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Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.

This commit is contained in:
Mauricio Carneiro 2011-07-05 16:30:10 -04:00
parent cd53e5a131
commit 7d3dfdfdf2
1 changed files with 0 additions and 4 deletions
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4
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -19,9 +19,6 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
class MethodsDevelopmentCallingPipeline extends QScript { class MethodsDevelopmentCallingPipeline extends QScript {
qscript => qscript =>
@Argument(shortName="gatk", doc="gatk jar file", required=true)
var gatkJarFile: File = _
@Argument(shortName="outputDir", doc="output directory", required=true) @Argument(shortName="outputDir", doc="output directory", required=true)
var outputDir: String = "./" var outputDir: String = "./"
@ -185,7 +182,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
logging_level = "INFO"; logging_level = "INFO";
jarFile = gatkJarFile;
memoryLimit = 4; memoryLimit = 4;
phone_home = if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3 phone_home = if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3
} }