I have set up a local install of galaxy, and have it integrated with SGE on our cluster using the CLI runner. I have been able to set up job_conf.xml and job_resource_params_conf.xml so that scheduling parameters can be entered in the web interface for tools. I was hoping to use this approach to set up SGE parameters (queue, project, #cores, etc), but I'm at a loss as to how to make those parameters accessible to the code that creates the submission script.
Can anyone point me to sample code as to how to use parameters specified in job_resource_params_conf.xml in the CLI runners? Or if there is a better way to do this, please let me know.