.. _manualinstallation:

Installation as a Python package
================================

Prerequisites
-------------

-  GHMM (http://ghmm.org/)
-  GraphViz (http://www.graphviz.org/)

For preprocessing BED files with preprocess\_dataset (tested only on Linux and macOS):

- bedtools (https://github.com/arq5x/bedtools2)
- RNAshapes 2.1.6 (https://bibiserv.cebitec.uni-bielefeld.de/download/tools/rnashapes.html)
- RNAstructure 5.8.1 (http://rna.urmc.rochester.edu/rnastructure.html)

Installation of prerequisites
-----------------------------

1. Install prerequisites for GHMM as described on
   http://ghmm.sourceforge.net/installation.html. The commands for
   Ubuntu are:

.. code-block:: bash

    sudo apt-get update
    sudo apt-get install build-essential automake autoconf libtool
    sudo apt-get install python-dev
    sudo apt-get install libxml++2.6-dev
    sudo apt-get install swig

2. Download and unpack GHMM from https://sourceforge.net/projects/ghmm/
3. Install GHMM as described on http://ghmm.sourceforge.net/installation.html. The commands for Ubuntu are:

.. code-block:: bash

    cd ghmm
    sh autogen.sh
    sudo ./configure
    sudo make
    sudo make install
    sudo ldconfig

4. Install GraphViz. On Ubuntu:

.. code-block:: bash

    sudo apt-get install graphviz
    sudo apt-get install libgraphviz-dev

5. Install pip if not already installed. On Ubuntu:

.. code-block:: bash

    sudo apt-get install python-pip

6. Install PyGraphViz:

.. code-block:: bash

    sudo PKG_CONFIG_ALLOW_SYSTEM_LIBS=OHYESPLEASE pip install pygraphviz

7. Install bedtools as described on http://bedtools.readthedocs.io/en/latest/content/installation.html
8. Download and install RNAshapes from https://bibiserv.cebitec.uni-bielefeld.de/download/tools/rnashapes.html.
9. Download and install RNAstructure from http://rna.urmc.rochester.edu/register.html.

Installation of ssHMM
---------------------

1. Download ssHMM from https://github.molgen.mpg.de/heller/ssHMM
2. Install ssHMM:

.. code-block:: bash

    #as root
    sudo python setup.py install

    #as non-root
    python setup.py install --user

This will install ssHMM and the following python package dependencies: numpy, graphviz, pygraphviz, weblogo, future, logging_exceptions, forgi. If setuptools fails to install any of the dependencies, try to install it separately (e.g. with ``sudo pip install numpy``).