Resources For Getting Started With Terminal

If you're new to using the terminal (command line), these resources will help you get comfortable with basic commands, navigation, and text editing.

Why Learn the Command Line?

Most scientific software, including SBGrid tools, requires basic terminal usage. You don't need to be an expert—just comfortable opening a terminal, navigating directories, and editing simple text files.

Note for macOS users: macOS is Unix-based, so Linux/Unix tutorials apply to your system too.

Full Beginner Tutorials

Best for: Complete beginners who want a structured, step-by-step introduction.

The Unix Shell (Software Carpentry)
Comprehensive tutorial covering files, directories, pipes, loops, and shell scripts. Designed for researchers with no prior programming experience.
Library Carpentry: The UNIX Shell
Similar to Software Carpentry but tailored for library and information professionals. Great hands-on exercises.
Ubuntu's Command Line for Beginners
Linux-focused tutorial with clear explanations and practical examples. Works well for any Linux distribution.
Codecademy: Intro to the Command Line (free account required)
Interactive browser-based lessons with exercises. Good for learners who prefer hands-on practice.

Quick Reference & Cheat Sheets

Best for: Users who know the basics but need quick reminders.

tldr pages
Simplified, community-driven "man pages" with practical examples. Install as a command-line tool or use in your browser.
tldr in-browser (offline-capable)
Browser-based version of tldr that works offline. Bookmark for quick reference.

Text Editor Help

Best for: Getting unstuck when editing configuration files.

Nano Cheat Sheet (official)
Quick reference for Nano keyboard shortcuts. Most importantly: CTRL+O (save), CTRL+X (exit).
How to Quit Vim Without Saving
Accidentally opened Vim? Type :q! and press Enter to escape. Article also explains vimtutor for learning Vim basics.

Linux software environment

A Linux shell environment is a collection of settings and variables that define the behavior and preferences of the shell session. These settings include environment variables, shell options, and configuration files that influence how software and commands are executed.

Key Components of a Shell Environment

Environment Variables: Variables like PATH, HOME, and USER that store information used by the shell and applications. For example, PATH determines the directories the shell searches for executable files.
Configuration Files: Files such as .bashrc, .profile, and .bash_profile that are executed when a shell session starts. These files can set environment variables, define aliases, and configure shell options.
Shell Options: Settings that control the behavior of the shell, such as command history, auto-completion, and prompt customization.

Impact on Software Usage

Executable Search Path: The PATH variable affects which software can be run directly from the command line without specifying the full path.
Library Paths: Variables like LD_LIBRARY_PATH influence where the system looks for shared libraries, affecting software that relies on these libraries.
User Preferences: Environment variables can customize software behavior, such as setting the default editor with EDITOR or VISUAL.
Session Customization: Configuration files allow users to tailor their shell environment, enabling or disabling features, setting up aliases, and automating tasks.

Overall, the shell environment plays a crucial role in software usage by defining the context in which commands and applications are executed, thereby influencing their behavior and accessibility.

What You Need to Know for SBGrid

You don't need to master everything—just these basics:

Open a terminal (macOS: Terminal.app, Linux: your terminal app)
Navigate directories: cd, ls, pwd
Edit text files: Use nano for simplicity
Run commands: Type a command and press Enter
Understand file paths: Absolute (/programs/sbgrid.shrc) vs. relative (~/Documents)

The SBGrid documentation assumes you're comfortable with these basics. If something is unclear, refer back to these resources or contact support.

Return to: Using SBGrid on your computer