galaxyproject / galaxyproject/tools-iuc
Suggestions: Galaxy Ensembl VEP tool
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- Dominant language
- HTML
- Stars
- 201
- Forks
- 525
- Avg merge
- 23h 54m
- Merged PRs (30d)
- 59
Description
I'm just posting this in the hopes that IUC would consider updating the wrapper for Ensembl's VEP tool for annotating variants. VEP is challenging to install itself, even with a Docker image, and would be nice to include in a Galaxy workflow. Some of the functionalities that could be included are:
- HGVS annotations against Hg19 and Hg38
- Option to either use a cached reference genome or annotation files for offline annotation, or connect with ensembl's servers.
- Ability to generate and customize a PDF or HTML report
Thanks!
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
The issue names no repository files, tests, or entry points. Start by checking the project's current Ensembl VEP wrapper and installation requirements, then assess the requested HGVS Hg19/Hg38 annotation, offline or server-backed operation, and PDF/HTML reporting. Done requires an agreed scope and a defined Galaxy wrapper implementation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100