.. _installation:

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

.. toctree::
    :hidden:

    Conda
    Docker
    Manually

We distribute ssHMM both as a Python package and as a Docker image (similar to a virtual machine). There are three ways to install ssHMM:

:ref:`Conda installation <condainstallation>`:

- quick and easy installation
- requires `Conda <https://conda.io>`_
- recommended for most users

:ref:`Docker installation <dockerinstallation>`:

- quick and easy installation
- requires `Docker <https://en.wikipedia.org/wiki/Docker_%28software%29>`_
- requires sudo rights
- all dependencies of ssHMM are pre-installed in the image
- recommended for Linux beginners

:ref:`Manual installation <manualinstallation>`:

- more difficult installation
- dependencies of ssHMM have to be installed manually
- recommended only for experienced users