The Unix Shell

Files and Directories

The part of the operating system responsible for managing files and directories is called the file system. It organizes our data into files, which hold information, and directories (also called “folders”), which hold files or other directories.

Several commands are frequently used to create, inspect, rename, and delete files and directories. To start exploring them, let’s open a shell window:

$

The dollar sign is a prompt, which shows us that the shell is waiting for input; your shell may use a different character as a prompt and may add information before the prompt. When typing commands, either from these lessons or from other sources, do not type the prompt, only the commands that follow it.

Type the command whoami, then press the Enter key (sometimes marked Return) to send the command to the shell. The command’s output is the ID of the current user, i.e., it shows us who the shell thinks we are:

$ whoami

jessica

More specifically, when we type whoami the shell:

1. finds a program called whoami,
2. runs that program,
3. displays that program’s output, then
4. displays a new prompt to tell us that it’s ready for more commands.

Next, let’s find out where we are by running a command called pwd (which stands for “print working directory”). At any moment, our current working directory is our current default directory, i.e., the directory that the computer assumes we want to run commands in unless we explicitly specify something else. Here, the computer’s response is /Users/jessica, which is Jessica’s home directory:

$ pwd

/Users/jessica

To understand what a “home directory” is, let’s have a look at how the file system as a whole is organized. For the sake of example, we’ll be illustrating the filesystem on our scientist Jessica’s computer. After this illustration, you’ll be learning commands to explore your own filesystem, which will be constructed in a similar way, but not be exactly identical.

On Jessica’s computer, the filesystem looks like this:

The File System

At the top is the root directory that holds everything else. We refer to it using a slash character / on its own; this is the leading slash in /Users/jessica.

Inside that directory are several other directories: bin (which is where some built-in programs are stored), data (for miscellaneous data files), Users (where users’ personal directories are located), tmp (for temporary files that don’t need to be stored long-term), and so on.

We know that our current working directory /Users/jessica is stored inside /Users because /Users is the first part of its name. Similarly, we know that /Users is stored inside the root directory / because its name begins with /.

Underneath /Users, we find one directory for each user with an account on Jessica’s machine, her colleagues the Mummy and Wolfman.

Home Directories

The Mummy’s files are stored in /Users/imhotep, Wolfman’s in /Users/larry, and Jessica’s in /Users/jessica. Because Jessica is the user in our examples here, this is why we get /Users/jessica as our home directory.
Typically, when you open a new command prompt you will be in your home directory to start.

Now let’s learn the command that will let us see the contents of our own filesystem. We can see what’s in our home directory by running ls, which stands for “listing”:

$ ls

Applications Documents    Library      Music        Public
Desktop      Downloads    Movies       Pictures

(Again, your results may be slightly different depending on your operating system and how you have customized your filesystem.)

ls prints the names of the files and directories in the current directory in alphabetical order, arranged neatly into columns. We can make its output more comprehensible by using the flag -F, which tells ls to add a trailing / to the names of directories:

$ ls -F

Applications/ Documents/    Library/      Music/        Public/
Desktop/      Downloads/    Movies/       Pictures/

Here, we can see that our home directory contains mostly sub-directories. Any names in your output that don’t have trailing slashes, are plain old files. And note that there is a space between ls and -F: without it, the shell thinks we’re trying to run a command called ls-F, which doesn’t exist.

We can also use ls to see the contents of a different directory. Let’s take a look at our Documents directory by running ls -F Documents, i.e., the command ls with the arguments -F and Documents. The second argument — the one without a leading dash — tells ls that we want a listing of something other than our current working directory:

$ ls -F Documents

data/

Your output should be a list of all the files and sub-directories on your Documents, including the directory data you created at the start of the lesson. Take a look at your Documents to confirm that your output is accurate.

As you may now see, using a bash shell is strongly dependent on the idea that your files are organized in an hierarchical file system.
Organizing things hierarchically in this way helps us keep track of our work: it’s possible to put hundreds of files in our home directory, just as it’s possible to pile hundreds of printed papers on our desk, but it’s a self-defeating strategy.

Now that we know the directories are located on our Documents, we can do two things.

First, we can look at its contents, using the same strategy as before, passing a directory name to ls:

$ ls -F Documents/data/

Global/  NEON-DS-Airborne-Remote-Sensing/  NEON-DS-Landsat-NDVI/  NEON-DS-Site-Layout-Files/

Second, we can actually change our location to a different directory, so we are no longer located in our home directory.

The command to change locations is cd followed by a directory name to change our working directory. cd stands for “change directory”, which is a bit misleading: the command doesn’t change the directory, it changes the shell’s idea of what directory we are in.

Let’s say we want to move to the NEON-DS-Site-Layout-Files directory we saw above. We can use the following series of commands to get there:

$ cd Documents
$ cd data
$ cd NEON-DS-Site-Layout-Files

These commands will move us from our home directory onto our Documents, then into the data directory and finally into the NEON-DS-Site-Layout-Files directory. cd doesn’t print anything, but if we run pwd after it, we can see that we are now in /Users/jessica/Documents/data/NEON-DS-Site-Layout-Files. If we run ls without arguments now, it lists the contents of /Users/jessica/Documents/data/NEON-DS-Site-Layout-Files, because that’s where we now are:

$ pwd

/Users/jessica/Documents/data/NEON-DS-Site-Layout-Files

$ ls -F

HARV/  NDVI_animation.gif  README.GTF  SJER/

We now know how to go down the directory tree: how do we go up? We might try the following:

cd Documents

-bash: cd: Documents: No such file or directory

But we get an error! Why is this?

With our methods so far, cd can only see sub-directories inside your current directory. There are different ways to see directories above your current location; we’ll start with the simplest.

There is a shortcut in the shell to move up one directory level that looks like this:

$ cd ..

.. is a special directory name meaning “the directory containing this one”, or more succinctly, the parent of the current directory. Sure enough, if we run pwd after running cd .., we’re back in /Users/jessica/Documents/data/:

$ pwd

/Users/jessica/Documents/data

As for the ls command, we can pass several directories to the cd command

$ cd ../..

We moved up two directories and we are now in `/Users/jessica“:

$ pwd

/Users/jessica

The special directory .. doesn’t usually show up when we run ls. If we want to display it, we can give ls the -a flag:

$ ls -F -a

./                  Desktop/          Movies/ 
../                 Documents/        Music/
.bash_profile       Downloads/        Pictures/
Applications/       Library/          Public/

-a stands for “show all”; it forces ls to show us file and directory names that begin with ., such as .. (which, if we’re in /Users/jessica, refers to the /Users directory) As you can see, it also displays another special directory that’s just called ., which means “the current working directory”. It may seem redundant to have a name for it, but we’ll see some uses for it soon.

These then, are the basic commands for navigating the filesystem on your computer: pwd, ls and cd. Let’s explore some variations on those commands. What happens if you type cd on its own, without giving a directory?

$ cd

How can you check what happened? pwd gives us the answer!

$ pwd

/Users/jessica

It turns out that cd without an argument will return you to your home directory, which is great if you’ve gotten lost in your own filesystem.

Let’s try returning to the NEON-DS-Site-Layout-Files directory from before. Last time, we used three commands, but we can actually string together the list of directories to move to NEON-DS-Site-Layout-Files/ in one step:

$ cd Documents/data/NEON-DS-Site-Layout-Files

Check that we’ve moved to the right place by running pwd and ls -F.

If we want to move up one level from the shell directory, we could use cd ... But there is another way to move to any directory, regardless of your current location.

So far, when specifying directory names, or even a directory path (as above), we have been using relative paths. When you use a relative path with a command like ls or cd, it tries to find that location from where we are, rather than from the root of the file system.

However, it is possible to specify the absolute path to a directory by including its entire path from the root directory, which is indicated by a leading slash. The leading / tells the computer to follow the path from the root of the file system, so it always refers to exactly one directory, no matter where we are when we run the command.

This allows us to move to our NEON-DS-Site-Layout-Files directory from anywhere on the filesystem (including from inside data). To find the absolute path we’re looking for, we can use pwd and then extract the piece we need to move to NEON-DS-Site-Layout-Files.

$ pwd

/Users/jessica/Documents/data/NEON-DS-Site-Layout-Files

$ cd /Users/jessica/Documents/

Run pwd and ls -F to ensure that we’re in the directory we expect.

Relative path resolution

Using the filesystem diagram below, if pwd displays /Users/thing, what will ls ../backup display?

1. ../backup: No such file or directory
2. 2012-12-01 2013-01-08 2013-01-27
3. 2012-12-01/ 2013-01-08/ 2013-01-27/
4. original pnas_final pnas_sub

File System for Challenge Questions

pnas_sub/ pnas_final/ original/