Cross-link between Galaxy and UCSC for additional hub genomes

[jennaj]

Discussion and use case
https://help.galaxyproject.org/t/no-link-for-ucsc-to-visualise-datasets/12260/

From UCSC. This would either be in addition to the ucsc.builds.txt
You will also need all genbank-ids that we have here on our side… as a text file: https://hgdownload.soe.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt

What might work

1. Use all of the links/tools as they are now, and (optionally) supplement the builds list.

Known wrinkles so far

1. The UCSC browser serves the dbkey/database from the Table browser with a specific identifier format that differs slightly from the root identifier, and it is current server specific. This is being looked at (followup discussion could be here).
2. Use like a custom genome? Users source the fasta, indexed at runtime, but can use the pre-existing database keys? Seems like a yes unless we want to generate indexes.

[maximilianh]

We are now considering these changes:

1. send the GCA_xxxx ID as db_key to Galaxy
2. accept the GCA_xxxx ID in all incoming links.
3. send a list of GCA_xxx IDs (Jen already has the URL, see above) that we accept to Galaxy and ask that Galaxy pulls this file every day or so.

Does this sound reasonable?

[bgruening]

Hi @maximilianh. not or now?

[maximilianh]

Oh boy, I read over it, but didn't see the typo, sorry. Thanks @bgruening.

We fixed (2) on genome-test yesterday, but still need to do (1)

[bgruening]

Some cool progress, if we have this in place it would be soooo good for our users! 👍

[maximilianh]

Yes, and then the future steps will be, one day: 1) make liftOver alignments or maybe even add entire assemblies in Galaxy (as discussed over beer with Anton, I think in Montpellier) 2) somehow let UCSC grab these alignments or assembly files

…

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