I'm trying to configure my job_conf.xml to send all jobs to a SGE cluster. I can now execute most jobs successfully. However, since I have my galaxy installed in a local location (e.g. /opt/galaxy) instead of a network location, internal galaxy scripts do not execute correctly (e.g. Get Data->Upload File, which is upload1.py) since this local location is not present on the cluster. I was wondering if there's an easy way to route all of these jobs to the local job runner? Note that I don't want to move this galaxy on to a network location.
I found this page describing how to route jobs, (https://wiki.galaxyproject.org/Admin/Config/Jobs#Job_Destinations) but I'm not sure how I would isolate either only the jobs that require local galaxy code, or only the toolshed and custom tool xmls I've added to galaxy (other than laboriously listing them and their destinations under <tools> in job_conf.xml one by one). Is there an easier way?