Merge branch 'develop' into add-cnmops-kopisu

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

@@ -40,16 +40,22 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
   def defaultResidentFactor: Double = 1.2
   var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
 
+  val useSge: Boolean = config("use_sge", default = true)
+
   var residentFactor: Double = config("resident_factor", default = defaultResidentFactor)
 
   private var _coreMemory: Double = 2.0
   def coreMemory = _coreMemory
 
+  /** This value is for SGE and is defined in seconds */
+  protected val maxWalltimeLimit: Option[Int] = config("max_walltime_limit")
+
   var retry = 0
 
   override def freezeFieldValues(): Unit = {
     setResources()
-    if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
+    if (useSge && vmem.isDefined) jobResourceRequests :+= s"h_vmem=${vmem.get}"
+    if (useSge && maxWalltimeLimit.isDefined) jobResourceRequests :+= s"h_rt=${maxWalltimeLimit.get}"
     super.freezeFieldValues()
   }
 

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

@@ -16,11 +16,10 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 
-import htsjdk.samtools.SAMSequenceDictionary
-import htsjdk.samtools.reference.{ FastaSequenceFile, IndexedFastaSequenceFile }
+import htsjdk.samtools.reference.IndexedFastaSequenceFile
 import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
-import nl.lumc.sasc.biopet.utils.{ BamUtils, ConfigUtils, FastaUtils, Logging }
-import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
+import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, FastaUtils, Logging }
 
 import scala.collection.JavaConversions._
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala

@@ -29,7 +29,6 @@ class Pysvtools(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input file", required = true)
   var input: List[File] = Nil
 
-  @Argument(doc = "Set flanking amount")
   var flanking: Option[Int] = config("flanking")
 
   var exclusionRegions: List[File] = config("exclusion_regions", default = Nil)