sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d64ae46bb98735dcee8ee178e0e65e168f371b2ab264aaa17b6504e187e58107 | Shell | 3,388 | 66 | #!/usr/bin/env bash
scripts_dir='/net/shendure/vol8/projects/BCBL/Mixing/bin'
dropseq_scripts_dir='/net/shendure/vol1/home/abros/bin/Drop-seq_tools-1.12'
dropseq_ref_dir='/net/shendure/vol8/projects/BCBL/Mixing/ref/mus10_ref/mm10'
fastq1=$1
fastq2=$2
output_dir=$3
mkdir $output_dir
# Convert fastq to unaligned bam:... |
c97a5d8f6a38e3a3fb684d88e87862de04b8f49741b58567bef908b505192ac2 | Shell | 3,417 | 98 | #!/bin/bash
set -xe
export OS=$(uname)
if [ "${OS}" = "Linux" ]; then
export DS_ROOT_TASK=${HOME}
export PYENV_ROOT="${DS_ROOT_TASK}/pyenv-root"
export DS_CPU_COUNT=$(nproc)
fi;
if [ "${OS}" = "${TC_MSYS_VERSION}" ]; then
export DS_ROOT_TASK=${TASKCLUSTER_TASK_DIR}
export PYENV_ROOT="${TASKCLUSTE... |
0d4d0b7c6662622b8a2dcc3e2163e68fc4672b7595a26e9ce848b7cb30faf23a | Shell | 3,429 | 113 | #!/bin/bash
#SBATCH --account=p33_norment
#SBATCH --time=24:00:00
#SBATCH --job-name=ABCD_E
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=32G
#
# Metrics SMT/DKI/RSI/NODDI
# Ivan I. Maximov, Ullevål Oslo
# 24.08.2018, version 1.0
# 23.11.2018, ver 1.1
source /cluster/bin/jobsetup
module load MATLAB/2020b
module load... |
35373a484e55c4926c71adc50412f81a0d52bc14b5d67e1313598e066c4a9ff7 | Shell | 3,429 | 120 | #! /bin/bash
filepath=/Users/wang/Desktop/Research_projects/BBSC/Functional/fmri/derivatives/freesurfer-v7.2.0
cd $filepath
ls | grep -i sub- >$filepath/subjList.txt # command grep is trying to filter the input with 'sub-'. -i ignore the high or low cases
for sub in $(cat $filepath/subjList.txt); do
export SUB... |
5ac66a592eb9812f52cba76bac996dff42d6f8aa9002ad33108fce5fccbe330c | Shell | 3,432 | 125 | #!/bin/bash
#SBATCH -J ace_fin
#SBATCH --time=48:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=48
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=3700
#SBATCH --mail-type=END
#SBATCH --mail-user=<wojciech.stark@warwick.ac.uk>
module purge
module load GCCcore/10.2.0
module load Python/3.8.6
# module load GCCcore/1... |
7509aa1b87bcc2edd61fe4eb9ebd95a8217be3e52b33bf24a9be27dcd6f0800c | Shell | 3,436 | 126 | #!/usr/bin/env bash
#
# Custom runtime environment for MacOS X installation
#
#
# Initialize runtime environment.
# Usage: initEnv <runtime-env-name>
# initEnv will be called at module runtime for each required <runtime-env-name>
#
# See env-default.sh for canonical runtime environment names
#
function initEnv()... |
cb21b63b918b85cdb907ef80f9a24b6063fcc208f63428c3da9e75e01a7bbf7c | Shell | 3,483 | 109 | #!/usr/bin/env bash
set -euo pipefail
endpoint=""
upload_mode=""
input=""
output=""
consolidate_header="0"
consolidate_citations="0"
include_raw_citations="0"
include_raw_affiliations="0"
start_page="-1"
end_page="-1"
while [[ $# -gt 0 ]]; do
case "$1" in
--endpoint) endpoint="$2"; shift 2 ;;
--up... |
d919be2bb81be56ce79b21c6d82aa2565cf9a4275aead210b6b60058c05f8a99 | Shell | 3,487 | 80 | #!/bin/sh
# This bash script is for running minimum working examples
# of transfer learning for continuous integration tests
# to be run on CI.
set -xe
ru_dir="./data/smoke_test/russian_sample_data"
ru_csv="${ru_dir}/ru.csv"
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
if [ ! -f "${ldc93s... |
6c791c258db31c37a852744c92cd3dc56f3d6e91065b15f12e9501b5452d132b | Shell | 3,547 | 101 | #!/bin/bash
cd "$(dirname $0)"
root_path="$(pwd)"
# demo=$1
export LD_LIBRARY_PATH=/usr/local/cuda/compat:$LD_LIBRARY_PATH
export PYTHONPATH=$root_path:$PYTHONPATH
# export FLAGS_allocator_strategy=naive_best_fit
# export GLOG_v=6
# export GLOG_vmodule=auto_growth_best_fit_allocator=4,stream_safe_cuda_allocator=4
ex... |
95aa795647ae67946bf7626552f8883a3861b4c56ab5c8af60721b4f03c16590 | Shell | 3,550 | 151 | #!/bin/bash
if [ "*${1}*" == "**" ]; then
DOINSTALL="false"
else
DOINSTALL="true"
fi
BISWEBOS=`uname | cut -f1 -d_`
ARM=`uname -a | cut -f2 -d/ | cut -f2 -d_`
ARMARCH=""
if [ ${ARM} == "ARM64" ]; then
ARM="TRUE"
ARMARCH=-DCMAKE_OSX_ARCHITECTURES="arm64;x86_64"
else
ARM="FALSE"
fi
echo "___"
ech... |
abc0c74c4e6b84f4439b74c1db9fdae358d734bf3e05e0dedac2656e502532b3 | Shell | 3,550 | 73 | #!/bin/zsh
## This cript is trying to conver the volume data into suface data in fsaverage5
# 1. transfer the data into fsaverage; 2. smooth the data with kernel 6;
# 3. downsample the data into fsaverge5; 4. add nan to medialwall
# This function is used to convert the MNI data into surface data using WU method (Wu... |
2ed34da0f3fc44bd8b58a3921e4253c6c0d651a77b8692f895f6e6ae4e16de23 | Shell | 3,553 | 66 | ### 1. positive selection analysis using MEME framework
#!/bin/bash
###################################################################
# @description : For postive or diveisity selection of sites, with mixed effected model
###################################################################
### Note: please exam... |
ec7f5c5cddb53a07d7f922d83abf62febf1d4a1f3371bd45b6b4ffe8337af1d8 | Shell | 3,604 | 146 | #!/bin/bash
usage() {
echo $0
echo ""
echo " register same subject epis "
echo " -t target_image target epi for registration (required)"
echo " -m movable_image movable epi for registration (required)"
echo " -i images quoted list of images to transform"
echo " -o images ... |
6741fb769432399939eb543ff7e35a1f5e37c1255638e5ed927104b3322533f1 | Shell | 3,639 | 110 | #!/bin/bash
declare -i i=0
for enc_method in one_hot blosum62 atchley pca; do
for lr in 0.0001; do
for n_dense in 1; do
for n_units in [16] [32] [64]; do
for dropout_flag in True; do
for p_dropout in 0.2 0.5; do
i+=1
cur_name=${enc_method}_${n_dense}_${n_units}_... |
7a42d0c6326147abe99c845aa6a011947d7470dfb6ca8409fe86fabb26f08cc9 | Shell | 3,640 | 113 | #/usr/bin/env bash
EXECDIR="$(cd "$(dirname "$0")" && pwd)"
PATH=$EXECDIR:$PATH
init_dir()
{
local DIRNAME=$1
[ ! -d $DIRNAME ] && mkdir -p $DIRNAME;
[ ! -d $DIRNAME ] && { echo -e "ERROR: Directory $DIRNAME DOES NOT exists."; exit 1; }
}
usage()
{
echo -e "usage: $0 [-h] [OPTIONS]
This is a bash wra... |
88193ea5dd596117660b7b1eaaa8ea58efc0ce3368b68561857e51be44201a66 | Shell | 3,647 | 110 | #!/bin/bash
declare -i i=0
for enc_method in one_hot blosum62 atchley pca; do
for lr in 0.0001; do
for n_dense in 1; do
for n_units in [16] [32] [64]; do
for dropout_flag in True; do
for p_dropout in 0.2 0.5; do
i+=1
cur_name=${enc_method}_${n_dense}_${n_units}_... |
a7a7cf2d45ab416c17bc8de5701ac08f371febfeaec27347e25fd7e646c6b437 | Shell | 3,651 | 110 | #!/bin/bash
declare -i i=0
for enc_method in one_hot blosum62 atchley pca; do
for lr in 0.0001; do
for n_dense in 1; do
for n_units in [16] [32] [64]; do
for dropout_flag in True; do
for p_dropout in 0.2 0.5; do
i+=1
cur_name=${enc_method}_${n_dense}_${n_units}_... |
378f3791518625e494743be92b95703bbb7ca07b9f6921bb3ee5d26c673b608f | Shell | 3,717 | 117 | #!/bin/bash
ERLANG_COOKIE="MYSECRETCOOKIE"
cleanup() {
echo "Stopping and removing existing RabbitMQ containers..."
docker stop rabbit1 rabbit2 rabbit3 2>/dev/null
docker rm rabbit1 rabbit2 rabbit3 2>/dev/null
echo "Removing existing Docker network..."
docker network rm rabbitmq-cluster 2>/dev/nu... |
0fa3f5253ef76e839566d5d329696edfe4518ea4755690b343c9a2836965c7d3 | Shell | 3,738 | 102 | #!/bin/bash -eu
trap 'catch' ERR
catch() {
grep OPT arpackmm.run.log
grep Error arpackmm.run.log
exit 1
}
# For all these eigen problems, the first eigen value is about 382 or (382, 0.).
for stdPb in "--A As.mtx" "--nonSymPb --A An.mtx" "--nonSymPb --cpxPb --A Az.mtx"
do
# Choose B matrix according to A.
e... |
366a28d1d05f77413a5b733f4010d853877e71dcf0cf4bb83c757526e4f1a74e | Shell | 3,746 | 116 | #!/bin/bash
#
# T1w Structural processing with bash:
#
# Preprocessing workflow for structural T1w.
#
# This workflow makes use of FREESURFER, FSL (fslchfiletype)
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micaopen/templates
#
# ARGUMENTS order:
# $1 : BIDS directory
# $2 : partici... |
9ad5839f0ea445876381598f790d77c328c31f11c5bc3088512112cc06ca104a | Shell | 3,751 | 42 | #!/bin/sh
## -e : Make sure all errors cause the script to fail
## -x be verbose; write what we are doing, as we do it
set -ex
# for non-LTS && EOL'ed ubuntu, the mirror url must be modified to run `apt update`
cmd=ls
if [ $2 = ":eoan" ]; then
cmd="sed -i 's/\(security\|archive\).ubuntu/old-releases.ubuntu/g' /etc... |
06a705f0b5db182bd64d070070473bb1608b5e127fa537e58345f5da4fd88694 | Shell | 3,764 | 130 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: converted to SLURM array (one task per subject), set -euo pipefail,
# source config, removed sbatch --wait, input validation, safer loops
#SBATCH --job-name=dtitk-extractdiff
#SBATCH --mem=500M
#SBATCH --partition=luna-cpu-short
#SBATCH --qos=anw-cpu
#SB... |
dd4e726585a55d258105249396076dbd539f7d43f76479a941ad59c945829751 | Shell | 3,781 | 126 | #!/bin/sh
##
## CHANGE ME to galaxy's database name
##
DATABASE=galaxyprod
##
## AWK script to extract the relevant fields of SGE's qacct report
## and write them all in one line.
AWKSCRIPT='
$1=="jobnumber" { job_number = $2 }
$1=="qsub_time" { qsub_time = $2 }
$1=="start_time" { start_time = $2 }
$1=="end_time" ... |
0146263f3e440faee9485b703b3a490709ca6f8be5d29ab9fd4cb6226069573f | Shell | 3,792 | 131 | #!/bin/bash
set -xe
set_ldc_sample_filename()
{
local _bitrate=$1
if [ -z "${_bitrate}" ]; then
echo "Bitrate should not be empty"
exit 1
fi;
case "${_bitrate}" in
8k)
ldc93s1_sample_filename='LDC93S1_pcms16le_1_8000.wav'
;;
16k)
ldc93s1_sample_filename='LDC93S1_pcms16le_1_16... |
35d67f33ec353b640ed33a8b18165ba6f9263290c78fd7294de9fb8dff26e4bc | Shell | 3,793 | 30 | export BIOHOME=/home/bb/valejose/home
export PYTHONPATH=$BIOHOME/bioseq2seq
export CHKPT_DIR="$BIOHOME/bioseq2seq/experiments/checkpoints/coding_noncoding"
export test_set="$BIOHOME/bioseq2seq/data/mammalian_200-1200_test_RNA_nonredundant_80.fa"
export val_set="$BIOHOME/bioseq2seq/data/mammalian_200-1200_val_RNA_nonred... |
eabcd44ff7357861464a9f43c5a51353a5a712bf4b76254afb1f9284098ef850 | Shell | 3,808 | 109 | #!/bin/bash
#
# Check the shell completion scripts. Run by 'make -C completion check'.
#
# 1. drift: does spec/vsearch.yaml still agree with src/cli.cc?
# 2. staleness: do the checked-in scripts match what the generators emit?
# 3. syntax: does each script parse in the shell it targets?
#
# Usage: check_comp... |
427818236db0f33d97d3df1833707323716d12a8f9c6ab4cb75d02dfd74ed66c | Shell | 3,820 | 102 | ## prepare input files for implicit solvent calculations
#vmd dispdev text -e write-dcd-A.tcl
#vmd dispdev text -e write-dcd-B.tcl
#vmd dispdev text -e write-dcd-AB.tcl
#
##calculate implicit energies
#namd2 test-AB.namd > test-AB.log
#namd2 test-A.namd > test-A.log
#namd2 test-B.namd > test-B.log
rm -rf entro*... |
0e3f2b24a818a3419406050ccdc75874b21c55be16e60b71cf017d6b533e312f | Shell | 3,864 | 124 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
unset command_line_specified_study_folder
unset command_line_specified_subj
unset command_line_specified_run_local
local index=0
local numArgs=${#arguments[@]}
local argument
while [ ${index} -lt ${numArgs} ]; do
argum... |
40473f67108687c94c877c42081b8bfb703e92a49222c937afda7f84011af07f | Shell | 3,879 | 148 | #!/bin/sh
# inspect_explore.sh
#
# inspect_explore.sh [ options ] img mask
#
# Created by Paddy Slator on 30/04/2020.
# Author: Paddy Slator, p.slator@ucl.ac.uk
#
#
# LICENSE
# <inspect toolbox for qMRI analysis>
# Copyright (C) <2020> <Paddy J. Slator, p.slator@ucl.ac.uk>
#
# This program is free software: you c... |
1de7ee110db4beee0a951b61aad1c7e3294bf974ae3ae6a1d11ee07ba76ab949 | Shell | 3,883 | 115 | #!/usr/bin/env bash
#==========================================================================
#
# Copyright NumFOCUS
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# htt... |
607629838c200db96a1e81590c6ebeb8af668def3ee0a0f401000e542ed9d471 | Shell | 3,901 | 142 | #!/bin/bash
# Script to check integrity of all ethoscope databases
# Load environment variables if available
if [ -f /etc/ethoscope/environment ]; then
source /etc/ethoscope/environment
fi
# Default settings (can be overridden by environment variables)
DATA_DIR="${ETHOSCOPE_RESULTS_DIR:-/ethoscope_data/results}"
... |
2c173ab6250d6767ec447617a3cf81d83a426cfbe5504786acdd5c2866b2e4da | Shell | 3,940 | 115 | #!/usr/bin/env bash
#
# Build Debian binary packages via dpkg-buildpackage, using
# packaging/debian/debian/ as the packaging directory.
#
# Usage:
# bash scripts/build-deb-packages.sh
#
# Environment variables:
# DIST_DIR Directory to write .deb files (default: <repo>/dist)
# BUILD_MODE "all" = ... |
8c8c4300a3f60ad30fc8379c4e9dc54268560f8a7beddc042bc0358c63e4071e | Shell | 3,951 | 110 | # Brain Extraction shell script (non-SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
#!/bin/bash
# echo "Bash version ${BASH_VERSION}..."
# export QSUB_CODE="qsub -l h_rt=1:00:00 -l h_vmem=1.9G -l tmem=1.9G -l s_stack=10240 -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error "
if [ $# -lt 2 ]
then
echo ""
echo "******... |
8ef066474aeae34a332eea4b38b89ddee261e215ea65a906956e75c5283336b6 | Shell | 3,963 | 105 | #!/bin/bash --login
ID=0 # a number between 0 and 14 inclusive to determine the repetition and the fold indices
FOLD=$(( $(( $ID % 5 )) + 1 )) # remainder gives 0 - 4 but should be 1 - 5, so we add + 1
REP=$(( $ID / 5 )) # 0 - 2
echo TASK_ID=$ID, rep=$REP, fold=$FOLD
BATCH_SIZE=16
NUM_WORKERS=0
GPUS=1
DATA_DIR="$... |
08bd22364b910dc500ad8ad9696f400e2b18b87f8e5423025c4efa0784132df6 | Shell | 4,045 | 98 | #!/bin/bash
rm -rf en.*.txt energy*.txt
###extract potential energies rows
#tim=40 #s folders from s1 to s54
#count=1
countcpu=0
tocpu=19
#while [ "$count" -le "$tim" ]
#do
# cd s"$count"
# echo "this is s"$count""
while [ "$countcpu" -le "$tocpu" ]
do
echo "md is "$countcpu""
# echo "Current working di... |
412937430dd4b444e85fbaafd0708fdb521940f57a1de48c088b7e97de61909e | Shell | 4,085 | 113 | #!/usr/bin/env bash
############################################################
# run-with-singularity.sh (v0.1)
# Wrapper script for running a GenePattern module in a local
# singularity container
#
# Usage:
# run-with-singularity.sh [run-with-env-args]
#
# Configuration
# Copy this file to your ./resources/wr... |
54022cebd18ebb78cbd40fccd8eaf3fb6851a33a461970ce4a73868ce1636d2c | Shell | 4,086 | 99 | #################
## directories ##
SETDIR=/projects/pfenninggroup/singleCell/Logan_BU_Striatum_snRNA-seq
GWASDIR=/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments
CODEDIR=${SETDIR}/code/raw_code/ldsc_interferon_response
DATADIR=${SETDIR}/data/tidy_data/ldsc_interferon_response
ANNOTDIR=${D... |
9c04e5c2eac1928065d32f8ab56c86214d708db539a2e5f12f41e23fe7518c1d | Shell | 4,144 | 140 | #!/usr/bin/env bash
#
# Cross-compile the OpenCC command-line executable for Windows x64 using Zig.
#
# This script is intentionally a direct compiler invocation instead of a full
# release build. It is useful as a fast smoke test for Windows-facing C++ code
# paths when developing on Unix-like hosts:
#
# - _WIN32 p... |
3122616ba41db7c9c0182c33d9fec505b7d9a9dff25b3a71f413f8e7e6fd4a54 | Shell | 4,158 | 96 | export IPYTHONDIR="`pwd`/.ipython"
export IPYTHON_PROFILE=default
numNeurons=1000
simNamePart='1k_testing'
export PD_DATA_DIR="../../../BasalGangliaData/Parkinson/PD2026"
ipcluster start -n 5 --profile=$IPYTHON_PROFILE --ip=127.0.0.1&
sleep 20
######################################################################
# ... |
33619584a28b5c7abe5acf8b79896e2a7bb048916c3212c3d938be48d979c956 | Shell | 4,173 | 159 | #!/bin/bash
## run a single fun of fsl analysis
##
## $Id: fsl_contrast.sh,v 1.3 2008-07-22 21:13:49 ohinds Exp $
usage() {
echo "usage: $0 [options] subj run model"
echo " options:"
echo " -h hpf: high pass filter cutoff (default 32 seconds)"
echo " -d drop: drop scans from the begi... |
c4f1fa1f1b4c360e7e96f2fb3559b6248f2ba62aa27c8a5ee8a69e2fc955298c | Shell | 4,193 | 78 | #!/bin/bash -e
# Copyright 2021 Beijing DP Technology Co., Ltd.
#
# 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 app... |
fd1ac516d3efee02a01049546d28f37dc818ac2158ac1b4294a8fbf480da1d37 | Shell | 4,198 | 128 | #!/usr/bin/env bash
#==========================================================================
#
# Copyright NumFOCUS
#
# 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
#
# htt... |
6c626eacc4961f8f65ac3fd41c364ec35ebd278d220fc5f8e07e5c5345bcf5a4 | Shell | 4,200 | 195 | #!/bin/bash
#SBATCH -J mace_sts
#SBATCH --time=48:00:00
#SBATCH --nodes=8
#SBATCH --ntasks-per-node=48
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=3700
#SBATCH --mail-type=END
#SBATCH --mail-user=<wojciech.stark@warwick.ac.uk>
module purge
module load GCCcore/13.2.0
module load Python/3.11.5
source ~/mace/bin/act... |
095eec18a7a1fcad7749922ed5bebfd5f65526e7b92df350bee7d79953ddda3e | Shell | 4,227 | 118 | #!/bin/bash
declare -i i=0
for enc_method in one_hot blosum62 atchley pca; do
for lr in 0.0001; do
for n_dense in 1; do
for n_units in [16] [32] [64]; do
for dropout_flag in True; do
for p_dropout in 0.2 0.5; do
for leftout in B0702 B0801 C0701; do
i+=1
... |
9821a07c21c776d7397391b2d3e5634f0f222dbcce7d49701dc66834a7659375 | Shell | 4,235 | 109 | #!/bin/bash
# example:
# bash 02d.naiveoverlap.sh -i c1 \
# -p /projects/ps-renlab2/kaw033/CEMBAv2/CEMBA_data/snapatac2 \
# -o /projects/ps-renlab2/kaw033/CEMBAv2/CEMBA_data/snapatac2
while getopts ':i:p:o:h' opt; do
case "$opt" in
i)
cl="$OPTARG"
echo "Processing option 'i' with '${OPTARG}' argum... |
c824fb883cc1e43797e110d617b8b8967af98390d3773d2da1756c22d1427db8 | Shell | 4,264 | 91 | #!/bin/bash
# Migration from Legacy Syntax Example
# Shows how to convert old commands to the current centered-nearest contract
echo "=================================================="
echo "Migration from Legacy to Centered-Nearest Grouping"
echo "=================================================="
echo ""
echo "SC... |
4f956d360de18488581c81c1ee72087ed8fa4ec3e11a2e0034404c079add4ec3 | Shell | 4,269 | 136 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, existence checks, improved error handling
set -euo pipefail
Usage() {
cat <<EOF
(C) C.Vriend - AmsUMC - 02a-DTITK_prepinterreg.sh
Prepare inter-subject registration by collecting subject templates
into a single interr... |
75b26331d02155f70f497d7c5a541586b23c62a097b211444025b39c2be8de78 | Shell | 4,320 | 126 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: SLURM job-array parallelisation of per-subject QC step
set -euo pipefail
Usage() {
cat <<EOF
(C) C.Vriend - AmsUMC - 03b-DTITK_warpqc.sh
Computes the mean warped DTI image across all subjects, extracts
the L3 eigenvalue map for registra... |
343d3457bff60d35524a5b0da83500979d6060affff5dc0755d22566b6f6e605 | Shell | 4,353 | 112 | #!/bin/bash
# Set up source and build directories
build="/wynton/group/gladstone/biocore/projects/ADPPG/Huang/NicoleKoutsodendris-NK01-snRNAseq-pathology-mm10-oct-2021/analysis_hapoe_chr/parameters/adppg-mm10-apoe-chr-mapt-chr-2021-A_build"
mkdir -p "$build"
# Check if the source files exist in reference_sources/ fo... |
9e7691880b92816da056407ce46f3ca2d2d6040c8572458dac080a65f2871847 | Shell | 4,378 | 71 | epochs=20000;
lr=1e-4;
logfile=out.log
# Perform the weak scaling
np=2;
# 2 GPUs
CUDA_VISIBLE_DEVICES=0,1 horovodrun -np ${np} -H localhost:${np} python hvd_hval.py --N 64 --lr ${lr} --seed 1234 --epochs ${epochs} --save 2> /dev/null&
echo "$np"-1234> "$logfile";
CUDA_VISIBLE_DEVICES=2,3 horovodrun -np ${np} -H local... |
2207e7eb0e4eacfc4616ccd61c7e97cb33c552c228f2e77c0dc372042b0f61a2 | Shell | 4,394 | 190 | #!/bin/bash
#SBATCH --job-name=mace_sts
#SBATCH --time=48:00:00
#SBATCH --nodes=10
#SBATCH --ntasks-per-node=128
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=3850
#SBATCH --account=su007-rjm
#SBATCH --mail-type=END
#SBATCH --mail-user=<wojciech.stark@warwick.ac.uk>
module purge
module load GCCcore/11.3.0 Python/3.... |
7c86017853911d26ad09758af99e89a713d144f79e987753d4faea7cac25740d | Shell | 4,394 | 71 | epochs=20000;
lr=1e-4;
logfile=out.log
# Perform the weak scaling
np=2;
# 2 GPUs
CUDA_VISIBLE_DEVICES=0,1 horovodrun -np ${np} -H localhost:${np} python hvd_hval.py --N 256 --lr ${lr} --seed 1234 --epochs ${epochs} --save 2> /dev/null&
echo "$np"-1234> "$logfile";
CUDA_VISIBLE_DEVICES=2,3 horovodrun -np ${np} -H loca... |
7b3e211072f0e7463cdbe71ea03694e87a2288919008d2bd5290a0f142705e86 | Shell | 4,402 | 71 | epochs=30000;
lr=1e-4;
logfile=out.log
# Perform the weak scaling
np=2;
# 2 GPUs
CUDA_VISIBLE_DEVICES=0,1 horovodrun -np ${np} -H localhost:${np} python hvd_hval.py --N 500 --lr ${lr} --seed 1234 --epochs ${epochs} --save 2> /dev/null&
echo "$np"-1234> "$logfile";
CUDA_VISIBLE_DEVICES=2,3 horovodrun -np ${np} -H loca... |
56490c96f0f1f4ab0f087e2bb0505081739ec20b69f779162f2c1dd1e7587d3b | Shell | 4,414 | 125 | #!/usr/bin/env bash
############################################################
# run-with-docker.sh (v0.2)
# Wrapper script for running a GenePattern module in a local
# docker container
#
# Usage:
# run-with-docker.sh [run-with-env-args]
#
# Configuration
# Copy this file to your ./resources/wrapper_scripts ... |
8f7d0e3655e8883e091784fbb808e21c853d8c403b1f610dc132819e6fc41c87 | Shell | 4,421 | 108 | #!/bin/bash
#########################################
# Demonstrate the comman usage of the
# Multi-Atlas Segmentation (MAS) pipeline
#########################################
# Add niftk installation location to system paths: `PATH` and `LD_LIBRARY_PATH`.
# This will only work if user followed the installation inst... |
cb5baaad21a663d6775303de010fe5c144f0b5cee9fd0fc5e8be23084feaeaf6 | Shell | 4,438 | 168 | #!/bin/bash
if [ "*${1}*" == "**" ]; then
DOINSTALL="false"
else
DOINSTALL="true"
fi
BISMAKEJ="-j4"
GENERATOR="Unix Makefiles"
IDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
BDIR="$( cd ${IDIR}/../build && pwd )"
SRCDIR="$( cd ${BDIR}/.. && pwd )"
BISWEBOS=`uname | cut -f1 -d_`
MOCHA=`which mocha`... |
db9994cff17a5a48a6c0e273145c36b4720b8e9cde12f150222a0af39b472974 | Shell | 4,494 | 106 | #!/bin/bash
set -e
set -x
bcecmd=/Users/yexianbin/mac-bcecmd-0.5.4/bcecmd
python_bin=/usr/bin/python3 ## should be installed with paddle
CKPT_BOS_PATH=$1 # 指定一个 BOS 下的 ckp 路径，自动下载下来部署。比如：bos:/helixvs-temp/backdoor/r012_698k_online.pdparams
EXTRACT_PARAM=$2 # 是否需要从 ckp 中提取 'model' 字段下的参数，默认应该不需要，假定模型侧已经处理... |
21753b9b9142d1d6915b97e2d237dea119a0b96fd78b448d03efafe88c33082d | Shell | 4,516 | 92 | export CHKPT_DIR="experiments/checkpoints/final"
export OUT_DIR="experiments/output"
export test_rna="data/mammalian_200-1200_test_RNA_nonredundant_80.fa"
export test_prot="data/mammalian_200-1200_test_PROTEIN_nonredundant_80.fa"
export val_rna="data/mammalian_200-1200_val_RNA_nonredundant_80.fa"
export val_prot="data/... |
0e220caf60dda6e42638ca0bfe94e1910b83f975fe027ffde345935ad5cf427b | Shell | 4,536 | 182 | # preprocess single run fmri data using fsl
usage() {
echo $0 [options] input_file output_file
echo " options:"
echo " -m [1|0]: whether to motion correct (default 1)"
echo " -M [1|0]: whether to regress out motion (default 1)"
echo " -f num : smoothing fwhm in mm (default 6)"
echo " ... |
c3e07a738a5e1988398b40216100cf2a271dba8ea03b09c7916889ac30f3308d | Shell | 4,541 | 182 | # preprocess single run fmri data using fsl
usage() {
echo $0 [options] input_file output_file
echo " options:"
echo " -m [1|0]: whether to motion correct (default 1)"
echo " -M [1|0]: whether to regress out motion (default 1)"
echo " -f num : smoothing fwhm in mm (default 6)"
echo " ... |
bc3a128ae38ac885da78553b870dec1cd660e82b134c1c48b2a32622deca0c01 | Shell | 4,558 | 189 | #!/bin/bash
#SBATCH --job-name=mace_sts
#SBATCH --time=48:00:00
#SBATCH --nodes=10
#SBATCH --ntasks-per-node=128
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=3850
#SBATCH --account=su007-rjm
#SBATCH --mail-type=END
#SBATCH --mail-user=<wojciech.stark@warwick.ac.uk>
module purge
module load GCCcore/11.3.0 Python/3.... |
5c202aa6411e54177a18ed832bc00105a0bd6c8dd91be36a9a01ca7e47cf8edf | Shell | 4,620 | 174 | #!/bin/sh
#
#
#___INFO__MARK_BEGIN__
##########################################################################
#
# The Contents of this file are made available subject to the terms of
# the Sun Industry Standards Source License Version 1.2
#
# Sun Microsystems Inc., March, 2001
#
#
# Sun Industry Standards Source ... |
d6500b47e8dd42f1ef88d0effb9203bbc5d23f0bade3d6fac41468ae9dc4d3a2 | Shell | 4,629 | 121 | #! /bin/sh
#
# Copyright (C) 2003, 2005-2007, 2011, 2015-2016 Free Software Foundation, Inc.
#
# This program 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; either version 2.1 of the License, or
# (at ... |
02c7941652c573e521e8ce5283914a848495f311a7a140e3b8bc46dd02c6e893 | Shell | 4,646 | 93 | #!/bin/bash
set -xe
target=$1
source $(dirname $0)/tc-all-vars.sh
MAKE_TARGETS="lmplz filter build_binary"
CMAKE_BUILD="cmake --build . -j ${DS_CPU_COUNT} --target ${MAKE_TARGETS}"
CMAKE_DEFINES="-DFORCE_STATIC=ON"
case "${target}" in
--android-arm64)
export Boost_DIR="${DS_ROOT_TASK}/DeepSpeech/ds/ndk_... |
3fef047cb630d968eaa8ba65a8e34a34245f150f19774a4aaa6ac9dc0e09e95c | Shell | 4,671 | 172 | #!/usr/bin/env bash
#
# Wrapper script for running an Rscript command
# Calls run-with-env.
#
# Usage: run-script
# -n, dry-run
# [-c <env-custom>],
# [-a <env-arch>],
# -l <libdir>,
# -p <patches>,
# [-d (TRUE|FALSE)], debug mode (defaul=FALSE)
# [-m (TRUE|FALSE)], mkdirs (default=TRUE) ... |
8fab44a8e88269b57d7e94bbb8f2cf77ff0c312774382aec697a3a2f99ee4fd4 | Shell | 4,696 | 139 | #!/bin/bash
#
# Copyright 2020, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of condit... |
326f97684261fc1a26e32c20acbf4db1e432250107fffcc604449f947f57142c | Shell | 4,701 | 128 | #!/bin/bash
usage() {
echo "Usage: $0 -c [cicero_dir] -a [peakannot_file] -g [group] -m [meta_col]"
exit 1
}
while getopts ":c:a:g:m:" o; do
case "${o}" in
c)
cicero_dir=${OPTARG};;
a)
peakannot_file=${OPTARG};;
g)
group=${OPTARG};;
m)
... |
f3609adcd49c7c361ec4f606c9952286093cbbcd81df3247411704085eab9d80 | Shell | 4,744 | 169 | #!/bin/bash
# Test runner for append functionality tests
# This script runs all tests related to the database append feature
echo "==================================="
echo "Running Ethoscope Append Tests"
echo "==================================="
# Get the directory where this script is located
SCRIPT_DIR="$( cd "... |
5248e94de798d064f2babf0ff0ed17ef80c94c2d7f4deef6ec67d3a0d1d90dc8 | Shell | 4,808 | 88 | # Separate the labels into left-right hemisphere
# Step 1: make a left-right flipped version of the template image and
# corresponding mask (Done in Matlab NIFTI Tool)
# Step 2: register the image to the flipped counterpart to get affine matrix
# Step 3: half the affine matrix
# Step 4: Apply the halved affine ... |
52e481a524cf3825d609a641ce7100a8f599bc206b29e66d03c8a5228abdaee3 | Shell | 4,817 | 51 | #################################################################################################################################
# BSP performances on simulations using increasing number of genes and cells. See Figure 2C,2D, and Supplementary Figure 3
###################################################################... |
ac953c86508eb7e356d4b7c285b86fa96625253016a34fa663c7a76761616079 | Shell | 4,837 | 140 | #!/bin/bash
get_batch_options() {
local arguments=("$@")
unset command_line_specified_study_folder
unset command_line_specified_subj
unset command_line_specified_run_local
local index=0
local numArgs=${#arguments[@]}
local argument
while [ ${index} -lt ${numArgs} ]; do
argum... |
d2242ef6305da3ccb163e8d83791e6430b339966b7584395c09d905da903d9af | Shell | 4,892 | 125 | #!/usr/bin/env bash
usage="$(basename "$0") [--help] [-s n] -- DAFi pipeline script to transform, gate, and generate reports on the flowcytometry FCS files
where:
--help show this help text
--nclusters specify number of initial clusters to use for the k-means clustering on the whole sample (default: 200)
... |
8ad6e8156fb6bf833fa161c03bcf881da0cfd4f4fce9bde450de8c17a02ee9ad | Shell | 4,917 | 153 | #!/usr/bin/env bash
usage="$(basename "$0") [--help] [-s n] -- DAFi pipeline script to transform, gate, and generate reports on the flowcytometry FCS files
where:
--help show this help text
--no_opt disables intel AVX2 level optimization in case of compatibility issues (default: AVX2 enabled if detected)
... |
ab1244394c7155ffb3146365c611bb575d5641ea6ae6ab0ae89f80d73965c4c1 | Shell | 4,932 | 44 | #!/bin/bash
source activate kallistobus
cd /data/users/jared/ENS/6mo_LMMP/preprocessing
mkdir -p bus_output
cd bus_output
echo "Processing fastqs from TH"
kallisto bus -i ../bustools_required_files_10xv2_mm/mm_cDNA_introns_mm_10xv2.idx -o ./TH \
-x 10xv2 -t 16 \
/mnt/morbo/Data/Sequencing/Raw_Backup/Kulkarni/Kulkarni... |
53b297c4e436af7731b060d557cdc1f791c61a6d12202c533e962eff134aeadf | Shell | 5,001 | 195 | #!/bin/bash
echo "----------------------------------------------------------"
cat<<TF
##### # #### # # ###### #####
# # # # # # # # #
##### # #### # # ##### #####
# # # # # ## # # # #
# # # # # ## ## # ... |
8ab47401355a9eb3eb260dc8964825eeac96f2c55df89fb0f2312ad60b89b61a | Shell | 5,025 | 178 | #!/usr/bin/env bash
# RNAcode sometimes fails because of bugs. Since the manual suggests
# to call RNAcode on splitted alignments it is feasible to run
# RNAcode separately on the parts. This is implemented here. Command
# line parameters just passed on to RNAcode.
#
# - the script ensures that the region ids are co... |
abbb5bb44f334fde4c02ec671e6f906a4977907e155c21adf2ee1b06d46482fc | Shell | 5,062 | 120 | #/bin/bash
##################################
### Set variables beneath this ###
##################################
# Save OLD PATH
export OLD_PATH=$PATH
#------------------------------------------------------------------------------#
# SOFTWARE CONFIGURATION for MICAPIPE
# Afni binaries
PATH=$(IFS=':';p=($PATH);uns... |
066048ba2fe92600a0bfa761bd9c5f0bf99ee486057b4510e372d18a838de874 | Shell | 5,126 | 153 | #!/usr/bin/env bash
#
# Build and smoke-test a trimmed CPack source package.
#
# Usage:
# bash scripts/build-source-package.sh build <profile>
# bash scripts/build-source-package.sh smoke-test <profile> [tarball]
# bash scripts/build-source-package.sh all <profile>
#
# Profiles (see OPENCC_SOURCE_PACKAGE_PROFILE ... |
bd58d76ee962ddd8600b22534e28a3f211136edea4ccf110561f57657297dd52 | Shell | 5,144 | 162 | #!/bin/bash
set -e
{
usage="$(basename "$0") [-h] [-m <gffcompare tmap file>] [-t <transcripts.fa file>] [-g <genome name>]
This script will produce an annotated csv table of transcripts, by using the tmap output file from add-ncbi-annotation pipeline.
Arguments:
-h show this help text
-m NCBI gffcompare t... |
4ee5266b7184e9d12a268909576ddd8f241f68c1f7c8a5c70966f7ef94d86938 | Shell | 5,184 | 156 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, source config, removed sleep,
# --parsable job tracking, safer loops, input validation, trap cleanup
set -euo pipefail
Usage() {
cat <<EOF
(C) C.Vriend - AmsUMC - 02d-DTITK_interreg-diffeo.sh
Perform iterative diffeomorph... |
010357501c7d63960234d2f2cac85f35b21e23929ef50a9eed65c45bda0d6fd8 | Shell | 5,196 | 179 | #!/bin/bash
set -xe
generic_download_tarxz()
{
target_dir=$1
url=$2
if [ -z "${target_dir}" -o -z "${url}" ]; then
echo "Empty name for target directory or URL:"
echo " target_dir=${target_dir}"
echo " url=${url}"
exit 1
fi;
mkdir -p ${target_dir} || true
${WGET} ${url} -O - | ${UNXZ} |... |
fe906d3cc2d3358903208c4eef18e0138af66ff0d3f9f81492cc2efb90bf6ea9 | Shell | 5,261 | 148 | #!/bin/bash
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
set -e
# Sync with Github repo for latest DAFi scripts and notebooks
cd /var/DAFi-gating
git pull
cd $HOME
if [ -d "work" ]; then
cp /var/DAFi-gating/Notebooks/*.ipynb ~/work
else
cp /var/DAFi-gating/Not... |
d388d23bdb36123df84978defa4eebe4e1381f987082e0a27810485bea145171 | Shell | 5,366 | 170 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, source config, removed sleep,
# --parsable job tracking, safer loops, input validation
set -euo pipefail
Usage() {
cat <<EOF
(C) C.Vriend - AmsUMC - 02c-DTITK_interreg-affine.sh
Perform iterative affine inter-subject regi... |
388cc3cc1490e05cd3d9f55a4a1dc96319084ca1c54fb1385fca3dd08ef88e7c | Shell | 5,414 | 75 | # EDSR baseline model (x2) + JPEG augmentation
#python main.py --model EDSR --scale 2 --patch_size 96 --save edsr_baseline_x2 --reset
#python main.py --model EDSR --scale 2 --patch_size 96 --save edsr_baseline_x2 --reset --data_train DIV2K+DIV2K-Q75 --data_test DIV2K+DIV2K-Q75
# EDSR baseline model (x3) - from EDSR ba... |
39ef19d25fecbfa081692791567bf11d88d195ee968a50e632dd63ee1a7c4f42 | Shell | 5,477 | 159 | # https://support.10xgenomics.com/single-cell-atac/software/release-notes/references#GRCh38-2020-A
# Genome metadata
genome="rn6"
version="2014"
# Set up source and build directories
build="${genome}-${version}-build"
mkdir -p "$build"
# Download source files if they do not exist in reference-sources/ folder
source... |
f990049aa72910cda2cb972403ab471fc7e9306ae7d5bbab972763674dff7e06 | Shell | 5,632 | 123 | # This example script is a walk through of a typical use for pyrho
# We will infer a recombination map using 10 arbitrary diploid individuals from
# ACB for the first 200 SNPs of chromosome 1.
# This script assumes that you've successfully installed pyrho.
# All of the pyrho commands have a number of options. If any... |
773532a0dc169b81e48244b771894d777183e1f015246251bec4d77f68fda381 | Shell | 5,658 | 164 | #!/bin/sh
# This file can be downloaded at http://tinyurl.com/oyuh92j
######################################
# To build the sd card, follow instructions @ http://archlinuxarm.org/platforms/armv6/raspberry-pi
# Then run this script.
# After boot, one can log a s `root` (password = `root`)
# And run: `systemctl start sl... |
3f7e7fdfe99179894714d67c78a28e7f5822d7c5dbb93a1cff845c1a5b58d090 | Shell | 5,748 | 191 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, source config, input validation,
# output existence checks, safer variable handling, fixed log naming
#SBATCH --job-name=dtitk-atlas2template
#SBATCH --mem=16G
#SBATCH --partition=luna-cpu-short
#SBATCH --qos=anw-cpu
#SBATCH --cpus-per... |
184dcfa5b35d3b2c7d973b8b3e48c51b7a8f3b284450c41f2cbb729bdcfe1593 | Shell | 5,750 | 170 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, source config, removed sleep,
# dependency-based array submission, improved error handling
set -euo pipefail
Usage() {
cat <<EOF
(C) C.Vriend - AmsUMC - 02b-DTITK_interreg-rigid.sh
Perform rigid and affine inter-subject r... |
a348204ad59f08a9bd65d3d651bb1692d429a5ac6234349f5c710ddabfb1aa53 | Shell | 5,751 | 205 | #!/usr/bin/env bash
# number of gpus per node
ngpus=1
# number of cores per node (for reconcile only?)
ncores=40
# total number of wafers in the dataset
nwafers=3
# wafers nimgs before exclude lists:
# [739 959 894] = 2592 slices
# Processed wafers nimgs:
# [737 955 881] = 2573 slices
# total number of slices in so... |
028f91e715662b3c0cfbab7c8a1f6428388cd493ea34af00a1e2e10b78f171a8 | Shell | 6,026 | 179 | #!/bin/bash
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
set -e
# A POSIX variable
OPTIND=1 # Reset in case getopts has been used previously in the shell.
# Sync with Github repo for latest DAFi scripts and notebooks
while getopts "u?f?:" opt; do
c... |
7b76a7b0bfc8e45ab02a57d0ff487bc129451202745d6a9d400487563d99499b | Shell | 6,114 | 114 | #!/usr/bin/env bash
# =============================================================================
# BCR-seq preprocessing: pRESTO -> IgBLAST -> Change-O
# 5'RACE (SMARTer template-switch), IgG-targeted mouse heavy/light libraries.
# Produces a productive AIRR-format rearrangement database per sample.
#
# Run inside t... |
08c1b18dfe91bcb0234ab8b3ad12a09bb2c2f2563982dfb0edafa828e8a91068 | Shell | 6,187 | 109 | #!/bin/bash
set -ex
target=$1
source $(dirname $0)/tc-all-vars.sh
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
pushd ${DS_ROOT_TASK}/DeepSpeech/ds/
case "${target}" in
--android-arm64|--android-armv7|--android-x86_64)
source $(dirname $0)/tc-android-utils.sh
wget -q https://github... |
53ebb8c4839836b75d15b6bdfd8b6b958771fd2bbf894df00e919300673fba47 | Shell | 6,234 | 158 | #!/bin/bash
set -e
echo "=== Galaxy GCP Batch Job Execution ==="
echo "Job: ${job_id_tag}"
echo "Tool: ${tool_id}"
echo "Container: ${container_image}"
echo "Timestamp: $$(date)"
echo "Host: $$(hostname)"
echo ""
# Debug network and NFS connectivity
echo "=== Network and NFS Connectivity Debug ==="
echo "Testing NFS s... |
0ff38fdfe6e49d9217903cae57632d3bd99fb1a327249056fe5d46e54df38acb | Shell | 6,261 | 113 | #!/bin/bash
# $ -S /bin/bash
# $ -N job-simulation_MsCaviar_helenhua
# $ -cwd = run from this current working directory (relative paths)
# -o stdout-Simulation.out
# $ -l h_data=6G,h_rt=24:00:00
# $ -t 1-10:1
# source ~/.bash_profile
# source ~/.bashrc
. /u/local/Modules/default/init/modules.sh
module load python/anac... |
91495ac3980675ab98ee73d3fdddebced4b4ba05943093b7de39abc456fd7101 | Shell | 6,313 | 116 | RESULT_DIR="$HOME/experiments/hecktor2021/survival_plus_x/petct"
EXPERIMENTS=(
"multitask+cnn_with-seg_with-densenet"
"multitask+cnn_with-seg_without-densenet"
"multitask+cnn_without-seg_with-densenet"
"multitask+cnn_without-seg_without-densenet"
"multitask+vit_with-seg_with-densenet"
"multitas... |
8684f6850cc3d57da5066b64d9fb66b6b845930a0963a132f9735f8b06517b2b | Shell | 6,369 | 164 | #!/bin/bash
# echo "Bash version ${BASH_VERSION}..."
# Structural Parcellation shell script (SGE)
# Author: Da Ma (d.ma.11@ucl.ac.uk)
# $1: enquiry image
# $2: atlas folder "in_vivo" or "ex_vivo"
# $3: if exist, read user defined parameters
if [[ $# -lt 2 ]]
then
echo "*********************************************... |
5c49ec714cc4638aa352f4cd38d3c3ddd31fa2c7f2d862b5f78ac1b2b18fd5e8 | Shell | 6,380 | 196 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, source config, input validation,
# safer loops, pre-flight checks, fixed broken backslash in original
set -euo pipefail
Usage() {
cat <<EOF
(C) C.Vriend - AmsUMC - 008-DTITK_write-output.sh
Copies final pipeline outputs (... |
c16e380fceb1c4efda72231c9c7c2aa8c512091a113ca3f37e67937e0870c4dd | Shell | 6,439 | 175 | #!/usr/bin/env bash
############################################################
# r-common.sh
# Common R functions for GenePattern wrapper scripts
#
# Environment variables ...
# GP_SCRIPT_DIR, full path to the wrapper scripts directory
# GP_R_VERSION, the version of R, e.g. '2.15'
#
# ... for R site-library cu... |
11ff0d5950449dcca1f52c7288495c742909d945ce07596da9dfcb4b88796828 | Shell | 6,450 | 226 | #!/usr/bin/env bash
############################################################
# env-hashmap.sh
# bash3 compatible alternative to an associative array
# Usage:
# source env-hashmap.sh
# Declared variables:
# __gp_module_envs
# __gp_env_map_keys
# __gp_env_map_vals
# Declared functions:
# putValue can... |
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