if you didn't know already the Torrent Server uses SGE, for those of us who are more used to PBS or LSF, this guide below might help you walk through some of the commands if you need to say create your own reference index or do tmap on the TS
Array jobs for clusters running SGEhttp://wiki.gridengine.info/wiki/index.php/Simple-Job-Array-Howto
Converting between PBS and SGE scriptshttp://wiki.ibest.uidaho.edu/index.php/Tutorials:_SGE_PBS_Converting
Above url has a fantastic conversion table that lists options that are new to me as well!
For a more concise, quick and dirty guide see here