Creating a Repository

Objectives

• Create a local Git repository.
• Describe the purpose of the .git directory.

Once Git is configured, we can start using it.

We're going to use the Genomic Variant Calling workshop as the basis for our repository

First, let's navigate into the directory for the lesson ~/obss_2023/intro-git and create a new directory vc_project there for our repository to live in:

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$ cd ~/obss_2023/intro-git
$ mkdir vc_project
$ cd vc_project

Then we tell Git to make vc_project a repository -- a place where Git can store versions of our files:

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$ git init

It is important to note that git init will create a repository that can include subdirectories and their files---there is no need to create separate repositories nested within the vc_project repository, whether subdirectories are present from the beginning or added later. Also, note that the creation of the vc_project directory and its initialization as a repository are completely separate processes.

If we use ls to show the directory's contents, it appears that nothing has changed:

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$ ls

But if we add the -a flag to show everything, we can see that Git has created a hidden directory within vc_project called .git:

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$ ls -a

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.   ..  .git

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

Next, we will change the default branch to be called main. This might be the default branch depending on your settings and version of git. See the setup episode for more information on this change.

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$ git checkout -b main

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Switched to a new branch 'main'

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

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$ git status

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On branch main

No commits yet

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.

Places to Create Git Repositories

Along with tracking information about variant calling (the project we have already created), We would also like to track information about ecoli. Lets creates an ecoli project inside our vc_project project with the following sequence of commands:

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$ cd ~/obss_2023/intro-git   # return to Desktop directory
$ cd vc_project     # go into vc_project directory, which is already a Git repository
$ ls -a          # ensure the .git subdirectory is still present in the vc_project directory
$ mkdir ecoli    # make a subdirectory vc_project/ecoli
$ cd ecoli       # go into ecoli subdirectory
$ git init       # make the ecoli subdirectory a Git repository
$ ls -a          # ensure the .git subdirectory is present indicating we have created a new Git repository

Is the git init command, run inside the ecoli subdirectory, required for tracking files stored in the ecoli subdirectory?

Solution

No. we do not need to make the ecoli subdirectory a Git repository because the vc_project repository can track any files, sub-directories, and subdirectory files under the vc_project directory. Thus, in order to track all information about moons, we only needed to add the ecoli subdirectory to the vc_project directory.

Additionally, Git repositories can interfere with each other if they are "nested": the outer repository will try to version-control the inner repository. Therefore, it's best to create each new Git repository in a separate directory. To be sure that there is no conflicting repository in the directory, check the output of git status. If it looks like the following, you are good to go to create a new repository as shown above:

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$ git status

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fatal: Not a git repository (or any of the parent directories): .git

Correcting git init Mistakes

A nested repository is redundant and may cause confusion down the road. We would like to remove the nested repository. How can we undo the last git init in the ecoli subdirectory?

Solution -- USE WITH CAUTION!

Background

Removing files from a Git repository needs to be done with caution. But we have not learned yet how to tell Git to track a particular file; we will learn this in the next episode. Files that are not tracked by Git can easily be removed like any other "ordinary" files with

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$ rm filename

Similarly a directory can be removed using rm -r dirname or rm -rf dirname. If the files or folder being removed in this fashion are tracked by Git, then their removal becomes another change that we will need to track, as we will see in the next episode.

Solution

Git keeps all of its files in the .git directory. To recover from this little mistake, we can just remove the .git folder in the ecoli subdirectory by running the following command from inside the vc_project directory:

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$ rm -rf ecoli/.git

But be careful! Running this command in the wrong directory will remove the entire Git history of a project you might want to keep. Therefore, always check your current directory using the command pwd.

keypoints

• git init initializes a repository.
• Git stores all of its repository data in the .git directory.