GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
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Specify adapter type through CLI option when adding track #4517

Open kwentine opened 1 month ago

kwentine commented 1 month ago

Context

In swedgene we programmatically call add-track with arguments taken from YAML configuration files to generate various config.json.

Some of the feature tracks are hosted remotely, with opaque URLs (example)

We cannot point JBrowse to opaque URL using add-track because it perplexes guessAdapter(), so we may need to download local copies and name them explicitly to keep our automation going.

Request

Support an --adaterType option akin to --trackType that would allow:

jbrowse add-track --adapterType=GtfAdapter  "https://figshare.scilifelab.se/ndownloader/files/123456"