I've looked around in the docs and haven't been able to figure out how this works.

I'm working with the SGE template which appears to have three "levels" of code/text to be parsed by brew:

## text like this: comments
#$ -text like this: arguments to qsub
bare text like this: shell commands

When and where do the #$ lines get passed on to qsub (if that is indeed what happens)? Thanks for any help wrapping my mind around this!