Plugin development for Bioclipse - from scratch

I switched laptop recently, so I needed to set up my development environment for Bioclipse 2.2 plugin development from scratch. Since the instructions for how to do this are spread over a couple of blogs and the wiki, I used the occasion to create an integrated howto, for my own documentation as well as for anyone interested.

For the initial steps I'm following this tutorial, and may refer to it as "the wiki page". This tutorial might contain a bit more details though, specific for Ubuntu (9.04).

My system

I'm running Ubuntu 9.04. My Java version is "java-1.5.0-sun-" located in "/usr/lib/jvm/java-1.5.0-sun-".

Installing Eclipse

I first downloaded Eclipse (the "Eclipse for RCP/Plug-in Developers (182 MB)" version) from (according to some, the classic package will do fine as well).

When starting up Eclipse, you get to choose a place to store the workspace. I created a workspace called "bioclipse-master" where I'll keep the master branch of Bioclipse checked out.

Installing the Apache Commons Codec feature

  • Click "Help > Install New Software"
  • Click the "Available software sites" link to the right
  • Enable the Ganymede Update site (URL: , click OK
  • Back in the "Install New Software" windows, in the "Work with" drop-down, choose the update site you just added above.
  • Filter for "apache"
  • Select the "Apache Commons Codec" feature and complete the wizard.

Checking out the Bioclipse source

I checked out the bioclipse source by going to the workspace folder I created earler

cd [your-specific-location-of-eclipse-workspaces]/bioclipse-master

and then checking out from git (requires that you have git installed):
git clone git://

Importing Bioclipse into Eclipse

Then, inside Eclipse, I imported the newly created project folder by means of:

  • File > Import...
  • General > Existing Projects into Workspace
  • Selected the "bioclipse.core" folder as root folder
  • Finish

Finalizing settings and building Bioclipse

  • I opened the "target.platform" file (find it by pressing [Ctrl] + [Shift] + [R] (For "Resouce") and type the first letters in "target".)
  • Clicked "set as target platform" in the top right corner
  • I pressed the green button at the top right.

Voila! Running Bioclipse 2.2! :)

Checking out the Bioclipse SDK

The Bioclipse SDK (Software Development Kit) provides with an easy wizard to get you started building your next Bioclipse plugin, creating a Biomanager for the plugin, and code stubs for you to fill in with your code.

  • Go to "Help > Install new software"
  • Click the link "available software sites"
  • Add the site (Name it "Bioclipse SDK" for example)
  • Back in the "Install new software" windows, choose the newly created update site in the "Work with:" drop-down.
  • "Bioclipse SDK feature" should now appear in the field below. Select it and complete the wizard.

Using the Bioclipse SDK Wizard

See also Egon's original instructions, for creating a Bioclipse plugin using the Bioclipse SDK.

  • File > New > Project
  • Choose "Plug-in Development > Plug-in Project"
  • In the next two screens, fill in the ID, Version, Name, and Provider as you like (Hint: The name preferrably should start with "net.bioclipse...").
  • In the screen after that, when choosing "Templates", choose "Bioclipse Manager Plug-in".

Done! Now you should have a new project in your navigator.

Start coding

in the navigator.

See also