Merge remote-tracking branch 'remotes/origin/develop' into feature-centrifuge

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

@@ -18,7 +18,7 @@ import java.io.{ File, FileInputStream, PrintWriter }
 import java.security.MessageDigest
 
 import nl.lumc.sasc.biopet.utils.Logging
-import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import org.broadinstitute.gatk.utils.runtime.ProcessSettings
 import org.ggf.drmaa.JobTemplate
 
@@ -40,6 +40,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
   def defaultRemoteCommand = "bash"
   private val remoteCommand: String = config("remote_command", default = defaultRemoteCommand)
 
+  val preCommands: List[String] = config("pre_commands", default = Nil, freeVar = false)
+
   private def changeScript(file: File): Unit = {
     val lines = Source.fromFile(file).getLines().toList
     val writer = new PrintWriter(file)
@@ -111,7 +113,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
    * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
    */
   protected[core] def preProcessExecutable() {
-    val exe = BiopetCommandLineFunction.preProcessExecutable(executable)
+    val exe = BiopetCommandLineFunction.preProcessExecutable(executable, preCommands)
     exe.path.foreach(executable = _)
     addJobReportBinding("md5sum_exe", exe.md5.getOrElse("N/A"))
   }
@@ -219,7 +221,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
    */
   override final def commandLine: String = {
     preCmdInternal()
-    val cmd = cmdLine +
+    val cmd = preCommands.mkString("\n", "\n", "\n") +
+      cmdLine +
       stdinFile.map(file => " < " + required(file.getAbsoluteFile)).getOrElse("") +
       stdoutFile.map(file => " > " + required(file.getAbsoluteFile)).getOrElse("")
     addJobReportBinding("command", cmd)
@@ -240,13 +243,18 @@ object BiopetCommandLineFunction extends Logging {
   private[core] val executableCache: mutable.Map[String, String] = mutable.Map()
 
   case class Executable(path: Option[String], md5: Option[String])
-  def preProcessExecutable(executable: String): Executable = {
+  def preProcessExecutable(executable: String, pre_commands: List[String] = Nil): Executable = {
     if (!BiopetCommandLineFunction.executableMd5Cache.contains(executable)) {
       if (executable != null) {
         if (!BiopetCommandLineFunction.executableCache.contains(executable)) {
           try {
             val buffer = new StringBuffer()
-            val cmd = Seq("which", executable)
+            val tempFile = File.createTempFile("which.", ".sh")
+            val writer = new PrintWriter(tempFile)
+            pre_commands.foreach(cmd => writer.println(cmd + " > /dev/null 2> /dev/null"))
+            writer.println(s"which $executable")
+            writer.close()
+            val cmd = Seq("bash", tempFile.getAbsolutePath)
             val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
             if (process.exitValue == 0) {
               val file = new File(buffer.toString)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala

@@ -155,7 +155,9 @@ object GensToVcf extends ToolCommand {
             .make()
       }
 
-      val infoMap = infoHeaderKeys.map(_.map(x => ("GENS_" + x) -> infoValues.get(infoHeaderMap.get(x))).toMap).getOrElse(Map())
+      val infoMap = infoHeaderKeys
+        .map(_.map(x => ("GENS_" + x) -> infoValues.get(infoHeaderMap.get(x)).replaceAll(";", ",")).toMap)
+        .getOrElse(Map())
 
       val builder = (new VariantContextBuilder)
         .chr(cmdArgs.contig)