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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.
# $Header: //tmp/pathsoft/artemis/art,v 1.1 2004-06-09 10:09:25 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
EXTLIBDIR=/nfs/pathsoft/external/javalib
ARTEMIS_HOME=`dirname "$PRG"`/.
LIBDIR=/nfs/pathsoft/prod/javalibs
#TMP_CLASSPATH=/nfs/team81/kmr/psu/jobcontrol/ant-build/classes/main:$LIBDIR/psu_all.jar:$EXTLIBDIR/oracle.jar:$EXTLIBDIR/jdbc-2.0-stdext.jar:$EXTLIBDIR/activation-1.0.1.jar:$EXTLIBDIR/mail-1.2.jar:$EXTLIBDIR/velocity-dep-1.2.jar:$EXTLIBDIR/gnu-getopt-1.0.9.jar:$PSU_PROD_CLASSPATH
TMP_CLASSPATH=
if [ "$CLASSPATH" = "" ]
then
CLASSPATH=$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar
else
CLASSPATH=$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$CLASSPATH
fi
export CLASSPATH
ARTEMIS_PROPERTIES="-Dartemis.environment=UNIX"
# Allow URLs to work from behind firewalls
if [ "$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:\/\/\(.*\):\(.*\)/ -DproxyHost=\1 -DproxyPort=\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
usage: $0 [-options options_file] [EMBL/GENBANK/SEQUENCE_FILE [+FEATURE_FILE] [+FEATURE_FILE] ...] ...
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=$JAVA_VM
fi
if [ "$QUIET" = no ]
then
echo starting Artemis with flags: $FLAGS $ARTEMIS_PROPERTIES 1>&2
fi
$JAVA $FLAGS $ARTEMIS_PROPERTIES Diana $*