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MOLGENIS - for scientific data: management, exploration, integration and analysis
Java JavaScript CSS Other

Merge pull request #3057 from bartcharbon/master

performance enhancement KEGG, HGNC and CGD annotator
latest commit 0804d59bbc
@tommydeboer tommydeboer authored
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molgenis-charts update version to 1.8.0-SNAPSHOT
molgenis-core-ui Fix for github issue #2840
molgenis-core update version to 1.8.0-SNAPSHOT
molgenis-data-annotators fix unit test
molgenis-data-csv update version to 1.8.0-SNAPSHOT
molgenis-data-elasticsearch - Moved code that decides if an entity is referenced by another entit…
molgenis-data-examples update version to 1.8.0-SNAPSHOT
molgenis-data-googlespreadsheet update version to 1.8.0-SNAPSHOT
molgenis-data-jpa update version to 1.8.0-SNAPSHOT
molgenis-data-mapper Merge pull request #3055 from bartcharbon/master
molgenis-data-mysql - Moved code that decides if an entity is referenced by another entit…
molgenis-data-rest-client update version to 1.8.0-SNAPSHOT
molgenis-data-rest removed comment
molgenis-data-semanticsearch update version to 1.8.0-SNAPSHOT
molgenis-data-system update version to 1.8.0-SNAPSHOT
molgenis-js update version to 1.8.0-SNAPSHOT
molgenis-model-registry update version to 1.8.0-SNAPSHOT
molgenis-ontology-core update version to 1.8.0-SNAPSHOT
molgenis-scripts update version to 1.8.0-SNAPSHOT
molgenis-security-core update version to 1.8.0-SNAPSHOT
molgenis-security Fix for github issue #2840
.gitignore Add factory paths to git ignore
eclipse-java-molgenis-style.xml eclipse molgenis java code formatter: insert new line after annotatio…
pom.xml update version to 1.8.0-SNAPSHOT

Build Status

Welcome to MOLGENIS

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.

1. Install software needed

install java8 JDK (not JRE) from

install eclipse (we used Luna) from

install mysql from (we used 5.6.23 DMG)

install git from

2. Configure mysql

open terminal and start mysql client (command differs in Windows, Linux, Mac):

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

Note, if not running you can start the MySQL server from the System Preferences

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'
  • 'm2e-apt'

go to 'Eclipse' -> 'Preferences'

  • 'installed JREs' and select 'java 8'
  • 'Maven' -> 'Annotation Processing' and select 'Automatically Configure JDT APT'


4. 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 -b <tag name: see>

More information about forking can be found here:

5. Configure the default admin password

Create the file ~/.molgenis/omx/ and add user and database properties:


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 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 (this takes a while!)

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.

7. Keep your code up to date

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

8. Troubleshooting

When I build I get maven build error 'env not available'.

Solution: start Eclipse from commandline.

When I try to start an application, the console tells me 'Address already in use'!

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`
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