MOLGENIS is an collaborative open source project on a mission to generate great software infrastructure for life science research. Each app in the MOLGENIS family comes with rich data management interface and plug-in integration of analysis tools in R, Java and web services.

The procedure below tells you how to checkout the molgenis project and build one of the example apps

Go to the directory where you keep your git repositories, e.g.

cd ~/git

Create a new workspace directory, e.g.

mkdir workspace
cd workspace

Clone the repo into this directory

git clone https://github.com/<yourname>/molgenis.git

Now you have a folder molgenis in your workspace directory.

(tested with latest eclipse download, J2EE Juno 4.2 SR1, Mac OSX 64bit)

MOLGENIS is created with help of Maven and Freemarker. You need a few eclipse plugins to work with those.

start eclipse:

~/Software/eclipse-juno-4.2/eclipse

When asked chose (new) workspace directory. I choose to simply same directory ~/git/workspace as before

Now install the plugins by choosing {{{Help -> Eclipse marketplace}}}. Add the following (you can restart Eclipse when done):

• maven integration for eclipse
• Apt M2E connector
• JBoss Tools (ONLY SELECT THE 'FreeMarker IDE feature' later in the wizard!)
• testng

Now you have configure Eclipse. Restart eclipse.

Start Eclipse, select your workspace if asked.

Click: File -> Import ... -> Existing Maven Projects

Set root directory to your git checkout folder. E.g. ~/git/workspace (this means you can still see the 'molgenis' folder).

Eclipse discovers all molgenis modules (should be all checked).

Click next/okay; eclipse will now import the modules. Also Eclipse will automatically install maven connector plugins when needed (restart follows)

If still open, close the 'Welcome' screen

Eclipse will automatically build and download jars

Right mouse 'molgenis' -> Run as -> Maven install

After generation eclipse will compile automagically

Assumed is that you installed mysql Log in via terminal using your root credentials

mysql -u root -p

Give create a database with permissions to molgenis user

create database omicsconnect;
grant all privileges on omicsconnect.* to molgenis@localhost identified by 'molgenis';
flush privileges;

Load schema:

TODO: this should use JPA so that database need not to this additional setup

use omicsconnect;
\. /path/git/molgenis13.2/molgenis-app-omicsconnect/target/generated-sources/molgenis/sql/create_tables.sql

TODO: this needs to be improved so it starts immediately without generate/build if not needed

Right click 'molgenis-app-omicsconnect' -> Run as ... -> Maven build ...

In the 'goals' box type in 'jetty:start'

Choose Run. Now jetty will be started.

Open your browser at http://localhost:8080/