From 595e482df864932a7e8f45b2331ef25b2c0a3976 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 25 Oct 2015 09:39:34 +0100
Subject: [PATCH] Set defaults for gc limits
---
.../sasc/biopet/core/BiopetJavaCommandLineFunction.scala | 8 +++-----
1 file changed, 3 insertions(+), 5 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index 86e97f4c7..572287102 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -21,9 +21,9 @@ import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunction {
executable = config("java", default = "java", submodule = "java", freeVar = false)
- javaGCThreads = config("java_gc_threads")
- javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
- javaGCTimeLimit = config("java_gc_timelimit")
+ javaGCThreads = config("java_gc_threads", default = 4)
+ javaGCHeapFreeLimit = config("java_gc_heap_freelimit", default = 10)
+ javaGCTimeLimit = config("java_gc_timelimit", default = 50)
override def defaultVmemFactor: Double = 2.0
@@ -38,8 +38,6 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
if (javaMainClass != null && javaClasspath.isEmpty)
javaClasspath = JavaCommandLineFunction.currentClasspath
-
- //threads = getThreads(defaultThreads)
}
/** Creates command to execute extension */
--
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