From 62cc447adae8d17100ec0cd0101b6c9792c3be51 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 9 Mar 2015 14:23:44 +0100
Subject: [PATCH] RCommandlineFunction Trait
Conflicts:
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
---
.../RscriptCommandLineFunction.scala | 84 +++++++++++++++++++
1 file changed, 84 insertions(+)
create mode 100644 public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
new file mode 100644
index 000000000..26ddc7d2e
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
@@ -0,0 +1,84 @@
+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(" ")
+ }
+}
--
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