galaxyproject / galaxyproject/idc

Cross-link between Galaxy and UCSC for additional hub genomes

Open
#47 5 comments 0 reactions 0 assignees View on GitHub
enhancement question
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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.