BENCHMARK RECIPE

1

Deploying GATK Best Practices Pipeline Below are the scripts files accompanying and as documented in the Infrastructure for

Deploying GATK Best Practices Pipeline paper.

____________________________________________________________________________

GATK Best Practices Pipeline_README

The following scripts are designed to take the same arguments to keep it consistent for running tests. For

single threaded baseline analysis with no optimizations, run the data_colletion_gatk_best_practices_pl

script with NumThreads as “1”.

For both thread level and process level parallelism analysis, use the

data_collection_gatk_best_practices_optimized.pl script with NumThreads as proposed in the paper.

____________________________________________________________________________________________

Data Collection Script for GATK Best Practices Pipeline (wgs_end2end_data_collection_gatk_best_practices.pl)

#!/usr/bin/perl

if (scalar(@ARGV) < 5) {

die("Usage: SampleName NumThreads InputDataDirectory TempOutputDirectory profiling \n[if profiling is enabled, then the

following is required]: collectstatspath interval stats \n");

}

my $sample = $ARGV[0];

my $numThreads = $ARGV[1];

my $inDataDir = $ARGV[2];

my $tmpDir = "".$ARGV[3];

my $profiling = $ARGV[4]; #by default profiling is turned ON if invoked from the workflow profiler

# arguments for collect_stats

my $collectstatspath = $ARGV[5];

my $interval = $ARGV[6]; # by default sampling interval is 30s from the workflow profiler.

my $stats = $ARGV[7];

#my $numLanes =$ARGV[1];

my $called = "$0 @ARGV";

my $numLanes = 0;

my $sampleprefix = $sample.'_'.$numThreads.'T';

BENCHMARK RECIPE

2

Data Collection Script for GATK Best Practices Pipeline (cont)

# INPUT FASTQ FILES

#OTHER FORMATS FOR FQ: "_1.fastq.gz; #"_1.fastq";

my $fqFile1, $fqFile2;

$fqFile1 = $inDataDir.$sample."_1.fq";

$fqFile2 = $inDataDir.$sample."_2.fq";

# Pipeline executables and its directories

### SPECIFY PATH IN THE VARIABLES BELOW ###

my $toolsDir = '/PATH/TO/TOOLS_DIR';

my $homosapiensrefgenomeDir = '/PATH/TO/REF';

# TOOLS

my $bwaDir = "$toolsDir/bwa";

my $bwa = "$bwaDir/bwa";

my $gatkDir = "$toolsDir/gatk-protected/target";

my $gatk = "$gatkDir/GenomeAnalysisTK.jar";

my $picardDir ="$toolsDir/picard/dist";

my $picard = "$picardDir/picard.jar";

# HOMOSAPIENSREFGENOME

my $refgenomeFastaFile = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.fasta";

my $refgenomeBwtFile = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.fasta.bwt";

my $dbSNPvcf = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.dbsnp.vcf";

my $dbSNPindel = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.known_indels.vcf";

# EXOME TARGET INTERVALS

my $exome_targets_intervals = "$homosapiensrefgenomeDir/nexterarapidcapture_exome_uniqueintervals.bed";

unless(-d $inDataDir) {

die("Error: The InputDataDirectory $inDataDir doesn't exist\n");

}

unless(-d $tmpDir) {

die("Error: The TempOutputDirectory $tmpDir doesn't exist\n");

}

# Output file names for each stage of the pipeline

my $baseName = $sample;

my $baseNameLane = $baseName.'_'.$numLanes.'L_'.$numThreads.'T';

my $bwamem_samFile = $tmpDir.$baseNameLane.".sam";

my $sort_bamFile = $tmpDir.$baseName."_sorted.bam";

my $duplicateMetricsFile = $tmpDir.$baseName."_dup.metrics";

my $bamDupRemFile = $tmpDir.$baseName."_dupRem.bam";

my $bamRealignFile = $tmpDir.$baseName."_realign.bam";

my $realnInterval = $tmpDir.$baseName."_realn.intervals";

my $finalBam = $tmpDir.$baseName."_final.bam";

my $HCvcf = $tmpDir.$baseName."_HaplotypeCaller.vcf";

my $genomeImportFile = $refgenomeFastaFile.".fai";

#ADD the relevant platform

my $readGroupHeader = "\@RG\\tID:$baseNameLane\\tLB:$baseName\\tSM:$baseName\\tPL:PLATFORM";

my $recalOut = $tmpDir .$baseName."_recal.grp";

my $dryRun = 0;

my $pwd = `pwd`;

chomp $pwd;

my $host = `hostname`;

chomp $host;

my $uname = `whoami`;

chomp $uname;

my $runningTime = time;

my $commandsfile = $tmpDir.$uname."_".$sampleprefix."_processing.log";

my $outputfile = $tmpDir.$uname."_".$sampleprefix."_output.log";

open(LOG,">$commandsfile");

BENCHMARK RECIPE

3

Data Collection Script for GATK Best Practices Pipeline (cont)

print LOG "#$called (version $version) in $pwd on $host.\n";

print LOG "#Started at ".`date +"%F %T"`."\n";

print LOG "#temporary files created in $tmpDir\n";

my $procTime = time;

my $procFlag = 0;

sub run_and_log {

my $command = $_[0];

my $execute = !$dryRun;

my $exitValue = 0; #a command we don't run is considered successful

my $redirect;

if (@_ >1){

$execute=!$_[1];

}

#several of the programs like to output to STDERR, so we link that to log file

$redirect = "1>>$outputfile 2>&1";

#that is because we redirect STDOUT in many cases, so let's not mess with it.

$redirect = "2>>$outputfile" if $command =~ m/>/;

# $redirect = "" if $command =~ m/>/;

$command = $command." ".$redirect;

if ($procFlag == 0){

$procFlag++;

} else {

$procTime = time - $procTime;

printf LOG "#Processing Time %02d:%02d:%02d\n",int($procTime /3600),int(($procTime % 3600)

/60),int($procTime %60);

$procTime = time;

}

print LOG "#not run\n" if !$execute;

print LOG "#".`date +"%F %T"`;

print LOG $command."\n";

$exitValue = system($command) if $execute;

#necessary if we use `` instead of system()

#$exitValue = $? >>8;

##If the command failed, we want to stop it here.

if ($exitValue != 0){

my $error = "Command failed with return value $exitValue : $command \n";

print LOG $error;

close LOG;

die $error;

}

}

sub Start_profiling {

my ($tag) = @_;

if ($profiling) {

system("$collectstatspath $stats -d $interval -td $tmpDir -n $sampleprefix -tag $tag -l 5 -u 1 -s 600 &");

}

}

sub Stop_Profiling {

BENCHMARK RECIPE

4

Data Collection Script for GATK Best Practices Pipeline (cont)

if ($profiling) {

system("$collectstatspath --kill-all");

}

}

my $stage_tag=BwaMem;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "$bwa mem -t $numThreads -Ma -R \'$readGroupHeader\' $refgenomeFastaFile $fqFile1 $fqFile2 >

$bwamem_samFile";

Stop_Profiling();

sleep(60);

my $stage_tag=SortSam;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Xmx8g -jar $picard SortSam I=$bwamem_samFile O=$sort_bamFile SO=coordinate

CREATE_INDEX=true";

Stop_Profiling();

sleep(60);

my $stage_tag=MarkDuplicates;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Xmx8g -jar $picard MarkDuplicates I=$sort_bamFile O=$bamDupRemFile

M=$duplicateMetricsFile CREATE_INDEX=true TMP_DIR=$tmpDir";

Stop_Profiling();

sleep(60);

my $stage_tag=RealignerTargetCreator;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Xmx8g -jar $gatk -T RealignerTargetCreator -nt $numThreads -R $refgenomeFastaFile -o

$realnInterval -known:indels,vcf $dbSNPindel -I $bamDupRemFile";

Stop_Profiling();

sleep(60);

my $stage_tag=IndelRealigner;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Xmx8g -Djava.io.tmpdir=$tmpDir -jar $gatk -T IndelRealigner -R $refgenomeFastaFile -

targetIntervals $realnInterval -known:indels,vcf $dbSNPindel -I $bamDupRemFile -o $bamRealignFile --

filter_bases_not_stored";

Stop_Profiling();

sleep(60);

my $stage_tag=BaseRecalibrator;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Xmx4g -jar $gatk -T BaseRecalibrator -I $bamRealignFile -R $refgenomeFastaFile -

knownSites:mask,vcf $dbSNPvcf -o $recalOut";

Stop_Profiling();

sleep(60);

BENCHMARK RECIPE

5

Stages of GATK Best Practices Pipeline (cont)

my $stage_tag=PrintReads;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Xmx8g -jar $gatk -T PrintReads -R $refgenomeFastaFile -I $bamRealignFile -BQSR $recalOut

-o $finalBam";

Stop_Profiling();

sleep(60);

my $stage_tag=HaplotypeCaller;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Xmx8g -jar $gatk -T HaplotypeCaller -R $refgenomeFastaFile -I $finalBam -o $HCvcf -ERC

GVCF --variant_index_type LINEAR --variant_index_parameter 128000";

Stop_Profiling();

sleep(60);

$runningTime = time - $runningTime;

printf LOG "#done in %02d:%02d:%02d\n",int($runningTime /3600),int(($runningTime % 3600)

/60),int($runningTime %60);

exit 0;

Data Collection Script for GATK Best Practices Pipeline Optimized (wgs_end2end_data_collection_gatk_best_practices_optimized.pl)

#!/usr/bin/perl

if (scalar(@ARGV) < 5) {

die("Usage: SampleName NumThreads InputDataDirectory TempOutputDirectory profiling \n[if profiling is

enabled, then the following is required]: collectstatspath interval stats \n");

}

my $sample = $ARGV[0];

my $numThreads = $ARGV[1];

my $inDataDir = $ARGV[2];

my $tmpDir = "".$ARGV[3];

my $profiling = $ARGV[4]; #by default profiling is turned ON if invoked from the workflow profiler

# arguments for collect_stats

my $collectstatspath = $ARGV[5];

my $interval = $ARGV[6]; # by default sampling interval is 30s from the workflow profiler.

my $stats = $ARGV[7];

#my $numLanes =$ARGV[1];

my $called = "$0 @ARGV";

my $numLanes = 0;

my $sampleprefix = $sample.'_'.$numThreads.'T';

BENCHMARK RECIPE

6

Data Collection Script for GATK Best Practices Pipeline Optimized (cont)

# INPUT FASTQ FILES

#OTHER FORMATS FOR FQ: "_1.fastq.gz; #"_1.fastq";

my $fqFile1, $fqFile2;

$fqFile1 = $inDataDir.$sample."_1.fq";

$fqFile2 = $inDataDir.$sample."_2.fq";

# Pipeline executables and its directories

### SPECIFY PATH IN THE VARIABLES BELOW ###

my $toolsDir = '/PATH/TO/TOOLS_DIR';

#SCALA_SCRIPTS: Scripts to be passed to Queue.jar

my $QueueBroadBestPracticesDir = '/PATH/TO/SCALA_SCRIPTS';

my $homosapiensrefgenomeDir = '/PATH/TO/REF';

# TOOLS

my $bwaDir = "$toolsDir/bwa";

my $bwa = "$bwaDir/bwa";

my $gatkDir = "$toolsDir/gatk-protected/target";

my $gatk = "$gatkDir/GenomeAnalysisTK.jar";

my $gatk_queue = "$QueueBroadBestPracticesDir/Queue.jar";

my $picardDir ="$toolsDir/picard/dist";

my $picard = "$picardDir/picard.jar";

# HOMOSAPIENSREFGENOME

my $refgenomeFastaFile = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.fasta";

my $refgenomeBwtFile = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.fasta.bwt";

my $dbSNPvcf = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.dbsnp.vcf";

my $dbSNPindel = "$homosapiensrefgenomeDir/Homo_sapiens_assembly19.known_indels.vcf";

# QUEUE

my $nfs_ExampleIndelRealigner = "$QueueBroadBestPracticesDir/ExampleIndelRealigner.scala";

my $nfs_ExampleBaseRecalibrator = "$QueueBroadBestPracticesDir/ExampleBaseRecalibrator.scala";

my $nfs_ExamplePrintReads = "$QueueBroadBestPracticesDir/ExamplePrintReads.scala";

my $nfs_ExampleHaplotypeCaller = "$QueueBroadBestPracticesDir/ExampleHaplotypeCaller.scala";

# REMOVE QUEUE RELATED FOLDERS AFTER COMPLETION

my $cwd = `cwd`;

print "$cwd\n";

my $queueDir = $cwd . "/.queue";

print "$queueDir\n";

my $jobReport = $cwd . "*.jobreport.txt";

my $ExampleDir = $tmpDir . "/Example*";

unless(-d $inDataDir) {

die("Error: The InputDataDirectory $inDataDir doesn't exist\n");

}

unless(-d $tmpDir) {

die("Error: The TempOutputDirectory $tmpDir doesn't exist\n");

}

# Output file names for each stage of the pipeline

my $baseName = $sample;

my $baseNameLane = $baseName.'_'.$numLanes.'L_'.$numThreads.'T';

my $bwamem_samFile = $tmpDir.$baseNameLane.".sam";

my $sort_bamFile = $tmpDir.$baseName."_sorted.bam";

my $duplicateMetricsFile = $tmpDir.$baseName."_dup.metrics";

BENCHMARK RECIPE

7

Data Collection Script for GATK Best Practices Pipeline Optimized (cont)

my $bamDupRemFile = $tmpDir.$baseName."_dupRem.bam";

my $bamRealignFile = $tmpDir.$baseName."_realign.bam";

my $realnInterval = $tmpDir.$baseName."_realn.intervals";

my $finalBam = $tmpDir.$baseName."_final.bam";

my $HCvcf = $tmpDir.$baseName."_HaplotypeCaller.vcf";

my $genomeImportFile = $refgenomeFastaFile.".fai";

#ADD the relevant platform

my $readGroupHeader = "\@RG\\tID:$baseNameLane\\tLB:$baseName\\tSM:$baseName\\tPL:PLATFORM";

my $recalOut = $tmpDir .$baseName."_recal.grp";

my $dryRun = 0;

my $pwd = `pwd`;

chomp $pwd;

my $host = `hostname`;

chomp $host;

my $uname = `whoami`;

chomp $uname;

my $runningTime = time;

my $commandsfile = $tmpDir.$uname."_".$sampleprefix."_processing.log";

my $outputfile = $tmpDir.$uname."_".$sampleprefix."_output.log";

open(LOG,">$commandsfile");

print LOG "#$called (version $version) in $pwd on $host.\n";

print LOG "#Started at ".`date +"%F %T"`."\n";

print LOG "#temporary files created in $tmpDir\n";

my $procTime = time;

my $procFlag = 0;

sub run_and_log {

my $command = $_[0];

my $execute = !$dryRun;

my $exitValue = 0; #a command we don't run is considered successful

my $redirect;

if (@_ >1){

$execute=!$_[1];

}

#several of the programs like to output to STDERR, so we link that to log file

$redirect = "1>>$outputfile 2>&1";

#that is because we redirect STDOUT in many cases, so let's not mess with it.

$redirect = "2>>$outputfile" if $command =~ m/>/;

# $redirect = "" if $command =~ m/>/;

$command = $command." ".$redirect;

if ($procFlag == 0){

$procFlag++;

} else {

$procTime = time - $procTime;

printf LOG "#Processing Time %02d:%02d:%02d\n",int($procTime /3600),int(($procTime % 3600)

/60),int($procTime %60);

$procTime = time;

BENCHMARK RECIPE

8

Data Collection Script for GATK Best Practices Pipeline Optimized (cont)

}

print LOG "#not run\n" if !$execute;

print LOG "#".`date +"%F %T"`;

print LOG $command."\n";

$exitValue = system($command) if $execute;

#necessary if we use `` instead of system()

#$exitValue = $? >>8;

##If the command failed, we want to stop it here.

if ($exitValue != 0){

my $error = "Command failed with return value $exitValue : $command \n";

print LOG $error;

close LOG;

die $error;

}

}

sub Start_profiling {

my ($tag) = @_;

if ($profiling) {

system("$collectstatspath $stats -d $interval -td $tmpDir -n $sampleprefix -tag $tag -l 5 -u 1 -s 600 &");

}

}

sub Stop_Profiling {

if ($profiling) {

system("$collectstatspath --kill-all");

}

}

my $stage_tag=BwaMem;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "$bwa mem -t $numThreads -Ma -R \'$readGroupHeader\' $refgenomeFastaFile $fqFile1 $fqFile2 >

$bwamem_samFile";

Stop_Profiling();

sleep(60);

my $stage_tag=SortSam;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Dsamjdk.try_use_intel_deflater=true -jar $picard SortSam I=$bwamem_samFile

O=$sort_bamFile SO=coordinate CREATE_INDEX=true TMP_DIR=$tmpDir";

Stop_Profiling();

sleep(60);

my $stage_tag=MarkDuplicates;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Dsamjdk.try_use_intel_deflater=true -jar $picard MarkDuplicates I=$sort_bamFile

O=$bamDupRemFile M=$duplicateMetricsFile CREATE_INDEX=true TMP_DIR=$tmpDir";

Stop_Profiling();

sleep(60);

BENCHMARK RECIPE

9

Data Collection Script for GATK Best Practices Pipeline Optimized (cont)

my $stage_tag=RealignerTargetCreator;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -jar $gatk -T RealignerTargetCreator -nt $numThreads -R $refgenomeFastaFile -o $realnInterval

-known:indels,vcf $dbSNPindel -I $bamDupRemFile";

Stop_Profiling();

sleep(60);

my $stage_tag=IndelRealigner;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Djava.io.tmpdir=$tmpDir -jar $gatk_queue -R $refgenomeFastaFile -I $bamDupRemFile -indels

$dbSNPindel -S $nfs_ExampleIndelRealigner -l DEBUG -run -jobRunner CMPShell" ;

Stop_Profiling();

system("rm -rf $queueDir; rm -r $jobReport; rm -rf $ExampleDir");

sleep(60);

my $stage_tag=BaseRecalibrator;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Djava.io.tmpdir=$tmpDir -jar $gatk_queue -I $bamRealignFile -R $refgenomeFastaFile -D

$dbSNPvcf -S $nfs_ExampleBaseRecalibrator -l DEBUG -run -jobRunner CMPShell" ;

Stop_Profiling();

system("rm -rf $queueDir; rm -r $jobReport; rm -rf $ExampleDir");

sleep(60);

my $stage_tag=PrintReads;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Djava.io.tmpdir=$tmpDir -jar $gatk_queue -R $refgenomeFastaFile -I $bamRealignFile -B

$recalOut -l DEBUG -S $nfs_ExamplePrintReads -run -jobRunner CMPShell" ;

Stop_Profiling();

system("rm -rf $queueDir; rm -r $jobReport; rm -rf $ExampleDir");

sleep(60);

my $stage_tag=HaplotypeCaller;

Start_profiling($stage_tag);

print "$stage_tag\n";

run_and_log "java -Djava.io.tmpdir=$tmpDir -jar $gatk_queue -R $refgenomeFastaFile -I $finalBam -l DEBUG -S

$nfs_ExampleHaplotypeCaller -run -jobRunner CMPShell";

Stop_Profiling();

system("rm -rf $queueDir; rm -r $jobReport; rm -rf $ExampleDir");

sleep(60);

$runningTime = time - $runningTime;

printf LOG "#done in %02d:%02d:%02d\n",int($runningTime /3600),int(($runningTime % 3600)

/60),int($runningTime %60);

exit 0;

_____

BENCHMARK RECIPE

10

CMPShell_README.scala

Steps to run Queue using CMPShell:

1) The 'cmpshell' directory needs to be created with the CMPShellJobRunner.scala and CMPShellJobManager.scala

and added here : scala/src/org/broadinstitute/sting/queue/engine/cmpshell

2) Queue.jar must be recompiled to use 'CMPShell'

3) Pass 'CMPShell' as the argument to -jobRunner when running Queue.jar.

CMPShell.JobRunner.scala

Package org.broadinstitute.sting.queue.engine.shell

Import org.broadinstitute.sting.queue.function.CommandLineFunction

import org.broadinstitute.sting.queue.engine.{RunnerStatus, CommandLineJobRunner}

import java.util.Date

import org.broadinstitute.sting.utils.Utils

import org.broadinstitute.sting.utils.runtime.{ProcessSettings, OutputStreamSettings, ProcessController}

import java.util.concurrent.{Executors, ExecutorService}

import Array._

/**

* Runs jobs one at a time locally

* @param function Command to run.

*/

class CMPShellJobRunner(val function: CommandLineFunction, pool: ExecutorService, creationCount: Int) extends

CommandLineJobRunner {

// Controller on the thread that started the job

private var controller: ProcessController = null

/**

* Runs the function on the local shell.

*/

def start() {

var executionMachineName = Utils.resolveHostname()

val commandSep = Array(";")

val sshCommandLine = Array("ssh", executionMachineName)

val scriptCommandLine = Array("sh", jobScript.getAbsolutePath)

var inputCommandLine = Array[String]()

if (!function.jobEnvironmentNames.isEmpty) {

inputCommandLine = function.jobEnvironmentNames.mkString("").split(" ")

inputCommandLine = concat(inputCommandLine, commandSep);

}

val commandLine = concat(sshCommandLine, inputCommandLine, scriptCommandLine)

val stdoutSettings = new OutputStreamSettings

val stderrSettings = new OutputStreamSettings

val mergeError = (function.jobErrorFile == null)

stdoutSettings.setOutputFile(function.jobOutputFile, true)

if (function.jobErrorFile != null)

stderrSettings.setOutputFile(function.jobErrorFile, true)

if (logger.isDebugEnabled) {

stdoutSettings.printStandard(true)

stderrSettings.printStandard(true)

}

BENCHMARK RECIPE

11

CMPShellJobRunner.scala (cont)

val processSettings = new ProcessSettings(

commandLine, mergeError, function.commandDirectory, null,

null, stdoutSettings, stderrSettings)

updateJobRun(processSettings)

updateStatus(RunnerStatus.RUNNING)

val runIt = new Thread( new Runnable {

def run() {

getRunInfo.exechosts = executionMachineName

getRunInfo.startTime = new Date()

controller = ProcessController.getThreadLocal

val exitStatus = controller.exec(processSettings).getExitValue

getRunInfo.doneTime = new Date()

updateStatus(if (exitStatus == 0) RunnerStatus.DONE else RunnerStatus.FAILED)

}

})

pool.execute( runIt)

}

def updateJobStatus() = {

true

}

/**

* Possibly invoked from a shutdown thread, find and

* stop the controller from the originating thread

*/

def tryStop() {

// Assumes that after being set the job may be

// reassigned but will not be reset back to null

if (controller != null) {

try {

controller.tryDestroy()

} catch {

case e =>

logger.error("Unable to kill shell job: " + function.description)

}

}

}

}

CMPShellJobManager.scala

package org.broadinstitute.sting.queue.engine.shell

import org.broadinstitute.sting.queue.function.CommandLineFunction

import org.broadinstitute.sting.queue.engine.CommandLineJobManager

BENCHMARK RECIPE

12

CMPShellJobManager.scala (cont)

import java.util.concurrent.{Executors, ExecutorService}

class CMPShellJobManager extends CommandLineJobManager[CMPShellJobRunner] {

protected var pool: ExecutorService = null

var creationCount : Int = 0;

def runnerType = classOf[CMPShellJobRunner]

def create(function: CommandLineFunction) = {

creationCount += 1

new CMPShellJobRunner(function, pool, creationCount)

}

override def init() {

creationCount = 0;

pool = Executors.newFixedThreadPool( 64)

}

override def exit() {

pool.shutdown()

}

override def updateStatus(runners: Set[CMPShellJobRunner]) = {

var updatedRunners = Set.empty[CMPShellJobRunner]

runners.foreach(runner => if (runner.updateJobStatus()) {updatedRunners += runner})

updatedRunners

}

override def tryStop(runners: Set[CMPShellJobRunner]) { runners.foreach(_.tryStop()) }

}

For more information: • Intel Life Sciences code optimizations: www.intel.com/healthcare/optimizecode

• GATK optimizations & reference architecture:

http://www.intel.com/content/www/us/en/healthcare-it/solutions/genomicscode-gatk.html

• GATK Best Practices Guide: https://www.broadinstitute.org/gatk/guide/best-practices.php

Copyright © 2016 Intel Corporation. All rights reserved. Intel, the Intel logo are trademarks of Intel Corporation in the U.S. and other countries. * Other names and brands may be claimed as the property of others. 02/16