Bioconda

A Conda package for CheckM is available on Bioconda as checkm-genome. It installs CheckM along with its dependencies:

conda create -n checkm -c conda-forge -c bioconda checkm-genome
conda activate checkm

The Bioconda package has been generously put together and maintained by community members (if this is you, please let us know so we can acknowledge you here!). It may lag behind the latest release on PyPI.

CheckM >= 1.3.0 requires gPlace instead of pplacer. If gPlace is not installed with the Bioconda package, install it from PyPI (this requires Python >= 3.12):

pip3 install gtdb-gplace

Finally, download and configure the reference data.