switch to core rscript extension

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RScriptCommandLineFunction.scala

-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
-
-import java.io.{ File, FileOutputStream }
-
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.Input
-
-/**
- * Trait for RScript wrappers
- */
-trait RScriptCommandLineFunction extends BiopetCommandLineFunction {
-
-  @Input(doc = "R script file", required = false)
-  var RScript: File = _
-
-  executable = config("exe", default = "Rscript", submodule = "rscript")
-
-  protected var RScriptName: String = _
-
-  def setRScript(script: String) {
-    setRScript(script, "")
-  }
-
-  def setRScript(script: String, subpackage: String) {
-    RScriptName = script
-    // TODO: set .queue/tmp as a library-wide constant
-    RScript = new File(".queue/tmp/" + subpackage + RScriptName)
-
-    if (!RScript.getParentFile.exists)
-      RScript.getParentFile.mkdirs
-
-    val is = getClass.getResourceAsStream(subpackage + RScriptName)
-    val os = new FileOutputStream(RScript)
-
-    org.apache.commons.io.IOUtils.copy(is, os)
-    os.close()
-  }
-
-  def RScriptCommand: String = {
-    required(executable) + required(RScript)
-  }
-}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala

@@ -17,16 +17,16 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.RScriptCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Wrapper for the plot_heatmap.R script, used internally in Gentrap
  */
-class PlotHeatmap(val root: Configurable) extends RScriptCommandLineFunction {
+class PlotHeatmap(val root: Configurable) extends RscriptCommandLineFunction {
 
-  setRScript("plot_heatmap.R", "/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/")
+  protected var script: File = config("script", default = "plot_heatmap.R")
 
   @Input(doc = "Input table", required = true)
   var input: File = null
@@ -38,12 +38,12 @@ class PlotHeatmap(val root: Configurable) extends RScriptCommandLineFunction {
   var useLog: Boolean = config("use_log", default = false)
   var tmmNormalize: Boolean = config("tmm_normalize", default = false)
 
-  def cmdLine = {
-    RScriptCommand +
-      conditional(tmmNormalize, "-T") +
-      conditional(useLog, "-L") +
-      required("-C", countType) +
-      required("-I", input) +
-      required("-O", output)
-  }
+  override def cmd = super.cmd ++
+    (if (tmmNormalize) Seq("-T") else Seq()) ++
+    (if (useLog) Seq("-L") else Seq()) ++
+    (countType match {
+      case Some(t) => Seq("-C", t)
+      case _ => Seq()
+    }) ++
+    Seq("-I", input.getAbsolutePath, "-O", output.getAbsolutePath)
 }