ReproPhylo is a reproducible phylogenetics pipeline. See http://hulluni-bioinformatics.github.io/ReproPhylo/.
This Vagrantfile creates a Ubuntu 14.04 LTS image with a working ReproPhylo installation.
Run the following to start the VM:
git clone https://github.com/gawbul/vagrant-reprophylo
cd vagrant-reprophylo
vagrant up
vagrant ssh
Once in the VM you can run ./notebook.sh to start the Jupyter notebook server.
This will be accessible through your web browser at https://localhost:8888/.
The default password for the notebook server is reprophylo.