sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
e4149896d82e0d556ca5b692f08fcd44b3f1a713b18a9844c73e8d1554dc4d6a | Shell | 1,317 | 2 | python /mnt/disks/gmiller_data1/pnet-simu-private/src/pnet/run_model_on_preharmonized_data.py --epochs=4 --cpus=2 --data_config_f=/mnt/disks/gmiller_data1/pnet/configs/data.yaml --datasets="somatic_amp somatic_del somatic_mut germline_rare_common_missense" --evaluation_set=validation --input_data_dir=/mnt/disks/gmiller... |
845c0783d3b070e7100db18669599860290b929bdc1b8da7dbd5dab198a7e073 | Shell | 1,332 | 34 | #!/usr/bin/env bash
# run_rescal.sh
set -xe # echo each command and exit on error
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1 # force Python stdio unbuffered
echo "[$(date)] Activated env and set DGLBACKEND. L... |
6641d8d8b6787b9e9fc598d6a395b811f303ddaa2ee8946fd9de2e2d85d7194f | Shell | 1,334 | 34 | #!/bin/bash -l
#SBATCH --job-name=eval_binaural_swc
#SBATCH --output=outLogs/binaural_swc_test_2024_%A_%a.out
#SBATCH --error=outLogs/binaural_swc_test_2024_%A_%a.err
#SBATCH --mem=12Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=0:10:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:1 --constraint=20GB
#SBATCH --... |
4e2cc02ef47cb8ba3459f957ba80db55f516d18fcbea90d7a903a7ea78fa80d3 | Shell | 1,342 | 41 | # Temporarily change directory to $HOME to install software
pushd .
cd $HOME
# Make sure some level of pip is installed
python -m ensurepip
# Install Miniconda
if [ "$TRAVIS_OS_NAME" == "osx" ]; then
# Make OSX md5 mimic md5sum from linux, alias does not work
md5sum () {
command md5 -r "$@"
}
M... |
701ca7b93ff222dbdc3744ac20bb27212665c6e22957e5ae27aa8eca2509163a | Shell | 1,343 | 39 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$WORKDIR"' EXIT
cd "$WORKDIR" || exit
cfl2png... |
262b0391b897c59854a593728531bcd9462dfc019d2211431accd5f122692c4a | Shell | 1,349 | 31 | #!/bin/bash -l
#SBATCH --job-name=eval_model
#SBATCH --output=outLogs/sim_all_target_dist_positions_%A_%a.out
#SBATCH --error=outLogs/sim_all_target_dist_positions_%A_%a.err
#SBATCH --mem=8Gb
#SBATCH --cpus-per-task=2
#SBATCH --time=3:00:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:a100:1 --constraint=20GB
... |
ec59f111dcc18468d48a08946374dbefc5e6a05ae96a5a33d6f8d4897299ea23 | Shell | 1,361 | 41 | #!/bin/bash
user=$1 # gadgetron-matlab user e.g. fil-physics # For github
gad_matV=$2 # e.g. 1900083a562b98a176658ebc741c1b8f247e8285
mV=$3 # e.g. R2022b # Matlab version
# exit on error
set -e
# X Authority from bind mounted /home/mr
# Explicitly refernce /root so will fail if accidently executed as user o... |
8a69a80d863fd995d31040b28e4f9fb8ea5d3a2457bdd2d598ba9fd518fc68d7 | Shell | 1,368 | 39 | #!/bin/bash
# Common setup for all Jenkins scripts
# shellcheck source=./common_utils.sh
source "$(dirname "${BASH_SOURCE[0]}")/common_utils.sh"
set -ex -o pipefail
# Source ROCm environment variables (paths may vary between tarball/wheel installs)
if [[ "${BUILD_ENVIRONMENT}" == *rocm* ]] && [[ -f /etc/rocm_env.sh ]... |
b52352fca9c9fdf6020470b85ad56275eb7cabd71b791942550f158cef36c827 | Shell | 1,383 | 31 | #!/bin/bash -l
#SBATCH --job-name=eval_model
#SBATCH --output=outLogs/sim_human_azim_spotlight_exmpt_alt_arch_%A_%a.out
#SBATCH --error=outLogs/sim_human_azim_spotlight_exmpt_alt_arch_%A_%a.err
#SBATCH --mem=12Gb
#SBATCH --cpus-per-task=2
#SBATCH --time=2:00:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:1 --... |
d42ca3f3b9af9c0341452e7358d3af21b760e7816f5ded4d1a577cd5e53df4db | Shell | 1,391 | 31 | #!/bin/bash -l
#SBATCH --job-name=eval_model
#SBATCH --output=outLogs/sim_core_target_dist_positions_ssn_dist_%A_%a.out
#SBATCH --error=outLogs/sim_core_target_dist_positions_ssn_dist_%A_%a.err
#SBATCH --mem=8Gb
#SBATCH --cpus-per-task=2
#SBATCH --time=3:00:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:a100:... |
de64be9309ba4ef8b90dfdedc1a16ace51cedc1db6bcf39fe52cf0ee4e4fd1d0 | Shell | 1,405 | 37 | #!/bin/bash
# Install a persistent, system-wide Rust toolchain.
#
# PyTorch's build compiles the torch._rust extension (see setup.py
# _build_rust_extensions), so cargo must be on PATH for the build user at build
# time. This script is shared by the Ubuntu CI build images and the
# almalinux/manylinux CD wheel-builder ... |
b05ecf027a26db603ed64fc60a5fdd11638d16d32d6d633203af81d3c8da5772 | Shell | 1,414 | 36 | #!/bin/bash
# So this script takes *csv files and makes them into readable FASTA formats for igblast
# Should also extract relevant biophysical properties for these sequences while we're at it
# ASSUME FOR NOW THAT EVERY XLSX FILE HAS A HEADER. Should (maybe?) be some way to detect this
# Honestly detection should be... |
e96fd98d782a30b370d20f8dd91f2a9674863be784dbb64c43b8644dac1285a3 | Shell | 1,414 | 36 | #!/bin/bash
# So this script takes *csv files and makes them into readable FASTA formats for igblast
# Should also extract relevant biophysical properties for these sequences while we're at it
# ASSUME FOR NOW THAT EVERY XLSX FILE HAS A HEADER. Should (maybe?) be some way to detect this
# Honestly detection should be... |
a079c46efcdb2e15560bf7676b2a3c007695c4ef7139cff67fe00c3d92c4b373 | Shell | 1,435 | 43 | #!/bin/bash
# exit when any command fails
set -e
# keep track of the last executed command
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
cleanup() {
exit_code=$?
if [ ${exit_code} == 0 ]
then
echo "Completed execution"
else
echo "\"${last_command}\" failed with exit code... |
a4b0d6c65d4df6504000d73d2ab16d5d67f3020aa80036d418c7da8de41d781f | Shell | 1,437 | 55 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
if [ -z "$IOS_CMAKE_TOOLCHAIN_FILE" ]
then
echo "IOS_CMAKE_TOOLCHAIN_FILE not set... |
c8f3c9164ee6332a6a3ebae3e1f743a2e14701480828fcf05c2639ecb86dab9c | Shell | 1,437 | 55 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
if [ -z "$IOS_CMAKE_TOOLCHAIN_FILE" ]
then
echo "IOS_CMAKE_TOOLCHAIN_FILE not set... |
91000d439db89b3dc2aefa81d65f11bfb7dd9f3ee8142b4bf7611f92d5e201ae | Shell | 1,440 | 55 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
if [ -z "$IOS_CMAKE_TOOLCHAIN_FILE" ]
then
echo "IOS_CMAKE_TOOLCHAIN_FILE not set... |
936b01a847a42431abcb28ef0c6da44da56e9050ad30ee4ae5339393679bc47d | Shell | 1,440 | 55 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
if [ -z "$IOS_CMAKE_TOOLCHAIN_FILE" ]
then
echo "IOS_CMAKE_TOOLCHAIN_FILE not set... |
bd71468eec5c79512bdad38b3e4a694681444d4e766f5a39e373d215fde209b8 | Shell | 1,442 | 58 | # this script may not work properly.
# neurodocker minify is not supported on amd64.
# tried with Rosetta2, but 'neurodocker minify' command failed with internal retrozip error.
#!/bin/bash
set -euo pipefail
mkdir -p tmp
# 1. Convert to .mif and embed FSL gradients
mrconvert tests/data/D3/meso_slice.nii.gz tmp/in.... |
b0113523f99c1216e4d4d7d1515f84da74090c15f889c74343778db0618bdb80 | Shell | 1,450 | 46 | #!/bin/bash
#
# CBIG_check_whether_function_used_in_other_functions_wrapper.sh $file_path "silent"
# Wrapper function to search for all instances of a function name
# inside a predefined set of directories
# Input can be the function name, a file name, or full path of a file
file_name=$(basename "$1")
verbose=$2
#... |
9957298b8922035e45ff6f0aec12e4ff763ed5cb9351e69a43ffcdc2eef7b833 | Shell | 1,457 | 55 | #!/bin/bash
# Exit on errors
set -e
# ==========================================================
# Environment Setup
# ==========================================================
source ~/miniconda3/etc/profile.d/conda.sh
export TMPDIR=$HOME/tmp
export TEMP=$HOME/tmp
export TMP=$HOME/tmp
export TRITON_CACHE_DIR=$HOME/... |
6a4f2b36aa0fef55c47bd66865e9fdd02f2eff51e778d1cc60ce0635f08142aa | Shell | 1,476 | 35 | #!/bin/bash -l
#SBATCH --job-name=eval_model
#SBATCH --output=outLogs/sim_human_threshold_exmpt_v02_%A_%a.out
#SBATCH --error=outLogs/sim_human_threshold_exmpt_v02_%A_%a.err
#SBATCH --mem=8Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=1:00:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:1 --constraint=20GB
#SBAT... |
095a44641561ce363b3133b8a2c49d993286e72f777308e01d871ba6d863db5a | Shell | 1,481 | 55 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
if [ -z "$IOS_CMAKE_TOOLCHAIN_FILE" ]
then
echo "IOS_CMAKE_TOOLCHAIN_FILE not set... |
521c2ad19e5c6a889bf273c87640daea029d0c19ea6dcdcce5344004bd0a2150 | Shell | 1,489 | 40 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$WORKDIR"' EXIT
cd "$WORKDIR" || exit
cfl2png... |
8f5b1ff6883388279d1d6e4b5ec970dedc8d65edf5fe1e5fe596324210e928ef | Shell | 1,492 | 48 | #!/bin/bash
#$ -S /bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id: ashs_atlas_lf_qsub.sh 94 2013-04-24 18:21:56Z yushkevich $
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevi... |
9db04932dbbeaa7fa296c320e19b5e524acbe905250aa75a20708e6efb77ede0 | Shell | 1,496 | 52 | #!/bin/bash
#pull down chr21 of hg38 for test
wget -O chr21.fa.gz https://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chr21.fa.gz
gzip -df chr21.fa.gz
echo "downloaded chr21 hg38 fasta file"
#test for several strides
for stride in 100 500 1000
do
echo $stride
python ../src/helpers/make_gc_matched_n... |
d2de66ebaa536ae6699723667eb0ea9605b7ddccfea8f0b8d13ac633cd542e05 | Shell | 1,498 | 62 | #!/usr/bin/env bash
# CPU build script for s390x only.
# x86 and aarch64 CPU builds use linux-binary-manywheel.yml.
set -ex
export TH_BINARY_BUILD=1
export USE_CUDA=0
# Keep an array of cmake variables to add to
if [[ -z "$CMAKE_ARGS" ]]; then
CMAKE_ARGS=()
fi
ARCH=$(uname -m)
echo "Building CPU wheel for archi... |
7480797524aba54f19d096cae948a07ddf91e2432057852714baaf33f6baf16d | Shell | 1,503 | 50 | #!/bin/bash
# This script will generate example input data
# Written by Ru(by) Kong and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
##########################
# Specify output directory
##########################
out_dir=`realpath ${1}`
if [ -d $out_dir ]; then
rm -r $out_... |
49ba78f8afe84afe839bf37a0e2d78ab02d70ffa8f79ee13a08e353f77707746 | Shell | 1,507 | 61 | #!/bin/bash -l
#SBATCH --time=24:00:00
#SBATCH -p su_lab,encore
#SBATCH --mem=25G
#SBATCH --array 1-22
#SBATCH -o outs/Stage2_%A_%a.out
conda activate scTWAS_new
date
batch_suffix=''
ct=Bulk
run_subtype=FALSE
FUSION="${datadir}/software/FUSION/fusion_twas-master/"
WGT="scTransform_by_celltype_afterAgg"
posdic="${... |
7466e212a29b26842ad8fac18f614e1f3235ab3011072114f2190158c28a2545 | Shell | 1,513 | 37 | #!/bin/bash
#SBATCH -J samtools_bam_to_fastq
#SBATCH -c 8 # Request one core
#SBATCH -t 0-0:45 # Runtime in D-HH:MM format
#SBATCH -p short # Partition to run in
#SBATCH --mem=2G # Memory total in MiB (for all cores)... |
02740b1776bd50ce000707eaf205be699d79e56ed905ca0074d7a6321def538d | Shell | 1,515 | 54 | #!/bin/bash
#$ -S /bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id$
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevich, University of Pennsylvania
#
# This file is part of ... |
e698e16c9827a5703ef71a1e827fb4628c4a62c237e7e7264205d69e46f3ed5b | Shell | 1,526 | 37 | #! /bin/sh
#
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE CHANGE: Please specify location of CBIG repository
export CBIG_CODE_DIR=/data/users/ngohgia/storage/CBIG
# PLEASE CHANGE: define location... |
a37cade43e98505a59dc0061ed749d4db2f52af099fe27a0f939b5a83feff059 | Shell | 1,528 | 41 | #!/bin/bash
# This script submit a job to HPC for CBIG_fMRI_Preproc2016 single subject unit test.
# Written by Xingyu Lyu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
outdir=$1 # Your output directory
fmrinii_dir="$CBIG_TESTDATA_DIR/stable_projects/preprocessing"
fmrinii_di... |
3abe54368b4358ea7553bfdb426d183ce2ca125026f267b1562e651d0fba62d1 | Shell | 1,555 | 43 |
# Download submodules and move them to lib.
cat > submodules.txt <<EOF
kalign 0.3.0 makovalab-psu kalign-dunovo c0ef2de4a958aed47311ea86591debb3bada871143a6923bc6338ab2f99f2d5b
utillib 0.1.1-alpha NickSto utillib 961f5a3481d1c0dbe00c258b9df2de541e5605f3de4ff25bcc3cec22922e7c06
ET 0.3 N... |
8e74e6b78649d73d59100da9f7225baae88a4431b7566d94784b6120bfc77a29 | Shell | 1,555 | 25 | #!/bin/zsh
Rscript 08.DNNs/02b.tune_gPCs_cv.R --model 1 --fold 1 > logs/gPCs_cv_1_1.log
Rscript 08.DNNs/02b.tune_gPCs_cv.R --model 1 --fold 2 > logs/gPCs_cv_1_2.log
Rscript 08.DNNs/02b.tune_gPCs_cv.R --model 1 --fold 3 > logs/gPCs_cv_1_3.log
Rscript 08.DNNs/02b.tune_gPCs_cv.R --model 1 --fold 4 > logs/gPCs_cv_1_4.log
... |
44777cf9ceff9e65dd27ed72eb9a19a87132c223e2d45037e48a1d9210d5d228 | Shell | 1,563 | 41 | #!/bin/bash
# This script submit a job to HPC for CBIG_fMRI_Preproc2016 motion correction unit test.
# Written by XUE Aihuiping and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
outdir=$1 # Your output directory
fmrinii_dir="$CBIG_TESTDATA_DIR/stable_projects/preprocessing"
fmri... |
c539603ad7824146d6fb60db0c16b73df17bf27f51e716034fbc040718ee3b43 | Shell | 1,563 | 25 | #!/bin/zsh
Rscript 08.DNNs/02b.tune_gPCs_cv.R --model 1 --fold 6 > logs/gPCs_cv_1_6.log
Rscript 08.DNNs/02b.tune_gPCs_cv.R --model 1 --fold 7 > logs/gPCs_cv_1_7.log
Rscript 08.DNNs/02b.tune_gPCs_cv.R --model 1 --fold 8 > logs/gPCs_cv_1_8.log
Rscript 08.DNNs/02b.tune_gPCs_cv.R --model 1 --fold 9 > logs/gPCs_cv_1_9.log
... |
6cd50ea63f881fde4161592868797a4b976cf8635af111b1856d594cee0e73f8 | Shell | 1,566 | 56 | #!/bin/bash
# YOLOv5 🚀 by Ultralytics, GPL-3.0 license
# Download COCO 2017 dataset http://cocodataset.org
# Example usage: bash data/scripts/get_coco.sh
# parent
# ├── yolov5
# └── datasets
# └── coco ← downloads here
# Arguments (optional) Usage: bash data/scripts/get_coco.sh --train --val --test --segments
if... |
68b37852bae80a2401c0e965054ad1b51f8740d6990b377105153ae9bd3759d8 | Shell | 1,588 | 49 | #!/bin/bash
# exit when any command fails
set -e
# keep track of the last executed command
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
cleanup() {
exit_code=$?
if [ ${exit_code} == 0 ]
then
echo "Completed execution"
else
echo "\"${last_command}\" failed with exit cod... |
a12b3e93bc2c7a33e0fa79c2d62c800fe8e560889de841b5200bf20cd96f2d48 | Shell | 1,605 | 60 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
if [ -z "$IOS_CMAKE_TOOLCHAIN_FILE" ]
then
echo "IOS_CMAKE_TOOLCHAIN_FILE not set... |
10135d42e972e51fb67c550aaeff360ad485e3c60ac6a1a023c689614f93a172 | Shell | 1,622 | 46 | #!/bin/bash
# This script runs CBIG_fMRI_Preproc2016 single subject unit test within a Docker container.
# ! Warning: Since Docker is not installed on the compute nodes, this unit test runs directly on the compiler.
# ! Therefore, please choose a time when the compiler is not busy to run this unit test.
#
# Wr... |
944fb19c9fabd70b91d9b9a2b90ae1682e3f21467ab7a840044c85ba5a68e4bf | Shell | 1,623 | 63 | #!/bin/sh
#
# Vivado(TM)
# ISEWrap.sh: Vivado Runs Script for UNIX
# Copyright 1986-1999, 2001-2013 Xilinx, Inc. All Rights Reserved.
#
HD_LOG=$1
shift
# CHECK for a STOP FILE
if [ -f .stop.rst ]
then
echo "" >> $HD_LOG
echo "*** Halting run - EA reset detected ***" >> $HD_... |
8be681b9bba7158fefee8564940877c17d775d5cd7732406eea6690d14521f8b | Shell | 1,629 | 49 | #!/bin/bash
# Stop on error
set -e
# Settings for deployment container
IMAGE_FORK=fil-physics # Docker image from which the container
IMAGE_VERSION=V16 # will be created
CONTAINER_SUFFIX=0_public_rc1 # container version
# Settings for Matlab
GAD_MAT_FORK=baskadym # GitHub fork (e.g. fil-physics or your G... |
e554770e9b90c882b585b3d8ae2e84dc4b7b50f2961f78cbcd05994a45274778 | Shell | 1,637 | 58 | #!/usr/bin/env bash
# This script can also be used to test whether your diff changes any codegen output.
#
# Run it before and after your change:
# .ci/pytorch/codegen-test.sh <baseline_output_dir>
# .ci/pytorch/codegen-test.sh <test_output_dir>
#
# Then run diff to compare the generated files:
# diff -Naur <bas... |
4ea88c09b293cadc36115d59291c3698ba4edfe32a90942a8af35785fb72b41c | Shell | 1,639 | 53 | #!/bin/bash
root=/Volumes/Research/fieree01lab
#root=/mnt
datapath=$root/labspace/Santiago/PyDesigner/ValidationData/subj_1_22oct21/LTE_ZTE_variableTE
dwi1=20211022_194435sc1DIFF2isoTE92LTEs031a001.nii.gz
# dwi2=20211022_194435sc1FWF2isoTE92PTEs005a001.nii.gz
# dwi3=20211022_194435sc1FWF2isoTE92STEs007a001.nii.gz
# dw... |
b40a0fe43b5293fe97bb56250cf2ed4308f57b77a0140c90cf5bffb4b474d702 | Shell | 1,644 | 41 | #!/bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id$
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevich, University of Pennsylvania
#
# This file is part of ASHS
#
# ASHS i... |
d22b4c4725f44eee5b45f3a2e135721b029f51514bc0a35712877e479b41df30 | Shell | 1,657 | 49 | #!/bin/bash
# exit when any command fails
set -e
# keep track of the last executed command
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
cleanup() {
exit_code=$?
if [ ${exit_code} == 0 ]
then
echo "Completed execution"
else
echo "\"${last_command}\" failed with exit code... |
c72c65d13b59eb2505aa714c79aefd44070d6ae0ede037c5a4ebf403269bce44 | Shell | 1,658 | 57 | #!/bin/bash
set -eux
PYTORCH_DIR="$(cd $(dirname $0)/..; pwd -P)"
PYTORCH_ANDROID_DIR=$PYTORCH_DIR/android
source "$PYTORCH_ANDROID_DIR/common.sh"
check_android_sdk
check_gradle
# Run android instrumented tests on x86 emulator
ADB_PATH=$ANDROID_HOME/platform-tools/adb
echo "Expecting running emulator"
$ADB_PATH d... |
80540c3248897bebba5b2ae8a6cb1275f09135d5488917cc12d3830beff394e8 | Shell | 1,671 | 51 | #!/bin/bash
# YOLOv5 🚀 by Ultralytics, GPL-3.0 license
# Download ILSVRC2012 ImageNet dataset https://image-net.org
# Example usage: bash data/scripts/get_imagenet.sh
# parent
# ├── yolov5
# └── datasets
# └── imagenet ← downloads here
# Arguments (optional) Usage: bash data/scripts/get_imagenet.sh --train --val... |
b9ec9a21ca62e11e700521b2f77732a8cc2aa105c77f5bad4a693e9479a40d5b | Shell | 1,671 | 56 | #!/bin/bash
# Script used only in CD pipeline
set -ex
# install dependencies
dnf -y install gmp-devel libmpc-devel texinfo flex bison
cd /usr/local/src
# fetch source for gcc 13
git clone --depth 1 --single-branch -b releases/gcc-13.3.0 https://github.com/gcc-mirror/gcc.git gcc-13.3.0
mkdir -p gcc-13.3.0/build-gomp... |
f3fbea178890a33308dc0ef4dfb5f48cd9895b30b533700c3357bc33e15e7af5 | Shell | 1,676 | 56 | #!/bin/bash
# Script for installing sccache on the xla build job, which uses xla's docker
# image, which has sccache installed but doesn't write the stubs. This is
# mostly copied from .ci/docker/install_cache.sh. Changes are: removing checks
# that will always return the same thing, ex checks for for rocm, CUDA, ch... |
c86c8e7df9fee847de34b13488d6dcc3a07a97bff271090fbbcab6d626d6de44 | Shell | 1,678 | 69 | #!/bin/bash
# ================================
# CONFIGURACIÓN DEL USUARIO
# ================================
bids_root_dir="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Raw_T1/sampled_imgs_ADNI"
out_root="/data/Lautaro/Documentos/BrainAgeCOVID/DATOS/Raw_T1/Image_quality/ADNI"
container_path="/home/lautaro/mriqc-0.15... |
3988ffcc86d3d14a32afbd3a5f523df60e146f7659b8e9bfd7b1c80db24cd1ff | Shell | 1,682 | 64 | #!/bin/bash
#v0.1 Feb 23rd 2016
#Arash Nazeri, Jon Pipitone, and Tina Roostaei, Kimel Family Translational
#Imaging-Genetics Research Lab
#This script depends on ANTs v2.1 and FSL v4.1.9 (or higher)
#
#Developed at Kimel Family Translational Imaging Genetics Ressearch
#Laboratory (TIGR), Research Imaging Centre, Campb... |
56500872ee4b39364e234e87d75d7d12a91066f5d9c8ef6df23965ab3eddc6aa | Shell | 1,688 | 51 | #!/bin/bash
# Work around bug where devtoolset replaces sudo and breaks it.
if [ -n "$DEVTOOLSET_VERSION" ]; then
export SUDO=/bin/sudo
else
export SUDO=sudo
fi
as_jenkins() {
# NB: unsetting the environment variables works around a conda bug
# https://github.com/conda/conda/issues/6576
# NB: Pass on PATH a... |
274cf3ebbf3dc4f48ca1e7b992418ad69f37dd9f4ced318b3f5ad8296cb863f1 | Shell | 1,711 | 58 | #!/bin/bash
#$ -S /bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id$
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevich, University of Pennsylvania
#
# This file is part of ... |
51e944d323d4e66a10ec946c83c0b08e078e46a6b2ce91d8283d941a646fd534 | Shell | 1,712 | 45 | #!/bin/bash
set -ex
if [ -n "$CLANG_VERSION" ]; then
if [[ $UBUNTU_VERSION == 22.04 ]]; then
# work around ubuntu apt-get conflicts
sudo apt-get -y -f install
wget --no-check-certificate -O - https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
if [[ $CLANG_VERSION -ge 18 ]]; then
... |
15f48f733b0964dcc5f81ce4391b195bfab7010bf099751bf5cf218cddcbb7f8 | Shell | 1,719 | 45 | #!/bin/bash
#SBATCH -J salmon
#SBATCH -c 5 # Request one core
#SBATCH -t 0-0:40 # Runtime in D-HH:MM format
#SBATCH -p short # Partition to run in
#SBATCH --mem=20G # Memory total in MiB (for all cores)
#SBATCH -o lo... |
c056a405190b775cf6bb12d1535b2ef4313d6dcf0dc2a8337e61b8a792701867 | Shell | 1,728 | 67 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
RAW=$(readlink -f ../01_data_brain/ksp_2D)
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "... |
026c68d179b0bb97a7c3d00abff5f6c5198f738db9ee9203f9377c409ddab674 | Shell | 1,744 | 68 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
if [ -z "$ANDROID_NDK" ]
then
echo "ANDROID_NDK not set; please set it to the And... |
6fb0c699b54f3dac9833820d474115f055a430aee8b4714f6659979745369857 | Shell | 1,748 | 40 | #!/usr/bin/env bash
# Build a docker image on the remote BuildKit pool used by OSDC/ARC runners,
# which have no host docker daemon. Registers a remote buildx builder, then runs
# the passed command ("$@", e.g. a build.sh or `make ... -image`) and retries
# only connection-phase failures while the autoscaled pool is co... |
dd991898fbb6e7258f95a52ef1a44e612144cfea6041400de650f55ba6dac52c | Shell | 1,750 | 62 | #!/bin/bash
#$ -S /bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id$
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevich, University of Pennsylvania
#
# This file is part of ... |
34ace060473aa47de082ba404484b45e389a8113a4f1bb55f1bf8f437a7d117e | Shell | 1,753 | 60 | #!/usr/bin/env bash
set -eou pipefail
GIT_TOP_DIR=$(git rev-parse --show-toplevel)
TMPFILE=$(mktemp)
trap "rm -rf ${TMPFILE}" EXIT
# By default just run against the latest commit
BASE=${BASE:-HEAD~1}
HEAD=${HEAD:-HEAD}
ancestor=$(git merge-base "${BASE}" "${HEAD}")
echo "INFO: Checking against the following stats"... |
f9651d93b29f16554af39a5fe74e4ed6cc82372bf3e3c38c7268467f8f6e9bbd | Shell | 1,756 | 47 | #!/bin/bash
# exit when any command fails
set -e
# keep track of the last executed command
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
cleanup() {
exit_code=$?
if [ ${exit_code} == 0 ]
then
echo "Completed execution"
else
echo "\"${last_command}\" failed with exit code... |
f041f9fd4760eaecddfa054220345e16d4d55aad6dc7c03596c439f2417c9d7e | Shell | 1,759 | 59 | #!/bin/bash
#$ -S /bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id$
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevich, University of Pennsylvania
#
# This file is part of ... |
c9553b3e06114da38aaeaea8d5158fd4c71e6bf624daad53379568680cc69dc0 | Shell | 1,762 | 68 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
if [ -z "$ANDROID_NDK" ]
then
echo "ANDROID_NDK not set; please set it to the And... |
5c868353c32a2e4ff0b0b4c56034abf5cdb1b26f4f882bcdbc1e2075805effd3 | Shell | 1,768 | 68 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
if [ -z "$ANDROID_NDK" ]
then
echo "ANDROID_NDK not set; please set it to the And... |
f9d8a67247201a5757baaee315861e05e68246b7356c0cdf39aae862f80cd8c4 | Shell | 1,782 | 58 | #!/bin/bash
setup_torch_trace() {
if [[ "${ENABLE_TORCH_TRACE:-0}" != "1" ]]; then
return
fi
local trace_dir="${RUNNER_TEMP:-/tmp}/torch_traces"
mkdir -p "$trace_dir"
export TORCH_TRACE="$trace_dir"
echo "TORCH_TRACE enabled: writing structured trace logs to $trace_dir"
}
collect_tlparse_output() {
... |
517c15381cf8cd243a51db78a026a96fde4268bd4801a7ea6bebdd13ea17e702 | Shell | 1,784 | 22 | #!/bin/bash
set -e
python 000_run_multi.py -n CNN_pH_kfold_val_pure -d results/baseline_sub -c1 ckpt/baseline_sub -l 1 -t substrates_classes
python 000_run_multi.py -n CNN_pH_kfold_nval_pure -d results/baseline_inh -c1 ckpt/baseline_inh -l 1 -t inhibitors_classes
python 000_run_multi.py -n CNN_pH_kfold_val_stop -d r... |
49b047e5825e4e42e7ad3fbb279d0f118bcf8e3d6a7fd4816ad24acb628b959e | Shell | 1,790 | 57 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$WORKDIR"' EXIT
cd "$WORKDIR" || exit
if [[ -... |
af49bb843640d406aed4ce1e7d37a5ab6fd0e9d5498d5018db8089d76e1a1728 | Shell | 1,801 | 25 | module load miniconda
conda activate ldsc
python /gpfs/gibbs/project/alagpulinsa/zx228/ldsc/ldsc.py \
--h2 /vast/palmer/pi/alagpulinsa/Ziang/LDSC_sumstats_munged/T1D.sumstats.gz \
--ref-ld-chr /vast/palmer/pi/alagpulinsa/Brain_developement_atac_data/Prenatal/hg19_combined/Prenatal_chr,/vast/palmer/pi/alagpulinsa/B... |
777b9044b84185a256ebcf3f0dd523e3043c260a036840560274d927a240ff6f | Shell | 1,809 | 75 | #!/bin/bash
set -ex
source "$(dirname "${BASH_SOURCE[0]}")/common_utils.sh"
clone_executorch() {
EXECUTORCH_PINNED_COMMIT=$(get_pinned_commit executorch)
# Clone the Executorch
git clone https://github.com/pytorch/executorch.git
# and fetch the target commit
pushd executorch
git checkout "${EXECUTORCH_... |
35e4ff5dce4fbf6d496b28b9dff94c53498569dee68c3412969facc40ca1e154 | Shell | 1,831 | 55 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
RAW=$(readlink -f ../01_data_brain/ksp_2D)
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$W... |
66c7e26e67af59d24621764112bbe6b8966fee894c421dcccbf1774d89796d49 | Shell | 1,831 | 49 | #!/bin/bash
# If you want to rebuild, run this with REBUILD=1
# If you want to build with CUDA, run this with USE_CUDA=1
# If you want to build without CUDA, run this with USE_CUDA=0
if [ ! -f pyproject.toml ]; then
echo "ERROR: Please run this build script from PyTorch root directory."
exit 1
fi
SCRIPT_PARENT_D... |
11b53f37d559ead4f969bf78f4a2ec6ba0be4cffa1e6d0bf5c0467cda83cff6f | Shell | 1,834 | 46 | #!/bin/bash
#SBATCH --job-name=saz22 # Job name # Partition (queue) name
#SBATCH --ntasks=1 # Single task job
#SBATCH --cpus-per-task=1 # Number of cores per task - match this to the num_threa... |
5af9da69ac4bd87aa2e8df7560eea8f6f578e9236763a6e0fce3924e24d946b0 | Shell | 1,840 | 50 | #!/bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id$
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevich, University of Pennsylvania
#
# This file is part of ASHS
#
# ASHS i... |
ee198652d2ddc304b16f9b0831139b4d3150e76a3d34d9c26eb5cf7a4856c99e | Shell | 1,852 | 62 | #!/bin/bash
set -ex
source "$(dirname "${BASH_SOURCE[0]}")/common_utils.sh"
# Get the pinned JAX version (same for all CUDA versions)
JAX_VERSION=$(get_pinned_commit /ci_commit_pins/jax)
function install_jax_cpu() {
echo "Installing JAX ${JAX_VERSION} (CPU only)"
pip_install "jax[cpu]==${JAX_VERSION}"
# Veri... |
90d47fba5db607e1af93467c09aa7a4f281619d90a4f7b54ba71a65408abded5 | Shell | 1,856 | 31 | #! /bin/bash
prefix="/opt/local"
# WX_CONF="${prefix}/Library/Frameworks/wxWidgets.framework/Versions/wxWidgets/3.1/bin/wx-config"
# WX_CONF="/Users/cs/wxPython-4.0.7.post2/build/wxbld/wx-config"
PYVER="3.13"
WX_CONF="${prefix}/Library/Frameworks/Python.framework/Versions/${PYVER}/bin/wx-config"
MYCC=`${WX_CONF} --cc`... |
7bb76e777152ce0d389f3c2034cf04bbb212344e303eeebfa30c975734025ba1 | Shell | 1,870 | 45 | #!/usr/bin/env bash
# Per-Python macOS arm64 wheel build orchestrator. Mirrors
# .ci/wheel/linux/build.sh: this script owns the stage contract; the Python
# modules (build_env_setup.py / build_install_deps.py / build_wheel.py /
# repair_wheel.py) are non-orchestrating stages that stay version-agnostic.
#
# Scope: wheel... |
7c2861f8bcbec7833027570ece6c621c6efdb9759d4e91a936c118309f3a3779 | Shell | 1,903 | 50 | #! /bin/bash
WX_CONFIG=/opt/local/bin/wx-config
WXPY_DIR=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
mkdir -p stimfit.app
mkdir -p stimfit.app/Contents
mkdir -p stimfit.app/Contents/Frameworks
mkdir -p stimfit.app/Contents/MacOS
mkdir -p stimfit.app/Contents/libs
cp -v -r ... |
d9cb8e03b4bdf0ffc5c31eab5a4409602ffc0191f92bd7e8f5d17260d0390dbc | Shell | 1,911 | 54 | #!/bin/bash
# This script submit a job to HPC for CBIG_fMRI_Preproc2016 single subject unit test within a Singularity container.
# Written by Fang Tian and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# First, define the directory to store the Singularity image
IMG_DIR="$HOME/sto... |
1b79732e9dadecf0a5a7d170cd13fef45159b72341b03e47ceb1d41756182cf8 | Shell | 1,917 | 48 | #!/usr/bin/env bash
# run_rescal_eval_all_shuffles.sh
set -xe
source ~/miniconda3/etc/profile.d/conda.sh
conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
TOTAL_CORES=$(nproc)
NUM_PROC=$((TOTAL_CORES - 15))
DATA_PATH="/storage/Arushi/090526_EvoAge/kg_formation/training_3/Shuffled_EvoAge_tes... |
921d2b6722d798d0e76e4f1e50698087822cfa5b2ceb5efaf1eef7f5df883e4c | Shell | 1,940 | 45 | #! /bin/bash
# Written by Tianchu Zeng and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
echo "Executing this script will install a new environment called CBIG_py3_aws and install package aws-cli."
read -p "Are you sure? (y/n) " answer
if echo "$answer" | grep -iq "^y"; then
... |
b39c6a434093b9b03217c278eb72d421a07b2a77edb8a95ef5f6d715b326d174 | Shell | 1,950 | 72 | # !/bin/bash
# outcount and motion censor for functional bold runs
# set data directories
dataDir=/media/yuhui/LCT
cd ${dataDir}
for patDir in subj_folder; do
{
cd ${dataDir}/${patDir}
for runDir in bold.sft; do
{
cd ${dataDir}/${patDir}/${runDir}
run_dsets=($(ls -f rbold*.nii.gz))
run_num=${#run_dsets[@]... |
66c38e086dd632b2db2bfc864ea8e87f6307e5dd30c392304fb51c67edb96007 | Shell | 1,955 | 64 | #!/bin/bash
#$ -S /bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id$
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevich, University of Pennsylvania
#
# This file is part of ... |
32138e020a336126f2c251208fcb10ad460c722fe898abb27e1cd23d9e669df1 | Shell | 1,957 | 60 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... |
be25fd7a984d8086b0ed97d4ed2e113c20b3c529f50f46e0d3cba12b2745aeae | Shell | 1,971 | 69 | #!/usr/bin/env bash
date
echo "Step 3 calling peaks with macs 3"
printf "\n"
######
peakdir="Your/directory/for/the/output/peak/file"
printf "Your directory for the output peak file %s\n" "${peakdir}"
# change genomeForMacs3 if data is not from human. Follow the macs3 manual
genomeForMacs3="hs"
printf "Your genome ... |
5b7ecee71c5596e6c658b98e16b28676348eae7ec51fc5ef94634089a39adee8 | Shell | 1,980 | 54 | #!/bin/bash
set -ex
source "$(dirname "${BASH_SOURCE[0]}")/common_utils.sh"
COMMIT=$(get_pinned_commit halide)
test -n "$COMMIT"
# Resolve the Python env prefix that Halide's bindings get installed into
if command -v conda >/dev/null 2>&1; then
eval "$(conda shell.bash hook)"
conda activate py_$ANACONDA_PYTHON_V... |
b285887ee3ac9ab477efd9422c091378d7cfdc7afe2c5a2fdffb48afe235cb2e | Shell | 1,990 | 48 | # this is a script for retro-recon of B1 maps
# it runs with remote connection to the server and for retro-recon without Siemens console
# to enable remote reconstruction it overwrites the display variable in container, which is currently set to run correctly when you use X-server on the hostmachine (the actual physica... |
bbb98b6eb932a5152209f2e3728b21434a33531c1eeeba0e70497be60a431fb5 | Shell | 2,026 | 43 | #!/bin/bash
# Shared validator entry point for the hardened PR review.
#
# Both hooks call this. The model CANNOT invoke it directly — Bash is refused in
# that job — so its on-demand check is the write itself: every Write to the
# findings file runs this and injects the result back. Rewriting is unlimited,
# so the lo... |
54265a4f8277d3da7c4568c229c7239dea36a891c3ae34aa5d1e36255403b6d4 | Shell | 2,030 | 47 | #!/bin/bash
# PostToolUse(Write) hook — advisory, and the reason the whole loop works.
#
# HOW FEEDBACK ACTUALLY REACHES THE MODEL. On exit 0 a hook's stderr goes to the
# transcript and NOWHERE the model can read, so a validator that merely printed
# errors and exited 0 would be inert — the model would rewrite nothing... |
c1d45f3d4795647ef8f40a6d3da60abb7de91f97c6a28cbad9e6a7f15ae38c64 | Shell | 2,100 | 60 | #!/bin/bash -
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id$
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevich, University of Pennsylvania
#
# This file is part of ASHS
#
# ASH... |
b23f8d10593fb10c42fc4e84f63b1b7a65dc32bd9c8a62ddec12be28dc81a7be | Shell | 2,112 | 86 | #!/bin/sh
if [ ${#ANTSPATH} -le 3 ] ; then
echo we guess at your ants path
export ANTSPATH=${ANTSPATH:="$HOME/bin/ants/"} # EDIT THIS
fi
if [ ! -s ${ANTSPATH}/ANTS ] ; then
echo we cant find the ANTS program -- does not seem to exist. please \(re\)define \$ANTSPATH in your environment.
exit
fi
NUMPARAM... |
aee76fad967b61307b6a7d13eb256421063a018d6817ab082fda23341491cf50 | Shell | 2,120 | 63 | #!/bin/bash
#############################################
# CBIG Speed Up Gradient Diffusion Emdedding
#############################################
# AUTHOR #################################
# RU(BY) KONG
# 2020/10/01
##########################################
##########################################
# CBIG_SPGr... |
41003f167b79c103345cbf761fd8c9d81938d9887396fd38aaebf36477d5c363 | Shell | 2,150 | 74 | #!/bin/bash
set -eux
##############################################################################
# Common util functions for Android build scripts.
##############################################################################
if [ -z "$PYTORCH_DIR" ]; then
echo "PYTORCH_DIR not set!"
exit 1
fi
retry () {
... |
7989c38c944a6dfbe7196aa76e7ada389845d06b9f014e9b049032afd432f239 | Shell | 2,151 | 61 | #!/usr/bin/env bash
# run inside the r-maaslin2 micromamba environment
#### BARE MINIMUM COVARIATES
# Early 30-120 Infants Full
Rscript run-maaslin.R \
--dir_job '../' \
--job_prefix 'mice_1mo_to_4mo_Low_vs_High' \
--job_suffix '' \
--fixed_effects 'BSID_Group,Infant_Age,Seq_Depth' \
--fixed_effe... |
660b32481dc5f9f9714e22a492d2492f6a6066b2ef01ab523d679b0e109aaad4 | Shell | 2,153 | 65 | #!/bin/bash
#v0.2.1 July 21st 2015
#Arash Nazeri, Jon Pipitone, and Tina Roostaei, Kimel Family Translational
#Imaging-Genetics Research Lab
#This script depends on ANTs v2.1 and FSL v4.1.9 (or higher)
#
#Developed at Kimel Family Translational Imaging Genetics Ressearch
#Laboratory (TIGR), Research Imaging Centre, Ca... |
9430b9d377f322c9a1cfad8fea5672d4697fd28bca42435d0710760bedc04a61 | Shell | 2,157 | 61 | #!/usr/bin/env bash
# run inside the r-maaslin2 micromamba environment
#### BARE MINIMUM COVARIATES
# Early 30-120 Infants Full
Rscript run-maaslin.R \
--dir_job '../' \
--job_prefix 'mice_1mo_to_4mo_Low_vs_TypicalHigh' \
--job_suffix '' \
--fixed_effects 'BSID_Low,Infant_Age,Seq_Depth' \
--fixed... |
d596c64a35c4dd119fb0d5749924c1f8b946fc21c66aa325d6cc6a4d2ac541dd | Shell | 2,185 | 62 | #!/usr/bin/env bash
set -ex
CACHE_DIRECTORY="/tmp/.lintbin"
CLANG_LINTERS="CLANGTIDY,CLANGTIDY_EXECUTORCH_COMPATIBILITY,CLANGFORMAT"
PYREFLY_LINTERS="PYREFLY"
case "${LINTER_GROUP:-}" in
clang)
ADDITIONAL_LINTRUNNER_ARGS="--take ${CLANG_LINTERS} ${CHANGED_FILES}"
;;
pyrefly)
ADDITIONAL... |
d07dfa6fe2483cd279756642369f11b3c6b47b99776dd78fc32ac63a8c6b90a2 | Shell | 2,208 | 51 | #!/bin/bash
cicero_dir='/cluster/share/atac_group/mafas5/chen_ws/cicero/output'
meta_col='subclass'
echo "Merge distal-proximal conns: ${meta_col}"
out_all_conns_sta="${cicero_dir}/macaca.whole.${meta_col}.merge.conns.sta.all"
cat ${cicero_dir}/*.conns.sta \
| sed -e "1i cluster\ttotConns\tddConns\tppConn... |
7f4e380d4f7b96f0a8fbcb559c6002e67818c202bca99f5f46375bf2dcf5bc2d | Shell | 2,222 | 72 | #!/bin/bash
# Build a FIL physics docker container image
if [ "$EUID" -ne 0 ]
then echo "Please run as root"
exit
fi
# Stop on error
set -e
# Settings for deployment image
IMAGE_FORK=fil-physics
IMAGE_VERSION=V16
IMAGE_NAME=${IMAGE_FORK}:${IMAGE_VERSION}
BASE_NAME=${IMAGE_NAME}-base
MATLAB_CONTAINER_URL=https:... |
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