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Turning off PHONE HOME option in the MDCP 

* MDCP is for internal use and there is no need to report to the Amazon cloud.
   * Reporting to ASW_S3 is not allowing jobs to finish, this is probably a bug.
This commit is contained in:
Mauricio Carneiro 2012-01-27 11:13:30 -05:00
parent f8f2152f9c
commit 052a4bdb9c
1 changed files with 1 additions and 4 deletions
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5
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -25,9 +25,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
@Argument(shortName="noIndels", doc="do not call indels with the Unified Genotyper", required=false) @Argument(shortName="noIndels", doc="do not call indels with the Unified Genotyper", required=false)
var noIndels: Boolean = false var noIndels: Boolean = false
@Argument(shortName="LOCAL_ET", doc="Doesn't use the AWS S3 storage for ET option", required=false)
var LOCAL_ET: Boolean = false
@Argument(shortName="mbq", doc="The minimum Phred-Scaled quality score threshold to be considered a good base.", required=false) @Argument(shortName="mbq", doc="The minimum Phred-Scaled quality score threshold to be considered a good base.", required=false)
var minimumBaseQuality: Int = -1 var minimumBaseQuality: Int = -1
@ -203,7 +200,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
logging_level = "INFO"; logging_level = "INFO";
memoryLimit = 4; memoryLimit = 4;
phone_home = if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3 phone_home = GATKRunReport.PhoneHomeOption.NO_ET
} }
def bai(bam: File) = new File(bam + ".bai") def bai(bam: File) = new File(bam + ".bai")