#!/bin/bash
#
# run cytoscape from a jar file
#
# $Revision: 5850 $
# $Date: 2004-05-19 14:16:08 -0700 (Wed, 19 May 2004) $
# 
# this is a linux-only version 
#-------------------------------------------------------------------------------
cytoscapeHomeTester=${CYTOSCAPE_HOME:-undefined}

if [ $cytoscapeHomeTester = undefined ]; then 
    echo " --- CYTOSCAPE_HOME is undefined, exiting...";
    exit
  else 
    if [ -r $CYTOSCAPE_HOME ]; then
      echo $CYTOSCAPE_HOME is readable
    else
      echo $CYTOSCAPE_HOME is defined, but not readable, exiting...
      exit
    fi
  fi


export LD_LIBRARY_PATH=$CYTOSCAPE_HOME/lib
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/X11R6/lib

java -Xmx1024MB -Djava.library.path=$CYTOSCAPE_HOME \
		-classpath cytoscape.jar:.:$CLASSPATH \
		cytoscape.CyMain \
                -b $CYTOSCAPE_DATA/annotation/manifest $*

