aws_batch.sh

#!/bin/bash

# read in flagged arguments
while getopts ":i:o:d:" arg; do
  case $arg in
    i) # specify input folder
      data_dir=${OPTARG}
      ;;
    o) # specifcy output folder
      output_dir=${OPTARG}
      ;;
    d) # specify data version
      data_version=${OPTARG}
  esac
done
if [ -z ${data_dir+x} ];
    then
        echo "${data_version}"
        Rscript /pre_load_data.R "${data_version}"
else
    #IFS=',' read -r -a a_projects <<< "${projects}"
    batch_index=${AWS_BATCH_JOB_ARRAY_INDEX}
    export HDF5_USE_FILE_LOCKING=FALSE
    pert_name=$(echo "${projects}" | jq -r --argjson index ${batch_index} '.[$index].pert_name')
    folder_name=$(echo "${projects}" | jq -r --argjson index ${batch_index} '.[$index].project_id')
    echo "${data_dir}/${folder_name}/${pert_name}" "${output_dir}/${folder_name}/${pert_name}"
    Rscript /run_script.R "${data_dir}/${folder_name}/${pert_name}" "${output_dir}/${folder_name}/${pert_name}" "${data_version}"
fi

exit_code=$?

echo "$exit_code"
exit $exit_code