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