sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
59681d1453de03b1423417cb1a542463422a871164d017984bd1c93aeb2544eb | Shell | 4,277 | 95 | #!/bin/sh
. "$(dirname "$0")/lib.sh"
mode=${1:-full}
ACTUAL_FILE=$(numeric_actual_file iad_basic)
: > "$ACTUAL_FILE"
announce "iad basic numeric cases ($mode)"
run_common_cases() {
run_iad_numeric r0 -V 0 -r 0
run_iad_numeric r1 -V 0 -r 1
run_iad_numeric r04 -V 0 -r 0.4
run_iad_numeric r04_t01 -V 0 ... |
b74cca5e169fc0824d8106d15f693afe578810161cc3c6b9ca3010f2da9572fc | Shell | 4,303 | 95 | #!/usr/bin/env bash
# Build a macOS arm64 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/set... |
aa0fac8d4c698dec70ac4bb574dd4da8268d5c165ad9856a9185504a1b4efabe | Shell | 4,363 | 122 | #!/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
ct=$1
model_hidden_batch=$2
if [[ "$model_hidden_batch" == "TRUE" ]]; then
QCOVAR_suffix='_with_hidden_batch'
else
QCOVAR_suffix=''
fi
if [[ "$match_suffix... |
1ed506402d84b56d2c507173768349ec44e838608b2a650583a2fc721dd5194d | Shell | 4,368 | 166 | #!/bin/bash
set -euo pipefail
# Configure, build, and install Stimfit on macOS using CMake,
# including production of a macOS .app bundle.
#
# Usage:
# ./build_macos_cmake.sh
# ./build_macos_cmake.sh --with-python
# ./build_macos_cmake.sh --without-python
# ./build_macos_cmake.sh --with-python --install-prefix... |
2cdbdaa6c544119ed8bbd0cd83eebf0ed7f232013a1a1be17e7ec1c17cfdb0d8 | Shell | 4,382 | 215 | #!/bin/bash
VERSION="0.0.1"
function Usage {
cat <<USAGE
Usage:
`basename $0` [-h] [-r] [-j nb_jobs] command arg_list
Optional arguments:
-h: Shows help
-r: Replace asterix * in the command string with argument
-j: Number of cpu cores to use (default 2)
Examples:
`basename $0` somec... |
1dda873b854dbf5b10c8ade7db5de7b51d3c8c232cb0348258ac15c48b23ce2e | Shell | 4,385 | 112 | #! /bin/bash
# Written by Wei Hou Tan and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
echo "Executing this script will install Python packages used by CBIG."
read -p "Are you sure? (y/n) " answer
if echo "$answer" | grep -iq "^y"; then
# store current directory
WORKDIR... |
ca32f388dd02b2fe5f0f6d5b1f7762f0d60e3ca76e291ec6a8f6e0c82889757a | Shell | 4,438 | 156 | #!/bin/bash
#v0.2.1 July 28th 2015
#Arash Nazeri and Jon Pipitone, 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, Campbell Family Men... |
de6b5789779f69d00636ce61e18b6fef186f10d064719f4029c60a4b6e5fa432 | Shell | 4,459 | 72 | #!/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
# echo an error message before exiting
trap 'echo "\"${last_command}\" command filed with exit code $?."' EXIT
# DNASE is SE data
# ATAC is PE
dnase_in_b... |
b3fef85aa92274ffd64407ba6c0af062ea6d38aad6623d527a2041d7fb4c3021 | Shell | 4,492 | 132 | #!/bin/bash
# Exit on errors
set -e
# ==========================================================
# Configurations & Paths (Relative paths preferred)
# ==========================================================
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$SCRIPT_DIR"
# Conda python binaries
CONDA_B... |
3c2fe2d125ae58d041f14ddd59b651447c78123f74c98575bdb2288476b9438a | Shell | 4,534 | 125 | #!/usr/bin/env bash
# Script used only in CD pipeline
set -exou pipefail
TOPDIR=$(git rev-parse --show-toplevel)
image="$1"
shift
if [ -z "${image}" ]; then
echo "Usage: $0 IMAGE:ARCHTAG"
exit 1
fi
# Go from imagename:tag to tag
DOCKER_TAG_PREFIX=$(echo "${image}" | awk -F':' '{print $2}')
GPU_ARCH_VERSION=""... |
fc416a2d17169911ca1abc077d4e500aa1c235ec1447db2b8ad5cdeb15be174f | Shell | 4,569 | 142 | #!/bin/bash
#$ -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 ... |
e0a75b63b66f50e5998ddbe7df422bbbc789810c2f444c355b2531173a4efbad | Shell | 4,590 | 136 | #!/bin/bash
# Exit on errors
set -e
# ==========================================================
# Help documentation
# ==========================================================
show_help() {
echo "Usage: ./run_pipeline.sh [options]"
echo ""
echo "Options:"
echo " -s, --step <steps> Comma-separa... |
5efd2bd357380ed4779f56127ee6c57de8daadfeb8e31ca61bcd884f724beba3 | Shell | 4,630 | 156 | #!/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
Usage="Usage: \$ $(basename "$0") [options] command [command args]
Measure the resources used by a command and all of its children.
Prints 8 tab-delimi... |
31186badb5dba01f76d7ae44233b50c2ea81139ffc0dca04df4ddd37d295838f | Shell | 4,633 | 143 | #!/bin/bash
# exit when any command fails
set -e
# keep track of the last executed command
trap 'last_command=$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... |
0e2223ca30d18bb0d2edd43d1e915de69952fb6e17b6bb50816060f93c7ac98d | Shell | 4,665 | 154 | #!/bin/bash
#v 0.1 March 10th 2016
#Arash Nazeri, Kimel Family Translational Imaging-Genetics Research Lab
#This script depends on FSL v4.1.9 (or higher)
#
#Developed at Kimel Family Translational Imaging Genetics Ressearch
#Laboratory (TIGR), Research Imaging Centre, Campbell Family Mental
#Health Institute,Centre for... |
e7c27981215e5e0349dd7451313ea9fef0ba7b516154cfb5ee294f3da0b9179b | Shell | 4,681 | 108 | #!/bin/bash
## This is an adaptation of the 1000 Connectome script written by Xi-Nian Zuo, Maarten Mennes & Michael Milham.
## For more information see www.nitrc.org/projects/fcon_1000
set -e
trap 'echo "$0 : An ERROR has occured."' ERR
Usage() {
echo ""
echo "Usage: `basename $0` <ALFF-out> <bold4D-in> <ma... |
5d7779fbdfa98caf50b11ae746213095f395459b769a24a57bef27ef1432c33e | Shell | 4,723 | 120 | #!/bin/sh
# The Monte Carlo lost-light calculation must treat the two slides
# separately. It used to read only the top-slide parameters and apply them
# to both faces, so a slide on the bottom was either duplicated or lost
# entirely. These are relationships between runs rather than frozen numbers,
# since the Mont... |
2e59e46423a550164383f34c8d32567edb92bdfa24aa27ae488f35353b9bfe44 | Shell | 4,773 | 153 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : fifo_mean.sh
# Simulator : Aldec Riviera-PRO Simulator
# Description : Simulation script for compiling, elaborating and verifying the project sourc... |
86a7f7af0bcf95a12f485c5ace19aabe637fe75562b366256d8faa062756cf96 | Shell | 4,776 | 153 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : fifo_mean.sh
# Simulator : Aldec Active-HDL Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source... |
06c258a52d124496d7e2743b218c1a41cea3a4b153e69e782be8d2a9a03385c4 | Shell | 4,786 | 153 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : mult_gen_0.sh
# Simulator : Aldec Riviera-PRO Simulator
# Description : Simulation script for compiling, elaborating and verifying the project sour... |
aa47cfaced4f3a51224a684c6c4efb51339c33206fe5e68a46a8155dd7d074e8 | Shell | 4,789 | 153 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : mult_gen_0.sh
# Simulator : Aldec Active-HDL Simulator
# Description : Simulation script for compiling, elaborating and verifying the project sourc... |
f1912decbcf90a101de5cb8d2d119931544bd4378a9a313181e0b50e84414ae7 | Shell | 4,797 | 112 | #!/bin/bash
set -ex -o pipefail
PYTORCH_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)"
source "${PYTORCH_ROOT}/.ci/pytorch/common_utils.sh"
FLASH_ATTENTION_DIR="${PYTORCH_ROOT}/third_party/flash-attention"
FLASH_ATTENTION_HOPPER_DIR="${FLASH_ATTENTION_DIR}/hopper"
[[ -z "$FA_FINAL_PACKAGE_DIR" ]] && fat... |
5213fbc1fc9aaf85914e0e29bc480c54e46ddd5cc7bd86a2b2b46c9959d296bb | Shell | 4,837 | 198 | #!/bin/bash
set -euo pipefail
# Configure, build, install, and optionally package Stimfit on GNU/Linux using CMake.
#
# Usage:
# ./build_linux_cmake.sh
# ./build_linux_cmake.sh --without-python
# ./build_linux_cmake.sh --with-python --install-prefix build/linux-python/install
# ./build_linux_cmake.sh --install... |
6a267b58a1fc84d07c6ad4ed0aba2cf25f75e56203f2ca0c49d0674513b60390 | Shell | 4,869 | 167 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : fifo_mean.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the projec... |
9daf579f9ecfcca6fdfe1f47a58f4ffc54c2ff7c4be2abbba299d32ebf720e62 | Shell | 4,882 | 167 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : mult_gen_0.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the proje... |
84b03b75aaf5a7ed8984f1e381937e9fecafd3a6bb2f0c3cbf0f999e3650f2e8 | Shell | 4,911 | 176 | #!/bin/bash
#v 0.1 March 14th 2016
#Arash Nazeri, Kimel Family Translational Imaging-Genetics Research Lab
#This script depends on FSL v4.1.9 (or higher)
#
#Developed at Kimel Family Translational Imaging Genetics Ressearch
#Laboratory (TIGR), Research Imaging Centre, Campbell Family Mental
#Health Institute,Centre for... |
f4f8e298a47ac10deb04281abee043e7f6f32307a08d40daa9a84ac257725111 | Shell | 4,916 | 77 | #!/bin/bash
if [ -z "$1" ]; then
echo "BrainSuite v17a cortical surface extraction script"
echo "Authored by David W Shattuck (http://shattuck.bmap.ucla.edu)"
echo "UCLA Brain Mapping Center"
echo "for more information, please see: http://brainsuite.org"
echo "usage: $0 input_image"
echo " where input_imag... |
3517bc04521855e282923c52f6e49774d802527d7106d45ab7e71487fdf6818d | Shell | 4,962 | 89 | mm10ToHg38_CHAIN_FILE="/cluster/share/atac_group/PublishedData/liftover/mm10.hg38.all.chain.gz"
macFas5ToHg38_CHAIN_FILE="/cluster/share/atac_group/PublishedData/liftover/macFas5.hg38.all.chain.gz"
Hg38Tomm10_CHAIN_FILE="/cluster/share/atac_group/PublishedData/liftover/hg38ToMm10.over.chain.gz"
Hg38TomacFas5_CHAIN_F... |
4e5b037b0bcb34be3dee219f0af131fce842c68cda44f4396b3bf92d7897a883 | Shell | 4,965 | 128 | #!/bin/bash
set -ex
# Build sccache from source at v0.16.0 with the nvcc 13.3 dryrun-parsing fix
# backported from mozilla/sccache#2722 (see
# patches/sccache-nvcc-13.3-dryrun-parsing.patch). The prebuilt release binary
# mis-parses nvcc 13.3+ --dryrun output (it skips the device compile, leaving
# "fatbinary: Could ... |
c9af7390f398f79702842645f04e6a262867684cfa63dd5f0f915fb04df78eed | Shell | 4,993 | 156 | #!/bin/bash
# This is where the local pytorch install in the docker image is located
pt_checkout="${GITHUB_WORKSPACE:-/var/lib/jenkins/workspace}"
source "$pt_checkout/.ci/pytorch/common_utils.sh"
echo "python_doc_push_script.sh: Invoked with $*"
set -ex -o pipefail
# for statements like ${1:-${DOCS_INSTALL_PATH:-... |
a70723447310005504b377d98196f4e74a25f555cc320c2b493e30c11e4b97a4 | Shell | 5,026 | 174 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : fifo_mean.sh
# Simulator : Mentor Graphics Questa Advanced Simulator
# Description : Simulation script for compiling, elaborating and verifying the... |
e12bd3fdbb9efe3edf399fc547d7e8540a2b5e82b953c7456fb07b4990363a68 | Shell | 5,039 | 174 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : mult_gen_0.sh
# Simulator : Mentor Graphics Questa Advanced Simulator
# Description : Simulation script for compiling, elaborating and verifying th... |
994613d082d5b5411f683e170a8ee238853243692420101985518655f7a16735 | Shell | 5,079 | 110 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO FUNCTIONAL IMAGE Registration (FUNC to STD)
## Xi-Nian Zuo, Aug. 13, 2011; Revised at IPCAS, Feb. 12, 2013.
## Ting Xu 202204, BIDS format input
###########... |
26b62c6ce6c23db4f0ebb1b613cf3ed845948b2cde294f0b94260dfc0939d8b7 | Shell | 5,106 | 121 |
#!/usr/bin/env bash
# set -xe
# source ~/miniconda3/etc/profile.d/conda.sh
# conda activate dglke_env
export DGLBACKEND=pytorch
export PYTHONUNBUFFERED=1
# Dynamically detect CPU cores and use n - 1
TOTAL_CORES=$(nproc)
NUM_PROC=$((TOTAL_CORES - 15))
echo "[$(date)] Running TESTING only on CPU with $NUM_PROC threa... |
1a3b63e686132cba6b75ece4c1849e894b3ae31a8be5d7b9e1efbaa801f9ce54 | Shell | 5,142 | 180 | #! /bin/sh
# get the input file
file=$1
echo ""
echo "You are checking file: $file"
# check if the input file is a Matlab script
if [[ "`echo $file | cut -d '.' -f2`" != "m" ]]; then
echo "This file is not a Matlab script, quit."
exit 1;
fi
###############
# Move the comment block below the function name
#########... |
330ed7bf51497fde9dc05320e6d4220d32d5a953ef90a5cd1a6dd2ccbede1165 | Shell | 5,310 | 160 | #!/bin/bash
NUMPARAMS=$#
MAXITERATIONS=30x90x20
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... |
016af6692857797db6150e81bacc27d9c1cef3a84af4b8ae0b75b51e08d31af4 | Shell | 5,328 | 170 | #!/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 ... |
283842493d4b3e0eb8286684b4af4152d35107f2e14f832ee40581fbe38bc250 | Shell | 5,486 | 175 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : fifo_mean.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying the pro... |
4cfdee7825ca1305960dad28c8023de09fdad7a1fbdf9497abfb89196a05dcb7 | Shell | 5,490 | 118 | #!/bin/bash
# ROCm-specific utility functions shared across CI scripts
ROCM_UTILS_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
# Build rocm-composable-kernel (ck4inductor) wheel
# Usage: build_rocm_ck_wheel <output_dir>
build_rocm_ck_wheel() {
local raw_output_dir="${1:?build_rocm_ck_wheel: output directory ... |
f89632e0747aa96fe3de6224f0a65cc811e8ab7266ab3ca95ff065643b07c887 | Shell | 5,495 | 175 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : fifo_mean.sh
# Simulator : Cadence Xcelium Parallel Simulator
# Description : Simulation script for compiling, elaborating and verifying the projec... |
9e6047a11232f02e8a8695f452fa1d66dc47a074c3217c80240add86f5631c47 | Shell | 5,511 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : mult_gen_0.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying the pr... |
4d4ed318747713a4838306645ebdbcb8d3a9b520b8c64bed933ba5559a772cdc | Shell | 5,520 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : mult_gen_0.sh
# Simulator : Cadence Xcelium Parallel Simulator
# Description : Simulation script for compiling, elaborating and verifying the proje... |
9f8e7b1848e302c872b7e39f7600150939590e2b2a2f21ab00223284c51ff7a5 | Shell | 5,552 | 131 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO SEGMENTATION OF FUNCTIONAL SCAN
## Xi-Nian Zuo, Aug. 13, 2011; Revised at IPCAS, Feb. 12, 2013.
## Ting Xu, 202204, BIDS format input
######################... |
879ea0de7a06b1fd72743f4495be6af09f1b907eb82ac111a7e1d3c220a1a1e1 | Shell | 5,689 | 226 | #!/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
MaxParallelDefault=4
OldPathDefault=~/code/dunovo.old
NewPathDefault=~/code/dunovo.new
Usage="Usage: \$ $(basename "$0") [options] infile"
function ma... |
e2ad2e9f219112fcfa5b78a76b72825ed7c867af7107b0ed88f6bfc3f2702d87 | Shell | 5,836 | 141 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO SEGMENTATION OF ANTOMICAL SCAN (FREESURFER)
## Revised from Xi-Nian Zuo https://github.com/zuoxinian/CCS
## Ting Xu, BIDS format input
#####################... |
cb4db776fae359e0a94d8471bc2fd928e80df3885f8ee16d3c67986c3509e8b6 | Shell | 5,875 | 117 | #!/bin/bash
# PreToolUse(Write) — the actual boundary on where the model may write.
#
# WHY THIS EXISTS RATHER THAN A PATH-QUALIFIED --allowedTools RULE. A rule like
# `Write(//path/to/file)` depends on how the CLI normalises and globs a path,
# and when it does not match, the tool call is simply refused with no reason... |
2f1c325ee5fce0fef5c4c2bb6e1f344895886bebd35048e459b95e1d1745bfa8 | Shell | 5,936 | 253 | #!/usr/bin/env bash
if [ "x$BASH" = x ] || [ ! "$BASH_VERSINFO" ] || [ "$BASH_VERSINFO" -lt 4 ]; then
echo "Error: Must use bash version 4+." >&2
exit 1
fi
set -ue
STAT_NAMES=(cpu mem vsz rss)
SleepDefault=5
DebugPrintInterval=5 # minutes
Usage="Usage: \$ $(basename "$0") [options] [-u | -k key | -p ppid | command... |
2d05c94023fe6d2a60eb608314316736398daec57e21759ff67cc8624bc5917f | Shell | 6,017 | 84 | #Example single-cell sequencing
#start with tagged, refined, corrected.sorted.dedup.bam that has been group dedup'd
REF=/path/to/gencode44/GRCh38.p14.genome.fa
ANNOT=/path/to/gencode44/gencode.v44.chr_patch_hapl_scaff.annotation.gtf
TENK=/data/cliu/PacBio_Kinnex/SQ2_PBMC_10k/ #10k sample data
FIVEK=/data/cliu/PacBio... |
f03c749c7e9fce274f3da3002985a02c6523e9149c080d75f6db09cde62c8b4b | Shell | 6,035 | 211 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : mult_gen_0.sh
# Simulator : Xilinx Vivado Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source f... |
06e3de14de22d0dc7044d91dcc74d134765e40feff59e893841b568908107627 | Shell | 6,050 | 132 | #!/usr/bin/env bash
#
# Install the Python.org Python requested by $DESIRED_PYTHON and expose
# it on PATH for the subsequent build_env_setup.py / build_install_deps.py /
# build_wheel.py invocations.
#
# Windows analog of `.ci/wheel/linux/set_desired_python.sh`. The Linux variant
# just prepends a manylinux-image-ship... |
dfc9ca1e217812c21daa3ecb3d32dc98d67b3d67097e769a8b6c52f6ddaf96a4 | Shell | 6,056 | 166 | #!/bin/bash
#SBATCH --job-name=ParkQC
#SBATCH --time=12:00:00
#SBATCH --mem=16G
# Load conda
source ~/miniconda3/etc/profile.d/conda.sh
# Activate environment
conda activate MultiQCEnv
fastqc /groups/Ismagilov_Group/AW/Parkinsons/20250415_DataForAna/AllFastq/*.fastq.gz -o /groups/Ismagilov_Group/AW/Parkinsons/202504... |
91bafc8566ca9a75bea8901e33970f8836d34008dbc2074e615f7f00d3d41a92 | Shell | 6,088 | 213 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : fifo_mean.sh
# Simulator : Xilinx Vivado Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source fi... |
64428bb7fe11f9d48db65cc1e5c3026d248eaa901a699c2a6d058ad06fe7a275 | Shell | 6,163 | 37 | #!/bin/bash
echo 'SubjID,L_bankssts_thickavg,L_caudalanteriorcingulate_thickavg,L_caudalmiddlefrontal_thickavg,L_cuneus_thickavg,L_entorhinal_thickavg,L_fusiform_thickavg,L_inferiorparietal_thickavg,L_inferiortemporal_thickavg,L_isthmuscingulate_thickavg,L_lateraloccipital_thickavg,L_lateralorbitofrontal_thickavg,L_li... |
769d9fb46fa2f6cdba8b1140089ee3e2d965673633780f9ce2db88718e0b4e7c | Shell | 6,415 | 153 | #!/usr/bin/env bash
##########################################################################################################################
## docker image: https://hub.docker.com/r/tingsterx/ccs-bids
## export PATH for docker
. /neurodocker/startup.sh
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=4
##################... |
5ae5dbb48b6668784dd4e7eb62304cfa801f324843ef28bdffcc6c9101353e9d | Shell | 6,453 | 176 | #!/bin/bash
# Exit on errors
set -e
# ==========================================================
# Configurations & Paths (Relative paths preferred)
# ==========================================================
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$SCRIPT_DIR"
# Conda python and executable b... |
c2ff5e48d8bae3b973264f58b8841f823faf35d04ebcdf5917704bb51fc34297 | Shell | 6,624 | 133 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO IMAGE REGISTRATION (FLIRT/FNIRT)
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATIONS*****!!!!!
##
## R-fMRI master: Xi-Nian Zuo. Dec. 07, 2010, Institute of Psyc... |
91ae581c446006f25453f1526e1ae32897700d5cc54d27dcc01644defcd6834b | Shell | 6,632 | 150 | module purge
module load MATLAB
module load miniconda
source /vast/palmer/apps/avx2/software/miniconda/24.9.2/etc/profile.d/conda.sh
conda activate conjFDR
PARA_DIR="/home/yd357/pi_paths/pi_alag/Tools/pleiofdr/codes/step2_run_pleioFDR/code"
PLEIOFDR_DIR="${PARA_DIR}/pleiofdr"
TRAIT_FOLDER="/home/yd357/pi_paths/pi_alag... |
390e7a0f1ea26abaa5ce28efc172d5d74d369431cf605fb93506a3166afee815 | Shell | 6,853 | 87 | #Example bulk sequencing analysis
#Author: Christine Liu
##Workman ONT samples (dRNA and cDNA)
SAMPLES=(NA12878-cDNA_All_Guppy_4.2.2 NA12878-DirectRNA_All_Guppy_4.2.2)
DATA_DIR=/path/to/data/
OUT_DIR=/path/to/output/
REF=/path/to/gencode48/GRCh38.primary_assembly.genome.fa
for SAMP in ${SAMPLES[@]}
do
pbmm2 align... |
8883462eaf9ccb1e89b85d694e67da413c0e1fff8b754bfe48b565815bf03cce | Shell | 6,896 | 233 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : mult_gen_0.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying the proj... |
852dba2b304ec6f319387e4852b4a0cf9c121c103abac226759532b98a05e5d6 | Shell | 6,932 | 242 | #!/bin/bash
#
# Developed by Fred Weinhaus 10/22/2007 .......... revised 1/1/2008
#
# USAGE: grid [-s spacing] [-c color] [-t thickness] [-o opacity] infile outfile
# USAGE: grid [-h or -help]
#
# OPTIONS:
#
# -s spacing x,y spacing between grid lines; default=16,16 or 16;
# second ... |
a27cbf0e765dff66885e8a0e9c8f94be650ca792bd02c9b1ce56044903dcb0b1 | Shell | 6,969 | 108 | #!/bin/bash -l
#SBATCH --job-name=eval_model
#SBATCH --output=outLogs/eval_precedence_alt_archs_%A_%a.out
#SBATCH --error=outLogs/eval_precedence_alt_archs_%A_%a.err
#SBATCH --mem=10Gb
#SBATCH --cpus-per-task=2
#SBATCH --time=3:00:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:1 --constraint=20GB
#SBATCH --ar... |
880e51583516f8729c6f6e8e2912c43220dcc4b941eda083b6337e23d28e6127 | Shell | 7,072 | 168 | #!/bin/bash
# shellcheck source=./common.sh
source "$(dirname "${BASH_SOURCE[0]}")/common.sh"
if [[ ${BUILD_ENVIRONMENT} == *onnx* ]]; then
pip install click mock tabulate networkx==2.0
pip -q install "file:///var/lib/jenkins/workspace/third_party/onnx#egg=onnx"
fi
# Skip tests in environments where they are not... |
d41940e850eaa2f19f44dac65b6290f64bf17c2147500cee27d55db5145eaf88 | Shell | 7,130 | 243 | #!/bin/bash
set -ex
arch_path=''
targetarch=${TARGETARCH:-$(uname -m)}
if [ ${targetarch} = 'amd64' ] || [ "${targetarch}" = 'x86_64' ]; then
arch_path='x86_64'
else
arch_path='sbsa'
fi
NVSHMEM_VERSION=3.7.2
CUDA_CUPTI_VERSION=13.3.75
function install_cuda {
version=$1
runfile=$2
major_minor=${version%.*}... |
12b0ffe452de77bd2ff50d2bd967003d5557aaead7fc1f7647a6662e93542391 | Shell | 7,203 | 241 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.3 (64-bit)
#
# Filename : fifo_mean.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying the proje... |
577da30e7a33e14c40c5772b15f86c01d5698f28e4833838aa00005e466d0fdb | Shell | 7,241 | 105 | #!/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 --... |
b29b1fa8266b8506b787b61fb247c6f4bd203e10ab11ef6ce3b1233085e30ab4 | Shell | 7,387 | 190 | #!/usr/bin/env bash
echo $@
##########################################################################################################################
## SCRIPT TO PREPROCESS THE FUNCTIONAL SCAN
## parameters are passed from 0_preprocess.sh
##
## Written by the Underpants Gnomes (a.k.a Clare Kelly, Zarrar Shehzad, Maa... |
1da4b7da747209eeb4442ac1509cb9dd55c55a7bddcdbc6a128629a5ccf9ebff | Shell | 7,588 | 159 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO PREPROCESS THE ANATOMICAL SCAN (INTEGRATE AFNI/FSL/FREESURFER/ANTS)
## Revised from Xi-Nian Zuo https://github.com/zuoxinian/CCS
## Ting Xu, Denoise using ANTS... |
e85576389a7059fbd0066cf2a78958b9b8d56c4d381573ac6430f9393d5f7f2d | Shell | 7,608 | 212 | #!/bin/bash
set -ex
# 1. Guard Clause
# This ensures the script exits harmlessly on non-TPU builds
if [ -z "${TORCH_TPU}" ]; then
echo "TORCH_TPU is not set. Skipping TorchTPU installation..."
exit 0
fi
source "$(dirname "${BASH_SOURCE[0]}")/common_utils.sh"
# 2. Tokens
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOUR... |
06213f633b55d24bf795303a90fe7e8d6f265a973b7a0e36120290fcd7a17fe0 | Shell | 7,929 | 193 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO PREPROCESS THE FUNCTIONAL SCAN (INTEGRATE AFNI AND FSL)
## Xi-Nian Zuo (zuoxinian@gmail.com). Aug. 13, 2011; Revised at IPCAS, Feb. 12, 2013.
## Ting Xu 202204... |
19743f2f8b82bcefb7789b01ed4d89d3c4fbcf1fe54b476735a02c6d2020d427 | Shell | 8,155 | 179 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO REGRESS OUT NUISANCE COVARIATES FROM RESTING_STATE SCAN
## Revised from Xi-Nian Zuo https://github.com/zuoxinian/CCS
## Ting Xu, 202204, BIDS format input
#... |
82ec9fb916529119289ce563f45bd2ee6dd284ab75680913d2fcc926d18c9011 | Shell | 8,186 | 150 | # !/bin/bash
# set data directories
top_dir=/media/yuhui/LCT
cd $top_dir
for patDir in subj_folder; do
{
cd ${top_dir}/${patDir}
for runDir in bold.sft; do
{
cd ${top_dir}/${patDir}/${runDir}
run_dsets=($(ls -f rbold*.nii.gz))
run_num=${#run_dsets[@]}
for subj in rbold; do
{
# ==============... |
e947d9ee46de34b76ee61ef21b726d749582dd8e9f0b56e2bef720cbd0f356f6 | Shell | 8,220 | 105 | #!/bin/bash -l
#SBATCH --job-name=eval_model
#SBATCH --output=outLogs/sim_human_threshold_exmpt_v02_all_archs_%A_%a.out
#SBATCH --error=outLogs/sim_human_threshold_exmpt_v02_all_archs_%A_%a.err
#SBATCH --mem=8Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=3:00:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:1 --c... |
0b0462718097c21399cd0836c14d5b355fa7334c4fd713dbb83362faba2fc8d4 | Shell | 8,570 | 212 | #!/bin/bash
# shellcheck disable=SC2002,SC2004,SC2086,SC2129,SC2155
set -eux -o pipefail
export TZ=UTC
tagged_version() {
GIT_DIR="${workdir}/pytorch/.git"
GIT_DESCRIBE="git --git-dir ${GIT_DIR} describe --tags --match v[0-9]*.[0-9]*.[0-9]*"
if [[ ! -d "${GIT_DIR}" ]]; then
echo "Abort, abort! Git dir ${GIT_... |
bc15dcb658bd477ba70fb7b9cb4084554f99b44181fec0bcf71e199e706e3619 | Shell | 8,589 | 282 | #!/usr/bin/env bash
if [ x$BASH = x ] || [ ! $BASH_VERSINFO ] || [ $BASH_VERSINFO -lt 4 ]; then
echo "Error: Must use bash version 4+." >&2
exit 1
fi
set -ue
Project=dunovo
DefaultChunkMbs=512
RefdirDefault=refdir
EtDomain='nstoler.com'
RequiredCommands='bowtie bowtie-build samtools awk'
verbosity=2
Usage="Usage:... |
a58f1a47cb982cd9d70098bea429665f6cd4232a63fea1ec260e7547e1a29b06 | Shell | 8,613 | 130 | #!/bin/bash -l
#SBATCH --job-name=eval_model
#SBATCH --output=outLogs/sim_byrne_et_al_2023_%A_%a.out
#SBATCH --error=outLogs/sim_byrne_et_al_2023_%A_%a.err
#SBATCH --mem=8Gb
#SBATCH --cpus-per-task=4
#SBATCH --time=3:00:00
#SBATCH --partition=use-everything
#SBATCH --gres=gpu:1 --constraint=20GB
#SBATCH --array=0-44 #0... |
f5df4e948225336a46da78282ce2404e6d468e8913d8d53b0b3ed3e0d8ebb9af | Shell | 8,712 | 286 | #!/bin/bash
#$ -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 ... |
da2002c29b7eacc3d33f8cfe3d6901356ea52efa235cf2d79c7a5fe5fb64f1f1 | Shell | 9,358 | 244 | #!/bin/bash
set -xe
# Script used in CI and CD pipeline
# Intel® software for general purpose GPU capabilities.
# Refer to https://www.intel.com/content/www/us/en/developer/articles/tool/pytorch-prerequisites-for-intel-gpus.html
# Users should update to the latest version as it becomes available
function install_ubu... |
2f67bb6422e4013cd2de2b825c77001df353f2b1e588cef7cdb1384887f2aab6 | Shell | 9,379 | 218 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO REGRESS OUT NUISANCE COVARIATES FROM RESTING_STATE SCAN
## Revised from Xi-Nian Zuo https://github.com/zuoxinian/CCS
## Ting Xu, 202204, BIDS format input
#... |
2feb23a2159284f261dfc9ff92e13c8924dd5e54a084bca08990b3cefdbcdcfa | Shell | 9,504 | 276 | #!/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... |
76f98acceffe9afed136ce494acd6f5a9b84870208e71fc5cf05f0fa668f313f | Shell | 10,469 | 240 | #!/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... |
32603ab378fa51da9534beb0bd60ced7bab9e21acea8917c273092fc4bff0751 | Shell | 10,619 | 308 | #!/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... |
f7b39e457be1b3b2fb207f52d4139300f59685a7c84ed67ed935b9a297bde09c | Shell | 11,097 | 285 | #!/bin/bash
# shellcheck disable=SC2086,SC2006,SC2207,SC2076,SC2155,SC2046,SC1091,SC2143
# TODO: Re-enable shellchecks above
set -eux -o pipefail
# This script checks the following things on binaries
# 1. The gcc abi matches DESIRED_DEVTOOLSET
# 2. MacOS binaries do not link against OpenBLAS
# 3. There are no protob... |
7f12624ec3e4b2d5aefac0978be07b1c3f2d87eaa4f35148101c4a66cb56a3f1 | Shell | 11,252 | 220 | ########################################################################################
#> References per sample
########################################################################################
- 1LP, 2LP, 4LP, 6LP, 8LP, 9LP, EP1NSmono: /n/scratch/users/c/cao385/refs/tdTomato/GRCh38
- 3LP, 5LP, EP1NSrat, VBT24... |
d04504233bda78b3118bd58adce61bff6f6cc01173f257f59ec32e98e334fad1 | Shell | 11,297 | 94 | wget https://storage.googleapis.com/finngen-public-data-r11/summary_stats/finngen_R11_Q17_ANKYLOGLOSSIA.gz
wget https://storage.googleapis.com/finngen-public-data-r11/summary_stats/finngen_R11_Q17_APVR.gz
wget https://storage.googleapis.com/finngen-public-data-r11/summary_stats/finngen_R11_Q17_ASD.gz
wget https://stora... |
788c1e23491a3db0e13400b507edd408338708a81bbff0676aa645ca3c2c0c9e | Shell | 11,487 | 332 | #!/usr/bin/env bash
# meant to be called only from the neighboring build.sh and build_cpu.sh scripts
set -e pipefail
SOURCE_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
# Require only one python installation
if [[ -z "$DESIRED_PYTHON" ]]; then
echo "Need to set DESIRED_PYTHON env variable"
... |
dc789531f99193d9b9a5808f76e6d6704d473ebf77dfb5429bb6e3ec6b08b521 | Shell | 12,178 | 313 | #!/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 ... |
648a504888f9e22f70babcdc94742e2c3fc509c77fe30d329f648e4ce091012c | Shell | 12,314 | 257 | #!/bin/sh
. "$(dirname "$0")/lib.sh"
announce "iad option parsing and behavior"
ACTUAL_FILE=$(numeric_actual_file iad_options)
: > "$ACTUAL_FILE"
help="$TEST_TMP/iad_help.out"
"$IAD_EXECUTABLE" -h > "$help" 2>&1
assert_contains "$help" "Usage: iad"
assert_contains "$help" "-1 '# # # # #'"
assert_contains "$help" "-... |
4169350a33a811cb636fa4c60ca88edc688e0e2d6414c75ba976e94e1f73c5fa | Shell | 12,804 | 78 | zcat < XiongZ_31763980.txt.gz| csvcut -d " " -Sc CHR,BP,SNP,EA,OA,ExR-EnR_BETA,ExR-EnR_SE,ExR-EnR_P | sed -e 's/ExR-EnR_//g' | gzip -c > XiongZ_31763980.ExR-EnR.csv.gz
zcat < XiongZ_31763980.txt.gz| csvcut -d " " -Sc CHR,BP,SNP,EA,OA,ExR-EnL_BETA,ExR-EnL_SE,ExR-EnL_P | sed -e 's/ExR-EnL_//g' | gzip -c > XiongZ_31763980... |
44119b8079fff4c244de163d4df254cb1e113244918bd2d122df82f630d63f2c | Shell | 12,904 | 356 | #!/usr/bin/env bash
if [ x$BASH = x ] || [ ! $BASH_VERSINFO ] || [ $BASH_VERSINFO -lt 4 ]; then
echo "Error: Must use bash version 4+." >&2
exit 1
fi
set -ue
Start=${Start:=}
BarcodeLen=${BarcodeLen:=12}
SpacerLen=${SpacerLen:=5}
StartClip=${StartClip:=5}
EndClip=${EndClip:=5}
BwaCmd=${BwaCmd:="bwa"}
SamtoolsCmd=$... |
bd2f864532ac5573879ebe481adee3c6e44163f01725ee01fd60e13ce500e0f5 | Shell | 13,038 | 263 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO Boundary-based FUNCTIONAL IMAGE Registration
## Revised from Xi-Nian Zuo https://github.com/zuoxinian/CCS
## Ting Xu 202204, BIDS format input
#############... |
878a79ec1907bc85ae92c36364d486bc9834ff5b4da2aeb93cd52f6635c4d1e5 | Shell | 13,415 | 142 | #!/bin/bash
set -e
# rm -rf results/meta* ckpt/meta*
# rm -rf results/meta_sub* ckpt/meta_sub*
# traditional
# python 000_run_multi.py -n CNN_pH_kfold_nval_meta_freeze -d results/meta_inh -c1 ckpt/meta_inh -l 1 -t inhibitors_classes
# python 000_run_multi.py -n CNN_pH_kfold_meta_freeze -d results/meta_sub -c1 ckpt/me... |
691eed4d77d10fa91960bb2b9bf1fcd298db63bdbd891ca835c241c339b43a8a | Shell | 13,427 | 142 | #!/bin/bash
set -e
# rm -rf results/meta* ckpt/meta*
# rm -rf results/meta_sub* ckpt/meta_sub*
# traditional
# python 000_run_multi.py -n CNN_pH_kfold_nval_meta_freeze -d results/meta_inh -c1 ckpt/meta_inh -l 1 -t inhibitors_classes
# python 000_run_multi.py -n CNN_pH_kfold_meta_freeze -d results/meta_sub -c1 ckpt/me... |
0ef363dfc2528d01cc052c30c8106eeb9f42b1c76244dc61b00617ab93a0b2a0 | Shell | 13,684 | 146 | #!/bin/bash
set -e
# rm -rf results/meta* ckpt/meta*
# rm -rf results/meta_sub* ckpt/meta_sub*
# traditional
python 000_run_multi.py -n CNN_pH_kfold_val_meta_stop -d results/meta_sub -c1 ckpt/meta_sub -l 1 -t substrates_classes
python 000_run_multi.py -n CNN_pH_kfold_val_meta_full -d results/meta_sub -c1 ckpt/meta_su... |
bb46a16264898e47343b728328d53bca0cad1f4924edbc141e6d5751ffeb486a | Shell | 14,838 | 444 | #!/bin/bash
# Common util **functions** that can be sourced in other scripts.
# note: printf is used instead of echo to avoid backslash
# processing and to properly handle values that begin with a '-'.
log() { printf '%s\n' "$*"; }
error() { log "ERROR: $*" >&2; }
fatal() { error "$@"; exit 1; }
retry () {
"$@"... |
602493f139ed2754877787ea562c7288e3fa3c109656906aca783e6934851bee | Shell | 15,152 | 417 | #!/bin/bash
set -x
# shellcheck disable=SC2034
# shellcheck source=./macos-common.sh
source "$(dirname "${BASH_SOURCE[0]}")/macos-common.sh"
# Test that OpenMP is enabled
pushd test
if [[ ! $(python -c "import torch; print(int(torch.backends.openmp.is_available()))") == "1" ]]; then
echo "Build should have OpenMP e... |
094641744995bbd276870aeefacabb83ea9506dfbac50d3edc432c14d2ec03fb | Shell | 17,206 | 500 | #!/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... |
053b73887d606e900632ed37b6bedb2908850674d679c9fc2ead36984a385c85 | Shell | 17,355 | 524 | #!/usr/bin/env bash
if [ x$BASH = x ] || [ ! $BASH_VERSINFO ] || [ $BASH_VERSINFO -lt 4 ]; then
echo "Error: Must use bash version 4+." >&2
exit 1
fi
# get the name of the test directory
dirname=$(dirname $0)
cmd_prefix="$dirname/../"
Usage="Usage: \$ $(basename $0) [options] [test1 [test2]]
Options:
-p: Assume sc... |
5d16e189d7fbecbfd4637a3cad7c6433cd5fadac1e1fd317b92f145254d1af64 | Shell | 17,420 | 425 | #!/bin/bash
# shellcheck disable=SC2086,SC2048,SC2068,SC2145,SC2034,SC2207,SC2143
# TODO: Re-enable shellchecks above
set -eux -o pipefail
# Essentially runs pytorch/test/run_test.py, but keeps track of which tests to
# skip in a centralized place.
#
# TODO Except for a few tests, this entire file is a giant TODO. Wh... |
33c05e6cac9b7a4fb809f041751f60c0490627d5c6988eac08b41ae3d3ba8c3a | Shell | 17,506 | 497 | #!/usr/bin/env bash
# meant to be called only from the neighboring build.sh and build_cpu.sh scripts
# NOTE: This script is only used for ROCm and s390x builds.
# CPU/CUDA x86 and aarch64 builds use build_wheel.sh + repair_wheel.sh.
set -ex
SOURCE_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )... |
214cdd8179d25642b6945f55e82b1ef73f538e4f7ee334e2b91735f196d22475 | Shell | 17,611 | 451 |
#!/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... |
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