Learn just enough terminal commands to work with Python environments and Git. You only need about 10 commands to get started!
•UV package manager runs from the terminal
•Git clone downloads course notebooks via terminal
•Navigate folders to find and organize your projects
Don't worry - it's much simpler than it looks! Most biology students master these basics in under an hour.
A modern terminal with AI assistance - perfect for beginners!
✓AI explains commands and errors
✓Smart auto-completion
✓Modern, intuitive interface
✓Command history search
Alternative: You can also use your system's built-in terminal (Terminal on Mac, Windows Terminal, or any Linux terminal). All commands work the same!
These are the only commands you need for this course. Master these and you're good to go!
Print Working Directory - Shows where you are right now
pwdList - Shows all files and folders in the current location
lsChange Directory - Move to a different folder
cd Documents/biology-pythonGo up one level in the folder structure
cd ..Make Directory - Create a new folder
mkdir my-projectGet help for any command (works with most commands)
git --helpDownload a repository from GitHub
git clone https://github.com/HocheggerLab/y3-bio-python.gitCreate a Python virtual environment
uv venvActivate your Python virtual environment
source .venv/bin/activateActivate your Python virtual environment on Windows
.venv\\Scripts\\Activate.ps1Press Tab while typing and the terminal will auto-complete file and folder names. This saves tons of time!
Here's exactly what you'll do to set up the course notebooks:
Launch Warp (or your default terminal)
This shows your current location
Move to your Documents folder
Creates a new folder for course materials
Move into your new folder
Downloads all course notebooks and materials
Windows users: use .venv\Scripts\Activate.ps1
You're ready to start coding. That's all the terminal you need!
If you get "command not found", the tool might not be installed or not in your PATH.
Solution: Re-check installation instructions for that tool (git, uv, etc.)
The folder or file doesn't exist at that location.
Solution: Use ls to see what's actually there, check your spelling
You don't have permission to access that file or folder.
Solution: Make sure you're working in your own home directory (Documents, Desktop, etc.)
💡Press Tab for auto-completion and↑ to see previous commands!
This page covers everything you need for this course, but if you're curious to dive deeper into shell scripting and terminal power-user techniques:
Interactive course to master the command line: