From 13ca628ad9b292b597d1356b695c191f4a5e4936 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 18 Mar 2016 07:26:52 +0100
Subject: [PATCH] Raise memory
---
.../nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala | 2 ++
.../sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala | 2 +-
.../lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala | 2 ++
3 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
index 60a76d860..db9ed0f7e 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
@@ -38,6 +38,8 @@ class MergeOtuMaps(val root: Configurable) extends BiopetCommandLineFunction wit
var failuresFp: Option[File] = None
+ override def defaultCoreMemory = 4.0
+
override def beforeGraph(): Unit = {
super.beforeGraph()
require(input.nonEmpty)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
index 371752d37..07fef8aef 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
@@ -33,7 +33,7 @@ class PickClosedReferenceOtus(val root: Configurable) extends BiopetCommandLineF
var outputDir: File = null
override def defaultThreads = 3
- override def defaultCoreMemory = 12.0
+ override def defaultCoreMemory = 16.0
def versionCommand = executable + " --version"
def versionRegex = """Version: (.*)""".r
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
index cbf010ca7..d9295dee0 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
@@ -56,6 +56,8 @@ class SplitLibrariesFastq(val root: Configurable) extends BiopetCommandLineFunct
def outputSeqs = new File(outputDir, "seqs.fna")
+ override def defaultCoreMemory = 4.0
+
override def beforeGraph(): Unit = {
super.beforeGraph()
require(input.nonEmpty)
--
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