Coding

bash Script Template

#!/bin/bash

# ------------------------------------------------------------------------------
# author:       Neo Shin
# date:         2023-08-09
# function:     script.sh --airc_id <airc_id> --sub <sub> --date <20230201> --ses <1|2|3>
# description:  script to run through slurm or SGE
# ------------------------------------------------------------------------------

# ------------------------------------------------------------------------------
# parallel engine settings
# ------------------------------------------------------------------------------
# SLURM settings
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1        # can be increased if needed
#SBATCH --mem=4G                 # can be increased if needed
#SBATCH --partition=kenrod
#SBATCH --output=jid-%A-%a_jname-%x.log
#SBATCH --mail-type=FAIL
#SBATCH --time=2-00:00:00        # day-hours:minutes:seconds format

# SGE settings
#$ -V
#$ -S /bin/bash
#$ -o jid-$JOB_ID-$TASK_ID_jname-$JOB_NAME.log
#$ -j y
#$ -m a
#$ -M ${USER}@utdallas.edu

# ------------------------------------------------------------------------------
# modules
# ------------------------------------------------------------------------------
module load bashHelperKennedyRodrigue
source bashHelperKennedyRodrigueFunctions.sh

# ------------------------------------------------------------------------------
# args/hdr
# ------------------------------------------------------------------------------
parse_args "$@"
req_args=(airc_id sub date ses)
check_req_args ${req_args[@]}
print_header
set -e

# ------------------------------------------------------------------------------
# paths
# ------------------------------------------------------------------------------
root_dir=`get_root_dir kenrod`

declare -A in_paths
in_paths[nii_dir]="${root_dir}/to/the/input/directory"
in_paths[code_dir]=`dirname $0`

declare -A out_paths
out_paths[nii_dir]="${root_dir}/to/the/output/directory"
out_paths[test]="${root_dir}/to/the/output/file"

# ------------------------------------------------------------------------------
# check paths
# ------------------------------------------------------------------------------
# Stops script if the input directories do not exist
check_in_paths ${in_paths[@]}

# Stop script if the output directory exists and overwrite was not enabled
if [[ -d ${out_paths[nii_dir]} ]] && [ ! -z "$(ls -A ${out_paths[nii_dir]})" ] && [[ ${overwrite} -eq 0 ]]; then
    echo "error: non-empty directory exists and overwrite set to 0 (out_paths: ${out_paths})"
    exit 1;
fi

# ------------------------------------------------------------------------------
# main
# ------------------------------------------------------------------------------
cmd="<insert command here>"
eval_cmd -c "${cmd}" -o ${out_paths[test]} --overwrite ${overwrite} --print ${print}

# ------------------------------------------------------------------------------
# end
# ------------------------------------------------------------------------------
print_footer

Command Example

To run this script:

# SLURM
sbatch /path/to/script/script.sh --airc_id 3tb1111 --sub 0001 --date 20230101 --ses 3

# SGE
module load sge
qsub /path/to/script/script.sh --airc_id 3tb1111 --sub 0001 --date 20230101 --ses 3

Flex Uber

If scripts are created using the script template, consider making use of the flex_uber or flex_wrapper functions.