Lecture 2: Introduction to Bash

This lecture introduces you to the Unix command line (bash shell). You’ll learn how to navigate files and directories, manipulate files, and use powerful tools like pipes and pattern matching.

Note

This tutorial is based on The Carpentries “The Unix Shell” lesson, licensed CC-BY 4.0.

Section 1: Setup

Before we dive into bash commands, we need to set up our working environment using GitHub Codespaces.

Step 1: Create a GitHub Account

Note

Use your PSU email because GitHub provides a lot of functionality for free to educational users.

If you don’t already have one, go to github.com and create a free account.

Step 2: Create a New Repository

  1. Click the + icon in the top right corner and select New repository
  2. Name your repository bashing (or any other meaningful name you prefer)
  3. Select Public or Private based on your preference
  4. Check Add a README file
  5. Click Create repository

Step 3: Open a Codespace

GitHub Codespaces provides a complete VS Code environment in your browser:

  1. Go to your newly created repository
  2. Click the green Code button
  3. Select the Codespaces tab
  4. Click Create codespace on main

After a moment, you’ll have a full VS Code environment running in your browser!

Step 4: Open the Terminal

In VS Code (within Codespaces):

  1. Use the menu: Terminal → New Terminal
  2. Or use the keyboard shortcut: Ctrl+` (backtick)

A terminal panel will open at the bottom of the screen. This is where you’ll type bash commands.

Step 5: Verify Everything Works

Let’s test that everything is working. Type the following command and press Enter:

ls

You should see a list of files in your current directory (at minimum, a README.md file). If you see this output, you’re ready to go!

Try one more command:

pwd

This shows your current directory (pwd = “print working directory”). You should see something like /workspaces/bashing.

Section 2: Bash Basics

Background

Humans and computers commonly interact through a graphical user interface (GUI) - clicking icons and using menus. While intuitive, GUIs don’t scale well for repetitive tasks.

Imagine copying the third line from 1000 text files in 1000 directories into a single file. With a GUI, this would take hours of clicking. With the Unix shell, it takes seconds.

The Unix shell is both a command-line interface (CLI) and a scripting language. It allows you to automate repetitive tasks quickly and efficiently.

The Shell

The shell is a program where users type commands. The most popular Unix shell is Bash (Bourne Again SHell).

When you open a terminal, you see a prompt (usually ending in $ or >), indicating the shell is waiting for input:

$
Important

When typing commands from examples, do not type the $ - only type the commands that follow it.

Setup Test Data

Let’s download some test data to practice with:

cd ~
mkdir -p Desktop
cd Desktop
wget -c https://github.com/swcarpentry/shell-novice/raw/2929ba2cbb1bcb5ff0d1b4100c6e58b96e155fd1/data/shell-lesson-data.zip
unzip -u shell-lesson-data.zip

Now let’s explore this data.

Working with Files and Directories

mkdir - Make Directory

Create a new directory:

cd ~/Desktop/shell-lesson-data
mkdir thesis
ls -F

Create nested directories with -p:

mkdir -p project/data project/results
ls -FR project

Creating Files

Create an empty file with touch:

cd thesis
touch draft.txt
ls

Or use a text editor. In VS Code, you can: - Click File → New File - Or run code draft.txt to open in the editor

cp - Copy

Copy a file:

cd ~/Desktop/shell-lesson-data
cp notes.txt thesis/notes-backup.txt
ls thesis

Copy a directory (requires -r for recursive):

cp -r thesis thesis_backup
ls

mv - Move (or Rename)

Rename a file:

mv thesis/draft.txt thesis/quotes.txt
ls thesis

Move a file to a different directory:

mv thesis/quotes.txt .
ls

rm - Remove

WarningDeleting is Forever!

The shell doesn’t have a trash bin. Once deleted, files are gone permanently.

Remove a file:

rm quotes.txt
ls quotes.txt

Remove a directory (requires -r):

rm -r thesis_backup

Use -i for interactive confirmation:

rm -i notes.txt

Wildcards

Wildcards let you match multiple files:

Wildcard Matches
* Zero or more characters
? Exactly one character

Examples in molecules/ directory:

cd ~/Desktop/shell-lesson-data/molecules
ls *.pdb          # All .pdb files
ls p*.pdb         # Files starting with 'p'
ls ???ane.pdb     # Three characters + 'ane.pdb'

Section 3: More Bash

Now let’s explore more powerful features: pipes, filters, and searching.

Pipes and Filters

wc - Word Count

Count lines, words, and characters:

cd ~/Desktop/shell-lesson-data/molecules
wc cubane.pdb
wc -l *.pdb    # Lines only

Redirecting Output

Save output to a file with >:

wc -l *.pdb > lengths.txt
cat lengths.txt
Warning

> overwrites files! Use >> to append instead.

sort - Sort Lines

sort -n lengths.txt    # Numeric sort

head and tail

View the beginning or end of files:

head -n 3 lengths.txt    # First 3 lines
tail -n 2 lengths.txt    # Last 2 lines

The Pipe Operator |

Connect commands - output of one becomes input to the next:

wc -l *.pdb | sort -n
wc -l *.pdb | sort -n | head -n 1

This is the pipes and filters philosophy: small tools that do one thing well, combined together.

Redirects and pipes: wc outputs to shell, wc > file outputs to file, wc | sort | head builds a pipeline

cat - Concatenate

Display file contents:

cat lengths.txt

Combine multiple files:

cat file1.txt file2.txt > combined.txt

Finding Things

grep - Search File Contents

Find lines matching a pattern:

cd ~/Desktop/shell-lesson-data/writing
grep "not" haiku.txt

Useful options:

Option Description
-w Match whole words only
-n Show line numbers
-i Case insensitive
-r Search recursively in directories
-v Invert match (lines NOT matching)

Examples:

grep -n "the" haiku.txt
grep -w "The" haiku.txt
grep -i "the" haiku.txt
grep -r "Yesterday" .

find - Search for Files

The find command searches for files by name or properties. Consider this directory structure:

A file tree showing writing directory with subdirectories data, thesis, tools and files

Find files by name or properties:

find . -type f              # All files
find . -type d              # All directories
find . -name "*.txt"        # Files ending in .txt

Combining find and grep

Find files, then search within them:

grep "FE" $(find .. -name "*.pdb")

The $() runs the command inside and substitutes its output.

Section 4: Wrap Up

Committing Your Work

You’ve created files and directories in your Codespace. Let’s save this work to GitHub using VS Code’s built-in Git support.

Step 1: Open Source Control

Click the Source Control icon in the left sidebar (or press Ctrl+Shift+G).

Step 2: Stage Changes

You’ll see a list of changed files. Click the + icon next to each file to stage it, or click + next to “Changes” to stage all.

Step 3: Write a Commit Message

In the message box at the top, type a brief description of your changes:

Add shell lesson practice files

Step 4: Commit

Click the checkmark icon (or press Ctrl+Enter) to commit your changes.

Step 5: Push to GitHub

Click Sync Changes to push your commits to GitHub. Your work is now saved!

Summary

You’ve learned:

  • Navigation: pwd, ls, cd
  • File operations: mkdir, touch, cp, mv, rm
  • Viewing files: cat, head, tail
  • Redirection: >, >>, |
  • Processing: wc, sort, grep, find
  • Version control: Committing with VS Code

These commands form the foundation for working efficiently on the command line. The more you practice, the more natural they become!

Key Points

  • The shell reads commands and runs programs
  • pwd, ls, and cd navigate the file system
  • cp, mv, and rm manage files and directories
  • * and ? are wildcards that match filenames
  • | pipes connect commands together
  • grep finds patterns in files; find finds files by name