Add pip/python instructions

[creisle]

Summary

• Adds instructions for running the README steps without conda (basic pip/python virtualenv)
• Adds a setup.py file to avoid having to set the PYTHONPATH manually before each command
• Does some linting on the README file to add new lines and code types to fenced code blocks

PS. Not sure if you want contributions at this point but I did this for myself when I was trying out the baseline and thought it might be helpful. Feel free to decline if not.

Note: to actually publish this on pypi you'll probably want to change the top-level namespace rather than installing from the src directory since the sub-package names are pretty general.

If you are open to changes I have a second PR in-place I can add later which adds a snakemake file so users can run 1 command for all the README steps

[Raldir]

Hey Caralyn, your efforts are much appreciated! Since it does appear that having the repo and pypi is appreciated, I'll set it set-up and merge it with your PR.

[creisle]

ok sounds good! let me know if you need anything from my end. Happy to help :)

[Raldir]

The repository is on pypi now and your PR has been merged. Feel free to create a new PR with your snakemake.