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--- RNAMAP2D v. 1.6.3                           ---
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A tool for calculation, analysis and visualization of contact maps for RNAs and protein-RNA structures.

(c) 2009 - 2012 Michal J. Pietal, Natalia Szostak, 
         Kristian Rother and Janusz M. Bujnicki

See LICENSE.rtf for detatls on availability conditions.


----------- INSTALLATION ON WINDOWS -----------

Please download the binary version, double click on an archive and extract it to any folder. Then, enter the folder and click the file RNAMap2D.exe to start the program.


----------- INSTALLATION ON UBUNTU LINUX -----------

On Ubuntu Linux, the following packages need to be installed via apt-get
or synaptic:

python                    (version 2.6.4)
python2.6-dev		  (version 2.6.4)
python-wxgtk2.8           (version 2.8.10)
python-imaging            (version 1.1.6)
python-numeric            (version 24.2)
python-numpy              (version 1.3)
python-egenix-mxtexttools (version 3.1.2)
python-excelerator        (version 0.6.3)
g++			  (version 1.4.4)

Also, PyCogent Version 1.4 is required (see http://sourceforge.net/projects/pycogent/).

In addition, BioPython version 1.42 needs to be installed from source (see http://biopython.org/wiki/Download ).
 IMPORTANT: uncomment all lines mentioning 'KDTree' in setup.py before running 'python setup.py build'.
 If you have a newer BioPython version installed already, you can copy Bio/ and Martel/ from the build/lib.linux.. directory to the RNAMap2D directory.

Please note, that other program versions, especially of wxPython and BioPython will not work.


----------- INSTALLATION ON ANY OTHER LINUX -----------

The installation of the Linux distribution requires some third-party programs.
Please make sure all the following libraries are installed:

Python 2.6                    = 2.6.2    (available at http://www.python.org )
Python Imaging Library (PIL)  = 1.1.6    (available at http://www.pythonware.com/products/pil/ )
Numeric                       = 24.2     (available at http://sourceforge.net/projects/numpy/files/Old Numeric/)
                                           (after installing, the Lib folder should be copied into python's dist-packages/ dir as Numeric )
Numpy                         = 1.3      (available at http://numpy.scipy.org/ ) 
mxTextTools                   = 3.1.1    (available at http://www.egenix.com/products/python/mxBase/)
wxPython                      = 2.8.10   (available at http://sourceforge.net/projects/wxpython/files/wxPython/ )
PyExcelerator                 = 0.6.4    (available at http://sourceforge.net/projects/pyexcelerator/ )
BioPython                     = 1.42     (available at http://biopython.org/wiki/Download )
					IMPORTANT: uncomment all lines mentioning 'KDTree' in setup.py before running 'python setup.py build'.
					If you have a newer BioPython version installed already, you can copy Bio/ and Martel/ from the
					build/lib.linux.. directory to the RNAMap2D directory.
PyCogent 		      = 1.4 is 	(available at http://sourceforge.net/projects/pycogent/)

g++ and python2.6-dev packages are either present or easy to download in any other Linux systems. Please refer to the respective manuals.

We support the listed modules only, whilst rnamap should work on above, we give no warranty on it since it was not tested on other library combinations. That's why we strongly recommend to use the strict library versions (as listed), all the more they're all available to the date of program's release.


----------- INSTALLATION ON MAC -----------

The installation for MacOSX has the same prerequisites than generic Linux instructions (see: above).

The authors however, plan to release a standalone MacOSX (Intel) binary without prerequisites, as soon as they gain accesss to the computer for binary build.

The software was not tested under MacOSX on Intel architecture, however python code is portable so MacOSX Intel release is considered beta but should work without any problems.


----------- INSTALLATION OF RNAVIEW ON LINUX or MACOSX (OPTIONAL) -----------

RNAMAP2D can use the RNAView program to calculate base pairs. If it is not found, RNAMAP2D will use its own module for that.

To make RNAView available to RNAMAP2d, please install

rnaview     (available at http://ndbserver.rutgers.edu/services/download/ ) 
	     after the installation create a link to the RNAView binary in /usr/bin by typing: 
             sudo ln -s /?/?/?/RNAVIEW/bin/rnaview /usr/bin

             and add to your ~/.bashrc file the line:
             export RNAVIEW=/usr

Note that $RNAVIEW variable has to be set to /usr as well.


----------- USAGE -----------

Linux: 

Unpack the archive (using tar -zvxf command)

Change directory to rnamap2d and type: python RNAMAP2D.py (if multiple Python instalations are present, type python2.6 instead of python).
This will start a self-explanatory GUI.


MacOSX:

Unpack the archive (using tar -zvxf command)

Change directory to rnamap2d and type: pythonw RNAMAP2D.py (if multiple Python instalations are present, type pythonw2.6 instead of pythonw).
This will start a self-explanatory GUI.


Windows:

Unpack the archive by double clicking it.

Then enter rnamap2d directory and double click the RNAMAP2D.exe file

For more information about usage please see the RNAmap2D manual and tutorial available from the homepage: http://iimcb.genesilico.pl/rnamap2d.html


----------- TROUBLESHOOTING -----------

- The library msvcp90.dll under Windows may be missing.
Plese download it from: http://www.dll-files.com/dllindex/dll-files.shtml?msvcp90

- An already installed wxPython 2.6 may interfere with your wxPython 2.8 package. Use python2.6 command instead of python to run the program.