Get from a clean OS install up to the point where you can generate, run and use a MOLGENIS

Install Java,Tomcat,MySQL and Eclipse

MOLGENIS is known to run happily on Windows, Linux and Mac. We here assume the procedure for the windows installation; for other operating system distributions we refer to respective documentations. To get started, download and install the most recent:

1. Java 6 JDK ​http://java.sun.com/javase/downloads/
   Just install the most recent standard JDK with standard options.
   
2. Tomcat >=5 web server ​http://tomcat.apache.org/
   Rember the root password you are asked. Don't run Tomcat as a service; we will start and stop it ourself.
   
3. Mysql >=5.1 database ​http://dev.mysql.com/downloads/mysql/5.1.html
   During installation of the windows version you need to tick 'innodb'. Remember your root password.
   
4. Eclipse Integrated Development Environment ​http://www.eclipse.org/downloads/
   You need to install the J2EE version (which allows you to start/stop tomcat)
   
5. (Optional) Graphviz
   MOLGENIS autogenerates documentation for your application. This requires the GraphViz? package from ​http://www.graphviz.org/Download.php Make sure your PATH is set to run 'dot.exe' from the commandline. In windows this is set in the control panel -> System -> Environment variables.

Create a database in MySQL

Setup a MySQL database (once per MOLGENIS instance) MOLGENIS typically uses MySQL as data storage back-end although also PostgreSQL may be used. Here the procedure for MySQL is described to create a database and give MOLGENIS permission to populate it.

1. Open mysql.exe as root user. Under windows in "C:\Program Files\MySQL Server 5.1\bin\mysql.exe - u root -p
   Type your mysql root password remembered from step 3 above!
2. Create a database 'molgenis' and give rights to the molgenis generator to change it using password 'molgenis'.
   Type: create database molgenis; grant all privileges on molgenis.* to molgenis@localhost identified by 'molgenis'; flush privileges;