Command Line Basics

This section introduces the terminal: what it is, why researchers use it, and the core commands for navigating and organizing files. Master these basics and any Unix system — a cluster, a remote server, an HPC node — will feel familiar.

The Terminal

A terminal is a text interface to your computer. Instead of clicking icons, you type commands. It is how researchers talk to servers, automate repetitive work, and do in seconds what a mouse would take days to do.

Open yours now:

  • Mac: Press Cmd+Space, type Terminal, press Enter.
  • Windows: Download and install Git Bash, then open “Git Bash” from the Start menu.

You should see a blinking cursor. That is where you type commands.

🟢 Green sticky = I’m done and ready    🔴 Red sticky = I need help

Put a sticky note on your laptop lid so instructors can see where you are.

Why This Matters

With a terminal open, here is what you can now do:

  GUI (Finder / Explorer) CLI (Terminal)
Speed Click → drag → drop, one file at a time 300 files moved in one second
Navigate Browse folders by clicking cd, ls, pwd — anywhere, instantly
Organize Rename files one by one Wildcards sort an entire dataset at once
Power Limited to what the app exposes Run scripts, schedule jobs, automate anything

And later this morning, when you SSH into the Yens, every command you learn right now runs identically on a machine 500× more powerful than your laptop:

  Your laptop Stanford Yens
Cores ~8–16 32–512 per node
RAM ~8–32 GB 250 GB – 3 TB per node
Commands $ ls $ cd $ pwd $ ls $ cd $ pwd
Access direct ssh SUNetID@yen.stanford.edu

Same commands. More power.

Class discussion — file organization

You have been working on your research projects for about a month. Before we go further:

  • What kinds of files do you actually have? (raise your hand — we will whiteboard this)
  • Where do they live right now?
  • What happens when you need to find something from three weeks ago?
One example structure (expand after discussion)

Organizing files is not a rule for its own sake — it is what makes your work reproducible, shareable, and recoverable when something goes wrong. Here is one common structure for a research project:

A research project folder named my_project holds four separate items: a data folder for raw data that is never modified, a scripts folder for your code, a results folder for the outputs your scripts generate, and a README file describing what the project is and how to run it. 📁 my_project/ 📁 data/ raw data — never modify it 📁 scripts/ your code — the analysis you write 📁 results/ outputs your scripts generate — safe to delete & rebuild 📄 README.md what this project is & how to run it

One project folder, four separate jobs: keep raw data untouched, your code in one place, the results your code regenerates in another, and a README that explains it all — so nothing important ever gets mixed up or overwritten.

There are many ways to organize files — this is one example. What matters is that the structure is consistent and that raw data is never mixed with outputs.

Exercise

Your terminal is open. In this exercise you will use the command line to find where you are, move around the file system, and create and delete files and folders.

Goal: Use the command line to navigate your file system and reorganize a directory of files — without touching a mouse.

A wizard at a workbench conjuring folders and files with a wand — a folder becomes a file, which becomes two files, each duplicated below

Everything you’d normally do by clicking and dragging — making a folder, creating a file, copying it — you’re about to do by typing. Same result, no mouse.

Investigation

Find your current working directory and list the files in it.

pwd
ls
  • pwd — print working directory: where you are right now
  • ls — list files and directories here

Reading the code blocks in this course. Commands come first, in a grey box; what each one does is explained underneath. Copy the box, run it, then read the list to see what happened.

Later pages sometimes put a short note inside the box instead, after a #. Everything from the # onward is written for you and is not part of the command, so type or paste only what comes before it. On a Mac the Terminal’s shell (zsh) won’t accept those notes at the prompt — paste one and you’ll get a complaint like too many arguments. Nothing is broken; just re-run without the # part.

Now look for hidden files — files whose names start with a dot are invisible to a plain ls:

ls -lah

A flag modifies the behavior of a command. -lah is three flags combined into one:

  • -l — long format: one file per line, with details
  • -a — all files, including hidden ones
  • -h — human-readable file sizes

Together they tell ls to show everything, in detail, with file sizes you can actually read. You can look up any command’s flags by searching online — for example, “ls command flags”.

Tab completion: Start typing a filename or path and press Tab — the shell completes it. Press Tab twice to see all matches. Use it constantly; it prevents typos and saves time.

Movement

Use cd to change directories. ~ is your home directory; .. means one level up.

cd ~/Desktop
pwd
cd ..
pwd
  • cd ~/Desktop — go to your Desktop. Once you type D, press Tab to autocomplete; press Tab twice to see all options if nothing completes
  • pwd — confirm where you landed
  • cd .. — go up one level
  • pwd — confirm you moved up

A Mac may ask permission the first time. A box appears saying “Terminal would like to access files in your Desktop folder.” Click OK — that is macOS checking that you meant to let your own shell see your own files. If you click Don’t Allow, cd ~/Desktop and ls will come up empty. (You can change your mind later under System Settings → Privacy & Security → Files and Folders.)

Creation

Create a new folder on your Desktop, create a file inside it, and duplicate it.

mkdir -p ~/Desktop/spell_chamber
cd ~/Desktop/spell_chamber
touch scroll.txt
cp scroll.txt scroll_copy.txt
ls
  • mkdir -p — create a new folder. The -p flag makes any missing parent folders too, and stays quiet if the folder already exists — so the command is safe to run twice
  • cd — enter it
  • touch — create a new, empty file
  • cp — make a copy of that file
  • ls — confirm both files are here

Deletion

Clean up — remove everything you just created.

⚠️ rm is permanent. There is no undo, no trash can. Double-check what you are removing before you run it.

rm scroll.txt
rm scroll_copy.txt
rm -r ~/Desktop/spell_chamber
  • rm scroll.txt — remove the file
  • rm scroll_copy.txt — remove the copy
  • rm -r — remove the folder and all its contents (-r = recursive)

🟢 Green sticky = I’m done and ready    🔴 Red sticky = I need help

Put a sticky note on your laptop lid so instructors can see where you are.

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