From a93b0bbdb739cb456d9ae1128d0d3d793340e225 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Feb 2015 18:52:55 +0100
Subject: [PATCH] Fix bug on relative files
---
.../sasc/biopet/core/BiopetCommandLineFunctionTrait.scala | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 9382f779a..6210f8a6d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -52,9 +52,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
checkExecutable
afterGraph
- super.freezeFieldValues()
-
- if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
+ if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent + "/." + firstOutput.getName + "." + configName + ".out")
if (threads == 0) threads = getThreads(defaultThreads)
if (threads > 1) nCoresRequest = Option(threads)
@@ -65,6 +63,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
}
if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
+
+ super.freezeFieldValues()
}
protected def checkExecutable {
--
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