Commit 9f2940e0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change limits to coreMemory

parent 1ff52e09
......@@ -44,7 +44,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
override val versionExitcode = List(0, 1)
override def versionCommand = executable + " --version"
override val defaultVmem = "6G"
override val defaultCoreMemory = 4.0
override val defaultThreads = 8
var sam: Boolean = config("sam", default = true)
......
......@@ -33,7 +33,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 8
/** default vmem for cluster jobs */
override val defaultVmem = "8G"
override val defaultCoreMemory = 6.0
/** input file */
@Input(doc = "Input file (SAM or BAM)", required = true)
......
......@@ -35,7 +35,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 8
/** default vmem for cluster jobs */
override val defaultVmem = "16G"
override val defaultCoreMemory = 10.0
/** input file */
@Input(doc = "Input FASTQ file(s)", required = true) //var input: List[File] = _
......
......@@ -33,7 +33,7 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
var decomrpess = true
var memory: Option[Int] = config("memory")
override val defaultVmem = (memory.getOrElse(1000) * 2 / 1000) + "G"
override val defaultCoreMemory = memory.getOrElse(1000).toDouble / 1000
override val defaultThreads = 2
override def beforeCmd {
......
......@@ -36,7 +36,7 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
protected var script: File = _
protected var scriptName: String = _
protected var arguments: ListBuffer[String] = ListBuffer()
override val defaultVmem: String = "4G"
override val defaultCoreMemory = 2.0
executable = config("exe", default = "Rscript", submodule = "R")
......
......@@ -64,7 +64,7 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
override val versionExitcode = List(0, 1)
/// Stampy uses approx factor 1.1 times the size of the genome in memory.
override val defaultVmem = "4G"
override val defaultCoreMemory = 4.0
override val defaultThreads = 8
override def versionCommand = executable + " --help"
......
......@@ -63,7 +63,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
var outFileNamePrefix: String = _
var runThreadN: Option[Int] = config("runThreadN")
override val defaultVmem = "6G"
override val defaultCoreMemory = 4.0
override val defaultThreads = 8
/** Sets output files for the graph */
......
......@@ -32,7 +32,7 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
override val versionExitcode = List(0, 1)
override def versionCommand = executable + " --version"
override val defaultVmem = "6G"
override val defaultCoreMemory = 4.0
override val defaultThreads = 8
@Input(doc = "FastQ file(s) R1", shortName = "R1")
......
......@@ -46,7 +46,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
if (input.getName.endsWith(".bam")) inputTag = "-abam"
}
override val defaultVmem = "6G"
override val defaultCoreMemory = 4.0
/** Returns command to execute */
def cmdLine = required(executable) + required("coverage") +
......
......@@ -60,7 +60,7 @@ class BwaAln(val root: Configurable) extends Bwa {
var n2: Boolean = config("2", default = false)
var Y: Boolean = config("Y", default = false)
override val defaultVmem = "5G"
override val defaultCoreMemory = 4.0
override val defaultThreads = 8
/** Returns command to execute */
......
......@@ -69,7 +69,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var Y: Boolean = config("Y", default = false)
var I: Option[String] = config("I")
override val defaultVmem = "6G"
override val defaultCoreMemory = 4.0
override val defaultThreads = 8
def cmdLine = {
......
......@@ -26,7 +26,7 @@ abstract class Conifer extends PythonCommandLineFunction {
override val versionExitcode = List(0)
override def versionCommand = executable + " " + python_script + " --version"
override val defaultVmem = "8G"
override val defaultCoreMemory = 5.0
override val defaultThreads = 1
def cmdLine = getPythonCommand
......
......@@ -31,7 +31,7 @@ abstract class Gatk extends BiopetJavaCommandLineFunction {
val analysisType: String
override val defaultVmem = "5G"
override val defaultCoreMemory = 3.0
@Input(required = true)
var reference: File = config("reference")
......
......@@ -59,7 +59,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var pairs: Boolean = config("pairs", default = false)
override val defaultVmem = "6G"
override val defaultCoreMemory = 4.0
override def beforeGraph {
super.beforeGraph
......
......@@ -60,8 +60,7 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0, 1)
override val defaultVmem = "8G"
memoryLimit = Option(3.0)
override val defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
required("TMP_DIR=" + jobTempDir) +
......
......@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/** General Sambamba extension */
abstract class Sambamba extends BiopetCommandLineFunction {
override val defaultVmem = "4G"
override val defaultCoreMemory = 2.0
override val defaultThreads = 2
override def subPath = "sambamba" :: super.subPath
......
......@@ -84,7 +84,7 @@ object BreakdancerConfig {
class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "breakdancer-max", freeVar = false)
override val defaultVmem = "6G"
override val defaultCoreMemory = 4.0
override val defaultThreads = 1 // breakdancer can only work on 1 single thread
override val versionRegex = """.*[Vv]ersion:? (.*)""".r
......
......@@ -28,7 +28,7 @@ class Clever(val root: Configurable) extends BiopetCommandLineFunction {
private lazy val versionexecutable: File = config("version_exe", default = (new File(executable).getParent + "/ctk-version"))
override val defaultVmem = "4G"
override val defaultCoreMemory = 3.0
override val defaultThreads = 8
override def versionCommand = versionexecutable.getAbsolutePath
......
......@@ -23,7 +23,7 @@ import java.io.File
class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "pindel", freeVar = false)
override val defaultVmem = "8G"
override val defaultCoreMemory = 5.0
override val defaultThreads = 8
override val versionRegex = """Pindel version:? (.*)""".r
......
......@@ -29,7 +29,6 @@ abstract class Varscan extends BiopetJavaCommandLineFunction {
* override val versionRegex = """VarScan v(.*)""".r
*/
override val defaultVmem = "8G"
memoryLimit = Option(3.0)
override val defaultCoreMemory = 5.0
}
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