README file for VisualCNA v 1.0, 07/2014

Dependencies
============
VisualCNA is written in Python and has been tested on Python version 2.7.
Accordingly, we recommend to have Python version 2.7 or higher.

Because VisualCNA requires several other Python libraries and the PyMol software
(https://www.python.org), these libraries (dependencies) and PyMol must have
been installed before installing VisualCNA.
    
A list of dependencies is provided below. Please note that, depending on the
Linux installation you have installed, you might need to resolve additional
dependencies. 

In the case of unresolved dependencies, the installation of VisualCNA
(see below) will exit with an error message. After installing the missing
dependency, restart the installation of VisualCNA (see below).

Dependencies for Python libraries
    - GNU GCC with C++ feature (tested on version 4.7.1)
    - cmake
    - gFortran (tested on version 4.7.1)
    - BLAS
    - LAPACK
    - GNU make

Dependencies for PyMol
    - OpenGL
    - GLUT library for OpenGL (or freeglut)
    - libpng (Also required for saving images of data plots)
    - Tcl/Tk (for the external GUI)
    - FreeType2 (if you want to have nice fonts)

Apart from these dependencies, the command line CNA software available from 
http://cpclab.uni-duesseldorf.de/software is also required by
visualCNA for running CNA calculations. However, VisualCNA can be installed
without the CNA software, in that case it can only be used to analyze results
generated externally using CNA or visualizing example cases shipped along
(see below).
 
Installation instructions
=========================

Installation of VisualCNA does not require root privileges; you only need to
provide the path to the installation directory where you have writing
permissions when asked during the installation process.

Steps for installation
1. Extract visualCNA_1.0.tar.gz by executing "tar zxvf visualCNA_1.0.tar.gz"
   (without quotes).
   (You have already performed this step, since you are reading this file)
2. Change directory to visualCNA by executing "cd visualCNA" (without quotes)
3. Run the install.sh script by executing "./install.sh" (without quotes) and
   follow the on-screen instructions for installation of VisualCNA.
   (Make sure that the install.sh script is executable; if not, run
   "chmod +x install.sh" (without quotes))

    
There are two installation situations depending on whether (I) or not (II) you
have already installed the command-line CNA software available at
http://cpclab.uni-duesseldorf.de/software. 

I) The command-line CNA software is required as a backend for VisualCNA in case
you would like to perform your own thermal unfolding simulations.

II) When installed without the command-line CNA software, VisualCNA can be used
to analyze results generated externally by CNA or to view example cases shipped
along with VisualCNA.

    
Installation situations
=======================
I)  When you have the command-line CNA software installed
    
Upon execution of the install.sh script, you will be asked to provide the path
to the installation directory. In case you have the command-line CNA software
installed, you need to provide the root directory of this software. For example,
provide <DIR> as the path to the installation directory if the CNA executable is
located in <DIR>/CNA/CNA.sh .

After confirming that your input is correct, the installation will proceed
automatically.

After a successful installation, the executable to run VisualCNA is located in
the directory <DIR>/CNA. To launch VisualCNA, run "<DIR>/CNA/visualCNA"
(without quotes).

II) When you do not have the command-line CNA software installed
    
(Note that VisualCNA can only be used for analyzing results externally generated
by CNA in this case. However, you cannot perform your own thermal unfolding
simulations.)
    
In this situation, you can provide any directory where you have writing
permissions as installation directory. For example, VisualCNA will be installed
in <DIR>/CNA in case you provide <DIR> as the installation directory. After
successful installation, you can launch VisualCNA by "<DIR>/CNA/visualCNA"
(without quotes).


Tutorials and user guide
========================
VisualCNA is an intuitive and easy to use GUI for running CNA and analyzing
results from it. For a quick introduction into how to use VisualCNA, we
recommend to watch tutorial videos available on YouTube:
    https://www.youtube.com/user/cpclabduesseldorf
    
In addition to tutorial videos, a PDF file of a user guide explaining CNA and
VisualCNA along with a step-by-step guide for different tasks performed with
VisualCNA is provided in the <DIR>/CNA/doc folder of the VisualCNA installation. 


Contact for bug reports/suggestions/queries
===========================================
In case you have trouble with installing VisualCNA, find a bug, or have a
question or suggestion, please contact:
    support@cnanalysis.de
        
We will be happy to get back to you as soon as possible.

