This is a prelude to using Condor-G. I used the following incantation:
-bash-3.00$ more meshgen.cmd
universe = vanilla
executable = /globalhome/gateway/geofest.binaryexec/autoref.pl
output = autoref.out
error = autoref.err
log = autoref.log
arguments = /globalhome/gateway/condor_test/testgeoupdate rare
environment = "PATH=/globalhome/gateway/geofest.binaryexec/"
#getenv = true
initialdir = /globalhome/gateway/condor_test
should_transfer_files = IF_NEEDED
when_to_transfer_output = ON_EXIT
The key thing here was the "environment" attribute, since the autoref.pl script is of course a perl script that calls other executables. These executables need to be in the PATH.
You can also do this by setting the PATH environment variable in your shell and then using the getenv attribute. This will work OK for the command line but will not be much use in a web service version. OK, you could get it to work, but this is the kind of thing that will break 6 months later when you move to a new machine.
None of the condor examples I could find discuss this, but it is well documented in the condor_submit manual page.