#!/bin/sh

source $HOME/.bashrc

echo "CIPRES_THREADSPP=$CIPRES_THREADSPP"
echo "CIPRES_NP=$CIPRES_NP"

module purge
module load intel
module load beagle/2.1

export BEAST_HOME="/projects/ps-ngbt/opt/gordon/beast2/2.1.0"

#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


#Begin XSLT transformation
mv ${INPUTFILENAME} ${INPUTFILENAME}~
xsltproc - ${INPUTFILENAME}~ << EOF > ${INPUTFILENAME}
<?xml version="1.0"?>

<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">

<xsl:template match="@*|node()">
        <xsl:copy>
                <xsl:apply-templates select="@*|node()"/>
        </xsl:copy>
</xsl:template>

<xsl:template match="distribution[@spec='TreeLikelihood' or @spec='likelihood.TreeLikelihood' or @spec='evolution.likelihood.TreeLikelihood' or @spec='beast.evolution.likelihood.TreeLikelihood']/@spec">
        <xsl:attribute name="spec">
                <xsl:value-of select="'beast.evolution.likelihood.ThreadedTreeLikelihood'"/>
        </xsl:attribute>
</xsl:template>

<!-- You can just replace the content of this template with the appropriate script to run ParticleFilter -->
<!-- See http://www.beast2.org/wiki/index.php/Performance_Suggestions#Particle_Filter -->
<xsl:template match="run[@spec='ParticleFilter' or @spec='inference.ParticleFilter' or @spec='beast.inference.ParticleFilter']/text()">
        <contact-CIPRES-admins-if-you-absolutely-need-particlefilter>
        Please do not use ParticleFilter on CIPRES.
        Contact CIPRES administrators if this is absolutely necessary for your science.
        </contact-CIPRES-admins-if-you-absolutely-need-particlefilter>
</xsl:template>

<xsl:template match="run[@spec='PathSampler' or @spec='inference.PathSampler' or @spec='beast.inference.PathSampler']/text()">
	<contact-CIPRES-admins-if-you-absolutely-need-pathsampling>
	Please do not use PathSampler on CIPRES.
	Contact CIPRES administrators if this is absolutely necessary for your science.
	</contact-CIPRES-admins-if-you-absolutely-need-pathsampling>
</xsl:template>

</xsl:stylesheet>

EOF
rm ${INPUTFILENAME}~
#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' ${INPUTFILENAME}
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

echo "running:"

cmdline="java -Xmx15000m -Djava.library.path="$BEAST_HOME/lib:$BEAGLE_HOME/lib" -cp "$BEAST_HOME/lib/beast.jar:$BEAST_HOME/BEASTii/lib/BEASTii.addon.jar" beast.app.beastapp.BeastMain ${BEASTARGS} ${INPUTFILENAME}"
echo $cmdline
$cmdline