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Refactor toward support for running Galaxy in docker-galaxy-stable. #479

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merged 2 commits into from May 20, 2016

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jmchilton commented May 17, 2016

  • 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.

xref #15

@jmchilton jmchilton force-pushed the jmchilton:docker_galaxy_refactor branch from 2b8bf7b to 8be43ee May 19, 2016

Refactor toward support for running Galaxy in docker-galaxy-stable.
 - 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.

@jmchilton jmchilton force-pushed the jmchilton:docker_galaxy_refactor branch from 8be43ee to 8121af5 May 20, 2016

Revise job conf handling.
 - 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``.

@jmchilton jmchilton force-pushed the jmchilton:docker_galaxy_refactor branch from 8121af5 to c4dfd55 May 20, 2016

@jmchilton jmchilton merged commit 1a8db8b into galaxyproject:master May 20, 2016

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