Version Control in BioinformaticsOur Experience Using GitNeil SaundersMATHEMATICS, INFORMATICS AND STATISTICSwww.csiro.au
Genesis - YammerVersion Control: Slide 2 of 21
Why?       Surely everyone uses version control?Version Control: Slide 3 of 21
Evolution of a self-taught programmer                                 “One file, no versions”Version Control: Slide 4 of 21
Evolution of a self-taught programmer                                 “Versions as multiple files”Version Control: Slide 5 ...
Evolution of a self-taught programmer                                 Version Control!Version Control: Slide 6 of 21
Choices       http://en.wikipedia.org/wiki/Comparison of revision control software         • lists 34 software packages   ...
Git                                 http://git-scm.com/Version Control: Slide 8 of 21
Start with a good file hierarchy                                 and a good .gitignore fileVersion Control: Slide 9 of 21
Initialize the repository                                  git initVersion Control: Slide 10 of 21
Add files                                  git add .Version Control: Slide 11 of 21
Commit changes                        git commit -a -m “Initial commit”Version Control: Slide 12 of 21
That may be all you needVersion Control: Slide 13 of 21
Repositories       Redmine + GitoliteVersion Control: Slide 14 of 21
Cloning a remote repository              git clone gitolite@www.bioinformatics.csiro.au:malaria.gitVersion Control: Slide ...
Pushing to a remote repository                                  git push origin masterVersion Control: Slide 16 of 21
Updating from a remote repository                                  git fetch origin                                  git p...
More advanced - all Git commandsVersion Control: Slide 18 of 21
Github: social codingVersion Control: Slide 19 of 21
BioMed Central + Github          http://blogs.biomedcentral.com/bmcblog/2013/02/28/github-and-                            ...
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Version control in bioinformatics - Neil Saunders

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Version control is an important aspect of reproducible bioinformatics research. However, it is still not employed as widely as we would like.
In this presentation I aim to:
(1) Provide a basic introduction to Git, a popular open-source distributed version control system
(2) Illustrate how we use Git to manage projects in the CMIS Bioinformatics & Biostatistics group

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Version control in bioinformatics - Neil Saunders

  1. 1. Version Control in BioinformaticsOur Experience Using GitNeil SaundersMATHEMATICS, INFORMATICS AND STATISTICSwww.csiro.au
  2. 2. Genesis - YammerVersion Control: Slide 2 of 21
  3. 3. Why? Surely everyone uses version control?Version Control: Slide 3 of 21
  4. 4. Evolution of a self-taught programmer “One file, no versions”Version Control: Slide 4 of 21
  5. 5. Evolution of a self-taught programmer “Versions as multiple files”Version Control: Slide 5 of 21
  6. 6. Evolution of a self-taught programmer Version Control!Version Control: Slide 6 of 21
  7. 7. Choices http://en.wikipedia.org/wiki/Comparison of revision control software • lists 34 software packages • of which 26 are “actively developed” • and 10 use the distributed repository modelVersion Control: Slide 7 of 21
  8. 8. Git http://git-scm.com/Version Control: Slide 8 of 21
  9. 9. Start with a good file hierarchy and a good .gitignore fileVersion Control: Slide 9 of 21
  10. 10. Initialize the repository git initVersion Control: Slide 10 of 21
  11. 11. Add files git add .Version Control: Slide 11 of 21
  12. 12. Commit changes git commit -a -m “Initial commit”Version Control: Slide 12 of 21
  13. 13. That may be all you needVersion Control: Slide 13 of 21
  14. 14. Repositories Redmine + GitoliteVersion Control: Slide 14 of 21
  15. 15. Cloning a remote repository git clone gitolite@www.bioinformatics.csiro.au:malaria.gitVersion Control: Slide 15 of 21
  16. 16. Pushing to a remote repository git push origin masterVersion Control: Slide 16 of 21
  17. 17. Updating from a remote repository git fetch origin git pull originVersion Control: Slide 17 of 21
  18. 18. More advanced - all Git commandsVersion Control: Slide 18 of 21
  19. 19. Github: social codingVersion Control: Slide 19 of 21
  20. 20. BioMed Central + Github http://blogs.biomedcentral.com/bmcblog/2013/02/28/github-and- biomed-central/Version Control: Slide 20 of 21

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