sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
1ac24a082c8a676f87f9dc652fc870a33db146569c2281b4aa6d43ea52e8fd71 | Shell | 12,939 | 357 | #!/bin/bash
source $FREESURFER_HOME/SetUpFreeSurfer.sh
######## this script is only meant to be run following brain extraction, denoising, Bias field correction and segmentation.
######## This script is dependent on files generated in the previous outputs.
####### This is the beginning of Step 4 for surface genera... |
7458141e62c2be1aeb3eaf59270bbd54cd9e800ac89353afb79ec0039d067fdb | Shell | 13,092 | 453 | #!/usr/bin/env bash
### REGENIE TEST SCRIPT
# Functions used
help_msg="Update to most recent REGENIE version (using 'git pull')."
fail_msg="Step 1 of REGENIE did not finish successfully."
err_msg="Uh oh, REGENIE did not build successfully. $help_msg"
print_err () {
echo "$err_msg"; exit 1
}
print_simple_err () {
... |
be00dca458975f4d55bdef80e08cb9765095c05edfe5585fc3a8c875f22da36a | Shell | 13,211 | 461 | #!/usr/bin/env bash
### REGENIE TEST SCRIPT
# Functions used
help_msg="Rebuild the regenie package using conda install --force-install (or consider compiling from source)"
fail_msg="Step 1 of REGENIE did not finish successfully."
err_msg="Uh oh, REGENIE did not build successfully. $help_msg"
print_err () {
echo "$... |
84a92a643ce6d22b80e90c7f2dfa04b6c4a51b246facfcab4d5ac5f4cbe9b5f7 | Shell | 13,276 | 308 | #!/bin/bash
# Written by Yapei Xie and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# Master KRR submission script.
# Usage: bash CBIG_LBC_run_step3_KRR.sh <mode>
# mode = main : standard 8-condition prediction
# mode = transfer : model transfer (FC_Y0 model applied to... |
76b36a4ac78eac5010b9a697809add6798bac7f216188286cb4d8160fa72f649 | Shell | 13,448 | 324 | #!/usr/bin/env bash
# ─────────────────────────────────────────────────────────────────
# Unified environment setup for cluster_pipeline
#
# Usage:
# bash scripts/setup_env.sh # full install (recommended)
# bash scripts/setup_env.sh --quick # Python-only, skip ext tools
#
# What it does:
# 1. Crea... |
ba408a69b766d8b467f7706f841e0f841def32b960a603a01a745b65dea9fe9b | Shell | 13,544 | 347 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# ------------------- #
# GENERAL DEFINITIONS
# ------------------- #
source $MRCATDIR/setupMrCat.sh
labelFile=$MRCATDIR/data/macaque/F99/subcortLabel_2mm.nii.gz
anaDir="/Volumes/rsfMRI/anaes... |
d218deb2c687c3144be78dba25673a93245e1d7596d540799b94b638fc45fc3a | Shell | 13,566 | 472 | #!/usr/bin/env bash
### REGENIE TEST SCRIPT
# Functions used
help_msg="Update to most recent REGENIE version (using 'git pull') and re-compile the software."
fail_msg="Step 1 of REGENIE did not finish successfully."
err_msg="Uh oh, REGENIE did not build successfully. $help_msg"
print_err () {
echo "$err_msg"; exit... |
a1122a9ad9a76cdb0cda15eb0525dd773568e725a56603d151498a78ae87dc1f | Shell | 13,651 | 432 | #!/usr/bin/env bash
### REGENIE TEST SCRIPT TO USE WITH DOCKER IMAGE ###
# Functions used
help_msg="Check the docker image and re-build if needed."
fail_msg="Step 1 of REGENIE did not finish successfully."
err_msg="Docker image did not build successfully."
print_err () {
echo "$err_msg"; exit 1
}
print_simple_err ... |
bb5b4a3c8f7ad9f6227678614350346354b283899a927fec19816e566fe5ee4a | Shell | 13,675 | 306 | #!/bin/bash
# Copyright 2017 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following di... |
f53b647e722a52735dfe27f464dab55ce0b9fe5ce515d88a653270ecc36a9f21 | Shell | 13,770 | 265 | code='/mnt/d/Code/HeartModelling'
#echo "Making sample 4 ----------------------------------------------------------------"
#
#python ${code}/s4_interpolation.py \
#--dataPath1 /mnt/d/Paper3/Models/invivo/mi/cx/sample4/aha_segments/pc_aha.vtk \
#--dataPath2 /mnt/d/Paper3/Models/invivo/mi/cx/sample4... |
206f992487b60fc539adef4e9768407f52d5236c95b2576ddef6782cc18937df | Shell | 13,846 | 317 | #!/bin/bash
# Check if the SUBJECT variable is provided
if [ -z "$1" ]; then
echo "No subject provided."
exit 1
fi
# Get the subject name
SUBJECT_DIR="/home/danieldude123/project"
# Access the subject passed from the main script
SUBJECT="$1"
# Define directories and paths
script_dir="/home/danieldu... |
5a59febfd596a1bf092e04aa02135712db1c8fdfa9f67082ee82812d683c0dc1 | Shell | 13,861 | 302 | #!/bin/bash -e
## v3.2 of STARsolo wrappers is set up to guess the chemistry automatically
## newest version of the script uses STAR v2.7.10a with EM multimapper processing
## in STARsolo which on by default; the extra matrix can be found in /raw subdir
SIF="/nfs/cellgeni/singularity/images/reprocess_10x.sif"
CMD=... |
8070d3a990d9f688b099838f9c5de865808606f191a70f4f64c6e499dec4fdef | Shell | 13,924 | 367 | #!/bin/bash
# terminate script on error or if a command fails before piping to another command
set -eu
set -o pipefail
########################################################################################################################
# helper functions
show_help() {
cat << EOF
Manage the SV discovery pipeline o... |
5e1cf644edb22fd24b43670d4c0aac527611ca9d35aab2cc20ba884358f0a032 | Shell | 14,021 | 304 | #!/bin/bash
#
#This is a shell program to batch reconstruct images using 28 different methods.
#
# Last change: 2015-08-17. by Hanchuan Peng adding the anisotropic filtering.
#
function write_neuron_tracing_command {
outputScript=$1;
METHOD=$2;
vaa3dProgramPath=$3;
inimgfileTracing=$4;
finalfileFolder=$5;
... |
f90cca6e65ebe1d65e7872efc3d02a80e52314e64ccc1a385139d9e990577721 | Shell | 14,434 | 341 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# TODO: if for some SUBJ/SESS one run is acquired, but for others multiple, only
# the runs with multiple end up in the SUBJRUN/SESSRUN folder. You could
# consider to copy the SUBJ/SESS SBCA ... |
b3c8f6ba89a633d1c7b5a9fae265be3c70a7147e70b659c3ad0d850acee38284 | Shell | 14,484 | 249 | #!/bin/sh
########################
#nohup ./VirusMeta.sh /media/StorageOne/HTS VirusMeta 2014_G7_MSNEW2 nextseq UNBIASED DNA /media/StorageTwo/blc_2014_G7_MSNEW2/Data/Intensities/BaseCalls > 2014_G7_MSNEW2.log
export path_htsa_dir=$1 #path to HTSA analysis dir
export path_pipeline=$2
export Project_name=$3
export pla... |
4928f3ea5ed0f20d9cfe9ff11bd7cb8f620b122d3fe11f30e6db5f94625f74ea | Shell | 14,727 | 253 | #!/bin/bash
# Check if the SUBJECT variable is provided
if [ -z "$1" ]; then
echo "No subject provided."
exit 1
fi
# Get the subject name
SUBJECT="$1"
# Define directories and paths
script_dir="/home/danieldude123/scripts/manoj_saranathan_pulvinar"
SUBJECT_DIR="/home/danieldude123/data/${SUBJECT}/T1w/Diffusion/m... |
88213ec06e0e8d312b712fac52983118d1e479de500ad10e6c8e620f182f0beb | Shell | 14,727 | 312 | #!/bin/bash
# Executables =====================================================================================
PIE_EXE=./bin/pie-solver
MT_EXE=meshtool
P3_EXE=python3
CARP_EXE=openCARP
GIZMO_EXE=./bin/gizmo
# Default Variables ===============================================================================
NP=32
N_RU... |
985b397259173cdab73047e7732b2a19c521c2f73731b19c798b176ee87927c5 | Shell | 14,765 | 470 | #!/usr/bin/env bash
set -euo pipefail
# =========================================================================
# download_1kgp.sh
#
# Download 1000 Genomes Project Phase 3 VCF files (GRCh38) from Ensembl
# and build a MeRIT configuration file with cohort and sample sections.
#
# This is a convenience script for set... |
d6fe964e1a8eaa1441bc909083b6d3838c7beaec96e0a533373d7a6eea9cbfd4 | Shell | 14,841 | 371 | #!/usr/bin/env bash
################################################################################
# run_all_analyses.sh -- pipeline runner for chess-expertise-2025
#
# Usage:
# ./run_all_analyses.sh [LEVEL]
#
# LEVEL (default: group)
# all - run every stage in order: fmriprep -> spm -> subject-level ->... |
5f05c6af35cc81b1a84897b4732ea5f363605f7f8cff9d249715b03c759222ee | Shell | 14,880 | 302 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 07/10/2014 Davit Bzhalava
##########################################################################################
#
# It is variant caller, SNP caller, plotter
#
# /media/StorageOn... |
5ea7b2edef3affcc4435c1d24cdfdb9fab4798c41509b9d140fae472497e560c | Shell | 14,970 | 493 | #!/bin/bash
set -uo pipefail
function download_geo_family() {
local SERIES=$1
## download the so-called soft_family file, and use it to generate same files as above
local PAD=`echo $SERIES | perl -ne 's/\d{3}$/nnn/; print'`
wget -O ${SERIES}_family.soft.gz https://ftp.ncbi.nlm.nih.gov/geo/series/$PAD/$SERIE... |
ab31398ebe0ebab5902ccaa0f562988435a413766b04f862d8a5c993c86ba55d | Shell | 15,011 | 431 | #!/usr/bin/env bash
MLFLOW_HOME="$(pwd)"
directory="$MLFLOW_HOME/.venvs/mlflow-dev"
REPO_ROOT=$(git rev-parse --show-toplevel)
rd="$REPO_ROOT/requirements"
VENV_DIR="$directory/bin/activate"
# Progress file to resume the script from where it exited previously
PROGRESS_FILE="$MLFLOW_HOME/dev-env-setup-progress"
showHe... |
5334ae62fb15e54be557713771b1dc7d374ca9b13191001e9922d822cf094dce | Shell | 15,674 | 427 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cuttlefish
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=soGenome
#SBATCH --error=error_%j.txt
#SBATCH --output=output_%j.txt
# --- helper functions --- #
function echo_error()
{
echo "$@" 1>&2
}
function guard_error(... |
c93e3c89a550f5869240dc15332fb366c0b52ac5cb2ad925ddd5711ad75a6806 | Shell | 16,135 | 227 |
#!/bin/bash
#PBS -l walltime=12:00:00
#PBS -N L3stats-ttest
#PBS -q normal
#PBS -m ae
#PBS -M matt.mattoni@temple.edu
#PBS -l nodes=1:ppn=28
# load modules and go to workdir
# module load fsl/6.0.2
# source $FSLDIR/etc/fslconf/fsl.sh
cd $PBS_O_WORKDIR
umask 0000
# ensure paths are correct
shareddir=/gpfs/scratch/tug... |
a3319cbcab2e3f2ece0c47a2c8cc0c5ebb355acf7f3f5f623903a8101067ef56 | Shell | 16,345 | 401 | #!/usr/bin/env bash
#ssset -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
#--------------------------------------------------------------------------
# Registration of functional/diffusion (EPI) to structural (T1w) images.
#
# Usage
# type \'sh register_EPI_T1.... |
db851b53293d7cbb56b0e485675c3e6efcda155fda7529678cca8ca9f2dad1a0 | Shell | 16,345 | 431 | #!/bin/bash
# Copyright 2024 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
f017ee60d712eae69dec337c26371e807be3d32f78537d613a2d93e03c984a17 | Shell | 16,445 | 591 | #!/bin/bash
set -e
# Inputs to the script
MANIFEST=
JSON=
TEMPLATE_DIR=
# Script name and dir
SCRIPT_DIRECTORY=$(dirname "$0")
SCRIPT_BASE_NAME=$(basename "$0")
SCRIPT="$SCRIPT_DIRECTORY/$SCRIPT_BASE_NAME"
# Starting iteration
START_ITER=0
# Initial template (subject or image)
INIT_TEMPLATE_IMAGE=
INIT_TEMPLATE_MAS... |
02842d1cd904051602a26d0bedafc99aa41203133fd5614d588d76e01d0da694 | Shell | 16,455 | 232 |
#!/bin/bash
#PBS -l walltime=4:00:00
#PBS -N L2stats-subj-qc
#PBS -q normal
#PBS -m ae
#PBS -M matt.mattoni@temple.edu
#PBS -l nodes=1:ppn=28
# load modules and go to workdir
# module load fsl/6.0.2
# source $FSLDIR/etc/fslconf/fsl.sh
cd $PBS_O_WORKDIR
umask 0000
# ensure paths are correct
shareddir=/gpfs/scratch/tu... |
fd4549a9e8a964696ebc407e53410f8774578f979e9a412b0d682994fa022bb3 | Shell | 16,571 | 423 | #!/bin/bash -e
set -e # To abort the whole script if one function returns an error.
# See https://github.com/SchulzLab/STARE for more information and usage.
# Adapted from TEPIC: https://github.com/SchulzLab/TEPIC
version_num="1.0.5"
help="STARE version ""$version_num""
Usage: ./STARE.sh
[-a/--annotation gene annotat... |
e6ee9779517ae52581c94577fdcaa7bf0d69a40295ba747bb329b0f1735f5457 | Shell | 16,687 | 381 | #!/bin/bash
# =============================================================================
# STARsolo CLI - 10x Genomics platform
# =============================================================================
# Automatic chemistry detection (v1 / v2 / v3 / v4 / multiome),
# strand-specificity detection, and paired-en... |
c4901ddb178f5cda0419613a6e287f9efee9ae672efc98a9d2f238d8b0c3b553 | Shell | 16,899 | 406 | #SAMPLE 5 -----------------------------------------------------------------
#python /mnt/d/HeartModelling/HeartModelling/auxiliar/rbm/ldrb_s1_getFacetFunction.py \
#--dataPath /mnt/d/Paper3/Models/invivo/mi/cx/sample5 \
#--domainType BiV
#
#python /mnt/d/HeartModelling/HeartModelling/auxiliar/transmuralComposition/pe... |
3b79e3e8fc1f91c55fbce018bbfabed9a615be744e6499cb21db42c4427d6a1c | Shell | 17,264 | 433 | #!/usr/bin/env bash
set -e # stop immediately on error
# ------------------------------ #
# usage
# ------------------------------ #
usage() {
cat <<EOF
bet_macaque.sh: brain extraction tailored for macaque brains
Usage: sh bet_macaque.sh <input> [<output>] [options]
Example: sh bet_macaque.sh nodif -t T2st... |
e172aaceb18dacbe52cc19eafd7437ae1dcefbc68902c4a407fd1f55db1b1701 | Shell | 17,522 | 464 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# cut out the first n seconds (default: 15) until a steady state of radio-frequency excitation
# ------------------------------ #
# Help
# ------------------------------ #
usage() {
cat <<E... |
a800cb15280e615ac65bc23f84a89fb6b3f731a821948af28be29e168de42c76 | Shell | 17,972 | 264 | #!/bin/sh
# /media/StorageOne/HTS/VirusMeta/SAM_BAM/circos_FPKM/circos_pipeline_v2.sh /media/StorageOne/HTS/Projects/2013_H7_RNA-2libr /media/StorageOne/HTS/Projects/2013_H7_RNA-2libr/Data/Intensities/BaseCalls/forward.fastq.gz /media/StorageOne/HTS/Projects/2013_H7_RNA-2libr/Data/Intensities/BaseCalls/reverse.fastq.g... |
79a431bb52408a9d51e8b2dc3c372736c04ef1b6571e1aebd4334cf2b193b5d7 | Shell | 18,053 | 437 | #!/bin/bash -e
## v3.2 of STARsolo wrappers is set up to guess the chemistry automatically
## newest version of the script uses STAR v2.7.10a with EM multimapper processing
## in STARsolo which on by default; the extra matrix can be found in /raw subdir
# --- Function Definitions ---
# Finds paired-end FASTQ files b... |
b92641900ce08900c6b1fcac028e773d9977e9e3f048c84f90f34757badeaa28 | Shell | 18,102 | 351 | #!/bin/bash
# Stop on error
set -e
if [[ "$#" -lt 2 ]]; then
echo
echo "ACTIVATE PIPELINE'S CONDA ENVIRONMENT BEFORE RUNNING THIS SCRIPT!"
echo
echo "This script installs data for genome [GENOME] on a directory [DEST_DIR]."
echo "A TSV file [DEST_DIR]/[GENOME].tsv will be generated. Use it for pipeline."
e... |
2d7c46369b8bb654aab3ff1cd76bbb7e9005254823de88829084315b890787d2 | Shell | 18,346 | 542 | #!/bin/bash
# Main script to apply the template pipeline from Rick Lange
# Revisited by Lea to be more general
# Could be launch from the Wrapper
# ------------------------------ #
# usage
# ------------------------------ #
usage() {
cat <<EOF
templating.sh: run the template pipeline to make multimodal template fr... |
3145c2064aff92ab75b34ef786c92e00991977f93a7b98240fcf1cc26c6d3345 | Shell | 18,824 | 318 | #!/bin/bash
# Check if the SUBJECT variable is provided
if [ -z "$1" ]; then
echo "No subject provided."
exit 1
fi
# Access the subject passed from the main script
SUBJECT="$1"
# Define directories and paths
script_dir="/home/danieldude123/scripts/manoj_saranathan_pulvinar"
SUBJECT_DIR="/home/danieldud... |
ae4f32f43c4622becb62fa9c30d67d717c01647f8e165c9290934dc1d5bfc1fd | Shell | 18,977 | 435 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# examples
#sh Coord2ROI.sh --warpmethod=coord --coord=./Oliver/ROIs/TS_coords.txt --dil=5 --refa=F99 --refb=./Oliver/MI00539_proc/f_mean.nii.gz --maskb=refb --closestvox --warpb2a=./Oliver/M... |
203d42651fa0ee30e844007fad92fa80c6f0973e25dd9099a9c98759a80e8ae8 | Shell | 19,128 | 689 | #!/bin/bash
VERSION="1"
# Version 1 by Falk Lüsebrink
# falk dot luesebrink at dzne dot de
# 16.07.2024
# Changes made to the original script:
# 1) NearestNeighbor interpolation instead of linear interpolation
# 2) Changed size of matrix for "large images" to 1024
# trap keyboard interrupt (control-c)
trap control_... |
194fa79e3d47fb2599d7353abea62b52ae9c8191a3d4ef2ea2a84bd85590c79a | Shell | 19,643 | 655 | #! /bin/sh
# Copyright (C) 2011-2024 Free Software Foundation, Inc.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# This program ... |
c98b0af4dbdeb0fb084895c6486636bf51a7fa34ba8a5188d43d4dd5d2b38ce7 | Shell | 19,693 | 591 | ##SAMPLE 4 -----------------------------------------------------------------
#echo "Processing SAMPLE 4"
#
## HE ---------------------------
#python /mnt/d/Code/HeartModelling/s5_perrottiEndoMidEpi.py \
#--dataPath /mnt/d/Paper3/Models/invivo/mi/cx/sample4 \
#--outName mesh_he \
#--infAsHealthy
#
#python /mnt/... |
cd3426e82ac9a35e301eab31fa2746f08d2e6b939acc5ca464bd58e4e9ec8631 | Shell | 19,934 | 390 | #!/bin/bash
##
## Ambra Villani's RNA-seq experimental design
##
## 9th May 2023
## Izaskun Mallona
# Tasks:
# 1. Compare Ambra's WT to Abud's and McQuade's TREM and iPSC by (sub)treatment
# 2. Compare Ambra's mutants to Ambra's WTs
# - Double check BAM files to see if they're mutant
# 3. Compare Ambra's mutants to M... |
084320f9bb035c0c31fa2b602a1468d3047c0347b22bca5caec8d503227bfb77 | Shell | 20,298 | 512 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# clean your functional data timeseries using regression of noise components
# TODO: make the matlab command nice, with try-catch and error messages
# TODO: set the nCompSignal dependent on n... |
ee80d02ae213f979f81e12f0f3757b008ba08f7ea5a9f61b5aafce5becec3798 | Shell | 20,316 | 297 | #!/bin/bash
# Stop on error
set -e
if [[ "$#" -lt 2 ]]; then
echo
echo "This script downloads/installs data for genome [GENOME] on a directory [DEST_DIR]."
echo "A TSV file [DEST_DIR]/[GENOME].tsv will be generated. Use it for pipeline."
echo
echo "Supported genomes: hg19, mm9, hg38 and mm10"
echo
echo "... |
ec5d213e942930ab6774175a47badef3dcd4b3aa14967b864dc731911aac1081 | Shell | 20,475 | 493 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# examples
# sh registerT1wCT.sh --t1w=MNI --t1wmask=MNI_brain_mask --ct=LeetSkull --dir=~/projects/nima/ACCBF/registerT1wCT
# sh registerT1wCT.sh --t1w=MNI --t1wmask=MNI_brain_mask --ct=DrySk... |
52b08c692e54ef3d810e443258103fffee73d916ce58c1498c7d1424981e50a0 | Shell | 20,739 | 477 | #!/usr/bin/env bash
# Benchmark: end-to-end partial-parse performance across commands, scenarios, and selectors.
#
# Usage:
# DBT_BENCH_PROJECT=~/tmp/scale_6k \
# DBT_BIN=~/fs/target/release/dbt \
# bash fs/sa/crates/dbt-metadata/benches/partial_parse_bench.sh
#
# Outputs a Markdown table to stdout and writes per... |
d2757950d00882c653a0e3241895aacb46d07146921680aea228b4f6459fe619 | Shell | 20,792 | 860 | #!/bin/bash
####
################################## START OF EMBEDDED SGE COMMANDS ##########################
#$ -S /bin/bash
#$ -cwd
#$ -N pp_old_wrap
####$ -m a #### send mail when job begins
####$ -m e #### send mail when job ends
####$ -m n #### no mail is sent
#$ -m s #### send mail in case the job is suspended
##... |
7bdbf9103f3f08e3f04fd059eeb8cdcff42b821e7bf06e78eafc1106f20248d6 | Shell | 20,862 | 533 | #!/bin/bash
# Written by Yapei Xie and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#
# Combined wrapper for FC harmonization and stability:
# Step 1: Prepare FC_Y0Y2.csv (MATLAB, inline)
# Step 2: Run longCombat on FC_Y0Y2.csv (R, cluster job)
# ... |
396a4d84722d00e428f3ac8a461d0b091add735d10b81838381984495eb9df38 | Shell | 21,094 | 455 | #!/usr/bin/env bash
SCRIPT_NAME=$(basename "$0")
Usage="Usage: ./${SCRIPT_NAME} --bam_fn=BAM --ref_fn=REF --output=OUTPUT_DIR --threads=THREADS --platform=PLATFORM --model_path=MODEL_PREFIX [--bed_fn=BED] [options]"
# INFO: whole calling workflow of clair3
set -e
ARGS=`getopt -o b:f:t:m:p:o:r::c::s::h::g \
-l bam_fn:,... |
103a4b47bd65e298eb415d2ad6573acd30c25bcba40332106d09fdf8ce1b48c5 | Shell | 21,177 | 532 | #!/bin/bash
#alias python='python'
#####################################################################################
# Example Use #
# Script modified on 29the august, 2019
# A python script Collapse_Ranhex_Odt.py ( Dipankar / Dumaatravaie ) had replaced the bash script Collapse_Ranhex_Odt.sh
# Fixed the issue wi... |
74cbe9bcd97280ec54deb3c00bc6dad0a5cc38999ec5b448cabdd37e38f692c9 | Shell | 21,562 | 300 | # Creaing the 425k list
R
clist <- c("A1","A2","ADC_OMNI","ADC_GSA","ADC13n15","ADC14","ACT1","ACT3","ROSMAP1","ROSMAP2","NIALOAD","MAYO","TGEN2","UPITT","EOAD_ADFUS","IDIBAPS","UMA_550")
for(i in clist){ assign(i,data.table::fread(paste0("/hihg/studies/AD/analysis/projects/ADGC/Neuropath/GWAS_Covariates/Variants/MedRa... |
8159ddfac23f2f6cc155a839d26a2dfc6b16f0ec2dcf7d5249fc9259980b0062 | Shell | 21,801 | 500 | #!/bin/bash
# Copyright 2024 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
d62520e4fb64e8055b8932fcbbf5aafc1e7208dd3ea13a91db5395ee94794146 | Shell | 22,449 | 717 | #!/bin/sh
# Exit immediately if a command exits with a non-zero status.
# Treat unset variables as an error when substituting.
set -eu
# Function to be called on script exit for cleanup purposes.
cleanup() {
# Clean up any temporary directories
if [ -n "${td:-}" ]; then
rm -rf "$td"
fi
# Remov... |
a9af65776a7e700193609d120aa1e9351dcd7b98aaf17fceef964c196a8cab13 | Shell | 22,524 | 581 | #!/bin/bash
#alias python='python'
#####################################################################################
# Example Use #
# Script modified on 29the august, 2019
# A python script Collapse_Ranhex_Odt.py ( Dipankar / Dumaatravaie ) had replaced the bash script Collapse_Ranhex_Odt.sh
# Fixed the issue wi... |
af6fa8cdf5875240b30f3514db22f874376ca8a83d0c1bbc4067a4df3f6a6535 | Shell | 22,990 | 665 | #!/bin/bash
Usage() {
echo " "
echo "Preclinical Surface Reconstruction"
echo ""
echo "Usage: `basename $0` [options] -i <T1.nii.gz> -r <processes to run>"
echo ""
echo "Compulsory Arguments "
echo "-i <T1 image> : Image from which to reconstruct the surface "
echo "-r < precon_all>... |
4f3e1d31d507f6cd561f8cb9135c66a5979855758b9930dde4e93375a7eb2e3f | Shell | 23,239 | 525 | #!/usr/bin/env bash
SCRIPT_NAME=$(basename "$0")
Usage="Usage: ./${SCRIPT_NAME} --bam_fn=BAM --ref_fn=REF --output=OUTPUT_DIR --threads=THREADS --platform=PLATFORM --model_path=MODEL_PREFIX [--bed_fn=BED] [options]"
# INFO: whole calling workflow of clair3
set -e
ARGS=`getopt -o b:f:t:m:p:o:r::c::s::h::g \
-l bam_fn:,... |
08a34d68d9f9522f105eebc3eb0b91f5034658722d8999ccec63f1728282548c | Shell | 23,387 | 260 | # 捕捉中断/终止信号，终止所有后台任务
trap 'echo "中断信号收到，正在终止所有子任务..."; pkill -P $$; exit 1' SIGINT SIGTERM
## ---------------------- seed 2025 ------------------------
## A. AVE-CI and K-S-CI in "LwF, SS-IL, AV-CIL" four method
## ----------1. LwF method
#pushd LwF
#
#CUDA_VISIBLE_DEVICES=4 python train_incremental_lwf.py --dataset A... |
879e704789b84042c92f044087c756dbb4a20641ef0d5939875194a3425637ed | Shell | 24,429 | 535 | #!/bin/bash
# Pipeline for preprocessing cleaned, converted, and BIDS-standardized functional
# and structural magnetic resonance imaging data acquired at 7T in the scope of
# a tactile population receptive field (pRF) experiment.
# ***************************************
# Generated: 13.10.2022 (FL)
# Last modifie... |
7c4326386d6cf1bbbc5b22dfc9e404ebbb73357270a5a361d241a38d57381e47 | Shell | 24,502 | 204 | #!/bin/bash
# more information with hubert-ecg-evaluate --help
hubert-ecg-evaluate /path/to/ribeiro_test_set.csv /path/to/ribeiro_test/ 64 /path/to/hubert_small_55k_tnmg.pt --downsampling_factor=5 --save_id=ribeiro_small
hubert-ecg-evaluate /path/to/ningbo_test.csv . 64 /path/to/hubert_small_16.5k_ningbo0.pt --dow... |
68eea36224c35c053aaae9cd884e1e6305d217935d94a1e8b832804ac7eb4b4d | Shell | 24,897 | 567 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script will create a liftover chain file that goes from b37 -> hg38
#
# EXAMPLE:
# ./createLiftoverChainFileForB37ToHg38.sh
#
... |
7c9575370a12cec0b63112008e3d260a2c5a51776ca6e46f102fb8b2bbdfebf1 | Shell | 24,951 | 567 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script will create a liftover chain file that goes from hg38 -> b37
#
# EXAMPLE:
# ./createLiftoverChainFileForHg38ToB37.sh
#
... |
6b037bd864c953c8359c95734a2b087dae6e400132aaaaa86a28aa111eb5ecf2 | Shell | 24,953 | 595 | #!/usr/bin/env bash
set -e # stop immediately on error
# preprocessing of a macaque structural image
# 1. brain extraction
# 2. bias correction
# 3. reference registration
# these steps are dependent on each other and could therefore be repeated for
# the best results
# TODO: calculate the flirt cost based on the ... |
24bef7782e07ac210211e35afb7b999b1c1c879abc9f3d154dd7fc0e60446f6e | Shell | 25,493 | 635 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
f7970231aa4525240b8419ca81414de3207cfb21d5da8b20b0df190e5a4c21ec | Shell | 26,448 | 175 | #!/bin/bash
# small model size
hubert-ecg-evaluate /path/to/ningbo_test.csv . 64 /path/to/hubert_small_random_38.5k_ningbo0.pt --downsampling_factor=5 --tta --n_augs=7 --save_id=ningbo0_small_random --tta_aggregation=max
hubert-ecg-evaluate /path/to/ningbo_test.csv . 64 /path/to/hubert_small_random_30.5k_ningbo1.pt -... |
ffa36c3dfb51b50a0cbdffe219410ece2134601145750e93ca2a526ba38f607f | Shell | 28,747 | 692 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# This is an example resting state fMRI pipeline. It takes you from raw nifti_gz
# data to a preprocessed, registered dataset and dense connectome. The idea is
# that it is as modular as possi... |
c209089210c5d0d483a55007492168a46195bc069f84961213b248fa4c13c748 | Shell | 38,577 | 943 | #!/bin/bash
# Copyright 2020 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
36bc7bd168d04948d1e75ba1b3cd6eaad864b6854ca34aecb64d8d70ed7b1849 | Shell | 38,665 | 909 | #!/bin/bash
# Copyright 2023 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
bc4de93ab2cc5e3ba99ead2431d6040fa279da418fef5949c7a2ab4d35996518 | Shell | 39,884 | 949 | #!/bin/bash
# Copyright 2020 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
9d29a893da06df60abab5ca056d6834738220098f2d0b597e562c658bd93c3d9 | Shell | 43,221 | 191 | #!/bin/bash
hubert-ecg-finetune 3 /path/to/ribeiro_train.csv /path/to/ribeiro_val.csv 6 5 64 auroc --training_steps=70000 --downsampling_factor=5 --largeness=small --label_start_index=3 --use_loss_weights --random_init --dynamic_reg --val_interval=5000 --finetuning_layerdrop=0.0 --wandb_run_name=SMALL_random_ribeiro
... |
96e70cc1de6bc77eeecb9dda6e64de61a317133cfde301fb5029081943076092 | Shell | 43,759 | 903 | #!/bin/bash
# Author: Sai Ma <sai.ma2@mssm.edu>
# Last modified date: 2022/10/07
# Designed for processing share-V2
# input file
# 1) yaml
# 2) BCL or fastq or demultiplexed fastqs
# when there are 4 fastqs per lane, fastqs need to be named as "*S1_L001/2/3/4_R1/R2/I1/I2_001.fastq.gz" or "_S1_R1/R2/I1/I2_001.fastq.gz"... |
5d3ee11934c969132a2bf078035f67efde0a9f0a8f80884ca1bf1594fb8f15c0 | Shell | 44,598 | 992 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
f071073bb026a00dc08843552ffbacfe71754aa3fe6242f6884dd4165dbd6a8c | Shell | 49,597 | 441 | #!/bin/bash
set -e
# ------------------------------------------------------------------------------
# Verify other needed environment variables are set
# ------------------------------------------------------------------------------
#if [ -z "${MSMBINDIR}" ]; then
# log_Err_Abort "MSMBINDIR environment variable mus... |
d605003f50f352326871bb12a17150a0524e3536db99b9e8348833e2d5302983 | Shell | 55,053 | 1,582 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
e1c887fa8cfcc0dc305ad35ce53a22141242c7b094fd46f2ea8c7fab5e48fd2c | Shell | 56,677 | 327 | #!/bin/bash
# Commands to run to perform the fine-tuning of HuBERT-ECG SMALL, BASE and LARGE models on the PTB-XL All dataset as done in the paper
#!/bin/bash
### FINE-TUNING SMALL MODEL SIZE ###
# RIBEIRO
# We cannot disclose the Ribeiro dataset. Ask the original authors for access.
hubert-ecg-finetune 3 path/to/r... |
df5cb00d4ccef5a7c7175e48ecf968acf00964ddbd15bc9e88c33b16ce8dd941 | Shell | 57,908 | 1,082 | jupyter nbconvert plots_across_methods.ipynb --to python
# python plots_across_methods.py \
# --methods "mindeye1_subj01, \
# braindiffuser_subj01, \
# final_subj01_pretrained_40sess_24bs, \
# pretrained_subj01_40sess_hypatia_vd2, \
# pretrained_subj01_40sess_hypatia_vd_dual_proj_avg, \
# subj0... |
eba35a759f9abbd0c3eb69b72b51eefdc47be280841f3a8c93bdb77d57be12cd | Shell | 60,791 | 1,609 | #!/bin/bash
VERSION="1"
# Version 1 by Falk Lüsebrink
# falk dot luesebrink at dzne dot de
# 19.07.2024
# Changes made to the original script:
# 1) No affine registration
# 2) Default values changed (e.g., no bias field correction)
# 3) Gradient step size reduced to 0.1 (from 0.2)
# 4) NearestNeighbor interpolation i... |
3471fa4c4aac193488bdc9776ebae4dc54c125d1c55ce3311899dddd2735a971 | Shell | 61,492 | 1,750 | #!/bin/sh
set -eu
CONSOLE_WIDTH=68
MAX_VISIBLE_OPTIONS=5
if [ -t 0 ]; then
TTY_DEVICE="/dev/stdin"
else
TTY_DEVICE="/dev/tty"
fi
terminal_state=""
setup_tmp_dir=""
cursor_hidden="false"
spinner_pid=""
spinner_output_file=""
spinner_error_file=""
curl_auth_config=""
selection_header_open=""
selection_default_index=0... |
80a633f7e3e5c23698406ff6132eaed1b8e473c5f32d1e55a23c070e6c4bb1a9 | Shell | 200,000 | 7,058 | #! /bin/sh
## DO NOT EDIT - This file generated from ./build-aux/ltmain.in
## by inline-source v2014-01-03.01
# libtool (GNU libtool) 2.4.6
# Provide generalized library-building support services.
# Written by Gordon Matzigkeit <gord@gnu.ai.mit.edu>, 1996
# Copyright (C) 1996-2015 Free Software Foundati... |
b03f9f4e27a0be66cb1b2360371a9703c596aa7f3f524b5f86ebd40089a59f1d | Shell | 200,000 | 905 | #!/bin/bash
dsi_studio --action=trk --source=C57BL6_mouse.fib.gz --seed=injection_densities/100140756_injection_density.wp50.nii.gz --output=trk_outputs/100140756_seed.tt.gz --export=stat,tdi
dsi_studio --action=trk --source=C57BL6_mouse.fib.gz --seed=injection_densities/100140756_injection_density.wp50.nii.gz --end=pr... |
b8ac2d6fe6e08fc62733690fab4e4d31b5a3ea74498cbe693e858ad3a163be10 | Shell | 200,000 | 762 | #!/bin/bash
dsi_studio --action=trk --source=C57BL6_mouse.fib.gz --seed=injection_densities/100140756_injection_density.wp50.nii.gz --end=projection_densities/100142580_projection_density.wp50.nii.gz --output=trk_outputs/100140756_seed__100142580_end.tt.gz --export=stat,tdi
dsi_studio --action=trk --source=C57BL6_mouse... |
9005b20ea66df16b24efe0508e1fd84080390bd9505c62f3f909a9084a4a83a5 | Stan | 646 | 14 | /*
hBayesDM is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
hBayesDM is distributed in the hope that it will be useful,
... |
7ee5916828feb193e51a86b943ab6735030467f4b29ca430f60b0b3568d0f13d | Stan | 2,551 | 101 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
... |
bc060359a2eded2c16658063f3268a3d8a08762eb3683ee72083bcd859a42b34 | Stan | 2,551 | 101 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
... |
4e44dd2831cbdd3bcb6ba3e26d62c3244ab14df27add9db43a91a2d6bf6431f9 | Stan | 2,571 | 102 | //#include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
a... |
6a48f3c663011c4a09a93e9b905a71ae3848a620f9255045c596b9703c9ec4b9 | Stan | 2,573 | 101 | //#include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
a... |
cfe18a4ae67bfd049b02e22c83424e2a333fba7ad49e3ffdc12d2ec3af3ebc2b | Stan | 2,580 | 102 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
... |
fe394549655b9963c911a71d2ecb797f3d5c43995ac4440f0be5fa6314f780b3 | Stan | 2,589 | 102 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
... |
d5d32b432fd020fc35f98ec7ad85cb598430fe703649fd0d68a10a9e5d47e6eb | Stan | 2,590 | 102 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
... |
631320a565f58485dd6b2dafdd4e4023e710d443de0018805dec50b375ef0f8b | Stan | 2,809 | 108 | //#include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
a... |
6db857dda12e4688a6c091fd2dc0b1cd4d1cb27c8bb79c8f30abdf393971e213 | Stan | 2,810 | 108 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
... |
819b80e045c443ca9c35c1d9d09ce08e19f942f0bb6bc584c21397ffce4ddb39 | Stan | 2,811 | 108 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
... |
75d181ee3ef521daa354f6742ebeb8c01dfa56196ff1cdad0ede8368c2f6606f | Stan | 2,818 | 108 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
... |
ecf3cb7abfd0cabba9f196d1bc59b1b1adbede220a3582604f97aa0cf3f4cc51 | Stan | 2,828 | 108 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
... |
3e6ce49b810812abbc2cdc745f31c0e85b7940c86263968c1e68a03649342bec | Stan | 3,048 | 114 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
array[N] int<lower=1, upper=T> Tsubj; // number of trials per subject
array[N, T] real<lower=0> effort_a; // effort of offer
array[N, T] real<lower=0> amount_a; // reward of offer
... |
37bd7857b1f71bf2b0226938ac749e1e4dd63aac37b1f9a74139c027176a68e7 | Stan | 3,821 | 133 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
int<lower=1> N_time; // number of testing sessions
array[N, N_time] int<lower=1, upper=T> T_subj; // number of trials per subject per session
array[N, N_time, T] real<lower=0> effort... |
93255457de1bae470e1cd50c331d409c36fbe2e1a7cc37614d29106d72ae8c01 | Stan | 4,004 | 138 | functions {
real partial_log_lik(array[,] int choice_slice,
int start, int end,
array[,] int reward,
array[] real persev,
array[] real alpha,
array[] real beta,
int nTrials) {
... |
e1a65ebea011c4fb81f8cc24c15574f7865fc0e3451e1ece13b7a17b949db040 | Stan | 4,346 | 147 | //#include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
int<lower=1> N_time; // number of testing sessions
array[N, N_time] int<lower=1, upper=T> T_subj; // number of trials per subject per session
array[N, N_time, T] real<lower=0> effort_... |
e1176d9f5e171bd187b704319e67d72ddf5c68d7be8713e4b95489bff790d793 | Stan | 4,362 | 146 | // #include /pre/license.stan
data {
int<lower=1> N; // number of subjects
int<lower=1> T; // max number of trials per subject
int<lower=1> N_time; // number of testing sessions
array[N, N_time] int<lower=1, upper=T> T_subj; // number of trials per subject per session
array[N, N_time, T] real<lower=0> effort... |
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