I have had Galaxy running on a local BAS, and after success with that we’re ready to create an instance on our local cluster computing service. The local cluster uses PBS/Torque.

I’m familiar with the basics of configuration, but our particular scheduler rewards those who specify accurate walltimes. I would like to be able to define specific walltimes for each tool. I’m mapping out a strategy for how best to specify accurate walltimes. For instance, if someone is running tophat, it will take longer if they’re mapping against a complex reference genome like human, as opposed to nematode. I’d like to use different walltimes to account for that.

Is there anyone who has tackled this and would be willing to share their approach with me?

Thanks!

Dan