sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b234a2e838eab8f1098d84df3ffe7bc0645b2d66d425fd01977a3ac387c0eeb5 | Shell | 2,358 | 69 | #!/bin/bash
# Memory-Constrained Example
# Use case: Working with limited GPU/CPU memory
# This example shows strategies for memory-limited environments
echo "=================================================="
echo "Memory-Constrained Example"
echo "Goal: Train effectively with limited memory"
echo "=================... |
e1cbd1b97b50fc61dcc35063e1fe0b07b340ef99f376a2abf303c5d126c07c02 | Shell | 2,358 | 70 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pfen1
#SBATCH --exclude=compute-1-11,compute-1-12,compute-1-35
#SBATCH --time 3-00:00:00
#SBATCH --job-name=grnboost
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=46G
#SBATCH --error=logs/untar_%A.txt
#SBATCH --output=logs/untar_%A.txt
################... |
bf1bd454d7da938b898f435dd86a5c6ec5c2f0579ead7fac6bc15e23413519df | Shell | 2,370 | 64 | #!/bin/bash
set -xe
install_nuget()
{
PROJECT_NAME=$1
if [ -z "${PROJECT_NAME}" ]; then
exit "Please call with a valid PROJECT_NAME"
exit 1
fi;
nuget="${PROJECT_NAME}.${DS_VERSION}.nupkg"
export PATH=$PATH:$(cygpath ${ChocolateyInstall})/bin
mkdir -p "${TASKCLUSTER_TMP_DIR}/repo/"
mkdir -p "$... |
c1fa25bda1e8a585b41e94b65c4ca21d892fae3a6e277a8be638064d45de77e9 | Shell | 2,382 | 68 | #!/bin/bash
set -xe
# How to generate / update valgrind suppression lists:
# https://wiki.wxwidgets.org/Valgrind_Suppression_File_Howto#How_to_make_a_suppression_file
#
# $ valgrind --leak-check=full --show-reachable=yes --error-limit=no --gen-suppressions=all --log-file=minimalraw.log ./minimal
# $ cat ./minimalraw.... |
48114b2db3a89cda5ba3861a2005a0b7785c4befb7550d43dd9ec48fcf3addd1 | Shell | 2,384 | 62 | #!/bin/bash
set -xe
source $(dirname $0)/tf-vars.sh
mkdir -p ${CI_ARTIFACTS_DIR} || true
cp ${DS_ROOT_TASK}/tensorflow/bazel_*.log ${CI_ARTIFACTS_DIR} || true
OUTPUT_ROOT="${DS_ROOT_TASK}/tensorflow/bazel-bin"
for output_bin in \
tensorflow/lite/exper... |
1f79ca0bbafd18383386256509d412a47eee6c0504290caa12d84671c7492232 | Shell | 2,397 | 83 | #!/bin/bash
cd $(dirname $0)
cd ..
source ~/.bashrc
source ./scripts/utils.sh
root_path="$(pwd)/../../../.."
export PYTHONPATH="$root_path/":$PYTHONPATH
datasets="bace bbbp clintox sider tox21 toxcast"
compound_encoder_config="model_configs/geognn_l8.json"
init_model="./pretrain_models-chemrl_gem/class.pdparams"
log_... |
1b3afbc23743635c445408bdbedb7c9a2756fb8d711e75138861d27ed95cd0dd | Shell | 2,409 | 51 | #!/bin/bash
set -ex
source $(dirname $0)/tf_tc-vars.sh
pushd ${DS_ROOT_TASK}/tensorflow/
BAZEL_BUILD="bazel ${BAZEL_OUTPUT_USER_ROOT} build -s --explain bazel_monolithic_tf.log --verbose_explanations --experimental_strict_action_env --config=monolithic"
# Start a bazel process to ensure reliability on Windo... |
e765ed91f8d14648975db07edad8afbcb0997bcb806644c8222f0edf300b50b4 | Shell | 2,420 | 71 | #! /bin/bash
# this script will aggregate a 10x genomics multiome gex and atac library
# bgadd -L 10 /parkerw/cellranger
# to run LSF detached
# export LSF_DOCKER_VOLUMES="$HOME:$HOME \
# $STORAGE1/reference:$HOME/reference \
# $STORAGE1/cellranger_multi_counts:$HOME/cellranger_multi_counts \
# $SCRATCH1/ckd:$HOME/gi... |
4f77c0d48080aa05397296912f328327bbcbdc25a781c39e76d2e4e10ab682e3 | Shell | 2,427 | 62 | #!/bin/bash
set -xe
source $(dirname $0)/tf_tc-vars.sh
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
cp ${DS_ROOT_TASK}/tensorflow/bazel_*.log ${TASKCLUSTER_ARTIFACTS} || true
OUTPUT_ROOT="${DS_ROOT_TASK}/tensorflow/bazel-bin"
for output_bin in \
tensorfl... |
e67ce1c0885a19ca0869f0b48db73072bbc228f637c383da7747ea708b3a37de | Shell | 2,428 | 41 | # shellcheck shell=bash disable=SC2004,SC2006,SC2015,SC2086,SC2154,SC2166
if [ -z "$GALAXY_MEMORY_MB" -a -n "$SLURM_JOB_ID" ]; then
GALAXY_MEMORY_MB=`scontrol -do show job "$SLURM_JOB_ID" | sed 's/.*\( \|^\)Mem=\([0-9][0-9]*\)\( \|$\).*/\2/p;d'` 2>$metadata_directory/memory_statement.log
fi
if [ -n "$SGE_HGR_h_vme... |
1bbb9306123a0cb0ab932df949cb2b847e9318548e3865357b7135cec5189e49 | Shell | 2,452 | 34 | ########### job submission parameters (only needed for cluster version) ###############
# Recommended job submission parameters large FOV (e.g. 256*512*256), normally ex vivo scan normally ex vivo scan
export QSUB_CMD="qsub -l h_rt=5:00:00 -pe smp 4 -R y -l h_vmem=1G -l tmem=1G -j y -S /bin/sh -b y -cwd -V -o job_outp... |
7569168be5a6f7a51d5905342aabf1b3b6df380165fd88ad9c95e341c93cbbfd | Shell | 2,477 | 85 | #!/bin/bash
cd $(dirname $0)
cd ..
source ~/.bashrc
source ./scripts/utils.sh
root_path="$(pwd)/../../../.."
export PYTHONPATH="$root_path/":$PYTHONPATH
datasets="esol freesolv lipophilicity qm7 qm8 qm9"
compound_encoder_config="model_configs/geognn_l8.json"
init_model="./pretrain_models-chemrl_gem/regr.pdparams"
log... |
3e4bbaad9d4a5a56bb3bcc1961371bd65e07d874932b2c7b0f81f2a58edac8fd | Shell | 2,479 | 86 | #!/bin/bash
set -xe
export OS=$(uname)
if [ "${OS}" = "Linux" ]; then
export DS_ROOT_TASK=${CI_TASK_DIR}
export PYENV_ROOT="${DS_ROOT_TASK}/pyenv-root"
export DS_CPU_COUNT=$(nproc)
fi;
if [ "${OS}" = "${CI_MSYS_VERSION}" ]; then
export CI_TASK_DIR="$(cygpath ${CI_TASK_DIR})"
export DS_ROOT_TASK=$... |
c948c81adf9e9b488f5f466267cd2979037d9029505d5f81f034f6abefa19b4e | Shell | 2,489 | 95 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, source config, removed sleep,
# input validation, fixed log naming
#SBATCH --job-name=dtitk-diffeo
#SBATCH --mem=500M
#SBATCH --partition=luna-cpu-short
#SBATCH --qos=anw-cpu
#SBATCH --cpus-per-task=1
#SBATCH --time=00-00:30:00
#SBATCH... |
2347a5ceea1974e3e57a200b908d3782dd726bf1e062bcf5db63c9f61b556372 | Shell | 2,492 | 69 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.08.29
# usage: ./leave_one_out_parcellation.sh $1 $2 $3
# $1: atlas (in_vivo ex_vivo)
# $2: STEPS parameter k (kernel size in terms of voxel number)
# $3: STEPS parameter n (number of top ranked local atlas to select for label ... |
4b6af45f4a34b84cff61dab0ba06225cabf5a4c35dcb8aa6d3b72b093ca6281a | Shell | 2,499 | 83 | # Structural Parcellation shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.08.29 to be modified ...
#!/bin/bash
# echo "Bash version ${BASH_VERSION}..."
# $1: enquiry image
# $2: atlas folder "in_vivo" or "ex_vivo"
if [ ! -d job_output ]
then mkdir job_output
fi
if [ ! -d job_error ]
then... |
d96a315d3c95d48219e20b3aff12ec466ee567b56c0d0d8b0493a703f9a1135b | Shell | 2,509 | 76 | #!/usr/bin/env bash
usage="$(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)
... |
b6aeb600712bb2e15951951b6b1547c66a1f9b8fb4e989fd886e6ab68a11082b | Shell | 2,516 | 31 | python3 Scripts/reformattime.py BrainPaper/HeathLabCD4/OriginalData/movie1cd4.csv 30.68 30
python3 Scripts/reformattime.py BrainPaper/HeathLabCD4/OriginalData/movie2cd4.csv 30 30
python3 Scripts/reformattime.py BrainPaper/HeathLabCD4/OriginalData/movie3cd4.csv 32.76 30
python3 Scripts/reformattime.py BrainPaper/HeathLa... |
d77e1860a3c5cd98bac2f760ed04278e7a57c513c0df8a8c5422bc7ffb1db248 | Shell | 2,516 | 31 | python3 Scripts/reformattime.py BrainPaper/HeathLabCD8/OriginalData/movie1cd8.csv 30.68 30
python3 Scripts/reformattime.py BrainPaper/HeathLabCD8/OriginalData/movie2cd8.csv 30 30
python3 Scripts/reformattime.py BrainPaper/HeathLabCD8/OriginalData/movie3cd8.csv 32.76 30
python3 Scripts/reformattime.py BrainPaper/HeathLa... |
904a09fb3268d80656e570afd326732f5543b7fbd90eb59dfb659fd710474a0f | Shell | 2,521 | 56 | #/bin/bash
#
# initializes dependencies & paths necessary to run micapipe & related functions
#
#
# 2021 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------------------------------------------------------------------------------------------------------------------------------------
# Save OLD PATH
exp... |
679e34319a3beb422cf9c0fabbb926c368d3237c25af2cafc02d2feef5665dd8 | Shell | 2,550 | 73 | #!/bin/bash
#
#SBATCH --job-name=MLS_firstlvl
#SBATCH --array=05,106,11,118,123,210,24,27,29,44,54,64,88,92,97%20
#SBATCH --time=00:15:00
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=4GB
#SBATCH -p ${PROFILE}
# Outputs ----------------------------------
#SBATCH --output=../logs/FirstLvl.%A_%a.out
#SBATCH --error=../... |
5fc0d73c8af8e69b701d21e57b1d9deff5bfaa92908e8df37ec769b81adfa078 | Shell | 2,560 | 95 | #!/usr/bin/env bash
############################################################
# run-rscript-pkgs.sh
# Run an 'Rscript' module, installing R packages if necessary
# Usage:
# ./run-rscript-pkgs.sh \
# [--dry-run] \
# [--debug] \
# -v r-version \
# -c env-custom \
# -e name=value ...
# --
#... |
8cb4705de302ff44d6fb73678ae754a87287331c8ec4398d60887b8dd0646417 | Shell | 2,563 | 77 | #!/bin/bash
set -e
if [ $# -lt 1 ]; then
echo "Usage: ./run_mysql_server_singularity.sh [DB_DIR] [PORT] [CONTAINER_NAME] \
[MYSQL_USER] [MYSQL_PASSWORD] [MYSQL_DB_NAME]"
echo
echo "Example: run_mysql_server_singularity.sh ~/cromwell_data_dir 3307"
echo
echo "[DB_DIR]: This directory will be mapped to '/var/l... |
7363534fb715c86d0fa8abcccefebdb49fcef7ffc5b45de0e2522f2a2e17ef0f | Shell | 2,566 | 17 | #!/bin/bash
python trans_neg2pos.py H293-1.sorted.bam.filter.bam.pos.sort.bam.pos.rough.txt H293-1.sorted.bam.filter.bam.neg.sort.bam.neg.rough.txt > H293-1.site.txt
python trans_neg2pos.py H293-2.sorted.bam.filter.bam.pos.sort.bam.pos.rough.txt H293-2.sorted.bam.filter.bam.neg.sort.bam.neg.rough.txt > H293-2.site.txt
... |
7ff85be3791183d8571eb0079764a1855b945655155466550ae5a89c7ccda194 | Shell | 2,577 | 58 | #!/bin/bash
set -e
# Makes programs, downloads sample data, trains a GloVe model, and then evaluates it.
# One optional argument can specify the language used for eval script: matlab, octave or [default] python
make
#if [ ! -e text8 ]; then
# if hash wget 2>/dev/null; then
# wget http://mattmahoney.net/dc/text8.z... |
41b05cd4f5a23663d5078cacf7eea264179b3b7081cea192be754de8c84cc862 | Shell | 2,585 | 76 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pfen1
#SBATCH --time 3-00:00:00
#SBATCH --job-name=STARsolo
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=12
#SBATCH --mem=80G
#SBATCH --error=logs/STARsolo_%A_%a.txt
#SBATCH --output=logs/STARsolo_%A_%a.txt
#SBATCH --array=1-24%4
source ~/.bashrc
###################... |
52284e26e0df46f995e35449bf568618a219d034ccbdf0c8031ba027ec0140e7 | Shell | 2,593 | 47 | #!/bin/bash
set -u
set -x
#z5OMP.8.ca.female.chrVCF.impute.pairs.gz
#run from /media/storageA/lisa/dipc/
name=$1 #example: for files dipc.z5OMP.25.R1.fastq.gz and dipc.z5OMP.25.R2.fastq.gz the name is "z5OMP.25"
# resolve haplotypes via imputation
hickit -i $name.ca.male.contacts.pairs.gz -u -o - | bgzip > $name.ca.m... |
7d1f04259f7e59a6dc7d28587ca23ed6bb28793d6163fd189a9d7116e5afaa8a | Shell | 2,601 | 54 | #!/bin/bash
dwipreprocdir=/home/anw/cvriend/my-scratch/dwi-preproc
dwidtitkdir=/home/anw/cvriend/my-scratch/dwi-dtitk
module load dtitk/2.3.1
module load fsl/6.0.6.5
module load Anaconda3/2022.05
conda activate /scratch/anw/share/python-env/mrtrix
cd ${dwipreprocdir}
for subj in $(ls -d sub-*); do
echo ${subj}
... |
4f46391b35270db750e5751a51499e56834da561ea448a4cc2645b37d7fe8a6d | Shell | 2,609 | 88 | #!/bin/bash
#$ -pe local 8
#$ -l mem_free=10G,h_vmem=20G,h_fsize=100G
#$ -V
#$ -cwd
# run on JHPCE cluster
# qsub code/scripts/spaceranger/spaceranger_MiSeq.sh
############################
# Script to run Space Ranger
############################
# locations of files:
# -------------------
# spaceranger reference: /... |
ddfca52397f88e4c76273bb102605c6d7d1b963e7b2a99daa414c6525bf92a2a | Shell | 2,609 | 47 | #!/bin/bash
set -u
set -x
#z5OMP.8.ca.female.chrVCF.impute.pairs.gz
#run from /media/storageA/lisa/dipc/
name=$1 #example: for files dipc.z5OMP.25.R1.fastq.gz and dipc.z5OMP.25.R2.fastq.gz the name is "z5OMP.25"
# resolve haplotypes via imputation
hickit -i $name.ca.female.contacts.pairs.gz -u -o - | bgzip > $name.ca... |
58d92a728816f6be896c8c1e0c4cb91d138a136664159f430ba844f2d5e58923 | Shell | 2,615 | 74 | #!/bin/bash
usage() {
echo "Usage: $0 -c [cicero_dir] -m [meta_col]"
exit 1
}
while getopts ":c:a:g:m:" o; do
case "${o}" in
c)
cicero_dir=${OPTARG};;
m)
meta_col=${OPTARG};;
*)
usage ;;
esac
done
shift $((OPTIND-1))
if [ -z "${cicero_dir}"... |
e18b2ca0ecedb0e01f664daf13dab04b7970fd8c680a056d8f31345ae99eb929 | Shell | 2,620 | 92 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, source config, removed sleep,
# input validation, fixed log naming
#SBATCH --job-name=dtitk-rigid
#SBATCH --mem=500M
#SBATCH --partition=luna-cpu-short
#SBATCH --qos=anw-cpu
#SBATCH --cpus-per-task=1
#SBATCH --time=00-00:10:00
#SBATCH ... |
3df3f4cb736eda545fa3cb4235f8f9924147a7ff489552bebcfaa6d51168e37f | Shell | 2,631 | 70 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.08.29
# usage: ./leave_one_out_labfusion.sh atlas $1 $2 $3
# $1: atlas (in_vivo ex_vivo)
# $2: STEPS parameter k (kernel size in terms of voxel number)
# $3: STEPS parameter n (number of top ranked local atlas to select for lab... |
bf9e6149d7e6276f1344c6c7e11d025c2d215fa0885de6520eec9d827a3a06e5 | Shell | 2,632 | 57 | #! /usr/bin/awk -f
# A script to extract the actual suppression info from the output of (for example) valgrind --leak-check=full --show-reachable=yes --error-limit=no --gen-suppressions=all ./minimal
# The desired bits are between ^{ and ^} (including the braces themselves).
# The combined output should either be appen... |
bf3eba09b4135ca27cc18dc33341cf0fde45af1adeef64a675876f436a20d8b6 | Shell | 2,658 | 92 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, source config, removed sleep,
# input validation, fixed log naming
#SBATCH --job-name=dtitk-aff
#SBATCH --mem=500M
#SBATCH --partition=luna-cpu-short
#SBATCH --qos=anw-cpu
#SBATCH --cpus-per-task=1
#SBATCH --time=00-0:30:00
#SBATCH --n... |
da57a9825905d6a43013083f2cfb742c2b48a99b0e296c6831ac645add72ee12 | Shell | 2,659 | 91 | #!/usr/bin/env bash
# ================================================
# PyTorch Installer for Napari – Auto-Detect ANY version (Linux/Mac)
# Searches a user-selected path (default: ~/.local) and installs torch using pip
# ================================================
set -euo pipefail
PYTORCH_VERSION="2.5.0"
ech... |
3bac7878034de5dd0cdf9dde27d7311d79fec265cc133b7661a3caa55879cba4 | Shell | 2,668 | 58 | #!/bin/bash
set -e
# Makes programs, downloads sample data, trains a GloVe model, and then evaluates it.
# One optional argument can specify the language used for eval script: matlab, octave or [default] python
make
#if [ ! -e text8 ]; then
# if hash wget 2>/dev/null; then
# wget http://mattmahoney.net/dc/text8.z... |
1c4e179250f40aeedd3e25c93a1851681901dbe709341e7c1787eed1cb11ba77 | Shell | 2,671 | 117 | #!/usr/bin/env bats
setup () {
bats_require_minimum_version 1.5.0
dir=$(dirname "$BATS_TEST_FILENAME")
cd "$dir"
cpus=$(nproc)
exe="$dir/../bin/barrnap --threads $cpus"
dbs="bac arc fun"
tab=$'\t'
TRNA="${tab}tRNA${tab}"
RRNA="${tab}rRNA${tab}"
NCRNA="${tab}ncRNA${tab}"
OPERON="${tab}operon${tab}... |
c971ee6f417a25f3d07e04df636e33a5596608506a763c3d3f605026fb10688a | Shell | 2,676 | 113 | #!/bin/bash
set -xe
OS=$(uname)
if [ "${OS}" != "Darwin" ]; then
echo "This should only run on OSX."
exit 1
fi;
flavor=$1
source $(dirname "$0")/tc-tests-utils.sh
if [ -z "${TASKCLUSTER_TASK_DIR}" ]; then
echo "No TASKCLUSTER_TASK_DIR, aborting."
exit 1
fi
do_prepare_homebrew()
{
local _brew_instanc... |
b85d3de947ccb690cdf6e39e745f8a7fa6df060645b4e1aa3ab461df105311f5 | Shell | 2,688 | 94 | #!/bin/bash
set -euo pipefail
VENV=${1:?usage: $0 VENV}
PYTHON="$VENV/bin/python"
GALAXY="$VENV/bin/galaxy"
URL=http://localhost:8080
TRIES=120
WORK_DIR=$(mktemp -d -t galaxy-installed-startupXXXXXX)
LOG_FILE="$WORK_DIR/galaxy.log"
GALAXY_PID=
STOP_TIMEOUT=30
# Galaxy runs in its own process group, whose id is GALAX... |
68b90d0df46b1b105beb5ac653e937c4574496b35e6120f408ef0360d03bab04 | Shell | 2,692 | 55 | #!/bin/bash
set -ex
set -o pipefail
source $(dirname $0)/tf-vars.sh
pushd ${DS_ROOT_TASK}/tensorflow/
BAZEL_BUILD="bazel ${BAZEL_OUTPUT_USER_ROOT} build -s --explain bazel_monolithic_tf.log --verbose_explanations --experimental_strict_action_env --config=monolithic"
# Start a bazel process to ensure reliabi... |
13dd2c707b9f90669077bf3779ca480420ffd88a382fa10b9594de1f69b70b2b | Shell | 2,698 | 75 | #!/bin/bash
#########################################
# Demonstrate the comman usage of the
# Multi-Brain Separation (MBS) pipeline
#########################################
# Add niftk installation location to system paths: `PATH` and `LD_LIBRARY_PATH`.
# This will only work if user followed the installation instruc... |
12398c9fc4e95c592f0c5459dec0aa15df7ee88728b174809afca548164a2f2d | Shell | 2,723 | 59 | #!/bin/bash
set -e
# Makes programs, downloads sample data, trains a GloVe model, and then evaluates it.
# One optional argument can specify the language used for eval script: matlab, octave or [default] python
make
#if [ ! -e text8 ]; then
# if hash wget 2>/dev/null; then
# wget http://mattmahoney.net/dc/text8.z... |
a640339964b4fb4d50046bee084469bff1831fbe3577d69bfde4fe1cca743ea6 | Shell | 2,726 | 77 | #!/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... |
8b3ef3e67a2c8cd965b86a398a778599c911d01f82a67ac68b2c102cc2939c94 | Shell | 2,727 | 83 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
extract_python_versions "$1" "pyver" "pyver_pkg" "py_unicode_type" "pyconf" "pyalias"
bitrate=$2
decoder_src=$3
if [ "$decoder_src" = "--pypi" ]; then
# Disable automatically picking up decoder package built in this CI group
export DECODER_ARTIF... |
9829515057c019a937ba1fb7f3a4985c2b6c11e5fb727f064b646ee40ecf0e2f | Shell | 2,732 | 84 | #!/usr/bin/env bash
usage="$(basename "$0") [--help] [-s n] -- LJI132 DAFi pipeline script to transform, gate, and generate reports on the flowcytometry FCS
files based on LJI Panel
where:
--help show this help text
--no_opt disables intel AVX2 level optimization in case of compatibility issues (default: A... |
afbeac1ea3b67942d4738aa1b0295773ec291c433f9d7481d6292be17732b89d | Shell | 2,739 | 51 | #################################################################################################################################
# nnSVG performances on simulations using increasing number of genes and cells. See Figure 2C,2D, and Supplementary Figure 3
#################################################################... |
c2dac948255a25c2ff8eadce535705b9b444a5fb7ecfb04d1489d3885a91df2d | Shell | 2,739 | 51 | #################################################################################################################################
# SPARK performances on simulations using increasing number of genes and cells. See Figure 2C,2D, and Supplementary Figure 3
#################################################################... |
2b0d7d24e4810412b0f0285070f1091e07aafea696a99644d42cf803e855a460 | Shell | 2,747 | 103 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, safer loops, explicit error tracking,
# non-zero exit on failures, input validation
set -euo pipefail
Usage() {
cat <<EOF
(C) C.Vriend - AmsUMC - 01b-DTITK_checkfit.sh
Check that DTI-TK conversion and intra-subject regist... |
91bd186aa42d56d1d31ec49203d4aefcf5bd60ec2248fa2c0a33a81fca712c5a | Shell | 2,754 | 89 | #!/bin/bash
# start_uwsgi.sh - Start Cellxgene Gateway with uWSGI
#
# PREREQUISITES:
# - uWSGI installed (pip install uwsgi)
# - Virtual environment activated
# - .env file with CELLXGENE_LOCATION and CELLXGENE_DATA (or CELLXGENE_BUCKET)
#
# USAGE:
# ./start_uwsgi.sh
# Exit on error
set -e
# Get the directory where ... |
d4a5bb8e102515abda1c06745dc9de8f80db928d31ed9d2945ddfcc43d8cbc40 | Shell | 2,780 | 51 | #################################################################################################################################
# SPARKX performances on simulations using increasing number of genes and cells. See Figure 2C,2D, and Supplementary Figure 3
################################################################... |
4600aee0c4439eae8840b8c6f7de77e179996a506b1cf81a10a3a17623d86b6a | Shell | 2,782 | 68 | #!/bin/bash
# 01_build_haplotype_fasta.sh
# Build paternal/maternal haplotype-specific fasta files compatible with C.Origami.
#
# Strategy:
# - Use a *phased* single-sample VCF (e.g. GIAB GM12878 v4.2.1, 1000G phased calls,
# WhatsHap output, etc.).
# - Restrict to bi-allelic SNPs only — indels would shift down... |
c9e8ba6efa9a20344882223c4da800efbafdeba506f9effc5a8601f08be52312 | Shell | 2,782 | 92 | #!/bin/bash
set -xe
package_native_client()
{
tensorflow_dir=${DS_TFDIR}
deepspeech_dir=${DS_DSDIR}
artifacts_dir=${TASKCLUSTER_ARTIFACTS}
artifact_name=$1
if [ ! -d ${tensorflow_dir} -o ! -d ${deepspeech_dir} -o ! -d ${artifacts_dir} ]; then
echo "Missing directory. Please check:"
echo "tensorflow... |
688c1ff3f0098ef57cb95eca6c7a6d4cf5bb2458edd81c87b988bd162c521acd | Shell | 2,787 | 92 | #!/bin/bash
# Pipeline to reproduce pancancer pathways TP53 machine learning classifier
#
# Usage: bash tp53_analysis.sh
#
# Output: Will train a pan cancer model to detect TP53 aberration. Will also
# train a unique classifier within each specific cancer type
# Set Constants
tp53_diseases='BLCA,BRCA,CESC,COA... |
d2cc048fa8dff0f7c211a97b06a00e17786ea6e75da8fe7c3a1e31ef2f4d5d45 | Shell | 2,787 | 92 | #!/bin/bash
set -xe
package_native_client()
{
tensorflow_dir=${DS_TFDIR}
deepspeech_dir=${DS_DSDIR}
artifacts_dir=${CI_ARTIFACTS_DIR}
artifact_name=$1
if [ ! -d ${tensorflow_dir} -o ! -d ${deepspeech_dir} -o ! -d ${artifacts_dir} ]; then
echo "Missing directory. Please check:"
echo "tensorflow_dir=... |
0962c2b53cad69c41b0af791617ea43110151e1dab7bd4a33e7f07be18ca859d | Shell | 2,798 | 87 | #!/bin/bash
set -e
genome=${1}
if [ "$1" == "-h" ]; then
echo ""
echo "Usage: ./`basename $0` [genome]"
echo ""
echo "This program will download and index the specified genome from the uscs server (goldenpath) including annotation"
echo ""
echo "[genome]: UCSC Prefix of the genome assembly. Check names h... |
145eef11863cf2de255fb2125522af4f61c52df3e0718b1d385dbae3aa001dd0 | Shell | 2,800 | 71 | #!/bin/bash
# ============== User Configuration ==============
inputjson=${1}
outpath=${2}
mkdir -p ${outpath}
# Python and Environment Configuration
PYTHON_BIN="PATH/TO/YOUR/PYTHON"
export LD_LIBRARY_PATH="PATH/TO/YOUR/ENV/lib:$LD_LIBRARY_PATH"
ENV_BIN="PATH/TO/YOUR/ENV/bin"
# Database Paths
DATA_DIR="PATH/TO/DATA"... |
722914f347b067c2777a21cef05f75c80cb45b3e356fd1ffaafcdd747d7234f8 | Shell | 2,800 | 87 | #!/bin/bash
set -e
genome=${1}
if [ "$1" == "-h" ]; then
echo ""
echo "Usage: ./`basename $0` [genome]"
echo ""
echo "This program will download and index the specified genome from the uscs server (goldenpath) including annotation"
echo ""
echo "[genome]: UCSC Prefix of the genome assembly. Check names h... |
4988b966975f5e091b74cf4086366741a9c35fe6444dbc3f39225f3ec626eff0 | Shell | 2,828 | 77 | #!/bin/bash
# ./scripts/runtime_batch.sh "RepECN" 48 "repecn_t repecn_s repecn_b" "2 3 4" "--save_result --no_count --n_GPUs 1 --times 50"
# ./scripts/runtime_batch.sh "ALAN" 48 "v1t v1s v1b" "2 3 4" "--save_result --no_count --n_GPUs 1 --times 50"
# ./scripts/runtime_batch.sh "RACN" 48 "no" "2 3 4" "--save_result --n... |
1fbb1216f1265c8f4358c8f366acdf2f6729b32548714e938b5dc533dcae1a6a | Shell | 2,867 | 52 | #!/bin/bash -l
#
sub=$1 #participant ID
indir=$2 #path to input directory
outdir=$3 #path to output folder for images
tmpdir=$4 #path to temporary directory where command files will be generated
# load all defaults
module load freesurfer/7.1.0
qcdir=$outdir
dataDir=$indir
mkdir -p ${qcdir}
cd ${dataDir}/${sub}
sess... |
edec662bbd5edb0c71f018c003ea2724a8e459f32c907d2ea4ed28c30a44cc39 | Shell | 2,884 | 90 | #!/bin/bash
#
#SBATCH --job-name=AHRB_firstlvl
#SBATCH --array=1-108%20 # sub-26 doesnt have run2
#SBATCH --time=00:20:00
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=4GB
#SBATCH -p ${PROFILE}
# Outputs ----------------------------------
#SBATCH --output=../logs/FirstLvl.%A_%a.out
#SBATCH --error=../logs/FirstLvl.%A... |
86337150cd61042a949416369c0e319b694f4c07bdcb8f66b6edf3071de2308f | Shell | 2,903 | 51 | #################################################################################################################################
# SpatialDE performances on simulations using increasing number of genes and cells. See Figure 2C,2D, and Supplementary Figure 3
#############################################################... |
8a1d62f2992c509db7595e04f4a5141285cd870ff169579d6e2872ad93d39e89 | Shell | 2,911 | 89 | #!/bin/bash
# update-node-cli.sh - Update ethoscope node from git repository
# Usage: ./update-node-cli.sh [--all]
set -e
# Check if --all flag is provided
ALL_FLAG=false
if [[ "$1" == "--all" ]]; then
ALL_FLAG=true
fi
echo "Starting ethoscope node update..."
# 1. Find the source of /opt/ethoscope git repo
if ... |
80aaefd1c47f5f220c8e2985f5c2be39e89d21b2e59ba722864f4665dafa7c1b | Shell | 2,914 | 89 | #!/bin/bash
SAMPLES=$1
CONTRASTS=$2
shift 2
if [[ -z "$SAMPLES" ]];
then
cat <<EOF
Usage: dasa.sh SAMPLES CONTRASTS [nextflow-args]
Any nextflow-args, if supplied, are passed to the nextflow run command.
Pipeline parameters that can be specified in nextflow.config:
SAMPLES is a tab-delimited file describing exper... |
1d37c82ee6ce9b41987c697393944b6b793b6f36c692c158a4c17fc57b3e2ad3 | Shell | 2,919 | 90 | #!/bin/bash
#set -e
SAMPLES=$1
CONTRASTS=$2
#CONFIG=$3
shift 2
if [[ -z "$SAMPLES" ]];
then
cat <<EOF
Usage: dasa.sh SAMPLES CONTRASTS [nextflow-args]
Any nextflow-args, if supplied, are passed to the nextflow run command.
Pipeline parameters that can be specified in nextflow.config:
SAMPLES is a tab-delimited f... |
756aedf7bb7813d8ba17a35262f514d64ecb903df9fd4e970ac5d0d9f51e7e21 | Shell | 2,946 | 92 | #!/bin/sh
# Upgrade dependencies by default, export the existing lock with --export-only,
# or verify the lock and its requirements exports without changes with --check.
set -e
this_directory="$(cd "$(dirname "$0")" > /dev/null && pwd)"
workspace_root="$(cd "$this_directory/../../.." > /dev/null && pwd)"
requirements... |
d0486e6d63a3711f1f2d53ace278919bd748fb14b840b23dfc2ecb3796cfb142 | Shell | 2,950 | 54 | #!/bin/bash
#
# Main routing point to call all processing-related functions in MICAPIPE and SCRIPTS_CUSTOM folders
# Change the FUNC_ID variable to choose your function.
# All function calls are passed through the cluster (qbatch)
# * * NOTE: THIS IS INTENDED TO BE RUN ON THE BIC AT MCGILL! PLEASE ADAPT FOR YOUR PURPO... |
b574e1a8dd0bb0d4dca6033b8feb88f50aa3ae1980119377fe8b7bc3f071b7d7 | Shell | 2,958 | 99 | #!/usr/bin/env bash
usage="$(basename "$0") [--help] [-s n] -- DAFi pipeline script to transform, gate, and generate reports on the flowcytometry FCS files
where:
--help show this help text
--no_opt disables intel AVX2 level optimization in case of compatibility issues (default: AVX2 enabled if detected)
... |
ec6017d7397ab4765c69b93945c034bb4af3b449ce815bf1db4e74a13e506ddc | Shell | 2,971 | 91 | #!/bin/bash
cd "$(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
expo... |
99ae504491bacf9122b1afb7ed0adb60ba79e5aa9b3e3f3f2f50fe45a05edd45 | Shell | 2,993 | 89 | #!/bin/sh
set -x
export SRC_DIR="/tmp/SimpleITK"
export BLD_DIR="/tmp/SimpleITK-build"
export OUT_DIR="/work/io"
SIMPLEITK_GIT_TAG=${SIMPLEITK_GIT_TAG:-v1.1rc1}
PYTHON_VERSIONS=${PYTHON_VERSIONS:-$(ls /opt/python | sed -e 's/cp2[0-6][^ ]\+ \?//g')}
NPROC=$(grep -c processor /proc/cpuinfo)
export MAKEFLAGS="-j ${NP... |
852199b646306e077e603fe2821ec73b941fda47dfa405eaf9c1ddf8f85a444c | Shell | 3,016 | 70 | #!/bin/sh
# Build one release asset from an unpacked source distribution.
#
# Driven entirely by the environment so the workflow matrix stays data and
# this stays the only copy of the logic. Run it inside the build container
# (Linux, Windows) or directly on the runner (macOS); it assumes only a C++
# compiler, make, ... |
abe4e9ce6e506b3f97f96b019f0adfea9b9a959ea16186626611b301704cd841 | Shell | 3,026 | 91 | #!/bin/bash
# start_gunicorn.sh - Start Cellxgene Gateway with Gunicorn
#
# PREREQUISITES:
# - Gunicorn installed (included with cellxgene 1.3.0, or: pip install gunicorn)
# - Virtual environment activated
# - .env file with CELLXGENE_LOCATION and CELLXGENE_DATA (or CELLXGENE_BUCKET)
#
# USAGE:
# ./start_gunicorn.sh
... |
d525fe2e5180c7ee1cde9f60b97c7166e1498c927ef50c4e3dfc23c64e8f3036 | Shell | 3,030 | 100 | #!/bin/sh
# Converts a mysqldump file into a Sqlite 3 compatible file. It also extracts the MySQL `KEY xxxxx` from the
# CREATE block and create them in separate commands _after_ all the INSERTs.
# Awk is choosen because it's fast and portable. You can use gawk, original awk or even the lightning fast mawk.
# The mys... |
27c0763f935c34c8f8c1f8e0ffde70040a5508ceb2f26a0ff272305661f4f67b | Shell | 3,038 | 64 | ## script changed from original by for bioconda-lefse by jfg 2017.10.31
## adapted from the original lefse run.sh available at:
## https://bitbucket.org/nsegata/lefse/src/54694b4b0d9e335ff1ecafff8db4f1e0cf7004da/example/run.sh?at=default&fileviewer=file-view-default
##
##
# Download a 3-classes example (with subclass... |
a72274169d27e2b429c0e6bd65edff954cb8a1c87a61b5f5cf8ea4766375ec4a | Shell | 3,062 | 103 | #!/usr/bin/env bash
usage="$(basename "$0") [--help] [-s n] -- LJI132 DAFi pipeline script to transform, gate, and generate reports on the flowcytometry FCS
files based on LJI Panel
where:
--help show this help text
--no_opt disables intel AVX2 level optimization in case of compatibility issues (default: A... |
e91dc841d1be72346551753252c1a142a762d2470ea0ccee5213461679411e2c | Shell | 3,074 | 83 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_sampl
results_dir2=results_sampl_production
train_path=../data/logP/train.csv
val_path=../data/logP/val.csv
test_path=../data/logP/test.csv
path=../data/logP/logP_without_overlap.csv
#Hyperparameter optimizati... |
fd76a53df7193adb473b089bdd39d2ae59ac1760b168aed748a1f3d0048a757c | Shell | 3,097 | 91 | #!/usr/bin/env bash
#
# agent-vm.setup.sh: Package installation script that runs inside the base VM
# Inspired by https://github.com/sylvinus/agent-vm
# And https://github.com/anthropics/claude-code/blob/main/.devcontainer/Dockerfile
#
# This script is executed inside the VM.
#
set -euo pipefail
export DEBIAN_FRONTEN... |
ddf334c4714482ebacbca9f785f72864a239bb6a9ae0f008648898e1759d1a67 | Shell | 3,100 | 126 | #!/bin/sh
# inspect_explore_all.sh
#
# inspect_explore_all.sh [ options ] img mask
#
# Created by Paddy Slator on 01/01/2020.
# 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 softwar... |
0066b7c1f33ef2ff6e90c7858e3d13eebad4b819ed1f9cd8244bb871a68064e5 | Shell | 3,101 | 50 | epochs=30000;
lr=1e-4;
logfile=out.log
np=2;
# 2 GPUs
CUDA_VISIBLE_DEVICES=0,1 horovodrun -np ${np} -H localhost:${np} python hvd_hval.py --N 2000 --lr ${lr} --seed 1234 --epochs ${epochs} --save 2> /dev/null&
echo "$np"-1234> "$logfile";
CUDA_VISIBLE_DEVICES=2,3 horovodrun -np ${np} -H localhost:${np} python hvd_hval... |
1a2f3bad41250d425db9eba8e4bfc80bf83b3606560d6a05b8bb50fd3ac110eb | Shell | 3,127 | 90 | #!/bin/bash
#
#SBATCH --job-name=MLS_firstlvl
#SBATCH --array=1,3,8,12-18,22,26,28,30-34,37,39-41,46,48,50,51,53,56,58,60-63,67,72,75-79,81-83,85,87,89-91,93-95,98-99,101-102,104-105,109-110,112-114,116,119,121-122,127-132,136,139,144,149,151,155-156,158-160,162,164-165,167-168,175-176,183,185,195,197,199-200,204,207,2... |
7b92aaefb551ff5277588bdb101adf2a72e67efff0f6859e8abc134d3fdb9039 | Shell | 3,130 | 52 | 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 2000 --lr ${lr} --seed 1234 --epochs ${epochs} --save 2> /dev/null&
echo "$np"-1234> "$logfile";
CUDA_VISIBLE_DEVICES=2,3 horovodrun -np ${np} -H loc... |
c1e82305e080e3743105e2bf94994b5403b3805f8c995e5094f0f848ab0481d3 | Shell | 3,143 | 94 | #!/bin/bash
#
# Compute geodesic distance along cortical mesh:
#
# Generates geodesic distance matrices along native cortical surface using specified parcellations
#
# This workflow makes use of wb_command and custom python scripts
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micapipe/tree... |
2e656503de74e9fbc6411daeb0721d6e5f85959ed2d00f9f6d713f9dae35defe | Shell | 3,173 | 115 | #!/bin/bash
echo "----------------------------------------------------------"
cat<<TF
##### # #### # # ###### #####
# # # # # # # # #
##### # #### # # ##### #####
# # # # # ## # # # #
# # # # # ## ## # ... |
52fa53583ca31ed48cf59cb56330066aadb03eecd4cabb4bd5504c0b707f82dc | Shell | 3,194 | 110 | #!/usr/bin/env bash
usage="$(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)
... |
5e761a6d5ab449017831393fd218ecb03e6d55d3c0ca2983a8aba6cb63c07ef0 | Shell | 3,195 | 111 | #!/bin/bash
#set -eu
module rm compiler/rocm/2.9
module load compiler/rocm/4.0.1
module load apps/anaconda3/5.2.0
source activate ~/conda-envs/paddle_dcu
allhost=$1
demo=$2
echo "-------------input params ${SLURM_NODEID}--------------"
echo "${SLURM_NODEID} allhost:$allhost demo:$2"
echo "SLURM_NODEID:${SLURM_NODEID}... |
6ab5c002e2396802c0cf7c6272ccf2170af471fc35e4ee9f9c68ca2254a4a065 | Shell | 3,195 | 83 | #!/usr/bin/env bash
# run_all.sh — paper 7 deposit end-to-end smoke + headline reproduction.
#
# Wraps the canonical sequence documented in RUN_PAPER.md:
# 1. Smoke test (tests/test_canonical_pipeline.py): verifies the bundled
# feature JSONs reproduce paper 7's headline numbers byte-identical
# (held-out f... |
9c8437152490b1835c42cbd86ebd94fbb6d4cea4d146ee5875aa00951413d139 | Shell | 3,213 | 84 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pool1
#SBATCH --time=3-0:00:00
#SBATCH --job-name=ldsc
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=10G
#SBATCH --error=logs/est_herit_%A_%a.txt
#SBATCH --output=logs/est_herit_%A_%a.txt
#SBATCH --array=1-78
log2results() {
awk -F '\t' '/Total Observe... |
d7af1c89ff28c201c9f4c39e9986f6cd00c026d693639fc963964d44c60b5d67 | Shell | 3,229 | 66 | #!/usr/bin/env bash
export dir="/nfs/stak/users/valejose/hpc-share/bioseq2seq"
export scripts="${dir}/experiments/scripts"
source $scripts/templates.sh
# regular test set predictions
#bash $scripts/run.sh $dir/txt/pred_bioseq2seq.txt
#bash $scripts/run.sh $dir/txt/pred_bioseq2seq_weighted.txt
#bash $scripts/run.sh $di... |
f69a9a11f17d014f1533a2d5a62a131c4de7156cb1f92d94fa10bd3f9d392d04 | Shell | 3,249 | 61 | #!/bin/bash
##########################################################################
## ##
## Copyright (c) 2023 Philipp Lösel. All rights reserved. ##
## ##
## This... |
9551eaeb200d6a8b7ac86f13ff4764f1efbe3d64fdcd0205f118dc14b97f45f7 | Shell | 3,273 | 119 | #! /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... |
5a98428b105555f11890ccb31211433fddd586ee322e9a676fbb82933460fd36 | Shell | 3,277 | 149 | #!/bin/bash
#SBATCH --account=p33
#SBATCH --time=48:00:00
#SBATCH --job-name=ABCD_2
#SBATCH --mem-per-cpu=8G
#
# TOPUP for DWI/IVIM data
# Ivan I. Maximov, Ullevål Oslo
# 24.08.2018, version 1.0
# 23.11.2018, ver 1.1
# Define variables here. All nii files should be noise/gibbs ringing corrected
source /cluster/bin/jo... |
67456eed770b15a8de584cd372ee02976b08ddd4081d6497d7dc3f941d616f56 | Shell | 3,288 | 109 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
kenlm_url=$1
maybe_py_or_android="$2"
maybe_android=""
maybe_py=""
if [ ! -z "${maybe_py_or_android}" -a "${maybe_py_or_android}" != "android" ]; then
maybe_py=${maybe_py_or_android}
extract_python_versions "${maybe_py}" "pyver" "pyver_pkg" "py_un... |
9190586e69bb4276e43af5a47152487dff69ff8d8905aacfb26776ddc9639bea | Shell | 3,337 | 92 | #!/bin/bash
## Helpers shared by the scripts in this folder. Source it, do not run
## it:
##
## source "$(dirname "${0}")/manpage_tools.sh"
##
## All of these scripts are launched from vsearch/man/ and convert the
## markdown sources of the manual into something else (manual pages,
## GitHub-flavoured markdown, PD... |
bbfe8c7cc45f914b8e25e8452dc43f61230b5f69723c2e61d5929af80407ca2b | Shell | 3,343 | 47 | python ~/bin_python/I_script/trans_neg2pos.py 1.rough.txt 1neg.rough.txt > 1.sites.txt
python ~/bin_python/I_script/trans_neg2pos.py 2.rough.txt 2neg.rough.txt > 2.sites.txt
python ~/bin_python/I_script/trans_neg2pos.py 3.rough.txt 3neg.rough.txt > 3.sites.txt
python ~/bin_python/I_script/trans_neg2pos.py 4.rough.txt 4... |
fb399622307fdb2e76e46d5c28f9a9324e2723e15164de95291fa8c97f50bfee | Shell | 3,347 | 59 | #!/bin/bash
project_path=$1
subject=$2
cd ${project_path}
#Create tsv file with header for each value to store
if [ ! -f DATA/processed_data.tsv ]
then
echo "Subject Vscale Brain_norm GM_norm WM_norm vscf_norm"\
"pgrey_norm L_Thalmus L_Caudate L_Putamen L_Palidum Brainstem"\
"L_Hippo L_Amygdala L_... |
5f502ed9ad74bfcfa5bcd162acc636a972a7ceb942865ba1d935bf849331492b | Shell | 3,348 | 89 | #!/bin/sh
# Check one packaged release asset before it is published.
#
# usage: verify-asset.sh <assets-dir> <version>
# ASSET asset base name, e.g. linux-aarch64-static (required)
# LD the LDFLAGS the asset was linked with, so that
# -static-libstdc++ can be checked to have taken effe... |
b04d54cd36fa7b3399bbc2aa1c347e7d24ee9eb9fcacffa55169ad4e31ac3a92 | Shell | 3,351 | 92 | #!/bin/bash
#
# run_clang_tidy.sh -- quick clang-tidy check of one or more source files, to
# catch warnings a refactoring may have introduced (used like cppcheck, but with
# clang-tidy's much larger check set).
#
# It needs a compile_commands.json describing how the project is built. Generate
# it once with `bear` (re... |
827ce77864893f58e0a1a7e7f99aa77b9e1d7f443113ba17c599ad1fe7b31711 | Shell | 3,369 | 112 | #!/bin/bash
set -ex
source $(dirname $0)/tf_tc-vars.sh
install_android=
install_cuda=
case "$1" in
"--linux-cuda"|"--windows-cuda")
install_cuda=yes
;;
"--android-armv7"|"--android-arm64")
install_android=yes
;;
esac
# $1 url
# $2 sha256
download()
{
fname=`basename $1`
${WGET} $1 ... |
a01ed8ed63f8a6f0cd6c8abbf770e9a9cd71526364654119491e2d111c6061d4 | Shell | 3,371 | 116 | #!/bin/bash
# Written by C. Vriend - AmsUMC Jan 2023
# Modified: set -euo pipefail, source config, removed sleep,
# input validation, safer loops, output existence check
#SBATCH --job-name=dtitk-extdiff
#SBATCH --mem-per-cpu=1G
#SBATCH --partition=luna-cpu-short
#SBATCH --qos=anw-cpu
#SBATCH --cpus-per-task=1
#SBATCH ... |
a20e67a81f6f19f89d3559c495cf955a1a20495a8c5487b28f8262e3f543574a | Shell | 3,371 | 112 | #!/bin/bash
set -ex
source $(dirname $0)/tf-vars.sh
install_android=
install_cuda=
case "$1" in
"--linux-cuda"|"--windows-cuda")
install_cuda=yes
;;
"--android-armv7"|"--android-arm64")
install_android=yes
;;
esac
# $1 url
# $2 sha256
download()
{
fname=`basename $1`
${WGET} $1 -O ... |
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