INSTALL

Two steps:
    1. Setup MySQL
    2. Setup & run python



1. Setup MySQL
==============

There are two ways to setup the MySQL - minimal and django. Minimal just sets up the database so that the phasing program logs to it and you devise your own method of interrogating the database. django uses python's django project to setup the database and includes a website for interacting with the database.

Minimal MySQL Setup
===================
1. Edit CXParams.py - "db" section
2. Run script 'init_CXPhasing_mysql.py'. You will be prompted for super username and password to setup the database and initial tables.

2. Setup Python
===============
1. Make a copy of CXParams.py and give it a name relevant to the sample/measurement, e.g CXParams_sample1.py. 
2. Create a softlink to CXParams_sample1.py called CXParams.py ("ln -sf CXParams_sample.py CXParams.py"). The phasing scripts will always look for a file called CXParams.py so the softlink allows you to quickly change which set of parameters will be used by the algorithm.
3. In your CXParams.py edit the "io" section to have meaningul directory names for your system. Leave all the other values the same.
4. Run bin/phasing -st
5. It will complain about what python modules you need to install. I need to make a list of dependencies still.
6. It will attempt to create a log file in /var/log/CXPhasing but you will need to create that directory manually or change the log file directory in CXParams.io.log_dir.