Merge branch 'feature-rcommandline' into 'develop'

Feature rcommandline

R commandline function cherry-picked

See merge request !121

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.{ FileOutputStream, File }
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.Input
+
+import scala.collection.mutable.ListBuffer
+
+/**
+ * Created by wyleung on 17-2-15.
+ */
+trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
+  /**
+   * Will initially handle Cluster supported commands
+   *
+   */
+  // TODO: write support for running with InProcesFunction
+
+  @Input(doc = "R script", required = false)
+  protected var script: File = _
+  protected var scriptName: String = _
+  protected var arguments: ListBuffer[String] = ListBuffer()
+  override val defaultVmem: String = "4G"
+
+  executable = config("exe", default = "Rscript", submodule = "R")
+
+  /**
+   * Adding arguments in order
+   *
+   * @param argName
+   * @param argValue
+   * @param dash , is the dashsign a - or -- ?
+   * @param sep using a space or "=" to specify the "connector" between argName and argValue
+   */
+  def addArgument(argName: String, argValue: String, dash: String = "-", sep: String = " ") = {
+    arguments += "%s%s%s%s".format(dash, argName, sep, argValue)
+  }
+  def addPositionalArgument(argValue: String, dash: String = "-", sep: String = " ") = {
+    arguments += "%s".format(argValue)
+  }
+
+  /**
+   * Set the Rscript to run
+   *
+   * @param filename RScript file location
+   */
+  def setScript(filename: String): Unit = {
+    val f: File = new File(filename)
+    f.getAbsoluteFile.exists() match {
+      case true => {
+        script = f
+        scriptName = f.getName
+      }
+      case false => setScript(f, "")
+    }
+
+  }
+
+  /**
+   * Gets the R-script from within Biopet
+   *
+   * throws ResourceNotFound if script doesn't exist
+   */
+  def setScript(filename: File, subpackage: String): Unit = {
+    val RScript: File = new File(".queue/tmp/" + subpackage + filename)
+    if (!RScript.getParentFile.exists) RScript.getParentFile.mkdirs
+
+    val is = getClass.getResourceAsStream(subpackage + RScript.getName)
+    val os = new FileOutputStream(RScript)
+
+    org.apache.commons.io.IOUtils.copy(is, os)
+    os.close()
+
+    script = RScript
+    scriptName = RScript.getName
+  }
+
+  override def cmdLine: String = {
+    required(executable) +
+      required(script) +
+      arguments.mkString(" ")
+  }
+}