NationalGenomicsInfrastructure/ngi_pipeline — pull request #111 by Galithil (2014-11-07 10:48:20+00:00)
Title: fixed the logging

cl.load uses the bcbio method to read yaml configuration files. The code originates in scilifelab logger.
There's no point in using bcbio to read yaml files.
context managers are for @mariogiov
the empty string second argument is there because if the config file does not have the required key, config.get() returns None (default behavior) and os.path.join breaks on trying to join None objects.
The problematic code is located here : lib/python2.7/posixpath.py, line 77.
There is no testing for None, but there is one for ''.