Commit 252849b4 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 38.63+dfsg

parent b1a11c26

README.md

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@@ -3,4 +3,4 @@ 
# Language: Java, Bash

# Information about documentation is in /docs/readme.txt.



# Version 38.43
 
# Version 38.62

a_sample_mt.sh

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@@ -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

}

addadapters.sh

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@@ -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

analyzeaccession.sh

+1 −20
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@@ -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

analyzegenes.sh

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@@ -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