qmfetcher_hpc

#!/bin/bash
#
# Shell script to run the QMFetcher program from inside the QMTools Docker container.
# This script mounts the required directories and call the tool inside the container.
#
# echo "ARGS=$*"

PROG=$0

export SIF=${SIF:-/contrib/singularity/shared/neuroimaging}

if [ $# -lt 1  -o "$1" = "-h" -o "$1" = "--help" ]
then
  echo "usage: $PROG [-h] [-v] [-n NUM_RECS] [-o filename] [-q filepath] [--use-oldest] [--url-only] modality"
  echo '  where:'
  echo '    modality       Modality of the MRIQC group file. Must be one of: bold, T1w, or T2w.'
  echo ''
  echo '  options:'
  echo '    -h, --help     Show this help message and exit.'
  echo '    -v, --verbose  Print informational messages during processing.'
  echo '    -n NUM_RECS, --num-recs NUM_RECS'
  echo '                   Number of records to fetch (maximum) from a query.'
  echo '    -o filename, --output-filename filename'
  echo '                   Optional name of file to hold query results in the fetched directory.'
  echo '    -q filepath, --query-file filepath'
  echo '                   Path to a query parameters file in or below the current directory.'
  echo '    --use-oldest   Fetch oldest records.'
  echo '    --url-only     Generate the query URL and exit program.'
  echo ''
  echo "  example 1: $PROG -v bold"
  echo "  example 2: $PROG -v T1w -n 27 --use-oldest -o T1w_oldies"
  echo "  example 3: $PROG -v T1w -n 27 --use-oldest --url-only"
  echo "  example 4: $PROG -v bold -o Siemens7T.tsv -q queries/samples/siemens7T.qp"
  echo "  example 5: $PROG -v bold -o Siemens7T.tsv -q queries/samples/siemens7T.qp --url-only"
  exit 1
fi

apptainer exec --pwd / --bind ${PWD}/fetched:/fetched --bind ${PWD}/queries:/queries ${SIF}/qmtools_latest.sif qmfetcher $@