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gbids/run_docker.sh
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run_docker.sh
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#!/bin/bash
# Copyright (C) 2018, 2019 S3IT, University of Zurich
#
# This program is free software: you can redistribute it and/or
# modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# utility functions
me=$(basename "$0")
function die () {
rc="$1"
shift
(echo -n "$me: ERROR: ";
if [ $# -gt 0 ]; then echo "$@"; else cat; fi) 1>&2
exit $rc
}
## usage info
usage () {
cat <<__EOF__
Usage:
$me [options] DOCKER_TO_RUN BIDS_INPUT OUTPUT_FOLDER ANALYSIS_TYPE SUBJECT_LABEL
Run BIDS/App docker containe 'DOCKER_TO_RUN'
Options:
-d Enable verbose logging
-h Print this help text
__EOF__
}
## parse command-line
short_opts='dh'
long_opts='debug,help'
getopt -T > /dev/null
rc=$?
if [ "$rc" -eq 4 ]; then
# GNU getopt
args=$(getopt --name "$me" --shell sh -l "$long_opts" -o "$short_opts" -- "$@")
if [ $? -ne 0 ]; then
die 1 "Type '$me --help' to get usage information."
fi
# use 'eval' to remove getopt quoting
eval set -- $args
else
# old-style getopt, use compatibility syntax
args=$(getopt "$short_opts" "$@")
if [ $? -ne 0 ]; then
die 1 "Type '$me --help' to get usage information."
fi
set -- $args
fi
while [ $# -gt 0 ]; do
case "$1" in
--debug|-d) set -x ;;
--help|-h) usage; exit 0 ;;
--) shift; break ;;
esac
shift
done
## sanity checks
# the SCRIPT argument has to be present
if [ $# -lt 5 ]; then
die 1 "Missing required arguments. Type '$me --help' to get usage help."
fi
## main
echo "[`date`]: Start"
DOCKER_TO_RUN="$1"
DOCKER_DATA="$2"
DOCKER_OUTPUT="$3"
ANALYSIS="$4"
SUBJECT="$5"
echo "running: sudo docker run -i --rm -v $DOCKER_DATA:/bids -v $DOCKER_OUTPUT:/output $DOCKER_TO_RUN /bids /output $ANALYSIS --participant_label $SUBJECT"
# sudo docker run -i --rm -v $DOCKER_DATA:/bids -v $DOCKER_OUTPUT:/output $DOCKER_TO_RUN /bids /output $ANALYSIS --participant_label $SUBJECT
RET=$?
# Fix local filesystem permission
echo "fixing local filesystem permission"
# chown -R $UID:$GID $DOCKER_OUTPUT
echo "[`date`]: Done with code $RET"
exit $RET
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