To install gubbins it's recommended that you install it into a python virtual environment.

First follow the instruction to create a python VE here on this page (confirmed to work in python3 anaconda). Give it its own VE instance and activate it.

Then just run these conda installer commands to install it to your instance.

conda config --add channels r

conda config --add channels defaults

conda config --add channels conda-forge

conda config --add channels bioconda

conda install gubbins

To run gubbins you'll need to load your choice of anaconda and activate the vm you chose to install to in order to put gubbins in your path.

-- AdminUser - 20 Aug 2018