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

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

2. Genesis - Yammer
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3. Why?
Surely everyone uses version control?
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4. Evolution of a self-taught programmer
“One file, no versions”
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5. Evolution of a self-taught programmer
“Versions as multiple files”
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6. Evolution of a self-taught programmer
Version Control!
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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
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8. Git
http://git-scm.com/
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9. Start with a good file hierarchy
and a good .gitignore file
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10. Initialize the repository
git init
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11. Add files
git add .
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12. Commit changes
git commit -a -m “Initial commit”
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13. That may be all you need
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14. Repositories
Redmine + Gitolite
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15. Cloning a remote repository
git clone gitolite@www.bioinformatics.csiro.au:malaria.git
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16. Pushing to a remote repository
git push origin master
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17. Updating from a remote repository
git fetch origin
git pull origin
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18. More advanced - all Git commands
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19. Github: social coding
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20. BioMed Central + Github
http://blogs.biomedcentral.com/bmcblog/2013/02/28/github-and-
biomed-central/
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