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OmyxLab OmyxLab Bioinformatic Fridays

Lesson 3 — Pushing to GitHub

Learning Objectives

Section titled “Learning Objectives”
  • Create a new repository on GitHub through the web interface.
  • Connect a local repository to a GitHub remote with git remote add.
  • Upload commits to GitHub with git push.
  • Download updates from GitHub with git pull.
  • Clone an existing GitHub repository with git clone.
  • Understand the difference between origin, main, and HEAD.

Conceptual Overview

Section titled “Conceptual Overview”

What is a remote?

Section titled “What is a remote?”

A remote is a version of your repository that lives somewhere else — in this case, on GitHub’s servers. You can have several remotes, but the most common one is called origin by convention. When you push, you are sending your local commits to the remote. When you pull, you are fetching commits from the remote and merging them into your local branch.

The push/pull cycle

Section titled “The push/pull cycle”
Local machine                   GitHub (origin)
─────────────                   ───────────────
edit files
git add
git commit   ──── git push ──►  repository
             ◄─── git pull ───  (updated by a collaborator)

HTTPS vs SSH

Section titled “HTTPS vs SSH”

GitHub supports two ways to authenticate when pushing:

  • HTTPS — you use your GitHub username and a Personal Access Token (PAT) as the password.
  • SSH — you use the SSH key you set up in Lesson 1. No password needed after setup.

This module uses SSH throughout because it is more convenient once configured.

Worked Examples

Section titled “Worked Examples”

1) Create a repository on GitHub

Section titled “1) Create a repository on GitHub”
  1. Go to https://github.com/new in your browser.
  2. Fill in the fields:
    • Repository name: my_analysis (match the folder name from Lesson 2)
    • Description: Bioinformatics analysis scripts and notes
    • Visibility: Public (or Private — both work the same way)
    • Do NOT tick “Add a README file”, “Add .gitignore”, or “Choose a license” — you already have these locally.
  3. Click Create repository.

GitHub will show a page titled “Quick setup”. Leave this page open — you will need the SSH URL in the next step.

2) Copy the SSH remote URL

Section titled “2) Copy the SSH remote URL”

On the “Quick setup” page, make sure SSH is selected (not HTTPS). The URL looks like:

git@github.com:YourUsername/my_analysis.git

Copy this URL.

3) Add the remote to your local repository

Section titled “3) Add the remote to your local repository”

Go back to your terminal and navigate to your project:

Terminal window
cd ~/projects/my_analysis

Add the remote. origin is the name you give to this remote — it is a universal convention:

Terminal window
git remote add origin git@github.com:YourUsername/my_analysis.git

No output is expected when this command succeeds.

Verify it was added:

Terminal window
git remote -v

Output:

origin  git@github.com:YourUsername/my_analysis.git (fetch)
origin  git@github.com:YourUsername/my_analysis.git (push)

Two lines appear: one for fetching (downloading) and one for pushing (uploading). Both point to the same URL.

4) Push your commits to GitHub

Section titled “4) Push your commits to GitHub”

git push -u origin main uploads your local main branch to the remote named origin. The -u flag links the local branch to the remote branch — after this first push you only need to type git push in future.

Terminal window
git push -u origin main

Output:

Enumerating objects: 14, done.
Counting objects: 100% (14/14), done.
Delta compression using up to 8 threads
Compressing objects: 100% (10/10), done.
Writing objects: 100% (14/14), 1.23 KiB | 1.23 MiB/s, done.
Total 14 (delta 2), reused 0 (delta 0), pack-reused 0
remote: Resolving deltas: 100% (2/2), done.
To git@github.com:YourUsername/my_analysis.git
 * [new branch]      main -> main
branch 'main' set up to track 'origin/main'.

Go to https://github.com/YourUsername/my_analysis in your browser. Your files are now online.

5) Make a change locally and push it

Section titled “5) Make a change locally and push it”

Edit notes.md:

Terminal window
nano notes.md

Add a new line at the bottom:

- Pushed repository to GitHub successfully

Save and exit. Stage, commit, and push:

Terminal window
git add notes.md
git commit -m "Note successful GitHub push"
git push

Output:

Enumerating objects: 5, done.
Counting objects: 100% (5/5), done.
Delta compression using up to 8 threads
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 320 bytes | 320.00 KiB/s, done.
Total 3 (delta 1), reused 0 (delta 0), pack-reused 0
To git@github.com:YourUsername/my_analysis.git
   f4a52b1..8e12ab3  main -> main

Refresh the GitHub page for your repository. The commit message appears in the file list.

6) View commits on GitHub

Section titled “6) View commits on GitHub”

On your repository page, click the clock icon that shows the number of commits (e.g. “7 commits”) near the top right of the file list. GitHub shows the full commit history with messages, authors, and timestamps — the same information as git log.

7) Edit a file directly on GitHub

Section titled “7) Edit a file directly on GitHub”

GitHub allows you to edit files in the browser. This is useful for small changes like fixing a typo in a README.

  1. Go to your repository page on GitHub.
  2. Click on README.md.
  3. Click the pencil icon (Edit this file) in the top right.
  4. Add a line at the bottom: Maintained by: Your Name
  5. Scroll down to the “Commit changes” section.
  6. Enter the message: Add maintainer name to README
  7. Click Commit changes.

The change now exists on GitHub but not yet on your local machine.

8) Pull the change to your local machine

Section titled “8) Pull the change to your local machine”

git pull fetches the latest commits from the remote and merges them into your current branch.

Terminal window
git pull

Output:

remote: Enumerating objects: 5, done.
remote: Counting objects: 100% (5/5), done.
remote: Compressing objects: 100% (3/3), done.
Unpacking objects: 100% (3/3), done.
From github.com:YourUsername/my_analysis
   8e12ab3..9f23bc4  main       -> origin/main
Updating 8e12ab3..9f23bc4
Fast-forward
 README.md | 1 +
 1 file changed, 1 insertion(+)

Confirm the change is now in your local file:

Terminal window
tail -n 3 README.md

Output:

Samples: SRR1553607, SRR1553608, SRR1553609
Maintained by: Your Name

9) Clone an existing repository

Section titled “9) Clone an existing repository”

git clone downloads a complete copy of a remote repository (all files and full history) to your local machine. This is how you start working on a repository that already exists on GitHub — for example, a collaborator’s project or a public tool.

Clone the Bioinformatic Fridays repository as an example (read-only, no login needed):

Terminal window
cd ~
git clone git@github.com:wave-cu/Bioinformatic_Fridays.git

Output:

Cloning into 'Bioinformatic_Fridays'...
remote: Enumerating objects: 45, done.
remote: Counting objects: 100% (45/45), done.
remote: Compressing objects: 100% (38/38), done.
Receiving objects: 100% (45/45), 25.14 KiB | 1.40 MiB/s, done.

Explore the cloned repository:

Terminal window
ls Bioinformatic_Fridays

Output:

Module_1_Linux  Module_2_Conda  Module_3_Omics  Module_4_Recap_Exercises  Module_5_Project  Module_6_Problem_Solving  Module_7_Bash_Scripting  README.md

The entire repository, including all history, is now on your machine.

10) Understand git status after a push

Section titled “10) Understand git status after a push”

After pushing, your working directory and remote are in sync. Run:

Terminal window
cd ~/projects/my_analysis
git status

Output:

On branch main
Your branch is up to date with 'origin/main'.


nothing to commit, working tree clean

“Your branch is up to date with ‘origin/main’” means your local branch matches what is on GitHub exactly.

Exercises

Section titled “Exercises”

  1. Go to https://github.com/YourUsername/my_analysis. Can you see all the files from Lesson 2? Click on run_fastqc.sh and read its contents.

  2. Create a new file called methods.md locally with a short description of your analysis approach. Stage, commit, and push it. Refresh GitHub to confirm it appears.

  3. Use the GitHub web editor to add a line to sample_list.txt (add SRR1553610). Then run git pull locally and confirm the new line is present.

  4. Run git log --oneline after pulling. How does the history compare to what you see on the GitHub commits page?

  5. Challenge: Clone any public GitHub repository you are curious about. Run git log --oneline inside it. How many commits does it have?

Solutions

Section titled “Solutions”

Solution 1

Section titled “Solution 1”

Go to https://github.com/YourUsername/my_analysis. Files listed: README.md, notes.md, sample_list.txt, run_fastqc.sh, environment.md, .gitignore.

Solution 2

Section titled “Solution 2”
Terminal window
cd ~/projects/my_analysis
nano methods.md

File content:

## Methods


1. Quality control with FastQC
2. Adapter trimming with Trimmomatic
3. Alignment to reference genome with BWA-MEM
4. Variant calling with GATK HaplotypeCaller
Terminal window
git add methods.md
git commit -m "Add analysis methods overview"
git push

Solution 3

Section titled “Solution 3”

On GitHub: navigate to sample_list.txt, click the pencil icon, add SRR1553610 on a new line, commit the change.

Back in the terminal:

Terminal window
git pull
cat sample_list.txt

Output:

SRR1553607
SRR1553608
SRR1553609
SRR1553610

Solution 4

Section titled “Solution 4”
Terminal window
git log --oneline

The list should match the commits shown on the GitHub commits page exactly, in the same order.

Solution 5

Section titled “Solution 5”
Terminal window
git clone git@github.com:wave-cu/Bioinformatic_Fridays.git ~/bfridays_clone
cd ~/bfridays_clone
git log --oneline | wc -l

The number printed is the total commit count.