Package cue to make it installable

[pontushojer]

Hi!

Thanks for developing this exciting tool!

I have been testing Cue and made some edits to make it a bit easier to use.

This PR makes Cue into a proper python package, making it installable. Now one can simply run this in you working directory to call SVs:

call.py --data_config data.yml --model_config model.yml 

This also make it possible to build cue and publish it on PyPi to make it even more accessible.

Hope you find this useful!

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PS. I also run into an issue where matplotlib tried to generate images using the interactive backend which did not work for me as I was running on a server. Therefor I have added the following in some python files.

import matplotlib
matplotlib.use('Agg')