3. Navigating Files and Directories

Exploring the File System

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, we’ll go to our open shell window.

To determine our location, we’ll use the pwd command, short for “print working directory.” In the shell, we’re always in one place at one time, our current working directory, where commands typically operate. Knowing your location before running a command is essential, and pwd shows where you are:

$ pwd

/Users/nelle

Here, the computer’s response is /Users/nelle, which is Nelle’s home directory:

Home Directory Variation

The home directory path varies across operating systems. On Linux, it might be /home/nelle, while on Windows, it resembles C:\Documents and Settings\nelle or C:\Users\nelle. In future examples, we’ve used Mac output as the default, output may differ slightly between Linux and Windows, but it’s generally similar to our Mac examples.

To understand what a “home directory,” let’s look at the organization of the file system. We’ll use our scientist Nelle’s computer as an example. Later, you’ll learn commands to explore your own file system, which will look similar, but may not be identical.

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

At the top is the root directory that holds everything else. Denoted by / 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.

We know that our current working directory /Users/nelle is stored inside /Users, and /Users is stored inside the root directory / because it begins with /.

Slashes

The / character has two meanings: at the start of a name, it denotes the root directory, while inside a name, it’s a separator.

Underneath /Users, we find one directory for each user with an account on Nelle’s machine, her colleagues imhotep and larry.

User directories are as follows: imhotep’s in /Users/imhotep, larry’s in /Users/larry, and Nelle’s in /Users/nelle. We’re using Nelle as the example, so /Users/nelle is our home directory. Usually, when you open a new command prompt, you will be in your home directory.

To view the contents of our own file system, we can see what’s in our home directory by running ls, short for “listing”:

$ ls

Desktop     Downloads   Movies      Pictures
Documents   Library     Music       Public

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

ls prints the name of file and directories in the current directory. To understand the output more, we can add on the -F option (also called a switch or flag). It classifies output by adding markers to indicate what they are:

• a trailing / indicates that this is a directory
• @ indicates a link
• * indicates an executable

Depending on your default options, the shell might also use colors to indicate whether each entry is a file or directory.

$ ls -F

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.)

Here, we can see that our home directory contains mostly sub-directories. Any names in your output that don’t have a classification symbol, are plain old files.

General syntax of a shell command

Consider the command below as a general example of a command, which we will dissect into its component parts:

$ ls -F /

ls is the command, with an option -F and an argument /. We’ve already encountered options (also called switches or flags) which either start with a single dash (-) or two dashes (--), and they change the behaviour of a command. Arguments specify what a command operates on, like files and directories. Options and arguments are sometimes called parameters. A command can take multiple options and arguments, but it doesn’t require them.

Each part is separated by spaces. Omitting the space between ls and -F makes the shell search for a non-existent command called ls-F. Capitalization is also important, ls -r differs from ls -R.

Putting all that together, our command above gives us a listing of files and directories in the root directory /. An example of the output you might get from the above command is given below:

$ ls -F /

Applications/	Volumes/	etc@		sbin/
Library/	bin/		home@		tmp@
System/		cores/		opt/		usr/
Users/		dev/		private/	var@

Getting help

ls has lots of other options. There are two common ways to find out how to use a command and what options it accepts:

First, we can pass a --help option to the command, such as:

$ ls --help

Second, we can read its manual with man, such as:

$ man ls

Depending on your environment you might find that only one of these works (either man or --help).

We’ll describe both ways below.

The --help option

Many bash commands, and programs that people have written that can be run from within bash, support a --help option to display more information on how to use the command or program.

$ ls --help

Usage: ls [OPTION]... [FILE]...
List information about the FILEs (the current directory by default).
Sort entries alphabetically if none of -cftuvSUX nor --sort is specified.

Mandatory arguments to long options are mandatory for short options too.
  -a, --all                  do not ignore entries starting with .
  -A, --almost-all           do not list implied . and ..
      --author               with -l, print the author of each file

...
...
...

GNU coreutils online help: <https://www.gnu.org/software/coreutils/>
Report any translation bugs to <https://translationproject.org/team/>
Full documentation <https://www.gnu.org/software/coreutils/ls>
or available locally via: info '(coreutils) ls invocation'

The man command

The other way to learn about ls is to use the man command.

$ man ls

This will turn your terminal into a page with a description of the ls command and its options and, if you’re lucky, some examples of how to use it.

To navigate through the man pages, you may use ↑ and ↓ to move line-by-line, or try B and Spacebar to skip up and down by a full page. To search for a character or word in the man pages, use / followed by the character or word you are searching for. Sometimes a search will result in multiple hits. If so, you can move between hits using N (for moving forward) and Shift+N (for moving backward).

To quit the man pages, press Q.

Manual pages on the web

Of course there is a third way to access help for commands: searching the internet via your web browser. When using internet search, including the phrase unix man page in your search query will help to find relevant results.

GNU provides links to its manuals including the core GNU utilities, which covers many commands introduced within this lesson.

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 -F option and the argument Desktop. The argument Desktop tells ls that we want a listing of something other than our current working directory:

$ ls -F Desktop

data-shell/

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

As you can see, using a bash shell relies on a hierarchical file system organization which is important for effective work management. While you can store many files in your home directory, similar to stacking papers on a desk, it’s not an efficient approach.

Now that we know the data-shell directory is located on our Desktop, 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 Desktop/data-shell

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

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

To change locations, use cd followed by a directory name. cd means “change directory,” but it doesn’t change the directory itself; 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. You will notice that cd doesn’t print anything. This is normal. Many shell commands will not output anything to the screen when successfully executed. 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

/Users/nelle/Desktop/data-shell/data

$ ls -F

amino-acids.txt  animal-counts/  animals.txt  elements/  morse.txt  pdb/  planets.txt  salmon.txt  sunspot.txt

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

$ cd data-shell

-bash: cd: data-shell: 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/nelle/Desktop/data-shell:

$ pwd

/Users/nelle/Desktop/data-shell

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

$ ls -F -a

./  ../  .bash_profile  creatures/  data/  molecules/  north-pacific-gyre/  notes.txt  pizza.cfg  solar.pdf  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 options can be combined with a single - and no spaces between the options: 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

/Users/nelle

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

When moving up one level from the data directory, we used cd .., but there’s another way to navigate to any directory, regardless of our current location.

So far we have been using relative paths, where we specify directory names or directory paths (as above) based on our current location. When you use a relative path with a command like ls or cd, it tries to find the location based on our current location instead of from the root of the file system.

However, we can specify the absolute path to a directory by including its entire path from the root directory, denoted by the leading slash /. It tells the computer to follow the path from the root of the file system so it always points the same directory, no matter what our current location is.

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

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

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

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

Exercise: Relative Path Resolution

---

Using the filesystem diagram below, if pwd displays /Users/thing, what will ls -F ../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/

Solution

1. No: there is a directory backup in /Users.
2. No: this is the content of Users/thing/backup, but with .. we asked for one level further up.
3. No: see previous explanation.
4. Yes: ../backup/ refers to /Users/backup/.

Exercise: ls Reading Comprehension

---

Using the filesystem diagram below, if pwd displays /Users/backup, and -r tells ls to display things in reverse order, what command(s) will result in the following output:

Output:

 pnas_sub/ pnas_final/ original/

Is the correct command to produce the above output:

1. ls pwd
2. ls -r -F
3. ls -r -F /Users/backup

Solution

1. No: pwd is not the name of a directory.
2. Yes: ls without directory argument lists files and directories in the current directory.
3. Yes: uses the absolute path explicitly.

Nelle’s Pipeline: Organizing Files

Knowing just this much about files and directories, Nelle starts organizing the data from the protein assay machine. She creates a north-pacific-gyre directory (to remind herself where the data came from) and then a 2012-07-03 directory (the start date of sample processing). She used to use names like conference-paper and revised-results, hard to understand after a couple of years (leading to names like revised-revised-results-3).

Each of her physical samples is labelled according to her lab’s convention with a unique ten-character ID, such as “NENE01729A”. This is what she used in her collection log to record the location, time, depth, and other characteristics of the sample, so she decides to use it as part of each data file’s name. Since the assay machine’s output is plain text, she will call her files NENE01729A.txt, NENE01812A.txt, and so on. All 1520 files will go into the same directory.

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.