diff --git a/update_galaxy_client.sh b/update_galaxy_client.sh index d419d55613aae789ca64e9affad1657a52c993a5..955e607ac65b432949f3000d93908d206199a9f7 100755 --- a/update_galaxy_client.sh +++ b/update_galaxy_client.sh @@ -31,15 +31,15 @@ while getopts ":i" opt; do esac done shift "$((OPTIND-1))" # Shift off the options and optional --. -LWR_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" +PULSAR_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" GALAXY_DIRECTORY=$1 GALAXY_PULSAR_DIRECTORY=$GALAXY_DIRECTORY/lib/pulsar/ if [ "$invert" -ne "1" ]; then rm -rf $GALAXY_RUNNERS_DIRECTORY/client - cp -r $LWR_DIRECTORY/pulsar/client $GALAXY_PULSAR_DIRECTORY + cp -r $PULSAR_DIRECTORY/pulsar/client $GALAXY_PULSAR_DIRECTORY else - rm -rf $LWR_DIRECTORY/pulsar/client - cp -r $GALAXY_PULSAR_DIRECTORY/client $LWR_DIRECTORY/pulsar + rm -rf $PULSAR_DIRECTORY/pulsar/client + cp -r $GALAXY_PULSAR_DIRECTORY/client $PULSAR_DIRECTORY/pulsar fi diff --git a/update_galaxy_utils.sh b/update_galaxy_utils.sh index 78da82039a56b48b9f12f780405de3b9444e3003..fbae9a9b0461d403aa4043f60056dfc1ff3bce8c 100755 --- a/update_galaxy_utils.sh +++ b/update_galaxy_utils.sh @@ -32,7 +32,7 @@ while getopts ":i" opt; do done shift "$((OPTIND-1))" # Shift off the options and optional --. -LWR_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" +PULSAR_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" GALAXY_DIRECTORY=$1 GALAXY_LIB_DIR=$GALAXY_DIRECTORY/lib/galaxy GALAXY_RUNNERS_DIRECTORY=$GALAXY_LIB_DIR/jobs/runners @@ -40,28 +40,28 @@ GALAXY_RUNNERS_DIRECTORY=$GALAXY_LIB_DIR/jobs/runners if [ "$invert" -ne "1" ]; then rm -rf $GALAXY_RUNNERS_DIRECTORY/util - cp -r $LWR_DIRECTORY/pulsar/managers/util $GALAXY_RUNNERS_DIRECTORY + cp -r $PULSAR_DIRECTORY/pulsar/managers/util $GALAXY_RUNNERS_DIRECTORY rm -rf $GALAXY_LIB_DIR/objectstore - cp -r $LWR_DIRECTORY/galaxy/objectstore $GALAXY_LIB_DIR + cp -r $PULSAR_DIRECTORY/galaxy/objectstore $GALAXY_LIB_DIR rm -rf $GALAXY_LIB_DIR/tools/deps - cp -r $LWR_DIRECTORY/galaxy/tools/deps $GALAXY_LIB_DIR/tools + cp -r $PULSAR_DIRECTORY/galaxy/tools/deps $GALAXY_LIB_DIR/tools rm -rf $GALAXY_LIB_DIR/jobs/metrics - cp -r $LWR_DIRECTORY/galaxy/jobs/metrics $GALAXY_LIB_DIR/jobs + cp -r $PULSAR_DIRECTORY/galaxy/jobs/metrics $GALAXY_LIB_DIR/jobs else - rm -rf $LWR_DIRECTORY/pulsar/managers/util - cp -r $GALAXY_RUNNERS_DIRECTORY/util $LWR_DIRECTORY/pulsar/managers + rm -rf $PULSAR_DIRECTORY/pulsar/managers/util + cp -r $GALAXY_RUNNERS_DIRECTORY/util $PULSAR_DIRECTORY/pulsar/managers - rm -rf $LWR_DIRECTORY/galaxy/objectstore - cp -r $GALAXY_LIB_DIR/objectstore $LWR_DIRECTORY/galaxy + rm -rf $PULSAR_DIRECTORY/galaxy/objectstore + cp -r $GALAXY_LIB_DIR/objectstore $PULSAR_DIRECTORY/galaxy - rm -rf $LWR_DIRECTORY/galaxy/tools/deps - cp -r $GALAXY_LIB_DIR/tools/deps $LWR_DIRECTORY/galaxy/tools + rm -rf $PULSAR_DIRECTORY/galaxy/tools/deps + cp -r $GALAXY_LIB_DIR/tools/deps $PULSAR_DIRECTORY/galaxy/tools - rm -rf $LWR_DIRECTORY/galaxy/jobs/metrics - cp -r $GALAXY_LIB_DIR/jobs/metrics $LWR_DIRECTORY/galaxy/jobs + rm -rf $PULSAR_DIRECTORY/galaxy/jobs/metrics + cp -r $GALAXY_LIB_DIR/jobs/metrics $PULSAR_DIRECTORY/galaxy/jobs fi