AlexsLemonade / AlexsLemonade/refinebio
Add Capabilities to Process and Smash Externally Supplied Data
- Dominant language
- Python
- Stars
- 135
- Forks
- 21
- PR merge metrics
- No merged PRs in 30d
Description
### Context
It's quite likely that there will be researchers who will want to combine `refine.bio`-provided data with their own private data repositories.
It'd be great if we provided some functionality to make this easier for them by either running through our processors, gene-converters and smasher. Off the top of my head, I'm imagining that this could be new management command to live inside a processor/smasher Dockerfile and a small script with documentation to wire everything up together. But I'm certainly open to suggestions here!
This would also improve our own testing abilities.
### Problem or idea
I think this could be a good project for @Willv19 to take on if @kurtwheeler doesn't have a grander plan in mind.
### Solution or next step
Next step would probably to put some bounds on the requirements here - what kind of private data is a researcher most likely to have? Will it need to be processed, or just gene-conversion, or even just smashing?
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by defining the private-data use cases and whether processing, gene conversion, smashing, or all three are required. Then inspect the processor and smasher Dockerfiles, existing management commands, and related scripts; done means a bounded implementation with a documented, runnable workflow and tests for the supported path.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, python
- Domain
- bioinformatics, data, documentation, tooling
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100