Command Line Basics

If you have never used a command line before, don't worry — this section covers everything you need to know to get started. The command line is simply a text-based way of interacting with a computer. Instead of clicking on icons, you type commands. It may feel unfamiliar at first, but you will quickly find that it is a powerful and efficient way to work.

If you want to go deeper after this workshop, UF Research Computing has a more comprehensive Linux tutorial at https://github.com/UFResearchComputing/Linux_training.

Opening a Terminal

Mac: Open the Terminal app by going to Applications → Utilities → Terminal, or search for "Terminal" in Spotlight (Cmd+Space).

Windows: We recommend installing Git Bash or MobaXTerm which gives you a Linux-style terminal on Windows. Once installed, open it from the Start menu. Alternatively, Windows 10 and 11 have a built-in Linux terminal called WSL (Windows Subsystem for Linux) which you can enable through the Microsoft Store.

Once your terminal is open, you will see a command prompt that looks something like this:

username@computer:~$

This tells you your username, the name of the computer you are on, and your current directory (~ is shorthand for your home directory). You type commands after the $ and press Enter to run them.

Navigating the Filesystem

First, make sure you are in your home directory. Everyone's will look different, but ~ is a universal shorthand that always means "your home directory" no matter what system you are on:

cd ~
pwd

Your output will look something like /home/username on Linux, /Users/username on Mac, or something similar on Windows. That's expected — everyone's will be different.

ls — list files

ls lists the files and directories in your current directory. Your home directory may have some files already — that's fine:

ls

The -l flag gives you a long format with permissions, size, and date. Adding h makes file sizes human-readable (KB, MB, GB). Adding a includes hidden files that start with a dot:

ls -l

ls -lh

ls -la

cd — change directory

cd moves you into a different directory. cd .. goes up one level, cd ~ always takes you back to your home directory, and cd - takes you back to wherever you just were:

cd ..

cd ~

cd -

Setting Up a Practice Directory

Before we go further, let's create a dedicated space to practice in so we don't clutter your home directory.

mkdir — make directory

cd ~
mkdir command_line_practice
cd command_line_practice
pwd

Your path will look different, but you should see command_line_practice at the end.

Now let's create some subdirectories. The -p flag lets you create nested directories all at once:

mkdir notes
mkdir -p data/raw
ls

data notes

Creating Files

cat with redirection — quick file creation

The quickest way to create a small file is to use a heredoc — the << 'EOF' syntax tells the shell to treat everything that follows as file content until it sees EOF on a line by itself, making it safe to copy and paste:

cat > notes/hello.txt << 'EOF'
Hello world, this is my first file.
I am learning the command line.
This is line three.
EOF

Let's create a second file:

cat > notes/genes.txt  << 'EOF'
TP53 is a tumor suppressor gene.
BRCA1 is associated with breast cancer risk.
EGFR is a common target in lung cancer therapy.
TP53 mutations are found in many cancer types.
EOF

See the files you created:

ls notes

nano — interactive text editor

nano is a simple text editor that runs in the terminal and is better for longer files. To open or create a file:

nano notes/myfile.txt

Type whatever you like, then use these commands to save and exit:

Action	Keys
Exit and Save	Ctrl+X then Y
Cut a line	Ctrl+K
Paste	Ctrl+U
Search	Ctrl+W

The bottom of the nano screen always shows available commands, so you don't need to memorize them.

Viewing File Contents

cat — print entire file

cat notes/hello.txt

Hello world, this is my first file.
I am learning the command line.
This is line three.

head and tail — print the beginning or end of a file

head prints the first 10 lines of a file by default, and tail prints the last 10. The -n flag lets you specify how many lines you want. head is particularly useful for quickly checking the format of large files without printing the whole thing:

head notes/genes.txt

head -n 2 notes/genes.txt

tail -n 2 notes/genes.txt

Managing Files and Directories

cp — copy

To copy a file, give cp the source and the destination. The -r flag copies a whole directory and everything inside it:

cp notes/hello.txt notes/hello_backup.txt
ls notes/

genes.txt hello.txt hello_backup.txt myfile.txt

cp -r notes data/
ls data/

notes raw

mv — move or rename

mv works for both moving a file to a new location and renaming it — it's the same operation:

mv notes/hello_backup.txt data/
mv notes/myfile.txt notes/myfile_renamed.txt
ls notes/

genes.txt hello.txt myfile_renamed.txt

rm — remove

rm notes/myfile_renamed.txt
ls notes/

genes.txt hello.txt

There is no trash bin on the command line

Deleted files are gone permanently. Always double-check before using rm -r.

Input/Output Redirection

By default, commands print their output to the screen. The > operator redirects that output into a file instead, creating it if it doesn't exist and overwriting it if it does. The >> operator appends to a file rather than overwriting it:

ls -lh notes/ > data/file_list.txt

ls -lh data/ >> data/file_list.txt

Let's check what ended up in the file:

cat data/file_list.txt

-rw-r--r-- 1 username group 142 Apr 8 10:00 genes.txt
-rw-r--r-- 1 username group 73 Apr 8 10:00 hello.txt
...

Saving output to a file is useful for keeping records of what a command produced, or for checking the output of long-running jobs later.

Pipes

Pipes (|) let you chain commands together, sending the output of one command as the input to the next:

cat notes/genes.txt | head -2

TP53 is a tumor suppressor gene.
BRCA1 is associated with breast cancer risk.

ls -lh notes/ | grep "genes"

-rw-r--r-- 1 username group 142 Apr 8 10:00 genes.txt

Searching with grep

grep — search for a pattern

grep searches for a pattern in a file and prints every line that matches. The -i flag makes the search case-insensitive, and -c counts the number of matching lines instead of printing them:

grep "TP53" notes/genes.txt

TP53 is a tumor suppressor gene.
TP53 mutations are found in many cancer types.

grep -i "brca" notes/genes.txt

grep -c "TP53" notes/genes.txt

2

Combined with pipes, grep is very powerful for filtering output:

cat notes/genes.txt | grep "cancer"

BRCA1 is associated with breast cancer risk.
EGFR is a common target in lung cancer therapy.
TP53 mutations are found in many cancer types.

Getting Help

Almost every command has a manual page you can access with man, and most also accept --help for a quick summary of options. When in doubt, these are your first resources before searching online:

man ls

type q to get out of the manual

Cleaning Up

Once you're done practicing, you can remove the whole practice directory.

Reminder

rm -r permanently deletes everything inside. Make sure you are in your home directory (cd ~) and are removing the right directory before running this.

cd ~
rm -r command_line_practice