This is badly out of date, as I have transitioned from primarily working in MacOS back to Windows.
Some of my research in Chemical Graph Theory is greatly aided by being able to generate and view the fullerenes and fullerene patches I'm investigating. The Combinatorial Algorithms and Algorithmic Graph Theory group at Ghent University provides a tool called CaGe, which implements the fullgen algorithm (and others!) to construct all sorts of nice graphs.
I have XCode installed, but more importantly, downloaded a JDK from Oracle. Then at the command line (Terminal) I did the following
Run /usr/libexec/java_home. Copy the output of this using command-C.
In the directory where you've unpacked CaGe.zip, run ./INSTALL.sh; when prompted for the directory of your java installation, paste (command-v) and follow it with /bin.
This made CaGe compile for me on a brand-new iMac.