I understand how to add the jar files to the classpath in eclipse but I am not sure what to do with the .so files. I’ve spent awhile now try to figure this out and most of the link I have found say not to add things to the $LD_LIBRARY_PATH. Anyhow, I am not very proficient at using linux yet, so I do not even know how to add to this path. If someone could help me I would really appreciate it.
Just pass the directory where the .so files are as “java.library.path” system property. You can do this by adding a “-Djava.library.path=/path/to/the/jogl/binaries” on the commandline when launching a JOGL application. It’s not needed for compiling.
Here is a step by step description how to install jogl in eclipse (I pasted it from a post for the pre JSR jogl, so some files may be named different):
- download the jogl.jar,gluegen.jar, docs, sources and the appropriate jogl-natives
- make a directory for jogl (e.g. under /use/share/jogl)
- put the jogl.jar and the sources in this directory
- extract the jogl-natives and the gluegen-natives into that directory (you should have some .dlls after that)
- extract the javadoc_public.zip into this directory into the subdirectory docs
- run eclipse and open your project or create a new one
- select Project-Properties from the menu, select Java Build Path
- Use “Add External Jar” to add the jogl.jar and gluegen.jar from the above directory
- expand the new item in the tree
- as source select the jogl-src.zip file in the above directory
- as javadoc location select the subdirectory docs in the above directory
- as native library select the above directory (containing the .so’s)
- That’s it. You should now be able to use jogl in eclipse.
Despite the above advice clearly being straight from beelzebub
http://homepages.inf.ed.ac.uk/rmcnally/beast.png
it’s pretty much spot on. For all his faults, Satan knows his tech 
On a more general note, you can add stuff to the $PATH, $LD_LIBRARY_PATH, and in fact set any environment variable or run any command by editing the .bashrc file that lives in your home directory.
Files that start with a “.” are hidden, and so won’t show up by default in your file manager - there’s usually a menu option to show them.
This file is a list of command that get run whenever you open a command prompt, and is probably full of cryptic-looking stuff that controls the command history and filename colouring. So if you’ve got, say, some application installed in /home/foo/bin that you want to add to the $PATH, you add something like “export PATH=/home/foo/bin:$PATH” to the file.
[quote]it’s pretty much spot on. For all his faults, Satan knows his tech Wink
[/quote]
Yeah. Now I have reached my full power through the manifestation of this symbol, the time is right to subdue the world and bring darkness to it’s inhabitants. You all will serve me as my slaves and I will have unlimited power for the rest of eternity as long as I don’t submit any new post MUAHAHAHAHA…
Edit: damn - screwed it :o :’(