Intro to Git

Obligitory XKCD

It's really pretty simple...

Git is a tool for snapshotting with some really powerful tools for navigating and combining those snapshots

Installation

Follow Instructions

Initial configuration

Some common configuration options here. At a bare minimum, make sure you set your name and email 

$ git config --global user.name "John Iacona"
$ git config --global user.email j.iacona@kew.org

Github

Repo exists on Github, you want it on your computer


$ git clone git@github.com:RBGKew/bioinfo-utils.git

Code exists on your computer, you want it on Github


$ git init
$ git remote add origin git@github.com:RBGKew/shiny-new-repository.git
$ git add .
$ git push -u origin master

File lifecycle

A file can exist in one of 4 states in git

  1. Untracked
  2. Modified
  3. Staged
  4. Committed
git status is your friend

Untracked

Create a new file for your bio and add it to git 

$ vim docs/people/john-iacona.md
$ git add docs/people/john-iacona.md

Modified

Add your bio and see what has changed 

$ vim docs/people/john-iacona.md
$ git diff

Staged

Once you are happy with your changes, add them to the staging area 

$ git add docs/people/john-iacona.md

Committed

Finally, make an official snapshot of all staged changes 

$ git commit -m "Super useful commit message"

Aside about commit messages

other obligatory xkcd...

Commit messages should document what you have done for others and your future-self

Think about what you've done


$ git log
If you are using my .gitconfig file, the following aliases can be useful. 

$ git lol
$ git lola

Push it (real good)

Remote

Another copy of a repo. origin is the most common 

$ git push -u origin HEAD

So fetch

If the remote repo has progressed beyond yours, you have to fetch changes and merge them with yours 

$ git fetch
$ git merge origin/master

fetch vs. pull

pull tries to fetch and merge in one step.


$ git pull

Resources

http://rbgkew.github.io/doc/git.html