Installation
============

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

Please use Selene with Python 3.6+.

Install `PyTorch <https://pytorch.org/get-started/locally/>`_. 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:

.. code-block::

   conda install -c bioconda selene-sdk

Installing selene with pip
---------------------------

.. code-block:: sh

   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:

.. code-block::

   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 <https://conda.io/docs/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file>`_ 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

.. code-block:: sh

   python setup.py build_ext --inplace

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

.. code-block:: sh

   python setup.py install

Additional dependency for running the CLI (versions 0.4.8 and below)
--------------------------------------------------------------------

Please install ``docopt`` before running the command-line script ``selene_cli.py`` provided in the repository. 
In newer versions of Selene, the CLI can be run by calling ``python -m selene_sdk`` from anywhere in bash (assuming you have installed the library, through conda/pip/local install - ``python setup.py install``).