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