Awhile back, I wrote a post about getting QIIME2 up and running with jupyterhub. I have never been able to get it running “out-of-the-box”. The issue that I am running into is that the
PATH variable used by the single user notebooks is not the path that jupyter hub uses and so when a call to an exernal package is made the package will not be found.
I realize this is not an issue with QIIME, but rather with jupyterhub, however given the potential use of jupyterhub for classes or workshops (or companies) I wanted to post this in case anyone else has run into a similar issue or has found a solution.
One workaround I have found is to update the path from inside of the notebook where QIIME is being run:
import os os.environ['PATH'] = '/home/jovyan/my-conda-envs/qiime2-2018.8/bin:' + os.environ['PATH']
I also posted an issue about this on jupyterhub