To run Gephi on Mac OS 10.8.5, I needed to make a few adjustments and wanted to record them for posterity.

I found this thread very useful.

• I needed to install Java version 6. Oracle does not provide it; you need to get it from Apple. I found it here. Annoyingly, it was not in the standard software updates. Some sites (like Gephi’s?) tell you that Java 6 is automatically installed with Apple updates and that’s simply not true.
• I already had Java version 7 and that won’t currently work with Gephi. I downloaded that to make Rapidminer run!
• There’s nothing in either Gephi or RapidMiner that tells you what is missing when Java is missing or of the wrong version, by the way — they just fail to work.
• Once Java 6 was installed, I had to change two lines of code. First, in /Applications/Gephi.app/Contents/MacOS/Gephi, I needed to type jdkhome=`/usr/libexec/java_home -v 1.6` on the lines above the if-then snippet that tells Gephi where to look for Java. So search for $jdkhome in this file and add the line hardcoding jdkhome before the if statement.
• I also had to change the Gephi configuration file: I opened /Applications/Gephi.app/Contents/Resources/gephi/etc/gephi.conf and changed jdkhome there to jdkhome="/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/".
• Doing just one of these things was not enough.

Now I have graphs!