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#!/bin/bash -
#
# This script will start the Artemis circular plot on a UNIX system.
#
QUIET=no
usage () {
echo "SYNOPSIS"
echo " DNA Plotter: DNA Image Generation Tool"
echo "USAGE"
echo " $0 [options]"
echo "OPTIONS"
echo " -t FILE Read a template file"
echo
echo "EXAMPLES"
echo " % dnaplotter"
echo " % dnaplotter -t <template file>"
echo
echo "HOMEPAGE"
echo " http://www.sanger.ac.uk/science/tools/dnaplotter/"
echo
exit 0
}
#
# Parse arguments.
#
TEMPLATE_FILE_ARG=
APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
while test $# != 0
do
case $1 in
-t) TEMPLATE_FILE_ARG="$1 $2"; shift ;;
-D*) APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES $1" ;;
-quiet) QUIET=yes ; APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Drun_quietly=true" ;;
-help) usage ;;
--help) usage ;;
-h) usage ;;
*) usage ;;
esac
shift
done
#
# "-mx2g" sets the maximum amount of memory to use.
# This may need to be increased when dealing with large files
#
if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]
then
FLAGS="-mx2g -ms100m -noverify"
else
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
fi
if [[ "$QUIET" = "no" ]]
then
echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
fi
java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/java/dnaplotter.jar $TEMPLATE_FILE_ARG
result=$?
exit $result
exit $?
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