Split BaseSpace into two apps
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
We want to let users select which references to map to. Configure two apps on BaseSpace: Micall HIV and Micall Hepatitis-C. In the callback.js configuration, we can list the references to use as command line arguments.
- HIV: PROT/RT, INT, V3LOOP, GP41
- HCV: NS3, NS5a, NS5b
The summary report for each app will have a column for the sample name and a column for each of the drug classes with Y/N for each sample name.
For now, remove the G2P step from the BaseSpace version. Rename the g2p app result to report.
Contributor guide
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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
Start by reading the callback.js configuration and trace how BaseSpace app references, reports, and the g2p result are handled. The work is complete when separate HIV and HCV apps use the listed references, reports include sample and drug-class Y/N columns, the G2P step is absent, and the result is named report.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- javascript, python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100