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Fixed issues with Queue packaging of Picard QC classes: separate jar's are needed fromPicard. User needs to specify the -picardBase argument to point to input path for jars. 

> Also, reenable joint cleaning as now it works.
> DEV-125 #resolve
> DEV-90 #resolve
This commit is contained in:
Guillermo del Angel 2012-10-23 14:08:31 -04:00
parent 41b5f25bf3
commit 5fac5bf12e
3 changed files with 0 additions and 3 deletions
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1
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
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@ -13,7 +13,6 @@ import net.sf.picard.analysis.MetricAccumulationLevel
*/
class CalculateHsMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction {
analysisName = "CalculateHsMetrics"
javaMainClass = "net.sf.picard.analysis.directed.CalculateHsMetrics"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
var input: Seq[File] = Nil

1
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala
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@ -12,7 +12,6 @@ import java.io.File
*/
class CollectGcBiasMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction {
analysisName = "CollectGcBiasMetrics"
javaMainClass = "net.sf.picard.analysis.CollectGcBiasMetrics"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
var input: Seq[File] = Nil

1
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
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@ -12,7 +12,6 @@ import java.io.File
*/
class CollectMultipleMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction{
analysisName = "CollectMultipleMetrics"
javaMainClass = "net.sf.picard.analysis.CollectMultipleMetrics"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
var input: Seq[File] = Nil