Commit fac95be4 authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'develop' into add-cnmops-kopisu

parents 02e65123 3c836e0c
......@@ -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()
}
......
......@@ -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._
......
......@@ -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)
......
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