From 7d3dfdfdf2e92f502c4394d338ca01c5de6287e5 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Tue, 5 Jul 2011 16:30:10 -0400 Subject: [PATCH 1/2] Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter. --- .../queue/qscripts/MethodsDevelopmentCallingPipeline.scala | 4 ---- 1 file changed, 4 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala index d71c6ae5d..f5b639185 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala @@ -19,9 +19,6 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport class MethodsDevelopmentCallingPipeline extends QScript { qscript => - @Argument(shortName="gatk", doc="gatk jar file", required=true) - var gatkJarFile: File = _ - @Argument(shortName="outputDir", doc="output directory", required=true) var outputDir: String = "./" @@ -185,7 +182,6 @@ class MethodsDevelopmentCallingPipeline extends QScript { trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; - jarFile = gatkJarFile; memoryLimit = 4; phone_home = if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3 } From 5298e3a942be54c05a8d765c7aaca99e9c061f8a Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Tue, 5 Jul 2011 16:30:41 -0400 Subject: [PATCH 2/2] Making the outputDir optional. Default = ./ --- .../queue/qscripts/MethodsDevelopmentCallingPipeline.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala index f5b639185..a961beca1 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala @@ -19,7 +19,7 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport class MethodsDevelopmentCallingPipeline extends QScript { qscript => - @Argument(shortName="outputDir", doc="output directory", required=true) + @Argument(shortName="outputDir", doc="output directory", required=false) var outputDir: String = "./" @Argument(shortName="skipCalling", doc="skip the calling part of the pipeline and only run VQSR on preset, gold standard VCF files", required=false)