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#!/bin/bash
show_help() {
echo "usage: docker run --rm -e v1=a -e v2=b -v /host/path/to/file:/simdata ghcr.io/virtualcell/vcell-opt:latest [OPTIONS] optProblem.json results.json report.txt"
echo " or singularity run --bind /host/path/to/file:/simdata ghcr_io_virtualcell_vcell_opt_latest.img [OPTIONS] optProblem.json results.json report.txt"
echo " [OPTIONS]"
echo " -h | --help show this message"
echo " -e | --env var=value add environment variable (needed for Singularity only)"
echo " this option can be repeated to define multiple variables"
exit 1
}
if [ "$#" -lt 1 ]; then
show_help
fi
while :; do
case $1 in
-h|--help)
show_help
exit
;;
-e|--env)
shift
export $1
;;
-?*)
printf 'ERROR: Unknown option: %s\n' "$1" >&2
echo ""
show_help
;;
*) # Default case: No more options, so break out of the loop.
break
esac
shift
done
echo "$@"
if [ "$#" -lt 1 ]; then
show_help
fi
#shopt -s -o nounset
arguments=$*
echo "script args = $arguments"
#arguments=${arguments//$datadir_external/$datadir_internal}
#arguments=${arguments//$htclogdir_external/$htclogdir_internal}
cd /usr/local/app/vcell/installDir/python/vcell_opt || exit 1
poetry run python -m vcell_opt.optService $arguments
exit $? |