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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
This commit is contained in:
kshakir 2010-10-21 11:23:34 +00:00
parent b954a5a4d5
commit 990677ec36
1 changed files with 2 additions and 2 deletions
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4
perl/runPipelineSanityCheck.pl
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@ -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");