From 990677ec365c09475a4a66cefd453e892e64653c Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 Oct 2010 11:23:34 +0000
Subject: [PATCH] Also removed contig intervals from the pipeline sanity check
 perl scsript.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4540 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/runPipelineSanityCheck.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/perl/runPipelineSanityCheck.pl b/perl/runPipelineSanityCheck.pl
index b8556afd9..f50758ab8 100755
--- a/perl/runPipelineSanityCheck.pl
+++ b/perl/runPipelineSanityCheck.pl
@@ -163,8 +163,8 @@ $ENV{'PATH'} = "$args{'testRepositoryDir'}/shell:$args{'testRepositoryDir'}/pyth
 &execute("cd $args{'testRepositoryDir'} && ant dist playground oneoffs queue",  0, 1200, $args{'run'}, $args{'logFile'}, $args{'email'});
 &execute("cd $args{'testRepositoryDir'} && svn info",                           1, 10,   $args{'run'}, $args{'logFile'}, $args{'email'});
 
-&execute("cd $args{'testOutputDir'} && java -jar $args{'testRepositoryDir'}/dist/Queue.jar -jobProject QueuePipelineTest -S $args{'testRepositoryDir'}/scala/qscript/fullCallingPipeline.q -Y $args{'testInputYAML'} -refseqTable /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg18.txt --gatkjar $args{'testRepositoryDir'}/dist/GenomeAnalysisTK.jar -contigIntervals /humgen/gsa-hpprojects/analysis/pipeline/resources/whole_genome.intervals -titv 3.0 -skipCleaning -bsub", 0, 120, $args{'run'}, $args{'logFile'}, $args{'email'});
-&execute("cd $args{'testOutputDir'} && java -jar $args{'testRepositoryDir'}/dist/Queue.jar -jobProject QueuePipelineTest -S $args{'testRepositoryDir'}/scala/qscript/fullCallingPipeline.q -Y $args{'testInputYAML'} -refseqTable /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg18.txt --gatkjar $args{'testRepositoryDir'}/dist/GenomeAnalysisTK.jar -contigIntervals /humgen/gsa-hpprojects/analysis/pipeline/resources/whole_genome.intervals -titv 3.0 -skipCleaning -bsub -run", 0, 2400, $args{'run'}, $args{'logFile'}, $args{'email'});
+&execute("cd $args{'testOutputDir'} && java -jar $args{'testRepositoryDir'}/dist/Queue.jar -jobProject QueuePipelineTest -S $args{'testRepositoryDir'}/scala/qscript/fullCallingPipeline.q -Y $args{'testInputYAML'} -refseqTable /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg18.txt --gatkjar $args{'testRepositoryDir'}/dist/GenomeAnalysisTK.jar -titv 3.0 -skipCleaning -bsub", 0, 120, $args{'run'}, $args{'logFile'}, $args{'email'});
+&execute("cd $args{'testOutputDir'} && java -jar $args{'testRepositoryDir'}/dist/Queue.jar -jobProject QueuePipelineTest -S $args{'testRepositoryDir'}/scala/qscript/fullCallingPipeline.q -Y $args{'testInputYAML'} -refseqTable /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg18.txt --gatkjar $args{'testRepositoryDir'}/dist/GenomeAnalysisTK.jar -titv 3.0 -skipCleaning -bsub -run", 0, 2400, $args{'run'}, $args{'logFile'}, $args{'email'});
 
 &log("All tests completed successfully");