act

#!/bin/bash -

#
# This script will start ACT on a UNIX system.
#

QUIET=no
PRG=$0

usage () {
	echo "SYNOPSIS"
	echo "       Artemis Comparison Tool (ACT): Genome Comparison Tool"
	echo "USAGE"
	echo "        $0 [options] <SEQUENCE_1> <COMPARISON_1_2> <SEQUENCE_2> ..."
	echo "OPTIONS"
	echo "        SEQUENCE                   An EMBL, GenBank, FASTA, or GFF3 file"
	echo "        FEATURE                    An Artemis TAB file, or GFF file"
	echo "        COMPARISON                 A BLAST comparison file in tabular format"
	echo
	echo "        -options FILE              Read a text file of options from FILE"
	echo "        -chado                     Connect to a Chado database (using PGHOST, PGPORT, PGDATABASE, PGUSER environment variables)"
	echo
	echo "        -Dblack_belt_mode=?         Keep warning messages to a minimum [true,false]"
	echo "        -DuserplotX=FILE[,FILE2]    For sequence 'X' open one or more userplots"
	echo "        -DloguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data)"
	echo "        -DbamX=FILE[,FILE2,...]     For sequence 'X' open one or more BAM, CRAM, VCF, or BCF files"
	echo "        -Dchado="h:p/d?u"           Get ACT to open this CHADO database"
	echo "        -Dread_only                 Open CHADO database read-only"
	echo "EXAMPLES"
	echo "        % act"
	echo "        % act af063097.embl af063097_v_b132222.crunch b132222.embl"
	echo "        % act -Dblack_belt_mode=true -Dbam1=MAL_0h.bam -Dbam2=MAL_7h.bam,var.raw.new.bcf"
	echo "        % act -Duserplot2=/pathToFile/userPlot"
	echo
	echo "HOMEPAGE"
	echo "        http://www.sanger.ac.uk/resources/software/act/"
    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.
#
APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
while test $# != 0
do
    case $1 in
	    -options)   APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dextra_options=$2"; shift ;;
	    -chado)     APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dchado=$PGHOST:$PGPORT/$PGDATABASE?$PGUSER -Dibatis" ;;
	    -D*)        APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES $1" ;;
	    -quiet)     QUIET=yes ; APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Drun_quietly=true" ;;
	    -help)      usage ;;
	    --help)     usage ;;
	    -h)         usage ;;
	    *)          break ;;
    esac
    shift
done

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 -Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=ACT"
fi

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

$JAVA $FLAGS $APPLICATION_PROPERTIES uk.ac.sanger.artemis.components.ActMain $*
exit $?