  
  Section of Biomedical Image Analysis
  Goddard Building
  3701 Hamilton Walk, 6th Floor
  Philadelphia, PA 19104

  Web:   http://www.cbica.upenn.edu/sbia/
  Email: sbia-software at uphs.upenn.edu

  Copyright (c) 2016 University of Pennsylvania. All rights reserved.
  See http://www.cbica.upenn.edu/sbia/software/license.html or COPYING file.



INTRODUCTION
============

  This is the installation guide for MOE software. Please make sure you have the required 
  dependencies before proceeding.

Quick Summary of Installation
=============================

This software has been primarily implemented for Linux operating systems. It is implemented in Python.

----------------
 Dependencies
----------------
- Python 2.7.9
- Python library numpy 1.7.2
- Python library scipy 0.15.1
- Python library pandas 0.16.2
- Python library sklearn 0.15
- Python library matplotlib 1.4.3

Make sure all dependencies are met before proceeding with install.

-------------------------------------
Testing and Installation
-------------------------------------
From within the src/ folder, run: 

1) ./make test

This runs test.py from within the src directory. 

We have provided synthetic two dimensional data for four test cases. In each of these cases, data points denoted by circles are the reference (control) samples, while points denoted by triangles are the affected (patient) cases which are made up of heterogeneous sub-groups. These are located in src/test/Case∗. 

Test cases are used to check if the cross-validation accuracy in four test cases is greater than that of linear-SVM.

Proceed to the install step only if test passes in all four cases.


2) ./make install ${installDir}

Installation requires the installation directory as a user-input. 
This creates four folders within installDir - bin, libexec, share and doc.
bin/ contains the main executible moe.
libexec/ has all python scripts.
share/ has the test data.
doc/ has the doxygen documentation.

3) Add the binary folder to the system path:

export PATH=${PATH}:${installDir}/bin/

----------------------------
Code documentation
----------------------------

The "make install" step (above) generates doxygen documentation in "${installDir}/doc/*".
