galaxyproject / galaxyproject/tools-devteam
Update SICER to include more genome builds (ideally all on the instance)
- Dominant language
- Python
- Stars
- 37
- Forks
- 94
- PR merge metrics
- No merged PRs in 30d
Description
The list of builds is outdated. At a minimum add the latest builds from the same organisms already included: mm10, hg38, dm6, sacCer3, rn5, rn6.
The "pombe" and "tair8" are not dbkeys in current Galaxy releases ... (??) but there are alternatives.
Quote from sicer_wrapper.py
> # HACK! FIXME: allow using all specified builds, would currently require hacking SICER's "GenomeData.py" on the fly.
>
> VALID_BUILDS = [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]
Contributor guide
Research direction
Read the quoted VALID_BUILDS section in sicer_wrapper.py and the referenced SICER GenomeData.py. Compare the requested builds and the available alternatives for pombe and tair8 with current Galaxy dbkeys. Done means the SICER tool supports the requested current builds without the outdated list limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, tooling
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100