Compile MOLGENIS locally

Get the code

create acount on

'fork' on

copy the cloneURL

open terminal (mkdir if needed) and type

cd ~/git 
git clone[YOURACCOUNT]/molgenis

Optionally select stable molgenis version:

git fetch --tags origin
git checkout <tag name: see>

More information about forking can be found here:

Configure postgresql

If you are unfamiliar with PostGreSQL, follow one of their PostGreSQL installation guides. Once you have a PostGreSQL server running, open up the included pgAdmin application that is supplied with most PostGreSQL installations, and perform the following actions:

  • Add a database 'molgenis'
  • Add a user 'molgenis' (password 'molgenis') under Login Roles
  • Add 'can create databases' privilege to user 'molgenis'

Now that your database server and properties file have been configured.

Set admin password

Create directory ~/.molgenis/omx/

mkdir -p ~/.molgenis/omx/

Create the file ~/.molgenis/omx/

nano ~/.molgenis/omx/

... and add user and database properties to this file:


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.


In IntelliJ


Update your code

Add the original molgenis repository as a remote location.

cd ~/git/molgenis
git remote add blessed

Perform regular updates so the latest changes are merged with your local clone.

git pull blessed master

And push back any merges or commits of your own to your online fork.

git push origin master

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