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#!/bin/sh -
# This script will start Artemis on a UNIX system. This script should
# be left in the same directory as the rest of the Artemis
# distribution, so that the java class files can be found. If
# necessary a symbolic link can be made to this script from
# /usr/local/bin/ or elsewhere.
# resolve links - $0 may be a link
PRG=$0
progname=`basename $0`
#PSU_PROD_JAVA_VERSION=1.4.2
#. $PSU_CONFIG_DIR/shell/java_environment.sh
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '.*/.*' > /dev/null; then
PRG="$link"
else
PRG="`dirname $PRG`/$link"
fi
done
ARTEMIS_HOME=`dirname "$PRG"`/.
LIBDIR=/nfs/pathsoft/prod/javalibs
CLASSPATH=$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$ARTEMIS_HOME/lib/jemAlign.jar:$ARTEMIS_HOME/lib/jakarta-regexp-1.2.jar:$ARTEMIS_HOME/lib/macos.jar:$ARTEMIS_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
# batik jars
CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/batik/batik-awt-util.jar:$ARTEMIS_HOME/lib/batik/batik-dom.jar:$ARTEMIS_HOME/lib/batik/batik-ext.jar:$ARTEMIS_HOME/lib/batik/batik-svggen.jar:$ARTEMIS_HOME/lib/batik/batik-util.jar:$ARTEMIS_HOME/lib/batik/batik-xml.jar:$ARTEMIS_HOME/lib/batik/batik-codec.jar
# j2ssh jars
CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/j2ssh/commons-logging.jar:$ARTEMIS_HOME/lib/j2ssh/j2ssh-core.jar:$ARTEMIS_HOME/lib/j2ssh/
# iBatis jars
CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$ARTEMIS_HOME/lib/ibatis/:$ARTEMIS_HOME/lib/ibatis/log4j-1.2.14.jar:$ARTEMIS_HOME/lib/ibatis/cglib-nodep-2.2.jar
export CLASSPATH
# picard jars
CLASSPATH=$ARTEMIS_HOME/lib/picard/sam.jar:$ARTEMIS_HOME/lib/picard/picard.jar:$ARTEMIS_HOME/lib/commons-net-2.2.jar:$CLASSPATH
export CLASSPATH
ARTEMIS_PROPERTIES="-Dartemis.environment=UNIX"
# Allow URLs to work from behind firewalls
if [ "$http_proxy" = "" ]
then
http_proxy=$HTTP_PROXY
fi
if [ "$http_proxy" = "" ]
then
http_proxy=$HTTP_proxy
fi
if [ "$http_proxy" != "" ]
then
ARTEMIS_PROPERTIES="$ARTEMIS_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
fi
# "-mx500m" sets the maximum amount of memory that Artemis can use. This may
# need to be increased when dealing with large files
MEM="-mx500m -ms20m"
if [ "$JVM_FLAGS" = "" ]
then
FLAGS="$MEM -noverify"
else
FLAGS="$MEM -noverify $JVM_FLAGS"
fi
QUIET=no
DEBUG=no
if [ $# = 0 ]
then
:
else
if [ "$1" = "-h" -o "$1" = "--help" -o "$1" = "-help" ]
then
cat <<EOF
SYNOPSIS
Artemis: Genome Browser and Annotation Tool
USAGE
$0 [options] <SEQUENCE_FILE> [+FEATURE_FILE ...]
OPTIONS
SEQUENCE_FILE An EMBL, GenBank, FASTA, or GFF3 file
FEATURE_FILE An Artemis TAB file, or GFF file
-options FILE Read a text file of options from FILE
-debug Run using the debugging JVM instead
-fast | -fast64 Use the FastVM (hp Tru64 UNIX) with 32/64 bit pointers
-Dblack_belt_mode=? Keep warning messages to a minimum [true,false]
-Doffset=XXX Open viewer at base position XXX [integer >= 1]
-Duserplot=FILE[,FILE2] Open one or more userplots
-Dloguserplot=FILE[,FILE2] Open one or more userplots, take log(data)
-Dbam=FILE[,FILE2,...] Open one or more BAM, VCF or BCF files
-DbamClone=n Open all BAMs in multiple (n > 1) panels
-Dbam[1,2,..]=FILE[,FILE2,..] Open BAMs in separate panels
-Dshow_snps Show SNP marks in BamView
-Dshow_snp_plot Open SNP plot in BamView
-Dshow_cov_plot Open coverage plot in BamView
-Dshow_forward_lines=? Hide/show forward frame lines [true,false]
-Dshow_reverse_lines=? Hide/show reverse frame lines [true,false]
-Dchado="h:p/d?u" Get Artemis to open this CHADO database
-Dread_only Open CHADO database read-only
EXAMPLES
% art AJ006275.embl
% art contigs.fa +annotation.gff +islands.tab
% art -Dblack_belt_mode=true -Dbam=ecoli_hiseq.bam E_coli_K12.gbk
% art -Duserplot=repeatmap.plot,geecee.plot Plasmid.gff3
HOMEPAGE
http://www.sanger.ac.uk/resources/software/artemis/
EOF
exit 0
fi
while test $# != 0
do
case $1 in
-options) FLAGS="$FLAGS -Dextra_options=$2"; shift ;;
-D*) FLAGS="$FLAGS $1" ;;
-fast) FAST_FLAG="-fast " ;; # -fast must be the first argument
-fast64) FAST_FLAG="-fast64 " ;; # -fast64 must be the first argument
-quiet) QUIET=yes ; FLAGS="$FLAGS -Drun_quietly=true" ;;
-debug) DEBUG=yes ;;
*) break ;;
esac
shift
done
fi
FLAGS=$FAST_FLAG$FLAGS
if [ "$JAVA_VM" = "" ]
then
if [ "$DEBUG" = yes ]
then
JAVA=java_g
else
JAVA=java
fi
else
JAVA=$JAVA_VM
fi
PLATTMP=`uname`
if [ "$PLATTMP" = "Darwin" ]
then
FLAGS="$FLAGS -Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=Artemis"
fi
if [ "$QUIET" = no ]
then
echo starting Artemis with flags: $FLAGS $ARTEMIS_PROPERTIES 1>&2
fi
$JAVA -Djdbc.drivers=org.postgresql.Driver $FLAGS $ARTEMIS_PROPERTIES uk.ac.sanger.artemis.components.ArtemisMain $*
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