Lesson 2 — Your First Repository

Learning Objectives

• Understand what a Git repository is and what the .git folder contains.
• Initialise a new repository with git init.
• Stage files with git add and understand the staging area.
• Record a snapshot with git commit and write a good commit message.
• Check repository status with git status and git log.
• Create a .gitignore file to exclude files Git should not track.

Conceptual Overview

What is a repository?

A Git repository (or “repo”) is a folder that Git is tracking. When you run git init inside a folder, Git creates a hidden subfolder called .git. That folder holds the entire history of every file in the project — every version you have ever committed. You should never edit files inside .git directly.

The three areas

Understanding these three areas is the key to understanding Git:

Area	What it is
Working directory	The files as they exist on your filesystem right now
Staging area (index)	A preparation zone — files you have marked as “ready to commit”
Repository (history)	The permanent record of all commits

The workflow is always the same:

1. Edit files in your working directory.
2. Stage the changes you want to record with git add.
3. Commit the staged changes with git commit.

What makes a good commit message?

A commit message should complete the sentence “If applied, this commit will…”

• Good: Add quality-control script for FASTQ files
• Good: Fix off-by-one error in read counter
• Too vague: update or fix or changes

Short messages (under 72 characters) are fine for most commits.

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Worked Examples

1) Create a project folder and initialise a repository

mkdir -p ~/projects/my_analysis
cd ~/projects/my_analysis
git init

Output:

Initialized empty Git repository in /home/youruser/projects/my_analysis/.git/

git init only needs to be run once per project. The .git folder is now present:

ls -a

Output:

.  ..  .git

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2) Create your first file

nano README.md

Type the following inside nano, then press Ctrl+O to save and Ctrl+X to exit:

# My Analysis

This repository contains scripts and notes for my bioinformatics project.

Confirm the file exists:

ls

Output:

README.md

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3) Check the repository status

git status tells you what Git sees in your working directory and staging area.

git status

Output:

On branch main

No commits yet

Untracked files:
  (use "git add <file>..." to include in what will be committed)
  README.md

nothing added to commit but untracked files present (use "git add" to track)

“Untracked files” means Git can see the file but is not recording changes to it yet.

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4) Stage the file

git add moves a file from the working directory into the staging area.

git add README.md

No output is expected when this command succeeds. Check the status again:

git status

Output:

On branch main

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)
  new file:   README.md

The file is now in the staging area — it is ready to be committed.

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5) Make your first commit

git commit -m records the staged changes with the message provided after -m.

git commit -m "Add project README"

Output:

[main (root-commit) a3f92c1] Add project README
 1 file changed, 3 insertions(+)
 create mode 100644 README.md

The hash (a3f92c1) will be different on your machine — it is unique to your commit.

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6) View commit history

git log lists all commits from newest to oldest.

git log

Output:

commit a3f92c1d4e5f678901234567890abcdef1234567 (HEAD -> main)
Author: Your Name <you@example.com>
Date:   Thu Jun 26 09:00:00 2025 +0000

    Add project README

git log --oneline gives a compact one-line-per-commit view. This is useful when the history is long.

git log --oneline

Output:

a3f92c1 (HEAD -> main) Add project README

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7) Make a second commit

Add a new file to practice the full workflow again:

nano notes.md

Type the following, then save and exit:

## Session notes

- Installed FastQC
- Downloaded SRR1553607 dataset

Stage and commit:

git add notes.md
git commit -m "Add session notes"

Output:

[main b7c10d2] Add session notes
 1 file changed, 4 insertions(+)
 create mode 100644 notes.md

View the updated history:

git log --oneline

Output:

b7c10d2 (HEAD -> main) Add session notes
a3f92c1 Add project README

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8) Stage multiple files at once

Create two more files:

nano sample_list.txt

Type the following, then save and exit:

SRR1553607
SRR1553608
SRR1553609

nano run_fastqc.sh

Type the following, then save and exit:

#!/usr/bin/env bash
# Run FastQC on all FASTQ files in the current directory
fastqc *.fastq -o fastqc_results/

Stage both files in one command:

git add sample_list.txt run_fastqc.sh

Check status:

git status

Output:

On branch main
Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
  new file:   run_fastqc.sh
  new file:   sample_list.txt

Commit:

git commit -m "Add sample list and FastQC script"

Output:

[main c1e20f3] Add sample list and FastQC script
 2 files changed, 5 insertions(+)
 create mode 100755 run_fastqc.sh
 create mode 100644 sample_list.txt

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9) Create a .gitignore file

A .gitignore file tells Git which files and folders to ignore completely. This is important for:

• Large data files that do not belong in a repository (.fastq, .bam, .vcf)
• Temporary files created by tools (*.log, *.tmp)
• System files (.DS_Store on macOS)

nano .gitignore

Type the following, then save and exit:

# Large sequencing data files
*.fastq
*.fastq.gz
*.bam
*.bam.bai
*.vcf
*.vcf.gz

# Tool output directories
fastqc_results/
trimmed/
aligned/

# Temporary and system files
*.log
*.tmp
.DS_Store
__pycache__/

Stage and commit the .gitignore:

git add .gitignore
git commit -m "Add .gitignore for sequencing data and temp files"

Output:

[main d2f31a4] Add .gitignore for sequencing data and temp files
 1 file changed, 15 insertions(+)
 create mode 100644 .gitignore

Test it — create a dummy FASTQ file and check whether Git ignores it:

touch test_sample.fastq
git status

Output:

On branch main
nothing to commit, working tree clean

Git does not list test_sample.fastq because .gitignore excludes *.fastq. Remove the test file:

rm test_sample.fastq

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10) See what changed in a file

Edit notes.md to add a line:

nano notes.md

Add a new line at the bottom:

- FastQC completed successfully on all samples

Save and exit. Now run git diff to see what changed before staging:

git diff notes.md

Output:

diff --git a/notes.md b/notes.md
index 3b4f2a1..e7c90d2 100644
--- a/notes.md
+++ b/notes.md
@@ -2,3 +2,4 @@

 - Installed FastQC
 - Downloaded SRR1553607 dataset
+- FastQC completed successfully on all samples

Lines starting with + are additions. Lines starting with - are deletions. Stage and commit the change:

git add notes.md
git commit -m "Update notes with FastQC results"

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Exercises

1. Run git log --oneline in ~/projects/my_analysis. How many commits do you have?

2. Create a new file called environment.md that lists the tools you have installed (at least two). Stage and commit it with an appropriate message.

3. Edit README.md to add a second line describing your project. Run git diff before staging to confirm the change is shown. Then stage and commit.

4. Add *.csv and *.tsv to your .gitignore. Create a dummy file called metadata.csv and verify with git status that Git ignores it. Then remove the dummy file.

5. Challenge: Run git log --oneline again. Your history should now have at least 6 commits. Write down what each commit does in your own words.

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Solutions

Solution 1

git log --oneline

Output (yours will show 4 commits from the worked examples):

d2f31a4 (HEAD -> main) Add .gitignore for sequencing data and temp files
c1e20f3 Add sample list and FastQC script
b7c10d2 Add session notes
a3f92c1 Add project README

Solution 2

nano environment.md

File content:

## Software environment

- FastQC 0.12.1
- Trimmomatic 0.39
- BWA 0.7.17

git add environment.md
git commit -m "Add software environment notes"

Solution 3

nano README.md

Add a second line, for example:

Samples: SRR1553607, SRR1553608, SRR1553609

git diff README.md

Output shows the new line with a + prefix.

git add README.md
git commit -m "Add sample list to README"

Solution 4

Open .gitignore and add two lines:

nano .gitignore

Add at the bottom:

*.csv
*.tsv

Save and exit.

touch metadata.csv
git status

Output:

On branch main
nothing to commit, working tree clean

metadata.csv does not appear. Remove it:

rm metadata.csv

Solution 5

git log --oneline

Output (6 or more commits depending on your exercises):

f4a52b1 (HEAD -> main) Add sample list to README
e3c41a0 Add software environment notes
d2f31a4 Add .gitignore for sequencing data and temp files
c1e20f3 Add sample list and FastQC script
b7c10d2 Add session notes
a3f92c1 Add project README