Thank you both for your input and time. I ended up following the instructions here: http://circos.ca/tutorials/lessons/configuration/perl_and_modules/ and now I can successfully run the program when logged in as root. It turns out the newest GD package is incompatible with the other modules and 2.53 should be used instead. Still not able to install GD in my other non-root profiles but this is a minor inconvenience.