af_0.conda +name : sdeper +version : 1.7.0 +build : pyhdfd78af_0 +build number: 0 +size : 71 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/sdeper-1.7.0-pyhdfd78af_0.conda +md5 : e78b66c9054766c4e6f90d6ed894dbe0 +timestamp : 2025-10-05 14:26:39 UTC +dependencies: + - distinctipy 1.2.2 + - libopencv + - libprotobuf + - matplotlib-base 3.5.2 + - networkx 2.8.4 + - numba 0.59.1 + - numpy 1.26.4 + - opencv + - openpyxl 3.0.10 + - pandas 1.4.3 + - py-opencv + - python >=3.9,<=3.10 + - reportlab + - scanpy 1.9.1 + - scikit-learn + - scikit-misc + - scipy + - seaborn-base 0.13.2 + - tensorflow + - umap-learn + + +sdeper 1.7.1 pyhdfd78af_0 +------------------------ diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/searchgui.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/searchgui.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..28f789ee16c0db228926bbca4703b84ff752d112 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/searchgui.manual_bundle.txt @@ -0,0 +1,586 @@ +# Tool: searchgui +software_name: searchgui +tier: T1 +domain: t1_backfill_overall +downloads: 753333 +summary: User-friendly graphical tool for using proteomics identification search engines. +description: SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MetaMorpheus, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. +dependencies: blast >=2.16.0, fontconfig, fonts-conda-ecosystem, metamorpheus 1.1.0, mono >=6.0.0, openjdk >=21, python, xtandem 15.12.15.2 +execution_environment: Java +execution_environment_reason: inferred from Java runtime dependencies + +## URLs +home_url: https://github.com/compomics/searchgui +doc_url: https://github.com/compomics/searchgui/blob/master/README.md +dev_url: https://github.com/compomics/searchgui + +## CLI Help Source +java:-help +## CLI Help Content +$ conda run -n bioenv_java java -help +[rc=0] + +Usage: java [options] [args...] + (to execute a class) + or java [options] -jar [args...] + (to execute a jar file) + or java [options] -m [/] [args...] + java [options] --module [/] [args...] + (to execute the main class in a module) + or java [options] [args] + (to execute a single source-file program) + + Arguments following the main class, source file, -jar , + -m or --module / are passed as the arguments to + main class. + + where options include: + + -cp + -classpath + --class-path + A : separated list of directories, JAR archives, + and ZIP archives to search for class files. + -p + --module-path ... + A : separated list of directories, each directory + is a directory of modules. + --upgrade-module-path ... + A : separated list of directories, each directory + is a directory of modules that replace upgradeable + modules in the runtime image + --add-modules [,...] + root modules to resolve in addition to the initial module. + can also be ALL-DEFAULT, ALL-SYSTEM, + ALL-MODULE-PATH. + --list-modules + list observable modules and exit + -d + --describe-module + describe a module and exit + --dry-run create VM and load main class but do not execute main method. + The --dry-run option may be useful for validating the + command-line options such as the module system configuration. + --validate-modules + validate all modules and exit + The --validate-modules option may be useful for finding + conflicts and other errors with modules on the module path. + -D= + set a system property + -verbose:[class|module|gc|jni] + enable verbose output + -version print product version to the error stream and exit + --version print product version to the output stream and exit + -showversion print product version to the error stream and continue + --show-version + print product version to the output stream and continue + --show-module-resolution + show module resolution output during startup + -? -h -help + print this help message to the error stream + --help print this help message to the output stream + -X print help on extra options to the error stream + --help-extra print help on extra options to the output stream + -ea[:...|:] + -enableassertions[:...|:] + enable assertions with specified granularity + -da[:...|:] + -disableassertions[:...|:] + disable assertions with specified granularity + -esa | -enablesystemassertions + enable system assertions + -dsa | -disablesystemassertions + disable system assertions + -agentlib:[=] + load native agent library , e.g. -agentlib:jdwp + see also -agentlib:jdwp=help + -agentpath:[=] + load native agent library by full pathname + -javaagent:[=] + load Java programming language agent, see java.lang.instrument + -splash: + show splash screen with specified image + HiDPI scaled images are automatically supported and used + if available. The unscaled image filename, e.g. image.ext, + should always be passed as the argument to the -splash option. + The most appropriate scaled image provided will be picked up + automatically. + See the SplashScreen API documentation for more information + @argument files + one or more argument files containing options + -disable-@files + prevent further argument file expansion + --enable-preview + allow classes to depend on preview features of this release +To specify an argument for a long option, you can use --= or +-- . + + + + +## URL Docs Extract +### https://github.com/compomics/searchgui/blob/master/README.md +searchgui/README.md at master · CompOmics/searchgui · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} CompOmics / searchgui Public Notifications You must be signed in to change notification settings Fork 15 Star 47 Code Issues 18 Pull requests 0 Actions Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Wiki Security and quality Insights Files Expand file tree master Breadcrumbs searchgui / README.md Copy path Blame More file actions Blame More file actions Latest commit History History History 205 lines (122 loc) · 14.6 KB master Breadcrumbs searchgui / README.md Top File metadata and controls Preview Code Blame 205 lines (122 loc) · 14.6 KB Raw Copy raw file Download raw file Outline Edit and raw actions SearchGUI Introduction Read Me Troubleshooting Bioinformatics for Proteomics Tutorial SearchGUI Publications: Barsnes H and Vaudel M: SearchGUI: a highly adaptable common interface for proteomics search and de novo engines. J Proteome Res. 2018;17(7):2552-2555 . Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L: SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 2011;11(5):996-9 . If you use SearchGUI as part of a publication, please refer to the most recent publication. v4.3.17 - Windows ReleaseNotes v4.3.17 - Mac and Linux ReleaseNotes (Click on figure to see the full size version) Introduction SearchGUI is a a highly adaptable open-source common interface for configuring and running proteomics search and de novo engines, currently supporting X! Tandem , MyriMatch , MS Amanda , MS-GF+ , OMSSA , Comet , Tide , Andromeda , MetaMorpheus , Sage , Novor and DirecTag . To start using SearchGUI, unzip the downloaded file, and double-click the SearchGUI-X.Y.Z.jar file . No additional installation required! To visualize and analyze the search results we recommend PeptideShaker . For developer access to the search results we recommend the use of compomics-utilities . Go to top of page Read Me From the Command Line Bioconda Docker Easybuild Database Help User Defined Modifications Spectrum Data Formats Result Analysis To start identifying peptides and proteins using SearchGUI, download the latest version, unzip the downloaded file, and double-click on the SearchGUI-X.Y.Z.jar file. From the Command Line The main purpose of SearchGUI is to make it simpler to use multiple search engines at the same time. A graphical user interface is the best choice for smaller projects. SearchGUI can also be used via the command line, and be incorporated in different analysis pipelines. For details about the command line see: SearchCLI . Go to top of page Bioconda SearchGUI is available as a Miniconda package in the bioconda channel here . You can install SearchGUI with: conda install -c conda-forge -c bioconda searchgui Go to top of page Docker A Docker container is available via the Biocontainers repository. You can make use of the container via: docker run quay.io/biocontainers/searchgui:X.Y.Z--1 searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI Replace X.Y.Z with the wanted SearchGUI version number. You need to have in mind that Docker images don't contain your data into them. If you want to use any data file into a dockerised tool, you will need to map (using -v Docker parameter) your local folder containing it into the Docker internal file system, like docker run -v /home/my_user/resources:/myresources quay.io/biocontainers/searchgui:X.Y.Z--1 searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI -out myresources/parameters_output -db /myresources/uniprot-human-reviewed.fasta In this example we are also writing the ouput of the command ( -out parameter) into the mapped folder in order to write it into our own file system (instead on Docker's container one) and have access to it from our computer after the execution. Go to top of page Easybuild A Easybuild easyconfig file is available in the Easybuild development branch . SearchGUI can be installed with: eb -S SearchGUI-X.Y.Z-Java-1.8.0_152.eb module load SearchGUI/X.Y.Z-Java-1.8.0_152 Replace X.Y.Z with the wanted SearchGUI version number. The easyconfig provides aliases for the common CLI commands: SearchCLI PathSettingsCLI FastaCLI IdentificationParametersCLI Go to top of page User Defined Modifications It is straightforward to add/edit modifications via the graphical user interface. Modifications will be available in other instances of SearchGUI and PeptideShaker for the same user/computer. Not all modifications are correctly handled by the search engines. For example, X! Tandem is not compatible with modifications at termini on specific amino acids. Using such a modification will result in nonsense matches which can be filtered out afterwards. This functionality is available by default in PeptideShaker . Go to top of page Spectrum Data Formats SearchGUI supports mzML and mgf files as the direct input format for the spectrum files. In addition, ThermoRawFileParser is included, which supports out-of-the-box conversion of Thermo raw files into mzML and mgf. Furthermore, by referencing the location of your ProteoWizard installtion you may also provide additional raw file types as input, which will then be converted using msconvert . Note that this option is only available via the graphical user interface. From the command line you have to run the msconvert command line separatelty. Go to top of page Result Analysis To visualize and analyze the SearchGUI results we recommend the use of PeptideShaker . PeptideShaker is a search engine independent platform for visualization of peptide and protein identification results from multiple search engines. Go to top of page Troubleshooting Does Not Start I - Do you have Java installed? Download the latest version of Java here and try again. (You only need the JRE version (and not the JDK version) to run SearchGUI.) Does Not Start II - Have you unzipped the zip file? You need to unzip the file before double clicking the jar file. If you get the message "A Java Exception has occurred", you are most likely trying to run SearchGUI from within the zip file. Unzip the file and try again. Does Not Start III - Is SearchGUI installed in a path containing special characters, i.e. [ , % , æ, ø, å, etc? If so, move the whole folder to a different location or rename the folder(s) causing the problem and try again. (Note that on Linux SearchGUI has to be run from a path not containing spaces). Unidentified Developer - If you run SearchGUI on a Mac you can get the warning "SearchGUI" can't be opened because it is from an unidentified developer . To escape this warning control-click on the file icon and then select "Open." This will give you the option of opening it regardless of its unidentified source. This only has to be done once for each SearchGUI version. Search Engine Issues - Important: If you have problems with the search engines, please verify that the search engines are working outside of SearchGUI first. To test your installation run the search engine executable on the command line. This should result in output describing what the script does. If you get this, it works, and SearchGUI should run without problems. If not, see below. X! Tandem XML Syntax Error - If X! Tandem gives the error "Syntax error parsing XML", the problems is most likely that the path to your database or mgf files contains special characters not supported on your operating system. If this happens try renaming the folders containing the special characters or move the files to folders not containing special characters. Linux Support - Users wanting to use SearchGUI on Linux may have to install the search engines first, see the tools web pages for available search engine versions. Important: Please verify that the search engines are working outside of SearchGUI before using them inside SearchGUI. Linux Support II - If you get problems running makeblastdb (need to prepare FASTA files for OMSSA searches) make sure that you have the required 32 bit libraries. To install the libraries you can use "sudo apt-get install ia32-libs". MS Amanda Log - If you encounter problems with MS Amanda it may help to inspect the MS Amanda log files. On Windows these are located here: C:\ProgramData\MSAmanda . MS Amanda on Linux and Mac - Running MS Amanda on Linux or Mac requires that you have .NET Core installed. .NET 5.0 or newer is required. MyriMatch on Linux - If you get the error " locale::facet::_S_create_c_locale name not valid ", this can be fixed by running the command " export LC_ALL=C " before running SearchGUI/MyriMatch. To make this fix permanent, put the export line in your .bash_profile (~/.bash_profile). If you still have problems, please contact the MyriMatch developers . MyriMatch on Linux II - If you get the error " myrimatch: loadlocale.c:129: _nl_intern_locale_data: Assertion cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed. " (or other locale-related variable than LC_TIME ), this can be fixed by running the command " export LC_TIME=C " before running SearchGUI/MyriMatch. To make this fix permanent, put the export line in your .bash_profile (~/.bash_profile). MyriMatch on Windows - If Myrimatch finishes almost immediately and SearchGUI log shows something like " MyriMatch finished for * (47.0 milliseconds). Could not find MyriMatch result file ", myrimatch executable may not be running properly. Into its internal path (similar to \resources\MyriMatch\windows\windows_64bit, depending on your platform) you can execute it just writing myriMatch . If it throws errors about missing libraries like MSVCR100.dll or MSVCP100.dll you will need to install the last version available of them from Microsoft. MSVCR100.dll and MSVCP100.dll need this specific Microsoft Visual C++ package: Microsoft Visual C++ 2010 Service Pack 1 Redistributable Package MFC Security Update . Other versions of Visual C++ redistributable libraries may be obtained here: The latest supported Visual C++ downloads MetaMorpheus requirements - 64-bit operating system and .NET Core 3.1. See https://github.com/smith-chem-wisc/MetaMorpheus for more details. Linux and Mac OSX File Permissions - On Linux and Mac OSX you may have to edit the permissions for the executable files in order for SearchGUI to work. Allow execution for all users. 32 bits vs 64 bits - Please make sure that your using versions of the search engines that are compatible with your OS. Note that the latest releases of OMSSA are only available in 64 bits versions. For older versions of OMSSA see the OMSSA archive. However, it is always recommended to use the latest version if possible. Also note that OMSSA versions up until version 2.1.9 does not support precursor mass tolerance in ppm. Xlib/X11 errorrs - When running the command lines on systems without a grahpical user interface you may get errors related to X11. If that happens try adding -Djava.awt.headless=true to the command line. Problem Not Solved? Or Problem Not List? - Contact the developers of SearchGUI by setting up an issue describing the problem. If the issue is related to the installation of the search engines, please contact the search engine developers directly. Go to top of page Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/compomics/searchgui +GitHub - CompOmics/searchgui: Highly adaptable common interface for proteomics search and de novo engines · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} CompOmics / searchgui Public Notifications You must be signed in to change notification settings Fork 15 Star 47 Code Issues 18 Pull requests 0 Actions Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Wiki Security and quality Insights CompOmics/searchgui master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,091 Commits 1,091 Commits resources resources splashscreen splashscreen src src .gitignore .gitignore README.md README.md README.txt README.txt nb-configuration.xml nb-configuration.xml nbactions.xml nbactions.xml pom.xml pom.xml View all files Repository files navigation README SearchGUI Introduction Read Me Troubleshooting Bioinformatics for Proteomics Tutorial SearchGUI Publications: Barsnes H and Vaudel M: SearchGUI: a highly adaptable common interface for proteomics search and de novo engines. J Proteome Res. 2018;17(7):2552-2555 . Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L: SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 2011;11(5):996-9 . If you use SearchGUI as part of a publication, please refer to the most recent publication. v4.3.17 - Windows ReleaseNotes v4.3.17 - Mac and Linux ReleaseNotes (Click on figure to see the full size version) Introduction SearchGUI is a a highly adaptable open-source common interface for configuring and running proteomics search and de novo engines, currently supporting X! Tandem , MyriMatch , MS Amanda , MS-GF+ , OMSSA , Comet , Tide , Andromeda , MetaMorpheus , Sage , Novor and DirecTag . To start using SearchGUI, unzip the downloaded file, and double-click the SearchGUI-X.Y.Z.jar file . No additional installation required! To visualize and analyze the search results we recommend PeptideShaker . For developer access to the search results we recommend the use of compomics-utilities . Go to top of page Read Me From the Command Line Bioconda Docker Easybuild Database Help User Defined Modifications Spectrum Data Formats Result Analysis To start identifying peptides and proteins using SearchGUI, download the latest version, unzip the downloaded file, and double-click on the SearchGUI-X.Y.Z.jar file. From the Command Line The main purpose of SearchGUI is to make it simpler to use multiple search engines at the same time. A graphical user interface is the best choice for smaller projects. SearchGUI can also be used via the command line, and be incorporated in different analysis pipelines. For details about the command line see: SearchCLI . Go to top of page Bioconda SearchGUI is available as a Miniconda package in the bioconda channel here . You can install SearchGUI with: conda install -c conda-forge -c bioconda searchgui Go to top of page Docker A Docker container is available via the Biocontainers repository. You can make use of the container via: docker run quay.io/biocontainers/searchgui:X.Y.Z--1 searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI Replace X.Y.Z with the wanted SearchGUI version number. You need to have in mind that Docker images don't contain your data into them. If you want to use any data file into a dockerised tool, you will need to map (using -v Docker parameter) your local folder containing it into the Docker internal file system, like docker run -v /home/my_user/resources:/myresources quay.io/biocontainers/searchgui:X.Y.Z--1 searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI -out myresources/parameters_output -db /myresources/uniprot-human-reviewed.fasta In this example we are also writing the ouput of the command ( -out parameter) into the mapped folder in order to write it into our own file system (instead on Docker's container one) and have access to it from our computer after the execution. Go to top of page Easybuild A Easybuild easyconfig file is available in the Easybuild development branch . SearchGUI can be installed with: eb -S SearchGUI-X.Y.Z-Java-1.8.0_152.eb module load SearchGUI/X.Y.Z-Java-1.8.0_152 Replace X.Y.Z with the wanted SearchGUI version number. The easyconfig provides aliases for the common CLI commands: SearchCLI PathSettingsCLI FastaCLI IdentificationParametersCLI Go to top of page User Defined Modifications It is straightforward to add/edit modifications via the graphical user interface. Modifications will be available in other instances of SearchGUI and PeptideShaker for the same user/computer. Not all modifications are correctly handled by the search engines. For example, X! Tandem is not compatible with modifications at termini on specific amino acids. Using such a modification will result in nonsense matches which can be filtered out afterwards. This functionality is available by default in PeptideShaker . Go to top of page Spectrum Data Formats SearchGUI supports mzML and mgf files as the direct input format for the spectrum files. In addition, ThermoRawFileParser is included, which supports out-of-the-box conversion of Thermo raw files into mzML and mgf. Furthermore, by referencing the location of your ProteoWizard installtion you may also provide additional raw file types as input, which will then be converted using msconvert . Note that this option is only available via the graphical user interface. From the command line you have to run the msconvert command line separatelty. Go to top of page Result Analysis To visualize and analyze the SearchGUI results we recommend the use of PeptideShaker . PeptideShaker is a search engine independent platform for visualization of peptide and protein identification results from multiple search engines. Go to top of page Troubleshooting Does Not Start I - Do you have Java installed? Download the latest version of Java here and try again. (You only need the JRE version (and not the JDK version) to run SearchGUI.) Does Not Start II - Have you unzipped the zip file? You need to unzip the file before double clicking the jar file. If you get the message "A Java Exception has occurred", you are most likely trying to run SearchGUI from within the zip file. Unzip the file and try again. Does Not Start III - Is SearchGUI installed in a path containing special characters, i.e. [ , % , æ, ø, å, etc? If so, move the whole folder to a different location or rename the folder(s) causing the problem and try again. (Note that on Linux SearchGUI has to be run from a path not containing spaces). Unidentified Developer - If you run SearchGUI on a Mac you can get the warning "SearchGUI" can't be opened because it is from an unidentified developer . To escape this warning control-click on the file icon and then select "Open." This will give you the option of opening it regardless of its unidentified source. This only has to be done once for each SearchGUI version. Search Engine Issues - Important: If you have problems with the search engines, please verify that the search engines are working outside of SearchGUI first. To test your installation run the search engine executable on the command line. This should result in output describing what the script does. If you get this, it works, and SearchGUI should run without problems. If not, see below. X! Tandem XML Syntax Error - If X! Tandem gives the error "Syntax error parsing XML", the problems is most likely that the path to your database or mgf files contains special characters not supported on your operating system. If this happens try renaming the folders containing the special characters or move the files to folders not containing special characters. Linux Support - Users wanting to use SearchGUI on Linux may have to install the search engines first, see the tools web pages for available search engine versions. Important: Please verify that the search engines are working outside of SearchGUI before using them inside SearchGUI. Linux Support II - If you get problems running makeblastdb (need to prepare FASTA files for OMSSA searches) make sure that you have the required 32 bit libraries. To install the libraries you can use "sudo apt-get install ia32-libs". MS Amanda Log - If you encounter problems with MS Amanda it may help to inspect the MS Amanda log files. On Windows these are located here: C:\ProgramData\MSAmanda . MS Amanda on Linux and Mac - Running MS Amanda on Linux or Mac requires that you have .NET Core installed. .NET 5.0 or newer is required. MyriMatch on Linux - If you get the error " locale::facet::_S_create_c_locale name not valid ", this can be fixed by running the command " export LC_ALL=C " before running SearchGUI/MyriMatch. To make this fix permanent, put the export line in your .bash_profile (~/.bash_profile). If you still have problems, please contact the MyriMatch developers . MyriMatch on Linux II - If you get the error " myrimatch: loadlocale.c:129: _nl_intern_locale_data: Assertion cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed. " (or other locale-related variable than LC_TIME ), this can be fixed by running the command " export LC_TIME=C " before running SearchGUI/MyriMatch. To make this fix permanent, put the export line in your .bash_profile (~/.bash_profile). MyriMatch on Windows - If Myrimatch finishes almost immediately and SearchGUI log shows something like " MyriMatch finished for * (47.0 milliseconds). Could not find MyriMatch result file ", myrimatch executable may not be running properly. Into its internal path (similar to \resources\MyriMatch\windows\windows_64bit, depending on your platform) you can execute it just writing myriMatch . If it throws errors about missing libraries like MSVCR100.dll or MSVCP100.dll you will need to install the last version available of them from Microsoft. MSVCR100.dll and MSVCP100.dll need this specific Microsoft Visual C++ package: Microsoft Visual C++ 2010 Service Pack 1 Redistributable Package MFC Security Update . Other versions of Visual C++ redistributable libraries may be obtained here: The latest supported Visual C++ downloads MetaMorpheus requirements - 64-bit operating system and .NET Core 3.1. See https://github.com/smith-chem-wisc/MetaMorpheus for more details. Linux and Mac OSX File Permissions - On Linux and Mac OSX you may have to edit the permissions for the executable files in order for SearchGUI to work. Allow execution for all users. 32 bits vs 64 bits - Please make sure that your using versions of the search engines that are compatible with your OS. Note that the latest releases of OMSSA are only available in 64 bits versions. For older versions of OMSSA see the OMSSA archive. However, it is always recommended to use the latest version if possible. Also note that OMSSA versions up until version 2.1.9 does not support precursor mass tolerance in ppm. Xlib/X11 errorrs - When running the command lines on systems without a grahpical user interface you may get errors related to X11. If that happens try adding -Djava.awt.headless=true to the command line. Problem Not Solved? Or Problem Not List? - Contact the developers of SearchGUI by setting up an issue describing the problem. If the issue is related to the installation of the search engines, please contact the search engine developers directly. Go to top of page About Highly adaptable common interface for proteomics search and de novo engines compomics.github.io/projects/searchgui.html Topics java bioinformatics proteomics protein-identification Resources Readme Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 47 stars Watchers 18 watching Forks 15 forks Report repository Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Java 93.0% HTML 2.6% XSLT 2.3% Perl 1.8% GDB 0.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/compomics/searchgui +GitHub - CompOmics/searchgui: Highly adaptable common interface for proteomics search and de novo engines · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} CompOmics / searchgui Public Notifications You must be signed in to change notification settings Fork 15 Star 47 Code Issues 18 Pull requests 0 Actions Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Wiki Security and quality Insights CompOmics/searchgui master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,091 Commits 1,091 Commits resources resources splashscreen splashscreen src src .gitignore .gitignore README.md README.md README.txt README.txt nb-configuration.xml nb-configuration.xml nbactions.xml nbactions.xml pom.xml pom.xml View all files Repository files navigation README SearchGUI Introduction Read Me Troubleshooting Bioinformatics for Proteomics Tutorial SearchGUI Publications: Barsnes H and Vaudel M: SearchGUI: a highly adaptable common interface for proteomics search and de novo engines. J Proteome Res. 2018;17(7):2552-2555 . Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L: SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 2011;11(5):996-9 . If you use SearchGUI as part of a publication, please refer to the most recent publication. v4.3.17 - Windows ReleaseNotes v4.3.17 - Mac and Linux ReleaseNotes (Click on figure to see the full size version) Introduction SearchGUI is a a highly adaptable open-source common interface for configuring and running proteomics search and de novo engines, currently supporting X! Tandem , MyriMatch , MS Amanda , MS-GF+ , OMSSA , Comet , Tide , Andromeda , MetaMorpheus , Sage , Novor and DirecTag . To start using SearchGUI, unzip the downloaded file, and double-click the SearchGUI-X.Y.Z.jar file . No additional installation required! To visualize and analyze the search results we recommend PeptideShaker . For developer access to the search results we recommend the use of compomics-utilities . Go to top of page Read Me From the Command Line Bioconda Docker Easybuild Database Help User Defined Modifications Spectrum Data Formats Result Analysis To start identifying peptides and proteins using SearchGUI, download the latest version, unzip the downloaded file, and double-click on the SearchGUI-X.Y.Z.jar file. From the Command Line The main purpose of SearchGUI is to make it simpler to use multiple search engines at the same time. A graphical user interface is the best choice for smaller projects. SearchGUI can also be used via the command line, and be incorporated in different analysis pipelines. For details about the command line see: SearchCLI . Go to top of page Bioconda SearchGUI is available as a Miniconda package in the bioconda channel here . You can install SearchGUI with: conda install -c conda-forge -c bioconda searchgui Go to top of page Docker A Docker container is available via the Biocontainers repository. You can make use of the container via: docker run quay.io/biocontainers/searchgui:X.Y.Z--1 searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI Replace X.Y.Z with the wanted SearchGUI version number. You need to have in mind that Docker images don't contain your data into them. If you want to use any data file into a dockerised tool, you will need to map (using -v Docker parameter) your local folder containing it into the Docker internal file system, like docker run -v /home/my_user/resources:/myresources quay.io/biocontainers/searchgui:X.Y.Z--1 searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI -out myresources/parameters_output -db /myresources/uniprot-human-reviewed.fasta In this example we are also writing the ouput of the command ( -out parameter) into the mapped folder in order to write it into our own file system (instead on Docker's container one) and have access to it from our computer after the execution. Go to top of page Easybuild A Easybuild easyconfig file is available in the Easybuild development branch . SearchGUI can be installed with: eb -S SearchGUI-X.Y.Z-Java-1.8.0_152.eb module load SearchGUI/X.Y.Z-Java-1.8.0_152 Replace X.Y.Z with the wanted SearchGUI version number. The easyconfig provides aliases for the common CLI commands: SearchCLI PathSettingsCLI FastaCLI IdentificationParametersCLI Go to top of page User Defined Modifications It is straightforward to add/edit modifications via the graphical user interface. Modifications will be available in other instances of SearchGUI and PeptideShaker for the same user/computer. Not all modifications are correctly handled by the search engines. For example, X! Tandem is not compatible with modifications at termini on specific amino acids. Using such a modification will result in nonsense matches which can be filtered out afterwards. This functionality is available by default in PeptideShaker . Go to top of page Spectrum Data Formats SearchGUI supports mzML and mgf files as the direct input format for the spectrum files. In addition, ThermoRawFileParser is included, which supports out-of-the-box conversion of Thermo raw files into mzML and mgf. Furthermore, by referencing the location of your ProteoWizard installtion you may also provide additional raw file types as input, which will then be converted using msconvert . Note that this option is only available via the graphical user interface. From the command line you have to run the msconvert command line separatelty. Go to top of page Result Analysis To visualize and analyze the SearchGUI results we recommend the use of PeptideShaker . PeptideShaker is a search engine independent platform for visualization of peptide and protein identification results from multiple search engines. Go to top of page Troubleshooting Does Not Start I - Do you have Java installed? Download the latest version of Java here and try again. (You only need the JRE version (and not the JDK version) to run SearchGUI.) Does Not Start II - Have you unzipped the zip file? You need to unzip the file before double clicking the jar file. If you get the message "A Java Exception has occurred", you are most likely trying to run SearchGUI from within the zip file. Unzip the file and try again. Does Not Start III - Is SearchGUI installed in a path containing special characters, i.e. [ , % , æ, ø, å, etc? If so, move the whole folder to a different location or rename the folder(s) causing the problem and try again. (Note that on Linux SearchGUI has to be run from a path not containing spaces). Unidentified Developer - If you run SearchGUI on a Mac you can get the warning "SearchGUI" can't be opened because it is from an unidentified developer . To escape this warning control-click on the file icon and then select "Open." This will give you the option of opening it regardless of its unidentified source. This only has to be done once for each SearchGUI version. Search Engine Issues - Important: If you have problems with the search engines, please verify that the search engines are working outside of SearchGUI first. To test your installation run the search engine executable on the command line. This should result in output describing what the script does. If you get this, it works, and SearchGUI should run without problems. If not, see below. X! Tandem XML Syntax Error - If X! Tandem gives the error "Syntax error parsing XML", the problems is most likely that the path to your database or mgf files contains special characters not supported on your operating system. If this happens try renaming the folders containing the special characters or move the files to folders not containing special characters. Linux Support - Users wanting to use SearchGUI on Linux may have to install the search engines first, see the tools web pages for available search engine versions. Important: Please verify that the search engines are working outside of SearchGUI before using them inside SearchGUI. Linux Support II - If you get problems running makeblastdb (need to prepare FASTA files for OMSSA searches) make sure that you have the required 32 bit libraries. To install the libraries you can use "sudo apt-get install ia32-libs". MS Amanda Log - If you encounter problems with MS Amanda it may help to inspect the MS Amanda log files. On Windows these are located here: C:\ProgramData\MSAmanda . MS Amanda on Linux and Mac - Running MS Amanda on Linux or Mac requires that you have .NET Core installed. .NET 5.0 or newer is required. MyriMatch on Linux - If you get the error " locale::facet::_S_create_c_locale name not valid ", this can be fixed by running the command " export LC_ALL=C " before running SearchGUI/MyriMatch. To make this fix permanent, put the export line in your .bash_profile (~/.bash_profile). If you still have problems, please contact the MyriMatch developers . MyriMatch on Linux II - If you get the error " myrimatch: loadlocale.c:129: _nl_intern_locale_data: Assertion cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed. " (or other locale-related variable than LC_TIME ), this can be fixed by running the command " export LC_TIME=C " before running SearchGUI/MyriMatch. To make this fix permanent, put the export line in your .bash_profile (~/.bash_profile). MyriMatch on Windows - If Myrimatch finishes almost immediately and SearchGUI log shows something like " MyriMatch finished for * (47.0 milliseconds). Could not find MyriMatch result file ", myrimatch executable may not be running properly. Into its internal path (similar to \resources\MyriMatch\windows\windows_64bit, depending on your platform) you can execute it just writing myriMatch . If it throws errors about missing libraries like MSVCR100.dll or MSVCP100.dll you will need to install the last version available of them from Microsoft. MSVCR100.dll and MSVCP100.dll need this specific Microsoft Visual C++ package: Microsoft Visual C++ 2010 Service Pack 1 Redistributable Package MFC Security Update . Other versions of Visual C++ redistributable libraries may be obtained here: The latest supported Visual C++ downloads MetaMorpheus requirements - 64-bit operating system and .NET Core 3.1. See https://github.com/smith-chem-wisc/MetaMorpheus for more details. Linux and Mac OSX File Permissions - On Linux and Mac OSX you may have to edit the permissions for the executable files in order for SearchGUI to work. Allow execution for all users. 32 bits vs 64 bits - Please make sure that your using versions of the search engines that are compatible with your OS. Note that the latest releases of OMSSA are only available in 64 bits versions. For older versions of OMSSA see the OMSSA archive. However, it is always recommended to use the latest version if possible. Also note that OMSSA versions up until version 2.1.9 does not support precursor mass tolerance in ppm. Xlib/X11 errorrs - When running the command lines on systems without a grahpical user interface you may get errors related to X11. If that happens try adding -Djava.awt.headless=true to the command line. Problem Not Solved? Or Problem Not List? - Contact the developers of SearchGUI by setting up an issue describing the problem. If the issue is related to the installation of the search engines, please contact the search engine developers directly. Go to top of page About Highly adaptable common interface for proteomics search and de novo engines compomics.github.io/projects/searchgui.html Topics java bioinformatics proteomics protein-identification Resources Readme Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 47 stars Watchers 18 watching Forks 15 forks Report repository Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Java 93.0% HTML 2.6% XSLT 2.3% Perl 1.8% GDB 0.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge searchgui --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +searchgui 2.1.4 0 +----------------- +file name : searchgui-2.1.4-0.tar.bz2 +name : searchgui +version : 2.1.4 +build : 0 +build number: 0 +size : 124.5 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.1.4-0.tar.bz2 +md5 : f34eb8ed4dbf20f2ba8bdb69ef8c10c2 +dependencies: + - java-jdk >=6 + + +searchgui 2.1.4 1 +----------------- +file name : searchgui-2.1.4-1.tar.bz2 +name : searchgui +version : 2.1.4 +build : 1 +build number: 1 +size : 124.3 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.1.4-1.tar.bz2 +md5 : be036f4ebf601d64434e7d6393b9941c +dependencies: + - java-jdk >=6 + + +searchgui 2.1.4 2 +----------------- +file name : searchgui-2.1.4-2.tar.bz2 +name : searchgui +version : 2.1.4 +build : 2 +build number: 2 +size : 124.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.1.4-2.tar.bz2 +md5 : 3c557e4eafa381fb06fcf4c56ee35a87 +dependencies: + - java-jdk >=6 + + +searchgui 2.1.4 3 +----------------- +file name : searchgui-2.1.4-3.tar.bz2 +name : searchgui +version : 2.1.4 +build : 3 +build number: 3 +size : 124.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.1.4-3.tar.bz2 +md5 : b8d7bba989275fa747ff52126f80d546 +dependencies: + - java-jdk >=6 + + +searchgui 2.1.4 py27_1 +---------------------- +file name : searchgui-2.1.4-py27_1.tar.bz2 +name : searchgui +version : 2.1.4 +build : py27_1 +build number: 1 +size : 124.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.1.4-py27_1.tar.bz2 +md5 : 07c87971cce3c3eed1182bf287675104 +dependencies: + - java-jdk >=6 + - python 2.7* + + +searchgui 2.1.4 py34_1 +---------------------- +file name : searchgui-2.1.4-py34_1.tar.bz2 +name : searchgui +version : 2.1.4 +build : py34_1 +build number: 1 +size : 124.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.1.4-py34_1.tar.bz2 +md5 : 57e19074165d074ea55596bc0f1eedeb +dependencies: + - java-jdk >=6 + - python 3.4* + + +searchgui 2.1.4 py35_1 +---------------------- +file name : searchgui-2.1.4-py35_1.tar.bz2 +name : searchgui +version : 2.1.4 +build : py35_1 +build number: 1 +size : 124.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.1.4-py35_1.tar.bz2 +md5 : 03effdf1b968761ee40eeb36f0793a7e +dependencies: + - java-jdk >=6 + - python 3.5* + + +searchgui 2.1.4 py36_1 +---------------------- +file name : searchgui-2.1.4-py36_1.tar.bz2 +name : searchgui +version : 2.1.4 +build : py36_1 +build number: 1 +size : 124.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.1.4-py36_1.tar.bz2 +md5 : 8edc6e9ed225a0dc94dbdcc11290dce4 +dependencies: + - java-jdk >=6 + - python 3.6* + + +searchgui 2.9.0 0 +----------------- +file name : searchgui-2.9.0-0.tar.bz2 +name : searchgui +version : 2.9.0 +build : 0 +build number: 0 +size : 117.6 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.9.0-0.tar.bz2 +md5 : 03f6fd531f5e4330d0b12b79f952700f +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + + +searchgui 2.9.0 2 +----------------- +file name : searchgui-2.9.0-2.tar.bz2 +name : searchgui +version : 2.9.0 +build : 2 +build number: 2 +size : 117.6 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.9.0-2.tar.bz2 +md5 : f32a51cfbdbaa691c932c554188eb136 +timestamp : 2018-06-21 22:49:33 UTC +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python + + +searchgui 2.9.0 py27_1 +---------------------- +file name : searchgui-2.9.0-py27_1.tar.bz2 +name : searchgui +version : 2.9.0 +build : py27_1 +build number: 1 +size : 117.6 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.9.0-py27_1.tar.bz2 +md5 : aba4f51ce9ef5eb2aca8556012f2d5e5 +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 2.7* + + +searchgui 2.9.0 py34_1 +---------------------- +file name : searchgui-2.9.0-py34_1.tar.bz2 +name : searchgui +version : 2.9.0 +build : py34_1 +build number: 1 +size : 117.6 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.9.0-py34_1.tar.bz2 +md5 : b0763bea9b663420667a87a21286045e +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 3.4* + + +searchgui 2.9.0 py35_1 +---------------------- +file name : searchgui-2.9.0-py35_1.tar.bz2 +name : searchgui +version : 2.9.0 +build : py35_1 +build number: 1 +size : 117.6 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.9.0-py35_1.tar.bz2 +md5 : 16668fdfc6dca528151928178211abe2 +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 3.5* + + +searchgui 2.9.0 py36_1 +---------------------- +file name : searchgui-2.9.0-py36_1.tar.bz2 +name : searchgui +version : 2.9.0 +build : py36_1 +build number: 1 +size : 117.6 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-2.9.0-py36_1.tar.bz2 +md5 : 10c70be42da3e4c591bd7c50d175d1d1 +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 3.6* + + +searchgui 3.1.4 0 +----------------- +file name : searchgui-3.1.4-0.tar.bz2 +name : searchgui +version : 3.1.4 +build : 0 +build number: 0 +size : 128.3 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.1.4-0.tar.bz2 +md5 : 57300ddd4f9ead161da9f6bbdf8391ec +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + + +searchgui 3.1.4 2 +----------------- +file name : searchgui-3.1.4-2.tar.bz2 +name : searchgui +version : 3.1.4 +build : 2 +build number: 2 +size : 128.3 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.1.4-2.tar.bz2 +md5 : 83aa7030c7af70ebe28c173a90e4a060 +timestamp : 2018-06-21 23:57:37 UTC +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python + + +searchgui 3.1.4 py27_1 +---------------------- +file name : searchgui-3.1.4-py27_1.tar.bz2 +name : searchgui +version : 3.1.4 +build : py27_1 +build number: 1 +size : 128.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.1.4-py27_1.tar.bz2 +md5 : f50e28040b100cda11cd8b785c67acb6 +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 2.7* + + +searchgui 3.1.4 py34_1 +---------------------- +file name : searchgui-3.1.4-py34_1.tar.bz2 +name : searchgui +version : 3.1.4 +build : py34_1 +build number: 1 +size : 128.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.1.4-py34_1.tar.bz2 +md5 : 72fa8985a3dfab82814cd115cad243ac +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 3.4* + + +searchgui 3.1.4 py35_1 +---------------------- +file name : searchgui-3.1.4-py35_1.tar.bz2 +name : searchgui +version : 3.1.4 +build : py35_1 +build number: 1 +size : 128.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.1.4-py35_1.tar.bz2 +md5 : fad789239f1864305207b2a263af86f0 +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 3.5* + + +searchgui 3.1.4 py36_1 +---------------------- +file name : searchgui-3.1.4-py36_1.tar.bz2 +name : searchgui +version : 3.1.4 +build : py36_1 +build number: 1 +size : 128.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.1.4-py36_1.tar.bz2 +md5 : da2648f3542a56147044d31aaeb0b9b5 +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 3.6* + + +searchgui 3.2.3 1 +----------------- +file name : searchgui-3.2.3-1.tar.bz2 +name : searchgui +version : 3.2.3 +build : 1 +build number: 1 +size : 128.3 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.2.3-1.tar.bz2 +md5 : 4890c4b49c7b8e66cc31683c53cca7bf +timestamp : 2018-06-21 23:48:03 UTC +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python + + +searchgui 3.2.3 py27_0 +---------------------- +file name : searchgui-3.2.3-py27_0.tar.bz2 +name : searchgui +version : 3.2.3 +build : py27_0 +build number: 0 +size : 128.3 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.2.3-py27_0.tar.bz2 +md5 : df034e0f0fd1f9d41ff32aadbd0ed2ac +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 2.7* + + +searchgui 3.2.3 py34_0 +---------------------- +file name : searchgui-3.2.3-py34_0.tar.bz2 +name : searchgui +version : 3.2.3 +build : py34_0 +build number: 0 +size : 128.3 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.2.3-py34_0.tar.bz2 +md5 : f165aebdde6f8c301dad3474e4eb0ce2 +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 3.4* + + +searchgui 3.2.3 py35_0 +---------------------- +file name : searchgui-3.2.3-py35_0.tar.bz2 +name : searchgui +version : 3.2.3 +build : py35_0 +build number: 0 +size : 128.3 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.2.3-py35_0.tar.bz2 +md5 : 0fd98f1b6ae441e590a028d14a102005 +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 3.5* + + +searchgui 3.2.3 py36_0 +---------------------- +file name : searchgui-3.2.3-py36_0.tar.bz2 +name : searchgui +version : 3.2.3 +build : py36_0 +build number: 0 +size : 128.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/searchgui-3.2.3-py36_0.tar.bz2 +md5 : 74774005fecbefccf77d30ca89f0523a +dependencies: + - java-jdk >=6 + - mono >=4.0.0 + - python 3.6* + + +searchgui 3.2.5 1 +----------------- +file name : searchgui-3.2.5-1.tar.bz2 +name : searchgui +version : 3.2.5 +build : 1 +build number: 1 +size : 128.4 MB +license : Apache License, Version 2.0 +subdir : linux-64 +url : https://conda.anaconda.org/b diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/seqfu.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/seqfu.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..dadf7540ba6e322ca7cc7ce3033c10f4ebcbb2e3 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/seqfu.manual_bundle.txt @@ -0,0 +1,526 @@ +# Tool: seqfu +software_name: seqfu +tier: T1 +domain: t1_backfill_overall +downloads: 166742 +summary: DNA sequence utilities. +description: A collection of utilities to work with FASTX (FASTA or FASTQ) files +that accept gzipped input. +Tools to interleave and deinterleave, to calculate stats, and extract +portions of sequence datasets. +dependencies: libgcc >=14, libstdcxx >=14, libzlib >=1.3.2,<2.0a0, pcre >=8.45,<9.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: http://github.com/quadram-institute-bioscience/seqfu/ +doc_url: +dev_url: + +## CLI Help Source +cli:seqfu +## CLI Help Content +$ conda run -n bioenv_cli seqfu --help +[rc=0] +SeqFu 1.22.3 - FASTX Tools + + ____ _____ + / ___| ___ __ _| ___| _ + \___ \ / _ \/ _` | |_ | | | | + ___) | __/ (_| | _|| |_| | + |____/ \___|\__, |_| \__,_| + |_|  + · bases : count bases in FASTA/FASTQ files + · check : check FASTQ file for errors + · count [cnt] : count FASTA/FASTQ reads, pair-end aware + · deinterleave [dei] : deinterleave FASTQ + · derep [der] : feature-rich dereplication of FASTA/FASTQ files + · interleave [ilv] : interleave FASTQ pair ends + · lanes [mrl] : merge Illumina lanes + · list [lst] : print sequences from a list of names + · metadata [met] : print a table of FASTQ reads (mapping files) + · rotate [rot] : rotate a sequence with a new start position + · sort [srt] : sort sequences by size (uniques) + · stats [st] : statistics on sequence lengths + + · cat : concatenate FASTA/FASTQ files + · grep : select sequences with patterns + · head : print first sequences + · rc : reverse complement strings or files + · tab : tabulate reads to TSV (and viceversa) + · tail : view last sequences + · view : view sequences with colored quality and oligo matches + +Type 'seqfu version' or 'seqfu cite' to print the version and paper, respectively. +Add --help after each command to print its usage. + + + +## URL Docs Extract +### http://github.com/quadram-institute-bioscience/seqfu/ +GitHub - quadram-institute-bioscience/seqfu: Legacy repository (https://telatin.github.io/seqfu2) · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} quadram-institute-bioscience / seqfu Public Notifications You must be signed in to change notification settings Fork 1 Star 2 Code Issues 0 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights quadram-institute-bioscience/seqfu master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 105 Commits 105 Commits FASTX-Reader @ 09843ce FASTX-Reader @ 09843ce proch-n50 @ 0e4dd8f proch-n50 @ 0e4dd8f seqfu2 @ ab09094 seqfu2 @ ab09094 .gitignore .gitignore .gitmodules .gitmodules LICENSE LICENSE PRERELEASE.md PRERELEASE.md README.md README.md View all files Repository files navigation README MIT license SeqFu SeqFu SeqFu 1.x has been rewritten in Nim, expended and moved to a new house. Some of the tools shipped with the initial Perl implementation of Seqfu 0.x are available with Proch::N50 (see below). Repository Documentation n50 (moved) Moved to github.com/telatin/proch-n50 📦 See Metacpan page Citation Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files . Bioengineering 2021, 8, 59. doi.org/10.3390/bioengineering8050059 About Legacy repository ( https://telatin.github.io/seqfu2 ) telatin.github.io/seqfu2 Topics bioinformatics fasta fastq paired-end conda-packages Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 2 stars Watchers 2 watching Forks 1 fork Report repository Contributors Uh oh! There was an error while loading. Please reload this page . Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge seqfu --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +seqfu 0.1.0 pl526_0 +------------------- +file name : seqfu-0.1.0-pl526_0.tar.bz2 +name : seqfu +version : 0.1.0 +build : pl526_0 +build number: 0 +size : 14 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/seqfu-0.1.0-pl526_0.tar.bz2 +md5 : ffdd4f9673b4d260dd8b027e0b2561d1 +timestamp : 2020-03-17 16:25:30 UTC +dependencies: + - interleafq + - n50 + - perl >=5.26.2,<5.26.3.0a0 + - perl-exporter + - perl-fastx-abi + - perl-fastx-reader + - perl-file-which + - perl-getopt-long + - perl-json-pp + - perl-pod-usage + - perl-text-asciitable + + +seqfu 0.2.0 pl526_0 +------------------- +file name : seqfu-0.2.0-pl526_0.tar.bz2 +name : seqfu +version : 0.2.0 +build : pl526_0 +build number: 0 +size : 46 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/seqfu-0.2.0-pl526_0.tar.bz2 +md5 : 021ee3e91faee17a464e9d347bc746ff +timestamp : 2020-04-15 08:46:38 UTC +dependencies: + - interleafq + - n50 + - perl >=5.26.2,<5.26.3.0a0 + - perl-exporter + - perl-fastx-abi + - perl-fastx-reader + - perl-file-which + - perl-getopt-long + - perl-json-pp + - perl-pod-usage + - perl-text-asciitable + + +seqfu 0.2.0 pl526_1 +------------------- +file name : seqfu-0.2.0-pl526_1.tar.bz2 +name : seqfu +version : 0.2.0 +build : pl526_1 +build number: 1 +size : 46 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/seqfu-0.2.0-pl526_1.tar.bz2 +md5 : 552997e8ac03e46b7bac9fe31594df7c +timestamp : 2020-04-25 08:55:58 UTC +dependencies: + - interleafq >=0.99 + - n50 >=1.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-exporter + - perl-fastx-abi + - perl-fastx-reader >=0.88 + - perl-file-which + - perl-getopt-long + - perl-json-pp + - perl-pod-usage + - perl-text-asciitable + + +seqfu 0.5.0 pl526_0 +------------------- +file name : seqfu-0.5.0-pl526_0.tar.bz2 +name : seqfu +version : 0.5.0 +build : pl526_0 +build number: 0 +size : 48 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/seqfu-0.5.0-pl526_0.tar.bz2 +md5 : d9444f6402e2e578452335e5f5bab994 +timestamp : 2020-05-06 17:22:34 UTC +dependencies: + - interleafq >=0.99 + - n50 >=1.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-exporter + - perl-fastx-abi + - perl-fastx-reader >=0.88 + - perl-file-which + - perl-getopt-long + - perl-json-pp + - perl-pod-usage + - perl-text-asciitable + + +seqfu 0.5.1 pl526_0 +------------------- +file name : seqfu-0.5.1-pl526_0.tar.bz2 +name : seqfu +version : 0.5.1 +build : pl526_0 +build number: 0 +size : 48 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/seqfu-0.5.1-pl526_0.tar.bz2 +md5 : f7400ef48d99cf3d01c2cfef16f0a9bc +timestamp : 2020-06-07 11:17:16 UTC +dependencies: + - interleafq >=0.99 + - n50 >=1.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-exporter + - perl-fastx-abi + - perl-fastx-reader >=0.88 + - perl-file-which + - perl-getopt-long + - perl-json-pp + - perl-pod-usage + - perl-text-asciitable + + +seqfu 0.5.1 pl526_1 +------------------- +file name : seqfu-0.5.1-pl526_1.tar.bz2 +name : seqfu +version : 0.5.1 +build : pl526_1 +build number: 1 +size : 48 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/seqfu-0.5.1-pl526_1.tar.bz2 +md5 : 05402be433e9538e2ff604b204d05ae5 +timestamp : 2020-07-25 15:40:53 UTC +dependencies: + - interleafq >=0.99 + - n50 >=1.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-biox-seq + - perl-exporter + - perl-fastx-abi + - perl-fastx-reader >=0.88 + - perl-file-which + - perl-getopt-long + - perl-json-pp + - perl-pod-usage + - perl-text-asciitable + + +seqfu 0.6.0 pl526_0 +------------------- +file name : seqfu-0.6.0-pl526_0.tar.bz2 +name : seqfu +version : 0.6.0 +build : pl526_0 +build number: 0 +size : 50 KB +license : mit +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/seqfu-0.6.0-pl526_0.tar.bz2 +md5 : 452bb3a0940822521195a817935ccf4b +timestamp : 2020-07-27 11:10:38 UTC +dependencies: + - interleafq >=0.99 + - n50 >=1.3.0 + - perl >=5.26.2,<5.26.3.0a0 + - perl-biox-seq + - perl-exporter + - perl-fastx-abi + - perl-fastx-reader >=0.88 + - perl-file-which + - perl-getopt-long + - perl-json-pp + - perl-pod-usage + - perl-text-asciitable + + +seqfu 0.8.2 hed695b0_0 +---------------------- +file name : seqfu-0.8.2-hed695b0_0.tar.bz2 +name : seqfu +version : 0.8.2 +build : hed695b0_0 +build number: 0 +size : 264 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.8.2-hed695b0_0.tar.bz2 +md5 : 14b2a9c83e0831cf33d1bfe7b361bfcd +timestamp : 2020-12-20 08:58:11 UTC +dependencies: + - libgcc-ng >=7.5.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.8.5 hed695b0_0 +---------------------- +file name : seqfu-0.8.5-hed695b0_0.tar.bz2 +name : seqfu +version : 0.8.5 +build : hed695b0_0 +build number: 0 +size : 441 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.8.5-hed695b0_0.tar.bz2 +md5 : 164e19a065066f9c516afdaa109761a8 +timestamp : 2021-02-10 15:25:04 UTC +dependencies: + - libgcc-ng >=7.5.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.8.7 hed695b0_0 +---------------------- +file name : seqfu-0.8.7-hed695b0_0.tar.bz2 +name : seqfu +version : 0.8.7 +build : hed695b0_0 +build number: 0 +size : 453 KB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.8.7-hed695b0_0.tar.bz2 +md5 : e9083bc5ebf19fa0fecac2900c225edd +timestamp : 2021-02-17 17:27:22 UTC +dependencies: + - libgcc-ng >=7.5.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.8.8 hed695b0_0 +---------------------- +file name : seqfu-0.8.8-hed695b0_0.tar.bz2 +name : seqfu +version : 0.8.8 +build : hed695b0_0 +build number: 0 +size : 1.5 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.8.8-hed695b0_0.tar.bz2 +md5 : cd3c074500820ebca08d33761f32e8a4 +timestamp : 2021-02-25 19:11:42 UTC +dependencies: + - libgcc-ng >=7.5.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.8.10 hed695b0_0 +----------------------- +file name : seqfu-0.8.10-hed695b0_0.tar.bz2 +name : seqfu +version : 0.8.10 +build : hed695b0_0 +build number: 0 +size : 1.1 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.8.10-hed695b0_0.tar.bz2 +md5 : 1692ec607a0961dd80cdd1390efb012c +timestamp : 2021-02-26 18:18:37 UTC +dependencies: + - libgcc-ng >=7.5.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.8.11 hed695b0_0 +----------------------- +file name : seqfu-0.8.11-hed695b0_0.tar.bz2 +name : seqfu +version : 0.8.11 +build : hed695b0_0 +build number: 0 +size : 1.7 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.8.11-hed695b0_0.tar.bz2 +md5 : 67b683fb35354975f93577a28debbcc8 +timestamp : 2021-03-02 11:02:17 UTC +dependencies: + - libgcc-ng >=7.5.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.8.12 hed695b0_0 +----------------------- +file name : seqfu-0.8.12-hed695b0_0.tar.bz2 +name : seqfu +version : 0.8.12 +build : hed695b0_0 +build number: 0 +size : 1.7 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.8.12-hed695b0_0.tar.bz2 +md5 : 1faf294bc1196648638215f6cd1852c5 +timestamp : 2021-03-04 19:56:11 UTC +dependencies: + - libgcc-ng >=7.5.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.8.13 hed695b0_0 +----------------------- +file name : seqfu-0.8.13-hed695b0_0.tar.bz2 +name : seqfu +version : 0.8.13 +build : hed695b0_0 +build number: 0 +size : 2.2 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.8.13-hed695b0_0.tar.bz2 +md5 : c894c384c77666ade633b65b4b3f353d +timestamp : 2021-03-29 15:50:38 UTC +dependencies: + - libgcc-ng >=7.5.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.9.0 h38613fd_1 +---------------------- +file name : seqfu-0.9.0-h38613fd_1.tar.bz2 +name : seqfu +version : 0.9.0 +build : h38613fd_1 +build number: 1 +size : 2.1 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.9.0-h38613fd_1.tar.bz2 +md5 : e090d17fdeb1be3769650d800e7cb031 +timestamp : 2021-03-31 20:12:29 UTC +dependencies: + - libgcc-ng >=9.3.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.9.0 hed695b0_0 +---------------------- +file name : seqfu-0.9.0-hed695b0_0.tar.bz2 +name : seqfu +version : 0.9.0 +build : hed695b0_0 +build number: 0 +size : 2.2 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.9.0-hed695b0_0.tar.bz2 +md5 : 486f6d94e8015b8fb746f0a26e12f26e +timestamp : 2021-03-30 11:29:33 UTC +dependencies: + - libgcc-ng >=7.5.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.9.1 h38613fd_0 +---------------------- +file name : seqfu-0.9.1-h38613fd_0.tar.bz2 +name : seqfu +version : 0.9.1 +build : h38613fd_0 +build number: 0 +size : 2.4 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.9.1-h38613fd_0.tar.bz2 +md5 : c356e16439d7d4937d64d60dd4a9b838 +timestamp : 2021-04-07 12:28:22 UTC +dependencies: + - libgcc-ng >=9.3.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.9.5 h38613fd_0 +---------------------- +file name : seqfu-0.9.5-h38613fd_0.tar.bz2 +name : seqfu +version : 0.9.5 +build : h38613fd_0 +build number: 0 +size : 2.4 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.9.5-h38613fd_0.tar.bz2 +md5 : 6e11c77acc68541e1411034b0aea4a56 +timestamp : 2021-04-13 14:03:20 UTC +dependencies: + - libgcc-ng >=9.3.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 0.9.6 h38613fd_0 +---------------------- +file name : seqfu-0.9.6-h38613fd_0.tar.bz2 +name : seqfu +version : 0.9.6 +build : h38613fd_0 +build number: 0 +size : 2.4 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-0.9.6-h38613fd_0.tar.bz2 +md5 : 64580783401bd737dc9c1b07fea044d0 +timestamp : 2021-04-20 17:03:17 UTC +dependencies: + - libgcc-ng >=9.3.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 1.0.0 h38613fd_0 +---------------------- +file name : seqfu-1.0.0-h38613fd_0.tar.bz2 +name : seqfu +version : 1.0.0 +build : h38613fd_0 +build number: 0 +size : 2.4 MB +license : mit +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqfu-1.0.0-h38613fd_0.tar.bz2 +md5 : f026bde186eaf547e3ff0a4a26b3c108 +timestamp : 2021-05-06 11:52:39 UTC +dependencies: + - libgcc-ng >=9.3.0 + - pcre >=8.44,<9.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +seqfu 1.1.0 h38613fd_0 +-------------------- diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/seqkit.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/seqkit.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..264731d683ed2f29dd72340d071e88585a05dbfe --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/seqkit.manual_bundle.txt @@ -0,0 +1,642 @@ +# Tool: seqkit +software_name: seqkit +tier: T1 +domain: t1_backfill_overall +downloads: 726902 +summary: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. +description: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. +dependencies: +execution_environment: Other +execution_environment_reason: fallback runtime classification + +## URLs +home_url: https://github.com/shenwei356/seqkit +doc_url: https://bioinf.shenwei.me/seqkit +dev_url: https://github.com/shenwei356/seqkit + +## CLI Help Source +cli:seqkit +## CLI Help Content +$ conda run -n bioenv_cli seqkit --help +[rc=0] +SeqKit -- a cross-platform and ultrafast toolkit for FASTA/Q file manipulation + +Version: 2.13.0 + +Author: Wei Shen + +Documents : http://bioinf.shenwei.me/seqkit +Source code: https://github.com/shenwei356/seqkit +Please cite: https://doi.org/10.1002/imt2.191 + + +Seqkit utilizes the pgzip (https://github.com/klauspost/pgzip) package to +read and write gzip file, and the outputted gzip file would be slighty +larger than files generated by GNU gzip. + +Seqkit writes gzip files very fast, much faster than the multi-threaded pigz, +therefore there's no need to pipe the result to gzip/pigz. + +Seqkit also supports reading and writing xz (.xz) and zstd (.zst) formats since v2.2.0. +Bzip2 format is supported since v2.4.0. + +Compression level: + format range default comment + gzip 1-9 5 https://github.com/klauspost/pgzip sets 5 as the default value. + xz NA NA https://github.com/ulikunitz/xz does not support. + zstd 1-4 2 roughly equals to zstd 1, 3, 7, 11, respectively. + bzip 1-9 6 https://github.com/dsnet/compress + +Usage: + seqkit [command] + +Commands for Basic Operation: + faidx create the FASTA index file and extract subsequences + scat real time recursive concatenation and streaming of fastx files + seq transform sequences (extract ID, filter by length, remove gaps, reverse complement...) + sliding extract subsequences in sliding windows + stats simple statistics of FASTA/Q files + subseq get subsequences by region/gtf/bed, including flanking sequences + translate translate DNA/RNA to protein sequence (supporting ambiguous bases) + watch monitoring and online histograms of sequence features + +Commands for Format Conversion: + convert convert FASTQ quality encoding between Sanger, Solexa and Illumina + fa2fq retrieve corresponding FASTQ records by a FASTA file + fq2fa convert FASTQ to FASTA + fx2tab convert FASTA/Q to tabular format (and length, GC content, average quality...) + tab2fx convert tabular format to FASTA/Q format + +Commands for Searching: + amplicon extract amplicon (or specific region around it) via primer(s) + fish look for short sequences in larger sequences using local alignment + grep search sequences by ID/name/sequence/sequence motifs, mismatch allowed + locate locate subsequences/motifs, mismatch allowed + +Commands for Set Operation: + common find common/shared sequences of multiple files by id/name/sequence + duplicate duplicate sequences N times + head print the first N FASTA/Q records, or leading records whose total length >= L + head-genome print sequences of the first genome with common prefixes in name + pair match up paired-end reads from two fastq files + range print FASTA/Q records in a range (start:end) + rmdup remove duplicated sequences by ID/name/sequence + sample sample sequences by number or proportion + sample2 sample sequences by number or proportion (version 2) + split split sequences into files by id/seq region/size/parts (mainly for FASTA) + split2 split sequences into files by size/parts (FASTA, PE/SE FASTQ) + +Commands for Edit: + concat concatenate sequences with the same ID from multiple files + mutate edit sequence (point mutation, insertion, deletion) + rename rename duplicated IDs + replace replace name/sequence by regular expression + restart reset start position (rotate) for circular genomes + sana sanitize broken single line FASTQ files + +Commands for Ordering: + shuffle shuffle sequences + sort sort sequences by id/name/sequence/length + +Commands for BAM Processing: + bam monitoring and online histograms of BAM record features + +Commands for Miscellaneous: + merge-slides merge sliding windows generated from seqkit sliding + sum compute message digest for all sequences in FASTA/Q files + +Additional Commands: + genautocomplete generate shell autocompletion script (bash|zsh|fish|powershell) + version print version information and check for update + +Flags: + --alphabet-guess-seq-length int length of sequence prefix of the first FASTA record based on + which seqkit guesses the sequence type (0 for whole seq) + (default 10000) + --compress-level int compression level for gzip, zstd, xz and bzip2. type "seqkit -h" + for the range and default value for each format (default -1) + -h, --help help for seqkit + --id-ncbi FASTA head is NCBI-style, e.g. >gi|110645304|ref|NC_002516.2| + Pseud... + --id-regexp string regular expression for parsing ID (default "^(\\S+)\\s?") + -X, --infile-list string file of input files list (one file per line), if given, they are + appended to files from cli arguments + -w, --line-width int line width when outputting FASTA format (0 for no wrap) (default 60) + -o, --out-file string out file ("-" for stdout, suffix .gz for gzipped out) (default "-") + --quiet be quiet and do not show extra information + -t, --seq-type string sequence type (dna|rna|protein|unlimit|auto) (for auto, it + automatically detect by the first sequence) (default "auto") + --skip-file-check skip input file checking when given a file list if you believe + these files do exist + -j, --threads int number of CPUs. can also set with environment variable + SEQKIT_THREADS) (default 4) + +Use "seqkit [command] --help" for more information about a command. + + + +## URL Docs Extract +### https://bioinf.shenwei.me/seqkit +SeqKit - Ultrafast FASTA/Q kit Skip to content SeqKit - Ultrafast FASTA/Q kit Home Initializing search GitHub SeqKit - Ultrafast FASTA/Q kit GitHub Home Home Table of contents Features Installation Method 1: Download binaries Method 2: Install via Pixi Method 3: Install via conda Method 4: Install via homebrew Subcommands Citation Contributors Acknowledgements Contact License Starchart Download Usage FAQs Tutorial Benchmark Notes More tools Table of contents Features Installation Method 1: Download binaries Method 2: Install via Pixi Method 3: Install via conda Method 4: Install via homebrew Subcommands Citation Contributors Acknowledgements Contact License Starchart SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation Try SeqKit in your browser (Tutorials and Exercises provided by sandbox.bio ) Documents: http://bioinf.shenwei.me/seqkit ( Usage , FAQs , Tutorial , and Benchmark ) Source code: https://github.com/shenwei356/seqkit Latest version: Please cite : Others : Features Easy to install ( download ) Providing statically linked executable binaries for multiple platforms (Linux/Windows/macOS, amd64/arm64) Light weight and out-of-the-box, no dependencies, no compilation, no configuration conda install -c bioconda seqkit Easy to use Ultrafast (see technical-details and benchmark ) Seamlessly parsing both FASTA and FASTQ formats Supporting ( gzip / xz / zstd / bzip2 / lz4 compressed) STDIN/STDOUT and input/output file, easily integrated in pipe Reproducible results (configurable rand seed in sample and shuffle ) Supporting custom sequence ID via regular expression Supporting Bash/Zsh autocompletion Versatile commands ( usages and examples ) Practical functions supported by 38 subcommands Installation Method 1: Download binaries Go to Download Page , where you can find download links to various platforms. Method 2: Install via Pixi pixi global install -c bioconda seqkit Method 3: Install via conda conda install -c bioconda seqkit Method 4: Install via homebrew brew install seqkit Subcommands Category Command Function Input Strand-sensitivity Multi-threads Basic operation seq Transform sequences: extract ID/seq, filter by length/quality, remove gaps… FASTA/Q stats Simple statistics: #seqs, min/max_len, N50, Q20%, Q30%… FASTA/Q ✓ subseq Get subsequences by region/gtf/bed, including flanking sequences FASTA/Q + or/and - sliding Extract subsequences in sliding windows FASTA/Q + only faidx Create the FASTA index file and extract subsequences (with more features than samtools faidx) FASTA + or/and - translate translate DNA/RNA to protein sequence FASTA/Q + or/and - watch Monitoring and online histograms of sequence features FASTA/Q scat Real time concatenation and streaming of fastx files FASTA/Q ✓ Format conversion fq2fa Convert FASTQ to FASTA format FASTQ fx2tab Convert FASTA/Q to tabular format FASTA/Q fa2fq Retrieve corresponding FASTQ records by a FASTA file FASTA/Q + only tab2fx Convert tabular format to FASTA/Q format TSV convert Convert FASTQ quality encoding between Sanger, Solexa and Illumina FASTA/Q Searching grep Search sequences by ID/name/sequence/sequence motifs, mismatch allowed FASTA/Q + and - partly, -m locate Locate subsequences/motifs, mismatch allowed FASTA/Q + and - partly, -m amplicon Extract amplicon (or specific region around it), mismatch allowed FASTA/Q + and - partly, -m fish Look for short sequences in larger sequences FASTA/Q + and - Set operation sample Sample sequences by number or proportion FASTA/Q sample2 Sample sequences by number or proportion (version 2) FASTA/Q rmdup Remove duplicated sequences by ID/name/sequence FASTA/Q + and - common Find common sequences of multiple files by id/name/sequence FASTA/Q + and - duplicate Duplicate sequences N times FASTA/Q split Split sequences into files by id/seq region/size/parts (mainly for FASTA) FASTA preffered split2 Split sequences into files by size/parts (FASTA, PE/SE FASTQ) FASTA/Q head print the first N FASTA/Q records, or leading records whose total length >= L FASTA/Q head-genome Print sequences of the first genome with common prefixes in name FASTA/Q range Print FASTA/Q records in a range (start:end) FASTA/Q pair Patch up paired-end reads from two fastq files FASTA/Q Edit replace Replace name/sequence by regular expression FASTA/Q + only rename Rename duplicated IDs FASTA/Q concat Concatenate sequences with same ID from multiple files FASTA/Q + only restart Reset start position (rotate) for circular genomes FASTA/Q + only mutate Edit sequence (point mutation, insertion, deletion) FASTA/Q + only sana Sanitize broken single line FASTQ files FASTQ Ordering sort Sort sequences by id/name/sequence/length FASTA preffered shuffle Shuffle sequences FASTA preffered BAM processing bam Monitoring and online histograms of BAM record features BAM Miscellaneous sum Compute message digest for all sequences in FASTA/Q files FASTA/Q ✓ merge-slides Merge sliding windows generated from seqkit sliding TSV Notes: Strand-sensitivity: + only : only processing on the positive/forward strand. + and - : searching on both strands. + or/and - : depends on users' flags/options/arguments. Multiple-threads: Using the default 4 threads is fast enough for most commands, some commands can benefit from extra threads. Citation Wei Shen*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. doi:10.1002/imt2.191 . Contributors Wei Shen Botond Sipos : bam , scat , fish , sana , watch . others Acknowledgements We thank all users for their valuable feedback and suggestions. We thank all contributors for improving the code and documentation. We appreciate Klaus Post for his fantastic packages ( compress and pgzip ) which accelerate gzip file reading and writing. Contact Create an issue to report bugs, propose new functions or ask for help. License MIT License Starchart Made with Material for MkDocs + +### https://github.com/shenwei356/seqkit +GitHub - shenwei356/seqkit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} shenwei356 / seqkit Public Notifications You must be signed in to change notification settings Fork 180 Star 1.5k Code Issues 11 Pull requests 3 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights shenwei356/seqkit master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 884 Commits 884 Commits .github .github benchmark benchmark doc doc seqkit seqkit tests tests .gitignore .gitignore .travis.yml .travis.yml CHANGELOG.md CHANGELOG.md Dockerfile Dockerfile LICENSE LICENSE README-v0.3.1.1.md README-v0.3.1.1.md README.md README.md go.mod go.mod go.sum go.sum seqkit2.jpg seqkit2.jpg View all files Repository files navigation README MIT license SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation Try SeqKit in your browser (Tutorials and Exercises provided by sandbox.bio ) Documents: http://bioinf.shenwei.me/seqkit ( Usage , FAQs , Tutorial , and Benchmark ) Source code: https://github.com/shenwei356/seqkit Latest version: Please cite : Others : Features Easy to install ( download ) Providing statically linked executable binaries for multiple platforms (Linux/Windows/macOS, amd64/arm64) Light weight and out-of-the-box, no dependencies, no compilation, no configuration conda install -c bioconda seqkit Easy to use Ultrafast (see technical-details and benchmark ) Seamlessly parsing both FASTA and FASTQ formats Supporting ( gzip / xz / zstd / bzip2 / lz4 compressed) STDIN/STDOUT and input/output file, easily integrated in pipe Reproducible results (configurable rand seed in sample and shuffle ) Supporting custom sequence ID via regular expression Supporting Bash/Zsh autocompletion Versatile commands ( usages and examples ) Practical functions supported by 38 subcommands Installation Method 1: Download binaries Go to Download Page , where you can find download links to various platforms. Method 2: Install via Pixi pixi global install -c bioconda seqkit Method 3: Install via conda conda install -c bioconda seqkit Method 4: Install via homebrew brew install seqkit Subcommands Category Command Function Input Strand-sensitivity Multi-threads Basic operation seq Transform sequences: extract ID/seq, filter by length/quality, remove gaps… FASTA/Q stats Simple statistics: #seqs, min/max_len, N50, Q20%, Q30%… FASTA/Q ✓ subseq Get subsequences by region/gtf/bed, including flanking sequences FASTA/Q + or/and - sliding Extract subsequences in sliding windows FASTA/Q + only faidx Create the FASTA index file and extract subsequences (with more features than samtools faidx) FASTA + or/and - translate translate DNA/RNA to protein sequence FASTA/Q + or/and - watch Monitoring and online histograms of sequence features FASTA/Q scat Real time concatenation and streaming of fastx files FASTA/Q ✓ Format conversion fq2fa Convert FASTQ to FASTA format FASTQ fx2tab Convert FASTA/Q to tabular format FASTA/Q fa2fq Retrieve corresponding FASTQ records by a FASTA file FASTA/Q + only tab2fx Convert tabular format to FASTA/Q format TSV convert Convert FASTQ quality encoding between Sanger, Solexa and Illumina FASTA/Q Searching grep Search sequences by ID/name/sequence/sequence motifs, mismatch allowed FASTA/Q + and - partly, -m locate Locate subsequences/motifs, mismatch allowed FASTA/Q + and - partly, -m amplicon Extract amplicon (or specific region around it), mismatch allowed FASTA/Q + and - partly, -m fish Look for short sequences in larger sequences FASTA/Q + and - Set operation sample Sample sequences by number or proportion FASTA/Q sample2 Sample sequences by number or proportion (version 2) FASTA/Q rmdup Remove duplicated sequences by ID/name/sequence FASTA/Q + and - common Find common sequences of multiple files by id/name/sequence FASTA/Q + and - duplicate Duplicate sequences N times FASTA/Q split Split sequences into files by id/seq region/size/parts (mainly for FASTA) FASTA preffered split2 Split sequences into files by size/parts (FASTA, PE/SE FASTQ) FASTA/Q head print the first N FASTA/Q records, or leading records whose total length >= L FASTA/Q head-genome Print sequences of the first genome with common prefixes in name FASTA/Q range Print FASTA/Q records in a range (start:end) FASTA/Q pair Patch up paired-end reads from two fastq files FASTA/Q Edit replace Replace name/sequence by regular expression FASTA/Q + only rename Rename duplicated IDs FASTA/Q concat Concatenate sequences with same ID from multiple files FASTA/Q + only restart Reset start position (rotate) for circular genomes FASTA/Q + only mutate Edit sequence (point mutation, insertion, deletion) FASTA/Q + only sana Sanitize broken single line FASTQ files FASTQ Ordering sort Sort sequences by id/name/sequence/length FASTA preffered shuffle Shuffle sequences FASTA preffered BAM processing bam Monitoring and online histograms of BAM record features BAM Miscellaneous sum Compute message digest for all sequences in FASTA/Q files FASTA/Q ✓ merge-slides Merge sliding windows generated from seqkit sliding TSV Notes: Strand-sensitivity: + only : only processing on the positive/forward strand. + and - : searching on both strands. + or/and - : depends on users' flags/options/arguments. Multiple-threads: Using the default 4 threads is fast enough for most commands, some commands can benefit from extra threads. Citation Wei Shen*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. doi:10.1002/imt2.191 . Contributors Wei Shen Botond Sipos : bam , scat , fish , sana , watch . others Acknowledgements We thank all users for their valuable feedback and suggestions. We thank all contributors for improving the code and documentation. We appreciate Klaus Post for his fantastic packages ( compress and pgzip ) which accelerate gzip file reading and writing. Contact Create an issue to report bugs, propose new functions or ask for help. License MIT License Starchart About A cross-platform and ultrafast toolkit for FASTA/Q file manipulation bioinf.shenwei.me/seqkit Topics golang bioinformatics cross-platform tool toolkit fasta manipulation sequence fastq Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 1.5k stars Watchers 26 watching Forks 180 forks Report repository Releases 94 SeqKit v2.13.0 (10-year-old birthday version) Latest Feb 27, 2026 + 93 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Go 91.6% Shell 5.5% R 2.1% Other 0.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/shenwei356/seqkit +GitHub - shenwei356/seqkit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} shenwei356 / seqkit Public Notifications You must be signed in to change notification settings Fork 180 Star 1.5k Code Issues 11 Pull requests 3 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights shenwei356/seqkit master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 884 Commits 884 Commits .github .github benchmark benchmark doc doc seqkit seqkit tests tests .gitignore .gitignore .travis.yml .travis.yml CHANGELOG.md CHANGELOG.md Dockerfile Dockerfile LICENSE LICENSE README-v0.3.1.1.md README-v0.3.1.1.md README.md README.md go.mod go.mod go.sum go.sum seqkit2.jpg seqkit2.jpg View all files Repository files navigation README MIT license SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation Try SeqKit in your browser (Tutorials and Exercises provided by sandbox.bio ) Documents: http://bioinf.shenwei.me/seqkit ( Usage , FAQs , Tutorial , and Benchmark ) Source code: https://github.com/shenwei356/seqkit Latest version: Please cite : Others : Features Easy to install ( download ) Providing statically linked executable binaries for multiple platforms (Linux/Windows/macOS, amd64/arm64) Light weight and out-of-the-box, no dependencies, no compilation, no configuration conda install -c bioconda seqkit Easy to use Ultrafast (see technical-details and benchmark ) Seamlessly parsing both FASTA and FASTQ formats Supporting ( gzip / xz / zstd / bzip2 / lz4 compressed) STDIN/STDOUT and input/output file, easily integrated in pipe Reproducible results (configurable rand seed in sample and shuffle ) Supporting custom sequence ID via regular expression Supporting Bash/Zsh autocompletion Versatile commands ( usages and examples ) Practical functions supported by 38 subcommands Installation Method 1: Download binaries Go to Download Page , where you can find download links to various platforms. Method 2: Install via Pixi pixi global install -c bioconda seqkit Method 3: Install via conda conda install -c bioconda seqkit Method 4: Install via homebrew brew install seqkit Subcommands Category Command Function Input Strand-sensitivity Multi-threads Basic operation seq Transform sequences: extract ID/seq, filter by length/quality, remove gaps… FASTA/Q stats Simple statistics: #seqs, min/max_len, N50, Q20%, Q30%… FASTA/Q ✓ subseq Get subsequences by region/gtf/bed, including flanking sequences FASTA/Q + or/and - sliding Extract subsequences in sliding windows FASTA/Q + only faidx Create the FASTA index file and extract subsequences (with more features than samtools faidx) FASTA + or/and - translate translate DNA/RNA to protein sequence FASTA/Q + or/and - watch Monitoring and online histograms of sequence features FASTA/Q scat Real time concatenation and streaming of fastx files FASTA/Q ✓ Format conversion fq2fa Convert FASTQ to FASTA format FASTQ fx2tab Convert FASTA/Q to tabular format FASTA/Q fa2fq Retrieve corresponding FASTQ records by a FASTA file FASTA/Q + only tab2fx Convert tabular format to FASTA/Q format TSV convert Convert FASTQ quality encoding between Sanger, Solexa and Illumina FASTA/Q Searching grep Search sequences by ID/name/sequence/sequence motifs, mismatch allowed FASTA/Q + and - partly, -m locate Locate subsequences/motifs, mismatch allowed FASTA/Q + and - partly, -m amplicon Extract amplicon (or specific region around it), mismatch allowed FASTA/Q + and - partly, -m fish Look for short sequences in larger sequences FASTA/Q + and - Set operation sample Sample sequences by number or proportion FASTA/Q sample2 Sample sequences by number or proportion (version 2) FASTA/Q rmdup Remove duplicated sequences by ID/name/sequence FASTA/Q + and - common Find common sequences of multiple files by id/name/sequence FASTA/Q + and - duplicate Duplicate sequences N times FASTA/Q split Split sequences into files by id/seq region/size/parts (mainly for FASTA) FASTA preffered split2 Split sequences into files by size/parts (FASTA, PE/SE FASTQ) FASTA/Q head print the first N FASTA/Q records, or leading records whose total length >= L FASTA/Q head-genome Print sequences of the first genome with common prefixes in name FASTA/Q range Print FASTA/Q records in a range (start:end) FASTA/Q pair Patch up paired-end reads from two fastq files FASTA/Q Edit replace Replace name/sequence by regular expression FASTA/Q + only rename Rename duplicated IDs FASTA/Q concat Concatenate sequences with same ID from multiple files FASTA/Q + only restart Reset start position (rotate) for circular genomes FASTA/Q + only mutate Edit sequence (point mutation, insertion, deletion) FASTA/Q + only sana Sanitize broken single line FASTQ files FASTQ Ordering sort Sort sequences by id/name/sequence/length FASTA preffered shuffle Shuffle sequences FASTA preffered BAM processing bam Monitoring and online histograms of BAM record features BAM Miscellaneous sum Compute message digest for all sequences in FASTA/Q files FASTA/Q ✓ merge-slides Merge sliding windows generated from seqkit sliding TSV Notes: Strand-sensitivity: + only : only processing on the positive/forward strand. + and - : searching on both strands. + or/and - : depends on users' flags/options/arguments. Multiple-threads: Using the default 4 threads is fast enough for most commands, some commands can benefit from extra threads. Citation Wei Shen*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. doi:10.1002/imt2.191 . Contributors Wei Shen Botond Sipos : bam , scat , fish , sana , watch . others Acknowledgements We thank all users for their valuable feedback and suggestions. We thank all contributors for improving the code and documentation. We appreciate Klaus Post for his fantastic packages ( compress and pgzip ) which accelerate gzip file reading and writing. Contact Create an issue to report bugs, propose new functions or ask for help. License MIT License Starchart About A cross-platform and ultrafast toolkit for FASTA/Q file manipulation bioinf.shenwei.me/seqkit Topics golang bioinformatics cross-platform tool toolkit fasta manipulation sequence fastq Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 1.5k stars Watchers 26 watching Forks 180 forks Report repository Releases 94 SeqKit v2.13.0 (10-year-old birthday version) Latest Feb 27, 2026 + 93 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Go 91.6% Shell 5.5% R 2.1% Other 0.8% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge seqkit --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +seqkit 0.3.4.1 0 +---------------- +file name : seqkit-0.3.4.1-0.tar.bz2 +name : seqkit +version : 0.3.4.1 +build : 0 +build number: 0 +size : 2.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.3.4.1-0.tar.bz2 +md5 : acf7399c950af8202782d6fd051912e1 +dependencies: [] + + +seqkit 0.4.3 0 +-------------- +file name : seqkit-0.4.3-0.tar.bz2 +name : seqkit +version : 0.4.3 +build : 0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.4.3-0.tar.bz2 +md5 : c6c09b7cb269403c7387f6d95e202c13 +dependencies: [] + + +seqkit 0.4.4 0 +-------------- +file name : seqkit-0.4.4-0.tar.bz2 +name : seqkit +version : 0.4.4 +build : 0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.4.4-0.tar.bz2 +md5 : 78b3c6ec9d3726698287706f9ae2d8e7 +dependencies: [] + + +seqkit 0.4.5 0 +-------------- +file name : seqkit-0.4.5-0.tar.bz2 +name : seqkit +version : 0.4.5 +build : 0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.4.5-0.tar.bz2 +md5 : 37b012684edae9770910cd1c09c2d322 +dependencies: [] + + +seqkit 0.5.0 0 +-------------- +file name : seqkit-0.5.0-0.tar.bz2 +name : seqkit +version : 0.5.0 +build : 0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.5.0-0.tar.bz2 +md5 : ec9a8a3367217ec1d33c9c039e31daaf +dependencies: [] + + +seqkit 0.5.1 0 +-------------- +file name : seqkit-0.5.1-0.tar.bz2 +name : seqkit +version : 0.5.1 +build : 0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.5.1-0.tar.bz2 +md5 : 8a769a9b2a30e332582d31650d4c3a62 +dependencies: [] + + +seqkit 0.5.2 0 +-------------- +file name : seqkit-0.5.2-0.tar.bz2 +name : seqkit +version : 0.5.2 +build : 0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.5.2-0.tar.bz2 +md5 : 9293cba8ea2355af5a07852bdcb8a315 +dependencies: [] + + +seqkit 0.5.3 0 +-------------- +file name : seqkit-0.5.3-0.tar.bz2 +name : seqkit +version : 0.5.3 +build : 0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.5.3-0.tar.bz2 +md5 : c19983baf66d13279725f53baf5d307f +dependencies: [] + + +seqkit 0.5.4 0 +-------------- +file name : seqkit-0.5.4-0.tar.bz2 +name : seqkit +version : 0.5.4 +build : 0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.5.4-0.tar.bz2 +md5 : 0c9cb2989a7fae9d991bb2ba4ec80a49 +dependencies: [] + + +seqkit 0.5.5 0 +-------------- +file name : seqkit-0.5.5-0.tar.bz2 +name : seqkit +version : 0.5.5 +build : 0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.5.5-0.tar.bz2 +md5 : 51c53b2fc54290a0deb15d17a94462cf +dependencies: [] + + +seqkit 0.6.0 0 +-------------- +file name : seqkit-0.6.0-0.tar.bz2 +name : seqkit +version : 0.6.0 +build : 0 +build number: 0 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.6.0-0.tar.bz2 +md5 : 2d672dd0e526dd810bedca755ae48490 +dependencies: [] + + +seqkit 0.7.0 0 +-------------- +file name : seqkit-0.7.0-0.tar.bz2 +name : seqkit +version : 0.7.0 +build : 0 +build number: 0 +size : 1.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.7.0-0.tar.bz2 +md5 : c7308b95f5a5e2923aa7479227330dba +dependencies: [] + + +seqkit 0.7.1 0 +-------------- +file name : seqkit-0.7.1-0.tar.bz2 +name : seqkit +version : 0.7.1 +build : 0 +build number: 0 +size : 2.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.7.1-0.tar.bz2 +md5 : 277d498f34290b71e275a14d8b4a11c8 +dependencies: [] + + +seqkit 0.7.2 0 +-------------- +file name : seqkit-0.7.2-0.tar.bz2 +name : seqkit +version : 0.7.2 +build : 0 +build number: 0 +size : 2.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.7.2-0.tar.bz2 +md5 : 01d6706a9c48f1ea9f43174c6faec1f9 +dependencies: [] + + +seqkit 0.8.0 0 +-------------- +file name : seqkit-0.8.0-0.tar.bz2 +name : seqkit +version : 0.8.0 +build : 0 +build number: 0 +size : 2.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.8.0-0.tar.bz2 +md5 : 557149dd22ae1fabc35ba967220408db +dependencies: [] + + +seqkit 0.8.0 1 +-------------- +file name : seqkit-0.8.0-1.tar.bz2 +name : seqkit +version : 0.8.0 +build : 1 +build number: 1 +size : 2.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.8.0-1.tar.bz2 +md5 : 9a8e2d0401a984da45736ee465b28589 +dependencies: + - pigz + + +seqkit 0.8.0 2 +-------------- +file name : seqkit-0.8.0-2.tar.bz2 +name : seqkit +version : 0.8.0 +build : 2 +build number: 2 +size : 2.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.8.0-2.tar.bz2 +md5 : e1ceb102f9df8f5572aaec1277cb0d07 +timestamp : 2018-06-21 21:12:27 UTC +dependencies: + - pigz + + +seqkit 0.8.1 2 +-------------- +file name : seqkit-0.8.1-2.tar.bz2 +name : seqkit +version : 0.8.1 +build : 2 +build number: 2 +size : 2.1 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.8.1-2.tar.bz2 +md5 : 423cb3567bd0b5f57fd3f7b8867d762c +timestamp : 2018-06-29 09:53:31 UTC +dependencies: [] + + +seqkit 0.9.0 2 +-------------- +file name : seqkit-0.9.0-2.tar.bz2 +name : seqkit +version : 0.9.0 +build : 2 +build number: 2 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.9.0-2.tar.bz2 +md5 : 05fc6e64a5fff5f486577ee1b2c39ed0 +timestamp : 2018-09-26 12:59:54 UTC +dependencies: [] + + +seqkit 0.9.1 2 +-------------- +file name : seqkit-0.9.1-2.tar.bz2 +name : seqkit +version : 0.9.1 +build : 2 +build number: 2 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.9.1-2.tar.bz2 +md5 : a9bede49980822c838ee33b0c14d2b91 +timestamp : 2018-10-12 03:51:45 UTC +dependencies: [] + + +seqkit 0.9.2 2 +-------------- +file name : seqkit-0.9.2-2.tar.bz2 +name : seqkit +version : 0.9.2 +build : 2 +build number: 2 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.9.2-2.tar.bz2 +md5 : 6b8cc63972e45836db47935037716147 +timestamp : 2018-11-16 15:11:28 UTC +dependencies: [] + + +seqkit 0.9.3 1 +-------------- +file name : seqkit-0.9.3-1.tar.bz2 +name : seqkit +version : 0.9.3 +build : 1 +build number: 1 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.9.3-1.tar.bz2 +md5 : 2bf10cf4c21887b256b049e904c78902 +timestamp : 2018-12-03 21:30:02 UTC +dependencies: [] + + +seqkit 0.10.0 1 +--------------- +file name : seqkit-0.10.0-1.tar.bz2 +name : seqkit +version : 0.10.0 +build : 1 +build number: 1 +size : 2.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.10.0-1.tar.bz2 +md5 : fdc677e974bd2783859ff6aa2a1f4099 +timestamp : 2018-12-24 10:34:09 UTC +dependencies: [] + + +seqkit 0.10.1 1 +--------------- +file name : seqkit-0.10.1-1.tar.bz2 +name : seqkit +version : 0.10.1 +build : 1 +build number: 1 +size : 2.9 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.10.1-1.tar.bz2 +md5 : 62a2c11332a59431663b806686bae928 +timestamp : 2019-02-27 13:42:06 UTC +dependencies: [] + + +seqkit 0.10.2 0 +--------------- +file name : seqkit-0.10.2-0.tar.bz2 +name : seqkit +version : 0.10.2 +build : 0 +build number: 0 +size : 3.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.10.2-0.tar.bz2 +md5 : 04e5c9c32a91d05b4515289649294803 +timestamp : 2019-07-31 09:41:10 UTC +dependencies: [] + + +seqkit 0.11.0 0 +--------------- +file name : seqkit-0.11.0-0.tar.bz2 +name : seqkit +version : 0.11.0 +build : 0 +build number: 0 +size : 6.5 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.11.0-0.tar.bz2 +md5 : f3b43bf9f113271b31133d5404a169be +timestamp : 2019-09-25 06:17:09 UTC +dependencies: [] + + +seqkit 0.12.0 0 +--------------- +file name : seqkit-0.12.0-0.tar.bz2 +name : seqkit +version : 0.12.0 +build : 0 +build number: 0 +size : 6.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.12.0-0.tar.bz2 +md5 : 5e9808ffb131ada218d56f139bec14df +timestamp : 2020-02-18 16:19:58 UTC +dependencies: [] + + +seqkit 0.12.1 0 +--------------- +file name : seqkit-0.12.1-0.tar.bz2 +name : seqkit +version : 0.12.1 +build : 0 +build number: 0 +size : 6.6 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.12.1-0.tar.bz2 +md5 : 651c3afeb3c1f8d00935ea70688d3ae7 +timestamp : 2020-04-21 15:02:23 UTC +dependencies: [] + + +seqkit 0.13.0 0 +--------------- +file name : seqkit-0.13.0-0.tar.bz2 +name : seqkit +version : 0.13.0 +build : 0 +build number: 0 +size : 6.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.13.0-0.tar.bz2 +md5 : 4a310889800efe14fcb084e299ed1d24 +timestamp : 2020-07-07 12:16:40 UTC +dependencies: [] + + +seqkit 0.13.1 0 +--------------- +file name : seqkit-0.13.1-0.tar.bz2 +name : seqkit +version : 0.13.1 +build : 0 +build number: 0 +size : 6.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.13.1-0.tar.bz2 +md5 : 6f72a13dd45109ff2b2b024746b66000 +timestamp : 2020-07-09 11:42:10 UTC +dependencies: [] + + +seqkit 0.13.2 0 +--------------- +file name : seqkit-0.13.2-0.tar.bz2 +name : seqkit +version : 0.13.2 +build : 0 +build number: 0 +size : 6.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/seqkit-0.13.2-0.tar.bz2 +md5 : 1358e77b8ab8aa50b4c2d3d27d1350f9 +timestamp : 2020-07-13 09:26:40 UTC +dependencies: [] + + +seqkit 0.14.0 0 +--------------- +file name : seqkit-0.14.0-0.tar.bz2 +name : seqkit +ve diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sina.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sina.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..933a52ef86f1f19d27ce32da9134f8297032bbd1 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sina.manual_bundle.txt @@ -0,0 +1,310 @@ +# Tool: sina +software_name: sina +tier: T1 +domain: t1_backfill_overall +downloads: 119005 +summary: Reference based multiple sequence alignment +description: SINA allows incorporating additional sequences into an existing +multiple sequence alignment (MSA) without modifying the original +alignment. While adding sequences to an MSA with SINA is usually +faster than re-computing the entire MSA from an augmented set of +unaligned sequences, the primary benefit lies in protecting +investments made into the original MSA such as manual curation of the +alignment, compute intensive phylogenetic tree reconstruction and +taxonomic annotation of the resulting phylogeny. + +Additionally, SINA includes a homology search which uses the +previously computed alignment to determine the most similar +sequences. Based on the search results, a LCA based classification of +the query sequence can be computed using taxonomic classifications +assigned to the sequences comprising the reference MSA. + +SINA is used to compute the small and large subunit ribosomal RNA +alignments provided by the SILVA_ project and is able to use the ARB_ +format reference databases released by the project. +dependencies: arb-bio-tools, boost-cpp >=1.70.0,<1.70.1.0a0, glib >=2.58.3,<3.0a0, libarbdb 6.0.6 haa8b8d8_8, libgcc-ng >=7.5.0, libstdcxx-ng >=7.5.0, tbb >=2020.2,<2021.0.0a0, zlib >=1.2.11,<1.3.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/epruesse/SINA +doc_url: https://sina.readthedocs.io +dev_url: + +## CLI Help Source +cli:sina +## CLI Help Content +$ conda run -n bioenv_cli sina --help +[rc=127] + +/bin/bash: /225040511/miniconda3/envs/bioenv_cli/lib/libtinfo.so.6: no version information available (required by /bin/bash) +/225040511/miniconda3/envs/bioenv_cli/lib/sina/bin/sina.real: error while loading shared libraries: libboost_program_options.so.1.54.0: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run sina --help` failed. (See above for error) + + +## URL Docs Extract +### https://github.com/epruesse/SINA +GitHub - epruesse/SINA: SINA - Reference based multiple sequence alignment · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} epruesse / SINA Public Notifications You must be signed in to change notification settings Fork 4 Star 41 Code Issues 27 Pull requests 0 Discussions Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Security and quality Insights epruesse/SINA master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 871 Commits 871 Commits .circleci .circleci ci_scripts ci_scripts doc doc include include m4 m4 src src test_data @ 078f87f test_data @ 078f87f tests tests tools tools .bumpversion.cfg .bumpversion.cfg .gitignore .gitignore .gitmodules .gitmodules .travis.yml .travis.yml LICENSE LICENSE Makefile.am Makefile.am README.rst README.rst arb_LICENSE.txt arb_LICENSE.txt arb_PUBLIB_LICENSE.txt arb_PUBLIB_LICENSE.txt autogen.sh autogen.sh configure.ac configure.ac View all files Repository files navigation README GPL-3.0 license SINA - reference based multiple sequence alignment SINA aligns nucleotide sequences to match a pre-existing MSA using a graph based alignment algorithm similar to PoA. The graph approach allows SINA to incorporate information from many reference sequences building without blurring highly variable regions. While pure NAST implementations depend highly on finding a good match in the reference database, SINA is able to align sequences relatively distant to references with good quality and will yield a robust result for query sequences with many close reference. Features Speed. Aligning 100,000 full length rRNA against the SILVA NR takes 40 minutes on a mid-sized 2018 desktop computer. Aligning 1,000,000 V4 amplicons takes about 60 minutes. Accuracy. SINA is used to build the SILVA SSU and LSU rRNA databases. Classification. SINA includes an LCA based classification module. ARB. SINA is able to directly read and write ARB format files such as distributed by the SILVA project. Online Version An online version for submitting small batches of sequences is made available by the SILVA project as part of their ACT: Alignment, Classification and Tree Service . In addition to SINA's alignment and classification stages, ACT allows directly building phylogenetic trees with RAxML or FastTree from your sequences and (optionally) additional sequences chosen using SINA's add-neighbors feature. Installing SINA The preferred way to install SINA locally is via Bioconda . If you have a working Bioconda installation, just run: conda create -n sina sina conda activate sina Alternatively, self-contained images are available at https://github.com/epruesse/SINA/releases . Choose the most recent tar.gz appropriate for your operating system and unpack: tar xf sina-1.7.3-dev-dev-linux.tar.gz cd sina-1.7.3-dev-dev ./sina Documentation The full documentation is available at https://sina.readthedocs.io . The algorithm is explained in the paper: Elmar Pruesse, Jörg Peplies, Frank Oliver Glöckner; SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28 (14): 1823-1829. doi:10.1093/bioinformatics/bts252 About SINA - Reference based multiple sequence alignment sina.readthedocs.io Topics bioinformatics alignment sequence 16s rrna silva Resources Readme License GPL-3.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 41 stars Watchers 6 watching Forks 4 forks Report repository Releases 15 Minor fix (build issue w/o TBB Malloc) Latest Dec 13, 2020 + 14 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C++ 82.2% M4 9.7% Perl 4.2% Shell 2.1% Makefile 0.7% C 0.6% TeX 0.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge sina --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +sina 1.3.0 0 +------------ +file name : sina-1.3.0-0.tar.bz2 +name : sina +version : 1.3.0 +build : 0 +build number: 0 +size : 4.1 MB +license : Personal Use and Evaluation License (PUEL) for SINA Stand‐Alone Software +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.3.0-0.tar.bz2 +md5 : 7ec9a59164b9834885b0da07920670fa +dependencies: [] + + +sina 1.3.1 0 +------------ +file name : sina-1.3.1-0.tar.bz2 +name : sina +version : 1.3.1 +build : 0 +build number: 0 +size : 9.0 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.3.1-0.tar.bz2 +md5 : 4b8e5996923217f67a5a7cfb0f38f5ec +dependencies: + - arb-bio + - boost 1.64.* + - libgcc + + +sina 1.3.1 h4ef8376_2 +--------------------- +file name : sina-1.3.1-h4ef8376_2.tar.bz2 +name : sina +version : 1.3.1 +build : h4ef8376_2 +build number: 2 +size : 2.1 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.3.1-h4ef8376_2.tar.bz2 +md5 : 02cbf655023d12339b378f25d79c3e39 +timestamp : 2018-09-05 23:39:03 UTC +dependencies: + - arb-bio-tools + - boost >=1.67.0,<1.67.1.0a0 + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +sina 1.3.4 h4ef8376_2 +--------------------- +file name : sina-1.3.4-h4ef8376_2.tar.bz2 +name : sina +version : 1.3.4 +build : h4ef8376_2 +build number: 2 +size : 2.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.3.4-h4ef8376_2.tar.bz2 +md5 : 74c1ba06a65af9dfdd0cfbd0facd7eae +timestamp : 2018-09-09 01:49:40 UTC +dependencies: + - arb-bio-tools + - boost >=1.67.0,<1.67.1.0a0 + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +sina 1.3.5 h4ef8376_2 +--------------------- +file name : sina-1.3.5-h4ef8376_2.tar.bz2 +name : sina +version : 1.3.5 +build : h4ef8376_2 +build number: 2 +size : 2.2 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.3.5-h4ef8376_2.tar.bz2 +md5 : a37dcbf0db7e0790e781b16dd9f27d1c +timestamp : 2018-09-20 11:13:13 UTC +dependencies: + - arb-bio-tools + - boost >=1.67.0,<1.67.1.0a0 + - libstdcxx-ng >=4.9 + - zlib >=1.2.11,<1.3.0a0 + + +sina 1.4.0 h4ef8376_0 +--------------------- +file name : sina-1.4.0-h4ef8376_0.tar.bz2 +name : sina +version : 1.4.0 +build : h4ef8376_0 +build number: 0 +size : 4.0 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.4.0-h4ef8376_0.tar.bz2 +md5 : a0ee83687bd4baa324afac9b3456767a +timestamp : 2018-11-11 06:58:01 UTC +dependencies: + - arb-bio-tools + - boost >=1.67.0,<1.67.1.0a0 + - libstdcxx-ng >=4.9 + - tbb >=2019.2,<2021.0.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +sina 1.5.0 hc7f9b0f_0 +--------------------- +file name : sina-1.5.0-hc7f9b0f_0.tar.bz2 +name : sina +version : 1.5.0 +build : hc7f9b0f_0 +build number: 0 +size : 1.5 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.5.0-hc7f9b0f_0.tar.bz2 +md5 : a6d6d47c50f5d6b7e54991ee2e0d72a0 +timestamp : 2019-02-16 01:03:17 UTC +dependencies: + - arb-bio-tools + - boost-cpp >=1.68.0,<1.68.1.0a0 + - glib >=2.58.2,<3.0a0 + - libarbdb 6.0.6 haa8b8d8_8 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - tbb >=2019.3,<2021.0.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +sina 1.6.0 hc7f9b0f_0 +--------------------- +file name : sina-1.6.0-hc7f9b0f_0.tar.bz2 +name : sina +version : 1.6.0 +build : hc7f9b0f_0 +build number: 0 +size : 1.6 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.6.0-hc7f9b0f_0.tar.bz2 +md5 : ef2aaf3e80b1f77c1852a990ceee3b28 +timestamp : 2019-04-27 02:08:14 UTC +dependencies: + - arb-bio-tools + - boost-cpp >=1.68.0,<1.68.1.0a0 + - glib >=2.58.3,<3.0a0 + - libarbdb 6.0.6 haa8b8d8_8 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - tbb >=2019.5,<2021.0.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +sina 1.6.1 h9aa86b4_0 +--------------------- +file name : sina-1.6.1-h9aa86b4_0.tar.bz2 +name : sina +version : 1.6.1 +build : h9aa86b4_0 +build number: 0 +size : 1.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.6.1-h9aa86b4_0.tar.bz2 +md5 : 58fa3c752984932c6137185c67f1a5ee +timestamp : 2020-03-09 05:26:22 UTC +dependencies: + - arb-bio-tools + - boost-cpp >=1.70.0,<1.70.1.0a0 + - glib >=2.58.3,<3.0a0 + - libarbdb 6.0.6 haa8b8d8_8 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - tbb >=2020.1,<2021.0.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +sina 1.7.0 h9aa86b4_0 +--------------------- +file name : sina-1.7.0-h9aa86b4_0.tar.bz2 +name : sina +version : 1.7.0 +build : h9aa86b4_0 +build number: 0 +size : 1.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.7.0-h9aa86b4_0.tar.bz2 +md5 : 913b4e2e0d42a18ed986012f58ec5990 +timestamp : 2020-08-02 01:27:51 UTC +dependencies: + - arb-bio-tools + - boost-cpp >=1.70.0,<1.70.1.0a0 + - glib >=2.58.3,<3.0a0 + - libarbdb 6.0.6 haa8b8d8_8 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - tbb >=2020.1,<2021.0.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +sina 1.7.1 h9aa86b4_0 +--------------------- +file name : sina-1.7.1-h9aa86b4_0.tar.bz2 +name : sina +version : 1.7.1 +build : h9aa86b4_0 +build number: 0 +size : 1.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.7.1-h9aa86b4_0.tar.bz2 +md5 : 52b62dd5fd6eab2c0a724528aade7b0e +timestamp : 2020-08-19 01:27:25 UTC +dependencies: + - arb-bio-tools + - boost-cpp >=1.70.0,<1.70.1.0a0 + - glib >=2.58.3,<3.0a0 + - libarbdb 6.0.6 haa8b8d8_8 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - tbb >=2020.1,<2021.0.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +sina 1.7.2 h9aa86b4_0 +--------------------- +file name : sina-1.7.2-h9aa86b4_0.tar.bz2 +name : sina +version : 1.7.2 +build : h9aa86b4_0 +build number: 0 +size : 1.9 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sina-1.7.2-h9aa86b4_0.tar.bz2 +md5 : b185afaee972c6ccf232c8a316493a33 +timestamp : 2020-12-13 21:29:58 UTC +dependencies: + - arb-bio-tools + - boost-cpp >=1.70.0,<1.70.1.0a0 + - glib >=2.58.3,<3.0a0 + - libarbdb 6.0.6 haa8b8d8_8 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - tbb >=2020.2,<2021.0.0a0 + - zlib >=1.2.11,<1.3.0a0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/slow5tools.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/slow5tools.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..86a632d8cf7066704380ef9f2dd4d79cdac9d52b --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/slow5tools.manual_bundle.txt @@ -0,0 +1,488 @@ +# Tool: slow5tools +software_name: slow5tools +tier: T1 +domain: t1_backfill_overall +downloads: 381688 +summary: Toolkit for S/BLOW5 format. +description: Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. +dependencies: hdf5 >=1.14.3,<1.14.4.0a0, libgcc >=13, libstdcxx >=13, libzlib >=1.3.1,<2.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/hasindu2008/slow5tools +doc_url: +dev_url: https://github.com/hasindu2008/slow5tools + +## CLI Help Source +cli:slow5tools +## CLI Help Content +$ conda run -n bioenv_cli slow5tools --help +[rc=0] +Usage: slow5tools [OPTIONS] [COMMAND] [ARG] +Tools for using slow5 files. + +OPTIONS: + -h, --help Display this message and exit. + -v, --verbose Verbosity level. + -V, --version Output version information and exit. + +COMMANDS: + f2s or fast5toslow5 convert fast5 file(s) to SLOW5/BLOW5 + s2f or slow5tofast5 convert SLOW5/BLOW5 file(s) to fast5 + merge merge SLOW5/BLOW5 files + split split SLOW5/BLOW5 files + index create a SLOW5/BLOW5 index file + get display the read entry for each specified read id + view view the contents of a SLOW5/BLOW5 file or convert between different SLOW5/BLOW5 formats and compressions + stats prints statistics of a SLOW5/BLOW5 file to the stdout + cat quickly concatenate SLOW5/BLOW5 files of same type (same header, extension, compression) [experimental] + quickcheck quickly checks if a SLOW5/BLOW5 file is intact + +ARGS: Try 'slow5tools [COMMAND] --help' for more information. + + + +## URL Docs Extract +### https://github.com/hasindu2008/slow5tools +GitHub - hasindu2008/slow5tools: Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} hasindu2008 / slow5tools Public Notifications You must be signed in to change notification settings Fork 7 Star 105 Code Issues 0 Pull requests 0 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights hasindu2008/slow5tools master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,573 Commits 1,573 Commits .github/ workflows .github/ workflows build build docs docs scripts scripts slow5lib @ e4bf785 slow5lib @ e4bf785 src src test test .gitattributes .gitattributes .gitignore .gitignore .gitmodules .gitmodules .travis.yml .travis.yml CMakeLists.txt CMakeLists.txt Dockerfile Dockerfile LICENSE LICENSE Makefile Makefile README.md README.md config.mk.in config.mk.in configure.ac configure.ac installdeps.mk installdeps.mk View all files Repository files navigation README MIT license slow5tools Slow5tools is a simple toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. About SLOW5 format: SLOW5 is a new file format for storing signal data from Oxford Nanopore Technologies (ONT) devices. SLOW5 was developed to overcome inherent limitations in the standard FAST5 signal data format that prevent efficient, scalable analysis and cause many headaches for developers. SLOW5 can be encoded in human-readable ASCII format, or a more compact and efficient binary format (BLOW5) - this is analogous to the seminal SAM/BAM format for storing DNA sequence alignments. The BLOW5 binary format supports zlib (DEFLATE) compression, or other compression methods (see notes ), thereby minimising the data storage footprint while still permitting efficient parallel access. Detailed benchmarking experiments have shown that SLOW5 format is an order of magnitude faster and significantly smaller than FAST5. Full documentation: https://hasindu2008.github.io/slow5tools Publication (SLOW5 format): https://www.nature.com/articles/s41587-021-01147-4 Publication (slow5tools): https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02910-3 SLOW5 specification: https://hasindu2008.github.io/slow5specs slow5 ecosystem: https://hasindu2008.github.io/slow5 To convert to and from ONT's new POD5 format, you use blue_crab . If POD5 format and the associated POD5 C/C++ API reaches maturity/stability and adheres to C++11 standard, capabilities for POD5 <-> SLOW5 conversion will be added to slow5tools. slow5tools is strictly adhering to C++11 standard for wider compatibility. Quick start If you are a Linux user on x86_64 architecture and want to quickly try slow5tools out, download the compiled binaries from the latest release . For example: VERSION=v1.4.0 wget " https://github.com/hasindu2008/slow5tools/releases/download/ $VERSION /slow5tools- $VERSION -x86_64-linux-binaries.tar.gz " && tar xvf slow5tools- $VERSION -x86_64-linux-binaries.tar.gz && cd slow5tools- $VERSION / ./slow5tools Binaries should work on most Linux distributions as the only dependency is zlib which is available by default on most distributions. For compiled binaries to work, your processor must support SSSE3 instructions or higher (processors after 2007 have these) and your operating system must have GLIBC 2.17 or higher (Linux distributions from 2014 onwards typically have this). You can also use conda to install slow5tools as conda install slow5tools -c bioconda -c conda-forge . For converting latest vbz compressed FAST5, you will need to setup the ONT vbz plugin as explained in faq:Q3 . Table of Contents Quick start Building Building a release Building from GitHub Other building options Usage Examples Troubleshooting/Questions Upcoming features and optimisations Notes Acknowledgement Citation Building Building a release Users are recommended to build from the latest release tar ball. A compiler that supports C++11 is needed to build slow5tools. Quick example for Ubuntu : sudo apt-get install libhdf5-dev zlib1g-dev # install HDF5 and zlib development libraries VERSION=v1.4.0 wget " https://github.com/hasindu2008/slow5tools/releases/download/ $VERSION /slow5tools- $VERSION -release.tar.gz " && tar xvf slow5tools- $VERSION -release.tar.gz && cd slow5tools- $VERSION / ./configure make The commands to install hdf5 (and zlib) development libraries on some popular distributions : On Debian/Ubuntu : sudo apt-get install libhdf5-dev zlib1g-dev On Fedora/CentOS : sudo dnf/yum install hdf5-devel zlib-devel On Arch Linux: sudo pacman -S hdf5 On OS X : brew install hdf5 zlib Building from GitHub WARNING: Building from GitHub is meant for advanced users to test latest features. For production purposes, use the latest release version that is thoroughly tested. Building from the Github repository additionally requires autoreconf which can be installed on Ubuntu using sudo apt-get install autoconf automake ( brew install autoconf automake on macOS). To build from GitHub: sudo apt-get install libhdf5-dev zlib1g-dev autoconf automake #install HDF5 and zlib development libraries and autotools git clone --recursive https://github.com/hasindu2008/slow5tools cd slow5tools autoreconf # autoreconf --install for macos ./configure make Other building options If you only want to manipulate S/BLOW5 files, you can disable FAST5/HDF5 for even easier compilation. Call ./configure --disable-hdf5 && make or completely bypass the configure step and just call make disable_hdf5=1 . You can optionally enable zstd compression support when building slow5lib by invoking make zstd=1 . This requires zstd 1.3 or higher development libraries installed on your system ( libzstd1-dev package for apt , libzstd-devel for yum/dnf and zstd for homebrew ). SLOW5 files compressed with zstd offer smaller file size and better performance compared to the default zlib . However, zlib runtime library is available by default on almost all distributions unlike zstd and thus files compressed with zlib will be more 'portable' (also see notes ). For enabling zstd on Apple Silicon (e.g., Mac M1) also see faq . If you cannot install the zstd library system wide you can locally build zstd and build slow5tools against that: scripts/install-zstd.sh # download and compiles zstd in the current folder ./configure --enable-localzstd make # don't run make zstd=1. libzstd.a is statically linked this time. slow5tools from version 0.3.0 onwards by default requires vector instructions (SSSE3 or higher for Intel/AMD and neon for ARM). If your processor is an ancient processor with no such vector instructions, invoke make as make no_simd=1 . If you cannot install the hdf5 library system wide you can locally build HDF5 (takes ages) and build slow5tools against that: scripts/install-hdf5.sh # download and compiles HDF5 in the current folder ./configure --enable-localhdf5 make On Mac M1 or in any system if ./configure cannot find the hdf5 libraries installed through the package manager, you can specify the location as LDFLAGS=-L/path/to/shared/lib/ CPPFLAGS=-I/path/to/headers/ . For an example for Apple Silicon (e.g., Mac M1) see faq . You can build a docker image as follows. git clone https://github.com/hasindu2008/slow5tools && cd slow5tools docker build . docker run -v /path/to/local/data/data/:/data/ -it :image_id ./slow5tools To support large files on 32-bit systems use: CFLAGS="-D_FILE_OFFSET_BITS=64" make . Usage Visit the man page for all the commands and options. A guide on using BLOW5 for archiving and steps to verify if data integrity is preserved is here . A script for performing real-time FAST5 to BLOW5 conversion during sequencing is provided here . Examples # convert a directory of fast5 files into BLOW5 files (default compression: zlib+svb-zd) slow5tools f2s fast5_dir -d blow5_dir # convert a single fast5 file into a SLOW5 ASCII slow5tools f2s file.fast5 -o file.slow5 # convert a directory of fast5 files into BLOW5 files with zstd+svb-zd compression (similar to ONT's vbz compression) slow5tools f2s fast5_dir -d blow5_dir -c zstd -s svb-zd # concatenate all BLOW5 fils in a directory into a single BLOW5 file (works only if all the BLOW5 files have the same header, otherwise use merge) slow5tools cat blow5_dir -o file.blow5 # merge all BLOW5 files in a directory into a single BLOW5 file (default compression: zlib+svb-zd) slow5tools merge blow5_dir -o file.blow5 # merge all BLOW5 files in a directory into a single BLOW5 file with zstd+svb-zd compression (similar to ONT's vbz compression) slow5tools merge blow5_dir -o file.blow5 -c zstd -s svb-zd # to view a BLOW5 file in SLOW5 ASCII on standard out slow5tools view file.blow5 # Convert a BLOW5 file into SLOW5 ASCII slow5tools view file.blow5 -o file.slow5 # convert a SLOW5 file to BLOW5 (default compression) slow5tools view file.slow5 -o file.blow5 # index a slow5/blow5 file slow5tools index file.blow5 # extract records from a slow5/blow5 file corresponding to given read ids slow5tools get file.blow5 readid1 readid2 -o output.slow5 # extract records from a slow5/blow5 file based on a list of read ids slow5tools get file.blow5 -l readids_list.txt -o output.slow5 # split a BLOW5 file into separate BLOW5 files based on the read groups slow5tools split file.blow5 -d blow5_dir -g # split a BLOW5 file (single read group) into separate BLOW5 files such that there are 4000 reads in one file slow5tools split file.blow5 -d blow5_dir -r 4000 # split a BLOW5 file into separate BLOW5 files by barcode given the buttery-eel barcode summary file slow5tools split file.blow5 -d blow5_dir -x barcode_summary.txt # split a BLOW5 file into separate BLOW5 files based on a custom TSV file slow5tools split file.blow5 -d blow5_dir -x custom.tsv --demux-rid readid --demux-code category # convert a directory of blow5 files to fast5 slow5tools s2f blow5_dir -d fast5 # print summary statistics (e.g., number of read groups, compression method, number of records, etc) slow5tools stats file.blow5 # quickly check if a blow5 file is intact slow5tools quickcheck file.blow5 # print all per-read metadata (except the raw signal) slow5tools skim file.blow5 # print the list of read IDs slow5tools skim --rid file.blow5 # print the SLOW5 header slow5tools skim --hdr file.blow5 Visit here for example workflows. See here for example bash one-liners with slow5tools. Troubleshooting/Questions Visit the frequently asked questions or open an issue . Upcoming features and optimisations Following are some features and optimisations in our todo list which will be implemented based on the need. If anyone is interested please request here . Contributions are welcome. pipelining input, processing and output in merge, get, etc. (improved runtime upto 2X, please find the implementation here ) reading from stdin for view binary releases for ARM64 processors on Linux and for MacOS any other useful features Notes slow5lib from version 0.3.0 onwards has built in StreamVByte compression support to enable even smaller file sizes, which is applied to the raw signal by default when producing BLOW5 files. zlib compression is then applied by default to each record. If zstd is used instead of zlib on top of StreamVByte , it is similar to ONT's latest vbz compression. BLOW5 files compressed with zstd+StreamVByte are still significantly smaller than vbz compressed FAST5 files. Acknowledgement slow5tools uses klib . Some code snippets have been taken from Minimap2 and Samtools . Citation Please cite the following in your publications when using SLOW5 file format: Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al. Fast nanopore sequencing data analysis with SLOW5. Nat Biotechnol 40, 1026-1029 (2022). https://doi.org/10.1038/s41587-021-01147-4 @article{gamaarachchi2022fast, title={Fast nanopore sequencing data analysis with SLOW5}, author={Gamaarachchi, Hasindu and Samarakoon, Hiruna and Jenner, Sasha P and Ferguson, James M and Amos, Timothy G and Hammond, Jillian M and Saadat, Hassaan and Smith, Martin A and Parameswaran, Sri and Deveson, Ira W}, journal={Nature biotechnology}, pages={1--4}, year={2022}, publisher={Nature Publishing Group} } Please cite the following in your publications when using slow5tools: Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al. Flexible and efficient handling of nanopore sequencing signal data with slow5tools. Genome Biol 24, 69 (2023). https://doi.org/10.1186/s13059-023-02910-3 @article{samarakoon2023flexible, title={Flexible and efficient handling of nanopore sequencing signal data with slow5tools}, author={Samarakoon, Hiruna and Ferguson, James M and Jenner, Sasha P and Amos, Timothy G and Parameswaran, Sri and Gamaarachchi, Hasindu and Deveson, Ira W}, journal={Genome Biology}, volume={24}, number={1}, pages={69}, year={2023}, publisher={Springer} } About Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. hasindu2008.github.io/slow5tools Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 105 stars Watchers 6 watching Forks 7 forks Report repository Releases 16 slow5tools-v1.4.0 Latest Jan 28, 2026 + 15 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C 59.0% Shell 36.5% Python 1.7% Makefile 0.9% C++ 0.9% M4 0.5% Other 0.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/hasindu2008/slow5tools +GitHub - hasindu2008/slow5tools: Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} hasindu2008 / slow5tools Public Notifications You must be signed in to change notification settings Fork 7 Star 105 Code Issues 0 Pull requests 0 Discussions Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights hasindu2008/slow5tools master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,573 Commits 1,573 Commits .github/ workflows .github/ workflows build build docs docs scripts scripts slow5lib @ e4bf785 slow5lib @ e4bf785 src src test test .gitattributes .gitattributes .gitignore .gitignore .gitmodules .gitmodules .travis.yml .travis.yml CMakeLists.txt CMakeLists.txt Dockerfile Dockerfile LICENSE LICENSE Makefile Makefile README.md README.md config.mk.in config.mk.in configure.ac configure.ac installdeps.mk installdeps.mk View all files Repository files navigation README MIT license slow5tools Slow5tools is a simple toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. About SLOW5 format: SLOW5 is a new file format for storing signal data from Oxford Nanopore Technologies (ONT) devices. SLOW5 was developed to overcome inherent limitations in the standard FAST5 signal data format that prevent efficient, scalable analysis and cause many headaches for developers. SLOW5 can be encoded in human-readable ASCII format, or a more compact and efficient binary format (BLOW5) - this is analogous to the seminal SAM/BAM format for storing DNA sequence alignments. The BLOW5 binary format supports zlib (DEFLATE) compression, or other compression methods (see notes ), thereby minimising the data storage footprint while still permitting efficient parallel access. Detailed benchmarking experiments have shown that SLOW5 format is an order of magnitude faster and significantly smaller than FAST5. Full documentation: https://hasindu2008.github.io/slow5tools Publication (SLOW5 format): https://www.nature.com/articles/s41587-021-01147-4 Publication (slow5tools): https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02910-3 SLOW5 specification: https://hasindu2008.github.io/slow5specs slow5 ecosystem: https://hasindu2008.github.io/slow5 To convert to and from ONT's new POD5 format, you use blue_crab . If POD5 format and the associated POD5 C/C++ API reaches maturity/stability and adheres to C++11 standard, capabilities for POD5 <-> SLOW5 conversion will be added to slow5tools. slow5tools is strictly adhering to C++11 standard for wider compatibility. Quick start If you are a Linux user on x86_64 architecture and want to quickly try slow5tools out, download the compiled binaries from the latest release . For example: VERSION=v1.4.0 wget " https://github.com/hasindu2008/slow5tools/releases/download/ $VERSION /slow5tools- $VERSION -x86_64-linux-binaries.tar.gz " && tar xvf slow5tools- $VERSION -x86_64-linux-binaries.tar.gz && cd slow5tools- $VERSION / ./slow5tools Binaries should work on most Linux distributions as the only dependency is zlib which is available by default on most distributions. For compiled binaries to work, your processor must support SSSE3 instructions or higher (processors after 2007 have these) and your operating system must have GLIBC 2.17 or higher (Linux distributions from 2014 onwards typically have this). You can also use conda to install slow5tools as conda install slow5tools -c bioconda -c conda-forge . For converting latest vbz compressed FAST5, you will need to setup the ONT vbz plugin as explained in faq:Q3 . Table of Contents Quick start Building Building a release Building from GitHub Other building options Usage Examples Troubleshooting/Questions Upcoming features and optimisations Notes Acknowledgement Citation Building Building a release Users are recommended to build from the latest release tar ball. A compiler that supports C++11 is needed to build slow5tools. Quick example for Ubuntu : sudo apt-get install libhdf5-dev zlib1g-dev # install HDF5 and zlib development libraries VERSION=v1.4.0 wget " https://github.com/hasindu2008/slow5tools/releases/download/ $VERSION /slow5tools- $VERSION -release.tar.gz " && tar xvf slow5tools- $VERSION -release.tar.gz && cd slow5tools- $VERSION / ./configure make The commands to install hdf5 (and zlib) development libraries on some popular distributions : On Debian/Ubuntu : sudo apt-get install libhdf5-dev zlib1g-dev On Fedora/CentOS : sudo dnf/yum install hdf5-devel zlib-devel On Arch Linux: sudo pacman -S hdf5 On OS X : brew install hdf5 zlib Building from GitHub WARNING: Building from GitHub is meant for advanced users to test latest features. For production purposes, use the latest release version that is thoroughly tested. Building from the Github repository additionally requires autoreconf which can be installed on Ubuntu using sudo apt-get install autoconf automake ( brew install autoconf automake on macOS). To build from GitHub: sudo apt-get install libhdf5-dev zlib1g-dev autoconf automake #install HDF5 and zlib development libraries and autotools git clone --recursive https://github.com/hasindu2008/slow5tools cd slow5tools autoreconf # autoreconf --install for macos ./configure make Other building options If you only want to manipulate S/BLOW5 files, you can disable FAST5/HDF5 for even easier compilation. Call ./configure --disable-hdf5 && make or completely bypass the configure step and just call make disable_hdf5=1 . You can optionally enable zstd compression support when building slow5lib by invoking make zstd=1 . This requires zstd 1.3 or higher development libraries installed on your system ( libzstd1-dev package for apt , libzstd-devel for yum/dnf and zstd for homebrew ). SLOW5 files compressed with zstd offer smaller file size and better performance compared to the default zlib . However, zlib runtime library is available by default on almost all distributions unlike zstd and thus files compressed with zlib will be more 'portable' (also see notes ). For enabling zstd on Apple Silicon (e.g., Mac M1) also see faq . If you cannot install the zstd library system wide you can locally build zstd and build slow5tools against that: scripts/install-zstd.sh # download and compiles zstd in the current folder ./configure --enable-localzstd make # don't run make zstd=1. libzstd.a is statically linked this time. slow5tools from version 0.3.0 onwards by default requires vector instructions (SSSE3 or higher for Intel/AMD and neon for ARM). If your processor is an ancient processor with no such vector instructions, invoke make as make no_simd=1 . If you cannot install the hdf5 library system wide you can locally build HDF5 (takes ages) and build slow5tools against that: scripts/install-hdf5.sh # download and compiles HDF5 in the current folder ./configure --enable-localhdf5 make On Mac M1 or in any system if ./configure cannot find the hdf5 libraries installed through the package manager, you can specify the location as LDFLAGS=-L/path/to/shared/lib/ CPPFLAGS=-I/path/to/headers/ . For an example for Apple Silicon (e.g., Mac M1) see faq . You can build a docker image as follows. git clone https://github.com/hasindu2008/slow5tools && cd slow5tools docker build . docker run -v /path/to/local/data/data/:/data/ -it :image_id ./slow5tools To support large files on 32-bit systems use: CFLAGS="-D_FILE_OFFSET_BITS=64" make . Usage Visit the man page for all the commands and options. A guide on using BLOW5 for archiving and steps to verify if data integrity is preserved is here . A script for performing real-time FAST5 to BLOW5 conversion during sequencing is provided here . Examples # convert a directory of fast5 files into BLOW5 files (default compression: zlib+svb-zd) slow5tools f2s fast5_dir -d blow5_dir # convert a single fast5 file into a SLOW5 ASCII slow5tools f2s file.fast5 -o file.slow5 # convert a directory of fast5 files into BLOW5 files with zstd+svb-zd compression (similar to ONT's vbz compression) slow5tools f2s fast5_dir -d blow5_dir -c zstd -s svb-zd # concatenate all BLOW5 fils in a directory into a single BLOW5 file (works only if all the BLOW5 files have the same header, otherwise use merge) slow5tools cat blow5_dir -o file.blow5 # merge all BLOW5 files in a directory into a single BLOW5 file (default compression: zlib+svb-zd) slow5tools merge blow5_dir -o file.blow5 # merge all BLOW5 files in a directory into a single BLOW5 file with zstd+svb-zd compression (similar to ONT's vbz compression) slow5tools merge blow5_dir -o file.blow5 -c zstd -s svb-zd # to view a BLOW5 file in SLOW5 ASCII on standard out slow5tools view file.blow5 # Convert a BLOW5 file into SLOW5 ASCII slow5tools view file.blow5 -o file.slow5 # convert a SLOW5 file to BLOW5 (default compression) slow5tools view file.slow5 -o file.blow5 # index a slow5/blow5 file slow5tools index file.blow5 # extract records from a slow5/blow5 file corresponding to given read ids slow5tools get file.blow5 readid1 readid2 -o output.slow5 # extract records from a slow5/blow5 file based on a list of read ids slow5tools get file.blow5 -l readids_list.txt -o output.slow5 # split a BLOW5 file into separate BLOW5 files based on the read groups slow5tools split file.blow5 -d blow5_dir -g # split a BLOW5 file (single read group) into separate BLOW5 files such that there are 4000 reads in one file slow5tools split file.blow5 -d blow5_dir -r 4000 # split a BLOW5 file into separate BLOW5 files by barcode given the buttery-eel barcode summary file slow5tools split file.blow5 -d blow5_dir -x barcode_summary.txt # split a BLOW5 file into separate BLOW5 files based on a custom TSV file slow5tools split file.blow5 -d blow5_dir -x custom.tsv --demux-rid readid --demux-code category # convert a directory of blow5 files to fast5 slow5tools s2f blow5_dir -d fast5 # print summary statistics (e.g., number of read groups, compression method, number of records, etc) slow5tools stats file.blow5 # quickly check if a blow5 file is intact slow5tools quickcheck file.blow5 # print all per-read metadata (except the raw signal) slow5tools skim file.blow5 # print the list of read IDs slow5tools skim --rid file.blow5 # print the SLOW5 header slow5tools skim --hdr file.blow5 Visit here for example workflows. See here for example bash one-liners with slow5tools. Troubleshooting/Questions Visit the frequently asked questions or open an issue . Upcoming features and optimisations Following are some features and optimisations in our todo list which will be implemented based on the need. If anyone is interested please request here . Contributions are welcome. pipelining input, processing and output in merge, get, etc. (improved runtime upto 2X, please find the implementation here ) reading from stdin for view binary releases for ARM64 processors on Linux and for MacOS any other useful features Notes slow5lib from version 0.3.0 onwards has built in StreamVByte compression support to enable even smaller file sizes, which is applied to the raw signal by default when producing BLOW5 files. zlib compression is then applied by default to each record. If zstd is used instead of zlib on top of StreamVByte , it is similar to ONT's latest vbz compression. BLOW5 files compressed with zstd+StreamVByte are still significantly smaller than vbz compressed FAST5 files. Acknowledgement slow5tools uses klib . Some code snippets have been taken from Minimap2 and Samtools . Citation Please cite the following in your publications when using SLOW5 file format: Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al. Fast nanopore sequencing data analysis with SLOW5. Nat Biotechnol 40, 1026-1029 (2022). https://doi.org/10.1038/s41587-021-01147-4 @article{gamaarachchi2022fast, title={Fast nanopore sequencing data analysis with SLOW5}, author={Gamaarachchi, Hasindu and Samarakoon, Hiruna and Jenner, Sasha P and Ferguson, James M and Amos, Timothy G and Hammond, Jillian M and Saadat, Hassaan and Smith, Martin A and Parameswaran, Sri and Deveson, Ira W}, journal={Nature biotechnology}, pages={1--4}, year={2022}, publisher={Nature Publishing Group} } Please cite the following in your publications when using slow5tools: Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al. Flexible and efficient handling of nanopore sequencing signal data with slow5tools. Genome Biol 24, 69 (2023). https://doi.org/10.1186/s13059-023-02910-3 @article{samarakoon2023flexible, title={Flexible and efficient handling of nanopore sequencing signal data with slow5tools}, author={Samarakoon, Hiruna and Ferguson, James M and Jenner, Sasha P and Amos, Timothy G and Parameswaran, Sri and Gamaarachchi, Hasindu and Deveson, Ira W}, journal={Genome Biology}, volume={24}, number={1}, pages={69}, year={2023}, publisher={Springer} } About Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. hasindu2008.github.io/slow5tools Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Stars 105 stars Watchers 6 watching Forks 7 forks Report repository Releases 16 slow5tools-v1.4.0 Latest Jan 28, 2026 + 15 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C 59.0% Shell 36.5% Python 1.7% Makefile 0.9% C++ 0.9% M4 0.5% Other 0.5% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge slow5tools --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +slow5tools 0.2.0 h0326b38_3 +--------------------------- +file name : slow5tools-0.2.0-h0326b38_3.tar.bz2 +name : slow5tools +version : 0.2.0 +build : h0326b38_3 +build number: 3 +size : 876 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.2.0-h0326b38_3.tar.bz2 +md5 : 24fae66257d9d5f4bbfda8c15a4d1fc3 +timestamp : 2022-09-15 06:59:24 UTC +dependencies: + - hdf5 >=1.12.1,<1.12.2.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.12,<1.3.0a0 + - zlib >=1.2.12,<1.3.0a0 + + +slow5tools 0.2.0 h0326b38_4 +--------------------------- +file name : slow5tools-0.2.0-h0326b38_4.tar.bz2 +name : slow5tools +version : 0.2.0 +build : h0326b38_4 +build number: 4 +size : 876 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.2.0-h0326b38_4.tar.bz2 +md5 : 51ee3b445fd42f3af538feb47e325d87 +timestamp : 2023-05-13 11:10:51 UTC +dependencies: + - hdf5 >=1.12.1,<1.12.2.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +slow5tools 0.2.0 h3447091_2 +--------------------------- +file name : slow5tools-0.2.0-h3447091_2.tar.bz2 +name : slow5tools +version : 0.2.0 +build : h3447091_2 +build number: 2 +size : 874 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.2.0-h3447091_2.tar.bz2 +md5 : 6efc129976a39b2eb03fbd38f7dc33a4 +timestamp : 2022-02-24 16:27:27 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +slow5tools 0.2.0 h500492e_4 +--------------------------- +file name : slow5tools-0.2.0-h500492e_4.tar.bz2 +name : slow5tools +version : 0.2.0 +build : h500492e_4 +build number: 4 +size : 838 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.2.0-h500492e_4.tar.bz2 +md5 : 6e9a084321b79ea64a0cdb8859d42c84 +timestamp : 2023-05-14 23:13:27 UTC +dependencies: + - hdf5 >=1.12.2,<1.12.3.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +slow5tools 0.2.0 h500492e_5 +--------------------------- +file name : slow5tools-0.2.0-h500492e_5.tar.bz2 +name : slow5tools +version : 0.2.0 +build : h500492e_5 +build number: 5 +size : 838 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.2.0-h500492e_5.tar.bz2 +md5 : b2a2731721c380088b60b65d07471fd9 +timestamp : 2023-05-16 07:24:28 UTC +dependencies: + - hdf5 >=1.12.2,<1.12.3.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib + + +slow5tools 0.2.0 h56e2c18_6 +--------------------------- +file name : slow5tools-0.2.0-h56e2c18_6.tar.bz2 +name : slow5tools +version : 0.2.0 +build : h56e2c18_6 +build number: 6 +size : 853 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.2.0-h56e2c18_6.tar.bz2 +md5 : b89fcbc0dbaff699eef94002707844a7 +timestamp : 2024-06-04 14:58:04 UTC +dependencies: + - hdf5 >=1.14.3,<1.14.4.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<2.0a0 + - zlib + + +slow5tools 0.2.0 he001e6d_0 +--------------------------- +file name : slow5tools-0.2.0-he001e6d_0.tar.bz2 +name : slow5tools +version : 0.2.0 +build : he001e6d_0 +build number: 0 +size : 910 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.2.0-he001e6d_0.tar.bz2 +md5 : 41baca855b12b1046159bf8cc8542b90 +timestamp : 2021-08-24 03:53:28 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - zlib >=1.2.11,<1.3.0a0 + + +slow5tools 0.2.0 he001e6d_1 +--------------------------- +file name : slow5tools-0.2.0-he001e6d_1.tar.bz2 +name : slow5tools +version : 0.2.0 +build : he001e6d_1 +build number: 1 +size : 910 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.2.0-he001e6d_1.tar.bz2 +md5 : 8b3e1192776c7ff82be9190d36d55b10 +timestamp : 2021-09-23 11:44:26 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - zlib >=1.2.11,<1.3.0a0 + + +slow5tools 0.2.0 hee927d3_7 +--------------------------- +file name : slow5tools-0.2.0-hee927d3_7.tar.bz2 +name : slow5tools +version : 0.2.0 +build : hee927d3_7 +build number: 7 +size : 852 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.2.0-hee927d3_7.tar.bz2 +md5 : c5bbfee76b9135ff6f91c1607ba5fc89 +timestamp : 2024-12-14 02:36:58 UTC +dependencies: + - hdf5 >=1.14.3,<1.14.4.0a0 + - libgcc >=13 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + - zlib + + +slow5tools 0.3.0 h3447091_1 +--------------------------- +file name : slow5tools-0.3.0-h3447091_1.tar.bz2 +name : slow5tools +version : 0.3.0 +build : h3447091_1 +build number: 1 +size : 1.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.3.0-h3447091_1.tar.bz2 +md5 : e4dadd520b4bbcbb5500d9b230965eff +timestamp : 2022-02-24 03:25:44 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +slow5tools 0.3.0 he001e6d_0 +--------------------------- +file name : slow5tools-0.3.0-he001e6d_0.tar.bz2 +name : slow5tools +version : 0.3.0 +build : he001e6d_0 +build number: 0 +size : 1.0 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.3.0-he001e6d_0.tar.bz2 +md5 : d56c7093a5b72788b54bba11ef3bfb75 +timestamp : 2021-09-23 11:33:17 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - zlib >=1.2.11,<1.3.0a0 + + +slow5tools 0.4.0 h3447091_0 +--------------------------- +file name : slow5tools-0.4.0-h3447091_0.tar.bz2 +name : slow5tools +version : 0.4.0 +build : h3447091_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.4.0-h3447091_0.tar.bz2 +md5 : 8f76bc19228e3dc33668bd6f739bfd7e +timestamp : 2022-03-29 12:21:26 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +slow5tools 0.5.0 h3447091_0 +--------------------------- +file name : slow5tools-0.5.0-h3447091_0.tar.bz2 +name : slow5tools +version : 0.5.0 +build : h3447091_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.5.0-h3447091_0.tar.bz2 +md5 : 910ef98c9c5d7899839993767e6f685a +timestamp : 2022-05-26 09:28:58 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.11,<1.3.0a0 + - zlib >=1.2.11,<1.3.0a0 + + +slow5tools 0.5.1 h3447091_0 +--------------------------- +file name : slow5tools-0.5.1-h3447091_0.tar.bz2 +name : slow5tools +version : 0.5.1 +build : h3447091_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.5.1-h3447091_0.tar.bz2 +md5 : 8cc25106086b89ce83b8a84c51fedf2d +timestamp : 2022-06-28 04:26:41 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.12,<1.3.0a0 + - zlib >=1.2.12,<1.3.0a0 + + +slow5tools 0.5.1 h3447091_1 +--------------------------- +file name : slow5tools-0.5.1-h3447091_1.tar.bz2 +name : slow5tools +version : 0.5.1 +build : h3447091_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.5.1-h3447091_1.tar.bz2 +md5 : f44cac4ac1058e896c0efb90c0ab0b66 +timestamp : 2022-08-01 16:18:57 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.12,<1.3.0a0 + - zlib >=1.2.12,<1.3.0a0 + + +slow5tools 0.6.0 h0326b38_2 +--------------------------- +file name : slow5tools-0.6.0-h0326b38_2.tar.bz2 +name : slow5tools +version : 0.6.0 +build : h0326b38_2 +build number: 2 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.6.0-h0326b38_2.tar.bz2 +md5 : 885a90f6a2601f00b8464cd66a7dc306 +timestamp : 2022-09-15 07:06:05 UTC +dependencies: + - hdf5 >=1.12.1,<1.12.2.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.12,<1.3.0a0 + - zlib >=1.2.12,<1.3.0a0 + + +slow5tools 0.6.0 h3447091_0 +--------------------------- +file name : slow5tools-0.6.0-h3447091_0.tar.bz2 +name : slow5tools +version : 0.6.0 +build : h3447091_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.6.0-h3447091_0.tar.bz2 +md5 : 60da34aa7d02bfe76374445a89b63a25 +timestamp : 2022-08-13 05:54:50 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.12,<1.3.0a0 + - zlib >=1.2.12,<1.3.0a0 + + +slow5tools 0.6.0 h3447091_1 +--------------------------- +file name : slow5tools-0.6.0-h3447091_1.tar.bz2 +name : slow5tools +version : 0.6.0 +build : h3447091_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.6.0-h3447091_1.tar.bz2 +md5 : 93ea5408c9cba76deb998952a4b2e001 +timestamp : 2022-08-15 19:58:24 UTC +dependencies: + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.12,<1.3.0a0 + - zlib >=1.2.12,<1.3.0a0 + + +slow5tools 0.7.0 h0326b38_0 +--------------------------- +file name : slow5tools-0.7.0-h0326b38_0.tar.bz2 +name : slow5tools +version : 0.7.0 +build : h0326b38_0 +build number: 0 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.7.0-h0326b38_0.tar.bz2 +md5 : b41a34bd4725acee180e632decae29b1 +timestamp : 2023-03-30 11:57:49 UTC +dependencies: + - hdf5 >=1.12.1,<1.12.2.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +slow5tools 0.7.0 h0326b38_1 +--------------------------- +file name : slow5tools-0.7.0-h0326b38_1.tar.bz2 +name : slow5tools +version : 0.7.0 +build : h0326b38_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/slow5tools-0.7.0-h0326b38_1.tar.bz2 +md5 : 220c5d2bfceae08efeae40d0f8599b27 +timestamp : 2023-05-13 11:25:34 UTC +dependencies: + - hdf5 >=1.12.1,<1.12.2.0a0 + - libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + - zlib >=1.2.13,<1.3.0a0 + + +slow5tools 0.7.0 h500492e_1 +--------------------------- +file name : slow5tools-0.7.0-h500492e_1.tar.bz2 +name : slow5tools +version : 0.7.0 +build : h500492e_1 +build number: 1 +size : 1.2 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/ diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snakemake-interface-common.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snakemake-interface-common.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..33954ad3514abc6e0684f568c35a1ce972fdc7b1 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snakemake-interface-common.manual_bundle.txt @@ -0,0 +1,383 @@ +# Tool: snakemake-interface-common +software_name: snakemake-interface-common +tier: T1 +domain: t1_backfill_overall +downloads: 356370 +summary: Common functions and classes for Snakemake and its plugins. +description: Common functions and classes for Snakemake and its plugins. +dependencies: argparse-dataclass >=2.0.0, configargparse >=1.7, packaging >=24.0,<26.0, python >=3.8 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/snakemake/snakemake-interface-common +doc_url: +dev_url: https://github.com/snakemake/snakemake-interface-common + +## URL Docs Extract +### https://github.com/snakemake/snakemake-interface-common +GitHub - snakemake/snakemake-interface-common: Common functions and classes for Snakemake and its plugins · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} snakemake / snakemake-interface-common Public Notifications You must be signed in to change notification settings Fork 7 Star 0 Code Issues 6 Pull requests 5 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights snakemake/snakemake-interface-common main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 179 Commits 179 Commits .github/ workflows .github/ workflows src/ snakemake_interface_common src/ snakemake_interface_common tests tests .gitattributes .gitattributes .gitignore .gitignore CHANGELOG.md CHANGELOG.md LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml setup.cfg setup.cfg View all files Repository files navigation README MIT license snakemake-interface-common Common functions and classes for Snakemake and its plugins. About Common functions and classes for Snakemake and its plugins Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 0 stars Watchers 0 watching Forks 7 forks Report repository Releases 54 v1.23.0 Latest Mar 8, 2026 + 53 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/snakemake/snakemake-interface-common +GitHub - snakemake/snakemake-interface-common: Common functions and classes for Snakemake and its plugins · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} snakemake / snakemake-interface-common Public Notifications You must be signed in to change notification settings Fork 7 Star 0 Code Issues 6 Pull requests 5 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights snakemake/snakemake-interface-common main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 179 Commits 179 Commits .github/ workflows .github/ workflows src/ snakemake_interface_common src/ snakemake_interface_common tests tests .gitattributes .gitattributes .gitignore .gitignore CHANGELOG.md CHANGELOG.md LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml setup.cfg setup.cfg View all files Repository files navigation README MIT license snakemake-interface-common Common functions and classes for Snakemake and its plugins. About Common functions and classes for Snakemake and its plugins Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 0 stars Watchers 0 watching Forks 7 forks Report repository Releases 54 v1.23.0 Latest Mar 8, 2026 + 53 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge snakemake-interface-common --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +snakemake-interface-common 1.3.2 pyhdfd78af_0 +--------------------------------------------- +file name : snakemake-interface-common-1.3.2-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.3.2 +build : pyhdfd78af_0 +build number: 0 +size : 11 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.3.2-pyhdfd78af_0.tar.bz2 +md5 : 5c82892cd931a92cff2124580f4d5add +timestamp : 2023-08-31 04:16:30 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.3.3 pyhdfd78af_0 +--------------------------------------------- +file name : snakemake-interface-common-1.3.3-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.3.3 +build : pyhdfd78af_0 +build number: 0 +size : 11 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.3.3-pyhdfd78af_0.tar.bz2 +md5 : 605beaf5c0530076db3b54ff14eea5cd +timestamp : 2023-09-11 07:29:13 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.4.1 pyhdfd78af_0 +--------------------------------------------- +file name : snakemake-interface-common-1.4.1-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.4.1 +build : pyhdfd78af_0 +build number: 0 +size : 15 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.4.1-pyhdfd78af_0.tar.bz2 +md5 : f09ae4264e387e8e8feb7a2be9eb9f6a +timestamp : 2023-09-19 14:21:32 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.7.1 pyhdfd78af_0 +--------------------------------------------- +file name : snakemake-interface-common-1.7.1-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.7.1 +build : pyhdfd78af_0 +build number: 0 +size : 16 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.7.1-pyhdfd78af_0.tar.bz2 +md5 : 2d9b707f1862b61cd44e20993c68aca4 +timestamp : 2023-09-21 18:32:16 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.7.3 pyhdfd78af_0 +--------------------------------------------- +file name : snakemake-interface-common-1.7.3-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.7.3 +build : pyhdfd78af_0 +build number: 0 +size : 16 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.7.3-pyhdfd78af_0.tar.bz2 +md5 : 8c3d1b797f808a317c6360d0d8141c79 +timestamp : 2023-09-22 08:26:08 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.8.0 pyhdfd78af_0 +--------------------------------------------- +file name : snakemake-interface-common-1.8.0-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.8.0 +build : pyhdfd78af_0 +build number: 0 +size : 16 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.8.0-pyhdfd78af_0.tar.bz2 +md5 : 88608d342aad7c300b2b5ddc322411fe +timestamp : 2023-09-23 12:30:31 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.10.0 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.10.0-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.10.0 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.10.0-pyhdfd78af_0.tar.bz2 +md5 : 752b8587125160d36cc7b9a531e25362 +timestamp : 2023-09-27 12:24:21 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.12.0 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.12.0-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.12.0 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.12.0-pyhdfd78af_0.tar.bz2 +md5 : fd1b96ea5509c65392bd2dea71b2e5a3 +timestamp : 2023-10-11 15:31:29 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.13.0 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.13.0-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.13.0 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.13.0-pyhdfd78af_0.tar.bz2 +md5 : 569716c0cc196390d497d0f55da45a09 +timestamp : 2023-10-14 07:34:10 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.14.0 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.14.0-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.14.0 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.14.0-pyhdfd78af_0.tar.bz2 +md5 : 1800526a192c6f51afa6696da08de230 +timestamp : 2023-10-17 06:27:10 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.14.1 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.14.1-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.14.1 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.14.1-pyhdfd78af_0.tar.bz2 +md5 : 75fc3c16317d4cbafab6b3f7bb41b6ae +timestamp : 2023-10-26 08:31:13 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.14.2 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.14.2-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.14.2 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.14.2-pyhdfd78af_0.tar.bz2 +md5 : b99319434883045cbff687a137bd25e6 +timestamp : 2023-11-02 13:29:49 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.14.3 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.14.3-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.14.3 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.14.3-pyhdfd78af_0.tar.bz2 +md5 : ebde6dba507b042ae51e9dc41492861c +timestamp : 2023-11-17 12:28:58 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.14.4 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.14.4-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.14.4 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.14.4-pyhdfd78af_0.tar.bz2 +md5 : cb97c1d8dcb65f1b60c136f32a864f98 +timestamp : 2023-11-27 10:34:51 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.14.5 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.14.5-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.14.5 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.14.5-pyhdfd78af_0.tar.bz2 +md5 : 56b5897d97467640b59f9e7d8e503249 +timestamp : 2023-12-06 10:35:39 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.15.0 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.15.0-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.15.0 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.15.0-pyhdfd78af_0.tar.bz2 +md5 : 4a86becbea8ac29004908c1ca870a499 +timestamp : 2023-12-08 16:32:44 UTC +dependencies: + - python >=3.7.0,<4.0.0 + + +snakemake-interface-common 1.15.0 pyhdfd78af_1 +---------------------------------------------- +file name : snakemake-interface-common-1.15.0-pyhdfd78af_1.tar.bz2 +name : snakemake-interface-common +version : 1.15.0 +build : pyhdfd78af_1 +build number: 1 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.15.0-pyhdfd78af_1.tar.bz2 +md5 : 0b649894cc54bbe8d39f9bbd9f534dca +timestamp : 2023-12-18 21:57:04 UTC +dependencies: + - argparse-dataclass >=2.0.0,<3.0.0 + - configargparse >=1.7,<2.0 + - python >=3.8.0,<4.0.0 + + +snakemake-interface-common 1.15.1 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.15.1-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.15.1 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.15.1-pyhdfd78af_0.tar.bz2 +md5 : 7a47ae5413bacd72ac0c66f60abebc97 +timestamp : 2024-01-16 12:26:59 UTC +dependencies: + - argparse-dataclass >=2.0.0,<3.0.0 + - configargparse >=1.7,<2.0 + - python >=3.8.0,<4.0.0 + + +snakemake-interface-common 1.15.2 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.15.2-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.15.2 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.15.2-pyhdfd78af_0.tar.bz2 +md5 : 8a1aa65c805b95abf741393a591b075f +timestamp : 2024-01-23 10:33:10 UTC +dependencies: + - argparse-dataclass >=2.0.0,<3.0.0 + - configargparse >=1.7,<2.0 + - python >=3.8.0,<4.0.0 + + +snakemake-interface-common 1.15.3 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.15.3-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-common +version : 1.15.3 +build : pyhdfd78af_0 +build number: 0 +size : 17 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.15.3-pyhdfd78af_0.tar.bz2 +md5 : 6a69ed3f5324594b518b3b69b314423f +timestamp : 2024-02-02 18:29:48 UTC +dependencies: + - argparse-dataclass >=2.0.0,<3.0.0 + - configargparse >=1.7,<2.0 + - python >=3.8.0,<4.0.0 + + +snakemake-interface-common 1.16.0 pyhdfd78af_0 +---------------------------------------------- +file name : snakemake-interface-common-1.16.0-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-com diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snakemake-interface-report-plugins.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snakemake-interface-report-plugins.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..6de28588367f49aec8c2a0cc74012f19131c540f --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snakemake-interface-report-plugins.manual_bundle.txt @@ -0,0 +1,134 @@ +# Tool: snakemake-interface-report-plugins +software_name: snakemake-interface-report-plugins +tier: T1 +domain: t1_backfill_overall +downloads: 307149 +summary: This package provides a stable interface for interactions between Snakemake and its report plugins. +description: This package provides a stable interface for interactions between Snakemake and its report plugins. +dependencies: python >=3.11.0,<4.0.0, snakemake-interface-common >=1.16.0,<2.0.0 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/snakemake/snakemake-interface-report-plugins +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/snakemake/snakemake-interface-report-plugins +GitHub - snakemake/snakemake-interface-report-plugins: The interface for Snakemake report plugins. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} snakemake / snakemake-interface-report-plugins Public Notifications You must be signed in to change notification settings Fork 2 Star 4 Code Issues 2 Pull requests 1 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights snakemake/snakemake-interface-report-plugins main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 28 Commits 28 Commits .github/ workflows .github/ workflows snakemake_interface_report_plugins snakemake_interface_report_plugins tests tests .gitignore .gitignore CHANGELOG.md CHANGELOG.md LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml setup.cfg setup.cfg View all files Repository files navigation README MIT license Snakemake interface for report plugins This package defines the interface between Snakemake and its report plugins. Plugins should implement the following skeleton to comply with this interface. It is recommended to use Snakedeploy to set up the skeleton (and automated testing) within a python package. from dataclasses import dataclass , field from snakemake_interface_common . exceptions import WorkflowError from snakemake_interface_report_plugins . reporter import ReporterBase from snakemake_interface_report_plugins . settings import ReportSettingsBase # Optional: # Define additional settings for your reporter. # They will occur in the Snakemake CLI as --report-<reporter-name>-<param-name> # Omit this class if you don't need any. # Make sure that all defined fields are Optional (or bool) and specify a default value # of None (or False) or anything else that makes sense in your case. @ dataclass class ReportSettings ( ReportSettingsBase ): myparam : Optional [ int ] = field ( default = None , metadata = { "help" : "Some help text" , # Optionally request that setting is also available for specification # via an environment variable. The variable will be named automatically as # SNAKEMAKE_REPORT_<reporter-name>_<param-name>, all upper case. # This mechanism should ONLY be used for passwords and usernames. # For other items, we rather recommend to let people use a profile # for setting defaults # (https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles). "env_var" : False , # Optionally specify a function that parses the value given by the user. # This is useful to create complex types from the user input. "parse_func" : ..., # If a parse_func is specified, you also have to specify an unparse_func # that converts the parsed value back to a string. "unparse_func" : ..., # Optionally specify that setting is required when the reporter is in use. "required" : True , # Optionally specify multiple args with "nargs": True }, ) # Required: # Implementation of your reporter class Reporter ( ReporterBase ): def __post_init__ ( self ): # initialize additional attributes # Do not overwrite the __init__ method as this is kept in control of the base # class in order to simplify the update process. # See https://github.com/snakemake/snakemake-interface-report-plugins/snakemake_interface_report_plugins/reporter.py # for attributes of the base class. # In particular, the settings of above ReportSettings class are accessible via # self.settings. def render ( self ): # Render the report, using attributes of the base class. ... About The interface for Snakemake report plugins. Resources Readme License MIT license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 4 stars Watchers 0 watching Forks 2 forks Report repository Releases 8 v2.0.1 Latest Mar 9, 2026 + 7 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 100.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge snakemake-interface-report-plugins --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +snakemake-interface-report-plugins 1.0.0 pyhdfd78af_0 +----------------------------------------------------- +file name : snakemake-interface-report-plugins-1.0.0-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-report-plugins +version : 1.0.0 +build : pyhdfd78af_0 +build number: 0 +size : 13 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.0.0-pyhdfd78af_0.tar.bz2 +md5 : 48807a1a5a669975f09920777152d6ca +timestamp : 2024-02-19 10:02:01 UTC +dependencies: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.16.0,<2.0.0 + + +snakemake-interface-report-plugins 1.1.0 pyhdfd78af_0 +----------------------------------------------------- +file name : snakemake-interface-report-plugins-1.1.0-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-report-plugins +version : 1.1.0 +build : pyhdfd78af_0 +build number: 0 +size : 13 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.1.0-pyhdfd78af_0.tar.bz2 +md5 : 3a7dd19cd530b27b59aed6cb606a7987 +timestamp : 2024-10-04 15:26:29 UTC +dependencies: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.16.0,<2.0.0 + + +snakemake-interface-report-plugins 1.1.1 pyhdfd78af_0 +----------------------------------------------------- +file name : snakemake-interface-report-plugins-1.1.1-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-report-plugins +version : 1.1.1 +build : pyhdfd78af_0 +build number: 0 +size : 13 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.1.1-pyhdfd78af_0.tar.bz2 +md5 : 136bcee2bee666a611ad5813a742cdba +timestamp : 2025-07-11 09:24:54 UTC +dependencies: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.16.0,<2.0.0 + + +snakemake-interface-report-plugins 1.2.0 pyhdfd78af_0 +----------------------------------------------------- +file name : snakemake-interface-report-plugins-1.2.0-pyhdfd78af_0.tar.bz2 +name : snakemake-interface-report-plugins +version : 1.2.0 +build : pyhdfd78af_0 +build number: 0 +size : 13 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.2.0-pyhdfd78af_0.tar.bz2 +md5 : b8867f869630ee014a615db08093b1ab +timestamp : 2025-07-29 16:27:55 UTC +dependencies: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.16.0,<2.0.0 + + +snakemake-interface-report-plugins 1.3.0 pyhd4c3c12_0 +----------------------------------------------------- +file name : snakemake-interface-report-plugins-1.3.0-pyhd4c3c12_0.conda +name : snakemake-interface-report-plugins +version : 1.3.0 +build : pyhd4c3c12_0 +build number: 0 +size : 14 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.3.0-pyhd4c3c12_0.conda +md5 : e6fd8cfb23b294da699e395dbc968d11 +timestamp : 2025-10-31 11:35:44 UTC +dependencies: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.16.0,<2.0.0 + + +snakemake-interface-report-plugins 2.0.1 pyh84498cf_0 +----------------------------------------------------- +file name : snakemake-interface-report-plugins-2.0.1-pyh84498cf_0.conda +name : snakemake-interface-report-plugins +version : 2.0.1 +build : pyh84498cf_0 +build number: 0 +size : 15 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-2.0.1-pyh84498cf_0.conda +md5 : 48c9665b5f82e3d4f85f0e357371f44f +timestamp : 2026-03-09 06:12:53 UTC +dependencies: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.16.0,<2.0.0 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snakemake.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snakemake.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..468aba7f365bcc46b8baaec9d4f5683bfb3dd3a8 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snakemake.manual_bundle.txt @@ -0,0 +1,537 @@ +# Tool: snakemake +software_name: snakemake +tier: T1 +domain: t1_backfill_overall +downloads: 1698791 +summary: A popular workflow management system aiming at full in-silico reproducibility. +description: Snakemake is a workflow management system that aims to reduce the complexity of creating +workflows by providing a fast and comfortable execution environment, together with a clean +and modern specification language in python style. Snakemake workflows are essentially Python +scripts extended by declarative code to define rules. Rules describe how to create output +files from input files. +dependencies: eido, pandas <3, peppy, pygments, slack_sdk, snakemake-minimal 9.19.0.* +execution_environment: Other +execution_environment_reason: fallback runtime classification + +## URLs +home_url: https://snakemake.github.io +doc_url: https://snakemake.readthedocs.io/en/stable +dev_url: https://github.com/snakemake/snakemake + +## URL Docs Extract +### https://snakemake.readthedocs.io/en/stable +Snakemake | Snakemake 9.19.0 documentation Skip to content Snakemake 9.19.0 documentation Homepage Plugin catalog Workflow catalog Wrappers API docs Toggle navigation menu ⌘ K Snakemake 9.19.0 documentation Homepage Plugin catalog Workflow catalog Wrappers API docs Getting started Installation Migration between Snakemake versions Best practices Tutorial: General use Setup Basics: An example workflow Advanced: Decorating the example workflow Additional Features Tutorial: Interaction, Visualization, and Reporting Executing workflows Command line interface Job Grouping Between workflow caching Using executor plugins Interoperability Monitoring Provenance Defining workflows Writing Workflows Snakefiles and Rules Configuration Modularization Storage support Utils Distribution and Reproducibility Reports Automatically generating unit tests Integrating foreign workflow management systems Project Info Citing and Citations More Resources Frequently Asked Questions Contributing Codebase and architecture Credits Changelog License Snakemake The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment. Finally, workflow runs can be automatically turned into interactive portable browser based reports, which can be shared with collaborators via email or the cloud and combine results with all used parameters, code, and software. Snakemake is highly popular , with >11 new citations per week ( old and new paper). It has been mentioned in two Nature technology features ( here and here ) and has more than 1 million downloads on anaconda.org . For an introduction, please visit https://snakemake.github.io . Getting started To get a first impression, please visit https://snakemake.github.io . To properly understand what Snakemake can do for you please read our “rolling” paper . News about Snakemake are published via Bluesky and Mastodon . To learn Snakemake, please do the Tutorial: General use , and see the FAQ . Best practices for writing Snakemake workflows can be found here . Support For releases, see Changelog . Check frequently asked questions (FAQ) . In case of questions , please post on stack overflow . To discuss with other Snakemake users, use the discord server . Please do not post questions there. Use stack overflow for questions. For bugs and feature requests , please use the issue tracker . For contributions , visit Snakemake on Github and read the guidelines . Check out our code of conduct and refer to it for requests or concerns in that direction. Citation When using Snakemake, please cite our “rolling” paper Mölder, F., Jablonski, K.P., Letcher, B., Hall, M.B., Tomkins-Tinch, C.H., Sochat, V., Forster, J., Lee, S., Twardziok, S.O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S., Köster, J., 2021. Sustainable data analysis with Snakemake. F1000Res 10, 33. This paper will also be regularly updated when Snakemake receives new features. See Citations for more information. Maintainers The Snakemake maintainers are: Johannes Köster (lead developer) David Lähnemann Christian Meesters Michael B. Hall Filipe G. Vieira Morten E. Lund Michael Jahn Cade Mirchandani Resources Snakedeploy Snakedeploy is a toolbox for maintenance and deployment/setup tasks around Snakemake and Snakemake workflows. Snakemake Wrappers Repository The Snakemake Wrapper Repository is a collection of reusable wrappers that allow to quickly use popular tools from Snakemake rules and workflows. Snakemake Workflow Catalog An automatically scraped catalog of publicly available Snakemake workflows for any kind of data analysis. Snakemake Workflows Project This project provides a collection of high quality modularized and reusable workflows. The provided code should also serve as a best-practices of how to build production ready workflows with Snakemake. Everybody is invited to contribute. Snakemake Cluster Profiles Project This project provides Snakemake configuration profiles for various execution environments. Please consider contributing your own if it is still missing. Snakemake API documentation The documentation of the Snakemake API for programmatic access and development on Snakemake. Conda-Forge Conda-Forge is a community driven distribution of Conda packages that can be used from Snakemake for creating completely reproducible workflows by defining the used software versions and providing binaries. Bioconda Bioconda, a partner project of conda-forge, is a community driven distribution of bioinformatics-related Conda packages that can be used from Snakemake for creating completely reproducible workflows by defining the used software versions and providing binaries. Installation On this page Getting started Support Citation Maintainers Resources © 2014-2026, Johannes Koester Built with Sphinx 9.1.0 + +### https://snakemake.github.io +Snakemake image/svg+xml Snakemake Docs Github Mastodon Bluesky image/svg+xml A framework for reproducible data analysis >14 new citations per week ( old + new paper ) >1,200,000 downloads Open source , MIT licensed affiliated project Join the Snakemake hackathon 2026 at TU Munich , Germany! Read the paper Read the docs Tutorial Workflow catalog Readability and automation With Snakemake, data analysis workflows are defined via an easy to read, adaptable, yet powerful specification language on top of Python. Steps are defined by "rules", which denote how to generate a set of output files from a set of input files (e.g. using a shell command). Wildcards (in curly braces) provide generalization. Dependencies between rules are determined automatically. rule select_by_country: input : "data/worldcitiespop.csv" output : "by-country/{country}.csv" shell : "xsv search -s Country '{wildcards.country}' " "{input} > {output}" Portability By integration with the Conda package manager and containers , all software dependencies of each workflow step are automatically deployed upon execution. rule select_by_country: input : "data/worldcitiespop.csv" output : "by-country/{country}.csv" conda : "envs/xsv.yaml" shell : "xsv search -s Country '{wildcards.country}' " "{input} > {output}" Scripting integration Rapidly implement analysis steps via direct script and jupyter notebook integration supporting Python, R, Julia, Rust, Bash, without requiring any boilerplate code. rule select_by_country: input : "data/worldcitiespop.csv" output : "by-country/{country}.csv" script : "scripts/select_by_country.R" Modularization Easily create and employ re-usable tool or library wrappers , split your data analysis into well-separated modules , and compose multi-modal analyses by easily combining entire workflows various sources. rule convert_to_pdf: input : "{prefix}.svg" output : "{prefix}.pdf" wrapper : "0.47.0/utils/cairosvg" "Turing completeness" Being a syntactical extension of Python , you can implement arbitrary logic beyond the plain definition of rules. Rules can be generated conditionally, arbitrary Python logic can be used to perform aggregations, configuration and metadata can be obtained and postprocessed in any required way. def get_data (wildcards): # use arbitrary Python logic to # aggregate over the required input files return ... rule plot_histogram: input : get_data output : "plots/hist.svg" script : "scripts/plot-hist.py" Human Readability The logic of production workflows can become complex by involving lots of lookups and dynamic decisions. Snakemake offers semantic helper functions for lookups, branching and aggregation that avoid the need for plain Python code as shown above, and allow to express complex logic in a human-readable and self-contained way. rule plot_histogram: input : branch ( lookup (dpath="histogram/somedata", within=config), then ="data/somedata.txt", otherwise ="data/someotherdata.txt" ) output : "plots/hist.svg" script : "scripts/plot-hist.py" Dynamic workflows Snakemake allows to define workflows that are dynamically updated at runtime. By defining so-called checkpoints , the workflow can be dynamically adapted at runtime. Further, input can be provided as Python queues , thereby enabling a workflow to continuously receive new input data (e.g. while a certain measurement is conducted). rule all: input : from_queue (all_results, finish_sentinel=...) checkpoint somestep: input : "samples/{sample}.txt" output : "somestep/{sample}.txt" shell : "somecommand {input} > {output}" Transparency and data provenance Automatic, interactive, self-contained reports ensure full transparency from results down to used steps, parameters, code, and software. The reports can moreover contain embedded results (from images, to PDFs and even interactive HTML ) enabling a comprehensive reporting that combines analysis results with data provenance information. Scalability Workflows scale seamlessly from single to multicore, clusters or the cloud, without modification of the workflow definition and automatic avoidance of redundant computations. Configurability Snakemake is extremely flexible and configurable. Numerous options allow adapt the behavior to the needs of the data analysis at hand and the underlying infrastructure. Options can be provided via the command line interface or persisted via system-wide, user-specific, and workflow specific profiles . executor : slurm software-deployment-method : - conda latency-wait : 60 default-storage-provider : fs shared-fs-usage : - persistence - software-deployment - sources - source-cache local-storage-prefix : /local/work/$USER/snakemake-scratch Extensibility Snakemake has a powerful plugin system that allows to extend various functionalities with alternative implementations. Via stable and well-defined interfaces, plugins can evolve independently of Snakemake, and mutual update requirements are minimized. Currently, execution backends and remote storage support is implemented via plugins. In the future, we will extend this to other areas, such as workflow scheduling, reporting, software deployment, and more. Authors and Contributors  ⓘ Johannes Köster Per Unneberg Chris Tomkins-Tinch Rasmus Ågren Tim Booth Vanessasaurus snakemake-bot Filipe G. Vieira Henning Timm David Laehnemann Chris Burr Manuel Holtgrewe Marcel Martin Michael Hall Cade Mirchandani Ryan C. Thompson Wibowo Arindrarto Elmar Pruesse Morten Enemark Lund Felix Mölder Aoran Hu Ryan Dale Ben Beasley Fredrik Boulund Peter Van Dyken Simon Ye Derek Croote Oliver Stolpe Jake VanCampen Justin Fear Kemal Eren Mattias de Hollander Maarten-vd-Sande Dr. K. D. Murray Michael K. Wilkinson Maarten Kooyman Kim Christian Arnold Jermiah Joseph Jay Hesselberth Hyeshik Chang Cornelius Roemer Troy Comi John Eppley Mattias Frånberg Felix Wiegand Christian Meesters mhulsman Nils Homer Patrik Smeds Kyle Beauchamp Liang-Bo Wang Joseph K Aicher Mike Taves Lars Bilke Kevin Sayers C. Titus Brown Anfeng Li Sven Twardziok Sultan Orazbayev Matt Shirley G. D. McBain endrebak Adam Labadorf Anthony Underwood Elias Kuthe Haizi Zheng Jan Forster John Blischak Don Freed Dmitry Kalinkin Marco-Masera Peter Cock Vito Zanotelli Shinji Matsumoto Rohan-Ibn-Tariq Benjamin Yeh Ryan A. Hagenson Sichong Silas Kieser Vlad Savelyev Soo Lee Sven Schrinner wligtenberg Hatem Florian R. Hölzlwimmer Thomas Vandal Tomás Di Domenico rebecca-palmer darrin t schultz Bruno P. Kinoshita Ashwin V. Mohanan Andreas Wilm crimsonDaMi Arya Massarat Christian Brueffer Christopher Schröder David Alexander David Koppstein Jeremy Leipzig Joona Lehtomäki Koen van Greevenbroek Kyle Meyer Nicolas Ochsner Nils Giordano Pay Giesselmann Yoshiki Vázquez Baeza Alex Leonard Sebastian Schmidt nikostr jlncrnt dkuzminov cclienti Zeb Burke-Conte Vince Till Hartmann Hielke Walinga Wolfgang Kopp Ward D DrYak Ethan Holleman Sebastian Jesse Connell John Marshall Jon Stutters Patrick Kunzmann Norbert Auer Lucas Frérot Michael R. Crusoe Matthew Monk Hugo Lapré Doğukan J.J. Ezra Herman JS Légaré Heath O'Brien Dmytro Kazanzhy Devon Ryan Christian Foivos Gypas Alexander Kleinjohann Frédéric Chevalier Thomas Weber Thom Griffioen Roy Jacobson Rich Abdill Peter Schiffels Nelis Drost Naveen Michael Schubert Marawan Abdelgawad Lance Parsons Jo Hausmann Adam Morris Jens Zentgraf Sebastian Ohlmann Sean Davis Seth Ariel Green Quinn Blenkinsop Raphael Müller ScottMastro Renan Valieris Renato Alves RezaMadi Samuel Gaist Rick Tankard Rob Schaefer Sam-Tygier Robben Migacz Sam Nicholls Robert Schauner Ryunosuke O'Neil Romain Feron Rodrigo Luger Connor Jops Matt Stone Matthias Peter Matthias Wolf Michal Stolarczyk Mike DePalatis Mitchell Robert Vollger Mohammad Samman Moustapha Sall Murillo F. Rodrigues Nicholas A. Del Grosso Nick Semenkovich Noah Oliver Küchler Paul Bransford Paul K. Korir Paul L. Maurizio Paul Moore Perry Pete Bachant Peter Steinbach Philipp Helo Rehs Pierre Marijon Zbigniew Jędrzejewski-Szmek Bailey Harrington bcouturi Bilgehan Nevruz bingxiao chaen Eric Jelli Johannes HAMPP johannaschmitz maxim-h moschetti nbelakovski nhartwic ningOTI ocaisa olgert denas phmoferring rlehnigk roshnipatel snajder-r stydodt tdayris Valentin Schneider-Lunitz xhejtman Žiga Avsec Stefan Pfenninger-Lee Stephan Druskat Susana Posada Céspedes Tadas Bareikis Tanguy Lallemand Taylor Reiter Terry Jones Tet Woo Lee Thomas Grainger Thomas Mulvaney Thomas Sibley Tim Heap Tim Tröndle Tobias Ternent Travis Wrightsman Valentin Pestel Valentyn Bezshapkin Vincent Vini Salazar pirovc Vladimir Mikryukov Wim Jeantine-Glenn Yaman Qalieh Yaroslav Halchenko Ye Yuan CowanCS1 Daniel Lusk Dario Beraldi Derrick Miller Diego Rubert Dr. Fabian Schlegel Dustin Rodrigues Edmund Miller Edouard Choinière Egor Kosaretskiy Emmanouil "Manolis" Maragkakis Eric Normandeau Fabian Neumann Flo Fong Chun Chan Afonso Santos Frank Löffler Frankie Robertson Fritjof Lammers Jean-Sebastien Gounot Gaspard Reulet George Wu Giacomo Tagliabue gibran hemani Adam Ciuris Alistair Miles Andrew Berger Andrii Oriekhov Aniket Pradhan arnikz BAKEZQ Balázs Brankovics Ben Evans Ben Jolly Branch Vincent Brian Fulton-Howard Brice Letcher Byron J. Smith Cail McLean Daley Carl Mathias Kobel Chang Ye Chaz Reid Charlie Pauvert Chris Lamb Christian Klarhorst ChristofferCOASD Clemens Lange ClementFombonne Colin J. Brislawn Justin Hiemstra Karatuğ Ozan Bircan Karel Břinda Kevin Hoffschlag Knut Dagestad Rand Kostis Anagnostopoulos Kyle Johnsen LarsStegemanGT Leonardo Schwarz Leopoldo Pla Sempere Louis Vignoli Ludwig Neste Luis Kress Lukas Klein LvKvA Maarten0110 Maciek Bąk Marcel Bargull Marcin Magnus Marco Vidal García Mark Keller Martin Holub Martin Stancsics Mathieu Bernard Matthew Feickert Giles Harper-Donnelly Giulio Centorame Grégoire Denay Hamdiye Uzuner Henry Webel Ido Tamir Jakub Kaczmarzyk James Chuang James Shaw Jan Eil Jason Greenbaum scholtalbers Jeremy Magland Jesse Bloom Jesse Wallace Jigar Patel Joe Sapp Johannes Heuel Johannes Schumann John Bates John Hennig John Huddleston (major) john (major) Josh Cook JulioV Groups, Institutes, Companies, and Organizations  ⓘ University of Duisburg-Essen Science for Life Laboratory Broad Institute of MIT and Harvard On Sabbatical The GLOBE Institute – University of Copenhagen CERN CUBI Core Unit Bioinformatics, Berlin Institute of Health University of Queensland | UQCCR UC Santa Cruz Icahn School of Medicine at Mount Sinai group.one @AnyBody 上海交通大学 Karolinska Institutet Pairwise Netherlands Institute of Ecology (NIOO-KNAW) Solynta Gekkonid Scientific LHCb Oyat Consulting Data Science @google EMBL Princess Margaret Cancer Centre, University Health Network University of Colorado School of Medicine Seoul National University @neherlab @nextstrain Princeton University Spotify Universität Duisburg-Essen University of Mainz @fulcrumgenomics Clinical Genomics Uppsala / Uppsala University Earth Sciences New Zealand (formerly GNS Science) Helmholtz Centre for Environmental Research AWS University of California, Davis BIH @cid-harvard @novartis NTNU Regeneron Pharmaceuticals Sentieon UZH Zurich Washington University School of Medicine @seqera.io Exact Sciences University Medicine Essen Technical University of Munich Université de Montréal @cnio-bu University of Vienna Barcelona Supercomputing Center @ENCCS ImmunoScape Gymrek Lab, UCSD @insilicoconsulting University of Duisburg Essen DKTK/DKFZ @TileDB-Inc Stanford University ETH DKRZ @BiomeSense ETHZ University of Helsinki Institute for Health Metrics and Evaluation @bihealth Max Delbrück center for molecular medicine @sib-swiss Alva Genomics University of Pennsylvania University College London VantAI IMS Nanofabrication GmbH Sorbonne Université, Paris @common-workflow-language Brabant Water Esox Biologics @GenomicsUA @lyft Genedata AG Bioinformatics Software Engineer at Novartis Institutes for BioMedical Research (NIBR) @RWTH-EBC @txbiomed Data Science Centre, EMBL @Syngenta University of Chicago Center for eResearch, University of Auckland @TRON-Bioinformatics Saarland University University of Colorado Anschutz School of Medicine Kahnemnan-Treisman Center A. C. Camargo Cancer Center @idiap WEHI University of Utah Center for High Performance Computing @nanoporetech Anthropic @fulcrumgenomics Ascend Analytics @Elembio Medical College of Wisconsin University of Pittsburgh / Center for Craniofacial and Dental Genetics Freie Universität Berlin @USF-HII DataDotOrg NIAID Caltech www.hzdr.de HHU Düsseldorf Seqoia Red Hat Amsterdam UMC @mpinb @open-energy-transition University of Basel Duke-NUS @BlueRiverTechnology Gustave Roussy TU Delft German Aerospace Center (DLR) IOB @open-energy-transition Novartis LPC Caen - IN2P3 - CNRS Sunagawa Lab @ ETH Zürich University of Tartu Dartmouth College, @dandi, @Debian, @DataLad, @neurodebian, @PyMVPA, @fail2ban University of Michigan, Ann Arbor WCIP | University of Glasgow Helmholtz-Zentrum Dresden-Rossendorf e.V. @seqeralabs National Institutes of Health IBIS (Institut de Biologie Intégrative et des Systèmes) TU Berlin Roche Friedrich Schiller University Jena University of Jyväskylä Swiss Ornithological Institute Montreal Clinical Research Institute 4Catalyzer @tempuslabs Wellcome Sanger Institute SPD @Adobe Westerdijk Fungal Bioidiversity Institute Sarepta Therapeutics @manaakiwhenua Mount Sinai Hospital (@marcoralab) CNRS The Gladstone Institutes Wesleyan University Norges Miljø- & Biovitenskapelige Universitet (NMBU) Freelancer for hire. Maybe. Paul Scherrer Institute Morgridge Instute for Research 𝐈𝐍𝐑𝐈𝐀🇫🇷 Nat. Inst. for DigitSci & Tech Predictive Neuroscience Lab, University Hospital Essen Oslo University Hospital @JRC-IET, C3 Georgia Tech FGCZ, ETHZ | UZH Treelogic & University of Alacant Pasqal Stockholm Universitetet TRON gGmbH Mainz Hochschule Darmstadt City, University of London Harvard, USA @Quantco LPNHE - CNRS - Sorbonne Université University of Wisconsin-Madison Institute for Molecular Bioscience, University of Queensland @bio-raum @CVUA-RRW DTU biosustain VBCF Stony Brook Medicine La Jolla Institute for Allergy and Immunology @LJI-Bioinformatics @IEDB Fred Hutchinson Cancer Research Center; Howard Hughes Medical Institute CSIRO Erlangen Centre for Astroparticle Physics @blab @nextstrain Daylily Informatics Vertex Pharmaceuticals + +### https://github.com/snakemake/snakemake +GitHub - snakemake/snakemake: This is the development home of the workflow management system Snakemake. For general information, see · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} snakemake / snakemake Public Notifications You must be signed in to change notification settings Fork 637 Star 2.8k Code Issues 983 Pull requests 131 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights snakemake/snakemake main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 5,848 Commits 5,848 Commits .github .github apidocs apidocs docs docs examples examples images images misc misc playground playground src/ snakemake src/ snakemake tests tests .dockerignore .dockerignore .gitattributes .gitattributes .gitignore .gitignore .gitpod.yml .gitpod.yml .readthedocs.yml .readthedocs.yml .sonarcloud.properties .sonarcloud.properties .test_durations .test_durations .wci.yml .wci.yml CHANGELOG.md CHANGELOG.md CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md Dockerfile Dockerfile LICENSE.md LICENSE.md MANIFEST.in MANIFEST.in README.md README.md doc-environment.yml doc-environment.yml pyproject.toml pyproject.toml release-please-config.json release-please-config.json setup.py setup.py View all files Repository files navigation README Code of conduct MIT license Snakemake The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Snakemake is highly popular, with on average more than 7 new citations per week in 2021, and almost 400k downloads. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment. Homepage: https://snakemake.github.io Copyright (c) 2012-2022 Johannes Köster johannes.koester@uni-due.com (see LICENSE) About This is the development home of the workflow management system Snakemake. For general information, see snakemake.github.io Topics snakemake reproducibility workflow-management Resources Readme License MIT license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 2.8k stars Watchers 16 watching Forks 637 forks Report repository Releases 358 v9.19.0 Latest Mar 28, 2026 + 357 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 93.3% JavaScript 3.2% HTML 0.7% Makefile 0.6% Jinja 0.4% Shell 0.4% Other 1.4% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge snakemake --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +snakemake 3.4.2 py34_1 +---------------------- +file name : snakemake-3.4.2-py34_1.tar.bz2 +name : snakemake +version : 3.4.2 +build : py34_1 +build number: 1 +size : 119 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.4.2-py34_1.tar.bz2 +md5 : e9416fcafc25ba2933dc4293fab1d13b +dependencies: + - docutils + - python 3.4* + - pyyaml + + +snakemake 3.4.2 py35_1 +---------------------- +file name : snakemake-3.4.2-py35_1.tar.bz2 +name : snakemake +version : 3.4.2 +build : py35_1 +build number: 1 +size : 118 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.4.2-py35_1.tar.bz2 +md5 : 523af0a606841b51c3b56209982de3d0 +dependencies: + - docutils + - python 3.5* + - pyyaml + + +snakemake 3.5.1 py35_1 +---------------------- +file name : snakemake-3.5.1-py35_1.tar.bz2 +name : snakemake +version : 3.5.1 +build : py35_1 +build number: 1 +size : 128 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.5.1-py35_1.tar.bz2 +md5 : 9e5462b041ac35209ff177a558fca95d +dependencies: + - docutils + - python 3.5* + - pyyaml + + +snakemake 3.5.2 py35_1 +---------------------- +file name : snakemake-3.5.2-py35_1.tar.bz2 +name : snakemake +version : 3.5.2 +build : py35_1 +build number: 1 +size : 129 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.5.2-py35_1.tar.bz2 +md5 : a493e216f15e7c2a6cf447648ea08aa1 +dependencies: + - docutils + - python 3.5* + - pyyaml + + +snakemake 3.5.3 py35_1 +---------------------- +file name : snakemake-3.5.3-py35_1.tar.bz2 +name : snakemake +version : 3.5.3 +build : py35_1 +build number: 1 +size : 143 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.5.3-py35_1.tar.bz2 +md5 : efa6290b8409b7a50a1fc37c854bac8a +dependencies: + - docutils + - python 3.5* + - pyyaml + + +snakemake 3.5.4 py34_1 +---------------------- +file name : snakemake-3.5.4-py34_1.tar.bz2 +name : snakemake +version : 3.5.4 +build : py34_1 +build number: 1 +size : 142 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.5.4-py34_1.tar.bz2 +md5 : 3a6515a8f2dc810a6d4bfaaca1d1a805 +dependencies: + - docutils + - python 3.4* + - pyyaml + + +snakemake 3.5.4 py35_1 +---------------------- +file name : snakemake-3.5.4-py35_1.tar.bz2 +name : snakemake +version : 3.5.4 +build : py35_1 +build number: 1 +size : 142 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.5.4-py35_1.tar.bz2 +md5 : 5bb71c5639c0647d5dabcc501a34b198 +dependencies: + - docutils + - python 3.5* + - pyyaml + + +snakemake 3.5.5 py34_1 +---------------------- +file name : snakemake-3.5.5-py34_1.tar.bz2 +name : snakemake +version : 3.5.5 +build : py34_1 +build number: 1 +size : 145 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.5.5-py34_1.tar.bz2 +md5 : c61b72cf92967a49496f6f207fcca62a +dependencies: + - docutils + - python 3.4* + - pyyaml + + +snakemake 3.5.5 py35_1 +---------------------- +file name : snakemake-3.5.5-py35_1.tar.bz2 +name : snakemake +version : 3.5.5 +build : py35_1 +build number: 1 +size : 144 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.5.5-py35_1.tar.bz2 +md5 : 35c60d86919e1a095f55de88c21ab048 +dependencies: + - docutils + - python 3.5* + - pyyaml + + +snakemake 3.6.0 py34_0 +---------------------- +file name : snakemake-3.6.0-py34_0.tar.bz2 +name : snakemake +version : 3.6.0 +build : py34_0 +build number: 0 +size : 146 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.6.0-py34_0.tar.bz2 +md5 : d19f4307e09db778b3de2c1919d3577d +dependencies: + - docutils + - python 3.4* + - pyyaml + + +snakemake 3.6.0 py35_0 +---------------------- +file name : snakemake-3.6.0-py35_0.tar.bz2 +name : snakemake +version : 3.6.0 +build : py35_0 +build number: 0 +size : 146 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.6.0-py35_0.tar.bz2 +md5 : 74a2bac60a6f6664f635c5203b0e20e7 +dependencies: + - docutils + - python 3.5* + - pyyaml + + +snakemake 3.6.1 py34_0 +---------------------- +file name : snakemake-3.6.1-py34_0.tar.bz2 +name : snakemake +version : 3.6.1 +build : py34_0 +build number: 0 +size : 147 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.6.1-py34_0.tar.bz2 +md5 : 15ec0995046ba9bc53a909f6d314c18b +dependencies: + - docutils + - python 3.4* + - pyyaml + + +snakemake 3.6.1 py35_0 +---------------------- +file name : snakemake-3.6.1-py35_0.tar.bz2 +name : snakemake +version : 3.6.1 +build : py35_0 +build number: 0 +size : 146 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.6.1-py35_0.tar.bz2 +md5 : f790adaa6c0f8d017d18e105266bf4b8 +dependencies: + - docutils + - python 3.5* + - pyyaml + + +snakemake 3.7.0 py35_0 +---------------------- +file name : snakemake-3.7.0-py35_0.tar.bz2 +name : snakemake +version : 3.7.0 +build : py35_0 +build number: 0 +size : 148 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.7.0-py35_0.tar.bz2 +md5 : 1bef30aa75c9518d991553d42609cb78 +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - moto >=0.4.14 + - pysftp >=0.2.8 + - python 3.5* + - pyyaml + - requests >=2.8.1 + + +snakemake 3.7.1 py34_0 +---------------------- +file name : snakemake-3.7.1-py34_0.tar.bz2 +name : snakemake +version : 3.7.1 +build : py34_0 +build number: 0 +size : 148 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.7.1-py34_0.tar.bz2 +md5 : 72c5e0e662b8337cfdfc26502d8ee824 +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - pysftp >=0.2.8 + - python 3.4* + - pyyaml + - requests >=2.8.1 + + +snakemake 3.7.1 py35_0 +---------------------- +file name : snakemake-3.7.1-py35_0.tar.bz2 +name : snakemake +version : 3.7.1 +build : py35_0 +build number: 0 +size : 148 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.7.1-py35_0.tar.bz2 +md5 : f603a9efd1a72737ead1985cd4010b3b +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - pysftp >=0.2.8 + - python 3.5* + - pyyaml + - requests >=2.8.1 + + +snakemake 3.8.0 py34_0 +---------------------- +file name : snakemake-3.8.0-py34_0.tar.bz2 +name : snakemake +version : 3.8.0 +build : py34_0 +build number: 0 +size : 155 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.8.0-py34_0.tar.bz2 +md5 : 129209000522d3dff7bddecc7d3b6b90 +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - pysftp >=0.2.8 + - python 3.4* + - pyyaml + - requests >=2.8.1 + - wrapt + + +snakemake 3.8.0 py35_0 +---------------------- +file name : snakemake-3.8.0-py35_0.tar.bz2 +name : snakemake +version : 3.8.0 +build : py35_0 +build number: 0 +size : 154 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.8.0-py35_0.tar.bz2 +md5 : 1c9fe6cc5b935784796f3f9b7f690c50 +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - pysftp >=0.2.8 + - python 3.5* + - pyyaml + - requests >=2.8.1 + - wrapt + + +snakemake 3.8.1 py34_0 +---------------------- +file name : snakemake-3.8.1-py34_0.tar.bz2 +name : snakemake +version : 3.8.1 +build : py34_0 +build number: 0 +size : 155 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.8.1-py34_0.tar.bz2 +md5 : 5876198788588588bedf4aced6e52a69 +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - pysftp >=0.2.8 + - python 3.4* + - pyyaml + - requests >=2.8.1 + - wrapt + + +snakemake 3.8.1 py35_0 +---------------------- +file name : snakemake-3.8.1-py35_0.tar.bz2 +name : snakemake +version : 3.8.1 +build : py35_0 +build number: 0 +size : 155 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.8.1-py35_0.tar.bz2 +md5 : 3a66aa142c9480ee4404eb6fa0fe00bf +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - pysftp >=0.2.8 + - python 3.5* + - pyyaml + - requests >=2.8.1 + - wrapt + + +snakemake 3.8.2 py34_0 +---------------------- +file name : snakemake-3.8.2-py34_0.tar.bz2 +name : snakemake +version : 3.8.2 +build : py34_0 +build number: 0 +size : 156 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.8.2-py34_0.tar.bz2 +md5 : c22b845b54a0bc81e3e8e5b1767572f5 +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - pysftp >=0.2.8 + - python 3.4* + - pyyaml + - requests >=2.8.1 + - wrapt + + +snakemake 3.8.2 py35_0 +---------------------- +file name : snakemake-3.8.2-py35_0.tar.bz2 +name : snakemake +version : 3.8.2 +build : py35_0 +build number: 0 +size : 155 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.8.2-py35_0.tar.bz2 +md5 : 32f5dc23e0fe6b7c67fee16c3f0a40b4 +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - pysftp >=0.2.8 + - python 3.5* + - pyyaml + - requests >=2.8.1 + - wrapt + + +snakemake 3.9.0 py34_0 +---------------------- +file name : snakemake-3.9.0-py34_0.tar.bz2 +name : snakemake +version : 3.9.0 +build : py34_0 +build number: 0 +size : 161 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.9.0-py34_0.tar.bz2 +md5 : dfcd57f483707679ccf110a873e99a7d +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - pysftp >=0.2.8 + - python 3.4* + - pyyaml + - requests >=2.8.1 + - wrapt + + +snakemake 3.9.0 py35_0 +---------------------- +file name : snakemake-3.9.0-py35_0.tar.bz2 +name : snakemake +version : 3.9.0 +build : py35_0 +build number: 0 +size : 161 KB +license : MIT License +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snakemake-3.9.0-py35_0.tar.bz2 +md5 : 45bd70423256d96c5c643a2ce5aeec1e +dependencies: + - docutils + - dropbox >=5.2 + - filechunkio >=1.6 + - ftputil >=3.2 + - pysftp >=0.2.8 + - python 3.5* + - pyyaml + - requests >=2.8.1 + - wrapt + + +snakemake 3.9.1 py34_0 +---------------------- +file name : snakemake-3.9.1-py34_0.tar.bz2 +name : snakemake +version : 3.9 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snippy.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snippy.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..91b0598764a69714f3ac174831055bc3e9b67257 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snippy.manual_bundle.txt @@ -0,0 +1,620 @@ +# Tool: snippy +software_name: snippy +tier: T1 +domain: t1_backfill_overall +downloads: 142061 +summary: Rapid bacterial SNP calling and core genome alignments +description: Rapid bacterial SNP calling and core genome alignments +dependencies: any2fasta >=0.4, bcftools >=1.10, bedtools >=2.28.0, bwa >=0.7.17, freebayes >=1.3.1, minimap2 >=2.17, openjdk >=11, parallel >=20170422, perl, perl-bioperl >=1.7.2, samclip >=0.4, samtools >=1.10,<=1.20, seqtk >=1.3, snp-sites >=2.4, snpeff >=4.3,<=5.0, tabixpp 1.1.0.*, vcflib >=1.0.0_rc3,<=1.0.2, vt >=0.5772,<2015 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/tseemann/snippy +doc_url: +dev_url: + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/tseemann/snippy +GitHub - tseemann/snippy: :scissors: Rapid haploid variant calling and core genome alignment · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} tseemann / snippy Public Notifications You must be signed in to change notification settings Fork 122 Star 583 Code Issues 215 Pull requests 4 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights tseemann/snippy master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 443 Commits 443 Commits .github/ workflows .github/ workflows bin bin etc etc perl5/ Snippy perl5/ Snippy test test .gitignore .gitignore CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md LICENSE LICENSE README.md README.md environment.yml environment.yml View all files Repository files navigation README Code of conduct License Snippy Rapid haploid variant calling and core genome alignment Synopsis Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomic tree). Quick Start % snippy --cpus 16 --outdir mysnps --ref Listeria.gbk --R1 FDA_R1.fastq.gz --R2 FDA_R2.fastq.gz <cut> Walltime used: 3 min, 42 sec Results folder: mysnps Done. % ls mysnps snps.vcf snps.bed snps.gff snps.csv snps.tab snps.html snps.bam snps.txt reference/ ... % head -5 mysnps/snps.tab CHROM POS TYPE REF ALT EVIDENCE FTYPE STRAND NT_POS AA_POS LOCUS_TAG GENE PRODUCT EFFECT chr 5958 snp A G G:44 A:0 CDS + 41/600 13/200 ECO_0001 dnaA replication protein DnaA missense_variant c.548A>C p.Lys183Thr chr 35524 snp G T T:73 G:1 C:1 tRNA - chr 45722 ins ATT ATTT ATTT:43 ATT:1 CDS - ECO_0045 gyrA DNA gyrase chr 100541 del CAAA CAA CAA:38 CAAA:1 CDS + ECO_0179 hypothetical protein plas 619 complex GATC AATA GATC:28 AATA:0 plas 3221 mnp GA CT CT:39 CT:0 CDS + ECO_p012 rep hypothetical protein % snippy-core --prefix core mysnps1 mysnps2 mysnps3 mysnps4 Loaded 4 SNP tables. Found 2814 core SNPs from 96615 SNPs. % ls core.* core.aln core.tab core.tab core.txt core.vcf Installation Conda Install Bioconda then: conda install -c conda-forge -c bioconda snippy Check installation Ensure you have the desired version: snippy --version Check that all dependencies are installed and working: snippy --check Calling SNPs Input Requirements a reference genome in FASTA or GENBANK format (can be in multiple contigs) sequence read file(s) in FASTQ or FASTA format (can be .gz compressed) format a folder to put the results in Output Files Extension Description .tab A simple tab-separated summary of all the variants .csv A comma-separated version of the .tab file .html A HTML version of the .tab file .vcf The final annotated variants in VCF format .bed The variants in BED format .gff The variants in GFF3 format .bam The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates. .bam.bai Index for the .bam file .log A log file with the commands run and their outputs .aligned.fa A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov ( does not have variants ) .consensus.fa A version of the reference genome with all variants instantiated .consensus.subs.fa A version of the reference genome with only substitution variants instantiated .raw.vcf The unfiltered variant calls from Freebayes .filt.vcf The filtered variant calls from Freebayes .vcf.gz Compressed .vcf file via BGZIP .vcf.gz.csi Index for the .vcf.gz via bcftools index ) ⚠️ ❌ Snippy 4.x does NOT produce the following files that Snippy 3.x did Extension Description .vcf.gz.tbi Index for the .vcf.gz via TABIX .depth.gz Output of samtools depth -aa for the .bam file .depth.gz.tbi Index for the .depth.gz file Columns in the TAB/CSV/HTML formats Name Description CHROM The sequence the variant was found in eg. the name after the > in the FASTA reference POS Position in the sequence, counting from 1 TYPE The variant type: snp msp ins del complex REF The nucleotide(s) in the reference ALT The alternate nucleotide(s) supported by the reads EVIDENCE Frequency counts for REF and ALT If you supply a Genbank file as the --reference rather than a FASTA file, Snippy will fill in these extra columns by using the genome annotation to tell you which feature was affected by the variant: Name Description FTYPE Class of feature affected: CDS tRNA rRNA ... STRAND Strand the feature was on: + - . NT_POS Nucleotide position of the variant withinthe feature / Length in nt AA_POS Residue position / Length in aa (only if FTYPE is CDS) LOCUS_TAG The /locus_tag of the feature (if it existed) GENE The /gene tag of the feature (if it existed) PRODUCT The /product tag of the feature (if it existed) EFFECT The snpEff annotated consequence of this variant (ANN tag in .vcf) Columns in TXT format Name Description ID Reference + Sample LENGTH Length of the reference ALIGNED Number of sites aligned to UNALIGNED Number of sites unaligned VARIANT Number of sites different from the reference HET Number of sites heterozygous or poor quality genotype represented with an n ( --minqual ) MASKED Number of sites masked in reference represented with an X ( --mask ) LOWCOV Number of sites low coverage in this sample represented with an N ( --mincov ) Variant Types Type Name Example snp Single Nucleotide Polymorphism A => T mnp Multiple Nuclotide Polymorphism GC => AT ins Insertion ATT => AGTT del Deletion ACGG => ACG complex Combination of snp/mnp ATTC => GTTA The variant caller The variant calling is done by Freebayes . The key parameters under user control are: --mincov - the minimum number of reads covering a site to be considered (default=10) --minfrac - the minimum proportion of those reads which must differ from the reference --minqual - the minimum VCF variant call "quality" (default=100) Looking at variants in detail with snippy-vcf_report If you run Snippy with the --report option it will automatically run snippy-vcf_report and generate a snps.report.txt which has a section like this for each SNP in snps.vcf : ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >LBB_contig000001:10332 snp A=>T DP=7 Q=66.3052 [7] 10301 10311 10321 10331 10341 10351 10361 tcttctccgagaagggaatataatttaaaaaaattcttaaataattcccttccctcccgttataaaaattcttcgcttat ........................................T....................................... ,,,,,, ,,,,,,,,,,,,,,,,,,,,,t,,,,,,,,,,t,,t,,,,,,,,,,,,,,,,g,,,,,,,g,,,,,,,,,t, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, .......T..................A............A....... .........................A........A.....T........... .........C.............. .....A.....................C..C........CT.................TA............. ,a,,,,,a,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t,t,,,g,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,ga,,,,,,,c,,,,,,,t,,,,,,,,,,g,,,,,,t,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ............T.C..............G...............G...... ,,,,,,,g,,,,,,,,g,,,,,,,,,,, g,,,,,,,,,,,,,,,,,,,, If you wish to generate this report after you have run Snippy, you can run it directly: cd snippydir snippy-vcf_report --cpus 8 --auto > snps.report.txt If you want a HTML version for viewing in a web browser, use the --html option: cd snippydir snippy-vcf_report --html --cpus 16 --auto > snps.report.html It works by running samtools tview for each variant, which can be very slow if you have 1000s of variants. Using --cpus as high as possible is recommended. Options --rgid will set the Read Group ( RG ) ID ( ID ) and Sample ( SM ) in the BAM and VCF file. If not supplied, it will will use the --outdir folder name for both ID and SM . --mapqual is the minimum mapping quality to accept in variant calling. BWA MEM using 60 to mean a read is "uniquely mapped". --basequal is minimum quality a nucleotide needs to be used in variant calling. We use 13 which corresponds to error probability of ~5%. It is a traditional SAMtools value. --maxsoft is how many bases of an alignment to allow to be soft-clipped before discarding the alignment. This is to encourage global over local alignment, and is passed to the samclip tool. --mincov and --minfrac are used to apply hard thresholds to the variant calling beyond the existing statistical measure.. The optimal values depend on your sequencing depth and contamination rate. Values of 10 and 0.9 are commonly used. --targets takes a BED file and only calls variants in those regions. Not normally needed unless you are only interested in variants in specific locii (eg. AMR genes) but are still performing WGS rather than amplicon sequencing. --contigs allows you to call SNPs from contigs rather than reads. It shreds the contigs into synthetic reads, as to put the calls on even footing with other read samples in a multi-sample analysis. Core SNP phylogeny If you call SNPs for multiple isolates from the same reference, you can produce an alignment of "core SNPs" which can be used to build a high-resolution phylogeny (ignoring possible recombination). A "core site" is a genomic position that is present in all the samples. A core site can have the same nucleotide in every sample ("monomorphic") or some samples can be different ("polymorphic" or "variant"). If we ignore the complications of "ins", "del" variant types, and just use variant sites, these are the "core SNP genome". Input Requirements a set of Snippy folders which used the same --ref sequence. Using snippy-multi To simplify running a set of isolate sequences (reads or contigs) against the same reference, you can use the snippy-multi script. This script requires a tab separated input file as follows, and can handle paired-end reads, single-end reads, and assembled contigs. # input.tab = ID R1 [R2] Isolate1 /path/to/R1.fq.gz /path/to/R2.fq.gz Isolate1b /path/to/R1.fastq.gz /path/to/R2.fastq.gz Isolate1c /path/to/R1.fa /path/to/R2.fa # single end reads supported too Isolate2 /path/to/SE.fq.gz Isolate2b /path/to/iontorrent.fastq # or already assembled contigs if you don't have reads Isolate3 /path/to/contigs.fa Isolate3b /path/to/reference.fna.gz Then one would run this to generate the output script. The first parameter should be the input.tab file. The remaining parameters should be any remaining shared snippy parameters. The ID will be used for each isolate's --outdir . % snippy-multi input.tab --ref Reference.gbk --cpus 16 > runme.sh % less runme.sh # check the script makes sense % sh ./runme.sh # leave it running over lunch It will also run snippy-core at the end to generate the core genome SNP alignment files core.* . Output Files Extension Description .aln A core SNP alignment in the --aformat format (default FASTA) .full.aln A whole genome SNP alignment (includes invariant sites) .tab Tab-separated columnar list of core SNP sites with alleles but NO annotations .vcf Multi-sample VCF file with genotype GT tags for all discovered alleles .txt Tab-separated columnar list of alignment/core-size statistics .ref.fa FASTA version/copy of the --ref .self_mask.bed BED file generated if --mask auto is used. Why is core.full.aln an alphabet soup? The core.full.aln file is a FASTA formatted mutliple sequence alignment file. It has one sequence for the reference, and one for each sample participating in the core genome calculation. Each sequence has the same length as the reference sequence. Character Meaning ATGC Same as the reference atgc Different from the reference - Zero coverage in this sample or a deletion relative to the reference N Low coverage in this sample (based on --mincov ) X Masked region of reference (from --mask ) n Heterozygous or poor quality genotype (has GT=0/1 or QUAL < --minqual in snps.raw.vcf ) You can remove all the "weird" characters and replace them with N using the included snippy-clean_full_aln . This is useful when you need to pass it to a tree-building or recombination-removal tool: % snippy-clean_full_aln core.full.aln > clean.full.aln % run_gubbins.py -p gubbins clean.full.aln % snp-sites -c gubbins.filtered_polymorphic_sites.fasta > clean.core.aln % FastTree -gtr -nt clean.core.aln > clean.core.tree Options If you want to mask certain regions of the genome, you can provide a BED file with the --mask parameter. Any SNPs in those regions will be excluded. This is common for genomes like M.tuberculosis where pesky repetitive PE/PPE/PGRS genes cause false positives, or masking phage regions. A --mask bed file for M.tb is provided with Snippy in the etc/Mtb_NC_000962.3_mask.bed folder. It is derived from the XLSX file from https://gph.niid.go.jp/tgs-tb/ If you use the snippy --cleanup option the reference files will be deleted. This means snippy-core can not "auto-find" the reference. In this case you simply use snippy-core --reference REF to provide the reference in FASTA format. Advanced usage Increasing speed when too many reads Sometimes you will have far more sequencing depth that you need to call SNPs. A common problem is a whole MiSeq flowcell for a single bacterial isolate, where 25 million reads results in genome depth as high as 2000x. This makes Snippy far slower than it needs to be, as most SNPs will be recovered with 50-100x depth. If you know you have 10 times as much data as you need, Snippy can randomly sub-sample your FASTQ data: # have 1000x depth, only need 100x so sample at 10% snippy --subsample 0.1 ... <snip> Sub-sampling reads at rate 0.1 <snip> Only calling SNPs in particular regions If you are looking for specific SNPs, say AMR releated ones in particular genes in your reference genome, you can save much time by only calling variants there. Just put the regions of interest into a BED file: snippy --targets sites.bed ... Finding SNPs between contigs Sometimes one of your samples is only available as contigs, without corresponding FASTQ reads. You can still use these contigs with Snippy to find variants against a reference. It does this by shredding the contigs into 250 bp single-end reads at 2 &times; --mincov uniform coverage. To use this feature, instead of providing --R1 and --R2 you use the --ctgs option with the contigs file: % ls ref.gbk mutant.fasta % snippy --outdir mut1 --ref ref.gbk --ctgs mut1.fasta Shredding mut1.fasta into pseudo-reads. Identified 257 variants. % snippy --outdir mut2 --ref ref.gbk --ctgs mut2.fasta Shredding mut2.fasta into pseudo-reads. Identified 413 variants. % snippy-core mut1 mut2 Found 129 core SNPs from 541 variant sites. % ls core.aln core.full.aln ... This output folder is completely compatible with snippy-core so you can mix FASTQ and contig based snippy output folders to produce alignments. Correcting assembly errors The de novo assembly process attempts to reconstruct the reads into the original DNA sequences they were derived from. These reconstructed sequences are called contigs or scaffolds . For various reasons, small errors can be introduced into the assembled contigs which are not supported by the original reads used in the assembly process. A common strategy is to align the reads back to the contigs to check for discrepancies. These errors appear as variants (SNPs and indels). If we can reverse these variants than we can "correct" the contigs to match the evidence provided by the original reads. Obviously this strategy can go wrong if one is not careful about how the read alignment is performed and which variants are accepted. Snippy is able to help with this contig correction process. In fact, it produces a snps.consensus.fa FASTA file which is the ref.fa input file provided but with the discovered variants in snps.vcf applied! However, Snippy is not perfect and sometimes finds questionable variants. Typically you would make a copy of snps.vcf (let's call it corrections.vcf ) and remove those lines corresponding to variants we don't trust. For example, when correcting Roche 454 and PacBio SMRT contigs, we primarily expect to find homopolymer errors and hence expect to see ins more than snp type variants. In this case you need to run the correcting process manually using these steps: % cd snippy-outdir % cp snps.vcf corrections.vcf % $EDITOR corrections.vcf % bgzip -c corrections.vcf > corrections.vcf.gz % tabix -p vcf corrections.vcf.gz % vcf-consensus corrections.vcf.gz < ref.fa > corrected.fa You may wish to iterate this process by using corrected.fa as a new --ref for a repeated run of Snippy. Sometimes correcting one error allows BWA to align things it couldn't before, and new errors are uncovered. Snippy may not be the best way to correct assemblies - you should consider dedicated tools such as PILON or iCorn2 , or adjust the Quiver parameters (for Pacbio data). Unmapped Reads Sometimes you are interested in the reads which did not align to the reference genome. These reads represent DNA that was novel to your sample which is potentially interesting. A standard strategy is to de novo assemble the unmapped reads to discover these novel DNA elements, which often comprise mobile genetic elements such as plasmids. By default, Snippy does not keep the unmapped reads, not even in the BAM file. If you wish to keep them, use the --unmapped option and the unaligned reads will be saved to a compres + +## Conda Search Info +$ conda search -c bioconda -c conda-forge snippy --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +snippy 2.9 1 +------------ +file name : snippy-2.9-1.tar.bz2 +name : snippy +version : 2.9 +build : 1 +build number: 1 +size : 12 KB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-2.9-1.tar.bz2 +md5 : 0814599faff61fad2a1c235f115255ff +dependencies: + - bwa + - freebayes + - parallel + - perl-bioperl + - perl-threaded + - samtools + - snpeff + - vcflib + - vcftools + + +snippy 2.9 pl5.22.0_0 +--------------------- +file name : snippy-2.9-pl5.22.0_0.tar.bz2 +name : snippy +version : 2.9 +build : pl5.22.0_0 +build number: 0 +size : 12 KB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-2.9-pl5.22.0_0.tar.bz2 +md5 : 4a2c40278ef559867ffef6d73f15ede3 +dependencies: + - bwa + - freebayes + - parallel + - perl 5.22.0* + - perl-bioperl + - samtools + - snpeff + - vcflib + - vcftools + + +snippy 3.0 0 +------------ +file name : snippy-3.0-0.tar.bz2 +name : snippy +version : 3.0 +build : 0 +build number: 0 +size : 13 KB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-3.0-0.tar.bz2 +md5 : cbe97c5c914d6958ba897105db927a51 +dependencies: + - bwa + - freebayes + - parallel + - perl-bioperl + - perl-threaded + - samtools + - snpeff + - vcflib + - vcftools + + +snippy 3.0 1 +------------ +file name : snippy-3.0-1.tar.bz2 +name : snippy +version : 3.0 +build : 1 +build number: 1 +size : 13 KB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-3.0-1.tar.bz2 +md5 : 9c8b3878e12bb608c03c7c69a730d1c1 +dependencies: + - bwa + - freebayes + - htslib + - parallel + - perl-bioperl + - perl-threaded + - samtools + - snpeff + - vcflib + - vcftools + + +snippy 3.0 pl5.22.0_1 +--------------------- +file name : snippy-3.0-pl5.22.0_1.tar.bz2 +name : snippy +version : 3.0 +build : pl5.22.0_1 +build number: 1 +size : 17 KB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-3.0-pl5.22.0_1.tar.bz2 +md5 : 5e6620b7b7f5dde4e30fb5d0841e26ff +dependencies: + - bwa + - freebayes + - htslib + - parallel + - perl 5.22.0* + - perl-bioperl + - samtools + - snpeff + - vcflib + - vcftools + + +snippy 3.1 0 +------------ +file name : snippy-3.1-0.tar.bz2 +name : snippy +version : 3.1 +build : 0 +build number: 0 +size : 52.9 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-3.1-0.tar.bz2 +md5 : 79baea6aae46332603cba9c1be1c2810 +dependencies: + - bwa + - freebayes + - htslib + - parallel + - perl-bioperl + - perl-list-moreutils + - perl-threaded + - samtools + - snpeff + - vcflib + - vcftools + + +snippy 3.1 4 +------------ +file name : snippy-3.1-4.tar.bz2 +name : snippy +version : 3.1 +build : 4 +build number: 4 +size : 52.9 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-3.1-4.tar.bz2 +md5 : a0b92991953e92859cefed2a95502625 +timestamp : 2018-06-21 03:08:27 UTC +dependencies: + - bwa >=0.7.12 + - freebayes >=1.1.0 + - parallel >=20130422 + - perl + - perl-bioperl 1.6.924 + - perl-list-moreutils >=0.413 + - samtools >=1.3 + - snpeff >=4.1 + - vcflib + - vcftools >=0.1.14 + + +snippy 3.1 pl5.22.0_1 +--------------------- +file name : snippy-3.1-pl5.22.0_1.tar.bz2 +name : snippy +version : 3.1 +build : pl5.22.0_1 +build number: 1 +size : 52.9 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-3.1-pl5.22.0_1.tar.bz2 +md5 : dca06ad956655402e730e0a37603de9e +dependencies: + - bwa >=0.7.12 + - freebayes >=0.9.20 + - htslib >=1.4 + - parallel >=20130422 + - perl 5.22.0* + - perl-bioperl ==1.6.924 + - perl-list-moreutils >=0.413 + - samtools >=1.3 + - snpeff >=4.1 + - vcflib + - vcftools >=0.1.14 + + +snippy 3.1 pl5.22.0_2 +--------------------- +file name : snippy-3.1-pl5.22.0_2.tar.bz2 +name : snippy +version : 3.1 +build : pl5.22.0_2 +build number: 2 +size : 52.9 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-3.1-pl5.22.0_2.tar.bz2 +md5 : ba6a1788b8ff0180a37016daefb7b755 +dependencies: + - bwa >=0.7.12 + - freebayes >=1.1.0 + - htslib >=1.4 + - parallel >=20130422 + - perl 5.22.0* + - perl-bioperl ==1.6.924 + - perl-list-moreutils >=0.413 + - samtools >=1.3 + - snpeff >=4.1 + - vcflib + - vcftools >=0.1.14 + + +snippy 3.1 pl5.22.0_3 +--------------------- +file name : snippy-3.1-pl5.22.0_3.tar.bz2 +name : snippy +version : 3.1 +build : pl5.22.0_3 +build number: 3 +size : 52.9 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-3.1-pl5.22.0_3.tar.bz2 +md5 : bd9fde659ad36d3387ed7ec6252b3711 +dependencies: + - bwa >=0.7.12 + - freebayes >=1.1.0 + - parallel >=20130422 + - perl 5.22.0* + - perl-bioperl ==1.6.924 + - perl-list-moreutils >=0.413 + - samtools >=1.3 + - snpeff >=4.1 + - vcflib + - vcftools >=0.1.14 + + +snippy 3.2 pl5.22.0_1 +--------------------- +file name : snippy-3.2-pl5.22.0_1.tar.bz2 +name : snippy +version : 3.2 +build : pl5.22.0_1 +build number: 1 +size : 60.3 MB +license : GPL2 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-3.2-pl5.22.0_1.tar.bz2 +md5 : e4bd27c6c4a982888f6c19871cfff1b1 +dependencies: + - bwa >=0.7.12 + - freebayes >=1.1 + - parallel >=20130422 + - perl 5.22.0* + - perl-bioperl + - perl-file-slurp + - perl-list-moreutils + - perl-time-piece + - samtools >=1.3 + - snpeff >=4.3 + - vcflib + - vcftools >=0.1.14 + + +snippy 4.0.2 0 +-------------- +file name : snippy-4.0.2-0.tar.bz2 +name : snippy +version : 4.0.2 +build : 0 +build number: 0 +size : 18.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-4.0.2-0.tar.bz2 +md5 : aa25f8d350a3474903a9b03b61cab30b +timestamp : 2018-08-14 18:31:16 UTC +dependencies: + - bcftools >=1.8 + - bwa >=0.7.17 + - emboss >=6.0 + - freebayes >=1.1 + - minimap2 >=2.10 + - parallel >=20170422 + - perl + - perl-bioperl + - perl-list-moreutils + - perl-time-piece + - samclip >=0.2 + - samtools >=1.8 + - seqtk >=1.2 + - snp-sites >=2.4 + - snpeff >=4.3 + - vcflib + - vt >=0.5772 + + +snippy 4.0.5 0 +-------------- +file name : snippy-4.0.5-0.tar.bz2 +name : snippy +version : 4.0.5 +build : 0 +build number: 0 +size : 18.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-4.0.5-0.tar.bz2 +md5 : 48874c7524f0f05ec86eeb7d70697771 +timestamp : 2018-08-16 08:08:08 UTC +dependencies: + - bcftools >=1.8 + - bwa >=0.7.17 + - emboss >=6.0 + - freebayes >=1.1 + - minimap2 >=2.10 + - parallel >=20170422 + - perl + - perl-bioperl >=1.7.2 + - perl-list-moreutils + - perl-time-piece + - samclip >=0.2 + - samtools >=1.8 + - seqtk >=1.2 + - snp-sites >=2.4 + - snpeff >=4.3 + - vcflib + - vt >=0.5772 + + +snippy 4.0.7 0 +-------------- +file name : snippy-4.0.7-0.tar.bz2 +name : snippy +version : 4.0.7 +build : 0 +build number: 0 +size : 18.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-4.0.7-0.tar.bz2 +md5 : e9c4d773780432869f652a2ef7a9e1a9 +timestamp : 2018-08-28 05:10:01 UTC +dependencies: + - bcftools >=1.8 + - bwa >=0.7.17 + - emboss >=6.0 + - freebayes >=1.1 + - minimap2 >=2.10 + - parallel >=20170422 + - perl + - perl-bioperl >=1.7.2 + - perl-list-moreutils + - perl-time-piece + - samclip >=0.2 + - samtools >=1.8 + - seqtk >=1.2 + - snp-sites >=2.4 + - snpeff >=4.3 + - vcflib + - vt >=0.5772 + + +snippy 4.1.0 0 +-------------- +file name : snippy-4.1.0-0.tar.bz2 +name : snippy +version : 4.1.0 +build : 0 +build number: 0 +size : 18.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-4.1.0-0.tar.bz2 +md5 : 0292fa6486ebaf481be6e5f362e1d989 +timestamp : 2018-08-28 08:22:49 UTC +dependencies: + - bcftools >=1.8 + - bwa >=0.7.17 + - emboss >=6.0 + - freebayes >=1.1 + - minimap2 >=2.10 + - parallel >=20170422 + - perl + - perl-bioperl >=1.7.2 + - perl-list-moreutils + - perl-time-piece + - samclip >=0.2 + - samtools >=1.8 + - seqtk >=1.2 + - snp-sites >=2.4 + - snpeff >=4.3 + - vcflib + - vt >=0.5772 + + +snippy 4.2.3 0 +-------------- +file name : snippy-4.2.3-0.tar.bz2 +name : snippy +version : 4.2.3 +build : 0 +build number: 0 +size : 18.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-4.2.3-0.tar.bz2 +md5 : d8b79e5f4174c9c3028c01000c6e2d1a +timestamp : 2018-10-03 07:54:31 UTC +dependencies: + - bcftools >=1.8 + - bedtools + - bwa >=0.7.17 + - emboss >=6.0 + - freebayes >=1.1 + - minimap2 >=2.10 + - parallel >=20170422 + - perl + - perl-bioperl >=1.7.2 + - perl-time-piece + - samclip >=0.2 + - samtools >=1.8 + - seqtk >=1.2 + - snp-sites >=2.4 + - snpeff >=4.3 + - vcflib + - vt >=0.5772 + + +snippy 4.3.3 0 +-------------- +file name : snippy-4.3.3-0.tar.bz2 +name : snippy +version : 4.3.3 +build : 0 +build number: 0 +size : 18.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-4.3.3-0.tar.bz2 +md5 : 77b85e2c049297a722c0affa6528f673 +timestamp : 2018-10-26 05:59:34 UTC +dependencies: + - bcftools >=1.8 + - bedtools + - bwa >=0.7.17 + - emboss >=6.0 + - freebayes >=1.1 + - minimap2 >=2.10 + - parallel >=20170422 + - perl + - perl-bioperl >=1.7.2 + - perl-time-piece + - samclip >=0.2 + - samtools >=1.8 + - seqtk >=1.2 + - snp-sites >=2.4 + - snpeff >=4.3 + - vcflib + - vt >=0.5772 + + +snippy 4.3.5 0 +-------------- +file name : snippy-4.3.5-0.tar.bz2 +name : snippy +version : 4.3.5 +build : 0 +build number: 0 +size : 18.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-4.3.5-0.tar.bz2 +md5 : 02ceba8fd49e0b2e255c59147f832af6 +timestamp : 2018-11-09 14:19:51 UTC +dependencies: + - bcftools >=1.8 + - bedtools + - bwa >=0.7.17 + - emboss >=6.0 + - freebayes >=1.1 + - minimap2 >=2.10 + - parallel >=20170422 + - perl + - perl-bioperl >=1.7.2 + - perl-time-piece + - samclip >=0.2 + - samtools >=1.8 + - seqtk >=1.2 + - snp-sites >=2.4 + - snpeff >=4.3 + - vcflib + - vt >=0.5772 + + +snippy 4.3.6 0 +-------------- +file name : snippy-4.3.6-0.tar.bz2 +name : snippy +version : 4.3.6 +build : 0 +build number: 0 +size : 18.9 MB +license : GPL-2.0 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snippy-4.3.6-0.tar.bz2 +md5 : 34f716924e1b31db893d967c53d37015 +timestamp : 2018-11-27 23:29:16 UTC +dependencies: + - bcftools >=1.8 + - bedtools + - bwa >=0.7.17 + - emboss >=6.0 + - freebayes >=1.1 + - minimap2 >=2.10 + - parallel >=20170422 + - perl + - perl-bioperl >=1.7.2 + - perl-time-piece + - samclip >=0.2 + - samtools >=1.8 + - seqtk >=1.2 + - snp-sites >=2.4 + - snpeff >=4.3 + - vcflib + - vt >=0.5772 + + +snippy 4.4.0 0 +-------------- +file name : snippy-4.4.0-0.tar.bz2 +name : snippy +version : 4.4.0 +build : 0 +build number: 0 +size : 18.9 MB +license : GPL-2.0 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snippy-4.4.0-0.tar.bz2 +md5 : 152da2436aeaad08fbfd diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snpeff.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snpeff.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0f3d3d5f072a5eb9fda04da05cad46c40be03dd --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/snpeff.manual_bundle.txt @@ -0,0 +1,631 @@ +# Tool: snpeff +software_name: snpeff +tier: T1 +domain: t1_backfill_overall +downloads: 586606 +summary: Genetic variant annotation and effect prediction toolbox +description: Genetic variant annotation and effect prediction toolbox +dependencies: openjdk >=21, python, zlib +execution_environment: Java +execution_environment_reason: inferred from Java runtime dependencies + +## URLs +home_url: http://snpeff.sourceforge.net/ +doc_url: +dev_url: + +## CLI Help Source +java:-help +## CLI Help Content +$ conda run -n bioenv_java java -help +[rc=0] + +Usage: java [options] [args...] + (to execute a class) + or java [options] -jar [args...] + (to execute a jar file) + or java [options] -m [/] [args...] + java [options] --module [/] [args...] + (to execute the main class in a module) + or java [options] [args] + (to execute a single source-file program) + + Arguments following the main class, source file, -jar , + -m or --module / are passed as the arguments to + main class. + + where options include: + + -cp + -classpath + --class-path + A : separated list of directories, JAR archives, + and ZIP archives to search for class files. + -p + --module-path ... + A : separated list of directories, each directory + is a directory of modules. + --upgrade-module-path ... + A : separated list of directories, each directory + is a directory of modules that replace upgradeable + modules in the runtime image + --add-modules [,...] + root modules to resolve in addition to the initial module. + can also be ALL-DEFAULT, ALL-SYSTEM, + ALL-MODULE-PATH. + --list-modules + list observable modules and exit + -d + --describe-module + describe a module and exit + --dry-run create VM and load main class but do not execute main method. + The --dry-run option may be useful for validating the + command-line options such as the module system configuration. + --validate-modules + validate all modules and exit + The --validate-modules option may be useful for finding + conflicts and other errors with modules on the module path. + -D= + set a system property + -verbose:[class|module|gc|jni] + enable verbose output + -version print product version to the error stream and exit + --version print product version to the output stream and exit + -showversion print product version to the error stream and continue + --show-version + print product version to the output stream and continue + --show-module-resolution + show module resolution output during startup + -? -h -help + print this help message to the error stream + --help print this help message to the output stream + -X print help on extra options to the error stream + --help-extra print help on extra options to the output stream + -ea[:...|:] + -enableassertions[:...|:] + enable assertions with specified granularity + -da[:...|:] + -disableassertions[:...|:] + disable assertions with specified granularity + -esa | -enablesystemassertions + enable system assertions + -dsa | -disablesystemassertions + disable system assertions + -agentlib:[=] + load native agent library , e.g. -agentlib:jdwp + see also -agentlib:jdwp=help + -agentpath:[=] + load native agent library by full pathname + -javaagent:[=] + load Java programming language agent, see java.lang.instrument + -splash: + show splash screen with specified image + HiDPI scaled images are automatically supported and used + if available. The unscaled image filename, e.g. image.ext, + should always be passed as the argument to the -splash option. + The most appropriate scaled image provided will be picked up + automatically. + See the SplashScreen API documentation for more information + @argument files + one or more argument files containing options + -disable-@files + prevent further argument file expansion + --enable-preview + allow classes to depend on preview features of this release +To specify an argument for a long option, you can use --= or +-- . + + + + +## Conda Search Info +$ conda search -c bioconda -c conda-forge snpeff --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +snpeff 3_6 hdfd78af_0 +--------------------- +file name : snpeff-3_6-hdfd78af_0.tar.bz2 +name : snpeff +version : 3_6 +build : hdfd78af_0 +build number: 0 +size : 18.6 MB +license : LGPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snpeff-3_6-hdfd78af_0.tar.bz2 +md5 : 85a9d348ea3b9869ffc4db9008a6e697 +timestamp : 2022-06-02 14:41:26 UTC +dependencies: + - openjdk >=8 + - python + - zlib + + +snpeff 4.1l 0 +------------- +file name : snpeff-4.1l-0.tar.bz2 +name : snpeff +version : 4.1l +build : 0 +build number: 0 +size : 42.9 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.1l-0.tar.bz2 +md5 : de3c6e9dc5da349849590cb98230baff +dependencies: [] + + +snpeff 4.1l 1 +------------- +file name : snpeff-4.1l-1.tar.bz2 +name : snpeff +version : 4.1l +build : 1 +build number: 1 +size : 42.9 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.1l-1.tar.bz2 +md5 : 69e26023af77338144f86a8f98459dd0 +dependencies: + - java-jdk + + +snpeff 4.1l 2 +------------- +file name : snpeff-4.1l-2.tar.bz2 +name : snpeff +version : 4.1l +build : 2 +build number: 2 +size : 42.9 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.1l-2.tar.bz2 +md5 : 97036ccdc1da521a64900e67df8b1174 +dependencies: + - java-jdk + + +snpeff 4.1l 3 +------------- +file name : snpeff-4.1l-3.tar.bz2 +name : snpeff +version : 4.1l +build : 3 +build number: 3 +size : 42.9 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.1l-3.tar.bz2 +md5 : 2ffc168de7610465f0119cd82b267d35 +dependencies: + - java-jdk >=8 + + +snpeff 4.1l 4 +------------- +file name : snpeff-4.1l-4.tar.bz2 +name : snpeff +version : 4.1l +build : 4 +build number: 4 +size : 18.3 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.1l-4.tar.bz2 +md5 : 3e1538842f1bb9c8b59b9b0ec12ef472 +dependencies: + - java-jdk >=8 + + +snpeff 4.1l 5 +------------- +file name : snpeff-4.1l-5.tar.bz2 +name : snpeff +version : 4.1l +build : 5 +build number: 5 +size : 18.3 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.1l-5.tar.bz2 +md5 : 45514470528e871361da54d4b4e793ce +timestamp : 2018-06-21 02:08:36 UTC +dependencies: + - java-jdk >=8 + + +snpeff 4.1l 6 +------------- +file name : snpeff-4.1l-6.tar.bz2 +name : snpeff +version : 4.1l +build : 6 +build number: 6 +size : 18.3 MB +license : LGPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snpeff-4.1l-6.tar.bz2 +md5 : ccfd0a92b99ab20b61e882390f86030a +timestamp : 2019-10-16 08:27:55 UTC +dependencies: + - openjdk >=8 + + +snpeff 4.1l 7 +------------- +file name : snpeff-4.1l-7.tar.bz2 +name : snpeff +version : 4.1l +build : 7 +build number: 7 +size : 18.3 MB +license : LGPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snpeff-4.1l-7.tar.bz2 +md5 : ae7f9573d8ca2d7e5e1268adfa0e8569 +timestamp : 2019-10-26 14:01:09 UTC +dependencies: + - openjdk >=8 + + +snpeff 4.1l hdfd78af_8 +---------------------- +file name : snpeff-4.1l-hdfd78af_8.tar.bz2 +name : snpeff +version : 4.1l +build : hdfd78af_8 +build number: 8 +size : 18.3 MB +license : LGPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snpeff-4.1l-hdfd78af_8.tar.bz2 +md5 : 0ae9de43809019532fa87d323d25c889 +timestamp : 2021-03-25 11:54:17 UTC +dependencies: + - openjdk >=8 + + +snpeff 4.2 0 +------------ +file name : snpeff-4.2-0.tar.bz2 +name : snpeff +version : 4.2 +build : 0 +build number: 0 +size : 43.8 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.2-0.tar.bz2 +md5 : 8cc4255dd30094d335a026fdfa75b72e +dependencies: + - java-jdk + + +snpeff 4.3b 0 +------------- +file name : snpeff-4.3b-0.tar.bz2 +name : snpeff +version : 4.3b +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3b-0.tar.bz2 +md5 : 3f9bb167747a2a568497a13488c8b9dd +dependencies: + - java-jdk + + +snpeff 4.3g 0 +------------- +file name : snpeff-4.3g-0.tar.bz2 +name : snpeff +version : 4.3g +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3g-0.tar.bz2 +md5 : 2de5fe04c1148cb26b27b0f6ddce16f2 +dependencies: + - java-jdk + + +snpeff 4.3i 0 +------------- +file name : snpeff-4.3i-0.tar.bz2 +name : snpeff +version : 4.3i +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3i-0.tar.bz2 +md5 : 776f9804a74eac5219ffc77ddf569d3b +dependencies: + - java-jdk + + +snpeff 4.3k 0 +------------- +file name : snpeff-4.3k-0.tar.bz2 +name : snpeff +version : 4.3k +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3k-0.tar.bz2 +md5 : c376b5e891932028d93abf360465cc50 +dependencies: + - openjdk + + +snpeff 4.3 0 +------------ +file name : snpeff-4.3-0.tar.bz2 +name : snpeff +version : 4.3 +build : 0 +build number: 0 +size : 44.3 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3-0.tar.bz2 +md5 : 45f4f7331e4fe9e6df7b3e2134b2df5a +dependencies: + - java-jdk + + +snpeff 4.3 1 +------------ +file name : snpeff-4.3-1.tar.bz2 +name : snpeff +version : 4.3 +build : 1 +build number: 1 +size : 44.3 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3-1.tar.bz2 +md5 : bbd84947d1abf2a578c43c0a95e45a26 +dependencies: + - java-jdk + + +snpeff 4.3 2 +------------ +file name : snpeff-4.3-2.tar.bz2 +name : snpeff +version : 4.3 +build : 2 +build number: 2 +size : 44.3 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3-2.tar.bz2 +md5 : f5952c67def6399c8d520473f28ab218 +dependencies: + - java-jdk + + +snpeff 4.3 3 +------------ +file name : snpeff-4.3-3.tar.bz2 +name : snpeff +version : 4.3 +build : 3 +build number: 3 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3-3.tar.bz2 +md5 : fa674fe85d76e988f33073db50e693bc +dependencies: + - java-jdk + + +snpeff 4.3.1k 0 +--------------- +file name : snpeff-4.3.1k-0.tar.bz2 +name : snpeff +version : 4.3.1k +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3.1k-0.tar.bz2 +md5 : addccb905fb69a07fb654bfc8d4ab7df +dependencies: + - openjdk + + +snpeff 4.3.1m 0 +--------------- +file name : snpeff-4.3.1m-0.tar.bz2 +name : snpeff +version : 4.3.1m +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3.1m-0.tar.bz2 +md5 : ea3fdfed31565c1f168374cc3400eaa8 +dependencies: + - openjdk + + +snpeff 4.3.1o 0 +--------------- +file name : snpeff-4.3.1o-0.tar.bz2 +name : snpeff +version : 4.3.1o +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3.1o-0.tar.bz2 +md5 : 6abb3bb6d5c479f77956587ecd022a5d +dependencies: + - openjdk + + +snpeff 4.3.1p 0 +--------------- +file name : snpeff-4.3.1p-0.tar.bz2 +name : snpeff +version : 4.3.1p +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3.1p-0.tar.bz2 +md5 : 7b85af8142ff2b2ed3ade1fa4e74e87d +dependencies: + - openjdk + + +snpeff 4.3.1p 1 +--------------- +file name : snpeff-4.3.1p-1.tar.bz2 +name : snpeff +version : 4.3.1p +build : 1 +build number: 1 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3.1p-1.tar.bz2 +md5 : 7fd6b318dc1fe71dc8c42c435e6606d7 +dependencies: + - openjdk + + +snpeff 4.3.1q 0 +--------------- +file name : snpeff-4.3.1q-0.tar.bz2 +name : snpeff +version : 4.3.1q +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3.1q-0.tar.bz2 +md5 : 7d5a75c2ecd6a39b8e111dd194fa074c +dependencies: + - openjdk + + +snpeff 4.3.1r 0 +--------------- +file name : snpeff-4.3.1r-0.tar.bz2 +name : snpeff +version : 4.3.1r +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3.1r-0.tar.bz2 +md5 : 2e8eece3bf3493abed92afd18817d849 +dependencies: + - openjdk + + +snpeff 4.3.1t 0 +--------------- +file name : snpeff-4.3.1t-0.tar.bz2 +name : snpeff +version : 4.3.1t +build : 0 +build number: 0 +size : 19.7 MB +license : LGPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/snpeff-4.3.1t-0.tar.bz2 +md5 : 63f7e68ed43c4794942ce56f6a78f529 +dependencies: + - openjdk + + +snpeff 4.3.1t 1 +--------------- +file name : snpeff-4.3.1t-1.tar.bz2 +name : snpeff +version : 4.3.1t +build : 1 +build number: 1 +size : 19.7 MB +license : LGPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snpeff-4.3.1t-1.tar.bz2 +md5 : 14ddd68d1cc90a5cf28cac32e21a7ad4 +timestamp : 2018-06-21 02:30:58 UTC +dependencies: + - openjdk + + +snpeff 4.3.1t 2 +--------------- +file name : snpeff-4.3.1t-2.tar.bz2 +name : snpeff +version : 4.3.1t +build : 2 +build number: 2 +size : 19.7 MB +license : LGPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snpeff-4.3.1t-2.tar.bz2 +md5 : e84e3a3c30ad087c561b1a0863e60eda +timestamp : 2019-03-09 17:25:18 UTC +dependencies: + - openjdk + - zlib + + +snpeff 4.3.1t 3 +--------------- +file name : snpeff-4.3.1t-3.tar.bz2 +name : snpeff +version : 4.3.1t +build : 3 +build number: 3 +size : 19.7 MB +license : LGPLv3 +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/snpeff-4.3.1t-3.tar.bz2 +md5 : 9c26bc82ad29afb964159cef82e5cf55 +timestamp : 2019-10-10 19:19:07 UTC +dependencies: + - openjdk + - python + - zlib + + +snpeff 4.3.1t 4 +--------------- +file name : snpeff-4.3.1t-4.tar.bz2 +name : snpeff +version : 4.3.1t +build : 4 +build number: 4 +size : 19.7 MB +license : LGPLv3 +subdir : noarch +url : https:// diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sorted_nearest.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sorted_nearest.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..4693a52b2de6c5282b9da4072072d08ec543dc59 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sorted_nearest.manual_bundle.txt @@ -0,0 +1,431 @@ +# Tool: sorted_nearest +software_name: sorted_nearest +tier: T1 +domain: t1_backfill_overall +downloads: 204953 +summary: Find nearest interval. +description: Find nearest interval. +dependencies: libgcc >=13, numpy, python >=3.11,<3.12.0a0, python_abi 3.11.* *_cp311 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/endrebak/sorted_nearest +doc_url: +dev_url: https://github.com/endrebak/sorted_nearest + +## URL Docs Extract +### https://github.com/endrebak/sorted_nearest +GitHub - pyranges/sorted_nearest: Cython helper library for pyranges. Find nearest interval in linear time at C speed. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} pyranges / sorted_nearest Public Notifications You must be signed in to change notification settings Fork 5 Star 2 Code Issues 3 Pull requests 2 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights pyranges/sorted_nearest master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 66 Commits 66 Commits .github/ workflows .github/ workflows examples examples sorted_nearest sorted_nearest tests tests .gitignore .gitignore .travis.yml .travis.yml CHANGELOG CHANGELOG LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in build_wheel.sh build_wheel.sh pyproject.toml pyproject.toml setup.py setup.py View all files Repository files navigation BSD-3-Clause license Copyright 2018 Endre Bakken Stovner Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. About Cython helper library for pyranges. Find nearest interval in linear time at C speed. License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 2 stars Watchers 1 watching Forks 5 forks Report repository Releases 1 0.0.31 Latest Jun 22, 2020 Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Cython 82.0% C 12.2% Python 5.1% Shell 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/endrebak/sorted_nearest +GitHub - pyranges/sorted_nearest: Cython helper library for pyranges. Find nearest interval in linear time at C speed. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} pyranges / sorted_nearest Public Notifications You must be signed in to change notification settings Fork 5 Star 2 Code Issues 3 Pull requests 2 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights pyranges/sorted_nearest master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 66 Commits 66 Commits .github/ workflows .github/ workflows examples examples sorted_nearest sorted_nearest tests tests .gitignore .gitignore .travis.yml .travis.yml CHANGELOG CHANGELOG LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in build_wheel.sh build_wheel.sh pyproject.toml pyproject.toml setup.py setup.py View all files Repository files navigation BSD-3-Clause license Copyright 2018 Endre Bakken Stovner Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. About Cython helper library for pyranges. Find nearest interval in linear time at C speed. License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 2 stars Watchers 1 watching Forks 5 forks Report repository Releases 1 0.0.31 Latest Jun 22, 2020 Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Cython 82.0% C 12.2% Python 5.1% Shell 0.7% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge sorted_nearest --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done +sorted_nearest 0.0.17 py27h14c3975_0 +------------------------------------ +file name : sorted_nearest-0.0.17-py27h14c3975_0.tar.bz2 +name : sorted_nearest +version : 0.0.17 +build : py27h14c3975_0 +build number: 0 +size : 202 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.17-py27h14c3975_0.tar.bz2 +md5 : ac05a61b5698a34faf9256b22c6a0d50 +timestamp : 2019-05-09 08:03:11 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy >1.16.3* + - python >=2.7,<2.8.0a0 + + +sorted_nearest 0.0.17 py27h14c3975_1 +------------------------------------ +file name : sorted_nearest-0.0.17-py27h14c3975_1.tar.bz2 +name : sorted_nearest +version : 0.0.17 +build : py27h14c3975_1 +build number: 1 +size : 207 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.17-py27h14c3975_1.tar.bz2 +md5 : 45486925ca33b6c0ea38f5e131b92433 +timestamp : 2019-05-09 10:26:24 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy >=1.16.3 + - python >=2.7,<2.8.0a0 + + +sorted_nearest 0.0.17 py36h14c3975_0 +------------------------------------ +file name : sorted_nearest-0.0.17-py36h14c3975_0.tar.bz2 +name : sorted_nearest +version : 0.0.17 +build : py36h14c3975_0 +build number: 0 +size : 206 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.17-py36h14c3975_0.tar.bz2 +md5 : b796a711234af6e29f36c77e69ea01a5 +timestamp : 2019-05-09 08:04:31 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy >1.16.3* + - python >=3.6,<3.7.0a0 + + +sorted_nearest 0.0.17 py36h14c3975_1 +------------------------------------ +file name : sorted_nearest-0.0.17-py36h14c3975_1.tar.bz2 +name : sorted_nearest +version : 0.0.17 +build : py36h14c3975_1 +build number: 1 +size : 211 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.17-py36h14c3975_1.tar.bz2 +md5 : 38df6188c6880cc8138367fda4ada729 +timestamp : 2019-05-09 10:27:50 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy >=1.16.3 + - python >=3.6,<3.7.0a0 + + +sorted_nearest 0.0.17 py37h14c3975_0 +------------------------------------ +file name : sorted_nearest-0.0.17-py37h14c3975_0.tar.bz2 +name : sorted_nearest +version : 0.0.17 +build : py37h14c3975_0 +build number: 0 +size : 206 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.17-py37h14c3975_0.tar.bz2 +md5 : 2108dc261c0270f305ebfebbed710c01 +timestamp : 2019-05-09 08:05:51 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy >1.16.3* + - python >=3.7,<3.8.0a0 + + +sorted_nearest 0.0.17 py37h14c3975_1 +------------------------------------ +file name : sorted_nearest-0.0.17-py37h14c3975_1.tar.bz2 +name : sorted_nearest +version : 0.0.17 +build : py37h14c3975_1 +build number: 1 +size : 211 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.17-py37h14c3975_1.tar.bz2 +md5 : 1477346ef2d8b3003bed555f0137fb92 +timestamp : 2019-05-09 10:25:12 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy >=1.16.3 + - python >=3.7,<3.8.0a0 + + +sorted_nearest 0.0.18 py27h14c3975_1 +------------------------------------ +file name : sorted_nearest-0.0.18-py27h14c3975_1.tar.bz2 +name : sorted_nearest +version : 0.0.18 +build : py27h14c3975_1 +build number: 1 +size : 207 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.18-py27h14c3975_1.tar.bz2 +md5 : dcd16edf740edd0a8c94a34d82cbb9bb +timestamp : 2019-05-13 11:46:18 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy >=1.16.3 + - python >=2.7,<2.8.0a0 + + +sorted_nearest 0.0.18 py36h14c3975_1 +------------------------------------ +file name : sorted_nearest-0.0.18-py36h14c3975_1.tar.bz2 +name : sorted_nearest +version : 0.0.18 +build : py36h14c3975_1 +build number: 1 +size : 211 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.18-py36h14c3975_1.tar.bz2 +md5 : 4de9d4f71722cde0ea2b48be6ddd19e4 +timestamp : 2019-05-13 11:47:35 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy >=1.16.3 + - python >=3.6,<3.7.0a0 + + +sorted_nearest 0.0.18 py37h14c3975_1 +------------------------------------ +file name : sorted_nearest-0.0.18-py37h14c3975_1.tar.bz2 +name : sorted_nearest +version : 0.0.18 +build : py37h14c3975_1 +build number: 1 +size : 211 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.18-py37h14c3975_1.tar.bz2 +md5 : 6487acd7f4a12beabe9c6f46c9a05b77 +timestamp : 2019-05-13 11:48:52 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy >=1.16.3 + - python >=3.7,<3.8.0a0 + + +sorted_nearest 0.0.19 py27h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.19-py27h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.19 +build : py27h3010b51_1 +build number: 1 +size : 207 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.19-py27h3010b51_1.tar.bz2 +md5 : 1de94e9d6a26f69a7f46ccbe38f04c18 +timestamp : 2019-05-14 11:46:39 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=2.7,<2.8.0a0 + + +sorted_nearest 0.0.19 py36h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.19-py36h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.19 +build : py36h3010b51_1 +build number: 1 +size : 211 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.19-py36h3010b51_1.tar.bz2 +md5 : ade025a55f7d6a0f8589fec1e82f2a52 +timestamp : 2019-05-14 11:45:30 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=3.6,<3.7.0a0 + + +sorted_nearest 0.0.19 py37h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.19-py37h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.19 +build : py37h3010b51_1 +build number: 1 +size : 211 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.19-py37h3010b51_1.tar.bz2 +md5 : e359e6c374aec6a750bebd31d1b41f65 +timestamp : 2019-05-14 11:44:09 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=3.7,<3.8.0a0 + + +sorted_nearest 0.0.20 py27h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.20-py27h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.20 +build : py27h3010b51_1 +build number: 1 +size : 207 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.20-py27h3010b51_1.tar.bz2 +md5 : a9994a18a84d8290b99553c0c9a4051a +timestamp : 2019-05-15 13:01:28 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=2.7,<2.8.0a0 + + +sorted_nearest 0.0.20 py36h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.20-py36h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.20 +build : py36h3010b51_1 +build number: 1 +size : 211 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.20-py36h3010b51_1.tar.bz2 +md5 : 3b660fbb859bf34eafde7489dd048737 +timestamp : 2019-05-15 13:00:14 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=3.6,<3.7.0a0 + + +sorted_nearest 0.0.20 py37h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.20-py37h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.20 +build : py37h3010b51_1 +build number: 1 +size : 211 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.20-py37h3010b51_1.tar.bz2 +md5 : a2ac8ddadbec4d1179213ebe03c4a15d +timestamp : 2019-05-15 13:02:56 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=3.7,<3.8.0a0 + + +sorted_nearest 0.0.22 py27h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.22-py27h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.22 +build : py27h3010b51_1 +build number: 1 +size : 532 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.22-py27h3010b51_1.tar.bz2 +md5 : db937478c8679ed41da1e826ad9a624a +timestamp : 2019-05-16 11:23:16 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=2.7,<2.8.0a0 + + +sorted_nearest 0.0.22 py36h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.22-py36h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.22 +build : py36h3010b51_1 +build number: 1 +size : 537 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.22-py36h3010b51_1.tar.bz2 +md5 : ddaf4a1fc54826900ae3a9f6b03984b1 +timestamp : 2019-05-16 11:21:55 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=3.6,<3.7.0a0 + + +sorted_nearest 0.0.22 py37h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.22-py37h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.22 +build : py37h3010b51_1 +build number: 1 +size : 535 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.22-py37h3010b51_1.tar.bz2 +md5 : 3c2111466349e2a2792939d63c34bf99 +timestamp : 2019-05-16 11:20:21 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=3.7,<3.8.0a0 + + +sorted_nearest 0.0.23 py27h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.23-py27h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.23 +build : py27h3010b51_1 +build number: 1 +size : 531 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.23-py27h3010b51_1.tar.bz2 +md5 : c6ee5d82c895b0fb3a3d5fccd8d3ddab +timestamp : 2019-05-28 10:54:20 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=2.7,<2.8.0a0 + + +sorted_nearest 0.0.23 py36h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.23-py36h3010b51_1.tar.bz2 +name : sorted_nearest +version : 0.0.23 +build : py36h3010b51_1 +build number: 1 +size : 534 KB +license : BSD +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sorted_nearest-0.0.23-py36h3010b51_1.tar.bz2 +md5 : 46d93c1714f5db06c40ddf50b5dbda7b +timestamp : 2019-05-28 10:57:40 UTC +dependencies: + - cython + - libgcc-ng >=7.3.0 + - numpy + - python >=3.6,<3.7.0a0 + + +sorted_nearest 0.0.23 py37h3010b51_1 +------------------------------------ +file name : sorted_nearest-0.0.23-py37h3010b51_1 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/spapros.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/spapros.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..d7fcfe270355a36541ddaa315737a44e366caaf1 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/spapros.manual_bundle.txt @@ -0,0 +1,105 @@ +# Tool: spapros +software_name: spapros +tier: T1 +domain: single_cell +downloads: 631 +summary: Probe set selection for targeted spatial transcriptomics. +description: Probe set selection for targeted spatial transcriptomics. +dependencies: bandit >=1.7.6, click >=8.0.1, jinja2 >=3.0.1, jupyter-sphinx >=0.3.2, leidenalg >=0.8.7, matplotlib-base >=3.6.3, nox >=2023.04.22, nox-poetry >=1.0.3, numpy <2, pandas >=2.0.0,<3.0.0, pandoc >=2.1, pillow >=10.0.2, python >=3.11,<3.14, pyyaml >=6.0.1, questionary >=1.10.0, rich >=10.1.0, ruamel.yaml >=0.17.10, scanpy >=1.9.8, seaborn-base >=0.11.1, upsetplot >=0.7.0, venndata >=0.1.0, xgboost >=1.6.1 +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://github.com/theislab/spapros +doc_url: https://spapros.readthedocs.io/en/latest +dev_url: https://github.com/theislab/spapros + +## URL Docs Extract +### https://spapros.readthedocs.io/en/latest +Welcome to spapros’s documentation! — spapros docs spapros 0.1.6 CONTENTS: Installation Usage API Tutorials Credits Contributor Covenant Code of Conduct spapros Welcome to spapros’s documentation! View page source Welcome to spapros’s documentation!  Spapros is a python package that provides a pipeline for probe set selection and evaluation for targeted spatial transcriptomics data. Key Features  Select probe sets for spatial transcriptomics which identify cell types of interest, capture general transcriptomic variation, and incorporate prior knowledge Evaluate probe sets with an extensive pipeline Indices and tables  Index Module Index Search Page Next © Copyright 2022, Lukas Heumos. Built with Sphinx using a theme provided by Read the Docs . + +### https://github.com/theislab/spapros +GitHub - theislab/spapros: Python package for Probe set selection for targeted spatial transcriptomics. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} theislab / spapros Public Notifications You must be signed in to change notification settings Fork 8 Star 48 Code Issues 10 Pull requests 9 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights theislab/spapros main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 645 Commits 645 Commits .github .github data data docs docs makefiles makefiles spapros spapros tests tests .bandit.yml .bandit.yml .cookietemple.yml .cookietemple.yml .darglint .darglint .editorconfig .editorconfig .flake8 .flake8 .gitattributes .gitattributes .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml .prettierignore .prettierignore .readthedocs.yml .readthedocs.yml CHANGELOG.rst CHANGELOG.rst CODE_OF_CONDUCT.rst CODE_OF_CONDUCT.rst Dockerfile Dockerfile LICENSE LICENSE Makefile Makefile README.md README.md codecov.yml codecov.yml cookietemple.cfg cookietemple.cfg noxfile.py noxfile.py poetry.lock poetry.lock pyproject.toml pyproject.toml requirements.txt requirements.txt requirements_dev.yaml requirements_dev.yaml View all files Repository files navigation README Contributing MIT license spapros Installation You can install spapros via pip from PyPI : pip install spapros Alternatively, you can install spapros using conda or mamba : mamba install -c bioconda spapros Usage Visit our documentation for installation, tutorials, examples and more. Overview Selecting the right gene set is critical for targeted spatial transcriptomics, where only a limited number of genes can be profiled in an experiment. To select the set of genes, typically a scRNA-seq reference is used. Based on such a reference Spapros aims to select a set of genes that simultaneously optimizes for cell type identification and transcriptional variation, while optionally ensuring compatibility with probe design requirements. Below you find A list of questions that guide your specific experimental design A short description of the selection pipeline A short overview of the gene set evaluation For more details see our paper , API documentation and tutorials . Experimental design questions Each experiment has a specific research question and potential experimental/budget constraints. These specificities should be considered in the experimental design. Typical questions that arise for the gene set selection are: Are you only interested in cell type identification (e.g. cell type proportions and niche compositions)? Or also in within-cell type variation? How many genes do you want to profile? Are you interested in a specific disease signature? Are there pre-selected genes that you want to profile? Are there cell types or signals that are expected in the spatial data but not in the scRNA-seq reference? How good are the cell type annotations in the scRNA-seq reference? Additionally, more technical questions that should be considered are: How many cell type clusters are there in the scRNA-seq reference? On which compute resources can you run the selection? I have multiple selected gene panels. How can I find out which one is the best? If you have additional experimental design questions, please don't hesitate to either open a github issue or contact us directly . Answers to these questions , to choose the most appropriate method and parameters for the probe set selection: Run the selection with n_pca_genes=0 (see e.g. Cell type classification only which refers to SpaprosCTo of our paper). Note that in this case less than n genes could be selected. If that happens, just run the selection multiple times (as done e.g. in Selection for high numbers of genes (>150) ). This refers to the default parameter setting of Spapros. In case of more than 150 genes, it's recommended to sequentially run the selection multiple times (see Selection for high numbers of genes (>150) ). While Spapros tries to capture general variation, your main focus might lie on a subtle disease signature. In this case, you can either define additional "diseased" cell type clusters or manually identify additional DE genes (e.g. per cell type) and add them as pre-selection (see Select a few additional genes ). You can use the preselected_genes argument to add a set of pre-selected genes (see Select a few additional genes ). This problem can not be solved by Spapros' selection on the scRNA-seq reference. Some literature genes must be added manually (or can be provided as a marker list, see Selection with curated marker list ). We highly recommend to use a well prepared scRNA-seq reference for the selection, to tailor the set of annotated cell types to the given research question. However, a selection on a generic leiden clustering will still capture the main variation in the dataset (in that case do not use n_pca_genes=0 ). The time and memory consumption of Spapros selections grow with the number of cell types. In case of > 100 cell type clusters, you might want to split the data into coarse cell type groups (e.g. immune cells vs. others) and run the selection separately on each group. We recommend to run Spapros on a node of a compute cluster. For the benchmarks in the paper we used 12 cpus and 64GB memory. With the Spapros package we provide an evaluation scheme to evaluate and compare gene sets (see Evaluation of gene sets and Advanced evaluation ). Selection pipeline Spapros is an end-to-end probe set selection pipeline. The pipeline performs optimized gene selection while optionally designing the probe sequence and accounting for technology-specific technical constraints. These aspects are considered jointly to deliver an optimal combinatorial probe set. If you are only interested in the gene panel selection jump to gene panel selection , otherwise the probe design and filter section is relevant. probe design and filter Note that the probe design component of Spapros is implemented in the oligo designer toolsuite package . Follow our tutorial on the end-to-end selection to run the probe design filter, the gene panel selection and the probe design (see End-to-end selection ). As a first step in the selection process, Spapros’ probe design component can be used to filter the full list of possible genes to exclude genes for which probes cannot be designed due to technology-specific technical constraints. These constraints include the availability of sufficient unique possible probe sequences, as well as sequence properties like GC-content and melting temperature requirements. Moreover, binding locations of the final probes for a given gene cannot overlap. Thus, we generate non-overlapping probe sets with optimal thermodynamic and sequence properties with a graph-based search algorithm. This probe design component supports a range of technologies, including SCRINSHOT, MERFISH, SeqFISH and HybISS, and is extensible to new technologies. Additionally, Spapros’ probe design filter can be used independently of the gene set selection process, making it compatible with other selection methods. gene panel selection For the gene panel selection, Spapros selects genes that describe the overall variation in the scRNA-seq reference using a PCA-based selection procedure on a pre-selection of highly variable genes. To ensure cell types can be recovered using the gene set, Spapros uses the PCA-selected genes to predict cell type labels using a binary classification tree for each cell type. The genes used in these trees represent candidate cell type marker genes, and the tree itself provides a combinatorial rule, describing how the cell types can be identified in the generated spatial transcriptomics data. To ensure that all user-defined cell types can be identified, Spapros compares the classification performance for each cell type to the performance of reference trees. These trees are generated via a custom approach that iteratively optimizes for classifying similar cell identities. In each iteration Spapros performs DE selections on critical cell type subsets and retrains the trees on the extended gene pool. If any discrepancy in performance is found with the DE trees (that represent the optimal performance target), Spapros iteratively adds DE genes to the list of possible genes to improve classification performance. Finally, genes are ranked based on their feature importance in classification trees to allow for a user-defined number of selected genes. To facilitate downstream analysis in studies that solely focus on detecting cell type frequencies, it may be of interest to select only genes for cell type recovery rather than detecting additional spatial signals. For this, we provide SpaprosCTo ( n_pca_genes=0 ), which exclusively utilizes DE trees for selection. technical constraints and prior knowledge To account for technical constraints of expression levels a smoothed multiplicative penalty kernel is applied to the scores of PCA and DE based selections. See our tutorial on expression constraints for more details. While Spapros can select and design probe sets using only a reference scRNA-seq dataset and a list of cell types as input, users can also add prior knowledge and constraints to bias the algorithm toward user-defined genes. See our tutorials on pre-selected genes and marker lists for more details. Gene set evaluation Spapros includes an evaluation suite to assess the quality of selected gene sets. Key metrics include: Variation recovery: Evaluating the preservation of fine and global transcriptional variation. Cell type recovery: Measuring how well the gene set distinguishes predefined cell types. Gene redundancy: Assessing the redundancy of the selected genes. Technical constraints: Ensuring adherence to design limitations, such as expression thresholds and probe sequence requirements. Note that this group is based on custom expression constraints (see Expression constraints ). The metrics of group 1 and 2 are aggregated into an overall performance score in our comparison tables. Based on the specific experimental design demands the most appropriate metric can be chosen. Find more details and discussion on the evaluations in our tutorials our paper and an overview of our plotting functions for visualizing the results . How to cite If you use Spapros in your research, please cite the following publication: Kuemmerle, L. B., Luecken, M. D., et al. (2024). Probe set selection for targeted spatial transcriptomics. Nature Methods . https://doi.org/10.1038/s41592-024-02496-z Credits This package was created with cookietemple using Cookiecutter based on Hypermodern Python Cookiecutter . About Python package for Probe set selection for targeted spatial transcriptomics. Resources Readme License MIT license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 48 stars Watchers 2 watching Forks 8 forks Report repository Releases 7 0.1.6 Latest Nov 8, 2025 + 6 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.1% Other 0.9% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/theislab/spapros +GitHub - theislab/spapros: Python package for Probe set selection for targeted spatial transcriptomics. · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} theislab / spapros Public Notifications You must be signed in to change notification settings Fork 8 Star 48 Code Issues 10 Pull requests 9 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights theislab/spapros main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 645 Commits 645 Commits .github .github data data docs docs makefiles makefiles spapros spapros tests tests .bandit.yml .bandit.yml .cookietemple.yml .cookietemple.yml .darglint .darglint .editorconfig .editorconfig .flake8 .flake8 .gitattributes .gitattributes .gitignore .gitignore .pre-commit-config.yaml .pre-commit-config.yaml .prettierignore .prettierignore .readthedocs.yml .readthedocs.yml CHANGELOG.rst CHANGELOG.rst CODE_OF_CONDUCT.rst CODE_OF_CONDUCT.rst Dockerfile Dockerfile LICENSE LICENSE Makefile Makefile README.md README.md codecov.yml codecov.yml cookietemple.cfg cookietemple.cfg noxfile.py noxfile.py poetry.lock poetry.lock pyproject.toml pyproject.toml requirements.txt requirements.txt requirements_dev.yaml requirements_dev.yaml View all files Repository files navigation README Contributing MIT license spapros Installation You can install spapros via pip from PyPI : pip install spapros Alternatively, you can install spapros using conda or mamba : mamba install -c bioconda spapros Usage Visit our documentation for installation, tutorials, examples and more. Overview Selecting the right gene set is critical for targeted spatial transcriptomics, where only a limited number of genes can be profiled in an experiment. To select the set of genes, typically a scRNA-seq reference is used. Based on such a reference Spapros aims to select a set of genes that simultaneously optimizes for cell type identification and transcriptional variation, while optionally ensuring compatibility with probe design requirements. Below you find A list of questions that guide your specific experimental design A short description of the selection pipeline A short overview of the gene set evaluation For more details see our paper , API documentation and tutorials . Experimental design questions Each experiment has a specific research question and potential experimental/budget constraints. These specificities should be considered in the experimental design. Typical questions that arise for the gene set selection are: Are you only interested in cell type identification (e.g. cell type proportions and niche compositions)? Or also in within-cell type variation? How many genes do you want to profile? Are you interested in a specific disease signature? Are there pre-selected genes that you want to profile? Are there cell types or signals that are expected in the spatial data but not in the scRNA-seq reference? How good are the cell type annotations in the scRNA-seq reference? Additionally, more technical questions that should be considered are: How many cell type clusters are there in the scRNA-seq reference? On which compute resources can you run the selection? I have multiple selected gene panels. How can I find out which one is the best? If you have additional experimental design questions, please don't hesitate to either open a github issue or contact us directly . Answers to these questions , to choose the most appropriate method and parameters for the probe set selection: Run the selection with n_pca_genes=0 (see e.g. Cell type classification only which refers to SpaprosCTo of our paper). Note that in this case less than n genes could be selected. If that happens, just run the selection multiple times (as done e.g. in Selection for high numbers of genes (>150) ). This refers to the default parameter setting of Spapros. In case of more than 150 genes, it's recommended to sequentially run the selection multiple times (see Selection for high numbers of genes (>150) ). While Spapros tries to capture general variation, your main focus might lie on a subtle disease signature. In this case, you can either define additional "diseased" cell type clusters or manually identify additional DE genes (e.g. per cell type) and add them as pre-selection (see Select a few additional genes ). You can use the preselected_genes argument to add a set of pre-selected genes (see Select a few additional genes ). This problem can not be solved by Spapros' selection on the scRNA-seq reference. Some literature genes must be added manually (or can be provided as a marker list, see Selection with curated marker list ). We highly recommend to use a well prepared scRNA-seq reference for the selection, to tailor the set of annotated cell types to the given research question. However, a selection on a generic leiden clustering will still capture the main variation in the dataset (in that case do not use n_pca_genes=0 ). The time and memory consumption of Spapros selections grow with the number of cell types. In case of > 100 cell type clusters, you might want to split the data into coarse cell type groups (e.g. immune cells vs. others) and run the selection separately on each group. We recommend to run Spapros on a node of a compute cluster. For the benchmarks in the paper we used 12 cpus and 64GB memory. With the Spapros package we provide an evaluation scheme to evaluate and compare gene sets (see Evaluation of gene sets and Advanced evaluation ). Selection pipeline Spapros is an end-to-end probe set selection pipeline. The pipeline performs optimized gene selection while optionally designing the probe sequence and accounting for technology-specific technical constraints. These aspects are considered jointly to deliver an optimal combinatorial probe set. If you are only interested in the gene panel selection jump to gene panel selection , otherwise the probe design and filter section is relevant. probe design and filter Note that the probe design component of Spapros is implemented in the oligo designer toolsuite package . Follow our tutorial on the end-to-end selection to run the probe design filter, the gene panel selection and the probe design (see End-to-end selection ). As a first step in the selection process, Spapros’ probe design component can be used to filter the full list of possible genes to exclude genes for which probes cannot be designed due to technology-specific technical constraints. These constraints include the availability of sufficient unique possible probe sequences, as well as sequence properties like GC-content and melting temperature requirements. Moreover, binding locations of the final probes for a given gene cannot overlap. Thus, we generate non-overlapping probe sets with optimal thermodynamic and sequence properties with a graph-based search algorithm. This probe design component supports a range of technologies, including SCRINSHOT, MERFISH, SeqFISH and HybISS, and is extensible to new technologies. Additionally, Spapros’ probe design filter can be used independently of the gene set selection process, making it compatible with other selection methods. gene panel selection For the gene panel selection, Spapros selects genes that describe the overall variation in the scRNA-seq reference using a PCA-based selection procedure on a pre-selection of highly variable genes. To ensure cell types can be recovered using the gene set, Spapros uses the PCA-selected genes to predict cell type labels using a binary classification tree for each cell type. The genes used in these trees represent candidate cell type marker genes, and the tree itself provides a combinatorial rule, describing how the cell types can be identified in the generated spatial transcriptomics data. To ensure that all user-defined cell types can be identified, Spapros compares the classification performance for each cell type to the performance of reference trees. These trees are generated via a custom approach that iteratively optimizes for classifying similar cell identities. In each iteration Spapros performs DE selections on critical cell type subsets and retrains the trees on the extended gene pool. If any discrepancy in performance is found with the DE trees (that represent the optimal performance target), Spapros iteratively adds DE genes to the list of possible genes to improve classification performance. Finally, genes are ranked based on their feature importance in classification trees to allow for a user-defined number of selected genes. To facilitate downstream analysis in studies that solely focus on detecting cell type frequencies, it may be of interest to select only genes for cell type recovery rather than detecting additional spatial signals. For this, we provide SpaprosCTo ( n_pca_genes=0 ), which exclusively utilizes DE trees for selection. technical constraints and prior knowledge To account for technical constraints of expression levels a smoothed multiplicative penalty kernel is applied to the scores of PCA and DE based selections. See our tutorial on expression constraints for more details. While Spapros can select and design probe sets using only a reference scRNA-seq dataset and a list of cell types as input, users can also add prior knowledge and constraints to bias the algorithm toward user-defined genes. See our tutorials on pre-selected genes and marker lists for more details. Gene set evaluation Spapros includes an evaluation suite to assess the quality of selected gene sets. Key metrics include: Variation recovery: Evaluating the preservation of fine and global transcriptional variation. Cell type recovery: Measuring how well the gene set distinguishes predefined cell types. Gene redundancy: Assessing the redundancy of the selected genes. Technical constraints: Ensuring adherence to design limitations, such as expression thresholds and probe sequence requirements. Note that this group is based on custom expression constraints (see Expression constraints ). The metrics of group 1 and 2 are aggregated into an overall performance score in our comparison tables. Based on the specific experimental design demands the most appropriate metric can be chosen. Find more details and discussion on the evaluations in our tutorials our paper and an overview of our plotting functions for visualizing the results . How to cite If you use Spapros in your research, please cite the following publication: Kuemmerle, L. B., Luecken, M. D., et al. (2024). Probe set selection for targeted spatial transcriptomics. Nature Methods . https://doi.org/10.1038/s41592-024-02496-z Credits This package was created with cookietemple using Cookiecutter based on Hypermodern Python Cookiecutter . About Python package for Probe set selection for targeted spatial transcriptomics. Resources Readme License MIT license Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 48 stars Watchers 2 watching Forks 8 forks Report repository Releases 7 0.1.6 Latest Nov 8, 2025 + 6 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.1% Other 0.9% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge spapros --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +spapros 0.1.5 pyhdfd78af_0 +-------------------------- +file name : spapros-0.1.5-pyhdfd78af_0.tar.bz2 +name : spapros +version : 0.1.5 +build : pyhdfd78af_0 +build number: 0 +size : 98 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/spapros-0.1.5-pyhdfd78af_0.tar.bz2 +md5 : 9e1c02b670c2a6ede5a9d43249d78949 +timestamp : 2024-06-20 10:17:11 UTC +dependencies: + - bandit >=1.7.6 + - click >=8.0.1 + - jinja2 >=3.0.1 + - jupyter-sphinx >=0.3.2 + - leidenalg >=0.8.7 + - matplotlib-base >=3.6.3 + - nox >=2023.04.22 + - nox-poetry >=1.0.3 + - numpy 1.26.4 + - pandas >=1.3.0,<2.0.0 + - pandoc >=2.1 + - pillow >=10.0.2 + - python >=3.9,<3.10 + - pyyaml >=6.0.1 + - questionary >=1.10.0 + - rich >=10.1.0 + - ruamel.yaml >=0.17.10 + - scanpy >=1.9.8 + - seaborn >=0.11.1 + - upsetplot >=0.7.0 + - venndata >=0.1.0 + - xgboost >=1.6.1 + + +spapros 0.1.6 pyhdfd78af_0 +-------------------------- +file name : spapros-0.1.6-pyhdfd78af_0.conda +name : spapros +version : 0.1.6 +build : pyhdfd78af_0 +build number: 0 +size : 105 KB +license : MIT +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/spapros-0.1.6-pyhdfd78af_0.conda +md5 : 387e528d4f9ddcff4b8b30735f3dba88 +timestamp : 2025-11-24 02:44:24 UTC +dependencies: + - bandit >=1.7.6 + - click >=8.0.1 + - jinja2 >=3.0.1 + - jupyter-sphinx >=0.3.2 + - leidenalg >=0.8.7 + - matplotlib-base >=3.6.3 + - nox >=2023.04.22 + - nox-poetry >=1.0.3 + - numpy <2 + - pandas >=2.0.0,<3.0.0 + - pandoc >=2.1 + - pillow >=10.0.2 + - python >=3.11,<3.14 + - pyyaml >=6.0.1 + - questionary >=1.10.0 + - rich >=10.1.0 + - ruamel.yaml >=0.17.10 + - scanpy >=1.9.8 + - seaborn-base >=0.11.1 + - upsetplot >=0.7.0 + - venndata >=0.1.0 + - xgboost >=1.6.1 diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sra-tools.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sra-tools.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf3c626bccef3bbd33577eef0dcd8a0579a7fb4a --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/sra-tools.manual_bundle.txt @@ -0,0 +1,501 @@ +# Tool: sra-tools +software_name: sra-tools +tier: T1 +domain: t1_backfill_overall +downloads: 620587 +summary: The SRA Toolkit and SDK from NCBI. +description: "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries +for using data in the INSDC Sequence Read Archives." +dependencies: ca-certificates, curl, ossuuid, perl, perl-uri, perl-xml-libxml +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/ncbi/sra-tools +doc_url: https://github.com/ncbi/sra-tools/wiki +dev_url: https://github.com/ncbi/sra-tools + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/ncbi/sra-tools/wiki +Home · ncbi/sra-tools Wiki · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} ncbi / sra-tools Public Notifications You must be signed in to change notification settings Fork 279 Star 1.3k Code Issues 21 Pull requests 9 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights Home Jump to bottom Andrew Klymenko edited this page Jul 15, 2024 · 46 revisions Welcome to the sra-tools wiki! For a full history of SRA Toolkit's changes, please refer to CHANGES.md . Toggle table of contents Pages 26 Loading Home Loading 01. Downloading SRA Toolkit Uh oh! There was an error while loading. Please reload this page . Loading 02. Installing SRA Toolkit Uh oh! There was an error while loading. Please reload this page . Loading 03. Quick Toolkit Configuration Uh oh! There was an error while loading. Please reload this page . Loading 04. Cloud Credentials Uh oh! There was an error while loading. Please reload this page . Loading 05. Toolkit Configuration Uh oh! There was an error while loading. Please reload this page . Loading 06. Connection Timeouts Uh oh! There was an error while loading. Please reload this page . Loading 07. Network Access Uh oh! There was an error while loading. Please reload this page . Loading 08. prefetch and fasterq dump Uh oh! There was an error while loading. Please reload this page . Loading 09. Downloading NGS SDK Uh oh! There was an error while loading. Please reload this page . Loading Avoid using ascp directly for downloads Uh oh! There was an error while loading. Please reload this page . Loading Building and Installing from Source Uh oh! There was an error while loading. Please reload this page . Loading Building from source : configure options explained Uh oh! There was an error while loading. Please reload this page . Loading Download On Demand Uh oh! There was an error while loading. Please reload this page . Loading FAQ Uh oh! There was an error while loading. Please reload this page . Loading Firewall and Routing Information Uh oh! There was an error while loading. Please reload this page . Loading First help on decryption dbGaP data Uh oh! There was an error while loading. Please reload this page . Loading HowTo: Access SRA Data Uh oh! There was an error while loading. Please reload this page . Loading HowTo: Binary Installation Uh oh! There was an error while loading. Please reload this page . Loading HowTo: convert BAM to cSRA Uh oh! There was an error while loading. Please reload this page . Loading HowTo: fasterq dump Uh oh! There was an error while loading. Please reload this page . Loading Network and Connection Errors Uh oh! There was an error while loading. Please reload this page . Loading Obsolete software Uh oh! There was an error while loading. Please reload this page . Loading Read Names Uh oh! There was an error while loading. Please reload this page . Loading SRA tools docker Uh oh! There was an error while loading. Please reload this page . Loading sratools driver tool Uh oh! There was an error while loading. Please reload this page . Show 11 more pages… Clone this wiki locally Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/ncbi/sra-tools +GitHub - ncbi/sra-tools: SRA Tools · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} ncbi / sra-tools Public Notifications You must be signed in to change notification settings Fork 279 Star 1.3k Code Issues 21 Pull requests 9 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights ncbi/sra-tools master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 8,201 Commits 8,201 Commits build build libs libs ngs ngs scripts scripts setup setup shared shared test test tools tools tools2 tools2 vdb-cache-less-experiment vdb-cache-less-experiment .gitattributes .gitattributes .gitignore .gitignore CHANGES.md CHANGES.md CMakeLists.txt CMakeLists.txt LICENSE LICENSE Makefile Makefile README-blastn README-blastn README-vdb-config README-vdb-config README.md README.md configure configure View all files Repository files navigation README License PUBLIC DOMAIN NOTICE National Center for Biotechnology Information This software/database is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the author's official duties as a United States Government employee and thus cannot be copyrighted. This software/database is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction. Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose. Please cite the author in any work or product based on this material. The NCBI SRA (Sequence Read Archive) Contact: email: sra@ncbi.nlm.nih.gov Download Visit our download page for pre-built binaries. Change Log Please check the CHANGES.md file for change history. SRA Toolkit complies with NCBI Web Policies Please visit our wiki for information on using, configuring, and building the toolkit. The SRA Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. March 25, 2026 : SRA Toolkit Release 3.4.1 This release updates release notes. It adds some release notes that were missed in 3.3.0 and 3.4.0. It contains no changes to functionality. March 17, 2026 : SRA Toolkit Release 3.4.0 Improved error messages and handling of invalid data in fasterq-dump. The cache-mgr utility has been retired and will no longer be updated. December 2, 2025 : SRA Toolkit Release 3.3.0 Reads longer than 65K are now supported by fasterq-dump. Added the Geneus and Salus platforms. Releases for all linux distributions are built using AlmaLinux 8 currently. There are versions labelled for invididual linux distributions that are tested and confirmed to build on those platforms. Javadocs for the SRA Toolkit and cache-mgr have been deprecated and will not be present in future releases. March 18, 2025 : SRA Toolkit Release 3.2.1 Fixed fasterq-dump crash when using WGS references. Fixed fasterq-dump failures when accessing runs via HTTP. Releases built on CentOS will no longer be provided. January 14, 2025 : SRA Toolkit Release 3.2.0 Restored function to list contents of cart files in prefetch. Prefetch will now print a phid in error message to aid in help desk ticket diagnotics. Builds will complete on machines without a static C++ library. CMake now permits building of individual targets. May 21, 2024 : SRA Toolkit Release 3.1.1 Improved prefetch error and information messages for users. Fixed errors and warnings when building on Windows. March 5, 2024 : SRA Toolkit Release 3.1.0 Using prefetch --eliminate-quals will now dowload SRA Lite data or report that a Lite version is not available. Reduced frequency of global timeouts for cloud users. vdb-validate will report an error if data (blob) checksums are missing. Added support for AlmaLinux. Fixed hanging on macOS and BSD. December 19, 2023 : SRA Toolkit Release 3.0.10 Fixed a bug in using JWT with some cloud storage. Added build support for arm64 processors. August 29, 2023 : SRA Toolkit 3.0.7 Updated vdb-config to improve AWS credential interface and usage by SRA Toolkit. Fixed a bug in AWS credentials with prefetch. Fixed a bug resulting in 'reference not found' messages for reference sequences stored inside a run. July 10, 2023 : SRA Toolkit 3.0.6 Prefetch now supports the latest GCP access tokens. Fixed a bug in vdb-config for Windows users. To ensure output of techinical reads, fasterq-dump will now automatically switch to --split-files mode if --include-technical option is used. May 9, 2023 : SRA Toolkit 3.0.5 Added support for PacBio to fasterq-dump. Added features to output reference sequences to fasterq-dump. Fixed a bug in dbGaP data access when using ngc files. January 3, 2023 : SRA Toolkit 3.0.3 Fixed a regression in sra-stat. December 12, 2022 : SRA Toolkit 3.0.2 Fixed 'buffer insufficient while converting string within text module' failure for prefetch on Mac. November 15, 2022 : SRA Toolkit 3.0.1 Removed interactive requirement to configure SRA Toolkit. Changes to the repository structure: To better serve disparate groups of users, the tools/ directory of the sra-tools repository is divided into several subdirectories: external/ - the tools that comprise the end user facing sra-toolkit. These are the tools that are installed on a toolkit user's machine. This is the default make target internal/ - the tools oriented towards the toolkit's developers and NCBI-internal users loaders/ - the tools used in archive loading pipelines, such as the NCBI SRA test-tools/ - the tools used in the NCBI-internal testing of the toolkit. The default 'make' command will now only build the external tools. To build other categories of tools, use these targets/flags: 'make all' - to build everything, including the test projects (located in sra-tools/test/) 'make BUILD_TOOLS_INTERNAL=ON' - to build the external and the internal tools 'make BUILD_TOOLS_LOADERS=ON' - to build the external tools and the loaders 'make BUILD_TOOLS_TEST_TOOLS=ON' - to build the external tools and the test tools 'make TOOLS_ONLY=ON' - to skip building the test projects The build flags shown above can be combined on the same command line, for instance 'make BUILD_TOOLS_LOADERS=ON BUILD_TOOLS_INTERNAL=ON TOOLS_ONLY=ON' will build everything except the test tools and the test projects. August 4, 2022 : Security Update Due to updated security at NCBI, versions of the SRA Toolkit 2.9.6 and older will no longer be able to connect to the NCBI data location service. We advise impacted users to update to the latest version of the SRA Toolkit. February 10, 2022 : SRA Toolkit 3.0.0 NCBI's SRA changed the source build system to use CMake in toolkit release 3.0.0. This change is an important step to improve developers' productivity as it provides unified cross platform access to support multiple build systems. This change affects developers building NCBI SRA tools from source. Old makefiles and build systems are no longer supported. This change also includes the structure of GitHub repositories, which underwent consolidation to provide an easier environment for building tools and libraries (NGS libs and dependencies are consolidated). Consolidation of NGS libraries and dependencies provides better usage scope isolation and makes building more straightforward. Affected repositories ncbi/ngs This repository is frozen. All future development will take place in GitHub repository ncbi/sra-tools (this repository), under subdirectory ngs/ . ncbi/ncbi-vdb This project's build system is based on CMake. The libraries providing access to SRA data in VDB format via the NGS API have moved to GitHub repository ncbi/sra-tools . Old (base URL: https://github.com/ncbi/ncbi-vdb ) New (base URL: https://github.com/ncbi/sra-tools ) libs/ngs ngs/ncbi/ngs libs/ngs-c++ ngs/ncbi/ngs-c++ libs/ngs-jni ngs/ncbi/ngs-jni libs/ngs-py ngs/ncbi/ngs-py libs/vdb-sqlite libs/vdb-sqlite test/ngs-java test/ngs-java test/ngs-python test/ngs-python ncbi/sra-tools (This repository) This project's build system is based on CMake. The project acquired some new components, as listed in the table above. October 25, 2021. SRA Toolkit 2.11.3: fixed a bug in fasterq-dump: fasta and fasta-unsorted parameters work correctly. October 7, 2021. SRA Toolkit 2.11.2: SRA data are now available either with full base quality scores (SRA Normalized Format), or with simplified quality scores (SRA Lite), depending on user preference. Both formats can be streamed on demand to the same filetypes (fastq, sam, etc.), so they are both compatible with existing workflows and applications that expect quality scores. However, the SRA Lite format is much smaller, enabling a reduction in storage footprint and data transfer times, allowing dumps to complete more rapidly. The SRA toolkit defaults to using the SRA Normalized Format that includes full, per-base quality scores, but users that do not require full base quality scores for their analysis can request the SRA Lite version to save time on their data transfers. To request the SRA Lite data when using the SRA toolkit, set the "Prefer SRA Lite files with simplified base quality scores" option on the main page of the toolkit configuration- this will instruct the tools to preferentially use the SRA Lite format when available (please be sure to use toolkit version 2.11.2 or later to access this feature). The quality scores generated from SRA Lite files will be the same for each base within a given read (quality = 30 or 3, depending on whether the Read Filter flag is set to 'pass' or 'reject'). Data in the SRA Normalized Format with full base quality scores will continue to have a .sra file extension, while the SRA Lite files have a .sralite file extension. For more information please see our data format page. August 17, 2021: SRA Toolkit 2.11.1. March 15, 2021: SRA Toolkit 2.11.0. December 16, 2020: SRA Toolkit 2.10.9. June 29, 2020: SRA Toolkit 2.10.8. May 20, 2020: SRA Toolkit 2.10.7. May 18, 2020: SRA Toolkit 2.10.6. April 1, 2020: SRA Toolkit 2.10.5. February 26, 2020: SRA Toolkit 2.10.4. February 18, 2020: SRA Toolkit 2.10.3. Release 2.10.2 of sra-tools provides access to all the public and controlled-access dbGaP of SRA in the AWS and GCP environments (Linux only for this release) . This vast archive's original submission format and SRA-formatted data can both be accessed and computed on these clouds, eliminating the need to download from NCBI FTP as well as improving performance. The prefetch tool also retrieves original submission files in addition to ETL data for public and controlled-access dbGaP data. With release 2.10.0 of sra-tools we have added cloud-native operation for AWS and GCP environments (Linux only for this release) , for use with the public SRA. prefetch is capable of retrieving original submission files in addition to ETL data. With release 2.9.1 of sra-tools we have finally made available the tool fasterq-dump , a replacement for the much older fastq-dump tool. As its name implies, it runs faster, and is better suited for large-scale conversion of SRA objects into FASTQ files that are common on sites with enough disk space for temporary files. fasterq-dump is multi-threaded and performs bulk joins in a way that improves performance as compared to fastq-dump , which performs joins on a per-record basis (and is single-threaded) . fastq-dump is still supported as it handles more corner cases than fasterq-dump , but it is likely to be deprecated in the future. You can get more information about fasterq-dump in our Wiki at https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump . About SRA Tools Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1.3k stars Watchers 53 watching Forks 279 forks Report repository Releases 75 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C 63.0% C++ 31.0% Perl 1.6% Python 1.3% Java 1.0% CMake 0.9% Other 1.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/ncbi/sra-tools +GitHub - ncbi/sra-tools: SRA Tools · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} ncbi / sra-tools Public Notifications You must be signed in to change notification settings Fork 279 Star 1.3k Code Issues 21 Pull requests 9 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights ncbi/sra-tools master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 8,201 Commits 8,201 Commits build build libs libs ngs ngs scripts scripts setup setup shared shared test test tools tools tools2 tools2 vdb-cache-less-experiment vdb-cache-less-experiment .gitattributes .gitattributes .gitignore .gitignore CHANGES.md CHANGES.md CMakeLists.txt CMakeLists.txt LICENSE LICENSE Makefile Makefile README-blastn README-blastn README-vdb-config README-vdb-config README.md README.md configure configure View all files Repository files navigation README License PUBLIC DOMAIN NOTICE National Center for Biotechnology Information This software/database is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the author's official duties as a United States Government employee and thus cannot be copyrighted. This software/database is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction. Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose. Please cite the author in any work or product based on this material. The NCBI SRA (Sequence Read Archive) Contact: email: sra@ncbi.nlm.nih.gov Download Visit our download page for pre-built binaries. Change Log Please check the CHANGES.md file for change history. SRA Toolkit complies with NCBI Web Policies Please visit our wiki for information on using, configuring, and building the toolkit. The SRA Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. March 25, 2026 : SRA Toolkit Release 3.4.1 This release updates release notes. It adds some release notes that were missed in 3.3.0 and 3.4.0. It contains no changes to functionality. March 17, 2026 : SRA Toolkit Release 3.4.0 Improved error messages and handling of invalid data in fasterq-dump. The cache-mgr utility has been retired and will no longer be updated. December 2, 2025 : SRA Toolkit Release 3.3.0 Reads longer than 65K are now supported by fasterq-dump. Added the Geneus and Salus platforms. Releases for all linux distributions are built using AlmaLinux 8 currently. There are versions labelled for invididual linux distributions that are tested and confirmed to build on those platforms. Javadocs for the SRA Toolkit and cache-mgr have been deprecated and will not be present in future releases. March 18, 2025 : SRA Toolkit Release 3.2.1 Fixed fasterq-dump crash when using WGS references. Fixed fasterq-dump failures when accessing runs via HTTP. Releases built on CentOS will no longer be provided. January 14, 2025 : SRA Toolkit Release 3.2.0 Restored function to list contents of cart files in prefetch. Prefetch will now print a phid in error message to aid in help desk ticket diagnotics. Builds will complete on machines without a static C++ library. CMake now permits building of individual targets. May 21, 2024 : SRA Toolkit Release 3.1.1 Improved prefetch error and information messages for users. Fixed errors and warnings when building on Windows. March 5, 2024 : SRA Toolkit Release 3.1.0 Using prefetch --eliminate-quals will now dowload SRA Lite data or report that a Lite version is not available. Reduced frequency of global timeouts for cloud users. vdb-validate will report an error if data (blob) checksums are missing. Added support for AlmaLinux. Fixed hanging on macOS and BSD. December 19, 2023 : SRA Toolkit Release 3.0.10 Fixed a bug in using JWT with some cloud storage. Added build support for arm64 processors. August 29, 2023 : SRA Toolkit 3.0.7 Updated vdb-config to improve AWS credential interface and usage by SRA Toolkit. Fixed a bug in AWS credentials with prefetch. Fixed a bug resulting in 'reference not found' messages for reference sequences stored inside a run. July 10, 2023 : SRA Toolkit 3.0.6 Prefetch now supports the latest GCP access tokens. Fixed a bug in vdb-config for Windows users. To ensure output of techinical reads, fasterq-dump will now automatically switch to --split-files mode if --include-technical option is used. May 9, 2023 : SRA Toolkit 3.0.5 Added support for PacBio to fasterq-dump. Added features to output reference sequences to fasterq-dump. Fixed a bug in dbGaP data access when using ngc files. January 3, 2023 : SRA Toolkit 3.0.3 Fixed a regression in sra-stat. December 12, 2022 : SRA Toolkit 3.0.2 Fixed 'buffer insufficient while converting string within text module' failure for prefetch on Mac. November 15, 2022 : SRA Toolkit 3.0.1 Removed interactive requirement to configure SRA Toolkit. Changes to the repository structure: To better serve disparate groups of users, the tools/ directory of the sra-tools repository is divided into several subdirectories: external/ - the tools that comprise the end user facing sra-toolkit. These are the tools that are installed on a toolkit user's machine. This is the default make target internal/ - the tools oriented towards the toolkit's developers and NCBI-internal users loaders/ - the tools used in archive loading pipelines, such as the NCBI SRA test-tools/ - the tools used in the NCBI-internal testing of the toolkit. The default 'make' command will now only build the external tools. To build other categories of tools, use these targets/flags: 'make all' - to build everything, including the test projects (located in sra-tools/test/) 'make BUILD_TOOLS_INTERNAL=ON' - to build the external and the internal tools 'make BUILD_TOOLS_LOADERS=ON' - to build the external tools and the loaders 'make BUILD_TOOLS_TEST_TOOLS=ON' - to build the external tools and the test tools 'make TOOLS_ONLY=ON' - to skip building the test projects The build flags shown above can be combined on the same command line, for instance 'make BUILD_TOOLS_LOADERS=ON BUILD_TOOLS_INTERNAL=ON TOOLS_ONLY=ON' will build everything except the test tools and the test projects. August 4, 2022 : Security Update Due to updated security at NCBI, versions of the SRA Toolkit 2.9.6 and older will no longer be able to connect to the NCBI data location service. We advise impacted users to update to the latest version of the SRA Toolkit. February 10, 2022 : SRA Toolkit 3.0.0 NCBI's SRA changed the source build system to use CMake in toolkit release 3.0.0. This change is an important step to improve developers' productivity as it provides unified cross platform access to support multiple build systems. This change affects developers building NCBI SRA tools from source. Old makefiles and build systems are no longer supported. This change also includes the structure of GitHub repositories, which underwent consolidation to provide an easier environment for building tools and libraries (NGS libs and dependencies are consolidated). Consolidation of NGS libraries and dependencies provides better usage scope isolation and makes building more straightforward. Affected repositories ncbi/ngs This repository is frozen. All future development will take place in GitHub repository ncbi/sra-tools (this repository), under subdirectory ngs/ . ncbi/ncbi-vdb This project's build system is based on CMake. The libraries providing access to SRA data in VDB format via the NGS API have moved to GitHub repository ncbi/sra-tools . Old (base URL: https://github.com/ncbi/ncbi-vdb ) New (base URL: https://github.com/ncbi/sra-tools ) libs/ngs ngs/ncbi/ngs libs/ngs-c++ ngs/ncbi/ngs-c++ libs/ngs-jni ngs/ncbi/ngs-jni libs/ngs-py ngs/ncbi/ngs-py libs/vdb-sqlite libs/vdb-sqlite test/ngs-java test/ngs-java test/ngs-python test/ngs-python ncbi/sra-tools (This repository) This project's build system is based on CMake. The project acquired some new components, as listed in the table above. October 25, 2021. SRA Toolkit 2.11.3: fixed a bug in fasterq-dump: fasta and fasta-unsorted parameters work correctly. October 7, 2021. SRA Toolkit 2.11.2: SRA data are now available either with full base quality scores (SRA Normalized Format), or with simplified quality scores (SRA Lite), depending on user preference. Both formats can be streamed on demand to the same filetypes (fastq, sam, etc.), so they are both compatible with existing workflows and applications that expect quality scores. However, the SRA Lite format is much smaller, enabling a reduction in storage footprint and data transfer times, allowing dumps to complete more rapidly. The SRA toolkit defaults to using the SRA Normalized Format that includes full, per-base quality scores, but users that do not require full base quality scores for their analysis can request the SRA Lite version to save time on their data transfers. To request the SRA Lite data when using the SRA toolkit, set the "Prefer SRA Lite files with simplified base quality scores" option on the main page of the toolkit configuration- this will instruct the tools to preferentially use the SRA Lite format when available (please be sure to use toolkit version 2.11.2 or later to access this feature). The quality scores generated from SRA Lite files will be the same for each base within a given read (quality = 30 or 3, depending on whether the Read Filter flag is set to 'pass' or 'reject'). Data in the SRA Normalized Format with full base quality scores will continue to have a .sra file extension, while the SRA Lite files have a .sralite file extension. For more information please see our data format page. August 17, 2021: SRA Toolkit 2.11.1. March 15, 2021: SRA Toolkit 2.11.0. December 16, 2020: SRA Toolkit 2.10.9. June 29, 2020: SRA Toolkit 2.10.8. May 20, 2020: SRA Toolkit 2.10.7. May 18, 2020: SRA Toolkit 2.10.6. April 1, 2020: SRA Toolkit 2.10.5. February 26, 2020: SRA Toolkit 2.10.4. February 18, 2020: SRA Toolkit 2.10.3. Release 2.10.2 of sra-tools provides access to all the public and controlled-access dbGaP of SRA in the AWS and GCP environments (Linux only for this release) . This vast archive's original submission format and SRA-formatted data can both be accessed and computed on these clouds, eliminating the need to download from NCBI FTP as well as improving performance. The prefetch tool also retrieves original submission files in addition to ETL data for public and controlled-access dbGaP data. With release 2.10.0 of sra-tools we have added cloud-native operation for AWS and GCP environments (Linux only for this release) , for use with the public SRA. prefetch is capable of retrieving original submission files in addition to ETL data. With release 2.9.1 of sra-tools we have finally made available the tool fasterq-dump , a replacement for the much older fastq-dump tool. As its name implies, it runs faster, and is better suited for large-scale conversion of SRA objects into FASTQ files that are common on sites with enough disk space for temporary files. fasterq-dump is multi-threaded and performs bulk joins in a way that improves performance as compared to fastq-dump , which performs joins on a per-record basis (and is single-threaded) . fastq-dump is still supported as it handles more corner cases than fasterq-dump , but it is likely to be deprecated in the future. You can get more information about fasterq-dump in our Wiki at https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump . About SRA Tools Resources Readme License View license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1.3k stars Watchers 53 watching Forks 279 forks Report repository Releases 75 tags Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C 63.0% C++ 31.0% Perl 1.6% Python 1.3% Java 1.0% CMake 0.9% Other 1.2% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge sra-tools --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +sra-tools 2.6.2 0 +----------------- +file name : sra-tools-2.6.2-0.tar.bz2 +name : sra-tools +version : 2.6.2 +build : 0 +build number: 0 +size : 89.6 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.6.2-0.tar.bz2 +md5 : a2b878a19f2212c9cb8b60b9a97eeb6a +dependencies: [] + + +sra-tools 2.6.3 0 +----------------- +file name : sra-tools-2.6.3-0.tar.bz2 +name : sra-tools +version : 2.6.3 +build : 0 +build number: 0 +size : 90.4 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.6.3-0.tar.bz2 +md5 : 7bb312bc06964bc27586721078e906f1 +dependencies: [] + + +sra-tools 2.7.0 0 +----------------- +file name : sra-tools-2.7.0-0.tar.bz2 +name : sra-tools +version : 2.7.0 +build : 0 +build number: 0 +size : 83.3 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.7.0-0.tar.bz2 +md5 : 1cb3039c7dacd83c949530b98987853a +dependencies: [] + + +sra-tools 2.8.0 0 +----------------- +file name : sra-tools-2.8.0-0.tar.bz2 +name : sra-tools +version : 2.8.0 +build : 0 +build number: 0 +size : 99.7 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.8.0-0.tar.bz2 +md5 : eadb3754e866d2259844e79fc16118e3 +dependencies: [] + + +sra-tools 2.8.1 0 +----------------- +file name : sra-tools-2.8.1-0.tar.bz2 +name : sra-tools +version : 2.8.1 +build : 0 +build number: 0 +size : 99.8 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.8.1-0.tar.bz2 +md5 : 8ad133be3965669006b15417bad2dc3b +dependencies: [] + + +sra-tools 2.8.2 0 +----------------- +file name : sra-tools-2.8.2-0.tar.bz2 +name : sra-tools +version : 2.8.2 +build : 0 +build number: 0 +size : 102.1 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.8.2-0.tar.bz2 +md5 : 7f8bcab69b2e9f9a87682dc0a68a2146 +dependencies: [] + + +sra-tools 2.8.2 h550f44e_1 +-------------------------- +file name : sra-tools-2.8.2-h550f44e_1.tar.bz2 +name : sra-tools +version : 2.8.2 +build : h550f44e_1 +build number: 1 +size : 101.8 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.8.2-h550f44e_1.tar.bz2 +md5 : 25019c2266fbeb66ee6e5e8bbe5802c2 +timestamp : 2018-06-16 17:29:25 UTC +dependencies: + - libgcc-ng >=4.9 + + +sra-tools 2.9.0 h470a237_1 +-------------------------- +file name : sra-tools-2.9.0-h470a237_1.tar.bz2 +name : sra-tools +version : 2.9.0 +build : h470a237_1 +build number: 1 +size : 37.3 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.9.0-h470a237_1.tar.bz2 +md5 : 5c85986a8127c2928a01d0f3b8cdd9ed +timestamp : 2018-06-19 20:17:07 UTC +dependencies: + - libgcc-ng >=4.9 + - ncbi-ngs-sdk + - ncbi-vdb + + +sra-tools 2.9.1 h470a237_0 +-------------------------- +file name : sra-tools-2.9.1-h470a237_0.tar.bz2 +name : sra-tools +version : 2.9.1 +build : h470a237_0 +build number: 0 +size : 36.8 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.9.1-h470a237_0.tar.bz2 +md5 : 6e1b0611f051684a67b8f264a6d061d3 +timestamp : 2018-06-26 15:19:04 UTC +dependencies: + - libgcc-ng >=4.9 + + +sra-tools 2.9.1_1 h470a237_0 +---------------------------- +file name : sra-tools-2.9.1_1-h470a237_0.tar.bz2 +name : sra-tools +version : 2.9.1_1 +build : h470a237_0 +build number: 0 +size : 38.0 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.9.1_1-h470a237_0.tar.bz2 +md5 : ed5f34daa4a75ebfd60c2a955b46bd8d +timestamp : 2018-07-02 23:13:52 UTC +dependencies: + - libgcc-ng >=4.9 + + +sra-tools 2.9.6 hf484d3e_0 +-------------------------- +file name : sra-tools-2.9.6-hf484d3e_0.tar.bz2 +name : sra-tools +version : 2.9.6 +build : hf484d3e_0 +build number: 0 +size : 45.1 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.9.6-hf484d3e_0.tar.bz2 +md5 : 010360b3ab732be603d3798b5d1bacc4 +timestamp : 2019-06-12 20:39:44 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + + +sra-tools 2.10.0 pl526he1b5a44_0 +-------------------------------- +file name : sra-tools-2.10.0-pl526he1b5a44_0.tar.bz2 +name : sra-tools +version : 2.10.0 +build : pl526he1b5a44_0 +build number: 0 +size : 47.3 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.10.0-pl526he1b5a44_0.tar.bz2 +md5 : 4fa63a77ca7de673be36c22791106fca +timestamp : 2019-08-21 06:49:44 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - ncbi-ngs-sdk + - perl >=5.26.2,<5.26.3.0a0 + - perl-uri + - perl-xml-libxml + + +sra-tools 2.10.1 pl526haddd2b5_0 +-------------------------------- +file name : sra-tools-2.10.1-pl526haddd2b5_0.tar.bz2 +name : sra-tools +version : 2.10.1 +build : pl526haddd2b5_0 +build number: 0 +size : 47.3 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.10.1-pl526haddd2b5_0.tar.bz2 +md5 : 5e5fa3072e60b4dd0c30d40147ea8921 +timestamp : 2019-12-19 12:51:24 UTC +dependencies: + - hdf5 >=1.10.5,<1.10.6.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - libxml2 >=2.9.10,<2.10.0a0 + - ncbi-ngs-sdk + - perl >=5.26.2,<5.26.3.0a0 + - perl-uri + - perl-xml-libxml + + +sra-tools 2.10.3 pl526haddd2b5_0 +-------------------------------- +file name : sra-tools-2.10.3-pl526haddd2b5_0.tar.bz2 +name : sra-tools +version : 2.10.3 +build : pl526haddd2b5_0 +build number: 0 +size : 50.8 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.10.3-pl526haddd2b5_0.tar.bz2 +md5 : 83339db179c7e656976bd83880c459cd +timestamp : 2020-03-02 17:37:57 UTC +dependencies: + - hdf5 >=1.10.5,<1.10.6.0a0 + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - libxml2 >=2.9.10,<2.10.0a0 + - ncbi-ngs-sdk + - perl >=5.26.2,<5.26.3.0a0 + - perl-uri + - perl-xml-libxml + + +sra-tools 2.10.7 pl526haddd2b5_0 +-------------------------------- +file name : sra-tools-2.10.7-pl526haddd2b5_0.tar.bz2 +name : sra-tools +version : 2.10.7 +build : pl526haddd2b5_0 +build number: 0 +size : 60.4 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.10.7-pl526haddd2b5_0.tar.bz2 +md5 : 767cd6c86662ac26fc0d4a16590e229e +timestamp : 2020-06-02 20:08:07 UTC +dependencies: + - hdf5 >=1.10.5,<1.10.6.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - libxml2 >=2.9.10,<2.10.0a0 + - ncbi-ngs-sdk + - ossuuid + - perl >=5.26.2,<5.26.3.0a0 + - perl-uri + - perl-xml-libxml + + +sra-tools 2.10.7 pl526haddd2b5_1 +-------------------------------- +file name : sra-tools-2.10.7-pl526haddd2b5_1.tar.bz2 +name : sra-tools +version : 2.10.7 +build : pl526haddd2b5_1 +build number: 1 +size : 60.3 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.10.7-pl526haddd2b5_1.tar.bz2 +md5 : 4849b9bd635c65678ba7862796e880cc +timestamp : 2020-06-02 21:34:03 UTC +dependencies: + - hdf5 >=1.10.5,<1.10.6.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - libxml2 >=2.9.10,<2.10.0a0 + - ncbi-ngs-sdk + - ossuuid + - perl >=5.26.2,<5.26.3.0a0 + - perl-uri + - perl-xml-libxml + + +sra-tools 2.10.7 pl526haddd2b5_2 +-------------------------------- +file name : sra-tools-2.10.7-pl526haddd2b5_2.tar.bz2 +name : sra-tools +version : 2.10.7 +build : pl526haddd2b5_2 +build number: 2 +size : 60.4 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.10.7-pl526haddd2b5_2.tar.bz2 +md5 : 1aa9fddef8b079cd57ff5a8e58b45da8 +timestamp : 2020-07-01 10:20:03 UTC +dependencies: + - curl + - hdf5 >=1.10.5,<1.10.6.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - libxml2 >=2.9.10,<2.10.0a0 + - ncbi-ngs-sdk + - ossuuid + - perl >=5.26.2,<5.26.3.0a0 + - perl-uri + - perl-xml-libxml + + +sra-tools 2.10.8 pl526haddd2b5_0 +-------------------------------- +file name : sra-tools-2.10.8-pl526haddd2b5_0.tar.bz2 +name : sra-tools +version : 2.10.8 +build : pl526haddd2b5_0 +build number: 0 +size : 60.5 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.10.8-pl526haddd2b5_0.tar.bz2 +md5 : 2f630479c7211345be24622b4bb9e621 +timestamp : 2020-07-02 21:13:14 UTC +dependencies: + - curl + - hdf5 >=1.10.5,<1.10.6.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - libxml2 >=2.9.10,<2.10.0a0 + - ncbi-ngs-sdk + - ossuuid + - perl >=5.26.2,<5.26.3.0a0 + - perl-uri + - perl-xml-libxml + + +sra-tools 2.10.9 pl526haddd2b5_0 +-------------------------------- +file name : sra-tools-2.10.9-pl526haddd2b5_0.tar.bz2 +name : sra-tools +version : 2.10.9 +build : pl526haddd2b5_0 +build number: 0 +size : 61.9 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.10.9-pl526haddd2b5_0.tar.bz2 +md5 : 533ad8f4100c1c714ab8e123d3384cb6 +timestamp : 2020-12-16 19:18:17 UTC +dependencies: + - curl + - hdf5 >=1.10.5,<1.10.6.0a0 + - libgcc-ng >=7.5.0 + - libstdcxx-ng >=7.5.0 + - libxml2 >=2.9.10,<2.10.0a0 + - ncbi-ngs-sdk + - ossuuid + - perl >=5.26.2,<5.26.3.0a0 + - perl-uri + - perl-xml-libxml + + +sra-tools 2.11.0 pl5262h314213e_0 +--------------------------------- +file name : sra-tools-2.11.0-pl5262h314213e_0.tar.bz2 +name : sra-tools +version : 2.11.0 +build : pl5262h314213e_0 +build number: 0 +size : 64.5 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.11.0-pl5262h314213e_0.tar.bz2 +md5 : 1c2d2b6dafa5fc5cc758392d5cca742e +timestamp : 2021-04-27 07:12:08 UTC +dependencies: + - ca-certificates + - curl + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - libxml2 >=2.9.10,<2.10.0a0 + - ncbi-ngs-sdk + - ossuuid + - perl >=5.26.2,<5.26.3.0a0 + - perl-uri + - perl-xml-libxml + + +sra-tools 2.11.0 pl5262h314213e_1 +--------------------------------- +file name : sra-tools-2.11.0-pl5262h314213e_1.tar.bz2 +name : sra-tools +version : 2.11.0 +build : pl5262h314213e_1 +build number: 1 +size : 64.6 MB +license : Public Domain +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.11.0-pl5262h314213e_1.tar.bz2 +md5 : cdb98fb37f739dceee16c72dd851abb8 +timestamp : 2021-11-10 19:35:38 UTC +dependencies: + - ca-certificates + - curl + - hdf5 >=1.10.6,<1.10.7.0a0 + - libgcc-ng >=9.4.0 + - libstdcxx-ng >=9.4.0 + - libxml2 >=2.9.12,<2.10.0a0 + - ncbi-ngs-sdk + - ossuuid diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/stacks.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/stacks.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b43713a96d97073814e94ce6627b2952168bdec --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/stacks.manual_bundle.txt @@ -0,0 +1,563 @@ +# Tool: stacks +software_name: stacks +tier: T1 +domain: t1_backfill_overall +downloads: 341460 +summary: Stacks is a software pipeline for building loci from short-read sequences. +description: Stacks is a software pipeline for building loci from short-read sequences. +dependencies: libgcc >=13, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, perl, perl-bioperl-core, perl-file-spec, perl-file-temp, perl-posix, python, r-base >=4, samtools, velvet, zlib +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://catchenlab.life.illinois.edu/stacks/ +doc_url: +dev_url: + +## CLI Help Source +rscript:--help +## CLI Help Content +$ conda run -n bioenv_r_bioc Rscript --help +[rc=127] + +Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + +ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error) + + +## URL Docs Extract +### https://catchenlab.life.illinois.edu/stacks/ +Stacks Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Download Stacks Version 2.68 Recent Changes [updated August 23, 2024] Stacks Pipeline Genetic Maps Stacks can be used to generate mappable markers from RAD-seq data. Thousands of markers can be generated from a single generation, F1 map as well as markers for traditional F2 and backcross designs. Stacks can export data to JoinMap, OneMap , or R/qtl. These data can be used for examining genomic structure as well as assembling genomic assemblies. Population Genomics Stacks can be used to identify SNPs within or among populations. Stacks provides tools to generate summary statistics and to compute population genetic measures such as F IS and π within populations and F ST between populations, allowing for genome scans. Data can be exported in VCF format and for use in programs such as STRUCTURE or GenePop . Data can also be exported for cline analysis in HZAR format . Any SNP dataset in VCF format can also be imported into the Stacks populations module. SNPs generated from re-sequencing or RNA-seq, among other methods, can now be filtered/smoothed in the same way RAD data can. Phylogenetics Stacks can export GBS/RAD data for phylogenetic analysis. Identified SNPs can be concatenated and exported in Phylip format; these SNPs can be specified as fixed within and variable among populations, or simply all variable sites (encoded in IUPAC notation ). Stacks can also export SNPs with their full flanking sequence -- the RAD locus. These data can be exported in Phylip format (either as concatenated or partitioned data) which can be fed into any standard phylogenetics package such as PhyML or RAxML . Getting started with Stacks Stacks Manual Stacks Version 1 Manual Frequently Asked Questions How should I cite the use of Stacks? What are the requirements to run Stacks? How do I optimize the various parameters in Stacks? Is there a protocol that I can follow for running Stacks? Are previous versions of Stacks available? Can Stacks perform gapped alignments within and among samples? Can Stacks handle double-digested data? How about combinatorial barcodes? more... Tutorials How do the major Stacks parameters control the de novo formation of stacks and loci? Pipeline components The Stacks pipeline is designed modularly to perform several different types of analyses. Programs listed under Raw Reads are used to clean and filter raw sequence data. Programs under Core represent the main Stacks pipeline — building loci (ustacks), creating a catalog of loci (cstacks, and matching samples back against the catalog (sstacks), transposing the data (tsv2bam), adding paired-end reads to the analysis and calling genotypes, and population genomics analysis. Programs under Execution Control will run the whole pipeline. Raw reads process_radtags process_shortreads clone_filter kmer_filter Core ustacks cstacks sstacks tsv2bam gstacks populations Execution control denovo_map.pl ref_map.pl Utility programs stacks-dist-extract stacks-integrate-alignments stacks-private-alleles The process_radtags program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the restriction enzyme cutsite are intact (correcting minor errors). Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct, the read is discarded. Reads that pass quality thresholds are demultiplexed if barcodes are supplied. The process_shortreads program performs the same task as process_radtags for fast cleaning of randomly sheared genomic or transcriptomic data. This program will trim reads that are below the quality threshold instead of discarding them, making it useful for genomic assembly or other analyses. The clone_filter program will take a set of reads and reduce them according to PCR clones. This is done by matching raw sequence or by referencing a set of random oligos that have been included in the sequence. The kmer_filter program allows paired or single-end reads to be filtered according to the number or rare or abundant kmers they contain. Useful for both RAD datasets as well as randomly sheared genomic or transcriptomic data. The ustacks program will take as input a set of short-read sequences and align them into exactly-matching stacks. Comparing the stacks it will form a set of loci and detect SNPs at each locus using a maximum likelihood framework. A catalog can be built from any set of samples processed by the ustacks program. It will create a set of consensus loci, merging alleles together. In the case of a genetic cross, a catalog would be constructed from the parents of the cross to create a set of all possible alleles expected in the progeny of the cross. Sets of stacks constructed by the ustacks program can be searched against a catalog produced by the cstacks program. In the case of a genetic map, stacks from the progeny would be matched against the catalog to determine which progeny contain which parental alleles. The tsv2bam program will transpose data so that it is oriented by locus, instead of by sample. In additon, if paired-ends are available, the program will pull in the set of paired reads that are associate with each single-end locus that was assembled de novo . The gstacks - For de novo analyses, this program will pull in paired-end reads, if available, assemble the paired-end contig and merge it with the single-end locus, align reads to the locus, and call SNPs. For reference-aligned analyses, this program will build loci from the single and paired-end reads that have been aligned and sorted. This populations program will compute population-level summary statistics such as π, F IS , and F ST . It can output site level SNP calls in VCF format and can also output SNPs for analysis in STRUCTURE or in Phylip format for phylogenetics analysis. The denovo_map.pl program executes each of the Stacks components to create a genetic linkage map, or to identify the alleles in a set of populations. The ref_map.pl program takes reference-aligned input data and executes each of the Stacks components, using the reference alignment to form stacks, and identifies alleles. It can be used in a genetic map of a set of populations. The load_radtags.pl program takes a set of data produced by either the denovo_map.pl or ref_map.pl progams (or produced by hand) and loads it into the database. This allows the data to be generated on one computer, but loaded from another. Or, for a database to be regenerated without re-executing the pipeline. The stacks-dist-extract script will pull data distributions from the log and distribs files produced by the Stacks component programs. The stacks-integrate-alignments script will take loci produced by the de novo pipeline, align them against a reference genome, and inject the alignment coordinates back into the de novo -produced data. The stacks-private-alleles script will extract private allele data from the populations program outputs and output useful summaries and prepare it for plotting. Implementation Stacks is implemented in C++, with some helper programs in Perl, and is parallelized using the OpenMP libraries. It will compile on GNU-based Linux systems or BSD-based Apple OS X systems. Stacks is released under the GNU GPL license . Stacks was developed by Julian Catchen < > and Nicolas Rochette < >, with contributions from Angel Amores < >, Paul Hohenlohe < >, and Bill Cresko < >. Mailing List Subscribe to the stacks-user mailing list for technical help, and to discuss the use and development of Stacks. Publications Here are a few publications that have used the Stacks pipeline for data analysis. These papers show a variety of uses for the Stacks pipeline. N. Rochette, A. Rivera‐Colón, and J. Catchen. Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics . Molecular Ecology , 28(21):4737-4754. 2019. [ reprint ] N. Rochette & J. Catchen. Deriving genotypes from RAD-seq short-read data using Stacks . Nature Protocols , 12:2640–2659, 2017. [ reprint ] J. Paris, J. Stevens, & J. Catchen. Lost in parameter space: a road map for Stacks . Methods in Ecology and Evolution , 8(10):1360-1373, 2017. [ reprint ] S. Bassham, J. Catchen, E. Lescak, F. von Hippel, W. Cresko. Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback . Genetics , 209:921-939, 2018. [ reprint ] J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics . Molecular Ecology , 22(11):3124-3140, 2013. [ reprint ] J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping loci de novo from short-read sequences . G3: Genes, Genomes, Genetics , 1:171-182, 2011. [ reprint ] A. Amores, J. Catchen, A. Ferrara, Q. Fontenot and J. Postlethwait. Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication . Genetics , 188:799–808, 2011. [ reprint ] P. Hohenlohe, S. Amish, J. Catchen, F. Allendorf, G. Luikart. RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow trout and westslope cutthroat trout . Molecular Ecology Resources , 11(s1):117-122, 2011. [ reprint ] K. Emerson, C. Merz, J. Catchen, P. Hohenlohe, W. Cresko, W. Bradshaw, C. Holzapfel. Resolving postglacial phylogeography using high-throughput sequencing . Proceedings of the National Academy of Science , 107(37):16196-200, 2010. [ reprint ] + +## Conda Search Info +$ conda search -c bioconda -c conda-forge stacks --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +stacks 1.37 0 +------------- +file name : stacks-1.37-0.tar.bz2 +name : stacks +version : 1.37 +build : 0 +build number: 0 +size : 11.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.37-0.tar.bz2 +md5 : a72b5603a821e13e406cd4631ba48aaa +dependencies: + - perl-threaded + + +stacks 1.37 1 +------------- +file name : stacks-1.37-1.tar.bz2 +name : stacks +version : 1.37 +build : 1 +build number: 1 +size : 11.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.37-1.tar.bz2 +md5 : 112ee220cee7d0110f145b8464deab7d +dependencies: + - libgcc + - perl-threaded + - velvet + + +stacks 1.37 h9a82719_4 +---------------------- +file name : stacks-1.37-h9a82719_4.tar.bz2 +name : stacks +version : 1.37 +build : h9a82719_4 +build number: 4 +size : 1021 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.37-h9a82719_4.tar.bz2 +md5 : f64df0ed7cdd4ae1004f2ebcdfc47129 +timestamp : 2021-03-25 01:28:19 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - perl + - velvet + - zlib >=1.2.11,<1.3.0a0 + + +stacks 1.37 ha92aebf_2 +---------------------- +file name : stacks-1.37-ha92aebf_2.tar.bz2 +name : stacks +version : 1.37 +build : ha92aebf_2 +build number: 2 +size : 2.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.37-ha92aebf_2.tar.bz2 +md5 : 65fe3577df9b9c4fc1bb51687ffc03bb +timestamp : 2018-07-06 16:47:00 UTC +dependencies: + - libgcc-ng >=4.9 + - perl + - velvet + - zlib >=1.2.11,<1.3.0a0 + + +stacks 1.37 hd03093a_5 +---------------------- +file name : stacks-1.37-hd03093a_5.tar.bz2 +name : stacks +version : 1.37 +build : hd03093a_5 +build number: 5 +size : 989 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.37-hd03093a_5.tar.bz2 +md5 : 3d37b46c2c860e56d2b67e51a1db6b60 +timestamp : 2022-02-22 23:49:26 UTC +dependencies: + - libgcc-ng >=10.3.0 + - libstdcxx-ng >=10.3.0 + - libzlib >=1.2.11,<1.3.0a0 + - perl + - velvet + - zlib >=1.2.11,<1.3.0a0 + + +stacks 1.37 he513fc3_3 +---------------------- +file name : stacks-1.37-he513fc3_3.tar.bz2 +name : stacks +version : 1.37 +build : he513fc3_3 +build number: 3 +size : 910 KB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.37-he513fc3_3.tar.bz2 +md5 : 9e46083eb904faf6dbe21d56e77c6836 +timestamp : 2019-10-26 12:48:30 UTC +dependencies: + - libgcc-ng >=7.3.0 + - libstdcxx-ng >=7.3.0 + - perl + - velvet + - zlib >=1.2.11,<1.3.0a0 + + +stacks 1.40 0 +------------- +file name : stacks-1.40-0.tar.bz2 +name : stacks +version : 1.40 +build : 0 +build number: 0 +size : 12.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.40-0.tar.bz2 +md5 : 2a42582481bff25d33960c80a7645109 +dependencies: + - libgcc + - perl-threaded + - velvet + - zlib + + +stacks 1.40 1 +------------- +file name : stacks-1.40-1.tar.bz2 +name : stacks +version : 1.40 +build : 1 +build number: 1 +size : 14.6 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.40-1.tar.bz2 +md5 : c5e3b9c0684a85a43e9a095e63678240 +dependencies: + - libgcc + - perl-threaded + - samtools 0.1.19 + - sparsehash + - velvet + - zlib + + +stacks 1.40 2 +------------- +file name : stacks-1.40-2.tar.bz2 +name : stacks +version : 1.40 +build : 2 +build number: 2 +size : 14.6 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.40-2.tar.bz2 +md5 : 12370e36b75c25eea83953397355b551 +dependencies: + - libgcc + - perl-threaded + - samtools 0.1.19 + - sparsehash + - velvet + - zlib 1.2.11* + + +stacks 1.40 pl5.22.0_3 +---------------------- +file name : stacks-1.40-pl5.22.0_3.tar.bz2 +name : stacks +version : 1.40 +build : pl5.22.0_3 +build number: 3 +size : 14.6 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.40-pl5.22.0_3.tar.bz2 +md5 : 53a3943a57f8934a1de3c57bb79a4c60 +dependencies: + - libgcc + - perl 5.22.0* + - samtools 0.1.19 + - sparsehash + - velvet + - zlib 1.2.11* + + +stacks 1.42 1 +------------- +file name : stacks-1.42-1.tar.bz2 +name : stacks +version : 1.42 +build : 1 +build number: 1 +size : 18.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.42-1.tar.bz2 +md5 : 6e6f8db734819800143966aaaeb71a7b +dependencies: + - libgcc + - perl-threaded + - sparsehash + - velvet + - zlib + + +stacks 1.42 2 +------------- +file name : stacks-1.42-2.tar.bz2 +name : stacks +version : 1.42 +build : 2 +build number: 2 +size : 18.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.42-2.tar.bz2 +md5 : 01a36463656e25d69cc6410e77372e89 +dependencies: + - libgcc + - perl-threaded + - sparsehash + - velvet + - zlib + + +stacks 1.42 3 +------------- +file name : stacks-1.42-3.tar.bz2 +name : stacks +version : 1.42 +build : 3 +build number: 3 +size : 18.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.42-3.tar.bz2 +md5 : 03a513db9e05bff62154cd9f32506e4e +dependencies: + - libgcc + - perl-threaded + - sparsehash + - velvet + - zlib + + +stacks 1.42 4 +------------- +file name : stacks-1.42-4.tar.bz2 +name : stacks +version : 1.42 +build : 4 +build number: 4 +size : 18.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.42-4.tar.bz2 +md5 : 585cf2008d958319d01715164e1c4fc2 +dependencies: + - libgcc + - perl-threaded + - sparsehash + - velvet + - zlib 1.2.11* + + +stacks 1.42 pl5.22.0_5 +---------------------- +file name : stacks-1.42-pl5.22.0_5.tar.bz2 +name : stacks +version : 1.42 +build : pl5.22.0_5 +build number: 5 +size : 18.4 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.42-pl5.22.0_5.tar.bz2 +md5 : f02907a7bb3625099cec8ecda920b596 +dependencies: + - libgcc + - perl 5.22.0* + - sparsehash + - velvet + - zlib 1.2.11* + + +stacks 1.43 0 +------------- +file name : stacks-1.43-0.tar.bz2 +name : stacks +version : 1.43 +build : 0 +build number: 0 +size : 18.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.43-0.tar.bz2 +md5 : 0b1d1fbb0f5d7fb9ef51df718cae3cb3 +dependencies: + - libgcc + - perl-threaded + - sparsehash + - velvet + - zlib + + +stacks 1.43 1 +------------- +file name : stacks-1.43-1.tar.bz2 +name : stacks +version : 1.43 +build : 1 +build number: 1 +size : 18.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.43-1.tar.bz2 +md5 : 14090c71555964ce72f329f0a1ad5dbb +dependencies: + - libgcc + - perl-threaded + - sparsehash + - velvet + - zlib 1.2.11* + + +stacks 1.43 pl5.22.0_2 +---------------------- +file name : stacks-1.43-pl5.22.0_2.tar.bz2 +name : stacks +version : 1.43 +build : pl5.22.0_2 +build number: 2 +size : 18.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.43-pl5.22.0_2.tar.bz2 +md5 : f6b598056e8bb36e561053e748b75fea +dependencies: + - libgcc + - perl 5.22.0* + - sparsehash + - velvet + - zlib 1.2.11* + + +stacks 1.44 0 +------------- +file name : stacks-1.44-0.tar.bz2 +name : stacks +version : 1.44 +build : 0 +build number: 0 +size : 18.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.44-0.tar.bz2 +md5 : bad2dda061c8d61039b2c6ba97cf7452 +dependencies: + - libgcc + - perl-threaded + - sparsehash + - velvet + - zlib + + +stacks 1.44 he941832_3 +---------------------- +file name : stacks-1.44-he941832_3.tar.bz2 +name : stacks +version : 1.44 +build : he941832_3 +build number: 3 +size : 5.2 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.44-he941832_3.tar.bz2 +md5 : 81079e214b7013026684e7a392895555 +timestamp : 2018-07-06 20:49:38 UTC +dependencies: + - libstdcxx-ng >=4.9 + - perl + - sparsehash + - velvet + - zlib >=1.2.11,<1.3.0a0 + + +stacks 1.44 pl5.22.0_1 +---------------------- +file name : stacks-1.44-pl5.22.0_1.tar.bz2 +name : stacks +version : 1.44 +build : pl5.22.0_1 +build number: 1 +size : 18.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.44-pl5.22.0_1.tar.bz2 +md5 : 97ca0cce2e44d5d9f135b70df07cf287 +dependencies: + - libgcc + - perl 5.22.0* + - sparsehash + - velvet + - zlib + + +stacks 1.44 pl5.22.0_2 +---------------------- +file name : stacks-1.44-pl5.22.0_2.tar.bz2 +name : stacks +version : 1.44 +build : pl5.22.0_2 +build number: 2 +size : 18.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.44-pl5.22.0_2.tar.bz2 +md5 : 529a57ef9b6055ee8b79d6002eedeedb +dependencies: + - libgcc + - perl 5.22.0* + - sparsehash + - velvet + - zlib 1.2.11* + + +stacks 1.46 boost1.61_1 +----------------------- +file name : stacks-1.46-boost1.61_1.tar.bz2 +name : stacks +version : 1.46 +build : boost1.61_1 +build number: 1 +size : 24.5 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.46-boost1.61_1.tar.bz2 +md5 : f6038b345742a1ff73f721bbcb3215f6 +dependencies: + - boost 1.61* + - libgcc + - perl 5.22.0* + - sparsehash + - velvet + - zlib + + +stacks 1.46 boost1.64_1 +----------------------- +file name : stacks-1.46-boost1.64_1.tar.bz2 +name : stacks +version : 1.46 +build : boost1.64_1 +build number: 1 +size : 24.6 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.46-boost1.64_1.tar.bz2 +md5 : bf6836252533c7645fa75e4a3f8d2a15 +dependencies: + - boost 1.64* + - libgcc + - perl 5.22.0* + - sparsehash + - velvet + - zlib + + +stacks 1.46 h9a82719_3 +---------------------- +file name : stacks-1.46-h9a82719_3.tar.bz2 +name : stacks +version : 1.46 +build : h9a82719_3 +build number: 3 +size : 5.2 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.46-h9a82719_3.tar.bz2 +md5 : 9f7d636f29343cf322037f19c0dde3b0 +timestamp : 2021-03-25 00:05:45 UTC +dependencies: + - libgcc-ng >=9.3.0 + - libstdcxx-ng >=9.3.0 + - openmp + - perl + - perl-bioperl-core + - perl-file-spec + - perl-file-temp + - perl-posix + - samtools + - sparsehash + - velvet + - zlib >=1.2.11,<1.3.0a0 + + +stacks 1.46 hd03093a_4 +---------------------- +file name : stacks-1.46-hd03093a_4.tar.bz2 +name : stacks +version : 1.46 +build : hd03093a_4 +build number: 4 +size : 5.0 MB +license : GPL +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stacks-1.46-hd03093a_4.tar.bz2 +md5 : 0dcabe0479be2aebdd990c8afb295808 +timestamp : 2022-02-22 23:31: diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/star-fusion.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/star-fusion.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ea969829cd8de841aa21c5e24af97027bf0eb63 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/star-fusion.manual_bundle.txt @@ -0,0 +1,597 @@ +# Tool: star-fusion +software_name: star-fusion +tier: T1 +domain: t1_backfill_overall +downloads: 448501 +summary: STAR-Fusion fusion variant caller. All dependencies required to run FusionInspector and FusionAnnotator are included. +description: STAR-Fusion fusion variant caller. All dependencies required to run FusionInspector and FusionAnnotator are included. +dependencies: bbmap, blast, bzip2, gmap, htslib, igv-reports, openssl, perl, perl-carp, perl-carp-assert, perl-db_file, perl-json-xs, perl-perlio-gzip, perl-set-intervaltree, perl-uri, python, samtools <1.10, star 2.7.11b, trinity <2.9 +execution_environment: Perl +execution_environment_reason: inferred from package/dependencies (Perl ecosystem) + +## URLs +home_url: https://github.com/STAR-Fusion/STAR-Fusion +doc_url: https://github.com/STAR-Fusion/STAR-Fusion/wiki +dev_url: https://github.com/STAR-Fusion/STAR-Fusion + +## CLI Help Source +perl:-h +## CLI Help Content +$ conda run -n bioenv_perl perl -h +[rc=0] + +Usage: perl [switches] [--] [programfile] [arguments] + -0[octal] specify record separator (\0, if no argument) + -a autosplit mode with -n or -p (splits $_ into @F) + -C[number/list] enables the listed Unicode features + -c check syntax only (runs BEGIN and CHECK blocks) + -d[:debugger] run program under debugger + -D[number/list] set debugging flags (argument is a bit mask or alphabets) + -e program one line of program (several -e's allowed, omit programfile) + -E program like -e, but enables all optional features + -f don't do $sitelib/sitecustomize.pl at startup + -F/pattern/ split() pattern for -a switch (//'s are optional) + -i[extension] edit <> files in place (makes backup if extension supplied) + -Idirectory specify @INC/#include directory (several -I's allowed) + -l[octal] enable line ending processing, specifies line terminator + -[mM][-]module execute "use/no module..." before executing program + -n assume "while (<>) { ... }" loop around program + -p assume loop like -n but print line also, like sed + -s enable rudimentary parsing for switches after programfile + -S look for programfile using PATH environment variable + -t enable tainting warnings + -T enable tainting checks + -u dump core after parsing program + -U allow unsafe operations + -v print version, patchlevel and license + -V[:variable] print configuration summary (or a single Config.pm variable) + -w enable many useful warnings + -W enable all warnings + -x[directory] ignore text before #!perl line (optionally cd to directory) + -X disable all warnings + +Run 'perldoc perl' for more help with Perl. + + + + +## URL Docs Extract +### https://github.com/STAR-Fusion/STAR-Fusion/wiki +Home · STAR-Fusion/STAR-Fusion Wiki · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} STAR-Fusion / STAR-Fusion Public Notifications You must be signed in to change notification settings Fork 84 Star 254 Code Issues 155 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights Home Jump to bottom Edit New page Brian Haas edited this page Aug 19, 2025 · 109 revisions Announcements: Interested in finding cancer mutations too? Checkout our companion CTAT Mutations Pipeline project . STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT) . STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. Our STAR-Fusion manuscript is published in Genome Biology https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1842-9 Obtaining and Installing STAR-Fusion See STAR-Fusion installation instructions wiki pages . Getting started A short tutorial is available. Running STAR-Fusion There are two ways to run STAR-Fusion. The typical case is that you're staring with FASTQ files. Alternatively, in the context of a more comprehensive transcriptome analysis pipeline leveraging STAR and the human genome from our CTAT genome lib, you may have a 'Chimeric.junction.out' file generated as one of the outputs from an earlier STAR alignment run. If so, you can 'kickstart' STAR-Fusion by using just this 'Chimeric.junction.out' file. These execution modes are detailed below: Running STAR-Fusion starting with FASTQ files (typical): Given paired-end of FASTQ files, run STAR-Fusion like so: STAR-Fusion --genome_lib_dir /path/to/your/CTAT_resource_lib \ --left_fq reads_1.fq \ --right_fq reads_2.fq \ --output_dir star_fusion_outdir If you have single-end FASTQ files, just use the --left_fq parameter: STAR-Fusion --genome_lib_dir /path/to/your/CTAT_resource_lib \ --left_fq reads_1.fq \ --output_dir star_fusion_outdir If you set the environmental variable 'CTAT_GENOME_LIB' to the '/path/to/your/ctat_genome_lib_build_dir' resulting from the above build process or from the plug-n-play installation, then you won't need to specify --genome_lib_dir as a STAR-Fusion parameter. Note, unless you have relatively long single-end reads (ex. at least 100 base length), you will be underpowered for detecting fusion transcripts. If you're running the STAR alignment as part of STAR-Fusion, then you'll need ~40G RAM available. The STAR-Fusion downstream processing doesn't require much RAM. Alternatively, Kickstart mode: running STAR yourself, and then running STAR-Fusion using the existing outputs It's not always the case that you want to have STAR-Fusion run STAR directly, as you may have already run STAR earlier on, or prefer to run STAR separately to use the outputs in other processes such as for expression estimates or variant detection. Parameters that we recommend for running STAR (as of STAR-v2.7.2a) as part of STAR-Fusion are as follows: STAR --genomeDir ${star_index_dir} \ --readFilesIn ${left_fq_filename} ${right_fq_filename} \ --outReadsUnmapped None \ --twopassMode Basic \ --readFilesCommand "gunzip -c" \ --outSAMstrandField intronMotif \ # include for potential use with StringTie for assembly --outSAMunmapped Within Note, the "--twopassMode Basic" setting leads to data-set dependent behavior - ie., if you subsample your reads, there's no guarantee you'll find the same fusion even if the fusion reads are in that subsample. For sample-independent performance, use "--twopassMode None" and including the following parameters that are relevant to fusion detection and STAR-Fusion execution: --chimSegmentMin 12 \ # ** essential to invoke chimeric read detection & reporting ** --chimJunctionOverhangMin 8 \ --chimOutJunctionFormat 1 \ # **essential** includes required metadata in Chimeric.junction.out file. --alignSJDBoverhangMin 10 \ --alignMatesGapMax 100000 \ # avoid readthru fusions within 100k --alignIntronMax 100000 \ --alignSJstitchMismatchNmax 5 -1 5 5 \ # settings improved certain chimera detections --outSAMattrRGline ID:GRPundef \ --chimMultimapScoreRange 3 \ --chimScoreJunctionNonGTAG -4 \ --chimMultimapNmax 20 \ --chimNonchimScoreDropMin 10 \ --peOverlapNbasesMin 12 \ --peOverlapMMp 0.1 \ --alignInsertionFlush Right \ --alignSplicedMateMapLminOverLmate 0 \ --alignSplicedMateMapLmin 30 Essential parameters for use with STAR-Fusion are indicted. Others are current settings used when the alignment is performed with STAR-Fusion. This will (in part) generate a file called 'Chimeric.out.junction', which is used by STAR-Fusion like so: STAR-Fusion --genome_lib_dir /path/to/your/CTAT_resource_lib \ -J Chimeric.out.junction \ --output_dir star_fusion_outdir Note, if you use this -J Chimeric.out.junction file, it is essential that the new '--chimOutJunctionFormat 1' parameter was used, since this integrates alignment statistics at the end of the junction file, which are used for estimating the FFPM fusion ~expression estimates. Output from STAR-Fusion The output from STAR-Fusion is found as a tab-delimited file named 'star-fusion.fusion_predictions.tsv', along with an abridged version that excludes the identification of the evidence fusion reads and called 'star-fusion.fusion_predictions.abridged.tsv', with the following format: #FusionName JunctionReadCount SpanningFragCount SpliceType LeftGene LeftBreakpoint RightGene RightBreakpoint LargeAnchorSupport FFPM LeftBreakDinuc LeftBreakEntropy RightBreakDinuc RightBreakEntropy annots THRA--AC090627.1 27 93 ONLY_REF_SPLICE THRA^ENSG00000126351.8 chr17:38243106:+ AC090627.1^ENSG00000235300.3 chr17:46371709:+ YES_LDAS 23875.8456 GT 1.8892 AG 1.9656 ["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr17:8.12Mb]"] THRA--AC090627.1 5 93 ONLY_REF_SPLICE THRA^ENSG00000126351.8 chr17:38243106:+ AC090627.1^ENSG00000235300.3 chr17:46384693:+ YES_LDAS 19498.6072 GT 1.8892 AG 1.4295 ["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr17:8.12Mb]"] ACACA--STAC2 12 52 ONLY_REF_SPLICE ACACA^ENSG00000132142.15 chr17:35479453:- STAC2^ENSG00000141750.6 chr17:37374426:- YES_LDAS 12733.7844 GT 1.9656 AG 1.9656 ["ChimerSeq","CCLE","Klijn_CellLines","FA_CancerSupp","INTRACHROMOSOMAL[chr17:1.60Mb]"] RPS6KB1--SNF8 10 43 ONLY_REF_SPLICE RPS6KB1^ENSG00000108443.9 chr17:57970686:+ SNF8^ENSG00000159210.5 chr17:47021337:- YES_LDAS 10545.1651 GT 1.3753 AG 1.8323 ["Klijn_CellLines","FA_CancerSupp","ChimerSeq","CCLE","INTRACHROMOSOMAL[chr17:10.95Mb]"] TOB1--SYNRG 8 30 ONLY_REF_SPLICE TOB1^ENSG00000141232.4 chr17:48943419:- SYNRG^ENSG00000006114.11 chr17:35880751:- YES_LDAS 7560.6844 GT 1.4566 AG 1.8892 ["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr17:12.97Mb]"] VAPB--IKZF3 4 46 ONLY_REF_SPLICE VAPB^ENSG00000124164.11 chr20:56964573:+ IKZF3^ENSG00000161405.12 chr17:37934020:- YES_LDAS 9948.269 GT 1.9656 AG 1.7819 ["FA_CancerSupp","Klijn_CellLines","CCLE","ChimerSeq","ChimerPub","INTERCHROMOSOMAL[chr20--chr17]"] ZMYND8--CEP250 2 44 ONLY_REF_SPLICE ZMYND8^ENSG00000101040.15 chr20:45852970:- CEP250^ENSG00000126001.11 chr20:34078463:+ NO_LDAS 9152.4075 GT 1.8295 AG 1.8062 ["FA_CancerSupp","CCLE","ChimerSeq","INTRACHROMOSOMAL[chr20:11.74Mb]"] AHCTF1--NAAA 3 38 ONLY_REF_SPLICE AHCTF1^ENSG00000153207.10 chr1:247094880:- NAAA^ENSG00000138744.10 chr4:76846964:- YES_LDAS 8157.5805 GT 1.7232 AG 1.8062 ["FA_CancerSupp","CCLE","INTERCHROMOSOMAL[chr1--chr4]"] VAPB--IKZF3 1 46 ONLY_REF_SPLICE VAPB^ENSG00000124164.11 chr20:56964573:+ IKZF3^ENSG00000161405.12 chr17:37922746:- NO_LDAS 9351.3729 GT 1.9656 AG 1.9329 ["FA_CancerSupp","Klijn_CellLines","CCLE","ChimerSeq","ChimerPub","INTERCHROMOSOMAL[chr20--chr17]"] VAPB--IKZF3 1 46 ONLY_REF_SPLICE VAPB^ENSG00000124164.11 chr20:56964573:+ IKZF3^ENSG00000161405.12 chr17:37944627:- NO_LDAS 9351.3729 GT 1.9656 AG 1.8892 ["FA_CancerSupp","Klijn_CellLines","CCLE","ChimerSeq","ChimerPub","INTERCHROMOSOMAL[chr20--chr17]"] STX16--RAE1 4 33 ONLY_REF_SPLICE STX16^ENSG00000124222.17 chr20:57227143:+ RAE1^ENSG00000101146.8 chr20:55929088:+ YES_LDAS 7361.719 GT 1.9899 AG 1.9656 ["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr20:1.27Mb]"] AHCTF1--NAAA 1 38 ONLY_REF_SPLICE AHCTF1^ENSG00000153207.10 chr1:247094431:- NAAA^ENSG00000138744.10 chr4:76846964:- NO_LDAS 7759.6498 GT 1.9086 AG 1.8062 ["FA_CancerSupp","CCLE","INTERCHROMOSOMAL[chr1--chr4]"] STX16-NPEPL1--RAE1 4 24 INCL_NON_REF_SPLICE STX16-NPEPL1^ENSG00000254995.4 chr20:57227143:+ RAE1^ENSG00000101146.8 chr20:55929088:+ YES_LDAS 5571.0306 GT 1.9899 AG 1.9656 INTRACHROMOSOMAL[chr20:1.27Mb] RAB22A--MYO9B 6 11 ONLY_REF_SPLICE RAB22A^ENSG00000124209.3 chr20:56886178:+ MYO9B^ENSG00000099331.9 chr19:17256207:+ YES_LDAS 3382.4115 GT 1.6895 AG 1.9656 ["FA_CancerSupp","ChimerSeq","CCLE","INTERCHROMOSOMAL[chr20--chr19]"] MED1--ACSF2 4 11 ONLY_REF_SPLICE MED1^ENSG00000125686.7 chr17:37595418:- ACSF2^ENSG00000167107.8 chr17:48548389:+ YES_LDAS 2984.4807 GT 1.9656 AG 1.9656 ["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr17:10.90Mb]"] MED13--BCAS3 2 12 ONLY_REF_SPLICE MED13^ENSG00000108510.5 chr17:60129898:- BCAS3^ENSG00000141376.16 chr17:59469338:+ YES_LDAS 2785.5154 GT 1.5546 AG 1.9086 ["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr17:0.55Mb]"] MED1--STXBP4 1 15 ONLY_REF_SPLICE MED1^ENSG00000125686.7 chr17:37607291:- STXBP4^ENSG00000166263.9 chr17:53218671:+ NO_LDAS 3183.4461 GT 1.3996 AG 1.7968 ["CCLE","FA_CancerSupp","Klijn_CellLines","INTRACHROMOSOMAL[chr17:15.44Mb]"] MED13--BCAS3 1 12 ONLY_REF_SPLICE MED13^ENSG00000108510.5 chr17:60129898:- BCAS3^ENSG00000141376.16 chr17:59465979:+ NO_LDAS 2586.55 GT 1.5546 AG 0.8366 ["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr17:0.55Mb]"] STARD3--DOK5 2 7 ONLY_REF_SPLICE STARD3^ENSG00000131748.11 chr17:37793484:+ DOK5^ENSG00000101134.7 chr20:53259997:+ NO_LDAS 1790.6885 GT 1.8892 AG 1.9656 ["FA_CancerSupp","CCLE","INTERCHROMOSOMAL[chr17--chr20]"] DIDO1--TTI1 1 10 ONLY_REF_SPLICE DIDO1^ENSG00000101191.12 chr20:61569148:- TTI1^ENSG00000101407.8 chr20:36642259:- NO_LDAS 2188.6192 GT 1.6402 AG 1.9329 ["FA_CancerSupp","ChimerSeq","CCLE","INTRACHROMOSOMAL[chr20:24.85Mb]"] DIDO1--TTI1 1 10 ONLY_REF_SPLICE DIDO1^ENSG00000101191.12 chr20:61569148:- TTI1^ENSG00000101407.8 chr20:36634799:- NO_LDAS 2188.6192 GT 1.6402 AG 1.8892 ["FA_CancerSupp","ChimerSeq","CCLE","INTRACHROMOSOMAL[chr20:24.85Mb]"] BRD4--RFX1 1 8 ONLY_REF_SPLICE BRD4^ENSG00000141867.13 chr19:15443101:- RFX1^ENSG00000132005.4 chr19:14109129:- NO_LDAS 1790.6884 GT 1.9086 AG 1.8892 ["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr19:1.23Mb]"] BRD4--RFX1 1 8 ONLY_REF_SPLICE BRD4^ENSG00000141867.13 chr19:15443101:- RFX1^ENSG00000132005.4 chr19:14094407:- NO_LDAS 1790.6884 GT 1.9086 AG 1.8295 ["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr19:1.23Mb]"] TRPC4AP--MRPL45 1 8 ONLY_REF_SPLICE TRPC4AP^ENSG00000100991.7 chr20:33665849:- MRPL45^ENSG00000174100.5 chr17:36478009:+ NO_LDAS 1790.6884 GT 1.6895 AG 1.9086 ["CCLE","Klijn_CellLines","FA_CancerSupp","INTERCHROMOSOMAL[chr20--chr17]"] The JunctionReads column indicates the number of RNA-Seq fragments containing a read that aligns as a split read at the site of the putative fusion junction. The SpanningFrags column indicates the number of RNA-Seq fragments that encompass the fusion junction such that one read of the pair aligns to a different gene than the other paired-end read of that fragment. Those predictions that have very few JunctionReads and/or SpanningReads are going to be enriched for false positives. Note, depending on the site of the fusion breakpoint and length of the reads, it may not be possible to have SpanningFragments and all evidence may show up in the form of JunctionReads. The breakpoints are formatted like so: 'chr17:38243106:+' indicating the chromosome, coordinate, and strand corresponding to the expressed transcript for each corresponding left or right side of the fusion transcript. The genomic strand should correspond to the transcribed orientation of the annotated gene from which that fusion part was derived. The number of fusion-supporting reads depends on both the expression of the fusion transcript and the number of reads sequenced. The deeper the sequenced data set, the greater the number of artifactual fusions that will appear with minimal supporting evidence, and so taking into account the sequencing depth is important to curtail overzealous prediction of fusion transcripts with ever-so-minimal supporting evidence. We provide normalized measures of the fusion-supporting rna-seq fragments as FFPM (fusion fragments per million total reads) measures. A filter of 0.1 sum FFPM (meaning at least 1 fusion-supporting rna-seq fragment per 10M total reads) tends to be effective at excluding fusion artifacts, and is the current default for filtering fusions from the final output. Adjust the 'STAR-Fusion --min_FFPM' parameter, or set it to zero to disable FFPM-based filtering. The 'LargeAnchorSupport' column indicates whether there are split reads that provide 'long' (set to length of 25 bases) alignments on both sides of the putative breakpoint. Those fusions supported only by split reads (no spanning fragments) and lack LargeAnchorSupport are often highly suspicious and tend to be false positives. Those with LargeAnchorSupport are labeled as 'YES_LDAS' (where LDAS = long double anchor support.... yes, more jargon). 'SpliceType' indicates whether the proposed breakpoint occurs at reference exon junctions as provided by the reference transcript structure annotations (ex. gencode). 'LeftBreakEntropy' and 'RightBreakEntropy' represent the Shannon entropy of the 15 exonic bases flanking the breakpoint. The maximum entropy is 2, representing highest complexity. The lowest would be zero (involving a 15 base mononucleotide run). Low entropy sites should generally be treated as less confident breakpoints. The abridged output file contents are shown above. See the unabridged 'star-fusion.fusion_predictions.tsv' output file for the identity of the RNA-Seq fragments identified as junction or spanning fragments, where the individual read names are provided as comma-delimited lists in each corresponding column. The final column 'annots' provides a simplified annotation for fusion transcript, leveraging FusionAnnotator (bundled with STAR-Fusion). For the human source or plug-n-play genome libs, the fusion annotation info is based on CTAT_HumanFusionLib , which includes many popular resources for annotating fusions known to be relevant to cancer, as well as fusions thought to be red herrings that will be automatically filtered from the final output. Rules for filtering out fusions based on annotations are encoded in a small Perl module found as '${CTAT_GENOME_LIB}/AnnotFilterRule.pm', and for the provided human genome lib involves excluding 'red herring' categories (described here - not a fish picture ;-) ) in addition to fusions involving mitochondrial genes or HLA loci (common artifacts). To exclude any annotation-based filtering, use the 'STAR-Fusion --no_annotation_filter' parameter. If there are alternatively spliced isoforms for fusion transcripts, the same fusion pair will be listed as multiple entries but with different breakpoints identified. Further Inspection, Visualization, and Validation? We have a companion tool called FusionInspector that provides a more in-depth view of the evidence supporting the predicted fusions. FusionInspector can also run Trinity to de novo reconstruct your predicted fusion transcripts based on the identified fusion-supporting RNA-Seq reads. As of STAR-Fusion v1.1.0, FusionInspector is integrated into STAR-Fusion as a submodule. FusionInspector can be run in either 'inspect' or 'validate' mode when executed downstream from STAR-Fusion: ' --FusionInspector inspect ': only the reads identified by STAR-Fusion as evidence supporting the fusion prediction are aligned directly to a target set of fusion-gene contigs for exploration using IGV. ' --FusionInspector validate ': involves a more rigorous process of reevaluating the entire set of input reads, aligning the reads to a combination of the reference genome and a set of fusion-gene contigs based on the STAR-Fusion predictions. Reads mapping better to the fusion-gene contigs than the reference genome are identified and reported, fusions are re-scored/quantified, and fusion transcript allelic fractions are computed. If either mode is invoked, STAR-Fusion will run FusionInspector and create a FusionInspector/ output subdirectory containing all relevant output files. See the FusionInspector Wiki for documentation on output files and loading results into IGV for visualization, or leveraging the html-based igv-reports. An example html-report interactive fusion visualization is shown below: Examine Effect of Fusions on Coding Regions It is sometimes the case that fusion transcripts generate novel fusion proteins with altered functions. You can further explore the impact of the fusion event on coding regions by invoking the '--examine_coding_effect' parameter. The coding effect results are appended as additional columns in the STAR-Fusion tab-delimited output file. An example set of columns include: #FusionName BCR--ABL1 ... CDS_LEFT_ID ENST00000305877.8 CDS_LEFT_RANGE 1-2782 CDS_RIGHT_ID ENST00000318560.5 CDS_RIGHT_RANGE 80-3393 PROT_FUSION_TYPE INFRAME FUSION_MODEL chr22|+|[0]23523148-23524426[0]|[1]23595986-23596167[2]|[0]23603137-23603241[2]|[0]23603542-23603727[2]|[0]23610595-23610702[2]|[0]236 + +### https://github.com/STAR-Fusion/STAR-Fusion +GitHub - STAR-Fusion/STAR-Fusion: STAR-Fusion codebase · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} STAR-Fusion / STAR-Fusion Public Notifications You must be signed in to change notification settings Fork 84 Star 254 Code Issues 155 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights STAR-Fusion/STAR-Fusion master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 693 Commits 693 Commits Docker Docker FusionAnnotator @ b261840 FusionAnnotator @ b261840 FusionFilter @ ff7ca33 FusionFilter @ ff7ca33 FusionInspector @ 3418788 FusionInspector @ 3418788 PerlLib PerlLib STAR-Fusion.github.io @ 4bb25fc STAR-Fusion.github.io @ 4bb25fc STAR-Fusion.wiki @ 9b7b28b STAR-Fusion.wiki @ 9b7b28b WDL WDL bioconda_recipe/ star-fusion bioconda_recipe/ star-fusion ctat-genome-lib-builder @ f557014 ctat-genome-lib-builder @ f557014 docs docs plugins plugins testing testing util util .dockstore.yml .dockstore.yml .gitmodules .gitmodules ChangeLog ChangeLog LICENSE LICENSE Makefile Makefile README.md README.md STAR-Fusion STAR-Fusion notes notes View all files Repository files navigation README BSD-3-Clause license STAR-Fusion Click the wiki link at top for the STAR-Fusion documentation. To download the software, click the 'Releases' tab and download the 'FULL'-labeled version. Note, if you're going to clone the code from github, do it recursively like so: git clone --recursive https://github.com/STAR-Fusion/STAR-Fusion.git About STAR-Fusion codebase Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 254 stars Watchers 15 watching Forks 84 forks Report repository Releases 39 STAR-Fusion-v1.15.1 Release Latest Jul 1, 2025 + 38 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 89.9% WDL 5.5% Python 2.6% Makefile 1.0% Shell 0.6% Dockerfile 0.3% R 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +### https://github.com/STAR-Fusion/STAR-Fusion +GitHub - STAR-Fusion/STAR-Fusion: STAR-Fusion codebase · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} STAR-Fusion / STAR-Fusion Public Notifications You must be signed in to change notification settings Fork 84 Star 254 Code Issues 155 Pull requests 0 Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Wiki Security and quality Insights STAR-Fusion/STAR-Fusion master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 693 Commits 693 Commits Docker Docker FusionAnnotator @ b261840 FusionAnnotator @ b261840 FusionFilter @ ff7ca33 FusionFilter @ ff7ca33 FusionInspector @ 3418788 FusionInspector @ 3418788 PerlLib PerlLib STAR-Fusion.github.io @ 4bb25fc STAR-Fusion.github.io @ 4bb25fc STAR-Fusion.wiki @ 9b7b28b STAR-Fusion.wiki @ 9b7b28b WDL WDL bioconda_recipe/ star-fusion bioconda_recipe/ star-fusion ctat-genome-lib-builder @ f557014 ctat-genome-lib-builder @ f557014 docs docs plugins plugins testing testing util util .dockstore.yml .dockstore.yml .gitmodules .gitmodules ChangeLog ChangeLog LICENSE LICENSE Makefile Makefile README.md README.md STAR-Fusion STAR-Fusion notes notes View all files Repository files navigation README BSD-3-Clause license STAR-Fusion Click the wiki link at top for the STAR-Fusion documentation. To download the software, click the 'Releases' tab and download the 'FULL'-labeled version. Note, if you're going to clone the code from github, do it recursively like so: git clone --recursive https://github.com/STAR-Fusion/STAR-Fusion.git About STAR-Fusion codebase Resources Readme License BSD-3-Clause license Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 254 stars Watchers 15 watching Forks 84 forks Report repository Releases 39 STAR-Fusion-v1.15.1 Release Latest Jul 1, 2025 + 38 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Perl 89.9% WDL 5.5% Python 2.6% Makefile 1.0% Shell 0.6% Dockerfile 0.3% R 0.1% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge star-fusion --info +[rc=0] +2 channel +Terms of +Service +accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done +star-fusion 0.4.0 pl5.18.2_0 +---------------------------- +file name : star-fusion-0.4.0-pl5.18.2_0.tar.bz2 +name : star-fusion +version : 0.4.0 +build : pl5.18.2_0 +build number: 0 +size : 232.8 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-0.4.0-pl5.18.2_0.tar.bz2 +md5 : 818c001e75e82065bf45aa7947bc7d2b +dependencies: + - blast + - perl 5.18.2* + - perl-db-file + - perl-set-intervaltree + + +star-fusion 0.5.3 pl5.18.2_0 +---------------------------- +file name : star-fusion-0.5.3-pl5.18.2_0.tar.bz2 +name : star-fusion +version : 0.5.3 +build : pl5.18.2_0 +build number: 0 +size : 640 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-0.5.3-pl5.18.2_0.tar.bz2 +md5 : ba3c2b6227453d9d1b295aafaa84e4dc +dependencies: + - blast + - perl 5.18.2* + - perl-db-file + - perl-set-intervaltree + + +star-fusion 0.5.3 pl5.22.0_0 +---------------------------- +file name : star-fusion-0.5.3-pl5.22.0_0.tar.bz2 +name : star-fusion +version : 0.5.3 +build : pl5.22.0_0 +build number: 0 +size : 640 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-0.5.3-pl5.22.0_0.tar.bz2 +md5 : 379c87e4a3bdf3216eaaa878aabf54f9 +dependencies: + - blast + - perl 5.22.0* + - perl-db-file + - perl-set-intervaltree + + +star-fusion 0.5.4 1 +------------------- +file name : star-fusion-0.5.4-1.tar.bz2 +name : star-fusion +version : 0.5.4 +build : 1 +build number: 1 +size : 644 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-0.5.4-1.tar.bz2 +md5 : 735726e9f227be18d25fd0e6642cd839 +dependencies: + - blast + - perl-db-file + - perl-set-intervaltree + - perl-threaded + - perl-uri + + +star-fusion 0.5.4 2 +------------------- +file name : star-fusion-0.5.4-2.tar.bz2 +name : star-fusion +version : 0.5.4 +build : 2 +build number: 2 +size : 645 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-0.5.4-2.tar.bz2 +md5 : 99b45d56afb0c635e2c14cf6e1cace11 +dependencies: + - blast + - bowtie + - gmap + - perl-db-file + - perl-set-intervaltree + - perl-threaded + - perl-uri + - star + + +star-fusion 0.5.4 pl5.22.0_0 +---------------------------- +file name : star-fusion-0.5.4-pl5.22.0_0.tar.bz2 +name : star-fusion +version : 0.5.4 +build : pl5.22.0_0 +build number: 0 +size : 644 KB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-0.5.4-pl5.22.0_0.tar.bz2 +md5 : c6fea56f1a3813c79ae948a2334b97c4 +dependencies: + - blast + - perl 5.22.0* + - perl-db-file + - perl-set-intervaltree + - perl-uri + + +star-fusion 0.7.0 1 +------------------- +file name : star-fusion-0.7.0-1.tar.bz2 +name : star-fusion +version : 0.7.0 +build : 1 +build number: 1 +size : 652 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-0.7.0-1.tar.bz2 +md5 : 09c4ce62d1ab407403352540cb73fee7 +timestamp : 2018-06-16 16:49:24 UTC +dependencies: + - blast + - bowtie + - gmap + - perl + - perl-db-file + - perl-set-intervaltree + - perl-uri + - star + + +star-fusion 0.7.0 pl5.22.0_0 +---------------------------- +file name : star-fusion-0.7.0-pl5.22.0_0.tar.bz2 +name : star-fusion +version : 0.7.0 +build : pl5.22.0_0 +build number: 0 +size : 651 KB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-0.7.0-pl5.22.0_0.tar.bz2 +md5 : 043b879ccfc63d62374995aec7f2bea4 +dependencies: + - blast + - bowtie + - gmap + - perl 5.22.0* + - perl-db-file + - perl-set-intervaltree + - perl-uri + - star + + +star-fusion 1.0.0 pl5.22.0_0 +---------------------------- +file name : star-fusion-1.0.0-pl5.22.0_0.tar.bz2 +name : star-fusion +version : 1.0.0 +build : pl5.22.0_0 +build number: 0 +size : 1.4 MB +license : MIT +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.0.0-pl5.22.0_0.tar.bz2 +md5 : 07ddd0882e60eec06d1adc1dbf982f59 +dependencies: + - blast + - bowtie + - gmap + - perl 5.22.0* + - perl-db-file + - perl-set-intervaltree + - perl-uri + - star + + +star-fusion 1.1.0 pl5.22.0_0 +---------------------------- +file name : star-fusion-1.1.0-pl5.22.0_0.tar.bz2 +name : star-fusion +version : 1.1.0 +build : pl5.22.0_0 +build number: 0 +size : 11.9 MB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.1.0-pl5.22.0_0.tar.bz2 +md5 : 82ef1d31727889944ab8bb3d1038e932 +dependencies: + - blast + - bowtie + - gmap + - perl 5.22.0* + - perl-db-file + - perl-set-intervaltree + - perl-uri + - star + + +star-fusion 1.2.0 pl5.22.0_0 +---------------------------- +file name : star-fusion-1.2.0-pl5.22.0_0.tar.bz2 +name : star-fusion +version : 1.2.0 +build : pl5.22.0_0 +build number: 0 +size : 12.0 MB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.2.0-pl5.22.0_0.tar.bz2 +md5 : 2719e1358c64f97043c6cda885736276 +dependencies: + - blast + - bowtie + - gmap + - perl 5.22.0* + - perl-db-file + - perl-set-intervaltree + - perl-uri + - star + + +star-fusion 1.3.2 pl5.22.0_0 +---------------------------- +file name : star-fusion-1.3.2-pl5.22.0_0.tar.bz2 +name : star-fusion +version : 1.3.2 +build : pl5.22.0_0 +build number: 0 +size : 12.2 MB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.3.2-pl5.22.0_0.tar.bz2 +md5 : df45655c0b6cbe7ea5699f7342e7309a +dependencies: + - blast + - bowtie + - gmap + - perl 5.22.0* + - perl-db-file + - perl-set-intervaltree + - perl-uri + - star + + +star-fusion 1.3.2 pl5.22.0_1 +---------------------------- +file name : star-fusion-1.3.2-pl5.22.0_1.tar.bz2 +name : star-fusion +version : 1.3.2 +build : pl5.22.0_1 +build number: 1 +size : 12.2 MB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.3.2-pl5.22.0_1.tar.bz2 +md5 : f3817890d5a7220e62e066e63012db55 +dependencies: + - blast + - bowtie + - gmap + - perl 5.22.0* + - perl-carp + - perl-db-file + - perl-io-gzip + - perl-json-xs + - perl-set-intervaltree + - perl-uri + - star + + +star-fusion 1.3.2 pl5.22.0_2 +---------------------------- +file name : star-fusion-1.3.2-pl5.22.0_2.tar.bz2 +name : star-fusion +version : 1.3.2 +build : pl5.22.0_2 +build number: 2 +size : 12.2 MB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.3.2-pl5.22.0_2.tar.bz2 +md5 : deb69208d92ed5f7e127370312fd4add +dependencies: + - blast + - bowtie + - gmap + - perl 5.22.0* + - perl-carp + - perl-db-file + - perl-io-gzip + - perl-json-xs + - perl-set-intervaltree + - perl-uri + - star <=2.5 + + +star-fusion 1.4.0 1 +------------------- +file name : star-fusion-1.4.0-1.tar.bz2 +name : star-fusion +version : 1.4.0 +build : 1 +build number: 1 +size : 12.2 MB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.4.0-1.tar.bz2 +md5 : f17061f97bed95e3b06aef4aa72e962f +timestamp : 2018-06-16 16:54:57 UTC +dependencies: + - blast + - bowtie + - gmap + - perl + - perl-carp + - perl-db-file + - perl-io-gzip + - perl-json-xs + - perl-set-intervaltree + - perl-uri + - star >2.5 + + +star-fusion 1.4.0 2 +------------------- +file name : star-fusion-1.4.0-2.tar.bz2 +name : star-fusion +version : 1.4.0 +build : 2 +build number: 2 +size : 12.2 MB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.4.0-2.tar.bz2 +md5 : 162fcbcdcf5cb78dc6a5858c744d507e +timestamp : 2018-07-04 08:37:39 UTC +dependencies: + - bbmap + - blast + - bowtie + - gmap + - perl + - perl-carp + - perl-db-file + - perl-io-gzip + - perl-json-xs + - perl-set-intervaltree + - perl-uri + - samtools + - star >2.5 + + +star-fusion 1.4.0 pl5.22.0_0 +---------------------------- +file name : star-fusion-1.4.0-pl5.22.0_0.tar.bz2 +name : star-fusion +version : 1.4.0 +build : pl5.22.0_0 +build number: 0 +size : 12.2 MB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.4.0-pl5.22.0_0.tar.bz2 +md5 : f53fcc78cfb9b9e09f21c659e29d6002 +dependencies: + - blast + - bowtie + - gmap + - perl 5.22.0* + - perl-carp + - perl-db-file + - perl-io-gzip + - perl-json-xs + - perl-set-intervaltree + - perl-uri + - star >2.5 + + +star-fusion 1.5.0 0 +------------------- +file name : star-fusion-1.5.0-0.tar.bz2 +name : star-fusion +version : 1.5.0 +build : 0 +build number: 0 +size : 7.7 MB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.5.0-0.tar.bz2 +md5 : 756a4cc73e8cf76067be99358d969a2e +timestamp : 2018-10-02 07:57:55 UTC +dependencies: + - bbmap + - blast + - bowtie + - gmap + - perl + - perl-carp + - perl-db-file + - perl-io-gzip + - perl-json-xs + - perl-set-intervaltree + - perl-uri + - samtools + - star >=2.6.1b + + +star-fusion 1.6.0 0 +------------------- +file name : star-fusion-1.6.0-0.tar.bz2 +name : star-fusion +version : 1.6.0 +build : 0 +build number: 0 +size : 8.1 MB +license : BSD-3-Clause +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-fusion-1.6.0-0.tar.bz2 +md5 : 0a987f3dc6f8037ac5b8b529b6fb5016 +timestamp : 2019-04-10 11:33:53 UTC +dependencies: + - bbmap + - blast + - bowtie + - gmap + - perl + - perl-carp + - perl-db-file + - perl-io-gzip + - perl-json-xs + - perl-set-intervaltree + - perl-uri + - samtools + - star >=2.7.0f + + +star-fusion 1.6.0 1 +------------------- +file name : star-fusion-1.6.0-1.tar.bz2 +name : star-fusion +version : 1.6.0 +build : 1 +build number: 1 +size : 7.7 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/star-fusion-1.6.0-1.tar.bz2 +md5 : ece799da43797faf25e26183bc90592f +timestamp : 2019-08-13 11:41:00 UTC +dependencies: + - bbmap + - blast + - bowtie + - gmap + - perl + - perl-carp + - perl-carp-assert + - perl-db-file + - perl-io-gzip + - perl-json-xs + - perl-set-intervaltree + - perl-uri + - samtools + - star >=2.7.0f + + +star-fusion 1.7.0 0 +------------------- +file name : star-fusion-1.7.0-0.tar.bz2 +name : star-fusion +version : 1.7.0 +build : 0 +build number: 0 +size : 9.0 MB +license : BSD-3-Clause +subdir : noarch +url : https://conda.anaconda.org/bioconda/noarch/star-fusion-1.7.0-0.tar.bz2 +md5 : 091ff79841744a1bc6def642a56bae6d +timestamp : 2019-08-17 21:33:28 UTC +dependencies: + - bbmap + - blast + - bowtie + - gmap + - perl + - perl-carp + - perl-carp-assert + - perl-db-file + - perl-io-gzip + - perl-json-xs + - perl-set-intervaltree + - perl-uri + - samtools + - star >=2.7.0f + + +star-fusion 1.7.0 1 +------------------- +file name : star-fusion-1.7.0-1.tar.bz2 +name : star-fusion +version : 1.7.0 +build : 1 +build number: 1 +size : 9.5 MB +license : BSD-3-Clause +subdir : noarch +url : diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/star.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/star.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..8ce4392ab0c521ab1523265186bdda0a0898ecec --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/star.manual_bundle.txt @@ -0,0 +1,505 @@ +# Tool: star +software_name: star +tier: T1 +domain: t1_backfill_overall +downloads: 1589721 +summary: An RNA-seq read aligner. +description: An RNA-seq read aligner. +dependencies: _openmp_mutex >=4.5, htslib >=1.21, htslib >=1.22.1,<1.24.0a0, libgcc >=13, libgomp, libstdcxx >=13, libzlib >=1.3.1,<2.0a0 +execution_environment: Compiled +execution_environment_reason: inferred from native/compiled dependencies + +## URLs +home_url: https://github.com/alexdobin/STAR +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/alexdobin/STAR +GitHub - alexdobin/STAR: RNA-seq aligner · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} alexdobin / STAR Public Notifications You must be signed in to change notification settings Fork 546 Star 2.2k Code Issues 973 Pull requests 17 Discussions Actions Projects Wiki Security and quality 0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Wiki Security and quality Insights alexdobin/STAR master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,210 Commits 1,210 Commits bin bin doc doc docs docs extras extras source source .gitignore .gitignore .gitmodules .gitmodules .travis.yml .travis.yml CHANGES.md CHANGES.md CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE README.md README.md RELEASEnotes.md RELEASEnotes.md _config.yml _config.yml View all files Repository files navigation README Code of conduct Contributing MIT license STAR 2.7.11b Spliced Transcripts Alignment to a Reference © Alexander Dobin, 2009-2024 https://www.ncbi.nlm.nih.gov/pubmed/23104886 AUTHOR/SUPPORT Alex Dobin, dobin@cshl.edu https://github.com/alexdobin/STAR/issues https://groups.google.com/d/forum/rna-star HARDWARE/SOFTWARE REQUIREMENTS x86-64 compatible processors 64 bit Linux or Mac OS X MANUAL https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf RELEASEnotes contains detailed information about the latest major release CHANGES contains detailed information about all the changes in all releases DIRECTORY CONTENTS source: all source files required for compilation bin: pre-compiled executables for Linux and Mac OS X doc: documentation extras: miscellaneous files and scripts COMPILING FROM SOURCE Download the latest release from and uncompress it # Get latest STAR source from releases wget https://github.com/alexdobin/STAR/archive/2.7.11b.tar.gz tar -xzf 2.7.11b.tar.gz cd STAR-2.7.11b # Alternatively, get STAR source using git git clone https://github.com/alexdobin/STAR.git Compile under Linux # Compile cd STAR/source make STAR For processors that do not support AVX extensions, specify the target SIMD architecture, e.g. make STAR CXXFLAGS_SIMD=sse Compile under Mac OS X # 1. Install brew (http://brew.sh/) # 2. Install gcc with brew: $ brew install gcc # 3. Build STAR: # run 'make' in the source directory # note that the path to c++ executable has to be adjusted to its current version $cd source $make STARforMacStatic CXX=/usr/local/Cellar/gcc/8.2.0/bin/g++-8 # 4. Make it availible through the terminal $cp STAR /usr/local/bin All platforms - non-standard gcc If g++ compiler (true g++, not Clang sym-link) is not on the path, you will need to tell make where to find it: cd source make STARforMacStatic CXX=/path/to/gcc If employing STAR only on a single machine or a homogeneously setup cluster, you may aim at helping the compiler to optimize in way that is tailored to your platform. The flags LDFLAGSextra and CXXFLAGSextra are appended to the default optimizations specified in source/Makefile. # platform-specific optimization for gcc/g++ make CXXFLAGSextra=-march=native # together with link-time optimization make LDFLAGSextra=-flto CXXFLAGSextra="-flto -march=native" FreeBSD ports STAR can be installed on FreeBSD via the FreeBSD ports system. To install via the binary package, simply run: pkg install star LIMITATIONS This release was tested with the default parameters for human and mouse genomes. Mammal genomes require at least 16GB of RAM, ideally 32GB. Please contact the author for a list of recommended parameters for much larger or much smaller genomes. FUNDING The development of STAR is supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number R01HG009318. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. About RNA-seq aligner Resources Readme License MIT license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Stars 2.2k stars Watchers 83 watching Forks 546 forks Report repository Releases 56 STAR 2.7.11b --- 2024/01/24 ::: Minor in one parameter. Latest Jan 26, 2024 + 55 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages C 62.8% C++ 32.3% TeX 3.2% Makefile 0.7% Awk 0.7% Roff 0.3% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge star --info +[rc=0] +2 channel Terms of +Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done +star 2.4.0j 0 +------------- +file name : star-2.4.0j-0.tar.bz2 +name : star +version : 2.4.0j +build : 0 +build number: 0 +size : 1.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.4.0j-0.tar.bz2 +md5 : 942996eebffb08dfc65ef8bac35478f5 +dependencies: [] + + +star 2.4.0j 1 +------------- +file name : star-2.4.0j-1.tar.bz2 +name : star +version : 2.4.0j +build : 1 +build number: 1 +size : 1.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.4.0j-1.tar.bz2 +md5 : bef0fd3c631fb8b056e27726fe0497fc +timestamp : 2018-06-16 17:02:19 UTC +dependencies: [] + + +star 2.4.0j h9ee0642_2 +---------------------- +file name : star-2.4.0j-h9ee0642_2.tar.bz2 +name : star +version : 2.4.0j +build : h9ee0642_2 +build number: 2 +size : 1.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.4.0j-h9ee0642_2.tar.bz2 +md5 : 53af8f2991fe489cbadfae2a422da11a +timestamp : 2021-03-26 15:32:54 UTC +dependencies: [] + + +star 2.4.2a 0 +------------- +file name : star-2.4.2a-0.tar.bz2 +name : star +version : 2.4.2a +build : 0 +build number: 0 +size : 2.6 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.4.2a-0.tar.bz2 +md5 : 544f9aa1c4954888bda958394ea86a3c +dependencies: [] + + +star 2.5.0a 0 +------------- +file name : star-2.5.0a-0.tar.bz2 +name : star +version : 2.5.0a +build : 0 +build number: 0 +size : 5.5 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.5.0a-0.tar.bz2 +md5 : 37088c5ca187d460d4a8a0b062ba6c90 +dependencies: [] + + +star 2.5.0b 0 +------------- +file name : star-2.5.0b-0.tar.bz2 +name : star +version : 2.5.0b +build : 0 +build number: 0 +size : 5.5 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.5.0b-0.tar.bz2 +md5 : ff9d7c972049011cdbed8ad798cf6230 +dependencies: [] + + +star 2.5.0c 0 +------------- +file name : star-2.5.0c-0.tar.bz2 +name : star +version : 2.5.0c +build : 0 +build number: 0 +size : 5.5 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.5.0c-0.tar.bz2 +md5 : a5c5cb1f26dea3c24a45eb4f8260bbb1 +dependencies: [] + + +star 2.5.1b 0 +------------- +file name : star-2.5.1b-0.tar.bz2 +name : star +version : 2.5.1b +build : 0 +build number: 0 +size : 7.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.5.1b-0.tar.bz2 +md5 : 24ab49dcf16c6a6ae73e69d57f46c604 +dependencies: [] + + +star 2.5.2a 0 +------------- +file name : star-2.5.2a-0.tar.bz2 +name : star +version : 2.5.2a +build : 0 +build number: 0 +size : 5.5 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.5.2a-0.tar.bz2 +md5 : 38605f26c473de9fd442ab177f774a0c +dependencies: [] + + +star 2.5.2b 0 +------------- +file name : star-2.5.2b-0.tar.bz2 +name : star +version : 2.5.2b +build : 0 +build number: 0 +size : 5.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.5.2b-0.tar.bz2 +md5 : 61ff72e5366d8ce590cebedddc7846d7 +dependencies: [] + + +star 2.5.3a 0 +------------- +file name : star-2.5.3a-0.tar.bz2 +name : star +version : 2.5.3a +build : 0 +build number: 0 +size : 5.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.5.3a-0.tar.bz2 +md5 : 13b7d44c462a3ba622407dfaf59c02ec +dependencies: [] + + +star 2.5.4a 0 +------------- +file name : star-2.5.4a-0.tar.bz2 +name : star +version : 2.5.4a +build : 0 +build number: 0 +size : 5.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.5.4a-0.tar.bz2 +md5 : 410cffc23afd60bca6b5197b7a0557d2 +dependencies: [] + + +star 2.6.0b 0 +------------- +file name : star-2.6.0b-0.tar.bz2 +name : star +version : 2.6.0b +build : 0 +build number: 0 +size : 5.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.6.0b-0.tar.bz2 +md5 : f5fc99184e1b512db81cf5bb26d9307d +dependencies: [] + + +star 2.6.0c 0 +------------- +file name : star-2.6.0c-0.tar.bz2 +name : star +version : 2.6.0c +build : 0 +build number: 0 +size : 5.7 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.6.0c-0.tar.bz2 +md5 : 986bed68e216e431dff50668c0805985 +dependencies: [] + + +star 2.6.0c 1 +------------- +file name : star-2.6.0c-1.tar.bz2 +name : star +version : 2.6.0c +build : 1 +build number: 1 +size : 5.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.6.0c-1.tar.bz2 +md5 : afa86e13f56d11fe79fc8b41c74dbcae +timestamp : 2018-06-16 17:00:29 UTC +dependencies: [] + + +star 2.6.0c 2 +------------- +file name : star-2.6.0c-2.tar.bz2 +name : star +version : 2.6.0c +build : 2 +build number: 2 +size : 5.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.6.0c-2.tar.bz2 +md5 : 08ee062e2f161e23560fcc3b8f898312 +timestamp : 2019-03-09 08:49:54 UTC +dependencies: [] + + +star 2.6.0c h9ee0642_3 +---------------------- +file name : star-2.6.0c-h9ee0642_3.tar.bz2 +name : star +version : 2.6.0c +build : h9ee0642_3 +build number: 3 +size : 5.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.6.0c-h9ee0642_3.tar.bz2 +md5 : 022f00e4790377bc4408a0effb8d2478 +timestamp : 2021-03-26 15:47:02 UTC +dependencies: [] + + +star 2.6.1a 1 +------------- +file name : star-2.6.1a-1.tar.bz2 +name : star +version : 2.6.1a +build : 1 +build number: 1 +size : 5.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.6.1a-1.tar.bz2 +md5 : 80e52945a6531111cd39de74c00e52ea +timestamp : 2018-08-16 11:35:27 UTC +dependencies: [] + + +star 2.6.1b 0 +------------- +file name : star-2.6.1b-0.tar.bz2 +name : star +version : 2.6.1b +build : 0 +build number: 0 +size : 5.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.6.1b-0.tar.bz2 +md5 : b0e3097359f780bc9de87c3b38426eb7 +timestamp : 2018-09-24 08:40:53 UTC +dependencies: [] + + +star 2.6.1d 0 +------------- +file name : star-2.6.1d-0.tar.bz2 +name : star +version : 2.6.1d +build : 0 +build number: 0 +size : 5.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.6.1d-0.tar.bz2 +md5 : 3be2e00b2947ca7a37781ecfd294d02e +timestamp : 2019-02-20 13:25:50 UTC +dependencies: [] + + +star 2.6.1d h9ee0642_1 +---------------------- +file name : star-2.6.1d-h9ee0642_1.tar.bz2 +name : star +version : 2.6.1d +build : h9ee0642_1 +build number: 1 +size : 5.8 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.6.1d-h9ee0642_1.tar.bz2 +md5 : 0db4890244448116e2191cdd9c76771a +timestamp : 2021-03-26 15:42:15 UTC +dependencies: [] + + +star 2.7.0b 0 +------------- +file name : star-2.7.0b-0.tar.bz2 +name : star +version : 2.7.0b +build : 0 +build number: 0 +size : 8.0 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.7.0b-0.tar.bz2 +md5 : 130ff60cd076acc05aabfcf6fa610f3c +timestamp : 2019-02-08 12:33:30 UTC +dependencies: [] + + +star 2.7.0d 0 +------------- +file name : star-2.7.0d-0.tar.bz2 +name : star +version : 2.7.0d +build : 0 +build number: 0 +size : 3.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.7.0d-0.tar.bz2 +md5 : 7870fbd8e8e6813b81999fa732d2ef9d +timestamp : 2019-02-20 13:23:08 UTC +dependencies: [] + + +star 2.7.0e 0 +------------- +file name : star-2.7.0e-0.tar.bz2 +name : star +version : 2.7.0e +build : 0 +build number: 0 +size : 3.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.7.0e-0.tar.bz2 +md5 : 0bc60eb796dc73909989a6b54478d1b3 +timestamp : 2019-03-17 09:17:29 UTC +dependencies: [] + + +star 2.7.0f 0 +------------- +file name : star-2.7.0f-0.tar.bz2 +name : star +version : 2.7.0f +build : 0 +build number: 0 +size : 3.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.7.0f-0.tar.bz2 +md5 : 62d581206e0f6f4ee5d6e919954ce08a +timestamp : 2019-04-10 10:26:55 UTC +dependencies: [] + + +star 2.7.1a 0 +------------- +file name : star-2.7.1a-0.tar.bz2 +name : star +version : 2.7.1a +build : 0 +build number: 0 +size : 3.3 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.7.1a-0.tar.bz2 +md5 : d36abf17ec0b27d6dfef4f683578eadd +timestamp : 2019-05-16 12:14:37 UTC +dependencies: [] + + +star 2.7.2a 0 +------------- +file name : star-2.7.2a-0.tar.bz2 +name : star +version : 2.7.2a +build : 0 +build number: 0 +size : 3.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.7.2a-0.tar.bz2 +md5 : 6356564e6fc8fc3248581b42b3aa25de +timestamp : 2019-08-13 23:31:31 UTC +dependencies: [] + + +star 2.7.2b 0 +------------- +file name : star-2.7.2b-0.tar.bz2 +name : star +version : 2.7.2b +build : 0 +build number: 0 +size : 3.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.7.2b-0.tar.bz2 +md5 : 4aa48b59920b67b1e6f171528e20d868 +timestamp : 2019-08-30 06:04:22 UTC +dependencies: [] + + +star 2.7.2c 0 +------------- +file name : star-2.7.2c-0.tar.bz2 +name : star +version : 2.7.2c +build : 0 +build number: 0 +size : 3.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.7.2c-0.tar.bz2 +md5 : 275c247b21c20fc7e2c2deca55640316 +timestamp : 2019-10-03 18:53:02 UTC +dependencies: [] + + +star 2.7.3a 0 +------------- +file name : star-2.7.3a-0.tar.bz2 +name : star +version : 2.7.3a +build : 0 +build number: 0 +size : 3.4 MB +license : GPLv3 +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/star-2.7.3a-0.tar.bz2 +md5 : d16d12158e2163c50918b8bafb05e034 +timestamp : 2019-10-08 20:35:07 UTC +dependencies: [] + + +star 2.7.3a h5ca1c30_1 +---------------------- +file name : star-2.7.3a-h5ca1c30_1.tar.bz2 +name : star +version : 2.7.3a +build : h5ca1c30_1 +build number: 1 +size : 1.7 MB +license : GPL-3.0-or-later +subdir : linux-64 +url : https://conda.anaconda.org/biocond diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/stream.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/stream.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..45f37b366a87640e6f2bd056455fef26d0dd8caf --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/stream.manual_bundle.txt @@ -0,0 +1,587 @@ +# Tool: stream +software_name: stream +tier: T1 +domain: t1_backfill_overall +downloads: 125038 +summary: STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping +description: STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping +dependencies: anndata, gunicorn, matplotlib-base >=3.2, networkx 2.1.*, numpy, plotly, python >=3, python-slugify, r-base 3.6.*, r-devtools, r-distutils, r-elpigraph.r, r-essentials, r-igraph, r-kernsmooth, r-rcpp, r-rcpparmadillo, r-vgam, r-xml, rpy2 2.9.*, scikit-learn >=0.23, scipy, seaborn, shapely, statsmodels, umap-learn, unzip, zip +execution_environment: R +execution_environment_reason: inferred from package/dependencies (R ecosystem) + +## URLs +home_url: https://github.com/pinellolab/stream +doc_url: +dev_url: + +## URL Docs Extract +### https://github.com/pinellolab/stream +GitHub - pinellolab/STREAM: STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} pinellolab / STREAM Public Notifications You must be signed in to change notification settings Fork 51 Star 182 Code Issues 54 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights pinellolab/STREAM master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 471 Commits 471 Commits .github/ workflows .github/ workflows stream stream tutorial tutorial .dockerignore .dockerignore .gitignore .gitignore .travis.yml .travis.yml CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md Dockerfile Dockerfile LICENSE LICENSE MANIFEST.in MANIFEST.in README.md README.md setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README Code of conduct AGPL-3.0 license STREAM (Latest version v1.1) Latest News Dec 17, 2021 Version 1.1 is now available. fixed incompatible issues related to the latest version of pandas fixed plotting issues related to the latest version of matplotlib and seaborn Jun 1, 2020 Version 1.0 is now available. The v1.0 has added a lot of new functionality: added QC metrics and plots added support of scATAC-seq analysis using peaks as features added support of interactive plots with plotly redesigned all plotting-related functions redesigned mapping procedure removed support of STREAM command line interface See v1.0 for more details. Jan 14, 2020 Version 0.4.1 is now available. We added support of feature top_pcs for Mapping Nov 26, 2019 Version 0.4.0 is now available. Numerous changes have been introduced. Please check v0.4.0 for details. Introduction STREAM ( S ingle-cell T rajectories R econstruction, E xploration A nd M apping) is an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. STREAM is now published in Nature Communications ! Please cite our paper Chen H, et al. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nature Communications , volume 10, Article number: 1903 (2019). if you find STREAM helpful for your research. STREAM is written using the class anndata Wolf et al. Genome Biology (2018) and available as user-friendly open source software and can be used interactively as a web-application at stream.pinellolab.org , as a bioconda package https://bioconda.github.io/recipes/stream/README.html and as a standalone command-line tool with Docker https://github.com/pinellolab/STREAM Installation with Bioconda (Recommended) $ conda install -c bioconda stream If you are new to conda environment: If Anaconda (or miniconda) is already installed with Python 3 , skip to 2) otherwise please download and install Python3 Anaconda from here: https://www.anaconda.com/download/ Open a terminal and add the Bioconda channel with the following commands: $ conda config --add channels defaults $ conda config --add channels bioconda $ conda config --add channels conda-forge Create an environment named env_stream , install stream , jupyter , and activate it with the following commands: For single cell RNA-seq analysis : $ conda create -n env_stream python=3.7 stream=1.0 jupyter $ conda activate env_stream For single cell ATAC-seq analysis : $ conda create -n env_stream python=3.7 stream=1.0 stream_atac jupyter $ conda activate env_stream To perform STREAM analyis in Jupyter Notebook as shown in Tutorial , type jupyter notebook within env_stream : $ jupyter notebook You should see the notebook open in your browser. Tutorial Example for scRNA-seq: 1.1-STREAM_scRNA-seq (Bifurcation).ipynb Example for scRNA-seq: 1.2-STREAM_scRNA-seq (Multifurcation) on 2D visulization.ipynb Example for scRNA-seq: 1.3-STREAM_scRNA-seq (Multifurcation) on original embedding.ipynb Example for scATAC-seq(using peaks): 2.1-STREAM_scATAC-seq_peaks.ipynb Example for scATAC-seq(using k-mers): 2.2-STREAM_scATAC-seq_k-mers.ipynb Example for scATAC-seq(using motifs): 2.3-STREAM_scATAC-seq_motifs.ipynb Example for mapping feature: 3-STREAM_mapping.ipynb Example for complex trajectories: 4-STREAM_complex_trajectories.ipynb Tutorials for v0.4.1 and earlier versions can be found here Installation with Docker With Docker no installation is required, the only dependence is Docker itself. Users will completely get rid of all the installation and configuration issues. Docker will do all the dirty work for you! Docker can be downloaded freely from here: https://store.docker.com/search?offering=community&type=edition To get an image of STREAM, simply execute the following command: $ docker pull pinellolab/stream Basic usage of docker run $ docker run [OPTIONS] IMAGE [COMMAND] [ARG...] Options: --publish , -p Publish a container’s port(s) to the host --volume , -v Bind mount a volume --workdir , -w Working directory inside the container To use STREAM inside the docker container: Mount your data folder and enter STREAM docker container: $ docker run --entrypoint /bin/bash -v /your/data/file/path/:/data -w /data -p 8888:8888 -it pinellolab/stream:1.0 Inside the container, launch Jupyter notebook: root@46e09702ce87:/data# jupyter notebook --ip 0.0.0.0 --port 8888 --no-browser --allow-root Access the notebook through your desktops browser on http://127.0.0.1:8888 . The notebook will prompt you for a token which was generated when you create the notebook. STREAM interactive website In order to make STREAM user friendly and accessible to non-bioinformatician, we have created an interactive website: http://stream.pinellolab.org The website can also run on a local machine. More details can be found https://github.com/pinellolab/STREAM_web Credits: H Chen, L Albergante, JY Hsu, CA Lareau, GL Bosco, J Guan, S Zhou, AN Gorban, DE Bauer, MJ Aryee, DM Langenau, A Zinovyev, JD Buenrostro, GC Yuan, L Pinello About STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data stream.pinellolab.org Topics visualization python scrna-seq lineage trajectory singlecell scatac-seq Resources Readme License AGPL-3.0 license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 182 stars Watchers 15 watching Forks 51 forks Report repository Releases 14 stream_v1.1 Latest Dec 18, 2021 + 13 releases Packages 0       Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 99.0% Other 1.0% Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time. + +## Conda Search Info +$ conda search -c bioconda -c conda-forge stream --info +[rc=0] +2 channel Terms of Service accepted +Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done +stream 0.2.0 py35r341h26a2512_0 +------------------------------- +file name : stream-0.2.0-py35r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.0 +build : py35r341h26a2512_0 +build number: 0 +size : 76 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.0-py35r341h26a2512_0.tar.bz2 +md5 : 2a60f24b4d52564497a388e5407f5deb +timestamp : 2018-09-06 19:42:44 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.5,<3.6.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.0 py36r341h26a2512_0 +------------------------------- +file name : stream-0.2.0-py36r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.0 +build : py36r341h26a2512_0 +build number: 0 +size : 75 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.0-py36r341h26a2512_0.tar.bz2 +md5 : 66fc60846391dcc6bff7bcf906436eb1 +timestamp : 2018-09-06 19:33:44 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.6,<3.7.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.1 py35r341h26a2512_0 +------------------------------- +file name : stream-0.2.1-py35r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.1 +build : py35r341h26a2512_0 +build number: 0 +size : 76 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.1-py35r341h26a2512_0.tar.bz2 +md5 : c86dc11fef0a2b848eda74f4a5f1d1e0 +timestamp : 2018-09-08 19:40:30 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.5,<3.6.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.1 py36r341h26a2512_0 +------------------------------- +file name : stream-0.2.1-py36r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.1 +build : py36r341h26a2512_0 +build number: 0 +size : 75 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.1-py36r341h26a2512_0.tar.bz2 +md5 : d96185b85bbc9b130cde669facc71598 +timestamp : 2018-09-08 19:48:18 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.6,<3.7.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.2 py35r341h26a2512_0 +------------------------------- +file name : stream-0.2.2-py35r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.2 +build : py35r341h26a2512_0 +build number: 0 +size : 76 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.2-py35r341h26a2512_0.tar.bz2 +md5 : 585a3b2489a690f2ef7ffc4d29f026ec +timestamp : 2018-09-17 04:39:42 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.5,<3.6.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.2 py36r341h26a2512_0 +------------------------------- +file name : stream-0.2.2-py36r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.2 +build : py36r341h26a2512_0 +build number: 0 +size : 76 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.2-py36r341h26a2512_0.tar.bz2 +md5 : 84f7d0f3d2dd094897fddd6333ab982a +timestamp : 2018-09-17 04:32:42 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.6,<3.7.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.3 py35r341h26a2512_0 +------------------------------- +file name : stream-0.2.3-py35r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.3 +build : py35r341h26a2512_0 +build number: 0 +size : 78 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.3-py35r341h26a2512_0.tar.bz2 +md5 : 3c3fdd14922cf58f2533deccfde054d0 +timestamp : 2018-09-25 00:04:44 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.5,<3.6.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.3 py36r341h26a2512_0 +------------------------------- +file name : stream-0.2.3-py36r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.3 +build : py36r341h26a2512_0 +build number: 0 +size : 78 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.3-py36r341h26a2512_0.tar.bz2 +md5 : 40253df635cf66a3c5f77e2c8191eab3 +timestamp : 2018-09-24 23:56:59 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.6,<3.7.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.4 py35r341h26a2512_0 +------------------------------- +file name : stream-0.2.4-py35r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.4 +build : py35r341h26a2512_0 +build number: 0 +size : 79 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.4-py35r341h26a2512_0.tar.bz2 +md5 : 1be4b62454ffd545327af72edfd3fb8a +timestamp : 2018-09-29 00:50:07 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.5,<3.6.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.4 py36r341h26a2512_0 +------------------------------- +file name : stream-0.2.4-py36r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.4 +build : py36r341h26a2512_0 +build number: 0 +size : 78 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.4-py36r341h26a2512_0.tar.bz2 +md5 : 91a48a461eed8597af4ee18b931b37f1 +timestamp : 2018-09-29 00:57:34 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.6,<3.7.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.5 py35r341h26a2512_0 +------------------------------- +file name : stream-0.2.5-py35r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.5 +build : py35r341h26a2512_0 +build number: 0 +size : 79 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.5-py35r341h26a2512_0.tar.bz2 +md5 : 186a9f325aacb257d016cc0e3ddfb62a +timestamp : 2018-09-30 10:45:53 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.5,<3.6.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.5 py36r341h26a2512_0 +------------------------------- +file name : stream-0.2.5-py36r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.5 +build : py36r341h26a2512_0 +build number: 0 +size : 78 KB +license : Affero +subdir : linux-64 +url : https://conda.anaconda.org/bioconda/linux-64/stream-0.2.5-py36r341h26a2512_0.tar.bz2 +md5 : 2877036131cad2552acbd39d9f76146b +timestamp : 2018-09-30 10:38:15 UTC +dependencies: + - anndata + - gunicorn + - libgcc-ng >=4.9 + - libgfortran >=3.0 + - libstdcxx-ng >=4.9 + - matplotlib + - networkx >=2.0 + - numpy + - python >=3.6,<3.7.0a0 + - python-slugify + - r-base >=3.4.1,<3.4.2.0a0 + - r-devtools + - r-distutils + - r-elpigraph.r + - r-essentials + - r-igraph + - r-kernsmooth + - r-rcpp + - r-rcpparmadillo + - r-vgam + - r-xml + - rpy2 + - scikit-learn + - scipy + - seaborn + - shapely + - statsmodels + - umap-learn + - unzip + - zip + + +stream 0.2.6 py35r341h26a2512_0 +------------------------------- +file name : stream-0.2.6-py35r341h26a2512_0.tar.bz2 +name : stream +version : 0.2.6 +build : py35r341h26a2512_0 +build number: 0 +size : 83 KB +license : Affero +subdir diff --git a/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/stringtie.manual_bundle.txt b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/stringtie.manual_bundle.txt new file mode 100644 index 0000000000000000000000000000000000000000..43c28d0986dc298498dd21f7b60992c11f1b29c1 --- /dev/null +++ b/BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/stringtie.manual_bundle.txt @@ -0,0 +1,564 @@ +# Tool: stringtie +software_name: stringtie +tier: T1 +domain: t1_backfill_overall +downloads: 700436 +summary: StringTie employs efficient algorithms for transcript structure recovery and abundance estimation from bulk RNA-Seq reads aligned to a reference genome. +description: StringTie employs efficient algorithms for transcript structure recovery and abundance estimation from bulk RNA-Seq reads aligned to a reference genome. +dependencies: bzip2 >=1.0.8,<2.0a0, htslib >=1.22.1,<1.24.0a0, libgcc >=13, liblzma >=5.8.1,<6.0a0, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, python +execution_environment: Python +execution_environment_reason: inferred from python dependency + +## URLs +home_url: https://ccb.jhu.edu/software/stringtie +doc_url: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual +dev_url: https://github.com/gpertea/stringtie + +## CLI Help Source +cli:stringtie +## CLI Help Content +$ conda run -n bioenv_cli stringtie --help +[rc=0] +StringTie v2.1.7 usage: + +stringtie [-G ] [-l ] [-o ] [-p ] + [-v] [-a ] [-m ] [-j ] [-f ] + [-c ] [-g ] [-u] [-L] [-e] [--viral] [-E ] + [--ptf ] [-x ] [-A ] [-h] {-B|-b } + [--mix] [--conservative] [--rf] [--fr] +Assemble RNA-Seq alignments into potential transcripts. +Options: + --version : print just the version at stdout and exit + --conservative : conservative transcript assembly, same as -t -c 1.5 -f 0.05 + --mix : both short and long read data alignments are provided + --rf : assume stranded library fr-firststrand + --fr : assume stranded library fr-secondstrand + -G reference annotation to use for guiding the assembly process (GTF/GFF3) + --ptf : load point-features from a given 4 column feature file + -o output path/file name for the assembled transcripts GTF (default: stdout) + -l name prefix for output transcripts (default: STRG) + -f minimum isoform fraction (default: 0.01) + -L long reads processing; also enforces -s 1.5 -g 0 (default:false) + -R if long reads are provided, just clean and collapse the reads but + do not assemble + -m minimum assembled transcript length (default: 200) + -a minimum anchor length for junctions (default: 10) + -j minimum junction coverage (default: 1) + -t disable trimming of predicted transcripts based on coverage + (default: coverage trimming is enabled) + -c minimum reads per bp coverage to consider for multi-exon transcript + (default: 1) + -s minimum reads per bp coverage to consider for single-exon transcript + (default: 4.75) + -v verbose (log bundle processing details) + -g maximum gap allowed between read mappings (default: 50) + -M fraction of bundle allowed to be covered by multi-hit reads (default:1) + -p number of threads (CPUs) to use (default: 1) + -A gene abundance estimation output file + -E define window around possibly erroneous splice sites from long reads to + look out for correct splice sites (default: 25) + -B enable output of Ballgown table files which will be created in the + same directory as the output GTF (requires -G, -o recommended) + -b enable output of Ballgown table files but these files will be + created under the directory path given as + -e only estimate the abundance of given reference transcripts (requires -G) + --viral : only relevant for long reads from viral data where splice sites + do not follow consensus (default:false) + -x do not assemble any transcripts on the given reference sequence(s) + -u no multi-mapping correction (default: correction enabled) + -h print this usage message and exit + +Transcript merge usage mode: + stringtie --merge [Options] { gtf_list | strg1.gtf ...} +With this option StringTie will assemble transcripts from multiple +input files generating a unified non-redundant set of isoforms. In this mode +the following options are available: + -G reference annotation to include in the merging (GTF/GFF3) + -o output file name for the merged transcripts GTF + (default: stdout) + -m minimum input transcript length to include in the merge + (default: 50) + -c minimum input transcript coverage to include in the merge + (default: 0) + -F minimum input transcript FPKM to include in the merge + (default: 1.0) + -T minimum input transcript TPM to include in the merge + (default: 1.0) + -f minimum isoform fraction (default: 0.01) + -g gap between transcripts to merge together (default: 250) + -i keep merged transcripts with retained introns; by default + these are not kept unless there is strong evidence for them + -l