sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
1170d6b0f561d5ad7b783393ff7e995de758c868e7d125bd38c277feb021d733 | Shell | 4,682 | 109 | #!/bin/bash
#SBATCH -c 16
#SBATCH -t 2-12:00
#SBATCH -p medium
#SBATCH --mem-per-cpu=15G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_production_v888v2_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_production_v888v2_%j.err
###############################################################################
# v... |
588f5df626620cb12dcd23b9677da03209e8976dee28f6a48e7d1a286eabdc1b | Shell | 4,684 | 106 | #!/usr/bin/env bash
#
# profile.sh — reproducible salmon quant profiling harness (Phase 1).
#
# Builds the `profiling` cargo profile (release + line-table debug info, unstripped
# — see [profile.profiling] in the root Cargo.toml; the shipped release/dist binary
# is unaffected) and runs `salmon quant` under a sampling ... |
6c1c31f1316762dc8de27f55c18f1d4eab30c36ff1a656db80c588b0af27682b | Shell | 4,686 | 126 | #!/bin/bash
# Copyright 2020 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
acd010fab77e41f8d8936f0674cda673a3abfad7c957f57a437c9fb5d88ebfb4 | Shell | 4,695 | 125 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO PREPROCESS THE FUNCTIONAL SCAN (INTEGRATE AFNI AND FSL)
##
## R-fMRI master: Xi-Nian Zuo. Aug. 13, 2011; Revised at IPCAS, Dec. 12, 2015; Jul. 14, 2017.
## R-f... |
b3202a997ed759eb04831bc17f495b829e41c5314ea5f18d9d288ddaf2330d6d | Shell | 4,702 | 104 | #!/bin/bash
#SBATCH -c 4
#SBATCH -t 0-15:00 # 15h walltime on medium (each stage
# ~30m-4h, 4 stages, leaves headroom)
#SBATCH -p medium
#SBATCH --mem=250G # data-push step OOMed at 150G last run
#SBATCH -o jobs/banc_edgelist_rebuil... |
bf750ce31322affbb7c2183308e633d06c47c4568d4191d1c184e391110119b7 | Shell | 4,726 | 120 | #!/bin/bash
#SBATCH -c 8
#SBATCH -t 0-06:00
#SBATCH -p short
#SBATCH --mem=96G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_optic_sweep_%A_%a.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_optic_sweep_%A_%a.err
#SBATCH --array=0-12
# Memory note: NTAC shards 9-12 (anchor frac >= 50%) OOM-killed at 32G on
# job 3658... |
6c59b4e803759924b74deecafc80d763581efa2f7080b546de13cffbc3eedf83 | Shell | 4,733 | 149 | #!/bin/bash
# Function to locate MATLAB
find_matlab() {
# Determine the platform
local platform=$(uname -s)
# Paths for macOS installation
if [[ "$platform" == "Darwin" ]]; then
# Common installation directory for macOS
local matlab_base="/Applications"
# Find MATLAB .app bund... |
59745d113c7bb890025f064b14e905a41ace647d09f0749b7608e6bcf560c226 | Shell | 4,743 | 169 | #!/usr/bin/env bash
set -euo pipefail
BG="../data/fmri/sub-template_T1w_template_brain.nii.gz"
CA12_L="../data/fmri/masks/sub-template_FULLCA12_L.nii.gz"
CA12_R="../data/fmri/masks/sub-template_FULLCA12_R.nii.gz"
DGCA3_L="../data/fmri/masks/sub-template_FULLDGCA3_L.nii.gz"
DGCA3_R="../data/fmri/masks/sub-template_FUL... |
dfa712888b5643d86bdc21adc26941061ffddce591bc39a3a5e336cd5caef3cf | Shell | 4,743 | 129 | #!/bin/sh
#============================================================
# iso2mesh inline documentation to wiki convertor
#
# Author: Qianqian Fang <q.fang at neu.edu>
#============================================================
printhelp=$1
if [ "$#" -ge 1 ]; then
echo "iso2mesh >> Iso2Mesh"
fi
print_help()
{... |
e6f4fce394ba1c14435151a0f362eec29527f832dede1578753021becee90f23 | Shell | 4,744 | 145 | #!/bin/bash
#parse arguments
die() {
printf '%s\n' "$1" >&2
exit 1
}
_help() {
printf "Usage: map_genes.sh [--tr1] [--t1] [--n1] [--tr2] [--t2] [--n2]\n\t[--tr1]: path to transcriptome/proteome 1\n\t[--t1]: is 1 a transcriptome [nucl] or proteome [prot]\n\t[--n1]: two character identifier of 1\n\t[--tr2]: path to ... |
be4134333647ecce608190dc9fc0074096c0c464be0aeaf2adb88b78c7112fb7 | Shell | 4,766 | 140 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# retrieve input argument to find correct instructions
instructDir="$1"
# ------------------- #
# GENERAL DEFINITIONS
# ------------------- #
source $MRCATDIR/setupMrCat.sh
structRootDir="/Vo... |
de92942b677926a35420eb134871ec95aa950dd4cd1dd3d8bf511cdcec6243a1 | Shell | 4,766 | 128 | #!/bin/bash
# Get top level of git repo
git --version > /dev/null
if [ $? -ne 0 ]
then
echo "Could not find git executable"
exit 1
fi
top_level=$(git rev-parse --show-toplevel)
if [ -z "$top_level" ]
then
echo "This is not a git repository"
exit 1
fi
if ! hash sed 2>/dev/null; then
echo "'sed' is not inst... |
555900ef8bafad81d532048d359856472a0cfdf03bd9d7342207e19f518a86f9 | Shell | 4,770 | 158 | #!/bin/sh
#
# Copyright (C) 2014 Genome Research Ltd.
#
# Author: James Bonfield <jkb@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including with... |
7562e46d4af1bef9847aecc8791747246d433ef5f635700b67cfd693047675d7 | Shell | 4,791 | 118 | ##################################
# pull docker image into singularity
singularity pull docker://cibersortx/fractions
singularity pull docker://cibersortx/hires
singularity pull docker://cibersortx/gep
GSE="GSE185862"
mixture="CIBERSORTx_adjusted_merged_matrix_TPM_M.txt"
# Define array of GOIs (Genes of Interest)
G... |
76bc9d8b5ed32a5ada9e59697dd0f6af8cdc3fd8d4270d5cbe4e82caa42b4bbb | Shell | 4,830 | 136 | #!/bin/bash
echo "The Heart modelling code is under ${HEART_MODELLING_CODE}"
echo "The Data is under ${PAPER3_DATA}"
#for i in 10 11 12
#do
# echo "MAKING CS SAMPLE ${i} --------------------------------------------------------------------------"
#
# python ${HEART_MODELLING_CODE}/auxiliar/conductionSystem/projectSu... |
245f24098512e17516b9b09f311c9405c2a72bef851defc6f851781615e97e4b | Shell | 4,845 | 120 | #!/bin/bash
export path_htsa_dir=$1
export path_pipeline=$2
export project_work_dir=$3
export work_fasta=$4
export PB_dir=$5
export aggregated_work_dir=$6
echo "annotating metagenomic sequences according using paracel blast..."
if [ -d $PB_dir ];
then
rm -r $PB_dir
fi
mkdir $PB_dir
cd $PB_dir
if [ -f $work_fast... |
41a296ba163d1c33e5e1a941931f0e2eb8ec9c015b0095784cb3fb869d29acda | Shell | 4,849 | 152 | #!/bin/bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); yo... |
f19b27375a43fa4034403e8203ed443eb48ec86ad092ad782310e452b4f01f7e | Shell | 4,854 | 97 | #!/usr/bin/env bash
set -euo pipefail
repo_root="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
stage_sql="${repo_root}/sofa2_sql/02_stage_components.sql"
score_sql="${repo_root}/sofa2_sql/03_hourly_raw_scores.sql"
window_sql="${repo_root}/sofa2_sql/04_window_final_scores.sql"
firstday_sql="${repo_root}/sofa2_sql/0... |
7044bd40dc48475753b12b3adf72af55a8d2167d027941742eb2fbe127cd8b32 | Shell | 4,856 | 122 | #!/bin/bash
set -e -u
script_name="SubcorticalProcessingASL.sh"
echo "${script_name}: START"
ASLVariable="$1"
echo "${script_name}: ASLVariable: ${ASLVariable}"
AtlasSpaceFolder="$2"
echo "${script_name}: AtlasSpaceFolder: ${AtlasSpaceFolder}"
ResultsFolder="$3"
echo "${script_name}: ResultsFolder: ${ResultsFol... |
54942ac92547efce12ada2f2dbcc485255389485f6b8dc6edc4cf86706c2a229 | Shell | 4,872 | 108 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO IMAGE REGISTRATION (FLIRT/FNIRT)
##
## R-fMRI master: Xi-Nian Zuo. Dec. 07, 2010, Institute of Psychology, CAS.
##
## Last Modified: Sept., 21, 2014.
## Ema... |
c373aa876850b03322bb32ee8d621040fe6acd908d961fa1fbd2175aacbe43f8 | Shell | 4,888 | 148 | #!/usr/bin/env bash
# extractSmoothness.sh
# Compute ACF-based effective FWHM (gaussian_NEWmodel) from AFNI 3dFWHMx
# for both multiecho-combined and single-echo (echo-2) images, at kernels 0 and 5 mm.
# Writes a TSV: sub ses task run acq kernel_mm fwhm_eff img
# Run with bash (not sh).
set -Eeuo pipefail
# --... |
b4e47059adbe0ddb762ccfbe6208400705dd2fc024bfad70bc9b0136f7c36980 | Shell | 4,896 | 117 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO QUALITY ASSURANCE OF ANATOMICAL SURFACE PROCESSING
##
## !!!!!*****ALWAYS CHECK YOUR SURFACES*****!!!!!
##
## Thanks go to Thomas Yeo for sharing his excell... |
746677783b1786f175b1b06e278cb6150605ed12d776cfd1973347468ffd2c72 | Shell | 4,897 | 165 | #!/bin/bash
# Setup script for Python environment for fly connectome tutorials
# Creates conda environment "sjcabs" with all required dependencies
set -e # Exit on error
echo "=========================================="
echo "Fly Connectome Tutorial - Python Setup"
echo "=========================================="
e... |
6d0ca42f03fb23a45be56ef0816a9c5aa67a6c26310d00e05b55928fab87c782 | Shell | 4,951 | 120 | #!/bin/bash
## check that STAR temporary dir is removed for all samples, and that archived unmapped reads are created
>&2 echo "Checking that all STARsolo jobs went to completion .."
for i in *
do
if [[ -d $i && -d $i/output && -s $i/Log.final.out ]]
then
if [[ -d $i/_STARtmp ]]
then
>&2 echo "WARN... |
d69af499e9f10cff22337498c2177f9601ad6521aa7e2da66149cf5da3d46eba | Shell | 4,962 | 115 | #!/bin/bash
#numbers=(2 4 12 14 17)
#for num in "${numbers[@]}"; do
# echo "Sample 4: AHA $num"
# python /mnt/d/Code/HeartModelling/generateSimFiles/genS1AHAFromTemplate.py \
# --templatePath /mnt/d/Paper4/Simulations/invivo/mi_EHT1/sample4/settings_mi_CL600_1800ms_stimAHA1_first3beats.json \
# --stimAHA ... |
888751a57e6bede13621e41c664727cfa9a8a8dab6951879001e3fb0331802a2 | Shell | 4,975 | 135 | #!/bin/bash
#
#This is a shell program to batch reconstruct images using 10 different methods using NeuronAssember.
#
function write_neuron_tracing_command {
outputScript=$1;
METHOD=$2;
vaa3dProgramPath=$3;
inimgfileTracing=$4;
finalfileFolder=$5;
smooth_inimgfileTracing=${inimgfileTracing}.g.v3draw;
#... |
9c73e6d0dc7b752ebdb8c8d2ef27d112419406ad51bda7548a96d66a9ce39a29 | Shell | 4,979 | 144 | #!/bin/bash
# Installation script for Membrane Kymograph Generator
# This script installs the application system-wide
set -e # Exit on error
# Colors for output
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
NC='\033[0m' # No Color
# Installation directories
INSTALL_DIR="/opt/membrane-kymograph"
BIN_LINK="... |
89b4e227b9002248184d8463c8ebc995abdb764dfeac1965dce8612f42532313 | Shell | 4,996 | 124 | #!/bin/bash
#PBS -l walltime=8:00:00
#PBS -N warpkit
#PBS -q normal
#PBS -l nodes=1:ppn=28
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
IFS=' ' read -r -a pairs <<< "$PAIRS"
maindir=/gpfs/scratch/tug87422/smithlab-shared/night-owls
toolsdir=/gpfs/scratch/tug87422... |
3536ab11491168388317145ce7aeceaf960d3e109189be087aa591df7e798e37 | Shell | 5,005 | 137 | ## Setting up base directory values
user_dir="/data/nsm/velottalab/riley/manuscript_pipeline"
tmp_dir="${user_dir}/data/tmp"
mkdir -p ${tmp_dir}
scripts_dir="${user_dir}/scripts"
### 1 - Trimming & FastQC ###
raw_reads_dir="/data/nsm/velottalab/rawdata/fish/alewife_wgs_n110"
trim_dir="${user_dir}/data/trim"
mkdir -p ... |
78d4aa10cbe0edf515853a1e1258a9667729bc9d8b5f601501035597946cb89c | Shell | 5,018 | 89 | #!/bin/bash
subj=$1
run(){
echo "$@"
"$@"
if [ ! $? -eq 0 ]; then
echo "failed"
exit 1
fi
}
T1=restore/T1/${subj}.nii.gz
T2=restore/T2/${subj}.nii.gz
outwb=surfaces/$subj/workbench
outtmp=surfaces/$subj/temp
LeftGreyRibbonValue="3"
LeftGreyRibbonValueIn="2"
RightGreyRibbonValue="42"
RightGreyRibbon... |
3f5e3f382ce11d4fd61f0c4b96516ed634088796b2bef5cff4367a215abe88e1 | Shell | 5,086 | 170 | #!/bin/bash
# Process monitor for DP_GP_cluster with auto-restart capability
# Usage: ./monitor_dp_gp.sh [--auto-restart] [--max-attempts=N]
set -euo pipefail
# Default configuration
AUTO_RESTART=false
MAX_ATTEMPTS=3
CHECK_INTERVAL=300 # 5 minutes
LOG_DIR="logs"
MONITOR_LOG="${LOG_DIR}/monitor_$(date +%Y%m%d_%H%M%S... |
2499a233aabe7c4441befad620717fadd4ba73a741710de5dec99b21a4abaa64 | Shell | 5,092 | 118 | #!/bin/sh
# This function replicates the variance component model results in the HCP dataset shown in Li et al., 2019
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################
# setup for CIRC cluster
########################
curr_dir=$(p... |
de06c86a5264b1814bf54d067cd5501fbe4894757fafa0cee00c2e5111f6e48d | Shell | 5,112 | 74 | #!/bin/bash
export path_htsa_dir=$1
export path_pipeline=$2
export diginorm_work_dir=$3
export PAIR1=$4
export PAIR2=$5
########################################
#DIGINORM
########################################
if [ -d $diginorm_work_dir ];
then
rm -r $diginorm_work_dir
fi
mkdir $diginorm_work_dir
cd $diginorm_w... |
16d1839682cfee91e6c091bb6a03c26c696b579d893c429ebd05d705905aaa5e | Shell | 5,116 | 121 | #!/bin/bash
#/media/StorageOne/HTS/VirusMeta/SAM_BAM/circos_plot_cov/circos_pipeline.sh /media/StorageOne/HTS/Projects/2011_N17_Viraskin2-HiSeq /media/StorageOne/HTS/Projects/2011_N17_Viraskin2-HiSeq/anecto_virus.fasta /media/StorageOne/HTS/Projects/2011_N17_Viraskin2-HiSeq/Data/Intensities/BaseCalls/forward.fastq /med... |
dfecbbdaca8114e1712344f92f420150eded710789a0caa45b6aafb6cc16b8d3 | Shell | 5,133 | 186 | #!/usr/bin/env bash
set -euo pipefail
usage() {
cat <<'EOF'
Usage:
scripts/release_smoke_test.sh local
scripts/release_smoke_test.sh pypi
scripts/release_smoke_test.sh open
Environment variables:
PYTHON Python executable to use for venv creation (default: python3)
UV ... |
30359a009bf06109cd25ef189cd111add3be287077044e6e51aac5e0038c21ed | Shell | 5,160 | 95 | #!/bin/bash
export work_fasta=$1
export project_work_dir=$2
export NR_dir=$3
export PB_dir=$4
export aggregated_dir=$5
export path_htsa_dir=/media/StorageOne/HTS
echo "annotating gis with taxonomy..."
#Privide each gi with species names
awk 'NR==FNR{hash[$1];next} ($1 in hash) {print $1,$3}' gi.blast_results $path... |
2beba9642aec0ec2ac65f1531222b0760760a9b778393955210ff5401394da10 | Shell | 5,176 | 149 | #!/bin/bash
if [ "$1" == "" ] || [ "$2" == "" ] || [ "$3" == "" ]
then
echo "ERROR: Usage: \"$0\" \"INPUT_DATA_DIR\" \"OUTPUT_DIR\" \"TYPE_BACKEND\" (= [--torch, --keras])"
exit 1
fi
input_data_dir=$1
output_dir=$2
type_backend=$3
workdir=$PWD
if [ "$type_backend" == "--torch" ]
then
in_rel_model_file="... |
ef1211f0dc9df9616a94f042a16e5755209e4e2c5b4ad8007d7cb79a412c2c7f | Shell | 5,179 | 88 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# ------------------- #
# GENERAL DEFINITIONS
# ------------------- #
source $MRCATDIR/setupMrCat.sh
studyDir="/Volumes/rsfMRI/anaesthesia"
anaDir="$studyDir/analysis"
mkdir -p $anaDir/dconn
... |
3143f4ee7499fd5fd03609f8cecef8153953f600e1e7e2f2cf7df401a9526754 | Shell | 5,180 | 77 | #!/bin/sh
export path_htsa_dir=/media/StorageOne/HTS #path to HTSA analysis dir
export path_pipeline=VirusMeta
work_file_directory=$1
fasta_file=$2
if [ ! -d "$work_file_directory" ]; then
mkdir "$work_file_directory"
fi
#prepare fasta file and replace _ with @ in ids
sed -i '/^>/s/.fasta/_fasta/g' $fasta_f... |
43291be032ad694bfb456ec509112af6bfba0b57de2da943db4a6c5644e81cba | Shell | 5,187 | 129 | #!/bin/bash
#SBATCH --job-name=soMAPHIC_scaffolds
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=250G
#SBATCH --error=joblog_error_mapHiC_scaffolds_%A_%a.txt
#SBATCH --output=joblog_output_mapHiC_scaffolds_%A_%a.txt
#SBATCH --array=0-1
#### source library... |
9fa7f0a9de3ae4e1caaa317da88f7b42b36e422a4262d1ca2a7cb49fdd0863e9 | Shell | 5,210 | 145 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Tue Apr 28 2020 00:37:21 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
d0e95e68631ddc1214940d48589889dedbe333ff52e62a62edd74d09e9bb905e | Shell | 5,222 | 93 | #!/bin/bash
set -e -u
echo -e "\n START: RibbonVolumeToSurfaceMapping"
Subject="$1" #"${SubjectID}_V1_MR"
ASLFolder="$2" #"$StudyFolder/$SubjectID/T1w/ASL/perfusion_estimation/native_space"
ASLVariable="$3" #"perfusion_calib"
ASLVariableVar="$4" # e.g. perfusion_var_calib
T1WorkingDirectory="$5" #"$StudyFolder/$Subj... |
38a6222e84a04ef40509f54ff8c91a21ecc0e3002e8a8e027dd2e59cbb075808 | Shell | 5,226 | 129 | #!/usr/bin/env bash
umask 0000
# This script will perform Level 1 statistics in FSL.
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
logdir=/gpfs/scratch/tug87422/smithlab-shared/nig... |
72ce5da276596bb8bc042a329c74bbe5a3973f5f8e37807a5ba300a20076c942 | Shell | 5,227 | 129 | #!/usr/bin/env bash
umask 0000
# This script will perform Level 1 statistics in FSL.
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
logdir=/gpfs/scratch/tug87422/smithlab-shared/nig... |
10950be3a4399b03e0f1a90f6170a4f4be0a8533ec77743c5c3f92e3c525dec6 | Shell | 5,239 | 140 | #!/usr/bin/env bash
#
# Performance-regression gate.
#
# Runs every perf_* benchmark in two build directories (the PR build and the
# base-branch build) under callgrind and compares their instruction counts.
# Instruction counts are deterministic (independent of CI runner load), so this
# is not flaky like wall-clock t... |
fb7b754990ce7828d1440842fa929e5b05892bec026bff5ce048eff6d8fbb1b9 | Shell | 5,240 | 157 | #!/bin/bash -l
######################################################################
## This script is used to compile libraries and to build Python
## distribution for OpenMM with CUDA support.
##
## Build artifacts (.whl and .tar.gz files) and an installation script
## (install.sh) are stored in the `output` direct... |
c6640adf9203140a425e66efc3b984e7a380bcd1529f3c0a562932b59237e659 | Shell | 5,265 | 105 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO CALCULATE ICA-BASED RESTING-STATE FUNCTIONAL CONNECTIVITY
##
## This script can be run on its own, by filling in the appropriate parameters
##
## Written by Xi... |
2e994e3a036a740bd31b83dca8896671edbeef0351b100acf24726099be6faf8 | Shell | 5,266 | 139 | #!/bin/bash
# This script will download and attempt to build and install
# 4dfp tools locally.
tools_dir=$(realpath $(dirname $(command -v $0)))
pushd $tools_dir > /dev/null
# if arg1 is 1, dont't use gcc > 7 flags
OLD_GCC=0
if [[ $# -gt 0 ]]; then
if [[ $1 -eq 1 ]]; then
OLD_GCC=1
fi
fi
# check if fi... |
5384d85b0a20c78a6927f59e72fef8e1fbf669bd47127dd5257e94c4db390ac7 | Shell | 5,283 | 156 | #!/bin/bash
source $FREESURFER_HOME/SetUpFreeSurfer.sh
Usage() {
echo " "
echo "Usage: `basename $0` [options] -s <Subject folder> "
echo ""
echo " Compulsory Arguments "
echo "-s <subject directory> : preprocesed directory containing all surface and fill files"
echo " Optional... |
60e6a7561b8f37709eb97bdbe1e65be707d2e4a886ec2e41516289c994f1ef09 | Shell | 5,287 | 119 | #!/bin/bash
# This is an example of our "registration fusion" implementation, modeled after
# Wu, Ngo, Greve, et al. (2018) Human Brain Mapping.
#
# this script is run within an fmriprep 20.2.3 (LTS) singularity container.
# it produces left and right hemispheric projections into volumetric space
# for a specified sub... |
8d03f6d9b9683aa3f152c3f52763e5d60680bf28a48aaa17efd8c218d708c440 | Shell | 5,287 | 125 | #!/bin/bash
is_float() {
[[ $1 =~ ^-?[0-9]*\.?[0-9]+$ ]]
}
NMOLECULES=16
BETA=10.0
# BETA="100.0"
#dataset_path="../../../Datasets/PDBBindOriginalCleaned/cleaned_dataset";
dataset_path="../../Datasets/PDBBind"
output_path="generated_250303_bb"
OPTIONS=$(getopt -o g --long use-glide -- "$@")
# OPTIONS=$(getopt -o ... |
335bc56b2be6a6019db193b3848b8b9f995120143b0a5e3d83784ca0e3d7c2bf | Shell | 5,311 | 92 | #!/bin/bash
export work_fasta=$1
export project_work_dir=$2
export path_htsa_dir=/media/StorageOne/HTS
echo "annotating gis with taxonomy..."
#Privide each gi with species names
awk 'NR==FNR{hash[$1];next} ($1 in hash) {print $1,$3}' gi.blast_results $path_htsa_dir/PublicData/taxdb_nt/gi_taxid_name.txt > gi_divisi... |
7e17d82a71c922d7799f56294e977bd4a00babb1addf654af2a5dc46e8bc1852 | Shell | 5,311 | 155 | #!/bin/bash
# This script lives in each of the upstream repos. Add this to .travis.yml to
# run after each successful build (assuming that the script is in the root of
# the repo):
# after_success:
# - ./trigger-dependent-build
#
# There are three variables to set - `$auth_token`, `$endpoint`, and
# `$repo_id` -... |
4908836ae28710bd54b5b3761df9542b6bc90f0b0fe0776ee70bb7ae26a27279 | Shell | 5,323 | 77 | #!/bin/bash -l
set -e
#cd in the directory of the script in order to use relative paths
script_path=$( cd "$(dirname "${BASH_SOURCE}")" ; pwd -P )
cd "$script_path"
WORKING_DIR=/home/runner/work/gatk
ln -fs $WORKING_DIR/scripts/cnv_wdl/cnv_common_tasks.wdl
ln -fs $WORKING_DIR/scripts/cnv_wdl/somatic/cnv_somatic_oncot... |
a4ffd353a94b2e05fb73c8316cfb59f2df74b7f109f43f48539785340cdcb8ea | Shell | 5,327 | 111 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO FINAL PREPROCESSING STEPS OF RESTING_STATE SCAN
##
## R-fMRI master: Xi-Nian Zuo.
## Email: zuoxn@psych.ac.cn or zuoxinian@gmail.com.
######################... |
8cd58b7f62aee34fa506076c44a9318905e9b1bb075665a49a58fcb6f6f00db5 | Shell | 5,357 | 158 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# register the functional image to the structural (and bias correct)
# TODO: this could be improved by either
# 1) using fieldmaps
# 2) using ANTs, see the new awake fMRI pipeline
# ----... |
147cce4a5a4a0890ec00eb5bc074fffd032e2a3c11f7b0b4852c76acb6029b59 | Shell | 5,359 | 163 | #!/bin/bash
#####
# Example:
# $CBIG_CODE_DIR/stable_projects/preprocessing/CBIG2022_DiffProc/ \
# MRtrix/CBIG_DiffProc_batch_tractography.sh \
# --subj_list /path/to/txtfile --dwi_dir /path/to/dwi_images \
# --output_dir /path/to/output --py_env name_of_AMICO_environment \
# --mask_outp... |
f1a373a4dc53fee008d0f0ecf6cb4268640f5da9de09edd7ccbd19af8e5c85e0 | Shell | 5,367 | 139 | #!/bin/sh
# This function replicate the linear ridge regression results in the HCP dataset shown in Li et al., 2019
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################
# setup for CIRC cluster
########################
curr_dir=$(pwd... |
76c8e676a2f7f8a7eec8a11dd9164682c04a34a1b96a62cbcbd3e1d5a27bb4ee | Shell | 5,373 | 161 | #!/bin/sh
#####
# This wrapper script submits job to the schduler to run the specified type of regression, using
# the specified input FCs. These scripts are for the ABCD dataset.
#
# Input:
# -regression:
# The type of regression to use. Can be "KRR" or "LRR".
# Append "_sh" for the split-half analysis u... |
b219ef62440d6166d0bbfacc739f19e8ce045f0a7efe8ae73da03e17c8d9c6a2 | Shell | 5,400 | 124 | #!/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 ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); y... |
bfac0a96c2c0fc2891c1671761d6186fb9f4213558f253231c7534f9d7aaf194 | Shell | 5,415 | 145 | #!/bin/bash
# =============================================================================
# STARsolo CLI - Shared library functions
# =============================================================================
# Sourced by bin/starsolo and all platform scripts. Never executed directly.
# ===========================... |
c76f0470a5618aeaf9575f5f4750bfbee49a85f58c0188ffa5e3fb59f920c84b | Shell | 5,427 | 128 | #!/bin/sh
#####
# This is a wrapper script to generate all the FCs used in the analysis for the ABCD dataset.
#
# For rest-FC matrices there are 3 types of FC matrices that are generated. It can be run for at the
# 419x419 FC resolution or 1019x1019 FC resolution. It is run from 2 mins to 20 mins in intervals of 2 m... |
33a298d403c3713ad43c033dfb12bbf7c726fd5b52847f561f15bbe2d846692b | Shell | 5,465 | 199 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script will give you the overlapping encode gene entries for all variants
# in a given VCF file.
# It must be internally configu... |
ed43cc6b56e2e6991182630d2f730b676d939e142a65aea8f1151dc189b31e64 | Shell | 5,476 | 201 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script will create a fasta file containing the transcript sequences
# that overlap variants in a given VCF file.
# It must be i... |
f17cc8e3dd65bf312afd41f82102db8d0cd260eb8f998a0234e1814038b06f92 | Shell | 5,478 | 158 | #!/bin/bash
# ==============================================================================
# Shinobi fMRI Setup Script
# ==============================================================================
# Sets up the shinobi_fmri environment: venv, dependencies, config.
#
# Usage:
# ./setup.sh [OPTIONS]
#
# Options:
#... |
8ddd5aba0a55aedbc32ecf66cb0f6a9fd58129329c8479c883aa22cc5481a65d | Shell | 5,514 | 146 | #!/bin/bash
# This script creates a Google Dataproc cluster used for running the GATK-SV pipeline.
set -eu
if [[ "$#" -lt 8 ]]; then
echo -e "Please provide:"
echo -e " [1] local directory of GATK build (required)"
echo -e " [2] project name (required)"
echo -e " [3] cluster name (required)"
e... |
44d09e7f79bb2bb28ebd1603462d2f7f6b37b99e9b95e7c5a8d1e937cda86eb3 | Shell | 5,523 | 185 | #!/bin/bash
# if FSLDIR is not defined, assume we need to read the FSL startup
if [ -z ${FSLDIR+x} ]; then
if [ -f /etc/fsl/fsl.sh ]; then
. /etc/fsl/fsl.sh
else
echo FSLDIR is not set and there is no system-wide FSL startup
exit 1
fi
fi
usage()
{
base=$(basename "$0")
echo "usage: $base <subje... |
7ab4e68f983e0a2051b191766607246b8cf4400547f7d45d1c69c5807e3cd674 | Shell | 5,543 | 74 | #!/bin/bash
#BSUB -J THCVD_NMTUI
#BSUB -o ./THCVD_NMTUI_%J.out
#BSUB -e ./THCVD_NMTUI_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 2
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
... |
7fcfdced915c9805c9e021dcba0ff02f1736406f93de365d1835df3b4b33d902 | Shell | 5,558 | 149 | #!/usr/bin/env bash
#
# Build (and optionally push) a GATK docker image to GCR using Google Cloud Build. Images are built
# in the cloud rather than locally. Pushing to dockerhub is not supported by this script.
#
# By default the images are pushed to the following GCR repository:
#
# us.gcr.io/broad-dsde-methods/broad... |
403f62473123f630bb659c3519f74eccceb0c47a665a3c04ec26ec4ed929c672 | Shell | 5,560 | 74 | #!/bin/bash
#BSUB -J VAL_ADC13t15
#BSUB -o ./VAL_ADC13t15_%J.out
#BSUB -e ./VAL_ADC13t15_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 5000
#BSUB -R "rusage[mem=5000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.0... |
3ca0196b3c2fcfbd918ca6aa116da97dca4d7116127bf1d6039fa47d94b8434f | Shell | 5,563 | 112 | #DWIToDTIEstimation=/Applications/Slicer5.2.2.app/Contents/Extensions-31382/SlicerDMRI/lib/Slicer-5.2/cli-modules/DWIToDTIEstimation
#DiffusionTensorScalarMeasurements=/Applications/Slicer5.2.2.app/Contents/Extensions-31382/SlicerDMRI/lib/Slicer-5.2/cli-modules/DiffusionTensorScalarMeasurements
#BRAINSFit=/Applications... |
1d50aa0afe1e34757a445622f7338927f2bd8065096c54ea78a773b7dc9e4f27 | Shell | 5,587 | 119 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO QUALITY ASSURANCE OF ANATOMICAL SURFACE PROCESSING
##
## !!!!!*****ALWAYS CHECK YOUR SURFACES*****!!!!!
##
## Thanks go to Thomas Yeo for sharing his excell... |
7f90f4214b586d9b5dcca86b75e2eec38bff6a0190130a28cb77ca389e1601af | Shell | 5,589 | 189 | #!/bin/bash
# install_reticulate_dependencies.sh
# Installation script for GCS Parquet reading dependencies
# Installs gcsfs, pyarrow, and pandas into r-reticulate environment
set -e
# Colors for output
RED='\033[0;31m'
GREEN='\033[0;32m'
BLUE='\033[0;34m'
YELLOW='\033[1;33m'
NC='\033[0m' # No Color
echo -e "${BLUE}... |
6eaa7b145cad15f1bf36ca0a87d41ddc4767f4a1bc0ab127eb36b42b418fcf24 | Shell | 5,590 | 156 | #!/bin/bash
###########################################################
### Full v850 data rebuild for BANC pipeline
###
### Produces all versioned data files and pushes to GCS.
### Prerequisite: v850 synapse CSV must be on GCS at:
### gs://lee-lab_brain-and-nerve-cord-fly-connectome/v850/synapses_v2_human_readable.c... |
866ce907150838a23ec6d4510a6fcc157dc2ca903b5d080bc386f15ae0b9f92f | Shell | 5,619 | 165 | BASE=/proj/berzelius-2021-29/users/x_patbr #Path to home
REWRITE=$BASE/FoldDock/src/analysis/dockq/rewrite_af_pdb.py
##Rewrite the AF2 output to contain 2 chains instead of 1 for the DockQ evaluation
################################
###########new_dimers###########
################################
##########AF std an... |
828888b682f33174ca558b797c3055b421b99766d732462731fc39a492fd9ef2 | Shell | 5,640 | 178 | #!/bin/bash
###############################################
# run GWAS (ldsc)
path0=/projects/ps-renlab/yangli/projects/CEMBA/01.joint_dat/rs1cemba/gwas/L2cluster
# liftOver and merge
wget http://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToHg19.over.chain.gz
wget http://hgdownload.soe.ucsc.edu/goldenPath/h... |
198307a0dc2082118fc0df8f426bf1c605514f66d7e56eaf379212b1a57d49f9 | Shell | 5,661 | 177 | #!/bin/bash
usage() {
cat << EOF
Usage: dl+direct [-h] [-s subject] [-b [-i inv2_file]] [-n] [-f] [-g] [-m model_file] [-k] T1_FILE OUTPUT_DIR
Process T1_FILE (nifti) with dl+direct and put results into OUTPUT_DIR.
Input is expected to be a skull-stripped T1w MRI. You may specify --bet to remove
the skull (using hd-be... |
63c3ccd8f067c4766ffebbe88c9e86ba79e9bc088c21e72d9c46e7d1ee3a14c8 | Shell | 5,679 | 156 | #!/bin/bash
#snakemake -k --jobs 999 --latency-wait 120 --max-jobs-per-second 8 --cluster-config cluster.json --cluster "qsub -N {cluster.name} -j {cluster.j} -M {cluster.M} -m {cluster.m} -l nodes={cluster.nodes}:ppn={cluster.ppn},walltime={cluster.walltime} -l mem={cluster.mem} -e {cluster.stderr} -o {cluster.stdout}... |
3f62ee77fe551fade1974c33472dcbf74039eaffefef0a4c9910f47713dc773a | Shell | 5,696 | 167 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# retrieve input argument to find correct instructions
instructDir="$1"
# ------------------- #
# GENERAL DEFINITIONS
# ------------------- #
source $MRCATDIR/setupMrCat.sh
studyDir="/Volumes... |
e3bb842d01f9db52f5e3a41522c1347b6930c428ff762f4fbfeaec934465c6c2 | Shell | 5,696 | 160 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# retrieve input argument to find correct instructions
instructDir="$1"
# ------------------- #
# GENERAL DEFINITIONS
# ------------------- #
source $MRCATDIR/setupMrCat.sh
structRootDir="/Vo... |
db6ef8036c1ee5ff0be4c97bab11c1d26348db58cdf6ec7013079b3c9ba57357 | Shell | 5,702 | 144 | #!/bin/bash
#####
# This script preprocesses T1 and diffusion data for tractography. Parcellations and tractograms are generated.
#
# Written by Leon Ooi and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#####
###############
# set up environment
###############
sub=$1
algo=$2
scr... |
d9343fcb855a8e6a3da85b39c3247a67c795853e776d7bdd5c7565f307db1f94 | Shell | 5,703 | 189 | #!/usr/bin/env bash
set -euo pipefail
# Package this repository for HPC transfer.
# - minimal mode (default): code + docs + configs, excludes heavy data and outputs
# - full mode: includes project data needed to run immediately (can be very large)
#
# Usage:
# bash scripts/package_for_hpc.sh
# bash scripts/package... |
52bd96ff31dad703c631914acada4a954a3e71a6add1d0280163d481601ee9bb | Shell | 5,710 | 124 | #!/bin/sh
#####
# This is a wrapper script to generate all the FCs used in the analysis for the HCP dataset. It generates
#
# For rest-FC matrices there are 5 types of FC matrices that are generated. It can be run for at the
# 419x419 FC resolution or 1019x1019 FC resolution. It is run from 2 mins to 58 mins in inter... |
cfd517ef45793065297238529617fe4f6e036392c4d5fff4b03a8f4ddc3b7266 | Shell | 5,721 | 149 | ##########################################################################################################################
## CCS SCRIPT TO CALCULATE REGIONAL HOMOGENEITY MEASURES OF THE LOW FREQUENCY OSCILLATIONS IN THE BOLD SIGNAL
##
## This script can be run on its own, by filling in the appropriate parameters
##
##... |
5a62027d7086d123943fc1da00c878d5ea11829c039eff8bf634fc17bc1985c8 | Shell | 5,762 | 130 | #!/usr/bin/env bash
##########################################################################################################################
## SCRIPT TO RUN GENERAL RESTING-STATE PREPROCESSING
##
## Written by the R-fMRI master: Xi-Nian Zuo.
## Email: zuoxn@psych.ac.cn.
##
#########################################... |
ce988550b0cb17ea62a712472d282d8b0ebc7edd7e893baad279e717aaebb738 | Shell | 5,774 | 148 | #!/usr/bin/env bash
# Q&A gate for fn-51 — missingness-vs-d calibration report.
# Implements events from PROCEDURE.md. Fail-loud when infrastructure is missing.
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../.." && pwd)"
cd "${ROOT}"
PROC_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
echo "=... |
6de49dccfeab744494ddd260ff8a3294de5cec7ad4fa8c3967e923471091974c | Shell | 5,778 | 200 | #!/bin/bash
# Batch cancel SLURM jobs
# Usage: ./batch_cancel.sh [OPTIONS]
show_help() {
cat << EOF
Batch cancel SLURM jobs
Usage:
./batch_cancel.sh [OPTIONS]
Options:
-r START END Cancel jobs in range (e.g., -r 12345 12350)
-n PATTERN Cancel jobs matching name pattern (e.g., -n shino... |
9ddd41d8a6ed808c019dd134a3a64e29965cbcc457ffef0971a65020ecd21380 | Shell | 5,795 | 147 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# examples
# sh transformCoordANTs.sh --coord=0,2,19 --transform=/Users/you/projects/thisProject/registerT1wCT/transform/LeetSkull_to_MNI_0GenericAffine.mat
# sh transformCoordANTs.sh --coord=... |
3e90f76198e22c716f6a3a4cf9007963d3a03599b47538a12e3b2cceca660163 | Shell | 5,797 | 151 | #SAMPLE 1 -----------------------------------------------------------------
echo "MAKING SAMPLE 1 --------------------------------------------------------------------------"
python /mnt/d/HeartModelling/HeartModelling/auxiliar/rbm/ldrb_s1_getFacetFunction.py \
--dataPath /mnt/d/Paper3/Models/invivo/he/sample1 \
--dom... |
becaee574580f0a2dd7663af49d2a9a72e1fa0f7283a368a26627981f6b2c064 | Shell | 5,840 | 118 | #!/bin/sh
echo "Cora"
echo "===="
echo "GCN"
python gcn.py --dataset=Cora --inference
python gcn.py --dataset=Cora --random_splits --inference
python gcn.py --dataset=Cora --inference --profile
python gcn.py --dataset=Cora --random_splits --inference --profile
echo "GAT"
python gat.py --dataset=Cora --inference
pyth... |
6bf33da653e8e8dfc0e0f6ebec0a878cc9ac3fa8fe21af1dafa19504b7554a1f | Shell | 5,859 | 106 | #!/bin/bash
# this should run after you've evaluated this in matlab
# create_CANLab2023_CIFTI_subctx('MNI152NLin6Asym','coarse',2,load_atlas('canlab2023_coarse_fsl6_2mm'))
# which will create a nifti file in this folder with all necessary subcortical volumes
#
# It assumes it's located in Atlases_and_parcellations/202... |
6d2c0e3f396d463f14a07d4b73ea1b206142a18ca2f697e5f973e18779b47b4b | Shell | 5,899 | 167 | #!/usr/bin/env bash
# ------------------------------------------------------------
# LSS extractor (MNI-only):
# - NAcc means (zstat/cope/varcope)
# - BRS_Cortical_3pt1 means (zstat/cope/varcope)
# - BRS correlation (zstat vs BRS map)
# - Last column: expected zstat path (sanity check)
# ----------------------... |
68dae6c26d40e212c2562a99c8711183bdd3c202662a3b868684161e8b30c982 | Shell | 5,918 | 167 | #!/bin/bash
#SBATCH -c 16 # 16 cores (OMP-parallel sparse ops in align.py)
#SBATCH -t 2-00:00 # 2 days
#SBATCH -p medium # medium partition (5d max, fits comfortably)
#SBATCH --mem=128G # whole-brain cosine+bil... |
a8d575466bb1fc2ef3c99a859a921f9da60029a61f9fc28f124f8d214a6e3515 | Shell | 5,926 | 126 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO QUALITY ASSURANCE OF ANATOMICAL SURFACE PROCESSING
##
## !!!!!*****ALWAYS CHECK YOUR SURFACES*****!!!!!
##
## Thanks go to Thomas Yeo for sharing his excell... |
2f0b1fd6833839f6133567882dfd9afa2d1218aaa45c47071b7b6923025013f1 | Shell | 5,944 | 136 | #!/bin/sh
export path_htsa_dir=$1
export path_pipeline=$2
export Project_name=$3;
export aggregated_work_dir=$4;
export sequencing_type=$5;
export SOAP_work_dir=$project_work_dir/soapdenovo
export SOAPtrans_work_dir=$project_work_dir/soapdenovo_trans
export megahit_work_dir=$project_work_dir/megahit
export omega_wor... |
e0bd8350ede5f847f9fc300be40ed2acbdabe79d9339af9b01b80b9381e38745 | Shell | 5,946 | 136 | #!/bin/sh
export path_htsa_dir=$1
export path_pipeline=$2
export Project_name=$3;
export aggregated_work_dir=$4;
export sequencing_type=$5;
export SOAP_work_dir=$project_work_dir/soapdenovo
export SOAPtrans_work_dir=$project_work_dir/soapdenovo_trans
export megahit_work_dir=$project_work_dir/megahit
export omega_wor... |
07dc83fbc3b88507ffce2e9031aad4ab01f4d864e0022dc5617213fed0b891a9 | Shell | 5,973 | 167 | #!/bin/bash
#SBATCH -c 16
#SBATCH -t 3-00:00
#SBATCH -p priority
#SBATCH --mem-per-cpu=10G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_sweep_%A_%a.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_sweep_%A_%a.err
#SBATCH --array=0-12
##############################################################################... |
3a30409aefa24759acd8a0981c2bf2725e2e03eef8e358320cc850807b86b0ab | Shell | 5,980 | 146 | #!/bin/bash
########################################################################
# #
# This pipeline is only for processing the multicenter diffusion data. #
# From Qiqi Tong, CBIST, Zhejiang University. #
# ... |
404f9a97617eac87a370294b0775ad363ee296643e19037abcce76fee557a1fc | Shell | 5,997 | 123 | #!/bin/bash
# This script copies SV analysis results from a Google Dataproc cluster
# to an appropriate bucket/directory on GCS. It also uploads contents of
# local output logs
# terminate script on error or if a command fails before piping to another command
set -eu
set -o pipefail
if [[ "$#" -lt 3 ]]; then
ech... |
dbd4dcbd659a5658a359db2ac4318aa3b3c997578f28b9f295c27d964d9ee59d | Shell | 6,029 | 152 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO REGRESS OUT NUISANCE COVARIATES FROM RESTING_STATE SCAN
## nuisance covariates are: global signal (option), white matter (WM, WHITE), CSF, and
## 6 motion p... |
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