Installation#

Installing geNomad#

You can install geNomad in you computer using either a general-purpose package manager (pixi, mamba, conda) or a Python-specific package manager (uv or pip).

Pixi is probably the simplest way to install geNomad. It takes care of all the dependencies for you and doesn’t require any environment management, meaning the genomad command will be available globally.

pixi global install -c conda-forge -c bioconda genomad
genomad --help

Mamba is a package manager that handles all your dependencies for you. To install geNomad using Mamba, you need to create a new environment and activate it before running the genomad command.

mamba create -n genomad -c conda-forge -c bioconda genomad
mamba activate genomad
genomad --help

Conda is a package manager that handles all your dependencies for you. To install geNomad using Conda, you need to create a new environment and activate it before running the genomad command.

conda create -n genomad -c conda-forge -c bioconda genomad
conda activate genomad
genomad --help

uv is a Python-specific package manager that lets you install geNomad as a global command within an isolated environment. However, it won’t take care of the non-Python dependencies required by geNomad (see note below).

uv tool install genomad
genomad --help

pip is a Python-specific package manager that lets you install geNomad as a global command. It is the standard tool for installing Python libraries and should be available to everyone with a Python installation. However, pip won’t take care of the non-Python dependencies required by geNomad (see note below).

pip install genomad
genomad --help

Non-python dependencies

Pixi, Mamba, and Conda will install both the Python dependencies and the non-Python dependencies required by geNomad. If you install geNomad using uv or pip, make sure to add MMseqs2 and ARAGORN to your $PATH.

Running geNomad using containers#

You can also execute geNomad using containerization tools, such as Docker and Podman. To pull the image, execute the command below.

docker pull antoniopcamargo/genomad

podman pull docker.io/antoniopcamargo/genomad

To start a geNomad container you have to mount a folder from the host system into the container with the -v argument. The following command mounts the current working directory ($(pwd)) under /app inside the container and then executes the genomad download-database and genomad end-to-end commands.

docker run -ti --rm -v "$(pwd):/app" antoniopcamargo/genomad download-database .
docker run -ti --rm -v "$(pwd):/app" antoniopcamargo/genomad end-to-end input.fna output genomad_db

podman run -u 0 -ti --rm -v "$(pwd):/app" antoniopcamargo/genomad download-database .
podman run -u 0 -ti --rm -v "$(pwd):/app" antoniopcamargo/genomad end-to-end input.fna output genomad_db