Add bio command line tool

[joverlee521]

Description of proposed changes

Based on #108 to work-around CI hanging issues

Update: bio recipe has been fixed in bioconda with bioconda/bioconda-recipes#55920. This PR is now only blocked on #105

I wanted to add bio to match docker-base since I found it on bioconda.

Checklist

• Checks pass

[tsibley]

However, it doesn't work when I tested locally, might need to look into the bioconda recipe.

The bioconda recipe is borked. And the PR which added it is an amazing example of what not to do: deleting failing tests one-by-one just to get CI to pass and then merging without review.

orz

[joverlee521]

The bioconda recipe is borked.

Can you elaborate? I'm not familiar enough with conda recipes to see what's wrong with it 😅

[victorlin]

The recipe tells Bioconda how to build the Conda package, and it looks like the package we're getting was not built correctly. I'd guess that something in the build config needs tweaking.

[joverlee521]

Created an issue in bioconda-recipes: bioconda/bioconda-recipes#55914

[tsibley]

Can you elaborate? I'm not familiar enough with conda recipes to see what's wrong with it 😅

@joverlee521 I would have, but I didn't look into how it's borked, but I did confirm the borkage. After its installed, for example, the Python libraries are not present in site-packages, although the installation metadata is.

[joverlee521]

See my hacky fix in bioconda/bioconda-recipes#55920

[victorlin]

Didn't test (not easily testable on Hutch network), but looks good given bio was added by all 3 builds in @tsibley's manually triggered CI run:

name: bio
version: 1.8.0
build: pyhdfd78af_0

[joverlee521]

Thanks for following up here @tsibley 🙏

[tsibley]

Since I was mucking around in this repo anyway, I figured I'd take care of this too. :-)

20250512T203714Z is the first version with bio.