Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/README.md
+++ b/README.md
@@ -3,4 +3,4 @@
 # Language: Java, Bash
 # Information about documentation is in /docs/readme.txt.

-# Version 38.43
+# Version 38.62
--- a/a_sample_mt.sh
+++ b/a_sample_mt.sh
@@ -3,7 +3,7 @@
 usage(){
 echo "
 Written by Brian Bushnell
-Last modified August 22, 2018
+Last modified July 31, 2019

 Description:  Does nothing.  Should be fast.

@@ -53,8 +53,6 @@ CP="$DIR""current/"

 z="-Xmx4g"
 z2="-Xms4g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -64,6 +62,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 		return
@@ -75,25 +74,7 @@ calcXmx () {
 calcXmx "$@"

 a_sample_mt() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		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 load pigz
-	fi
-	local CMD="java $EA $EOOM $z -cp $CP jgi.A_SampleMT $@"
+	local CMD="java $EA $EOOM $z -cp $CP templates.A_SampleMT $@"
 	echo $CMD >&2
 	eval $CMD
 }

--- a/addadapters.sh
+++ b/addadapters.sh
@@ -53,8 +53,6 @@ popd > /dev/null
 CP="$DIR""current/"

 z="-Xmx200m"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -64,29 +62,12 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 }
 calcXmx "$@"

 function addadapters() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		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 load pigz
-	fi
 	local CMD="java $EA $EOOM $z -cp $CP jgi.AddAdapters $@"
 	echo $CMD >&2
 	eval $CMD

--- a/analyzeaccession.sh
+++ b/analyzeaccession.sh
@@ -40,8 +40,6 @@ CP="$DIR""current/"

 z="-Xmx400m"
 z2="-Xms400m"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -51,29 +49,12 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 }
 calcXmx "$@"

 a_sample_mt() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		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 load pigz
-	fi
 	local CMD="java $EA $EOOM $z -cp $CP tax.AnalyzeAccession $@"
 	echo $CMD >&2
 	eval $CMD

--- a/analyzegenes.sh
+++ b/analyzegenes.sh
@@ -37,10 +37,8 @@ popd > /dev/null
 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
 CP="$DIR""current/"

-z="-Xmx1g"
-z2="-Xms1g"
-EA="-ea"
-EOOM=""
+z="-Xmx2g"
+z2="-Xms2g"
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -50,29 +48,12 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 }
 calcXmx "$@"

 function analyze() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		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 load pigz
-	fi
 	local CMD="java $EA $EOOM $z $z2 -cp $CP prok.AnalyzeGenes $@"
 	#echo $CMD >&2
 	eval $CMD

--- a/bbcms.sh
+++ b/bbcms.sh
@@ -116,8 +116,6 @@ CP="$DIR""current/"

 z="-Xmx4g"
 z2="-Xms4g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -127,6 +125,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 		return
@@ -138,24 +137,6 @@ calcXmx () {
 calcXmx "$@"

 bloomfilter() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		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 load pigz
-	fi
 	local CMD="java $EA $EOOM $z $z2 -cp $CP bloom.BloomFilterCorrectorWrapper $@"
 	echo $CMD >&2
 	eval $CMD

--- a/bbcountunique.sh
+++ b/bbcountunique.sh
@@ -64,8 +64,6 @@ CP="$DIR""current/"

 z="-Xmx1g"
 z2="-Xms1g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -75,6 +73,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 	return
@@ -86,24 +85,6 @@ calcXmx () {
 calcXmx "$@"

 bbcountunique() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		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 load pigz
-	fi
 	local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.CalcUniqueness $@"
 	echo $CMD >&2
 	eval $CMD

--- a/bbduk.sh
+++ b/bbduk.sh
@@ -3,7 +3,7 @@
 usage(){
 echo "
 Written by Brian Bushnell
-Last modified March 21, 2019
+Last modified April 11, 2019

 Description:  Compares reads to the kmers in a reference dataset, optionally 
 allowing an edit distance. Splits the reads into two outputs - those that 
@@ -205,7 +205,6 @@ minlength=10        (ml) Reads shorter than this after trimming will be
 mlf=0               (minlengthfraction) Reads shorter than this fraction of 
                    original length after trimming will be discarded.
 maxlength=          Reads longer than this after trimming will be discarded.
-                    Pairs will be discarded only if both are longer.
 minavgquality=0     (maq) Reads with average quality (after trimming) below 
                    this will be discarded.
 maqb=0              If positive, calculate maq from this many initial bases.
@@ -321,12 +320,11 @@ popd > /dev/null

 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
 CP="$DIR""current/"
-NATIVELIBDIR="$DIR""jni/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""

 z="-Xmx1g"
 z2="-Xms1g"
-EA="-ea"
-EOOM=""
 set=0
 silent=0
 json=0
@@ -338,6 +336,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 		return
@@ -349,32 +348,7 @@ calcXmx () {
 calcXmx "$@"

 bbduk() {
-	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 [[ $NERSC_HOST == cori ]]; then
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/usg
-		module unload java
-		module load java/1.8.0_144
-		module unload PrgEnv-intel
-		module load PrgEnv-gnu/7.1
-		module load samtools/1.4
-		module load pigz
-	fi
-	#local CMD="java -Djava.library.path=$NATIVELIBDIR $EA $z $z2 -cp $CP jgi.BBDuk $@"
-	local CMD="java $EA $z $z2 -cp $CP jgi.BBDuk $@"
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.BBDuk $@"
 	if [[ $silent == 0 ]] && [[ $json == 0 ]]; then
 		echo $CMD >&2
 	fi

--- a/bbest.sh
+++ b/bbest.sh
@@ -38,8 +38,6 @@ CP="$DIR""current/"

 z="-Xmx120m"
 z2="-Xms120m"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -49,35 +47,12 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 }
 calcXmx "$@"

 function bbest() {
-	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 jgi.SamToEst $@"
 #	echo $CMD >&2
 	eval $CMD

--- a/bbfakereads.sh
+++ b/bbfakereads.sh
@@ -58,8 +58,6 @@ popd > /dev/null
 CP="$DIR""current/"

 z="-Xmx600m"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -70,29 +68,12 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 }
 calcXmx "$@"

 function fakereads() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		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 load pigz
-	fi
 	local CMD="java $EA $EOOM $z -cp $CP jgi.FakeReads $@"
 	echo $CMD >&2
 	eval $CMD

--- a/bbmap.sh
+++ b/bbmap.sh
@@ -320,12 +320,11 @@ popd > /dev/null

 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
 CP="$DIR""current/"
-NATIVELIBDIR="$DIR""jni/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""

 z="-Xmx1g"
 z2="-Xms1g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -335,6 +334,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 		return
@@ -347,32 +347,7 @@ calcXmx "$@"


 bbmap() {
-	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 [[ $NERSC_HOST == cori ]]; then
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/usg
-		module unload java
-		module load java/1.8.0_144
-		module unload PrgEnv-intel
-		module load PrgEnv-gnu/7.1
-		module load samtools/1.4
-		module load pigz
-	fi
-	#local CMD="java -Djava.library.path=$NATIVELIBDIR $EA $z -cp $CP align2.BBMap build=1 overwrite=true fastareadlen=500 $@"
-	local CMD="java $EA $z -cp $CP align2.BBMap build=1 overwrite=true fastareadlen=500 $@"
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBMap build=1 overwrite=true fastareadlen=500 $@"
 	echo $CMD >&2
 	eval $CMD
 }

--- a/bbmapskimmer.sh
+++ b/bbmapskimmer.sh
@@ -20,12 +20,11 @@ popd > /dev/null

 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
 CP="$DIR""current/"
-NATIVELIBDIR="$DIR""jni/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""

 z="-Xmx1g"
 z2="-Xms1g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -35,6 +34,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 		return
@@ -46,32 +46,7 @@ calcXmx () {
 calcXmx "$@"

 mapPacBioSkimmer() {
-	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 $z -cp $CP align2.BBMapPacBioSkimmer build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambig=all minscaf=100 startpad=10000 stoppad=10000 midpad=6000 $@"
-	local CMD="java -Djava.library.path=$NATIVELIBDIR $EA $z -cp $CP align2.BBMapPacBioSkimmer build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambig=all minscaf=100 startpad=10000 stoppad=10000 midpad=6000 $@"
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBMapPacBioSkimmer build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambig=all minscaf=100 startpad=10000 stoppad=10000 midpad=6000 $@"
 	echo $CMD >&2
 	eval $CMD
 }

--- a/bbmask.sh
+++ b/bbmask.sh
@@ -81,8 +81,6 @@ CP="$DIR""current/"

 z="-Xmx1g"
 z2="-Xms1g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -92,6 +90,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 		return
@@ -103,24 +102,6 @@ calcXmx () {
 calcXmx "$@"

 bbmask() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		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 load pigz
-	fi
 	local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.BBMask $@"
 	echo $CMD >&2
 	eval $CMD

--- a/bbmerge-auto.sh
+++ b/bbmerge-auto.sh
@@ -25,12 +25,11 @@ popd > /dev/null

 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
 CP="$DIR""current/"
-NATIVELIBDIR="$DIR""jni/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""

 z="-Xmx14g"
 z2="-Xms14g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -40,6 +39,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 		return
@@ -51,26 +51,7 @@ calcXmx () {
 calcXmx "$@"

 function merge() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		module load pigz
-	elif [[ $NERSC_HOST == cori ]]; then
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/usg
-		module unload java
-		module load java/1.8.0_144
-		module load pigz
-	fi
-	#local CMD="java -Djava.library.path=$NATIVELIBDIR $EA $z $z2 -cp $CP jgi.BBMerge $@"
-	local CMD="java $EA $z $z2 -cp $CP jgi.BBMerge $@"
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.BBMerge $@"
 	echo $CMD >&2
 	eval $CMD
 }

--- a/bbmerge.sh
+++ b/bbmerge.sh
@@ -3,7 +3,7 @@
 usage(){
 echo "
 Written by Brian Bushnell and Jonathan Rood
-Last modified February 21, 2019
+Last modified June 26, 2019

 Description:  Merges paired reads into single reads by overlap detection.
 With sufficient coverage, can merge nonoverlapping reads by kmer extension.
@@ -233,12 +233,11 @@ popd > /dev/null

 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
 CP="$DIR""current/"
-NATIVELIBDIR="$DIR""jni/"
+JNI="-Djava.library.path=""$DIR""jni/"
+#JNI=""

 z="-Xmx1000m"
 z2="-Xms1000m"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -248,31 +247,13 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 }
 calcXmx "$@"

 function merge() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		module load pigz
-	elif [[ $NERSC_HOST == cori ]]; then
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/usg
-		module unload java
-		module load java/1.8.0_144
-		module load pigz
-	fi
-	#local CMD="java -Djava.library.path=$NATIVELIBDIR $EA $z $z2 -cp $CP jgi.BBMerge $@"
-	local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.BBMerge $@"
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.BBMerge $@"
 	echo $CMD >&2
 	eval $CMD
 }

--- a/bbnorm.sh
+++ b/bbnorm.sh
@@ -138,8 +138,6 @@ CP="$DIR""current/"

 z="-Xmx31g"
 z2="-Xms31g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -149,6 +147,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 	return
@@ -160,24 +159,6 @@ calcXmx () {
 calcXmx "$@"

 normalize() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		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 load pigz
-	fi
 	local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.KmerNormalize bits=32 $@"
 	echo $CMD >&2
 	eval $CMD

--- a/bbrealign.sh
+++ b/bbrealign.sh
@@ -79,8 +79,6 @@ CP="$DIR""current/"

 z="-Xmx4g"
 z2="-Xms4g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -90,6 +88,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 		return
@@ -101,30 +100,6 @@ calcXmx () {
 calcXmx "$@"

 bbrealign() {
-	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 $z2 -cp $CP var2.Realign $@"
 	echo $CMD >&2
 	eval $CMD

--- a/bbsplit.sh
+++ b/bbsplit.sh
@@ -97,12 +97,11 @@ popd > /dev/null

 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
 CP="$DIR""current/"
-NATIVELIBDIR="$DIR""jni/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""

 z="-Xmx1g"
 z2="-Xms1g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -112,6 +111,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 	return
@@ -123,31 +123,7 @@ calcXmx () {
 calcXmx "$@"

 function bbsplit() {
-	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 [[ $NERSC_HOST == cori ]]; then
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/usg
-		module unload java
-		module load java/1.8.0_144
-		module unload PrgEnv-intel
-		module load PrgEnv-gnu/7.1
-		module load samtools/1.4
-		module load pigz
-	fi
-	local CMD="java -Djava.library.path=$NATIVELIBDIR $EA $z -cp $CP align2.BBSplitter ow=t fastareadlen=500 minhits=1 minratio=0.56 maxindel=20 qtrim=rl untrim=t trimq=6 $@"
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBSplitter ow=t fastareadlen=500 minhits=1 minratio=0.56 maxindel=20 qtrim=rl untrim=t trimq=6 $@"
 	echo $CMD >&2
 	eval $CMD
 }

--- a/bbsplitpairs.sh
+++ b/bbsplitpairs.sh
@@ -59,8 +59,6 @@ popd > /dev/null
 CP="$DIR""current/"

 z="-Xmx200m"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -70,29 +68,12 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 }
 calcXmx "$@"

 splitpairs() {
-	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 pigz
-	elif [[ $NERSC_HOST == denovo ]]; then
-		module unload java
-		module load java/1.8.0_144
-		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 load pigz
-	fi
 	local CMD="java $EA $EOOM $z -cp $CP jgi.SplitPairsAndSingles $@"
 	echo $CMD >&2
 	eval $CMD

--- a/bbwrap.sh
+++ b/bbwrap.sh
@@ -40,12 +40,11 @@ popd > /dev/null

 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
 CP="$DIR""current/"
-NATIVELIBDIR="$DIR""jni/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""

 z="-Xmx1g"
 z2="-Xms1g"
-EA="-ea"
-EOOM=""
 set=0

 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
@@ -55,6 +54,7 @@ fi

 calcXmx () {
 	source "$DIR""/calcmem.sh"
+	setEnvironment
 	parseXmx "$@"
 	if [[ $set == 1 ]]; then
 		return
@@ -66,31 +66,7 @@ calcXmx () {
 calcXmx "$@"

 bbwrap() {
-	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 [[ $NERSC_HOST == cori ]]; then
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi
-		module use /global/common/software/m342/nersc-builds/denovo/Modules/usg
-		module unload java
-		module load java/1.8.0_144
-		module unload PrgEnv-intel
-		module load PrgEnv-gnu/7.1
-		module load samtools/1.4
-		module load pigz
-	fi
-	local CMD="java -Djava.library.path=$NATIVELIBDIR $EA $z -cp $CP align2.BBWrap build=1 overwrite=true fastareadlen=500 $@"
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBWrap build=1 overwrite=true fastareadlen=500 $@"
 	echo $CMD >&2
 	eval $CMD
 }