Navigating Files and Directories
Last updated on 2024-11-05 | Edit this page
Estimated time: 40 minutes
Overview
Questions
- How can I move around on my computer?
- How can I see what files and directories I have?
- How can I specify the location of a file or directory on my computer?
Objectives
- Explain the similarities and differences between a file and a directory.
- Translate an absolute path into a relative path and vice versa.
- Construct absolute and relative paths that identify specific files and directories.
- Use options and arguments to change the behaviour of a shell command.
- Demonstrate the use of tab completion and explain its advantages.
Introducing and navigating the filesystem in the shell (covered in Navigating Files and Directories section) can be confusing. You may have both terminal and GUI file explorer open side by side so learners can see the content and file structure while they’re using terminal to navigate the 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.
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:
OUTPUT
/Users/nelle
Here, the computer’s response is /Users/nelle
, which is
Nelle’s home directory:
Home Directory Variation
The home directory path will look different on different operating
systems. On Linux, it may look like /home/nelle
, and on
Windows, it will be similar to
C:\Documents and Settings\nelle
or
C:\Users\nelle
. (Note that it may look slightly different
for different versions of Windows.) In future examples, we’ve used Mac
output as the default - Linux and Windows output may differ slightly but
should be generally similar.
We will also assume that your pwd
command returns your
user’s home directory. If pwd
returns something different,
you may need to navigate there using cd
or some commands in
this lesson will not work as written. See Exploring Other Directories for
more details on the cd
command.
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 /
.
Slashes
Notice that there are two meanings for the /
character.
When it appears at the front of a file or directory name, it refers to
the root directory. When it appears inside a path, it’s just a
separator.
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
:
OUTPUT
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.
OUTPUT
Applications/ Documents/ Library/ Music/ Public/
Desktop/ Downloads/ Movies/ Pictures/
Here, we can see that the home directory contains only sub-directories. Any names in the output that don’t have a classification symbol are files in the current working directory.
Clearing your terminal
If your screen gets too cluttered, you can clear your terminal using
the clear
command. You can still access previous commands
using ↑ and ↓ to move line-by-line, or by
scrolling in your terminal.
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 — depending on your environment, you might find that
only one of these ways works:
- We can pass a
--help
option to any command (available on Linux and Git Bash), for example:
- We can read its manual with
man
(available on Linux and macOS):
We’ll describe both ways next.
Help for built-in commands
Some commands are built in to the Bash shell, rather than existing as
separate programs on the filesystem. One example is the cd
(change directory) command. If you get a message like
No manual entry for cd
, try help cd
instead.
The help
command is how you get usage information for Bash
built-ins.
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.
OUTPUT
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
... ... ...
When to use short or long options
When options exist as both short and long options:
- Use the short option when typing commands directly into the shell to minimize keystrokes and get your task done faster.
- Use the long option in scripts to provide clarity. It will be read many times and typed once.
The man
command
The other way to learn about ls
is to type
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.
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.
Exploring More ls
Options
You can also use two options at the same time. What does the command
ls
do when used with the -l
option? What about
if you use both the -l
and the -h
option?
Some of its output is about properties that we do not cover in this lesson (such as file permissions and ownership), but the rest should be useful nevertheless.
The -l
option makes ls
use a
long listing format, showing not only the
file/directory names but also additional information, such as the file
size and the time of its last modification. If you use both the
-h
option and the -l
option, this makes the
file size ‘human readable’, i.e. displaying something
like 5.3K
instead of 5369
.
Listing in Reverse Chronological Order
By default, ls
lists the contents of a directory in
alphabetical order by name. The command ls -t
lists items
by time of last change instead of alphabetically. The command
ls -r
lists the contents of a directory in reverse order.
Which file is displayed last when you combine the -t
and
-r
options? Hint: You may need to use the -l
option to see the last changed dates.
The most recently changed file is listed last when using
-rt
. This can be very useful for finding your most recent
edits or checking to see if a new output file was written.
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:
OUTPUT
shell-lesson-data/
Note that if a directory named Desktop
does not exist in
your current working directory, this command will return an error.
Typically, a Desktop
directory exists in your home
directory, which we assume is the current working directory of your bash
shell.
Your output should be a list of all the files and sub-directories in
your Desktop directory, including the shell-lesson-data
directory you downloaded at the setup for this
lesson. (On most systems, the contents of the Desktop
directory in the shell will show up as icons in a graphical user
interface behind all the open windows. See if this is the case for
you.)
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 Desktop 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
:
OUTPUT
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:
These commands will move us from our home directory into our Desktop
directory, then 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
/Users/nelle/Desktop/shell-lesson-data/exercise-data
.
If we run ls -F
without arguments now, it lists the
contents of
/Users/nelle/Desktop/shell-lesson-data/exercise-data
,
because that’s where we now are:
OUTPUT
/Users/nelle/Desktop/shell-lesson-data/exercise-data
OUTPUT
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:
ERROR
-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:
..
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/shell-lesson-data
:
OUTPUT
/Users/nelle/Desktop/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
:
OUTPUT
./ ../ 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?
How can you check what happened? pwd
gives us the
answer!
OUTPUT
/Users/nelle
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:
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
.
OUTPUT
/Users/nelle/Desktop/shell-lesson-data/exercise-data
Run pwd
and ls -F
to ensure that we’re in
the directory we expect.
Two More Shortcuts
The shell interprets a tilde (~
) character 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 two directories – i.e. if you execute
cd -
twice, you end up back in the starting directory.
The difference between cd ..
and cd -
is
that the former brings you up, while the latter brings you
back.
Try it! First navigate to ~/Desktop/shell-lesson-data
(you should already be there).
Then cd
into the exercise-data/creatures
directory
Now if you run
you’ll see you’re back in ~/Desktop/shell-lesson-data
.
Run cd -
again and you’re back in
~/Desktop/shell-lesson-data/exercise-data/creatures
Absolute vs Relative Paths
Starting from /Users/nelle/data
, which of the following
commands could Nelle use to navigate to her home directory, which is
/Users/nelle
?
cd .
cd /
cd /home/nelle
cd ../..
cd ~
cd home
cd ~/data/..
cd
cd ..
- No:
.
stands for the current directory. - No:
/
stands for the root directory. - No: Nelle’s home directory is
/Users/nelle
. - No: this command goes up two levels, i.e. ends in
/Users
. - Yes:
~
stands for the user’s home directory, in this case/Users/nelle
. - No: this command would navigate into a directory
home
in the current directory if it exists. - Yes: unnecessarily complicated, but correct.
- Yes: shortcut to go back to the user’s home directory.
- Yes: goes up one level.
Relative Path Resolution
Using the filesystem diagram below, if pwd
displays
/Users/thing
, what will ls -F ../backup
display?
../backup: No such file or directory
2012-12-01 2013-01-08 2013-01-27
2012-12-01/ 2013-01-08/ 2013-01-27/
original/ pnas_final/ pnas_sub/
- No: there is a directory
backup
in/Users
. - No: this is the content of
Users/thing/backup
, but with..
, we asked for one level further up. - No: see previous explanation.
- Yes:
../backup/
refers to/Users/backup/
.
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/
ls pwd
ls -r -F
ls -r -F /Users/backup
- No:
pwd
is not the name of a directory. - Yes:
ls
without directory argument lists files and directories in the current directory. - Yes: uses the absolute path explicitly.
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
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:
OUTPUT
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.
OUTPUT
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:
OUTPUT
Applications/ System/
Library/ Users/
Network/ Volumes/
Nelle’s Pipeline: Organizing Files
Knowing this much about files and directories, Nelle is ready to organize the files that the protein assay machine will create.
She creates a directory called north-pacific-gyre
(to
remind herself where the data came from), which will contain the data
files from the assay machine and her data processing scripts.
Each of her physical samples is labelled according to her lab’s
convention with a unique ten-character ID, such as ‘NENE01729A’. This ID
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
within the filename of each data file. Since the output of the assay
machine 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 shell-lesson-data
, Nelle
can see what files she has using the command:
This command 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:
and then presses Tab (the tab key on her keyboard), the shell automatically completes the directory name for her:
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’.
To see all of those files, she can press Tab twice more.
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 then form a directory tree.
-
pwd
prints the user’s current working directory. -
ls [path]
prints a listing of a specific file or directory;ls
on its own lists the current working directory. -
cd [path]
changes the current working directory. - Most commands take options that begin with a single
-
. - Directory names in a path are separated with
/
on Unix, but\
on Windows. -
/
on its own is the root directory of the whole file system. - An absolute path specifies a location from the root of the file system.
- A relative path specifies a location starting from the current location.
-
.
on its own means ‘the current directory’;..
means ‘the directory above the current one’.