[jrmcauliffe]

I don't have a Scientific Computing Workflow/Background, but the AWS recommended tool for automated deployment to AWS is Cloudformation

http://aws.amazon.com/cloudformation/

Connecting Spot instances to EBS volumes isn't really possible via their APIs though. Amazon's API seems to regard Spot Instances as stateless compute entities, you need to push the results to a real on-demand instance (with attached EBS Volume) or something like ec2.

If you have massive compute requirements, companies like

http://www.cyclecomputing.com/

will do the hard work for you, otherwise with a bit of configuration work you can spin up a master node with an ebs volume along with a set of spot instances (of any type) to perform the work.

Checkout the Cloudformation template examples. There's bound to be something that's pretty close to your use case (including software installs etc).