pip

CheckM is a Python program (CheckM >= 1.3.0 requires Python >= 3.11) and is available on PyPI as checkm-genome:

pip3 install checkm-genome

This will install CheckM and all other required Python libraries (see Python dependencies). If pip complains about breaking system packages, install CheckM into a virtual environment:

python3 -m venv .venv       # or: uv venv, if you prefer https://pypi.org/project/uv/
source .venv/bin/activate   # or: whatever the venv command tells you to run
pip3 install checkm-genome  # or: uv pip install checkm-genome

The bioinformatic tool dependencies (HMMER, Prodigal, and gPlace) need to be installed separately and placed on your system path. gPlace is installed from PyPI and requires Python >= 3.12:

pip3 install gtdb-gplace

If you are not too concerned about having the latest versions, your package manager may provide HMMER and Prodigal:

  • Debian, Ubuntu, etc.: apt install hmmer prodigal

  • Fedora: dnf install hmmer (Prodigal needs to be obtained separately, e.g. from Bioconda)

Alternatively, a Conda environment can be set up with the dependencies from Bioconda and CheckM installed with pip:

conda create -n checkm -c conda-forge -c bioconda python=3.12 hmmer prodigal
conda activate checkm
pip3 install checkm-genome gtdb-gplace

Finally, download and configure the reference data.