From 7d3dfdfdf2e92f502c4394d338ca01c5de6287e5 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 5 Jul 2011 16:30:10 -0400
Subject: [PATCH] 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
   }