sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ba1725e50ea47ed648efa591e4360c4f878556cbc64e9c14caf50a39affa2a05 | Shell | 1,430 | 47 | #!/bin/sh -e
SQLITE=$HOME/tools/sqlite3
SQLITE=sqlite3
OUT_FILE="sift.txt"
OUT_SORT_FILE="sift.sort.txt"
OUT_VCF="sift.vcf"
# Download files
for f in Human_CHR1.sqlite.gz Human_CHR10.sqlite.gz Human_CHR11.sqlite.gz Human_CHR12.sqlite.gz Human_CHR13.sqlite.gz Human_CHR14.sqlite.gz Human_CHR15.sqlite.gz Human_CHR16.sql... |
4cfadc719846c3c23dbc9577a5a9b0d06eee05561bc0fd78d4fdde372d0d5a69 | Shell | 1,438 | 31 | #!/usr/bin/env bash
set -e
# device specifier given from first argument, default value is -1
device=${1:--1}
# Preprocessor parse result must contain both pos/neg samples
tox21_num_data=100
for method in nfp ggnn
do
if [ ! -f "input" ]; then
rm -rf input
fi
# Tox21 classification task with only... |
b27e705ce609e1660f79e09dcd8d6706a043359f79ef0d731648cac5816f94d4 | Shell | 1,456 | 40 | #!/bin/bash
readarray -t IGNORED_FILES < $( dirname "$0" )/covignore.cfg
REUSE_COVERAGE_REPORT=${REUSE_COVERAGE_REPORT:-0}
REPO=${1:-"origin"}
BRANCH=${2:-"refactor_dev"}
git fetch $REPO $BRANCH
PY_FILES=""
for FILE_NAME in $(git diff --name-only ${REPO}/${BRANCH}); do
# Only test python files in mmdet/ existing... |
8afcad60f74284ec0dd86884be3d84b51d38ccef6a284748888fe7e6475d67ba | Shell | 1,466 | 49 | #!/bin/bash
# Check that llvm.fmuladd (emitted by clang for a*b+c) is instrumented by the
# PRISM backend, both scalar (-O0) and vectorized (-O3).
set -e
export SAMPLES=50
if [[ "$PRISM_BACKEND" != "up-down" && "$PRISM_BACKEND" != "sr" ]]; then
echo "Error: PRISM_BACKEND must be set to 'up-down' or 'sr'"
ex... |
aa59db4d3e25eb3a8232d16dfb934c8d6a6aba475e90999ebf2609c1cc86433e | Shell | 1,472 | 35 | python launcher_scripts/run_from_config.py configs/scarf/scarf_gen_predict_train_nist.yaml
# Assign intensities to enable easy training in next module
python data_scripts/forms/03_add_form_intens.py \
--pred-form-folder results/scarf_nist20/split_1_rnd1/preds_train_300/form_preds \
--true-form-folder data/spec_datas... |
c338a1999e1ec0261d8e6af17d3bd70ce5293ab1499b7296983a9b371d14f34a | Shell | 1,474 | 38 | #!/bin/bash
module load miniconda
conda activate ldsc
module load BEDTools
module load dSQ
### Credit: Flynn Chen ###
base_dir="/gpfs/gibbs/pi/gerstein/jz435/ShareZhangLab/PTSD/LDSC"
download_dir="/gpfs/gibbs/pi/gerstein/jz435/ShareZhangLab/PTSD/LDSC/jing_download"
outputs_dir="/gpfs/gibbs/pi/gerstein/jz435/ShareZ... |
365ae5c67add65910368344cd3d41dc224a0441e51fafc3cb4da27a671ef9668 | Shell | 1,478 | 51 | #!/bin/bash
set -e
echo "==== Neural Jacobian Field Setup ===="
# ---------- Python tooling ----------
echo "[1/6] Installing uv + NumPy compatibility"
pip install -U uv
uv pip install "numpy<2"
# ---------- PyTorch (CUDA 11.8) ----------
# echo "[2/6] Installing PyTorch CUDA 11.8"
# uv pip install torch==2.1.2+cu11... |
9a762797cc1ffa7f773a49410d34829e49f91a9883f7df41fa3b84b4cd39730a | Shell | 1,481 | 29 | #!/bin/bash
#SBATCH --job-name=bulk
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=100G
BULK1='/gpfs/gibbs/pi/girgenti/JZhang/commonData/PTSD/ATAC/PEC_bulk_ATAC_individual_merge_sort_cat.sorted.bed'
#path='/home/ah2428/girgenti_scratch60/atac/subclass_proj/PeakBeds_Subclass'
path='/gpfs/gibbs/pi/girgenti... |
08811e75090c5d3a9b9726221e2ad64116eabbf12e7708e21a160c96937a02ee | Shell | 1,482 | 42 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# 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 applica... |
e74c86a9aec02ddedfdcc4162b5ef889d2595ed2cc55bb6de3b345303066260c | Shell | 1,482 | 36 | ## The relevant files are currently on a shared Google
## drive at https://drive.google.com/drive/folders/1kC0I2UGl2ltrluI9NqDjaQJGw5iliw_J
## Monitor for changes and eventually migrate to nlp dataset
curl -L 'https://drive.google.com/uc?export=download&id=1Jjhbal535VVz2ap4v4r_rN1UEHTdLK5P' \
| grep -v "^#" | cut -f 2,... |
98e619f1b06bf785b531ba79ea85f04dc514bb3062d7b31bc68ca4af6e3c6fab | Shell | 1,487 | 44 | #!/bin/bash
#
# Copyright 2021 AlQuraishi Laboratory
#
# 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 ... |
9ec17c1f7d27a2ab4cf24ca804c2f5ec49c2eed7ff0e1da5cb5a1501ab1ce000 | Shell | 1,489 | 58 | #!/usr/bin/env sh
#
# Flattens a downloaded RODA database into the format expected by OpenFold
# Args:
# roda_dir:
# The path to the database you want to flatten. E.g. "roda/pdb"
# or "roda/uniclust30". Note that, to save space, this script
# will empty this directory.
# output_d... |
a03c01a3c7e2fd13fa4960f3efae926ba6567d065cb4a135c6e72b29ea6f96bf | Shell | 1,490 | 53 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=mlgpu_medium
#SBATCH --job-name=train-BERT-classifier
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=16
#SBATCH --time=1-00:00:00
#SBATCH --gres=gpu:a40:1
#SBATCH --exclusive
source /lustre/mlnvme/data/... |
499ead2f59e7134e42d820ae66f0fad2e4f15765914881906f05ebcebe83167c | Shell | 1,492 | 49 | #!/bin/bash
assemblyDir=Gencode_M25_Mus_musculus
genomeDir=$assemblyDir/STAR
genomeFastaFiles=$assemblyDir/GRCm38.p6.genome.fa
sjdbGTFfile=$assemblyDir/gencode.vM25.annotation.gtf
ftpPlace=ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25
varVCFfile=PRJEB43298/mgp_REL2005_snps_BC_chr_selected_for_sta... |
586fc4cc1a7faee2d5e74a6268770ed099a0b1c0b4ea91e655358152725daee9 | Shell | 1,500 | 39 | # Copyright 2020 The HuggingFace Team. All rights reserved.
#
# 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 applicabl... |
c51a4ca6b8ce9171e5c817de0e33cc1d86e88054f2304ea10de1349a8b1200d1 | Shell | 1,507 | 55 | #!/bin/bash
#: Title : test_siminput
#: Date : 2019-05-23
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../siminput
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
65754612a07998e78c1f6512ab6c0494c06ecbcfca032521efa9276950229f3e | Shell | 1,511 | 47 | #!/bin/bash
#
# Runs ANTs SyN registration for the whole cohort on the batch
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------------------------------------------------------------------------------------------------------------------------------------
rootdir=/data_/tardiflab/mwc/bids/de... |
a0d3a003f2a603cf7fe448987674f4c356f0e58e53fb7de73224387fcc700787 | Shell | 1,513 | 58 | #!/bin/bash
#: Title : test_dcmmlist
#: Date : 2017-11-08
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dcmmlist
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
2beff871957b471c5d3119f9db4858bcc81295c2731d3ad0336b018f1fd2955f | Shell | 1,516 | 50 | #!/bin/bash
cd $(dirname $0)
cd ..
source ~/.bashrc
source ./scripts/utils.sh
root_path="$(pwd)/../../.."
# export FLAGS_fraction_of_gpu_memory_to_use=0.6
export PYTHONPATH="$root_path/":$PYTHONPATH
# datasets="bace bbbp clintox hiv muv sider tox21 toxcast"
datasets="bace bbbp clintox sider tox21 toxcast"
compound_... |
ef41fe1de67ead4339c7beb75a5bbfd79ed74dc25dab40283e29631f6f4c34b3 | Shell | 1,521 | 31 | #!/bin/bash
# activate conda env:
source /home/iml/hannah.eichhorn/anaconda3/bin/activate
conda activate dev_iqm
# store current date in variable
now=$(date +"%y_%m_%d")
cd /home/iml/hannah.eichhorn/Code/_OWN_PUBLIC_REPS/ImageQualityMetricsMRI/
nohup python -u process_all_subjects.py --normalisation "percentile" --... |
c0fbe54cdf99572e01e409b1d5c49667d170fb3fe127e59150fc26f4a8964a12 | Shell | 1,522 | 69 | set -e
TIME=/usr/bin/time
BEDPATH=hic_data/GM12878_combined_22_100kb.bed
#Chromosome3D
#create input
INPUT_PATH=Chromosome3D/input/GM12878_combined_22_100kb.txt
if [ ! -e $INPUT_PATH ]
then
python chromosome3d_input.py $BEDPATH $INPUT_PATH
fi
#run
$TIME -f "%M" -o chromosome3d_chr22_100kb_memory.txt perl Chrom... |
5e6677ad49acb3b4f6801c496adc696007309efd2160324ab79d5e5095cd2942 | Shell | 1,529 | 55 | #!/bin/bash
#SBATCH --partition fhs-fast
#SBATCH --ntasks 1
#SBATCH --nodes 1
#SBATCH --tasks-per-node 5
#SBATCH --cpus-per-task 9
#SBATCH --mem-per-cpu 4G
#SBATCH --time 120:00:00
#SBATCH --job-name fit-nav
#SBATCH --outp... |
9b5539c451bb1d45b34cd8ae73369f7b634bfd701c8591969f96ecc986dc338d | Shell | 1,529 | 39 | # Copyright 2020 The HuggingFace Team. All rights reserved.
#
# 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 applicabl... |
72dfc747c1256ae85175fe81d72e5802bb6979b0c9c0c2eeec16dae8774ff153 | Shell | 1,533 | 40 | #!/bin/bash
module load miniconda
conda activate ldsc
module load BEDTools
module load dSQ
### Credit: Flynn Chen ###
base_dir="/gpfs/gibbs/pi/gerstein/jz435/ShareZhangLab/PTSD/LDSC"
download_dir="/gpfs/gibbs/pi/gerstein/jz435/ShareZhangLab/PTSD/LDSC/jing_download"
outputs_dir="/gpfs/gibbs/pi/gerstein/jz435/ShareZ... |
41755897cd9c9a82c1fd3485cab1482659a819f95029aa19773711960ff3960e | Shell | 1,534 | 38 | # Copyright 2020 The HuggingFace Team. All rights reserved.
#
# 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 applicabl... |
bcbe926cc190b148081be8935f290f731fa08b3c3cea3203daea3294b5a342f0 | Shell | 1,539 | 49 | #!/usr/bin/env bash
# =============================================================================
# run_all.sh — Run all example CLI scripts in order
# =============================================================================
# Usage (from anywhere):
# bash examples/10_cli/run_all.sh
# cd examples/10_cli && b... |
1ece1a84e0bf1fef4011fe9b1ac3d5557570b639f7def235269d693de88ae6c7 | Shell | 1,540 | 71 | set -e
TIME=/usr/bin/time
bash get_gm12878.sh 100000 22
bash get_gm12878.sh 10000 22
BEDPATH=hic_data/GM12878_combined_22_10kb.bed
#Chromosome3D
#create input
#INPUT_PATH=Chromosome3D/input/GM12878_combined_22_10kb.txt
#if [ ! -e $INPUT_PATH]
# then
# python chromosome3d_input.py $BEDPATH $INPUT_PATH
#fi
#run
#... |
2f88a23a127ed95ef1c0f51defc1bd6326acb9eb5102d5467b3819c60b971516 | Shell | 1,545 | 19 | cp ~/git/PhysiCell_rheiland_dev/sample_projects/biorobots/config/PhysiCell_settings.xml biorobots.xml
cp ~/git/PhysiCell_rheiland_dev/sample_projects/cancer_biorobots/config/PhysiCell_settings.xml cancer_biorobots.xml
cp ~/git/PhysiCell_rheiland_dev/sample_projects/cancer_immune/config/PhysiCell_settings.xml cancer_imm... |
db622272984cb749a1cb1749b1fbd6517efd8d19ed56bc497821066c8a40f130 | Shell | 1,549 | 44 | #!/bin/bash
#First paratemer $sub is the name of the folder of the subject that want to be processed
#Second parameter is the folder where the freesurfer folders are located
sub=$1
SUBJECTS_DIR=$2
fsaverage_subid=fsaverage
cd $SUBJECTS_DIR
if [ -f ${SUBJECTS_DIR}/${sub}/label/rh.aparc.annot ] && [ ! "${s... |
1b8dab046bb6b8bad80d06ad6c9ba1c1c6aefe273b906b8689079a6a47b94718 | Shell | 1,557 | 65 | #!/usr/bin/env bash
TYPE=$1
OPERATOR=$2
MODE=$3
PREC=$4
SEED=$5
SAMPLES=$6
OP=$7
echo "TYPE=${TYPE}"
echo "OPERATOR=${OPERATOR}"
echo "MODE=${MODE}"
echo "PREC=${PREC}"
echo "SEED=${SEED}"
echo "SAMPLES=${SAMPLES}"
echo "OP=${OP}"
declare -A options
options[FLOAT]=--precision-binary32
options[DOUBLE]=--precision-bin... |
c09b7a2c2fedee9575f211766d1468d0fc94c75390a82463736129291269de2b | Shell | 1,558 | 56 | #!/bin/bash
#: Title : test_fit2res
#: Date : 2014-10-04
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit2res
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
f5db8757ff73586c6d1af02d212934238c7b80c0c38c7b4799dae1aa05d306ad | Shell | 1,566 | 54 | #!/bin/bash
#
# get number of voxels in volumetric parcellation data
#
# Inputs:
# $1 : subject ID (integer)
# $2 : session ID (1 or 2)
# $3 : parcellation
#
#
# 2025 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#--------------------------------------------------------------------------------------------... |
b5479e185fb8f8b0ae7e2a221ff13dc580323641ba3e301f08ffd16d63f10bc1 | Shell | 1,569 | 57 | #!/bin/bash
#: Title : test_dft2res
#: Date : 2019-08-26
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dft2res
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
144f6f1b1b01f63e1d1511fc5fc61cd7e407ef8dcd0def44a953ccd6ad4078d7 | Shell | 1,572 | 5 | perl ./popoolation_1.2.2/Variance-sliding.pl --input ./pileups/MONAASAB3_filtered.pileup --output ./pileups/pianalysis/pi/MONAASAB3_bfilt.pi --measure pi --window-size 2500 --step-size 1250 --min-count 2 --min-qual 20 --pool-size 64 --min-coverage 5 --max-coverage 74 --min-covered-fraction 0.2 --fastq-type sanger
perl ... |
378981002b53f1699bc8ab72b3c460960d13ed6849a3af2768a3801b10c737b0 | Shell | 1,575 | 50 | #!/bin/bash
assemblyDir=Gencode_M25_Mus_musculus
genomeDir=$assemblyDir/STAR
genomeFastaFiles=$assemblyDir/GRCm38.p6.genome.fa
sjdbGTFfile=$assemblyDir/gencode.vM25.annotation.gtf
ftpPlace=ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25
varVCFfile=PRJEB43298/mgp_REL2005_snps_BC_chr_selected_for_sta... |
137b03649ae74ac01d7635c333b8992bd07a544937d3802321d1a67855b83f34 | Shell | 1,590 | 39 | #!/bin/bash
# Runs each single cell through `kallisto pseudoalign`.
# Run from data directory.
# Currently can only run on the same compute node on which it was compiled, spudling07.
# From the README of the modified kallisto
# https://github.com/govinda-kamath/clustering_on_transcript_compatibility_counts/blob/maste... |
f7c9ed92bef547c99372bf28ba0f0ee62da7cc058037ceafe99023eb1794dffe | Shell | 1,591 | 74 | #!/usr/bin/env bash
set -e
# This helper script is meant to be used by BBGLab member only
SRC_FOLDER="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
function run() {
nextflow run {SRC_FOLDER}/intogen.nf --input "$@" --output intogen_{today} --debug true -profile bbglab -resume --containers {SRC_FOLD... |
84e8f23a157b0a49f130f0739fe78a5b5eac3a69681bbf1199b290cd5030f143 | Shell | 1,607 | 78 | #!/bin/bash
# Template batch script for running sim_opt_dd across all scales
# base name of this script (without extension)
scriptname=$(basename $0 .sh)
echo -e "\n*** Running batch script '"$scriptname"' ***\n"
# path to Matlab code directory
codedir=$GITDIR/ssdi
# current directory (the directory this script is... |
beb9650f18141bd2399eedfab1d97e58ea0726a9cd6707f316578422994674dc | Shell | 1,622 | 30 | #!/bin/bash
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=8000
#SBATCH --exclude=n69,n74
#SBATCH --tmp=128MB
#SBATCH --time=30:00:00
#SBATCH --partition=aind
#SBATCH --output=/allen/programs/mindscope/workgroups/omfish/carsonb/hpc_outputs/%j_zarr_test.log
#SBATCH --mail-type=ALL
#SBATCH --mail-user=carson.berry@alle... |
8264195b3c7d7b2378e59ec4b37d5c03a444feffa69bff214b1e6b9c37cd7c42 | Shell | 1,632 | 45 | Rscript step1_fitNULLGLMM.R \
--plinkFile=./input/nfam_100_nindep_0_step1_includeMoreRareVariants_poly \
--phenoFile=./input/pheno_1000samples.txt_withdosages_withBothTraitTypes.txt \
--phenoCol=y_binary \
--covarColList=x1,x2 \
--sampleIDColinphenoFile=IID \
--traitT... |
f56f1bb0d77032e0493b528bec01a10e3744aa19e70479d7f89d1ebe771b6d94 | Shell | 1,641 | 67 | #!/bin/bash -x
#To trim these sequences and merge them:
#pushd .. && make clean && make && popd
#6 * 3 * 5 * 4
Z=( 26 )
M=( 0.02 )
N=( 0.87 )
X=( 0.125 )
M2=( 0.02 )
N2=( 0.9 )
Q=( 13)
rm trimmed_*
rm lendist_*
for z in "${Z[@]}"
do
for m in "${M[@]}"
do
for n in "${N[@]}"
do
for x in "${X[@]}"
d... |
c2820cf8019e606b1ba3ef27008abf0cd5b15d11319124270921ae4cedf009c7 | Shell | 1,648 | 33 | Rscript step2_SPAtests.R \
--vcfFile=./input/genotype_10markers_triallelic.missing.withVarianceallMissing.vcf.gz \
--vcfFileIndex=./input/genotype_10markers_triallelic.missing.withVarianceallMissing.vcf.gz.tbi \
--vcfField=GT \
--chrom=chr1 \
--minMAF=0.0001 \
--minMAC=1 ... |
c0cc7a6b1424a0a887c832ed121dfd7d49051ccf8b5188d18e8c1a469c10dd90 | Shell | 1,651 | 51 | #!/bin/bash
#
# Runs ANTs SyN registration testing for a range of parameter combinations on the batch
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------------------------------------------------------------------------------------------------------------------------------------
id="10"
S... |
b339a6a831d1680331666ce1ae01fa4adb3e9951a8d019c998270d544945d5ef | Shell | 1,654 | 63 | ## rna.inc.sh
## Functions of RNA-seq pipeline
##
## Copyright (c) 2017-2018 Institut Curie
## Author(s): Nicolas Servant
## Contact: nicolas.servant@curie.fr
## This software is distributed without any guarantee under the terms of the BSD-3 licence.
## See the LICENCE file for details
##
##
##
##
## GLOBAL VARIABLE AR... |
9c8be60dcfec822db6abb87aa265452b5ae7d29a2fd91c2719ee75997a722a53 | Shell | 1,656 | 34 | #!/bin/bash
function cleanFile
{
FILE=$1
shift
cat $FILE | awk '{print $2 "\t" $3 }' | egrep -v "^0 "
}
#cleanFile human-hic-len.freq > bE378K21-screen.dat1.cleaned
#cleanFile hummingbird-hic.freq > bE378K21-screen.dat2.cleaned
#cleanFile fMasArm1-hic.freq > bE378K21-screen.dat3.cleaned
#cleanFile tdevil-hic.freq >... |
cb792d3a6ee27427e1ac96f3f0aa5f11269934b7c221048bdeed0590382aa32e | Shell | 1,656 | 53 | #!/bin/bash
variant_orig=mgp_REL2005_snps_indels.vcf
variant_snps_BC=mgp_REL2005_snps_BC.vcf
variant=mgp_REL2005_snps_BC_chr_selected.vcf
variant_for_star=mgp_REL2005_snps_BC_chr_selected_for_star.vcf
variant_genes=mgp_REL2005_snps_BC_chr_selected_genes.vcf
mkdir -p PRJEB43298
pushd PRJEB43298
# Download variant fil... |
dcd57643a459237d211dc828239009c3f16f0da792f515c452d7497cc46e699a | Shell | 1,656 | 71 | #!/bin/bash
#SBATCH -N 1
#SBATCH -n 16
#SBATCH --time=15:00:00
#SBATCH --mem=250G
#SBATCH --job-name=kbpython
#SBATCH --account=def-jsjoyal
#SBATCH --mail-type=END
#SBATCH --mail-user=gael.cagnone.1@gmail.com
#SBATCH -o job.report
#SBATCH --no-requeue
source ~/ENV_python.3.7.4_scanpy/bin/activate
cd /home/gaelcge/pr... |
be1cd73dcf10830aede36ab1fd1c353d9fb3e325b918d71b896bbf5f9b4146e5 | Shell | 1,657 | 62 | #/bin/bash
OUT_DIR="/local/projects/scnn-investigation_haykel/protocols/sub-36/"
MASK_PATH="/local/projects/scnn-investigation_haykel/protocols/sub-36/brain_mask.nii.gz"
FIVE_TT_MIF="/local/projects/scnn-investigation_haykel/protocols/sub-36/t2w/5tt_from_drawem2.nii.gz"
# MSMT-CSD
FOD_PATH="/local/projects/scnn-inve... |
0fb20e189394faea721388f8da0c063b7109001fe53ac6d511f3810822f02c26 | Shell | 1,658 | 49 | #!/bin/bash
CONDA_INSTALL_URL=${CONDA_INSTALL_URL:-"https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"}
source scripts/vars.sh
# Install Miniconda locally
rm -rf lib/conda
rm -f /tmp/Miniconda3-latest-Linux-x86_64.sh
wget -P /tmp \
"${CONDA_INSTALL_URL}" \
&& bash /tmp/Miniconda3-latest-Li... |
9be8a559c2ed1b451e4ed778157fae6fa896c032d0caa5988c9ae07b51e4a284 | Shell | 1,660 | 51 | #!/bin/bash
#
# Runs ANTs SyN registration testing for a range of parameter combinations on the batch
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------------------------------------------------------------------------------------------------------------------------------------
id="10"
S... |
bb45eda8e3438a40568295109bfcbc5d2061a295e23266197c2c2d58f8efd3cd | Shell | 1,667 | 77 | #!/bin/bash
# Note that all __XYZ__ strings are replaced by launch_gce.py
WORKDIR="/train/workdir_base/__EXAMPLE__/__NAME__/__TIMESTAMP__"
mkdir -p /train
cd /train
# Login directly with:
# gcloud compute ssh $VM -- /sudo_tmux_a.sh
echo -e '#!/bin/bash\nsudo /tmux_a.sh' > /sudo_tmux_a.sh
chmod a+x /sudo_tmux_a.sh
e... |
45c44e97ea44afdd002537445a7176fd16d6aa93816b8bf497ba62ba32e1634f | Shell | 1,671 | 62 | #!/usr/bin/env bash
##---------------------------------------------------------------------
# wget everything that needs to be w-got (lolol)
# tar everything
# configure everything
# make everything
# rm the unnecessary install materials
##---------------------------------------------------------------------
#Save th... |
57bf72a0dab8ba0af2874719ae010892d4c9f78ab93d4340d1c9a1439db2c9dd | Shell | 1,678 | 82 | #!/bin/bash
############
# use ctrl+c to kill parallel exec
############
trap killgroup SIGINT
killgroup(){
echo killing...
kill -9 0
}
get_last_epoch() {
local epoch_prefix=$1
for ((i=1000;i>0;i-=2)); do
if [ -d "${epoch_prefix}$i" ]; then
echo $i
return
fi
don... |
f1cec75ba2cece007ce092c7d18a3533e6ec9d4d5364d601ebaed2d14f788d2e | Shell | 1,678 | 65 | #!/usr/bin/env bash
# =============================================================================
# 10_fill.sh — Statistics fill (--fill)
# =============================================================================
# Derive missing statistical columns via fill_data() on the CLI.
# See docs/Conversion.md for conver... |
151a5324d540a84c012dbb3a5d7100f2a914556872c1e5d46aeef9f76d864d19 | Shell | 1,685 | 38 | #!/bin/bash
#
# Finds a target sub-##_ses-# ID in an input plain text file and prints the comma-separated list of integer
# values for that dataset. These integers correspond to the Independent Components marked for removal in
# melodic-based denoising of rs-fMRI
#
#
# INPUTS:
# $1 : full path to text file with I... |
f832b1ce76ca573975c0abae46567a27f9a8266936fe526c29d32603662e575f | Shell | 1,686 | 73 | #!/bin/bash
print_banner() {
printf "\n\n\n\e[30m\e[42m$1\e[0m\n\n\n\n"
}
print_green() {
printf "\e[30m\e[42m$1\e[0m\n"
}
print_red() {
printf "\e[30m\e[41m$1\e[0m\n"
}
images=(
"gitlab-master.nvidia.com:5005/dl/dgx/pytorch:19.08-py3-devel"
"gitlab-master.nvidia.com:5005/dl/dgx/pytorch:master-py3-devel"
"pyt... |
ea881c8f077745cd884f1e0270d77d57b197674e8abaf01a575e04245f901196 | Shell | 1,693 | 56 | #!/bin/sh
#-------------------------------------------------------------------------------
# Files
#-------------------------------------------------------------------------------
in=$1 # Input VCF file
eff=`dirname $in`/`basename $in .vcf`.snpeff.vcf # SnpEff annotated VCF file
out=`dirname $in`/`basena... |
b8ebe7032f3c6415a322fd45d19bf8ca5680104372bb8f1724bb7d1f0712122e | Shell | 1,695 | 45 | # FD-LOCO
BEADS_DIR="/media/Data/smlm_z_data/fd-loco/Astigmatism_beads_stacks_2um";
OUTDIR="/home/miguel/Projects/smlm_z/publication/VIT_fd-loco4/";
PX_SIZE=110;
ZSTEP=10;
DEFAULT_LOCS='/home/miguel/Projects/data/fd-loco/roi_startpos_810_790_split.ome_locs.hdf5';
DEFAULT_SPOTS='/home/miguel/Projects/data/fd-loco/roi_st... |
d36f64e3cce31aab14b9cf052b836c6a675c97f5967391ed233a49730f23ff68 | Shell | 1,695 | 55 | #!/usr/bin/env bash
HELP_STR="usage: convertUserSessions.sh userName
userName must be %-encoded as it is in namedSessionDb"
# cgiDir for hg.conf{,.private} settings
cgiDir=/usr/local/apache/cgi-bin
# delay (in seconds) between calls to sessionDataConvert.sh to avoid hammering server & hgcentral
delay=3
# Look for a... |
23ba18a8c54759aa83cf4c35b49afc561c57023cfc5f052a675b0241d0f4d018 | Shell | 1,703 | 44 | #!/usr/bin/env bash
# for seqeval metrics import
pip install -r ../requirements.txt
## The relevant files are currently on a shared Google
## drive at https://drive.google.com/drive/folders/1kC0I2UGl2ltrluI9NqDjaQJGw5iliw_J
## Monitor for changes and eventually migrate to nlp dataset
curl -L 'https://drive.google.com... |
1a507978d8d52f947bc6dd4f2534b17e9b05b3df2af5e9f89741de2254bf37b5 | Shell | 1,704 | 64 | #!/usr/bin/env bash
CONFIG=$1
GPUS=$2
WORK_DIRS=${3:-'work_dirs'}
RETRY_PATH=${RETRY_PATH:-''}
NNODES=${NNODES:-1}
NODE_RANK=${NODE_RANK:-0}
PORT=${PORT:-29500}
MASTER_ADDR=${MASTER_ADDR:-"127.0.0.1"}
datasets=$(pwd)/rf100
export PYTHONPATH="../..":$PYTHONPATH
DEBUG=0
# example
datasets_list=("acl-x-ray", "tweeter-p... |
43510d9af21069ef22a9ea335d21e23c03857b2cb2231517d99a744f7f6877a3 | Shell | 1,709 | 44 | #!/bin/sh
# cleanLostTables.sh - run this as a cron job on your custom trash
# database. It needs the perl script: lostTables.pl
# Lost tables come about in the custom trash database when they have
# no corresponding entry in the metaInfo table. When they are in the
# metaInfo table, they will expire because of the ... |
ca0b7439ce55d410a08f896b3d03f640566aaab38f2391fbdd9030ba5a4de08a | Shell | 1,723 | 63 | wd=/mnt/data1/workspace/Anders/MelBrM
sif=/mnt/data1/public/singularity/dcibioinformaticsHTS-v0.9.sif
dukevcfs=${wd}/Proc/DNA/vcf2maf/Duke/paired/pass_vcf/*/*_PASS.vcf
mdaccvcfs=${wd}/Proc/DNA/vcf2maf/MDACC/paired/pass_vcf/*/*_PASS.vcf
# v=/mnt/data1/workspace/Anders/MelBrM/Proc/DNA/vcf2maf/Duke/paired/pass_vcf/10017_F... |
04b4e3a67aebfca2ca6eb7a37fb1178f63970ce43d1a6c3444ea1751dfd8a6ea | Shell | 1,729 | 44 | #!/bin/bash
# Check that binaries use the vector registers of one x86-64 level:
#
# check-isa.sh <level> LIBPRISM PATH...
#
# LIBPRISM (libprism-static.so) must use the level's widest registers: xmm
# only for x86-64-v1/v2, ymm for v3, zmm for v4. Anything narrower means
# Highway picked a narrower target than -march... |
13051d2d733251d8f0a2dcfb7f638001ba55ca815d63c863f54979e0515c5b0c | Shell | 1,730 | 60 | #!/bin/bash
#: Title : test_ainterp
#: Date : 2014-07-11
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../ainterp
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
6632283b8d7f6c064927568fd5ebe9faea384374a0edf9a9cddcd54b47102147 | Shell | 1,740 | 59 | #!/bin/bash
#: Title : test_fitedit
#: Date : 2014-10-04
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fitedit
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
5954ed228f69fffe3fafecc605679fbf53e8cfa229277150a853fe7ab95ee872 | Shell | 1,746 | 48 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=lm_long
#SBATCH --job-name=tokenize-sft
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64
#SBATCH --time=7-00:00:00
#SBATCH --mem=1900G
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/modules_intel.sh
which python3
ulim... |
ba581415fed58d609a74cf61750ec94be89196725494fd67749f0ad971215295 | Shell | 1,754 | 56 | #!/bin/bash
# --- convert paired vcfs to MAF format
wd=/data/dcibioinformatics/Anders/MelBrM_rerun
inputdir=${wd}/Proc/stage5/Duke/paired
bcftools=/scif/apps/bcftools/bcftools-1.18/bcftools
vcf2maf=${wd}/Code/GATK_rerun/wes_analysis/vcf2maf/vcf2maf_lwr.pl
veppath=/opt/vep/src/ensembl-vep
vepdata=/data/dcibioinformati... |
0ea319c565dc6083eb555c60360a662dbd05ba94cafb008ded0e3d4af84ffb09 | Shell | 1,755 | 61 | #!/bin/bash
#
# get number of vertices and surface are of parcels from surface data
#
# Inputs:
# $1 : subject ID (integer); doesn't support rescans
# $2 : parcellation
# $3 : hemipshere (lh rh)
#
#
# 2025 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#-----------------------------------------------------... |
988a25334bc1cd6437a71abb5e5ca7d256463b5b4c276831aec83ee2e0a1a90e | Shell | 1,756 | 56 | #!/bin/bash
# --- convert paired vcfs to MAF format
wd=/data/dcibioinformatics/Anders/MelBrM_rerun
inputdir=${wd}/Proc/stage5/MDACC/paired
bcftools=/scif/apps/bcftools/bcftools-1.18/bcftools
vcf2maf=${wd}/Code/GATK_rerun/wes_analysis/vcf2maf/vcf2maf_lwr.pl
veppath=/opt/vep/src/ensembl-vep
vepdata=/data/dcibioinformat... |
c7200ed19ff0099be8d82767eae9adfb3a0f91e002ca958084cc35831adfb056 | Shell | 1,763 | 80 | #!/bin/sh
TESTPROG=bedItemOverlapCount
tests=0
failures=0
verbose=""
export TESTPROG verbose tests failures
usage() {
echo "usage: `basename $0` [-verbose] [-home] [-help]"
echo -e "\tTesting the binary $TESTPROG\n"
echo -e "\t-verbose - show all test command lines and results"
echo -e "\t-home - use ... |
959fc26769cb7edd3e821aa7f68643cb37ae27804914e4f5d9635a508909c75c | Shell | 1,764 | 70 | #!/bin/bash -l
#SBATCH --account=the_tucanos
#SBATCH --partition=mlgpu_long
#SBATCH --job-name=Tucano-DPO
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --threads-per-core=1
#SBATCH --cpus-per-task=16
#SBATCH --time=7-00:00:00
#SBATCH --gres=gpu:a40:8
#SBATCH --exclusive
source /lustre/mlnvme/data/the_tucanos/m... |
79e604f7212271e8c8079f637649123666d6847abe70be6b495eddd40eb91aff | Shell | 1,765 | 64 | #!/bin/bash
check_status() {
if [ $? -ne 0 ]; then
echo "Test fail"
exit 1
fi
}
clean() {
rm -f *.log
}
clean
verificarlo-c test.c -o test
check_status
VFC_BACKENDS="libinterflop_mca.so --precision-binary32 23 --seed=1234" ./test 0 0 >23.log 2>/dev/null
VFC_BACKENDS="libinterflop_mca.so ... |
7d253f8abceeed332e3e6eb81b5475a8a216aa350c70f7e7d57f6372f13c606d | Shell | 1,766 | 38 | #!/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: REPLACING ORIGINAL STRUCTURAL IMAGES WITH DEFACED STRUCTURAL IMAGES
# PROJECT: SFGPI
# WRITTEN BY LENNART WITTKUHN... |
e47632c4a8cf10e983965ef4b849e9b079746bfdd8cb14ce2df1177b04d5df98 | Shell | 1,767 | 57 | #!/bin/bash
export VFC_BACKENDS_LOGGER=False
export N=30
check_status() {
if [[ $? != 0 ]]; then
echo "Test fail"
exit 1
fi
}
clean() {
rm -f bfr.* aft.*
}
run_test() {
BACKEND=$1
REAL=$2
P=$3
RES=$4
echo "Test ${BACKEND}"
VFC_BACKENDS="${BACKEND}" ./test_${REAL} ... |
f81c1ac4e6b4943d0ea35cf0d4a941df040b13fb88ab7713392c79eed0127775 | Shell | 1,772 | 47 | #!/usr/bin/env bash
# Run tests to check if slurm picks up begin time set by CATS
# This relies on a cluster already setup and running, if not run
# ./cluster/start.sh
set -eou pipefail
# Step a) Run cats inside the slurmctld container and extract start time
raw_output=$(docker exec -i slurmctld \
cats -d 5 --loc ... |
70f3099f204a81f8eb375951aaf4132771abeea511961fd774a4369ba7c4abca | Shell | 1,774 | 67 | #!/usr/bin/env bash
CONFIG=$1
GPUS=$2
WORK_DIRS=${3:-'work_dirs'}
RETRY_PATH=${RETRY_PATH:-''}
NNODES=${NNODES:-1}
NODE_RANK=${NODE_RANK:-0}
PORT=${PORT:-29500}
MASTER_ADDR=${MASTER_ADDR:-"127.0.0.1"}
PARTITION=${PARTITION:-'mm_dev'}
JOB_NAME=${JOB_NAME:-'benchmark'}
GPUS_PER_NODE=${GPUS_PER_NODE:-8}
CPUS_PER_TASK=${C... |
a9f57fccdb4914aa73bd75de805a9f8ab172e729b11a20100d74df0eaf8df451 | Shell | 1,777 | 68 | #!/bin/bash
set -e
set -o nounset
set -o pipefail
if [[ ${TRACE-0} == "1" ]]; then
set -o xtrace
fi
NUM_TESTS=8
# Run AntiFold on single PDB/CIF file
# Nb: Assumes first chain heavy, second chain light
echo -e "\n### Test 1 / $NUM_TESTS ###"
python antifold/main.py \
--pdb_file data/pdbs/6y1l_imgt.pdb
# Antibo... |
add2ff03696de61686e1c0100dbad12a7667abf522b23e388c934285a0ff5ef8 | Shell | 1,781 | 73 | #!/bin/bash
set -e
new_env() {
DIR=.$1
rm -rf $DIR
mkdir $DIR
cp -r *.c $DIR
cd $DIR
}
test1() {
new_env test1
rm -f *.ll
verificarlo-c -c test.c -emit-llvm --save-temps
if grep "fcmp ogt" test.*.2.ll || grep "fcmp ole" test.*.2.ll; then
echo "[TEST 1 | PASS] comparison ... |
377d6bad9ff67acdc64d0619dac55814e8747998ddcbfa90fb3877cc177b22c3 | Shell | 1,784 | 68 | #!/bin/bash
set -eu
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# User settings
#
# - Set the path to the elastix folder
# in the variable ELASTIX_PATH below.
# - Set the number of threads.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Path to elastix folder
ELASTIX_PATH=${HOME}/Downloads/elastix
# Number of threads
threa... |
8343c15d7bcc073815320c5bdbef818feeebd76e753c78f1d1613b43c37adc40 | Shell | 1,784 | 61 | #!/bin/bash
# need this bash wrapper, parasol cannot use the bash pipe syntax directly
# input are two SRA files with forward/reverse reads
# or alternatively two .fastq.gz files
# parameters:
# $1 = index
# $2 = output dir
# $3 = SRA input file
# $2 = SRA input file 2
set -e
set -o pipefail
# required until Erich p... |
93f47e0347d0d47595047bc15ffa85fcf610ac4dc5a56908fe8dc67db74d4913 | Shell | 1,784 | 47 | #!/bin/sh
A=$1
INDIR=tests/input
OUTDIR=tests/output
EXPDIR=tests/expected
rm -rf $OUTDIR
mkdir -p $OUTDIR
# Easy case: single sequence, one gap, consistent AGP and sequence.
$A $INDIR/test1.good.agp $INDIR/test1.fa \
> $OUTDIR/test1.good.fa.out 2>$OUTDIR/test1.good.fa.err
$A $INDIR/test1.good.agp $INDIR/test1.... |
06d29692655bb5b1070faf6e1f11e859518f9c6387d624dd95cd498ccfc816a2 | Shell | 1,785 | 65 | #!/bin/bash
#SBATCH --job-name=prf_mapping_sub-4
#SBATCH --mail-user=email
#SBATCH --mail-type=end
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=30G
#SBATCH --cpus-per-task=25
#SBATCH --time=4-00:00:00
#SBATCH --qos=standard
declare -a combinations
index=0
for sub in 0
do
for hem in 0 1
do
combin... |
12033fd24fd3d5438b8b52c46f5a5f9b13b8940b06d22a3c8465996c962edb20 | Shell | 1,785 | 65 | #!/bin/bash
#SBATCH --job-name=prf_mapping_sub-3
#SBATCH --mail-user=email
#SBATCH --mail-type=end
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=30G
#SBATCH --cpus-per-task=25
#SBATCH --time=4-00:00:00
#SBATCH --qos=standard
declare -a combinations
index=0
for sub in 0
do
for hem in 0 1
do
combin... |
583e396e14fd414c1cd50df3b28c55bd0e7e3c93d662563f8c8233f48e64220a | Shell | 1,785 | 65 | #!/bin/bash
#SBATCH --job-name=prf_mapping_sub-6
#SBATCH --mail-user=email
#SBATCH --mail-type=end
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=30G
#SBATCH --cpus-per-task=25
#SBATCH --time=4-00:00:00
#SBATCH --qos=standard
declare -a combinations
index=0
for sub in 0
do
for hem in 0 1
do
combin... |
674ac6ff92adf06e28725f9f1f84629d3f47d83262bce242584813b073c0f2f6 | Shell | 1,785 | 65 | #!/bin/bash
#SBATCH --job-name=prf_mapping_sub-5
#SBATCH --mail-user=email
#SBATCH --mail-type=end
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=30G
#SBATCH --cpus-per-task=25
#SBATCH --time=4-00:00:00
#SBATCH --qos=standard
declare -a combinations
index=0
for sub in 0
do
for hem in 0 1
do
combin... |
e2f4c21d1b610dc5fe44397af82114fdc9fe9aeadddfbe76f3b1ad17e9d7b1b2 | Shell | 1,785 | 65 | #!/bin/bash
#SBATCH --job-name=prf_mapping_sub-1
#SBATCH --mail-user=email
#SBATCH --mail-type=end
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=20G
#SBATCH --cpus-per-task=25
#SBATCH --time=4-00:00:00
#SBATCH --qos=standard
declare -a combinations
index=0
for sub in 0
do
for hem in 0 1
do
combin... |
edc989cd99c57989cfbbfbf69cb4a3976f72bc69f1c1e57f44765cf06ef97808 | Shell | 1,785 | 65 | #!/bin/bash
#SBATCH --job-name=prf_mapping_sub-2
#SBATCH --mail-user=email
#SBATCH --mail-type=end
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=30G
#SBATCH --cpus-per-task=25
#SBATCH --time=4-00:00:00
#SBATCH --qos=standard
declare -a combinations
index=0
for sub in 0
do
for hem in 0 1
do
combin... |
9b14dbdc1a160d6e59190a475366d70a454a724112bc650fa43d5f26ccab5fb2 | Shell | 1,786 | 53 | mkdir -p skmer_xval_results
conda activate skmer
export bp=maxdata
echo REFERENCES: $bp
rm -rf temp_query_$bp
find ./temp_ref_$bp/ -name '*.gz' | parallel -j 64 gunzip -f {}
mkdir -p temp_out_$bp
mkdir -p temp_query_$bp
mkdir -p temp_skmer_$bp
export RANDOM=426547
for sample in $(find 00000500K/ -name '*.fq.gz' -e... |
62bb9ea1ba4f18e56a9163c4030d2ee5c5f45c76e13ff70ad09f3bdf51cd7210 | Shell | 1,793 | 74 | #!/bin/bash
cd "$(dirname "$0")/.."
target=${1:-"GPU"} # options: GPU, CPU
# set the path to the location of
# built GSL libraries (GSL_BUILD_DIR) and
# libks (LIBKS_DIR)
if [[ -f "./set_dependency_paths.sh" ]]; then
# this file is not included in the repo
# and the only thing it does is:
# `export GSL_BU... |
b2449b9781b8f565d3034e3ccdb51ee9361148d7ea1e8ac8c63afc3d93c90c5a | Shell | 1,796 | 50 | #!/bin/bash -x
DATASET_NAME=${1} # has to be the same as the filename of DATASET_CONFIG
DATASET_CONFIG="${DATASET_NAME}.py"
GCP_PROJECT=kubric-xgcp
GCS_BUCKET=gs://research-brain-kubric-xgcp
REGION=us-central1
JOB_NAME=${2}
MACHINE_TYPE="n1-highmem-16"
NUM_WORKERS=20
if ! [[ $JOB_NAME =~ ^[a-zA-Z][-a-zA-Z0-9]*[a-zA-... |
6f8a0105954a939eb55e4ed35b71fa8250174c7e34eb462d975fce341745b7e8 | Shell | 1,801 | 53 | #!/bin/bash
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# 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 require... |
234b06b752c0a45c1a757049be970f76889ff761a8f0ddd62a76bedfa5f9dd32 | Shell | 1,802 | 63 | #!/bin/bash
#: Title : test_dcmdict
#: Date : 2017-04-13
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dcmdict
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
b776e757f8a5bacc5da3ca0f25feba269ca79935cef5af01411aaae54d0cd93a | Shell | 1,805 | 48 | #!/bin/sh
# This script sets up the freesurfer environment and executes
# freesurfer's automatic processing pipeline, resulting in a
# set of meshes that model the cerebral cortex. It takes two
# input arguments. Use as:
#
# ft_freesurferscript.sh <DIRNAME> <SUBJECTNAME>
#
# 1. <DIRNAME> is the directory that con... |
6a6e1c22d627edc77eb435fc9acef8fcb87a49f4b8064028ef6ddb6a2bf9f12f | Shell | 1,811 | 65 | #!/bin/bash
source "$(dirname "$0")/../paths.sh"
if [ "${BUILD_PRISM}" = "no" ]; then
echo "this test is not run when using --without-prism"
# Exit with 77 to mark the test skipped
# https://www.gnu.org/software/automake/manual/html_node/Scripts_002dbased-Testsuites.html
exit 77
fi
function run() {
... |
c110a1b768a012a03a5493141a85565da210caae9b0b4c63ec1eb841d4f932b1 | Shell | 1,852 | 51 | #!/bin/bash
input_dir=star_output_wasp/
input_file_suffix=_Aligned.sortedByCoord.out.bam.featureCounts.bam
output_dir=wasp_output_ase/
output_file_suffix=_ASE.tab
mkdir -p $output_dir
for input_file in $input_dir/*$input_file_suffix
do
sample_id=$(basename $input_file $input_file_suffix)
snps_file_wasp=$output_dir/... |
2c2b09c4a6e7c5d8c8fb1570fdc2e24476d88efb7d639f6fa9edc85e12242943 | Shell | 1,853 | 61 | #!/bin/sh
# the next line restarts using tclsh \
exec cg source "$0" "$@"
logverbose 2
if {![info exists argv]} {set argv {}}
set argv [job_init {*}$argv]
foreach {dest webcache} $argv break
if {![info exists dest]} {set dest /complgen/refseqnew}
if {![info exists webcache]} {set webcache $dest/webcache}
if {[info ex... |
20fdffebd7a6c95293276059c29fe7db2100d08cc76444a26c10f2ac64ffd49f | Shell | 1,854 | 53 | #!/bin/bash
set -e
# Silence backend loading banners to keep test output clean.
export VFC_BACKENDS_SILENT_LOAD=True
check_status() {
if [ $? -ne 0 ]; then
echo "Test fail"
exit 1
fi
}
# -----------------------------------------------------------------------
# 0. Prerequisites
# ------------... |
ecea7bd90ed6a9b37b8c17ea92a4e5e9b95639ae7a9f39e33656dc408a5af1d6 | Shell | 1,860 | 63 | #!/bin/bash
#: Title : test_llsqe3
#: Date : 2021-12-10
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../llsqe3
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
249e9f66ec8ba05b2860b380d9a77ecfc6a268d0bd938c412cccf16d41b55c93 | Shell | 1,872 | 77 | #!/usr/bin/env bash
# =============================================================================
# 01_basic_qc.sh — Basic Quality Control
# =============================================================================
# Run QC on a GWAS summary statistics file and save the cleaned output.
#
# Usage:
# bash 01_basi... |
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