AlexsLemonade / AlexsLemonade/refinebio

Add Capabilities to Process and Smash Externally Supplied Data

Open
#341 9 comments 0 reactions 0 assignees View on GitHub
backlog processor smasher
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

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