Getting Started

Table of Contents

1. Command Line Basics
   1. The filesystem
   2. Navigating the filesystem
2. File Names
3. Text Editing
4. Terminal Text Editing
5. Tutorials
   1. Learn Bash
   2. Learn Git

Command Line Basics

Most of the steps in this guide will require interacting with a Unix-style command line. You can learn the basics of the command line at Codecademy or linuxcommand.org. Familiarity with Unix and command line operations is assumed throughout this guide.

First, find your command line interface:

• On macOS, open Applications > Utilities > Terminal
• On a Linux desktop, look for an application named Terminal, Xterm, Console, or similar.
• On Windows, install Linux. Some of the commands needed are also available in Windows PowerShell.

When you open your terminal, you will see the prompt. Your prompt may differ, but generally the prompt will look something like

host:~ user$

This tells you that you are interacting with the computer named host, your current directory is the home (~) directory, and your username is user. When you connect to other computers, such as a computing cluster, the host part of the prompt will change. As you navigate your files from the command line, the directory (~) will change to show where you are.

In the following examples, the prompt is shown. You type the text following the $:

host:~ user$ ls

In these examples, sample output from what you type is shown on the lines following the prompt:

host:~ user$ ls
Desktop
Documents
Downloads

In most of this manual, only the commands to be entered will be provided, without indicating the prompt or following output. These commands will be shown like this:

ls

The filesystem

All of the files on a Unix-like system are organized in a file tree. The root of this tree, which contains all other files, is denoted /. When you first open a command line window, you will usually start with a current working directory corresponding to your home directory. On macOS, this directory has the absolute path of /Users/username, where username is specifc to the account you use to login to the system. On Linux, your home directory is usually /home/username. Notice that these directory names are absolute—they all start with /, the root directory, and describe how you navigate the file tree to get to the directory:

/
├── Users
    └── username

On many systems, you can drag-and-drop files from your graphical interface onto the command line, which will then show the absolute path of the file you dragged.

Navigating the filesystem

Let’s practicing navigating the files on your computer using the command line! Access your system’s command line interface and try the following examples. The file paths shown here reflect a macOS system. On other systems, the files you see will be different, but the same principles apply.

1. List files in the current directory

    host:~ user$ ls
    Desktop
    Documents
    Downloads
   

2. List files in Downloads

    host:~ user$ ls Downloads
    bhm211.pdf
    bhq005.pdf
    bhq050.pdf
    bhr113.pdf
    bhv234.pdf
    bhv239.pdf
    bhw184.pdf
   

3. Change the current directory to the child Downloads

    host:~ user$ cd Downloads
    host:Downloads user$ cd Downloads
   

4. List files again

    host:Downloads user$ ls
    bhm211.pdf
    bhq005.pdf
    bhq050.pdf
    bhr113.pdf
    bhv234.pdf
    bhv239.pdf
    bhw184.pdf
   

5. Get the full path to the current directory

    host:Downloads user$ pwd
    /Users/user/Downloads
   

6. List the parent directory using a relative path

    host:Downloads user$ ls ..
    Desktop
    Documents
    Downloads
   

7. Change back to the parent directory using an absolute path

    host:Downloads user$ cd /Users/user
    host:~ user$ ls
    Desktop
    Documents
    Downloads
   

File Names

It is good practice to restrict the characters you use in file names to alphanumeric characters (a-z and 0-9), standard dashes (-, not —), and underscores _. File names with spaces or special characters such as #$&|(){}[] are likely to create problems. If you want to emphasize word boundaries, you can

• CapitalizeTheFirstLetter
• use_underscores
• or-use-dashes
• or.periods

Text Editing

You will need to write short scripts and edit files. These files should generally be plain text, with Unix-style line endings. To avoid problems, it is best to use a text editor designed for this purpose and one that recognizes the language you are using (e.g. Bash, JSON, or Python). Do not use a word processor such as Word to create or edit the files used in this guide. Word processors tend to add extra characters, special characters (e.g. converting straight double quotes (") to pairs of curved opening (“) and closing quotes (”)) that will lead to errors.

An editor designed for programming will also have features to add color coding and automatic formatting to emphasize the structure of the code. These features will help you spot errors.

There are many options for such editors; Sublime is a free, lightweight editor for macOS, Linux, and Windows.

Terminal Text Editing

You can interactively edit files at the command line using nano. This is particularly useful when working on remote systems over the command line. Nano should be installed on most Unix systems.

To edit a new or existing file named testfile.txt:

1. Start nano:

   host:~ user$ nano testfile.txt
   

2. Type Ctrl+O to save the file
3. Type Ctrl+X to quit the editor

There are also more capable command line editors, such as Emacs and Vim, but these are not installed on all systems.

Tutorials

Learn Bash

Work through the 4 free modules of Learn the Command Line on Codeacademy. Don’t just copy and paste commands in the lessons—type them out.

Learn Git

Work through the 4 free modules of Learn Git on Codeacademy.

Table of contents

• Essential Software