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|
#!/bin/bash -
#
# This script will start the Artemis circular plot on a UNIX system.
#
QUIET=no
PRG=$0
usage () {
echo "SYNOPSIS"
echo " DNA Plotter: DNA Image Generation Tool"
echo "USAGE"
echo " $0 [options]"
echo "OPTIONS"
echo " -t FILE Read a template file"
echo
echo "EXAMPLES"
echo " % dnaplotter"
echo " % dnaplotter -t <template file>"
echo
echo "HOMEPAGE"
echo " http://www.sanger.ac.uk/science/tools/dnaplotter/"
echo
exit 1
}
add_proxy_properties() {
if [[ "$http_proxy" = "" ]]
then
http_proxy=$HTTP_PROXY
fi
if [[ "$http_proxy" = "" ]]
then
http_proxy=$HTTP_proxy
fi
if [[ "$http_proxy" != "" ]]
then
APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
fi
}
#
# Resolve links - $0 may be a link
#
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '.*/.*' > /dev/null; then
PRG="$link"
else
PRG="`dirname $PRG`/$link"
fi
done
#
# 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
APPLICATION_HOME=`dirname "$PRG"`
JAR_NAME=dnaplotter.jar
JAR_FILE=$APPLICATION_HOME/$JAR_NAME
#
# Use a custom Java version if necessary
#
if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
then
JAVA=`which java`
else
JAVA_HOME=$ARTEMIS_JAVA_JRE
JAVA=$ARTEMIS_JAVA_JRE/bin/java
fi
#
# Allow URLs to work from behind firewalls.
#
add_proxy_properties
#
# "-mx1g" 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
PLATTMP=`uname`
if [[ "$PLATTMP" = "Darwin" ]]
then
APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=Circular-Plot"
fi
if [[ "$QUIET" = "no" ]]
then
echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
fi
if [[ -e $JAR_FILE ]]
then
$JAVA $FLAGS $APPLICATION_PROPERTIES -jar $JAR_FILE $TEMPLATE_FILE_ARG
result=$?
else
CLASSPATH=$APPLICATION_HOME:$APPLICATION_HOME/lib/biojava.jar:$APPLICATION_HOME/lib/jemAlign.jar:$APPLICATION_HOME/lib/jakarta-regexp-1.2.jar:$APPLICATION_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/j2ssh/commons-logging.jar:$APPLICATION_HOME/lib/j2ssh/j2ssh-core.jar:$APPLICATION_HOME/lib/j2ssh/
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$APPLICATION_HOME/lib/ibatis/:$APPLICATION_HOME/lib/ibatis/log4j-1.2.14.jar:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
CLASSPATH=$CLASSPATH:$APPLICATION_HOME/lib/batik/batik-awt-util.jar:$APPLICATION_HOME/lib/batik/batik-dom.jar:$APPLICATION_HOME/lib/batik/batik-ext.jar:$APPLICATION_HOME/lib/batik/batik-svggen.jar:$APPLICATION_HOME/lib/batik/batik-util.jar:$APPLICATION_HOME/lib/batik/batik-xml.jar
CLASSPATH=$APPLICATION_HOME/lib/picard/picard.jar:$APPLICATION_HOME/lib/commons-net-3.6.jar:$CLASSPATH
CLASSPATH=$APPLICATION_HOME/lib/commons-lang-2.6.jar:$CLASSPATH
export CLASSPATH
$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
result=$?
fi
exit $result
exit $?
|
