Initial JBrowse configurations

[kwentine]

This PR allows to specify initial JBrowse configurations, that will be used as a starting point to generate de fully-fledged config.json.

To add an initial JBrowse configuration, create config.json alongside config.yaml in the species configuration directory.

The final config.json will include the elements in the initial configuration, plus all those specified in config.yaml However if a track or assembly is present both in the initial configuration and config.yaml, the latter will take precedence (no fine-grained merge is performed).

Intended use cases:

• Add initial sessions for each species
• Add tracks that require configuration more advanced than what jbrowse add-track can handle (BED files with column names and score column for example)
• Manually add hosted track that we don't want to download, but that would perplex add-track because of opaque URLS
  • Example: .bed file hosted at figshare/12345

[kwentine]

I'm so happy that you could engage so actively with the feature and test some of the use cases.

Along with supplying default sessions (which we can maybe dedicate a branch to), it opens the possibility for quite a lot of tweaking (color palette and logo for example).

Merging in main periodically to keep a feature branch up-to-date is a practice I follow as well when, like in this case:

• more than one person is involved

• there are non trivial conflicts

  The alternative (when one works alone and fancies a linear git history graph) is to rebase the feature branch on main and force-push.

[brinkdp]

Sounds good to dedicate a branch to continue investigating defaultSessions. There are indeed many interesting configuration points to try.