NMC DSP Getting Started on Linux

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Software Packages

In order to get started with the NMC Data Support Platform (NMC DSP) you need to obtain the following software packages:

downloading

  • Download and install the latest Java Runtime Environment and latest Java Software Developers Kit (SDK)
  • Download and install Eclipse for Java EE developers from: http://www.eclipse.org/downloads/ (~160 MB)
  • Apache Tomcat Core (5.5)
  • Download and install the latest PostgreSQL
  • The latest Molgenis release from: http://molgenis.sourceforge.net/

installing Apache Tomcat

Installing Apache Tomcat on Linux depends on your distribution, but if you use a GUI, the package manager should list Tomcat

installing PostgreSQL

Installing Apache Tomcat on Linux depends on your distribution, but if you use a GUI, the package manager should list PostgreSQL

Setting up your workspace

Where you would like your workspaces stored is of course a personal preference. Just create a directory in your homefolder and call it "mymolgenisworkspace".

You can now start Eclipse and select / change to your Molgenis workspace (File --> Switch Workspace --> Other --> ~/mymolgenisworkspace).

Adjusting Build path and Java Runtime

By default Eclipse might by use versions 1.5 of the JDK and JRE, however Molgenis requires 1.6 which was installed by the latest Linux Java packages you downloaded earlier. In order to get things working you need to change the project settings to use 1.6 instead of 1.5 by changing the Java Build Path and Java Compiler in the properties of the molgenis project (file --> properties).

Setting up Apache Tomcat for your project

Select the properties for Eclipse and configure a Tomcat server with JRE 1.6:

NMC DSP Leopard Eclipse Server RuntimeEnvironment 1.png

NMC DSP Leopard Eclipse Server RuntimeEnvironment 2.png

NMC DSP Leopard Eclipse Server RuntimeEnvironment 3.png

Generating

Now that you have everything set up correctly, and you have switched your Eclipse workspace to your Molgenis workspace, you can generate the Molgenis code by running MolgenisGenerate.java :

NMC DSP Leopard Eclipse MolgenisGenerate.png

Now that you have generated the Molgenis code, you can run it on your -previously defined- Tomcat server:

Running

The first time you would like to Run the Molgenis project you need to define how and where to Run your code:

  1. select molgenis3_2_distro
  2. right click --> Run As --> Run On Server
  3. create a new Tomcat server based on the server definitions created above

NMC DSP Leopard Eclipse Server RunOnServer-1.png

NMC DSP Leopard Eclipse Server RunOnServer-2.png

NMC DSP Leopard Eclipse Server RunOnServer-3.png

When you have configured this server once, it will appear in the servers tab where you can easily start / stop the project on your Tomcat server:

NMC DSP Leopard Eclipse Server RunOnServer-4.png