sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
1e13aa02bdaa2c1c83ba0d5c2231726668659ad8fdb8a6dc1dc5d01bfb97a0e9 | Shell | 865 | 22 | # https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
wget https://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
wget https://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
grep "^>" <(gunzip -c Ho... |
5d64f6788ccc553376fb9bf4bf5013ab7dca2ef9dd1fe85d6f310d15906e10f4 | Shell | 881 | 18 | #!/bin/bash
# run gadgetron in a fil gadgetron container as root
# launcher must specify FULL path to this script for polkit action to allow without further authentication
container_name=$1
# Strip off the end of the container name, from the first occurence of "c-" (e.g. fil-physicsc-V15.0 becomes fil-physics)
#gad_m... |
76bc003c6255ee5d31d9d72ba05878cd455f1b51aa2d6ed7dba3e96d863b7e2e | Shell | 884 | 33 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$WORKDIR"' EXIT
cd "$WORKDIR" || exit
bart tr... |
0f82f9cf99c5336e1b35719dff6e99b682fa94aac9cb0a056139ab00e916b663 | Shell | 892 | 26 |
#!/usr/bin/env bash
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
# Dynamically detect CPU cores and use n - 1
TOTAL_CORES=$(nproc)
NUM_PROC=22
echo "[$(date)] Running TESTING only on CPU with $NUM_PROC threads..."
exec stdbuf -o0 -e0 dglke_eval \
--model_name RESCAL \
--dataset Biomedical_1_to_1 \
--d... |
92f89caed4ec667a876e168e31590d177ecd7a76850eb083c7853e1ed569e460 | Shell | 898 | 25 |
#!/usr/bin/env bash
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
# Dynamically detect CPU cores and use n - 1
TOTAL_CORES=$(nproc)
NUM_PROC=22
echo "[$(date)] Running TESTING only on CPU with $NUM_PROC threads..."
exec stdbuf -o0 -e0 dglke_eval \
--model_name RESCAL \
--dataset Biomedical_121_12M \
--... |
6d73a3defc198e93d3f2f26b5f9a970d2c0d6a736ebe01ae78a269ddea625736 | Shell | 900 | 20 | #!/bin/bash
#SBATCH -J synapse_download
#SBATCH -c 4 # Request one core
#SBATCH -t 0-8:00 # Runtime in D-HH:MM format
#SBATCH -p short # Partition to run in
#SBATCH --mem=20G # Memory total in MiB (for all cores)
#SB... |
beacf4898c456625947d07d0433e8ed84743bee1baf4cd93cb92cd2992b18c82 | Shell | 916 | 32 | #!/usr/bin/env bash
# run inside the r-maaslin2 micromamba environment
#### BARE MINIMUM COVARIATES
# Early 30-120 Infants Full
Rscript run-maaslin.R \
--dir_job '../' \
--job_prefix 'mice_1mo_to_4mo_Low_vs_TypicalHigh' \
--job_suffix '' \
--fixed_effects 'BSID_Low,Infant_Age,Seq_Depth' \
--fixed... |
32a1fed1be1d9920009bf21152e2c396cff283ca46f3a71526e4f0b170ae71db | Shell | 917 | 11 | #!/bin/bash
set -e
python 000_run_multi.py -n CNN_pH_kfold_val_multi_stop -d results/multitask_sub -c1 ckpt/multitask_sub -l 1 -t substrates_refine substrates_classes
python 000_run_multi.py -n CNN_pH_kfold_val_multi_freeze -d results/multitask_sub -c1 ckpt/multitask_sub -l 1 -t substrates_refine substrates_classes
p... |
24bf0acc92fc0e6ba92c45d765d13ba0a6412cb1ed16b223b35e8a81316a788a | Shell | 930 | 44 | #!/bin/bash
# ==========================
# USO:
# ./copiar_stats.sh /ruta/a/subjects /ruta/a/carpeta_destino
# ==========================
SOURCE_DIR="$1"
DEST_DIR="$2"
# --- Verificaciones básicas ---
if [ -z "$SOURCE_DIR" ] || [ -z "$DEST_DIR" ]; then
echo "Uso: ./copiar_stats.sh <carpeta_subjects> <carpeta_d... |
3c24a8a71da1ac034ecca1f8f83943dee9a2f2bd64e0154de0a8516cfb16f262 | Shell | 940 | 30 | #!/bin/sh
curr_dir=`pwd`
for folder in */
do
echo "[TEST](start) $folder"
cd $curr_dir
cp -r $folder $CBIG_CODE_DIR/stable_projects/
git add $CBIG_CODE_DIR/stable_projects/$folder/*
cd $CBIG_CODE_DIR
sh $CBIG_CODE_DIR/hooks/pre-commit
git reset
rm -r $CBIG_CODE_DIR/stable_projects/$folder
echo "You should ge... |
dd383c15a6f082d5e1c89cd736aba0aa083af5439209e1f0cc88b5f505508a5e | Shell | 947 | 32 | #!/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
if [ 1 ... |
c0aeabce8d25b33501411edfb26754bdeabdf21725fe1988a0b1fa3ed664df07 | Shell | 950 | 13 | #!/bin/bash
#SBATCH --mem=16000
#SBATCH --time=10:00:00
#SBATCH --ntasks=4
echo ${subid}
/usr/usc/matlab/default/bin/matlab -nodisplay -nosplash -r "addpath(genpath('/home/rcf-proj2/aaj/git_sandbox/bfp/src')); bfp /home/rcf-proj2/aaj/git_sandbox/bfp/supp_data/hpcconfig.ini /home/rcf-proj2/aaj/ADHD_Peking/data/Peking_a... |
d1d242fd0a04877c5fceee239e20c9710459e4c71aa6df336507e952826488b9 | Shell | 960 | 20 | #!/bin/bash
# Script used only in CD pipeline
set -ex
# Anaconda
# Latest anaconda is using openssl-3 which is incompatible with all currently published versions of git
# Which are using openssl-1.1.1, see https://anaconda.org/anaconda/git/files?version=2.40.1 for example
MINICONDA_URL=https://repo.anaconda.com/minico... |
8e631ef3d9ca3d4b6f1700d56b12f44aecb55006893ffeec435e367cf94dc0b6 | Shell | 963 | 29 |
#!/usr/bin/env bash
set -xe
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
# Dynamically detect CPU cores and use n - 1
TOTAL_CORES=$(nproc)
NUM_PROC=$((TOTAL_CORES - 10))
echo "[$(date)] Running TESTING only on CPU with $NUM_PROC threads..."... |
9a857840cf983903b6f771c74c34ebcb42b470c5c5a25d428cb6e93442ee9b0b | Shell | 963 | 29 |
#!/usr/bin/env bash
set -xe
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
# Dynamically detect CPU cores and use n - 1
TOTAL_CORES=$(nproc)
NUM_PROC=$((TOTAL_CORES - 10))
echo "[$(date)] Running TESTING only on CPU with $NUM_PROC threads..."... |
9be0dd9039ab0dddfe22b9ed762108efb12f4722c8f43590618a4b05dce4f8e2 | Shell | 963 | 29 |
#!/usr/bin/env bash
set -xe
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
# Dynamically detect CPU cores and use n - 1
TOTAL_CORES=$(nproc)
NUM_PROC=$((TOTAL_CORES - 10))
echo "[$(date)] Running TESTING only on CPU with $NUM_PROC threads..."... |
d59836eed5e516cdb8ffce81c221f7908a6e1e10117fae48e9fae42fe7844bda | Shell | 963 | 29 |
#!/usr/bin/env bash
set -xe
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
# Dynamically detect CPU cores and use n - 1
TOTAL_CORES=$(nproc)
NUM_PROC=$((TOTAL_CORES - 20))
echo "[$(date)] Running TESTING only on CPU with $NUM_PROC threads..."... |
24775ba8975ff5cc825eb3160e24403bd9a1fcf70f2b90ec5db54443fd30351a | Shell | 966 | 29 |
#!/usr/bin/env bash
set -xe
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
# Dynamically detect CPU cores and use n - 1
TOTAL_CORES=$(nproc)
NUM_PROC=$((TOTAL_CORES - 20))
echo "[$(date)] Running TESTING only on CPU with $NUM_PROC threads..."... |
621807f313ac3afe9364f6a0ab67a1602ba337aafe5dfeb3e269d52a44bce6a9 | Shell | 966 | 42 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
mkdir -p build/local
CMAKE_ARGS=()
# CMake-level configuration
CMAKE_ARGS+=("-DCM... |
e7c69a48efb7e298f3092c68598217aaa1a6075df7d75913adfb535e22dfd2fa | Shell | 968 | 29 |
#!/usr/bin/env bash
set -xe
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
# Dynamically detect CPU cores and use n - 1
TOTAL_CORES=$(nproc)
NUM_PROC=$((TOTAL_CORES - 20))
echo "[$(date)] Running TESTING only on CPU with $NUM_PROC threads..."... |
26d15f68bc303b2691c7dfd0a14ceb91e3cbb13c4233c3911d1f64f4a07e6aac | Shell | 969 | 7 | #! /bin/bash
# arch_flags="-arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5"
arch_flags="" # -arch i386 -arch x86_64"
# ../../configure --enable-python --with-wx-config=/Users/cs/wxbin/bin/wx-config CXX="/usr/bin/g++-4.0" CC="/usr/bin/gcc-4.0" LD="/usr/bin/g++-4.0" CPPFLAGS="-DH5_USE_16_A... |
6cf41139f0672c5f30126d1d9f986bde729f1ff14458502571b3dea69e581ac7 | Shell | 985 | 32 | #!/bin/sh
. "$(dirname "$0")/lib.sh"
[ -x "$AD_EXECUTABLE" ] || fail "AD_EXECUTABLE is not executable: $AD_EXECUTABLE"
ACTUAL_FILE=$(numeric_actual_file ad_basic)
: > "$ACTUAL_FILE"
announce "ad basic cases"
run_ad_numeric ad_base -m -a 0.9 -b 1 -g 0.8 -q 8
run_ad_numeric ad_oblique -m -a 0.9 -b 1 -g 0.8 -i 45 -q 8... |
8936fd2b94806bdc334be77759470be309bcbe7f801357bd36f4f940c66b9a2a | Shell | 987 | 38 | #!/bin/bash
# Script used only in CD pipeline
set -ex
OPENBLAS_VERSION=${OPENBLAS_VERSION:-"v0.3.34"}
OPENBLAS_CHECKOUT_DIR="OpenBLAS"
if [[ "$(uname -m)" == "aarch64" ]]; then
OPENBLAS_TARGET="ARMV8"
elif [[ "$(uname -m)" == "riscv64" && "${GCC_VERSION}" -lt 15 ]]; then
# FIXME: zvfbfwma (vector bfloat16 instru... |
901b7eda66f6fc193bf44129d0d8477e7076fa5adeab0e43c126f7304ab23b18 | Shell | 991 | 20 | #!/bin/bash
#SBATCH -o /data/CARD_singlecell/PFC_atlas/logs/01_atac_model.out
#SBATCH -e /data/CARD_singlecell/PFC_atlas/logs/01_atac_model.err
#SBATCH --partition=gpu
#SBATCH --cpus-per-task=2
#SBATCH --mem=350000
#SBATCH --gres=gpu:v100x:2
#SBATCH --time=48:00:00
# This is so kludgy, but this the input files just n... |
5bc873ba678c9d5d748b50abc81988e680a8e86198d1f796975b536be3fbcadf | Shell | 992 | 21 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( 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... |
777a7a0fd0e4ff141f13a85d699ead4accb0540d509ffe788df389987f3e6099 | Shell | 996 | 30 |
# module load sratoolkit/3.0.2
#
# parallel -j 6 --bar \
# fastq-dump -O fastq --split-3 --gzip \
# {} ::: SRR8571937 SRR8571938 SRR8571939 SRR8571940 SRR8571941 SRR8571942 SRR8571943 SRR8571944 SRR8571945 SRR8571946 SRR8571947 SRR8571948 SRR8571949 SRR8571950 SRR8571951 SRR8571952
# Download from ENA instead o... |
e91c1565854eb42c9f159d0dd82d5f728afb70211d7ffdde0c8932719c7c07ff | Shell | 1,005 | 39 | #!/bin/bash
stf_select_presets() {
local with_python="$1"
local python_configure_preset="$2"
local no_python_configure_preset="$3"
local python_build_preset="${4:-}"
local no_python_build_preset="${5:-}"
if [[ "$with_python" -eq 1 ]]; then
STF_CONFIGURE_PRESET="$python_configure_preset"
STF_BUILD_... |
ae9bf2e9247b346e15b649271ab24d70c8110395b804a2078189959b41f48a83 | Shell | 1,019 | 30 | #!/usr/bin/env bash
# run_rotate_eval_cpu.sh
set -xe
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
# Dynamically detect CPU cores and use n - 1
TOTAL_CORES=$(nproc)
NUM_PROC=$((TOTAL_CORES - 10))
echo "[$(date)] Running TESTING only on CPU wi... |
bf719609892973c8501394bfb4ed1abc4425806ad959f211bfea2ad12486337c | Shell | 1,019 | 46 | #!/usr/bin/env bash
date
echo "Getting the motif using Homer2"
#####
oripeak="Your/narrowpeak.bed/file"
printf "Your narrowpeak.bed file -- %s\n" $oripeak
motifdir="Your/motif/directory"
printf "Your directory for the homer2 output files"
annoforHomer2="Your/annotation/bed12"
printf "Your annotation bed12 file for ... |
0bed4d907b35fb44fe4fbcbe4fd4c8da32715b11a788ee19a15f57000c6cb2fc | Shell | 1,023 | 36 | #!/usr/bin/env bash
# run inside the r-linda micromamba environment
# Early, First 4 months
printf "Analyzing early (1-4 months) mice\n"
Rscript run-lmm.R \
--dir_job ".." \
--job_prefix "mice_1mo_to_4mo_Low_vs_TypicalHigh" \
--job_suffix "" \
--formula "~ BSID_Low + Infant_Age + (1|Stool_ID)"
# Earl... |
a0f1592c8e8cfc1cc697ec8f951d3f99e24d9a4e2d1e800c3aab7611ebac30e5 | Shell | 1,027 | 35 | #!/bin/bash
# run this within tested container to perform integration tests
# warning: test_dir is wiped out before and after testing !!!
ref_container=fil-physicsc-V16.0
test_container=fil-physicsc-V16.0_public_rc1
ref_dir=/hostshare/container_test_data/reconstructed_reference_images/${ref_container}
gadmat_fork=ba... |
3df8228a92be738ae98b2189ee9a92d6608b91207f06798118f20b037c18955b | Shell | 1,036 | 34 | #!/bin/bash -l
#SBATCH --job-name=get_unit_acts
#SBATCH --output=outLogs/get_unit_acts_for_anova_%j.out
#SBATCH --error=outLogs/get_unit_acts_for_anova_%j.err
#SBATCH --mem=20Gb
#SBATCH --cpus-per-task=8
#SBATCH --time=12:00:00
#SBATCH --partition=mcdermott
#SBATCH --gres=gpu:a100:1
PROJECT... |
0a46a4e69ca413ab166710d718f4cdd7e8359d2a5bd9ef85a16c726f74bf30db | Shell | 1,041 | 31 | #!/bin/bash -l
#SBATCH --job-name=eval_binaural_textures
#SBATCH --output=outLogs/mono_texture_test_stim_%A_%a.out
#SBATCH --error=outLogs/mono_texture_test_stim_%A_%a.err
#SBATCH --mem=12Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=3:00:00
#SBATCH --partition=mcdermott
#SBATCH --gres=gpu:1 --constraint=20GB
#SBATCH --... |
95ea7e7dc28ea1da3862e27463f5b58d4e31d9a7bd598b5db386a586fba4f886 | Shell | 1,042 | 27 | #!/bin/bash -l
#SBATCH --job-name=unit_anova
#SBATCH --output=outLogs/unit_anova_%A_%a.out
#SBATCH --error=outLogs/unit_anova_%A_%a.err
#SBATCH --mem=100Gb
#SBATCH --cpus-per-task=64
#SBATCH --time=4:00:00
#SBATCH --partition=use-everything
#SBATCH --array=38-367 # 0-92 for full
PROJECT_ROOT... |
026f48e72dd11513696cc899f449e3f6d0fe539731c822d803c46dd2eff6045f | Shell | 1,052 | 41 | # # !/bin/bash
top_dir=/media/yuhui/LCT
cd $top_dir
for patDir in subj_folder; do
{
cd ${top_dir}/${patDir}
for runDir in mt.sft; do
{
cd ${top_dir}/${patDir}/${runDir}
run_dsets=($(ls -f bold*.nii.gz))
run_num=${#run_dsets[@]}
for subj in rbold rdant; do #
{
3dTcat -prefix all_runs.${subj}.nii.... |
3ea652027ba2badefb21c03779303bf64f05e40486928703f862cf0a2b2d5e4c | Shell | 1,068 | 27 | #!/bin/bash
# Function to retry functions that sometimes timeout or have flaky failures
retry () {
$* || (sleep 1 && $*) || (sleep 2 && $*) || (sleep 4 && $*) || (sleep 8 && $*)
}
# Use openmp from conda which supports 11.0. Otherwise we'll end up with
# whatever version comes with homebrew which only supports t... |
eddece76c1082eb3d288aabe01bfa63a15df2860ce63edc80f3cfac2160040a4 | Shell | 1,080 | 23 | #!/bin/zsh
#
# Clean rebuild + editable install of PIMMS.
#
# Why the deletes matter: Cython's cythonize() SKIPS regenerating a .c file when
# that .c is newer than its .pyx, and build_ext can reuse cached .o files under
# build/. So a plain reinstall may NOT pick up .pyx changes. Removing the
# generated C (pimms/*.c)... |
899207bdbd250332c049f51b056fa88427b83b6696858b77de933892ca66ffc9 | Shell | 1,081 | 24 | #filter studies for those with at least one significant association
#grep "genome-wide significant variants (P<5e-8)" finngen_*.mungesumstats_log/finngen_*_log_msg.txt | grep -v "0 genome-wide significant variants (P<5e-8)" | cut -f1 -d " " | uniq | sed -e 's/\./\t/g' -e 's/finngen_R11_//g' | cut -f1 > FINNGEN/signific... |
718c5c14688b354ef2e8d04e7d5cdd235ac851aa663d9509e105b0d1d9ebf2fa | Shell | 1,085 | 27 | #!/bin/bash
# Stop hook — blocking. The session may not end on a findings file that would
# lose findings at publication.
#
# Exit 2 is what Claude Code reads as "do not stop, here is why"; the stderr
# text becomes the model's next instruction.
#
# `stop_hook_active` guards the obvious loop: it is true when the model ... |
9242d886346583587d19d500e1ee9df117a00dddd8334094aaf108be3221714e | Shell | 1,092 | 42 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( 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
ba... |
02c0de601afb28013664f599e38954d0fb7b312e7a8cb45d76b5cd08284a718b | Shell | 1,093 | 34 | #!/bin/bash -l
#SBATCH --job-name=get_unit_acts
#SBATCH --output=outLogs/get_unit_acts_diff_sources_%A_%a.out
#SBATCH --error=outLogs/get_unit_acts_diff_sources_%A_%a.err
#SBATCH --mem=20Gb
#SBATCH --cpus-per-task=8
#SBATCH --time=12:00:00
#SBATCH --partition=mcdermott
#SBATCH --gres=gpu:a100... |
a0f60359a5902961706e6b7415fb2df33c33222fd75a9d7d8e2f929c1bd199d0 | Shell | 1,095 | 23 | #!/bin/zsh
Rscript 08.DNNs/03b.tune_soil_cv.R --model 1 --fold 1
Rscript 08.DNNs/03b.tune_soil_cv.R --model 1 --fold 2
Rscript 08.DNNs/03b.tune_soil_cv.R --model 1 --fold 3
Rscript 08.DNNs/03b.tune_soil_cv.R --model 1 --fold 4
Rscript 08.DNNs/03b.tune_soil_cv.R --model 1 --fold 5
Rscript 08.DNNs/03b.tune_soil_cv.R --m... |
fc08d515ef0705b2ab2d378f6db307b28bb1e1dda5b760f636d92b46ac1b3cdc | Shell | 1,095 | 23 | #!/bin/zsh
Rscript 08.DNNs/03b.tune_soil_cv.R --model 3 --fold 1
Rscript 08.DNNs/03b.tune_soil_cv.R --model 3 --fold 2
Rscript 08.DNNs/03b.tune_soil_cv.R --model 3 --fold 3
Rscript 08.DNNs/03b.tune_soil_cv.R --model 3 --fold 4
Rscript 08.DNNs/03b.tune_soil_cv.R --model 3 --fold 5
Rscript 08.DNNs/03b.tune_soil_cv.R --m... |
830db59bb31e0f95402f77bdf7a91a914853db9011e4ce330c82009afa14b736 | Shell | 1,096 | 51 | #!/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=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
#trap 'rm -rf... |
8e19ac33082b2de90f1c11e21e7b3c00d5938693ea9890f5c050db0d2233b583 | Shell | 1,106 | 37 | #!/bin/bash
INPUT_DIR="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Raw_T1/datos_check_de_preprocesamiento"
OUTPUT_DIR="${INPUT_DIR%/}/preprocessed_ANTS_affine"
mkdir -p "$OUTPUT_DIR"
MNI_TEMPLATE="/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz"
shopt -s nullglob
for nii in "$INPUT_DIR"/*.nii "$INPUT_DIR"/... |
ebb1e0d56265bcc3d6eb80c8a583f6ed169182bac49b4c7f632173735e479428 | Shell | 1,108 | 39 | #!/bin/bash
INPUT_DIR="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Raw_T1/datos_check_de_preprocesamiento"
OUTPUT_DIR="${INPUT_DIR%/}/preprocessed_ANTS_rigid"
mkdir -p "$OUTPUT_DIR"
MNI_TEMPLATE="/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz"
shopt -s nullglob
for nii in "$INPUT_DIR"/*.nii "$INPUT_DIR"/*... |
f97227ced803a345270cebdfbdc97d82418b5366e2dbbfdac34df28451b4fc99 | Shell | 1,123 | 25 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
adb push build/android/x86/convolution-test /data/local/tmp/convolution-test
adb pu... |
01d47c7e696a7a7d6b2098ac9ae868131e52a7160a50ded86a3c15c961a2c896 | Shell | 1,126 | 26 | #!/bin/sh
# Last successfully run on Dec 17th, 2019
# Written by Gia H. Ngo and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
... |
cfe4f3c0ff17dd21bea9eb8b2cbeea93fb8462b6da68a3176354cc064cc061c0 | Shell | 1,127 | 25 | #! /bin/sh
# Last successfully run on May 2nd 2017
# Written by [xxx] and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# ... |
d9f278c9568552a9532542bcb5c5ecb1cb43dbed6dfc779849ae834dc560111e | Shell | 1,127 | 25 | #! /bin/sh
# Written by [xxx] and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# Last successfully run on May 2nd 2017
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# ... |
96bf3e8a1a1fcd7571d2d56de64c0f03d7a043d051c1bc260aacd9aaa4a5cbf3 | Shell | 1,129 | 37 | #!/bin/bash
INPUT_DIR="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Raw_T1/FULL_ADNI_images"
OUTPUT_DIR="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Preprocessed/DeepBrainNet/ADNI"
mkdir -p "$OUTPUT_DIR"
MNI_TEMPLATE="/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz"
shopt -s nullglob
for nii in "$INPUT_DIR... |
da78da723d08183074ed7ecb83c8a448edd486f48dcd772aae572f823c5465ce | Shell | 1,131 | 38 | #!/bin/bash
#paths
INPUT_DIR="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Raw_T1/FULL_ADNI_images"
OUTPUT_DIR="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Preprocessed/BrainAgeNeXt/ADNI"
mkdir -p "$OUTPUT_DIR"
MNI_TEMPLATE="/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz"
shopt -s nullglob
for nii in "$IN... |
757a31d083f17ec74761c5dced5718a290b30dcd4de44eca2ab2694ae147bbfb | Shell | 1,136 | 39 | while read x; do
echo "reformatted_finngen <- MungeSumstats::format_sumstats(
path=\"FINNGEN/finngen_R11_"$x".gz\",
save_path = \"finngen_R11_"$x".formatted.tsv.bgz\",
force_new = TRUE,
ref_genome=\"GRCh38\",
convert_ref_genome=\"GRCh38\",
local_chain = \"GRCh37_to_GRCh38.chain\",
dbSNP = 155,
allele_f... |
cd9cabb657c86cff3c84c6aefa63ce94b45c9be9d35bd83e8f5e364f455cc335 | Shell | 1,139 | 31 | #!/bin/bash -l
#SBATCH --job-name=get_tscrpt
#SBATCH --output=outLogs/get_binaural_manifest_transcripts_%j.out
#SBATCH --error=outLogs/get_binaural_manifest_transcripts_%j.err
#SBATCH --mem=8Gb
#SBATCH --cpus-per-task=2
#SBATCH --time=1:00:00
#SBATCH --partition=mcdermott
#SBATCH --gres=gpu:a100:1
PROJECT_ROOT="$(cd... |
7b2a58537c470ceb59208683dd2d4e501276ed5f10cdae4d21d7c37c7d8537f8 | Shell | 1,140 | 25 | #!/bin/bash
#SBATCH --cpus-per-task 1
#SBATCH --mem-per-cpu=32G
#SBATCH --time 24:00:00
#SBATCH --array=0-303
#SBATCH --gres=lscratch:2000
#SBATCH --output=/data/CARD_singlecell/SN_atlas/cellbender/logs/pileup-%a.out
module load samtools
module load bcftools
# Make a temporary location
mkdir /lscratch/$SLURM_JOB_ID/... |
73a0e335e0e5accc99950b7fe4654d0ec38258c2c3abc76d530b3a9bba4c6592 | Shell | 1,142 | 40 | #!/bin/bash
set -ex
# Since version 24 the system ships with user 'ubuntu' that has id 1000
# We need a work-around to enable id 1000 usage for this script
if [[ $UBUNTU_VERSION == 24.04 ]]; then
# touch is used to disable harmless error message
touch /var/mail/ubuntu && chown ubuntu /var/mail/ubuntu && userd... |
76057738268a5ff2bdfa4463921aff73726e301c14c385b93f56ba88cffb8c55 | Shell | 1,147 | 47 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( 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
if [[ -... |
8c9552715e7c0d9a624924db63b48f704d663876e8c685bf55b002e28abc9873 | Shell | 1,147 | 39 | #!/bin/sh
set -eu
case "${1:-full}" in
veryshort)
"$(dirname "$0")/test_iad_basic.sh" --veryshort
;;
basic)
"$(dirname "$0")/test_iad_basic.sh"
"$(dirname "$0")/test_iad_forward.sh"
"$(dirname "$0")/test_iad_no_sphere.sh"
"$(dirname "$0")/test_iad_one_sphere_no_... |
a8ceaa9a57d5b47bd0dacb0a665c7c96c8335f96b225b2cae5364ad67fe8ff7a | Shell | 1,152 | 34 | #!/bin/bash
#
# CBIG_prepend_prefix_to_function_name_wrapper.sh $file_path
# Wrapper function to search for all instances of a function name (without prefix)
# inside a predefined set of directories and replace them by the new function name
# with the prefix prepended, if prompted
# Input can be the function name, a f... |
89166909066d3f9aed35b3c156a81d3ca52262e28ccc010b236a99e04ff437e1 | Shell | 1,155 | 41 | #!/usr/bin/env bash
set -e # Stop script execution if any run.sh fails
# List of directories to process
directories=(
"BioMistral"
"BioMistralFinetuned"
"medgemma"
)
echo "Starting sequential execution of run.sh scripts..."
echo "================================================="
for dir in "${directori... |
793fa2a5058ce8792ea4f9bcae0955ad4d0c86c275b92b1d576acc3f0b7774f8 | Shell | 1,159 | 37 | #!/bin/bash
#paths
INPUT_DIR="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Raw_T1/CP0173_skullstripped"
OUTPUT_DIR="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Preprocessed/DeepBrainNet/CP0173skullstripped"
mkdir -p "$OUTPUT_DIR"
MNI_TEMPLATE="/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz"
shopt -s nullglo... |
5dd3f0a345dc259ce5e2747aa78e2d2ffe7ad7d4eb7e27be5a1d8d13638a0b76 | Shell | 1,160 | 34 | #!/bin/bash
INPUT_DIR="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Raw T1/datos_check_de_preprocesamiento"
OUTPUT_DIR="${INPUT_DIR%/}/preprocessed_FLIRT_rigid"
mkdir -p "$OUTPUT_DIR"
# Ruta al template MNI (ajústalo si usás otra versión de FSL)
MNI_TEMPLATE="/usr/local/fsl/data/standard/MNI152_T1_1mm_brain"
# Recor... |
192ead970723e50b9e5a930ab909045680bf6414b82e4f074cd3f915adeb69e0 | Shell | 1,162 | 34 | #!/bin/bash
INPUT_DIR="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Raw T1/datos_check_de_preprocesamiento"
OUTPUT_DIR="${INPUT_DIR%/}/preprocessed_FLIRT_affine"
mkdir -p "$OUTPUT_DIR"
# Ruta al template MNI (ajústalo si usás otra versión de FSL)
MNI_TEMPLATE="/usr/local/fsl/data/standard/MNI152_T1_1mm_brain"
# Reco... |
43d121a16b9aaa87ee224489cc68060b71d54f3d67052d321373d34d37f22093 | Shell | 1,165 | 32 | #!/usr/bin/env bash
# initialize and activate
eval "$(conda shell.bash hook)"
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
echo "[$(date)] Activated env and set DGLBACKEND. Launching training…"
# prefix the training CLI with stdbuf to turn off buffering in any subprocess
exec stdbuf -... |
ffa84412e2676a5fe6e27f0c9c4212c5e643d929ea022d1d05404e3238e89b59 | Shell | 1,165 | 25 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
adb push build/android/arm64-v8a/convolution-test /data/local/tmp/convolution-test
... |
e06cced08b0140fd1fad4a87f6a1592a358fdbac2eed8bcd8cdf9da96860baf3 | Shell | 1,176 | 29 | #!/bin/zsh
#
# Remove PIMMS run-output files (trajectories, energies, analysis .dat files,
# restart snapshots, status logs, and the echoed parameter / angle files) from
# the repo root and every demo / validation directory. Input keyfiles
# (KEYFILE.kf), parameter files (params.prm) and any *new_restart.pimms inputs
#... |
7e6949a463d7b852b203df22a89a12e54acf74beb138699b410f50e81b75531c | Shell | 1,177 | 30 | #!/bin/bash -l
#SBATCH --job-name=eval_popham_swc
#SBATCH --output=outLogs/binaural_popham_swc_conds_all_stim_alt_archs_v10_%A_%a.out
#SBATCH --error=outLogs/binaural_popham_swc_conds_all_stim_alt_archs_v10_%A_%a.err
#SBATCH --mem=12Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=0:10:00
#SBATCH --partition=normal
#SBATCH... |
6672e0fae632f5e99bf81ee1e415df795f9d2936f60dc307332c2819127d505b | Shell | 1,179 | 25 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
adb push build/android/armeabi-v7a/convolution-test /data/local/tmp/convolution-tes... |
6df374a4b5bb4e99a6f03e3f685eb537dd0b849c33bb45b06259d389a1af4531 | Shell | 1,180 | 33 | #!/usr/bin/env bash
# initialize and activate
eval "$(conda shell.bash hook)"
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
echo "[$(date)] Activated env and set DGLBACKEND. Launching training…"
# prefix the training CLI with stdbuf to turn off buffering in any subprocess
exec stdbuf -... |
7415259488e2f060de9034d45b6929365dc318f0d45c8c993a30d0178d9bf0e4 | Shell | 1,181 | 30 | #!/bin/bash -l
#SBATCH --job-name=eval_cue_duration
#SBATCH --output=outLogs/cue_duration_test_stim_%A_%a.out
#SBATCH --error=outLogs/cue_duration_test_stim_%A_%a.err
#SBATCH --mem=4Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=0:10:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:1 --constraint=20GB
#SBATCH --a... |
237ef2a3fedc3cc95523dbd0f7d9f2dea88d42ae62c242b11e8537b0fa067ab7 | Shell | 1,188 | 33 | #!/usr/bin/env bash
# initialize and activate
eval "$(conda shell.bash hook)"
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
echo "[$(date)] Activated env and set DGLBACKEND. Launching training…"
# prefix the training CLI with stdbuf to turn off buffering in any subprocess
exec stdbuf -... |
d2b228243a426d65d47161626d7fb7683137eebce358def06352df2ea925d4db | Shell | 1,193 | 36 | #!/usr/bin/env bash
# run_complex.sh
# initialize and activate
eval "$(conda shell.bash hook)"
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
echo "[$(date)] Activated env and set DGLBACKEND. Launching training…"
# prefix the training CLI with stdbuf to turn off buffering in any subpr... |
4099d9a39c94e59cca761bd8b6cf23682f019eda62ae5d90b27a8f45ca09956d | Shell | 1,194 | 30 | #!/usr/bin/env bash
# Require only one python installation
if [[ -z "$DESIRED_PYTHON" ]]; then
echo "Need to set DESIRED_PYTHON env variable"
exit 1
fi
# If given a python version like 3.6m or 2.7mu, convert this to the format we
# expect. The binary CI jobs pass in python versions like this; they also only
#... |
6bb2d3bcb577291e34f906fd7d6a2521d801055e06b2c0c7250648c87b4d5d77 | Shell | 1,198 | 36 | #!/bin/bash
set -ex
# cuSPARSELt license: https://docs.nvidia.com/cuda/cusparselt/license.html
mkdir tmp_cusparselt && cd tmp_cusparselt
cusparselt_version=$1
arch_path='sbsa'
export TARGETARCH=${TARGETARCH:-$(uname -m)}
if [ ${TARGETARCH} = 'amd64' ] || [ "${TARGETARCH}" = 'x86_64' ]; then
arch_path='x86_64'
f... |
dd902c1897952208fca7c5f2cb36080d5a11a33c289974f8c2a29eba32950823 | Shell | 1,203 | 37 | #!/bin/bash
set -ex
# Most of the time, NCCL version won't diverge for different CUDA versions,
# so we can just use the default NCCL version.
NCCL_VERSION=$(cat ci_commit_pins/nccl.txt)
# If NCCL version diverges for different CUDA versions, uncomment the following
# block and add the appropriate files (using CUDA ... |
1c3d22f49c235d4f112380a406420c8fc1d649d2ab46ffeeadc5030d212c3be1 | Shell | 1,223 | 35 | #!/bin/bash
set -ex
# Where to create the venv. Defaults to the linter image location; the main CI
# image overrides it to a per-version path.
VENV_PATH="${VENV_PATH:-/var/lib/jenkins/ci_env}"
apt-get update
# Use deadsnakes in case we need an older python version
sudo add-apt-repository -y ppa:deadsnakes/ppa
if [[ ... |
24f8c397ec56fda896ca5b2d882aaa5a19e310404346ea1efea71a5b6fc43c18 | Shell | 1,230 | 43 | #!/bin/bash
#SBATCH --job-name=train_new_binaural_attn
#SBATCH --output=outLogs/train_v11_main_feature_gain_arch_%j.out
#SBATCH --error=outLogs/train_v11_main_feature_gain_arch_%j.err # train_v09_gender_bal_4M_w_no_cue_learned_ word_task_v09_cue_loc_task_
#SBATCH --mem=100Gb
#SBATCH -N 1
PROJECT_ROOT="$(cd "$(dirname ... |
fbc304957b60ce82345464dffc815ec0bd1304938cc7b923d770b1ba79718ad0 | Shell | 1,235 | 43 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
06ae3b0756687c4fc2919ecb09e3ca152069b0a3b44f7654600742447629b9d8 | Shell | 1,238 | 33 | #!/usr/bin/env bash
# run_rescal.sh
set -xe # echo each command and exit on error
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1 # force Python stdio unbuffered
echo "[$(date)] Activated env and set DGLBACKEND. Launching RESCAL training…"
# prefix the tr... |
04499a4c20056a91296043193dc7f02fe0938f1ab006ed39aa9f33c2b82bc5c3 | Shell | 1,242 | 36 | set -ex
LOCAL_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
ROOT_DIR=$(cd "$LOCAL_DIR"/../.. && pwd)
TEST_DIR="$ROOT_DIR/test"
gtest_reports_dir="${TEST_DIR}/test-reports/cpp"
pytest_reports_dir="${TEST_DIR}/test-reports/python"
# Figure out which Python to use
PYTHON="$(which python)"
if [[ "${BUILD_ENVIRONMENT}... |
2d172b9b32c0a4821f32c85b46f366f51dfc9c4c644d9d402279995799dfa59b | Shell | 1,242 | 37 | #!/bin/bash
#$ -S /bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id$
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevich, University of Pennsylvania
#
# This file is part of ... |
234b523e802b0ba3d319ec9c75889031bbb9ab69f92a4557e0feff301656442f | Shell | 1,245 | 28 | #!/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
cp $SCR... |
d09406e1924dd0321b438f9283e1ea352f3e48c8d91d281e484366140063165f | Shell | 1,246 | 31 | #!/bin/bash -l
#SBATCH --job-name=eval_popham_swc
#SBATCH --output=outLogs/binaural_popham_swc_conds_all_stim_%A_%a.out
#SBATCH --error=outLogs/binaural_popham_swc_conds_all_stim_%A_%a.err
#SBATCH --mem=12Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=0:10:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:1 --cons... |
290b2bb741652eb2128aed15bb9aa8554d4521d6b8b235850beda76cbd63bbae | Shell | 1,247 | 27 | #!/bin/bash
# AWS EC2 instance startup script https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/user-data.html
# This script will run only once on first instance start (for a re-start script see mime.sh)
# /home/ubuntu (ubuntu) or /home/ec2-user (amazon-linux) is working dir
# Use >300 GB SSD
cd home/ubuntu
if [ ! -... |
37c9807d3b5e819f682d15d94df8cb5bec937e4dee96d0f2c7df770353628e9e | Shell | 1,253 | 34 | #!/usr/bin/env bash
# run_simple.sh
set -xe # echo each command and exit on error
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1 # force Python stdio unbuffered
echo "[$(date)] Activated env and set DGLBACKEND. Launching SimplE training…"
# prefix the tr... |
51ca2b3106aacefd99df9e93113bb61271e27335107fb89c61df662d61693eec | Shell | 1,253 | 33 | #!/bin/bash
set -ex
source "$(dirname "${BASH_SOURCE[0]}")/common_utils.sh"
retry () {
"$@" || (sleep 10 && "$@") || (sleep 20 && "$@") || (sleep 40 && "$@")
}
# ONNXRuntime should be installed before installing
# onnx-weekly. Otherwise, onnx-weekly could be
# overwritten by onnx.
# Note: parameterized, pytest-... |
9e82c2520b2acefe121bdd6093134977123f5ad9154fd168eca504c596f0f437 | Shell | 1,255 | 43 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
66c44466f4004a468ad946c83cb02d206e08f3a9cda0be9f87d0aba218a0d185 | Shell | 1,258 | 43 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
71099f273e0ccf6830a37390f6292598ee126c7481ae1630d7e0ecd9af2eb766 | Shell | 1,273 | 34 | #!/usr/bin/env bash
# run_rescal.sh
set -xe # echo each command and exit on error
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1 # force Python stdio unbuffered
echo "[$(date)] Activated env and set DGLBACKEND. L... |
68d0a7b516010c9ccce3413eb2d79cad1b5175e64db0c1411f981a8f6ceecb42 | Shell | 1,279 | 33 | #!/usr/bin/env bash
# run_rescal.sh
set -xe # echo each command and exit on error
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1 # force Python stdio unbuffered
echo "[$(date)] Activated env and set DGLBACKEND. L... |
ab380fdba4e483b44297294985c95261b82ca6b5406b2948c1c4a24a4fa61199 | Shell | 1,279 | 34 | #!/usr/bin/env bash
# run_rotate.sh
set -xe # echo each command and exit on error
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1 # <— force Python stdio unbuffered
echo "[$(date)] Activated env and set DGLBACKEND... |
a545c23a32a0bc54370d0ac4ab4f2edf7d1fb6595c15d0e87cc4fb468cec20fa | Shell | 1,286 | 43 | module load miniconda
conda activate conjFDR
#source /home/yd357/pi_paths/pi_alag/env/pleioFDR_env/bin/activate
INPUT_DIR="/home/yd357/pi_paths/pi_alag/Tools/PLACO/data/GWAS"
OUTPUT_DIR="/home/yd357/pi_paths/pi_alag/Tools/pleiofdr/data/convert_GWAS"
CONVERT_DIR="/home/yd357/pi_paths/pi_alag/env/pleiofdr/python_conver... |
2c0753e73857bbd970c91242b82a0f8e7ecb5ab228883e052f655f81637444dc | Shell | 1,287 | 32 | #!/bin/bash -l
#SBATCH --job-name=eval_binaural_swc
#SBATCH --output=outLogs/binaural_swc_test_2024_v10_arch_search_%A_%a.out
#SBATCH --error=outLogs/binaural_swc_test_2024_v10_arch_search_%A_%a.err
#SBATCH --mem=12Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=0:15:00
#SBATCH --partition=use-everything
#SBATCH --gres=gp... |
81a43cc2cb80081471585307fa59bad0c7210832771325c2c0722d48c1f49eaf | Shell | 1,294 | 47 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
176defb627452e61b7b78da01cd6cfe2b99478950476b5a38e3a2625cf73f0bc | Shell | 1,296 | 38 | #!/bin/bash
# exit when any command fails
set -e
# keep track of the last executed command
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
cleanup() {
exit_code=$?
if [ ${exit_code} == 0 ]
then
echo "Completed execution"
else
echo "\"${last_command}\" failed with exit code... |
554a8eae69dc461705fa1bafad069b1e690cc2d26559b8ec04dd3023fc416a69 | Shell | 1,297 | 36 | ###############################################
#!/usr/bin/env bash
set -xe
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1 # force Python stdio unbuffered
echo "[$(date)] Activated env and set DGLBACKEND. Launching... |
8d0f21c464d067a519dbf0772e232a07e6273f894a8322b11a96b019405ed211 | Shell | 1,297 | 32 | #!/bin/bash -l
#SBATCH --job-name=eval_popham_swc
#SBATCH --output=outLogs/binaural_popham_swc_conds_all_stim_control_arch_%A_%a.out
#SBATCH --error=outLogs/binaural_popham_swc_conds_all_stim_control_arch_%A_%a.err
#SBATCH --mem=12Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=0:20:00
#SBATCH --partition=normal
#SBATCH -... |
98a963137c0c85a740edc3efdd3e87700a7c4e430dc0b8d3dc0debc834e4d0e2 | Shell | 1,301 | 34 | #!/usr/bin/env bash
# run_rescal.sh
set -xe # echo each command and exit on error
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1 # force Python stdio unbuffered
echo "[$(date)] Activated env and set DGLBACKEND. L... |
b154384cd1fdda223c6b83ae4be5225c6105ec9ea10444f76a24fe6cec057176 | Shell | 1,306 | 39 | #!/bin/bash
#SBATCH --cpus-per-task 1
#SBATCH --mem-per-cpu=32G
#SBATCH --time 96:00:00
#SBATCH --output=logs/snakemake-%j.out
module purge
module load apptainer
module load snakemake/7.7.0
# Pull profile, this will only run once, and is required for running on Biowulf
git clone https://github.com/NIH-HPC/snakemake_... |
95d65249559d082740cac713681ed5216999e674ec62431864f3a4e9e99c253e | Shell | 1,314 | 41 | #!/usr/bin/env bash
# Upload a binary to a bucket, supports dry-run mode
set -euo pipefail
# Optional inputs. By default upload to s3://ossci-linux
TARGET_OS=${TARGET_OS:-linux}
UPLOAD_BUCKET=${UPLOAD_BUCKET:-s3://ossci-${TARGET_OS}}
UPLOAD_SUBFOLDER=${UPLOAD_SUBFOLDER:-}
# Download to ${{ runner.temp }}/artifacts ... |
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