#!/bin/bash
#
#
if [ $# -lt 1 ] ; then
echo "usage : hrquestCml [-a ] [-f parameterfile.txt] [-m mrsi.txt] filename.mrui"
echo "        -a use full path for the mrui file to process "
echo ""
echo "Author: H. Ratiney"
echo ""
echo "Not enough argument.... exit the process"

exit 1
fi
mrsi=false
absolu=false
while [ $# -gt 0 ] ; do
    case $1 in
        -f) textfile=$2
            option="-f $textfile"
                shift 2 ;;
        -m) mrsitext=$2
            mrsi=true
                shift 2;;
        -a) absolu=true
                 shift 1;;
         *)  break   ;;
    esac
done

if [ $mrsi == true ]; then
option="$option -m $mrsitext"
fi

if [ $absolu == true ] ; then
thisdir=
else
thisdir=`pwd`/
fi

libdir=/cquest_exec
questClasspath=/cquest_exec

LD_LIBRARY_PATH=$questClasspath:$LD_LIBRARY_PATH:/usr/lib/:$libdir
#LD_LIBRARY_PATH=$questClasspath:$LD_LIBRARY_PATH:$libdir
export LD_LIBRARY_PATH
echo $LD_LIBRARY_PATH

#cd $questClasspath
pwd
#for k in $* do

java -Djava.library.path=$libdir:$LD_LIBRARY_PATH -classpath $questClasspath/cQuest_V1_lin.jar:$questClasspath/fft.jar  -Xss2m -Xmx512m cquest.quantitation.quest.run.QuestCmdLine $option ${thisdir}$*
#done
# work/test/base*.peaks