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.

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

By far, the most widely used modern version control system in the world today is Git. Git is a mature, actively maintained open source project originally developed in 2005 by Linus Torvalds, the famous creator of the Linux operating system kernel. A staggering number of software projects rely on Git for version control, including commercial projects as well as open source. Developers who have worked with Git are well represented in the pool of available software development talent and it works well on a wide range of operating systems and IDEs (Integrated Development Environments). https://www.atlassian.com/git/

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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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