Installation

EUGENe is a Python package, and can be installed using pip:

pip install 'eugene-tools'

We highly recommend using a virtual environment to install EUGENe to avoid conflicting dependencies with other packages. If you are unfamiliar with virtual environments, we recommend using Miniconda.

VERSION=3.9 # or 3.8-3.12
conda create -n eugene python=$VERSION

We also recommend installing mamba to speed up the installation process.

Developmental installation

To work with the latest version on GitHub, clone the repository and cd into its root directory.

git clone https://github.com/cartercompbio/EUGENe.git
cd EUGENe

Then, install the package in development mode:

pip install -e .

Extras for development [dev, docs] can be installed using:

pip install -e .[dev, docs]

Troubleshooting

If you have any issues installing, please open an issue on GitHub!