sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
45c8fb427c7d85a6cae63ed198aceb402ecb871487b3b6756892f657e6e53929 | Shell | 4,894 | 142 | #!/bin/bash
# 'KAS-Analyzer UCSC' was developed by Ruitu Lyu on 12-10-2021.
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer UCSC [ -h/--help ] [ -k KAS-seq ] [ -l UCSC track ] [ -c track colors ]"
exampleHelp="Example: nohup KAS-Analyzer UCS... |
4cf297869e0a72b8728a6785d4f821e43f3e502a88fe1ed935f32820ccf85b53 | Shell | 4,895 | 108 | #! /bin/bash
set -o errexit
# FYI: The first steps can only be executed if you have downloaded
# all of the images from eLife's Amazon Web Services
# repository. These steps are provided here for transparency,
# but they are commented to avoid errors.
# The remaining steps can be executed using th... |
e0c66b209d6aa02a178e9581fb76e841735735bd22eb224a5ab9ebf5765fc51f | Shell | 4,895 | 182 | #!/bin/bash
# Collects QC data for SV VCF output by SV pipeline
set -e
###USAGE
usage(){
cat <<EOF
usage: collectQC.sh [-h] [-F FAM] [-R] VCF SVTYPES OUTDIR
Helper tool to collect QC data for a VCF output by sv-pipeline
Positional arguments:
VCF VCF from sv-pipeline
SVTYPES List of SV type... |
0cbbb598eb0419e0b41ee8cfd45c0227fc052f7c1c3e37e3994a2599a738b1dd | Shell | 4,907 | 137 | #!/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> -d <deform_dir> -s <scri... |
9a8a15b15b265ab8f05573dca0677b3145baacc8410344e4fb5eea20f71bbff6 | Shell | 4,987 | 87 | #!bin/bash
SCRIPTDIR=~/HybridFlow/scripts
dicomDir=~/HybridFlow/dicomData
hematocrit=0.45
relaxivityconstant=4.2
workingDir=~/HybridFlow/processedData
fastdceProtocolName=fl3d_vibe_fast_DT1.7s_16slices_2mmiso
T1map_precontrastFile=MP2RAGE_T1_precontrast_ref.nii
T1map_postcontrast1File=MP2RAGE_T1_postcontrast1.nii
T... |
bea8bbc294d80ee24ae57aa052d7a68c061ae820777f7d26dad76581533ff5d8 | Shell | 4,994 | 125 | #!/bin/bash
set -e
# Requirements for this script
# installed versions of: FSL
# environment: FSLDIR
################################################ SUPPORT FUNCTIONS ##################################################
Usage() {
echo "`basename $0`: Script to make masks for ventricles and white matter"
echo... |
98a541136feef72fc0b394fdc53fe33a910deed9b549d71464d3d9e886d16775 | Shell | 5,013 | 108 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=30:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
d00c20da01072c9bc757eb9e63c19bbfbcf2f1beb597df40406b63f99cf90603 | Shell | 5,026 | 195 | #!/bin/bash
# Master wrapper to collect QC data & generate plots for SV VCF output by SV pipeline
set -e
###USAGE
usage(){
cat <<EOF
usage: vcf_qc.sh [-h] [-F FAM] [-R] VCF SVTYPES BENCHDIR OUTDIR
Perform several quality control (QC) analyses on an SV VCF from sv-pipeline
Positional arguments:
VCF V... |
912a95d6078277c510aface7db51b243cdcc46d41e898a1640d64e391095a6b0 | Shell | 5,027 | 107 | #!/bin/bash
# The "qmri-ald" program provides automated image-processing pipelines for
# structural MRI images primarily acquired in pediatric healthy controls
# and pediatric patients with cerebral adrenoleukodystrophy. The program
# provides preprocessing, processing, quantitative, and statistical analysis
# of MRI i... |
95df651adcd0ea2f5d9b04a7f3c034e78a2c84baa0ccfb2efe643f566f1fe8ed | Shell | 5,064 | 33 | python3 deploy.py --dataPath /media/Data/row001_auto/color/cam0_images/ --row_segmentation /media/Data/row001_auto/row01.pkl --output /home/cairlab/testResult/ds1/row001_auto/ --downsample 1
python3 deploy.py --dataPath /media/Data/row001_auto/color/cam0_images/ --row_segmentation /media/Data/row001_auto/row01.pkl --ou... |
0e346788144b339d23f9e86733a5729a5c93a8592d13a75e1256e2341c7572d1 | Shell | 5,082 | 143 | #!/usr/bin/env bash
install_miniforge() {
if [ "${OSTYPE}" = msys ]; then
# Windows is on GitHub Actions, whose built-in Python installations we added direct support for.
python --version
return 0
fi
local conda="${CONDA_EXE-}" # Try to get the activated conda executable
if [ -z "${conda}" ]; the... |
58c80038e33ab380c29f10ab56a51807efe1feb800d9632bc460bba202a80cb7 | Shell | 5,086 | 118 | #!/bin/bash
# align-star-se.sh
main() {
# Now in resources/usr/bin
#echo "* Download and install STAR..."
#git clone https://github.com/alexdobin/STAR
#(cd STAR; git checkout tags/STAR_2.4.0k)
#(cd STAR; make)
#wget https://github.com/samtools/samtools/archive/0.1.19.tar.gz
# If available,... |
b6fc2aefa2ef51a5226b9303868c8707a5f5550962d919870a0e8e04f121a120 | Shell | 5,091 | 122 | #!/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 all vali... |
8c1d798293c1bf8d7b46de27f2a0350bbcba61839f55fc5ed41a0c07a8d0bf51 | Shell | 5,109 | 169 | #!/bin/bash
# Ensures the output of the test will not be truncated.
echo CTEST_FULL_OUTPUT
echo
# 2 or 3 parameters should be provided, exit otherwise
# 3rd parameter is the path used by Nightly dashboard and 'make test'
if [ "$#" -le 1 ] || [ "$#" -gt 4 ]
then
echo "Usage (example): `basename $0` benchRT gamma"
... |
e491fe55c004dba7d84e2ca1360813501c009a58b49874d57bea6d9a64cceb80 | Shell | 5,123 | 31 | echo ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Deeplab Modified a1m1 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
#echo -e ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Deeplab Modified a1m1 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
python3 Xavier_SpeedTest.py --weight '/media/Data/ignored/newnet_resnet18_64_newHead_m1_a1/05022022_050501/b... |
9994d9167fe22deda6d4edb58964191a6f4a90026774235c90ba3a3cd48e80a8 | Shell | 5,131 | 106 | #!/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... |
564c361d4c8d026238d30e1e4872f77c4753a0de33824f2b7d20ad8cf4f45219 | Shell | 5,135 | 106 | #!/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... |
5dcdd28f7f700c3ccd99fc9a099af7ac3ef8e959af7030ec6093c47e14124e2d | Shell | 5,143 | 181 | #!/bin/bash
# Collects QC data for SV VCF output by SV pipeline
# Per-sample benchmarking comparisons to external dataset
set -e
###USAGE
usage(){
cat <<EOF
usage: collectQC.perSample_benchmarking.sh [options] VCFSTATS SAMPLES CONTIGS PERSAMPDIR.tar.gz SET2.tar.gz OUTDIR
Helper tool to collect per-sample bechmarki... |
d04ca367a73bbb4800dd11d0c0a860c4b5dcc058da95a97656e6ca871f584994 | Shell | 5,150 | 114 | #!/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... |
58c55f51e5ff0b4b1a380ddc764017df38010517ed609d39e316a40ba48671a6 | Shell | 5,154 | 114 | #!/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... |
d82a446454d2bea460cf68c8252dc234687a78f8020f049d6b8e80475e45b3b5 | Shell | 5,156 | 141 | #!/bin/bash
# 'KAS-Analyzer complexity' was developed by Ruitu Lyu on 1-10-2022.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer complexity [ -h/--help ] [ -o prefix ] [ -l labels ] [ -k KAS-seq ]"
exampleHelp="Example: nohup KAS-Analyzer complexity -o KAS-seq_complexity -l labels.txt -k KAS-se... |
14f15d2e92469ba925d7479dac0774e9c17e1d64efccfee0400d3c9ac97400b2 | Shell | 5,173 | 125 | #!/bin/sh
# CBIG_IndCBM_create_template.sh <surf_mesh> <binary_mask> <output_dir> -m(optional) <midline> \
# -l(optional) <lh_vertex> -r(optional) <rh_vertex>
# This function creates a cifti template combining the cerebral cortical surface and the cerebellum in the volume.
# Input:
# surf_mesh: Mesh neame for ... |
d414f5f4fd73d30bc11e0697ac69c709aee54ad9403cc934c75adb6df027a1e8 | Shell | 5,211 | 119 | #!/bin/bash
# comp-tophat 0.0.2
#set -x
#set +e
main() {
#echo "Value of test dataset: '$test_dir'"
#echo "Value of standard dataset: '$data_dir'"
#dx download project-BKjyBz00ZZ0PZF5V7Gv00zqG:/"$test_dir"/*
#dx download project-BKjyBz00ZZ0PZF5V7Gv00zqG:/test/"$data_dir"/*
#find
echo "*****"
... |
c08c78721eef67fcdab4a164494f14a38fe6a4e52d02aa9496bdf3c4ad856673 | Shell | 5,231 | 116 | #!/bin/bash
# comp-star-rsem 0.0.2
#set -x
#set +e
main() {
echo "*****"
echo "* Running: comp-star-rsem.sh"
echo "* samtools version: "`samtools 2>&1 | grep Version | awk '{print $2}'`
echo "* also using: cut, diff, ls, md5sum, tee, diss"
echo "*****"
set1_log_final_fn=`dx describe "$set1_lo... |
2eb2c3b1458c6a4fef1c291e2dd12ffef84c0d83a4bf3c4d16613651b4b8bf7b | Shell | 5,269 | 159 | #!/bin/bash
# 'KAS-Analyzer FRiP' was developed by Ruitu Lyu on 12-11-2021.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer FRiP [ -h/--help ] [ -o prefix ] [ -p peaks ] [ -l labels ] [ -k KAS-seq ]"
exampleHelp="Example: nohup KAS-Analyzer FRiP -o KAS-seq_FRiP -p peaks_files.txt -l labels.txt ... |
65df6c770ad9fb60ebf67ee8b39fed7dab189c6326efed39640c62248300e27a | Shell | 5,300 | 177 | #!/bin/bash
# Stitch fragmented CNVs present in a VCF, without subsetting with regard to PE/SR evidence
###USAGE
usage(){
cat <<EOF
usage: stitch_fragmented_CNVs.sh [-h] [-e <float>] [-m <int>] [-X <float>] INVCF OUTVCF
Stitch fragmented CNVs present in the same samples in a VCF
Positional arguments:
INVCF ... |
a484695cdf862a11d72758590f48bfeb400151a53e353e4ca28b6933b4487b8f | Shell | 5,323 | 100 | #!/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 ... |
8faf2145d0f753fdbe4e6c7549f238c0b13567c105300f22ce1024178d1bb41e | Shell | 5,338 | 129 | #!/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 <imgList> -d <idList> -s <subinfo>... |
d8eccf00b2cb6b6dd4bf0d08b8e27b5a8e1dc55ff13eb15ff5d7a0beb52cff6d | Shell | 5,374 | 195 | #!/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
## Bowtie2 wrap... |
0d1c03263a7b314da6cb44b97d34c1362158a58bb7d2b684557450097ba9be0c | Shell | 5,418 | 108 | #!/bin/bash
#/data/talkowski/Samples/common-mind/03_variant_filtering/filtered_vcfs##
##define metric file##
set -e
metric_file=$1
##define cutoff columns##
PE_log_pval_col=$(cat $metric_file|head -n 1|tr '\t' '\n'|fgrep -n PE_log_pval|awk -F':' '{print $1}')
SR_log_pval_col=$(cat $metric_file|head -n 1|tr '\t' '\... |
68985dd6243087e44dcb8bbaa7178cbdab2b9afc27bf7a6e50c326cdeb189bfb | Shell | 5,579 | 49 | #Building_vg_genomes_2022May01.sh
module load g/vg/1.20.0
#/gpfs/gpfs2/software/tabix/bgzip /gpfs/gpfs1/home/bmoyers/BrainTF_AlleleSpecificBinding/5397-JL-0001/phased_variants_PASSED.vcf
#/gpfs/gpfs2/software/tabix/tabix -p vcf /gpfs/gpfs1/home/bmoyers/BrainTF_AlleleSpecificBinding/5397-JL-0001/phased_variants_PA... |
0d6cbdeb3f65a401174b096b87c8c20fef5fafb2988c6111efba6fad071739c3 | Shell | 5,585 | 179 | #!/usr/bin/env bash
# Cause the script to exit if a single command fails.
set -e
# Show explicitly which commands are currently running.
set -x
ROOT_DIR=$(cd "$(dirname "${BASH_SOURCE:-$0}")"; pwd)
java -version
run_testng() {
local pid
local exit_code
"$@" &
pid=$!
if wait $pid; then
exi... |
6f91064d6148e193e58e3f95cd0be4f02fd80ab07bea3f218e7901505331999b | Shell | 5,622 | 187 | #!/bin/sh
kernel="ou10"
lr=0.001
num_epochs=500
python3 ../ntd/train_diffusion_model.py \
base.experiment=ajile_experiment \
base.tag=conv_ou_ec01 \
dataset=ajile \
dataset.pat_id=EC01 \
diffusion=diffusion_quad_50 \
diffusion_kernel=${kernel} \
network=cat_conv_ajile \
optimizer=base_... |
80e8a6f66015b5652adcc3d048263dc5941e908f2842940b497f28d66cea4b7a | Shell | 5,638 | 53 |
qsub -l mfree=30G -l centos=7 -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_15_Greg_ATAC_Code_nobackup /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_15_Greg_ATAC_Code_nobackup/runSingleNB9.sh peakMat useMNN 2 50
qsub -l mfree=30G -l centos=7 -wd /net/trapnell/vol1/home/r... |
d27d08ec9760a50d070f1b67bf7eeab73c255d2fccc645aa08788fc9cdbabf91 | Shell | 5,666 | 144 | #!/bin/bash
# align-tophat-pe.sh
main() {
# Now in resources/usr/bin
## install tophat 2.0.8
#wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.8.Linux_x86_64.tar.gz
## install bowtie2_2.1.0
#wget http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/bowtie2-2.1.0-linux-x86_64.z... |
bd2dc33133a83c65fd8b1d058edba376530150567e3e09e5ccbc87cef6c4e4c5 | Shell | 5,701 | 34 | echo ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Deeplab Modified a1m1 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
#echo -e ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Deeplab Modified a1m1 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
python3 Xavier_SpeedTest_val.py --weight '/media/Data/ignored/newnet_resnet18_64_newHead_m1_a1/05022022_0505... |
a941f879b23732dbe1bf8313142240d55e77dc431ac8dbf7423044cda9bea5ce | Shell | 5,740 | 158 | #!/bin/bash
## HiC-Pro
## Copyleft 2015-2016 Institut Curie
## Author(s): Alex Barrera, Nicolas Servant
## 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, June 2007.
##
##... |
433911377330c82f347b964072c09425500650470d18eecf78ea5e3dc36918ff | Shell | 5,755 | 157 | #!/bin/bash
# 02_Masks.sh
#our EPIs cover C5, C6, C7 and C8
#what to do
build_horn_masks=1
build_dilated_quadrant_masks=1
build_cord_mask=1
build_quadrant_masks=1
delete_warping_files=1
#Directories
atlas_dir=/data/u_dabbagh_software/sct_5.5/data/PAM50/atlas #insert here your path to the SCT PAM50 atlas
template_dir... |
8ab4634e0a02fa81d07ca1fc7746d9d20af42ffd678381e70d8c4cbfa1aff94e | Shell | 5,837 | 156 | #!/bin/bash
# 02_2ndLevel.sh
#what shall be done
prep_sessionwise=1
run_dhl_sessionwise=1
run_cord_sessionwise=1
run_cord_dil_sessionwise=1
prep_avg=1
run_dhl_avg=1
run_cord_avg=1
run_cord_dil_avg=1
get_copezstat=1
#Directories
template_dir=/data/u_dabbagh_software/sct_5.5/data/PAM50/template
project_dir=/data/pt_0... |
6fb459ed874c7cce7c0e657dfed530a4809a96d1c75e589aa57accc52063c9f6 | Shell | 5,866 | 51 | echo ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Deeplab Modified a1m1 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
echo -e ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Deeplab Modified a1m1 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
python3 build_trt.py --weight '/media/Data/ignored/newnet_resnet18_64_newHead_m1_a1/19022022_190547/best_mode... |
33d5866866b81967c26cd6ab3c599c2257bf2112cda8efa8051175e273736789 | Shell | 5,895 | 185 | #!/bin/sh
#
# Example:
# sh ./CBIG_ASDf_unit_test.sh ~/storage/Temporaray/CBIG_ASDf_unit_test
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################################
# Set paths and create log file
###################################... |
f39715bc0837378203c1a4460ffb00f6d0a7b6f84d208281e700cd5376861e96 | Shell | 5,900 | 201 | #!/bin/bash
# Stitch fragmented CNVs present in a VCF
###USAGE
usage(){
cat <<EOF
usage: stitch_fragmented_CNVs.sh [-h] [-d] [-e <float>] [-m <int>] [-X <float>] INVCF OUTVCF
Stitch fragmented CNVs present in the same samples in a VCF
Positional arguments:
INVCF Original input VCF
OUTVCF ... |
e0d8a1bceabca71f465bc473dc2c05883a42e30b219684dfe5ba957f73f7fbd3 | Shell | 5,964 | 138 | #! /bin/bash
# # Format of arguments:
# # --promoterUpstream $1 --promoterDownstream $2 --coaccessCutoff $3 --maxNdistalSites $4 --peakSize $5
# qsub -P trapnelllab -l mfree=40G -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_07_redoATACtoExprData_nobackup/ /net/trapnell/vol1/home/readdf/trapLabDi... |
f8c023ffb8f9d07ca8ab5386d6fbde54c08a2211b3dcd38a9491e11221c0a617 | Shell | 5,968 | 181 | # @todo - better / more robust parsing of inputs from env vars.
## -------------------
## Constants
## -------------------
# @todo - apt repos/known supported versions?
# @todo - GCC support matrix?
# List of sub-packages to install.
# @todo - pass this in from outside the script?
# @todo - check the spec... |
f49693f7fc21f3f3b939e1edad9566cd1e5aa16af27595c1df282660aeadffd0 | Shell | 5,985 | 93 | #!/bin/csh -f
# Combines results from Amplitude Modulated analysis, compares the group t values to 0
# Amplitude modulated lexical frequency coef = [4]
set top_dir = top_dir/
cd $top_dir/Group_Analysis/AmpMod_LogZScore_WordFreq_PhonoDen
3dttest++ \
-prefix LexFreq_in_phonoden_out_noRF_AmpMod_vs_0_ttest \
-mask ../ma... |
f536eb239a4648d60ca2efa2a7a0e9d25668c0a2194a957d5d68f524b8e92c58 | Shell | 5,997 | 198 | #!/bin/sh
# This script serves as a toy example of using the code in folder step1_FC2doc
# and step2_polarLDA in Tang2020_ASDFactors
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#############################################
# Specify output director... |
e55b74e2007df975d82bcda6c70a3e14304067c6521bfa9f17adf1ce3a4312e2 | Shell | 6,001 | 93 | #!/bin/csh -f
# Combines results from Amplitude Modulated analysis, compares the group t values to 0
# Amplitude modulated phonological neighborhood density coef = [6]
set top_dir = top_dir/
cd $top_dir/Group_Analysis/AmpMod_LogZScore_WordFreq_PhonoDen
3dttest++ \
-prefix Phonoden_in_LexFreq_out_noRF_AmpMod_vs_0_tte... |
fd0fab1e63b05606e7df28f2cc2e2ae73993cd3f44a80255b99a849fb19b862b | Shell | 6,002 | 198 | #!/bin/bash
set -x
# Cause the script to exit if a single command fails.
set -e
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE:-$0}")"; pwd)"
WORKSPACE_DIR="${ROOT_DIR}/.."
JAVA_DIRS_PATH=('java')
RAY_JAVA_MODULES=('api' 'runtime' 'serve')
JAR_BASE_DIR="$WORKSPACE_DIR"/.jar
mkdir -p "$JAR_BASE_DIR"
cd "$WORKSPACE_DIR/java... |
2b7776d2f56bac15d7daaf796285edcdcffb40f4a9da59cd3a3c981737f7bfdd | Shell | 6,022 | 183 | #!/bin/bash
set -Exeuo pipefail
function StandardizeVCFs() {
declare -n _raw_vcfs=$1
declare -n _samples=$2
local _caller=$3
local _contigs=$4
local _min_svsize=$5
local _prefix=$6
# Optional extra arguments forwarded verbatim to `svtk standardize`.
local _extra_args=("${@:7}")
echo "----------- S... |
881a0562e485e34d8c7ca9e1959daa2ed3eae88a25ae4e32c431f6d6024e0507 | Shell | 6,038 | 135 | #!/bin/bash
# 'KAS-Analyzer targetgenes' was developed by Ruitu Lyu on 1-22-2022.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer targetgenes [ -h/--help ] [ -o prefix ] [ -s assembly id ] [ -f features ] [ -l length ] [ -p peaks ]"
exampleHelp="Example:
Gene features:
nohup KAS-Analyzer targe... |
af790a2d539dd60716d991098d478aaf67caa71bbe700f62607da20d6ea8a755 | Shell | 6,151 | 137 | #!/bin/bash
set -e
MAINDIR=$(pwd)
display_usage() {
echo ""
tput bold
echo "Description"
tput sgr0
echo ""
echo "This script uses MRTrix and FSL to analyze diffusion data using a certain atlas."
echo ""
tput bold
echo "Usage"
tput sgr0
echo ""
echo "./$(basename $0) [Subject and type of session]"
echo ... |
c0b14dd1b5b9cf8b9d310d21bf5b5521bba62ad7f7b2617552df37cf894a269c | Shell | 6,183 | 121 | # shellcheck shell=bash
# Installed as /etc/profile.d/zz-rayci-pypi-proxy.sh in the forge and manylinux
# images, sourced by .buildkite/hooks/pre-command for steps that run directly on
# the agent, and by ci/ray_ci/macos/pypi_proxy.sh on the macOS fleet. One file
# makes the decision for every surface.
#
# Points pip, ... |
81d03b1f20a399310efe342ef0f45155eaba5ff45007b9f9ea4cc39b4db7d898 | Shell | 6,249 | 137 | #!/usr/bin/env bash
# Checks that the syncAndCrunch rsync calls skip directories named "scratch" (at any depth)
# but still copy files merely named like it. Uses synthetic trees in a temp dir whose path
# contains a space. Run with: bash tests/test_rsync_ignores_scratch.sh
#
# syncer.sh is run for real. The two rsync c... |
38f13d081d4f8ada38edfc61f4d242a62653e1c279f34a1118e85cfa11a39da3 | Shell | 6,338 | 155 | #!/bin/bash
# 02_2ndLevel.sh
#what shall be done
prep_sessionwise=1
run_dhl_sessionwise=1
run_cord_sessionwise=1
run_cord_dil_sessionwise=1
prep_avg=1
run_dhl_avg=1
run_cord_avg=1
run_cord_dil_avg=1
#Directories
template_dir=/data/u_dabbagh_software/sct_5.5/data/PAM50/template
project_dir=/data/pt_02306/main/data/pa... |
857b8a7d0b2521c7f9d0f3f777cc5de67aae72a2664febec4b41574008b3c573 | Shell | 6,372 | 157 | #!/bin/bash
# 01_DenoiseMoco.sh
# What shall be done
prepData=1
thermnoise=1
moco=1
moco_refined=1
csf_mask=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: " $se... |
6d280562f8938a1af7fbad52312cf6efbfdc9dfcf08898b4bc423f4850989ad1 | Shell | 6,432 | 134 |
module load bedtools/2.29.2
#DFR: I've run gatherInputFiles.R, which has output a master bed file and bed files for each cell type's expressed genes + linked sites. All are as unsorted bedfiles.
cd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_08_27_GWAS_work_nobackup
# Note the hyperparameters used,... |
db7506374264dfe775bd3f9974ba47c9d7d8020f332cb32562c664210617abb4 | Shell | 6,522 | 214 | #!/bin/bash
# 'KAS-Analyzer install' was developed by Ruitu Lyu on 12-10-2021.
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer install [ -h\--help ] [ -conda ] [ -check ] [ -t tools ] [ -KAS-Analyzer ]"
exampleHelp="Example: KAS-Analyzer ins... |
6cd7461f4bed1b88ef0f0cec29d22539036ea51e5e44ce11f415ba920cbeffcf | Shell | 6,547 | 155 | #!/bin/bash
# 'KAS-Analyzer fingerprint' was developed by Ruitu Lyu on 12-11-2021.
# Stop on error
set -e
# arguments
usageHelp="Usage: KAS-Analyzer fingerprint [ -h/--help ] [ -t threads ] [ -s assembly id ] [ -o prefix ] [ -l labels ] [ -k KAS-seq ] "
exampleHelp... |
8dd030d4b1220fbd639642e10499fdafd9dadc82d789bbb8065006b2e2411c1e | Shell | 6,557 | 228 | #!/bin/bash
# Collects QC data for SV VCF output by SV pipeline
# Summary, VCF-wide statistics only
set -e
###USAGE
usage(){
cat <<EOF
usage: collectQC.vcf_wide.sh [-h] [-F FAM] [-R] [-r REF] VCF SVTYPES OUTDIR
Helper tool to collect vcf-wide QC data for a VCF output by sv-pipeline
Positional arguments:
VCF ... |
697000be1c7232a27f162458a9b48ecafc7bb82d9ca6175889fe7b918d6e014a | Shell | 6,585 | 21 | PARTITION=$1
GPUS=${GPUS:-8}
GPUS_PER_NODE=${GPUS_PER_NODE:-8}
CPUS_PER_TASK=${CPUS_PER_TASK:-5}
SRUN_ARGS=${SRUN_ARGS:-""}
log_dir="work_dirs/slurm_logs"
mkdir -p "$log_dir"
SRUN_ARGS=${SRUN_ARGS} GPUS=$GPUS GPUS_PER_NODE=$GPUS_PER_NODE CPUS_PER_TASK=$CPUS_PRE_TASK ./tools/slurm_train.sh $PARTITION duo-atss_r5... |
c68d989682e90d670cd63cd4a0e86f8cb4854847b05ef7ff400ceca195d09ac9 | Shell | 6,595 | 88 | wrkdir=/data/talkowski/Samples/SFARI/DeepSeq/HarrisonCompare/GT_Filtering/phase1_RF/mosaic_CNV/mosaic_pipeline/clean
##Mosaic CNV check##
##We currently are only going to check Mosaic CNV###
##Restrict to events private to individual exclude family structure for this particular module##
##Must come from raw caller out... |
415bfbf38f973139818b11365c0d847731a6805c379803ade7f427833fd14fc5 | Shell | 6,601 | 117 | #!/bin/bash
# 01_FeatWithinRun.sh
#what shall be done
create_fsf=1
run_feat=1
normalize_feat=1
#normalization Directories
template_dir=/data/u_dabbagh_software/sct_5.5/data/PAM50/template #replace with your own sct folder
# Loop over subjects and sessions
for subject in {1..40}; do
for session in {1..2}; do
... |
0956caf9923bdd4a1a2b0374e2ddce69bad110428f19e6acb5afe343e408bb37 | Shell | 6,630 | 170 | #!/bin/bash
# rampage-align-pe.sh NOTE: This is misnamed as it now works with SE data.
main() {
# Now in resources/usr/bin
#echo "* Download and install STAR..."
#git clone https://github.com/alexdobin/STAR
#(cd STAR; git checkout tags/STAR_2.4.0k)
#(cd STAR; make)
#wget https://github.com/sam... |
f1856790ff900a7b1980ad4c8bc340dd394fb1b0fac36e699ee9b24c3c63d8d2 | Shell | 6,637 | 209 | #!/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 ##############################... |
f966555a0f217ab98b89eb7383aa5acc166ead174963f6d1299eccdb799f569a | Shell | 6,645 | 234 | #!/bin/bash
USAGESTR="
NAME
${SCRIPTNAME} Flashed reconstruction grid search and generation
SYNOPSIS
${SCRIPTNAME} <config> <output_base> [optional one-letter arguments]
OPTIONS
-j <jitter-sd> Standard deviation of Gaussian for perturbing spike times
In units of electrical samples at ... |
e8d0bfdb989ae7d1c8b2aa301de97abb00ea49a0e1ec9c3c5d9bc95b25156f35 | Shell | 6,677 | 174 | #!/bin/bash
#DonorSpecificMapping.sh
################################################################################
#This script is used to map reads to the donor-specific graph genomes, and then
# extract the reads which map to heterozygous locations for further counting
# and significance assessment.
#
# ... |
5a810adcbfad11d40c1cb3a820739584fc356148f65d6b74eafeba7ca1d06eb8 | Shell | 6,681 | 164 | #!/bin/bash
# 'KAS-Analyzer motif' was developed by Ruitu Lyu on 12-22-2021.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer motif [ -h/--help ] [ -t threads ] [ -o prefix ] [ -s assembly id ] [ -e enhancer position file ] [ -c control position file ] "
exampleHelp="Example: nohup KAS-Analyzer ... |
363f5587505923d6e60749cccc460794a65fc47bc75c741dc1e983857d6a1629 | Shell | 6,683 | 169 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2:-""}
output_dir=${3:-""}
input_json="$(realpath "${input_json}")"
if... |
df4dfe7e666cb4615e5e56b80d53b0d7a663b67685c5ce30c1a895da030c20e6 | Shell | 6,694 | 175 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2:-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if ... |
adce576ac338a2fce6d661b18793567c3e722d65c934fcab0237b7c6686a5fce | Shell | 6,746 | 173 | #!/bin/bash
# 'KAS-Analyzer RNaseH' was developed by Ruitu Lyu on 12-15-2022.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer RNaseH [ -h/--help ] [ -p threads ] [ -o prefix ] [ -r WT_R-loop.bed ] [ -f fold change ] [ -c WT_R-loop_density.txt ] [ -t RNaseH_R-loop_density.txt ]"
exampleHelp="Exa... |
ae05e792e1e9b5e739636f590897eac55bc98580137dbef9172773360063906b | Shell | 6,784 | 181 | #!/bin/bash
# STAR mapping / RSEM quantification pipeline
# usage: from an empty working directory, run
# ./STAR_RSEM.sh (read1) (read2 or "") (STARgenomeDir) (RSEMrefDir) (dataType) (nThreadsSTAR) (nThreadsRSEM)
# input: gzipped fastq file read1 [read2 for paired-end]
# STAR genome directory, RSEM reference ... |
c9bef787b70f0504b3aa1a476dc256577a93529fe8b36335a6bb7cadcf841332 | Shell | 6,786 | 192 | #!/bin/bash
set -Exeuo pipefail
function getJavaMem() {
# get JVM memory in MiB by getting total memory from /proc/meminfo
# and multiplying by java_mem_fraction
local mem_fraction=${java_mem_fraction:=0.85}
cat /proc/meminfo | \
awk -v MEM_FIELD="$1" -v frac="${mem_fraction}" '{
f[substr($1, 1, le... |
d7943fc421e466e825defd2814171ce8d189ae12646907bf30d8328d0f4d436b | Shell | 6,806 | 176 | #!/bin/bash
#
# The script runs our nnUNet model on the subject sub-01 with 10 sessions from the open-access courtois-neuromod dataset
# to evaluate the inter-subject stability.
#
# Namely:
# - segment spinal cord (using SCT)
# - detect PMJ label (using SCT)
# - segment rootlets (using our nnUNet model)
# - run... |
b2b8d42f8c6a2d785e1d7fa5dbd866fcef5fdc154da1d989322a2ddb06277b2d | Shell | 6,810 | 175 | #!/bin/bash
#
# The script runs our nnUNet model on a 10 subjects (2 sessions) from the marseille-rootlets dataset (private) to
# evaluate the inter-session stability.
#
# Namely:
# - segment spinal cord (using SCT)
# - detect PMJ label (using SCT)
# - segment rootlets (using our nnUNet model)
# - run inter-rat... |
e244f2905b29276fe245cbb203a853933861fc04e80e0e2393b5df33a2d2451f | Shell | 6,828 | 174 | #!/bin/bash
#
# The script runs our nnUNet model on a single subject with 19 sessions from the open-access spine-generic single-subject
# dataset (https://github.com/spine-generic/data-single-subject) to evaluate the inter-subject stability.
#
# Namely:
# - segment spinal cord (using SCT)
# - detect PMJ label (usin... |
70682e8f820803a6b25265b19f8ef870ef397d16e218e4ee08f3c3ff1ec7b3bf | Shell | 6,856 | 95 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=15:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
a3307aeb451ecf71b1349d519b047109356401d2de64167f28aca67f842597ab | Shell | 6,882 | 201 | #!/bin/bash
# This script is a bash implementation of the following workflow/task in WDL:
# Filename: wdl/Scramble.wdl
# Workflow: Scramble
set -Exeuo pipefail
if [ -z "${SV_SHELL_CLEAN_UP_WORKING_DIR:-}" ]; then
SV_SHELL_CLEAN_UP_WORKING_DIR=true
fi
# -------------------------------------------------------
# ===... |
f355db10cc83a3450d5b57978d4cedee4c6e3f17f4aaa431374c2b1d32e33b15 | Shell | 6,890 | 90 | #!/bin/bash
# Delete files that are surplus to requirements
rm ./tmp/footer.js
rm ./tmp/news.png
rm ./tmp/manual.png
rm ./tmp/oct.png
# Move custom javascript and css documents to a subfolder in the dir containing index.html
mkdir ./tmp/statistics-resampling/site-files
cp ./templates/javascript.js ./tmp/statistics-re... |
d70d5540a50b77b0808aa2a4ce598cd34ff3068794c61e213b2f194e97d451b0 | Shell | 6,899 | 46 | perl -I ../lib ../scripts/perl/addMatrixHeaders.pl -i ../sample-data/addMatrixHeaders/5C.naked.matrix.gz --xhf ../sample-data/addMatrixHeaders/5C.xHeaders.gz --yhf ../sample-data/addMatrixHeaders/5C.yHeaders.gz
perl -I ../lib ../scripts/perl/aggregateBED.pl -i ../sample-data/aggregrateBED/chrX.bed.gz --a mm9 --wsize 40... |
e2388228ec6cb0d752dfc8000efcefe1daf0d185cd30d753a3d0694b28f64ac7 | Shell | 6,902 | 170 | #!/bin/bash
set -ex
export CI="true"
export PYTHON="3.10"
export RAY_BUILD_ENV="macos-py${PYTHON}"
export RAY_USE_RANDOM_PORTS="1"
export RAY_DEFAULT_BUILD="1"
export LC_ALL="en_US.UTF-8"
export LANG="en_US.UTF-8"
export BUILD="1"
export DL="1"
export TORCH_VERSION=2.3.0
export TORCHVISION_VERSION=0.18.0
filter_out_... |
949a7e2b3e472e64f2350fa1ff53f7ccdefdd00ee53dce6c01e20997a1909511 | Shell | 6,959 | 181 | #!/bin/bash
set -Exeuo pipefail
if [ -z "${SV_SHELL_CLEAN_UP_WORKING_DIR:-}" ]; then
SV_SHELL_CLEAN_UP_WORKING_DIR=true
fi
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
o... |
ceede6149ae434697ce9ff5f157d9b05be12c841df20c2da9bcf1b26810a4f2f | Shell | 6,965 | 89 | #! /bin/bash
# Format of arguments:
# --promoterUpstream $1 --promoterDownstream $2 --coaccessCutoff $3 --maxNdistalSites $4 --peakSize $5
qsub -P trapnelllab -l mfree=40G -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_26_setup_ATAC_to_expr_data_nobackup/ /net/trapnell/vol1/home/readdf/trapLabDir... |
9c795c9091bcb562393c5dbcf9e2dd382ba0478c3170bbf6bfd9b2f15979e7a8 | Shell | 7,099 | 220 | #!/bin/bash
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer trim [ -h ] [ -a adapter ] [ -t threads ] [ -f ] [ -q quality ] [ -l length ] [ -1 read1 ] [ -2 read2 ]"
exampleHelp="Example:
Single-end:
nohup KAS-Analyzer trim -a i... |
3fd91f6760a5f76e20b66f148c6088c528123d4702d624004e425ac10d56e512 | Shell | 7,101 | 171 | #!/bin/bash
# align-star-pe.sh
main() {
# Now in resources/usr/bin
#echo "* Download and install STAR..."
#git clone https://github.com/alexdobin/STAR
#(cd STAR; git checkout tags/STAR_2.4.0k)
#(cd STAR; make)
#wget https://github.com/samtools/samtools/archive/0.1.19.tar.gz
# If available,... |
ce98371f5e93928538925cc9f3e11eae09092de5f5fcc4710aab221df419c5c2 | Shell | 7,109 | 181 | #!/bin/bash
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer idr [ -h ] [ -1 rep1 peaklist ] [ -2 rep2 peaklist ] [ -c peak caller] [ -t file type ] [ -r rank ] [ -o output file ]"
exampleHelp="Example:
narrowPeak (macs2):
nohup K... |
ffa5cd7807576c553ccbda70782fcaca1b331629b7444d07e49bd32289d45fb4 | Shell | 7,185 | 224 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2:-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
d3d70df4e5ba4e2bc5e12c51fce3acbc1de5b38c0eaa8e21ec8b90d327cf8f77 | Shell | 7,306 | 207 | #!/bin/bash
#-------------------------------------------------------------------------------
# This software has been developed by:
#
# Dpto. Sistemas y Recursos Naturales
# ETSI Montes, Forestal y del Medio Natural
# Universidad Politecnica de Madrid
# https://github.com/ggfhf/
#
# Licence: GNU General P... |
e3339e8ba0b96dca01e21ade7c170dd5957318817e763df254ee18d5fc73bb5c | Shell | 7,333 | 159 | #1. found the SNPs that need to be removed from subsequent.
cd /mnt/scratch/quanjian/WGS/orginial_rawdata/fq2gvcf/genotypeGVCF
# extract individual data from merged VCF file
bcftools view -s DB2,LS2,LB2,DS2 allChr.snp.excessHet.hardFilter.vcf.gz > F0_Stage70.snp.excessHet.hardFilter.vcf
# ectract genotype informa... |
b546be3c30c6b303d6754123426da78e67bee56d5b720690261581f1aa73a288 | Shell | 7,336 | 221 | #!/bin/bash
set -Exeuo pipefail
function MergeSample() {
local _sample_id=$1
local _std_cnmops=$2
local _large_cnmops=$3
local _gcnv=$4
local _dragen=$5
local _max_dist="${6:-"0.25"}"
echo "----------- Starting MergeSample -------------"
echo "_std_cnmops: ${_std_cnmops}"
echo "_large_cnmops: ${_la... |
37a878bcf2e31a2eccd935003d443d58a855e3e6ded73a69f656ad0a8bbfe8c4 | Shell | 7,338 | 209 | #!/usr/bin/env bash
# Script to generate tensors from UKBB data
################### VARIABLES ############################################
TENSOR_PATH=
NUM_JOBS=20
SAMPLE_IDS_START=1000000
SAMPLE_IDS_END=6030000
XML_FIELD= # exclude ecg data
MRI_FIELD= # exclude mri data
RECIPES_ARGS=
TENSORIZE_MODE="tensorize"
EN... |
0b9e1bedac147cddf9d27a2dd1f25bce4c09dbbffeb43cdd899a24e3496d4dfd | Shell | 7,367 | 208 | #!/bin/bash
#-------------------------------------------------------------------------------
# This software has been developed by:
#
# GI en Desarrollo de Especies y Comunidades Leñosas (WooSp)
# Dpto. Sistemas y Recursos Naturales
# ETSI Montes, Forestal y del Medio Natural
# Universidad Politecnica de ... |
6cbbe379cfd7358d8c844937d8face2a47d08079e19895b6960cf12d3e95c686 | Shell | 7,387 | 276 | #!/bin/bash
## HiC-Pro
## Copyleft 2017 Institut Curie
## Author(s): Nicolas Servant
## Contact: nicolas.servant@curie.fr
## This software is distributed without any guarantee under the terms of the BSD licence
##
## First version of converter between HiCPro and higlass.
## The cooler python package should... |
7acec80ef44f939915683fd0451e55555ddcc826fdd1fde73aa129fd5446787f | Shell | 7,497 | 21 | PARTITION=$1
GPUS=${GPUS:-8}
GPUS_PER_NODE=${GPUS_PER_NODE:-8}
CPUS_PER_TASK=${CPUS_PER_TASK:-5}
SRUN_ARGS=${SRUN_ARGS:-""}
log_dir="work_dirs/slurm_logs"
mkdir -p "$log_dir"
SRUN_ARGS=${SRUN_ARGS} GPUS=$GPUS GPUS_PER_NODE=$GPUS_PER_NODE CPUS_PER_TASK=$CPUS_PRE_TASK ./tools/slurm_train.sh $PARTITION urpc2020-at... |
0464d8501a92706131f41664710fa10f1b9304ad1d5c8cbcf272454ffa0904ed | Shell | 7,524 | 190 | #!/bin/bash
#
# The script runs our nnUNet model on a single subject (sub-010_ses-headUp) from the Spinal Cord Head Position MRI
# dataset (https://openneuro.org/datasets/ds004507/versions/1.0.1). 0.6mm iso T2w image of this subject was resampled
# to 0.8mm, 1.0mm, 1.2mm, 1.4mm, and 1.6mm iso resolution using the sct_r... |
d83e57dd70da5630fd165fbc8e808607fcb53b8657be176973da0c385cc0c38a | Shell | 7,632 | 216 | #!/bin/bash
# By running this script you can fully replicate the results from our paper
# See Readme.md for more info
# ------
# Step 0 -- Set environment variables
# ------
## 0.1 Folders
I=intermediates ### Here you will save the intermediate files. Modify if needed
R=results ### Here you will save the final... |
d1613347f31e4f58a9ae9c87a73b3da401011e2f41990d0ff999b940e8e80dd0 | Shell | 7,891 | 204 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
a78dd475c3167f500206fd093ea411bf0252867bbaebf342e58c2f57447af3f2 | Shell | 8,066 | 322 | ## hic.inc.sh
##
## Copyright (c) 2015 Institut Curie
## Author(s): Eric Viara, 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
###########################... |
3715405e6f0a051dae4676ce7c38abca45021a581055a0629fbdc2f8c583f30d | Shell | 8,105 | 275 | #!/bin/bash
#-------------------------------------------------------------------------------
# This software has been developed by:
#
# Dpto. Sistemas y Recursos Naturales
# ETSI Montes, Forestal y del Medio Natural
# Universidad Politecnica de Madrid
# https://github.com/ggfhf/
#
# Licence: GNU General P... |
8d7c1d02e40a0fa4ec7d3b0bf64ef3cc0b79c729424e795d568bbf27b3f33dbb | Shell | 8,180 | 276 | #!/bin/bash
#-------------------------------------------------------------------------------
# This software has been developed by:
#
# GI en Desarrollo de Especies y Comunidades Leñosas (WooSp)
# Dpto. Sistemas y Recursos Naturales
# ETSI Montes, Forestal y del Medio Natural
# Universidad Politecnica de ... |
6726444f646c96653cb0ef8ab8e80d15495829f1df32cec8940a2a1d07888d46 | Shell | 8,200 | 175 | #!/bin/bash
#
# This script performs:
# - segmentation of rootlets from T2w data (model model-spinal-rootlets_ventral_D106_r20240523),
# - segmentation of spinal cord from T2w data (sct_deepseg_sc)
# - segmentation of vertebral levels from T2w data (sct_label_vertebrae)
# - detection of PMJ from T2w data (sct_detect_pm... |
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