sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f937e34f7b609a6baa5aa94fd8408f5f5857a7e99e439394ebadea9c5d9dfc54 | Shell | 2,237 | 56 | #!/bin/bash
# parse command-line arguments
if [ $# -ne 3 ]; then
echo Usage: $(basename "$0") fusions.tsv Aligned.sortedByCoord.out.bam output_prefix
echo
echo "Description: This script takes fusion predictions from Arriba (fusions.tsv) and extracts the fusion-supporting alignments listed in the column 'read_identi... |
71123e163eb34e98eaab0a157726579d7e8689227e61d7ac6dac396b1b973f3c | Shell | 2,241 | 20 | cd PCR1
~/.local/bin/bbmap/bbduk.sh -Xmx6g in1=R1.fq.gz in2=R2.fq.gz out=stdout.fq ref=adapters ktrim=r k=23 mink=11 hdist=1 tpe tbo 2> log_filtering.out | ~/.local/bin/bbmap/bbmap.sh -Xmx6g in=stdin.fq ref=design_files.fasta ordered interleaved nodisk outu=unmapped.fq.gz scafstats=scafstats.txt 2> log_mapping.out
cd ... |
baa10008e97fb3c97028e8ffff246db85c8134cbe8ac3970bb775b3bc356a9c7 | Shell | 2,243 | 56 | #!/bin/bash
### Install the package from source with a given type in a defined conda environment with a define python version,
### and call it to check if it works
### example usage:
### ./pip_install.sh stable my_env 3.9
set -e -u
INSTALL_TYPE=$1 # stable, loose, etc..
ENV_NAME=${2:-alphadia}
PYTHON_VERSION=${3:-3.11... |
1c744e8a45d2366d4a292553515b881b922ae03f44a262245ca075001741ed40 | Shell | 2,247 | 74 | #!/bin/bash
#SBATCH --job-name=j_firstlevel
#SBATCH --partition=short
#SBATCH --time=48:00:00
#SBATCH -n 1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=4G
#SBATCH --output=logs/%x.%A-%a.out
#SBATCH --error=logs/%x.%A-%a.err
#############################################
freesurfer_version="X.X.X"
export FREESURFER_... |
4962e4be3fea0c012d4526136235ac2e3ead763b7cbe506f57ace4896d3d45c4 | Shell | 2,249 | 92 | #!/bin/bash
MASTER_URL="http://picsl-histoannot-server"
DOCKER_TAG="latest"
# Name of the template
TEMPLATE_NAME="picsl-histoannot-worker-template-${DOCKER_TAG}"
GROUP_NAME="picsl-histoannot-worker-group-${DOCKER_TAG}"
# Service account info
SVCACCT=$(gcloud config get-value account)
function delete_template()
{
i... |
7ace0a701386fd67fb0b3d99ed85825acf9faa9157c6b3d685e86a3c4384552b | Shell | 2,250 | 81 | #!/bin/bash
# These commands are specific to my working setup and would need to be changed
# if rerunning on a different setup.
module load singularityce
# ENVIRONMENT VARIABLES
WORKDIR=${WORKDIR}
CONTAINER_DIR=${CONTAINER_DIR}
SCRATCH_DIR=${SCRATCH_DIR}
export SINGULARITY_BINDPATH="/users,/scratch,/work,/data"
si... |
7a738db5adacf196ce91a29842f5232210c90eb42a2fe4f8bdd50d455fcaa00e | Shell | 2,251 | 78 | #!/bin/bash
# synthseg (robust, with cortical parcellation)
# (the script was run on a server via SLURM)
# for details, see: https://direct.mit.edu/imag/article/doi/10.1162/IMAG.a.930
# František Váša, frantisek.vasa@kcl.ac.uk
# data directory
hype_dir=[path_to_folder]/HYPE ### SET PATH TO MAIN FOLDER
in_dir=${hype_d... |
90f78ce5316e3e52d57d882c7ae7675bb5c6838e56c4631e8df5573a49f0eb22 | Shell | 2,261 | 20 | cd Bunny_P
~/.local/bin/bbmap/bbduk.sh -Xmx6g in1=R1.fq.gz in2=R2.fq.gz out=stdout.fq ref=adapters ktrim=r k=23 mink=11 hdist=1 tpe tbo 2> log_filtering.out | ~/.local/bin/bbmap/bbmap.sh -Xmx6g in=stdin.fq ref=design_files.fasta ordered interleaved nodisk outu=unmapped.fq.gz scafstats=scafstats.txt 2> log_mapping.out
... |
a12fa2d075013edbc03ce546e38136d5b8f6751660f76171b6fcf21401691e7a | Shell | 2,269 | 71 | #!/usr/bin/env bash
#Hongjian Jin, 1/10/2023, at St Jude Children's Research Hospital
usage() {
echo "Usage: $(basename ${0}) -L <fq.lst> [-o <outdir> -q <queue> -s <subset>]" 1>&2;
printf " describe usage here.\n"
printf "\nOptions:"
printf "\n\t-L fq.lst: [required] one fastq.gz filename per line"
... |
389660d11044973369c8fc7bb5ff8b1f74cadc5c8ec7bbaa14b3006ab91561f4 | Shell | 2,270 | 47 | #!/usr/bin/env bash
# Host-side launcher for the Docker variant of the CMA self-hosted sandbox demo.
#
# Builds the per-session image, then runs `ant beta:worker poll` on the host
# with --on-work pointed at on-work.sh, which `docker run`s a per-session
# container per claimed work item. The poller never executes tools... |
c4211712083ebb2bf948ad22631e6c60a64ffff99dc6a5075916c7fbfdc9a91a | Shell | 2,292 | 122 | #!/bin/bash
# deepTools generate BigWig from BAM
# script filename
script_path="${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 $... |
6c8fdac60bf6ecdf08d4202bbccc0911c2d7a3268925fd615d28c6aff6be9c29 | Shell | 2,297 | 46 | #!/bin/bash
path_to_wm=/home/ludovicocoletta/Documents/REMAP_subcortical/WM_FC/04_LNM_waypoints/seg/WM_re.nii.gz
path_to_cortical_thr=/home/ludovicocoletta/Documents/IntraOpMap_2022/04_preprocessed_rsfmri/00_draft/maps_2mm_cleaned_and_thr/leave_one_seed_out_results/report
path_to_subcortical_thr=/home/ludovicocoletta/... |
db70b8ab3cc3f283fd7642aa6451326da6ba2ccac35aa88d158343b9ac178c5d | Shell | 2,302 | 48 | #!/bin/bash
if [ -z "$GAZEBO_MODEL_PATH" ]; then
bash -c 'echo "export GAZEBO_MODEL_PATH=$GAZEBO_MODEL_PATH:"`pwd`/../assets/models >> ~/.bashrc'
else
bash -c 'sed "s,GAZEBO_MODEL_PATH=[^;]*,'GAZEBO_MODEL_PATH=`pwd`/../assets/models'," -i ~/.bashrc'
fi
#Load turtlebot variables. Temporal solution
chmod +x catkin_... |
6e2705caeff8d7eae4d94095717a93f2117a26f93bd1c617e2eaa83d1542043b | Shell | 2,314 | 48 | #!/bin/bash
# Resample ccf results from fsLR space to fsaverage space
set -u -x -e
sub=$1
path_anat_data=$2
path_output_dir=$3
path_HCPtemplates_standardmeshatlases=$4
path_fsaverage=$5
path_wbcommand=$6
threshold="00"
for hemi in L R; do
for model in real simulated; do
for param in r rss sigma v0i; do... |
aa073c21a2f480f97fff441d445389103d17dbf986bdf02fac946404765d6ff3 | Shell | 2,321 | 62 | #!/bin/bash
# ============================================================
# 02_processing_for_roi2roi_structgradients.sh
# ============================================================
# This script generates subject-level ROI-to-ROI structural
# connectomes using MRtrix (tck2connectome) and the Schaefer atlas.
##
# St... |
10f469f4f4ab1035f9715159b8dd492e4795fe638456d2b5813c6fd0c050f05a | Shell | 2,348 | 88 | #!/bin/bash
# Siwei 06 Aug 2021
# Siwei 31 Jun 2019
# collapse multiple extracted bed files into one
## list all .bed files
shopt -s nullglob
bed_array=(*.bed)
echo "${bed_array[@]}"
# beds=(CN_summits_extracted_max.bed
# DN_summits_extracted_max.bed
# GA_summits_extracted_max.bed
# NPC_summits_extracted_max.bed)
... |
80514905f616ba36f256e23583b081120abd30610b247146ab2bb99110ac93f0 | Shell | 2,352 | 49 | cp ENCFF124UYX.bam ENCFF124UYX_E10.5_H3K4me3.bam
cp ENCFF157KEH.bam ENCFF157KEH_E10.5_H3K4me3.bam
cp ENCFF045IPK.bam ENCFF045IPK_E10.5_H3K4me3.bam
cp ENCFF825AVI.bam ENCFF825AVI_E10.5_H3K4me3.bam
cp ENCFF760QYZ.bam ENCFF760QYZ_E11.5_H3K4me3.bam
cp ENCFF184CUE.bam ENCFF184CUE_E11.5_H3K4me3.bam
cp ENCFF717QDV.bam ENCFF71... |
73edcf106b92ac21b4c67ce5de913c512c8f2c8d9e8d4175005120722fd7468a | Shell | 2,365 | 52 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --job-name=RetInfer
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=50G
#SBATCH --account=a_ai_collab
#SBATCH --time=06:00:00
#SBATCH -o output_models_inference.txt
#SBATCH -e error_models_inference.txt
#SBATCH --partition=gpu_cuda
#SBATCH --qos=gpu
#SBATCH --gr... |
a1de3516daf3824604971736bc6aa4deb3492bd8b143888d157a2d8a2afc8c0f | Shell | 2,374 | 48 | #!/bin/bash
#-----------------------------------------------
# Filter: near read ends
#-----------------------------------------------
# Filter out variants within <int> bp from the end of the read
# Uncomment the line below for cluster computing, otherwise make sure you have these tools installed
# module load gcc/1... |
435310f98c4c30c62c97710d7739caba86be4fffdaa44680e919d1d192518998 | Shell | 2,390 | 70 | #!/bin/bash -e
# This takes one commandline argument, the name of the package. If no
# name is given, then we'll end up just using the name associated with
# an arbitrary .tar.gz file in the rootdir. That's fine: there's probably
# only one.
#
# Run this from the 'packages' directory, just under rootdir
## Set LIB ... |
22817d19fd84b53f00bceee64f1c2591ed8de07cfd5df49ee3a15bbbaa37e643 | Shell | 2,391 | 73 | #!/bin/bash
# SessionStart Hook - Skills Cookbook Environment Check
# This hook runs at the start of each Claude Code session to verify environment setup
set -e
echo "🔍 Skills Cookbook - Environment Check"
echo "======================================"
# Check if we're in a virtual environment
if [[ -z "$VIRTUAL_ENV... |
832fa8c78ffb10edbab31291aae69e1bdff28edacfa5e2bc4314255ec81604d3 | Shell | 2,393 | 86 | #!/usr/bin/bash -l
#SBATCH --job-name=mc-prediction
#SBATCH --output=/dev/null
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=3
#SBATCH --mem=9G
#SBATCH --time=1-00:00:00
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=abc@bio.aau.dk
#SBATCH --account=phn
#SBATCH --array=0-30
set -euo pipefail
# Runs the workfl... |
35264cc395183b5a5f719f5290db859b34672bd76340dce2428062eb1f7bfe5d | Shell | 2,402 | 66 | #!/bin/bash
ml freesurfer/7.3.2
# this script transforms the anlges from deepRetinotopy to the required angles for neuropythy and save them as ..._neuropythy
subjects_dir=""
while getopts s:r: flag
do
case "${flag}" in
s) subjects_dir=${OPTARG};;
r) path_to_validation_repo=${OPTARG};;
?)
... |
386742bed234d5c7e4337c56507600e8f6e40914a39fbf707470e629e642f18d | Shell | 2,416 | 81 | #!/bin/bash
# comments
# make dir for diagns
rm -rf ADiag
mkdir ADiag
#
rm -rf APhysData
mkdir APhysData
#
########################################## Comment out the ### lines if you want the same with multiple runs
#
DIR1="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
input1=$DIR1/paramet.i
#input2=$DIR1/SU... |
44d1eba32f152a795720b21c06cec9bb4928f95f52bc62199906048e44d663c9 | Shell | 2,419 | 59 | #!/bin/bash -l
# Set SCC project
#$ -P ivc-ml
# Request 4 CPUs
#$ -pe omp 3
#$ -m bea
# Request 1 GPU
#$ -l gpus=1
#$ -l gpu_memory=48G
#$ -l h_rt=48:00:00
# nvidia-smi
# echo $CUDA_VISIBLE_DEVICES
# module load miniconda
conda activate mmMRI
export WANDB_CACHE_DIR="/projectnb/ivc-ml/dlteif/.cache/"
echo $WANDB... |
b7e0e542a2b9aff2cfcc931df81ec7aa9250c10292e69f502bdbea3fbd0413c3 | Shell | 2,422 | 61 | #!/bin/bash
set -euf -o pipefail
clone_repo() {
local branch=$1
echo "cloning repo from branch $branch"
# rm "kaapana" folder if exists
if [ -d "kaapana" ]; then
echo "Deleting existing 'kaapana' folder"
rm -rf "kaapana"
fi
# clone repo from branch
if git clone -b "$branch" --single-branch http... |
d4ac7214297d44e38ac6e7a50da9a15e0c1e276a60129d33fc385035b2d078cf | Shell | 2,426 | 49 | #!/bin/bash
# Resample eccentiricity and polarangle from fsLR space to fsaverage space
set -u -x -e
sub=$1
path_anat_data=$2
path_output_dir=$3
path_HCPtemplates_standardmeshatlases=$4
path_fsaverage=$5
path_wbcommand=$6
threshold="00"
for hemi in L R; do
for model in real simulated; do
for param in ec... |
673b8d5a1820b76e30de9b1c35fb88cfdbe8eaaf3edf7b42eb2571be5f93acb5 | Shell | 2,427 | 52 | #!/usr/bin/env bash
# SPDX-License-Identifier: Apache-2.0
# Run the complete two-rank communication regression.
set -euo pipefail
SCRIPT_DIRECTORY="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)"
# Runtime configuration. Each value can be overridden in the environment.
# Two MPI ranks and two visible GPUs are r... |
c8783765eaad0309c10db0617aadf75df147048c0daca585af632a888498e329 | Shell | 2,432 | 68 | #!/usr/bin/env bash
# "Source step #2:" runs "DESeq2" differential expression gene (DEG) analyses with "R4 - Rscript (4.3.1 / 2023-06-16 / Beagle Scouts)"
# 'CLI' ARGs
COMPARISON=$1 # 'Comparison' to be done
BATCH=$2 # 'Batch' to be used
# My 'OBJs'
## It is recommended (but not required) to use only 'letters', 'n... |
935176740a38c594673a74bf73e2467e009c92fc521432e1fd22c247722ac0ad | Shell | 2,456 | 74 | #!/bin/bash
# Initialize a variable to store the directory path
directory=""
#'p:' represent need a command line argument with '-p', and opt is the variable name of -p
while getopts "p:" opt; do
#case starts a case
case $opt in
# p) represents a p case
p)
directory="$OPTARG"
;;
# \? represents the s... |
8d9fafbead0008eff63b93d81345e9fb8861f9f1ec6dfde82b0b734ba8d60979 | Shell | 2,458 | 60 | #!/bin/bash
# Exit immediately if a command exits with a non-zero status
set -e
# Usage: ./merge_test_decoys_wrapper.sh <output_prefix>
OUTPUT_PREFIX=$1
# Paths to the input GTF files
# different permutations of cryptic events, non-cryptic genes and non-cryptic events within cryptic-containing genes
# i.e. output o... |
5c398c7332b8f8b8a69282791b3122378114d0974f0681e4773f6124aa495b53 | Shell | 2,464 | 92 | #!/bin/bash
# This script is meant to be called in the "deploy" step defined in
# circle.yml. See https://circleci.com/docs/ for more details.
# The behavior of the script is controlled by environment variable defined
# in the circle.yml in the top level folder of the project.
set -ex
if [ -z $CIRCLE_PROJECT_USERNAME... |
a754f62e1594a2df0f4737ffcf0cc8c67d2a0d9a7a598ea856569fc28c83c524 | Shell | 2,467 | 57 | #!/bin/bash
set -eo pipefail
# An unset value disables the check in conftest entirely, so every job has to say what it
# is allowed to skip rather than silently skipping anything
test -n "${MNE_TEST_ALLOW_SKIP}" || {
echo "::error::MNE_TEST_ALLOW_SKIP is unset, so skips would go untracked"
exit 1
}
if [[ "${CI_O... |
3e8d05935210c4f5bf241f653aae8aaf057ca89b874ea44a017254a18332649a | Shell | 2,471 | 73 | #!/bin/bash
# Copyright (C) 2012 University of Oxford
#
# SHCOPYRIGHT
# last 2 parameters are subjdir and bindir
parameters=""
while [ ! -z "${2+x}" ]
do
case $1 in
"--nf="*) numfib=`echo $1 | cut -d '=' -f2` ;;
esac
all=$all" "$1
subjdir=$1
shift
done
bindir=$1
$bindir/bin/merge_parts_gpu... |
f06a3025882e8c403c4bf1b9dcf15801b1deae6b5076f474b84cb7ca2e74b066 | Shell | 2,477 | 61 |
#!/bin/bash
#merge R1 and R2 reads and then collapse reads so we have on read per region
#usearch version v11.0.667_i86linux64
#K Castellano
#merge forward and reverse reads
usearch -fastq_mergepairs Lv-D22-3FBS_S67_L001_R1_001_trim.fastq \
-reverse Lv-D22-3FBS_S67_L001_R2_001_trim.fastq \
-fastaout Lv-D22-3... |
4bef0137949b8bdcb31914efa307007a9db00c00fe2d4a4fb4089af0edf11123 | Shell | 2,485 | 77 | #!/usr/bin/env bash
#
# Licensed to the Apache Software Foundation (ASF) under one *
# or more contributor license agreements. See the NOTICE file *
# distributed with this work for additional information *
# regarding copyright ownership. The ASF licenses this file *
# to you under the Apache License... |
82faa9a102ff75288516c2a9f6c5962326d64a7cd59236fbbc55c5702643d165 | Shell | 2,486 | 87 | #!/bin/bash
##activate conda if required
#source /home/arh49/miniconda3/etc/profile.d/conda.sh
#source /usr/bin/Rscript
##usage: ./run_ewf_basecalling.sh arg1 arg2 arg3 arg4
##args as listed below
##need to implememtn check to get enofgh args. NBt do that later.
stable=$1
save_path=$2
bc_cfg=$3
rem_cfg=$4
##read i... |
24e5a55f5f113a0451781a61f942c29133d41c5cee91bb1f404b4c2fb647dd10 | Shell | 2,493 | 20 | cd PCR1
~/.local/bin/bbmap/bbduk.sh -Xmx6g in1=R1.fq.gz in2=R2.fq.gz out=stdout.fq ref=adapters ktrim=r k=23 mink=11 hdist=1 tpe tbo 2> log_filtering.out | ~/.local/bin/bbmap/bbmap.sh -Xmx6g in=stdin.fq ref=design_files.fasta ordered vslow k=8 maxindel=200 minratio=0.1 interleaved nodisk outu=unmapped.fq.gz scafstats=s... |
1c52cb2f797c504eb1419636356dea089bc8d7e858bfc48c2f371e778bbb77f5 | Shell | 2,496 | 44 |
dirT1=$STUDY_DIR/derivatives/$subj/anat
# Creating a mask from the T1_mprage (alternative way to get a mask and probably better for normaliz. purposes)
#---------------------------------------------------------
fslmaths ${dirT1}/${subj}_T1w_r_bfc.nii.gz -bin ${dirT1}/${subj}_T1w_r_bfc_mask.nii.gz
# Filling some very ... |
fc4c02bb6f3b38bb0cfc7c16627f46f35107d64f6591de25b9944a14a51acb6d | Shell | 2,503 | 86 | #!/bin/bash
# Test script to validate conda environment creation and pip requirements installation
# This script creates a test conda environment from environment.yaml and installs pip requirements
set -e # Exit on any error
set -u # Exit on undefined variables
is_truthy() {
case "${1:-}" in
1|true|TRUE... |
a72f3dff04b67c10585ae0e0ec0ff3665a57fcbea34d2f1fe5b1d0d4e7c7546e | Shell | 2,504 | 126 | #!/bin/bash
# run FastQC
# script filename
script_path="${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: WRONG... |
d9b4cdffce76250b9d0eb50057d0673afd71ad6a08f1efd1aecb71a116bb8efc | Shell | 2,509 | 63 | #!/bin/sh
#
#
data_path=/home/kenweber/Projects/Neuromuscular_Signature_R01_Pilot
output_path=/home/kenweber/trialwise
scripts_path=/home/kenweber/Neuromuscular_Signature_R01_Pilot
subjects=(sub-NSPilot006 sub-NSPilot007 sub-NSPilot009 sub-NSPilot010 sub-NSPilot012 sub-NSPilot014 sub-NSPilot015 sub-NSPilot016 sub-NS... |
0a6eefeeb439d687a6cd0e631c7d994eb1597ad565e9835fb090269b020ea157 | Shell | 2,515 | 74 | #!/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... |
b583865c443dd21c83d3a9aea5a5cbae46051056d641bbafddab096567a2286d | Shell | 2,516 | 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... |
1c2d48413203587ac0ce7832a6e8ad833ffa13645e3802e115fe5fd63f16d160 | Shell | 2,530 | 47 | #!/bin/bash
set -u -x -e
sub=$1
ses=$2
path_anat_data=$3
path_output_dir=$4
path_HCPtemplates_standardmeshatlases=$5
path_fsaverage=$6
path_wbcommand=$7
threshold="00"
for hemi in L R; do
if [ $hemi = "L" ]; then
hemi_down="left"
elif [ $hemi = "R" ]; then
hemi_down="right"
fi
for m... |
5c1176b0cb7277ae1f2b096329b41cfca940bf440018bfde987d0ad63862c6c2 | Shell | 2,530 | 47 | #!/bin/bash
set -u -x -e
sub=$1
ses=$2
path_anat_data=$3
path_output_dir=$4
path_HCPtemplates_standardmeshatlases=$5
path_fsaverage=$6
path_wbcommand=$7
threshold="00"
for hemi in L R; do
if [ $hemi = "L" ]; then
hemi_down="left"
elif [ $hemi = "R" ]; then
hemi_down="right"
fi
for m... |
b1cdcadfdf6ddc2543995cd2dd51af569ba15a81bc090485edb0fd7df432f8a7 | Shell | 2,531 | 73 | #!/bin/bash
# transforms the Wang template to individual subject surface space
# for run only emperical dataset.
set -x -u -e
echo "$0" "$@" # print function call
subject_label=$1
session_label=$2
subject_age_weeks=$3
path_derivatives=$4
path_anat_data=$5
path_func_data=$6
path_output_data=$7
file_volume_template_40wk... |
9a6a64fb41633f4fa4bdd76800671692fdae1f138001168f796b25a06a49236a | Shell | 2,541 | 49 | #!/bin/sh
set -e -o pipefail
# Root CA
# openssl genrsa -out root-ca-key.pem 2048
# openssl req -new -x509 -sha256 -key root-ca-key.pem -subj "/C=CA/ST=ONTARIO/L=TORONTO/O=ORG/OU=UNIT/CN=root.dns.a-record" -out root-ca.pem -days 730
# Admin cert
openssl genrsa -out admin-key-temp.pem 2048
openssl pkcs8 -inform PEM -ou... |
7bd3e8f1c80fed90e65237a45dfca6333704979aed74a1e1a3fa3e4ddd0c99f2 | Shell | 2,549 | 54 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --job-name=RetMaps
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=80G
#SBATCH --account=a_ai_collab
#SBATCH --time=48:00:00
#SBATCH -o output_models.txt
#SBATCH -e error_models.txt
#SBATCH --partition=gpu_cuda
#SBATCH --qos=gpu
#SBATCH --gres=gpu:h100:1 # f... |
2443cb61f2f0dbb1da134c7108df806a3884f1aa7c66af8165476d56e64c3ea6 | Shell | 2,583 | 55 | #!/bin/bash
#$ -cwd
#$ -N magma-gsa_step1-annot_MNT
#$ -o ./logs/magma-gsa_step1-annot_MNT23Aug2020.o
#$ -e ./logs/magma-gsa_step1-annot_MNT23Aug2020.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_F... |
c9bc0ca0f7a1c6405da4e1b98f0fc5f382e200f37937ed2968f1bb8f496781b2 | Shell | 2,588 | 84 | fastqc \
--outdir ${OUTPUT_DIR}/FASTQC/RAW \
--threads ${LSB_MAX_NUM_PROCESSORS} \
--format fastq \
--quiet \
${OUTPUT_DIR}/${FASTQ1} \
${OUTPUT_DIR}/${FASTQ2}
trim_galore \
--paired \
--gzip \
--clip_R1 15 \
--clip_R2 15 \
--cores ${LSB_MAX_NUM_PR... |
029fba60943a115ff35a04f8a39d5dacf829ba732b3c7cd4e512390cfb2d55ca | Shell | 2,596 | 91 | #!/bin/bash
# Siwei Aug 06 2021
# Siwei 31 Jun 2019
# collapse each single bed files to remove any overlapping peaks
# within 500 bp interval of the same file
# iterate through each bed file
for eachfile in *.bed
do
echo $eachfile
beds=($eachfile)
out=extracted/${eachfile/%.bed/_extracted_max.bed}
... |
c377b604305d6647ac368167c048ec7733cc1f62ba6b3551a352ed7943ba833e | Shell | 2,597 | 93 | # Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# arg1 = file, arg2 = file it depends on
action () {
if (test $mode = 0) then
rm -f ../$1
elif (! cmp -s $1 ../$1) then
if (test -z "$2" || test -e ../$2) then
cp $1 ..
if (test $mode = 2) then
... |
5a328b697f6889ffaba027e1173122abff9334807b498cc3738de0a08d00420f | Shell | 2,610 | 78 | #!/bin/bash
#SBATCH --job-name=j_firstlevel
#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 FREESURFER_... |
2814cf500ba781867ce8c51849ca6e559815f280baa24b96fd8db4a752b59d4b | Shell | 2,613 | 93 | #!/bin/bash
usage() {
echo "Usage: $0 [-w window_size] [-o out_bed_dir] <bed_files_directory> <reference.bed> <output.tsv>"
echo "Options:"
echo " -w Window size in base pairs (default: 0)"
echo " -o Output directory for overlapping BED files (optional)"
exit 1
}
# set default window-size (to be up... |
a0a8558a3be414d4fddd758cc156e98340191afb9c12d2c02cc52a007fab81b1 | Shell | 2,627 | 75 | # 4/1/2024
fastqc \
--outdir ${OUTPUT_DIR}/FASTQC/RAW \
--threads ${LSB_MAX_NUM_PROCESSORS} \
--format fastq \
--quiet \
${OUTPUT_DIR}/${FASTQ1} \
${OUTPUT_DIR}/${FASTQ2}
trim_galore \
--paired \
--gzip \
--clip_R1 15 \
--clip_R2 15 \
--cores ${LS... |
47f75bef0e20a34934d229cf4f88db217b5ad0166b5748a515bb832e2218c803 | Shell | 2,638 | 82 | #!/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... |
ecdc359d8483805fe6b498d0f9d21fa7380484a4da4701dba237fcd82624ef2b | Shell | 2,648 | 80 | #!/bin/bash
TEACHER="resnet110"
STUDENT="resnet8"
TEACHER_1="resnet110"
STUDENT_1="resnet20"
TEACHER_2="vgg19"
STUDENT_2="vgg8"
A=0.9
B=0
A1=0
B1=0.7
A11=0
B11=0.7
A2=1
B2=0.7
DATE="1_30"
cd /home/lthpc/zhongzh/RFD4Hist
python "/home/lthpc/zhongzh/RFD4Hist/train_student.py" \
--model_s $STUDENT \
--path_t "/hom... |
7ee358faae75bf287eb80612a537fe972fbb3d740dc1c1c8f077ef762d928816 | Shell | 2,679 | 57 | #!/bin/bash
#set number of cores
NUM_CORE=20
#run for scrambled expression data
#run cross every sample and every seed: fuma magma and seismic
for i in {1..10}
do
nohup Rscript src/null-sim/seismic_fuma_magma_null_sim.R data/expr/null_sim/expr_rda_rs/expr_ds_"$i".rda \
data/expr/null_sim/seed_table/sample... |
ec626bcdd9afe83e7e9d6e8045759637cf89c4f8f0aa9a5dba3b3536d2618164 | Shell | 2,685 | 67 | #!/bin/bash
# Siwei 21 Jan 2019
for EACHFILE in *.fastq.gz
do
echo $EACHFILE
####align for unpaired reads
bowtie2 -p 23 -X 2000 --mm --qc-filter --met 1 -t --sensitive -x ~/1TB/Databases/hg38/INDEX/Homo_sapiens_assembly38.fasta -U $EACHFILE --met-file align_metrics/${EACHFILE/%.fastq.gz/}_U.txt | samtools view -b ... |
027b4df1421970d31d1c7768092618aef77421cbb13a2a2ff07a05589b71025b | Shell | 2,693 | 21 | #!/bin/bash
#
#SBATCH --job-name=MMRegPanc1
#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-... |
439622b1a075cdc5729c0a6b8bca98f74bdaad5651b1c61569f6ce0983361dc4 | Shell | 2,693 | 21 | #!/bin/bash
#
#SBATCH --job-name=MMRegPanc1
#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-... |
8d9ffe01fefebaa341a679ebabb07cefec068b6e12b7a4bc93852aeaf8cad4de | Shell | 2,693 | 21 | #!/bin/bash
#
#SBATCH --job-name=MMRegPanc1
#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-... |
bf14a3c03d80fda4ae69d3483a213ed1dbdc1c5e068dbb0e819a27e9e0f06fa7 | Shell | 2,693 | 21 | #!/bin/bash
#
#SBATCH --job-name=MMRegPanc1
#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-... |
ff34b24a633ff7c432cfade778be175a71aa6b45888e8c773c592697fe664618 | Shell | 2,695 | 125 | #!/usr/bin/env bash
set -e
set -o pipefail
PROG=$(basename $0)
BOT_USER_NAME=scikit-build-bot
BOT_USER_EMAIL=scikit-build-bot@scikit-build.org
TARGET_BRANCH=gh-pages
err() { echo -e >&2 ERROR: $@\\n; }
die() { err $@; exit 1; }
#-------------------------------------------------------------------------------
help()... |
c10dc3fb3d272e7ff58079c4d37fe2da3e3925e4e0dc7130311e848eb39e9ee2 | Shell | 2,704 | 56 | #!/bin/bash
# In this example we process a scan containing multiple b-values acquired at one, single diffusion time
#
# The scan is stored in the https://github.com/radiomicsgroup/dMRIMC/tree/main/using_Histo_uSim/zenodo_mouse_data folder
# where you'll find:
# dwi_denoise_unring_sphmean_difftimefixed.nii --> scan wit... |
413505609304611f5c268ff4859c0843c1d987c9d441f1c2540a71ca0fa4c44f | Shell | 2,716 | 53 | #!/bin/bash
set -euo pipefail
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=${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... |
d9f74efc8a4d1f6618b24a0a7b068614acee17cf884cae01a319bda499684bcc | Shell | 2,726 | 91 | #!/bin/bash
# example prepare_vmd.sh /home/jtranch/Documents/lammps/src/dump_VSRSV.lammpstrj
# you will get a return file
echo "vmd script for file $1 is preparing..."
timestamp(){
date +%s
}
TS=$(timestamp)
FILE=view_${TS}.vmd
cat >${FILE} <<EOF
proc vmd_draw_arrow {mol start end} {
set middle [vecadd \$start ... |
4f7a795e5bae1dd7e3cf105ad6eb03964deebb90ffe39a29eb4290fe2d6d2936 | Shell | 2,737 | 77 | #!/bin/bash -ef
set -eo pipefail
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
ONLY_BINARY_ARG="--only-binary=:all:"
STD_ARGS="--progress-bar off --upgrade"
INSTALL_ARGS="-e"
EXTRAS=""
GROUP="test_extra"
if [ ! -z "$CONDA_ENV" ]; then
echo "Uninstalling MNE for CONDA_ENV=${CONDA_ENV... |
43fed4ed027e81e3c0b770d6f73e843ccf06829b6d0f6d162479b3354be6299b | Shell | 2,740 | 41 | #!/bin/bash
#$ -cwd
#$ -N magma-gsa_all_CAD_MNT
#$ -o ./logs/magma-gsa_all_CAD_MNT02Sep2020.o
#$ -e ./logs/magma-gsa_all_CAD_MNT02Sep2020.e
#$ -l bluejay,mem_free=24G,h_vmem=32G
echo "**** Job starts ****"
date
model="snp-wise"
ANNO=/dcs04/lieber/marmaypag/Tran_LIBD001/Matt/MNT_thesis/snRNAseq/10x_pilot_FINAL/MAGMA/G... |
6c6bd53b91fc3fde221b69d0e9b768f946306988f75fd6547c54e5505bd44270 | Shell | 2,750 | 60 | #!/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... |
c82947d74100823356c0a7ffa1f6a5b1f301a88a81537a4fef8da31e2b5ebe0a | Shell | 2,771 | 67 | #!/bin/bash
function create_track_count_per_seed {
seed=$1 # must be something like sub-1006_SEMANTIC_19_13_-7_whatever.nii.gz
func=$2
file_name=$(basename $seed _wm_gm_interface.nii.gz)
dir_name=$(dirname $seed)
splits=(${file_name//$func/A})
splits_2=(${splits//_/ })
sub_id=${sp... |
ea0399c8514a87c63fa645f416305c4d3fd5d80ce475a7020257b18bff016172 | Shell | 2,776 | 64 | #!/bin/bash
#SBATCH --partition=single
#SBATCH --ntasks=1
#SBATCH --time=48:00:00
#SBATCH --mem=12gb
#SBATCH --job-name=Melanoma_Brain_Metastasis
#SBATCH --output=ny_metastasis-%j.out
#SBATCH --export=NONE
## This script will setup a mcmicro folder structure for all files in a given folder, then
## run bfconvert on th... |
934bae24142a1a58f24091bd4769aa8e637916d0c7f75f31b2c43d34bf0d3830 | Shell | 2,791 | 45 | #!/bin/bash
#$ -cwd
#$ -N magma-gsa_step3-gsa_AD
#$ -o ./logs/magma-gsa_step3-gsa_AD_MNT18Jul2021.o
#$ -e ./logs/magma-gsa_step3-gsa_AD_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_FI... |
26101b434d32bb229cf4ce019192f1c254acc8d8ca6c569a8904234045a0e62d | Shell | 2,792 | 83 | #!/bin/bash
# =============================================================================
# generate-certs.sh — Create a self-signed CA and proxy certificate
# =============================================================================
#
# WHAT IS A SELF-SIGNED CA?
# A Certificate Authority (CA) is an entity that... |
c47179917647f0c3938f1b0b9a7e769b14911beeb791d3ad2da51d19667dcd17 | Shell | 2,793 | 66 | #!/bin/bash
c=$1
a=$2
my_cmd="
docker pull ghcr.io/rgcgithub/regenie/regenie:v3.5.gz
docker run \
--name regenie_run${c} \
-v "./:/proj_dir/" \
ghcr.io/rgcgithub/regenie/regenie:v3.5.gz regenie \
--step 2 \
--pred /proj_dir/ukb_step1_quant_pred.list \
--bgen /pro... |
e30f0714ff6656d4b437ef2af4ff883d467da13f3e9298874b02d43b6fb58164 | Shell | 2,805 | 79 | #!/usr/bin/env bash
###############################################################################
# Script: split_bam_and_bigwig.sh
#
# Purpose:
# For each paired-end, stranded RNA-seq BAM:
# 1. Split by *transcriptional sense and antisense* using proper flag combinations
# (dUTP/reverse-stranded protoco... |
418903304c39087a165e2001f878887ef7bbc4b1c25077d838dd0644576af69e | Shell | 2,807 | 94 | #!/bin/bash
# rigid registration of HFC+HFE (64mT) synthseg outputs to GE (3T) within individuals, for quantification of dice overlap
# (the script was run on a server via SLURM)
# for details, see: https://direct.mit.edu/imag/article/doi/10.1162/IMAG.a.930
# František Váša, frantisek.vasa@kcl.ac.uk
# data directory
... |
e60d319c9db57827e118a134305046e8b2d40b8ae4ef9116bea21f8d1f054dca | Shell | 2,850 | 47 | #!/bin/bash
NUM_CORE=15
# get the scDesign3 model
for i in {1..10}
do
nohup Rscript src/causal-sim/fit_scDesign3.R data/null_sim/expr_rda_rs/expr_ds_"${i}".rda data/causal_sim/standard_scdesign3_model/expr_ds_"${i}".cell_anno.txt \
data/causal_sim/standard_scdesign3_model/expr_ds_"${i}".scdesign3_para.rda 10 &
done... |
17515f22ceb05ca4c27bf2eb6e39ac98b844c5ee899d857dca8880f74f156ca1 | Shell | 2,851 | 79 | #!/bin/bash
# transforms the Wang template to individual subject surface space
set -x -u -e
echo "$0" "$@" # print function call
subject_label=$1
session_label=$2
subject_age_weeks=$3
path_derivatives=$4
path_anat_data=$5
path_func_data=$6
path_output_data=$7
file_volume_template_40wks=$8
name_volume_template_40wks=$9... |
fed83404f882e10a143e98e87ff0784bd57fd46325c1fba1c6ebef4cc12892ba | Shell | 2,871 | 79 | #!/bin/bash
# transforms the Wang template to individual subject surface space
set -x -u -e
echo "$0" "$@" # print function call
subject_label=$1
session_label=$2
subject_age_weeks=$3
path_derivatives=$4
path_anat_data=$5
path_func_data=$6
path_output_data=$7
file_volume_template_40wks=$8
name_volume_template_40wks=$9... |
0b7006f238e7be7ea4baf44b1926b6d5215bc626cd71396a725f9c174368bf0d | Shell | 2,891 | 62 | #!/usr/bin/env bash
# output to a log file rather than stdout
#!/bin/sh
# exec >> negbio_log_file
# exec 2>&1
BASE_FOLDER=$1
NEGBIO_PATH=$2
if [ -z "$BASE_FOLDER" ]
then
echo "You must call this script as: ./run_negbio.sh FOLDER_WITH_DATA_CSVS NEGBIO_GIT_PATH"
exit 1
else
echo "Source of data: $BASE_FOLD... |
0db83b041720e1b210b74374812dce8a25e6714bc751d8028d7afe3b4ed7dc8e | Shell | 2,926 | 102 | #!/usr/bin/env sh
CAFFE=/cs/vml2/msibrahi/workspaces/caffe-lstm
GIT_PROJ_DIR=$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... |
51150eed17a36f68df1bc8ddb3582a2f8dcdf28705856e5af13ff4531e6b912e | Shell | 2,937 | 113 | #!/bin/bash
##
## whole genome/exome/targeted sequencing somatic single/simple/short nucleotide variant calling
##
# specify maximum runtime for sbatch job
# SBATCHTIME=0:05:00
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
route_name=${script_name/%.sh/}
echo -e "\n =====... |
4e375fc23fdaa4da2852607cea83c278c15d357176e7dbf3175894f7a1fec029 | Shell | 2,942 | 69 | #!/bin/bash
# Check for the right number of arguments
if [ "$#" -ne 4 ]; then
echo "Usage: $0 CONTAINER_NAME DATA_PATH_RDA DATA_PATH_H5AD OUTPUT_PATH"
exit 1
fi
#get the base path and set it as the working directory
BASE_PATH=$(dirname "$(dirname "$(dirname "$(realpath "$0")")")")
echo "BASE_PATH IS" "$BASE_P... |
ad97a0c9c5e10e596fecf80a9aebac1dae6378f32b36b16d707ce42cfc7c49ee | Shell | 2,943 | 114 | #!/bin/bash
# 29 May 2021
# Siwei update dnsnp version to v154
# 11 May 2021
# Siwei rewrite in GATK4
# 11 Jun 2020
vcf_suffix="_995.vcf"
gatk4="/home/zhangs3/Data/Tools/gatk-4.1.8.1/gatk"
ref_path="/home/zhangs3/Data/Databases/Genomes/hg38"
ref_genome="/home/zhangs3/Data/Databases/Genomes/hg38/INDEX/Homo_sapiens_... |
bb9b4b2e34d49e9d6412a3448e4e4433fc507cde19427a2f77362c6d83d822f0 | Shell | 2,944 | 82 | #!/bin/bash
# set our directories
dir_out=$(pwd)
log_file="$dir_out/logfiles/log_runFSL-3.txt"
dir_tstt="$dir_out/results_tstt/"
if [ ! -d "$dir_tstt" ]; then
mkdir -p "$dir_tstt";
fi
nsim=5000
## Start with the hypotheses
hyp=1
if [ $hyp == 1 ]; then
code="SMP_all_cope6"
echo "$(date) start tstt $code" >> "$... |
5b5c4315e27f7c4aa1eab4826e217b69ade73c18dde246ed50924a5f36768187 | Shell | 2,950 | 68 | #!/bin/bash
# Usage: pooled_CRISPR_screen_Gecko_v2_reorient.sh
# Processes all .fastq.gz files in a folder
# All files must be gzipped and each file pair must be named as follows:
# fastq_filename_R1.fastq.gz, fastq_filename_R2.fastq.gz
# Launch bash script from directory containing the fastq files to be processed
#Cr... |
469d4afeb6385cfa988bb0399bc3be5bae153c6c3675261d208c684cccac1c3b | Shell | 2,952 | 167 | #!/bin/bash
##
## get reference of specified type for specified genome
##
# script filename
script_name=$(basename "${BASH_SOURCE[0]}")
# check for correct number of arguments
if [ ! $# == 2 ] ; then
echo -e "\n $script_name ERROR: WRONG NUMBER OF ARGUMENTS SUPPLIED \n" >&2
echo -e "\n USAGE: $script_name genome... |
47292dc544f09f3eaaee30471d36ab28d0464bb59c37ef6c5afacdd40b588ce5 | Shell | 2,955 | 89 | #!/bin/bash
set -eu -o pipefail
# default vals
extension_path=""
# help message
print_help() {
echo "Usage: $0 --dir <chart-path> --chart-name <chartname> [--no-import]"
echo
echo "Arguments:"
echo " --dir Path to the extension dir, should contain /extension and /processing-containers fold... |
0a8f8a75fbbfecc769f39c4daeff710c69d5c0bc0ffe50dde4fc512e1b913cdf | Shell | 2,964 | 106 | #! /bin/bash
set -xe
if [[ -z "${TMPDIR}" ]]; then
TMPDIR=/tmp
fi
set -u
if [ "$#" -lt "1" ] ; then
echo "Please provide an installation path such as /opt/ICGC"
exit 1
fi
# get path to this script
SCRIPT_PATH=`dirname $0`;
SCRIPT_PATH=`(cd $SCRIPT_PATH && pwd)`
# get the location to install to
INST_PATH=$1
... |
0b8d057c4e68c63fe937aac2aae99fa2fa4599496f810a265a39b767371844af | Shell | 2,973 | 62 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=07_deconvolution_CIBERSORTx_test2
#SBATCH -c 1
#SBATCH -o logs/07_deconvolution_CIBERSORTx_test2.txt
#SBATCH -e logs/07_deconvolution_CIBERSORTx_test2.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
ech... |
f0f171de209fe8a15b10052b1789ef5e4cdd4778b715f257eb8c26e0f1b79481 | Shell | 2,976 | 76 | #!/bin/bash
#-----------------------------------------------------------------------------------------
# Process anatomical data using ANTS:
# 1) Spatially-adaptive denoising
# 2) antsCorticalThickness for high-quality segmentation / brain extraction
# 3) Post-process segmentation posteriors
#_________________________... |
5d68f5240f0bb7fa8905dc2e83c2b7afe72a62c515c7295c4fef0b769d0803d9 | Shell | 2,980 | 109 | #!/bin/bash
#this file was used to perform fuma and magma analysis
print_help(){
echo "
All path should be relative path to the base directory (aka the parent directory of the bash script file).
Here are the required parameters:
-m | Mode: FUMA ('fuma') or MAGMA ('magma') analysis
-e | Expression file.... |
fe17dde2dcaf24fd1a27085f3a0ee110f932fdf8c70069d0031199a550839f5a | Shell | 2,984 | 94 | #!/bin/bash
# Script to extract the LGN maps from a input T1 image using Freesurfer
#
# Usage:
#
# segmentThalamus inputfile.nii
#
# To install FreeSurfer, download .deb package and install using:
#
# sudo dpkg-deb -x freesurfer_ubuntu22-7.3.2_amd64.deb /mnt/Software/FreeSurfer/7.3.2
#
# To add this directory a... |
2ca3354f8483224eac4d00406b2718f974c7d8a8d29b37c03bbc1dd5fb3a4e2e | Shell | 2,986 | 142 | #!/bin/bash
# bedtools generate bigWig from BAM
# script filename
script_name=$(basename "${BASH_SOURCE[0]}")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 3 ] ; then
echo -e "\n $script_name ERROR: WRONG NUM... |
7f838f73ffb1654b230ebd71af31695a9ee5d866974a453d906f8a30c60b0896 | Shell | 2,988 | 110 | #!/bin/bash
##
## chip-seq peak calling
##
# specify maximum runtime for sbatch job
# SBATCHTIME=12:00:00
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
route_name=${script_name/%.sh/}
echo -e "\n ========== ROUTE: $route_name ========== \n" >&2
# check for correct number... |
215c17eb43b34adfb1f36e56adcd59641943421d024bed2364e02d9491e8ce61 | Shell | 3,009 | 53 | #!/bin/bash
#$ -cwd
#$ -l mem_free=30G,h_vmem=30G,h_fsize=100G
#$ -pe local 1
#$ -N munge_gwas
#$ -o logs/munge-gwas_$JOB_ID.txt
#$ -e logs/munge-gwas_$JOB_ID_err.txt
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ... |
518a093dfc9b342963644c8de9e37cfc59884d26562bcbee992bc001b32f6e66 | Shell | 3,024 | 57 | #!/bin/bash
set -euo pipefail
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=${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 $movingfile _t1.nii.gz)_mask.nii.gz... |
ee94099d52528b712177e24a15a0535c37f5d6743be6046919c4c6f8dcbe87ae | Shell | 3,028 | 82 | #!/bin/bash
# set our directories
dir_out=$(pwd)
log_file="$dir_out/logfiles/log_runFSL-3.txt"
dir_tstt="$dir_out/results_tstt-cov/"
if [ ! -d "$dir_tstt" ]; then
mkdir -p "$dir_tstt";
fi
nsim=5000
## Start with the hypotheses
hyp=1
if [ $hyp == 1 ]; then
code="SMP_all_cope6"
echo "$(date) start tstt $code" >... |
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