From 8461cc3a22e93dd5074690fa44942e3a75802c2f Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 8 Oct 2009 18:13:49 +0000
Subject: [PATCH] /tmp is failing... We should be using hptmp anyways.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1793 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/1kgScripts/runCallingPipeline.pl  |  8 ++++----
 perl/1kgScripts/runCleaningPipeline.pl | 12 ++++++------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/perl/1kgScripts/runCallingPipeline.pl b/perl/1kgScripts/runCallingPipeline.pl
index c178f5913..1e5bb550c 100755
--- a/perl/1kgScripts/runCallingPipeline.pl
+++ b/perl/1kgScripts/runCallingPipeline.pl
@@ -41,7 +41,7 @@ my $bsub = "bsub -q $queue -o $indelsHigh.sdout";
 if ($wait) {
     $bsub .= " -w \"ended($wait)\"";
 }
-my $command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."3 -O $indelsHigh";
+my $command = "java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."3 -O $indelsHigh";
 execute("$bsub $command", $dry);
 
 my $indelsLow = "$outputHead.indels.low.calls";
@@ -49,7 +49,7 @@ $bsub = "bsub -q $queue -o $indelsLow.sdout -J $outputHead";
 if ($wait) {
     $bsub .= " -w \"ended($wait)\"";
 }
-$command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."1 -O $indelsLow";
+$command = "java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."1 -O $indelsLow";
 execute("$bsub $command", $dry);
 
 if ($snps) {
@@ -58,13 +58,13 @@ if ($snps) {
     if ($wait) {
 	$bsub .= " -w \"ended($wait)\"";
     }
-    $command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -varout $snpsFile -lod 0.0";
+    $command = "java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -varout $snpsFile -lod 0.0";
     execute("$bsub $command", $dry);
 
     my $filterFile = "$outputHead.snps.filtered.calls";
     my $vcfFile = "$outputHead.snps.vcf";
     $bsub = "bsub -q $queue -o $filterFile.sdout -w \"ended($outputHead)\"";
-    $command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T VariantFiltration -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -vcf $vcfFile -included $filterFile -sample $sample -B dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod,variant,Variants,$snpsFile,";
+    $command = "java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T VariantFiltration -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -vcf $vcfFile -included $filterFile -sample $sample -B dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod,variant,Variants,$snpsFile,";
     if ($badsnps) {
 	$command .= "cleaned,CleanedOutSNP,$badsnps,";
     }
diff --git a/perl/1kgScripts/runCleaningPipeline.pl b/perl/1kgScripts/runCleaningPipeline.pl
index 6025fa1cc..5b5a34dd6 100755
--- a/perl/1kgScripts/runCleaningPipeline.pl
+++ b/perl/1kgScripts/runCleaningPipeline.pl
@@ -31,7 +31,7 @@ GetOptions( "i=s" => \$inputBam,
 usage() if ( !$inputBam || !$outputBam );
 
 my $indelIntervals = "$outputBam.indels.intervals";
-my $command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $indelIntervals -oarg o -j $outputBam.intervals -q $queue";
+my $command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $indelIntervals -oarg o -j $outputBam.intervals -q $queue";
 if ($dry) {
     $command .= " -dry";
 }
@@ -41,7 +41,7 @@ if ($wait) {
 system($command);
 
 my $mismatchIntervals = "$outputBam.mismatches.intervals";
-$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T MismatchIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $mismatchIntervals -oarg o -j $outputBam.intervals -q $queue";
+$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T MismatchIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $mismatchIntervals -oarg o -j $outputBam.intervals -q $queue";
 if ($dry) {
     $command .= " -dry";
 }
@@ -51,7 +51,7 @@ if ($wait) {
 system($command);
 
 my $mergedIntervals = "$outputBam.merged.intervals";
-$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalMerger -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -intervals $indelIntervals -intervals $mismatchIntervals\" -o $mergedIntervals -oarg o -wait $outputBam.intervals -j $outputBam.merged -q $queue";
+$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalMerger -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -intervals $indelIntervals -intervals $mismatchIntervals\" -o $mergedIntervals -oarg o -wait $outputBam.intervals -j $outputBam.merged -q $queue";
 if ($dry) {
     $command .= " -dry";
 }
@@ -63,7 +63,7 @@ if ($inject) {
 } else {
     $cleanedBam = "$outputBam";
 }
-$command = "bsub -q $queue -o $outputBam.cleaner.script1 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -compress 1";
+$command = "bsub -q $queue -o $outputBam.cleaner.script1 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -compress 1";
 if ($inject) {
     $command .= " -cleanedOnly\" -j $outputBam.cleaner.clean";
 } else {
@@ -81,7 +81,7 @@ my $snpsFile = $badsnps;
 if (!$snpsFile) {
     $snpsFile = "$outputBam.badsnps";
 }
-$command = "bsub -q $queue -o $outputBam.cleaner.script2 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\"";
+$command = "bsub -q $queue -o $outputBam.cleaner.script2 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\"";
 if ($inject) {
     $command .= " -j $outputBam.cleaner.badsnps";
 } else {
@@ -101,7 +101,7 @@ if ($inject) {
     if ($jobName) {
 	$command .= " -J $jobName";
     }
-    $command .= " -w \"ended($outputBam.cleaner.*)\" java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T CleanedReadInjector -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam --output_bam $bam --cleaned_reads $cleanedBam -compress 1";
+    $command .= " -w \"ended($outputBam.cleaner.*)\" java -Djava.io.tmpdir=/broad/hptmp/ -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T CleanedReadInjector -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam --output_bam $bam --cleaned_reads $cleanedBam -compress 1";
     if ($dry) {
 	print "$command\n";
     } else {