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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
This commit is contained in:
depristo 2011-02-06 17:03:45 +00:00
parent 8b8b4fced1
commit c4707631e2
1 changed files with 10 additions and 1 deletions
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11
scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala
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@ -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,