sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
a6bd678a339fb4eae86ac64f51fce20a854aecdf383e4d30dd7115eb349ec50e | Shell | 6,548 | 155 | #!/usr/bin/env bash
# "Source step #2": runs the "KB (v0.28.2)" wrapper "Kallisto (v0.50.1) + Bustools (v0.43.2)" for generating the count matrices
## scRNA-seq: "10XV3" --> check Ivan emails about the AmpliDrop tech used!
### "CMDs" --> $ kb ref -i transcriptome.idx -g transcripts_to_genes.txt -f1 cdna.fa dna.primary... |
c5e319fa57b6345151bbd296ce4730917758bfe501f8a4bc80890eeafd69780f | Shell | 6,562 | 34 | #!/bin/bash
#
#SBATCH --job-name=MMReg025S
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-p... |
064f9d4e99fc5c375abbba44c8192d1647816e1238678626c0059ccfddf8a927 | Shell | 6,577 | 146 | #!/bin/bash
set -eu -o pipefail
if [ "$EUID" -ne 0 ]; then
echo -e "Please run the script with root privileges!"
exit 1
fi
# Check if FAST_DATA_DIR and SLOW_DATA_DIR are provided
if [ $# -lt 2 ]; then
echo "ERROR: Both FAST_DATA_DIR and SLOW_DATA_DIR must be provided."
echo "Usage: $0 <FAST_DATA_DIR> ... |
5e26d2f411e36aa9b47b9a755b191204c948ba8f27138c652bcd01a84eac52e9 | Shell | 6,595 | 34 | #!/bin/bash
#
#SBATCH --job-name=MMReg0125S
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-... |
3907fb2d8fc00e4a88e97314a1f29a3dfbf2123a812f82a208092942dd2974dd | Shell | 6,651 | 119 | #!/usr/bin/env bash
ml connectomeworkbench/1.5.0
ml freesurfer/7.3.2
ml deepretinotopy/1.0.11
source ~/miniforge3/etc/profile.d/conda.sh
conda activate deepretinotopy_validation
while getopts d:t:r: flag
do
case "${flag}" in
d) dataDir=${OPTARG};;
t) dirHCP=$(realpath "${OPTARG}");;
r) val... |
5dd60989d222b6b2f228dbb6b704056059f6f0a33e5c7a057dc4a09a20c8e52e | Shell | 6,702 | 110 | #!/bin/bash
set -eo pipefail
# Only measure coverage where it is cheap or uniquely valuable. On Python >= 3.14
# sys.monitoring is coverage's default core and can measure branches, making it
# nearly free. Below 3.14 coverage falls back to the C tracer (sys.monitoring
# cannot do branch coverage there), which roughly ... |
722ec98dc89efda0e3b480479c131a0cc1c1249bcdb0958f0e7ca1426ca1dc8e | Shell | 6,751 | 154 | #!/usr/bin/env bash
# "Source step #1": runs a recent version of "Kallisto (v0.46.2)" for pseudo-alignment of FASTQ files
# Sets 'colors' --> https://www.codegrepper.com/code-examples/shell/bash+background+color
## If I change the '0' by '1' right before the ';', the text turns 'bold'!
## If I change the '0' by '2' r... |
53957a4ff223db82b3a35c44336973606c239982d32eff259fba854ddd094641 | Shell | 6,834 | 180 | #!/bin/bash
cifar_path="/user_data/weifanw/cifar-100-python" # cifar saving path
cwd="/user_data/weifanw/familiarity_clean" # project directory
# ====================================================================================================
# params
task="effects"
wies_sweep=(10 15 20 25 30 35 40 45 50)
wie_f=... |
8093722c603795f4dfa12652c5cdaab57755b8a85ad421a4a23abb90b0a74154 | Shell | 6,955 | 211 | #!/bin/bash
# =============================================================================
# Docker smoke tests for Aydin
#
# Validates that Docker images build correctly and basic commands work.
# Requires Docker to be installed and running.
#
# Usage:
# ./docker/test-smoke.sh # Test CLI image only (fa... |
f06b74f689f6571d821e10056b602200873bad6ed4e2a4571ae1dfed547a7752 | Shell | 7,005 | 226 | #!/bin/bash
##
## RNA-seq variant calling using STAR aligner and GATK
##
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
route_name=${script_name/%.sh/}
echo -e "\n ========== ROUTE: $route_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 2 ] ; t... |
e6f2864281faceb1cdea5f7cdc587e4bd19ee0c66a540ec9ad7d9b7ea3607370 | Shell | 7,009 | 210 | #!/bin/bash
# Function to echo text in specified color using tput and printf
colored_echo() {
local color=$1
local text=$2
# Define color codes using tput
local black=$(tput setaf 0)
local red=$(tput setaf 1)
local green=$(tput setaf 2)
local yellow=$(tput setaf 3)
local blue=$(tput se... |
d1395863032ab1d35d6517084cb5721b6f32ca2e35cab32e96623ea8ec1df06c | Shell | 7,057 | 120 | #!/bin/bash
set -u -x -e
# GOAL: registration from fsaverage to hcp fs_lr to dhcpSym40 to native
# Use this registration to resample the wang template to individual surfaces
path_script=$(dirname $0)
sub=$1
ses=$2
path_bids_data=$3
path_output_data=$4
path_HCPtemplates_standardmeshatlases=$5
path_surfacetemplate=$6
p... |
f5abca57615291f682d8a0f008d4a4a80bf8e17ac2f14cedcccc2854680e70e4 | Shell | 7,083 | 182 | #!/bin/bash
# Description: AlphaFold non-docker version
# Author: Sanjay Kumar Srikakulam
usage() {
echo ""
echo "Please make sure all required parameters are given"
echo "Usage: $0 <OPTIONS>"
echo "Required Parameters:"
echo "-d <data_dir> Path to directory of supporti... |
87aa5d1046eb2191f5ec5ed151ffe79106f7749520018947076b99bc49ede6f8 | Shell | 7,088 | 154 | #!/bin/bash -l
#$ -P vkolagrp
#$ -t 1-40
#$ -pe omp 16
#$ -l mem_per_core=16G
#$ -N lpa_ppmi_patched_second_pass
#$ -j y
#$ -m bes
#$ -l h_rt=12:00:00
module load matlab
module load spm
module load fsl
module load miniconda
function conda_deactivate_all() {
while [ -n "$CONDA_PREFIX" ]; do
conda deactivat... |
56035f6a344c5b22189924f7cf90cc9cac4a7e3f24a5135465fabc7d6a0c48c6 | Shell | 7,100 | 163 | #!/bin/bash
declare -A ASSEMBLIES
ASSEMBLIES[hs37d5]="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz"
ASSEMBLIES[hg19]="http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/chromFa.tar.gz"
ASSEMBLIES[GRCh37]="http://ftp.ensembl.org/pub/grch37/release-87/... |
af2cdeb41dbfe3a108dc1c6a163f9ebdfb0aa071559c1d5bc2a86aacd404459c | Shell | 7,117 | 177 | #!/bin/bash
##v3 is built on v2 but replaces the R procesing of files with an awk script to generate input for R DSS (5 col files)
##activate conda if required
source /home/arh49/miniconda3/etc/profile.d/conda.sh
#source /usr/bin/Rscript
#modified so that it uses the same sample sheet input as provided to the wf-bas... |
b83cc89dd1e57732a990138e786b1dbf3e9591a144354057c8a85d4718b0d63a | Shell | 7,132 | 104 | #!/bin/bash
dx login --token TOKEN
my_cmd="for i in {1..22}; do echo \"chr\${i}_hqc\"; done > files_to_merge.txt && \
plink2 --pmerge-list files_to_merge.txt bfile --make-bed \
--out autosome_hqc \
--threads 32"
bed_file1="/notebooks/wes/sample_qc/high_quality_variants/chr1/chr1_hqc.bed"
bi... |
cbefcdd8b839e4c6a9eb2b9b9f86879248f555a0f91c894cd2697f39155cd1b3 | Shell | 7,152 | 269 | #!/bin/bash
#
#
# Created by Kenneth Weber on 10/18/2023. Modified by Valeria Oliva on 10/24/2023 for the Neuromuscular Signature Pilot.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR ... |
6d3eba77c2f3086ed701746c28742fa4c772b60bc3063e1b84e4156030af802a | Shell | 7,177 | 188 | #!/bin/bash
test -e ssshtest || curl -s https://raw.githubusercontent.com/ryanlayer/ssshtest/master/ssshtest
. ssshtest
STOP_ON_FAIL=1
data_path="test/data/"
func_path="test/func/"
imgs_without_json=$data_path"without_json"
imgs_with_json=$data_path"with_json"
printf "\n\nPlotCritic tests\n"
echo "#################... |
f239dfc1f6aea4c0c14f06832e26f5a502b50daa5bba8858406a05fb7184eee9 | Shell | 7,203 | 182 | #!/bin/bash
# Description: AlphaFold non-docker version
# Author: Sanjay Kumar Srikakulam
usage() {
echo ""
echo "Please make sure all required parameters are given"
echo "Usage: $0 <OPTIONS>"
echo "Required Parameters:"
echo "-d <data_dir> Path to directory of supporti... |
090609969053a0d25d577a3d60e549e23565847cab930f649b69675f6f0889f9 | Shell | 7,211 | 262 | #!/usr/bin/env bash
export ANTSPATH=${ANTSPATH:="/hpc/soft/ANTS/antsbin/bin/"}
# Registration to T1w seems to work a bit better
anat=/hpc/banco/Primavoice_Data_and_Analysis/analysis_sub-Maga/anat/segmentation/inia19_sub-Maga_ses-01_T1w0p6mmDenoised_cropped_debiased/sub-Maga_ses-01_T1w0p6mmDenoised_cropped_debiased-ri... |
ff4136414b2da21144ead376685f1a8d63ca29aff45e74ff79fc3f30f06df75d | Shell | 7,272 | 216 | #!/bin/bash
# Build MIMIC-IV in DuckDB: create the schema, load the data, then derive the
# concepts.
#
# Usage:
# ./build_mimic.sh <mimic_data_dir> [output_db]
#
# <mimic_data_dir> is the directory holding the hosp/ and icu/ subfolders.
# Compressed (.csv.gz) and uncompressed (.csv) data are both supported; DuckDB
#... |
bdfc82a2b155566023732de7964d05093a3141f5dcdbd8ca89c803501d3a7bfd | Shell | 7,327 | 278 | #!/bin/bash
# Bismark alignment
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ $# -lt 4 ] ; then
echo -e "\n $script_name ERROR:... |
3997e1aa7296296785b400a156e8c61a5d16d109fd4320bc131eb41a5e075aae | Shell | 7,331 | 225 | # package C library into a tarball
set -e
SCRIPT_PATH=$(dirname "$(realpath -s "$0")")
if [ -z "${INSTALL_PREFIX}" ]; then
INSTALL_PREFIX=$(realpath -s "${SCRIPT_PATH}/../../dp_c")
fi
mkdir -p "${INSTALL_PREFIX}"
echo "Installing DeePMD-kit to ${INSTALL_PREFIX}"
NPROC=$(nproc --all)
#------------------
BUILD_TMP_D... |
90e275a5bba2ce65e5e1458d089c58e72dcf5fa7d43fd335713d1caba491e725 | Shell | 7,386 | 125 | #!/bin/bash
set -u -x -e
# GOAL: registration from fsaverage to hcp fs_lr to dhcpSym40 to native
# Use this registration to resample the wang template to individual surfaces
path_script=$(dirname $0)
sub=$1
ses=$2
path_bids_data=$3
path_output_data=$4
path_HCPtemplates_standardmeshatlases=$5
path_surfacetemplate=$6
p... |
4bfb3fe2b30c742b9321aeaefaa8b464c8d74851d16277869d25d2cfe22a4116 | Shell | 7,398 | 330 | #!/bin/bash
# annotate regions with cytoband and overlapping genes using ANNOVAR
# expects tab-delimited input file with header row and 5 columns: chr, start, end, 0, 0
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== S... |
d799bd68312d6e0160cceb7f12e6e989248352ed7965162f54d4f15ad3f0df47 | Shell | 7,514 | 289 | #!/bin/bash
# HMMRATAC peak calling for ATAC-seq (original Java implementation)
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! ... |
70815cebd51bbe2b8b9ae4569648aee27b913b3b268972b95975b0504b72fd78 | Shell | 7,608 | 104 | #!/bin/bash
dx login --token TOKEN
my_cmd="for i in {1..22}; do echo \"chr\${i}_hqc_pruned\"; done > files_to_merge.txt && \
plink2 --pmerge-list files_to_merge.txt bfile --make-bed \
--out autosome_hqc_pruned \
--threads 32"
bed_file1="/notebooks/wes/sample_qc/high_quality_variants/chr1/ch... |
f7b95ca712c8873c4862e5fec91f43f46af673d6565bfdeab1a13c6a95993c74 | Shell | 7,637 | 322 | #!/bin/bash
# run Bowtie2 with ChIP-seq specific parameters
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ $# -lt 4 ] ; then
ech... |
cc484db65aa40abed561dbef0860421297d5d4149703706aef811e45f3e607fa | Shell | 7,658 | 322 | #!/bin/bash
# run Bowtie2 with ATAC-seq specific parameters
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 5 ] ; then
ec... |
cb111178bc2c045ba641db503d080aafb01b18ece97450414024f604e90c17ef | Shell | 7,762 | 249 | #!/bin/bash
# run RSEM
# script filename
script_name=$(basename "${BASH_SOURCE[0]}")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ $# -lt 5 ] ; then
echo -e "\n $script_name ERROR: WRONG NUMBER OF ARGUMENTS SUPPLIED ... |
7f032a826036220099b4adda9261261f619843d7277cb348d9704a4443c87404 | Shell | 7,841 | 151 | #!/bin/bash
# This script prepares the confounds used for performing nuisance regression. It currently uses 6 motion traces, WM , and CSF + their temporal derivatives (16 regressors in total). We assume that
# a) you have a T1 image of each subject that was segmented using the neural nets provided by Freesurfer.... |
a63d33ffd1874db0a92b711955b3dfd07d61a23425c1c89c4562e24394dabf55 | Shell | 7,957 | 104 |
#No stratification
python parameter_sweep_general_new.py subclass NotAllSame DownCounts Sestan_DLPFC 0
python parameter_sweep_general_new.py subclass_label NotAllSame DownCounts Allen_M1 0
python parameter_sweep_general_new.py subclass NotAllSame DownCounts Allen_MTG 0
python parameter_sweep_general_new.py subtype Not... |
0ab560ca8b96ae47229105edbb74638eae2733859d38f0cacfeda39d71aa834d | Shell | 8,025 | 338 | #!/bin/bash
# call nucleosomes in ATAC-Seq data using NucleoATAC
# script filename
script_name=$(basename "${BASH_SOURCE[0]}")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 4 ] ; then
echo -e "\n $script_name... |
37ad3439fb7ffea9ec5525a56a71c45d0c364e7c262168c50bc92a3046fd8ae0 | Shell | 8,060 | 230 | #!/bin/bash
#bedtools are required for the task
print_help(){
echo "
This script help you locate SNP and transform the locus (by chromosome id and location) to the corresponding variant rsid.
Only intersected SNPs will be printed out.
Note!!!! 1. All file path should be the same as the original files. 2. b... |
1bf59ebd30dde4aa370cbd5be24ca776e898e122ce260d9bb50229af282f3ea1 | Shell | 8,080 | 212 | #!/bin/bash
##
## EasyOptions 2015.2.28
## Copyright (c) 2013, 2014 Renato Silva
## BSD licensed
##
## This script is supposed to parse command line arguments in a way that,
## even though its implementation is not trivial, it should be easy and
## smooth to use. For using this script, simply document your... |
36bc163d61518012535e5e88927846630ed048373fbf68a287f805521d7aef38 | Shell | 8,172 | 202 | #!/usr/bin/env bash
# MIT License
#
# Copyright 2018 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, c... |
263023bebeb9db43cb3cf1503d0c3b6d687879ce1d573c9c16a14517b09609f9 | Shell | 8,348 | 251 | #!/bin/bash
# slurm specific parameters
#SBATCH --job-name=aslbrainage
#SBATCH --gres=gpu:a100:1
#SBATCH --partition=luna-gpu-long
#SBATCH --mem=64G
#SBATCH --cpus-per-task=1
#SBATCH --time=6-23:59
#SBATCH --nice=0
#SBATCH --qos=radv
#SBATCH --mail-type=BEGIN
set -eu
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
CSV_... |
084166040566d4341f5a566d02c937e1c95827314e45100d8892bcf40a4ff5f3 | Shell | 8,494 | 272 | #!/bin/bash
NORMAL="\\033[0;39m"
RED="\\033[0;31m"
BLUE="\\033[0;34m"
CURDIR=`pwd`
BASEDIR=$(dirname $0)
if [ -s add_to.bashrc ]; then
rm add_to.bashrc
fi
die() {
echo -e "$RED""Exit - ""$*""$NORMAL" 1>&2
exit 1
}
echo -e "$RED""Make sure internet connection works for your shell prompt under current user'... |
e81d5b9092d166911cd8ab9de4480826fc14da615446c61d0d29116e1bda5527 | Shell | 8,499 | 300 | #!/bin/bash
#----- Parse Input Arguments -----#
# from https://stackoverflow.com/a/39376824
# usage function
function usage()
{
cat << HEREDOC
Usage: $progname [options] [--ref genome.fa.gz] [--gtf annotation.gtf] [--vcf variants.vcf]
required arguments:
-r, --ref STR reference genome in fa... |
577afe4e5962f9614d0c4ea08485e325e8360719e942461dc634014c2bad8534 | Shell | 8,757 | 177 | #!/bin/bash
# =============================================================================
# kind-quickstart.sh — Run the full Tier 3 topology on a local kind cluster
# =============================================================================
#
# kind ("Kubernetes in Docker") spins up a real Kubernetes API server ... |
7645900c8854fbac5bd5a4441e8092fc0a592e2d7cbb723eb95175bde02659c3 | Shell | 9,108 | 331 | #!/bin/bash
# run STAR
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ $# -lt 4 ] ; then
echo -e "\n $script_name ERROR: WRONG NU... |
118040d00247a238c4685fb525efa94e3703c12f236588520457eb7545ffc3c6 | Shell | 9,162 | 122 | #!/bin/bash
# set the project
# gcloud config set project physionet-data
export TARGET_DATASET='mimiciii_derived'
BQ_FLAGS=(--use_legacy_sql=False --replace)
echo ''
echo '==='
echo 'Beginning to create concepts for MIMIC database.'
echo '==='
echo ''
# echo the commands called
set -x
echo 'Top level files..'
bq qu... |
78b130669030313e808389d6b317c0bdf9d5f45addfc8dd27b3003643bfd4f50 | Shell | 9,281 | 325 | #!/usr/bin/env bash
# Bias field correction using T1w & T2w images
HELP() {
cat <<HELP
T1xT2BiasFieldCorrection. Bias field correction using T1w & T2w images. Provides an attempt of brain extration if wanted.
Usage:
bash ${0##*/} -t1 <T1-input-file> -t2 <T2-input-file> [options]
Compulsory arguments:
... |
73278ee20a878cea5e746dabe9853ebf70a5eba4c9c701123fefc09a7898ad28 | Shell | 9,386 | 297 | #!/bin/bash
#
# v2 07/29/20 run jobs in parallel
#
# Created by Megan McAndrews and Kenneth Weber on 5/18/2016.
# Please cite:
# Weber II KA, Chen Y, Wang X, Kahnt T, Parrish TB. Lateralization of Cervical Spinal Cord Activity During an Isometric Upper Extremity Motor Task. NeuroImage 2016;125:233-243.
# Jenkins... |
dd915a5185f680c9fbbf18bd1a1730de9e33c7f5cc997b61ff82e977ac37b45a | Shell | 9,402 | 390 | #!/bin/bash
# call variants with LoFreq
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 4 ] ; then
echo -e "\n $script_na... |
5582ebbc486f61ddcf7501f4ba7be98ad522bd38efb607fece961aefad102e6c | Shell | 9,436 | 326 | #!/usr/bin/env bash
# Bias field correction using T1w & T2w images
HELP() {
cat <<HELP
T1xT2BiasFieldCorrection. Bias field correction using T1w & T2w images. Provides an attempt of brain extration if wanted.
Usage:
bash ${0##*/} -t1 <T1-input-file> -t2 <T2-input-file> [options]
Compulsory arguments:
... |
48385a40c988fe71c64268242826d585c4b2c6800b0859abab462dfd36c4070d | Shell | 9,619 | 302 | #!/bin/bash
# run Salmon (quasi-mapping-based mode)
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ $# -lt 4 ] ; then
echo -e "\n... |
74b0f5761aa6d067fcdf1f4d81c6ba11bb56096c9f25df720c47d4ae1930d6e7 | Shell | 9,638 | 365 | #!/bin/bash
# Bismark methylation extractor
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 5 ] ; then
echo -e "\n $scrip... |
e296339b734eb3d8e23f5ac0ca2e9f2d72cc9e9603fb925e6100aef1d359eb74 | Shell | 9,747 | 296 | #!/usr/bin/env bash
# Main script, sets source and destination folders, which csv file to read
# in order to get rawfile paths. Walks through the steps of a distributed
# search, waiting for each one to be finished before initializing
# the next one. For searches, the "inner.sh" script is called. For predicting
# spec... |
20d00562880bfa3e8b0a57980134f3cde03d6419f03872e90f20f50663faa489 | Shell | 9,771 | 329 | #!/usr/bin/env bash
# IterREGBET. Iterative registration of the in-file to the ref file (registered brain mask of the ref image is used at each iteration).
# To use when the input brain mask is not optimal (eg. an output of FSL BET).
# Will output a better brain mask of the in-file.
HELP() {
cat <<HELP
IterREGBE... |
d3d75000da95619ca8d8382233552044555ae53d49ffa081444467d11856f104 | Shell | 9,911 | 261 | # Run all the examples
LAMMPS=lmp_mpi
#LAMMPS=${HOME}/compile/lammps/build-test/lmp
BINPATH=${HOME}/compile/lammps/git/src
#BINPATH=${HOME}/compile/lammps/build-test
# -------------------------------------------------
# -------------------------------------------------
# Example 1 = run ab initio MD (AIMD)
# ---
#... |
5266ab5477f55386c2f9bd44ef84ed639decc7f0bc535f5efe68001f79eeed36 | Shell | 9,983 | 252 | #!/bin/bash
# This script performs the necessary processing and registration steps to
# prepare the planning images and target positions for loading into k-Plan.
#
# It should be called as a source script after defining the requisite
# variables.
#
# After running this script, load the following images into k-Plan:
# ... |
0dad900992a5303daea09158926d6c174616162c9e5e2c07485bfd56ce79bff1 | Shell | 10,126 | 331 | #!/bin/bash
#
# v2 07/29/20 run jobs in parallel
#
# Created by Megan McAndrews and Kenneth Weber on 5/18/2016.
# Please cite:
# Weber II KA, Chen Y, Wang X, Kahnt T, Parrish TB. Lateralization of Cervical Spinal Cord Activity During an Isometric Upper Extremity Motor Task. NeuroImage 2016;125:233-243.
# Jenkins... |
99137636c0dd71f322e668f45c7c3efee097ee461668996a983fdd11e760c483 | Shell | 10,281 | 431 | #!/bin/bash
# MACS peak calling
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ $# -lt 5 ] ; then
echo -e "\n $script_name ERROR:... |
aa41a6960e4d6d00ddbf40aaa2fd561f33a97a9950d4df78e870163c7012abcd | Shell | 10,326 | 226 | #!/usr/bin/env bash
# Auto-detect number of cores (leave 1 core free)
auto_cores=$(($(nproc) - 1))
[ $auto_cores -lt 1 ] && auto_cores=1 # Ensure at least 1 core
# Default values
n_jobs=$auto_cores
subject_id=""
output_dir=""
while getopts s:t:h:g:j:i:o: flag
do
case "${flag}" in
s) dirSubs=${OPTARG};;
... |
83936900f7d5dd21eddd5184a78a19a8c877463a004c19cc51b8984238183c87 | Shell | 10,603 | 440 | #!/bin/bash
# MACS peak calling
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ $# -lt 5 ] ; then
echo -e "\n $script_name ERROR:... |
506e9c6b48a54dbd024c4686d6fdc79fbd6d15566edb1d591b6f676294871d7b | Shell | 10,671 | 487 | # Create and run locally a Feat design for data preprocessing for a chosen task
# Author: Valeria Oliva
echo -n "Which sub? Only insert number >"
read subject
echo -n "where did you mount the Project folder? write path (e.g. for vale it is '/home/valeo/') >"
read projectpath
echo -n "session? 01 or 02 >"
read ses... |
8cab0585fb392a717a22b7947fa8f1fe3b5437dd3e83b884f8a52bcabd37f55d | Shell | 10,674 | 489 | # Create and run locally a Feat design for data preprocessing for all tasks
# Author: Valeria Oliva
echo -n "Which sub? Only insert number >"
read subject
echo -n "where did you mount the Project folder? write path (e.g. for vale it is '/home/valeo/') >"
read projectpath
echo -n "session? 01 or 02 >"
read ses
cd... |
c237cff39299852d16bfaf3ee3daaa1298d45117b7f6e35a4cc223585e79566c | Shell | 10,826 | 242 | #!/bin/bash
set -u -x -e
# Adapted from https://git.fmrib.ox.ac.uk/seanf/asymmetry-analysis/-/blob/master/hcp_surface.sh?ref_type=heads
# This script maps dHCP volumetric fMRI data to the surface
# It is largely a vanilla implementation of the HCP Surface Pipeline
# One of the main changes is that the fMRI is mapped in... |
0986f9402ec34f3d55d9b290573edc70083cdb5665fcb82e1625c661fb1a30e7 | Shell | 10,840 | 389 | #!/usr/bin/env bash
# FSL BET using T1w & T2w images
HELP() {
cat <<HELP
T1xT2BET. Brain extraction using T1w and T2w images.
Usage:
bash ${0##*/} -t1 <T1-input-file> -t2 <T2-input-file> [options]
Compulsory arguments:
-t1 Whole-head T1w image
-t2 Whole-head T2w image (use ... |
2186d1a660363596ee4c672c6527ef767260c4881b2fd39330a832bccf60a426 | Shell | 10,850 | 166 | #!/usr/bin/env bash
ml connectomeworkbench/1.5.0
ml freesurfer/7.3.2
ml deepretinotopy/1.0.11
source ~/miniforge3/etc/profile.d/conda.sh
conda activate deepretinotopy_validation
while getopts d:t:r: flag
do
case "${flag}" in
d) dataDir=${OPTARG};;
t) dirHCP=$(realpath "${OPTARG}");;
r) val... |
4a63495281a3459b0c0cccc8f91f543d2c761613c3700f11a765ab05a8ebebd3 | Shell | 10,851 | 389 | #!/usr/bin/env bash
# FSL BET using T1w & T2w images
HELP() {
cat <<HELP
T1xT2BET. Brain extraction using T1w and T2w images.
Usage:
bash ${0##*/} -t1 <T1-input-file> -t2 <T2-input-file> [options]
Compulsory arguments:
-t1 Whole-head T1w image
-t2 Whole-head T2w image (use ... |
63b90d6f0a85815881d25122ba59a8b64294fc5bea42b743176e82dbb3ae1590 | Shell | 10,913 | 409 | #!/bin/bash
# call variants with Mutect2 (2.1 part of GATK 4)
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 6 ] ; then
... |
43670d9a549556b7618dc374d6f9c851442165bf80172294e27e2b6e8d46c5bb | Shell | 10,944 | 11 | #!/usr/bin/env bash
export FREESURFER_HOME=/opt/ni_tools/freesurfer7.4.1
source /opt/ni_tools/freesurfer7.4.1/SetUpFreeSurfer.sh
cd /Volumes/Hera/preproc/7TBrainMech_rest
for id in sub-10129_ses-20180917.long.sub-10129 sub-10173_ses-20180802.long.sub-10173 sub-10173_ses-20200221.long.sub-10173 sub-10173_ses-20210830... |
7085102d3f54557ad3c7be83e5db915b2aa4a63d1cd5731a23df30d9d8688bfd | Shell | 11,099 | 454 | #!/bin/bash
# call somatic variants with Strelka
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 6 ] ; then
echo -e "\n $... |
5dbd6665a4edbf47b7623a4833987c12604b4c23ca3babc3bb504f2d212f718b | Shell | 11,250 | 417 | #!/bin/bash
# GATK realignment and recalibration
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 4 ] ; then
echo -e "\n $... |
19fd8d1debc8a10d71260e163b1f6f0f2e3f77cc7cbe445207aa7df2ca1e43ae | Shell | 11,267 | 285 | #!/usr/bin/env bash
###########################################################################################################################################################
# Author: Filipe Ferreira dos Santos
# Date: 03/22/2024
# This shell script aims to execute all "source_stepXXX.sh" scripts for the differenti... |
e77c94105d7317a0c4268717136b6402c912e16b19d3d4ad8ec0e63d0d7c2293 | Shell | 11,307 | 168 | #!/bin/bash
#$ -cwd
#$ -N magma-gsa_step3-geneSet_MNT
#$ -o ./logs/magma-gsa_step3-geneSet_MNT24Aug2020.o
#$ -e ./logs/magma-gsa_step3-geneSet_MNT24Aug2020.e
#$ -l bluejay,mem_free=32G,h_vmem=40G
echo "**** Job starts ****"
date
model="snp-wise"
ANNO=/dcs04/lieber/marmaypag/Tran_LIBD001/Matt/MNT_thesis/snRNAseq/10x_... |
d5b7e4bde5253887b31d68e442cb2f942bae0bb367f2b4d55ac2c00606af2aa9 | Shell | 11,314 | 297 | #!/bin/bash
cdir=$(dirname "$0")
. $cdir/common
cdir=$(normalpath "$cdir")
pn=$(basename $0)
commandline="$pn $*"
# Check that binaries are available
curdir=`dirname $0`
export PATH=${curdir}/../:${curdir}/../irtk:${curdir}/../niftyseg:$PATH
export LD_LIBRARY_PATH=${curdir}/../../lib/:$LD_LIBRARY_PATH
which ireg >... |
feca6669cbca4f6c8e3f4bf636cff7df01d33323f0552ab391400dbd5bf62ee2 | Shell | 11,443 | 288 | #!/usr/bin/env bash
###########################################################################################################################################################
# Author: Filipe Ferreira dos Santos
# Date: 11/21/2023
# This shell script aims to execute all "stXXX.sh" scripts for:
## - 'differential t... |
a9f835e0576db16ea1f8b52b7854aa32c9b2ea9346d9d88ea2aba4fe4cc0cdd0 | Shell | 11,680 | 22 | #!/usr/bin/env bash
for id in sub-10129_ses-20180917.long.sub-10129 sub-10173_ses-20180802.long.sub-10173 sub-10173_ses-20200221.long.sub-10173 sub-10173_ses-20210830.long.sub-10173 sub-10195_ses-20180129.long.sub-10195 sub-10195_ses-20191205.long.sub-10195 sub-10202_ses-20200103.long.sub-10202 sub-10202_ses-20210924.... |
4bcbf5db10ac7cf18a72c57e031a1dfe1db346e82d031bb8d93486867a431db1 | Shell | 11,694 | 447 | #!/bin/bash
# annotate VCF using ANNOVAR
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 3 ] ; then
echo -e "\n $script_n... |
0dc7d8091a5ced4f9c3c0ad7a74c76378b84c170350d8f8473e2f281576017dd | Shell | 11,762 | 265 | #!/bin/bash -l
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=20G
cd $SLURM_SUBMIT_DIR
date
hostname
###########################################################################################################################################
#Set up the environmental variables
FSLDIR=/sw/fsl
. ${FSLDIR}/etc/fslco... |
1f3b85ff22cae2efd2f07f3e1943f2c54147f14f8d57e677219a0a6896677b02 | Shell | 11,916 | 296 | #!/usr/bin/env bash
###########################################################################################################################################################
# Author: Filipe Ferreira dos Santos
# Date: 08/18/2024
# This shell script aims to execute all "stXXX.sh" scripts for executing the scRNA-seq... |
a58ec83c5cd7f31fadeace19c42d35be7c15997c5253a2c45992ecc688becad1 | Shell | 12,017 | 318 | #!/bin/bash
set -eu
# "Other" is rclone's generic S3-compatible profile (no vendor-specific
# quirks/defaults). Override via S3_PROVIDER if a specific backend needs one
# of rclone's named provider profiles (e.g. AWS, Minio, Ceph).
rclone_s3_args=(
--s3-provider "${S3_PROVIDER:-Other}"
--s3-endpoint "http://$S... |
d1dd96ad6a73d9d0e5c51c7dd5fe19467bf40c368f241a35485f25f1510b9af2 | Shell | 12,411 | 176 | #!/bin/bash
#$ -cwd
#$ -N magma-gsa_step3-geneSet_updated_MNT
#$ -o ./logs/magma-gsa_step3-geneSet_v1.08_MNT08Sep2020.o
#$ -e ./logs/magma-gsa_step3-geneSet_v1.08_MNT08Sep2020.e
#$ -l bluejay,mem_free=32G,h_vmem=40G
echo "**** Job starts ****"
date
model="snp-wise"
ANNO=/dcs04/lieber/marmaypag/Tran_LIBD001/Matt/MNT_... |
7bf44233aae7250b16c9eceedc8ee6815c6f9241eefa911445ca047d0c8b08a5 | Shell | 12,509 | 276 | #!/bin/bash
#set -e
#set -x
function cluster2D {
# Usage: cluster2D <input> <output> <axis> <threshold>
# e.g. cluster2D invol outvol y 0.9
invol=$1
outvol=$2
axis=$3
thresh=$4
tmpdir=`$FSLDIR/bin/tmpnam`
rm $tmpdir
mkdir $tmpdir
$FSLDIR/bin/fslsplit $invol $tmpdir/cl2d -$axis
for fn in $tmpdir/cl2d*... |
80007d549d5b03544dfe69fde7aca1b2fb0693338354d1bf2d857ae9c3d7345b | Shell | 12,547 | 278 | #!/usr/bin/env bash
#
# This is a script to process Split-seq reads. It is a modified version of \
# Drop-seq_alignment.sh provided alongside of Dropseqtools from Steve McCarroll's lab.
#
# Author: Rebekka Wegmann, Snijder lab, ETH Zurich
# Original version Copyright 2017 Broad Institute
# MIT License
#
#
# Permissio... |
bb0e7c821d1b0d10a14a2ac2473f9d3eb94cfc3a0632fddf5e0469db304b072a | Shell | 12,687 | 225 | #!/bin/bash -l
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=10G
export FREESURFER_HOME=/sw/freesurfer_7
source $FREESURFER_HOME/SetUpFreeSurfer.sh
echo $FREESURFER_HOME
export SUBJECTS_DIR=YOURSUBDIR/FS
FSLDIR=/sw/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
export PATH=$PAT... |
6de39a501375b1748c58830c99ed1fe286a75fe2f0124c5d8aabed418951c324 | Shell | 12,772 | 178 | #!/bin/bash
#$ -cwd
#$ -N magma-gsa_step3-GSA_rev
#$ -o ./logs/magma-gsa_step3-GSA_rev_MNT18Jul2021.o
#$ -e ./logs/magma-gsa_step3-GSA_rev_MNT18Jul2021.e
#$ -l bluejay,mem_free=20G,h_vmem=24G
echo "**** Job starts ****"
date
model="snp-wise"
ANNO=/dcs04/lieber/marmaypag/Tran_LIBD001/Matt/MNT_thesis/snRNAseq/10x_pilo... |
023c374d3f80bd6e9e60226f753904dde4f7ead1f0257a4d3c9febcd0b6c7f0d | Shell | 12,794 | 405 | #!/bin/bash
#-----------------------------------------------------------------------------------------
# Spatial registration:
# 1) EPI --> T1
# 2) T1 --> MNI (using predefined cost-function mask in target space)
# 3) Concatenate EPI --> T1 --> MNI
#_____________________________________________________________________... |
2d6d98f929791cc87c6e0607d7c818c93da97b0e92efb201bc8e87878f86df0e | Shell | 12,809 | 268 | #!/bin/bash
set -u -x -e
# Adapted from https://git.fmrib.ox.ac.uk/seanf/asymmetry-analysis/-/blob/master/hcp_surface.sh?ref_type=heads
# This script maps dHCP volumetric fMRI data to the surface
# It is largely a vanilla implementation of the HCP Surface Pipeline
# One of the main changes is that the fMRI is mapped in... |
fb3deb870b1b03e0f5df2a1e17e8738e2bca9cafdf93ceb6421be0fd5773f191 | Shell | 13,685 | 381 | #bin/bash
set -e
export OMP_THREAD_LIMIT=1
export OMP_NUM_THREADS=1
# disable stdout/stderr buffer
export PYTHONUNBUFFERED=1
TASK_NUM=$(printf "%03d" "$TASK_NUM")
TASK_NAME="Task${TASK_NUM}_${TASK_DESCRIPTION}"
# TASK_NUM=$(echo "$TASK" | cut -f1 -d"_" | tr -dc '0-9')
###########################################... |
dd79f2d11680d0ec8d2dd33d96873decd6b5d35ac3fe951a236138ae01d41ef5 | Shell | 14,063 | 423 | #!/bin/bash
set -e # Exit on any error
# =============================================================================
# CONFIGURATION
# =============================================================================
# Default configuration - can be overridden by config file or command line
CONFIG_FILE="${CONFIG_FILE:... |
6565900bec02becbf50940eeef952646d01bb78cd44609b93a253931381142f2 | Shell | 14,339 | 303 | #!/bin/bash
set -u -x -e
# Adapted from https://git.fmrib.ox.ac.uk/seanf/asymmetry-analysis/-/blob/master/hcp_surface.sh?ref_type=heads
# This script maps dHCP volumetric fMRI data to the surface
# It is largely a vanilla implementation of the HCP Surface Pipeline
# One of the main changes is that the fMRI is mapped in... |
a7804add97853d905cb9eeab231cc00b7e8f126469a32d316a6cec1c422bfb14 | Shell | 14,526 | 542 | #!/bin/bash
# call copy number variants with Control-FREEC (WES settings)
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == ... |
08ee73c4d565818890623d60f7aad8832ce8ee0c122473e1023d21a454210a52 | Shell | 14,729 | 46 | #!/usr/bin/env bash
for id in sub-10129_ses-20180917.long.sub-10129 sub-10173_ses-20180802.long.sub-10173 sub-10173_ses-20200221.long.sub-10173 sub-10173_ses-20210830.long.sub-10173 sub-10195_ses-20180129.long.sub-10195 sub-10195_ses-20191205.long.sub-10195 sub-10202_ses-20200103.long.sub-10202 sub-10202_ses-20210924.... |
54f895143b0186cf45137fdf9ad0ecedfc754d7dceced199f3f37db3122af94b | Shell | 14,779 | 480 | #!/usr/bin/env bash
# This BASH script is based on the template from https://github.com/kasperskytte/bash_template
# License is MIT, which means the author takes no responsibilities, but you can use it for anything you want
#exit when a command fails (use "|| true" to allow a command to fail)
set -o errexit
# exit whe... |
89eaeebdd4e6cff3c255bfb8121ed37724e8070547698a80e2e73b03c3d3ffb6 | Shell | 14,794 | 367 | #!/bin/bash
set -eu -o pipefail
# ============================================================================
# Kaapana migration 0.6.x -> 0.7.x (see docs/.../migration_guide_0.7.rst)
#
# upgrade the on-disk PostgreSQL clusters 17 -> 18
# move the admin project namespace + its workflow PVCs from `project-admin` to ... |
25fdee1ca7b02f725117ddd8692e850c18bc35ad67b31fdc4d3be9aab65702e6 | Shell | 15,287 | 522 | #!/bin/bash
set -eu -o pipefail
STORAGE_PROVIDER="${STORAGE_PROVIDER}"
STORAGE_CLASS_SLOW="${STORAGE_CLASS_SLOW}"
STORAGE_CLASS_FAST="${STORAGE_CLASS_FAST}"
STORAGE_CLASS_WORKFLOW="${STORAGE_CLASS_WORKFLOW}"
SERVICES_NAMESPACE="${SERVICES_NAMESPACE}"
ADMIN_NAMESPACE="${ADMIN_NAMESPACE}"
VOLUME_SLOW_DATA="${VOLUME_SLOW... |
8305240dd39839d9549d31d9c61d2b94d6de4871b185e0dddb182aad16fa4af2 | Shell | 16,088 | 310 | #!/usr/bin/env bash
# Auto-detect number of cores (leave 1 core free)
auto_cores=$(($(nproc) - 1))
[ $auto_cores -lt 1 ] && auto_cores=1 # Ensure at least 1 core
# Default values
n_jobs=$auto_cores
subject_id=""
output_dir=""
# Get the directory of the current script
script_dir=$(dirname "$(realpath "$0")")
while ... |
88e1d9f39b99010e790aa18357606b64506033affbade7250fe712100c07d8fb | Shell | 17,262 | 410 | #!/bin/bash
# Setup Specific
PIPELINE_AUTOMATION_DIR="~/fergusonLab/code/"
# Instance Constants
WORKDIR="/media/rs_256/ap_tests"
FASTQDIR="/data/rs_256/fastq"
BWDIR="/data/rs_256/workdir/aligned.aug10"
PEM_FILE="~/fergusonLab/210323.pem"
REMOTE_USER="ubuntu"
print_usage() {
echo "USAGE: bash $0 <EC2_instance> <... |
7d94f144367555b3bbfb76ceaf9f7886b6fe6d14e406b18538ebffc7246663c7 | Shell | 18,402 | 366 | #!/usr/bin/env zsh
# Configuration
data_folder=<... Path to the data folder ...>
temp_folder=<... Path to destination where experiment results will be written to ...>
contamination_package_path=<... Path to the matlab package from Roussels paper about acoustic contamination ...>
settings=config/settings.ini
stage=1
s... |
d570f548f2f8df9563010492290ffda6105ed4026f452cdb506df8c0ce65acae | Shell | 18,645 | 454 | #!/usr/bin/env bash
#-------------------------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
#-----------------... |
55ac06d9e39249c0f3a3013d843d2c110491c431591dcb62eb4c2e40410bab65 | Shell | 21,663 | 454 | #!/bin/bash
#
# Analayses spinal cord data for the Neuromuscular signature R01 project.
#
# Usage:
# sct_run_batch -c <PATH_TO_REPO>/etc/config_process_data.json # TODO
#
# The following global variables are retrieved from the caller sct_run_batch
# but could be overwritten by uncommenting the lines below:
# PATH_... |
8b783d23412f9af88abdf4bdb5f78bd10c131371fab0ec10bb02d3b0a561cc53 | Shell | 28,701 | 977 | #!/bin/bash
# $Id: install.sh 7942 2008-03-26 06:08:08Z xmldoc $
# $Source$ #
# install.sh - Set up user environment for a XML/XSLT distribution
# This is as an interactive installer for updating your
# environment to use an XML/XSLT distribution such as the DocBook
# XSL Stylesheets. Its main purpose is to configure... |
21db34725eeeac4593ad2533dc561cef06b2e039e7b073a42f6cbdad44824612 | Shell | 28,967 | 1,249 | # Create and run locally first level analysis in Feat for all tasks
# Author: Valeria Oliva
echo -n "Which sub? Only insert number >"
read subject
echo -n "where did you mount the Project folder? write path (e.g. for vale it is '/home/valeo/') >"
read projectpath
echo -n "session? 01 or 02 >"
read ses
cd ${proje... |
6d2815835c13bf54dfd65bbebbdd5d64c4088a69373d7aa6f659b28c01d36d44 | Shell | 28,994 | 1,249 | # Create and run locally first level analysis in Feat for a chosen task
# Author: Valeria Oliva
echo -n "Which sub? Only insert number >"
read subject
echo -n "where did you mount the Project folder? write path (e.g. for vale it is '/home/valeo/') >"
read projectpath
echo -n "session? 01 or 02 >"
read ses
echo -... |
5121e0f6be6d55a1f15a841f6da43655373fdc4e11217458fac5673b98ae661b | Shell | 29,633 | 865 | # main script functions
function filter_reference_files() {
echo "Preprocessing reads: $READS"
if [ ! -d "$OUTPUT_NAME/temp_files/refs" ]
then
mkdir -p "$OUTPUT_NAME/temp_files/refs"
fi
# filter GTF by ensembl id
grep $ENSG_ID $ANNOTATION > $OUTPUT_NAME/temp_files/refs/filt_chr.gtf
ANNOTATION_FILT=$OUTP... |
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