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biopet.biopet
Commits
595e482d
Commit
595e482d
authored
Oct 25, 2015
by
Peter van 't Hof
Browse files
Set defaults for gc limits
parent
18e22c1b
Changes
1
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
View file @
595e482d
...
...
@@ -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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