MOLGENIS is a collaborative open source project on a mission to generate great software infrastructure for life science research.
The procedure below tells you how to checkout the molgenis project and build one of the example apps.
install java8 JDK (not JRE) from http://www.oracle.com/technetwork/java/javase/downloads/index.html
install eclipse (we used Luna) from https://www.eclipse.org/downloads/
install mysql from (we used 5.6.23 DMG) http://dev.mysql.com/downloads/mysql/
install git from http://git-scm.com/download/
open terminal and start mysql client (command differs in Windows, Linux, Mac):
/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;
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'
- 'm2e-apt'
go to 'Eclipse' -> 'Preferences' -> 'installed JREs' and select 'java 8' go to 'Eclipse' -> 'Preferences' -> 'Maven' -> 'Annotation Processing' and select 'Automatically Configure JDT APT'
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
Optionally select stable molgenis version:
git fetch --tags origin
git checkout -b <tag name: see https://github.com/molgenis/molgenis/releases>
More information about forking can be found here: https://help.github.com/articles/fork-a-repo
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.
In eclpise, if still open, close the 'Welcome' screen.
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 push run button
Open your browser at http://localhost:8080/
You should see the application. Login as 'admin', 'admin' to be able to upload and view data, create users, etc etc.
Add the original molgenis repository as a remote location.
cd ~/git/molgenis
git remote add blessed https://github.com/molgenis/molgenis.git
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
Solution: start Eclipse from commandline.
Run the Maven target 'jetty:stop'. If that does not help, use your opering systems process manager to kill anything running on port 8080. For example:
kill -9 `lsof -i :8080 -t`