#!/bin/sh
#***********************************************************************
#
# Copyright (c) 1999-2005 The Institute for Genomic Research (TIGR).
# Copyright (c) 2005-2008, the Dana-Farber Cancer Institute (DFCI), 
# J. Craig Venter Institute (JCVI) and the University of Washington.
# All rights reserved.
#
# This software is OSI Certified Open Source Software.
# OSI Certified is a certification mark of the Open Source Initiative.
#
#***********************************************************************
#
# $RCSfile: tmev.sh,v $
# $Revision: 1.1 $
# $Date: 2007/12/12 21:52:48 $
# $Author: eleanorahowe $
# $State: Exp $
#
#***********************************************************************
#echo 'Setting CLASSPATH'

# Check for R
if [ ! -f `which R` ]
then
   if [ -f `which zenity` ]
   then
	zenity --text-info --width=600 --height=300 --title='*** MeV requires R ***' --filename=$BIRCH/script/tmev.msg
   else
	cat $BIRCH/script/tmev.msg
   fi
fi

# set environment variables
TMEV_HOME=$BIRCH/java/TM4/MeV

for jar in $TMEV_HOME/lib/*.jar 
do 
# make sure CLASSPATH is defined before we reference it 
if [ -z "$CLASSPATH" ] 
then 
CLASSPATH=.:$jar 
else 
CLASSPATH=$CLASSPATH:$jar
fi 
done 
export CLASSPATH

#**************************************
# R specific variables & compilations #
#**************************************

#echo 'Setting R-specific variables...'
#CurrDIR=`pwd`
#echo ${CurrDIR}

# Try to auto detect libjri.so file, if not found then try compiling. 
# This ensures the same libs are not compiled every time MeV is run
#if [ -a ${CurrDIR}/lib/libjri.so ]
#   then
#     echo "${CurrDIR}/lib/libjri.so exists"
#   else 
#     echo "Attempting to build jri Library"
#	 ./makejrilib.sh
#         if [ $? -ne 0 ]
#         then
#           echo "ERROR generating jri library...Aborting"
#           exit 1;
#         fi
#fi

# Set RHOME etc 
#R_HOME=/usr/lib/R
#R_HOME=/local/workspace01/zhangju/bin/R
#R_HOME=$BIRCH/local/pkg/R_language
#R_SHARE_DIR=/usr/share/R
#R_SHARE_DIR=$R_HOME/share
#export R_SHARE_DIR
#R_INCLUDE_DIR=/usr/include/R
#R_INCLUDE_DIR=$R_HOME/lib64/R/lib
#export R_INCLUDE_DIR

# For R shared libs
PATH=${PATH}:${R_HOME}/bin:${R_HOME}/lib
#JRI_LD_PATH=${CurrDIR}/lib:${R_HOME}/lib
JRI_LD_PATH=$TMEV_HOME/lib:${R_HOME}/lib
JRI_LD_PATH=$BIRCH/lib-$BIRCH_PLATFORM/MeV:$JRI_LD_PATH
if [ -z "$LD_LIBRARY_PATH" ] 
then
  LD_LIBRARY_PATH=$JRI_LD_PATH
else
  LD_LIBRARY_PATH=$JRI_LD_PATH:$LD_LIBRARY_PATH
fi
#export R_HOME
# echo R HOME: ${R_HOME}
export LD_LIBRARY_PATH
# echo LD LIBRARY PATH: ${LD_LIBRARY_PATH}
export PATH

echo 'Launching MeV'
#java -Djava.library.path=$LD_LIBRARY_PATH -Xss1M -Xmx1024m -cp $CLASSPATH org.tigr.microarray.mev.TMEV
java -Djava.library.path=$LD_LIBRARY_PATH -Xss1M -cp $CLASSPATH org.tigr.microarray.mev.TMEV