I have notice that the run.sh script is creating automatically all missing configuration and location files to make sure Galaxy can work properly at first launch. However, the script is not taking care of the actual settings of an existing universe_wsgi.ini file. As a result, if the universe_wsgi.ini file says that job_conf.xml is located at foo/bar location, the run.sh will create a job_conf.xml file at the root of the galaxy source code anyway.

I'm thinking of improving the run.sh behavior to respect file path declared in an existing universe_wsgi.ini file in order not to create unused config or location files. I have currently started to implement this behavior in a small Python script (more handy than pure sh).