sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
860e33c826f2107bf0f673e8b001c83a8e795192cad5df77d60284abee2b5831 | Shell | 2,094 | 53 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lice... |
c0259869f59fa51fa6ddcf550d62e5904ebd45320ccf74d7354e27d36008be62 | Shell | 2,099 | 46 | #! /bin/sh
# Last successfully run on Dec. 7, 2018 with git repository version v0.9.4-Li2019_GSR
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREES... |
20cbdd89ba1f98f32820634b84f9a1dc5cc878defc3aa66efad710a14f94708f | Shell | 2,103 | 61 | #!/bin/bash
# ------------------------------------------------------------------------------
# LDSC Genetic Correlation (rg) Analysis
# Description: Estimates genetic correlation between Fluid Intelligence and
# 246 Nodal Efficiency (NE) brain regions.
# ----------------------------------------------... |
5f269eea25201bf58f58e3f02419884fc62e195bf443b87bcd6f12409404a20d | Shell | 2,103 | 59 | #!/usr/bin/env bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Licen... |
73ffaf41929ab2a9a83103bea44ca71ec02da56f45d8a6f8897ce061d8a2cb61 | Shell | 2,103 | 64 | #!/bin/bash
#
#This is a shell program to batch reconstruct images using 21 different methods.
#
function write_vaa3d_job_config {
outputScript=$1;
jobpath=$2;
vaa3dProgramPath=$3;
echo "## Check which queue you may use" >> $outputScript;
# echo "#PBS -q dque" >> $outputScript;
echo "#PBS -q mindscope" >>... |
5adaf5a47a38345a2a82603f532287aa336c7cc799e4c17b5173d04a463365da | Shell | 2,104 | 54 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
eda59f50881d9b2ee71bc2c48640a292485c7c5eb0475c6f7e456c65283f3bc1 | Shell | 2,110 | 92 | #!/bin/sh
########################################
#SOAP_trans
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export SOAPtrans_work_dir=$3
export PAIR1=$4
export PAIR2=$5
if [ -d $SOAPtrans_work_dir ];
then
rm -r $SOAPtrans_work_dir
fi
mkdir $SOAPtrans_work_dir
cd $SOAPt... |
8ffa77a1250297749ca5dc40da1cc17d860e59a7118e8423cd03546d590905df | Shell | 2,116 | 68 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... |
ed320bc1d498b289fd0599295f1b78545f20ee7450304ea2e143bc1e843e7fab | Shell | 2,117 | 82 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script displays Gencode Transript information given a reference version
# and a list of transcript IDs.
# It must be internally ... |
d5ff19274ac236f83c6ba494028088eb27fb65aae6af6620a61e5d6394ece214 | Shell | 2,118 | 71 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}/data/results
SAVE_DIR=${RESL_DIR}/... |
d6f0eb8cc0ad54a621306f6fa7c64970dc5087521b859a7085badbf788293c7a | Shell | 2,120 | 78 | #!/bin/bash
#SBATCH --account=def-pbellec
#SBATCH --time=24:00:00
#SBATCH --job-name=shi_corr_betas
#SBATCH --output=logs/slurm/%x/%x_%j.out
#SBATCH --mem=64G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40
CHUNK_START=${1:-0}
LOG_DIR=${2:-}
VERBOSE_FLAG=${3:-}
CHUNK_SIZE=${4:-100}
# Note: LOW_LEVEL_FLAG removed - low-... |
1ff4a75da58602c7adc06aba5a3e6809a5eafc66cacfd8fafb47b492b321876b | Shell | 2,123 | 49 | #!/usr/bin/env sh
set -e
set -o pipefail
# You should cd to the project root
CWD=$(pwd)
# You should set the linuxdeploy and appimagetool path.
echo "Current working directory: ${CWD}"
echo "Path of linuxdeploy ${LINUX_DEPLOY_BIN}"
echo "Path of appimagetool ${APP_IMAGE_TOOL_BIN}"
echo "Path of appimagetool ${APP_IM... |
36ccba8b94abd8c97f443823932d80828f170b3bc66b3b50f6d6444ee0779968 | Shell | 2,123 | 88 | #!/bin/bash
set -e
OS=$(uname -s)
MW_MAIN_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"/..
OPENWORM_DIR=$MW_MAIN_DIR/../open-worm-analysis-toolbox
TIERPSYFEATURES_DIR=$MW_MAIN_DIR/../tierpsy-features
OPENCV_DIR=$MW_MAIN_DIR/../opencv
OPENCV_VER="3.2.0"
EXAMPLES_LINK="https://imperiallondon-my.sharepoint.co... |
68fcff1d2db5a37b50779bd373a53e395c6559da8dea9e035f119b1a0c8c12f7 | Shell | 2,123 | 49 | #!/bin/bash
# This script runs BayesTraits Discrete using Reversible-Jump method. Here I show the corelation between phenotypes,
# but this was also run for the site that showed corelated evolution with pair-bonding.
# The interpretation of the results of the Reversible-jump needs to be done manually (shown in output ... |
a4f53811a5f1da75791dbe31c09bc4bd66ebbcca3965e946c3dbf6525aa8a309 | Shell | 2,123 | 84 | #!/bin/bash
SCRIPTS_PATH=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/..
INSTALL_PATH=$SCRIPTS_PATH/../../pymeshlab
QT_DIR=""
MAC_M1=false
#checking for parameters
for i in "$@"
do
case $i in
-i=*|--install_path=*)
INSTALL_PATH="${i#*=}"
shift # past argument=value
;;
-qt=*|--qt_... |
2a73cb4d21eae5e08721bbf8c173cd24c6feb123512f912f03075e32f5bb8d9e | Shell | 2,125 | 56 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=GATK
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=20G
#SBATCH --chdir /data7/WGS_processing/src # TODO: set dir to project dir
#SBATC... |
8edc39893e7edea7a1adfa423a42d788e0c9ee870540a99d168a4d47a25a4d6b | Shell | 2,131 | 51 | #!/usr/bin/env bash
# Executes a subset of mlflow tests that is supported with fewer dependencies than the core mlflow package.
# Tests include most client interactions and compatibility points with the mlflow plugins around tracking, projects, models, deployments, and the cli.
# The SQL alchemy store's dependencies ... |
b47892dc635075d18664d5c034e4a0e388c44dfdd4f1f7838ad0c9dd4ddd7344 | Shell | 2,140 | 63 | #!/bin/sh
# This function replicates the variance component model results in the GSP dataset shown in Li et al., 2019
# Only two behavioral measures are included: Shipley_Vocab_Raw and Matrix_WAIS
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########... |
6efd747baf1c3a637667ebabd5c1e1bc88cfb6fa8ef43358310502970e544db0 | Shell | 2,141 | 59 | #!/bin/sh
# This function uses variance component model to estimate the explained variance of fluid intelligence score
# (PMAT24_A_CR) in the HCP dataset.
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################
# setup for CIRC cluster... |
1f6cdc0fc02e6d751f86d2cab71553bfa1fce968cb716f2b286aa03f26f19c2d | Shell | 2,142 | 57 | #!/bin/bash
#SBATCH --job-name=soMINIMAP
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=100G
#SBATCH --error=joblog_error_yahs_%A_%a.txt
#SBATCH --output=joblog_output_yahs_%A_%a.txt
#SBATCH --array=0-4
#### source library
path_script="/gpfs/scic/data/pro... |
b3aabea5476da4ba103489fd7864d26724c3b5aa47bebcc258f445c8536cac14 | Shell | 2,146 | 61 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Licens... |
7dbe064f8bca25787d023675e1facab845255b2acc30acc6b65eb952e82acb15 | Shell | 2,149 | 88 | #!/bin/bash
set -e
function usage ()
{
echo "Usage: $0 [-s <server name>] [-u <user name>] [-p <password>] [-d <local directory>] [-t <server dir>] [-i <include glob>] [-x <exclude glob>]" 1>&2
exit 1
}
directory="$(pwd)"
target="$(date -Id)"
includeCnt=0
excludeCnt=0
while getopts ":s:u:p:d:t:i:x:" key; do... |
f50e1f51b5ba01de9e85b0293ea638f7c73d8157c17548bfb8eba67a7fa42d48 | Shell | 2,149 | 45 | #!/bin/bash
# Output file for HTCondor submit
submit_file="submit_ridge_SHIP_Stroop_NAI.submit"
# Clear the existing submit file if it exists
> $submit_file
# Define the number of cores (CPUs)
num_cores=4
# Write the environment settings to the submit file
echo "# The environment" >> $submit_file
echo "universe ... |
cd5f7f4a1e4367f739ec9914534e5961c35994e9bd5d116bc3f6a60b1681bad6 | Shell | 2,151 | 51 | #!/bin/bash -l
set -e
MODE=$1
# We split up the test into CASE in COHORT to reduce overall test runtime
if [[ "$MODE" != "COHORT" ]] && [[ "$MODE" != "CASE" ]]; then
echo "First argument to this scripts needs to be COHORT or CASE"
exit 1
fi
#cd in the directory of the script in order to use relative paths
script_p... |
374f17b301046f0414e2fba6006760392e45c58a237a719c8c285412ffa96f14 | Shell | 2,154 | 89 | #!/bin/sh
########################################
#SOAP_trans
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export SOAPtrans_work_dir=$3
export diginorm_work_dir=$4
if [ -d $SOAPtrans_work_dir ];
then
rm -r $SOAPtrans_work_dir
fi
mkdir $SOAPtrans_work_dir
cd $SOAPtrans_... |
74b403b6f82b962081363c1a2af4b1a927fb8f9600b4dfb4703b764d18697412 | Shell | 2,154 | 57 | #!/bin/bash
# Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is 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... |
1d87b7489e2052014a1f87029046a43d3cbcebba3ccbe9e289b3e21968d0370c | Shell | 2,155 | 90 | #!/bin/sh
########################################
#SOAP_trans
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export SOAPtrans_work_dir=$3
export diginorm_work_dir=$4
if [ -d $SOAPtrans_work_dir ];
then
rm -r $SOAPtrans_work_dir
fi
mkdir $SOAPtrans_work_dir
cd $SOAPtrans_... |
d183adeadf5e8c5add992ca4338adc9844cd96cb1102e49e9659644a6da939b1 | Shell | 2,156 | 68 | #!/bin/sh
#####
# This wrapper script submits job to the scheduler to run LRR in the ABCD dataset.
# This runs the prediction procedure (10 site choose 3 cross validation).
#
# Input:
# -min:
# An integer indicating which FC to run regression for.
#
# -vers:
# The manner in which FC was calculated (See F... |
5d2ea4cd5bd9659050e48f98d412c3b4c1e5a529c9dea4a9dde56cdc9ffb9f66 | Shell | 2,157 | 28 | #!/usr/bin/env bash
#NOTE: This script has been checked in to aid in the release process for future Funcotator datasource bundles.
echo "Making Tarballs of each Datasource Directory..."
tar -zcvf funcotator_dataSources.v1.8.hg38.20230908s.tar.gz funcotator_dataSources.v1.8.hg38.20230908s
tar -zcvf funcotator_dataSou... |
6414fba2df039931a8bfc2a86cce2b348697bb8e513110e83fa15cd41c53599b | Shell | 2,157 | 72 | #!/bin/bash
## Example bash script to submit a job to compute the matrix and plot a heatmap of signal over peaks using deepTools. To run this script, do: qsub -t 1-n submit_deeptools_heatmap.sh CONFIG IDS
## CONFIG is the path to the file scripts/config.sh which contains environment variables set to commonly used path... |
e3cd027b83563d616d9e7635cdca92084210a9a00795b56ae6e3c67d60ed13f4 | Shell | 2,157 | 44 | #!/usr/bin/env bash
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Li... |
ec9ced4dda6253f865d922977dcad19b8e3013c4070a54f479756add60bf527b | Shell | 2,158 | 53 | ########this script run ccs_anat_preproc###########
#there are three inputs
# The first step of this script is to run on bash will move to python eventually
# 1.CCS_DIR
# 2.SUBJECTS_DIR
# 3.subject
######################################################
#set dirs
CCS_DIR=$1
SUBJECTS_DIR=$2
subject=$3
anat_dir=${CCS_DI... |
1086efc213ceaf5c9e6c079b45b64f39dacec458e9dc3939e1b35c56fddc3c75 | Shell | 2,160 | 66 | #!/bin/bash
#
# make brain mask exculding the ventricles
# using the data from FSL
#
# syntax: mkmask.sh <dim>
# <dim> = isotropic voxel size in mm
#
# (c) Alle Meije Wink 2015
# a.m.wink@gmail.com
# show or not show command before executing
function doit { echo $1; $1; }
#function doit { $1; }
# required parameter: ... |
7cbaf90e374186fe4563d73de5ef6e7b3ed04302ad34695c1c372c9ffefd79fc | Shell | 2,161 | 45 | #!/bin/bash
# Output file for HTCondor submit
submit_file="submit_SVM-rbf_SHIP_Stroop_NAI.submit"
# Clear the existing submit file if it exists
> $submit_file
# Define the number of cores (CPUs)
num_cores=4
# Write the environment settings to the submit file
echo "# The environment" >> $submit_file
echo "universe ... |
a82f451b7432e5b959927d785d40d922f087feab6847eb3a7a6efc77a280aba6 | Shell | 2,166 | 76 | #!/bin/bash
#$ -cwd
# error = Merged with joblog
#$ -o job_logs/job_log.$JOB_ID
#$ -j y
## Edit the line below as needed:
#$ -l h_rt=24:00:00,h_data=16G
## Modify the parallel environment
## and the number of cores as needed:
#$ -pe shared 1
# Get the current username
CURRENT_USER=$(whoami)
echo "User identified as ${... |
70b11207f3c6f9bc2dce24bec9d6694f41033a2a579b675474e413c7f75cfe40 | Shell | 2,173 | 87 | #!/bin/bash
########################################
#SOAP_trans
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export SOAPtrans_work_dir=$3
export diginorm_work_dir=$4
if [ -d $SOAPtrans_work_dir ];
then
rm -r $SOAPtrans_work_dir
fi
mkdir $SOAPtrans_work_dir
cd $SOAPtran... |
47f404a3f15aaf118ea49a7d3ac8a675fd79eeb14c70c254733589113a00813a | Shell | 2,175 | 58 | #!/usr/bin/env bash
# Reproduce Table 3 — six-metric benchmark across 5 architectures × 5 seeds × 100 epochs.
# Runtime: ~45 min on a 2-core CPU sandbox, ~10 min on RTX 3090.
#
# Usage:
# bash scripts/reproduce_table3.sh
set -euo pipefail
cd "$(dirname "$0")/.."
if [ ! -f "data/raw/gas_drift/Dataset/batch1.dat" ]... |
8090e9fdb921df47a7d031dd74ba04d3f074321ddfe13f30f004e00891bdea76 | Shell | 2,175 | 85 | #!/bin/bash
#
# Vivado(TM)
# ISEWrap.sh: Vivado Runs Script for UNIX
# Copyright 1986-2022 Xilinx, Inc. All Rights Reserved.
# Copyright 2022-2023 Advanced Micro Devices, Inc. All Rights Reserved.
#
cmd_exists()
{
command -v "$1" >/dev/null 2>&1
}
HD_LOG=$1
shift
# CHECK for a STOP FILE
if [ -f .stop.rst ]
... |
449dbda72df82754bba0d6096eed0637f32bd4e21f2d66b4bddb3d1ff8d7d890 | Shell | 2,176 | 59 | #!/bin/bash
PARSED=$1
RUN=`grep -w "BAM$" $PARSED | cut -f1 | head -$LSB_JOBINDEX | tail -1`
SIF="/nfs/cellgeni/singularity/images/reprocess_10x.sif"
CMD="singularity run --bind /nfs,/lustre $SIF"
## this has to be 10x bamtofastq, ideally the latest version
## TODO: need to somehow auto-detect when --cr11 is needed
... |
2163fc31b876117474667aeb5df2ac5987ece085f64408c27797c8bf2f5fafa5 | Shell | 2,184 | 77 | #!/bin/bash
is_float() {
[[ $1 =~ ^-?[0-9]*\.?[0-9]+$ ]]
}
NMOLECULES=16
BETA=10.0
# BETA="100.0"
#dataset_path="../../../Datasets/PDBBindOriginalCleaned/cleaned_dataset";
dataset_path="../../Datasets/PDBBind"
output_path="generated_250303_bb"
OPTIONS=$(getopt -o g --long use-glide -- "$@")
# OPTIONS=$(getopt -o ... |
0ee0fba8f698f7f77b9b588b1be463898db7494e062bac0d38f1893c780d34b6 | Shell | 2,187 | 42 | ##This script will create two files, which will be specified in the extractNeff.R with --sparseGRMFile and --sparseGRMSampleIDFile
#--sparseGRMFile=sparseGRM_relatednessCutoff_0.05_2000_randomMarkersUsed.sparseGRM.mtx
#--sparseGRMSampleIDFile=sparseGRM_relatednessCutoff_0.05_2000_randomMarkersUsed.sparseGRM.mtx.sample... |
28877c108eaabf7c160b58785625a827ddc5cd077dcc69ffe7e80a11430259ec | Shell | 2,187 | 73 | #!/bin/bash
#SBATCH --job-name=AdapterTrim
#SBATCH --time=72:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=50G
#cutadapt -f fastq --match-read-wildcards -m 22 \
# -a GGGGGGGGGG \
# -g GGAAGCAGTGGTATCAACGCAGAGTGAATGGGAAGCAGTGGTATCAACGC \
# -o HD_Plate2_5Knuclei_S4_R1_001_adapterTrim.fastq \
... |
7b8ad7d8eb77f56cd528e104ac39c431fd0484e682c113d0dfd887f32957a948 | Shell | 2,191 | 50 | #!/bin/bash
##
## 25th Apr 2025
:<<EOF
Request:
A last (I hope!) small request, which is however not essential. Would it be possible to have a test to check the difference of:
Slc37a2 transcript level: Slc37a2 mut 1 vs WT
Slc37a2 transcript level: Slc37a2 mut 2 vs WT
TREM2 transcript level: TREM2 mut vs WT
Not sure ... |
1974c1438f6d78e981cd9512cd51f6edce436f8d0b9fab06be01d079fbe965a7 | Shell | 2,193 | 49 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Sat Jan 22 2022 23:35:26 GMT-0600 (Central Standard Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
564912afd0244d3a7a0af38ff945d21b355a551fad23d940984029bbb5edccc7 | Shell | 2,193 | 53 | #!/bin/bash
# =============================================================================================
# Author: Javier Gonzalez-Castillo
# Date: 03/10/2023
#
# Description:
# This script sets the correct environment for cpm_batch.py to be able to proceed. It passes
# all provided inputs as inputs parameters to t... |
e3316b578189f8aad7b613c7be9d527fa256458d909375b70602201f1235646a | Shell | 2,197 | 53 | #!/bin/bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); yo... |
be4e4890f8d2e85751cd42be0a0d81c45f6ca0ee8fb921e52adac99056e69b63 | Shell | 2,199 | 63 | #!/bin/sh
#####
# This script calls the matlab function to run generate FC matrices in the ABCD dataset.
#
# Input:
# -output_dir:
# Path to store FC matrices
#
# -mins:
# The scan duration (in minutes) that is used to calculate the FC
#
# -vers:
# The manner in which to calculate the the first ... |
48c4fae2b0996bf75b6b6ad6a7a86c02be12a64151f66e8d138c0b1b634a86e1 | Shell | 2,202 | 60 | #!/usr/bin/env bash
# Creates a set of files that map records between GENCODE and RefSeq.
# Pulled directly from the ensemble database.
# Currently not used by Funcotator.
outFileBaseName="gencode_xrefseq"
outExt=".tsv"
hg19db="homo_sapiens_core_75_37"
hg38db="homo_sapiens_core_110_38"
hg19FileName=${outFileBaseNam... |
0f1b2041860b7777fde2a565b9442795f79ad965b773ae560a9a29d0cbe9982e | Shell | 2,204 | 94 | #!/bin/bash
CD=$PWD;
DD=/scratch2/ibrouwer2/appsms/appsms_import/sourcedata;
DF=${CD}/dicoms_list.txt;
OF=${CD}/dicoms_prot.txt;
# find one dicoms per (non-empty, file-containing) directory
if [[ ! -f $DF ]]; then
find $DD -type d -exec sh -c 'find "{}" -maxdepth 1 -type f -name \*dcm\* | sort | head -n 3 | tail ... |
029c202da45bdcba16498dabff54335b98c64fc54e8e06ada0d42f699e4b6aaa | Shell | 2,207 | 63 | #!/bin/bash
# =============================================================================
# STARsolo CLI - Drop-seq platform
# =============================================================================
# CB_UMI_Simple with no whitelist (12 bp CB, 8 bp UMI).
# =======================================================... |
efcdffe11acc7959d33dd490c01198dcd09362b08782ead8d4e23154b2342548 | Shell | 2,207 | 67 | #!/bin/sh
#####
# This wrapper script submits job to the schduler to run KRR in the ABCD dataset.
# This runs the prediction procedure (10 site choose 3 cross validation).
# Runs the predictions for subcortical connections specifically.
#
# Input:
# -min:
# An integer indicating which FC to run regression for.
... |
2e5093b159cc8c8152607ff30d4d22b4f612a3dcbe0ca9bca47cfc66b9d40acf | Shell | 2,210 | 50 | #!/bin/bash
# Copyright 2018 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
3ddbefd89617ad9a8c83e1c4e714c1e743ef4d0ae458262c05c2a091fb0e685e | Shell | 2,210 | 45 | #!/bin/bash
# Output file for HTCondor submit
submit_file="submit_AutoGluon_SHIP_Stroop_NAI.submit"
# Clear the existing submit file if it exists
> $submit_file
# Define the number of cores (CPUs)
num_cores=16
# Write the environment settings to the submit file
echo "# The environment" >> $submit_file
echo "univers... |
1927669a4f8a7dcb26b77773f8f534c7679e1144ae3ab880b40594e977035e91 | Shell | 2,211 | 67 | #!/bin/bash -v
################################################################################
#
# group_preprocess
# ----------------
#
# Extracts necessary dMRI and T1 files from HCP datasets and pre-process them
#
################################################################################
#
# Usag... |
1e24e0d7439abfc30f6503a3dd9e86627d638bcbaff85214b530b4701fb952dd | Shell | 2,211 | 69 | #!/bin/bash
# Startup script for Superset in Codespaces
echo "🚀 Starting Superset in Codespaces..."
echo "🌐 Frontend will be available at port 9001"
# Check if MCP is enabled
if [ "$ENABLE_MCP" = "true" ]; then
echo "🤖 MCP Service will be available at port 5008"
fi
# Find the workspace directory (Codespaces c... |
54388e67c894cd6895a587016fd00c1e23f2c6db1f42e2c23458bce1b5ce9313 | Shell | 2,215 | 46 | #!/bin/bash
# This script runs BayesTraits Discrete method on the datasets obtained in script 13.2. It tests for correlated evolution between
# the amino acid variant and the phenotype data (both discrete).
# This script shows the general script to run BayesTraits.
# For space purposes, the output files are not shown.... |
9570a78d8a75ca046eb7a7a601b9710e525d49add07d0ab4e63d258fb8034e8b | Shell | 2,215 | 52 |
#generate LD for all markers in bgen for each set in group file --annotation_in_groupTest=ALL
Rscript step3_LDmat.R \
--bgenFile=./input/genotype_100markers.bgen \
--bgenFileIndex=./input/genotype_100markers.bgen.bgi \
--SAIGEOutputFile=./output/LDmat \
--chrom=1 \
--AlleleOrder=ref-first \... |
454630b13a9fbdf919715ee5a9c7a8c97e8e992f8fbaee8f3ced7f5c394d4ea5 | Shell | 2,217 | 71 | #!/bin/bash
#SBATCH --account=def-pbellec
#SBATCH --time=12:00:00
#SBATCH --job-name=shi_mvpa_perm
#SBATCH --output=logs/slurm/%x/%x_%A_%a.out
#SBATCH --error=logs/slurm/%x/%x_%A_%a.err
#SBATCH --mem=128G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40
# Arguments from batch launcher:
# $1 = subject (e.g., sub-01)
# $2... |
46fc1df5c574b4753f3b13d4f87f174d14118847f99b99f0c00369e502655c5a | Shell | 2,218 | 57 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
2ff30bc85a25d0542246b4b8bb38314e8c2595b97c4a7212e2de7b36379bff73 | Shell | 2,220 | 64 | #!/bin/sh
#####
# This script calls the matlab function to run generate FC matrices in the ABCD dataset.
#
# Input:
# -output_dir:
# Path to store FC matrices
#
# -mins:
# The scan duration (in minutes) that is used to calculate the FC
#
# -vers:
# The manner in which to calculate the the first ... |
a2600037308c8cf2ba9f5b5cfebf0e956c3da3dd1ea36534d2340d139cc7d49b | Shell | 2,222 | 63 | #!/bin/bash
#!/bin/bash
#SBATCH -N 1 # Number of nodes. You must always set -N 1 unless you receive special instruction from the system admin
#SBATCH -n 1 # Number of CPUs. Equivalent to the -pe whole_nodes 1 option in SGE
#SBATCH --mail-type=END # Type of email notif... |
9638d0a6825c9ba05f620eed5585c264e8c3b688810241559eb8ffc48126fd63 | Shell | 2,225 | 24 | set -e
# Run this to regenerate the reference files for the tests.
#
# Usage:
# ./tests/update_test_files.sh <license_key>
TotalSegmentator -i tests/reference_files/example_ct_sm.nii.gz -o tests/reference_files/example_seg.nii.gz -bs --ml -d cpu
TotalSegmentator -i tests/reference_files/example_mr_sm.nii.gz -o tests/... |
65c953636555d4553a919eba5e35c425ccd8dcd39dcd83475dbb6ea6213ebb0f | Shell | 2,229 | 39 | # Enrichment.r
# -g = Two columns table of input genes with specific association from your study
# -l = list of two columns tables with gene - disease association. E.g. Gene1 SYN
# -p = make a bubble chart with OR and -log10(FDR)
# -b = background (protein coding = 19776, brain expressed = 15585, WGCNA list = 6029)
# -... |
6bb0effbda7f4301245c9232604221096f7a2867266c9e2da9c162776c784532 | Shell | 2,230 | 97 | #! /bin/sh
# $Id$
XML_VERSION='4.4'
XML_FILE="docbook-xml-${XML_VERSION}"
XML_URL="http://www.docbook.org/xml/${XML_VERSION}/${XML_FILE}.zip"
XSL_VERSION='1.72.0'
XSL_FILE="docbook-xsl-${XSL_VERSION}"
XSL_URL="http://downloads.sourceforge.net/docbook/${XSL_FILE}.tar.bz2"
#--------------------------------------------... |
2fb5b8747c0e03146bca74e5a8acfebb14d5ab8f219427240979818a58b2c893 | Shell | 2,233 | 82 | #!/bin/bash
set -e ${DEBUG:+-x}
# Redirect all scripts output + leaving stdout to container payload.
exec 3>&1
ENTRYPOINT_PATH=/label-studio/deploy/docker-entrypoint.d
exec_entrypoint() {
if /usr/bin/find -L "$1" -mindepth 1 -maxdepth 1 -type f -print -quit 2>/dev/null | read v; then
echo >&3 "$0: Looking for... |
cbb3f431dc712a84be5ad57efd16923109b61bd071cd567a44c16fa18e518c1d | Shell | 2,237 | 62 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO PREPROCESS THE DTI SCAN (INTEGRATE AFNI, FS AND FSL)
##
## R-fMRI master: Xi-Nian Zuo. Dec. 20, 2014.
##
## Last Modified: Dec., 20, 2014.
## Email: zuoxn@psyc... |
14e0751f516733636765c0bb8726f5dc010df3eac248c62912ee4f84d3fc512c | Shell | 2,242 | 60 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
3627bb45f5024b06230597af5146a0d2494cb4190b4473678f41b50a07ee0bf1 | Shell | 2,243 | 55 | #!/bin/bash
###################################################################
#created by Davit Bzhalava on 2014-11-21 #
#compares two sequence database with each other #
###################################################################
#/media/StorageOne/HTS/viralmeta_bi... |
ac5180eae0234fa393757deeacaa11f19d52cc0ef4bee1efe10c352a3570764b | Shell | 2,244 | 45 | #!/bin/bash
# Output file for HTCondor submit
submit_file="submit_CV_AutoGluon_SHIP_APOE_Stroop_NAI.submit"
# Clear the existing submit file if it exists
> $submit_file
# Define the number of cores (CPUs)
num_cores=1
# Write the environment settings to the submit file
echo "# The environment" >> $submit_file
echo "... |
28d153033c1d58ad534b92919ce951feb1c0eb4ee1a8012008b1363d712ca996 | Shell | 2,248 | 39 | #!/bin/bash
# fmriprep was used to align MNI152NLin6Asym 1mm T1 images (non-skull stripped) to the MNI152NLin2009cAsym:res-01 space,
# which is 1mm space in templateFlow that fmriprep uses to pull its templates. This produced ants format *.h5 files which
# are composite affine/warp files.
# these files were created by... |
afae1a38e693f8e8a4f5b5766c95ae732fdda77137c818be2b04314137c117dd | Shell | 2,252 | 63 | #!/bin/bash
# Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is 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... |
356a05336bf4b1198d03af18997d6d519980339c24aaaa248f2ecba87b24e25e | Shell | 2,256 | 65 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
#! /bin/sh
# Usage: bash <repo>/esm/scripts/download_weights.sh /path/to/weights/
# re run the command to continue downloading incomplete fil... |
eb595cc04a8f7ecfc56121f9e049e06ebc09a11dcce5ef59347675489509ddc0 | Shell | 2,257 | 82 | #!/usr/bin/env bash
set -ex
pip install -e .
cd Pendulum
python -u plot.py
cd ..
cd Lorenz-stenflo
python -u plot.py
python -u plot_time.py
python -u symbolic_refinement_rollout.py
python -u reproduce_symbolic_writeback.py
cd ..
cd Glycolytic
python -u plot.py
cd ..
cd CompoundPendulum
python -u plot.py
cd ..
cd ... |
ed35c65da7c098fe63f319a2bb13b9197b9361d796a2a003ecdf0184f43f1b41 | Shell | 2,260 | 49 | #!/bin/bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); yo... |
f5b81fef5cc36f8de37ca8ecc11aff26d8ed915c17ea9ba62f09ec244285bdfc | Shell | 2,260 | 82 | #!/bin/bash
# Build script for creating cross-platform executable with PyInstaller
echo "=== Membrane Kymograph - PyInstaller Build Script ==="
echo ""
# Check if virtual environment is active
if [[ "$VIRTUAL_ENV" == "" ]]; then
echo "⚠️ Warning: Virtual environment is not active."
echo "It's recommended to ... |
61d1b1f3dcc49bccd6f201cf8c07de7161dcfc1dbb80b26398c71e33cfae6ce9 | Shell | 2,261 | 70 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO generagte (i.e., merge all individual maps) 4D files for second-level group analysis
##
## This script can be run on its own, by filling in the appropriate par... |
33253575211fc4e83b0df69255af998b8b414d116bb9125da49d896434cbc641 | Shell | 2,263 | 78 | #!/bin/bash
SERIES=$1
if [[ -f $SERIES.urls.list ]]
then
>&2 echo "WARNING: File '$SERIES.urls.list' exists! This should not happen; overwriting the file.."
rm $SERIES.urls.list
fi
for i in `cat $SERIES.run.list`
do
TYPE="SRA" ## we always default to SRA. This could cause problems for very fresh datasets.
... |
47cfb2809f74fe9c63f9946c9ddb72b333dd0b429031be7a4bd8c3d7f610f8e4 | Shell | 2,266 | 85 | #!/bin/bash
function finish
{
cd "$oldcwd"
}
trap finish exit
oldcwd=$(pwd)
git --version > /dev/null
if [ $? -ne 0 ]
then
echo "Could not find git executable"
exit 1
fi
top_level=$(git rev-parse --show-toplevel)
if [ -z "$top_level" ]
then
echo "This is not a git repository"
exit 1
fi
cd $top_level
i... |
556ad62f657c39eee4fe99708d155fcb8fcb8696cd8fd41ea7da11084fa55dd3 | Shell | 2,270 | 62 | # Parameters
PLATFORM='ont'
INPUT_DIR="${HOME}/clair3_ont_quickDemo"
OUTPUT_DIR="${INPUT_DIR}/output"
THREADS=4
## Create local directory structure
mkdir -p ${INPUT_DIR}
mkdir -p ${OUTPUT_DIR}
# Download quick demo data
#GRCh38_no_alt Reference
wget -P ${INPUT_DIR} http://www.bio8.cs.hku.hk/clair3/demo/quick_demo/ont... |
7f200284aa0e2545358dd0732c4d315fd220d3daac0f5024963d263da1ce4027 | Shell | 2,271 | 67 | #!/usr/bin/bash
#SBATCH --partition=cpus
#SBATCH --time=300:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=256G
#SBATCH --job-name=soBRAKER
#SBATCH --error=joblog_braker_error_%j.txt
#SBATCH --output=joblog_braker_output_%j.txt
# define environment
path_biotools="/gpfs/scic/software/biotools"
path_... |
b23f77c7004145184c355fb995d877f7f96003cab32249754097f0b04cf303cc | Shell | 2,271 | 50 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
87d7a822bd714b059a56cacb02d83a6246258d4e39d4776c5a141ef26b478695 | Shell | 2,272 | 63 | #!/bin/bash
# Checks whether all files in a folder are identical to files with the same name in the other folder. And checks
# whether both have the same number of files.
help="[-a first folder, all files within will be compared to those with identical name in folder -b]\n
[-b second folder]\n
[-x files c... |
64e36ee41864fe5d0d5e2ac8e0608ddd6afa5b8d51098387ec5101b6d1eb91c6 | Shell | 2,273 | 64 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
input_dir=$pd/data/validations/ATAC_seq_BAM_nameSorted
output_dir=$pd/data/validations/ATAC_seq_peaks_noBL
mkdir -p $output_dir
# human iPSCs
rep1=${input_dir}/human_H1c2_iPSC.bam
rep2=${input_dir}/human_H2c1_iPSC.bam
sbatch --ou... |
e0628ca0b27f7faafe2395a93afc9f58c7ea8f00d71ff26f3c61af1c9e221d69 | Shell | 2,275 | 51 | file1='~/project/Au/regen/Xenopus/Xenopus_pep.fa'
type1='prot'
id1='Xe'
file2='~/project/Au/Au_genome/Au_pep.fa'
type2='prot'
id2='Au' #2-character ID (e.g. 'mo' for mouse)
bash ~/project/cross_species/SAMap/map_genes.sh --tr1 $file1 --t1 $type1 --n1 $id1 --tr2 $file2 --t2 $type2 --n2 $id2 --threads 60
Running blastx f... |
bfaef297b17d216a9ebb70e0b3cd2064126d437e70ca84a7746bb43db8acd438 | Shell | 2,276 | 50 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
e5017758624f019962ebef8511c9ca4d8206e57db5d96215129d2309b9887fde | Shell | 2,277 | 45 | #!/bin/bash
# Output file for HTCondor submit
submit_file="submit_dummy_SHIP_Stroop_NAI.submit"
# Clear the existing submit file if it exists
> $submit_file
# Define the number of cores (CPUs)
num_cores=4
# Write the environment settings to the submit file
echo "# The environment" >> $submit_file
echo "universe ... |
03a03df9ac570bb0887bb5258cca9c2dca89fe795269625d7fcb1c06eee2e4b9 | Shell | 2,278 | 68 | #!/bin/bash
# Script written by Alle Meije Wink based on a script from Veronica Popescu & Hugo Vrenken
#
# The should have as argument the input file.
#
# Dit script maakt eerst een warp van standard space brain naar patient brain. Die matrix
# toepassen op Hugo's / Veronica's 152 cut brain. Daarna de minimum Z bere... |
ef95d921cd8f1c09cf4132fb2d5305540713dd8fccc01929f9574cb7725ce7d7 | Shell | 2,280 | 89 | #!/bin/bash
#SBATCH -c 1 # Request cores
#SBATCH -t 0-04:00 # Runtime in D-HH:MM format
#SBATCH -p short # Partition to run in
#SBATCH --mem-per-cpu=25G # Memory per core
#SBATCH -o /home/zaa827/bancpipeline/jobs/o2_ranks_%j.ou... |
a0bf75fcae3afdc158dfa1a556685b4417967672166939a9c1697bb96f851349 | Shell | 2,284 | 71 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}/data/results
SAVE_DIR=${RESL_DIR}/... |
c39eb6324bf165cca9bac0b8da12a1c6d8a2da4f4ec54f4af42d11360d6a654c | Shell | 2,289 | 79 | #/usr/bin/env bash
#!/bin/bash
#PBS -l walltime=8:00:00
#PBS -N mriqc
#PBS -q normal
#PBS -l nodes=1:ppn=28
#PBS -l mem=100gb
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
module load singularity
cd $PBS_O_WORKDIR
umask 0000
# ensure paths are correct irrespective from wher... |
6e0de15debe3c5547425334e3ba64e97f8e11e8b57ec46a9658c15e8c0ee072e | Shell | 2,290 | 62 | # Parameters
PLATFORM='ilmn'
INPUT_DIR="${HOME}/clair3_illumina_quickDemo"
OUTPUT_DIR="${INPUT_DIR}/output"
THREADS=4
## Create local directory structure
mkdir -p ${INPUT_DIR}
mkdir -p ${OUTPUT_DIR}
# Download quick demo data
#GRCh38_no_alt Reference
wget -P ${INPUT_DIR} http://www.bio8.cs.hku.hk/clair3/demo/quick_de... |
87fbd5a928835c75df6089403ff75f6d912d4bd6dcd24a99074e2eb672b10ea2 | Shell | 2,291 | 41 | # Enrichment.r
# -g = Two columns table of input genes with specific association from your study
# -l = list of two columns tables with gene - disease association. E.g. Gene1 SYN
# -p = make a bubble chart with OR and -log10(FDR)
# -b = background (protein coding = 19776, brain expressed = 15585, WGCNA list = 6029)
# -... |
0495e0e5bccbfbad0d3f18fc88bcd14839f5c7760cf2cc62bfad7e1b8e26e47b | Shell | 2,292 | 68 | usage() {
cat <<EOF
Usage: $(basename "$0") <precon_dir> [animal]
precon_dir Path to an existing precon_all output directory
animal Optional animal/template name under \$PCP_PATH/standards
This script is for cases where standard N4 bias correction is not enough.
It can be useful for T1 i... |
679faa6a6e5b014672b6a8105f29799bd4b3eb9e678e893a02bb0e686188f9c5 | Shell | 2,294 | 41 | # Enrichment.r
# -g = Two columns table of input genes with specific association from your study
# -l = list of two columns tables with gene - disease association. E.g. Gene1 SYN
# -p = make a bubble chart with OR and -log10(FDR)
# -b = background (protein coding = 19776, brain expressed = 15585, WGCNA list = 6029)
# -... |
8399f67499fda84d67baf6ed0236aeb42328209d825b44af57d92f84165dc0c2 | Shell | 2,295 | 45 | #!/bin/bash
# Output file for HTCondor submit
submit_file="submit_linear_SHIP_Stroop_NAI.submit"
# Clear the existing submit file if it exists
> $submit_file
# Define the number of cores (CPUs)
num_cores=2
# Write the environment settings to the submit file
echo "# The environment" >> $submit_file
echo "universe ... |
1f387f4f5e2d2d630e7c305cc2396d723d59456d63510f7e716d771374b98c1f | Shell | 2,297 | 72 | #!/bin/sh
#####
# This wrapper script submits job to the schduler to run KRR in the ABCD dataset.
# This runs the reliability procedure (10 site choose 5 cross validation).
# Runs the procedure for a specific subsample.
#
# Input:
# -min:
# An integer indicating which FC to run regression for.
#
# -vers:
# ... |
33ea4ca2d3395d64a640dceaa3410e1668aa34b67edea4066822394bb72d57e7 | Shell | 2,298 | 52 | #!/bin/bash
set -e
path_tflite=$1
path_cpp=$2
board_type=$3
board_snr=$4
name="$board_type-$board_snr"
# Use EDGEVOLUTION_ROOT if set, otherwise derive from script location
PROJECT_DIR="${EDGEVOLUTION_ROOT:-$(cd "$(dirname "$0")/.." && pwd)}"
# Backport argparse.BooleanOptionalAction for Python < 3.9 (needed by Zeph... |
f761ccb5d19e1b3f2c9ee5b232e00c27c4052787ac3776e9692b9b92977bcd01 | Shell | 2,300 | 72 | #!/bin/bash
# real example call from starting dir:
#/data/liga_starad/ukb
# bash run_var_qc.sh -o experiments/arraySnps/all -p imputation/data/initial_snps/merged -i sample_infos/all_samples/ -m 16000 -t 2
helpFunction()
{
echo ""
echo "Usage: $0 -p plinkPrefix -i info_path -o outPath"
echo -e "\t-p prefi... |
03f5c830b674e9a0aaaa293d7302a896268a4ba49946ba4538b04e05ba46af92 | Shell | 2,301 | 84 | #! /bin/bash
# [fontforge](https://fontforge.org/en-US/) needs to be installed first
JSON_STRING="$(cat ./meta.json)"
JSON_REMOVE_NL=${JSON_STRING//$'\n'/ }
JSON_REMOVE_WHITESPACE=${JSON_REMOVE_NL//$' '/}
# font = fontforge.font();
# glyph = font.createChar(41, "A");
# glyph.importOutlines("/path/to/svg/foo.svg");
... |
ed3f930316359fdc2d40e44cbd14aa6fdcf61d2b6ce91197ae333f51a05d8aae | Shell | 2,302 | 45 | #!/bin/bash
# Output file for HTCondor submit
submit_file="submit_SHAP_XGBoost_SHIP_Stroop_NAI.submit"
# Clear the existing submit file if it exists
> $submit_file
# Define the number of cores (CPUs)
num_cores=1
# Write the environment settings to the submit file
echo "# The environment" >> $submit_file
echo "unive... |
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