I recommend some text changes here for clarity. I suggest changing this line to the following:

By default the QIIME temporary directory is set to ``/tmp/`` which will work for most cases but it can cause issues in two scenarios. First, if your dataset is large there may not be enough space on the filesystem containing ``/tmp``, and second when you are running in a parallel environment that makes use of multiple AWS instances, for example: :ref:`using-qiime-with-starcluster-and-the-ipython-notebook`. In both cases you will need to set up your ``tmp_dir`` variable within your ``qiime_config`` file to a different directory.