This document outlines a lesson on using version control with GitHub for bioinformatics. It introduces version control and GitHub, provides exercises for students to practice creating and collaborating on repositories, including adding and committing files, pushing and pulling changes, resolving conflicts, and submitting pull requests. The lesson aims to help researchers promote sharing, collaboration and reproducibility in their work.

1. Version Control with
GitHub for Bioinformatics
Rayna Harris
May 17, 2017

2. https://xkcd.com/1597/

3. Introductions
• Name and lab
• One sentence about your research
• Level of experience with version
• Favorite breakfast food

4. Blischak et al. 2016. A Quick Introduction to Version
Control with Git and GitHub. PLOS Comp Biol

5. http://b-maze.deviantart.com/art/Werewolf-vs-
Dracula-124893530
https://www.google.com/url?
sa=i&rct=j&q=&esrc=s&source=images&cd=&ved=0ahUKEwi
88ueDz_DTAhWEwiYKHaxFC7kQjRwIBw&url=https%3A%2F
%2Fwww.emaze.com%2F%40ALCOWQTC
%2F&psig=AFQjCNHl82zan3FdlfbN79LEZcf9le53nA&ust=149
4893424177155
http://b-maze.deviantart.com/art/Werewolf-vs-Dracula-124893530

6. • cd Desktop
• mkdir Dracula-Planets
• cd Dracula-Planets
• cd Desktop
• mkdir Wolfman-Planets
• cd Wolfman-Planets
Wolfman
Dracula
http://b-maze.deviantart.com/art/Werewolf-vs-Dracula-124893530

7. Blischak et al. 2016. A Quick Introduction to Version
Control with Git and GitHub. PLOS Comp Biol

8. Exercise
• Create a new file about a planet
• Add the file.
• Commit the file with a message
• Update the file with some additional information
• View the difference between the files
• Add and commit the updated file.
• Place your yellow sticky note on your computer when done

9. Brainstorm
• What are some files or types of files you might want
your version control system to ignore?
• Note: Github has a strict strict 100 MB size limit

10. http://b-maze.deviantart.com/art/Werewolf-vs-Dracula-124893530

11. Blischak et al. 2016. A Quick Introduction to Version
Control with Git and GitHub. PLOS Comp Biol

12. GitHub Online Repositories
• Go to github.com
• Sign in to your account
• Place your yellow sticky note on your computer
when done

15. Exercise
• Create a new repository
• desktop directory name == online repository name
• i.e. either Wolfman-Planets or Dracula-Planets
• Add the remote origin
• Push from the local desktop master to the online
remote origin
• Place yellow sticky note on laptop

16. Exercise
Add collaborators. Accept collaboration invites.
Navigate to each other’s online repos.

18. Exercise
• Navigate back to your desktop
• Clone the your collaborators repo with
• Navigate into the cloned repo
• Create earth.txt
• Add, commit, and push earth.txt
• Place yellow sticky note on laptop

19. http://starlogs.net/#tidyverse/ggplot2

20. Exercise
• Navigate back to the directory you created earlier.
• View the git status.
• Pull your collaborator’s changes. View the git status.
• Create a README.md file.
• Add, commit, and push the README.md file
• Place yellow sticky note on laptop

21. Brainstorm
• How can we promote discoverability and usability?
• How do we collaborate and attribute credit?
• How do we balance sharing and privacy?

22. http://b-maze.deviantart.com/art/Werewolf-vs-Dracula-124893530

23. Blischak et al. 2016. A Quick Introduction to Version
Control with Git and GitHub. PLOS Comp Biol

26. Exercise
• Navigate to CCBBatUT/WolfmanDraculaCollaboration
• View the issues
• Create a new file for one planet
• Submit a pull request with a commit message and an
additional comment
• View the issues again
• Place yellow sticky note on laptop

27. Supported by the Software Carpentry Foundation and The
Center Computational Biology and Bioinformatics and The

28. • Lesson template: http://swcarpentry.github.io/git-novice/
• Lesson publication: https://zenodo.org/record/
57571#.WRjDs1KZN-U
• Related video of this lesson: https://www.youtube.com/watch?
v=hKFNPxxkbO0
• Blischak et al. 2016: http://journals.plos.org/ploscompbiol/
article?id=10.1371/journal.pcbi.1005412m
• Example repos: https://github.com/mkuzak/planets and https://
github.com/CCBBatUT/WolfmanDraculaCollaboration
• Images: https://xkcd.com/1597/ and http://b-
maze.deviantart.com/art/Werewolf-vs-Dracula-124893530