Quickstart for developers on MAC:

1. Install software needed

install java8 SDK from http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

install eclipse (we used Luna) from https://www.eclipse.org/downloads/?osType=macosx

install mysql from (we used 5.6.23 DMG) http://dev.mysql.com/downloads/mysql/

install git from http://git-scm.com/download/mac

2. Configure mysql

open terminal and start mysql client via command:

/usr/local/mysql/bin/mysql -u root

in mysql client create database and permissions via command:

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

3. Configure Eclipse

start Eclipse from the commandline (via Dock will not work!)

when asked, create fresh workspace folder (not same folder as git!)

go to 'Help' -> 'Eclipse market place'

find and install plugins:

• 'JBoss Tools', during install only select Freemarker IDE
• 'TestNG for Eclipse'

go to 'Eclipse' -> 'Preferences' -> 'installed JREs' and select 'java 8'

4. Get the code

create acount on github.com

'fork' on http://github.com/molgenis/molgenis

copy the cloneURL

open terminal (mkdir if needed) and type

cd ~/git 
git clone http://github.com/[YOURACCOUNT]/molgenis

More information about forking can be found here: https://help.github.com/articles/fork-a-repo

5. Configure the default admin password

Create the directory /.molgenis/omx and create a file called molgenis-server.properties in this folder ( is your home folder)

Add user and database properties to this file, such as this example:

db_user=molgenis
db_password=molgenis
db_uri=jdbc:mysql://localhost/omx
admin.password=admin
user.password=admin

If these properties are not present, the MolgenisDatabasePopulator will fail (RuntimeException). This properties-file should be in your home folder, if the file is not there yet, just create it.

6. Import, build and run MOLGENIS in Eclipse

In eclipse, choose 'File' -> 'Import' -> 'Import existing Maven projects'

browse to your /git/molgenis directory

select (and wait to install all kinds of maven connectors)

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

Right mouse 'molgenis-app' -> Run as -> Maven build ... -> in goals type 'jetty:run' and

Frequently asked questions

1. I get maven build error 'env not available'. Solution: start Eclipse from commandline.