Installation

Installing geNomad

You can install geNomad in you computer using either a general-purpose package managers (mamba or conda) or a Python-specific package manager (pipx or pip). pip is the standard command to install Python libraries and should be available to everyone with a Python installation.

mamba

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

conda

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

pipx

pipx install genomad

pip

pip install genomad

pipx installation

We recommend using pipx over pip if possible. By using pipx you will avoid dependency conflicts that might arise if you try to install geNomad in an existing Python environment.

Conda and Mamba will install both the Python dependencies and the third-party software required by geNomad. If you install geNomad using pip or pipx, 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

docker pull antoniopcamargo/genomad

Podman

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

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

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