Hi skru, glad my code is being (potentially) useful.
activate_this.py doesn't create a virtual env, it enables it from a script that wasn't invoked from within a virtualenv. That's the whole problem this thread is about: what to do when your code needs to run in a virtualenv, but you also want your code to run from a scheduled task. So yes, it's more like the equivalent of "workon VIRTUALENV".
CLONEDIR is the directory of the repository I cloned from GitHub. It's where the target script lives, and I also need to set sys.path to include it so that imports work.
As Harry said, you can certainly do this without subprocess. That just doesn't work so well for me, because I want to run a script from my package from GitHub, but I don't want to commit this hack to the GitHub repository because it is PythonAnywhere-specific.
Lastly, yes, you run this script from PythonAnywhere's scheduler. My scheduled task is simply "/home/ACCOUNT/vep.py ARG1 ARG2", and this works.