Version Control in Bioinformatics: Our Experience Using Git

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Basic intro to Git for bioinformaticians yet to employ version control. Presented at CSS/FOAM 2013, Melbourne, Australia.

Technology

Version Control in Bioinformatics
Our Experience Using Git
Neil Saunders

MATHEMATICS, INFORMATICS AND STATISTICS
www.csiro.au

Genesis - Yammer

Version 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 of 21

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
• of which 26 are “actively developed”
• and 10 use the distributed repository model

Version Control: Slide 7 of 21

Git

http://git-scm.com/

Version Control: Slide 8 of 21

Start with a good ﬁle hierarchy

and a good .gitignore ﬁle

Version Control: Slide 9 of 21

Initialize the repository

git init

Version 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 need

Version Control: Slide 13 of 21

Repositories

Redmine + Gitolite

Version Control: Slide 14 of 21

Cloning a remote repository

git clone gitolite@www.bioinformatics.csiro.au:malaria.git

Version Control: Slide 15 of 21

Pushing to a remote repository

git push origin master

Version Control: Slide 16 of 21

Updating from a remote repository

git fetch origin
git pull origin

Version Control: Slide 17 of 21

More advanced - all Git commands

Version Control: Slide 18 of 21

Github: social coding

Version Control: Slide 19 of 21

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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Version Control in Bioinformatics: Our Experience Using Git

1. Version Control in Bioinformatics Our Experience Using Git Neil Saunders MATHEMATICS, INFORMATICS AND STATISTICS www.csiro.au

2. Genesis - Yammer Version Control: Slide 2 of 21

3. Why? Surely everyone uses version control? Version Control: Slide 3 of 21

4. Evolution of a self-taught programmer “One ﬁle, no versions” Version Control: Slide 4 of 21

5. Evolution of a self-taught programmer “Versions as multiple ﬁles” Version Control: Slide 5 of 21

6. Evolution of a self-taught programmer Version Control! Version Control: Slide 6 of 21

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 model Version Control: Slide 7 of 21

8. Git http://git-scm.com/ Version Control: Slide 8 of 21

9. Start with a good ﬁle hierarchy and a good .gitignore ﬁle Version Control: Slide 9 of 21

10. Initialize the repository git init Version Control: Slide 10 of 21

11. Add ﬁles git add . Version Control: Slide 11 of 21

12. Commit changes git commit -a -m “Initial commit” Version Control: Slide 12 of 21

13. That may be all you need Version Control: Slide 13 of 21

14. Repositories Redmine + Gitolite Version Control: Slide 14 of 21

15. Cloning a remote repository git clone gitolite@www.bioinformatics.csiro.au:malaria.git Version Control: Slide 15 of 21

16. Pushing to a remote repository git push origin master Version Control: Slide 16 of 21

17. Updating from a remote repository git fetch origin git pull origin Version Control: Slide 17 of 21

18. More advanced - all Git commands Version Control: Slide 18 of 21

19. Github: social coding Version Control: Slide 19 of 21

20. BioMed Central + Github http://blogs.biomedcentral.com/bmcblog/2013/02/28/github-and- biomed-central/ Version Control: Slide 20 of 21

Version Control in Bioinformatics: Our Experience Using Git

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