The notes below are modified from the excellent Unix Shell tutorial that is freely available on the Software Carpentry website. I highly recommend checking out the full version for further reading. The material is being used here under the terms of the Creative Commons Attribution license.

Navigating Files and 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.

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/nelle, which is Nelle's home directory:

$ pwd

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 this example, we'll be illustrating the filesystem on our scientist Nelle'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 Nelle'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/nelle.

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.

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

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/

ls has lots of other options. To find out what they are, we can type:

$ man ls

man is the Unix "manual" command: it prints a description of a command and its options, and (if you're lucky) provides a few examples of how to use it. To navigate through the man pages, you may use the up and down arrow keys to move line-by-line, or try the "b" and spacebar keys to skip up and down by full page. Quit the man pages by typing "q".

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.

We can also use ls to see the contents of a different directory. Let's take a look at our Desktop directory by running ls -F Desktop, i.e., the command ls with the arguments -F and Desktop. 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 Desktop

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

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 data directory we saw above. We can use the following series of commands to get there:

$ cd Desktop
$ cd data-shell
$ cd data

These commands will move us from our home directory onto our Desktop, then into the data-shell directory, then into the data directory. cd doesn't print anything, but if we run pwd after it, we can see that we are now in /Users/nelle/Desktop/data-shell/data. If we run ls without arguments now, it lists the contents of /Users/nelle/Desktop/data-shell/data, because that's where we now are:

$ pwd
$ ls -F
amino-acids.txt   elements/     pdb/            salmon.txt
animals.txt       morse.txt     planets.txt     sunspot.txt

We now know how to go down the directory tree, but how do we go up?

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/nelle/Desktop/data-shell:

$ pwd

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
./                  creatures/          notes.txt
../                 data/               pizza.cfg
.bash_profile       molecules/          solar.pdf
Desktop/            north-pacific-gyre/ writing/

-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/nelle, 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.

Note that in most command line tools, multiple parameters can be combined with a single - and no spaces between the parameters: ls -F -a is equivalent to ls -Fa.

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

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 data directory from before. Last time, we used three commands, but we can actually string together the list of directories to move to data in one step:

$ cd Desktop/data-shell/data

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 data 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 data-shell 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 data-shell.

$ pwd
$ cd /Users/nelle/Desktop/data-shell

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

Two More Shortcuts

The shell interprets the character ~ (tilde) at the start of a path to mean "the current user's home directory". For example, if Nelle's home directory is /Users/nelle, then ~/data is equivalent to /Users/nelle/data. This only works if it is the first character in the path: here/there/~/elsewhere is not here/there/Users/nelle/elsewhere.

Another shortcut is the - (dash) character. cd will translate - into the previous directory I was in, which is faster than having to remember, then type, the full path. This is a very efficient way of moving back and forth between directories. The difference between cd .. and cd - is that the former brings you up, while the latter brings you back. You can think of it as the Last Channel button on a TV remote.

Tab Completion

Now in her current directory data-shell, Nelle can see what files she has using the command:

$ ls north-pacific-gyre/2012-07-03/

This is a lot to type, but she can let the shell do most of the work through what is called tab completion. If she types:

$ ls nor

and then presses tab (the tab key on her keyboard), the shell automatically completes the directory name for her:

$ ls north-pacific-gyre/

If she presses tab again, Bash will add 2012-07-03/ to the command, since it's the only possible completion. Pressing tab again does nothing, since there are 19 possibilities; pressing tab twice brings up a list of all the files, and so on. This is called tab completion, and we will see it in many other tools as we go on.

Key Points:

  • "The file system is responsible for managing information on the disk."
  • "Information is stored in files, which are stored in directories (folders)."
  • "Directories can also store other directories, which forms a directory tree."
  • "cd path changes the current working directory."
  • "ls path prints a listing of a specific file or directory; ls on its own lists the current working directory."
  • pwd prints the user's current working directory.
  • whoami shows the user's current identity.
  • / on its own is the root directory of the whole file system.
  • A relative path specifies a location starting from the current location.
  • An absolute path specifies a location from the root of the file system.
  • Directory names in a path are separated with '/' on Unix, but '\\' on Windows.
  • '..' means 'the directory above the current one'; '.' on its own means 'the current directory'.
  • Most files' names are something.extension. The extension isn't required, and doesn't guarantee anything, but is normally used to indicate the type of data in the file.
  • Most commands take options (flags) which begin with a '-'.


Part 3: Working With Files and Directories