.. MacSyFinder - Detection of macromolecular systems in protein datasets
    using systems modelling and similarity search.            
    Authors: Sophie Abby, Bertrand Néron                                 
    Copyright © 2014  Institut Pasteur, Paris.                           
    See the COPYRIGHT file for details                                    
    MacsyFinder is distributed under the terms of the GNU General Public License (GPLv3). 
    See the COPYING file for details.  

.. _installation:


************
Installation
************


MacSyFinder dependencies
========================
MacSyFinder has two dependencies:
 - the *formatdb* (>=2.2.26) or *makeblastdb* (>=2.2.28) tools provided with the Blast suite of programs 
(http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) 
 - the program *Hmmer* version 3.0 (http://hmmer.janelia.org/). 

*formatdb* or *makeblastdb* and *hmmsearch* programs should be installed (*e.g.*, in the PATH) in order to use MacSyFinder. Otherwise, the paths to these executables must be specified in the command-line: see the :ref:`command-line options <hmmer-options>`. 
 
**Python version 2.7** is required to run MacSyFinder: https://docs.python.org/2.7/index.html 


Installation procedure
======================
First unarchive the source codes package, and enter the extracted folder::

  tar -xzvf macsyfinder-x.x.tar.gz
  cd macsyfinder-x.x
  
MacSyFinder installation follows classical "pythonic" installation procedure (see http://docs.python.org/2/install/)::

  python setup.py build
  (sudo) python setup.py install 

It is **highly recommanded** to run tests before performing the full installation::

  python setup.py build
  python setup.py test -vv
  (sudo) python setup.py install 
  
.. note::
  Super-user privileges (*i.e.*, ``sudo``) are necesserary if you want to install the program in the general file architecture.
  
  
.. note::
  If you do not have the privileges, or if you do not want to install MacSyFinder in the Python libraries of your system, 
  you can install MacSyFinder in a virtual environment (http://www.virtualenv.org/).

Procedures specific to MacSyFinder can be used instead of default. Please run the command for full options::
  

  python setup.py --help

The main ones are::
 
  python setup.py install --prefix /usr/local/home/bob/my_programs # Specifies an installation path

=> It will install MacSyFinder and required data (profiles folder and systems definition folders) in the Home directory of "bob", in the "my_progams" folder (useful if you do not have super-user privileges).

.. warning::
  When installing a new version of MacSyFinder, do not forget to uninstall the previous version installed ! 

Uninstalling MacSyFinder
========================

To uninstall MacSyFinder (the last version installed), run::

  (sudo) python setup.py uninstall