Not sure where they are by default in the QIIME AMI but that is where they should go...

While we aren't assuming EC2 here, we do need a tutorial that we can use unmodified at workshops. The unpacking off the OTUs takes a significant amount of time (> 5min if I recall) and should be extraneous in most cases. What about indicating that this tutorial assumes a standard QIIME install including the Greengenes OTUs and call it good?