Tour Of Hazel

Author
Affiliation

Seth Weaver

Bioinformatics Research Center

Published

July 23, 2026

Welcome to the Tour of Hazel! In this hands-on workshop we will accomplish two main goals:

  1. Navigate Hazel — walk through the HPC cluster’s layout and understand which storage spaces are appropriate for which computing tasks.
  2. Learn UNIX — pick up just enough shell commands to move around, manage files, and feel at home on the command line.

Use this guided walk through. When you see a command block that starts with a $, that is a command that you should type. Lines below that command (without a $) are the expected output of that command.

1 Getting Your Bearings

You have just logged in to Hazel, you likely see a log-on message. The first step is to find out where you are.

1.1 Where are you?

Use the pwd command — print working directory — to print the full path of your current location.

$ pwd
/home/sdweave2

You should see something like what’s shown above, except with your unity ID. Your unity ID is your username on hazel. You can always confirm your identity with:

$ echo $USER
sdweave2
TipConcept: Variables

The $ sign tells the shell to expand whatever follows it into its underlying value. $USER is a variable that the system pre-loads with your username. Try typing echo USER without the $ and notice the difference — the shell just prints the word USER instead of your name.

TipConcept: Paths

A path is the address of a file or directory on the filesystem. Paths that begin with / are absolute — they describe a location starting from the very top of the filesystem (called the root). The path /home/sdweave2 means: start at root (/), go into home, then go into sdweave2. You will see and type a lot of paths today.

3 Working with Files

Now that we know where we can go on Hazel, it’s time to start learning how to work on Hazel. Essential UNIX knowledge is how to create, move, copy, and delete files. We will practice those concepts now.

Navigate to your scratch directory (or home directory if scratch is not available) before continuing.

$ cd /shares/$GROUP/$USER
# or, if needed:
$ cd ~

Confirm where you are:

$ pwd
/shares/brc/sdweave2

3.1 How do I manipulate files and directories?

3.1.1 Create a directory

The first thing we will do is create a new directory for us to work in. Use mkdir to make a new directory:

$ mkdir new_dir

Verify it was created with ls — which will list the contents of the current directory

$ ls
new_dir

You should see new_dir listed, the blue color which you will see in the terminal indicates that it is a directory, not a file.

3.1.2 Create a file with a text editor

Hazel has several text editors available. Today, we will use nano, which is the most beginner-friendly. Type nano then the name of the file you want to create.

$ nano file.txt

You are now inside the nano editor. Type a few lines of text — anything you like. Perhaps: I'm creating a file! When you are done:

  • Press Ctrl+O then Enter to save the file
  • Press Ctrl+X to exit
TipText editor options

nano is great for beginners. As you grow more comfortable, you may encounter vim on HPC systems — powerful but with a steeper learning curve. nano is always a safe choice for quick edits.

3.1.3 View a file’s contents

Let’s verify that the file we just made contains the text we wrote. We can use cat, short for concatenate to print a file’s content to the terminal. Type cat then the name of the file.

$ cat file.txt
I'm creating a file!

You should see the text you just typed.

3.1.4 List files again — and notice something

Run ls again:

$ ls
file.txt new_dir

You can see file.txt and new_dir. But what if you wanted file.txt to be inside new_dir?

3.1.5 Move a file

To move a file to a new directory, use the mv command. Type mv, the name of the file and the name of the directory where the file will go:

$ mv file.txt new_dir/

Navigate into the directory and confirm it arrived:

$ cd new_dir
$ pwd
/shares/<group>/<user>/new_dir
$ ls
file.txt
Tip

mv can also be used to rename files. Type mv the current file name, then the new name. Example: mv file.txt new_name.txt. This will delete file.txt and now new_name.txt will contain its content.

3.1.6 Copy a file

Another core concept is copying files. This is done with the cp command. Type cp the name of the original file, then the name of the new file.

Make two copies of the file that we created earlier:

$ cp file.txt file2.txt
$ cp file.txt file3

Now run ls — you should see three all 3 files:

$ ls
file2.txt file3 file.txt

3.2 Wildcards

The * character is a wildcard that matches any sequence of characters. Use it with ls:

$ ls *.txt
file2.txt file.txt

As you can see, this lists only file.txt and file2.txt, skipping file3 because it has no .txt extension.

TipConcept: Wildcards

Any command that accepts a filename can accept a wildcard pattern. *.txt means “anything that ends in .txt”. Similarly, file* means “anything that starts with file”. Wildcards can be used to quickly move, list, or delete many files at once.

3.2.1 Delete a file

The final important concept for this section: deleting files. Use rm followed by a filename to remove that file. Practice this by removing file3

$ rm file3

Run ls to confirm it is gone.

WarningThere is no trash can

rm is permanent and immediate. There is no undo, no recycle bin, no “are you sure?” prompt. Once a file is removed, it is gone. Be deliberate before pressing Enter on any rm command.

4 Scripts: Automation of commands

So far, every command you have typed has been interactive — you ran it once, saw the result, and moved on. A script is a plain text file that contains a list of commands the shell runs for you, in order, all at once. Scripts are how you turn a series of manual steps into something repeatable and shareable.

4.1 Your first script

Make sure you are in your scratch (or home) directory:

$ cd /shares/$GROUP/$USER

Create a new file called hello.sh. The .sh extension is a convention that signals “this is a shell script.”

$ nano hello.sh

Type the following inside the editor:

#!/bin/bash
echo "Hello, $USER!"
TipThe shebang line

The very first line, #!/bin/bash, is called a shebang. It tells the operating system which program should interpret the script — in this case, /bin/bash. Always include it as the first line of your shell scripts.

Save and exit (Ctrl+O, Enter, Ctrl+X).

Now run the script by using ./ and the name of the script:

$ ./hello.sh
-bash: ./hello.sh: Permission denied

Oops! We got a permission denied error. This is becuase we forgot to tell the shell that hello.sh is an executable file. To do so, we must use the chmod command to change the mode of the file. The +x in front of the filename tells the shell that we want to make the file executable.

$ chmod +x hello.sh
Tip

Now if you run ls, you should see that hello.sh is in green text, a quick indication that the file is executable.

Now try to run the script again:

$ ./hello.sh
Hello, sdweave2!

4.2 Expanding the script

Open hello.sh again and replace the contents with a script that puts several of the commands you previously learned to work:

$ nano hello.sh
#!/bin/bash
PROJECT="my_project"

echo "Setting up workspace: $PROJECT"
mkdir $PROJECT

echo "Project: $PROJECT" > $PROJECT/notes.txt
cp $PROJECT/notes.txt $PROJECT/notes_backup.txt

echo "Files created:"
ls $PROJECT

echo "Contents of notes.txt:"
cat $PROJECT/notes.txt
TipConcept: User-defined variables

Define your own variables with the syntax NAME="value" — no spaces around the =. Expand them anywhere in the script with $NAME, just like system variables such as $USER. Changing PROJECT="my_project" to any other name would ripple through every command in the script automatically.

Save, exit, and run it:

$ ./hello.sh
Setting up workspace: my_project
Files created:
notes_backup.txt  notes.txt
Contents of notes.txt:
Project: my_project

In a handful of lines, the script created a directory, wrote a file, copied it, and reported back — the same steps you would have typed one at a time, now automated.

Use the commands ls, cd, cat, and others to explore fully what your script has created!

TipConcept: Output redirection

The > operator redirects the output of a command into a file instead of printing it to the terminal. echo "Project: $PROJECT" > $PROJECT/notes.txt writes that line directly into notes.txt. If the file does not exist it is created; if it does, it is overwritten.

5 Command Reference

Here is a quick reference for every command covered today.

Command What it does Example
pwd Print current directory path pwd
cd Change directory cd /shares/$GROUP/$USER
ls List directory contents ls *.txt
mkdir Make a new directory mkdir new_dir
nano Open a text editor nano file.txt
cat Print a file to the terminal cat file.txt
mv Move or rename a file mv file.txt new_dir/
cp Copy a file cp file.txt file2.txt
rm Delete a file (permanent!) rm file3
echo Print text or expand a variable echo $USER
> Redirect output into a file (overwrites) echo "text" > file.txt
chmod Change file permissions chmod +x hello.sh

6 Key Concepts

Five ideas that underpin everything you did today.

Concept What it means Quick example
Variables A named placeholder the shell expands when prefixed with $. System variables like $USER and $GROUP are pre-set; define your own with NAME="value" (no spaces around =). echo $USER → prints your username
Paths The address of a file or directory on the filesystem. Absolute paths start with / (root); ~ is shorthand for your home directory. /home/sdweave2, ~, /shares/brc/sdweave2
Wildcards The * character matches any sequence of characters. Any command that accepts filenames also accepts wildcard patterns to act on many files at once. ls *.txt lists only .txt files
Text editors Programs for creating and editing plain-text files in the terminal. nano is beginner-friendly: Ctrl+O saves, Ctrl+X exits. nano file.txt
Scripts A plain-text .sh file containing a sequence of shell commands, run all at once. Start with #!/bin/bash, make executable with chmod +x, then run with ./script.sh. ./hello.sh