Allowing the Queue to run the GATK via -cp instead of only from -jar.

Added an example of using a walker with Queue and a custom -classpath.
Removed an unused import statement in NamedFileWrapper.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4143 348d0f76-0448-11de-a6fe-93d51630548a

scala/qscript/examples/ExampleCustomWalker.scala

@@ -0,0 +1,49 @@
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.queue.extensions.gatk._
+
+/**
+ * A pipeline for Queue that runs a custom walker outside of the GATK jar.
+ * NOTE: This code is an unsupported example for soliciting feedback on how to improve Queue.
+ * Future syntax will simplify running the GATK so please expect the syntax below to change significantly.
+ */
+class ExampleCustomWalker extends QScript {
+  // The full packaged jar should be used.
+  // You can build this jar via 'ant package' and then find it under
+  // 'Sting/dist/packages/GenomeAnalysisTK-*/GenomeAnalysisTK.jar'
+  @Input(doc="The path to the packaged GenomeAnalysisTK.jar file.", shortName="gatk")
+  var gatkJar: File = null
+
+  @Input(doc="The reference file for the bam files.", shortName="R")
+  var referenceFile: File = null
+
+  // NOTE: Do not initialize List, Set, or Option to null
+  // as you won't be able to update the collection.
+  // By default set:
+  //   List[T] = Nil
+  //   Set[T] = Set.empty[T]
+  //   Option[T] = None
+  @Input(doc="One or more bam files.", shortName="I")
+  var bamFiles: List[File] = Nil
+
+  /**
+   * In script, you create and then add() functions to the pipeline.
+   */
+  def script = {
+    val myClasses = "myClassDir"
+
+    val customWalker = new CommandLineGATK {
+      // Set the name of your walker, for example this will be passed as -T MyCustomWalker
+      this.analysis_type = "MyCustomWalker"
+      // NOTE: At this time, you still need to specify the GATK jar or the pipeline won't validate.
+      this.jarFile = gatkJar
+      override def javaExecutable = "org.broadinstitute.sting.gatk.CommandLineGATK"
+      override def javaOpts = "%s -cp %s:%s".format(super.javaOpts, gatkJar, myClasses)
+    }
+
+    customWalker.reference_sequence = referenceFile
+    customWalker.input_file = bamFiles
+
+    // Add the newly created function to the pipeline.
+    add(customWalker)
+  }
+}

scala/src/org/broadinstitute/sting/queue/extensions/gatk/NamedFileWrapper.scala

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.queue.extensions.gatk
 
 import java.io.File
-import org.broadinstitute.sting.queue.function.FileProvider
 
 class NamedFileWrapper(private val file: File) {
   def toNamedFile = new NamedFile(file)

scala/src/org/broadinstitute/sting/queue/function/JarCommandLineFunction.scala

@@ -6,10 +6,9 @@ import java.io.File
 /**
  * Defines a command line function that runs from a jar file.
  */
-trait JarCommandLineFunction extends CommandLineFunction {
+trait JarCommandLineFunction extends JavaCommandLineFunction {
   @Argument(doc="jar")
   var jarFile: File = _
 
-  def commandLine = "java%s -Djava.io.tmpdir=%s -jar %s"
-    .format(optional(" -Xmx", memoryLimit, "g"), jobTempDir, jarFile)
+  def javaExecutable = "-jar " + jarFile
 }

scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala

@@ -0,0 +1,17 @@
+package org.broadinstitute.sting.queue.function
+
+/**
+ * Defines a command line function that runs java code.
+ */
+trait JavaCommandLineFunction extends CommandLineFunction {
+  /**
+   * Returns the java executable to run.
+   */
+  def javaExecutable: String
+
+  def javaOpts = "%s -Djava.io.tmpdir=%s"
+    .format(optional(" -Xmx", memoryLimit, "g"), jobTempDir)
+
+  def commandLine = "java%s %s"
+    .format(javaOpts, javaExecutable)
+}