bamview

#!/bin/bash -

#
# This script will start Bam View on a UNIX system.
#

QUIET=no

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 script path (inc symlinks)
#
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
    SOURCE="$(readlink "$SOURCE")"
    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script


APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
JAR_NAME=bamview.jar
JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED

#
# 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

#
# "-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

PLATTMP=`uname`
if [[ "$PLATTMP" = "Darwin" ]]
then
  	APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Xdock:name=BamView"
  	JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
  	ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
fi

if [[ "$QUIET" = "no" ]]
then
    echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
fi

$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.alignment.BamView $*
result=$?

exit $result