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executable file 104 lines (81 sloc) 2.715 kB
#!/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.
# $Header: //tmp/pathsoft/artemis/etc/gene_builder,v 1.1 2009-06-30 15:47:36 tjc Exp $
# resolve links - $0 may be a link
PRG=$0
progname=`basename $0`
while [ -h "$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 "$PRG"`/..
CLASSPATH=$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:$ARTEMIS_HOME/lib/postgresql-8.1-407.jdbc2ee.jar:$ARTEMIS_HOME/lib/chado-14-interface.jar:$CLASSPATH
# j2ssh jars
CLASSPATH=$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:$ARTEMIS_HOME/lib/retrotranslator-runtime-1.1.0.jar:$ARTEMIS_HOME/etc
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
if [ $# = 0 ]
then
:
else
while test $# != 0
do
case $1 in
-options) FLAGS="$FLAGS -Dextra_options=$2"; shift ;;
-D*) FLAGS="$FLAGS $1" ;;
*) break ;;
esac
shift
done
fi
FLAGS=$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
$JAVA -Djdbc.drivers=org.postgresql.Driver $FLAGS $ARTEMIS_PROPERTIES uk.ac.sanger.artemis.components.genebuilder.GeneEdit $*
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