can't install checkm2

[francesco-ricci]

Hello everyone,

I have tried to install checkm2 through all the recommended avenues, conda, mamba, etc. Can't make it.

When I use conda, the installation get stuck on the "Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source."

When I use mamba, the installation goes through but then when I run checkm2 -h, I get this sort of error "Traceback (most recent call last):
File "/home/fricci/miniconda3_p3.9/envs/checkm2/bin/checkm2", line 27, in
from checkm2 import predictQuality"

Does anybody have a clue?

Thanks
Francesco

[bikmi]

this caused by python3.6, specify to install python=3.8, mamba create -n checkm2 -c bioconda -c conda-forge checkm2 python=3.8, it works for me

[larssnip]

I get the same problem as Francesco. Adding python 3.8 as suggested by bikmi changes nothing, the error still persists. It says AttributeError: module 'numpy' has no attribute 'object'. This exact same error occurs when I try to pull and run docker containers for the same software, from various sources.

[byronverz9]

I also had an issue with the installation but managed to trial and error my way to an install with conda that worked for me:

conda create -n checkm2 -c conda-forge -c bioconda python=3.8 checkm2

If you're still struggling (or future people find this) maybe try that.

[larssnip]

I ended up using a singularity (apptainer) container from galaxy: https://depot.galaxyproject.org/singularity/

The 1.0.1 version, build pyh7cba7a3_0, seems to run without problems:

apptainer exec checkm2:1.0.1--pyh7cba7a3_0.sif checkm2 -h