pypi and bioconda install

[nick-youngblut]

Are there any plans to get CheckM2 on pypi (and then bioconda)?

Given how many pipelines/workflows include CheckM v1, it will be very helpful to have CheckM2 on bioconda

[chklovski]

Hi - yes, this will be done in the near future.

[SilasK]

The future is now. Let's put it on bioconda now or are there any reasons not to do it?

The only thing I would need is a release from the official GitHub, repo. I guess this one.

[SilasK]

Ah, and can you clarify the version?
Your latest commits contained info about v 0.1.3. But you have version 2. so it should be 2.1.3 .

Please don't with checkm2 v1.0.0 .

[chklovski]

I will make a release and add to bioconda over the next month or so. CheckM2 models may also may get updated to be in line with the newest GTDB release as well before I do that. Apologies for the delay.

Regarding versions, CheckM2 is a stand-alone tool that operates in many ways very differently from CheckM1, and therefore it makes sense to version it independently. So CheckM2 v1 may happen.

[jolespin]

Looking forward to this being available on conda. Once it's on Bioconda I will update my https://GitHub.com/jolespin/veba suite to use this instead of CheckM version 1.x. It would MASSIVELY simplify my pipeline but it's contingent on CheckM2 working out of the box on Conda (or PyPI).

Good luck with the publication btw. Looking forward to seeing it published. This tool is much needed in the field.

[atyakhtmpg]

Hello, the Bioconda is highly anticipated!

[chklovski]

Hi, thanks for your patience. Bioconda and pypi installation is now available from version 1.0.1 onwards.

[jolespin]

Awesome! Going to start adding it into my pipelines