conda package

[Zethson]

Hey,

I can't seem to find muon on any conda channel. Would suggest to add muon to conda-forge.

Cheers

[pavanvidem]

hey @Zethson is there already a PR for this? How about on bioconda along with already existing Scanpy?

[gtca]

We'll have it on confa-forge, I think scanpy is also leaning towards just using conda-forge. There's been one mildly annoying thing that we can't get .tar.gz source files from PyPI for some versions but I found the way around that should work.

I just opened a PR!

[Zethson]

@gtca actually, the discussion is open scverse/scanpy#2281
This discussion is also relevant for muon/mudata because nf-core needs updated containers for the nf-core scrnaseq pipeline.

[gtca]

Thanks for the reference!

needs updated containers

... which they don't want to build themselves?..

On that note, can't we just use GitHub Container Registry?

[Zethson]

... which they don't want to build themselves?..

Yes, rightfully so.

On that note, can't we just use GitHub Container Registry?

The question isn't hosting, but keeping the containers up to date. If scverse packages were in bioconda everything would be taken care of magically. But let's add this to the next scverse agenda ok? We have to find a solution here.

[gtca]

We can of course build them e.g. on: release here with actions.

Great, let's discuss in more detail next time then!

[Zethson]

@gtca I'd be happy if we could solve this at the hackathon. It will be very beneficial for pipelines since they automatically build containers for Bioconda packages etc.
Whether we should go for conda-forge or bioconda is a different matter ^_^

[ivirshup]

Since muon is on conda-forge now, should this issue be closed?

For getting a container built somewhere, something equivalent to scanpy could be done? (BioContainers/multi-package-containers#2209)

[Zethson]

Huh, since when did that happen?
https://anaconda.org/conda-forge/muon

I had no idea!