sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
dde639280ceeb282e0d48ea532b254323a9951115b2a537b01f4e5670d47443d | Shell | 3,622 | 152 | #!/usr/bin/env bash
#add parent directory to PYTONPATH
D=$(cd ../ && pwd)
export PYTHONPATH="${PYTHONPATH}:$D"
#default
CUT=false
MASK=false
BOUNDARY=false
USAGE="usage:\n\
'basename $0' -i <image file> -t <treshhold> [-m <mask-file>] [-c] [-s <size> -a <axis> -d <direction>] [-b] [-x]\n\
-i: Image file name to cr... |
a5725fcc6833a8ef0b198973aa06560d8cb44318cb4ef41cac4ab670c65719c5 | Shell | 3,647 | 73 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
3551eff1ab05dadbe172ad7638eaeeaca18677159ae80c25d24e99a7c4f6bc56 | Shell | 3,660 | 120 | #!/usr/bin/env bash
set -euxo pipefail
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE:-$0}")"; pwd)"
WORKSPACE_DIR="${ROOT_DIR}/.."
get_python_version() {
python -s -c "import sys; sys.stdout.write('%s.%s' % sys.version_info[:2])"
}
is_python_version() {
local expected result=0
expected="$1"
case "$(get_python_ve... |
5acf075dcb597fc48438fcd949d56ac0fcda5b58cbf34898de74944591e2f051 | Shell | 3,689 | 80 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
#... |
0dc2d6dbb101a041eeefd74ef89feefec33d18bce12122e4357a7a4431b1fb13 | Shell | 3,690 | 121 | #!/bin/bash
export PATH=$(pwd)/../bin/:$PATH
##export PATH=/bioinfo/local/curie/ngs-data-analysis/centos/HiC-Pro_2.10.1/bin/:$PATH
function die
{
echo -e "Unit testing failed !"
exit 1
}
## HiC-Pro should be install and in the PATH
which HiC-Pro > /dev/null;
if [ $? != "0" ]; then
echo -e "Can not procee... |
11d98989a8b38626c39268b354288f4fc127081adfe7e791f9faca31ef48cf3f | Shell | 3,691 | 101 | #! /bin/bash
# ============================================================
# bash to call genotypes from combined gvcfs
# ============================================================
# get command line options
# ============================================================
args=`getopt -o "r:,d:,i:,t:,p:,u:" -l "res... |
a5969a7351ad258b9abc198a83542bb4f1eb418715a28b8964082baa394ff62b | Shell | 3,725 | 68 | #!/bin/bash
# Set the number of cores to use
NCORES=20
# Ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
datadir=/ZPOOL/data/projects/rf1-sra-data/derivatives/fmriprep
tasks=("trust" "ugr" "sharedreward" "doors" "socia... |
5f80877f80856717ea6b13956e66241d986c633a0b345c08f1840858535bbd60 | Shell | 3,731 | 79 | #!/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... |
7357fd5bcbfe9b32fcf7e01740840b3bd2a7c5b2f6da2c08c8ae2a377f1069b1 | Shell | 3,736 | 106 | #!/usr/bin/env bash
set -ex
unset RAY_ADDRESS
if ! [ -x "$(command -v conda)" ]; then
echo "conda doesn't exist. Please download conda for this machine"
exit 1
else
echo "conda exists"
fi
# This is required to use conda activate
source "$(conda info --base)/etc/profile.d/conda.sh"
PYTHON_VERSION=$(pyth... |
740522d4d2939b5f390f8f3d77f897158e2e08bbc9c69a4add7d58d9a70ac0f2 | Shell | 3,742 | 96 | #!/bin/bash
# ---------------------------------------------------------
# Run differential celltype analysis for multi-region data:
# Updated: 10/14/2020
# OLD version of analysis
# ---------------------------------------------------------
source $HOME/data/DEVTRAJ/bin/mosaicism/config_mosaic.sh
conda activate mv_env
... |
c683fd292be96a7ccc406343d90ab25d2ee30ad863c5b9c4d4db35840235f4c3 | Shell | 3,750 | 105 | #!/bin/bash
# small-rna-prep-star.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_2.4.2a)
#(cd STAR; make)
# If available, will print tool versions to stderr and json string to stdout
... |
a6b3de8c9fa5ff606d3b7061af9c64a8408f25c75a08e1ac8e2b959a3d7d6ba9 | Shell | 3,766 | 116 | #!/bin/bash
# shellcheck disable=SC2086
# This script is for users to build docker images locally. It is most useful for users wishing to edit the
# base-deps, or ray images. This script is *not* tested.
GPU=""
BASE_IMAGE="ubuntu:22.04"
WHEEL_URL="https://s3-us-west-2.amazonaws.com/ray-wheels/latest/ray-3.0.0.dev0-cp3... |
1b5f5d1e3b26bc52c42ec7aa74241bc8387fbafd836a57e5f9c30631f8f7d926 | Shell | 3,770 | 109 | #! /bin/bash
# ============================================================
# bash to call combine GVCFs with parallel
# ============================================================
# get command line options
# ============================================================
args=`getopt -o "r:,d:,l:,i:,t:,p:,u:" -l "re... |
91241b76176e67e47cf917a1a143a31bd875c9549f34723868ec8abda9db0597 | Shell | 3,776 | 86 | #!/bin/bash
# rampage-peaks.sh
main() {
#echo "* Installing python-dev cython python-scipy python-networkx..."
#sudo apt-get install -y gcc python-dev cython python-scipy python-networkx | tee -a install.log 2>&1
#echo "* Installing pysam..."
#sudo easy_install pysam >> install.log 2>&1
echo "* Ins... |
2819e22c8af00e4b5287ae48cc043765cd44350581e42baa2b12d489f891f514 | Shell | 3,790 | 88 | #!/bin/bash
#Defines the identity of the pipeline being run. Will need to be updated accordingly.
pipeline="0"
#Defines a variable based on the location of files that have generated in fMRIPrep for processing in FEAT.
feat_folders="<directory root>/FEAT/Pipeline_${pipeline}/" #Full path removed for purpose of public ... |
d048da69f8ea93d662b33ed25f2a3d979e0adc26101c2e19912fcef964de1bdb | Shell | 3,796 | 75 | #!/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... |
7aa2c2680cd8bede8e7f1c7902b6d25af8b0283cfa06952471edb10f5583f748 | Shell | 3,797 | 75 | #!/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... |
e09f04c252cc730097320a463a57d7a37acbbed744bf319ac4da3aa3db62bebe | Shell | 3,827 | 98 | #!/bin/bash
# rampage-idr.sh
main() {
echo "* Installing Anaconda3-2.2.0 (python3.4.3, numpy-1.9.2 matplotlib-1.4.3..."
set -x
wget https://repo.continuum.io/archive/Anaconda3-2.2.0-Linux-x86_64.sh >> ../install.log 2>&1
bash Anaconda3-2.2.0-Linux-x86_64.sh -b
ana_bin=`echo ~/anaconda3/bin`
# p... |
7ab5399f86af6ad7f024e63d21304c4674d71791d592c1c00a4ea9737532405d | Shell | 3,835 | 139 | #!/bin/bash
## HiC-Pro
## Copyright (c) 2015 Institut Curie
## Author(s): Nicolas Servant
## Contact: nicolas.servant@curie.fr
## This software is distributed without any guarantee under the terms of the BSD-3 licence.
## See the LICENCE file for details
##
## Create SLURM Torque files
... |
e6723c97c264524f7e68c7732125bed86dd07d01eacb29fb97794c98a079acd2 | Shell | 3,837 | 106 | #!/bin/bash
# prep-star.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_2.4.0h)
#(cd STAR; make)
# If available, will print tool versions to stderr and json string to stdout
version... |
decfec76a024bc964239224f97f5cfa1b0bcbb58511b8017a89a329b4f3b1b19 | Shell | 3,839 | 91 | #!/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 ... |
03777d3b78f600be16fb628da4c1fd8ea69ad34f9f8d3795ee392733acff7e68 | Shell | 3,851 | 136 | #!/bin/bash
## HiC-Pro
## Copyright (c) 2015 Institut Curie
## Author(s): Guipeng Li, Nicolas Servant
## Contact: nicolas.servant@curie.fr
## This software is distributed without any guarantee under the terms of the BSD-3 licence.
## See the LICENCE file for details
## Adapted for LSF ... |
2a6e059c1c4acb65ba44d1c41e39aa93aed728b10c1d12625d12f2213857b83b | Shell | 3,879 | 89 | #!/bin/bash
#
set -euo pipefail
PE_counts=$1
metric_file=$2
##load metric file##
pe_count=$(awk '{if($1=="pe_count") print $2}' $metric_file)
median_hom=$(awk '{if($1=="median_hom") print $2}' $metric_file)
sd_het=$(awk '{if($1=="sd_het") print $2}' $metric_file)
zcat ${PE_counts} \
| { fgrep -v name || [[ $? ==... |
fa6fd44b69579d1572841d550ce712f071cdd3cc2ec4c91ea9be4c20425b53a3 | Shell | 3,880 | 151 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO_ROOT="$(cd "${SCRIPT_DIR}/.." && pwd)"
cd "${REPO_ROOT}"
MODE="all"
SCILENCE_ARGS=()
for arg in "$@"; do
case "${arg}" in
stage1|stage2_unknown|stage2_known|stage2|all)
MODE="${arg}"
;;
--scile... |
5b4b4e762e17b81a0455cfa681666eb832ea961341266aa70f5fcadf3bf76727 | Shell | 3,882 | 107 | #!/bin/bash
# prep-rsem.sh
main() {
# Now in resources/usr/bin
#echo "* Dowload and install RSEM..."
#git clone https://github.com/bli25wisc/RSEM.git
# (cd RSEM; git checkout tags/v1.2.19)
### get correct commit bit from submodule
#(cd RSEM; make)
# If available, will print tool versions t... |
ffe1bd9fb0132280feb06abd7c795842d757507361a29f0dfe3385e9d6db0df9 | Shell | 3,890 | 135 | #!/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
##
## Create PBS Tor... |
fd158f76470cf5968cadf17ed5622c211ceff1d20cc33cc45413e7a3e09ee77c | Shell | 3,892 | 78 | #!/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... |
d40e0120a10eeee15c9b44e391a987b68f42b1bc404ad4abaad24521a662414d | Shell | 3,920 | 92 | #!/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... |
7f36c53813685a003791ef124a7b20c7ddf2a9cf1b4fbc5feef400106f011445 | Shell | 3,924 | 92 | #!/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... |
f92c6be841b9b90c7eaa0bd6c2d0e3a7e99af24ac15e31912552c5599e436fe6 | Shell | 3,935 | 72 | #####Bash script to get read depth percent error using Allo and SmartMap. Example for ENCFF631JSV and ENCFF715KYL.
#Requirements: Bowtie2, macs2, samtools, bedtools, cutadapt, SmartMap, Allo, and sm_prep.sh (provided on github).
####Download and alignments####
wget -q https://www.encodeproject.org/files/ENCFF631JSV/@... |
7d27549066492cc78764950e07c4ec8856e53d28aa4aeb936f24f54bb6fc5b1f | Shell | 3,936 | 114 | #!/usr/bin/env bash
set -o errexit
#set -o pipefail
set -o nounset
#to run
#bash do_all.sh 2>&1 | tee <name>.log
#can replace pigz with gzip -c if prefered.
#SET THESE ARGUMENTS -- not passing these in -- just gets too messy.
BUCKET_ROOT="gs://ml4h-core/ukbb/2023-08-4" #gs://ml4cvd/projects/pbatra"
DATASET="ukbb7089... |
f4abf1856447890e94734b972c0e52f489472fd181ea53a1afe2c4aa898fb9a3 | Shell | 3,941 | 105 | #!/bin/bash
# 'KAS-Analyzer bedGraphToBigWig' was developed by Ruitu Lyu on 12-10-2021.
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer ToBigWig [ -h/--help ] [ -k KAS-seq ] [ -s assembly id ]"
exampleHelp="Example: nohup KAS-Analyzer ToBigW... |
4ccb091e02e2c696d591bd30a0d9ed71116281057b5acb615cceeebb8e4446bd | Shell | 3,954 | 82 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=2:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
c193a995d7390ccd8f45f31328e02546a53ad5db8d4c72ee21d132581e0c0232 | Shell | 3,957 | 102 | #!/bin/bash
# align-tophat-se.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... |
304e05c78b06cbc6b965f431c299afefe2a1200dc15d3bb106d79111ebed355d | Shell | 3,966 | 122 | #!/bin/bash
### PASTE AND RUN THIS IN THE /ichinose/ DIRECTORY
RUN_ID=210825_transcriptome_Nsyb_Repo
WORKING_DIR="./${RUN_ID}"
###Save pool.csv files in the /ichinose/ directory###
SAMPLE_LIST=
SAMPLE_ID=( $(cut -d ',' -f1 ${SAMPLE_LIST} ) )
DEPLETION_SOURCE="./190919_Neuro_Glia/genome/fly_ncrna"
GENOMEINDEX_DIR="./... |
2599a74281429377e9f9c3b345dc63fcbc3950dc2e0c1485c939d44b94732542 | Shell | 3,978 | 16 | 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 rtts-atss_r... |
4870fdb190d6db5762db55ee7a1834ad979e95bc6a5e474c607548b4cc103ea2 | Shell | 3,997 | 64 | #!/bin/bash
source /com/extra/ucsc/2015-04-21/load.sh
# v2 improves intron definition by using ucsc table browser introns and intron retention is now only searched in bsj spanning reads, not all reads as before
## Human
sample=old_hBr_circ
genomeSize=/home/mtv/software/IGVTools/genomes/hg19.chrom.sizes
fa=/home/mt... |
3fb1dedf9965cb7264d8524560e93f21329a671e1f467d70f22560186e5060e0 | Shell | 4,016 | 79 | #!/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... |
ca5bae25cd9a1aadf79011c6603f384497d7f7b7a9b31f28fae023470c8440ca | Shell | 4,016 | 79 | #!/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... |
51bb296e9dd78d5a06159089e3018e0801f719d46ad484e737ede221d83e5c3f | Shell | 4,019 | 101 | #!/bin/sh
# CBIG_IndCBM_compute_profile.sh <surf_mesh> <proj_dir>
# This function calls CBIG_MSHBM_generate_profiles.m and CBIG_MSHBM_avg_profiles.m to compute profiles based on a MSHBM
# folder structure. See CBIG_CODE_DIR/brain_parcellation/Kong2019_MSHBM for details.
# Input:
# surf_mesh: mesh name for your surf... |
77cc3a7285e3b8ef6e723cb9eeab8022a17f699105293447c6caec6f4cdbb39c | Shell | 4,055 | 92 | #!/bin/bash
# STAR mapping / RSEM quantification pipeline
# usage: from an empty working directory, run
# ./STAR_RSEM.sh (read1) (read2 or "") (STARgenomeDir) (RSEMrefDir) (dataType) (nThreadsSTAR)
# input: gzipped fastq file read1 [read2 for paired-end]
# STAR genome directory, RSEM reference directory - pre... |
e953784678ca266b8ad29270e56d955fb83f186db91d8f288cbc34b0f2e2ec10 | Shell | 4,085 | 134 | #!/bin/bash
if [ "$#" -ne 3 ]
then
echo "Usage (example): `basename $0` benchRT gamma Linux"
echo "The reference will be built from the benchRT/'output' folder content, based on the list of files provided in the reference/gamma.txt file. Linux is the architecture (not mandatory)."
exit 1
fi
echo
echo "The... |
8aa820e69b10f7bb4e44e6794e1a742c63f583db1ce5da0f09f7ba169aee0f25 | Shell | 4,119 | 184 | #!/bin/bash
echo "Initialazing Solr Schemas creation"
curl -X POST -H 'Content-type:application/json' --data-binary '{
"add-field":{
"name":"ATC",
"type":"string",
"indexed":false,
"stored":true},
"add-field":{
"name":"ATC_level",
"type":"pint",
"indexed":false,
"stored":t... |
669b06833bacdcfa5c3c5a31d7ff35d298aadec97746dac3f4a2083a202dca4f | Shell | 4,138 | 45 | echo ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Attanet resnet <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
#echo -e ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Attanet resnet <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
python3 Xavier_SpeedTest.py --weight '/media/Data/ignored/AttanetRN18/08022022_212634/best_model_epoch2865.pth' --net Atta... |
5f711c77cfaa3ef27749f51c9d6782a465aea02b47b0e7931049c317aeefd75e | Shell | 4,160 | 120 | #!/bin/bash
# This script is a bash implementation of the following workflow/task in WDL:
# Filename: wdl/CollectSVEvidence.wdl
# Workflow: CollectSVEvidence
set -Exeuo pipefail
if [ -z "${SV_SHELL_CLEAN_UP_WORKING_DIR:-}" ]; then
SV_SHELL_CLEAN_UP_WORKING_DIR=true
fi
# ------------------------------------------... |
5e10fc8bc51dfe1df5e3c32c2c0e8e1df67a2c6d31fbb4a0d25d9509ae303313 | Shell | 4,161 | 107 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if ... |
249dfc4d000ac3095db9cb84866f5e6f0690bdb97bd3db0cb93a562b5b0a8ba0 | Shell | 4,174 | 112 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2025, Open Brain Institute
# Author(s): Marwan Abdellah <marwan.abdellah@openbraininstitute.org>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
... |
ae785b950253df4d2518072dc48eebf7cd57526a9daefb905b6d93d0446a4c03 | Shell | 4,231 | 56 |
#! /bin/bash
# 7-21-21 run
for RNANAME in W134.Apex W135.Left.Vent W136.Apex W136.Left.Vent W139.Apex W139.Left.Vent W139.Right.Vent W139.Septum W142.Left.Vent W144.Apex W145.Apex W145.Left.Vent W146.Apex W146.Left.Vent; do
qsub -P trapnelllab -pe serial 16 -l centos=7 -l mfree=20G -wd /net/trapnell/vol1/home/readdf... |
6846f94fd91f1ac8bff385cc13fdd2c1f88e884d25a5602a1ebd05be4a7434a3 | Shell | 4,266 | 161 | #!/bin/bash
# Run FEAT once, and if FLAME fails with excessive outliers, retry with robust_yn=0
# using a fresh output directory to avoid stale intermediate state.
set -u
if [ $# -lt 2 ] || [ $# -gt 3 ]; then
echo "Usage: $0 <feat_binary> <fsf_file> [njobs]" >&2
exit 2
fi
feat_binary="$1"
fsf="$2"
njobs="${3:-}"... |
5407522be9bc21ae00ac9e82cf4fae376aa3f0c1f7cdd05b4629d7c3858fd1a7 | Shell | 4,281 | 53 | ##Generate merged idx for m6A-peaks across tissues
cat ~/2SMR/Results/*.m6A2ha.mr.fdr.res |grep -v exposure |cut -f 1 |sort -u |sed 's/_/\t/g' |awk -v OFS='\t' '{print $1,$2,$3}' |sort -k 1,1V -k 2,2n |\
bedtools merge -i - |awk '{print $0"\tm6A-"NR}' > ~/Downstream_analysis/Cross_tis_consistency/Merged.m6A_idx.m6A2ha... |
71e09a6e6f49484d1c02b1dbed3c2a9340a5d0fd27d3a54a80d2103d807c3671 | Shell | 4,297 | 84 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=2:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
d4e6286485d791cc0633b608fb40a988b99b85b4adf69109a0dc11da827b77d1 | Shell | 4,308 | 139 | #!/bin/bash
# 'KAS-Analyzer readsnum' was developped by Ruitu Lyu on 1-18-2022.
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer readsnum [ -h/--help ] [ -o prefix ] [ -f format ] "
exampleHelp="Example: nohup KAS-Analyzer readsnum -o KAS-seq... |
27b7d256f90f5f79b7685efca183b7f279f5759c669f4c7b33560947779bdbfc | Shell | 4,318 | 118 | #!/bin/bash
# prep-tophat.sh
main() {
# Now in resources/usr/bin
## install tophat 2.0.8
#wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.8.Linux_x86_64.tar.gz
## install bowtie2_2.1.0
#wget http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/bowtie2-2.1.0-linux-x86_64.zip/d... |
fc5bf48c475f57561327ff2f90050751db5b6f120ac912f8e5de888408fc9093 | Shell | 4,323 | 86 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
78aa16310d0b39494f16735cad32a435c3b30c5472b7812aee999ac085c33353 | Shell | 4,334 | 125 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
8ff9e8671eebbb7bd67210b430acda1bdcc184bb2aa2783a5dc31d5a25eafb87 | Shell | 4,348 | 128 | #!/bin/bash
# 'KAS-Analyzer fragmentsize' was developed by Ruitu Lyu on 12-14-2021.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer fragmentsize [ -h/--help ] [ -o prefix ] [ -l labels ] [ -k KAS-seq ]"
exampleHelp="Example: nohup KAS-Analyzer fragmentsize -o KAS-seq_fragmentsize -l labels.txt ... |
9ca89a1ac2e92e5ea6f92f77865261cefa6832d0835e0e077a15f4eeea0a0a1b | Shell | 4,350 | 141 | #!/bin/bash
SCRIPTNAME=$(basename $0)
USAGESTR="
NAME
${SCRIPTNAME} Evaluate eye movements reconstructions with MS-SSIM and LPIPS
Assumes that reconstructions have been previously produced using the
eye_movements_Reconstruct_grid_and_generate.sh shell script, and are
in the corresponding locations produced by that s... |
c4a0de3e22798c2b715987119dd96072b7034b637a573b14896e9c35a9503784 | Shell | 4,357 | 106 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --ntasks=1
#SBATCH --mem=128000
#SBATCH --time=16:00:00
#SBATCH --partition=prod
#SBATCH --job-name="synaptome"
#SBATCH --constraint=volta
#SBATCH --account=proj3
#SBATCH --output=/gpfs/bbp.cscs.ch/project/proj83/visualization-SSCXDIS-178/synaptome/trial-4... |
4fbc041b8790ca880a868d457e91f7d2405232f29a13f24ff6c07bb1afcce8a6 | Shell | 4,361 | 106 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --ntasks=1
#SBATCH --mem=128000
#SBATCH --time=16:00:00
#SBATCH --partition=prod
#SBATCH --job-name="synaptome"
#SBATCH --constraint=volta
#SBATCH --account=proj3
#SBATCH --output=/gpfs/bbp.cscs.ch/project/proj83/visualization-SSCXDIS-178/synaptome/trial-4... |
8fd1051a1c908eaf1656d0567d9b473f647cca1fb406801c01397d1c6c0eef1d | Shell | 4,387 | 24 | #!/bin/bash
cd /E-P-INs/Scripts/
module purge
source ~/.bashrc
conda activate bedtools
# ATACSeq Read Counts
bedtools multicov -bams /Neuro_7TP_ATACseq_OUT/ATACseq_0hr_rep1/ATACseq_0hr_rep1_shifted.bam /Neuro_7TP_ATACseq_OUT/ATACseq_0hr_rep2/ATACseq_0hr_rep2_shifted.bam -bed /E-P-INs/Network/Components/ABC_Network_Un... |
15f4eece073175d6d8e600278ae1fbe493d246ee0e3178d2d9b1958a949964c7 | Shell | 4,400 | 158 | #!/usr/bin/env bash
# Script to merge HD5 tensors
################### VARIABLES ############################################
DESTINATION=
SOURCES=
NUM_JOBS=96
INTERSECT=""
INPLACE=""
SAMPLE_IDS_START=1000000
SAMPLE_IDS_END=6030000
SCRIPT_NAME=$( echo $0 | sed 's#.*/##g' )
################### HELP TEXT ###########... |
8e3974d9e67e9ba1b23e1feafe502d742bd9c91b92ead4a95a260eb4956b0d99 | Shell | 4,402 | 94 | #!/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... |
7f757dcd0f50ffeded37ce2e46055f58aac71a1b75af44dfc6dbcc8e2a753846 | Shell | 4,408 | 85 | #!/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... |
de932baf6efbf036bda8516191f377d96768a97d9ad47c7f7120bea8325d5599 | Shell | 4,408 | 85 | #!/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... |
1839f0d91044ccf9c648e7afa45f272882f5a21aa486d768ecebd56b5d88f122 | Shell | 4,414 | 110 | #!/bin/bash
# small-rna-align.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_2.4.2a)
#(cd STAR; make)
#wget https://github.com/samtools/samtools/archive/0.1.19.tar.gz
# If availabl... |
3ebeb1997b291d5ccf68b75238451f41fdc898a924b2666f56a83b96ca7ca63b | Shell | 4,435 | 153 | #!/bin/bash
# Default settings
PORT=8000
COMMANDS=()
DEFAULT_COMMANDS=("run_nbs" "convert_nbs" "clear_nbs" "script_docs" "serve_docs")
RUN_DEFAULTS=true
# Initialize error collection
errors=()
# Function to handle errors
handle_error() {
local error_msg="$1"
echo -e "\n❌ Error: $error_msg"
errors+=("$err... |
e11ca84b5cc9ffc1cf37b108f7cac40a2ff7d1908c90a9070e0ea3e41111729e | Shell | 4,475 | 84 | #!/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... |
a599ac32e0d181b4fd7a360ea6159386a9d4f65de56032c2899bd827196267e8 | Shell | 4,498 | 88 | #!/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 ... |
995002daad4847f15f5930caf150d1d57ace05758e5c68223078da8bc4e66afa | Shell | 4,517 | 99 | #!/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 ... |
493131ecef58c586c0c493e8b0dbc8c5808e8354c37ed66fe070804a00b78f07 | Shell | 4,529 | 133 | #!/usr/bin/env bash
set -exuo pipefail
arg1="${1-}"
BAZELISK_VERSION="v1.16.0"
platform="unknown"
case "${OSTYPE}" in
msys)
echo "Platform is Windows."
platform="windows"
# No installer for Windows
;;
darwin*)
echo "Platform is Mac OS X."
platform="darwin"
;;
linux*)
echo "Pla... |
6fc2f6e750d57a2a8a5c4a5864c5b2e314b92dd1bd20229e9bd47bcb8a05c5c6 | Shell | 4,547 | 92 | # shellcheck shell=bash
# Point bazel's own downloader at the CI package mirror. Source this, then call
# rayci_bazel_downloader_config where the mirror has just been found reachable, or
# rayci_bazel_downloader_restore where ~/.bazelrc has just been rewritten.
#
# This is a separate mechanism from the pip index, and n... |
ce6fc1ee897e97c7672ba763e22c629ec4f4c959e00272f0310816663c298fbc | Shell | 4,553 | 159 | #!/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 ... |
cfe893bf1c242883144b347e647b3cf29d3a1440dd84d53c31a30f177cfa2684 | Shell | 4,560 | 57 | #!/bin/bash
# Make folders
mkdir -p $1
# Download data
if [[ $3 != "skip" ]]; then
echo -e "\033[1mDownloading test data\033[0m"
mkdir -p $2
wget -O $2/human_brain_100k.fq.gz https://www.dropbox.com/s/6i7gkb3r81u2kpn/human_brain_100k.fq.gz?dl=1
else
echo -e "\033[1mSkipping test data\033[0m"
fi
if [[... |
af40cca5116a99f8105babdda00a617104a49fcf3e32a64c7166fafe94f09891 | Shell | 4,590 | 140 | #!/usr/bin/env bash
# This script can be used to build and tag a 'ml4h' image, optionally push it to Google Container Registry,
# and again optionally, tag the image also as 'latest_<gpu|cpu>'.
#
# It assumes 'gcloud' has been installed, Docker has been configured to use 'gcloud' as a credential helper
# by running 'g... |
e32d2127fdc1e879dd30a531d79a44c07ad57d14260e54291744e16cab096bf4 | Shell | 4,606 | 133 | #!/bin/bash
image=$1
file=$2
#Describe the Y positions of reads
seq 50 +15 20000 > RANGE
#Extract the start X and Y position of the reads from the file input
StartX=$(cat $file | awk -v OFS="\t" '{if (NR >1) print $1}')
#EndX=$(cat $file | awk -v OFS="\t" '{if (NR >1) print $2}')
#StartX_bottom=$(cat $file | awk -v... |
dcb618d82b157929b5c8b0ad57fb9400b520d9d1308b1f6c3241d8eec4cc6015 | Shell | 4,614 | 98 | #!/bin/bash
#
# This script performs:
# - segmentation of rootlets using T2w model (model-spinal-rootlets_ventral_D106_r20240523) on the HC-Leipzig 7T MP2RAGE dataset
# Note: these segmentations are only initial and require manual corrections
# Authors: Katerina Krejci
#
# Uncomment for full verbose
set -x
# Immediat... |
c71b94cac36e60e364eb479339e6a34fd13b378f47401ef155384a75a742c669 | Shell | 4,624 | 146 | #!/bin/bash
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
set -Exeuo pipefail
if [ -z "${SV_SHELL_CLEAN_UP_WORKING_DIR:-}" ]; then
SV_SHELL_CLEAN_UP_WORKING_DIR=true
fi
function getJavaM... |
c0eaad3143c196f968914c0c00f895bb0c0e7a068761d15b946b5bec71693303 | Shell | 4,634 | 106 | #!/bin/bash
#SBATCH -c 1
#SBATCH -p normal
#SBATCH --mem=32g
#SBATCH --time=12:00:00
species=mouse
sample=20191227_28_mBrain_mRNA
if [ "$species" = "human" ] ; then
fa=~/long_read_circRNA_v2/data/human/hg19.fa
mRNA=~/long_read_circRNA_v2/data/human/Human_refFlat_hg19_Oct2018.unique.merge.bed
exon=~/long_read_circRNA... |
e908d4f6325b7996abd0b0c47ef68fd4906f4f748886433d2f519e232e53e8a4 | Shell | 4,634 | 84 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2020, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
924e524f944976c338de0e0dd88ab67951fd3e5fd5e254fee486d66a4d47de07 | Shell | 4,640 | 106 | #!/bin/bash
#SBATCH -c 1
#SBATCH -p normal
#SBATCH --mem=32g
#SBATCH --time=12:00:00
species=human
sample=20191230_20200102_hBrain_mRNA
if [ "$species" = "human" ] ; then
fa=~/long_read_circRNA_v2/data/human/hg19.fa
mRNA=~/long_read_circRNA_v2/data/human/Human_refFlat_hg19_Oct2018.unique.merge.bed
exon=~/long_read_c... |
b6a21e1abd4785d7b789c8d5f900c0bd634d0bff53ad6007e6a4d69162d0324a | Shell | 4,653 | 179 | #!/bin/bash
# Wrapper script to run cn.MOPS workflow from a list of binCov input files
set -e
#Usage statement
usage(){
cat <<EOF
usage: cnMOPS_workflow.sh [-h] [-r REBIN] [-o OUTDIR] [-c CLEANUP] [-x EXCLUDE] [-S SUBTRACT] [-M MATRIX] BINCOVS
Wrapper script to run cn.MOPS workflow from a list of binCov input file... |
e8e34a3568869db6ab5fb627634fcc274bbaff858404b72b7e842f1d41dea1a1 | Shell | 4,653 | 143 | #!/bin/bash
SCRIPTNAME=$(basename $0)
USAGESTR="
NAME
${SCRIPTNAME} Evaluate eye movements reconstructions in frequency domain
Assumes that reconstructions have been previously produced using the
eye_movements_Reconstruct_grid_and_generate.sh shell script, and are
in the corresponding locations produced by that scri... |
37b328eed34f11d6cabb659a83641fd70b814bb3378e916e5a1250ea5caaa757 | Shell | 4,654 | 154 | #!/bin/bash
# Gather relevant complex SV intervals for testing
set -e
###USAGE
usage(){
cat <<EOF
usage: gather_cpx_intervals_for_rd_gt.sh [-h] [-D <integer>] [-I integer] INVCF OUT
Reassign variant labels based on depth regenotyping in mod04b
Positional arguments:
INVCF Input VCF prior to re... |
b0c42a58cbc9cd6d7b98aae9addf2d54f79f37cae431053d514f3240d51c7eac | Shell | 4,662 | 119 | #!/bin/bash
# usage
if [ -z "$2" ]; then
echo "$0: read_filename data_descriptor [shasta_descriptor]"
exit 1
fi
# Set the exit code of a pipeline to that of the rightmost command
# to exit with a non-zero status, or zero if all commands of the pipeline exit
set -o pipefail
# cause a bash script to exit immediately ... |
cb62c02bd177796cac81ee42ab7705fdc73feb9a223018f68fc1e46bd48cb37f | Shell | 4,663 | 127 | #!/bin/bash
## HiC-Pro
## Copyright (c) 2015 Institut Curie
## Author(s): Nicolas Servant, Eric Viara
## Contact: nicolas.servant@curie.fr
## This software is distributed without any guarantee under the terms of the BSD-3 licence.
## See the LICENCE file for details
##
## Launcher for a... |
15af43448782b304dfcbdd8c1ce869c0e513d236cce03ba3943bddef7a0dcdaf | Shell | 4,675 | 91 | #!/bin/bash
# 01_Feat.sh
#what shall be done
create_fsf=1
run_feat=1
normalize_feat=1
#Directories
original_fsf=/data/pt_02306/main/code/github/pain-reliability-spinalcord/helper_functions/design.fsf
for subject in {1..40}; do
for session in {1..2}; do
printf -v sub "%02d" $subject
printf -v ses "%02d" $se... |
6beb6e4c0d0c9bb63c4a8ca870968131758014f4efe6c01448c387ee8094d6ad | Shell | 4,689 | 159 | #!/bin/bash
USAGESTR="
NAME
${SCRIPTNAME} Flashed reconstruction grid search and generation
SYNOPSIS
${SCRIPTNAME} <config> <output_base> [optional one-letter arguments]
OPTIONS
-y <path-to-yaml> Use specified YAML, rather than auto-generate
-o Just run the generation portion only; assumes... |
38b2e118dad88c2dd56bd2447998b4b6abcb4473e712f6f07e6de1b2b532c2a7 | Shell | 4,748 | 94 | #!/bin/bash
# 01_FeatDHR.sh
#what shall be done
create_fsf=1
run_feat=1
normalize_feat=1
#Directories
original_fsf=/data/pt_02306/main/code/github/pain-reliability-spinalcord/helper_functions/design.fsf
for subject in {1..40}; do
for session in {1..2}; do
printf -v sub "%02d" $subject
printf -v ses "%02d" ... |
7f6ef2dbac3ea0287d1ad73ec98768dccad6c553291be0fa7808a89f00a44fbf | Shell | 4,748 | 109 | #!/usr/bin/env bash
# bamclipper.sh
VERSION=1.1.1
NTHREAD=1
SAMTOOLS="samtools"
PARALLEL="parallel"
UPSTREAM=1
DOWNSTREAM=5
SAMTOOLS_VERSION_REQUIRED=1.3.1
PARALLEL_VERSION_REQUIRED=20130522
# show usage if no option is provided
if [[ "$#" -eq 0 ]]; then
echo >&2 "Program: BAMClipper (Remove primer sequence from ... |
37bcb37dfe7c6f5ff954229656eb32c808e9055ddfc769ec4a9ebc83ef79a059 | Shell | 4,758 | 91 | #!/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... |
b6dc81f2acb0e7714ea8b32d30e0bc40e0029a189bb0fbb221d53331742f3616 | Shell | 4,773 | 80 | #!/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... |
b180b9a1c6ba890ad4611ca1a4c4d108bf50ef560a96ac1a4e0bb52ef9a29b70 | Shell | 4,782 | 41 |
echo ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Attanet resnet <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
#echo -e ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Attanet resnet <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
python3 Xavier_SpeedTest_val.py --weight '/media/Data/ignored/AttanetRN18/08022022_212634/best_model_epoch2865.pth' --da... |
7740d5bc54232bd460e8bc0886e97acb48465e78b5a468501351f345015b9de7 | Shell | 4,784 | 83 | Phe1=$1
Phe2=$2
if [ $Phe1 = "m6A" ]; then
Phe1_s="m6A-"
else
Phe1_s=$Phe1
fi
if [ $Phe2 = "m6A" ]; then
Phe2_s="m6A-"
else
Phe2_s=$Phe2
fi
##generate .esi file for exposure modalities
for tis in Brain Lung Muscle Heart; do
for i in `seq 22`; do
awk -F '\t' '{if(NR==FNR){a[$0]=$0}else{if(a[$2]==... |
bea1169027b5ec6a1f6eec3a24e7cd013a25bfdc2b7525ae46be8fcacc4968a6 | Shell | 4,785 | 120 | #!/bin/bash
#Building_fasta_variant_sequences.sh
################################################################################
# The script below was used to create a fasta file of all the variant regions in
# a donor using phased variants in vcf format. It converts that vcf into a
# table of the passed var... |
1080cc01da98a8cdca329639ba69af8da32dbbd5ed84373784aec88eb50b4b13 | Shell | 4,798 | 102 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=50:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
b940d6887a71a7efecb985ac8c9143b4920de941dd30954bbe1a50b25e830c11 | Shell | 4,801 | 167 | #!/bin/bash
#
# This script runs all the lint checks.
#
set -exuo pipefail
clang_format() {
pip install -c python/requirements_compiled.txt clang-format
./ci/lint/check-git-clang-format-output.sh
}
pre_commit() {
# Run pre-commit on all files
# TODO(MortalHappiness): Run all pre-commit checks because current... |
bede9f8dccf3642c89a88119f6be8a10bfa377a33adacb03977cfbddb9597f62 | Shell | 4,826 | 143 | #!/bin/bash
# 'KAS-Analyzer statistics' was developed by Ruitu Lyu on 12-21-2021.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer statistics [ -h/--help ] [ -o prefix ] [ -l labels ] [ -s summary folder ]"
exampleHelp="Example: nohup KAS-Analyzer statistics -o KAS-seq_statistics -l labels.txt -... |
87a2083425c03749ec27615e91156039bd2fc0935864249913e00e036ce6e483 | Shell | 4,834 | 43 |
# qsub -P trapnelllab -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_12_scalableSubtyping_nobackup/ /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_12_scalableSubtyping_nobackup/singleSubtypeRun.sh TestFour 1,2 heartBroadMarkV2 20
# qsub -P trapnelllab -wd /net/trapnell/vol1/... |
52d1e10a90384c5dd20424be29f14a01f8bccb7d7ee9ed8c44c8eb2dc5109c97 | Shell | 4,844 | 97 | #!/bin/bash
# 01_Feat.sh
#what shall be done
create_fsf=1
run_feat=1
normalize_feat=1
#Directories
original_fsf=/data/pt_02306/main/code/github/pain-reliability-spinalcord/helper_functions/design.fsf
for subject in {1..40}; do
for session in {1..2}; do
printf -v sub "%02d" $subject
printf -v ses "%02d" $se... |
480fd51a0903836844a1d81d0fde32b42f7117ba031d9ffd738870646d88f5f9 | Shell | 4,888 | 92 | #####Bash script to get read allocation accuracy. Example for ENCFF873ZZU.
#Requirements: Bowtie, macs2, samtools, bedtools, cutadapt, and Allo
####Control file download, alignment, and allo run####
wget -q https://www.encodeproject.org/files/ENCFF873ZZU/@@download/ENCFF873ZZU.fastq.gz
gunzip ENCFF873ZZU.fastq.gz
bow... |
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