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Contains experimental modules that can find its way into molgenis
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Welcome to MOLGENIS

MOLGENIS is an collaborative open source project on a mission to generate great web applications for life science researchers.

The procedure below tells you how to checkout and build the molgenis suite, or use it to generate your own.

1. clone the molgenis repo

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<yourname>/molgenis.git

Now you have a folder molgenis in your workspace directory.

2. install and configure eclipse ==

(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:


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.

3. import the molgenis project into 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)

4. generate the code for the first time

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

5. create mysql database for omicsconnect app

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

6. run the omicsconnect app (example)

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/

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