Docker

A Dockerfile provided by a community member is available in the docker directory of the CheckM repository. The image installs HMMER and Prodigal from the Ubuntu package repository, installs the latest release of CheckM and gPlace from PyPI, and downloads the CheckM reference data into the image (CHECKM_DATA_PATH is set accordingly).

No pre-built image is provided. To build the image:

git clone https://github.com/Ecogenomics/CheckM.git
cd CheckM/docker
docker build -t checkm .

CheckM can then be run by mounting the directory containing your genomes into the container, e.g.:

docker run --rm -v /path/to/my_data:/data checkm \
    checkm lineage_wf -t 8 -x fa /data/bins /data/checkm_output