BioJava3 Eclipse with SVN


  • Make sure you have a copy of the latest eclipse (Galileo)
  • Make sure you have Java 1.6 installed. (if you are on OSX 10.4.x, install soylatte)
  • Install the m2eclipse Maven eclipse plugin (previously hosted by Sonatype). Be sure to include SCM integration, offered through the m2eclipse-extras package.
  • Install Subversive through eclipse update site (it’s the official eclipse plugin), or install subclipse plugin for subversion instead (latest versions: 1.8.16 and 1.6.18).


  • In the SVN Repository Exploring view: Right click on the folder /biojava/biojava-live/trunk and select Check Out as Maven project

Details for specific Eclipse Versions

Update for Eclipse Juno (I use Juno SR1)(October 2012)

There used to be some conflicts with SVN connectors, but thank God, things are good now. Now, it’s as simple as this:

  • From Help menu select “Install new software…”
  • select the Juno update site option (Juno -
  • Check “m2e - Maven Integration for Eclipse”, and “Subversive SVN Team Provider”
  • Go through the regular process (next, accept, & restart)
  • After installing both plugins, from File menu, select import…

  • “Checkout Maven Projects from SCM” looks like this.

  • beside the SCM URL label, there is a drop down box for SCM type, and a text field for URL. In the first time, the drop down box will be empty…
  • you will find a small line below containing “Find more SCM connectors in the m2e Marketplace”. Click m2e Marketplace.
  • In the “m2e team providers” section, select “m2e-Subversive”,

then the next/accept/etc. process.

  • When you start first call to SVN-based operation, eclipse will show you a window asking you to choose a connector. The safest way is to select SVNkit (pure java implementation). This choice will not install any conflicting binaries to your system, also, being Java-based, it is OS independent.. you will keep your head from all hassle related to win32/64 compatibility and such stuff.
  • congratulations! Everything is ready now. Go back to the “Checkout Maven Projects from SCM”, you will see an SVN option in the dropdown box. Select it, key in the URl, and import (here I use the developer’s access URL, which might be different from yours).

Update for Eclipse Helios SR2 (May 2011)

The above plugins are still available and work fine, however, below are the few important particulars.

  • Use update URLs from the plugins web site, do not use Eclipse market place, as in that case you will have to install all the components of the plugin manually and it will be very easy to forget to install something important, besides it does not always work.
  • Make sure you have full JDK 1.6 installed, JRE will not be sufficient (some Maven plugins will not work)
  • After JDK installation point Eclipse to the JDK location. For this edit eclipse.ini found in the Eclipse root directory. Insert -vm keyword with the location of your JDK and make sure that this keyword precedes -vmargs (!) for example


  • If you work on any other operating system but win32, you will have to install JavaHL library for the subclipse plugin manually. More information about it can be found here:
  • When adding the URL of BioJava development repository do not add the actual folder you want to check out, otherwise you may not be able to checkout it as maven project. For example if you want to checkout




as the repository URL and then navigate to trunk in the Eclipse SVN explorer.

Eclipse Indigo (August 29th 2011)

I downloaded the Eclipse j2ee version (OSX Lion) and used the Eclipse Marketplace to find and install the following plugins:

from Eclipse Marketplace:

- Subclipse 
- Maven Integration for Eclipse
- Maven Integration for Eclipse WTP (probably  not needed, but I do a lot of web stuff, so I added it)
- m2e-subclipse (SCM connector, bring Maven and subclipse together)

from Yoxos Marketplace

- SvnKit Client Adapter (needs to be enabled in Preferences->Team->SVN, SVN Interface ->SVNKit, Pure Java )

To check out BioJava you can do: new -> Maven ->checkout project from SCM, add biojava URL to …/biojava-live/trunk, press finish

A useful blog article providing more help for how to install Maven is here: 1

Here some instructions for where to find the various eclipse plugins: 2Andreas 04:43, 30 August 2011 (UTC)

Anonymous access with Git

In the past, anonymous access to BioJava source code via SVN has been problematic. Alternatively, you can retrieve the source code from the read-only BioJava github mirror using Eclipse.


  • Java 6 (1.6) JDK
  • Eclipse Indigo (3.7) or greater
  • m2eclipse (Eclipse update site)
  • EGit (pre-installed with Indigo)
  • Maven SCM Handler for EGit (m2e-egit) from Eclipse Marketplace

Additional setup:

  • Edit your eclipse.ini file to use the Java JDK as your VM (instructions above, required for Maven)
  • If necessary, set the HOME environment variable (required for EGit)

Import the BioJava Maven project from Git (StackOverflow answer):

  • Open the Git Repository perspective
  • Clone the BioJava git repository (
  • Expand the cloned repository, right-click “Working directory”, and pick “Import Maven Projects…”
  • Open the Java perspective
  • Select all of the projects, right-click and choose “Team > Share Project”, select “Git”, and check the “Use or create repository in parent folder of project” box