Users can clone and build the repository locally or install Selene through conda/pip.
Please use Selene with Python 3.6+.
Install PyTorch. If you have an NVIDIA GPU, install a version of PyTorch that supports it–Selene will run much faster with a discrete GPU.
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
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-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¶
docopt before running the command-line script
selene_cli.py provided in the repository.