Appion

The virtual environment is not needed after all for em_hole_finder on CentOS 7. Thanks to Jesper Lykkegaard Karlsen who wrote:

I installed em_hole_finder as described here:  https://github.com/hbradlow/em_hole_finder

After that I only needed to update a few python packages with pip:
pip install -U numpy
pip install -U scipy
Then I pointed the automasker.py required variable "HOLE_FIND_ACTIVATE" to a blank activate file. 

After that the automasker.py ran perfectly smooth. 

A more clean way of fixing this would of cause be to remove the requirement of the HOLE_FIND_ACTIVATE variable from automasker.py. But til the this little hack works fine.