---
title: GitHub Introduction
linkTitle: "GitHub"
weight: 2
type: docs
---

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<br/>

## GitHub in GEN242 

+ Note, this class will make heavy use of GitHub 
+ Homework assignments will be submitted and graded on GitHub Classroom
+ Course projects will also use private GitHub repositories: one repository for each course project (shared among students of each project)
+ Each student will need a personal GitHub account. They can be created [here](https://github.com/personal).
+ GitHub provides an unlimited number of free public repositories to each user. Via GitHub Education students can sign up for an extended number of free private GitHub accounts (see [here](https://education.github.com)).
+ For beginners this [quick guide](https://guides.github.com/activities/hello-world/) may be useful

## What are Git and GitHub?

+ Git is a version control system similar to SVN
+ GitHub is an online social coding service based on Git 
+ Combined Git/GitHub: environment for version control and social coding

## Installing Git
+ [Install](http://git-scm.com/book/en/Getting-Started-Installing-Git) on Windows, OS X and Linux
+ When using it from RStudio, it needs to find the Git executable

## Git Basics from Command-Line

Also try [interactive git tutorial](https://try.github.io/levels/1/challenges/1).

+ Finding help from command-line 

    ```sh
    git <command> --help
    ```

+ Initialize a directory as a Git repository

    ```sh
    git init
    ```
	
+ Add specific files to Git repository (staging area) 

   ```sh
   git add myfile
   ```

+ Add all files recursively 

  To ignore specific files (_e.g._ temp files), list them in a `.gitignore` file in your repository's root directory. Regular expressions are supported. See [here](https://help.github.com/articles/ignoring-files/) for more details.

   ```sh
   git add -A :/
   ```

+ After editing file(s) in your repos, record a snapshot of the staging area 

   ```sh
   git commit -am "some edits"
   ```

## GitHub Basics from Command-Line

1. Generate a new remote repository on GitHub online or use [hub](https://hub.github.com/) or [GitHub CLI](https://github.com/cli/cli#installation) command-line wrappers for this. To avoid errors with the online method, do not
   initialize the new repository with README, license, or `.gitignore` files. You can
   add these files after your project has been pushed to GitHub. 

   ```sh
   git remote add origin git@github.com:<user_name>/<repos_name>.git
   ```

2. Push updates to remote. Next time one can just use `git push`

    ```sh
    git push 
    ```

3. Clone existing remote repository
    
    ```sh
    git clone git@github.com:<user_name>/<repos_name>.git
    ```

4. Before working on project, update local git repos 

    ```sh
    git pull 
    ```

5. Make changes and recommit local to remote 

    ```sh
    git commit -am "some edits"; git push 
    ```
   

### Important When Working with Private GitHub Repositories!

In order to work with _private GitHub repositories_, like the ones used in GEN242, users need to activate in their GitHub account under `Settings` as authentication method either a [Personal Access Token](https://bit.ly/3u8GRkT) or an [SSH Key](https://bit.ly/3KcWixN). 
The latter SSH Key method is usually preferred. To push to a private GitHub repository from the HPCC cluster, you need to generate an SSH Key from your home account on the HPCC cluster using
the standard Linux `ssh-keygen` method as described [here](https://hpcc.ucr.edu/manuals/access/login/#ssh-keys), and then upload the 
newly generated public SSH Key of your HPCC account located under `~/.ssh/id_rsa.pub` to GitHub. The same method can be used to
create an SSH Key on a personal computer and then upload the public key to GitHub. Usually, one should create a dedicated key
pair for each computer one uses and upload the corresponding public keys to GitHub. If you are new to SSH Keys, then please read this [short introduction](https://hpcc.ucr.edu/manuals/access/login/#ssh-keys). 

<center><img title="github_ssh_key" src="../images/SSH_Keys.drawio.png" width="600"><img/></center>
<b>Fig 1:</b> SSH Keys required to work with private GitHub repos from a local computer as well as a remote system like the HPCC Cluster. The figure also includes the SSH Key required for password-less login to the remote system (here HPCC cluster). For generating SSH keys, see <a href="https://hpcc.ucr.edu/manuals/access/login/#ssh-keys">here</a>.

<br></br>

## Exercise

Run the following git/github excercise from the command-line. Do this after creating a GitHub repos according to the instructions above or online as outlined [here](https://girke.bioinformatics.ucr.edu/GEN242/assignments/homework/hw01/hw01/#b-homework-submission-to-a-private-github-repository).

```sh 
git clone git@github.com:<user or org>/<repo name> 
cd <repo name>
git pull
touch test # Creates empty file for testing
git add test # or use '-A' for all
git commit -am "some edits"
git push 
##-> Edit test file online and then run `git pull` to inspect changes
```

## Online file upload

Useful for new users who want to upload their homework assignments to GitHub but are not familiar enough with the command-line yet.

1. Press `Add file` button on your repository, and then `Upload files`. 
2. Under the file path window add required subdirectory structure and a dummy file name (e.g. `Homework/HW1/dummy.txt`)
3. After this press `Upload files` and upload any file (e.g. homework) to the newly create directory. After this the initial dummy file can be deleted. The latter is necessary since empty directories are not visible on GitHub.


## Using GitHub from RStudio

Note: one can also set up SSH Keys from RStudio. How to do this is explained [here](https://happygitwithr.com/ssh-keys). 

+ After installing Git (see [here](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)), set path to Git executable in Rstudio: 
	+ Tools `>` Global Options `>` Git/SVN

+ If needed, log in to GitHub account and create repository. Use option `Initialize this repository with a README`. 

+ Clone repository by copying & pasting URL from repository into RStudio's 'Clone Git Repository' window: 
    + File `>` New Project `>` Version Control `>` Git `>` Provide URL

+ Now do some work (_e.g._ add an R script), commit and push changes as follows: 
    + Tools `>` Version Control `>` Commit

+ Check files in staging area and press `Commit Button`

+ To commit changes to GitHub, press `Push Button`

+ Shortcuts to automate above routines are [here](https://support.rstudio.com/hc/en-us/articles/200711853-Keyboard-Shortcuts)

+ To resolve password issues, follow instructions [here](https://github.com/jennybc/stat540_2014/blob/master/seminars/seminar92_git.md). 

## Viewing static HTML files on GitHub

Simple viewing of HTML files on GitHub can be enabled by making the following
changes to a public repos. Without these adjustments, one needs to download an
HTML file from GitHub in order to view the rendered content. An example GitHub
repos for showcasing this feature is
[here](https://github.com/tgirke/View_HTML_on_GitHub/tree/master).

+ Make sure your GitHub repos is public
+ Go to `Settings`
+ Select `Pages` in menu on left
+ Select `Deploy from a branch` under `Source`
+ Select a branch in the `GitHub Pages` section
+ Save the changes and wait until a URL is provided for your site. 
+ To test, upload an HTML file and append its paths to the URL provided in previous step.