art

#!/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 1.5 2004-12-07 10:35:40 tjc Exp $

# 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

EXTLIBDIR=/nfs/pathsoft/external/javalib
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:$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:\/\/\(.*\):\(.*\)/ -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 uk.ac.sanger.artemis.components.ArtemisMain $*