From 043874a82e97e42baef8661805ea790815691b16 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 5 Mar 2015 12:49:34 +0100
Subject: [PATCH] Possible to not convert executable to CanonicalPath
---
.../sasc/biopet/core/BiopetCommandLineFunctionTrait.scala | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
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 0dcf13eea..115bca1b8 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
@@ -73,6 +73,9 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
super.freezeFieldValues()
}
+ /** can override this value is executable may not be converted to CanonicalPath */
+ val executableToCanonicalPath = true
+
/**
* Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
*/
@@ -87,7 +90,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if (process.exitValue == 0) {
executable = buffer.toString
val file = new File(executable)
- executable = file.getCanonicalPath
+ if (executableToCanonicalPath) executable = file.getCanonicalPath
+ else executable = file.getAbsolutePath
} else {
BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
}
--
GitLab