Alternative Module 2: Introduction to Bash on HiPerGator With JupyterLab

Using the bash101 Tutorial in JupyterLab (Open OnDemand)

This explains exactly how to open and use the bash101 tutorial Markdown file in JupyterLab, and how to create the required symlink so you can access the course share storage.

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What you will do

1. Create a symlink in your Home directory that points to /blue/psy4930/share.
2. Open the bash101 tutorial Markdown file in Markdown Preview.
3. Open a Terminal and run the commands in the tutorial.

Important: You are linking to the shared course location /blue/psy4930/share, not to an individual directory under /blue/psy4930.

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Step 1 — Start JupyterLab (Open OnDemand)

1. Log in to Open OnDemand: ood.rc.ufl.edu.
2. Start a JupyterLab session. It should be pinned to the bottom of the page as Jupyter Notebook. Or, you can click on the Interactive Apps menu, scroll down to Servers -> Jupyter Notebook). Single click on it. Use the course/cluster defaults but set Job Time Limit to 2 and then click Launch.
3. You might need to wait for a while, but the session typically starts quickly. When it's ready click on Connect to Jupyter.
4. When JupyterLab opens in a new tab, keep the File Browser visible (left side).

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Step 2 — Open a Terminal in JupyterLab

1. In JupyterLab, click the Launcher tab (or File → New → Launcher if you don't see one).
2. Scroll down to “Other,” click Terminal.
3. A terminal window will open. You will paste commands there.

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Step 3 — Create a symlink to /blue/psy4930/share

What this does

JupyterLab usually starts you in your home directory. A symlink is a shortcut that makes the course share storage easy to reach from home.

Commands (copy/paste)

In the Terminal, run:

cd
ln -s /blue/psy4930/share blue_psy4930

This creates a link named blue_psy4930 in your home directory. You should see blue_psy4930 in the list of folders on the left side of the JupyterLab window.

Verify the link worked

ls -l ~/blue_psy4930

You should see output like:

blue_psy4930 -> /blue/psy4930/share

If you see “File exists”

That means you already have something named blue_psy4930 in home.

1. Check what it is:

ls -ld ~/blue_psy4930
ls -l ~/blue_psy4930

2. If your instructor tells you to replace it, remove the old link and recreate it:

rm ~/blue_psy4930
ln -s /blue/psy4930/share ~/blue_psy4930

Note: rm ~/blue_psy4930 removes only the shortcut in your home folder, not the real course data in /blue.

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Step 4 — Navigate to your course folder and the bash101 folder

Go to the shared course area

Copy/paste:

cd ~/blue_psy4930
pwd
ls

Go to your personal course share folder

You will typically have a folder named with your username (gatorlink). Replace {gatorlinkID} with your own.

cd ~/blue_psy4930/{gatorlinkID}
pwd
ls

If you do not see your folder or cannot enter it, stop and contact the course instructor.

Go to the bash101 folder

If the tutorial has already created it, you can enter it:

cd ~/blue_psy4930/{gatorlinkID}/bash101
pwd
ls

If you have not created it yet, the tutorial’s Setup section will create it.

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Step 5 — Open the bash101 tutorial file in JupyterLab

Option A: The tutorial file is already in the course share folder

1. In the JupyterLab File Browser, click blue_psy4930.
2. Click the Module2 folder.
3. Find the tutorial .md file. There should only be one file in there. If there are more files or no files, someone did something they should not have done. Please contact your instructor.
4. Right‑click the .md file → Show Markdown Preview.

Option B: You need to upload the tutorial .md file

1. Download the file from the Module2 folder or from Canvas under Module 2.
2. In JupyterLab, open your folder: blue_psy4930/{gatorlinkID}/.
3. Upload the file:
   • Drag-and-drop the .md file into the file browser, or
   • Use File → Upload Files.
4. Right‑click the uploaded .md file → Show Markdown Preview.

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Step 6 — Arrange your screen (this matters)

You should have:

• The Markdown Preview (instructions) visible, and
• The Terminal visible.

In JupyterLab you can drag tabs to split the workspace. Keep both panes on-screen so you can read and run commands.

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Step 7 — Work through the tutorial

Rules that prevent most errors

• Run the tutorial top to bottom. Do not skip the Setup section.
• When the tutorial says “replace {gatorlinkID},” do it.
• If something fails, run pwd and ls to confirm where you are.
• Copilot/ChatGPT/Gemini/etc. can be useful for troubleshooting. Pay attention to errors!

The two most important “where am I?” commands

Copy/paste anytime you feel lost:

pwd
ls -la

If you need to get back to the tutorial working directory:

cd ~/blue_psy4930/{gatorlinkID}/bash101/work
pwd

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Troubleshooting (quick)

“No such file or directory”

You are probably in the wrong folder. Run:

pwd
ls

Then navigate back using:

cd ~/blue_psy4930/{gatorlinkID}

“Permission denied” when running a script

You likely need to make it executable:

chmod +x count_errors.sh

“I can’t find blue_psy4930 in the JupyterLab file browser”

• Confirm it exists in home:

  ls -l ~ | grep blue_psy4930

• If it exists, refresh the file browser (or reload the JupyterLab page).

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What to submit

Submit exactly what your instructor specifies. It should be:

• ~/blue_psy4930/{gatorlinkID}/bash101/work/notes/todo.txt
• ~/blue_psy4930/{gatorlinkID}/bash101/work/count_errors.sh
• A short log or screenshot showing the script ran successfully

If submission requirements differ in the current year, follow the course instructions on GitHub or Canvas.