Below is an example condor command script for running a job from my local grid client (a PC running FC7, globus, condor). I'm running a set of codes that I installed on the machine (lonestar) that I wanted to use. These codes are run by a perl script, so I had to set the PATH. I want to upload the input files from my desktop at submission time--the paths here are for my client machine. Note Condor-G will put these in $SCRATCH_DIRECTORY on lonestar, which doubles as your working directory (that is, autoref.pl will be executed here). To get the files back from lonestar to the PC, I used "transfer_output_files" and listed each file. Full paths for these aren't necessary. Condor will pull them back from $SCRATCH_DIRECTORY on the remote machine to your local directory.
# Here it is. Please gaze at it only through a welder's mask.
executable = /home/teragrid/myaccnt/geofest.binaryexec/autoref.pl
arguments = testgeoupdate rare
transfer_executable = false
universe = grid
grid_resource = gt2 tg-login.tacc.teragrid.org/jobmanager-fork
output = test.out.$(Cluster)
log = test.log.$(Cluster)
environment = PATH=/home/teragrid/myaccnt/geofest.binaryexec/:/bin/:/usr/bin