Gene-Environment iNteraction Simulator 2 Files

==============================================
PACKAGE NAME ---> GENS2
VERSION ----> 2.3.1
LICENCE---> GPL
CREATED BY-> Giovanni Scala <juen85[at]gmail.com>
==============================================

INDEX:

-> Requirements
-> About this package
-> Installation
-> Files and their Proper Directories
-> Playing this plugin
-> Known Bugs & Issues
-> Version History
-> Incompatibilities & Save game warnings
-> Credits & Usage


==============================================
REQUIREMENTS:
==============================================
Before running setup.py make sure following python modules are installed:

python >= 2.6
setuptools
simuPOP
numpy >= 1.6.0
scipy >= 0.9
matplotlib
openopt = 0.38 (full suite suggested) Available in this folder as OOSuite-0.38.zip
wxpython (optional)

==============================================
ABOUT THIS PACKAGE:
===============================================
This package contains python modules to run GENS2 simulation,
and libraries that can be used in simuPOP simulations 
( see simuPOP project for more info).


===============================================
INSTALLATION:
===============================================
You can alternatilvely choose between two methods in order to install and run GENS2: 
1) the classic installation procedure (requires manual installation of dependencies),
or 2) through the anaconda environmet (this one is easier but the tool can only be used 
in command line mode (no GUI) on some systems (e.g. MacOs X)). 

First method:
	1.	Install all required dependencies (see section REQUIREMENTS)
	2.	Extract the content of the archive in a folder and move to it.
	3. With administrative privileges run :
		python setup.py install 

Second metod (needs anaconda installed): 
	1. conda create --name gens2 setuptools numpy scipy wxpython matplotlib
	2. source activate gens2
	3. conda install -c bpeng simupop

	4. cd <open opt folder 0.38>
	5. python install_all.py

	6. cd <GENS2 folder> 
	7. python setup.py installed

	From this point onwards whenever you need to run GENS2, you just need to activate its environment with
	
		source activate gens2
===============================================
FILES USED AND THEIR PROPER DIRECTORIES:
===============================================
With this distribution are provided also a test population "test.pop"
and some configuration file "*.conf" for testing purpose.
If you want to try the application with testing values you must
copy those files in your working directory and select the provided 
test population.

Every time you run GENS2 it will be save a series o files with .conf 
extension to remember input through various simulations, if don't wont 
this just delete those files from your working directory.

===============================================
USING GENS2:
===============================================
There are three way to use GENS2 modules:
	-through a GUI based wizard using command 'python gensGUI.py'
	-through command line typing ' python GENS2.py arguments...] 
	 where 'arguments' indicate a series of argument passed to the application.
	 Type 'python GENS2.py -h' for help about parameters and their meaning.
	-through interactive terminal typing 'python GENS2.py --gui=False'

===============================================
KNOWN ISSUES OR BUGS:
===============================================
The present GENS2 distribution has been tested with the numpy version 1.10.1, scipy version 0.16.0 and openopt version 0.38.  Latest versions of openopt have some compatibility problems with the current implementation of GENS2. Although other versions may be suitable as well, we suggest to use them to avoid unexpected results. 

===============================================
VERSION HISTORY
===============================================
GENS 1.0
GENS 2.0-BETA
GENS 2.1-BETA
GENS 2.2-BETA
GENS 2.3
GENS 2.3.1