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GMOD / Apollo3

JBrowse 2 plugin for editing annotations on an Apollo server
Apache License 2.0
7 stars 4 forks source link

Multiple tracks to be centrally loaded #214

Closed nds closed 4 weeks ago

nds commented 1 year ago

We have a use case where we would like to "pre-load" tracks for the users. This will be a mix of GFFs and BAMs. We would like them to appear as separate tracks, and perhaps even be configured to display in different colours etc. At the moment, the admin users can load only GFFs centrally by using "Import features"; however, all information gets collapsed into the same track. This would be such a useful feature. Thank you.

garrettjstevens commented 1 year ago

This functionality is provided by JBrowse, which Apollo is a plugin for. Exactly how this is done depends on how your Apollo is deployed, but if the tracks you want to use have publicly available URLs it would be straightforward. Basically you would want to use the JBrowse CLI to modify your config.json. You can read about doing that here. If Apollo is deployed directly on a server you can do this in-place, and if you're using Docker you would then re-copy the config.json to your container, like here. If you can provide more details about where the track files will be and how Apollo is deployed, I can possibly provide more details.

sgiorgetti commented 1 year ago

Thanks @garrettjstevens - I have a couple of additional questions though.

If we pre-load some tracks by appropriately setting our config.json, what happens when we (admin) upload 1 more GFF via "Import Features"? I suppose they are loaded in a different track. May you confirm?

Also, if we (wicked admins) decided to import another set of features (GFF) via "Import Features" again, do these latter get collapsed into the same track?

garrettjstevens commented 1 year ago

Anything added via the "Import Features" menu item under the Apollo menu will get added to the Apollo track (shows up as "Annotations ()" in the track selector. That track will always show up when Apollo is loaded, even if it has nothing in it. If there are already features there, the imported features get added to the existing features in the Apollo track.

Any tracks added to the config.json will show up as separate tracks in the track selector.

sgiorgetti commented 1 year ago

Thanks @garrettjstevens !