#!/bin/sh

#export JAVA_HOME="/nfs/team71/phd/ap3/BIN/jdk1.6.0"
java -version;
which java

export CLASSPATH=""
echo $CLASSPATH

cd "/nfs/team71/phd/ap3/workspace/BioJavaHibernate"

echo "pdb2hibernate v0.1 ap3@sanger.ac.uk"


args=( "/nfs/team71/phd/ap3/WORK/PDB/" )

if [ "$1" ]
then
    args="$1"
fi

echo "running from " $PWD
echo "scanning     " $args
JDIR=$PWD"/jars";
echo "using jars from " $JDIR



cpath=""
for X in $JDIR/*.jar
do
  cpath=($cpath":"$X)
done

echo $cpath

#echo "java \
#    -Dorg.apache.commons.logging.LogFactory=org.apache.commons.logging.impl.LogFactoryImpl \
#    -Xbootclasspath/p${cpath} \
#    -Xmx300M  \
#    -jar pdb2hibernate.jar $args &"

#    -Xbootclasspath/p${cpath} \
#  -Xbootclasspath/p:./jars/hibernate3.jar:./jars/commons-logging-1.1.jar \

#     -Xbootclasspath/p:./jars/hibernate3.jar:./jars/commons-logging-1.1.jar \



java \
    -cp $cpath \
    -Xms400M -Xmx400M  \
    -Dorg.apache.commons.logging.LogFactory=org.apache.commons.logging.impl.LogFactoryImpl \
    -Dlog4j.configuration=log4j.properties \
     org.biojava.bio.structure.hibernate.DemoHibernateData $args >& /tmp/fillpdb.out &

echo "done"