sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
cfbb002509580ba90158538873b73bc5f86b5062bb62660aa39c103db2c27ee0 | Shell | 517 | 12 | #!/bin/bash
#SBATCH --job-name=SC
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=120G
#SBATCH --cpus-per-task=28
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/vn_preictal/scripts/slurm_output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyse... |
438368adc8934f2f65219af639d911eace2b6e9e42b19c204b4acd0faca1132d | Shell | 520 | 16 | #!/bin/bash
set -ex
# MKL
MKL_VERSION=2024.2.0
MKLROOT=/opt/intel
mkdir -p ${MKLROOT}
pushd /tmp
python3 -mpip install wheel
python3 -mpip download -d . mkl-static==${MKL_VERSION}
python3 -m wheel unpack mkl_static-${MKL_VERSION}-py2.py3-none-manylinux1_x86_64.whl
python3 -m wheel unpack mkl_include-${MKL_VERSION}-p... |
c180621e690ba23e956882696fef1ffa42d2ad43f2559b08760a1e39f291e4f5 | Shell | 521 | 16 | install required packages
python3 -m pip install --upgrade pip twine build
build and publish
rm -fr ./dist && python -m build # cleanup and build
CHANGE THE VERSION in the pyproject.toml file
python3 -m twine upload --verbose --repository pypi dist/* # choose between repo pypi and testpypi
uninstall the package
pip ... |
2204511d91d9ac6a8e8ade71f0c4a227920f5eca7835fd0e424666ee9191a558 | Shell | 522 | 26 | #!/bin/bash
#SBATCH --job-name=write_sc
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=120G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/wod/slurm-output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/w... |
7f23742e7dea20da06fe90e5b358ede12250c75fcce3fda24c28763a220b469d | Shell | 524 | 19 | while read x y; do
echo "reformatted_ruiz <- MungeSumstats::format_sumstats(
path=\"RUIZ/"$x".tsv\",
save_path = \""$y".formatted.tsv.bgz\",
force_new = TRUE,
ref_genome=\"GRCh37\",
convert_ref_genome=\"GRCh38\",
local_chain = \"GRCh37_to_GRCh38.chain\",
dbSNP = 155,
allele_flip_check = TRUE,
bi_alle... |
857808253fe19be613f0937fafe2fecf5124e775c597bb518bf5260a87a52b72 | Shell | 524 | 23 | #!/bin/bash
set -euo pipefail
FS_TGZ="fs.tgz"
FS_URL="https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu18_amd64-7.3.2.tar.gz"
FS_MODEL_PATH="freesurfer/models/synthstrip.1.pt"
MODEL_DIR="tests/models"
MODEL_OUT="${MODEL_DIR}/synthstrip_v7.3.2_test.pt"
wget -O "${FS_TGZ}" "${FS_URL... |
698926e04a887b785a3c383c173f42317e4bb89497e9955385afb08682ef854a | Shell | 526 | 14 | #!/bin/bash
#SBATCH --job-name=hspike_cluster
#SBATCH --partition=normal
#SBATCH --time=99:00:00
#SBATCH --mem=64G
#SBATCH --cpus-per-task=24
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/slurm/%j_%A-%a-%x-output.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/... |
c57221239dc438fc2b29b3e0e43ad4cb73326e8c4c7eb2da45d228ada657f87a | Shell | 527 | 14 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$WORKDIR"' EXIT
cd "$WORKDIR" || exit
bart jo... |
ebc653d6064e9c611b480fc16ba1667fdb7aa5e27b57436df77fde88e897b1eb | Shell | 530 | 13 | #!/bin/bash
#SBATCH --job-name=Seg
#SBATCH --partition=normal
#SBATCH --time=99:99:99
#SBATCH --mem=100G
#SBATCH --cpus-per-task=1
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/slurm_output/output-%j.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/stephen.whitm... |
4f823c17789152c8f73c96f49ed59e2414f459a92a30a0f12399e6725c21eb46 | Shell | 531 | 14 | #!/bin/bash
#SBATCH --job-name=preictal
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=32G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss02/charpier/analyses/vn_preictal/scripts/slurm_output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss02/charpier/ana... |
707311486a4b8e2b7704e2c11f9d81dd06d90c2f872614ab45e7af79496ccabc | Shell | 532 | 17 | #!/bin/bash
#SBATCH -J MACEH
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=12
#SBATCH --mem-per-cpu=3850
#SBATCH --cpus-per-task=1
#SBATCH --output=%j.out
#SBATCH --partition=compute
#SBATCH --account=su007-rjm
module purge
module load GCC/13.2.0 CUDA/11.8.0
python_path="/home/c/chenqian3/.conda... |
54ea5e2378988c212b13296840be918e440f1835db62f59ff2d9613305f5deab | Shell | 535 | 14 | #!/bin/bash
#SBATCH --job-name=hspike_cluster
#SBATCH --partition=normal
#SBATCH --time=99:00:00
#SBATCH --mem=220G
#SBATCH --cpus-per-task=24
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/slurm_output/%j_%A-%a-%x-output.txt
#SBATCH --error=/network/lustre/iss01/charpier/a... |
a168992b41a45264c39e9ddc0415c41b67c3d4eef3559ade0fc26d03871223db | Shell | 535 | 14 | #!/bin/bash
#SBATCH --job-name=hspike_cluster.m
#SBATCH --partition=normal
#SBATCH --time=99:00:00
#SBATCH --mem=64G
#SBATCH --cpus-per-task=8
#SBATCH --chdir=.
#SBATCH --error=/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/slurm_output/%A_%a_%j-%x_error.txt
#SBATCH --output=/network/lustre/iss01/charpier/an... |
3d7eedc1a5a78e98752c180f6bca1eafcf3e0a092a0af9312ec40c6954618044 | Shell | 538 | 17 | #!/bin/bash
#SBATCH --job-name=pnh_cluster
#SBATCH --partition=bigmem
#SBATCH --mem=220G
#SBATCH --cpus-per-task=24
#SBATCH --time=99:00:00
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/vn_pnh/slurm/%A-%a-%x-output.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/vn_pnh/slurm/%A-... |
6216d33c4dd5c249de4cde84038579ed1872dc9fa1b07fe76beab80dca72bce2 | Shell | 541 | 14 | #!/bin/bash
#SBATCH --job-name=hspike_FFT
#SBATCH --partition=normal
#SBATCH --time=99:00:00
#SBATCH --mem=64G
#SBATCH --cpus-per-task=8
#SBATCH --chdir=.
#SBATCH --error=/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/slurm/hspike_FFT_%A_%a_%j-%x_error.txt
#SBATCH --output=/network/lustre/iss01/charpier/anal... |
ecc8ed1a2800cef05e9a22324d5294c4b62ff51e20ca5595fd25787511ed7aea | Shell | 541 | 14 | #!/bin/bash
#SBATCH --job-name=hspike_FFT
#SBATCH --partition=normal
#SBATCH --time=99:00:00
#SBATCH --mem=64G
#SBATCH --cpus-per-task=8
#SBATCH --chdir=.
#SBATCH --error=/network/lustre/iss02/charpier/analyses/stephen.whitmarsh/slurm/hspike_FFT_%A_%a_%j-%x_error.txt
#SBATCH --output=/network/lustre/iss02/charpier/anal... |
f7b6f994233547c84c6fdde83e69d36cad75d6633ccaece91f000ff692921b20 | Shell | 542 | 14 | #!/bin/bash
#SBATCH --job-name=hspike_cluster_template
#SBATCH --partition=normal
#SBATCH --time=99:00:00
#SBATCH --mem=64G
#SBATCH --cpus-per-task=24
#SBATCH --chdir=.
#SBATCH --error=/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/slurm/%A_%a_%j-%x_error.txt
#SBATCH --output=/network/lustre/iss01/charpier/a... |
4a950d49efa47f258f641f0ffb037cce7d29f6a0315d03a964a6cb3f35e5b47e | Shell | 544 | 15 | #!/bin/bash
#SBATCH --job-name=write_sc
#SBATCH --partition=bigmem,normal
#SBATCH --time=99:99:99
#SBATCH --mem=32G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/vn_preictal/scripts/slurm_output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/ana... |
b34741e84699e72b2581784ef31b7879b82c2bdbad42ad2ae30572732e5ee596 | Shell | 544 | 15 | #!/bin/bash
#SBATCH --job-name=write_sc
#SBATCH --partition=bigmem,normal
#SBATCH --time=99:99:99
#SBATCH --mem=32G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/vn_preictal/scripts/slurm_output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/ana... |
74438ee82ddba78add7100392c23d5900e53d859497eacb0b537649b808f01cb | Shell | 545 | 17 | #!/bin/bash
#SBATCH --job-name=HspikeSC
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=120G
#SBATCH --cpus-per-task=28
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/slurm_output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/ana... |
56bc86dc1ea7e57fa7ac156452645ccdb20d77540007ae0d15016aad56facfb0 | Shell | 547 | 15 | #!/bin/bash
#SBATCH --job-name=preictal_project
#SBATCH --partition=bigmem,normal
#SBATCH --time=99:99:99
#SBATCH --mem=32G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/vn_peictal/scripts/slurm_output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charp... |
6991c08a5b8cada76b74d62ddd1bbb60ebe00ead55e51d6a911268328c4dfa8a | Shell | 549 | 15 | #!/bin/bash
#SBATCH --job-name=avg
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=8G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/lgi1/Git-Paul/slurm-output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/lgi1/G... |
3393c17d6314df4c45398edf6fa7e7fe1c46103830f66238877ce27f50ab081e | Shell | 553 | 17 | #!/bin/sh
# This script is to generate the 3D predictions
# The output of this script is a .csv file for **EACH** different cell type for which you want a prediction for
# e.g. OUTPUTc2.csv, OUTPUTc4.csv, etc...
# Each of these files... |
e5900928990fa2c4f608739a5fc683b47163dff41e5ce4971ee2db98c4d672c5 | Shell | 553 | 15 | #!/bin/bash
#SBATCH --job-name=batch
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=8G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/lgi1/Git-Paul/slurm-output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/lgi1... |
374f30e4eeb9b66e1585b99e3f87bd1a028dd1217f2b70efdbf294290d213f8a | Shell | 555 | 14 | #!/bin/bash
#SBATCH --job-name=hspike_spikestats
#SBATCH --partition=bigmem
#SBATCH --time=99:00:00
#SBATCH --mem=64G
#SBATCH --cpus-per-task=8
#SBATCH --chdir=.
#SBATCH --error=/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/slurm/SpikeStats_%A_%a_%j-%x_error.txt
#SBATCH --output=/network/lustre/iss01/charpi... |
565d9665150f35d27e696ba33b861bb9f2276184e0a53fb0e472bf2507dacba2 | Shell | 555 | 14 | #!/bin/bash
#SBATCH --job-name=hspike_spikestats
#SBATCH --partition=normal
#SBATCH --time=99:00:00
#SBATCH --mem=64G
#SBATCH --cpus-per-task=8
#SBATCH --chdir=.
#SBATCH --error=/network/lustre/iss02/charpier/analyses/stephen.whitmarsh/slurm/SpikeStats_%A_%a_%j-%x_error.txt
#SBATCH --output=/network/lustre/iss02/charpi... |
b38bcbbb56b7ed951f86e2b9e831d8a247af3248a751f0b0670c98a066c8f045 | Shell | 556 | 26 | VERSION=0.0.74
#change version in the pyproject.toml
deactivate
pip install toml
python <<EOF
import toml
f = 'pyproject.toml'
d = toml.load(open(f, 'r'))
d['project']['version'] = "${VERSION}"
toml.dump(d, open(f, 'w'))
EOF
# push the bumped version to git
git add .vscode/bump_version.sh
git add pyproject.toml
git ... |
dedb347389fdc204c5f90c62d523ce6ea9074653baeceb852796d913fa3ff338 | Shell | 558 | 18 | #!/bin/bash
#SBATCH --job-name=avg
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=50G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/lgi1/Git-Paul/slurm-output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/lgi1/... |
3bb2a00230fb4669f1b846b8b95446101b8007cb4e4a670561fdfd2706f4d98d | Shell | 563 | 23 | #!/usr/bin/env bash
# Set hard fail on error
set -e
# cd to the script directory to avoid pathing issues
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
cd $DIR/../examples
# run readme examples
echo "Running config_sample.yaml example"
yass sort config_sample.yaml --clean
echo "Running config_sample_comple... |
e10c6f257f64512a3012dadc5812569dd8445e7cab3f5afd391937948c0fce2b | Shell | 568 | 18 | while read p; do
echo "reformatted_xiongz <- MungeSumstats::format_sumstats(
path=\"XiongZ_31763980."$p".csv.gz\",
save_path = \"XiongZ_31763980."$p".formatted.tsv.gz\",
force_new = TRUE,
ref_genome=\"GRCh37\",
convert_ref_genome=\"GRCh38\",
dbSNP = 155,
allele_flip_check = TRUE,
bi_allelic_filter = FA... |
85d64d7baef50f218e7675595a53805cc9531523317af97a5f73d36c41d4f6b8 | Shell | 569 | 17 | #!/bin/bash
#SBATCH --job-name=spyking-circus
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=120G
#SBATCH --cpus-per-task=28
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/vn_preictal/scripts/slurm_output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/char... |
a7c85f57a511e72353098df996eaa77fa5cb987a115ccb01ceebcae899f39e72 | Shell | 576 | 16 | #!/bin/bash
#SBATCH --job-name=spyking-circus
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=120G
#SBATCH --cpus-per-task=28
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/louis.cousyn/Scripts/slurm_output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/cha... |
6b2f30f21674eb2e89dbc3071a787486ba46f2c20ab4f78cc2a8bb2b99c3b54d | Shell | 586 | 19 | #!/bin/sh
. "$(dirname "$0")/lib.sh"
announce "iad no-sphere fixture cases"
cp "$ROOT_DIR/tests/rxt/0_sphere/basic_A.rxt" "$TEST_TMP/basic_A.rxt"
cp "$ROOT_DIR/tests/rxt/0_sphere/sample_A.rxt" "$TEST_TMP/sample_A.rxt"
(
cd "$TEST_TMP"
"$IAD_EXECUTABLE" -M 0 -q 4 basic_A.rxt > basic_A.stdout 2>&1
"$IAD_E... |
fcaa22fc847bee765cfbf5f61f7f4b4c63318a9a34f6b263f30cd46bbe6882aa | Shell | 586 | 15 | #!/bin/bash
#SBATCH --job-name=hspike_cluster_template
#SBATCH --partition=normal
#SBATCH --time=99:00:00
#SBATCH --mem=64G
#SBATCH --cpus-per-task=8
#SBATCH --chdir=.
#SBATCH --error=/network/lustre/iss02/charpier/analyses/stephen.whitmarsh/slurm/hspike_cluster_template_%A_%a_%j-%x_error.txt
#SBATCH --output=/network/... |
71d1fd8d2b571c2d06d97e07732e7b912dd880e38e8e87a8c3a4d090bf24ab26 | Shell | 591 | 27 | #!/bin/bash
set -ex
if [ -n "${UBUNTU_VERSION}" ]; then
apt update
apt-get install -y doxygen git graphviz nodejs npm libtinfo5
fi
# Do shallow clone of PyTorch so that we can init lintrunner in Docker build context
git clone https://github.com/pytorch/pytorch.git --depth 1
chown -R jenkins pytorch
pushd pytorc... |
dafe7a2512dc9b05dc81685a658037a1d1fba8a3ae5286376cc6300d12c9d464 | Shell | 594 | 18 | #!/bin/bash
#SBATCH --job-name=hspike_cluster
#SBATCH --partition=normal
#SBATCH --time=99:00:00
#SBATCH --mem=32G
#SBATCH --cpus-per-task=8
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/stephen.whitmarsh/slurm/%A-%a-%x-output.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/step... |
b1c191a23f06604308a30fdc9a3bda1f0819402841dae73d398e34516b12063a | Shell | 600 | 14 | #!/bin/sh
. "$(dirname "$0")/lib.sh"
ACTUAL_FILE=$(numeric_actual_file iad_one_sphere_no_mc)
: > "$ACTUAL_FILE"
announce "iad one-sphere deterministic cases"
run_iad_numeric one_reflectance -V 0 -r 0.4 -S 1 -M 0 -1 "200 13 13 2 0.95"
run_iad_numeric one_rt -V 0 -r 0.4 -t 0.1 -S 1 -M 0 -1 "200 13 13 2 0.95"
run_iad_n... |
63dd2767f1f582321f416d6e28aeb1bfc7b62ef2db10fbf0e0a893ed27b39101 | Shell | 601 | 19 | #!/bin/bash
#SBATCH --job-name=write_sc
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=120G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/lgi1/Git-Paul/slurm-output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses... |
c857c6732582d8ab05ad22e6df5b534c33739c28ce479a32cc2657191f5c5488 | Shell | 602 | 16 | #!/bin/bash
#SBATCH --job-name=patlgi1
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=16G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/lgi1/Git-Paul/slurm-output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/l... |
b97a2568c4ed556c15a265da81675d8dba3a752104b4996f561efd1e16e6bfbc | Shell | 603 | 19 | #!/bin/bash
#SBATCH --job-name=dtx_spikes
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=120G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/lgi1/Git-Paul/slurm-output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/analys... |
0de3c8a4ce2f3e8a04ccfbce613f676a90d1c0154e7d1f9d3ba2db87789e44ab | Shell | 610 | 5 | mkdir results/chrombpnet/ATAC_PE/K562/ATAC_PE_12.30.2021/chrombpnet_model/interpret/tfhits/
python src/evaluation/invivo_footprints/tf_modiscohits.py --outdir=results/chrombpnet/ATAC_PE/K562/ATAC_PE_12.30.2021/chrombpnet_model/interpret/tfhits/ \
results/chrombpnet/ATAC_PE/K562/ATAC_PE_12.30.2021/chrombpnet_model/inte... |
30dc2068a69f7cbd88293714630afcae229d2f37df702a22fdd5620916101f3b | Shell | 616 | 25 | #!/bin/bash
# intersect on prim - mets matched filtered and VEP annotated vcf
wxsDir=~/Dropbox/projects/mayo-brain-mets/results/wxs
vcfDir=$wxsDir/variant-calls/maf
sampleList=$vcfDir/wxs-prim-bm-sample-map.txt
echo "#-------- Prim-Mets Matched VCF Intersect -------#"
while read line;do
sample=`echo $line`
patien... |
5d4e08d0d40348b5b2348705e8cfee3923530d06164afe34963f5465d8c54617 | Shell | 618 | 17 | #!/bin/bash
# YOLOv5 🚀 by Ultralytics, GPL-3.0 license
# Download COCO128 dataset https://www.kaggle.com/ultralytics/coco128 (first 128 images from COCO train2017)
# Example usage: bash data/scripts/get_coco128.sh
# parent
# ├── yolov5
# └── datasets
# └── coco128 ← downloads here
# Download/unzip images and lab... |
f923efbc438e7927b2cbd1306b0013937a15443d2cc84f68d7066c402703e8c6 | Shell | 620 | 16 | #!/bin/bash
#SBATCH --job-name=aw
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=16G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/lgi1/Git-Paul/slurm-output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/lgi1/G... |
0734fcc2666a26e80ea2a223140873b10b41c41dbc0af8d71329d52eb8f88e98 | Shell | 622 | 16 | #!/bin/bash
#SBATCH --job-name=an
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=16G
#SBATCH --cpus-per-task=2
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/lgi1/Git-Paul/slurm-output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/charpier/analyses/lgi1/G... |
b0565a194ffec7beabfcbc836afbcb81787f41f0a42dd57aef6029d50f281eee | Shell | 623 | 25 | #! /bin/bash
set -euo pipefail
if [ "$#" -ne 1 ]; then
echo "Usage: $0 <new-version>"
echo "Example: $0 0.16.12"
exit 1
fi
NEW_VERSION="$1"
VERSION_FILE="VERSION"
if [ ! -f "${VERSION_FILE}" ]; then
echo "Error: ${VERSION_FILE} not found"
exit 1
fi
OLD_VERSION="$(tr -d '\r\n' < "${VERSION_FILE}... |
1dc5e00f3929a2b27ae4d52559cce0bd5509761841be15bbef62b6ec06eb88d7 | Shell | 624 | 23 | #!/bin/bash
set -eux
yum install -y llvm-devel lld
LLVM_VERSION="$(rpm -q --qf '%{VERSION}' llvm-devel)"
LLVM_REPO="https://github.com/llvm/llvm-project.git"
git clone --depth 1 --filter=blob:none --sparse --branch "llvmorg-${LLVM_VERSION}" "${LLVM_REPO}" /llvm
git -C /llvm sparse-checkout set bolt cmake llvm
cma... |
fa9f5e7344b372b3eca83bbcac0189a4b2e11c1a0ff5120b52d4f61f60e3aa4e | Shell | 624 | 19 | #!/bin/bash -l
#SBATCH --job-name=make_swc_stim
#SBATCH --output=outLogs/make_swc_mono_expt_stim_2024_%A_%a.out
#SBATCH --error=outLogs/make_swc_mono_expt_stim_202_%A_%a.err
#SBATCH --mem=4Gb
#SBATCH --time=1:00:00
#SBATCH --partition=use-everything
#SBATCH --cpus-per-task=1
#SBATCH --array=60# 0-60
PROJECT_ROOT="$(c... |
11e86ca7de85bd344163943c3ffaa685b89de6063e1719bb4db8e0283d61a421 | Shell | 628 | 23 | #!/bin/bash -l
#SBATCH --job-name=get_thresh
#SBATCH --output=outLogs/get_human_thresholds_%j.out
#SBATCH --error=outLogs/get_human_thresholds_%j.err
#SBATCH --mem=8Gb
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
#SBATCH --partition=mcdermott
PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
cd "$PRO... |
768654695b76093ed41c34525093cc2102c534d3e0658bfe235996e853c17b9f | Shell | 629 | 16 | #!/bin/sh
# Clean and re-run every test_* fixture simulation with the PIMMS from THIS
# working tree, then regenerate the expected-output baselines. Run from this
# directory. (The old version of this script was an accidental copy of
# clean_up_tests.sh - it never ran anything - and both stopped at test_13.)
set -e
REP... |
efa0e55a8e2a8a0841c600a99c29a30a4e07c1fc7db1b84172af81a9ce7c2ed2 | Shell | 634 | 24 | #!/bin/bash
set -ex -o pipefail
SCRIPT_PARENT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
# shellcheck source=./common.sh
source "$SCRIPT_PARENT_DIR/common.sh"
run_tests() {
echo Running smoke_test.py...
python ./.ci/pytorch/smoke_test/smoke_test.py --package torchonly
echo Running test_autogra... |
c0bbdf445db60e6dfac9b19edc24ce20cd2b0a0177881ff79ab0244428289249 | Shell | 638 | 19 | #!/bin/bash
#SBATCH --job-name=make_popham_stim
#SBATCH --output=outLogs/make_swc_popham_expmt_stim_2024_%A_%a.out
#SBATCH --error=outLogs/make_swc_popham_expmt_stim_2024_%A_%a.err
#SBATCH --mem=4Gb
#SBATCH --time=1:00:00
#SBATCH --partition=use-everything
#SBATCH --cpus-per-task=1
#SBATCH --array=0-143# 0-143; 144 to... |
35e92e4aadf345187d784c434de996b5dc1942b46728eafb8e720dfbdc1a5008 | Shell | 640 | 22 | #!/bin/bash
# YOLOv5 🚀 by Ultralytics, GPL-3.0 license
# Download latest models from https://github.com/ultralytics/yolov5/releases
# Example usage: bash data/scripts/download_weights.sh
# parent
# └── yolov5
# ├── yolov5s.pt ← downloads here
# ├── yolov5m.pt
# └── ...
python - <<EOF
from utils.downloads... |
6a3c45676761e1fc78d2220b897fe2c4a198c43299be8973d83d9d0d95e3f427 | Shell | 641 | 18 | while read p x; do
echo "genesOut <- MAGMA.Celltyping::map_snps_to_genes(
path_formatted = \"/Users/cotneyj/Desktop/scRNA-Seq_GWAS/"$x".formatted.tsv.bgz\",
genome_build = \"GRCh38\",
N = 6169,
population = \"amr\",
upstream_kb = 100,
downstream_kb = 100
)" >> generate_ruiz_celltype_associations_for_R.tx... |
74ce987f156297e145d0d44ef095976729ab018675a2adf48e1dcda2ebc40af7 | Shell | 646 | 16 | #!/bin/bash
#SBATCH --job-name=spyking-circus
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=120G
#SBATCH --cpus-per-task=28
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/louis.cousyn/Scripts/slurm_output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/cha... |
ff35d533754695caa533da11780a23163b8bb61bf7d1cd1055ad0c9a2b7e6c82 | Shell | 651 | 23 | #!/bin/bash
train_mol_path='./data/training'
val_mol_path='./data/validation'
train_corpus_path='./data/training.corpus'
val_corpus_path='./data/validation.corpus'
vocab_path='./data/vocab'
# python bermol/vocab.py \
# --train_mol_path $train_mol_path \
# --val_mol_path $val_mol_path \
# --train_corpus_pa... |
042987b6d734cb98dcc4007ec39b5722df9c568bd781260ad2c3746f82a8b84a | Shell | 655 | 27 | #!/usr/bin/env bash
# Script used only in CD pipeline
set -eou pipefail
function do_install() {
cuda_version=$1
cuda_version_nodot=${1/./}
MAGMA_VERSION="2.6.1"
magma_archive="magma-cuda${cuda_version_nodot}-${MAGMA_VERSION}-1.tar.bz2"
cuda_dir="/usr/local/cuda-${cuda_version}"
(
set... |
dec823d5da7476264e228e8278324d47a3fd693aad32825e064817c58bd7c059 | Shell | 655 | 15 | #!/bin/bash
#SBATCH --mem=16000
#SBATCH --time=10:00:00
#SBATCH --ntasks=4
echo ${subid}
module load gcc/8.3.0 motif zlib mesa
module load matlab
#subid=sub-patient032094
matlab -nodisplay -nosplash -r "addpath(genpath('/project/ajoshi_27/code_farm/bfp/src')); setenv('BrainSuiteMCR','/project/ajoshi_27/MATLAB_Runtime... |
8500de795553af1523c57915ca4e1db6b7e5bd27a6a9390c34fd0880b703598a | Shell | 657 | 22 | #! /bin/bash
prefix="/opt/local"
PYVER=2.7
MYCC=/usr/bin/clang
MYCXX=/usr/bin/clang++
MYLD=ld
cmake_args="-S ../.. \
-B build-macports-module \
-DSTF_BUILD_MODULE=ON \
-DSTF_WITH_BIOSIG=ON \
-DSTF_BIOSIG_PROVIDER=SUBMODULE \
-DCMAKE_C_COMPILER=${MYCC} \
... |
2e1df468a1cbd62134dde5e83450367b2d94421a79eddfbbbd04e1d1366fdd69 | Shell | 659 | 14 | #!/bin/sh
. "$(dirname "$0")/lib.sh"
ACTUAL_FILE=$(numeric_actual_file iad_two_sphere_no_mc)
: > "$ACTUAL_FILE"
announce "iad two-sphere deterministic cases"
run_iad_numeric two_reflectance -V 0 -r 0.4 -S 2 -M 0 -1 "200 13 13 2 0.95" -2 "200 13 0 2 0.95"
run_iad_numeric two_rt -V 0 -r 0.4 -t 0.1 -S 2 -M 0 -1 "200 13... |
8ae065bf0a6c7dd4c6ca3e86064f35abd5ed592c697dc7dfc488d60748b3659b | Shell | 662 | 17 | for dataset in "PFC" "MTG"
do
## Preprocessing
Rscript --no-save --no-restore --verbose 1-preprocess.R ${dataset} > out-${dataset}.txt 2>&1
mv out-${dataset}.txt data/out-${dataset}.txt
for ps_model in "random_forest_cv"
do
## DE test
Rscript --no-save --no-restore --verbose 2-... |
6e38703d72c2fbd79216a5aaa9062d831cd0f30601634f77bd06661ff4c1929d | Shell | 672 | 17 | #! /bin/sh
set -e
echo "black check"
black . --check
echo "mypy check"
mypy tensorcircuit
echo "pylint check"
pylint tensorcircuit tests examples/*.py
pylint --recursive=y examples/reproduce_papers
pylint --recursive=y examples/challenge_suite
echo "pytest check"
pytest -n auto --cov=tensorcircuit -vv -W ignore::Depre... |
843da0f7dd65e1522fa31be969e2b398d44a8715c45591c6d8a86121ddea1796 | Shell | 672 | 29 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
RAW=$(readlink -f ../01_data_brain/ksp_2D)
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$W... |
631e70aa7cbf5e97c69f06c5efc0bbbaa41da2bbfb54ec317361f337a5cf67e7 | Shell | 676 | 15 | #!/bin/bash
#SBATCH --mem=16000
#SBATCH --time=10:00:00
#SBATCH --ntasks=4
echo ${subid}
module load gcc/8.3.0 motif zlib mesa
module load matlab
#subid=sub-patient032094
matlab -nodisplay -nosplash -r "addpath(genpath('/project/ajoshi_27/code_farm/bfp/src')); setenv('BrainSuiteMCR','/project/ajoshi_27/MATLAB_Runtime... |
54e9ad905f938dbaf5be078677f98f77d6f3787d829ba84369331b2d78366643 | Shell | 679 | 19 | #!/bin/bash -l
#SBATCH --job-name=make_swc_stim
#SBATCH --output=outLogs/make_swc_binaural_azim_spotlight_stim_2024_%A_%a.out
#SBATCH --error=outLogs/make_swc_binaural_azim_spotlight_stim_2024_%A_%a.err
#SBATCH --mem=4Gb
#SBATCH --time=0:10:00
#SBATCH --partition=use-everything
#SBATCH --cpus-per-task=1
#SBATCH --arra... |
b512647baec391078e4555a21e953098094b2f3e4adfd44b725677253959a9d7 | Shell | 679 | 31 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
DAT=/home/ibi/archive/vol/2025-07-04_IRT/meas_MID00064_FID65030_IBI_Radial_2025_02_27_08cb2e6.dat
download()
(
URL=$1
... |
4ffda4dbd7efb13b27ab0116dfcc51a290bfed835e7f04faf1c489c32f959dac | Shell | 682 | 27 | #!/bin/bash
# Script used only in CD pipeline
set -eux
ACL_VERSION=${ACL_VERSION:-"v53.2.0"}
ACL_INSTALL_DIR="/acl"
# Clone ACL
git clone https://github.com/ARM-software/ComputeLibrary.git -b "${ACL_VERSION}" --depth 1 --shallow-submodules
ACL_CHECKOUT_DIR="ComputeLibrary"
# Build with scons
pushd $ACL_CHECKOUT_DIR... |
b5e3cc47d75d222a8aa8ef9a535e3448219b6a39022042ebfd16f522d385c92e | Shell | 685 | 25 | #!/bin/bash
#SBATCH --job-name=jupyter_notebook
#SBATCH --output=outLogs/notebook_%j.out
#SBATCH --error=outLogs/notebook_%j.err
#SBATCH --mem=12Gb
#SBATCH --time=3:00:00
#SBATCH --partition=normal
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:1 --constraint=20GB
#SBATCH -x dgx001,dgx002
PROJECT_ROOT="$(cd "$(dirname ... |
c7c08eb613162edda6a21b968dffd6c5f44bf0fae01dda8c8a5fc93c91c8b574 | Shell | 693 | 15 | #!/bin/sh
# Written by Gia H. Ngo and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_CBIG_Ngo2019AuthorTopic
# remove unused stable projects
rm -r Standalone_CBIG_Ngo2019AuthorTopic/stable_projects/brain_parcellation
rm -r Sta... |
1cce3b4c30c263d7d3dd91aa40fde3e681276ac98de34ce36e2198e2a639b8ef | Shell | 696 | 18 | while read p; do
echo "genesOut <- MAGMA.Celltyping::map_snps_to_genes(
path_formatted = \"/Users/justincotney/Desktop/scRNA-Seq_GWAS/XiongZ_31763980."$p".formatted.tsv.bgz\",
genome_build = \"GRCh38\",
N = 10115,
population = \"eur\",
upstream_kb = 100,
downstream_kb = 100
)" >> generate_celltype_associ... |
6f7b0c9e983679f09aba3c84dc5c08c2db73d339dc9b686e61b80dd06851935b | Shell | 699 | 20 | #!/bin/bash
set -ex
if [ -n "$GCC_VERSION" ]; then
# Need the official toolchain repo to get alternate packages
add-apt-repository ppa:ubuntu-toolchain-r/test
apt-get update
apt-get install -y g++-$GCC_VERSION gfortran-$GCC_VERSION
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-"$GCC_VERSION" ... |
1ee65d7deb57e2319c65f6cb12cc88c050f3a010425096c2114529085b40ea0f | Shell | 707 | 24 | #!/bin/bash
#SBATCH --job-name=jupyter_notebook
#SBATCH --output=outLogs/notebook_%j.out
#SBATCH --error=outLogs/notebook_%j.err
#SBATCH --mem=6Gb
#SBATCH --time=3:00:00
#SBATCH --partition=mcdermott
#SBATCH --cpus-per-task=2
#SBATCH -x node043,node084,node093,node107,node034,node109,node112,node110
PROJECT_ROOT="$(c... |
a5775bf8c7e5d4b5a7eae3a3c2f31dac51e85c2414561d39d199491a1e410847 | Shell | 709 | 34 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
./figure_01_phase_singularity/run.sh
./figure_01_phase_singularity/fig.sh
./figure_02_detection/run.sh
./figure_02_detection/fig.sh
.... |
a2d9a5bfbda3cd15bf27e653cf72ab21ce563d0046d35a2e00867dbe9a4d9641 | Shell | 715 | 23 | #!/bin/bash
#SBATCH --job-name=get_tscrpt
#SBATCH --output=outLogs/get_swc_prolific_transcripts_%A_%a.out
#SBATCH --error=outLogs/get_swc_prolific_transcripts_%A_%a.err
#SBATCH --mem=8Gb
#SBATCH --cpus-per-task=2
#SBATCH --time=1:00:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:a100:1
#SBATCH --array=0-40# ... |
feb40fed24fd849fe639f1d4b63baba068cf431cafc2c93745f5a6d98f50cdf1 | Shell | 718 | 17 | #!/bin/bash
#SBATCH --job-name=spyking-circus
#SBATCH --partition=normal,bigmem
#SBATCH --time=99:99:99
#SBATCH --mem=120G
#SBATCH --cpus-per-task=28
#SBATCH --chdir=.
#SBATCH --output=/network/lustre/iss01/charpier/analyses/louis.cousyn/Scripts/slurm_output/output-%j_%a-%x.txt
#SBATCH --error=/network/lustre/iss01/cha... |
8495fe83c790c7322aaaecb113522260f79353ee168419c4e816bbb3494054ba | Shell | 721 | 22 | #!/bin/bash
# Step 1: Create a new conda environment with Python 3.10
conda create -n liten python=3.10 -y
# Step 2: Activate the new environment
source activate liten
# Step 3: Install PyTorch 2.4.0, TorchVision 0.19.0, and Torchaudio 2.4.0 with CUDA 12.1 support
pip install torch==2.4.0 torchvision==0.19.0 torchau... |
a192edeada2167fe37d948f1c466341fe4ee66067c4c2dba7a8ee48e0927786d | Shell | 730 | 18 | #!/bin/bash
set -ex
source "$(dirname "${BASH_SOURCE[0]}")/common_utils.sh"
# Cache the test models at ~/.cache/torch/hub/
IMPORT_SCRIPT_FILENAME="/tmp/torchvision_import_script.py"
as_jenkins echo 'import torchvision; torchvision.models.mobilenet_v2(pretrained=True); torchvision.models.mobilenet_v3_large(pretrained... |
a3853babd1737e43c2d0e2e217fec943cdee28f6de613448ab31842c1e6fa11f | Shell | 734 | 23 | #!/usr/bin/env bash
# Script that installs magma from tarball inside conda environment.
# It replaces anaconda magma-cuda package which is no longer published.
# Execute it inside active conda environment.
# See issue: https://github.com/pytorch/pytorch/issues/138506
set -eou pipefail
cuda_version_nodot=${1/./}
anaco... |
ec11cf3974bb6b7b3d149acd687e4e92fee28ccbf8d66f59c3fb86dad74490b7 | Shell | 753 | 25 | #!/bin/bash
set -ex
# cudss license: https://docs.nvidia.com/cuda/cudss/license.html
mkdir tmp_cudss && cd tmp_cudss
if [[ ${CUDA_VERSION:0:4} =~ ^12\.[1-4]$ ]]; then
arch_path='sbsa'
export TARGETARCH=${TARGETARCH:-$(uname -m)}
if [ ${TARGETARCH} = 'amd64' ] || [ "${TARGETARCH}" = 'x86_64' ]; then
... |
834d276a5220fd3c033dfb91bd5cf3e5e7fbdfd68fc4d506cad643066dc10b72 | Shell | 754 | 26 | #!/bin/sh
# Check how many lines there are in module - excludes blank lines
printf "\n\n\n\n CHECK MODULE SIZE:"
printf "\nNumber of lines of code & comments in FOOOF: "
find ./fooof -name "*.py" -type f -exec grep . {} \; | wc -l
# Check number of files using cloc
printf "\n\n\n CLOC OUTPUT (EXCLUDING TESTS): \n"
cl... |
fc421acad8dd168eb0a3eea3b37dd80715e7901e8bedd40e831e2414734d0475 | Shell | 754 | 20 | #!/bin/bash
set -ex
source /etc/rocm_env.sh
# AMD SMI is staged under the ROCm root and is intended to be imported by
# adding its share directory to Python's search path.
AMDSMI_SHARE_DIR="${ROCM_PATH}/share/amd_smi"
if [ -d "${AMDSMI_SHARE_DIR}/amdsmi" ]; then
echo "Exposing amdsmi from: ${AMDSMI_SHARE_DIR}"
S... |
7c1945b97560155c6058485f8ac5840d6bc7a28471f55a5e0b02c7ab772362da | Shell | 758 | 25 | #!/bin/bash
# run this within tested container to perform integration tests
# warning: test_dir is wiped out before and after testing !!!
# hint: to run this script from inside the test container
# e.g. ./run_tests_in_container.sh /hostshare/container_test_data/reconstructed_reference_images/fil-physicsc-V13.4 /hostsh... |
33bacc8b977bb5b6f567cbf60a68f7340a8775a9a744792c4061072352f93584 | Shell | 762 | 33 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
RAW=$(readlink -f ../01_data_brain/ksp_2D3)
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$... |
19b756e4a67d2bd669881799b402c9eb8b8bf70f956f27bc736148d8bbf169f1 | Shell | 767 | 23 | #!/bin/bash -l
#SBATCH --job-name=make_popham_stim
#SBATCH --output=outLogs/make_swc_popham_expmt_stim_2024_for_model_%A_%a.out
#SBATCH --error=outLogs/make_swc_popham_expmt_stim_2024_for_model_%A_%a.err
#SBATCH --mem=3Gb
#SBATCH --time=1:30:00
#SBATCH --partition=use-everything
#SBATCH --cpus-per-task=1
#SBATCH --arr... |
e4837f2ea85bf243b0e5d49e656162475ff2f603bad85176b42d13a788545be8 | Shell | 773 | 20 | #!/bin/bash
set -ex
function install_nvpl {
mkdir -p /opt/nvpl/lib /opt/nvpl/include
wget https://developer.download.nvidia.com/compute/nvpl/redist/nvpl_blas/linux-sbsa/nvpl_blas-linux-sbsa-0.3.0-archive.tar.xz
tar xf nvpl_blas-linux-sbsa-0.3.0-archive.tar.xz
cp -r nvpl_blas-linux-sbsa-0.3.0-archive... |
433b6ddaf8ff937c0c359ce4a2a7814cf71827d304380e9cef32748668bd908e | Shell | 780 | 26 | # AWS EC2 instance startup 'MIME' script https://aws.amazon.com/premiumsupport/knowledge-center/execute-user-data-ec2/
# This script will run on every instance restart, not only on first start
# --- DO NOT COPY ABOVE COMMENTS WHEN PASTING INTO USERDATA ---
Content-Type: multipart/mixed; boundary="//"
MIME-Version: 1.0... |
b1349eab220de059d6830304f2a2f51ef526c0f6b9519d4d9e959a2c99a02bb8 | Shell | 789 | 25 | #! /bin/bash
set -e
conda init
CONDA_ENVPY=$(conda info --base)/envs/ascent/bin/python
CONDA_BASE=$(conda info --base)/etc/profile.d/conda.sh
source $CONDA_BASE
conda create -n ascent
eval "$(conda shell.bash hook)"
conda activate ascent
conda install python=3.7
$CONDA_ENVPY -m pip install --upgrade pip setuptools whee... |
c708d5f8c6732099bf904f569ad95491c8326fad63941ee3b2eb65c4a9a733de | Shell | 790 | 25 | #! /bin/bash
set -e
conda init
CONDA_ENVPY=$(conda info --base)/envs/ascent/bin/python
CONDA_BASE=$(conda info --base)/etc/profile.d/conda.sh
source $CONDA_BASE
conda create -n ascent
eval "$(conda shell.bash hook)"
conda activate ascent
conda install python=3.11
$CONDA_ENVPY -m pip install --upgrade pip setuptools whe... |
d7f2e656d7e70d8256e2b271e6ca09afdee82ff88d86016faf6962811c888c64 | Shell | 790 | 26 | #!/bin/bash
#SBATCH --job-name=vqe_test
#SBATCH --output=vqe_test_%j.out
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=1
#SBATCH --gres=gpu:1 # consistent with the number of cards per node
#SBATCH --cpus-per-task=8
#SBATCH --partition=qdagnormal ... |
67b44fd3ff302c092a74ba8b30849468a1e01c2ec224e55d86d7293b428f1d54 | Shell | 792 | 11 | cd /media/lautaro/SSDLauti/reconallNCN
echo "SubjID,LLatVent,RLatVent,Lthal,Rthal,Lcaud,Rcaud,Lput,Rput,Lpal,Rpal,Lhippo,Rhippo,Lamyg,Ramyg,Laccumb,Raccumb,ICV" > LandRvolumes.csv
for subj_id in `ls -d *`; do
printf "%s," "${subj_id}" >> LandRvolumes.csv
for x in Left-Lateral-Ventricle Right-Lateral-Ventricle Left-... |
35203e2141c116e70f7df91417d61f76b5ecff9f36ef7a305da1461b17e138bd | Shell | 801 | 18 | allpeakFile="${projroot}/mba.whole.sa2.final.peak.srt.bed"
tssBed="${projroot}/meta/gencode.vM23.gene.tssUpDn1k.bed"
allpeakOvlpTssBed1="${outdir}/mba.whole.sa2.peakOvlpTSS.bed"
allpeakOvlpTssBed2="${outdir}/mba.whole.sa2.peakOvlpTSS.proximal.distal.bed"
allpeakOvlpTssBed3="${outdir}/mba.whole.sa2.peakOvlpTSS.p... |
fccb6aa8fe2de68b9fab7450b502d9147b5acf9941753c6b4730b17e4198a8bf | Shell | 807 | 26 | #! /bin/bash
set -e
conda init
CONDA_ENVPY=$(conda info --base)/envs/ascent/bin/python
CONDA_BASE=$(conda info --base)/etc/profile.d/conda.sh
source $CONDA_BASE
conda create -n ascent
eval "$(conda shell.bash hook)"
conda activate ascent
conda install python=3.11
$CONDA_ENVPY -m pip install --upgrade pip setuptools whe... |
fe12174c21731c177c65b61da1a65b11eec15916b1edaaac1ae37a522abe071a | Shell | 807 | 25 | #!/bin/zsh
# This script is to conbine all the 3D predictions into a
# single spatial dataframe in which the 3d tissue space
# is divided into a set of n x n x n grids (size $n). In
# each grid is the COUNT/Number of each cell-type.
# to generate this grid - the contours of the 3d tissue are used (mygdpdata.geojson)... |
8b86d876d61436f2b407587e7cf479a8a8f63db3396ff212ae1b033f4ddffa6b | Shell | 821 | 24 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$WORKDIR"' EXIT
cd "$WORKDIR" || exit
bart ex... |
c5fa13ccaf0ec0c80c0aab16acd9fec27291e3970c4829ec7ad7af2c68e081e7 | Shell | 827 | 21 | #!/bin/bash -l
#SBATCH --job-name=make_unfamiliar_stim
#SBATCH --output=outLogs/make_safe_swc_unfamiliar_distractor_stim_2024_%A_%a.out
#SBATCH --error=outLogs/make_safe_swc_unfamiliar_distractor_stim_2024_%A_%a.err
#SBATCH --mem=3Gb
#SBATCH --time=00:10:00
#SBATCH --partition=use-everything
#SBATCH --cpus-per-task=1
... |
c0f5f896110af60118f8acadba4a3a355a5e721fbbb62b71445505c4e7da8a4f | Shell | 832 | 19 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$WORKDIR"' EXIT
cd "$WORKDIR" || exit
bart re... |
723f706903548801e12677d68e7b3736c5faff061fcea1f1febe364bc169c259 | Shell | 835 | 27 | #!/bin/bash
set -ex
if [ -n "$KATEX" ]; then
apt-get update
# Ignore error if gpg-agent doesn't exist (for Ubuntu 16.04)
apt-get install -y gpg-agent || :
curl --retry 3 -sL https://deb.nodesource.com/setup_16.x | sudo -E bash -
sudo apt-get install -y nodejs
curl --retry 3 -sS https://dl.yarnpkg.com/de... |
fe3929aa0cb6468e8f54029bdc85b3490fe69d505f89bd3cfca3dca3bccf97dd | Shell | 843 | 32 | #!/usr/bin/bash
# Script to generate joint single cell count and meta files
# from 10X public data found at : https://support.10xgenomics.com/single-cell-gene-expression/datasets/
# in the subsection "Single Cell 3' Paper: Zheng et al. 2017"
# Create necessary folders
for ndir in raw tars all; do
if [ ! -d $ndir... |
a4841cf234a146aaeadf6ed3aab302c36ee6d6dc3d3c6d4d3c94cd14e922afeb | Shell | 846 | 23 | #!/bin/sh
. "$(dirname "$0")/lib.sh"
announce "iad forward calculations"
out="$TEST_TMP/forward.out"
"$IAD_EXECUTABLE" -z -a 0.9 -b 1 -g 0.8 -q 8 > "$out" 2>&1
assert_contains "$out" "R total = 0.0424"
assert_contains "$out" "T total = 0.8456"
assert_contains "$out" "T unscattered = 0.3679"
"$IAD_... |
f44b75157554870d14acda6213b30049afa30e6bf9b5831b51d5de77f2f43154 | Shell | 861 | 24 | #!/bin/bash
set +e
set -x
# Get the service name
RUNNER_SERVICE=$(cat "${RUNNER_WORKSPACE}/../../.service")
echo "GitHub self-hosted runner service: ${RUNNER_SERVICE}"
if [[ -n "${RUNNER_SERVICE}" ]]; then
echo "The self-hosted runner has encountered an unrecoverable error and will be shutdown"
pushd "${RUNNER_... |
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