sokrypton / sokrypton/ColabFold
pairing endpoint + mode=env
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Description
I see https://github.com/soedinglab/MMseqs2-App has an option for passing mode=env to the pairing endpoint but the colabfold config file https://github.com/sokrypton/ColabFold/blob/main/MsaServer/config.json has the environmentalpair config commented out. Looking at the generated pair.sh shell script I would assume this would make the endpoint error but when I hit the pair endpoint with mode=env I get a response. Is there a different environmentalpair db used by the deployed endpoint, or is it not running tip on MMseqs2-App (git history still looks like the environmentalpair config has been there for a while), or am I maybe wrong and MMseqs2-App isn't the right backend repo to look at.
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
Start with MsaServer/config.json and the generated pair.sh shell script, then compare their environmentalpair settings with the deployed pairing endpoint and the referenced MMseqs2-App repository. Done means establishing which backend and database configuration serves mode=env and recording the confirmed configuration or discrepancy.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- json, shell
- Domain
- api, backend, bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100