Developing Fiji in Eclipse

Revision as of 11:39, 28 May 2009 by Axtimwalde (talk | contribs) (To be continued ...)
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This tutorial is about how to setup Eclipse for developing Fiji on a *nix operating system.

Install Eclipse

Install Eclipse using your preferred package manager or download the appropriate binaries of the Eclipse IDE for Java Developers. Launch Eclipse and decide for a workspace location (e.g. ~/worspace). For me, Eclipse is not stable with Sun Java 6. That is, you will eventually have to install Java 5 as an alternative JRE and make a custom launcher for Eclipse, e.g.

/usr/lib/jvm/java-1.5.0-sun/bin/java -cp /usr/lib/eclipse/startup.jar org.eclipse.core.launcher.Main

Install Git

Install Git using your preferred package manager or download from the Git website.

Checkout Fiji

Go into your Eclipse workspace and clone the Fiji repository

cd ~/workspace
git clone ssh://

This will create the folder ~/workspace/fiji where you have the core Fiji repository.

In order to run Fiji properly, it is suggested to use the JRE which is shipped with Fiji. This is a platform dependent submodule of the Fiji repository. Check it out with

cd ~/workspace/fiji
git submodule init java/linux-amd64
git submodule update java/linux-amd64

Check out all submodules that you want to work with e.g.

cd ~/workspace/fiji
git submodule init ImageJA
git submodule update ImageJA
git submodule init mpicbg
git submodule update mpicbg
git submodule init TrakEM2
git submodule update TrakEM2
git submodule init VIB
git submodule update VIB

Fiji comes with its own build system that we will later use from Eclipse. Test, if Fiji builds properly

cd ~/workspace/fiji

Create the Eclipse Project

Launch Eclipse and create a new Java project