Merge branch 'feature-raise_memory' into 'develop'

Raised default residental memory for java jobs



See merge request !447

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

@@ -24,6 +24,7 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
   javaGCHeapFreeLimit = config("java_gc_heap_freelimit", default = 10)
   javaGCTimeLimit = config("java_gc_timelimit", default = 50)
 
+  override def defaultResidentFactor: Double = 1.5
   override def defaultVmemFactor: Double = 2.0
 
   /** Constructs java opts, this adds scala threads */

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

@@ -37,9 +37,10 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
   var vmem: Option[String] = config("vmem")
   def defaultCoreMemory: Double = 2.0
   def defaultVmemFactor: Double = 1.4
+  def defaultResidentFactor: Double = 1.2
   var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
 
-  var residentFactor: Double = config("resident_factor", default = 1.2)
+  var residentFactor: Double = config("resident_factor", default = defaultResidentFactor)
 
   private var _coreMemory: Double = 2.0
   def coreMemory = _coreMemory

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

@@ -60,7 +60,7 @@ abstract class Picard extends BiopetJavaCommandLineFunction with Version {
   def versionRegex = """Version: (.*)""".r
   override def versionExitcode = List(0, 1)
 
-  override def defaultCoreMemory = 3.0
+  override def defaultCoreMemory = 4.0
 
   override def getVersion = {
     if (jarFile == null) Picard.getBiopetPicardVersion