Version Control in Bioinformatics: Our Experience Using Git

Version Control in BioinformaticsOur Experience Using Git

Neil Saunders

MATHEMATICS, INFORMATICS AND STATISTICSwww.csiro.au

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Genesis - Yammer

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Why?

Surely everyone uses version control?

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Evolution of a self-taught programmer

“One file, no versions”

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Evolution of a self-taught programmer

“Versions as multiple files”

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Evolution of a self-taught programmer

Version Control!

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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

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Git

http://git-scm.com/

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Start with a good file hierarchy

and a good .gitignore file

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Initialize the repository

git init

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Add files

git add .

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Commit changes

git commit -a -m “Initial commit”

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That may be all you need

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Repositories

Redmine + Gitolite

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Cloning a remote repository

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

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Pushing to a remote repository

git push origin master

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Updating from a remote repository

git fetch origingit pull origin

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More advanced - all Git commands

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Github: social coding

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BioMed Central + Github

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