Linux Essentials

Why Learn Linux & The Command-Line Interface

Modern biological research is conducted primarily on Linux-based systems. Most research computing infrastructure, including the HPC clusters and cloud resources at TACC, runs Linux and supports software developed for Linux environments.

These systems are accessed through a command-line interface (CLI), a text-based interface where users type commands to interact directly with a computer. In research computing, the CLI is used to log into remote systems, manage files, and launch computational analyses.

../_images/welcome-to-CLI.jpeg

A simple echo command typed into a terminal window, demonstrating the command-line interface.

Learning how to use the Linux command line interface is therefore an essential skill for modern biologists. Once you are comfortable working in a Linux environment, you can work on virtually any research computing system in the world.

What You Will Learn

In this section, students will learn how to:

  • Describe basic functions of essential Linux commands

  • Use Linux commands to navigate a file system and manipulate files

  • Transfer data to / from a remote Linux file system

  • Edit files directly on a Linux system using a command line utility (vim)

Topics covered in this module include:

  • Creating and navigating folders (pwd, ls, mkdir, cd, rmdir)

  • Creating and manipulating files (touch, rm, mv, cp)

  • Looking at the contents of files (cat, less, head, tail, grep)

  • Network and file transfers (ssh, scp)

  • Text editing (vim)

Log in to the Class Server

All computing for this course will take place on Linux virtual machines (VMs). To reach them, you will connect in two steps:

  1. First, we’ll connect to student-login.tacc.utexas.edu. This is a persistent Linux VM at TACC that acts as a login gateway (jump host).

  2. Second, from student-login, you’ll connect to your own personal course VM. This VM is named mbs-337 and is hosted on JetStream2.

../_images/ssh-process.png

Controlled access architecture for Jetstream2 VMs.

To connect from your own computer, you will use the Secure Shell (SSH) protocol through a CLI or an SSH client. The exact steps depend slightly on your computer’s operating system.

Mac / Linux

MacOS and Linux machines both include a terminal application by default. To open a terminal on macOS:

  1. Press Command + Spacebar to open Spotlight search

  2. Type Terminal

  3. Press Enter

From the terminal, connect to the TACC login VM (replace username with your TACC username):

ssh username@student-login.tacc.utexas.edu
(enter password)
(enter MFA token)

Windows

Windows does not include a native Linux shell by default to run the SSH protocol. That’s okay – you just need to download an SSH client, which is a program that securely connects your computer to a remote Linux system. We recommend PuTTY (Choose the 64-bit x86 installer).

To connect:

Open the application 'PuTTY'
Enter Host Name: student-login.tacc.utexas.edu
(Click 'Open')
(Enter username)
(Enter password)
(Enter MFA token)

Chromebook

Chromebooks can run a Linux shell using ChromeOS’s built-in Linux support:

  1. Open Settings

  2. Go to Advanced -> Developers

  3. Enable Linux development environment

Once enabled, you can open the Terminal app from your launcher and connect using SSH:

ssh username@student-login.tacc.utexas.edu
(enter password)
(enter MFA token)

Confirming Your Login

You have successfully connected to student-login when you see a message similar to this:

------------------------------------------------------------------------------
------------------------------------------------------------------------------
Welcome to the Texas Advanced Computing Center
   at The University of Texas at Austin

** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/

TACC Support:
https://portal.tacc.utexas.edu/tacc-consulting

------------------------------------------------------------------------------
kbeavers@student-login:~$

Once you are connected to student-login, the next step is the same for everyone regardless of the operating system of your computer (since we are now all on the same Linux login host).

From the student-login prompt, type:

ssh mbs-337

You won’t need to provide a username or password this time, since your credentials are automatically forwarded from the login VM.

If the connection is successful, you will see Jetstream2 status information similar to the following:

══════════════════════════https://jetstream.status.io/══════════════════════════

Overall Jetstream2 Status:   Operational

Active Status Items:
◦   Scarce availability of g3.xl resources

Scheduled Maintenance:
◦   (2026-01-02T12:00:00.000Z - 2026-01-03T00:00:00.000Z) Upcoming maintenance outage on January 2, 2026

════════════════════════════════════════════════════════════════════════════════

At this point, you are successfully logged in to your personal Linux VM for the course and ready to begin working!

Creating and Navigating Folders

On most personal computers, your location is shown visually using a graphical interface. For example, you might use your mouse to navigate to your Desktop or open files inside your Documents folder.

In a Linux CLI, there is no visual file browser. Instead, you interact with the system by typing commands that ask the computer where you are and what files exist.

Tip

The text you see before your cursor is called the command prompt, and it provides useful information about your current session:

ubuntu@mbs-337:~$

  • ubuntu = who you are logged in as (this is the default user account on Ubuntu VMs)

  • mbs-337 = the system you are connected to

  • ~ = your current location (more on this later)

You type commands after the $ symbol

Where Am I?

To print your current location in the filesystem, use pwd (print working directory). In Linux, the terms “directory” and “folder” mean the same thing, and we’ll use them interchangeably:

$ pwd
/home/ubuntu

This is your home directory. This is where you start when you log in, and where your files and folders are stored.

What’s Here?

To see what files and folders exist in your current directory, use the ls (list) command:

$ ls

If nothing is printed, that simply means the directory is empty.

Creating Directories

Let’s create some directories using mkdir (make directory):

$ mkdir folder1
$ mkdir folder2
$ mkdir folder3

Let’s list the contents again:

$ ls
folder1 folder2 folder3

Moving Around

Now that we have some folders to work with, let’s navigate into one of them. To move into a directory, use cd (change directory). This is analogous to double-clicking a folder on Windows or Mac.

$ pwd
/home/ubuntu
$ cd folder1
$ pwd
/home/ubuntu/folder1

Now that we are inside folder1, make a few subdirectories:

$ mkdir subfolderA
$ mkdir subfolderB
$ mkdir subfolderC
$ ls
subfolderA subfolderB subfolderC

Navigate into subfolderA, then use ls to list the contents. What do you expect to see?

$ cd subfolderA
$ pwd
/home/ubuntu/folder1/subfolderA
$ ls

There is nothing there because we have not made any files or directories here yet.

Next, we will navigate back to the home directory. So far we have seen how to navigate “down” into folders, but how do we navigate back “up” to the parent folder? There are different ways to do this.

You can specify the full path, which is the “address” to a file or directory within the filesystem:

$ pwd
/home/ubuntu/folder1/subfolderA
$ cd /home/ubuntu/folder1
$ pwd
/home/ubuntu/folder1

Or, we could use the shortcut .., which refers to the parent directory (the directory immediately above the current one).

$ pwd
/home/ubuntu/folder1
$ cd ..
$ pwd
/home/ubuntu

Tip

From anywhere on the system, you can return to your home directory using ~ (remember our command prompt from earlier?) or simply cd with no arguments.

$ cd ~
$ pwd
/home/ubuntu
$ cd folder1
$ pwd
/home/ubuntu/folder1
$ cd
/home/ubuntu

Removing Directories

Now let’s look at how to remove directories.

The command rmdir (remove directory) can be used to delete a directory only if it is empty:

$ mkdir junkfolder
$ ls
folder1 folder2 folder3 junkfolder
$ rmdir junkfolder
$ ls
folder1 folder2 folder3

Removing Non-Empty Directories

Let’s remove the other directories that we made. To remove a directory and everything inside it, use rm -r

  • rm means remove

  • -r means recursive (delete everything inside, all the way down)

Warning

rm -r permanently deletes files and directories. There is no recycle bin on Linux systems, so use this command very carefully!

Let’s remove folder1 and all of its contents:

$ rm -r folder1
$ ls
folder2 folder3

Question

Which command should we use to remove folder2 and folder3?

Creating and Manipulating Files

So far, we’ve learned how to navigate the filesystem and perform operations with directories. But what about files? Just like on Windows or MacOS, Linux allows you to create, move, copy, rename, and delete files with the CLI.

Creating and Removing Files

First, let’s make sure we are in our home directory and create a few directories and files.

We’ll use the touch command to create an empty file:

$ cd     # cd on an empty line will automatically take you back to the home directory
$ pwd
/home/ubuntu
$ mkdir folder1
$ mkdir folder2
$ mkdir folder3
$ touch file_a
$ touch file_b
$ touch file_c
$ ls
file_a  file_b  file_c  folder1  folder2  folder3

These files we have created are all empty. Removing a file is done with the rm (remove) command.

$ touch junkfile
$ rm junkfile

Moving and Copying Files

Files are moved or renamed using mv and copied using cp. These commands work similarly to how you would expect on a Windows or Mac computer — the context around the move or copy operation determines what the result will be. In other words, mv and cp work on paths.

To demonstrate this, let’s move file_a into folder1 and file_b into folder2. We’ll also copy file_c into folder3.

$ mv file_a folder1/
$ mv file_b folder2/
$ cp file_c folder3/

Question

Take a moment to predict what the command ls would print if we used it in our current directory.

$ ls
file_c folder1  folder2  folder3
$ ls folder1
file_a
$ ls folder2
file_b
$ ls folder3
file_c

Two files have been moved into folders, and file_c has been copied - so there is still a copy of file_c in the home directory.

Move and copy commands can also be used to change the name of a file:

$ cp file_c file_c_copy
$ mv file_c file_c_new_name

Tip

By now, you may have discovered that Linux is very unforgiving of typos. Three habits will save you a lot of frustration:

  • Press <Tab> to auto-complete file and directory names

  • Use <UpArrow> to cycle through previous commands

  • Avoid spaces and special characters in file names. Stick to:

A-Z   # capital letters
a-z   # lowercase letters
0-9   # digits
-     # hyphen
_     # underscore
.     # period

Before we move on, let’s clean up once again by removing the files and folders we just created.

$ rm -r folder1
$ rm -r folder2
$ rm -r folder3

How do we remove file_c_copy and file_c_new_name?

$ rm file_c_copy
$ rm file_c_new_name

Looking at the Contents of Files

So far, we’ve been working with empty files and folders. Real research data, of course, is not empty. Let’s start exploring the contents of actual files using more Linux commands.

First, make sure you are in your home directory and copy a public file from the system into your own workspace.

$ cd ~
$ pwd
/home/ubuntu
$ cp /usr/share/dict/words .
$ ls
words

Try to use <Tab> to autocomplete the name of the file. Also, please notice the single dot . at the end of the copy command, which indicates that you want to copy the file to your current location (the home directory).

The words file is a standard dictionary file found on many Linux systems. It contains 479,828 words, each on its own line. To print the entire contents of the file to the screen, use cat.

$ cat words
A
AA
AAA
AA's
AB
ABC
ABC's
ABCs
ABM
ABM's
...

This is a long file! Printing everything to the screen is not very useful. Instead, we can view files one screen at a time with the less command:

$ less words

Scrolling through the data is the same, but now we can also search the data. Press the / forward slash key, and type a word that you would like to search for. The screen will jump down to the first match of that word. The n key will cycle through other matches, if they exist. You can exit this view by pressing the q key.

Finally, you can view just the beginning or the end of a file with the head and tail commands. For example:

$ head words
$ tail words

By default, these commands show 10 lines, which is often enough for a quick check.

Redirecting Output to Files

Up to this point, all command output has gone to the screen. Linux allows you to redirect this output into files instead.

Use > to redirect the output of a command to a new file:

$ cat words > words_new.txt
$ head words > first_10_lines.txt

A single greater than sign > will redirect and overwrite any contents in the target file. A double greater than sign >> will redirect and append any output to the end of the target file.

Question

What would happen if I ran the following?

$ tail words >> first_10_lines.txt

What about this?

$ tail words > words_new.txt

Be careful with these redirect commands – it is easy to accidentally overwrite or change the contents of files without meaning to!

Searching Files with Grep

Another essential tool is the grep command, which searches a file for a specific pattern, and returns all lines that match the pattern. For example:

$ grep "banana" words
banana
banana's
bananas

Quotes around the search term are not always required, but they are a good habit — especially when searching for patterns that include spaces or special characters.

Network and File Transfers

In biological research, you’ll often need to transfer files between your local computer and remote computing systems. HPC systems like your course VM have computational resources and specialized software that aren’t available on typical personal computers. File transfer allows you to leverage the strengths of both systems by moving data and results between them as needed.

To log in or transfer files to a remote Linux file system you must know the hostname (the unique network identifier of the computer you are connecting to) and the username (who you are). If you are already on a Linux file system, those are easy to determine using the following commands:

$ whoami
ubuntu
$ hostname
mbs-337

As we learned earlier, connecting to your course VM requires two steps because we use a jump host:

  1. First, we connected to student-login.tacc.utexas.edu (the jump host)

  2. Then, from the jump host, we connected to mbs-337 (your course VM)

Logging out of a remote system is done using the logout command, or the shortcut <Ctrl+d>:

[ubuntu@mbs-337]$ logout
[kbeavers@student-login]$ logout
[local]$

Copying files from your local computer to your Jetstream2 VM requires a two-step process using the scp command (Windows users can use WinSCP):

Step 1: Transfer from your local computer to the jump host

[local]$ scp my_file username@student-login.tacc.utexas.edu:~
(enter password)
(enter MFA token)

Step 2: Transfer from the jump host to your course VM

[local]$ ssh username@student-login.tacc.utexas.edu
(enter password)
(enter MFA token)
[student-login]$ scp my_file mbs-337:~

Notice that when transferring from student-login to mbs-337, you don’t need to specify a username or password because your credentials are automatically forwarded.

Copying files from your VM to your local computer

To copy files in the opposite direction, reverse the process:

[student-login]$ scp mbs-337:/home/ubuntu/my_file .
[student-login]$ logout
[local]$ scp username@student-login.tacc.utexas.edu:/home/username/my_file .
(enter password)
(enter MFA token)

Tip

Important: Where to Run File Transfer Commands

When transferring files between your local computer and a remote system, you must run the command from your local computer. This is because remote systems typically cannot initiate connections to local machines behind inbound firewall restrictions.

For transfers between student-login and mbs-337, you can run the command from either machine because you are already authenticated.

Transferring Directories

To copy entire directories, use the recursive flag (scp -r):

[local]$ scp -r my_folder username@student-login.tacc.utexas.edu:/home/username
[student-login]$ scp -r my_folder mbs-337:/home/ubuntu

This covers the basics of copying files. For more advanced file transfer options, you can explore tools like rsync in your own time.

Text Editing with VIM

VIM is a text editor used on Linux file systems.

Open a file (or create a new file if it does not exist):

$ vim file_name

There are two “modes” in VIM that we will talk about today. They are called “insert mode” and “normal mode”. In insert mode, the user is typing text into a file as seen through the terminal (think about typing text into TextEdit or Notepad). In normal mode, the user can perform other functions like save, quit, cut and paste, find and replace, etc. (think about clicking the menu options in TextEdit or Notepad). The two main keys to remember to toggle between the modes are i and Esc.

Entering VIM insert mode:

> i

Entering VIM normal mode:

> Esc

A summary of the most important keys to know for normal mode are:

# Navigating the file:

arrow keys        move up, down, left, right
    Ctrl+u        page up
    Ctrl+d        page down

         0        move to beginning of line
         $        move to end of line

        gg        move to beginning of file
         G        move to end of file
        :N        move to line N

# Saving and quitting:

        :q        quit editing the file
        :q!       quit editing the file without saving

        :w        save the file, continue editing
        :wq       save and quit

Review of Topics Covered

Part 1: Creating and navigating folders

Command

Effect

pwd

print working directory

ls

list files and directories

ls -l

list files in column format

mkdir dir_name/

make a new directory

cd dir_name/

navigate into a directory

rmdir dir_name/

remove an empty directory

rm -r dir_name/

remove a directory and its contents

. or ./

refers to the present location

.. or ../

refers to the parent directory

Part 2: Creating and manipulating files

Command

Effect

touch file_name

create a new file

rm file_name

remove a file

rm -r dir_name/

remove a directory and its contents

mv file_name dir_name/

move a file into a directory

mv old_file new_file

change the name of a file

mv old_dir/ new_dir/

change the name of a directory

cp old_file new_file

copy a file

cp -r old_dir/ new_dir/

copy a directory

<Tab>

autocomplete file or folder names

<UpArrow>

cycle through command history

Part 3: Looking at the contents of files

Command

Effect

cat file_name

print file contents to screen

cat file_name > new_file

redirect output to new file

less file_name

scroll through file contents

head file_name

output beginning of file

tail file_name

output end of a file

grep pattern file_name

search for ‘pattern’ in a file

~/

shortcut for home directory

<Ctrl+c>

force interrupt

>

redirect and overwrite

>>

redirect and append

Part 4: Network and file transfers

Command

Effect

hostname

print hostname

whoami

print username

ssh username@hostname

remote login

logout

logout

scp local remote

copy a file from local to remote

scp remote local

copy a file from remote to local

<Ctrl+d>

logout of host

Part 5: Text editing with VIM

Command

Effect

vim file.txt

open “file.txt” and edit with vim

i

toggle to insert mode

<Esc>

toggle to normal mode

<arrow keys>

navigate the file

:q

quit editing the file

:q!

quit editing the file without saving

:w

save the file, continue editing

:wq

save and quit

Additional Resources