Installation instructions for QPalma Version 0.9.9
  
The package requires python version 2.5 or newer, and is built from 
source, so the header files and libraries for python must be installed, 
as well as the core binaries.

Installation Instructions
-------------------------

You need the following packages

- SWIG  ( >=1.3.31 )
- numpy ( >=1.0.4 )

You can obtain SWIG from http://www.swig.org and numpy from
http://numpy.scipy.org/ or ask your sysadmin to install the packages.

Once you have the above packages installed you can start installing
QPalma.

Assuming you downloaded QPalma-0.9.9.tar.gz type:

   tar -xzvf QPalma-0.9.9.tar.gz

   cd QPalma-0.9.9

   ./setup_qpalma.sh

and follow the instructions to build the necessary C++ extension
modules and the python code.

The setup script creates a configuration file ./bin/qpalma_config.sh
(please edit it manually if necessary).  During the setup process, the
optimization package MOSEK with a trial license will be downloaded and
installed in the directory ./modules/mosek. The downloaded trial
license is restricted to 300 variables. You can obtain a trial license
without this restriction (but limited to 30 days) from
https://www.mosek.com/cgi-bin/trial.py. Copy the obtained license into
the file modules/mosek/5/licenses/mosek.lic to get it to work.

To run qpalma, run either of the following commands:

./bin/qpalma_train
./bin/qpalma_filter
./bin/qpalma_align

or try one of the example scripts in ./examples. 


Further information
-------------------

   More extensive documentation can be found under the doc/ directory of the
   QPalma distribution.

Contact
-------

   Fabio De Bona, fabio@tuebingen.mpg.de
   Gunnar Raetsch, Gunnar.Raetsch@tuebingen.mpg.de
   
   (or qpalma@tuebingen.mpg.de to contact both of us)
