Replaced pattern matched pipeline spec with annotated objects.

Old version is no longer available.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3558 348d0f76-0448-11de-a6fe-93d51630548a

ivy.xml

@@ -42,8 +42,8 @@
     <dependency org="commons-io" name="commons-io" rev="1.3.2" conf="default"/>
      
     <!-- Scala dependancies -->
-    <dependency org="org.scala-lang" name="scala-compiler" rev="2.8.0.RC2" conf="scala->default"/>
+    <dependency org="org.scala-lang" name="scala-compiler" rev="2.8.0.RC5" conf="scala->default"/>
-    <dependency org="org.scala-lang" name="scala-library" rev="2.8.0.RC2" conf="scala->default"/>
+    <dependency org="org.scala-lang" name="scala-library" rev="2.8.0.RC5" conf="scala->default"/>
 
     <!-- Queue additional dependencies -->
     <dependency org="commons-lang" name="commons-lang" rev="2.5" conf="queue->default"/>

java/src/org/broadinstitute/sting/queue/util/ClassType.java

@@ -0,0 +1,40 @@
+/*
+ * Copyright (c) 2010, 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.util;
+
+import java.lang.annotation.*;
+
+/**
+ * Specifies the type of an input our output field.
+ * Retains it during runtime to work around type erasure.
+ * Written in java because scala doesn't support RetentionPolicy.RUNTIME
+ */
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target({ElementType.FIELD})
+public @interface ClassType {
+    Class value();
+}

java/src/org/broadinstitute/sting/queue/util/Input.java

@@ -0,0 +1,38 @@
+/*
+ * Copyright (c) 2010, 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.util;
+
+import java.lang.annotation.*;
+
+/**
+ * Specifies an input to a QueueFunction
+ * Written in java because scala doesn't support RetentionPolicy.RUNTIME
+ */
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target({ElementType.FIELD})
+public @interface Input {
+}

java/src/org/broadinstitute/sting/queue/util/Internal.java

@@ -0,0 +1,40 @@
+/*
+ * Copyright (c) 2010, 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.util;
+
+import java.lang.annotation.*;
+
+/**
+ * Specifies an internal setting for a QueueFunction.
+ * Not an input or output but should be copied with a function.
+ * Internals should have default values that should be handled, i.e. they are always @Optional
+ * Written in java because scala doesn't support RetentionPolicy.RUNTIME
+ */
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target({ElementType.FIELD})
+public @interface Internal {
+}

java/src/org/broadinstitute/sting/queue/util/Optional.java

@@ -0,0 +1,38 @@
+/*
+ * Copyright (c) 2010, 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.util;
+
+import java.lang.annotation.*;
+
+/**
+ * Specifies an input or output to a QueueFunction is optional
+ * Written in java because scala doesn't support RetentionPolicy.RUNTIME
+ */
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target({ElementType.FIELD})
+public @interface Optional {
+}

java/src/org/broadinstitute/sting/queue/util/Output.java

@@ -0,0 +1,38 @@
+/*
+ * Copyright (c) 2010, 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.util;
+
+import java.lang.annotation.*;
+
+/**
+ * Specifies an output to a QueueFunction
+ * Written in java because scala doesn't support RetentionPolicy.RUNTIME
+ */
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target({ElementType.FIELD})
+public @interface Output {
+}

scala/src/org/broadinstitute/sting/queue/QArguments.scala

@@ -8,13 +8,13 @@ import java.io.{FileInputStream, File}
 import java.util.Properties
 
 class QArguments(args: Array[String]) {
-  var useBsub = false
+  var bsubAllJobs = false
   var dryRun = false
   val scripts = new ListBuffer[String]
   var inputPaths = List.empty[File]
   var argMap = Map.empty[String, String]
 
-  parseArgs(args)
+  val userArgs = parseArgs(args)
 
   private def parseArgs(args: Array[String]) = {
     var filtered = new ListBuffer[String]
@@ -26,13 +26,15 @@ class QArguments(args: Array[String]) {
     if (isFlagged(filtered, "-dry"))
       dryRun = true
     if (isFlagged(filtered, "-bsub"))
-      useBsub = true
+      bsubAllJobs = true
     for (arg <- getArgs(filtered, "-P"))
       addArg(arg)
     for (arg <- getArgs(filtered, "-I"))
       addFile(arg)
     for (arg <- getArgs(filtered, "-S"))
       scripts.append(arg)
+
+    List(filtered:_*)
   }
 
   private def isFlagged(filtered: ListBuffer[String], search: String) = {
@@ -65,22 +67,24 @@ class QArguments(args: Array[String]) {
     var file = new File(arg)
     if (arg.contains("=") && !file.exists) {
       val tokens = arg.split("=", 2)
-      argMap = argMap.updated(tokens(0), tokens(1))
+      argMap += tokens(0) -> tokens(1)
-    } else if (file.exists && arg.endsWith(".properties")) {
+    } else if (arg.endsWith(".properties")) {
+      if (!file.exists)
+        throw new QException("File not found: " + file.getAbsolutePath)
       var props = new Properties
       props.load(new FileInputStream(file))
       for ((name, value) <- props)
-        argMap = argMap.updated(name, value)
+        argMap += name -> value
+    } else {
+      throw new QException("Invalid property: " + arg)
     }
   }
 
   def addFile(arg: String): Unit = {
     var file = new File(arg)
-    if (arg.endsWith(".list")) {
+    inputPaths :+= file
+    if (arg.endsWith(".list"))
       new XReadLines(file).iterator.foreach(addFile(_))
-    } else {
-      inputPaths = inputPaths ::: List(file)
-    }
   }
 }
 

scala/src/org/broadinstitute/sting/queue/QCommandLine.scala

@@ -13,6 +13,7 @@ object QCommandLine extends Application with Logging {
       new QArguments(args)
     } catch {
       case exception => {
+        println(exception)
         println(usage)
         System.exit(-1)
       }
@@ -34,20 +35,13 @@ object QCommandLine extends Application with Logging {
       System.exit(-1)
     }
 
-    if (qArgs.inputPaths.size == 0) {
-      println("Error: No inputs specified")
-      println(usage)
-      System.exit(-1)
-    }
-
-
     val newArgs = new ListBuffer[String]
     newArgs.appendAll(args)
     QArguments.strip(newArgs, "-S")
     newArgs.prepend("-nocompdaemon", "-classpath", ClasspathUtils.manifestAwareClassPath, qArgs.scripts.head)
     MainGenericRunner.main(newArgs.toArray)
 
-    // NOTE: This line is not reached because something in MainGenericRunner is exiting the VM.
+    // NOTE: This line is not reached because the MainGenericRunner exits the VM.
     logger.debug("exiting")
   }
 }

scala/src/org/broadinstitute/sting/queue/QScript.scala

@@ -0,0 +1,103 @@
+package org.broadinstitute.sting.queue
+
+import org.broadinstitute.sting.queue.function.CommandLineFunction
+import org.broadinstitute.sting.queue.engine.QGraph
+
+/**
+ * Syntactic sugar for filling in a pipeline using a Scala script.
+ */
+object QScript {
+  // Type aliases so users don't have to import
+  type File = java.io.File
+  type Input = org.broadinstitute.sting.queue.util.Input
+  type Output = org.broadinstitute.sting.queue.util.Output
+  type Optional = org.broadinstitute.sting.queue.util.Optional
+  type ClassType = org.broadinstitute.sting.queue.util.ClassType
+  type CommandLineFunction = org.broadinstitute.sting.queue.function.CommandLineFunction
+  type GatkFunction = org.broadinstitute.sting.queue.function.gatk.GatkFunction
+
+  // The arguments for executing pipelines
+  private var qArgs: QArguments = _
+
+  // A default pipeline.  Can also use multiple 'new Pipeline()'
+  private val pipeline = new Pipeline
+
+  /**
+   * Initializes the QArguments and returns a list of the rest of the user args.
+   */
+  def setArgs(params: Array[String]) = {
+    qArgs = new QArguments(params)
+    qArgs.userArgs
+  }
+
+  /**
+   * Returns a list of files that were specified with "-I <file>" on the command line
+   * or inside a .list file.
+   */
+  def inputs(extension: String) = qArgs.inputPaths.filter(_.getName.endsWith(extension))
+
+  /**
+   * Exchanges the extension on a file.
+   */
+  def swapExt(file: File, oldExtension: String, newExtension: String) =
+    new File(file.getName.stripSuffix(oldExtension) + newExtension)
+
+  /**
+   * Adds one or more command line functions for dispatch later during run()
+   */
+  def add(functions: CommandLineFunction*) = pipeline.add(functions:_*)
+
+  /**
+   * Sets the @Input and @Output values for all the functions
+   */
+  def setParams(): Unit = pipeline.setParams()
+
+  /**
+   * Sets the @Input and @Output values for a single function
+   */
+  def setParams(function: CommandLineFunction): Unit = pipeline.setParams(function)
+
+  /**
+   * Executes functions that have been added to the pipeline.
+   */
+  def run() = pipeline.run()
+
+
+  /**
+   * Encapsulates a set of functions to run together.
+   */
+  protected class Pipeline {
+    private var functions = List.empty[CommandLineFunction]
+
+    /**
+     * Adds one or more command line functions for dispatch later during run()
+     */
+    def add(functions: CommandLineFunction*) =
+      this.functions :::= List(functions:_*)
+
+    /**
+     * Sets the @Input and @Output values for all the functions
+     */
+    def setParams(): Unit =
+      for (function <- functions) setParams(function)
+
+    /**
+     * Sets the @Input and @Output values for a single function
+     */
+    def setParams(function: CommandLineFunction): Unit =
+      for ((name, value) <- qArgs.argMap) function.setValue(name, value)
+
+    /**
+     * Executes functions that have been added to the pipeline.
+     */
+    def run() = {
+      val qGraph = new QGraph
+      qGraph.dryRun = qArgs.dryRun
+      qGraph.bsubAllJobs = qArgs.bsubAllJobs
+      for (function <- functions)
+        qGraph.add(function)
+      qGraph.fillIn
+      qGraph.run
+    }
+  }
+}

scala/src/org/broadinstitute/sting/queue/engine/CommandLineRunner.scala

@@ -0,0 +1,17 @@
+package org.broadinstitute.sting.queue.engine
+
+import org.broadinstitute.sting.queue.util.{Logging, ProcessUtils}
+import org.broadinstitute.sting.queue.function.CommandLineFunction
+
+/**
+ * Runs jobs one at a time locally
+ */
+trait CommandLineRunner extends Logging {
+  def run(function: CommandLineFunction, qGraph: QGraph) = {
+    var commandLine = function.commandLine
+    logger.info(commandLine)
+
+    if (!qGraph.dryRun)
+      ProcessUtils.runCommandAndWait(function.commandLine, function.commandDirectory)
+  }
+}

scala/src/org/broadinstitute/sting/queue/engine/DispatchJobRunner.scala

@@ -0,0 +1,56 @@
+package org.broadinstitute.sting.queue.engine
+
+import edu.mit.broad.core.lsf.LocalLsfJob
+import collection.JavaConversions._
+import management.ManagementFactory
+import java.io.File
+import java.util.ArrayList
+import org.broadinstitute.sting.queue.function.{DispatchFunction, QFunction}
+
+trait DispatchJobRunner {
+  type DispatchJobType
+  private var dispatchJobs = Map.empty[DispatchFunction, DispatchJobType]
+
+  protected def newJobName = DispatchJobRunner.nextJobName
+
+  def dispatch(function: DispatchFunction, qGraph: QGraph)
+
+  protected def addJob(function: DispatchFunction, dispatchJob: DispatchJobType) =
+    dispatchJobs += function -> dispatchJob
+
+  /**
+   * Walks up the graph looking for the previous LsfJobs
+   */
+  protected def previousJobs(function: QFunction, qGraph: QGraph) : List[DispatchJobType] = {
+    var previous = List.empty[DispatchJobType]
+
+    val source = qGraph.jobGraph.getEdgeSource(function)
+    for (incomingEdge <- qGraph.jobGraph.incomingEdgesOf(source)) {
+      incomingEdge match {
+
+        // Stop recursing when we find a job along the edge and return its job id
+        case dispatchFunction: DispatchFunction => previous :+= dispatchJobs(dispatchFunction)
+
+        // For any other type of edge find the LSF jobs preceding the edge
+        case qFunction: QFunction => previous :::= previousJobs(qFunction, qGraph)
+      }
+    }
+    previous
+  }
+}
+
+object DispatchJobRunner {
+  private val jobNamePrefix = "Q-" + {
+    var prefix = ManagementFactory.getRuntimeMXBean.getName
+    val index = prefix.indexOf(".")
+    if (index >= 0)
+      prefix = prefix.substring(0, index)
+    prefix
+  }
+  private var jobIndex = 0
+
+  private def nextJobName = {
+    jobIndex += 1
+    jobNamePrefix + "-" + jobIndex
+  }
+}

scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala

@@ -0,0 +1,57 @@
+package org.broadinstitute.sting.queue.engine
+
+import collection.JavaConversions._
+import edu.mit.broad.core.lsf.LocalLsfJob
+import org.broadinstitute.sting.queue.function.DispatchFunction
+import java.io.File
+import java.util.ArrayList
+import org.broadinstitute.sting.queue.util.Logging
+
+trait LsfJobRunner extends DispatchJobRunner with Logging {
+  type DispatchJobType = LocalLsfJob
+
+  def dispatch(function: DispatchFunction, qGraph: QGraph) = {
+    var jobName = function.jobName
+    if (jobName == null)
+      jobName = newJobName
+
+    var jobOutputFile = function.jobOutputFile
+    if (jobOutputFile == null)
+      jobOutputFile = new File(jobName + ".out")
+
+    var jobErrorFile = function.jobErrorFile
+    if (jobErrorFile == null)
+      jobErrorFile = new File(jobName + ".err")
+
+    val job = new LocalLsfJob
+    job.setName(jobName)
+    job.setOutputFile(jobOutputFile)
+    job.setErrFile(jobErrorFile)
+    job.setWorkingDir(function.commandDirectory)
+    job.setProject(function.jobProject)
+    job.setQueue(function.jobQueue)
+    job.setCommand(function.commandLine)
+
+    var extraArgs = List("-r")
+
+    if (function.memoryLimit.isDefined)
+      extraArgs :::= List("-R", "rusage[mem=" + function.memoryLimit.get + "]")
+
+    val previous = previousJobs(function, qGraph)
+    if (previous.size > 0)
+      extraArgs :::= List("-w", dependencyExpression(previous))
+
+    job.setExtraBsubArgs(new ArrayList(extraArgs))
+
+    addJob(function, job)
+
+    logger.info(job.getBsubCommand.mkString(" "))
+
+    if (!qGraph.dryRun)
+      job.start
+  }
+
+  private def dependencyExpression(jobs: List[LocalLsfJob]) = {
+    jobs.toSet[LocalLsfJob].map(_.getName).mkString("ended(\"", "\") && ended(\"", "\")")
+  }
+}

scala/src/org/broadinstitute/sting/queue/engine/Pipeline.scala

@@ -1,16 +0,0 @@
-package org.broadinstitute.sting.queue.engine
-
-import graphing.{ExplicitJobGrapher, TreeJobGrapher}
-import scheduling.ResourceNode
-
-/**
- * Syntactic sugar for filling in a pipeline using a Scala script.
- */
-object Pipeline {
-  def addRule(rule: (Any, Any), commandString: String): Unit = TreeJobGrapher.addRule(rule, commandString)
-  def run(args: Array[String], sources: Any, targets: Any): Unit = TreeJobGrapher.run(args, sources, targets)
-
-  def node() = ExplicitJobGrapher.node()
-  def addEdge(rule: (ResourceNode, ResourceNode), commandString: String): Unit = ExplicitJobGrapher.addEdge(rule, commandString)
-  def run(): Unit = ExplicitJobGrapher.run()
-}

scala/src/org/broadinstitute/sting/queue/engine/QCommand.scala

@@ -1,9 +0,0 @@
-package org.broadinstitute.sting.queue.engine
-
-/**
- * Defines a basic command to run
- * TODO: Allow overriding arguments per command such as the job queue
- */
-class QCommand(val commandString: String) extends QModelEdge {
-  override def toString = commandString
-}

scala/src/org/broadinstitute/sting/queue/engine/QFile.scala

@@ -1,43 +0,0 @@
-package org.broadinstitute.sting.queue.engine
-
-import org.apache.commons.lang.builder.{EqualsBuilder, HashCodeBuilder}
-import java.io.File
-import org.apache.commons.lang.StringUtils
-import org.broadinstitute.sting.queue.QException
-
-/**
- * Represents a file extension along with several tags.
- * TODO: Use the tags to map rules between wildcards, ex: *.vcf -> *.eval
- */
-class QFile(val fileType: String, val parts: String*) {
-  val extension = (List(parts:_*) ::: List(fileType)).mkString(".")
-  override def toString = extension
-  override def equals(p1: Any) = EqualsBuilder.reflectionEquals(this, p1)
-  override def hashCode = HashCodeBuilder.reflectionHashCode(this)
-
-  def matchesFile(path: String): Boolean = matchesFile(new File(path))
-  def matchesFile(file: File): Boolean = file.getAbsolutePath.endsWith(extension)
-  def baseName(path: String): String = baseName(new File(path))
-  def baseName(file: File): String = StringUtils.removeEnd(file.getAbsolutePath, extension)
-  def fullName(baseName: String) = baseName + extension
-}
-
-object QFile {
-  def getFiles(files: Any) : List[QFile] = {
-    files match {
-      case null => List.empty[QFile]
-      case Nil => List.empty[QFile]
-      case path: String => List(new QFile(path))
-      case file: QFile => List(file)
-      // Any List or Tuple add the members to this list
-      case product: Product => {
-        var list = List.empty[QFile]
-        for (fileList <- product.productIterator.toList.map(getFiles(_))) {
-          list :::= fileList
-        }
-        list
-      }
-      case x => throw new QException("Unknown file type: " + x)
-    }
-  }
-}

scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala

@@ -0,0 +1,71 @@
+package org.broadinstitute.sting.queue.engine
+
+import org.jgrapht.graph.SimpleDirectedGraph
+import scala.collection.JavaConversions
+import scala.collection.immutable.ListMap
+import org.broadinstitute.sting.queue.util.Logging
+import org.broadinstitute.sting.queue.function.{MappingFunction, CommandLineFunction, QFunction}
+
+class QGraph extends Logging {
+  var dryRun = true
+  var bsubAllJobs = false
+  val jobGraph = new SimpleDirectedGraph[QNode, QFunction](classOf[QFunction])
+  def numJobs = JavaConversions.asSet(jobGraph.edgeSet).filter(_.isInstanceOf[CommandLineFunction]).size
+
+  def add(command: CommandLineFunction) {
+    add(command, true)
+  }
+
+  /**
+   * Looks through functions with multiple inputs and outputs and adds mapping functions for single inputs and outputs.
+   */
+  def fillIn = {
+    // clone since edgeSet is backed by the graph
+    for (function <- JavaConversions.asSet(jobGraph.edgeSet).clone) {
+      val inputs = function.inputs
+      val outputs = function.outputs
+
+      if (inputs.size > 1)
+        for ((name, input) <- inputs)
+          addNullEdge(ListMap(name -> input), inputs)
+
+      if (outputs.size > 1)
+        for ((name, output) <- outputs)
+          addNullEdge(outputs, ListMap(name -> output))
+    }
+  }
+
+  def run = {
+    var isReady = true
+    for (function <- JavaConversions.asSet(jobGraph.edgeSet)) {
+      val missingValues = function.missingValues
+      if (missingValues.size > 0) {
+        isReady = false
+        logger.error(function match {
+          case cmd: CommandLineFunction => "Missing values for function: %s".format(cmd.commandLine)
+          case x => "Missing values:"
+        })
+        for (missing <- missingValues) {
+          logger.error("  " + missing)
+        }
+      }
+    }
+    
+    if (isReady || this.dryRun)
+      (new TopologicalJobScheduler(this) with LsfJobRunner).runJobs
+  }
+
+  private def add(f: QFunction, replace: Boolean) {
+    val inputs = QNode(f.inputs.values.filter(_ != null).toSet)
+    val outputs = QNode(f.outputs.values.filter(_ != null).toSet)
+    jobGraph.addVertex(inputs)
+    jobGraph.addVertex(outputs)
+    if (replace)
+      jobGraph.removeAllEdges(inputs, outputs)
+    jobGraph.addEdge(inputs, outputs, f)
+  }
+
+  private def addNullEdge(input: ListMap[String, Any], output: ListMap[String, Any]) = {
+    add(new MappingFunction(input, output), false)
+  }
+}

scala/src/org/broadinstitute/sting/queue/engine/QModelEdge.scala

@@ -1,7 +0,0 @@
-package org.broadinstitute.sting.queue.engine
-
-/**
- * Used for modeling before an edge gets
- * replicated into an actual ResourceEdge
- */
-class QModelEdge

scala/src/org/broadinstitute/sting/queue/engine/QNode.scala

@@ -0,0 +1,6 @@
+package org.broadinstitute.sting.queue.engine
+
+/**
+ * Represents a state between QFunctions the directed acyclic QGraph
+ */
+case class QNode (private val items: Set[Any])

scala/src/org/broadinstitute/sting/queue/engine/QRule.scala

@@ -1,3 +0,0 @@
-package org.broadinstitute.sting.queue.engine
-
-class QRule (val inputs: List[QFile], val outputs: List[QFile], var command: QCommand)

scala/src/org/broadinstitute/sting/queue/engine/TopologicalJobScheduler.scala

@@ -0,0 +1,31 @@
+package org.broadinstitute.sting.queue.engine
+
+import org.jgrapht.traverse.TopologicalOrderIterator
+import org.jgrapht.event.{EdgeTraversalEvent, TraversalListenerAdapter}
+import collection.JavaConversions._
+import org.broadinstitute.sting.queue.util.Logging
+import org.broadinstitute.sting.queue.function.{MappingFunction, CommandLineFunction, DispatchFunction, QFunction}
+
+/**
+ * Loops over the job graph running jobs as the edges are traversed
+ */
+abstract class TopologicalJobScheduler(private val qGraph: QGraph)
+    extends CommandLineRunner with DispatchJobRunner with Logging {
+
+  protected val iterator = new TopologicalOrderIterator(this.qGraph.jobGraph)
+
+  iterator.addTraversalListener(new TraversalListenerAdapter[QNode, QFunction] {
+    override def edgeTraversed(event: EdgeTraversalEvent[QNode, QFunction]) = event.getEdge match {
+      case f: DispatchFunction if (TopologicalJobScheduler.this.qGraph.bsubAllJobs) => dispatch(f, qGraph)
+      case f: CommandLineFunction => run(f, qGraph)
+      case f: MappingFunction => /* do nothing for mapping functions */
+    }
+  })
+
+  def runJobs = {
+    logger.info("Number of jobs: %s".format(this.qGraph.numJobs))
+    for (target <- iterator) {
+      // Do nothing for now, let event handler respond
+    }
+  }
+}

scala/src/org/broadinstitute/sting/queue/engine/graphing/ExplicitJobGrapher.scala

@@ -1,27 +0,0 @@
-package org.broadinstitute.sting.queue.engine.graphing
-
-import org.broadinstitute.sting.queue.engine.scheduling.{ResourceNode, ExecEdge}
-import org.broadinstitute.sting.queue.engine.QCommand
-
-class ExplicitJobGrapher extends JobGrapher
-
-object ExplicitJobGrapher {
-  private val grapher = new ExplicitJobGrapher
-
-  def node() = new ResourceNode
-
-  def addEdge(rule: (ResourceNode, ResourceNode), commandString: String): Unit = {
-    addEdge(rule._1, rule._2, new QCommand(commandString))
-  }
-
-  private def addEdge(source: ResourceNode, target: ResourceNode, command: QCommand) = {
-    val resourceEdge = new ExecEdge(command.commandString)
-    grapher.jobGraph.addVertex(source)
-    grapher.jobGraph.addVertex(target)
-    grapher.jobGraph.addEdge(source, target, resourceEdge)
-  }
-
-  def run() = {
-    grapher.run()
-  }
-}

scala/src/org/broadinstitute/sting/queue/engine/graphing/JobGrapher.scala

@@ -1,31 +0,0 @@
-package org.broadinstitute.sting.queue.engine.graphing
-
-import org.broadinstitute.sting.queue.QArguments
-import org.broadinstitute.sting.queue.engine.scheduling._
-import org.broadinstitute.sting.queue.util.Logging
-import org.jgrapht.graph.SimpleDirectedGraph
-
-abstract class JobGrapher() extends Logging {
-  /**
-   * Jobs to be run.
-   * Can be populated adhoc or during createJobGraph()
-   */
-  protected val jobGraph = new SimpleDirectedGraph[ResourceNode, ResourceEdge](classOf[ResourceEdge])
-
-  var qArgs: QArguments = _
-
-  def run() = {
-    createJobGraph()
-    val scheduler = createScheduler()
-    scheduler.runJobs
-  }
-
-  protected def createJobGraph() = {}
-
-  private def createScheduler() : JobScheduler = {
-    qArgs.useBsub match {
-      case false => new SimpleJobScheduler(jobGraph, qArgs)
-      case true => new DispatchJobScheduler(jobGraph, qArgs)
-    }
-  }
-}

scala/src/org/broadinstitute/sting/queue/engine/graphing/TreeJobGrapher.scala

@@ -1,143 +0,0 @@
-package org.broadinstitute.sting.queue.engine.graphing
-
-import org.jgrapht.graph.SimpleDirectedGraph
-import org.jgrapht.alg.BellmanFordShortestPath
-import org.broadinstitute.sting.queue.{QArguments, QException}
-import collection.mutable.ListBuffer
-import collection.JavaConversions._
-import org.broadinstitute.sting.queue.engine.scheduling.{ResourceEdge, ExecEdge, MapResourceNode}
-import org.broadinstitute.sting.queue.engine.{QModelEdge, QCommand, QFile, QRule}
-
-/**
- * Converts a set of rules provided by the user and a list of files into a graph of jobs to run
- */
-class TreeJobGrapher extends JobGrapher {
-  private val modelGraph = new SimpleDirectedGraph[List[QFile], QModelEdge](classOf[QModelEdge])
-
-  private val rules = new ListBuffer[QRule]
-  private var sourceFiles = List.empty[QFile]
-  private var targetFiles = List.empty[QFile]
-
-  // Used to tag a model edge for Element <-> List
-  private class QCollectionEdge extends QModelEdge
-
-  override protected def createJobGraph() = {
-    createModelGraph()
-    
-    var missingPaths = List.empty[Tuple2[QFile,QFile]]
-    for (sourceFile <- sourceFiles) {
-      for (targetFile <- targetFiles) {
-        var shortestPath = BellmanFordShortestPath.findPathBetween(modelGraph, List(sourceFile), List(targetFile))
-        if (shortestPath == null)
-          missingPaths = missingPaths ::: List((sourceFile, targetFile))
-        else
-          addPaths(shortestPath, qArgs)
-      }
-    }
-
-    for ((sourceFile, targetFile) <- missingPaths) {
-      logger.error(String.format("No command path found between %s --> %s", sourceFile, targetFile))
-    }
-
-    if (missingPaths.size > 0)
-      throw new QException("Not all inputs and outputs found in the pipeline graph")
-  }
-
-  private def createModelGraph() = {
-
-    // Look for rules with more than one input or output and add
-    // internal dependencies between the elements and the list
-    for (rule <- rules) {
-      if (rule.inputs.size > 1) {
-        for (input <- rule.inputs) {
-          modelGraph.addVertex(List(input))
-          modelGraph.addVertex(rule.inputs)
-          modelGraph.addEdge(List(input), rule.inputs, new QCollectionEdge)
-        }
-      }
-      if (rule.outputs.size > 1) {
-        for (output <- rule.outputs) {
-          modelGraph.addVertex(rule.outputs)
-          modelGraph.addVertex(List(output))
-          modelGraph.addEdge(rule.outputs, List(output), new QCollectionEdge)
-        }
-      }
-    }
-
-    // Add the explicit rules
-    for (rule <- rules) {
-      modelGraph.addVertex(rule.inputs)
-      modelGraph.addVertex(rule.outputs)
-      modelGraph.addEdge(rule.inputs, rule.outputs, rule.command)
-    }
-  }
-
-  private def addPaths(shortestPath: java.util.List[QModelEdge], qArgs: QArguments) {
-    for (inputFile <- qArgs.inputPaths.map(_.getAbsolutePath)) {
-      val source = modelGraph.getEdgeSource(shortestPath.head).head
-      if (source.matchesFile(inputFile)) {
-        val baseName = source.baseName(inputFile)
-        val target = modelGraph.getEdgeTarget(shortestPath.last).head
-        addPathsToTarget(baseName, List(target))
-      }
-    }
-  }
-
-  private def addPathsToTarget(baseName: String, targets: List[QFile]) : Unit = {
-    for (command <- modelGraph.incomingEdgesOf(targets)) {
-      val sources = modelGraph.getEdgeSource(command)
-      addJobGraphEdge(baseName, sources, targets, command)
-      addPathsToTarget(baseName, sources)
-    }
-  }
-
-  private def addJobGraphEdge(baseName: String, sources: List[QFile], targets: List[QFile], command: QModelEdge) {
-    val resourceSource = new MapResourceNode(mapFiles(baseName, sources))
-    val resourceTarget = new MapResourceNode(mapFiles(baseName, targets))
-    val resourceEdge = command match {
-      case qCommand: QCommand => new ExecEdge(qCommand.commandString)
-      case qTransition: QCollectionEdge => new ResourceEdge
-    }
-    jobGraph.addVertex(resourceSource)
-    jobGraph.addVertex(resourceTarget)
-    jobGraph.addEdge(resourceSource, resourceTarget, resourceEdge)
-  }
-
-  /**
-   * Creates a mapping of the files based on the baseName.
-   *   key: file extension
-   *   value: full name
-   * Used by the JobScheduler to lookup values as the commands are expanded at exec time.
-   */
-  private def mapFiles(baseName: String, files: List[QFile]) : Map[String, String] = {
-    Map(files.map(file => (file.extension, file.fullName(baseName))):_*)
-  }
-}
-
-/**
- * Syntactic sugar for filling in a pipeline using a Scala script.
- */
-object TreeJobGrapher {
-  private val grapher = new TreeJobGrapher
-
-  /**
-   * Sugar that allows addRule( inputs -> outputs, command )
-   */
-  def addRule(rule: (Any, Any), commandString: String): Unit = {
-    val inputs = QFile.getFiles(rule._1)
-    val outputs = QFile.getFiles(rule._2)
-    val command = new QCommand(commandString)
-    addRule(inputs, outputs, command)
-  }
-
-  private def addRule(inputs: List[QFile], outputs: List[QFile], command: QCommand): Unit = {
-    grapher.rules += new QRule(inputs, outputs, command)
-  }
-
-  def run(args: Array[String], sources: Any, targets: Any) = {
-    grapher.qArgs = new QArguments(args)
-    grapher.sourceFiles = QFile.getFiles(sources)
-    grapher.targetFiles = QFile.getFiles(targets)
-    grapher.run()
-  }
-}

scala/src/org/broadinstitute/sting/queue/engine/scheduling/DispatchJobScheduler.scala

@@ -1,79 +0,0 @@
-package org.broadinstitute.sting.queue.engine.scheduling
-
-import org.jgrapht.DirectedGraph
-import edu.mit.broad.core.lsf.LocalLsfJob
-import collection.JavaConversions._
-import management.ManagementFactory
-import java.io.File
-import java.util.ArrayList
-import org.broadinstitute.sting.queue.QArguments
-
-/**
- * Dispatches jobs to LSF and then returns.
- */
-class DispatchJobScheduler(jobGraph: DirectedGraph[ResourceNode, ResourceEdge], qArgs: QArguments)
-        extends TopologicalJobScheduler(jobGraph, qArgs) {
-  private var lsfJobs = Map.empty[ExecEdge, LocalLsfJob]
-  private var lsfJobIndex = 0
-  private val jvmName = ManagementFactory.getRuntimeMXBean.getName
-  private val jobNamePrefix = "Q-" + jvmName
-
-  def processExec(exec: ExecEdge) = {
-    lsfJobIndex += 1
-    val job = new LocalLsfJob
-    val jobName = jobNamePrefix + "-" + lsfJobIndex
-    val outputFile = jobName + ".out"
-    val errorFile = jobName + ".err"
-    val workingDir = lookup(exec, "jobWorkingDir", ".")
-    val lsfProject = lookup(exec, "jobProject", "Queue")
-    val queue = lookup(exec, "jobQueue", "broad")
-    val memory = lookup(exec, "jobMemory", "2")
-
-    var extraArgs = List("-r", "-R", "rusage[mem=" + memory + "]")
-
-    val sourceJobs = sourceLsfJobs(exec)
-    if (sourceJobs.size > 0) {
-      extraArgs :::= List("-w", dependencyExpression(sourceJobs))
-    }
-    job.setName(jobName)
-    job.setExtraBsubArgs(new ArrayList(extraArgs))
-    job.setProject(lsfProject)
-    job.setWorkingDir(new File(workingDir))
-    job.setProject(lsfProject)
-    job.setCommand(exec.commandString)
-    job.setOutputFile(new File(workingDir, outputFile))
-    job.setErrFile(new File(workingDir, errorFile))
-    job.setQueue(queue)
-
-    lsfJobs = lsfJobs.updated(exec, job)
-
-    logger.info(job.getBsubCommand.mkString(" "))
-
-    if (!qArgs.dryRun)
-      job.start
-  }
-
-  /**
-   * Walks up the graph looking for the previous LsfJobs for this node
-   */
-  private def sourceLsfJobs(edge: ResourceEdge) : List[LocalLsfJob] = {
-    var sourceJobs = List.empty[LocalLsfJob]
-
-    val source = this.jobGraph.getEdgeSource(edge)
-    for (incomingEdge <- this.jobGraph.incomingEdgesOf(source)) {
-      incomingEdge match {
-
-        // Stop recursing when we find a job along this edge and return it's job id
-        case exec: ExecEdge => sourceJobs :::= List(lsfJobs(exec))
-
-        // For any other type of edge find the LSF jobs preceeding the edge
-        case resourceEdge: ResourceEdge => sourceJobs :::= sourceLsfJobs(resourceEdge)
-      }
-    }
-    sourceJobs
-  }
-
-  private def dependencyExpression(jobs: List[LocalLsfJob]) = {
-    jobs.toSet[LocalLsfJob].map(_.getName).mkString("ended(\"", "\") && ended(\"", "\")")
-  }
-}

scala/src/org/broadinstitute/sting/queue/engine/scheduling/ExecEdge.scala

@@ -1,17 +0,0 @@
-package org.broadinstitute.sting.queue.engine.scheduling
-
-import org.apache.commons.lang.text.{StrLookup, StrSubstitutor}
-import java.lang.String
-
-class ExecEdge(private val templateCommandString: String)
-        extends ResourceEdge {
-  private var convertedCommandString: String = _
-  def commandString = convertedCommandString
-
-  override def traverse(graph: JobScheduler) = {
-    // Lookup any variable using the target node, or any of it's input nodes.
-    val sub = new StrSubstitutor(new StrLookup { def lookup(key: String) = graph.lookup(ExecEdge.this, key, null) })
-    convertedCommandString = sub.replace(templateCommandString)
-    graph.processExec(this)
-  }
-}

scala/src/org/broadinstitute/sting/queue/engine/scheduling/JobScheduler.scala

@@ -1,65 +0,0 @@
-package org.broadinstitute.sting.queue.engine.scheduling
-
-import org.jgrapht.DirectedGraph
-import org.broadinstitute.sting.queue.util.Logging
-import collection.JavaConversions._
-import org.broadinstitute.sting.queue.QArguments
-
-abstract class JobScheduler(protected val jobGraph: DirectedGraph[ResourceNode, ResourceEdge],
-        protected val qArgs: QArguments) extends Logging {
-
-  private var missingKeys = Set.empty[String]
-
-  def runJobs
-  def numJobs = jobGraph.edgeSet.size
-
-  def processExec(exec: ExecEdge) : Unit
-
-  /**
-   * Emulates storing of properties per node by looking up values on
-   * the current edge/target-node or any preceding nodes in the graph.
-   */
-  def lookup(edge: ResourceEdge, key: String, default: String) : String = {
-    val value = lookupRecursive(edge, key) match {
-      case Some(value) => value
-      case None => qArgs.argMap.getOrElse(key, default)
-    }
-    if (value == null)
-      missingKeys = missingKeys ++ Set(key)
-    value
-  }
-
-  protected def logMissingKeys = {
-    if (qArgs.dryRun && !missingKeys.isEmpty) {
-      logger.warn("Missing keys:")
-      for (key <- missingKeys)
-        logger.warn("  ${" + key + "}")
-    }
-  }
-
-  private def lookupRecursive(edge: ResourceEdge, key: String) : Option[String] = {
-    var value = edge.lookup(key)
-    if (value.isDefined)
-      return value
-
-    value = this.jobGraph.getEdgeTarget(edge).lookup(key)
-    if (value.isDefined)
-      return value
-
-    return lookupRecursive(this.jobGraph.getEdgeSource(edge), key)
-  }
-
-  private def lookupRecursive(node: ResourceNode, key: String) : Option[String] = {
-    var value = node.lookup(key)
-    if (value.isDefined)
-      return value
-
-    for (edge <- this.jobGraph.incomingEdgesOf(node)) {
-      value = lookupRecursive(edge, key)
-      if (value.isDefined)
-        return value
-    }
-
-    return None
-  }
-}

scala/src/org/broadinstitute/sting/queue/engine/scheduling/MapResourceNode.scala

@@ -1,5 +0,0 @@
-package org.broadinstitute.sting.queue.engine.scheduling
-
-class MapResourceNode (private val resources: Map[String,String]) extends ResourceNode {
-  override def lookup(key: String) : Option[String] = this.resources.get(key)
-}

scala/src/org/broadinstitute/sting/queue/engine/scheduling/ResourceEdge.scala

@@ -1,6 +0,0 @@
-package org.broadinstitute.sting.queue.engine.scheduling
-
-class ResourceEdge {
-  def traverse(graph: JobScheduler): Unit = {}
-  def lookup(key: String) : Option[String] = None
-}

scala/src/org/broadinstitute/sting/queue/engine/scheduling/ResourceNode.scala

@@ -1,9 +0,0 @@
-package org.broadinstitute.sting.queue.engine.scheduling
-
-import org.apache.commons.lang.builder.{HashCodeBuilder, EqualsBuilder}
-
-class ResourceNode() {
-  override def equals(p1: Any) = EqualsBuilder.reflectionEquals(this, p1)
-  override def hashCode = HashCodeBuilder.reflectionHashCode(this)
-  def lookup(key: String) : Option[String] = None
-}

scala/src/org/broadinstitute/sting/queue/engine/scheduling/SimpleJobScheduler.scala

@@ -1,19 +0,0 @@
-package org.broadinstitute.sting.queue.engine.scheduling
-
-import org.broadinstitute.sting.queue.util.ProcessUtils
-import org.broadinstitute.sting.queue.QArguments
-import org.jgrapht.DirectedGraph
-
-/**
- * Runs jobs one at a time locally
- */
-class SimpleJobScheduler(jobGraph: DirectedGraph[ResourceNode, ResourceEdge], qArgs: QArguments)
-        extends TopologicalJobScheduler(jobGraph, qArgs) {
-  def processExec(exec: ExecEdge) = {
-    var commandString = exec.commandString
-    logger.info(commandString)
-
-    if (!qArgs.dryRun)
-      ProcessUtils.runCommandAndWait(commandString)
-  }
-}

scala/src/org/broadinstitute/sting/queue/engine/scheduling/TopologicalJobScheduler.scala

@@ -1,29 +0,0 @@
-package org.broadinstitute.sting.queue.engine.scheduling
-
-import org.jgrapht.DirectedGraph
-import org.jgrapht.traverse.TopologicalOrderIterator
-import org.jgrapht.event.{EdgeTraversalEvent, TraversalListenerAdapter}
-import collection.JavaConversions._
-import org.broadinstitute.sting.queue.QArguments
-
-/**
- * Loops over the job graph running jobs as the edges are traversed
- */
-abstract class TopologicalJobScheduler(jobGraph: DirectedGraph[ResourceNode, ResourceEdge], qArgs: QArguments)
-        extends JobScheduler(jobGraph, qArgs) {
-
-  protected val iterator = new TopologicalOrderIterator(this.jobGraph)
-
-  iterator.addTraversalListener(new TraversalListenerAdapter[ResourceNode, ResourceEdge] {
-    override def edgeTraversed(event: EdgeTraversalEvent[ResourceNode, ResourceEdge]) =
-      event.getEdge.traverse(TopologicalJobScheduler.this)
-  })
-
-  override def runJobs = {
-    logger.info(String.format("Running %s jobs.", this.numJobs.toString))
-    for (target <- iterator) {
-      // Do nothing for now, let event handler respond
-    }
-    logMissingKeys
-  }
-}

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

@@ -0,0 +1,92 @@
+package org.broadinstitute.sting.queue.function
+
+import java.io.File
+import org.broadinstitute.sting.queue.util._
+import org.broadinstitute.sting.queue.engine.{CommandLineRunner, QGraph}
+
+trait CommandLineFunction extends QFunction with DispatchFunction {
+
+  /**
+   * The command line to run locally or via grid computing.
+   */
+  def commandLine: String
+
+  /**
+   * The directory where the command should run.
+   */
+  @Internal
+  var commandDirectory: File = new File(".")
+
+  /**
+   * Repeats parameters with a prefix/suffix if they are set otherwise returns "".
+   * Skips null, Nil, None.  Unwraps Some(x) to x.  Everything else is called with x.toString.
+   */
+  protected def repeat(prefix: String, params: Seq[_], suffix: String = "", separator: String = "") =
+    params.filter(param => hasValue(param)).map(param => prefix + toValue(param) + suffix).mkString(separator)
+
+  /**
+   * Returns parameter with a prefix/suffix if it is set otherwise returns "".
+   * Does not output null, Nil, None.  Unwraps Some(x) to x.  Everything else is called with x.toString.
+   */
+  protected def optional(prefix: String, param: Any, suffix: String = "") =
+    if (hasValue(param)) prefix + toValue(param) + suffix else ""
+
+  /**
+   * Sets a field value using the name of the field.
+   * Field must be annotated with @Input, @Output, or @Internal
+   * @returns true if the value was found and set
+   */
+  def setValue(name: String, value: String) = {
+    ReflectionUtils.getField(this, name) match {
+      case Some(field) =>
+        val isInput = ReflectionUtils.hasAnnotation(field, classOf[Input])
+        val isOutput = ReflectionUtils.hasAnnotation(field, classOf[Output])
+        val isInternal = ReflectionUtils.hasAnnotation(field, classOf[Internal])
+        if (isInput || isOutput || isInternal) {
+          ReflectionUtils.setValue(this, field, value)
+        }
+        true
+      case None => false
+    }
+  }
+
+  private lazy val fields = ReflectionUtils.getAllFields(this.getClass)
+  private def internals = ReflectionUtils.getFieldsAnnotatedWith(this, fields, classOf[Internal])
+  def inputs = ReflectionUtils.getFieldsAnnotatedWith(this, fields, classOf[Input])
+  def outputs = ReflectionUtils.getFieldsAnnotatedWith(this, fields, classOf[Output])
+
+  override def missingValues = {
+    val missingInputs = missingFields(inputs)
+    val missingOutputs = missingFields(outputs)
+    missingInputs | missingOutputs
+  }
+
+  private def missingFields(fields: Map[String, Any]) = {
+    var missing = Set.empty[String]
+    for ((name, value) <- fields) {
+      val isOptional = ReflectionUtils.getField(this, name) match {
+        case Some(field) => ReflectionUtils.hasAnnotation(field, classOf[Optional])
+        case None => false
+      }
+      if (!isOptional)
+        if (!hasValue(value))
+          missing += name
+    }
+    missing
+  }
+
+  private def hasValue(param: Any) = param match {
+    case null => false
+    case Nil => false
+    case None => false
+    case _ => true
+  }
+
+  private def toValue(param: Any): String = param match {
+    case null => ""
+    case Nil => ""
+    case None => ""
+    case Some(x) => x.toString
+    case x => x.toString
+  }
+}

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

@@ -0,0 +1,19 @@
+package org.broadinstitute.sting.queue.function
+
+import java.io.File
+import org.broadinstitute.sting.queue.util.Internal
+
+trait DispatchFunction extends QFunction with MemoryLimitedFunction {
+  def commandLine: String
+  var commandDirectory: File
+
+  var jobName: String = _
+  var jobOutputFile: File = _
+  var jobErrorFile: File = _
+
+  @Internal
+  var jobProject = "Queue"
+
+  @Internal
+  var jobQueue = "broad"
+}

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

@@ -0,0 +1,6 @@
+package org.broadinstitute.sting.queue.function
+
+trait IntervalFunction {
+  type Intervals = String
+  var intervals: Intervals
+}

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

@@ -0,0 +1,14 @@
+package org.broadinstitute.sting.queue.function
+
+import org.broadinstitute.sting.queue.engine.QGraph
+import scala.collection.immutable.ListMap
+
+/**
+ * Utility class to map a set of inputs to set of outputs.
+ * The QGraph uses this function internally to return
+ */
+class MappingFunction(private val in: ListMap[String, Any], private val out: ListMap[String, Any]) extends QFunction {
+  def inputs = in
+  def outputs = out
+  def run(qGraph: QGraph) = null
+}

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

@@ -0,0 +1,10 @@
+package org.broadinstitute.sting.queue.function
+
+import org.broadinstitute.sting.queue.util.{Input, Optional, ClassType}
+
+trait MemoryLimitedFunction {
+  @Input
+  @Optional
+  @ClassType(classOf[Int])
+  var memoryLimit: Option[Int] = None
+}

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

@@ -0,0 +1,10 @@
+package org.broadinstitute.sting.queue.function
+
+import org.broadinstitute.sting.queue.engine.QGraph
+import scala.collection.immutable.ListMap
+
+trait QFunction {
+  def inputs: ListMap[String, Any]
+  def outputs: ListMap[String, Any]
+  def missingValues = Set.empty[String]
+}

scala/src/org/broadinstitute/sting/queue/function/gatk/GatkFunction.scala

@@ -0,0 +1,35 @@
+package org.broadinstitute.sting.queue.function.gatk
+
+import java.io.File
+import org.broadinstitute.sting.queue.util.{ClassType, Input, Optional}
+import org.broadinstitute.sting.queue.function.{MemoryLimitedFunction, IntervalFunction, CommandLineFunction}
+
+trait GatkFunction extends CommandLineFunction with MemoryLimitedFunction with IntervalFunction {
+  @Input
+  @Optional
+  var javaTmpDir: String = _
+
+  @Input
+  var gatkJar: String = _
+
+  @Input
+  var referenceFile: String = _
+
+  @Input
+  @Optional
+  @ClassType(classOf[File])
+  var bamFiles: List[File] = Nil
+
+  @Input
+  @Optional
+  var dbsnp: File = _
+
+  @Input
+  @Optional
+  var intervals: Intervals = new Intervals("all")
+
+  protected def gatkCommandLine(walker: String) =
+    "java%s%s -jar %s -T %s -R %s%s%s "
+    .format(optional(" -Xmx", memoryLimit, "g"), optional(" -Djava.io.tmpdir=", javaTmpDir),
+      gatkJar, walker, referenceFile, repeat(" -I ", bamFiles), optional(" -D ", dbsnp), optional(" -L ", intervals))
+}

scala/src/org/broadinstitute/sting/queue/util/Logging.scala

@@ -7,7 +7,7 @@ import org.apache.log4j._
  */
 trait Logging {
   private val className = this.getClass.getName
-  lazy val logger = configuredLogger
+  protected lazy val logger = configuredLogger
 
   def configuredLogger = {
     Logging.configureLogging

scala/src/org/broadinstitute/sting/queue/util/ProcessUtils.scala

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.queue.util
 import org.broadinstitute.sting.utils.text.XReadLines
 import collection.mutable.ListBuffer
 import collection.JavaConversions._
+import java.io.File
 
 object ProcessUtils extends Logging {
 
@@ -15,10 +16,10 @@ object ProcessUtils extends Logging {
 
   val running = new ListBuffer[Process]() 
 
-  def runCommandAndWait(command: String) = {
+  def runCommandAndWait(command: String, directory: File) = {
     logger.debug("Running command: " + command)
 
-    var builder = new ProcessBuilder("sh", "-c", command)
+    var builder = new ProcessBuilder("sh", "-c", command).directory(directory)
 
     var process = builder.start
     running += process

scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala

@@ -0,0 +1,96 @@
+package org.broadinstitute.sting.queue.util
+
+import java.lang.reflect.Field
+import org.broadinstitute.sting.queue.QException
+import java.lang.annotation.Annotation
+import scala.concurrent.JavaConversions
+import scala.concurrent.JavaConversions._
+import scala.collection.immutable.ListMap
+
+object ReflectionUtils {
+  def getField(obj: AnyRef, name: String) = getAllFields(obj.getClass).find(_.getName == name)
+
+  def hasAnnotation(field: Field, annotation: Class[_ <: Annotation]) = field.getAnnotation(annotation) != null
+  
+  def getFieldsAnnotatedWith(obj: AnyRef, fields: List[Field], annotation: Class[_ <: Annotation]) =
+    ListMap(fields.filter(field => hasAnnotation(field, annotation))
+      .map(field => (field.getName -> fieldGetter(field).invoke(obj))) :_*)
+
+  def getAllTypes(clazz: Class[_]) = {
+    var types = List.empty[Class[_]]
+      var c = clazz
+      while (c != null) {
+        types :+= c
+        c = c.getSuperclass
+      }
+    types
+  }
+
+  def getAllFields(clazz: Class[_]) = getAllTypes(clazz).map(_.getDeclaredFields).flatMap(_.toList)
+
+  def setValue(obj: AnyRef, field: Field, value: String) = {
+
+    val getter = fieldGetter(field)
+    val setter = fieldSetter(field)
+
+    if (getter == null)
+      throw new QException("Field may be private?  Unable to find getter for field: " + field)
+
+    if (getter == null)
+      throw new QException("Field may be a val instead of var?  Unable to find setter for field: " + field)
+
+    if (classOf[Seq[_]].isAssignableFrom(field.getType)) {
+
+      if (!field.isAnnotationPresent(classOf[ClassType]))
+        throw new QException("@ClassType must be specified due to type erasure for field: " + field)
+
+      val fieldType = field.getAnnotation(classOf[ClassType]).asInstanceOf[ClassType].value
+      val typeValue = coerce(fieldType, value)
+
+      var list = getter.invoke(obj).asInstanceOf[Seq[_]]
+      list :+= typeValue
+      setter.invoke(obj, list)
+
+    } else if (classOf[Option[_]].isAssignableFrom(field.getType)) {
+
+      if (!field.isAnnotationPresent(classOf[ClassType]))
+        throw new QException("@ClassType must be specified due to type erasure for field: " + field)
+
+      val fieldType = field.getAnnotation(classOf[ClassType]).asInstanceOf[ClassType].value
+      val typeValue = coerce(fieldType, value)
+
+      setter.invoke(obj, Some(typeValue))
+
+    } else {
+
+      val fieldType = field.getType
+      val typeValue = coerce(fieldType, value)
+
+      setter.invoke(obj, typeValue.asInstanceOf[AnyRef])
+    }
+  }
+
+  private[util] def fieldGetter(field: Field) = field.getDeclaringClass.getMethod(field.getName)
+  private[util] def fieldSetter(field: Field) = field.getDeclaringClass.getMethod(field.getName+"_$eq", field.getType)
+
+  private def coerce(clazz: Class[_], value: String) = {
+    if (classOf[String] == clazz) value
+    else if (classOf[Boolean] == clazz) value.toBoolean
+    else if (classOf[Byte] == clazz) value.toByte
+    else if (classOf[Short] == clazz) value.toShort
+    else if (classOf[Int] == clazz) value.toInt
+    else if (classOf[Long] == clazz) value.toLong
+    else if (classOf[Float] == clazz) value.toFloat
+    else if (classOf[Double] == clazz) value.toDouble
+    else if (hasStringConstructor(clazz))
+      clazz.getConstructor(classOf[String]).newInstance(value)
+    else throw new QException("Unable to coerce value '%s' to type '%s'.".format(value, clazz))
+  }
+
+  private def hasStringConstructor(clazz: Class[_]) = {
+    clazz.getConstructors.exists(constructor => {
+      val parameters = constructor.getParameterTypes
+      parameters.size == 1 && parameters.head == classOf[String]
+    })
+  }
+}