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¶

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

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

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

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

Install GraphViz. On Ubuntu:

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

Install pip if not already installed. On Ubuntu:

sudo apt-get install python-pip

Install PyGraphViz:

sudo PKG_CONFIG_ALLOW_SYSTEM_LIBS=OHYESPLEASE pip install pygraphviz

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

Installation of ssHMM¶

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

#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).