jpayne@69: #!/bin/bash
jpayne@69: #See bbmap.sh for documentation.
jpayne@69: 
jpayne@69: usage(){
jpayne@69: 	bash "$DIR"bbmap.sh
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: JNI="-Djava.library.path=""$DIR""jni/"
jpayne@69: JNI=""
jpayne@69: 
jpayne@69: z="-Xmx1g"
jpayne@69: z2="-Xms1g"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: 	if [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 3200m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: mapPacBio() {
jpayne@69: 	if [[ $SHIFTER_RUNTIME == 1 ]]; then
jpayne@69: 		#Ignore NERSC_HOST
jpayne@69: 		shifter=1
jpayne@69: 	elif [[ $NERSC_HOST == genepool ]]; then
jpayne@69: 		module unload oracle-jdk
jpayne@69: 		module load oracle-jdk/1.8_144_64bit
jpayne@69: 		module load samtools/1.4
jpayne@69: 		module load pigz
jpayne@69: 	elif [[ $NERSC_HOST == denovo ]]; then
jpayne@69: 		module unload java
jpayne@69: 		module load java/1.8.0_144
jpayne@69: 		module load PrgEnv-gnu/7.1
jpayne@69: 		module load samtools/1.4
jpayne@69: 		module load pigz
jpayne@69: 	elif [[ $NERSC_HOST == cori ]]; then
jpayne@69: 		module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi
jpayne@69: 		module use /global/common/software/m342/nersc-builds/denovo/Modules/usg
jpayne@69: 		module unload java
jpayne@69: 		module load java/1.8.0_144
jpayne@69: 		module unload PrgEnv-intel
jpayne@69: 		module load PrgEnv-gnu/7.1
jpayne@69: 		module load samtools/1.4
jpayne@69: 		module load pigz
jpayne@69: 	fi
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP align2.BBMapPacBio build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambiguous=best minscaf=100 startpad=10000 stoppad=10000 midpad=6000 $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: mapPacBio "$@"