Hi Evan,
Can
 you include the full error you're receiving?
Thanks,
--nate
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.