This document explains how to get the code, install the necessary software and compile/run for the first time

Software needed

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/ (or use IntelliJ)

install MySQL (we used 5.6.23 DMG)

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

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;

Configure Eclipse

start Eclipse

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'

Restart (if you didn't do that already)

go to 'Eclipse' -> 'Preferences'

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

Restart

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

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

Set admin password

Create directory ~/.molgenis/omx/

mkdir -p ~/.molgenis/omx/

Create the file ~/.molgenis/omx/molgenis-server.properties

nano ~/.molgenis/omx/molgenis-server.properties

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

    db_user=molgenis  
    db_password=molgenis  
    db_uri=jdbc:mysql://localhost/molgenis  
    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.

Start MOLGENIS

In eclipse, if still open, close the 'Welcome' screen.

Choose 'File' -> 'Import' -> 'Import existing Maven projects'

Browse to your /git/molgenis directory

Select it, you will then be prompted to install some maven connectors, accept these (else MOLGENIS will not build properly in eclipse)

Right mouse 'molgenis' -> Run as -> Maven build ... In Goals type: clean install. Under Goals check Update Snapshots and Resolve Workspace artifacts. In the JRE tab, add the VM arguments:

```
-Xmx2g -Des.discovery.zen.ping.multicast.enabled=false -Des.network.host=localhost
```
Click run

Right mouse 'molgenis-app' -> Run as -> Maven build ... in goals type 'jetty:run' In the JRE tab, add the VM arguments:

```
-Xmx2g -Des.discovery.zen.ping.multicast.enabled=false -Des.network.host=localhost
```
Click run

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.

Update your code

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

Security

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 operating systems process manager to kill anything running on port 8080. For example:

kill -9 `lsof -i :8080 -t`

Start