sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
63623b88ffbec4f66134f7b3b85a9dd8df8f2107d0119b3f35930b8154c3036e | Shell | 1,180 | 24 | #!/bin/bash
#SBATCH --time=02:30:00
#SBATCH --mem=500M
#SBATCH --array=1-210
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/decoder-%A_%a.out
#SBATCH --cpus-per-task=1
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" variants.txt`
IFS=' ' read -a array <<< "$variants"
cd /m/cs/scratch/networks-pm/effects_externalfacto... |
353d7bc7c7345d189604ceb3d6f7820b366dd6fe6f57e5934849a01372577b2e | Shell | 1,182 | 39 |
# Function to display help
function show_help {
echo "Usage: $0 [options] <output_directory> <observations>"
echo "example: ./vcf_wav.sh ../Data 1998"
echo "Options:"
echo " -h, --help Show this help message and exit"
echo ""
echo "Arguments:"
echo " output_directory ... |
998cb66ad30fe37760c04059e96dcbb5d66289b0a47f6aa364d45e10ab0b5245 | Shell | 1,182 | 25 | #! /bin/bash
config_file_expert="configs/bcdc/bcdc_config_expert.json"
config_file_mclust="configs/bcdc/bcdc_config_mclust.json"
python visium_data_to_matrix_representation_converter.py --params ${config_file_mclust}
echo "========================================"
echo "Data convertend in matrix representation"
python... |
6f8c13f2025de369644aea4cd8459021efb01a4c6343601a38fb7538f1a5011c | Shell | 1,184 | 44 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
NCOLS=3
N2ROWS=1.4e5
# 1e6 causes out-of-memory
for n1rows in 1e3 0.2e4 0.4e4 0.6e4 0.8e4 1e4; do
echo "===== sqrt-bsxfun-dist2(): n1rows = $n1rows"
TOP_LOG=${TOP_LO... |
7efe201e099146eee123524d4ade357959d68dcc41099a04c4c062ea2c2e8b67 | Shell | 1,188 | 40 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -l <brainNameList> -d <brainDir>
... |
d2eff80c674dbc85b4835bdc4e034856cd1bb4f4e1fd793945723b345c5ab3b6 | Shell | 1,190 | 25 | #! /bin/bash
config_file_expert="configs/melanoma/melanoma_config_expert.json"
config_file_mclust="configs/melanoma/melanoma_config_mclust.json"
python st_data_to_matrix_representation_converter.py --params ${config_file_mclust}
echo "========================================"
echo "Data convertend in matrix representa... |
2103d50a295e3eff08b0393f5dee700f2fcb17d4eeb843af60b29341e4e0190e | Shell | 1,194 | 24 | #!/bin/bash
#SBATCH --time=04:00:00
#SBATCH --mem=20G
#SBATCH --array=11-24
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/glm-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" variants.txt`
IFS=' ' read -a array <<< "$variants"
cd /m/cs/scratch/networks-pm/effects_externalfactors_on_fu... |
9fcbab7a27fcb6480cdff13a44494658727601ee32a85a20da0414e9c1c4783a | Shell | 1,194 | 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 "$... |
5f28fd302cdbded2d65c1458c40b34bcfe1cc322e126c2b5b80e05698ac110d9 | Shell | 1,195 | 67 | #!/bin/bash
set -e
set -u
callsFile="${1}"
probsFile="${2}"
outputFolder="${3}"
fileName="${callsFile%.calls}"
chrNr="${fileName#*_}"
echo "$callsFile $probsFile output=$outputFolder $fileName $chrNr"
#exit 0
if [[ -z "$callsFile" ]]
then
echo "Error: set input"
exit
fi
if [[ -z "$outputFolder" ]]
then
echo "Er... |
1d30823bd07dcdd379f1cc5317dc875a9059172e438711dcaa11e429a2cce319 | Shell | 1,196 | 40 | #!/bin/bash
# syntax: ./script {lr_schedule} {start_ix} {stop_ix}
# start_ix and stop_ix are indices of genes in filename
# (everything between gets run in order)
# read the list of cancer genes from tsv file
filename="data/vogelstein_cancergenes.tsv"
read_genes_from_file() {
# create global gene array
decla... |
961cd2a6f1d104214c283b2245c4ac8125fc81b8774cb1c53ac894e70a1ced68 | Shell | 1,198 | 25 | #! /bin/bash
config_file_expert="configs/human_dlpfc/dlpfc_config_expert.json"
config_file_mclust="configs/human_dlpfc/dlpfc_config_mclust.json"
python visium_data_to_matrix_representation_converter.py --params ${config_file_mclust}
echo "========================================"
echo "Data convertend in matrix repres... |
3f3880fa1c76058bf5442ab3409b0094e441ace5e2b81a5103419ae7509ac15a | Shell | 1,199 | 40 | #!/bin/bash
# File: run_example.sh
# Author: Kelly Chang
# Date: Oct 2017
# Version: 1.0
#
# Description: Bash script to demonstrate the use of AP simulation scripts.
# This code is provided for example only.
#
# run control simulation
Rscript AP_simulation.R >& logfiles/con... |
e10b2f7ba646e96afd461224f204c62b97d64812d5b577b4b546e8c3669e413c | Shell | 1,199 | 64 | #!/bin/bash
RESULTS_DIR=./01_stratified_classification/results/sgd_max_iter
ERRORS_DIR=./sgd_max_iter_errors
# keep all the genes in the gene set, otherwise scripts default to 8000
MAD_PRESELECT=16042
mkdir -p $ERRORS_DIR
genes=(
"KRAS"
)
sgd_lasso_penalties=(
"0.00001"
"0.00005"
"0.0001"
"0.0005"
"0.0... |
1885c4ead643ac42946b1c7318d66686299bdaf92ab1f79d40628d7cca76945b | Shell | 1,204 | 16 | #!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_Kebets2019_TransdiagnosticComponents
# remove useless stable projects
rm -r Standalone_Kebets2019_TransdiagnosticComponents/stable_projects/brain_parcellat... |
47022d78dcfb7b7e3de400d95020e8567745e83ffed67759ddd460892fdb430d | Shell | 1,204 | 29 | #!/bin/sh
# Last successfully run on Dec 17th, 2019
# Written by Gia H. Ngo and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
... |
c7a28b1862acc09b9a63f8eb9b4f7c8038d269117485899af8b9afcada8a08bc | Shell | 1,204 | 32 | #!/bin/sh
# simple script to call chexpert labeler on many files
REPORT_PATH=$1
CHEXPERT_PATH=$2
if [ -z "$REPORT_PATH" ]
then
echo "You must call this script as: ./run_chexpert_on_files.sh FOLDER_WITH_DATA_CSVS CHEXPERT_GIT_PATH"
exit 1
else
echo "Source of data: $REPORT_PATH"
fi
if [ -z "$CHEXPERT_PATH... |
7354ed3f9f43cc4f4fb9a9606f0239efd196d7cd00c2b48ea637b95b1fb6290f | Shell | 1,205 | 36 | #!/bin/bash
#SBATCH --time=1:00:00 # walltime
#SBATCH --ntasks=4 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=102400M # memory per CPU core
#SBATCH -J "fc_matrix" # job name
# Set the max number of threads to use for programs using OpenMP. Should be <= ... |
121cac43691d942a8c500bb83434ae5bb61f9da54844d7c3210f44aee3c6f283 | Shell | 1,210 | 31 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../data"
mkdir -p outputs_from_test
# Using strc tool to extract chain A from each protein to be aligned
echo "Using strc tool to extract chain A from each protein to be aligned"
echo "" > pdb_list # Clean pdb_list file just in case
for i in ./test_inputs/*.pdb
do
... |
875307ae1a810d3b9442ba054c834f008fd1fadaa47ef2c2f2d767aeb5dc2a74 | Shell | 1,210 | 50 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
dcb624a1a124bda33f95b90cf54b5bdb517a0e53f39f38a9bd0613bd603635a7 | Shell | 1,210 | 36 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
7fe6e6e5dfb560ec2ba4cc1f41889ed9a05b3c9f7dbaa1eef1365c19f7e47c33 | Shell | 1,219 | 28 | #### GIN fine-tuning
runseed=$1
device=$2
split=species
### for GIN
for unsup in contextpred infomax edgepred masking
do
model_file=${unsup}
python finetune.py --model_file model_gin/${model_file}.pth --split $split --filename gin_${model_file} --epochs 50 --device $device --runseed $runseed --gnn_type gin
model_file... |
ccc786b8fb5077bd6d1948778620469cbbfa83f3f3b17cef1436cd22c71cf662 | Shell | 1,221 | 38 | #!/bin/bash
# Ugly little Bash script, generates a set of .h files for GFX using
# GNU FreeFont sources. There are three fonts: 'Mono' (Courier-like),
# 'Sans' (Helvetica-like) and 'Serif' (Times-like); four styles: regular,
# bold, oblique or italic, and bold+oblique or bold+italic; and four
# sizes: 9, 12, 18 and 2... |
9095b0aa1dd4f777ea13203402087477d5bc75e25ef761487925d7d6e594abc2 | Shell | 1,224 | 36 | #!/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... |
20a01bbaf62c69222415d7fe473e8e90bb6089a560a48d513cc221a6b4500f9c | Shell | 1,225 | 57 | #!/bin/bash -ex
VERSION=$1
USERNAME=$2
PASSWORD=$3
case "${VERSION}" in
3.1)
major_version="3"
hdp_version="3.1.0.0"
ubuntu_repo_version="14"
;;
3.0)
major_version="3"
hdp_version="3.0.1.0"
ubuntu_repo_version="14"
;;
2.6)
major_version="2"
hdp_version="2.6.1.0"
ubunt... |
1ad9b3f3a19da4c3dcf90feeb0440dfba3d3b1f3d5602b754b87b0497daf7311 | Shell | 1,226 | 30 | #!/bin/bash
id=$1
task=$2
thr=$3
anat_dir=${ABCD_DIR}/process/y0/recon_all
export SUBJECTS_DIR=$anat_dir
data_dir=${ABCD_DIR}/raw/images
############ process #############
echo $id
for bold in 01 02 03 04
do
imdir=${data_dir}/sub-${id}/ses-baselineYear1Arm1/func
imname=sub-${id}_ses-baselineYear1Arm1_task-${task}_ru... |
81f55f915af1c08922bdadfae5f770d8f10aa832172994e0430988b67c52063c | Shell | 1,227 | 47 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2015 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
9620a656ac71d6d807cd23311efb7145b407918d88dcfbc743f6949df68a9246 | Shell | 1,228 | 23 | mkdir laion400m/
mkdir laion400m/train laion400m/eval laion400m/al
mkdir laion400m/train/metadata laion400m/train/npy
mkdir laion400m/eval/metadata laion400m/eval/npy
mkdir laion400m/al/metadata laion400m/al/npy
for i in $(seq 0 99); do
wget https://deploy.laion.ai/8f83b608504d46bb81708ec86e912220/embeddings/metadat... |
b74686fd274c75d57d32dddffaacaa88f8d2139f82749baea37cc51a3d7c25b5 | Shell | 1,229 | 42 | #!/bin/sh
# test-hook.sh - test script for gphoto2's --hook-script option
# Copyright © 2006 Hans Ulrich Niedermann <gp@n-dimensional.de>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation;... |
a7ab4b34c45a33f7363409671a0b4e83b9408f792a681809528970b24de91b81 | Shell | 1,233 | 39 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
8dc6156b239e6c2d2e6919263b129b54c1a3f2c8e1b9b4b4ff9d49f0bd8fce4e | Shell | 1,235 | 45 | #!/bin/bash
# Fail fast
set -e
# Define path to directories on Adroit
export SCRATCH=/scratch/network/ROSENGROUP
export SOFTWARE=$SCRATCH/software
# Ensure results are written to scratch directory
export QUACC_RESULTS_DIR=$SCRATCH/jenkins
# GULP
export GULP_LIB=$SOFTWARE/gulp/gulp-6.1.2/Libraries
export PATH=$SOFTW... |
09887c9fc565678ddf37ac36e78fbb9a6ba5e8cd2f4be2a8d29fb35a3699b7f7 | Shell | 1,241 | 45 | #!/bin/bash
set -e
d=`dirname $0`
# Use 90% of RAM for H2O.
memTotalKb=`cat /proc/meminfo | grep MemTotal | sed 's/MemTotal:[ \t]*//' | sed 's/ kB//'`
memTotalMb=$[ $memTotalKb / 1024 ]
tmp=$[ $memTotalMb * 90 ]
xmxMb=$[ $tmp / 100 ]
# First try running java.
export JAVA_HOME=${d}/jdk1.7.0_80
echo JAVA_HOME is ${JA... |
632eab8c893ac7e6b77237de90c1323511643de612c9eb885de9ebb33a137501 | Shell | 1,242 | 22 | #!/bin/bash
# usage (from repo root):
#
# nohup bash ./tests/test.sh & echo $! > pidfile
#
singularity exec container.img python bin/text.py -t 2 -RS 5 -i 2 > text.out &&\
singularity exec container.img python bin/list.py -t 2 -RS 5 -i 2 > list.out && \
singularity exec container.img python bin/logo.py -t... |
ef0b9dbf35b57707a10587c8a0be926fa8c94af709f644ab12be00cb76c3b81b | Shell | 1,247 | 44 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -d <docs> -m <model> -o <outName>... |
a19f2165c83a1defa83dc8ccdc412ac00fc3e6314e02fa1fd0e8699153945a5d | Shell | 1,250 | 22 |
# human 38
wget -P data -cq http://ftp.ensembl.org/pub/release-79/gtf/homo_sapiens/Homo_sapiens.GRCh38.79.gtf.gz &
wget -P data -cq http://ftp.ensembl.org/pub/release-79/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz &
# mouse 39
wget -P data -cq http://ftp.ensembl.org/pub/release-109/gtf/mus_m... |
18a756c5367bf6ef2682c42c7b9d614a1adbf12c10acfc83afc56560821f92f5 | Shell | 1,253 | 47 | #!/bin/sh
#
# Vivado(TM)
# runme.sh: a Vivado-generated Runs Script for UNIX
# Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
#
echo "This script was generated under a different operating system."
echo "Please update the PATH and LD_LIBRARY_PATH variables below, before executing this script"
exit
if [ -z "$... |
7652d2e38977ed7bf7a15ac42cb5df3dd5859684bef35f5b60eac5b65cfac719 | Shell | 1,258 | 37 | #!/bin/bash
path2bwa=/hpc/hub_oudenaarden/bin/software/bwa-0.7.10
path2samtools=/hpc/hub_oudenaarden/bdebarbanson/bin/samtools-1.3.1
if [ $# -ne 3 ]
then
echo "Please, give:"
echo "1) input fastq file to map"
echo "2) root for output file (no .sam or .bam extension)"
echo "2) reference file [mouse, hu... |
b9b49edf2ee16a8bf2b465164fd36c07472aabb81acef1da424a132b2254d60b | Shell | 1,258 | 43 | #!/bin/bash
SCRIPT_DIR=$(cd $(dirname $0); pwd)
CWD=$PWD
if [ $# -eq 1 ]; then
CWD="$1"
fi
pushd ${CWD}
TOPLOG=$(\ls -1t top-*.log | head -n 1)
VMLOG=$(\ls -1t vmstat-*.log | head -n 1)
IOLOG=$(\ls -1t iostat-*.log | head -n 1)
NFSIOLOG=$(\ls -1t nfsiostat-*.log | head -n 1)
GPULOG=$(\ls -1t gpu-*.log | head -n... |
9b5e33bb458c9f2927954dc720e328448b88c3bbc82de87c6ff29dc3098e2ec9 | Shell | 1,261 | 31 | #!/bin/bash
if [ $# -ne 3 ]
then
echo "Please, give input (1) root file; (2) protocol [celseq1, celseq2, nla, scarsc]; (3) reference [mouse]"
exit
fi
p2s=/hpc/hub_oudenaarden/aalemany/bin/mapandgo2
submit=/hpc/hub_oudenaarden/group_scripts/submission.py
source /hpc/hub_oudenaarden/aalemany/virtualEnvironments... |
bfce8728260ef78ab6c65232a6d99252ef71d1e6b78aa499784b55386cf47ad9 | Shell | 1,261 | 29 | #!/bin/bash
#SBATCH --cpus-per-task 8
#SBATCH --mem-per-cpu 12G
#SBATCH --time 72:00:00
#SBATCH --ntasks 1
#SBATCH --nodes 1
#SBATCH --output=logs/%j.%x.out
#SBATCH --partition=tier2_cpu
#SBATCH --account=jeffrey_zacks
cd /scratch/n.tan/extended-event-modeling/ || echo "cd failed.."
source activate sem-viz-jupyter
e... |
a3b9948b647eb6485fa10218065ec3ecbb8ec189a0db5a42283929d3aa5502fd | Shell | 1,263 | 28 | #!/bin/bash
wget https://en.ids-imaging.com/files/downloads/ids-peak/software/linux-desktop/ids-peak_2.11.0.0-178_amd64.tgz
tar -xvzf ids-peak_2.11.0.0-178_amd64.tgz
sudo sh ids-peak_2.11.0.0-178_amd64/local/scripts/ids_install_udev_rule.sh
python3 -m pip install ids_peak_ipl
python3 -m pip install ids_peak
python3 -m ... |
fda11c6cb825491ffbcf24fa32ae4647c0e74dbb29425e159b5280a145ef43da | Shell | 1,267 | 67 | # fba; percentile
fba extract \
-1 $READ1 \
-2 $READ2 \
-w $CELL_BARCODE \
-f $FEATURE_BARCODE \
-o feature_barcoding_output.tsv.gz \
-r1_coords 0,16 \
-r2_coords 10,25 \
-cb_m 2 \
-fb_m 1
fba count \
-i feature_barcoding_output.tsv.gz \
-o matrix_featurecount.csv.gz \
-... |
857456aafdb10dde49b57ab931bc6ec27157615a01540c386abc86b1fa3c8508 | Shell | 1,271 | 50 | #!/bin/bash
DOCKERFILE=Dockerfile.mcalibmath
FUZZY_IMAGE_DEFAULT=verificarlo/fuzzy:v0.4.1-lapack
generate_docker() {
cat > ${DOCKERFILE} <<HERE
# Base image
FROM ${1}
# Copy fuzzy environment from fuzzy image
RUN mkdir -p /opt/mca-libmath
COPY --from=${2} /opt/mca-libmath/libmath.so /opt/mca-libmath/
COPY --fro... |
d9f485f493b6dd557a852a3fe992af83c2e256c6e270dc8e08eb3bb0eec6d304 | Shell | 1,271 | 41 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
f509a570a16b65274db08f7748100870dcb0dda6f6d04eaf7739bd800e1351a8 | Shell | 1,278 | 51 |
#======================================================
# get APOE haplotype SNP info for participants.
# APOE info at https://www.snpedia.com/index.php/APOE
#======================================================
rs429358_pos=44908684
rs7412_pos=44908822
cat data/adc/adc.bim | \
awk -v bp1=$rs429358_pos -v bp2=$r... |
2fce167dae63206ec0c1e7e3726d425864e5bea472be195376f946a4e85909ed | Shell | 1,283 | 28 | #!/bin/bash
#
# This script will convert GWAS sumstats to
# BED format.
#
# Gokberk Alagoz, 08.12.22
#
############################
module load bedtools/2.29.2
inDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/gSEM/"
outDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/gSEM/evo_results/"... |
7bb5f43832e56fcb8d22455d045055b0ddfcacd47b29a13e5869e318c8414a02 | Shell | 1,285 | 47 | if [ "$#" -lt 1 ]; then
echo "Usage: $0 <path_swconfig_json> <debug_mode> <print_swconfig> <sweep_progress>"
echo " path_swconfig_json: [*/swconfig*.json]"
echo " debug_mode: [true|false]"
echo " print_swconfig: [true|false]"
echo " sweep_progress: [0..100]"
exit 1
fi
# ... |
efec926e512b2442687e368ae7c2dcb07a677206f8289db9d2aa2133b9a6c8cd | Shell | 1,289 | 55 | #!/bin/bash
# Script to run plot_drug_response_regression.ipynb for several different
# drugs using papermill, writing the results to the fs_plots directory.
# Note that this must be run from the parent directory
# {repo_root}/08_cell_line_prediction.
kernel_name="pc-eval"
papermill_output_dir="./papermill_output_n... |
70ddb33dd43064459cbd706c8186394688b38530688997e475cf8278896cbeff | Shell | 1,290 | 40 | #!/bin/bash
function run_paratest(){
mincov=$1
min_count=$2
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/Dxy/syn_Dxy/results
dir_snp=/home/siyuan/jobs/suzukii_WGS/call_snp/amb/updated_poolsnp/paratest/test_maxcov/call_snp_maxcov_99/mincov_$mincov\_mincount_$min_count
dir_syn_snp=/home/siyuan/jobs/suzukii_WGS/genetic_... |
568f335dc4e9ec3220d6114de0450d6f0b6e7670be394b17ba4692d50c53cd7c | Shell | 1,293 | 65 | #!/bin/bash
# Run feature selection experiments across a few genes, with selected cancer
# types held out (either partially or completely)
RESULTS_DIR=./08_cell_line_prediction/results/tcga_to_ccle_lasso_poc
ERRORS_DIR=./ccle_lasso_poc_errors
# number of features to "preselect" to by mean absolute deviation
# -1 == ... |
89444a750715d692f6ca4d0b7fc3096891810a7e14feb81a6c9d2ea212a8d77b | Shell | 1,294 | 61 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
5e3098c72e029fb07d4ca1b22055ed845d30e533f8048697e1890273009b601e | Shell | 1,300 | 32 | #!/bin/bash
#Purpose: Rename surface-projected preproc output as consecutive sessionsand copy to new location so as to align with 12 consecutive runs selected for FC Matrices
#Inputs: CBIG2016 preproc output
#Outputs: Consecutively named sessions.
#PATHS
PREP_DIR=/fslgroup/fslg_fun_conn/compute/NSD_analysis/CBIG2016_... |
9415ca50f33f395ff73fba8a27dc3f44f99e1b3f1cd1ceb053d64c4f9d57412f | Shell | 1,304 | 42 | #!/bin/bash
#
#SBATCH --job-name=bez2018model
#SBATCH --out="trash/slurm-%A_%a.out"
#SBATCH --cpus-per-task=2
#SBATCH --mem=2000
#SBATCH --nodes=1
#SBATCH --time=2-00:00:00
#SBATCH --exclude=node[017-094,097,098],dgx001,dgx002
#SBATCH --array=0-49
##SBATCH --partition=mcdermott
#SBATCH --partition=use-everything
#SBATC... |
adbda483fe27dd970aec509aefcdc588ec0e3ab0aab36e7051759866eb1737cd | Shell | 1,309 | 49 | #MOLGENIS walltime=23:59:00 mem=20gb ppn=6
#string pennCNVVersion
#string intermediateDir
#string tmpTmpdir
#string tmpDir
#string workDir
#string tmpName
#string Project
#string logsDir
#string finalReport
#string samplesheet
#string pennCNVInputDir
#string pennCNVVersion
#string hmmFile
#string pfbFile
#string pennC... |
72762510d31f343e63544fec175ca817c7623896f28223b7e9fc3a4326b754d7 | Shell | 1,310 | 44 | #!/usr/bin/env sh
set -evx
. ci/get-nprocessors.sh
# if possible, ask for the precise number of processors,
# otherwise take 2 processors as reasonable default; see
# https://docs.travis-ci.com/user/speeding-up-the-build/#Makefile-optimization
if [ -x /usr/bin/getconf ]; then
NPROCESSORS=$(/usr/bin/getconf _NPROC... |
e6b6b0a1128e783e4512a74b44d01abcca05218f7e25b14072c0f523eb2f46ae | Shell | 1,314 | 36 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
0df2657f7addea5a1f4dda36b1e5b98fdfe449095e5cb99b17dc1489ddfa3967 | Shell | 1,323 | 46 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
4aad0daff65aa4f90964e0296e3e66b7c66e5db119b008b71a54451fe75f36ab | Shell | 1,329 | 34 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
1777ea5d87b67d9a7816a70222c845e1fcc1cc67b76ce49266a71800c035c947 | Shell | 1,330 | 46 | #!/bin/bash
BIOSHELL_DIR="/home/bioshell/src.git/bioshell"
OUT_DIR="/home/bioshell/public_html"
# Generate API documentation
function make_docs {
cd $BIOSHELL_DIR
( cat $BIOSHELL_DIR/doc/Doxyfile ; echo "OUTPUT_DIRECTORY="$OUT_DIR"/doc/" ) | doxygen -
}
# Compile - clang; param1 is the build type
function make_c... |
2d54abea79fa0dede6af5bc315eb1d399a5b3d2df82c515bc9ae84e67b0a514e | Shell | 1,330 | 31 | #!/bin/bash
#
# Use either WORKSPACE location for Jenkins or
# resolve path to scripts we need to check
# when executed manually outside Jenkins.
#
if [[ -z "${WORKSPACE:-}" ]]; then
MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
WORKSPACE="$(dirname ${MYDIR})"
fi
echo '################################################... |
e2922b083d6081518c4450db67981c56e53068a62210085dd6067b4bed63d37a | Shell | 1,330 | 51 | #!/bin/bash
# Run feature selection experiments for prediction of drug response (sensitive
# or resistant), with stratified train/test sets
RESULTS_DIR=./08_cell_line_prediction/results/drug_response_stratified
ERRORS_DIR=./drug_response_stratified_errors
# number of features to "preselect" to
# -1 == no preselectio... |
7a10e82f9e2ce8f366a04e88980b29523fc9d1a22df15cc9ed9c6a551de41c42 | Shell | 1,342 | 32 | #!/usr/bin/env bash
# Regenerate Phase-B byte-identity goldens from the repo's Perl NOMe_filtering
# (v0.25.1, self-contained Perl). Run from this directory (tests/data/phase_b).
#
# The Rust binary's DECOMPRESSED `.manOwar.txt.gz` output must be raw-byte-
# identical to each `.golden` (the gzip container itself is imp... |
45f52873e2db4f2127f50c3c42b88a8694f928ce61003a67755cb3795d6e9cb6 | Shell | 1,343 | 26 | export CARLA_ROOT=${1:-/home/kchitta/Documents/CARLA_0.9.10.1}
export WORK_DIR=${2:-/home/kchitta/Documents/misc/transfuser}
export CARLA_SERVER=${CARLA_ROOT}/CarlaUE4.sh
export PYTHONPATH=$PYTHONPATH:${CARLA_ROOT}/PythonAPI
export PYTHONPATH=$PYTHONPATH:${CARLA_ROOT}/PythonAPI/carla
export PYTHONPATH=$PYTHONPATH:$CAR... |
f320dd7afbd105502b82b6a1de78bc98cc1e36a845e4eb49c83b24fb2733aae5 | Shell | 1,348 | 48 | agfusion annotate \
--gene5prime FGFR2 \
--gene3prime DNM3 \
--junction5prime 130167703 \
--junction3prime 162019992 \
-db agfusion.mus_musculus.84.db \
--out FGFR2-DNM3
agfusion annotate \
--gene5prime ENSMUSG00000022770 \
--gene3prime ENSMUSG00000002413 \
--junction5prime 31684294 \
--junction3pr... |
fb9f162f2185b90693ff92ad38a010c8a40ad4637165bdc149e66733785320d1 | Shell | 1,355 | 33 | #!/bin/bash
#########################################################################
# Copyright (c) 2018-~ Beisi Xu && St Jude
# This source code is released for free distribution under the terms of the
# CreativeCommons BY-NC-SA 4.0 International License
#*Author: Beisi Xu < xubeisi [at] gmail DOT com >
# File... |
da5f0012700c5eaa898ca63627e510f46ba341ac75dbfd96a70b38e71f1b18fb | Shell | 1,364 | 55 | #!/bin/sh
# TODO: generalise to types of MRI format (NIFTY or DICOM)
# TODO: generalise to types of image format (png or jpg)
hibou() {
$3/python3 crop_nii.py -inpath $1 -outdir $2 -filename $4
}
chouette() {
med2image --inputFile $1 \
--outputDir $3 ... |
23a9b38c0bcacd61f2192c6aab446cb30182894f43da2959769b6ae418f01b32 | Shell | 1,366 | 50 | #!/bin/bash
# =============================================================================
# Description: Run LST toolbox from MATLAB rto
# adapted from TVB-pipeline by Schirner et al
# =============================================================================
# load MATLAB
# and SPM12
spm_folder=
matlab_path=
... |
f2a60ebfbab056a6712351151fd71d22421f041adf140d3b2bca634ecec1f3a6 | Shell | 1,370 | 38 | #!/bin/bash
function run_paratest(){
mincov=$1
min_count=$2
window_heter=$3
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/Fst/syn_Fst/results/Fst
sd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/Fst/scripts
script=$sd/filter_mpileup_by_cov_window.py
calc_script=$sd/calc_Fst_reynolds_ungapped_efs.py
dir_snp=/home/siyuan/j... |
ff1ac75f663dea11e813c5a533f8c4722e24437bf189a8fafc099dbcf7647d1c | Shell | 1,371 | 18 | # Download meshes at https://zenodo.org/records/10480304
# python3 main.py dendritic-spine-preprocess --input-mesh-file meshes-dendritic-spine/1spine_PM10_PSD11_ERM12_cyto1_ER2_coarser.xml --output-mesh-file meshes-dendritic-spine/1spine_mesh_coarser.h5 --num-refinements 0
# python3 main.py dendritic-spine-preprocess -... |
1dae8e828dd3ebbbafa8daccdb9d33a909d0d7f0038418605dac4d845fa3c248 | Shell | 1,372 | 50 | ## Use Xplor-NIH pdb2ens script to format pdbs
## convert from Xplor-NIH refinement outputs to standard PDB format
## Usage: bash format_pdb_xplor.sh path_to_pdbs
###############################################################################
# Help ... |
06b0dbe18a8a19a40d3b6d56d430045d4abda4943ff60a648a462989ed9c66f2 | Shell | 1,373 | 45 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
50a364b92093f20477f60d88837aef28c0d6855b017f99940183f8f3ede306ca | Shell | 1,374 | 36 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
f77d22c003da5ffcd7995d70551c1ac41a5d415e757b80cc3e1bea9a68f3e06d | Shell | 1,374 | 49 | #!/bin/bash
#=========================================================================
# create plink filesets for each chromosome in 1000 genomes phase 3 data,
# then merge into one plink fileset
#=========================================================================
# create file to list fileset prefixes to merg... |
6b32e51042927e33dac8bddf4fbd919d2d4e1a1a3809e43ac5d4d6fee66bd0d4 | Shell | 1,377 | 52 | #!/bin/bash
# Run feature selection experiments for prediction of drug response (sensitive
# or resistant), with stratified train/test sets
RESULTS_DIR=./08_cell_line_prediction/results/drug_response_stratified_regression
ERRORS_DIR=./drug_response_stratified_regression_errors
# number of features to "preselect" to
... |
26c0f465d1574201b2aca368a06236e613a2467a6f099eec7d2d719b8a275c5f | Shell | 1,378 | 53 | #!/bin/bash
#########################################################################
# Copyright (c) 2018-~ Beisi Xu && St Jude
# This source code is released for free distribution under the terms of the
# CreativeCommons BY-NC-SA 4.0 International License
#*Author: Beisi Xu < xubeisi [at] gmail DOT com >
# File... |
68afdb5e74ff3bdee929cc9f8776c2af06d7b7f444b4a7d9ea4d461888e5fb6e | Shell | 1,382 | 30 | #!/bin/bash
#SBATCH --ntasks 1
#SBATCH --array 1-10
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=16
#SBATCH --time=24:00:00
# srun inherits sbatch ntasks and nodes, so we need to specify for each step
# if there is no --ntasks 1, each step below will be ran 10 times (10 tasks)
# if there is no --nodes 1, each ste... |
1b4fd3ff53826bb2d2ff4a377618408708dba665dabf3867a50c0495daf47c6e | Shell | 1,385 | 58 | #!/bin/bash
set -e
### Save working directory
cwd=$(pwd)
function cleanup {
echo "Installation failed"
cd "${cwd}"
exec $SHELL
}
trap cleanup ERR
### Set workspace
export PUPIL_WS="$(dirname "$(realpath "$0")")/../build"
mkdir -p "${PUPIL_WS}"
### Install dependencies
sudo apt-get install -y \
pkg-config cm... |
3e72bcf3a8b8495859cfe31b712457012d9e05be4a25106ddb71c13456a991ba | Shell | 1,387 | 71 | #!/bin/bash
# Run feature selection experiments across a few genes, with selected cancer
# types held out (either partially or completely)
RESULTS_DIR=./08_cell_line_prediction/results/ccle_to_tcga_lasso_poc
ERRORS_DIR=./ccle_lasso_poc_errors
# number of features to "preselect" to by mean absolute deviation
# -1 == ... |
4f8559717e926c8bdd437dfafc55616a47c5e3372e8e776a8e73aa4643e96770 | Shell | 1,387 | 59 | #!/bin/bash
#******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2018 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Fr... |
5b0be2f51956d6d72ffcff7504923b1a8f54a181285abe716db1496306914f9a | Shell | 1,387 | 32 | export CARLA_ROOT=${1:-/home/kchitta/Documents/CARLA_0.9.10.1}
export WORK_DIR=${2:-/home/kchitta/Documents/transfuser}
export CARLA_SERVER=${CARLA_ROOT}/CarlaUE4.sh
export PYTHONPATH=$PYTHONPATH:${CARLA_ROOT}/PythonAPI
export PYTHONPATH=$PYTHONPATH:${CARLA_ROOT}/PythonAPI/carla
export PYTHONPATH=$PYTHONPATH:$CARLA_RO... |
2b8bfa0051ea5dac4948c8e19399cd64ed6e28b13b1679359ed76acbf5e54265 | Shell | 1,389 | 40 | #!/bin/bash
base=$(pwd)
res_parent_dir="${base}/results/figure2"
# 2-450 clusters
k_range='[2'
for i in {3..450}
do
k_range="${k_range},${i}"
done
k_range="${k_range}]"
# PCA on the full dataset
red_method="pca"
res_dir="${res_parent_dir}/all_${red_method}"
ARGUMENTS="++red_method=${red_method} ++reduction.n_dimen... |
f1d09a4f451a736f71cb6f2d45d2332e4d22c675d6796968c3d1a4dfd2c3ee05 | Shell | 1,389 | 59 | #!/usr/bin/env bash
set -euo pipefail
ENV_NAME=${ENV_NAME:-openmm_gpu}
CUDA_VERSION=${CUDA_VERSION:-}
REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
if ! command -v conda >/dev/null 2>&1; then
if [[ -x "$HOME/miniforge3/bin/conda" ]]; then
export PATH="$HOME/miniforge3/bin:$PATH"
fi
fi
if ! com... |
3f40fb1ed5c13a4b5497ccab75bbb2ca7ede40b0f39b9e27a792bb55843ae6f5 | Shell | 1,390 | 33 | #!/bin/bash -ex
# This script initializes the kerberos database and stores necessary keys in keytabs
MAPRED_USER=$1
mkdir -p /var/log/kerberos
kdb5_util create -P h2o
kadmin.local -q 'addprinc -pw h2o hdfs/localhost@H2O.AI'
kadmin.local -q 'addprinc -pw h2o mapred/localhost@H2O.AI'
kadmin.local -q 'addprinc -pw h2o ... |
7a237c8baf72d0d3cdf18fde9138c424f493c8b563557b84cbf9583d6210acf6 | Shell | 1,394 | 75 | #MOLGENIS walltime=01:59:00 mem=10gb ppn=1
#string Project
#string logsDir
#string optiCallDir
#string intermediateDir
#string genSampleDir
#string optiCallVersion
#string chrNr
set -e
set -u
set -o pipefail
inputFolder="${optiCallDir}"
outputFolder="${genSampleDir}"
mkdir -p "${outputFolder}"
makeTmpDir "${outputF... |
4e555a9de6e942824b3ecbf0c922087b19909b5bc65170159b29d64fff78979c | Shell | 1,397 | 44 | #!/bin/bash
#SBATCH --time=24:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=51250M # memory per CPU core
#SBATCH -J "HCPDprep" # job name
# Set the max number of threads to use for programs using OpenMP. Should be <= p... |
5024595a0e977f70a00c3c76fa04ef7d3a1272c2cb6ca5ed6f54d5e37a130213 | Shell | 1,399 | 42 | #!/bin/bash
export CARLA_ROOT=/path/to/CARLA
export SCENARIO_RUNNER_ROOT=/path/to/scenario_runner
export LEADERBOARD_ROOT=/path/to/leaderboard
export TEAM_CODE_ROOT=/path/to/team_code_transfuser
export PYTHONPATH="${CARLA_ROOT}/PythonAPI/carla/":"${SCENARIO_RUNNER_ROOT}":"${LEADERBOARD_ROOT}":${PYTHONPATH}
if [ -z "$C... |
2bfefc894de131263cf37128c313faa9f4501d6aa5b6765bdaaaf0eca5291cb8 | Shell | 1,401 | 32 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
285b9c99c5884aa8bba223d8986322ab6b60f9b93952444d10b60274d78b7fc4 | Shell | 1,403 | 36 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
a430791e15173f1cd7988bd8348c896ece305ca534ae239d51237b28d9ebe9de | Shell | 1,405 | 37 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
486ce9822b95b42da9e9360e1a4f22e274cd4f445d780a5f20182e5476d0bbdf | Shell | 1,411 | 41 | #!/bin/bash
function run_paratest(){
mincov=$1
min_count=$2
window_heter=$3
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/Fst/ungapped_window_efs/winheter_$window_heter\_mincov_$mincov\_mincount_$min_count
sd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/Fst/scripts
script=$sd/filter_mpileup_by_cov_window.py
calc_script=... |
2e45cf52d4e6e3846341bf8536db349c265f140b3fe2aad4cc51e6198046d7da | Shell | 1,412 | 50 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_b_hybrid_pt_800e'
DATA_PATH='YOUR_PATH/data/hybrid_train.csv'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 for 2 node, etc.
GPUS=${GPUS:-32}
GPUS_PER_NODE=${GPUS_PE... |
551fd3b448d22a0dae70d56ae9529cb75de52150e4c9fc0b743124455a7b3ddd | Shell | 1,414 | 34 | #!/bin/bash
# subsetVCF_v3.sh [chr1 vcf file] [sample subset file] [reference fasta] [outfile prefix] [','-separated chromosome numbers to process]
if [ "$#" -lt 5 ]
then
printf "\n%s\n\n" "subsetVCF_v3.sh [chr1 vcf file] [sample subset file] [reference fasta] [outfile prefix] [','-separated chromosomes numbers to p... |
65f59ac51f51441ae69dfc4c7d44f6793dc012aedda2fa45eb39ab88e5657f0a | Shell | 1,414 | 50 | #!/usr/bin/env bash
set -x
export MASTER_PORT=$((12000 + $RANDOM % 20000))
export OMP_NUM_THREADS=1
OUTPUT_DIR='YOUR_PATH/work_dir/vit_l_hybrid_pt_1200e'
DATA_PATH='YOUR_PATH/data/hybrid_train.csv'
JOB_NAME=$1
PARTITION=${PARTITION:-"video"}
# 8 for 1 node, 16 for 2 node, etc.
GPUS=${GPUS:-48}
GPUS_PER_NODE=${GPUS_P... |
729f0d2119aeca299e3f4d71a1b510185868a92ff43540ffb3e98f081ca2c75e | Shell | 1,418 | 33 | #!/bin/bash
#Purpose: Create label files in fs6 space - from individual parcellation files
#Inputs: parc2annot annotation files
#Outputs: .label.gii parcellation files
#Written by M. Peterson, Nielsen Brain and Behavior Lab under MIT License 2022
#SET PATHS
HOME=/fslgroup/fslg_spec_networks/compute
HOME_D=/fslgroup/g... |
fdff3a42fe07a23e1d6cf12da663cc703f86d6000ef3fc68ea3837fcbc6a2d3c | Shell | 1,422 | 64 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
0be31a8b113d63c97757cbd24ce7f9f6479a3e787ebe3c07de4a04b2b0ea9cc6 | Shell | 1,427 | 45 | #!/bin/bash
# Function to display usage instructions
print_help() {
echo "Usage: $0 [sweep|neutral] <number_of_replicates>"
echo
echo "Arguments:"
echo " sweep Generate sweep replicates."
echo " neutral Generate neutral replicates."
echo " number of replicates Number of replic... |
12451ae885c006b4b3e0eb6041039a58ece492a6c07c8b6afba7e7008892d253 | Shell | 1,428 | 52 | #MOLGENIS walltime=05:59:00 mem=10gb ppn=6
#string pythonVersion
#string beadArrayVersion
#string bpmFile
#string projectRawTmpDataDir
#string Project
#string SentrixBarcode_A
#list SentrixPosition_A
#string pennCNV_reportDir
#list Sample_ID
#string gapVersion
#string resultDir
#string logsDir
#string intermediateDir
... |
046738f83e439f8ba1de1010393abb25915df31795d703144b199a867f9361fe | Shell | 1,430 | 41 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
4a3617a852fc0131eed8fd9c8efc3472bc08b9c7467c6332ea232ebbfc5e97e1 | Shell | 1,430 | 32 | # Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... |
f2b8a0503bf10bcac9f1c528737b12667a2cbbd24ed4420af054e0f1f67a6462 | Shell | 1,431 | 41 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
21a1a2ea0c532d74e27d17e1bc681c40e32a6e1134b9f139cd721464e67b121f | Shell | 1,432 | 33 | #!/bin/bash
#Purpose: Create label files in fs6 space - from individual parcellation files
#Inputs: parc2annot annotation files
#Outputs: .label.gii parcellation files
#Written by M. Peterson, Nielsen Brain and Behavior Lab under MIT License 2022
#SET PATHS
HOME=/fslgroup/fslg_spec_networks/compute
HOME_D=/fslgroup/f... |
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