galaxyproject / galaxyproject/idc
Cross-link between Galaxy and UCSC for additional hub genomes
- Dominant language
- Shell
- Stars
- 10
- Forks
- 8
- PR merge metrics
- No merged PRs in 30d
Description
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.
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by reviewing ucsc.builds.txt and the UCSC_GI.assemblyHubList.txt source linked in the issue, then read the Galaxy discussion about missing UCSC visualization links. Determine which additional hub genomes and identifier formats are supported; done means the agreed cross-links work without breaking existing build links.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100