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).
What do you think about this concern ? Should I go for a pull request at any
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