Merge branch 'patch-executable_check' into 'develop'

Patch executable check

See merge request !114

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")
           }