Chris Cole wrote:

Is it possible to specify SGE parameters on a job-by-job basis? For example, say I want set off an array job or specify a parallel environment for certain jobs.

Hi Chris, The only way to specify parameters would be to configure an SGE queue that specifies them, and then assigning that queue to a specific tool. There's no way to do this currently on a per-job level. This page in the wiki explains setting a per-tool queue: http://g2.trac.bx.psu.edu/wiki/ClusteringGalaxy --nate