Git basics

Linus Torvalds ( is well known for creating the Linux operating system. Managing all the source code for Linux became onerous with existing systems, so he created "git" to do that, too. We'll learn enough git to get some things done.


Github is a for-profit business that provides git hosting services. They offer free accounts for individuals and groups. When you have completed an assignment, you will "push" it to Github. When assignments are due, I will "pull" your code down to check it. When you are done with class, you will have a public repository of code you can point to as evidence of your skills in both coding and source code management. So, the first step is that you create a Github account. Go do that.

Git commands

A binary called "git" should be installed on any HPC or Unix system you have. Git takes as its first argument a command. To see a list, enter git or git help. To see more information on a particular command such as "add," use git help add.

Create a repo

Using the Github web interface, create a new repository called "abe487." It's best to have the repo initialized with a "README." Copy the "Clone or Download" link and then on your machine (laptop/HPC), clone your repository and the "metagenomics-book" repo:

git clone <your repo>
[email protected]:kyclark/metagenomics-book.git
cp -r metagenomics-book/problems <your repo>

Notice that there is a subtle difference between these two commands:

  1. cp -r src dest
  2. cp -r src/ dest

The first one will copy the "src" directory and then its contents to "dest" while the second one will copy just the contents of "src" to "dest."

Committing your work

There are three git commands you must use to put your files into Github so that they can be seen by others:

  • add
  • commit
  • push

A basic workflow is:

$ echo hello > hello.txt
$ git add hello.txt
$ git commit -m 'added hello' !$
$ git push

The -m argument to commit is the commit message. If you don't specify a message, you will be dropped into your $EDITOR to type one.

If you cannot see your work the Github web interface, then I cannot check it out and grade it.

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