If you try to do this in Fedora you’ll quickly run into SElinux. This can easily be solved by specifying which java binary to use with Eclipse. You can do this by passing in -vm /path/to/java on the command line, or by adding this into the eclipse.ini file.

Another issue that you will have in both Ubuntu 9.10 and Fedora 12 is that certain UI buttons seem unresponsive. When clicking one of those buttons the UI is unresponsive for a few seconds, and when it wakes up it appears as if you had never clicked that button. This is due to the fact that both Ubuntu 9.10 and Fedora 12 ship with a new version of GTK, which contains a new feature which certain applications such as Eclipse can’t handle properly. The fix to this is quite easy, you can deactivate this new feature by setting the environmental variable GDK_NATIVE_WINDOWS to 1 (or true). You can do this by creating a script that does this before starting Eclipse, that way you don’t have to turn off this feature entirely but just for Eclipse.

The Fedora and Ubuntu versions of Eclipse that you can install via the distros’ package managers don’t have this problem, most likely because these versions of Eclipse turn off this GTK feature somehow (perhaps in the same way that I have described above).

You can read more about the GTK story here: http://blog.export.be/2009/10/fixing-eclipse-for-ubuntu-karmic-koala-9-10/. Kudos to the author, without that article it would have taken me a very long time to figure this one out