Thanks to excellent instructions in this paper and open source code, I was able to get PeptideBuilder examples running on my ubuntu machine. For me, I had to change the first line in runUnitTests.sh to

#!/bin/bash

Also, as noted in the paper, I needed the biopython library, which I obtained with pip:

pip install biopython # using sudo

The unit tests (so far) fail for me, for unknown reasons, but the evaluation.py code seems to produce structures that look good with PyMOL.

My question is a bit out there: I'm wondering if the authors or anyone else think it would be useful for me to post a link to a VirtualBox virtual machine that runs the code correctly (once I figure out the tweaks)? That way users could get around some of the quirks that arise from different linux installs and more quickly get to exploring and using PeptideBuilder? What do you think?