From a93c931949a568ad7bcea6ff072f76bdb4e0249d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Feb 2015 18:17:52 +0100
Subject: [PATCH] Make reference absolute
---
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
index 42a290825..9404a8950 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
@@ -54,7 +54,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
@Argument(doc = "Output Directory")
var outputDir: File = _
- var genomeDir: File = config("genomeDir", new File(reference.getParent, "/star"))
+ var genomeDir: File = config("genomeDir", new File(reference.getAbsoluteFile.getParent, "star"))
var runmode: String = _
var sjdbOverhang: Int = _
var outFileNamePrefix: String = _
--
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