Commit f6fc4c5e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix picard version, only work with a picard jar

parent a10bd09e
...@@ -30,6 +30,8 @@ import scala.io.Source ...@@ -30,6 +30,8 @@ import scala.io.Source
abstract class Picard extends BiopetJavaCommandLineFunction { abstract class Picard extends BiopetJavaCommandLineFunction {
override def subPath = "picard" :: super.subPath override def subPath = "picard" :: super.subPath
if (config.contains("picard_jar")) jarFile = config("picard_jar")
@Argument(doc = "VERBOSITY", required = false) @Argument(doc = "VERBOSITY", required = false)
var verbosity: Option[String] = config("verbosity") var verbosity: Option[String] = config("verbosity")
...@@ -51,10 +53,12 @@ abstract class Picard extends BiopetJavaCommandLineFunction { ...@@ -51,10 +53,12 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
@Argument(doc = "CREATE_MD5_FILE", required = false) @Argument(doc = "CREATE_MD5_FILE", required = false)
var createMd5: Boolean = config("createmd5", default = false) var createMd5: Boolean = config("createmd5", default = false)
//FIXME: picard version override def versionCommand = {
// override def versionCommand = executable + " " + javaOpts + " " + javaExecutable + " -h" if (jarFile != null) executable + " -cp " + jarFile + " " + javaMainClass + " -h"
// override val versionRegex = """Version: (.*)""".r else null
// override val versionExitcode = List(0, 1) }
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0, 1)
override val defaultVmem = "8G" override val defaultVmem = "8G"
memoryLimit = Option(3.0) memoryLimit = Option(3.0)
......
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