[galaxy-dev] Compiling dependencies in galaxy yields error

I was installing a tool from the galaxy toolshed and one of the dependencies was missing due to a bad link. I modified the install files to use the same version of the the software except from a local directory, however galaxy renders a large error when compiling. If I compile the source in the same location outside of galaxy it compiles and installs correctly. The specific package I am attempting to install is ghostscript for homer package.