diff --git a/packages/Queue.xml b/packages/Queue.xml
index 56e7ad2eb..916827dab 100644
--- a/packages/Queue.xml
+++ b/packages/Queue.xml
@@ -15,6 +15,9 @@
             <!-- Scala -->
             <package name="scala.**" />
 
+            <!-- Picard -->
+            <package name="net.sf.picard.**" />
+
             <!-- JNA, including embedded native libraries -->
             <dir name="com/sun/jna" />
         </dependencies>
diff --git a/scala/qscript/oneoffs/carneiro/justClean.scala b/scala/qscript/oneoffs/carneiro/justClean.scala
index 9b9781a71..36a7b5062 100755
--- a/scala/qscript/oneoffs/carneiro/justClean.scala
+++ b/scala/qscript/oneoffs/carneiro/justClean.scala
@@ -1,7 +1,5 @@
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk.{RealignerTargetCreator, RodBind, IndelRealigner}
-import org.broadinstitute.sting.commandline.ArgumentSource
-import org.broadinstitute.sting.queue.extensions.gatk.BamGatherFunction
 
 /**
  * Created by IntelliJ IDEA.
@@ -69,13 +67,6 @@ class justClean extends QScript {
     clean.memoryLimit = Some(6)
     clean.scatterCount = 84
 
-    clean.setupGatherFunction = {
-      case (gather: BamGatherFunction, source: ArgumentSource) =>
-        gather.memoryLimit = Some(6) // Memory limit you expect for the job
-        gather.jarFile = new File("/seq/software/picard/current/bin/MergeSamFiles.jar")
-    }
-
-
     add(clean);
   }
 }
diff --git a/scala/qscript/playground/FullCallingPipeline.q b/scala/qscript/playground/FullCallingPipeline.q
index a391371ad..54726160d 100755
--- a/scala/qscript/playground/FullCallingPipeline.q
+++ b/scala/qscript/playground/FullCallingPipeline.q
@@ -1,7 +1,7 @@
 import org.broadinstitute.sting.commandline.ArgumentSource
 import org.broadinstitute.sting.datasources.pipeline.Pipeline
 import org.broadinstitute.sting.queue.extensions.gatk._
-import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
+import org.broadinstitute.sting.queue.extensions.picard.PicardBamEmbeddedFunction
 import org.broadinstitute.sting.queue.extensions.samtools._
 import org.broadinstitute.sting.queue.function.ListWriterFunction
 import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, CloneFunction, ScatterFunction}
@@ -16,9 +16,6 @@ class FullCallingPipeline extends QScript {
   @Argument(doc="the YAML file specifying inputs, interval lists, reference sequence, etc.", shortName="Y")
   var yamlFile: File = _
 
-  @Input(doc="path to Picard FixMateInformation.jar.  See http://picard.sourceforge.net/ .", shortName="P", required=false)
-  var picardFixMatesJar: File = new java.io.File("/seq/software/picard/current/bin/FixMateInformation.jar")
-
   @Input(doc="path to GATK jar", shortName="G")
   var gatkJar: File = _
 
@@ -39,6 +36,8 @@ class FullCallingPipeline extends QScript {
 
   private var pipeline: Pipeline = _
 
+  private final val picardFixMatesClass = "net.sf.picard.sam.FixMateInformation"
+
   trait CommandLineGATKArgs extends CommandLineGATK {
     this.intervals = List(qscript.pipeline.getProject.getIntervalList)
     this.jarFile = qscript.gatkJar
@@ -110,7 +109,7 @@ class FullCallingPipeline extends QScript {
               gather.commandDirectory = new File("CleanedBams/IntermediateFiles/%s/ScatterGather/Gather_%s".format(sampleId, source.field.getName))
               gather.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId))
               gather.memoryLimit = Some(6)
-              gather.jarFile = qscript.picardFixMatesJar
+              gather.mainClass = picardFixMatesClass
               gather.assumeSorted = None
             case (gather: GatherFunction, source: ArgumentSource) =>
               gather.commandDirectory = new File("CleanedBams/IntermediateFiles/%s/ScatterGather/Gather_%s".format(sampleId, source.field.getName))
@@ -123,7 +122,7 @@ class FullCallingPipeline extends QScript {
           realigner.isIntermediate = true
 
           // Explicitly run fix mates if the function won't be scattered.
-          val fixMates = new PicardBamJarFunction {
+          val fixMates = new PicardBamEmbeddedFunction {
             @Input(doc="unfixed bam") var unfixed: File = _
             @Output(doc="fixed bam") var fixed: File = _
             def inputBams = List(unfixed)
@@ -132,7 +131,7 @@ class FullCallingPipeline extends QScript {
 
           fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId))
           fixMates.memoryLimit = Some(6)
-          fixMates.jarFile = qscript.picardFixMatesJar
+          fixMates.mainClass = picardFixMatesClass
           fixMates.unfixed = realigner.out
           fixMates.fixed = cleaned_bam
           fixMates.analysisName = "FixMates_"+sampleId
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala b/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
index abf4cbe09..1ec8f44a6 100755
--- a/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
@@ -310,11 +310,10 @@ class QGraph extends Logging {
    * Dry-runs the jobs by traversing the graph.
    */
   private def dryRunJobs() {
-    if (settings.startFromScratch) {
+    if (settings.startFromScratch)
       logger.info("Will remove outputs from previous runs.")
-      foreachFunction(_.resetToPending(false))
-    } else
-      updateGraphStatus(false)
+
+    updateGraphStatus(false)
 
     var readyJobs = getReadyJobs()
     while (running && readyJobs.size > 0) {
@@ -361,11 +360,10 @@ class QGraph extends Logging {
         settings.jobRunner = "Shell"
       commandLineManager = commandLinePluginManager.createByName(settings.jobRunner)
 
-      if (settings.startFromScratch) {
+      if (settings.startFromScratch)
         logger.info("Removing outputs from previous runs.")
-        foreachFunction(_.resetToPending(true))
-      } else
-        updateGraphStatus(true)
+
+      updateGraphStatus(true)
 
       var readyJobs = TreeSet.empty[FunctionEdge](functionOrdering)
       readyJobs ++= getReadyJobs()
@@ -458,7 +456,10 @@ class QGraph extends Logging {
    * @param cleanOutputs If true will delete outputs when setting edges to pending.
    */
   private def updateGraphStatus(cleanOutputs: Boolean) {
-    traverseFunctions(edge => checkDone(edge, cleanOutputs))
+    if (settings.startFromScratch)
+      foreachFunction(edge => edge.resetToPending(cleanOutputs))
+    else
+      traverseFunctions(edge => checkDone(edge, cleanOutputs))
     traverseFunctions(edge => recheckDone(edge))
   }
 
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
index 8a442f6f5..67dfbba64 100644
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
@@ -1,14 +1,19 @@
 package org.broadinstitute.sting.queue.extensions.gatk
 
 import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
-import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
+import org.broadinstitute.sting.queue.extensions.picard.PicardBamEmbeddedFunction
 
 /**
- * Merges BAM files using Picards MergeSamFiles.jar.
- * At the Broad the jar can be found at /seq/software/picard/current/bin/MergeSamFiles.jar.  Outside the broad see http://picard.sourceforge.net/")
+ * Merges BAM files using Picards net.sf.picard.sam.MergeSamFiles.
  */
-class BamGatherFunction extends GatherFunction with PicardBamJarFunction {
+class BamGatherFunction extends GatherFunction with PicardBamEmbeddedFunction {
+  this.mainClass = "net.sf.picard.sam.MergeSamFiles"
   this.assumeSorted = Some(true)
   protected def inputBams = gatherParts
   protected def outputBam = originalOutput
+
+  override def init() {
+    // Whatever the original function can handle, merging *should* do less.
+    this.memoryLimit = originalFunction.memoryLimit
+  }
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamEmbeddedFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamEmbeddedFunction.scala
new file mode 100644
index 000000000..deb251d89
--- /dev/null
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamEmbeddedFunction.scala
@@ -0,0 +1,37 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.queue.extensions.picard
+
+import org.broadinstitute.sting.queue.function.EmbeddedCommandLineFunction
+
+/**
+ * Wraps a Picard embedded class that operates on BAM files.
+ * See http://picard.sourceforge.net/ for more info.
+ *
+ * Since the command lines take slightly different arguments
+ * some values are optional.
+ */
+trait PicardBamEmbeddedFunction extends EmbeddedCommandLineFunction with PicardBamFunction {
+}
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
new file mode 100644
index 000000000..45c51c60c
--- /dev/null
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
@@ -0,0 +1,51 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.queue.extensions.picard
+
+import java.io.File
+import org.broadinstitute.sting.queue.function.CommandLineFunction
+
+/**
+ * Wraps a Picard function that operates on BAM files.
+ * See http://picard.sourceforge.net/ for more info.
+ *
+ * Since the various BAM utilities take slightly different arguments
+ * some values are optional.
+ */
+trait PicardBamFunction extends CommandLineFunction {
+  var validationStringency = "SILENT"
+  var sortOrder = "coordinate"
+  var compressionLevel: Option[Int] = None
+  var maxRecordsInRam: Option[Int] = None
+  var assumeSorted: Option[Boolean] = None
+
+  protected def inputBams: List[File]
+  protected def outputBam: File
+
+  abstract override def commandLine = super.commandLine +
+    Array(optional(" COMPRESSION_LEVEL=", compressionLevel), optional(" VALIDATION_STRINGENCY=", validationStringency),
+      optional(" SO=", sortOrder), optional( " MAX_RECORDS_IN_RAM=", maxRecordsInRam), optional(" ASSUME_SORTED=", assumeSorted),
+      " OUTPUT=" + outputBam, repeat(" INPUT=", inputBams), " TMP_DIR=" + jobTempDir).mkString
+}
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamJarFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamJarFunction.scala
index c86a389c1..31e95f0d1 100644
--- a/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamJarFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamJarFunction.scala
@@ -1,7 +1,30 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.queue.extensions.picard
 
 import org.broadinstitute.sting.queue.function.JarCommandLineFunction
-import java.io.File
 
 /**
  * Wraps a Picard jar that operates on BAM files.
@@ -10,18 +33,5 @@ import java.io.File
  * Since the jar files take slightly different arguments
  * some values are optional.
  */
-trait PicardBamJarFunction extends JarCommandLineFunction {
-  var validationStringency = "SILENT"
-  var sortOrder = "coordinate"
-  var compressionLevel: Option[Int] = None
-  var maxRecordsInRam: Option[Int] = None
-  var assumeSorted: Option[Boolean] = None
-
-  protected def inputBams: List[File]
-  protected def outputBam: File
-
-  override def commandLine = super.commandLine + "%s%s%s%s%s%s%s%s".format(
-    optional(" COMPRESSION_LEVEL=", compressionLevel), optional(" VALIDATION_STRINGENCY=", validationStringency),
-    optional(" SO=", sortOrder), optional( " MAX_RECORDS_IN_RAM=", maxRecordsInRam), optional(" ASSUME_SORTED=", assumeSorted),
-    " OUTPUT=" + outputBam, repeat(" INPUT=", inputBams), " TMP_DIR=" + jobTempDir)
+trait PicardBamJarFunction extends JarCommandLineFunction with PicardBamFunction {
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/function/EmbeddedCommandLineFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/EmbeddedCommandLineFunction.scala
new file mode 100644
index 000000000..e9987cdef
--- /dev/null
+++ b/scala/src/org/broadinstitute/sting/queue/function/EmbeddedCommandLineFunction.scala
@@ -0,0 +1,45 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.queue.function
+
+import java.io.File
+import org.broadinstitute.sting.queue.util.IOUtils
+import org.broadinstitute.sting.commandline.Argument
+
+/**
+ * Defines a command line function that runs java code from inside the existing class path.
+ */
+trait EmbeddedCommandLineFunction extends JavaCommandLineFunction {
+  @Argument(doc="Main class to run from the current classpath")
+  var mainClass: String = null
+
+  def javaExecutable = "-cp %s %s".format(EmbeddedCommandLineFunction.classpath, mainClass)
+}
+
+object EmbeddedCommandLineFunction {
+  private val classpath = System.getProperty("java.class.path")
+    .split(File.pathSeparatorChar).map(path => IOUtils.absolute(new File(path)))
+    .mkString("\"", "\"" + File.pathSeparator + "\"", "\"")
+}