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Version Control with GitHub for Bioinformatics

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Course presentation that complements teaching via live coding. Inspired by the Software Carpentry Git Novice Lesson. Available online: http://swcarpentry.github.io/git-novice/.

Citation: Ahmadia, A., Allen, J., Bachant, P., Banaszkiewicz, P., Barmby, P., Bekolay, T., … Wilson, G. (2015, May). Software Carpentry: Version Control with Git. Zenodo. http://doi.org/10.5281/zenodo.23544.

Created for the Fall 2017 Center for Computational Biology and Bioinforamtics Short Course on Version Control for Bioinformatics with GitHub. http://ccbb.utexas.edu/

Slides available at: https://www.slideshare.net/raynamharris/version-control-with-github-for-bioinformatics

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Version Control with GitHub for Bioinformatics

  1. 1. Version Control with GitHub for Bioinformatics Rayna Harris May 17, 2017
  2. 2. https://xkcd.com/1597/
  3. 3. Introductions • Name and lab • One sentence about your research • Level of experience with version • Favorite breakfast food
  4. 4. Blischak et al. 2016. A Quick Introduction to Version Control with Git and GitHub. PLOS Comp Biol
  5. 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. 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. 7. Blischak et al. 2016. A Quick Introduction to Version Control with Git and GitHub. PLOS Comp Biol
  8. 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. 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. 10. http://b-maze.deviantart.com/art/Werewolf-vs-Dracula-124893530
  11. 11. Blischak et al. 2016. A Quick Introduction to Version Control with Git and GitHub. PLOS Comp Biol
  12. 12. GitHub Online Repositories • Go to github.com • Sign in to your account • Place your yellow sticky note on your computer when done
  13. 13. 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
  14. 14. Exercise Add collaborators. Accept collaboration invites. Navigate to each other’s online repos.
  15. 15. 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
  16. 16. http://starlogs.net/#tidyverse/ggplot2
  17. 17. 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
  18. 18. Brainstorm • How can we promote discoverability and usability? • How do we collaborate and attribute credit? • How do we balance sharing and privacy?
  19. 19. http://b-maze.deviantart.com/art/Werewolf-vs-Dracula-124893530
  20. 20. Blischak et al. 2016. A Quick Introduction to Version Control with Git and GitHub. PLOS Comp Biol
  21. 21. 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
  22. 22. Supported by the Software Carpentry Foundation and The Center Computational Biology and Bioinformatics and The
  23. 23. • 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

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