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#!/bin/bash -
#
# This script will start Bam View on a UNIX system.
#
QUIET=no
PRG=$0
add_proxy_properties() {
if [[ "$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
APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
APPLICATION_HOME=`dirname "$PRG"`
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/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:$APPLICATION_HOME/lib/batik/batik-xml.jar:$APPLICATION_HOME/lib/batik/batik-codec.jar
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:$APPLICATION_HOME/lib/ibatis/cglib-nodep-2.2.jar
CLASSPATH=$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
#
# 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="-mx1g -ms100m -noverify"
else
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
fi
PLATTMP=`uname`
if [[ "$PLATTMP" = "Darwin" ]]
then
APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dcom.apple.mrj.application.apple.menu.about.name=BamView"
fi
if [[ "$QUIET" = "no" ]]
then
echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi
$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.alignment.BamView $*
exit $?