#!/bin/sh

source $HOME/.bashrc

echo "CIPRES_THREADSPP=$CIPRES_THREADSPP"
echo "CIPRES_NP=$CIPRES_NP"
echo "running:"

module purge

export BEAST_HOME="/projects/ps-ngbt/opt/gordon/beast2/2.1.3"
# Directory where all the installed packages are located.
export PACKAGE_HOME="/projects/ps-ngbt/opt/gordon/beast2/2.1.3/PACKAGES" 

#WE need to know which argument is the input file, since we will transform it.
BEASTARGS=""
while [ $# -gt 1 ]
do
	BEASTARGS+=$1
	BEASTARGS+=" "
	shift 1
done

INPUTFILENAME=$1
shift 1

set -e

export ALTERED_FILENAME=$(basename ${INPUTFILENAME} .xml)_altered.xml

#Begin XSLT transformation
apply_beast2_xslt.bash --useJava true ${INPUTFILENAME} > ${ALTERED_FILENAME}
#END XSLT


#Begin error message for users that used ParticleFilter
#TODO: Remove this section when you've added a CIPRES script for particle-filter to the XSLT
set +e
grep -q 'contact-CIPRES-admins' ${ALTERED_FILENAME}
if [  $? == "0" ] 
then
	echo "Please do not use ParticleFilter or PathSampler in your BEAST2 input files." 1>&2
	exit 1
fi
set -e
#End ParticleFilter

#inform user of alterations

echo "NOTICE : Your input file may have been altered to activate multi-threading."
echo "NOTICE : Your input file may have been altered to activate multi-threading." 1>&2

echo "running:"

cmdline="java -Xmx15000m -Djava.library.path="$BEAST_HOME/lib" -cp "$BEAST_HOME/lib/beast.jar:$BEAST_HOME/BEASTlabs/lib/BEASTlabs.addon.jar:$BEAST_HOME/BEAST_CLASSIC/lib/BEAST_CLASSIC.addon.jar:$PACKAGE_HOME/BDSKY/lib/BDSSM.addon.jar:$PACKAGE_HOME/SA/lib/SA.addon.jar:$PACKAGE_HOME/SubstBMA/lib/SubstBMA.addon.jar" beast.app.beastapp.BeastMain ${BEASTARGS} ${ALTERED_FILENAME}"
echo $cmdline
$cmdline