From f6fc4c5ec20eb5e992ab96d1820695118029b41a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 5 Mar 2015 19:13:07 +0100
Subject: [PATCH] Fix picard version, only work with a picard jar
---
.../lumc/sasc/biopet/extensions/picard/Picard.scala | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index 7d98514d9..22063d335 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -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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