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Version Control with GitHub for Bioinformatics
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.
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Version Control with GitHub for Bioinformatics
- 1. Version Control with GitHubfor Bioinformatics Rayna Harris May 17, 2017
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- 3. Introductions • Name andlab • 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
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- 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 anew 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 aresome files or types of files you might want your version control system to ignore? • Note: Github has a strict strict 100 MB size limit
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- 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 anew 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. Acceptcollaboration invites. Navigate to each other’s online repos.
- 18. Exercise • Navigate backto 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
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- 20. Exercise • Navigate backto 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 canwe promote discoverability and usability? • How do we collaborate and attribute credit? • How do we balance sharing and privacy?
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- 23. Blischak et al.2016. A Quick Introduction to Version Control with Git and GitHub. PLOS Comp Biol
- 26. Exercise • Navigate toCCBBatUT/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 theSoftware 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