Getting Started

This section explains what you need to get started from a clean OS install up to the point where you can generate, run and browse the MOLGENIS example that is shipped with the MOLGENIS distribution (in the next chapter).

Install the necessary software (only once)

MOLGENIS is known to run happily at 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;

Open the MOLGENIS workspace in Eclipse

Many 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 Just download and unzip. A directory 'molgenisXX_workspace' is created.