Force logging to a file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

@@ -15,10 +15,12 @@
  */
 package nl.lumc.sasc.biopet.core
 
+import org.apache.log4j.{ PatternLayout, Appender, WriterAppender, FileAppender }
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
-import java.io.File
+import java.io.{ PrintWriter, File }
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
+import scala.collection.JavaConversions._
 
 /** Wrapper around executable from Queue */
 trait PipelineCommand extends MainCommand with GatkLogging {
@@ -64,9 +66,18 @@ trait PipelineCommand extends MainCommand with GatkLogging {
       }
     }
 
+    val logDir: File = new File(Config.global.map.getOrElse("output_dir", "./").toString + File.separator + ".log")
+    logDir.mkdirs()
+    val logFile = new File(logDir, "biopet." + BiopetQCommandLine.timestamp + ".log")
+    val a = new WriterAppender(new PatternLayout("%-5p [%d] [%C{1}] - %m%n"), new PrintWriter(logFile))
+    logger.addAppender(a)
+
     var argv: Array[String] = Array()
     argv ++= Array("-S", pipeline)
     argv ++= args
+    if (!args.contains("--log_to_file") && !args.contains("-log")) {
+      argv ++= List("--log_to_file", logFile.getAbsolutePath.replace("biopet", "queue"))
+    }
     BiopetQCommandLine.main(argv)
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala

@@ -94,6 +94,8 @@ object BiopetQCommandLine extends GatkLogging {
     if (CommandLineProgram.result != 0)
       System.exit(CommandLineProgram.result)
   }
+
+  val timestamp = System.currentTimeMillis
 }
 
 /**
@@ -124,7 +126,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
       org.apache.commons.io.IOUtils.copy(is, os)
       os.close()
       val s = if (t.getName.endsWith("/")) t.getName.substring(0, t.getName.length - 1) else t.getName
-      pipelineName = s.substring(0, s.lastIndexOf(".")) + "." + System.currentTimeMillis
+      pipelineName = s.substring(0, s.lastIndexOf(".")) + "." + BiopetQCommandLine.timestamp
     }
 
     // override createByType to pass the correct exceptions