Navigating Files and Directories

Overview

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.

First, let’s find out where we are by running a command called pwd (which stands for ‘print working directory’). Directories are like places — at any time while we are using the shell, we are in exactly one place called our current working directory. Commands mostly read and write files in the current working directory, i.e. ‘here’, so knowing where you are before running a command is important. pwd shows you where you are:

pwd

/home/nelle

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

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 filesystem looks like an upside down tree. The topmost directory is the root directory that holds everything else. We refer to it using a slash character, /, on its own; this character 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 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 Nelle’s machine, her colleagues imhotep and larry.

The user imhotep’s files are stored in /Users/imhotep, user larry’s in /Users/larry, and Nelle’s in /Users/nelle. Nelle is the user in our examples here; therefore, we get /Users/nelle 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:

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. We can make its output more comprehensible by using the -F option which tells ls to classify the output by adding a marker to file and directory names to indicate what they are:

• a trailing / indicates that this is a directory

• @ indicates a link

• * indicates an executable

Depending on your shell’s default settings, 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/

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:

1. We can pass a --help option to any command (available on Linux and Git Bash), for example:

$ ls --help

2. We can read its manual with man:

$ man ls

We’ll describe both ways next.

The --help option

Most bash commands and programs that people have written to be run from within bash, support a --help option that displays 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 neither -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
  -b, --escape               print C-style escapes for nongraphic characters
      --block-size=SIZE      scale sizes by SIZE before printing them; e.g.,
                               '--block-size=M' prints sizes in units of
                               1,048,576 bytes; see SIZE format below
  -B, --ignore-backups       do not list implied entries ending with ~
  -c                         with -lt: sort by, and show, ctime (time of last
                               modification of file status information);
                               with -l: show ctime and sort by name;
                               otherwise: sort by ctime, newest first
  -C                         list entries by columns
      --color[=WHEN]         colorize the output; WHEN can be 'always' (default
                               if omitted), 'auto', or 'never'; more info below
  -d, --directory            list directories themselves, not their contents
  -D, --dired                generate output designed for Emacs' dired mode
  -f                         do not sort, enable -aU, disable -ls --color
  -F, --classify             append indicator (one of */=>@|) to entries
...        ...        ...

ls -j

ls: invalid option -- 'j'
Try 'ls --help' for more information.

The man command

The other way to learn about ls is to type:

man ls

This command will turn your terminal into a page with a description of the ls command and its options.

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.

Exploring Other Directories

Not only can we use ls on the current working directory, but we can use it to list 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

shell-lesson-data/

Your output should be a list of all the files and sub-directories in your home directory, including the shell-lesson-data directory you downloaded at the setup for this lesson.

Organizing things hierarchically helps us keep track of our work. While 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, it’s much easier to find things when they’ve been organized into sensibly-named subdirectories.

Now that we know the shell-lesson-data directory is located in our home directory, we can do two things.

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

ls -F shell-lesson-data

exercise-data/  north-pacific-gyre/

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 current working directory. In other words it changes the shell’s settings for what directory we are in. The cd command is akin to double-clicking a folder in a graphical interface to get into that folder.

Let’s say we want to move into the exercise-data directory we saw above. We can use the following series of commands to get there:

cd shell-lesson-data
cd exercise-data

These commands will move us from our home directory into the shell-lesson-data directory, then into the exercise-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 /home/username/shell-lesson-data/exercise-data.

If we run ls -F without arguments now, it lists the contents of /home/username/shell-lesson-data/exercise-data, because that’s where we now are:

pwd

/home/username/shell-lesson-data/exercise-data

ls -F

alkanes/  animal-counts/  creatures/  numbers.txt  writing/

We now know how to go down the directory tree (i.e. how to go into a subdirectory), but how do we go up (i.e. how do we leave a directory and go into its parent directory)? We might try the following:

cd shell-lesson-data

-bash: cd: shell-lesson-data: 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. It works as follows:

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 /home/username/shell-lesson-data:

pwd

/home/username/shell-lesson-data

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

ls -F -a

./  ../  exercise-data/  north-pacific-gyre/

-a stands for ‘show all’ (including hidden files); 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 three commands 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

pwd

/home/username

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

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

cd shell-lesson-data/exercise-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 shell-lesson-data directory from anywhere on the filesystem (including from inside exercise-data). To find the absolute path we’re looking for, we can use pwd and then extract the piece we need to move to shell-lesson-data.

pwd

/home/username/shell-lesson-data/exercise-data

cd /home/username/shell-lesson-data/exercise-data

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

Try it! First navigate to ~/Desktop/shell-lesson-data (you should already be there).

cd ~/shell-lesson-data

Try it! First navigate to ~/Desktop/shell-lesson-data (you should already be there).

cd exercise-data/creatures

Now if you run

cd -

you’ll see you’re back in ~/shell-lesson-data. Run cd - again and you’re back in ~/shell-lesson-data/exercise-data/creatures

General Syntax of a Shell Command

We have now encountered commands, options, and arguments, but it is perhaps useful to formalise some terminology.

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 which either start with a single dash (-), known as short options, or two dashes (--), known as long options. [Options] change the behavior of a command and Arguments tell the command what to operate on (e.g. files and directories). Sometimes options and arguments are referred to as parameters. A command can be called with more than one option and more than one argument, but a command doesn’t always require an argument or an option.

You might sometimes see options being referred to as switches or flags, especially for options that take no argument. In this lesson we will stick with using the term option.

Each part is separated by spaces. If you omit the space between ls and -F the shell will look for a command called ls-F, which doesn’t exist. Also, capitalization can be important. For example, ls -s will display the size of files and directories alongside the names, while ls -S will sort the files and directories by size, as shown below:

cd ~/shell-lesson-data
ls -s exercise-data

total 28
 4 animal-counts   4 creatures  12 numbers.txt   4 alkanes   4 writing

Note that the sizes returned by ls -s are in blocks. As these are defined differently for different operating systems, you may not obtain the same figures as in the example.

ls -S exercise-data

animal-counts  creatures  alkanes  writing  numbers.txt

Putting all that together, our command ls -F / 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 /

{{ 
Show HPC Folder
}}

Using Tab Completion

Change into the shell-lesson-data folder:

cd ~/shell-lesson-data

Let’s view the contents of the north-pacific-gyre folder

ls north-pacific-gyre/

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

ls nor

and then press the TAB key, the shell automatically completes the directory name:

ls north-pacific-gyre/

Pressing TAB again does nothing, since there are multiple possibilities; pressing TAB twice brings up a list of all the files.

If Nelle then presses G and then presses TAB again, the shell will append ‘goo’ since all files that start with ‘g’ share the first three characters ‘goo’.

ls north-pacific-gyre/goo

To see all of those files, she can press TAB twice more.

ls north-pacific-gyre/goo

goodiff.sh   goostats.sh