Actually, we're not assuming that they're running this on EC2, which means that some additional instructions would be required to make sure the files are where you'd now be expecting them. Minimizing steps that need to be taken for setup was the motivation for including that download here. I think I would prefer leaving that in place to make this easy (especially as it's usually people's first introduction to QIIME. What would you think adding the download back in, but saying in a new cell above it *If you already have a local copy of the Greengenes database, you can point to it as follows and not re-download.*