Version Control in BioinformaticsOur Experience Using Git

Neil Saunders

MATHEMATICS, INFORMATICS AND STATISTICSwww.csiro.au

Version Control: Slide 2 of 21

Genesis - Yammer

Version Control: Slide 3 of 21

Why?

Surely everyone uses version control?

Version Control: Slide 4 of 21

Evolution of a self-taught programmer

“One file, no versions”

Version Control: Slide 5 of 21

Evolution of a self-taught programmer

“Versions as multiple files”

Version Control: Slide 6 of 21

Evolution of a self-taught programmer

Version Control!

Version Control: Slide 7 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 8 of 21

Git

http://git-scm.com/

Version Control: Slide 9 of 21

Start with a good file hierarchy

and a good .gitignore file

Version Control: Slide 10 of 21

Initialize the repository

git init

Version Control: Slide 11 of 21

Add files

git add .

Version Control: Slide 12 of 21

Commit changes

git commit -a -m “Initial commit”

Version Control: Slide 13 of 21

That may be all you need

Version Control: Slide 14 of 21

Repositories

Redmine + Gitolite

Version Control: Slide 15 of 21

Cloning a remote repository

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

Version Control: Slide 16 of 21

Pushing to a remote repository

git push origin master

Version Control: Slide 17 of 21

Updating from a remote repository

git fetch origingit pull origin

Version Control: Slide 18 of 21

More advanced - all Git commands

Version Control: Slide 19 of 21

Github: social coding

Version Control: Slide 20 of 21

BioMed Central + Github

http://blogs.biomedcentral.com/bmcblog/2013/02/28/github-and-biomed-central/