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README.md

Synergy

Introduction

Synergy is a web application for exploring gene regulation in Synechocystis. The following documentation is mainly meant for developers. Documentation on how to use Synergy you can find over at http://synergy.plantgenie.org/documentation.

Synergy is based on CodeIgniter.

Requirements

  • Python 2.7+ with pip
  • PHP5+
  • Apache server with PHP5 support
  • MySQL
  • MEME suite

Installation

Basic setup

First of all, clone the repository (or just download it):

git clone https://github.com/maehler/Synergy.git

Of course, you will have to point you web server to this directory in order to serve it.

Inside the synergy directory, you must now create a python virtual environment that the application can use:

pip install virtualenv # If not already done
cd synergy
virtualenv .venv # Create virtual environment. Name is important!
source .venv/bin/activate # Activate the virtual environment
pip install -r requirements.txt # Install required modules, will take some time
...
deactivate # Deactivate the virtual environment

Database

You can download a dump of the database here: http://synergy.plantgenie.org/data/synergy.sql. When you have the dump, load it into a database that you have created, e.g. synergy_db

mysql -u user -p synergy_db < synergy_dump.sql

Next, you have to set the database credentials for both Python and CodeIgniter. For CodeIgniter, edit application/config/database.php and add the credentials for the $db['default'] variable.

For Python, create the file src/python/config/local.py where you add the database credentials in a dictionary named DATABASE

DATABASE = {
    'user': 'username',
    'host': 'localhost',
    'pass': 'password',
    'database': 'synergy_db'
}

Other constants

There are some other constants that Synergy needs to function properly.

In PHP you have to set the paths to the bin-directory of your MEME installation and a temporary directory for storing e.g. TOMTOM results. Add the following to application/config/constants.php:

define('MEME', '/absolute/path/to/meme/bin');
define('TMP', '/absolute/path/to/tmp/directory');

Preferably set the temporary directory to data/tmp in the Synergy repository, i.e. /path/to/synergy/data/tmp.