From c4707631e2c216c5359dbffb2c5cf6d6d3bebbd7 Mon Sep 17 00:00:00 2001 From: depristo Date: Sun, 6 Feb 2011 17:03:45 +0000 Subject: [PATCH] MethodsDevelopmentPipeline is now the test bed for large scale AWS_S3 logging. Can be disabled from command line if this is necessary git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5203 348d0f76-0448-11de-a6fe-93d51630548a --- .../rpoplin/MethodsDevelopmentCallingPipeline.scala | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala index 8619aa833..8f54ff1db 100755 --- a/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala @@ -1,5 +1,6 @@ import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.QScript +import org.broadinstitute.sting.gatk.phonehome.GATKRunReport class MethodsDevelopmentCallingPipeline extends QScript { qscript => @@ -31,7 +32,15 @@ class MethodsDevelopmentCallingPipeline extends QScript { @Argument(shortName="noCut", doc="adds the ApplyVariantCut walker to the pipeline", required=false) var noCut: Boolean = false - trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(3); } + @Argument(shortName="LOCAL_ET", doc="Doesn't use the AWS S3 storage for ET option", required=false) + var LOCAL_ET: Boolean = false + + trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { + logging_level = "INFO"; + jarFile = gatkJarFile; + memoryLimit = Some(3); + phone_home = Some(if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3) + } class Target( val baseName: String,