Refactor toward support for running Galaxy in docker-galaxy-stable. #479
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jmchilton
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- General cleanup of planemo.galaxy.config docstrings and such. - Refactor the configured Galaxy properties into ones relevant for Docker and not. - Create an interface for the GalaxyConfig object to be very explicit about what the rest of planemo expects from it. - Reduce this interface - mainly involves refactoring startup command generation so pid_file doesn't need to be used outside the config module. - Implement a BaseGalaxyConfig for GalaxyConfig object functionality that will be shared with a future Docker impementation - and put the local instance specific stuff in a LocalGalaxyConfig object.
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- Tell Galaxy that the webapp's server_name is ``main`` regardless - so that handler's can have fixed ``job_conf.xml`` files. - Provide a ``job_conf.xml`` if it isn't specified some other way. This prevents ``galaxy_root`` configuration (this should fix galaxyproject/planemo-machine#61). - Add Docker options to Galaxy target commands so job_conf.xml can be configured with Docker options appropriately - enable docker for Galaxy tools with ``--docker``.
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xref #15