Navigating Files and Directories
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.
Explain the steps in the shell’s read-run-print cycle.
Identify the actual command, flags, and filenames in a command-line call.
Demonstrate the use of tab completion, and explain its advantages.
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:
If you type the command:
into your shell, followed by pressing the ‘enter’ key,
your window should look like our example in this lesson.
This isn’t necessary to follow along (in fact, your prompt may have
other helpful information you want to know about). This is up to you!
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
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,
it shows us who the shell thinks we are:
More specifically, when we type
whoami the shell:
finds a program called
runs that program,
displays that program’s output, then
displays a new prompt to tell us that it’s ready for more commands.
In this lesson, we have used the username
with our hypothetical scientist Nelle) in example input and output throughout.
you type this lesson’s commands on your computer,
you should see and use something different,
namely, the username associated with the user account on your computer. This
username will be the output from
nelle should always be replaced by that username.
Remember, the Shell is a program that runs other programs rather than doing calculations itself. So the commands you type must be the names of existing programs. If you type the name of a program that does not exist and hit enter, you will see an error message similar to this:
-bash: mycommand: command not found
The Shell (Bash) tells you that it cannot find the program
because the program you are trying to run does not exist on your computer.
We will touch on quite a few commands in the course of this tutorial, but there
are actually many more than we can cover here.
let’s find out where we are by running a command called
(which stands for “print working directory”).
At any moment,
our current working directory
is our current default directory,
the directory that the computer assumes we want to run commands in
unless we explicitly specify something else.
the computer’s response is
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
and on Windows it will be similar to
C:\Documents and Settings\nelle or
(Note that it may look slightly different for different versions of Windows.)
On lxplus your home directory is placed on a filesystem which can be shared
between multiple computers called AFS.
If your CERN username is
cernuser then your home directory will be:
In future examples, we’ve used Mac output as the default - Linux and Windows output may differ slightly, but should be generally similar.
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:
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
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 is the first part of its name.
we know that
/Users is stored inside the root directory
because its name begins with
Notice that there are two meanings for the
When it appears at the front of a file or directory name,
it refers to the root directory. When it appears inside a name,
it’s just a separator.
we find one directory for each user with an account on Nelle’s machine,
her colleagues the Mummy and Wolfman.
The Mummy’s files are stored in
and Nelle’s in
/Users/nelle. Because Nelle is the user in our
examples here, this is why 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
which stands for “listing”:
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
arranged neatly into columns.
We can make its output more comprehensible by using the flag
(also known as a switch or an option) ,
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 flags. To find out what they are, we can type:
$ 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 -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 --file-type likewise, except do not append '*' --format=WORD across -x, commas -m, horizontal -x, long -l, single-column -1, verbose -l, vertical -C --full-time like -l --time-style=full-iso -g like -l, but do not list owner --group-directories-first group directories before files; can be augmented with a --sort option, but any use of --sort=none (-U) disables grouping -G, --no-group in a long listing, don't print group names -h, --human-readable with -l and/or -s, print human readable sizes (e.g., 1K 234M 2G) --si likewise, but use powers of 1000 not 1024 -H, --dereference-command-line follow symbolic links listed on the command line --dereference-command-line-symlink-to-dir follow each command line symbolic link that points to a directory --hide=PATTERN do not list implied entries matching shell PATTERN (overridden by -a or -A) --indicator-style=WORD append indicator with style WORD to entry names: none (default), slash (-p), file-type (--file-type), classify (-F) -i, --inode print the index number of each file -I, --ignore=PATTERN do not list implied entries matching shell PATTERN -k, --kibibytes default to 1024-byte blocks for disk usage -l use a long listing format -L, --dereference when showing file information for a symbolic link, show information for the file the link references rather than for the link itself -m fill width with a comma separated list of entries -n, --numeric-uid-gid like -l, but list numeric user and group IDs -N, --literal print raw entry names (don't treat e.g. control characters specially) -o like -l, but do not list group information -p, --indicator-style=slash append / indicator to directories -q, --hide-control-chars print ? instead of nongraphic characters --show-control-chars show nongraphic characters as-is (the default, unless program is 'ls' and output is a terminal) -Q, --quote-name enclose entry names in double quotes --quoting-style=WORD use quoting style WORD for entry names: literal, locale, shell, shell-always, shell-escape, shell-escape-always, c, escape -r, --reverse reverse order while sorting -R, --recursive list subdirectories recursively -s, --size print the allocated size of each file, in blocks -S sort by file size, largest first --sort=WORD sort by WORD instead of name: none (-U), size (-S), time (-t), version (-v), extension (-X) --time=WORD with -l, show time as WORD instead of default modification time: atime or access or use (-u); ctime or status (-c); also use specified time as sort key if --sort=time (newest first) --time-style=STYLE with -l, show times using style STYLE: full-iso, long-iso, iso, locale, or +FORMAT; FORMAT is interpreted like in 'date'; if FORMAT is FORMAT1<newline>FORMAT2, then FORMAT1 applies to non-recent files and FORMAT2 to recent files; if STYLE is prefixed with 'posix-', STYLE takes effect only outside the POSIX locale -t sort by modification time, newest first -T, --tabsize=COLS assume tab stops at each COLS instead of 8 -u with -lt: sort by, and show, access time; with -l: show access time and sort by name; otherwise: sort by access time, newest first -U do not sort; list entries in directory order -v natural sort of (version) numbers within text -w, --width=COLS set output width to COLS. 0 means no limit -x list entries by lines instead of by columns -X sort alphabetically by entry extension -Z, --context print any security context of each file -1 list one file per line. Avoid '\n' with -q or -b --help display this help and exit --version output version information and exit The SIZE argument is an integer and optional unit (example: 10K is 10*1024). Units are K,M,G,T,P,E,Z,Y (powers of 1024) or KB,MB,... (powers of 1000). Using color to distinguish file types is disabled both by default and with --color=never. With --color=auto, ls emits color codes only when standard output is connected to a terminal. The LS_COLORS environment variable can change the settings. Use the dircolors command to set it. Exit status: 0 if OK, 1 if minor problems (e.g., cannot access subdirectory), 2 if serious trouble (e.g., cannot access command-line argument). GNU coreutils online help: <http://www.gnu.org/software/coreutils/> Full documentation at: <http://www.gnu.org/software/coreutils/ls> or available locally via: info '(coreutils) ls invocation'
Many bash commands, and programs that people have written that can be
run from within bash, support a
--help flag to display more
information on how to use the commands or programs.
Unsupported command-line options
If you try to use an option (flag) that is not supported,
ls and other programs
will print an error message similar to this:
$ ls -j
ls: invalid option -- 'j' Try 'ls --help' for more information.
For more information on how to use
ls we can type
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.
man and Git for Windows
The bash shell provided by Git for Windows does not
man command. Doing a web search for
unix man page COMMAND (e.g.
unix man page grep)
provides links to numerous copies of the Unix manual
For example, GNU provides links to its
these include grep,
core GNU utilities,
which covers many commands introduced within this lesson.
To navigate through the
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 a full page.
man pages by typing “q”.
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
the shell thinks we’re trying to run a command called
which doesn’t exist.
Parameters vs. Arguments
According to Wikipedia, the terms argument and parameter mean slightly different things. In practice, however, most people use them interchangeably to refer to the input term(s) given to a command. Consider the example below:
ls -lh Documents
ls is the command,
-lh are the flags (also called options),
Documents is the argument.
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,
ls with the
-F flag and the argument
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.
As you may now see, using a bash shell is strongly dependent on the idea that your files are organized in a 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
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 -F Desktop/data-shell
creatures/ molecules/ notes.txt solar.pdf data/ north-pacific-gyre/ pizza.cfg writing/
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
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
data-shell directory, then into the
cd doesn’t print anything,
but if we run
pwd after it, we can see that we are now
If we run
ls without arguments now,
it lists the contents of
because that’s where we now are:
$ 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? 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.
if we run
pwd after running
cd .., we’re back in
The special directory
.. doesn’t usually show up when we run
ls. If we want
to display it, we can give
$ ls -F -a
./ creatures/ notes.txt ../ data/ pizza.cfg .bash_profile molecules/ solar.pdf Desktop/ north-pacific-gyre/ writing/
-a stands for “show all”;
ls to show us file and directory names that begin with
.. (which, if we’re in
/Users/nelle, refers to the
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 arguments can be combined
with a single
- and no spaces between the arguments:
ls -F -a is
Other Hidden Files
In addition to the hidden directories
., you may also see a file
.bash_profile. This file usually contains shell configuration
settings. You may also see other files and directories beginning
.. These are usually files and directories that are used to configure
different programs on your computer. The prefix
. is used to prevent these
configuration files from cluttering the terminal when a standard
The special names
.. don’t belong to
they are interpreted the same way by every program.
if we are in
ls .. will give us a listing of
When the meanings of the parts are the same no matter how they’re combined,
programmers say they are orthogonal:
Orthogonal systems tend to be easier for people to learn
because there are fewer special cases and exceptions to keep track of.
These then, are the basic commands for navigating the filesystem on your computer:
cd. Let’s explore some variations on those commands. What happens
if you type
cd on its own, without giving
How can you check what happened?
pwd gives us the answer!
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
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
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
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
$ cd /Users/nelle/Desktop/data-shell
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
~/data is equivalent to
/Users/nelle/data. This only works if it is the first character in the
here/there/~/elsewhere is not
Another shortcut is the
- (dash) character.
cd will translate
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.
Nelle’s Pipeline: Organizing Files
Knowing just 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
(to remind herself where the data came from).
she creates a directory called
which is the date she started processing the samples.
She used to use names like
but she found them hard to understand after a couple of years.
(The final straw was when she found herself creating
a directory called
Nelle names her directories “year-month-day”, with leading zeroes for months and days, because the shell displays file and directory names in alphabetical order. If she used month names, December would come before July; if she didn’t use leading zeroes, November (’11’) would come before July (’7’). Similarly, putting the year first means that June 2012 will come before June 2013.
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
NENE01812A.txt, and so on.
All 1520 files will go into the same directory.
Now in her current directory
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.
Absolute vs Relative Paths
which of the following commands could Amanda use to navigate to her home directory,
.stands for the current directory.
/stands for the root directory.
No: Amanda’s home directory is
No: this goes up two levels, i.e. ends in
~stands for the user’s home directory, in this case
No: this would navigate into a directory
homein 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
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
No: this is the content of
Users/thing/backup, but with
..we asked for one level further up.
No: see previous explanation.
ls Reading Comprehension
Assuming a directory structure as in the above Figure
(File System for Challenge Questions), if
ls to display things in reverse order,
what command will display:
pnas_sub/ pnas_final/ original/
ls -r -F
ls -r -F /Users/backup
Either #2 or #3 above, but not #1.
pwdis not the name of a directory.
lswithout directory argument lists files and directories in the current directory.
Yes: uses the absolute path explicitly.
Correct: see explanations above.
Exploring More ls Flags
What does the command
ls do when used with the
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.
-l flag 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. The
-h flag makes the file size
“human readable”, i.e. display something like
5.3K instead of
Listing Recursively and By Time
ls -R lists the contents of directories recursively, i.e., lists
their sub-directories, sub-sub-directories, and so on in alphabetical order
at each level. The command
ls -t lists things by time of last change, with
most recently changed files or directories first.
In what order does
ls -R -t display things? Hint:
ls -l uses a long listing
format to view timestamps.
The directories are listed alphabetical at each level, the files/directories in each directory are sorted by time of last change.
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 pathchanges the current working directory.
ls pathprints a listing of a specific file or directory;
lson its own lists the current working directory.
pwdprints the user’s current working directory.
whoamishows 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
..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