sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
5c2ed679fab5a9ca8e6a5cc685f64b3d6dff5281387c228dccddbfc0b523fb7f | Shell | 2,238 | 50 | module purge
module load miniconda
CONDA_BASE=$(conda info --base)
source "${CONDA_BASE}/etc/profile.d/conda.sh"
conda activate mixer_env
echo "Using Python: $(which python)"
echo "Python version: $(python --version)"
echo "Conda env: $CONDA_DEFAULT_ENV"
MIXER_DIR="/home/yd357/pi_paths/pi_alag/env/mixer"
OUTPUT_DI... |
def1efd166ed02a0c419afc7d68a630097ce62f25dac471572add851ff7315c5 | Shell | 2,266 | 54 | #!/bin/bash
set -ex -o pipefail
# Suppress ANSI color escape sequences
export TERM=vt100
# shellcheck source=./common.sh
source "$(dirname "${BASH_SOURCE[0]}")/common.sh"
# shellcheck source=./common-build.sh
source "$(dirname "${BASH_SOURCE[0]}")/common-build.sh"
echo "Environment variables"
env
echo "Testing FA3... |
afebfef69e5f87680fe426423f4035bf42c0241043ae06a35f4626854958f3d7 | Shell | 2,268 | 67 | #!/usr/bin/env bash
# run inside the r-linda micromamba environment
#### BARE MINIMUM COVARIATES
# Early 30-120 Infants Full
Rscript run-linda.R \
--dir_job '../' \
--job_prefix 'infants_1mo_to_4mo_Low_vs_High' \
--job_suffix '' \
--formula '~ BSID + Infant_Age + Seq_Depth + (1|Infant_ID)'
# Late In... |
be20e8a2623accd4f6d9ad9d549cf2481ae054f861be86aaa66f4eedb963141e | Shell | 2,336 | 69 | #!/bin/bash
# Download and install NIRFASTer
echo "Installing NIRFASTer..."
OS="$(uname -s)"
case "$OS" in
Linux*) OS_NAME="linux";;
Darwin*) OS_NAME="mac";;
CYGWIN*|MINGW*|MSYS*) OS_NAME="win";;
*) OS_NAME="Unknown";;
esac
echo "Operating System Detected: $OS_NAME"
if [ "$OS_NAME" =... |
5dcf3d7006d620a70d4fe7513743fcabf9935890e0b1e3f106c1f4b4fa6ae07a | Shell | 2,345 | 91 | #!/bin/bash
# Helper utilities for build
# Script used only in CD pipeline
OPENSSL_DOWNLOAD_URL=https://github.com/openssl/openssl/releases/download/OpenSSL_1_1_1l/ # @lint-ignore
CURL_DOWNLOAD_URL=https://curl.se/download
AUTOCONF_DOWNLOAD_URL=https://ftp.gnu.org/gnu/autoconf
function check_var {
if [ -z "$1"... |
57b84f1d9f1c59654641bc2c68467bc5ffaed2f5af2c8d45f92df664cf0755ac | Shell | 2,356 | 67 | #!/usr/bin/env bash
# run inside the r-linda micromamba environment
#### BARE MINIMUM COVARIATES
# Early 30-120 Infants Full
Rscript run-linda.R \
--dir_job '../' \
--job_prefix 'infants_1mo_to_4mo_Low_vs_Typical_vs_High' \
--job_suffix '' \
--formula '~ BSID + Infant_Age + Seq_Depth + (1|Infant_ID)'... |
24e81bdd87d070afb9963d7729490fecd68cfc599207567c2012c32a06f02573 | Shell | 2,359 | 74 | #!/bin/bash
#$ -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 ... |
398561615a61b923b4305e0476a058d10430920315c83ff9b5fc404bdcbfac53 | Shell | 2,393 | 84 | #!/usr/bin/env bash
#
# Request an ACCESS_TOKEN to be used by a GitHub APP
# Environment variable that need to be set up:
# * APP_ID, the GitHub's app ID
# * INSTALL_ID, the Github's app's installation ID
# * APP_PRIVATE_KEY, the content of GitHub app's private key in PEM format.
#
# https://github.com/orgs/community/d... |
c545d0795666096530be1c4b1859dbc415f1960ccc3c5986509748f31a25dc4f | Shell | 2,395 | 83 | #!/bin/bash
exe_name=$0
exe_dir=`dirname "$0"`
# If MCR R2023a is installed in a non-default location, define correct path
# on next line and uncomment it (remove the leading "#")
#BrainSuiteMCR="/path/to/your/MCR";
if [ -z "$BrainSuiteMCR" ]; then
if [ -e /usr/local/MATLAB/MATLAB_Runtime/R2023a ]; then
Brain... |
853d7ac491d26bc3189862d9b88968e15b3484a6d82b95882ca06f33793dddf5 | Shell | 2,396 | 72 | #!/bin/bash
# shellcheck disable=SC1090
set -eux -o pipefail
source "${BINARY_ENV_FILE:-/c/w/env}"
mkdir -p "$PYTORCH_FINAL_PACKAGE_DIR"
if [[ "$OS" != "windows-arm64" ]]; then
export CUDA_VERSION="${DESIRED_CUDA/cu/}"
export USE_SCCACHE=1
export SCCACHE_BUCKET=ossci-compiler-cache
export SCCACHE_IGNO... |
684aca7ffbb042e8bede7643386b30c55dc0dfa60b163cda8d2e6e4ba516358b | Shell | 2,424 | 52 | #!/usr/bin/env bash
set -eou pipefail
# Environment variables
# The script expects DESIRED_CUDA and PACKAGE_NAME to be set
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
MAGMA_VERSION=2.6.1
# Folders for the build
PACKAGE_FILES=${ROOT_DIR}/magma/package_files # source patches and metadata
PACKAGE_DIR=${... |
7aa4970d20a1eca6898e9eb8b00121e2987bb5b827b166011ec8ac31ef07229a | Shell | 2,471 | 66 | #!/bin/bash
# Helper dependencies build script for s390x
# Script used only in CD pipeline
# Stop at any error, show all commands
set -ex
# Function to retry functions that sometimes timeout or have flaky failures
retry () {
$* || (sleep 1 && $*) || (sleep 2 && $*) || (sleep 4 && $*) || (sleep 8 && $*)
}
retry ... |
c0277523eb1d7d07c031fcb2309784152e9023738644beaa9a62b8611a247aa0 | Shell | 2,475 | 111 | #!/bin/sh
set -eu
fail() {
echo "FAIL: $*" >&2
exit 1
}
case "${0}" in
*/*) CLI_DIR=$(CDPATH= cd -- "$(dirname -- "$0")" && pwd) ;;
*) CLI_DIR=$(pwd) ;;
esac
ROOT_DIR=${ROOT_DIR:-$(CDPATH= cd -- "$CLI_DIR/../.." && pwd)}
IAD_EXECUTABLE=${IAD_EXECUTABLE:-"$ROOT_DIR/iad"}
AD_EXECUTABLE=${AD_EXECUTABLE... |
f6679868fb7bdbb92ffaa13257b7b85e33128355e07b99b2f5d5d2ce92a1db98 | Shell | 2,510 | 37 | # exit when any command fails
set -e
# keep track of the last executed command
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
# echo an error message before exiting
trap 'echo "\"${last_command}\" command filed with exit code $?."' EXIT
python tf_modiscohits.py --outdir=count/k562_hits/ \
... |
73d9b96de69c408e850de3fa0ed677f537bfb458979ca2039fbf292c1995f1ee | Shell | 2,523 | 63 | #!/usr/bin/env bash
# Build a manylinux wheel for every CPython version in DESIRED_PYTHONS on
# a single runner. After the first full build, subsequent iterations only
# recompile libtorch_python + _C for the new Python ABI (libtorch_cpu is
# ABI-free and reused) via the cross-Python cache invalidation in
# tools/setup... |
b54f3451a579a2cc187e6db04eb013a93a6d32da74bf52eedec670df12dbf51a | Shell | 2,535 | 74 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
RAW=$(readlink -f ../01_data_brain/ksp_2D2)
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$... |
e099430943d0093f7a8c1e6521378ce0bdb5be2f4085bc5d992d9a2e70af5481 | Shell | 2,536 | 52 | #!/bin/bash -l
#SBATCH --job-name=eval_binaural_swc
#SBATCH --output=outLogs/binaural_swc_test_2024_control_archs_%A_%a.out
#SBATCH --error=outLogs/binaural_swc_test_2024_control_archs_%A_%a.err
#SBATCH --mem=32Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=0:45:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:1 ... |
9696ef5966efe8e38142e6bbf4f891b06276a0f2ddc99b38bcbf1f0aa8d9e7d4 | Shell | 2,537 | 67 | #!/bin/bash
# Start iAODE Training UI with integrated backend
set -e
echo "╔════════════════════════════════════════════════════════════════╗"
echo "║ iAODE Training UI - Integrated Application ║"
echo "╚════════════════════════════════════════════════════════════════╝"
echo ""
# Colors for output... |
418455eee677f9789d18fe677afc15f0950979ede0c5787929ea2f85cbd178a4 | Shell | 2,538 | 74 | #!/usr/bin/env bash
if [ x$BASH = x ] || [ ! $BASH_VERSINFO ] || [ $BASH_VERSINFO -lt 4 ]; then
echo "Error: Must use bash version 4+." >&2
exit 1
fi
set -ue
# Get the root directory of this repo.
scripts_dir=$(dirname $(dirname $(readlink -f $0)))
export PYTHONPATH=${PYTHONPATH:=$HOME/bx/code/indels/pybamparser/li... |
e9bab00653c1c611762d91f173553431f1bf87264c540450156d3a82ac1c7577 | Shell | 2,540 | 58 | #!/bin/bash
# shellcheck disable=SC2034
# shellcheck source=./macos-common.sh
source "$(dirname "${BASH_SOURCE[0]}")/macos-common.sh"
# shellcheck source=./common-build.sh
source "$(dirname "${BASH_SOURCE[0]}")/common-build.sh"
# Build PyTorch
if [ -z "${CI}" ]; then
export DEVELOPER_DIR=/Applications/Xcode9.app/Co... |
a53b75a7d83fa36ae9cd4f49d1ce98cd4adff5ed32d09ffbd92729df0fb220df | Shell | 2,564 | 79 | #!/bin/bash
exe_name=$0
exe_dir=`dirname "$0"`
# If MCR R2023a is installed in a non-default location, define correct path
# on next line and uncomment it (remove the leading "#")
#BrainSuiteMCR="/path/to/your/MCR";
if [ -z "$BrainSuiteMCR" ]; then
if [ -e /usr/local/MATLAB/MATLAB_Runtime/R2023a ]; then
Brain... |
751508c4c971855b2fb261404cd1a8dd98f53536611218d2c9da6b3755348a31 | Shell | 2,577 | 65 | #!/bin/sh
# The ez_RT family (ez_RT, ez_RT_unscattered, ez_RT_Cone, ez_RT_Oblique) takes
# indices of refraction but no slide optical depths, and each one sets both to
# zero internally. The slides refract but never absorb. That is deliberate --
# they are small interfaces for callers that cannot pass a structure --... |
fc55fe2f93c7f7c361359ed629a69d9f87a30f1bce0be96c097b5eacdf85c84e | Shell | 2,584 | 92 | #!/usr/bin/env bash
set -euo pipefail
export GCX_SERVER="${GCX_SERVER:-https://pytorchci.grafana.net}"
export GCX_CONTEXT="${GCX_CONTEXT:-pytorchci}"
# Cache a pinned, prebuilt gcx binary in a private directory and invoke it by
# absolute path, so nothing lands on the user's PATH. gcx's installer verifies
# the down... |
3332b1d98890aee11497b6abb9c5e6c838bff3356d9f506f3946d3025a7854ac | Shell | 2,613 | 78 | #!/bin/bash
set -ex -o pipefail
SCRIPT_PARENT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
# shellcheck source=./common.sh
source "$SCRIPT_PARENT_DIR/common.sh"
export TMP_DIR="${PWD}/build/win_tmp"
TMP_DIR_WIN=$(cygpath -w "${TMP_DIR}")
export TMP_DIR_WIN
export PROJECT_DIR="${PWD}"
PROJECT_DIR_WIN=$(cygpat... |
2edffafe12a345f7d352c373a2448a8ca40d2f53854ae84e9e5944854b8fdd8c | Shell | 2,616 | 38 | #!/usr/bin/env bash
# update_alternatives_clang.sh
# chmod u+x update_alternatives_clang.sh
#
update_alternatives() {
local version=${1}
local priority=${2}
local z=${3}
local slaves=${4}
local path=${5}
local cmdln
cmdln="--verbose --install ${path}${master} ${master} ${path}${master}-${v... |
b054fbeb754b5ae089261b3383dd6050b21d4930c96051a2631f581245b0c578 | Shell | 2,628 | 60 | #!/bin/sh
# This script is specific to CIRC HPC cluster.
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
ts=$(date +%Y-%m-%d_%H-%M-%S)
USERNAME=`whoami`
# [PLEASE EDIT THIS]
BASE_DIR="/data/users/${USERNAME}/storage/PROJECT_NAME_${ts}"
# The project folder
# The folde... |
3ee2a9cf6be88649a4795a4700d4fe2f157c2e625d068f7fd8d9eb4a0d907f54 | Shell | 2,643 | 82 | #!/bin/bash
exe_name=$0
exe_dir=`dirname "$0"`
# If MCR R2023a is installed in a non-default location, define correct path
# on next line and uncomment it (remove the leading "#")
#BrainSuiteMCR="/path/to/your/MCR";
if [ -z "$BrainSuiteMCR" ]; then
if [ -e /usr/local/MATLAB/MATLAB_Runtime/R2023a ]; then
Brain... |
4e4947f7430b5ffdd13e729479e436f0dd55a0f968dfc8ae535d5db6ac91fb1f | Shell | 2,645 | 49 | #!/bin/bash -l
#SBATCH --job-name=eval_model
#SBATCH --output=outLogs/sim_human_azim_spotlight_exmpt_control_arch_%A_%a.out
#SBATCH --error=outLogs/sim_human_azim_spotlight_exmpt_control_arch_%A_%a.err
#SBATCH --mem=20Gb
#SBATCH --cpus-per-task=2
#SBATCH --time=1:15:00
#SBATCH --partition=use-everything
#SBATCH --gres=... |
302869c92c772c2198fae1f359f51b7bb0235c65a6298aed8c19168ece29104d | Shell | 2,649 | 83 | #!/usr/bin/env bash
# Script used only in the CD pipeline, on an OSDC remote BuildKit builder (there
# is no local Docker daemon). The caller sets up the buildx builder, passes the
# target tag(s) as trailing `-t ...` args ("$@"), and gates publishing via
# WITH_PUSH.
set -exou pipefail
image="$1"
shift
if [ -z "${i... |
a508c0353afa36817580d17c3242781ec80e059f6df1f4090837cf166f6ae0a4 | Shell | 2,677 | 61 | #!/bin/bash
input_dir=$1
out_dir=$2
cl=$3
echo $cl
POOLED_PEAK="${input_dir}/${cl}-pool_peaks.narrowPeak"
function reuse_pooled_peak ()
{
local r=$1
if [ ! -f $1 ]; then
r=$2
fi
echo "$r"
}
if [ ! -f ${POOLED_PEAK} ]; then
exit 1
fi
REP1_PEAK=$(reuse_pooled_peak "${input_dir}/${cl}-rep... |
9ae1ca8f3e5a682ae825442d3d1953a20a115d7feeb2e5444294f61370171510 | Shell | 2,697 | 101 | #!/bin/bash
set -ex
install_ubuntu() {
# NVIDIA dockers for RC releases use tag names like `11.0-cudnn9-devel-ubuntu18.04-rc`,
# for this case we will set UBUNTU_VERSION to `18.04-rc` so that the Dockerfile could
# find the correct image. As a result, here we have to check for
# "$UBUNTU_VERSION" == "18.04"... |
ec9e7ce2f45dd953a7d371cb6aaf978d1f0052372c1927337d0b2047a88a8977 | Shell | 2,697 | 75 | #!/bin/bash
#$ -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 ... |
aa35f60b4b286851ea36f027d022a50f017015d9bfb43aeae76e9be06117dc8e | Shell | 2,701 | 81 | #!/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... |
2efff30b54241b85cb34e15e5748a82c52c18ef03e0c0404748f2d461ce43837 | Shell | 2,715 | 71 | #!/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 $SCRIPT_DIR
export DEBUG_LEVEL=4
export OMP_NUM_THREADS=1
export BART_USE_FFTW_WISDOM=1
RAW=$(readlink -f ../01_data_brain/ksp_slic... |
6f4a5c89f69952f0291b2c8ad2d3d157e106a1ab2f5b44810f023b6e073f17d3 | Shell | 2,724 | 92 | #!/bin/bash
set -ex
# Set ROCM_HOME isn't available, use ROCM_PATH if set or /opt/rocm
ROCM_HOME="${ROCM_HOME:-${ROCM_PATH:-/opt/rocm}}"
# Find rocm_version.h header file for ROCm version extract
rocm_version_h="${ROCM_HOME}/include/rocm-core/rocm_version.h"
if [ ! -f "$rocm_version_h" ]; then
rocm_version_h="${R... |
b4ceb959ec174b876e4862b14c0095a3fc6cdd3552c870b1ade1ff8bae18e3fc | Shell | 2,730 | 92 | #!/bin/bash
#$ -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 ... |
296b5106ba09c653d41fd81b15f50a6e9cb6af63694894b9a3fff6fe00953d99 | Shell | 2,744 | 80 | #!/bin/bash
exe_name=$0
exe_dir=`dirname "$0"`
# If MCR R2023a is installed in a non-default location, define correct path
# on next line and uncomment it (remove the leading "#")
#BrainSuiteMCR="/path/to/your/MCR";
if [ -z "$BrainSuiteMCR" ]; then
if [ -e /usr/local/MATLAB/MATLAB_Runtime/R2023a ]; then
Brain... |
c8f5517f8c1b2240fdb50a43ba6c726fcdaba864a9cf9c8613b287d182075614 | Shell | 2,757 | 94 | #!/usr/bin/env bash
set -eux
torch_version=$(unzip -p torch-* '**/METADATA' | grep '^Version: ' | cut -d' ' -f2)
nightly=$(echo ${torch_version} | cut -d'.' -f4)
# Copied from .ci/wheel/linux/build_common.sh
make_wheel_record() {
fpath=$1
if echo $fpath | grep RECORD >/dev/null 2>&1; then
echo "$fpath,,"
e... |
cb702589a3c9abbdb637e11de2b32c85f4d066003ddf4530ccf5f9ebb8dd95b2 | Shell | 2,757 | 78 | #!/bin/bash
set -ex
source "$(dirname "${BASH_SOURCE[0]}")/common_utils.sh"
function install_huggingface() {
pip_install -r huggingface-requirements.txt
}
function install_timm() {
local commit
commit=$(get_pinned_commit timm)
pip_install --no-deps "git+https://github.com/huggingface/pytorch-image-models@$... |
abafa48462653d6bcad4b459d2bba4e88129144469dc8181e16a3c9e3791d839 | Shell | 2,777 | 65 | #!/bin/sh
# A row must invert the same way wherever it appears.
#
# The adaptive grid is refined around the measurement it is built for, so a
# grid built for one row is the wrong grid for the next. It used to be built
# once per file and reused for every row after, which made the answer for a
# given wavelength depe... |
3be9b8841d7a41b094643d931c4194cc23bd3f66d28547d9edb72a7e7587c516 | Shell | 2,794 | 89 | #!/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 ... |
d3f31cbd081abbd84e9255c63b9dc584be260e0c5d27316d3ce4ef153f1fd56f | Shell | 2,850 | 78 | #!/usr/bin/env bash
# =============================================================================
# run_nnunet_eval.sh
# nnUNet inference + TTA post-processing for IC-UNet (Dataset100)
#
# Usage:
# bash run_nnunet_eval.sh
#
# Configure the variables below before running.
# Requires nnUNet to be installed and the fo... |
5efe892ee3b61de6193dfce265fac054b71fa654ead74a889e3861803cddea24 | Shell | 2,863 | 108 | # !/bin/bash
# set data directories
dataDir=/media/yuhui/LCT
cd ${dataDir}
for patDir in subj_folder; do
{
top_dir=${dataDir}/${patDir}
# task run
for filePre in bold; do
{
cd $top_dir/Func
sl_dsets=($(ls -f ${filePre}*.nii*))
run_num=${#sl_dsets[@]}
echo "*************** extract bold images, skip ... |
71cb575f67f78c9a69b5ee5d9ba81825f526ab5b6b7d6805070dda7c2d8f860d | Shell | 2,864 | 43 | # For internal testing. Just to check whether programs execute.
..\LN2_LAYER_SMOOTH -input sc_VASO_act.nii.gz -layer_file sc_layers.nii.gz -FWHM 1
..\LN_LAYER_SMOOTH -input sc_VASO_act.nii.gz -layer_file sc_layers.nii.gz -FWHM 0.3 -NoKissing
..\LN_BOCO -Nulled lo_Nulled_intemp.nii.gz -BOLD lo_BOLD_intemp.nii.gz -tria... |
681871018c8bc8a2f341e88d892f19b6e60c003783b1d0f62beeb41e9992022f | Shell | 2,868 | 97 | #!/bin/sh
###
# compare current branch with origin develop branch and list the changed files
###
curr_branch=$(git rev-parse --abbrev-ref HEAD)
files_to_be_checked=($(git diff --name-status $curr_branch..upstream/develop | awk '{ print $2 }'))
###
# define files to be checked
###
EXTENSIONS_TO_CHECK=("m" "sh" "csh")
... |
aa829e9c49dd4f466faf5380af9f02beaf540d139b69613ecf789044a3e9bd2e | Shell | 2,869 | 77 | #!/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... |
5f30ce8d088a8245bedee44c644b62c8a6865b6b8d0bb799f262ac7f9001c71e | Shell | 2,871 | 97 | #!/bin/bash
#PBS -N deeph_band
#PBS -l nodes=1:ppn=24
#PBS -l Qlist=n24
# calculate bands from band_i to band_f
# submit num_tasks tasks simultaneously
# place under same directory with hamiltonians_pred.h5, overlaps.h5
# == basic information ==
fermi_level=-3.9143371779349274
lowest_band=-3.1
num_band=100
band_i=1 #... |
423aae510cf33f8ca19b089c49b2132960576d7d3da04567ce8f15b7fa3d8c57 | Shell | 2,875 | 44 | #! /bin/bash
# For internal testing. Just to check whether programs execute.
../LN2_LAYER_SMOOTH -input sc_VASO_act.nii.gz -layer_file sc_layers.nii.gz -FWHM 1
../LN_LAYER_SMOOTH -input sc_VASO_act.nii.gz -layer_file sc_layers.nii.gz -FWHM 0.3 -NoKissing
../LN_BOCO -Nulled lo_Nulled_intemp.nii.gz -BOLD lo_BOLD_intemp... |
c465905796d75f8f485acf4f0febe72a689717fc297af3e06538c72dc308ab65 | Shell | 2,886 | 94 | #!/bin/bash
# Exit on errors
set -e
# ==========================================================
# Environment Setup
# ==========================================================
# Override CONDA_SH / CONDA_ENV if your conda lives elsewhere.
CONDA_SH="${CONDA_SH:-$HOME/miniconda3/etc/profile.d/conda.sh}"
CONDA_ENV="${... |
1991607967674224c2408c4d7a285380cc41d2b3f76b71e27aab5d9dd04341ae | Shell | 2,887 | 94 | #!/bin/bash
# Exit on errors
set -e
# ==========================================================
# Environment Setup
# ==========================================================
# Override CONDA_SH / CONDA_ENV if your conda lives elsewhere.
CONDA_SH="${CONDA_SH:-$HOME/miniconda3/etc/profile.d/conda.sh}"
CONDA_ENV="${... |
0d68b2daa1df60a9dbd91faf8bce4a2a9ef380b89f4087d78c13f9b5123e82f9 | Shell | 2,907 | 94 | #!/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 ... |
275af56163e7b37d4653b04476cb575898ef0e9ecbd559c1f74832e1ba6b59d0 | Shell | 2,908 | 94 | #!/bin/bash
# Exit on errors
set -e
# ==========================================================
# Environment Setup
# ==========================================================
# Override CONDA_SH / CONDA_ENV if your conda lives elsewhere.
CONDA_SH="${CONDA_SH:-$HOME/miniconda3/etc/profile.d/conda.sh}"
CONDA_ENV="${... |
bba8d230bcf060485906155d5da37407a490e01f42d30f11829c417bc1e01a48 | Shell | 2,908 | 48 | #!/bin/bash -l
#SBATCH --job-name=eval_model
#SBATCH --output=outLogs/sim_human_threshold_exmpt_v02_control_archs_%A_%a.out
#SBATCH --error=outLogs/sim_human_threshold_exmpt_v02_control_archs_%A_%a.err
#SBATCH --mem=8Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=1:15:00
#SBATCH --partition=use-everything
#SBATCH --gres=g... |
a5e012fff6ba13762dea5865081710283c26ba61f74fa1c2d68ded72ceeb68da | Shell | 2,918 | 133 | #!/usr/bin/env bash
date
echo "Step 2 mapping reads to a genome, and deduplicate with umi-tools, and spliting bams by strand"
# note of paired-end reads
# TRUE -- paired-end reads
# FALSE -- single-end reads
pair=FALSE
# the filename of your R1.fq.gz
inrawR1="YourInputRawFileR1.fq.gz"
if [ "${pair}" == FALSE ]; then... |
32abc1f595547596be960e03449a580b6267a6237488f61a5771fec811665317 | Shell | 2,940 | 66 | #!/bin/bash
# Required environment variables:
# $BUILD_ENVIRONMENT (should be set by your Docker image)
if [[ "$BUILD_ENVIRONMENT" != *win-* ]]; then
# Save the absolute path in case later we chdir (as occurs in the gpu perf test)
script_dir="$( cd "$(dirname "${BASH_SOURCE[0]}")" || exit ; pwd -P )"
if... |
dcf1c01301408c0302d5f7e655857299a697a873ab318d942afcfa0097d1d0b3 | Shell | 2,952 | 104 | #!/bin/sh
. "$(dirname "$0")/lib.sh"
announce "iad file workflow cases"
copy_fixture() {
src=$1
dest=$2
cp "$ROOT_DIR/tests/rxt/$src" "$TEST_TMP/$dest"
}
run_file_case() {
input=$1
output=$2
shift 2
"$IAD_EXECUTABLE" -M 0 -q 4 "$@" "$input" > "$TEST_TMP/file_case.out" 2>&1 || {
c... |
505f9e73689df841bdcdd3f4ed302355d07b2ba90ed95f76dbfe3236457dcc89 | Shell | 3,014 | 62 | #!/bin/bash
#Copyright 2025. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( 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... |
773f3e83e3f9817036843c1cc6e932723d6406e3d71232da6ff63ce59bcb6b74 | Shell | 3,018 | 101 | #!/bin/bash
#
# Train ESM-C 600M for Synapse Protein Localization (A2 Weighted Loss)
#
# This script fine-tunes the ESM-C 600M protein language model for predicting
# protein localization to 6 cellular compartments, with special focus on
# synapse prediction using weighted BCE loss.
#
# Requirements:
# - GPU with 40G... |
1e531a0c794334cde78cc16baa8ff4891520a78bdf2517502e80b64d21f3147c | Shell | 3,024 | 63 | #!/usr/bin/env bash
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
NUM_PROC=22
LOGDIR="./eval_logs"
mkdir -p "$LOGDIR"
echo "[$(date)] Running TESTING only on CPU with $NUM_PROC threads..."
run_eval () {
local tag=$1; shift
echo "[$(date)] Starting $tag"
stdbuf -o0 -e0 dglke_eval "$@" 2>&1 | tee "${LOGDI... |
ff10b2f458335b36be3c8a3c5ee4a734aff690b2f185418681239d2ecf742948 | Shell | 3,024 | 79 | #!/bin/sh
#
#this script compiles the code necessary to read neuralynx files from matlab.
#
# the first few lines are parameters that need to be adjusted (see README file).
#
#Version 12/05/11 urut/MPI
#updated 12/07/15 urut/Caltech
#
#== Should it compile for 32 or 64 bit matlab and which platform
PLATFORM="64PC" ... |
0e192b8e65e73a295f7c18f12e9d62f0d123a5b555e91108bc874b1e096775ca | Shell | 3,028 | 75 | #!/bin/bash
# exit when any command fails
set -e
# keep track of the last executed command
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
GPU=${1-0}
#create directory structure for workflow
data_dir=data
mkdir -p $data_dir
output_dir=outputs
mkdir -p $output_dir
output_data=$output_dir/d... |
1195944b4b5cfc1f4725f90dd70f80f663dde8e427fc6237d6c5e2934cf49615 | Shell | 3,028 | 94 | #!/bin/bash
#$ -S /bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id: ashs_atlas_loo_qsub.sh 86 2012-04-24 17:23:00Z yushkevich $
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkev... |
4d742c3b4f6a05f91ddbbdbd16040d121a53f4ffec6b44bea061fafccd87cb4b | Shell | 3,070 | 146 | #!/usr/bin/env bash
date
echo "Step 1 trimming adapters and filtering reads mapped to rRNA"
###
##
# note of paired-end reads
# TRUE -- paired-end reads
# FALSE -- single-end reads
pair=FALSE
# the filename of your R1.fq.gz
inrawR1="YourInputRawFileR1.fq.gz"
if [ "${pair}" == FALSE ]; then
echo "Single-end"
inra... |
0e3bb0c066f84a7ea1bdf78f9f95a6bb981cb2c0a880da707a75b5e003aa2eca | Shell | 3,120 | 83 | #!/bin/bash
# set data directories
top_dir=/media/yuhui/LCT
cd ${top_dir}
for patDir in subj_folder/mt.sft; do
{
sumaDir=${top_dir}/${patDir}/SUMA
cd ${sumaDir}
3dcalc -a aparc+aseg_REN_gm.nii.gz -expr "step(a-45)*1000" \
-prefix gm_boosted.nii.gz -overwrite
3dcalc -a aparc+aseg_REN_wmat.nii.gz -expr "amongs... |
3d5f8a90ab89cd82630532f4b610db1a85e4999f47d030ae36020a69812e84a7 | Shell | 3,122 | 95 | #!/bin/bash
#SBATCH --job-name=Stage1
#SBATCH --partition=su_lab,encore
#SBATCH --time=24:00:00
#SBATCH --mem-per-cpu=1G
#SBATCH -o outs/Stage1-%A_%a.out
#SBATCH --array 0-330
ct='Bulk'
model_hidden_batch=FALSE
match_suffix=FALSE
if [[ "$model_hidden_batch" == "TRUE" ]]; then
QCOVAR_suffix='_with_hidden_batch'
el... |
f9b899bd877ffc0f06411087aeaf25af55557565244a443d0f809a61dace0a73 | Shell | 3,136 | 83 | #!/bin/sh
#
# MS-DAP launch script
# https://github.com/ftwkoopmans/msdap
VERSION="1.2.3"
### OS
ISMACOS=$(uname -s | grep -i "darwin")
## if macOS
if [ ! -z "$ISMACOS" ]; then
echo "macOS"
command -v docker >/dev/null 2>&1 || { echo >&2 "ERROR: Docker is not installed"; exit 1; }
## Open Docker if, and only... |
1bdf6987c0534079025e5c0850d02bed0bb0b023dd496a019cfa7200d2a25397 | Shell | 3,150 | 80 | #!/bin/bash
# Exit on errors
set -e
# ==========================================================
# Configurations & Paths (Relative paths preferred)
# ==========================================================
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$SCRIPT_DIR"
CONDA_BASE="${CONDA_BASE:-$HOME... |
53af177bb3ee987d27aa888e8bc3bfc9ec92c8c3b500cf3147fd68c46d42c893 | Shell | 3,181 | 95 | #!/bin/bash
# Required arguments
filename=false
destination=false
freesurfer_license=false
script_name=$(basename "$0")
usage_string="Usage: bash $script_name --filename <filename> --destination <destination> --template <MNI152_T1_brain template from FSL> [--help]"
# Parses arguments
while [[ "$#" -gt 0 ]]; do
c... |
de6b8f50b061b0f45e585e864e33a713676373a0ba327238b0302c4fcbafa7e5 | Shell | 3,210 | 42 | #!/bin/zsh
Rscript 08.DNNs/06c.tune_int_cv.R --fold 1 --model 1 > logs/tune_int_1_1.log &
Rscript 08.DNNs/06c.tune_int_cv.R --fold 2 --model 1 > logs/tune_int_1_2.log &
Rscript 08.DNNs/06c.tune_int_cv.R --fold 3 --model 1 > logs/tune_int_1_3.log &
Rscript 08.DNNs/06c.tune_int_cv.R --fold 4 --model 1 > logs/tune_in... |
dfa799c200b695d70eb65c81a323cbb497c5224d616fd1c3ddc1afae3bb62d78 | Shell | 3,218 | 127 | #!/bin/bash
#######################################################################
#
# Program: ASHS (Automatic Segmentation of Hippocampal Subfields)
# Module: $Id: ashs_atlas_initdir_qsub.sh 81 2012-04-20 14:34:50Z yushkevich $
# Language: BASH Shell Script
# Copyright (c) 2012 Paul A. Yushkevich, Univers... |
a9cf4b08b2b7f6f561b5e2a01c501c42311d357613ef8b81d173a925a0766d5a | Shell | 3,221 | 73 | #!/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... |
832f58b6b0d7301b1efaf94f3dc04ece25085be9e58ae262d9a889d7861e1fd3 | Shell | 3,233 | 53 | module load miniconda
conda activate mixer_env
MIXER_DIR="/home/yd357/pi_paths/pi_alag/env/mixer"
OUTPUT_DIR="/home/yd357/pi_paths/pi_alag/Tools/MiXeR/data"
PARA_DIR="/home/yd357/pi_paths/pi_alag/Tools/MiXeR/codes/9.16/Step3_bivar"
# Read parameters from the job_params.txt, including step1 and step2
IFS=',' read -r... |
2d6e4aad6c5afe0f1b6c4c81ad81313fa1ceb1056f5b3aba34d081982a7e714e | Shell | 3,301 | 85 | #!/bin/bash
# find all available protein sequences in ./data/evo/00proseqs
# and align them using MUSCLE
# store the aligned sequences to ./data/evo/01proseqs_align
# link muscle command to local executable
muscle=/home/ceballos/muscle-linux-x86.v5.2
# create folder ./data/evo/01proseqs_align if not already created
... |
7e07bdc44a2522d54545ad2c838c2e58dcaf114384f368fb180d147ed1d59cb6 | Shell | 3,322 | 98 | #!/bin/bash
exe_name=$0
exe_dir=`dirname "$0"`
# If MCR R2023a is installed in a non-default location, define correct path
# on next line and uncomment it (remove the leading "#")
#BrainSuiteMCR="/path/to/your/MCR";
if [ -z "$BrainSuiteMCR" ]; then
if [ -e /usr/local/MATLAB/MATLAB_Runtime/R2023a ]; then
Brain... |
0a878431fcde85de77accfbda63aa0391a40bfa0872487bbaa4454beb8b7f6c4 | Shell | 3,324 | 101 | #!/bin/bash
set -x
if [ -z "$1" ]; then
echo "Need wheel location argument" && exit 1
fi
WHEELHOUSE_DIR=$1
PATCHELF_BIN=patchelf
ROCM_LIB=backends/amd/lib
ROCM_LD=backends/amd/llvm/bin
PREFIX=triton
fname_without_so_number() {
LINKNAME=$(echo $1 | sed -e 's/\.so.*/.so/g')
echo "$LINKNAME"
}
replace_neede... |
993069dddad3e5608a933bfc165fa507a14c3196c2f0de33d20be2dc57777527 | Shell | 3,328 | 113 | #!/usr/bin/env bash
if [ x$BASH = x ] || [ ! $BASH_VERSINFO ] || [ $BASH_VERSINFO -lt 4 ]; then
echo "Error: Must use bash version 4+." >&2
exit 1
fi
set -ue -o pipefail
TagLenDefault=12
InvariantDefault=5
Usage="Usage: \$ $(basename $0) [-t tag_len] [-i invariant_len] reads_1.fq reads_2.fq > families.tsv
Read raw... |
b6b3ca2bf7dd77b2694e95ff8f4786a02bb63de2fbae493f070a8ab05647bfea | Shell | 3,351 | 93 | #!/bin/bash
#
# Run Cytocraft Segmentation Leakage Robustness Analysis
# This script addresses Reviewer Comment 2 regarding robustness to systematic biological noise
#
# Multi-Cell-Type Tissue Model:
# - Multiple cell types with DIFFERENT chromosome structures (e.g., epithelial,
# fibroblast, immune cells each with ... |
93e61bd06b215a84a54dfb89f6722e2ceccdf50c81d7bcded612696dc807fe71 | Shell | 3,391 | 99 | #!/bin/sh
# Round trip through every slide configuration. For each one, -z computes
# R, T and unscattered T from known optical properties, and those three
# numbers are fed straight back into the inverse. The inverse must recover
# what we started with.
#
# Sample: a=0.8, b=5, g=0.9, index 1.5, 1 mm thick, so
# ... |
b1517b843614fad665a8fa4ea807ae6ef85a41b6bd4b03739874e9b6367113a2 | Shell | 3,400 | 70 | #! /bin/bash
WX_CONFIG=/Users/cs/wxbin/bin/wx-config
# WXPY_DIR=/Users/cs/wxPython-src-2.9.1.1/wxPython
# WXPY_VER=wx-2.9.1-osx_cocoa
# WXPY_INSTALL_DIR=/Users/cs/wxPython-2.9/dummy-install/lib/python2.5/site-packages
mkdir -p stimfit.app
mkdir -p stimfit.app/Contents
mkdir -p stimfit.app/Contents/Frameworks
mkdir -p... |
62596bf58b3e1f99d487b65253d8970a86403bde5b76701827832606e9076a17 | Shell | 3,430 | 144 | #!/usr/bin/env bash
if [ "x$BASH" = x ] || [ ! "$BASH_VERSINFO" ] || [ "$BASH_VERSINFO" -lt 4 ]; then
echo "Error: Must use bash version 4+." >&2
exit 1
fi
set -ue
unset CDPATH
TestDir=$(dirname $(readlink -f ${BASH_SOURCE[0]}))
DunovoDir=$(dirname "$TestDir")
BfxDir="$(dirname "$DunovoDir")/nick-bfx"
RefName="ove... |
9f4234176d238f71423107eb7e1a34da2ab6a2f58196b8f3cbc31b67b06a5e31 | Shell | 3,518 | 102 | #!/bin/bash
set -ex
# Optionally install conda
if [ -n "$ANACONDA_PYTHON_VERSION" ]; then
BASE_URL="https://github.com/conda-forge/miniforge/releases/latest/download" # @lint-ignore
CONDA_FILE="Miniforge3-Linux-$(uname -m).sh"
MAJOR_PYTHON_VERSION=$(echo "$ANACONDA_PYTHON_VERSION" | cut -d . -f 1)
MINOR_PYT... |
34b9d6bf1b7df3c7b9c0bb2c88ce1e13b396b5607224a7172ba52e7d217c8458 | Shell | 3,546 | 79 | #!/bin/bash
# this script creates reference reconstructed datasets for integration testing
# Reference container full name
ref_container=fil-physicsc-V15.9_bkd_rc1
# list of user parameter maps and stylesheets
epi_xml=/hostshare/Gadgetron_XML/IsmrmrdParameterMap_Siemens.xml
epi_xsl=/hostshare/Gadgetron_XML/IsmrmrdPar... |
e351e7396476a2bdaa060746f193b268a61f68eef2d2987f474567d0f81abcdf | Shell | 3,570 | 112 | #!/bin/bash
#$ -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 ... |
9eed3fcd3bdde7860b682a21e2f3be0fa3f2f61515803e3cb35cb38ecdeed41a | Shell | 3,586 | 132 | #!/usr/bin/env bash
# shellcheck disable=SC2231
set -euo pipefail
PACKAGE_TYPE=${PACKAGE_TYPE:-wheel}
PKG_DIR=${PKG_DIR:-/tmp/workspace/final_pkgs}
# Designates whether to submit as a release candidate or a nightly build
# Value should be `test` when uploading release candidates
# currently set within `designate_upl... |
404dbf9c05db34b865da19be2332b5627ec15a7f87c27494e59897c4fb33e512 | Shell | 3,606 | 87 | #!/bin/sh
# recon-all for anatomical mt run
dataDIR=/media/yuhui/LCT # replace with your own data directory
batchDir=/media/yuhui/LCT/Batch # where the reconall.expert100 is located
cd ${dataDIR}
for patID in subj_folder/mt.sft; do
{
echo "***************************** start with ${patID} *********************"
p... |
a3a00a567b746a283f73a3e629fb0ae458353da63663dbb920fb6aff1f49a4a5 | Shell | 3,757 | 120 | #!/bin/bash
# Script used only in CD pipeline
set -uex -o pipefail
PYTHON_DOWNLOAD_URL=https://www.python.org/ftp/python
GET_PIP_URL=https://bootstrap.pypa.io/get-pip.py
# Python versions to be installed in /opt/$VERSION_NO
CPYTHON_VERSIONS=${CPYTHON_VERSIONS:-"3.10.1 3.11.0 3.12.0 3.13.0 3.14.0 3.14.0t 3.15.0 3.15.0... |
1a3049e28b5fddf2abbb1244379c53db16a658f75640281eea11925514b94002 | Shell | 3,764 | 83 | #!/usr/bin/env bash
set -ex
SCRIPTPATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
PYTORCH_ROOT="${PYTORCH_ROOT:-$(cd "${SCRIPTPATH}/../../.." && pwd)}"
case "${GPU_ARCH_TYPE:-BLANK}" in
cuda|cuda-aarch64|cpu|cpu-aarch64|cpu-riscv64|cpu-cxx11-abi|xpu|rocm)
# New pipeline: pyprojec... |
ea96aaab54f565ceb639c8134593799e88b028c5d4bb239910b37ff2ff4c203d | Shell | 3,790 | 122 | #!/bin/bash
# This is where the local pytorch install in the docker image is located
pt_checkout="${GITHUB_WORKSPACE:-/var/lib/jenkins/workspace}"
# Since we're cat-ing this file, we need to escape all $'s
echo "cpp_doc_push_script.sh: Invoked with $*"
# for statements like ${1:-${DOCS_INSTALL_PATH:-docs/}}
# the or... |
2926cb6dc37fae14fe7f0e3229aa2049cb835de2bc1068025ac4f03dceee3df3 | Shell | 3,804 | 97 | #!/usr/bin/env bash
# Run from repo root with the virtualenv activated:
# source .venv/bin/activate && bash tests.sh
set -uo pipefail
IDAT_REF="cache/207513420108_R01C01_Grn.idat"
IDAT_MIX="cache/207513420108_R02C01_Grn.idat"
TMPDIR_TEST="$(mktemp -d)"
trap 'rm -rf "$TMPDIR_TEST"' EXIT
PASS=0
FAIL=0
pass() { echo... |
9706e2ab25e5ce97353188ce71d4ad6c3839a17c161e0ad3988f7e065de26ccb | Shell | 3,830 | 109 | #!/bin/bash
set -ex
mkdir -p /opt/triton
if [ -z "${TRITON}" ] && [ -z "${TRITON_CPU}" ]; then
echo "TRITON and TRITON_CPU are not set. Exiting..."
exit 0
fi
source "$(dirname "${BASH_SOURCE[0]}")/common_utils.sh"
get_pip_version() {
env_run pip list | grep -w $* | head -n 1 | awk '{print $2}'
}
if [ -n "${X... |
b5c5f486cf43ab7b5d34ff08839531d3c6d51a9726e364a52801be49c81bb547 | Shell | 3,911 | 112 | #!/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 ... |
da2ab363855690edf32c817aeb073787fb7c93cf2157e315fee1cf3e668b10b5 | Shell | 3,919 | 87 | #!/bin/bash
# this script creates reference reconstructed datasets for integration testing
# Reference container full name
ref_container=fil-physicsc-V15.9_bkd_rc1
# list of user parameter maps and stylesheets
epi_xml=/hostshare/Gadgetron_XML/IsmrmrdParameterMap_Siemens.xml
epi_xsl=/hostshare/Gadgetron_XML/IsmrmrdPar... |
bf2012276167509aa793ed2a24db1cd00656c82d98ba73076cf1f33bfa59bc7e | Shell | 3,964 | 109 | #!/bin/bash
trap 'exit 0' EXIT
# Claude Code stops the agent loop when a PostToolBatch hook exits 2, which is also what bash
# returns on a syntax error, so the trap must stay the first command.
export LC_ALL=C
MARKER="Time check"
MIN_BUDGET_MIN=25
# The CLI session starts 31-56 s after the job starts, and the job t... |
d9aa4d4ed5a05b5d308ae14118372662dda35cefe9af15cfce46954b69790ae5 | Shell | 4,038 | 111 | #!/bin/bash
# shellcheck disable=SC1091,SC2012,SC2154
OUTPUT_SCRIPT=${OUTPUT_SCRIPT:-/home/circleci/project/ci_test_script.sh}
# only source if file exists
if [[ -f /home/circleci/project/env ]]; then
source /home/circleci/project/env
fi
cat >"${OUTPUT_SCRIPT}" <<EOL
# =================== The following code will be... |
05848138090565800c1a209c4b46ada29d3ab96867c8b81721667eb5b5023386 | Shell | 4,040 | 102 | #!/bin/bash
#v0.1 Feb 21st 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... |
1666b992aac9aa87ee8144fb05dc0fd63e21ebc6dcbd64f942d4e42d0d463dff | Shell | 4,055 | 115 | #!/bin/sh
dataDIR=/media/yuhui/LCT
cd ${dataDIR}
for patID in subj*; do
{
patDir=${dataDIR}/${patID}
anatDIR=${dataDIR}/${patID}/mt.sft
funcDIR=${dataDIR}/${patID}/bold.sft
sumaDir=${dataDIR}/${patID}/mt.sft/SUMA
cd ${dataDIR}
for hemi in lh rh; do
{
cd ${dataDIR}
SUBJECTS_DIR=${dataDIR}
## PALS_B12... |
617ee059c09770fb137c1dcaee41679aa1a8d262ccdb258dd03ef63c25dcbfba | Shell | 4,072 | 106 | #!/bin/bash
set -ex
install_ubuntu() {
apt-get update
# kmod is used by GPU diagnostics; libc++ lets torch._C load at runtime.
apt-get install -y --no-install-recommends kmod libc++1 libc++abi1
# FIXME: Needed for rocSHMEM in ROCm7.14 since it had a dependency on libnuma.so
apt-get install -y libn... |
95f28b331f77b269b9986ce78b55c700633bcd1698daddc4190d904ce4d5cc04 | Shell | 4,103 | 95 | #!/bin/bash
group=$1
cicero_dir='/cluster/share/atac_group/mafas5/chen_ws/ASC/cicero'
input_dir='/cluster/share/atac_group/mafas5/chen_ws/ASC/cicero'
peakannot_file='/cluster/share/atac_group/mafas5/chen_ws/CREs/mba.whole.sa2.peakOvlpTSS.proximal.distal.ciceroPeakCoord.bed'
fitConn_file="${input_dir}/${group}-fitConn... |
67cf326a298698918ab782d66543d211833497a43f1a83315d6ab0f293ae3afb | Shell | 4,193 | 75 | #!/bin/bash
# Required environment variable: $BUILD_ENVIRONMENT
# (This is set by default in the Docker images we build, so you don't
# need to set it yourself.
# shellcheck source=./common.sh
source "$(dirname "${BASH_SOURCE[0]}")/common.sh"
echo "Testing pytorch"
# When adding more tests, please use HUD to see whi... |
a3ae44bba668b56d0ca755b519f4a5f9c3ca4c855f48e395c450f6b139dccfa1 | Shell | 4,224 | 105 | #!/bin/bash
# Top-level build script called from Dockerfile
# Script used only in CD pipeline
# Stop at any error, show all commands
set -ex
# openssl version to build, with expected sha256 hash of .tar.gz
# archive
OPENSSL_ROOT=openssl-1.1.1l
OPENSSL_HASH=0b7a3e5e59c34827fe0c3a74b7ec8baef302b98fa80088d7f9153aa16fa76... |
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