Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
2bf93f99
Commit
2bf93f99
authored
Mar 07, 2015
by
Peter van 't Hof
Browse files
Format scala docs
parent
8c9dcb5b
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
View file @
2bf93f99
...
...
@@ -17,9 +17,7 @@ package nl.lumc.sasc.biopet.core
import
org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
/**
* Biopet commandline class for java based programs
*/
/** Biopet commandline class for java based programs */
trait
BiopetJavaCommandLineFunction
extends
JavaCommandLineFunction
with
BiopetCommandLineFunctionTrait
{
executable
=
config
(
"java"
,
default
=
"java"
,
submodule
=
"java"
,
freeVar
=
false
)
...
...
@@ -27,25 +25,17 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
javaGCHeapFreeLimit
=
config
(
"java_gc_heap_freelimit"
)
javaGCTimeLimit
=
config
(
"java_gc_timelimit"
)
/**
* Constructs java opts, this adds scala threads
* @return
*/
/** Constructs java opts, this adds scala threads */
override
def
javaOpts
=
super
.
javaOpts
+
optional
(
"-Dscala.concurrent.context.numThreads="
,
threads
,
spaceSeparated
=
false
,
escape
=
false
)
/**
* Sets memory limit
*/
/** Sets memory limit */
override
def
beforeGraph
{
super
.
beforeGraph
if
(
memoryLimit
.
isEmpty
)
memoryLimit
=
config
(
"memory_limit"
)
}
/**
* Creates command to execute extension
* @return
*/
/** Creates command to execute extension */
override
def
commandLine
:
String
=
{
preCmdInternal
val
cmd
=
super
.
commandLine
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment