Computational Techniques for Life Sciences

Create a New Repository on the Command Line

First, let’s create a new folder in our $HOME directory on Stampede2 to organize our work:

$ cd ~/
$ mkdir my_first_repo/
$ cd my_first_repo/       # currently empty

Then we will use a Git command to initialize this directory as a new Git repository - or a place where Git can start to organize versions of our files.

$ git init
Initialized empty Git repository in /home1/03439/wallen/my_first_repo/.git/

If we use ls -la, we can see that Git has created a hidden directory within my_first_repo called .git:

$ ls -a
./  ../  .git/

Use the tree command to get a clearer view of the contents of the .git/ directory:

$ tree .git/
.git/
├── branches
├── config
├── description
├── HEAD
├── hooks
│   ├── applypatch-msg.sample
│   ├── commit-msg.sample
│   ├── post-update.sample
│   ├── pre-applypatch.sample
│   ├── pre-commit.sample
│   ├── prepare-commit-msg.sample
│   ├── pre-push.sample
│   ├── pre-rebase.sample
│   └── update.sample
├── info
│   └── exclude
├── objects
│   ├── info
│   └── pack
└── refs
    ├── heads
    └── tags

9 directories, 13 files

Git uses this special sub-directory to store all the information about the project, including all files and sub-directories located within the project’s directory. If we ever delete the .git sub-directory, we will lose the project’s history.

We can check that everything is set up correctly by asking Git to tell us the status of our project:

$ git status
On branch master

Initial commit

nothing to commit (create/copy files and use "git add" to track)

If you are using a different version of git, the exact wording of the output might be slightly different.

Exercise

1. Explore the files and folders in the .git/ directory
2. Can you find a file with your name and e-mail in it? How did it get there?