enable global options in a tool yaml file

[bgruening]

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]

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

[afgane]

@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]

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

[afgane]

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]

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

[bgruening]

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

[jmchilton]

Awesome - thanks a bunch @bgruening!

[afgane]

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]

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

[afgane]

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

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