Getting Started with the Shell

Last updated on 2026-08-04 | Edit this page

Overview

Questions

  • “How do I install and open a shell on my computer?”
  • “What is a shell, and why should I use it instead of only a graphical interface?”
  • “How do I move around directories and inspect files from the command line?”
  • “How do I do common file and folder operations in Bash?”
  • “How can I get help when I do not remember a command?”

Objectives

  • “Install a shell (Bash or equivalent) and open a terminal on your operating system.”
  • “Explain what a shell is and why it is useful for scientific and data workflows.”
  • “Open a terminal and run simple commands safely.”
  • “Navigate the filesystem with pwd, ls, and cd.”
  • “Create, move, copy, rename, and remove files and directories with core shell commands.”
  • “Use tab completion and built-in help (--help, man) to discover command usage.”

Install and open a shell

If you do not already have shell software installed, follow the Carpentries installation instructions:

After installation, open a new terminal window.

  • Windows: open Git Bash, WSL terminal, or another Bash-compatible terminal.
  • macOS: open Terminal (Applications -> Utilities -> Terminal).
  • Linux: open your system Terminal application.

Once the terminal opens, type:

BASH 

cd

This returns you to your home directory and gives everyone a consistent starting point for the lesson.

If your terminal is already configured and opens correctly, you can continue directly to the next section.

Why use the shell?

Many scientific workflows rely on command-line tools, including remote systems, HPC environments, and cloud processing pipelines. The shell helps you:

  • Automate repetitive tasks.
  • Combine simple tools into larger workflows.
  • Work efficiently on local and remote machines.

In this course we use Bash, one of the most common Unix shells. A shell reads the commands you type, runs programs, and prints the output.

For prep work, think of the shell as a universal interface: even when tools differ across institutions, the basic command-line workflow is often the same. Learning this now makes later lessons smoother because you can focus on data concepts instead of terminal basics.

Opening a shell and running first commands

Open a terminal and try:

BASH 

echo "Hello World"
whoami
date

Each line is a command. You are always working from a current directory.

These first commands help learners build confidence:

  • echo prints text, so you can confirm command syntax quickly.
  • whoami shows your current user, which is useful on shared systems.
  • date confirms system time and demonstrates command output.

BASH 

pwd

pwd prints the path of your current directory. It is good practice to run pwd whenever you are unsure where a command will run.

List directory contents

BASH 

ls
ls -F
ls -l
ls -la
  • ls lists items in the current directory.
  • -F marks directory names with /.
  • -l shows a detailed list.
  • -a includes hidden files.

Together, these options help you answer two quick questions before changing anything: “Where am I?” and “What is here?”

Change directory

BASH 

cd some_directory
cd ..
cd
  • cd some_directory enters a directory.
  • cd .. moves one level up.
  • cd without arguments returns to your home directory.

A useful mental model is a tree of folders. cd moves your location in that tree, and every relative path depends on your current location.

Paths can be:

  • Absolute: start from /, such as /home/username/data.
  • Relative: start from your current location, such as data/file.txt.
Challenge

Exercise 1: Basic navigation

  1. Print your current directory.
  2. List all files, including hidden ones.
  3. Move into a directory of your choice.
  4. Move back up one level.
  5. Return to your home directory.

BASH 

pwd
ls -la
cd some_directory
cd ..
cd

Working with files and directories

In command-line workflows, file and directory operations are the foundation for reproducible analysis. Before running scripts or notebooks, you usually create a clean folder structure and move files into predictable locations.

Create directories and files

BASH 

mkdir my_project
cd my_project
touch file1.txt file2.txt
ls

mkdir creates a new directory. touch creates an empty file if it does not exist, and updates a timestamp if it does.

In the example above, we created a new directory called my_project, entered it, and created two empty text files. The output of ls confirms the files exist.

Copy, move, and rename

BASH 

cp file1.txt file1_copy.txt
mv file1_copy.txt renamed.txt
mv renamed.txt ../renamed.txt

Use the cp command to copy files (it will create a duplicate). Use the mv command to move or rename files.

If you try ls after the last command, you will see that renamed.txt is no longer in the current directory because it was moved to the parent directory.

Remove files and directories

BASH 

rm file2.txt
rm -r some_directory

The rm command removes files. With the -r option, it removes directories and their contents recursively.

Be careful with rm and especially rm -r, since removal is usually permanent. For beginners, a safe habit is to run ls before and after removal so you can verify exactly what changed.

Viewing and editing text files

Write text to files with echo, >, and >>

You can use echo together with redirection operators to create and update text files directly from the shell.

BASH 

echo "Sea surface temperature notes" > notes.txt
echo "Added a second line" >> notes.txt
cat notes.txt

How this works:

  • > writes output to a file (and overwrites the file if it already exists).
  • >> appends output to the end of a file (keeps existing content).

This pattern is very common in command-line workflows and is used again in the Git lesson when creating and updating tracked files.

View file contents with cat

Use cat to print a text file in the terminal:

BASH 

cat data1.txt
cat data1.txt data_main.txt

This is useful for quickly checking file contents. For very large files, tools like less are often more practical than cat, but cat is perfect for small text files:

BASH 

less data1.txt

Edit files with nano

nano is a simple terminal text editor:

BASH 

nano notes.txt

In nano, type your text, then:

  • Press Ctrl+O to save.
  • Press Enter to confirm the filename.
  • Press Ctrl+X to exit.

nano is a good starter editor because it shows keyboard shortcuts directly in the interface.

Challenge

Exercise 2: cat and nano basics

  1. Create a file called notes.txt using nano.
  2. Add two short lines of text and save the file.
  3. Display the file contents using cat.

BASH 

nano notes.txt
cat notes.txt
Challenge

Exercise 3: echo and redirection

  1. Create a file called log.txt with one line using echo and >.
  2. Add a second line using echo and >>.
  3. Display the final file content with cat.

BASH 

echo "First log line" > log.txt
echo "Second log line" >> log.txt
cat log.txt

Getting help and using tab completion

Use built-in help:

BASH 

ls --help
man ls

Use tab completion by typing part of a filename or directory name, then pressing Tab. This reduces typos and speeds up command entry.

When learning new commands, combine these habits:

  • Check options with --help.
  • Try commands in a small practice directory first.
  • Use tab completion to avoid path mistakes.
Challenge

Exercise 4: File operations practice

  1. Create a directory called shell_practice.
  2. Enter it and create data1.txt and data2.txt.
  3. Create a subdirectory called backup.
  4. Copy data1.txt into backup.
  5. Rename data2.txt to data_main.txt.
  6. List the contents of the main directory and backup.
  7. Remove data1.txt from the main directory.

BASH 

mkdir shell_practice
cd shell_practice
touch data1.txt data2.txt
mkdir backup
cp data1.txt backup/
mv data2.txt data_main.txt
ls
ls backup
rm data1.txt

Summary

This episode introduced the shell as a practical interface for navigating files, running programs, and performing common file operations. These skills are foundational for later lessons where we work with scripts, remote systems, and larger scientific datasets.

Key Points
  • “The shell is a powerful interface for scientific workflows and automation.”
  • “pwd, ls, and cd are core commands for navigation.”
  • “mkdir, touch, cp, mv, and rm cover most basic file operations.”
  • “echo with > and >> lets you create files and append text from the command line.”
  • “cat displays text file contents quickly in the terminal.”
  • “nano is a beginner-friendly terminal editor for creating and updating text files.”
  • “Use --help, man, and tab completion to work faster and more safely.”