From 9156f68c45fac30141f2245356b571c31be62b0f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 26 Oct 2015 07:58:05 +0100
Subject: [PATCH] Fixed unknown executables
---
.../sasc/biopet/extensions/gatk/broad/GatkGeneral.scala | 2 +-
.../lumc/sasc/biopet/core/BiopetCommandLineFunction.scala | 6 +++---
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
index c0d8747dd..11b59f2fa 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
@@ -43,7 +43,7 @@ trait GatkGeneral extends CommandLineGATK with CommandLineResources with Referen
def versionCommand = "java" + " -jar " + jarFile + " -version"
override def getVersion = {
- executable = BiopetCommandLineFunction.preProcessExecutable(executable).path
+ BiopetCommandLineFunction.preProcessExecutable(executable).path.foreach(executable = _)
super.getVersion.collect { case v => "Gatk " + v }
}
}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index d12675210..c0046d053 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -99,7 +99,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
*/
protected[core] def preProcessExecutable() {
val exe = BiopetCommandLineFunction.preProcessExecutable(executable)
- executable = exe.path
+ exe.path.foreach(executable = _)
addJobReportBinding("md5sum_exe", exe.md5.getOrElse("N/A"))
}
@@ -199,7 +199,7 @@ object BiopetCommandLineFunction extends Logging {
private[core] val executableMd5Cache: mutable.Map[String, String] = mutable.Map()
private[core] val executableCache: mutable.Map[String, String] = mutable.Map()
- case class Executable(path: String, md5: Option[String])
+ case class Executable(path: Option[String], md5: Option[String])
def preProcessExecutable(executable: String): Executable = {
if (!BiopetCommandLineFunction.executableMd5Cache.contains(executable)) {
if (executable != null) {
@@ -236,7 +236,7 @@ object BiopetCommandLineFunction extends Logging {
}
}
}
- Executable(BiopetCommandLineFunction.executableCache(executable),
+ Executable(BiopetCommandLineFunction.executableCache.get(executable),
BiopetCommandLineFunction.executableMd5Cache.get(executable))
}
}
--
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