Quick tutorial on GitHub

Here, we'll assume you're working on one of MSKCC's clusters - luna, saba2, hal, unagi, miso-dev, or dashi-dev. All these nodes have git installed, but not always the same version.

Let's start with setting up a decent ~/.gitconfig, at least to tell git who you are. Modify name and email below to your own, preferably using the email that you registered with, at: https://github.com/settings/emails

git config --global user.name "Cookie Monster"
git config --global user.email monsterc@mskcc.org

To enable color highlighting in git's command-line interface, run the following:

git config --global color.status auto
git config --global color.diff auto
git config --global color.branch auto
git config --global color.interactive auto

You can also tell git to use a different text editor when you type commit messages:

git config --global core.editor vim

Find a nice folder where you can clone a local version of the repository, ~/src for example. Then here is how you would clone the CMO documentation repository into ~/src/cmo-docs:

git clone https://github.com/mskcc/cmo.git ~/src/cmo-docs

When cloning a private repo, the command above asks for your GitHub username and password. It does this every time you interact with the remote repository. You can run the following to make git remember your credentials for 2 hours:

git config --global credential.helper cache
git config --global credential.helper 'cache --timeout=7200'

Let's get into the repo, and edit a file. Use your own github ID below, in place of cmonster:

cd ~/src/cmo-docs
echo cmonster >> github_ids.txt

Now use git status to see all the files/folders that have been added/modified/removed:

git status

You will definitely see github_ids.txt as modified. Now let's see how it differs from the repo's committed version:

git diff github_ids.txt

Let's add this to the list of changes we want to commit. When writing code, you'd only do this step after you've checked over your code for bugs and it seems to work fine:

git add github_ids.txt

Let's use git status again to see all the changes that we are ready to commit:

git status

Now we can commit to those changes with a short message summarizing them:

git commit -m "Added my UID to github_ids.txt"

The commit you made is only reflected in your local copy of the repository. This especially helps in large collaborative projects where your small change might break everyone else's work. When you're confident and ready to share all your commits, then push to Github:

git push

That's it! You may be asked to enter your Github credentials, but you don't have to define any URL or path, because all the necessary configuration is in the .git subfolder. Take a peek:

cat .git/config

That's a basic tutorial to get you started. Look for much more at https://git-scm.com/documentation