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galaxyproject / idc

Simon's Data Club - Reference data for Galaxy servers
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Cross-link between Galaxy and UCSC for additional hub genomes #47

Open jennaj opened 2 months ago

jennaj commented 2 months ago

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 commented 2 months ago

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 commented 2 months ago

Hi @maximilianh. not or now?

maximilianh commented 2 months ago

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 commented 2 months ago

Some cool progress, if we have this in place it would be soooo good for our users! :+1:

maximilianh commented 2 months ago

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

On Tue, Apr 30, 2024 at 11:25 AM Björn Grüning @.***> wrote:

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

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