Note that the below procedure would not have been possible without the help of David van Enckevort. The document highlights the installation of the Molgenis web application. If you would like to develop or contribute (code) to the project, you are better off forking the github version.

Install Java 8 (my favorite is the Oracle JDK). There are many websites explaining how to do this, but the TL;DR version is:

sudo apt-get install software-properties-common
sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer # some annoying licence acceptance terms will pop up
sudo apt-get install oracle-java8-set-default

When you are done java -version and javac -version should yield the Java 8 version and build number.

You will also need to install Tomcat 7. This is straightforward with

sudo apt-get install tomcat7

1. Download the latest version of molgenis web application file (this is in the form of a Java war).
   1. Do this by searching for molgenis-app in the maven repository
   2. Download the war file by using wget. e.g.

      jp@maltabiobank:~/downloads$ wget http://search.maven.org/remotecontent?filepath=org/molgenis/molgenis-app/1.8.2/molgenis-app-1.8.2.war

2. Rename the downloaded war file to ROOT.war (case important). This is an annoying and necessary limitation
3. Copy the newly renamed ROOT.war to the Tomcat webs directory (by default this is in /var/lib/tomcat7/webapps)<code bash>

sudo cp -v ROOT.war /var/lib/tomcat7/webapps <code>

1. If you want to follow what is going on, *before* copying set a tail -f