This is designed to be used with pip.  To install this into your python setup, run something like:

pip setup.py install

from the folder containing this INSTALL.txt file.

This program requires a few prerequisite steps before you can use it.  Namely:

- Install or compile R using the --enable-R-shlib option when you
  configure it (Ubuntu's package comes with this option compiled)
- Run R, and run the following command to install the R libraries that
  this program uses.  Note that unless you run R as the superuser, the
  libraries will only be installed for you, and not for other users of
  the computer:
  
  install.packages('NMF',dependencies=TRUE)

Using EMMSA requires Numpy and Scipy, but these are not listed as dependencies in the setup file.  I had trouble getting these to work well with virtualenv.  I have omitted them so that installing EMMSA is not overly complicated, but if you want to actually run EMMSA, you need them.

There is also currently a similar problem with matplotlib.  Install it yourself, if you don't already have it.
