From 09c25863927795c6a94eb104d390bd60fd3ff920 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 2 Dec 2014 14:20:19 +0100
Subject: [PATCH] Fix on outputDir
---
.../main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
index 1f8649819..acfcdb94a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
@@ -47,7 +47,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
for (t <- out) outputFiles ::= new File(outputDirectory + File.separator + prefix + t)
}
- def cmdLine = required(executable) +
+ def cmdLine = required("cd", outputDirectory) + " && " + required(executable) +
optional("--outgroup", outgroup) +
optional("--starting_tree", startingTree) +
optional("--filter_percentage", filterPercentage) +
--
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