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galaxyproject / ephemeris

Library for managing Galaxy plugins - tools, index data, and workflows.
https://ephemeris.readthedocs.org/
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enable global options in a tool yaml file #26

Closed bgruening closed 7 years ago

bgruening commented 7 years ago

This PR will enable global options in a tool yaml files. Means 

  install_repository_dependencies: true
  install_resolver_dependencies: true
  install_tool_dependencies: false

can be specified as top arguments next to the Galaxy instance and API key. It will also change the default setting, to install resolver-dependencies and not tool-dependencies anymore.

bgruening commented 7 years ago

@mvdbeek if you have some time, can you look at this please?

afgane commented 7 years ago

@bgruening I think this is really needed and hence glad to see it. I'd just suggest to include a link to the docs explaining those or add a one line comment about each (because for a deployer that's not very invested in the tool dev, the differences between the three options are not really clear).

bgruening commented 7 years ago

@afgane where should this documentation go? In the example yaml?

afgane commented 7 years ago

That would probably be best. Alternatively, above each definition of the global var? (e.g., https://github.com/galaxyproject/ephemeris/pull/26/files#diff-3e2dc1314104230489feb0f417f2d40fR47)

mvdbeek commented 7 years ago

Maybe we should set repository_dependencies by default to true, to account for suites? Other than that looks good to me.

bgruening commented 7 years ago

Added some docs and changed the default value. Thanks for the review!

jmchilton commented 7 years ago

Awesome - thanks a bunch @bgruening!

afgane commented 7 years ago

I guess I should have been more explicit because what I meant by docs was to specify differences between tool, repository, and resolver dependencies...

bgruening commented 7 years ago

@afgane this are TS secrets no one knows exactly ;) I will try my best to add those.

afgane commented 7 years ago

That's how it feels every time I come cross them...

BTW, I'm really glad to see this switch that happened here.