= 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/ [[BR]]Just install the most recent standard JDK with standard options. [[BR]]
 1. Tomcat >=5 web server http://tomcat.apache.org/ [[BR]]Rember the root password you are asked. Don't run Tomcat as a service; we will start and stop it ourself. [[BR]]
 1. Mysql >=5.1 database http://dev.mysql.com/downloads/mysql/5.1.html  [[BR]]During installation of the windows version you need to tick 'innodb'. Remember your root password. [[BR]]
 1. Eclipse Integrated Development Environment http://www.eclipse.org/downloads/  [[BR]]You need to install the J2EE version (which allows you to start/stop tomcat)[[BR]]
 1. (Optional) Graphviz[[BR]]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.

== Open the MOLGENIS workspace using Eclipse ==
Most application developers use Eclipse to develop MOLGENIS applications. Therefore a ready made Eclipse project is the standard MOLGENIS distribution.
 1. Download the latest 'molgenis_workspace.zip' from http://molgenis.sourceforge.net[[BR]]
    ''Just download and unzip. A directory 'molgenisXX_workspace' is created.''


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