Commit 043874a8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Possible to not convert executable to CanonicalPath

parent 1571f046
...@@ -73,6 +73,9 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab ...@@ -73,6 +73,9 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
super.freezeFieldValues() 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 * 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 ...@@ -87,7 +90,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if (process.exitValue == 0) { if (process.exitValue == 0) {
executable = buffer.toString executable = buffer.toString
val file = new File(executable) val file = new File(executable)
executable = file.getCanonicalPath if (executableToCanonicalPath) executable = file.getCanonicalPath
else executable = file.getAbsolutePath
} else { } else {
BiopetQScript.addError("executable: '" + executable + "' not found, please check config") BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
} }
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment