sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
1f1639f9ba8c0dda001bea140af1e3d09ae0b66a7c8d2d67e7f249869e551f59 | Shell | 3,041 | 82 | smallrnaDir=/scratch/cqs/shengq2/references/smallrna/v4
genomeName=rheMac8
targetDir=${smallrnaDir}/${genomeName}
ensemblVersion=94
mirbaseVersion=22
if [ ! -s $targetDir ]; then
mkdir $targetDir
fi
cd $targetDir
if [ ! -s liftOver ]; then
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
chm... |
7c09858f71f93c1c53346af61c017cde807ec45334a92042fa7d087850cbebd7 | Shell | 3,048 | 81 | #!/bin/bash
# This script calculates the shift in the position of a target using two
# images that have been registered with the helmet reference image. The
# registration is performed using the brain extracted using bet, and mapped to
# space of the helmet registration image. The target coordinates should be in
# the... |
81c6415a3920bb68ddbaa3c6fd9e72edec1675d02e72be7296c7f2f74818b62d | Shell | 3,050 | 45 | #!/bin/bash
#$ -cwd
#$ -N magma-gsa_step3_PTSD-rev_MNT
#$ -o ./logs/magma-gsa_step3-PTSD_rev_MNT18Jul2021.o
#$ -e ./logs/magma-gsa_step3-PTSD_rev_MNT18Jul2021.e
#$ -l bluejay,mem_free=16G,h_vmem=20G
echo "**** Job starts ****"
date
model="snp-wise"
ANNO=/dcs04/lieber/marmaypag/Tran_LIBD001/Matt/MNT_thesis/snRNAseq/10... |
94efb52bb5677c5ed49a19e8bc2cd1e2095796cdb53fb49bb824d32775a7b6b0 | Shell | 3,051 | 57 | #!/bin/bash
#SBATCH -p scavenge # partition (queue)
#SBATCH -n 1 # number of cores
#SBATCH --output=scheduler_stdout.txt
#SBATCH --error=setup_stderr.txt
#SBATCH --job-name=CBASS
<<COMMENT
This scheduler script allows the parallel deployment of several experimental conditions to be... |
27e08c367df459b2a5455ffb26003d08f58bef7f90f67048cc2ff80f0efa0af3 | Shell | 3,067 | 57 | #!/bin/bash
set -e
set -o pipefail
# The regional EC2 mirror started 503ing on 2026-09-04 and apt spins on it for ~10 min before
# giving up, so fall back to the canonical one; self-healing, and removable once it is reliable
if ! curl -fsS --max-time 10 -o /dev/null "http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dis... |
95f47c117cf788de18da50e7cc5fd754429400e0c29f66f99f7af6594502c737 | Shell | 3,076 | 99 | #!/usr/bin/env bash
CODE_FN=code.tar.gz
# exit if any command fails...
set -e
# create output directory for condor logs early
# not sure exactly when/if this needs to be done
mkdir -p output/condor_logs
# echo some HTCondor job information
echo "Date: $(date)"
echo "Host: $(hostname)"
echo "System: $(uname -spo)"
e... |
179358d9c41dbc50f3b4a9fd5b4e5726bd5378910fd29e910b0ee879a4851e7c | Shell | 3,091 | 59 | #!/bin/bash
#SBATCH --job-name=j_func_preproc
#SBATCH --partition=short
#SBATCH --time=48:00:00
#SBATCH -n 1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=4G
#SBATCH --output=logs/%x.%A-%a.out
#SBATCH --error=logs/%x.%A-%a.err
#############################################
freesurfer_version="X.X.X"
export FREESURFE... |
97dbef580d6ae1c769afe6f275694ef29ae59989415ad4a471e4838ac2a6fb49 | Shell | 3,100 | 88 | #!/bin/sh
# ============================================================
# 00_processing_pet_data.sh
# ============================================================
# This script processes PET data by:
# 1. Regridding PET images to MNI space.
# 2. Z-scoring each image.
# 3. Computing weighted averages for receptor... |
d01b1f1659442add8174ef11f3454a4e0a277ea84026c7178aaa609d5f9dcf2f | Shell | 3,112 | 88 | smallrnaDir=/scratch/cqs/shengq1/references/smallrna/v3
genomeName=rheMac8
targetDir=${smallrnaDir}/${genomeName}
if [ ! -s $targetDir ]; then
mkdir $targetDir
fi
cd $targetDir
if [ ! -s liftOver ]; then
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
chmod 755 liftOver
fi
if [ ! -s rheMac... |
5f2dfac9a442e5316756743ff98c8535d750a9da8d44c64ba299efb31d4c5065 | Shell | 3,129 | 63 | #!/usr/bin/env bash
##
## @script.name [option] ARGUMENTS...
##
## Options:
## -h, --help All client scripts have this, it can be omitted.
## --var=VALUE index for variant column chr:pos:ref:alt. This or next four must be specified
## --chr=VALUE Columnn indexes
## --pos=V... |
9381e812bece7a4aa8bbc1e099d7b75c3e7925f8fe301e2f36890e0bea7f649d | Shell | 3,136 | 102 | #!/bin/bash
# this script is meant to be called from the working directory (will be handled by python caller)
if [[ $# -le 3 ]] ; then
echo 'Usage: ./$0 PROCESS_NUM START_STRUCT VARIANT NUM_STRUCTS'
exit 1
fi
PROCESS_NUM=$1
START_STRUCT=$2
VARIANT=$3
NUM_STRUCTS=$4
echo "PROCESS_NUM :" $PROCESS_NUM
echo "ST... |
3f0f5324ae93e02b30c15b714cea666c5f12d11e87132a9b30c0bbffad40cb93 | Shell | 3,151 | 59 | #!/bin/bash
#SBATCH --job-name=j_func_preproc
#SBATCH --partition=short
#SBATCH --time=48:00:00
#SBATCH -n 1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=4G
#SBATCH --output=logs/%x.%A-%a.out
#SBATCH --error=logs/%x.%A-%a.err
#############################################
freesurfer_version="X.X.X"
export FREESURFE... |
52545e2dc4d6531a2433d4b30ea3acf4b81e0a5deb52d0cac35b1caa95605c70 | Shell | 3,152 | 91 | #!/bin/bash
# script for third data release
# script to align native surfaces with template space
set -x -u -e
Usage() {
echo "align_to_template.sh <topdir> <subjid> <session> <age> <volumetric template> <volumetric template name> <surface template> <surface template name> <pre_rotation> <outdir> <config> <script ... |
21dedace0899c192196469eda78a3c1a1aac09200380748d32dfabe507339bcc | Shell | 3,210 | 75 | #!/bin/bash
# set our directories
dir_out=$(pwd)
log_file="$dir_out/log_runFSL-3.txt"
dir_ostt="$dir_out/results_ostt-cov"
if [ ! -d "$dir_ostt" ]; then
mkdir -p "$dir_ostt";
fi
nsim=5000
## Start with neural adaptation
ada=1
if [ $ada == 1 ]; then
code="SMP_all_cope4"
echo "$(date) start $code" >> "$log_file... |
952d1998e9ffbf5779d9f15961313e25bbaf5975b7cccf8fd2ac2d881a8e3305 | Shell | 3,220 | 127 | #!/bin/bash
# Siwei 19 Jan 2023
# Direct count for 20 SNP sites designed for ABE/CBE multiplex editing
# Disable BQSR, use the Phred value directly from CellRanger
# Siwei 08 Aug 2022
# Remove all filters, set minMappingQual=0
# Do not use VQSR recalibration
# Siwei 21 Jul 2022
# update SNP to dbsnp v154
# move all... |
1854b5c4b756239504b5c70b74c977e324402271d828f6ef7500adf7dfffd1f9 | Shell | 3,221 | 47 | # python "/home/zhong/Experiment/RFD_base_crd/train_student.py" \
# --path_t "/home/zhong/Experiment/RFD_base_crd/save/models/resnet110_ivygap_5_lr_0.05_decay_0.0005_trial_0/resnet110_best.pth" \
# --device cuda:4 --device_id 4 \
# --distill kd --model_s resnet32 -a 0.9 -b 0 --trial 1 \
# > 12_5_kd_resn... |
b06de06112c5ac67bb78a27a5e2d748f804b0256891e3cc20b46bbd474a185e9 | Shell | 3,226 | 70 | #!/bin/bash
set -ev
# 01. Set up environment
exec_dir=$( pwd )
cd "${exec_dir}"
an_dea_res_dir="${exec_dir}/scripts"
# 02. Set up config files
# 02a. Specify DEA summary config file path
cfg="${exec_dir}/configs/config_SUD_DEG_analysis.yaml"
echo "${cfg}"
# 02b. Specify DEG subcluster config file path
cfg_dsc="${exe... |
1afd9ba388ced50b6d863472602979d454bd2c6ee136ce52b930132b297de1b5 | Shell | 3,252 | 97 | # Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# arg1 = file, arg2 = file it depends on
# enforce using portable C locale
LC_ALL=C
export LC_ALL
action () {
if (test $mode = 0) then
rm -f ../$1
elif (! cmp -s $1 ../$1) then
if (test -z "$2" || test -e ../... |
a648c92452755f677173ff8021a4343b3f53380ab001219bd254151d54643326 | Shell | 3,266 | 46 | #!/bin/bash
#$ -cwd
#$ -N magma-gsa_step3_ADHD
#$ -o ./logs/magma-gsa_step3-ADHD_MNT18Jul2021.o
#$ -e ./logs/magma-gsa_step3-ADHD_MNT18Jul2021.e
#$ -l bluejay,mem_free=16G,h_vmem=20G
echo "**** Job starts ****"
date
model="snp-wise"
ANNO=/dcs04/lieber/marmaypag/Tran_LIBD001/Matt/MNT_thesis/snRNAseq/10x_pilot_FINAL/MA... |
d9da0cb24f3edf16703fda9c45540ff250fff8eddbb1510cd6f1509880c52afc | Shell | 3,271 | 80 | #!/bin/bash -e
set -o pipefail
# Works out what this build needs, before anything is restored or downloaded:
# build.txt and pattern.txt for the doc build, wanted_datasets.txt for
# circleci_download.sh, and cache_keys/<cache>.txt for the cache keys in
# .circleci/config.yml. A cache marked noop hashes to a key nothi... |
09d2f4e99e6385cc8a4b6c9f170eb552777fac976a65573d59b29b62ec3113e4 | Shell | 3,274 | 63 | #!/bin/bash
#-----------------------------------------------
# Filter: unique barcode pair
#-----------------------------------------------
# Filter out variants covered by multiple barcode pairs
# Uncomment the line below for cluster computing, otherwise make sure you have these tools installed
# module load gcc/14.... |
f65c4675c3dba0ec4faf6698f8f7e2e216ed344e3051123d2bee52e34fd2b975 | Shell | 3,290 | 101 | #!/bin/bash
#SBATCH -A LEYSER-SL2-CPU
#SBATCH -J prepare_reference
#SBATCH -D /rds/user/hm533/hpc-work/mammary_gland_transcriptomes/test_pipeline/ # your working directory
#SBATCH -o logs/slurm/00-prepare_reference.log
#SBATCH -p skylake # or `skylake-himem`
#SBATCH -c 1 # max 32 CPUs; de... |
3358ab294f2d9dd5abf6f25d2a554fe0f43a12336ee6c7130acf0b40b4d7979e | Shell | 3,325 | 80 | #!/bin/bash
curr_dir=`pwd`
sample=abcd
task=MID
# 2YearFollowUpYArm1
ses=2YearFollowUpYArm1
type=session # run or session
run=1
subj_list=${1}
inpfold=/scratch.global/${USER}/mid_rt_mod/firstlvl
outfold=/scratch.global/${USER}/mid_rt_mod/group
counter_start=0
run_randomise=custom # randomise or custom --> custom sit... |
720e1553fec7f3d4a12d8edfa0e7a2c426f2507662a3d2bb2cd6f699032a8940 | Shell | 3,326 | 116 | t#!/bin/bash
## Usage:
# sh apply_weights.sh
umask u=rwx,g=rwx,o=
mkdir -p logs
for region in NAc
do
for feature in gene
# for feature in gene exon jxn tx
do
# set of summary stats
for summstats in si sc dpw cpd aoi
do
SHORT="apply_weights_full_${region}_${feature}... |
ee907360ed14a8ffa1c9b476eb4834562f1f03f1507948d3be05aa54af3e63e4 | Shell | 3,328 | 110 |
fastqc \
--outdir ${OUTPUT_DIR}/FASTQC/RAW \
--threads ${LSB_MAX_NUM_PROCESSORS} \
--format fastq \
--quiet \
${OUTPUT_DIR}/${FASTQ1} \
${OUTPUT_DIR}/${FASTQ2}
trim_galore \
--paired \
--retain_unpaired \
--cores ${LSB_MAX_NUM_PROCESSORS} \
--output_dir... |
5cc714483756f3e64c5e26cea391d8fa017a944507bb878bedf78b003cc77388 | Shell | 3,330 | 75 | #!/bin/bash -e
set -o pipefail
# Fetches the datasets circleci_triage.sh listed in wanted_datasets.txt, which is
# only the ones this build's examples actually use; everything else was either
# restored from a cache or is not needed at all. Most datasets just want their
# data_path, so only the ones that need somethi... |
fa9586e255ef1621308baaae26140f6895bf74ada7927b214986d14462efb4ae | Shell | 3,351 | 97 | #!/bin/bash -l
PATTERN=$1
SAVE_FOLDER=$2
BRAINMASK_FOLDER=$3
mkdir -p $SAVE_FOLDER
for IMG in $PATTERN; do
TMP=$(basename -- "$IMG")
NAME=${TMP%-aseg.*}
mkdir -p $SAVE_FOLDER/$NAME
# Remove cerebellum, brain stem, 4th ventricle and optic chiasm
mri_binarize --i $IMG \
--replace ... |
7a4088f847a66004bc7c6cbbe8225a5d6f4d027dcf98ec0a871dd559f4630150 | Shell | 3,353 | 118 | #!/usr/bin/env sh
CAFFE=/cs/vml2/msibrahi/workspaces/caffe-lstm
GIT_PROJ_DIR=$CAFFE/examples/deep-activity-rec
DATASET_VIDEOS=/cs/vml2/msibrahi/Datasets/Greg-Volleyball/volleyball
DATASET_CONFIG=$GIT_PROJ_DIR/dataset-config
OUTPUT_DIR=$GIT_PROJ_DIR/ibrahim16-cvpr
TRAIN_SRC=trainval
TEST_SRC=test
WINDOW_NETWORK1=5
W... |
1cb5b995f489385ae3d1905a2ad2282150d13c3dd80da6848de86be8ae31be71 | Shell | 3,365 | 74 | #!/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... |
038b8d8572061f9c64adfbe7571c1d48828ddb9bb7f6a56d366b5bbc201ca2c6 | Shell | 3,393 | 109 | #!/bin/bash -l
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=10G
cd $SLURM_SUBMIT_DIR
date
hostname
export PATH=$PATH:/sw/afni/bin
FSLDIR=/sw/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
# feed session and subject here
subjects="YOURSUBID"
sessions="replace"
# Processing ... |
53314117f4ef74593245cde8848e6972cd0ec3684aa50907d0d3912e592a5a6b | Shell | 3,399 | 138 | #!/bin/bash
# 03 May 2023
# Siwei
# 11 May 2021
# Siwei rewrite in GATK4
# 11 Jun 2020
vcf_suffix="_995.vcf"
gatk4="/home/zhangs3/Data/Tools/gatk-4.2.6.1/gatk"
ref_path="/home/zhangs3/Data/Databases/Genomes/hg38"
ref_genome="/home/zhangs3/Data/Databases/Genomes/CellRanger_10x/refdata-cellranger-arc-GRCh38-2020-A/f... |
f698cddbd494655b9bfd98ac997023c1ad7d0f551a65239a7d0a5dd37a6a940e | Shell | 3,409 | 139 | #!/bin/bash
# 03 May 2023
# Siwei
# 11 May 2021
# Siwei rewrite in GATK4
# 11 Jun 2020
vcf_suffix="_all.vcf"
gatk4="/home/zhangs3/Data/Tools/gatk-4.2.6.1/gatk"
ref_path="/home/zhangs3/Data/Databases/Genomes/hg38"
ref_genome="/home/zhangs3/Data/Databases/Genomes/CellRanger_10x/refdata-cellranger-arc-GRCh38-2020-A/f... |
1d8394bc116422834ed71f9f502594549c6379be6174dcbca6e20d1b549f8064 | Shell | 3,437 | 69 | #!/bin/bash
# set our directories
cd ..
dir_data="fMRI_data"
dir_out="results_sig"
if [ ! -d "$dir_out" ]; then
mkdir -p "$dir_out";
fi
# look at the fusiform gyrus for the pwPE comparison based on eps_c cluster 7
fslmeants -i $dir_data/HGF_all_zstat4.nii.gz -o $dir_data/eps_c_rFG_meants.txt -m $dir_data/ROI_hgf_a... |
fbb1c334eee80678486eb3adab09a5a712f10c4fe5338073337ddc9b92e3e4ba | Shell | 3,437 | 93 | #!/bin/sh
# Copyright (c) 2021 Thomas Ward <thomas@thomasward.com>
# Copyright (c) 2019 MIT Laboratory for Computational Physiology
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without... |
8d43254cef28a75a6deb5b29d34bde6c3b54525c92427291eaeb3f2c26800529 | Shell | 3,457 | 126 | #!/bin/bash
# Sample script for benchmarking policy performance
# Suggested environment variables to export prior to executing script:
# KNL:
# OMP_NUM_THREADS=256 KMP_AFFINITY=compact
# Power:
# OMP_NUM_THREADS=64 OMP_PROC_BIND=true
# Constants and Variables:
# Vary: TEAMSIZE, and THREADRANGE
# for TEAMSIZE in {1... |
1987101caec0d60c8bd8c70cae6a67b76615a786aad2ab70998c84f05a20c7fa | Shell | 3,479 | 123 | #! /bin/bash
set -e
if [[ ! -z "$(ls -A $(pwd))" ]]; then
echo "Please run from an empty directory!"
exit 1
fi
if [[ -z $1 || ! $(basename $1) =~ ^labelbuddy-[0-9]+\.[0-9]+\.[0-9]+-Source.tar.gz$ ]]; then
cat <<EOF
Please specify source tarball path:
$(basename $0) /path/to/labelbuddy-x.x.x-Source.tar.g... |
074327fdf9b4fff950f60d8762dd8426ba1a26621ff730d54e514918ac8e07f1 | Shell | 3,482 | 93 | #!/bin/sh
# MAKE SURE FUSION.compute_weights.R IS IN YOUR PATH
# FILL IN THESE PATHS
GCTA="<PATH TO GCTA>"
PLINK="<PATH TO PLINK>"
GEMMA="<PATH TO GEMMA>"
# ALTERNATIVELY: ENSURE THAT plink, gcta, gemma CAN BE CALLED FROM PATH AND REMOVE --PATH_* FLAGS BELOW
# PATH TO DIRECTORY CONTAINING LDREF DATA (FROM FUSION WEBSIT... |
2a29e9a61b41f0ddf2ec83fbf3998f31f8ccc38fa565a45937dfab54383214c3 | Shell | 3,494 | 133 | #!/bin/bash
#
#
# Created by Sandrine Bédard on 11/19/2023.
#
# 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 PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLD... |
098e9397e1d1a04ff94174ed4fe024d436d5f43232d2a418b7075f124af3363c | Shell | 3,499 | 122 | #!/bin/bash
# Function to check if a Python package is installed
is_python_package_installed() {
conda activate flexutils-tensorflow
if pip list | grep -F "$1" &> /dev/null; then
return 0
else
return 1
fi
conda deactivate
}
# Function to echo text in specified color using tput and prin... |
5ed505397296d5cad8fc4144df2bc7bb98dbb843078e6cc35b7ec65505de1c92 | Shell | 3,515 | 85 | #!/bin/sh
#
# collect.sh - Node Exporter textfile collector generator
#
# Periodically collects and calculates filesystem usage statistics for the
# FAST and SLOW data directories and writes them in Prometheus textfile format
# into $TEXTFILE_DIR as:
# - kaapana_fast_size.prom
# - kaapana_slow_size.prom
#
# These met... |
318851d09fb44297baabcf74badaf2fab2fe0687b0366b1c9c72f322ea32391e | Shell | 3,520 | 142 | mkdir /vast/iaslab/FSMAP/scripts/revision_scripts/subregion_t_test
cd /vast/iaslab/FSMAP/scripts/revision_scripts/subregion_t_test
## PAG ##
for seed in DMPAG DLPAG LPAG VLPAG; do
mkdir -p /vast/iaslab/FSMAP/scripts/revision_scripts/subregion_t_test/$seed
for hemi in lh rh mni305; do
for subj in `cat /vast/ias... |
394ecd4f414730e37ae877528151bb4f8d4046afaf63160b180750253fabb4b2 | Shell | 3,541 | 109 | #!/bin/bash
print_help() {
echo "
Usage: $0 -l SNP_LOC_FILE -p SNP_P_VALUE_FILE -o OUTPUT_DIR -s COHORT_SIZE -m MAGMA_PATH -g GENE_LOC_FILE -b B_FILE [-w WINDOW_SIZES] [-h]
This script performs MAGMA annotation and analysis on SNP data.
Required parameters:
-l | SNP location file
-p | SNP p-value file
... |
949685d921bb41bfd317a6b1a13a2ce709939d1f2980e68b0813ddf4bfbdbfcd | Shell | 3,559 | 56 | #!/bin/bash
#$ -cwd
#$ -N magma-gsa_step2-gene_MNT
#$ -o ./logs/magma-gsa_step2-gene_MNT23Aug2020.o
#$ -e ./logs/magma-gsa_step2-gene_MNT23Aug2020.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_pilot_FIN... |
86274f3c089705b8a93c5d70e75e62321d606d21eb91ec3ad7750545fb140d55 | Shell | 3,599 | 111 | #!/bin/bash
# Script to build AnyLabeling in folder mode for macOS
# This creates a directory-based application instead of a bundled .app
# Set CPU or GPU mode
if [ "$1" == "GPU" ]; then
sed -i'' -e 's/\_\_preferred_device\_\_[ ]*=[ ]*\"[A-Za-z0-9]*\"/__preferred_device__ = "GPU"/g' anylabeling/app_info.py
SU... |
8d1805d965bd120369f735906f3e8031929b3d75c5028fc5edd518a8efe03463 | Shell | 3,612 | 94 | #!/bin/bash
#SBATCH --partition=GPU-a40 # select a partition i.e. "GPU-a100"
#SBATCH --gres=gpu:1 # Use GPU
#SBATCH --nodes=1 # select number of nodes
#SBATCH --ntasks-per-node=2 # select number of tasks per node
######SBATCH --mem=32GB
#SBATCH --time=2-00:00:... |
751c21a9450eb3f432e95159da5828b1f88efcb8bf23646f6bf5b89ceb1d8fa6 | Shell | 3,622 | 165 | #!/bin/bash
# labeling of reads and quantification of species with Centrifuge
# script filename
script_path="${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 [ ! $#... |
a7ecda14826e5f5715ad52ad6e31468124ff0b2a387bd2180a96e85f180ecb76 | Shell | 3,632 | 94 | #!/bin/bash
# This script generates the concepts in the BigQuery table mimiciv_derived.
export TARGET_DATASET=mimiciv_derived
export METADATA_TABLE="_metadata"
export MIMIC_VERSION="3.1"
# specify bigquery query command options
# note: max_rows=1 *displays* only one row, but all rows are inserted into the destination ... |
8d65e92f7b2584102c768354ad0074cc3a348c7504ed3a00cd49bad812755741 | Shell | 3,642 | 142 | #!/bin/bash
# small bash script to create a dummy BIDS data set
# defines where the BIDS data set will be created
start_dir=$(pwd) # relative to starting directory
raw_dir=${start_dir}/data/dummy/raw
subject_list='ctrl01 blind01 01' # subject list
session_list='01 02' # session list
create_raw_func_vism... |
27568950ff912efc52ed791b0ce3f6b50517a02c7d3167857bb28169a40cde73 | Shell | 3,643 | 94 | #!/bin/bash
#SBATCH --partition=GPU-a40 # select a partition i.e. "GPU-a100"
#SBATCH --gres=gpu:1 # Use GPU
#SBATCH --nodes=1 # select number of nodes
#SBATCH --ntasks-per-node=2 # select number of tasks per node
######SBATCH --mem=32GB
#SBATCH --time=2-00:00:... |
9a410eebb33a0e46bce76c4c0536ebb00dc55eda66b2cbfdb3bcb0009869bbae | Shell | 3,653 | 106 | #!/bin/bash
# Draw spheres as per Sarubbo et al., 2020 (NeuroImage).
# Expected inputs: a txt file with 4 columns for each of the categories of interest: sub_id (integers only), x, y, and z coords of stimulation points in MNI space. NO HEADERS
# Parameters to be edited, see SCRIPT STARTS HERE section :
# 1) Path ... |
8f55504fe62416b28550b9069da18c00a48144cd5322ee50bd6d64ab137563c2 | Shell | 3,676 | 130 | #!/bin/bash
##
## RNA-seq using Salmon transcript quantification
##
# script filename
script_path="${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 [ ! $# == 2 ] ; then
... |
19e1adbddeda3db9a2a598eaa3884867b92508d5cd5e9e0ec9dd61aae5a985f8 | Shell | 3,699 | 94 | # test libdeepmd_c.tar.gz works on a manylinux 2.28 runtime
set -e
SCRIPT_PATH=$(dirname "$(realpath -s "$0")")
MANYLINUX_IMAGE=${MANYLINUX_IMAGE:-quay.io/pypa/manylinux_2_28_x86_64:latest}
PYTHON_BIN=${PYTHON_BIN:-/opt/python/cp311-cp311/bin/python}
PYTORCH_DEPENDENCY_GROUP=${PYTORCH_DEPENDENCY_GROUP:-pin_pytorch_cpu... |
4a0bb5ef5896c8773c2596b9e74c04c3dab863a18c17d8c0df1f0264cf204fdd | Shell | 3,707 | 62 | #!/usr/bin/env bash
# Invoked by `ant beta:worker poll --on-work` once per claimed work item.
#
# The poller passes ANTHROPIC_{WORK_ID,ENVIRONMENT_ID,SESSION_ID,ENVIRONMENT_KEY}
# in the environment and the raw work JSON on stdin (drained, unused here).
# ANTHROPIC_BASE_URL is inherited from the poller process.
#
# Per... |
021842e93aabc45b6e090f4f9b5de157dd231789cb3b71fa4fa9c3f064c18c0b | Shell | 3,708 | 113 | #bin/bash
set -e -o pipefail
function radiomics {
echo "Starting Radiomics-Module..."
Xvfb :99 -screen 0 1024x768x24 &
export DISPLAY=:99
exec "$@"
loop_counter=0
organ=$(echo "$ORGAN" | awk '{print tolower($0)}')
echo 'INPUTDIR: ' $INPUTDIR
echo 'OUTPUTDIR: ' $OUTPUTDIR
echo '... |
dd054313cccf20068ee0417e65368a5191c737dbd20bee07d32cb656a8668b51 | Shell | 3,749 | 81 | source ./config.sh
source activate proteinnpt_env
export DMS_index=0 #Replace with index of desired DMS assay in the ProteinGym reference file (`utils/proteingym`)
#########################################################################
########################Zero-shot MSA Transformer########################
######... |
e70f3945ddc28bf8f643b1ccbb7ae1bd0ca016798e8c504b4137856708842283 | Shell | 3,801 | 139 | #!/bin/bash
##
## Cluster/Slurm status (check that common modules can be loaded and executed)
##
# specify maximum runtime for sbatch job
# SBATCHTIME=15:00
# standard route header (validate args and print settings)
code_dir=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." && pwd)
source "${code_dir}/scripts/route-h... |
d8aa5e8fca84df7fa8d104040185f274c0802b3edf4ababbeb8b2b534fb9bd9b | Shell | 3,819 | 13 | cd /data/apaeval/nf_rnaseq/bams_sorted/bams_by_chr
for i in `cat chr_list.txt`; do echo "SRR6795719 $i"; samtools view -b -o SRR6795719\_$i.bam ../SRR6795719.bam $i; samtools sort SRR6795718\_$i.bam --no-PG -O bam -o SRR6795719\_$i.sorted.bam -@ 4; rm SRR6795719\_$i.bam; mv SRR6795719\_$i.sorted.bam SRR6795719_$i.bam; ... |
41cb7c133acd7bf0b9049ceba0890455dcd21e6a0db118d3d79389ad30e9bef7 | Shell | 3,820 | 101 | #!/bin/bash
if [ -z "$ROS_DISTRO" ]; then
echo "ROS not installed. Check the installation steps: https://github.com/erlerobot/gym#installing-the-gazebo-environment"
fi
program="gazebo"
condition=$(which $program 2>/dev/null | grep -v "not found" | wc -l)
if [ $condition -eq 0 ] ; then
echo "Gazebo is not instal... |
c51427c44ea8bf43b9007216b0f0f2ff62306165958c4f68672e3a041d7a7555 | Shell | 3,820 | 43 | #!/bin/bash
set -euo pipefail
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=${THREADS_PER_COMMAND:-$(nproc)}
movingfile=$1
fixedfile=$2
outputdir=$3
shift 3
fixedmask=$(dirname ${fixedfile})/$(basename ${fixedfile} _t1.nii.gz)_mask.nii.gz
movingmask=$(dirname $movingfile)/$(basename $movingfile _t1.nii.gz)_mask.nii.gz... |
4499e87cb906f6086363540083cf8f3348e44a370033d1a64c5883e57d24600f | Shell | 3,841 | 115 | #!/bin/bash
##to work with espresso fasta
#tweaked so can feed it 6P4b as input
##activate conda if required
source /home/arh49/miniconda3/etc/profile.d/conda.sh
#source /usr/bin/Rscript
##v3 does both the no error model and the ont salmon quant
##actually salmon quant expects a random order of reads so any input ... |
b3f3737509a6dee566738ee291251354d758be4e4335daa788573704df51d2f8 | Shell | 3,843 | 128 | #!/bin/bash
# =============================================================================
# PyScenic 转录调控网络分析脚本
# =============================================================================
# 功能：使用PyScenic进行转录调控网络推断和调控强度分析
# 激活conda环境
conda init
conda activate pyscenic
# 设置工作目录到项目的pyscenic文件夹
PROJECT_ROOT="$(pwd)... |
970fb175a19c5695b65a861fbe5014dadfbc8d9c04b4b900e4c0332d701f6f7f | Shell | 3,850 | 120 | #!/bin/bash
APP_NAME=lammps-gui
DESTDIR=${PWD}/../LAMMPS_GUI
VERSION="$1"
echo "Delete old files, if they exist"
rm -rf ${DESTDIR} LAMMPS-Linux-x86_64-GUI-*.tar.gz
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
cp lammps-gui_build-prefix/bin/lammps-gui ${DES... |
2005b713aabe68621a25f50b2cd0bbfc5d206ad9b3e9a924f16bcc726f2eb30c | Shell | 3,866 | 71 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=2
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
#S... |
3750e198fac0ee396460b5391882de63f6b68a3cc441c0eed6bf41699915b123 | Shell | 3,964 | 100 | #!/bin/sh
# ============================================================
# 01.1_processing_for_roi2vox_structgradients_LEMON.sh
# ============================================================
# This script performs pulvinar-targeted tractography and mapping
# for the LEMON dataset using MRtrix and FSL tools.
#
# Steps:
... |
7a74ce758370dc981d85da702d7405b3fdcad7756b68120187d2da92ed8a518d | Shell | 3,967 | 75 | #!/bin/bash -e
# Copied from colabfold.mmseqs.com
MMSEQS="$1"
QUERY="$2"
DBBASE="$3"
BASE="$4"
DB1="$5"
DB2="$6"
DB3="$7"
USE_ENV="${8:-1}"
USE_TEMPLATES="${9:-0}"
FILTER="${10:-1}"
INDEX=${11:-1}
DB_LOAD_MODE="${12:-2}"
EXPAND_EVAL=inf
ALIGN_EVAL=10
DIFF=3000
QSC=-20.0
MAX_ACCEPT=1000000
if [ "${FILTER}" = "1" ]; the... |
be9c8b405f0b7e520696cddf251fed01a2a4bcc2cca7732bdd90cb7b7bcbc094 | Shell | 3,983 | 210 | #!/usr/bin/env bash
HELP() {
cat <<HELP
expand_BET_skull
Usage:
bash ${0##*/} -i <anat-file> -skull <skull-mask> -iskull <inskull-mask> -os <outskin-mask> [options]
Compulsory arguments:
-i Anatomic image (usually T1w)
-skull Skull mask provided by BET
-iskull Insku... |
5c2e72a6c09256a632e0fe262c36c360b393b0412d0390dac4a2f949bc6334b5 | Shell | 4,004 | 169 | #!/bin/bash
# get fragment size distribution
# script filename
script_path="${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 $scri... |
325c73f2f9427ad7a0bc46478fcb20ca221cfe15a6163990366e63ce1e039ada | Shell | 4,007 | 164 | #!/usr/bin/env sh
CAFFE=/cs/vml2/msibrahi/workspaces/caffe-lstm
GIT_PROJ_DIR=$CAFFE/examples/deep-activity-rec
DATASET_VIDEOS=/cs/vml2/msibrahi/Datasets/Greg-Volleyball/volleyball
DATASET_CONFIG=$GIT_PROJ_DIR/dataset-config
OUTPUT_DIR=$GIT_PROJ_DIR/ibrahim16-cvpr
TRAIN_SRC=trainval
TEST_SRC=test
WINDOW_NETWORK1=5
W... |
d3e1306f1690279b130d7f03899294ac34489f050a5d27002bd764e3d22d508e | Shell | 4,048 | 105 | #!/bin/bash -l
# Setup paths - subj ID should be passed as an argument when calling this function
export SUBJID=${1}
export SESS=ses-nyu3t01
# Main experimental directory
export EXP_DIR=/Volumes/server/Projects/attentionpRF/derivatives
export SUBJECTS_DIR=${EXP_DIR}/freesurfer
# Functional data directory
export FUN... |
af1643bd73bad6e7b9d32845834b4b22c6595cd496dd80fe6c74d3d56f663d4d | Shell | 4,062 | 141 | #!/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
DEFAULT_TRAINING_CSV="./data/training.csv"
DEFAUL... |
e4fa3ee0b8d5afb3833243af87928d71f3f5d93ec8d19807b601def6b62507ba | Shell | 4,071 | 142 | #!/usr/bin/env bash
CODE_FN=code.tar.gz
ENV_FN=metl-sim.tar.gz
ROSETTA_ENC_FN=rosetta_min_enc.tar.gz
ROSETTA_DEC_FN=rosetta_min.tar.gz
PASS_FILE=pass.txt
# exit if any command fails...
set -e
# create output directory for condor logs early
# not sure exactly when/if this needs to be done
mkdir -p output/condor_logs
... |
2b07f12962221bc80060fc7bf236ff0d365d06c901d8b22a2cbc98de9346435a | Shell | 4,077 | 73 | ml connectomeworkbench/1.5.0
ml freesurfer/7.3.2
ml deepretinotopy/1.0.8
dataDir=/BULK/LABDATA/NSD
cd $dataDir
# Run deepRetinotopy
echo "--------------------------------------------------------------------------------"
echo "[Step 1] Run deepRetinotopy..."
echo "-----------------------------------------------------... |
1f6af3e2f851770c85c0e12c70e8a38e4fe4a5389bc486160a0a7b01816c3184 | Shell | 4,087 | 120 | #!/bin/bash
DATE=21Fev20
# bfo
cd bfo/
../../../src/lmp_serial -in in.spin.bfo
cp log.lammps log.${DATE}.spin.bfo.g++.1
../../../src/lmp_serial -in in.spin.bfo
cp log.lammps log.${DATE}.spin.bfo.g++.4
rm log.lammps log.cite dump*.lammpstrj
cd ..
# fcc cobalt
cd cobalt_fcc/
../../../src/lmp_serial -in in.spin.cobalt_... |
6c46249c4f2c8964d6fe23815ee942f025328740f367376e39c168ec99060b2a | Shell | 4,113 | 27 | #!/bin/bash
gzip -dck ./ADMISSIONS.csv.gz | sed 1d | mclient -d mimic -s "COPY INTO MIMICIII.ADMISSIONS FROM STDIN USING DELIMITERS ',','\n','\"' NULL AS ''" - &&
gzip -dck ./DATETIMEEVENTS.csv.gz | sed 1d | mclient -d mimic -s "COPY INTO MIMICIII.DATETIMEEVENTS FROM STDIN USING DELIMITERS ',','\n','\"' NULL AS ... |
85f9a9b643811b08d63e763dae78e2b3dd36b5a2581b3590215850d446a3090b | Shell | 4,124 | 111 | #!/bin/sh
# Copyright (c) 2023 MIT Laboratory for Computational Physiology
# Copyright (c) 2021 Thomas Ward <thomas@thomasward.com>
#
# 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... |
ac0dedf88d795a5ee51f389a00b9eb1c2d9c3373f30da106d28bc457324edbf3 | Shell | 4,124 | 113 | #!/bin/bash
nline_per_set=2000
if test $# -ge 1; then
nline_per_set=$1
fi
rm -fr set.*
echo nframe is $(cat box.raw | wc -l)
echo nline per set is $nline_per_set
split box.raw -l $nline_per_set -d -a 3 box.raw
split coord.raw -l $nline_per_set -d -a 3 coord.raw
test -f energy.raw && split energy.raw -l $nline_per_... |
5aa48b31a4eae1dd19a93b606e2eda020f24bf66e88dd8b1281ab313db7a7759 | Shell | 4,139 | 108 | #!/bin/sh
# ============================================================
# 01_processing_for_roi2vox_structgradients.sh
# ============================================================
# This script performs pulvinar-targeted tractography and mapping
# across HCP subjects using MRtrix and FSL tools.
#
# Steps:
# 1. Spl... |
0705dc260d8be8d13f7837f5b5b706eeb6995f893cbdd258efa6415b12ea2208 | Shell | 4,158 | 124 | #!/bin/bash
if [ -z "$ROS_DISTRO" ]; then
echo "ROS not installed. Check the installation steps: https://github.com/erlerobot/gym#installing-the-gazebo-environment"
fi
program="gazebo"
condition=$(which $program 2>/dev/null | grep -v "not found" | wc -l)
if [ $condition -eq 0 ] ; then
echo "Gazebo is not instal... |
894284f87169374aa3087c38f4dc95146f4050b1638ed824a6bc72fafda0b444 | Shell | 4,161 | 104 | #!/bin/bash
# This script is used to register a T1 registration image with the helmet
# registration image. It performs the following steps:
# 1. Uses the 'bet' command to create a brain mask. Note, this may require setting
# the coordinates for the centre of the brain using the -c flag.
# 2. Inverts the brain... |
4a22131ec8aa94de0f536ce08230df98cb2da2032e1611af45f974930238d707 | Shell | 4,179 | 64 | #!/bin/bash
##### run FUMA and S-MAGMA for the TM FACS datasets and TM droplet datasets
bash src/tools/FUMA_MAGMA_batch.sh -m MAGMA -e data/expr/Tabula_muris/tm_facs.top10_magma.txt -g data/gwas/tm_gwas/magma_raw -o results/Tabula_muris/FACS/S-MAGMA
bash src/tools/FUMA_MAGMA_batch.sh -m FUMA -e data/expr/Tabula_muris/... |
0567729ad30e32b6867bb927ef09faf2a809f9e9ce55381282a09475e4bf614a | Shell | 4,190 | 98 | #!/bin/bash
# set our directories
dir_out=$(pwd)
log_file="$dir_out/logfiles/log_runFSL-3.txt"
dir_ostt="$dir_out/results_ostt"
if [ ! -d "$dir_ostt" ]; then
mkdir -p "$dir_ostt";
fi
nsim=5000
## Start with the hypothesis about the control participants
ctr=0
if [ $ctr == 1 ]; then
code="HGF_ctr_cope4"
echo "$... |
7a71e739f7e04d1d2f94de03dc652cd21f4ab89f72c50ab6645b39eee470b71b | Shell | 4,192 | 137 | #!/bin/bash
##
## ChIP-seq using Bowtie 2
##
# specify maximum runtime for sbatch job
# SBATCHTIME=48:00:00
# standard route header (validate args, print settings, prepare environment)
code_dir=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." && pwd)
source "${code_dir}/scripts/route-header.sh" "$@"
##############... |
fac09634b681e91209976231285d0e7df0aa44f77f34856f0d7377b52d708f15 | Shell | 4,267 | 120 | #!/bin/bash
DATE=14Apr20
# bfo
cd bfo/
../../../src/lmp_serial -in in.spin.bfo
cp log.lammps log.${DATE}.spin.bfo.g++.1
mpirun -np 4 ../../../src/lmp_mpi -in in.spin.bfo
cp log.lammps log.${DATE}.spin.bfo.g++.4
rm log.lammps log.cite dump*.lammpstrj
cd ..
# fcc cobalt
cd cobalt_fcc/
../../../src/lmp_serial -in in.sp... |
9c54ad0f73ef1399a5aa136b32723f815702075cc661c34730723e27502dbb5a | Shell | 4,273 | 164 | argv=$1 ### argv can be QC Pre DNA RNA
### all fastq file should in name or symbol link of ${prefix}${id}_R1.fq.gz/${prefix}${id}_R2.fq.gz form
### e.g.
### CZ565_R1.fq.gz
### CZ565_R2.fq.gz
### in the $path path
path=/projects/ps-renlab/fastq/2020/2020_08_05_ChIP_A/RRPE_08052020_ChIPA/
sample_id=`seq 565 596`
sample... |
c69fd35956f01ed540d788f0124613f0173ec090121cf674f123c3013532de37 | Shell | 4,281 | 110 | #!/bin/sh
# ============================================================
# 01.3_processing_for_roi2vox_structgradients_THOMAS.sh
# ============================================================
# This script performs pulvinar-targeted tractography and mapping
# using MRtrix and FSL, based on the Pulvinar THOMAS atlas.
#
... |
12f6cfc8f5f4518f611598bf69ed37e51ebbc9c7af52257c5fd42bb3a7099d10 | Shell | 4,294 | 130 | #!/bin/bash
APP_NAME=lammps-gui
VERSION="$1"
LAMMPS_GUI_APP="$2"
BUILD_DIR="${PWD}"
PACKAGING_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
STAGE_DIR="${BUILD_DIR}/dmg-staging"
DMG_FILE="LAMMPS-macOS-multiarch-GUI-${VERSION}.dmg"
PYTHON="${PYTHON:-python3}"
# dmgbuild creates the disk image and its Finder windo... |
3d4c6c5c065a458db39282a6039cd3575f4777b10beded99eaf484d907eda15f | Shell | 4,297 | 112 | #!/bin/bash
set -eu -o pipefail
# default vals
dockerfile=""
context_path=""
image_name=""
image_version=""
tar=""
import=""
# help message
print_help() {
echo "Usage: $0 --dir <context-path> --image-name <imagename> [--dockerfile <dockerfile>] [--image-version <imageversion>] [--no-import]"
echo
echo "Ar... |
68dc1a3c389e0d4c63cf0d77d3a538a612f0cdacb39e947ab43ac34be3a1c078 | Shell | 4,304 | 191 | #!/bin/bash
# GATK coverage stats
# script filename
script_path="${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 $script_name ERR... |
99e62136a7c25b75317f3be290765d64068fc76abf5c94342bd7b9759036a15f | Shell | 4,316 | 62 | #!/bin/bash
#$ -cwd
#$ -N magma-gsa_step2_non0median-run_MNT
#$ -o ./logs/magma-gsa_step2_v2-run_MNT02May2021.o
#$ -e ./logs/magma-gsa_step2_v2-run_MNT02May2021.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... |
a83272d2f9a5eae8eaa66383697e0b1268b297a971b6cf5b345bc19ff2528429 | Shell | 4,353 | 106 | #!/bin/bash
log() { echo "[base-desktop $(date -u +%H:%M:%S)] $*"; }
log "startup: begin"
if [ -n "$OPENBOX_ARGS" ]; then
sed -i "s#^command=/usr/bin/openbox\$#& ${OPENBOX_ARGS}#" /etc/supervisor/conf.d/supervisord.conf
fi
# Selkies encoder selection. The container is sometimes started with an NVIDIA GPU and so... |
154702e79e9bf4e3aa234840da81b7e2b1a24981cbf0f1f2a7d4520d3b7bb41e | Shell | 4,401 | 172 | #!/bin/bash
show_help() {
cat <<EOF
This is the JUMP proteomics pipeline bootstrapping script. Execute
with no arguments for a standard installation. An installation of
conda or minicoda is a prerequisite.
Bootstrapping will create a conda environment in this directory for
use with JUMP.
EOF
}
show_success... |
e769182dc2263f64ea78350cc85ec473b44ad2341cb5338050b89a0ab87e30fc | Shell | 4,412 | 138 | #!/bin/bash
##
## RRBS using Bismark
##
# script filename
script_path="${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 ] ; then
echo -e "\n $script_name ERR... |
012bee09847b2b686494a766d8a0c474b3db5c19e9a471ab14d41d69aab3f2c6 | Shell | 4,423 | 104 | #!/bin/bash
function tracking_in_subj_space {
path_to_sub=$1
func=$2
reg_of_int=$3
sub_id=$(basename $path_to_sub)
mkdir -p ${path_to_sub}/tracking_${reg_of_int}_reg
fslmerge -t \
${path_to_sub}/tracking_${reg_of_int}_reg/${sub_id}__5tt_${func}.nii.gz \
${path_... |
f6a96a30d47f0a85bba1089ac5467818cca40d17a5890567cbac8e143124189a | Shell | 4,425 | 91 | #!/bin/bash
set -eo pipefail
PLATFORM=$(python -c 'import platform; print(platform.system())')
echo "Installing pip-pre dependencies on ${PLATFORM}"
# uv rather than pip: it downloads in parallel and caches the wheels it builds
# for the git/archive deps below by resolved commit, so a warm UV_CACHE_DIR
# skips those... |
fd648eff602827469b1008ec3b84228eae25f46a09949a940ab05d848d62e01d | Shell | 4,446 | 201 | #!/bin/bash
# Split reads that contain Ns in their CIGAR string with GATK SplitNCigarReads
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of argume... |
834661dcda44087fb535fcfe370408f5ae7293b832af5f74df5ba35ba980c130 | Shell | 4,453 | 180 | #!/bin/bash
# run FastQ Screen (more generic version of qc-fastqscreen.sh)
# script filename
script_path="${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 [ ! $# ==... |
286b876ed36861e8f49fa5e316f3da61782f646a1af1d50dc728f3fa6220333d | Shell | 4,491 | 183 | #!/bin/bash
# run FastQ Screen
# script filename
script_path="${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 $script_name ERROR:... |
2112dc7eb0bb6f66ca2b4b883dd4012dcc0bf3649fa20abd09c34fb4993986b2 | Shell | 4,492 | 106 | #!/bin/bash
# ============================================================
# assess_SNR_LEMON.sh
# ============================================================
# Computes pulvinar SNR maps for functional (BOLD) and
# structural (DWI) MRI data from the LEMON dataset.
# Then averages SNR maps across all subjects.
#
# Dep... |
133c2a181659657f4855ce31457fb58746140b1c00f41d1a627d9f70f3be5166 | Shell | 4,505 | 83 | #!/bin/bash
#conda create -n bruker2nifti python=3.7
#pip install git+https://github.com/BrkRaw/brkraw.git
#add to .bashrc --> PATH=$PATH:/groupshare/traaffneu/preclinimg/software/Bru2
#qsub -l 'procs=1,mem=24gb,walltime=12:00:00' -I
#cd /home/traaffneu/margal/code/multirat_se/asset
# ./convert_bruker.sh
# ---- I... |
4b56d995a2d0a45fe86c332447c9dcf34689346ec5547b2c46026b09a6b970af | Shell | 4,522 | 105 | #!/bin/bash
# ============================================================
# assess_SNR_HCP.sh
# ============================================================
# This script computes SNR maps for each HCP subject, separately
# for functional (BOLD) and structural (DWI) MRI data, restricted
# to pulvinar ROIs. It then ave... |
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