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
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")
}
......
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