J/maanova is an open sourced desktop application developed by The Churchill
Group at The Jackson Laboratory with the aim of simplifying the analysis of
microarray experiments. J/maanova allows researchers to access a subset of the
functionality available in the R/maanova package through a graphical user
interface. See http://churchill.jax.org/software/jmaanova.shtml for details.

LICENSE
========
Copyright (c) 2010 The Jackson Laboratory

This software was developed by Gary Churchill's Lab at The Jackson
Laboratory (see http://churchill.jax.org).

This is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This software is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this software.  If not, see <http://www.gnu.org/licenses/>.

BUILDING
========
In order successfully complete these build instructions you must have:
* git
* ant >= 1.7.1
* java development kit (JDK) >= 1.5

To obtain and build the source code enter the following commands:
    git clone git://github.com/keithshep/j-maanova.git
    cd j-maanova
    git submodule init
    git submodule update
    ant

After the build completes you will have a full JNLP distribution built under:
    ./modules/main/web-dist

Assuming you have a bash shell you should also be able to run from the
command-line (without bothering with a JNLP install) by doing:
    cd modules/main
    ./run-jmaanova.bash

CONTRIBUTING
============
J/maanova is open sourced and we welcome contributions. It is probably a good
idea to get in contact with us if you intend to make a contribution so that we
can coordinate and advise you on whether or not we think we will be able to
accept the proposed changes.