Installation

Users can clone and build the repository locally or install Selene through conda/pip.

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 selene with pip:

pip install selene-sdk

Note that we do not recommend pip-installing older versions of Selene (below 0.4.0), as these releases were less stable.

We currently only have a source distribution available for pip-installation. We are looking into releasing wheels in the future.

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, Cython, and setuptools. Please make sure you have these 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.