From 5fac5bf12eb8c40af4809f0d4a31812a29d3b4a0 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Tue, 23 Oct 2012 14:08:31 -0400 Subject: [PATCH] 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 --- .../sting/queue/extensions/picard/CalculateHsMetrics.scala | 1 - .../sting/queue/extensions/picard/CollectGcBiasMetrics.scala | 1 - .../sting/queue/extensions/picard/CollectMultipleMetrics.scala | 1 - 3 files changed, 3 deletions(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala index aa36e29b6..3db498210 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala @@ -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 diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala index cba6ce2bb..fa655206d 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala @@ -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 diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala index b9af5258c..3695114c4 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala @@ -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