Configuration Instructions.txt

Once the Model SEED has been successfully installed, you must configure it to your running environment, and you must install the data associated with the Model SEED
1.) Customize the Model SEED configuration file
	a.) Copy the default configuration file Model-SEED-core/config/Settings.config to a new filename (e.g. MyModelSEED.config):
	b.) Edit you new configuration file filling in the following parameters (ignore the others for now):
		[Optional]
		SeedUsername=(your SEED account username)
		SeedPassword=(your SEED account password)
		dataDirectory=(location where your extracted the Model SEED flatfiles in step 1)
		[Optimizers]
		directoryGLPK=(location where glpk has been installed on your system)
		includeDirectoryCPLEX=(location where cplex include files are located if you have cplex, leave commented otherwise)
		libraryDirectoryCPLEX=(location where cplex library files are located if you have cplex, leave commented otherwise)
		licenceDirectoryCPLEX=(location of cplex license file if you have cplex, leave commented otherwise)
2.) Decide upon the database backend: either MySQL or SQL-lite
	a.) The Model SEED can use two different database implementations to store the relational database that comes with the Model SEED
		-MySQL: a heavy weight implementation with a separate installation that provides enhanced performance for heavy-duty use
		-SQL-lite: a light weight implementation built into Model SEED, requiring no effort to install or configure, but delivering reduced performance
	b.) By default, Model SEED assumes an SQL-lite database backend because this provides us with an easier installation process. If you're using SQL-lite, JUMP TO STEP (4)
	c.) If you're using MySQL, JUMP TO STEP (3)
3.) Install and load MySQL database
	a.) Set up an SQL server on your computer or identify a server with SQL that you have access to
	b.) Create or identify a user account in the SQL server that Model SEED can use to interact with the server, and give this user account privileges to make schemes.
	c.) Adjust database parameters in config file
		[Database]
		# type is either sqlite or mysql
		type=(set this to "mysql")
		# required for mysql
		username=(set to username for Model SEED account in MySQL database)
		password=(set to password for Model SEED account in MySQL database, leave commented if no password)
		host=(set to host location of computer where database is hosted, "localhost" if on local machine)
		socket=(points to location of MySQL ".sock" file)
		port=(set to port for MySQL database, defaults to 3306 if left commented)
	d.) Run this command: Model-SEED-core/bin/ms-config load "Name of your config file that you filled out in steps 2.b and 3.c"
	e.) Run this script: Model-SEED-core/bin/CreateDBScheme
	f.) If you're having trouble getting this script to run, remember you need to install the MySQL development headers/libraries as well as the standard installation.
	g.) Make sure your user account has privileges to view and modify the ModelDB scheme.
	h.) Should run with no errors.
	i.) Download the default database content from here:
	http://bioseed.mcs.anl.gov/~chenry/sql.tgz
	j.) Extract the SQL file, and import it into the "ModelDB" scheme created in step 3.e
4.) Set up MySQL database backend 
	a.) Download sqllite file http://bioseed.mcs.anl.gov/~devoid/ModelDB-sqlite.tgz
	b.) Extract to the Model-SEED-core/data/ directory
	c.) Load SQL-lite database from file:
	sqlite3 Model-SEED-core/data/ModelDB/ModelDB.db < Model-SEED-core/data/ModelDB/ModelDB.sqlite;
	d.) Delete the ModelDB.sqlite file
	e.) Run this command: Model-SEED-core/bin/ms-config load "Name of your config file that you filled out in steps 2.b and 4.b"
5.) Test the Model SEED
	a.) Run this command: Model-SEED-core/bin/ModelDriver