From a5a9f4b1b70f69f322e5ebb0b80106e26cff0d75 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 22 Oct 2015 15:29:30 +0200
Subject: [PATCH] refactor memorylimit
---
.../scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala | 4 ++--
.../scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala | 2 ++
.../lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala | 2 +-
3 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
index 300cd4cdb..11fffa46f 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
@@ -28,7 +28,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
var residentFactor: Double = config("resident_factor", default = 1.2)
private var _coreMemory: Double = 2.0
- def coreMemeory = _coreMemory
+ def coreMemory = _coreMemory
var retry = 0
@@ -89,7 +89,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
commands.foreach(_.setResources())
nCoresRequest = Some(commands.map(_.threads).sum)
- _coreMemory = commands.map(cmd => cmd.coreMemeory * (cmd.threads.toDouble / threads.toDouble)).sum
+ _coreMemory = commands.map(cmd => cmd.coreMemory * (cmd.threads.toDouble / threads.toDouble)).sum
memoryLimit = Some(_coreMemory * threads)
residentLimit = Some((_coreMemory + (0.5 * retry)) * residentFactor)
vmem = Some((_coreMemory * (vmemFactor + (0.5 * retry))) + "G")
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
index eaef86a39..b70865176 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
@@ -29,6 +29,8 @@ class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input wig file")
var inputWigFile: File = _
+ override def defaultCoreMemory = 3.0
+
@Input(doc = "Input chrom sizes file", required = true)
var inputChromSizesFile: File = _
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
index 5df2a3a7b..1e1459296 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
@@ -27,7 +27,7 @@ class SamtoolsSort(val root: Configurable) extends Samtools {
}
def cmdLine = required(executable) + required("sort") +
- optional("-m", (coreMemeory + "G")) +
+ optional("-m", (coreMemory + "G")) +
optional("-@", threads) +
optional("-O", outputFormat) +
required("-T", prefix) +
--
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