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biopet.biopet
Commits
f6fc4c5e
Commit
f6fc4c5e
authored
Mar 05, 2015
by
Peter van 't Hof
Browse files
Fix picard version, only work with a picard jar
parent
a10bd09e
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
View file @
f6fc4c5e
...
...
@@ -30,6 +30,8 @@ import scala.io.Source
abstract
class
Picard
extends
BiopetJavaCommandLineFunction
{
override
def
subPath
=
"picard"
::
super
.
subPath
if
(
config
.
contains
(
"picard_jar"
))
jarFile
=
config
(
"picard_jar"
)
@Argument
(
doc
=
"VERBOSITY"
,
required
=
false
)
var
verbosity
:
Option
[
String
]
=
config
(
"verbosity"
)
...
...
@@ -51,10 +53,12 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
@Argument
(
doc
=
"CREATE_MD5_FILE"
,
required
=
false
)
var
createMd5
:
Boolean
=
config
(
"createmd5"
,
default
=
false
)
//FIXME: picard version
// override def versionCommand = executable + " " + javaOpts + " " + javaExecutable + " -h"
// override val versionRegex = """Version: (.*)""".r
// override val versionExitcode = List(0, 1)
override
def
versionCommand
=
{
if
(
jarFile
!=
null
)
executable
+
" -cp "
+
jarFile
+
" "
+
javaMainClass
+
" -h"
else
null
}
override
val
versionRegex
=
"""Version: (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
override
val
defaultVmem
=
"8G"
memoryLimit
=
Option
(
3.0
)
...
...
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