diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
new file mode 100644
index 0000000000000000000000000000000000000000..00362623a7e780439539e30798ec288d56751f3b
--- /dev/null
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
@@ -0,0 +1,298 @@
+ /*
+* Copyright (c) 2012 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 nl.lumc.sasc.biopet.core
+
+import java.io.File
+import org.broadinstitute.sting.commandline._
+import org.broadinstitute.sting.queue.util._
+import org.broadinstitute.sting.queue.QCommandPlugin
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.queue.QScriptManager
+import org.broadinstitute.sting.queue.engine.{QStatusMessenger, QGraphSettings, QGraph}
+import collection.JavaConversions._
+import org.broadinstitute.sting.utils.classloader.PluginManager
+import org.broadinstitute.sting.utils.exceptions.UserException
+import org.broadinstitute.sting.utils.io.IOUtils
+import org.broadinstitute.sting.utils.help.ApplicationDetails
+import java.net.URL
+import java.util.{ResourceBundle, Arrays}
+import org.broadinstitute.sting.utils.text.TextFormattingUtils
+import org.apache.commons.io.FilenameUtils
+
+/**
+ * Entry point of Queue. Compiles and runs QScripts passed in to the command line.
+ */
+object BiopetQCommandLine extends Logging {
+ /**
+ * Main.
+ * @param argv Arguments.
+ */
+ def main(argv: Array[String]) {
+ val qCommandLine = new BiopetQCommandLine
+
+ val shutdownHook = new Thread {
+ override def run() {
+ logger.info("Shutting down jobs. Please wait...")
+ qCommandLine.shutdown()
+ }
+ }
+
+ Runtime.getRuntime.addShutdownHook(shutdownHook)
+
+ try {
+ CommandLineProgram.start(qCommandLine, argv)
+ try {
+ Runtime.getRuntime.removeShutdownHook(shutdownHook)
+ qCommandLine.shutdown()
+ } catch {
+ case e: Exception => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
+ }
+ if (CommandLineProgram.result != 0)
+ System.exit(CommandLineProgram.result)
+ } catch {
+ case e: Exception => CommandLineProgram.exitSystemWithError(e)
+ }
+ }
+}
+
+/**
+ * Entry point of Queue. Compiles and runs QScripts passed in to the command line.
+ */
+class BiopetQCommandLine extends CommandLineProgram with Logging {
+ @Input(fullName="script", shortName="S", doc="QScript scala file", required=false)
+ @ClassType(classOf[File])
+ var scripts: Seq[File] = Nil
+
+ @ArgumentCollection
+ val settings = new QGraphSettings
+
+ private val qScriptManager = new QScriptManager
+ private val qGraph = new QGraph
+ private var qScriptClasses: File = _
+ private var shuttingDown = false
+
+ private lazy val qScriptPluginManager = {
+ //qScriptClasses = IOUtils.tempDir("Q-Classes-", "", settings.qSettings.tempDirectory)
+ //qScriptManager.loadScripts(scripts, qScriptClasses)
+ var temp: Seq[URL] = Seq()
+ for (t <- scripts) temp :+= this.getClass.getResource(t.toString)
+ new PluginManager[QScript](qPluginType, temp)
+ }
+
+ private lazy val qCommandPlugin = {
+ new PluginManager[QCommandPlugin](classOf[QCommandPlugin])
+ }
+
+ private lazy val allCommandPlugins = qCommandPlugin.createAllTypes()
+
+ private lazy val qPluginType: Class[_ <: QScript] = {
+ allCommandPlugins.map(_.qScriptClass).headOption.getOrElse(classOf[QScript])
+ }
+
+ /**
+ * Takes the QScripts passed in, runs their script() methods, retrieves their generated
+ * functions, and then builds and runs a QGraph based on the dependencies.
+ */
+ def execute = {
+ var success = false
+ var result = 1
+ var functionsAndStatusSize = 0
+ try {
+ ClassFieldCache.parsingEngine = this.parser
+
+ if (settings.qSettings.runName == null)
+ settings.qSettings.runName = "runname"
+ if (IOUtils.isDefaultTempDir(settings.qSettings.tempDirectory))
+ settings.qSettings.tempDirectory = IOUtils.absolute(settings.qSettings.runDirectory, ".queue/tmp")
+ qGraph.initializeWithSettings(settings)
+
+ for (commandPlugin <- allCommandPlugins) {
+ loadArgumentsIntoObject(commandPlugin)
+ }
+
+ for (commandPlugin <- allCommandPlugins) {
+ if (commandPlugin.statusMessenger != null)
+ commandPlugin.statusMessenger.started()
+ }
+
+ qGraph.messengers = allCommandPlugins.filter(_.statusMessenger != null).map(_.statusMessenger).toSeq
+
+ // TODO: Default command plugin argument?
+ val remoteFileConverter = (
+ for (commandPlugin <- allCommandPlugins if (commandPlugin.remoteFileConverter != null))
+ yield commandPlugin.remoteFileConverter
+ ).headOption.getOrElse(null)
+
+ if (remoteFileConverter != null)
+ loadArgumentsIntoObject(remoteFileConverter)
+
+ val allQScripts = qScriptPluginManager.createAllTypes()
+ for (script <- allQScripts) {
+ logger.info("Scripting " + qScriptPluginManager.getName(script.getClass.asSubclass(classOf[QScript])))
+ loadArgumentsIntoObject(script)
+ allCommandPlugins.foreach(_.initScript(script))
+ // TODO: Pulling inputs can be time/io expensive! Some scripts are using the files to generate functions-- even for dry runs-- so pull it all down for now.
+ //if (settings.run)
+ script.pullInputs()
+ script.qSettings = settings.qSettings
+ try {
+ script.script()
+ } catch {
+ case e: Exception =>
+ throw new UserException.CannotExecuteQScript(script.getClass.getSimpleName + ".script() threw the following exception: " + e, e)
+ }
+
+ if (remoteFileConverter != null) {
+ if (remoteFileConverter.convertToRemoteEnabled)
+ script.mkRemoteOutputs(remoteFileConverter)
+ }
+
+ script.functions.foreach(qGraph.add(_))
+ logger.info("Added " + script.functions.size + " functions")
+ }
+ // Execute the job graph
+ qGraph.run()
+
+ val functionsAndStatus = qGraph.getFunctionsAndStatus
+
+ // walk over each script, calling onExecutionDone
+ for (script <- allQScripts) {
+ val scriptFunctions = functionsAndStatus.filterKeys(f => script.functions.contains(f))
+ script.onExecutionDone(scriptFunctions, success)
+ }
+ functionsAndStatusSize = functionsAndStatus.size
+
+ // write the final complete job report
+ logger.info("Writing final jobs report...")
+ qGraph.writeJobsReport()
+
+ if (qGraph.success) {
+ if (settings.run) {
+ allQScripts.foreach(_.pushOutputs())
+ for (commandPlugin <- allCommandPlugins)
+ if (commandPlugin.statusMessenger != null) {
+ val allInputs = allQScripts.map(_.remoteInputs)
+ val allOutputs = allQScripts.map(_.remoteOutputs)
+ commandPlugin.statusMessenger.done(allInputs, allOutputs)
+ }
+ }
+ success = true
+ result = 0
+ }
+ } finally {
+ if (!success) {
+ logger.info("Done with errors")
+ qGraph.logFailed()
+ if (settings.run) {
+ for (commandPlugin <- allCommandPlugins)
+ if (commandPlugin.statusMessenger != null)
+ commandPlugin.statusMessenger.exit("Done with errors: %s".format(qGraph.formattedStatusCounts))
+ }
+ }
+ }
+ logger.info("Script %s with %d total jobs".format(if (success) "completed successfully" else "failed", functionsAndStatusSize))
+ result
+ }
+
+ /**
+ * Returns true as QScripts are located and compiled.
+ * @return true
+ */
+ override def canAddArgumentsDynamically = true
+
+ /**
+ * Returns the list of QScripts passed in via -S and other plugins
+ * so that their arguments can be inspected before QScript.script is called.
+ * @return Array of dynamic sources
+ */
+ override def getArgumentSources = {
+ var plugins = Seq.empty[Class[_]]
+ plugins ++= qScriptPluginManager.getPlugins
+ plugins ++= qCommandPlugin.getPlugins
+ plugins.toArray
+ }
+
+ /**
+ * Returns the name of a script/plugin
+ * @return The name of a script/plugin
+ */
+ override def getArgumentSourceName(source: Class[_]) = {
+ if (classOf[QScript].isAssignableFrom(source))
+ qScriptPluginManager.getName(source.asSubclass(classOf[QScript]))
+ else if (classOf[QCommandPlugin].isAssignableFrom(source))
+ qCommandPlugin.getName(source.asSubclass(classOf[QCommandPlugin]))
+ else
+ null
+ }
+
+ /**
+ * Returns a ScalaCompoundArgumentTypeDescriptor that can parse argument sources into scala collections.
+ * @return a ScalaCompoundArgumentTypeDescriptor
+ */
+ override def getArgumentTypeDescriptors =
+ Arrays.asList(new ScalaCompoundArgumentTypeDescriptor)
+
+ override def getApplicationDetails : ApplicationDetails = {
+ new ApplicationDetails(createQueueHeader(),
+ Seq.empty[String],
+ ApplicationDetails.createDefaultRunningInstructions(getClass.asInstanceOf[Class[CommandLineProgram]]),
+ "")
+ }
+
+ private def createQueueHeader() : Seq[String] = {
+ Seq(String.format("Queue v%s, Compiled %s", getQueueVersion, getBuildTimestamp),
+ "Copyright (c) 2012 The Broad Institute",
+ "For support and documentation go to http://www.broadinstitute.org/gatk")
+ }
+
+ private def getQueueVersion : String = {
+ val stingResources : ResourceBundle = TextFormattingUtils.loadResourceBundle("StingText")
+
+ if ( stingResources.containsKey("org.broadinstitute.sting.queue.QueueVersion.version") ) {
+ stingResources.getString("org.broadinstitute.sting.queue.QueueVersion.version")
+ }
+ else {
+ "<unknown>"
+ }
+ }
+
+ private def getBuildTimestamp : String = {
+ val stingResources : ResourceBundle = TextFormattingUtils.loadResourceBundle("StingText")
+
+ if ( stingResources.containsKey("build.timestamp") ) {
+ stingResources.getString("build.timestamp")
+ }
+ else {
+ "<unknown>"
+ }
+ }
+
+ def shutdown() = {
+ shuttingDown = true
+ qGraph.shutdown()
+ if (qScriptClasses != null) IOUtils.tryDelete(qScriptClasses)
+ }
+}
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/PipelineCommand.scala
index ba76acc2ab12e13f1905cc39e2ea4c4683a8cd29..b2cc5050fc4e4b0e1b59f91f378217b6671c3720 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/PipelineCommand.scala
@@ -7,23 +7,25 @@
package nl.lumc.sasc.biopet.core
import java.io.FileOutputStream
-import org.broadinstitute.sting.queue.QCommandLine
+//import org.broadinstitute.sting.queue.QCommandLine
import org.broadinstitute.sting.queue.util.Logging
trait PipelineCommand extends Logging {
- val src = ""
- val extension = ".scala"
+// val src = ""
+// val extension = ".scala"
+ val pipeline = ""
def main(args: Array[String]): Unit = {
- val tempFile = java.io.File.createTempFile(src + ".", extension)
- val is = getClass.getResourceAsStream(src + extension)
- val os = new FileOutputStream(tempFile)
- org.apache.commons.io.IOUtils.copy(is, os)
- os.close()
+// val tempFile = java.io.File.createTempFile(src + ".", extension)
+// val is = getClass.getResourceAsStream(src + extension)
+// val os = new FileOutputStream(tempFile)
+// org.apache.commons.io.IOUtils.copy(is, os)
+// os.close()
var argv: Array[String] = Array()
- argv ++= Array("-S", tempFile.getAbsolutePath)
+ //argv ++= Array("-S", tempFile.getAbsolutePath)
+ argv ++= Array("-S", pipeline)
argv ++= args
- return QCommandLine.main(argv)
+ return BiopetQCommandLine.main(argv)
}
}
\ No newline at end of file
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index af4476e95e63636b2cfedbdb2625c0d995073010..c46e4f14b2d44a1309aea99ed53c7650ab20104d 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -271,5 +271,5 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
}
object Flexiprep extends PipelineCommand {
- override val src = "Flexiprep"
+ override val pipeline = "/nl/lumc/sasc/biopet/pipelines/flexiprep/"
}
diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
index 400ed4ad22923848ce1cab534ecae80aa2b52e9b..a0402a2b21f4ee332b4d5597c80799e3cbf0e38a 100644
--- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+++ b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
@@ -310,5 +310,5 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript
}
object Gatk extends PipelineCommand {
- override val src = "Gatk"
+ override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/"
}
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index db9681488b7bd5c7ba690fcf48e05a7b9c35a044..bd774d4311d15aae4731c0b3a02c3e2ad374ff32 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -192,5 +192,5 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri
}
object Mapping extends PipelineCommand {
- override val src = "Mapping"
+ override val pipeline = "/nl/lumc/sasc/biopet/pipelines/mapping/"
}