Added pre_command to executable check

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

@@ -113,7 +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"))
   }
@@ -243,13 +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)