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 92d71536e..3fd9a3c6d 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
@@ -38,6 +38,7 @@ 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 7c4c3f26a..14c10c581 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
@@ -37,6 +37,7 @@ 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 cac436906..3c122ee60 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
@@ -37,6 +37,7 @@ 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