Installation

Users can either clone and build the repository locally or install Selene through conda. We previously supported installation through pip, but are refraining from releasing the latest version of Selene through pip due to some issues we are observing when using the pip-installed torch and torchvision dependencies.

Installing with Anaconda

To install with conda (recommended for Linux users), run the following command in your terminal:

conda install -c bioconda selene-sdk

Installing from source

Selene can also be installed from source. First, download the latest commits from the source repository:

git clone https://github.com/FunctionLab/selene.git

The setup.py script requires NumPy. Please make sure you have this already installed.

If you plan on working in the selene repository directly, we recommend setting up a conda environment using selene-cpu.yml or selene-gpu.yml (if CUDA is enabled on your machine) and activating it.

Selene contains some Cython files. You can build these by running

python setup.py build_ext --inplace

If you would like to locally install Selene, you can run

python setup.py install

Additional dependency for running the CLI

Please install docopt before running the command-line script selene_cli.py provided in the repository.