sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1e2efb1bde7719a3eaa611f9c973549d5d467c4464308680716590d606dcf64c | Shell | 2,800 | 67 | #!/bin/bash
# 06_Normalization.sh
# What shall be done?
normalize_t2=1
normalize_epi=1
# Loop across sessions for data preparation
for subject in {1..40}; do
for session in {1..2}; do
printf -v sub "%02d" $subject
printf -v ses "%02d" $session
echo "subject: " $sub "session: " $ses
#Directories
... |
902d53c6f469dab83714e603608e1d2cadf71ed22ffb113cfa398f4c27ea8b6a | Shell | 2,818 | 87 | #!/bin/bash
# -----------------------------------------------------------------------------
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The A... |
4ceff8ef6a0dc814cae55f2f684f0defb1f2b0afefa5504d4d2285275ed7025a | Shell | 2,819 | 63 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=50:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
34cdbfb18d1d1e119d99c4c5eafa91955bd4c75c11e417a594bc733ba0a3ae4c | Shell | 2,822 | 89 | #!/bin/bash
## HiC-Pro
## Copyleft 2015-2018 Institut Curie
## Author(s): Nicolas Servant, Eric Viara
## Contact: nicolas.servant@curie.fr
## This software is distributed without any guarantee under the terms of the GNU General
## Public License, either Version 2, June 1991 or Version 3,... |
c7467e93772690e9dfc6a33ff85d8efd05dbaace68c5be5daeb55d65740ffd39 | Shell | 2,826 | 78 | #!/bin/bash -e
if [ $# -ne 5 ]; then
echo "usage v1: lrna_align_tophat_se.sh <tophat_index.tgz> <reads.fq.gz> <library_id> <ncpus> <bam_root>"
echo "Align single-end reads with TopHat/bowtie2. Is independent of DX and encodeD."
exit -1;
fi
tophat_index_tgz=$1 # TopHat Index archive.
reads_fq_gz=$2 ... |
c87e91d5f168a4ef6a17421321e7ef01fa3f43f971df2817c25114cd7b13d554 | Shell | 2,828 | 83 | #!/bin/bash
set -euo pipefail
if [[ ${BUILDKITE_COMMIT} == "HEAD" ]]; then
BUILDKITE_COMMIT="$(git rev-parse HEAD)"
export BUILDKITE_COMMIT
fi
# Get build ID from environment variables
BUILD_ID="${RAYCI_BUILD_ID:-}"
if [[ -z "${BUILD_ID}" ]]; then
if [[ -n "${BUILDKITE_BUILD_ID:-}" ]]; then
# Genera... |
6928a3774c83504114b4ff22860b45074dd66cc6b4fe231d180fa921863a11b3 | Shell | 2,834 | 75 | #!/bin/bash
#
# join_vcfs.sh
#
# Join VCFs which contain the same set of variants in different samples
#
set -euo pipefail
vcflist=$1
outfile=$2
#Make VCF header
echo -e "join_vcfs.sh :: $(date) :: MAKING VCF HEADER..."
first=$( sed -n '1p' ${vcflist} )
zcat ${first} | sed -n '1,1000p' | fgrep "##" > header.txt
zca... |
d1b4c655da0458d1a20f4594f5a1de8851cb1befa080aa961d0fd5dafcf719a4 | Shell | 2,842 | 60 | #!/usr/bin/env bash
# Set FSL Variable
OLD_FSLOUTPUTTYPE=$FSLOUTPUTTYPE
FSLOUTPUTTYPE=NIFTI
#!/bin/bash
wget http://repo.mouseimaging.ca/repo/DSURQE_40micron_nifti/DSURQE_40micron_average.nii
wget http://repo.mouseimaging.ca/repo/DSURQE_40micron_nifti/DSURQE_40micron_labels.nii
wget http://repo.mouseimaging.ca/repo/D... |
b4ea919a2073e771b9c075e78b038a5a2222a08b0d4a716d41891e00c5153933 | Shell | 2,857 | 66 | #!/bin/bash
#$ -N P0 #Job ID name sent to HPC cluster.
#$ -pe openmp 5 #Number of requested parallel environments.
#$ -o '/<directory root>/fMRIPrep/Pipeline_0/logs' #Folder where fMRIPrep logs files are saved out by the HPC cluster.
#$ -e logs #Resquests logs.
#$ -l m_mem_free=8G #Requested memory for HPC cluster... |
ab4aaca39388e9ba35f7cd517429b698fa233caf4d815867491cce46ad047e88 | Shell | 2,866 | 67 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=40:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
0df8a86b43e370625f38fcfbe3c8d90f8e6bd42697612e958556d548a8be07d3 | Shell | 2,873 | 58 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-06:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=32000 # Memory pool for all cores (see also... |
941ddb60fb4aef8f35382f12e277bf15fb7cdce2f50e119ae1b91fd096d914fc | Shell | 2,874 | 78 | #!/bin/bash -e
if [ $# -lt 6 ] || [ $# -gt 7 ]; then
echo "usage v1: lrna_index_tophat.sh <ref_fasta_gz> <spike_in_fasta_gz> <annotation_gtf_gz> <tiny_fq_gz> <annotation_version> <genome> [<gender>]"
echo "Creates TopHat index of reference genome, annotation and spike-ins for long-RNA-seq. Is independent of DX... |
47f66dd884ce905f1560a3a2577b43091aa2e8f95143582b249285128fcd91fe | Shell | 2,880 | 68 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
5d7608a638034896dbd173ab6cc637fa0b1cc2f21c9e3e6b37de5d6d6557e68a | Shell | 2,888 | 85 | #!/bin/bash
# This script is a bash implementation of the following workflow/task in WDL:
# Filename: wdl/CollectCoverage.wdl
# Task: CollectCounts
set -Exeuo pipefail
if [ -z "${SV_SHELL_CLEAN_UP_WORKING_DIR:-}" ]; then
SV_SHELL_CLEAN_UP_WORKING_DIR=true
fi
intervals=$1
cram_or_bam=$2
cram_or_bam_idx=$3
sample_... |
d52f7e6bfc312359dbd83af9de8377bbdf950714b0bd69a4b381c63d8b8766a4 | Shell | 2,891 | 66 | #!/bin/bash
#$ -N P9 #Job ID name sent to HPC cluster.
#$ -pe openmp 1 #Number of requested parallel environments.
#$ -o '/<directory root>/fMRIPrep/Pipeline_9/logs' #Folder where fMRIPrep logs files are saved out by the HPC cluster.
#$ -e logs #Resquests logs.
#$ -l m_mem_free=8G #Requested memory for HPC cluster... |
8745c09b3c1575da77776e1b87cf79ab522c07f0fb652947346ff3ef23be7481 | Shell | 2,896 | 66 | #!/bin/bash
#$ -N P8 #Job ID name sent to HPC cluster.
#$ -pe openmp 16 #Number of requested parallel environments.
#$ -o '/<directory root>/fMRIPrep/Pipeline_8/logs' #Folder where fMRIPrep logs files are saved out by the HPC cluster.
#$ -e logs #Resquests logs.
#$ -l m_mem_free=8G #Requested memory for HPC cluste... |
787bea3179ec63d1ba419f112dd2f8b76bf3ea6289f4bdeb2782fcfea8b69cfd | Shell | 2,900 | 66 | #!/bin/bash
#$ -N P4 #Job ID name sent to HPC cluster.
#$ -pe openmp 5 #Number of requested parallel environments.
#$ -o '/<directory root>/fMRIPrep/Pipeline_4/logs' #Folder where fMRIPrep logs files are saved out by the HPC cluster.
#$ -e logs #Resquests logs.
#$ -l m_mem_free=8G #Requested memory for HPC cluster... |
3c605091cb1d7224fabe8a1338ace0c1ce5e2159d34b89322b2dac21b7a3a4fe | Shell | 2,904 | 67 | #!/bin/bash
#$ -N P5 #Job ID name sent to HPC cluster.
#$ -pe openmp 5 #Number of requested parallel environments.
#$ -o '/<directory root>/fMRIPrep/Pipeline_5/logs' #Folder where fMRIPrep logs files are saved out by the HPC cluster.
#$ -e logs #Resquests logs.
#$ -l m_mem_free=8G #Requested memory for HPC cluster... |
6da0d7df88946b9071e7f41fbbb20c51834a68b6301557abf0399b866fa11e7c | Shell | 2,907 | 66 | #!/bin/bash
#$ -N P6 #Job ID name sent to HPC cluster.
#$ -pe openmp 5 #Number of requested parallel environments.
#$ -o '/<directory root>/fMRIPrep/Pipeline_6/logs' #Folder where fMRIPrep logs files are saved out by the HPC cluster.
#$ -e logs #Resquests logs.
#$ -l m_mem_free=8G #Requested memory for HPC cluster... |
76b2b0037b4f25cbeef9cb92f166071e14d8dd6c0f80769764c2bda4fe5a8080 | Shell | 2,908 | 67 | #!/bin/bash
#$ -N P2 #Job ID name sent to HPC cluster.
#$ -pe openmp 5 #Number of requested parallel environments.
#$ -o '/<directory root>/fMRIPrep/Pipeline_2/logs' #Folder where fMRIPrep logs files are saved out by the HPC cluster.
#$ -e logs #Resquests logs.
#$ -l m_mem_free=8G #Requested memory for HPC cluster... |
fff1d105c8643f8dadbc0428f24f30409270843aa1b726a448c96be49d16b19e | Shell | 2,908 | 67 | #!/bin/bash
#$ -N P3 #Job ID name sent to HPC cluster.
#$ -pe openmp 5 #Number of requested parallel environments.
#$ -o '/<directory root>/fMRIPrep/Pipeline_3/logs' #Folder where fMRIPrep logs files are saved out by the HPC cluster.
#$ -e logs #Resquests logs.
#$ -l m_mem_free=8G #Requested memory for HPC cluster... |
a8b03dcba511c2472a7817c58a6aaf805058213d1bba6a619c45a0aa0f6cbbb7 | Shell | 2,925 | 67 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
9350bb94a05e12ed13dd0a682991723806d708d2e15e4846a9eb1a7e3be4bb7f | Shell | 2,931 | 78 | #!/bin/bash -e
if [ $# -ne 6 ]; then
echo "usage v1: lrna_align_tophat_pe.sh <tophat_index.tgz> <read1.fq.gz> <read2.fq.gz> <library_id> <ncpus> <bam_root>"
echo "Align paired-end reads with TopHat/bowtie2. Is independent of DX and encodeD."
exit -1;
fi
tophat_index_tgz=$1 # TopHat Index archive.
read1_... |
dfe163ec4b14948a34e47cbb1ceb0a3db5eef2e9801f606141d2a8783bc5b66a | Shell | 2,931 | 56 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=20:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
fd3968679115eef077d3746aeb42922c378b7faa706377b566e3332281b7f315 | Shell | 2,934 | 67 | #!/bin/bash
#$ -N P1 #Job ID name sent to HPC cluster.
#$ -pe openmp 5 #Number of requested parallel environments.
#$ -o '/<directory root>/fMRIPrep/Pipeline_1/logs' #Folder where fMRIPrep logs files are saved out by the HPC cluster.
#$ -e logs #Resquests logs.
#$ -l m_mem_free=8G #Requested memory for HPC cluster... |
469e6de4fa96da27fcd60661fc17c161af81e600ce03d13c3f50c27b9f32e766 | Shell | 2,935 | 63 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2020, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
111ac260677dbf92bf3526e8ff6847b13cdb28c3a5a0d3a41d1dcb647f8ff53b | Shell | 2,937 | 63 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2020, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
6b28b391fdad565b84f161d5811a3dd567efc6d60aae0a7130f5f6fb9451e662 | Shell | 2,947 | 100 | #!/bin/bash
## HiC-Pro
## Copyleft 2015 Institut Curie
## Author(s): Nicolas Servant, Nelle Varoquaux
## Contact: nicolas.servant@curie.fr
## This software is distributed without any guarantee under the terms of the GNU General
## Public License, either Version 2, June 1991 or Version 3, ... |
2724e04d1362bd5a08c5cb0be117b63638f00c238f365828d9d7f2513c1bd6a0 | Shell | 2,958 | 97 | #! /bin/bash
script_dir="/net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_01_20_Vary_Motif_Pval_nobackup/bbi-sciatac-analyze/src"
humanFASTA="/net/bbi/vol1/data/genomes_stage/human/human_atac/Homo_sapiens.GRCh38.dna.toplevel.fa.finished"
mergedPeaks="/net/trapnell/vol1/HuBMAP/novaseq/210111_Riza_s... |
6ae297be43fc3a05733792eb6c9d87de3bb46dbce0e502b7d3eee1724177f06e | Shell | 2,966 | 84 | #!/bin/bash
STANDALONE=$1
#Standalone: Need to download atlas and transform beforehand
if [ -n "${STANDALONE}" ]; then
bash dsurqec.sh
bash ambmc.sh
rm lambmc*
rm ldsurqec_*
rm dsurqec_200*
rm ambmc_200*
fi
# Resize
ResampleImage 3 dsurqec_40micron_masked.nii _dsurqec_15micron_masked.nii 0.015x0.015x0.015 size... |
1ffdeee76551ef5e9b0af94673d557f58ba3ffc742ad27ea2af9b7e970d80719 | Shell | 2,975 | 67 | #!/bin/bash
#$ -N P7 #Job ID name sent to HPC cluster.
#$ -pe openmp 5 #Number of requested parallel environments.
#$ -o '/<directory root>/fMRIPrep/Pipeline_7/logs' #Folder where fMRIPrep logs files are saved out by the HPC cluster.
#$ -e logs #Resquests logs.
#$ -l m_mem_free=8G #Requested memory for HPC cluster... |
7738993a510e0bb87290d61ee3862ed86663508132ecc2a4ca0d275b8bb66095 | Shell | 2,978 | 122 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO_ROOT="$(cd "${SCRIPT_DIR}/.." && pwd)"
cd "${REPO_ROOT}"
MODE="all"
SCILENCE_ARGS=()
for arg in "$@"; do
case "${arg}" in
stage1|stage2|all)
MODE="${arg}"
;;
--scilence)
SCILENCE_ARGS+=(-... |
9d9b82ef482d33816e613eed4b199525f55aab6436c87dac47f5a6723ced669a | Shell | 2,987 | 77 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=30:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
5d1034136e74431a1522d2ae4538cdfc67114afe279df94d71e788666afb9ddb | Shell | 2,988 | 70 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2025, Open Brain Institute
# Author(s): Marwan Abdellah <marwan.abdellah@openbraininstitute.org>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
... |
426ece589bb93b64bd70c74be7ca54e5d79d04f52daa9d7e9ea1a7bd1df18398 | Shell | 2,997 | 75 | #!/bin/bash
# The "qmri-ald" program provides automated image-processing pipelines for
# structural MRI images primarily acquired in pediatric healthy controls
# and pediatric patients with cerebral adrenoleukodystrophy. The program
# provides preprocessing, processing, quantitative, and statistical analysis
# of MRI i... |
fbfd0aeb9f933c4244d6243bf1fd19b2e2e928bc7129458bd13b55185bc3d93a | Shell | 2,997 | 82 | #!/bin/bash
## HiC-Pro
## Copyright (c) 2015 Institut Curie
## Author(s): Nicolas Servant, Eric Viara
## 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
##
## Merge multiple... |
109c4b3a0587c64204cf5a5fcef7963fd95e68145e19ae37cd92d35d18b81efa | Shell | 3,031 | 68 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
607bb7c4a54e510103d37def2bd49cde46902ce601b310d65af9ffcddb05580b | Shell | 3,031 | 70 | #!/usr/bin/env bash
# server-conf-scripts are for configuration of a *fresh* VM and should not be
# treated as startup scripts. (They are not idempotent.)
GCP_BUCKET="ml4h-core"
# We assume we are running as a regular user, not root.
# Enable gcsfuse to allow mounting of the google storage bucket as if it were a dr... |
b264897b4105a4163541f706f3a9ee6f7380d3d6cff3d4d5b4d3c60170c00b50 | Shell | 3,040 | 66 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
68117d797f06b551dd1b652e1cf84d488d2cb5b0568259673f14179fe4d2842a | Shell | 3,049 | 117 | #!/bin/bash
# Simple script to split cn.MOPS calls by sample and copy state and merge
# across multiple runs (e.g. at different resolutions)
set -e
#Usage statement
usage(){
cat <<EOF
usage: cleancnMOPS.sh [-h] [-z] [-o OUTDIR] [-S SUBTRACT] SAMPLES GFFS
Helper tool to split cn.MOPS calls by sample and copy state ... |
4aeb0f23941614e5ed194c330c67485fd203427a63ab3e30f7a9017ab5cc78b2 | Shell | 3,050 | 45 | #!/bin/bash
# The "qmri-ald" program provides automated image-processing pipelines for
# structural MRI images primarily acquired in pediatric healthy controls
# and pediatric patients with cerebral adrenoleukodystrophy. The program
# provides preprocessing, processing, quantitative, and statistical analysis
# of MRI i... |
7405071567c26281659172649256b08757782e57f0e6039923e9e81cb743f7ce | Shell | 3,068 | 98 | #!/bin/bash
# 'KAS-Analyzer fastqc' was developped by Ruitu Lyu on 12-10-2021.
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer fastqc [ -h/--help ] [ -t threads ] [ -c contaminants ] [ -o output dir ] [ -k KAS-seq ] "
exampleHelp="Example: n... |
751c38bb620fd9824d5cea029e84791bf5f0e3103ee20d9edfe79596169f2ff7 | Shell | 3,083 | 60 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=2:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
179bb8a5227d59f74da88064ffec2765ffe9f4b1421977193cc70145bd46149e | Shell | 3,103 | 76 | #!/bin/bash
# comp-signals-pe 0.0.2
#set -x
#set +e
main() {
echo "*****"
echo "* Running: comp-signals-pe.sh"
echo "* Using: awk, tee, alexAwkBg.sh"
echo "*****"
# TODO: at some point the bam-to-bw scripts will stop uploading the bedGraphs.
# When that happens, this compare routine can... |
011bed25a30358b6aa7657dd9fbb22e4933975f024e49f7fe71f7c9ba80fb87d | Shell | 3,107 | 99 | #!/bin/bash
# Cause the script to exit if a single command fails.
set -e
# Show explicitly which commands are currently running.
set -x
DOWNLOAD_DIR=python_downloads
NODE_VERSION="14"
PY_MMS=("3.10" "3.11" "3.12" "3.13" "3.14")
if [[ -n "${SKIP_DEP_RES}" ]]; then
./ci/env/install-bazel.sh
curl -o- https://ra... |
2dc72e0413b79c3b3f327d4606e913f3ff48b68398edc2bf34e922aa2c0c1b4e | Shell | 3,122 | 131 | #!/bin/bash
# Collects QC data for SV VCF output by SV pipeline
# Cohort-level benchmarking comparisons to external dataset
set -e
###USAGE
usage(){
cat <<EOF
usage: collectQC.external_benchmarking.sh [-h] [-r REF] STATS SVTYPES CONTIGS BENCHDIR OUTDIR
Helper tool to collect cohort-level bechmarking data for a VCF... |
e5d77f6567a60767ad75f347e5a122e5280558b92c933f715146650babe0cd01 | Shell | 3,124 | 85 | # usage:
# ./dockerize.sh -> build deepface:latest locally from Dockerfile (onnx backend)
# ./dockerize.sh source=local -> same as above, local is the default source
# ./dockerize.sh source=hub -> pull serengil/deepface:latest from docker hub
# ./dockeriz... |
22bf3b3f2451e71209818cf59da502433c315c18fe4eaffbeaebc9abd23d1f36 | Shell | 3,128 | 99 | #!/bin/bash
#
# IntegrateGQ_PESR.sh
#
set -euo pipefail
vcf=$1
pegeno_indiv_file=$2
pegeno_variants_file=$3
srgeno_indiv_file=$4
srgeno_variants_file=$5
#Final Output for individual genotype file VID IID RD-Geno, RD-GQ, PE-Geno, PE-GQ, SR-Geno, SR-GQ, Combined-Geno, Combined-GQ#
##Final Output for variant genotype ... |
9bdc1ea1781738f95c5e385b5a8b1353ac9840040e9c4c21be8c11a7d74278ff | Shell | 3,139 | 98 | #!/bin/bash
# This script is a bash implementation of the following workflow/task in WDL:
# Filename: wdl/Whamg.wdl
# Workflow: Whamg
set -Exeuo pipefail
if [ -z "${SV_SHELL_CLEAN_UP_WORKING_DIR:-}" ]; then
SV_SHELL_CLEAN_UP_WORKING_DIR=true
fi
sample_id=$1
cram_file=$2
cram_index=$3
reference_fasta=$4
reference... |
2ddb828880493509881b9ef31c85d6768ad1d45a83add48b36da2db3289463a1 | Shell | 3,161 | 60 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
a818c25263d846a5de37326e04f2b9551e6faa5a5a2ef8cfee036013c01c5698 | Shell | 3,181 | 125 | #!/bin/bash
# Wrapper for bedtools map to compress raw binCov output into
# larger bin sizes
set -e
#Usage statement
usage(){
cat <<EOF
usage: compressCov.sh [-h] [-N] [-s] [-z] [-o OUTFILE] INPUT RATIO
Helper tool to automate compression of raw binCov.py output bed files or
bed-style coverage matrices into large... |
4fd3f47dba5e574542ec12e2d7f45a0ba57fb813846abfed98835559bd0d5886 | Shell | 3,197 | 107 | #!/usr/bin/env bash
# Cause the script to exit if a single command fails.
set -e
# Show explicitly which commands are currently running.
set -x
ROOT_DIR=$(cd "$(dirname "$0")/$(dirname "$(test -L "$0" && readlink "$0" || echo "/")")"; pwd)
if [[ ! "${OSTYPE}" =~ ^darwin ]]; then
echo "ERROR: This wheel test scrip... |
5186b58132d19b8fc55fc9068a31e0b41743f223c46cff05f495724a6df18a95 | Shell | 3,198 | 134 | #!/bin/bash
# Batch script to iterate binCov over a supplied list of contigs
set -e
#Usage statement
usage(){
cat <<EOF
usage: binCov_batch.sh [-h] [-b BINSIZE] [-m MODE] [-n] [-z] [-C] [-I INDEX]
[-L CONTIGS] [-x BLACKLIST] [-v OVERLAP]
BAM ID OUTDIR
Wrapper for seri... |
4feaac0b71d64e063ec44b8d908566fea4c5c44ccfb79341df9206510d205d7c | Shell | 3,210 | 69 | #!/bin/bash
set -e
prefix=$1 # e.g. data/demo/
device="cuda" # "cuda" or "cpu"
pixel_size=0.5 # desired pixel size for the whole analysis
n_genes=1000 # number of most variable genes to impute
# preprocess histology image
echo $pixel_size > ${prefix}pixel-size.txt
python rescale.py ${prefix} --image
python prepr... |
9a7c0f0f21f891c5faad7def1a5ca57509a16c1e8341426c1c87feba383a66ca | Shell | 3,210 | 62 | #!/bin/bash
#######################################################################################
#RNA QuantSeq Analysis: https://www.lexogen.com/quantseq-data-analysis/
#######################################################################################
#intall packages if don't have them:
#install fastqc with... |
3c64569ff3db13fb930547e17c2ae88874c162d97e9be483fa9ee875efbfedd9 | Shell | 3,245 | 83 | #!/bin/bash
#
# Run the >>> docstring examples in only the modules a pull request changed,
# across every library, in the docstringbuild image with the PR's Ray installed.
# Used by the "docstring-only" label's "doc: docstring examples" step in
# .buildkite/others.rayci.yml.
#
# Usage: run_docstring_examples.sh <build ... |
01327b5e2281af144ee302df3c618a0372216fab490dcc7bd22c331884c0970a | Shell | 3,255 | 52 | ##Generate DNAme bed files for ChromHMM annotations
#all tested DNAme
for tis in Lung Muscle; do
sed '1d' ~/2SMR/Results/${tis}.m6A2me.mr.fdr.res |cut -f 2 |sort -u |\
awk -v OFS='\t' '{if(NR==FNR){a[$1]=$1;b[$1]=$2;c[$1]=$3;d[$1]=$4}else{if(a[$0]==$0){print b[$0],c[$0],d[$0],$0}}}' ~/Database/infinium-methylationep... |
ba3275cfdf3b41cec4e2da32ca822e9e58428ed203b6150c5e2521719c575a15 | Shell | 3,261 | 110 | #!/bin/bash
## HiC-Pro
## Copyright (c) 2015-2018 Institut Curie
## Author(s): Nicolas Servant, Eric Viara
## Contact: nicolas.servant@curie.fr
## This software is distributed without any guarantee under the terms of the BSD-3 licence.
## See the LICENCE file for details
##
## build_raw... |
3dae4aef42c59104672fdc1146ddf463b5e9506767e67d359d7f5ce4177feb9c | Shell | 3,274 | 135 | #!/bin/bash
SCRIPTNAME=$(basename $0)
USAGESTR="
NAME
${SCRIPTNAME} Repeats eye movements reconstruction grid search and generation
Assumes that the grid search has already been completed using
eye_movements_reconstruct_grid_and_generate.sh
SYNOPSIS
${SCRIPTNAME} <config> <output_base> [optional one-letter argument... |
c6d4e2033617935cbec3e5c48337af2ee28765bed0b97f8ea1da1aaf8c86bedf | Shell | 3,295 | 62 | ### Script to find TF motif enrichments in promoters of DEGs
# JK September 16, 2019
# JK February 29, 2024
## gist of findMotifs.pl command:
# looking across top genes of interest for shared (enriched) motifs!
# findMotifs.pl will take your top genes and compare them to a background set of genes to make suremthat the... |
06fe58216fb12549c3c9708da9476a1d0a7558c61f61e53e81650a2b3fbb25f6 | Shell | 3,297 | 113 | #!/bin/bash
## HiC-Pro
## Copyright (c) 2015 Institut Curie
## Author(s): Nicolas Servant, Eric Viara
## 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
##
## Launcher of me... |
7f96e31f068c263acb1a6dfd3cebb40644c0940fb8f5bf80c8c4f7dcc583bcdf | Shell | 3,305 | 83 | #!/bin/bash
# 04_ExtractStats.sh
#on subject level we need:
#peak zstat & cope, #avg zstat & cope, all values in respective ROI zstat & cope
#rois:only c6, dh left, ventral horn right and respective dilated version
#on group level we need:
#uncorrected p values for each quadrant per segment,
#uncorrected p values wit... |
563589b3c75b823367b6ab3695a116945a3de16d1539a415e17f069418c99d07 | Shell | 3,312 | 107 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -r <reorientMa... |
3f0189bcd99450e7d38833165beec60c3764408edc89ec91f4960b6c43195dff | Shell | 3,321 | 72 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=20:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
4f1e84d44e7bd42ea9103580c4023fbb03de4ce18c24c705728baabe5cbb9ffd | Shell | 3,342 | 100 | #!/usr/bin/env bash
#############################
# gnomAD SV Discovery #
#############################
# gnomAD credits: http://gnomad.broadinstitute.org/
# Wrapper to run MELT (Gardner et al., Unpublished)
# Updated by ShuangBroad
# Several differences between this and Ryan L. Collins' version
# 1): read_... |
806ad1bc18fde1d49ca9b99317626359dd43fe2911d3befebdd4e56d52ab8a99 | Shell | 3,345 | 103 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2:-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
f20441e4a67e4979c4a8260f70c7c1f57368c4ab2760227b8e1c078759e67b84 | Shell | 3,348 | 92 | #!/bin/bash
# TODO: integrate this script into pull request workflow.
printError() {
printf '\033[31mERROR:\033[0m %s\n' "$@"
}
printInfo() {
printf '\033[32mINFO:\033[0m %s\n' "$@"
}
log_err() {
printError "Setting up clang-tidy encountered an error"
}
set -eo pipefail
trap '[ $? -eq 0 ] || log_err' ... |
fd4bdf124f44c532ad39bfe34f2da1cf5451099305a5d73a6a0db6af20e5b6d2 | Shell | 3,365 | 47 | #! /bin/bash
# 8-18-21 Runs
Rscript runGlmnetOnMotifs.R --featureSelection Binary_PromOnly_Motif_Counts
Rscript runGlmnetOnMotifs.R --featureSelection Binary_Combined_Motif_Counts
# 8-18-21 Runs
Rscript runGlmnetOnMotifs.R --featureSelection Binary_PromOnly_Motif_Counts --predictionTask _log2_CPM
Rscript runGlmn... |
2039d00c48014b1c6cc8cc5059f7ab232677133e8c1b616b1d010a042d08c48f | Shell | 3,370 | 64 | #run gcta.
gcta64=/mnt/analysis-psp/users/ukumar/programs/gcta_1.93.2/gcta64
#setup fam file
outdir=/mnt/analysis-psp/users/timchang/v3/pc/2211/results/hwe/gcta/
mkdir $outdir
cat /mnt/analysis-psp/users/timchang/v3/pc/2211/data/clin/mod/pspcon.2.fam | awk '{print $1, $2, $6}' | awk '{ $3 = ($3 == "1" ? 0 : 1) } 1' ... |
5f5a044059bdbe9687cbeffe0a28848310505b91ea2600dcfc0ec44aafa23eb0 | Shell | 3,373 | 83 | #!/bin/bash
# 04_ExtractStats.sh
#on subject level we need:
#peak zstat & cope, #avg zstat & cope, all values in respective ROI zstat & cope
#rois:only c6, dh left, ventral horn right and respective dilated version
#on group level we need:
#uncorrected p values for each quadrant per segment,
#uncorrected p values wit... |
513dfaed29a59e02524e1c3dace879f447d34da93c506e4dd54ebbf7e77b2556 | Shell | 3,375 | 111 | #!/usr/bin/env bash
# This script downloads LLVM prebuilt binaries, extract them to a user specified location, and setup Bazel
# with this location. Example usage:
#
# (Repository root) $ ci/env/install-llvm-binaries.sh <optional URL to LLVM> <optional target directory>
# (Repository root) $ bazel run --config=llvm //... |
a2c1e1eb906debc085bfef78017938711c30884f5b225c7d9250809b23bd5309 | Shell | 3,383 | 91 | #!/bin/bash
#BATCH -p DCU
#SBATCH -N 1
#SBATCH -n 9
#SBATCH --ntasks-per-node=9
#SBATCH -o %j.out
#SBATCH -e %j.err
cd /home1/Huashan1/zdd_data/Fuyan/conditional/
#ARMC5 chr16:31,458,080-31,467,167
gene='ARMC5'
path1='/home1/Huashan1/zdd_data/Fuyan/conditional'
plink --bfile /share_storage/home1/Vinceyang/UK... |
63102e27e41fbc9424c45a0dc4df02c02c6352fd50883b9ea594ef6b98e5ff68 | Shell | 3,403 | 96 | #!/usr/bin/env bash
# Installs the gVisor runtime (runsc) needed by the Ray sandbox tests.
# Written primarily for CI. Kept on "latest" for now
# Pinning a specific gVisor version is a separate follow-up tracked in issue #65352.
set -euxo pipefail
# Install directory. Defaults to /usr/local/bin (on PATH); overridabl... |
24768af1ba52df448661c3e2cf4ae332edb60d8bec4e251362c098149c709905 | Shell | 3,416 | 103 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
dee5e540220a44905374b9f2e1a61d406922858439e69f79eb6c4be035255216 | Shell | 3,416 | 98 | #!/bin/bash
# The "qmri-ald" program provides automated image-processing pipelines for
# structural MRI images primarily acquired in pediatric healthy controls
# and pediatric patients with cerebral adrenoleukodystrophy. The program
# provides preprocessing, processing, quantitative, and statistical analysis
# of MRI i... |
f07da024fa967c39c13c83c517a22251fc2dfe2fffdcd313a9e797323a708d5e | Shell | 3,421 | 113 | #!/usr/bin/env bash
# Script to enable running Python modules within Docker containers
# Note: If 'nvidia-docker' is specified as $DOCKER_COMMAND, this script must be run on a dl-image machine
# (rather than a 'ukbb-image' machine) on a GPU-enabled machine.
################### VARIABLES ##############################... |
8de5e17aceb68264ea608d2ed72944f9fb474ff23b8a71a3850e2b1c12d0bd4f | Shell | 3,430 | 78 | # Author: Zachary Chiang, Buenrostro Lab, Harvard University
# Runs processing of ex situ sequencing data
picard='/mnt/bin/picard/picard.jar'
genome=$1
prefix=$2
fastq_dir=$3
name=$4
genome_ver=`basename $genome`
# move to working directory and make subdirectories
cd /mnt/users/zack/projects/embryo_seq_expt002_no... |
67c45ac6761b782990ddab45ca0c599986ef675b648189aa0ff2f3e23c9bf61c | Shell | 3,434 | 88 | #!/bin/bash
set -e
MAINDIR=$(pwd)
display_usage() {
echo ""
tput bold
echo "Description"
tput sgr0
echo ""
echo "This script uses MRTrix and FSL to count the streamlines that pass through each ROI of a predefined atlas."
echo ""
tput bold
echo "Usage"
tput sgr0
echo ""
echo "./$(basename $0) [Subject an... |
c9f8527a09fecf9c4751e295bb732af6e18c20f30eae4a51e4be8d2ce834c7c8 | Shell | 3,442 | 33 | #! /bin/bash
# Koenig et al
curl https://ftp.ncbi.nlm.nih.gov/geo/series/GSE183nnn/GSE183852/suppl/GSE183852_DCM_Nuclei.Robj.gz > koenig_et_al_data/koenig_nuclei.Robj.gz
zcat koenig_et_al_data/koenig_nuclei.Robj.gz > koenig_et_al_data/koenig_nuclei.Robj
# Litvinukova et al
curl "https://storage.googleapis.com/d... |
a0792f22371bd35c231b57041a5811973c7386d2270c183fb5cedb1f51498b9a | Shell | 3,478 | 44 | #! /bin/bash
module load bedtools/2.29.2
echo "Starting peak matching and sequence extraction"
# First, set wd
cd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_07_redoATACtoExprData_nobackup
# For a defined promoter size and cicero linking hyperparams, get site info for each gene
Rscript definedPro... |
1d206cf9e804513e47451af2758beaefce83ffcd38f17842b789ee391b9998e1 | Shell | 3,489 | 135 | #!/bin/bash
FIND_CUDA () {
#CUDA RELATED VARIABLES
CUDA_LIBRARY_PATH=""
CUDA_MATH_LIBRARY_PATH=""
CUDA_INCLUDE_PATH=""
NVCC=""
CUDA_FOUND=""
LD_CONFIG=ldconfig
if [ "$OS" == "openSUSE Tumbleweed" ]; then
LD_CONFIG=/sbin/ldconfig
fi
if [ -z "$CUDA_LIBRARY_PATH" ]; then
CUDA_LIBRARY_PATH=$(dirname "$($L... |
f0a35254fadb6deda1d0869d4cdab48707ab5440f555aa61988b57a84ac9238e | Shell | 3,492 | 81 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
7e29425d4063b6f838f9582d94dc3e85d28677982b580f572d57ac1499117c28 | Shell | 3,496 | 103 | #!/bin/bash
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
set -Exeuo pipefail
input_json=${1}
output_json_filename=${2-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [ ... |
650b3f8cad01867f0a1d9b5db8c789e8dec5514093a37b98dcb0af0c8e5fce92 | Shell | 3,498 | 44 | #! /bin/bash
# module load bedtools/2.29.2
# echo "Starting peak matching and sequence extraction"
# # First, set wd
# cd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_07_redoATACtoExprData_nobackup
# # For a defined promoter size and cicero linking hyperparams, get site info for each gene
# Rscrip... |
07c07326e4151b6dc42f844ca302588cf18b4230a9356840eba517a86595231d | Shell | 3,501 | 44 | #! /bin/bash
module load bedtools/2.29.2
echo "Starting peak matching and sequence extraction"
# First, set wd
cd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_26_setup_ATAC_to_expr_data_nobackup
# For a defined promoter size and cicero linking hyperparams, get site info for each gene
Rscript defin... |
d28675ce3092ff74751a01105660fc0e76ab54032a75b5edceebabe38bd886e5 | Shell | 3,504 | 44 | #! /bin/bash
# module load bedtools/2.29.2
# echo "Starting peak matching and sequence extraction"
# # First, set wd
# cd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_07_redoATACtoExprData_nobackup
# # For a defined promoter size and cicero linking hyperparams, get site info for each gene
# Rscrip... |
d4c0c6dc2884bc6bf548064ca6e147fd22fda30b121206ade442319e93ac77b5 | Shell | 3,519 | 110 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <id_list> -s <script_dir> -o <out_... |
d0184dace95e19333b2a006e378c43bcddf52d21aa57bdc4238d776505861f05 | Shell | 3,525 | 105 | #!/bin/bash
# Wrapper to run NHP-HCP structural pipeline and surface fMRI processing
# How to run this script:
# sh /vols/Scratch/neichert/NHPPipelines/Examples/Scripts/the_wrapper_of_wrappers.sh
set -e
umask u+rw,g+rw # give group read/write permissions to all new files
# Before running the pipeline for the first... |
6933d6ef13c784d6fb5dab00ad635970be9803ae2da681a0ae042f5bc11247cf | Shell | 3,527 | 81 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
#... |
6c24c165359058c4dbaadab869ba4e1cba2c1fa499252db67e5355e5b081a7f2 | Shell | 3,528 | 101 | #!/bin/bash
#The pipeline ID we're using. This will need to be actively updated.
pipeline="0"
#The FEAT directory for this pipeline is defined.
feat_dir="/<directory root>/FEAT/Pipeline_${pipeline}/" #Full path removed for purpose of public sharing.
#Changes the working directory to the one containing FSF files for ... |
1775e90889faf6ca5bb52443d67277ab9c990e3c40712803483424e79e190b45 | Shell | 3,533 | 138 | #!/bin/bash
function myHelp () {
cat <<-END
syncer.sh
Purpose:
This bash script repeatedly calls rsync to pull data from a mounted directory
of an acquisition machine onto a local RAID array. It is called by syncAndCrunch.m
and runs in the background. syncer.sh will cease calling rsync once it finds a
file call... |
e5fc873a23048055fa85447ed11a424fbbc37ed9f0dfa93f8a6e7980fc303e29 | Shell | 3,536 | 106 | #!/bin/bash
set -e
umask u+rw,g+rw # give group read/write permissions to all new files
# before: RUN NHP HCP PIPELINE FOR T1w and T2w
# How to run this script:
# sh $myCode/RS/rest_vol_wrapper.sh
dataset='Jerome'
origdir=/vols/Data/sj/Nicole/${dataset}
SD=$origdir/derivatives
scriptsDir=/vols/Scratch/neichert/myC... |
c59e6a5340d7bd57bad54b5d828644d6157ba806a7cb860a69d73756489bfeaf | Shell | 3,551 | 44 | #! /bin/bash
module load bedtools/2.29.2
# echo "Starting peak matching and sequence extraction"
# # First, set wd
cd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_07_redoATACtoExprData_nobackup
# # For a defined promoter size and cicero linking hyperparams, get site info for each gene
Rscript defi... |
95fe41b6dfb7d2b173cac8e1112af6b2f8a5ea3b9cc6328d0137199e47e1a0dc | Shell | 3,564 | 132 | #!/bin/bash
# Stop on error
set -e
# Help information
usageHelp="Usage: KAS-Analyzer build [ -h ] [ -a aligner ] [ -g genome fasta ] [ -p index prefix ] [ -t threads ] [ -d index dir ]"
exampleHelp="Example: KAS-Analyzer build -a bowtie2 -g ./genome.fa -p hg19 -t 10 -d /Software/hg19_Bowtie2Index/ "
alignerHelp="-a [... |
cd9d162fd8ac7d9e93eda4b005c2f30f22a28f7b5755bbef545a91547c3e71c3 | Shell | 3,582 | 138 | #!/usr/bin/env bash
set -e
ROOT_DIR=$(cd "$(dirname "$0")/$(dirname "$(test -L "$0" && readlink "$0" || echo "/")")"; pwd)
function usage()
{
echo "Usage: copyright-format.sh [<args>]"
echo
echo "Options:"
echo " -h|--help print the help info"
echo " -c|--check check whether th... |
aed81436ab539834666b4f12078f11b31ab13e6eae7c5cb821828f690ed3e40a | Shell | 3,583 | 81 | #!/bin/bash
# CSHL small RNA pipeline: STAR mapping to the genome, bigWig generation
# usage: from an empty working directory, run
# ./STAR_RSEM.sh (read1) (STARgenomeDir) (nThreadsSTAR)
# input: gzipped fastq file read1 [read2 for paired-end]
# STAR genome directory, RSEM reference directory - prepared with ... |
ba6a6c2f4e78120bf543d5dfdc54ec912042d4562a1650e836392dd9f7f2bfd2 | Shell | 3,586 | 118 | #!/bin/bash
set -Exeuo pipefail
if [ -z "${SV_SHELL_CLEAN_UP_WORKING_DIR:-}" ]; then
SV_SHELL_CLEAN_UP_WORKING_DIR=true
fi
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}... |
3e5e778e63847877d02045c08811c720c7a9efe69029f3d167b08e92a3b0efa8 | Shell | 3,593 | 138 | #!/bin/bash
SCRIPTNAME=$(basename $0)
USAGESTR="
NAME
${SCRIPTNAME} Repeats flashed reconstruction grid search and generation
Assumes that the grid search has already been completed using
flash_reconstruct_grid_and_generate.sh
Assumes that the linear reconstruction filter training has already been
completed using f... |
3fd6d4798ce060e42a815ebcc679ac0a6972b024be3e3f7f2bf49094767b2681 | Shell | 3,596 | 134 | #!/bin/bash
## HiC-Pro
## Copyright (c) 2015 Institut Curie
## Author(s): Guipeng Li, 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
##
## Create SGE fi... |
0a99b7b008995350a0fd14050fab6e715208ee30aef38936d3e1e17089528c4d | Shell | 3,620 | 144 | #!/bin/bash
# Wrapper for PESR + depth merging in module 04b
set -e
###USAGE
usage(){
cat <<EOF
usage: PESR_RD_merge_wrapper.sh [-h] PESR_VCF RD_VCF CHROM OUT_VCF
Wrapper to handle PESR + RD merging in module 04b
Positional arguments:
PESR_VCF Input PESR VCF, bgzipped
RD_VCF ... |
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