Content from Introducing the Command Line

Last updated on 2024-01-29 | Edit this page

Overview

Questions

  • What is a command shell and why would I use one?

Objectives

  • Explain when and why command-line interfaces should be used instead of graphical interfaces.

Background

Humans and computers commonly interact in many different ways, such as through a keyboard and mouse, touch screen interfaces, or using speech recognition systems. The most widely used way to interact with personal computers is called a graphical user interface (GUI). With a GUI, we give instructions by clicking a mouse and using menu-driven interactions.

While the visual aid of a GUI makes it intuitive to learn, this way of delivering instructions to a computer scales very poorly. Imagine the following task: for a literature search, you have to copy the third line of one thousand text files in one thousand different directories and paste it into a single file. Using a GUI, you would not only be clicking at your desk for several hours, but you could potentially also commit an error in the process of completing this repetitive task. This is where we take advantage of the Unix shell. The Unix shell is both a command-line interface (CLI) and a scripting language, allowing such repetitive tasks to be done automatically and fast. With the proper commands, the shell can repeat tasks with or without some modification as many times as we want. Using the shell, the task in the literature example can be accomplished in seconds.

The Shell

The shell is a program where users can type commands. With the shell, it’s possible to invoke complicated programs like climate modeling software or simple commands that create an empty directory with only one line of code. The most popular Unix shell is Bash (the Bourne Again SHell — so-called because it’s derived from a shell written by Stephen Bourne). Bash is the default shell on most modern implementations of Unix and in most packages that provide Unix-like tools for Windows. Note that ‘Git Bash’ is a piece of software that enables Windows users to use a Bash like interface when interacting with Git.

Using the shell will take some effort and some time to learn. While a GUI presents you with choices to select, CLI choices are not automatically presented to you, so you must learn a few commands like new vocabulary in a language you’re studying. However, unlike a spoken language, a small number of “words” (i.e. commands) gets you a long way, and we’ll cover those essential few today.

The grammar of a shell allows you to combine existing tools into powerful pipelines and handle large volumes of data automatically. Sequences of commands can be written into a script, improving the reproducibility of workflows.

In addition, the command line is often the easiest way to interact with remote machines and supercomputers. Familiarity with the shell is near essential to run a variety of specialized tools and resources including high-performance computing systems. As clusters and cloud computing systems become more popular for scientific data crunching, being able to interact with the shell is becoming a necessary skill. We can build on the command-line skills covered here to tackle a wide range of scientific questions and computational challenges.

Let’s get started.

When the shell is first opened, you are presented with a prompt, indicating that the shell is waiting for input.

BASH 

$

The shell typically uses $ as the prompt, but may use a different symbol. In the examples for this lesson, we’ll show the prompt as $. Most importantly, do not type the prompt when typing commands. Only type the command that follows the prompt. This rule applies both in these lessons and in lessons from other sources. Also note that after you type a command, you have to press the Enter key to execute it.

The prompt is followed by a text cursor, a character that indicates the position where your typing will appear. The cursor is usually a flashing or solid block, but it can also be an underscore or a pipe. You may have seen it in a text editor program, for example.

Note that your prompt might look a little different. In particular, most popular shell environments by default put your user name and the host name before the $. Such a prompt might look like, e.g.:

BASH 

nelle@localhost $

The prompt might even include more than this. Do not worry if your prompt is not just a short $. This lesson does not depend on this additional information and it should also not get in your way. The only important item to focus on is the $ character itself and we will see later why.

So let’s try our first command, ls, which is short for listing. This command will list the contents of the current directory:

BASH 

$ ls

OUTPUT 

Desktop     Downloads   Movies      Pictures
Documents   Library     Music       Public

Command not found

If the shell can’t find a program whose name is the command you typed, it will print an error message such as:

BASH 

$ ks

OUTPUT 

ks: command not found

This might happen if the command was mis-typed or if the program corresponding to that command is not installed.

Nelle’s Pipeline: A Typical Problem

Nelle Nemo, a marine biologist, has just returned from a six-month survey of the North Pacific Gyre, where she has been sampling gelatinous marine life in the Great Pacific Garbage Patch. She has 1520 samples that she’s run through an assay machine to measure the relative abundance of 300 proteins. She needs to run these 1520 files through an imaginary program called goostats.sh. In addition to this huge task, she has to write up results by the end of the month, so her paper can appear in a special issue of Aquatic Goo Letters.

If Nelle chooses to run goostats.sh by hand using a GUI, she’ll have to select and open a file 1520 times. If goostats.sh takes 30 seconds to run each file, the whole process will take more than 12 hours of Nelle’s attention. With the shell, Nelle can instead assign her computer this mundane task while she focuses her attention on writing her paper.

The next few lessons will explore the ways Nelle can achieve this. More specifically, the lessons explain how she can use a command shell to run the goostats.sh program, using loops to automate the repetitive steps of entering file names, so that her computer can work while she writes her paper.

As a bonus, once she has put a processing pipeline together, she will be able to use it again whenever she collects more data.

In order to achieve her task, Nelle needs to know how to:

  • navigate to a file/directory
  • create a file/directory
  • check the length of a file
  • chain commands together
  • retrieve a set of files
  • iterate over files
  • run a shell script containing her pipeline

Key Points

  • A shell is a program whose primary purpose is to read commands and run other programs.
  • This lesson uses Bash, the default shell in many implementations of Unix.
  • Programs can be run in Bash by entering commands at the command-line prompt.
  • The shell’s main advantages are its high action-to-keystroke ratio, its support for automating repetitive tasks, and its capacity to access networked machines.
  • A significant challenge when using the shell can be knowing what commands need to be run and how to run them.

This chapter is from “Software Carpentry The Unix Shell”. It is licensed under the CC-BY-4.0.

Content from Navigating Files and Directories

Last updated on 2024-01-29 | Edit this page

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.

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:

BASH 

$ pwd

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 file system is made up of a root directory that contains sub-directories titled bin, data, users, and tmp

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.

Like other directories, home directories are sub-directories underneath "/Users" like "/Users/imhotep", "/Users/larry" or"/Users/nelle"

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:

BASH 

$ 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.

BASH 

$ ls -F

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:

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

BASH 

$ ls --help
  1. We can read its manual with man (available on Linux and macOS):

BASH 

$ man ls

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.

BASH 

$ ls --help

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
...        ...        ...

Unsupported command-line options

If you try to use an option that is not supported, ls and other commands will usually print an error message similar to:

BASH 

$ ls -j

ERROR 

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

The man command

The other way to learn about ls is to type

BASH 

$ 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.

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:

BASH 

$ ls -F Desktop

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:

BASH 

$ ls -F Desktop/shell-lesson-data

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:

BASH 

$ cd Desktop
$ cd shell-lesson-data
$ cd exercise-data

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:

BASH 

$ pwd

OUTPUT 

/Users/nelle/Desktop/shell-lesson-data/exercise-data

BASH 

$ ls -F

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:

BASH 

$ cd shell-lesson-data

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:

BASH 

$ 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/shell-lesson-data:

BASH 

$ pwd

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:

BASH 

$ ls -F -a

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.

Other Hidden Files

In addition to the hidden directories .. and ., you may also see a file called .bash_profile. This file usually contains shell configuration settings. You may also see other files and directories beginning with .. 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 ls command is used.

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?

BASH 

$ cd

How can you check what happened? pwd gives us the answer!

BASH 

$ pwd

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:

BASH 

$ cd Desktop/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.

BASH 

$ pwd

OUTPUT 

/Users/nelle/Desktop/shell-lesson-data/exercise-data

BASH 

$ cd /Users/nelle/Desktop/shell-lesson-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).

BASH 

$ cd ~/Desktop/shell-lesson-data

Then cd into the exercise-data/creatures directory

BASH 

$ cd exercise-data/creatures

Now if you run

BASH 

$ cd -

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?

  1. cd .
  2. cd /
  3. cd /home/nelle
  4. cd ../..
  5. cd ~
  6. cd home
  7. cd ~/data/..
  8. cd
  9. cd ..
  1. No: . stands for the current directory.
  2. No: / stands for the root directory.
  3. No: Nelle’s home directory is /Users/nelle.
  4. No: this command goes up two levels, i.e. ends in /Users.
  5. Yes: ~ stands for the user’s home directory, in this case /Users/nelle.
  6. No: this command would navigate into a directory home in the current directory if it exists.
  7. Yes: unnecessarily complicated, but correct.
  8. Yes: shortcut to go back to the user’s home directory.
  9. Yes: goes up one level.

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/
A directory tree below the Users directory where "/Users" contains the directories "backup" and "thing"; "/Users/backup" contains "original","pnas_final" and "pnas_sub"; "/Users/thing" contains "backup"; and"/Users/thing/backup" contains "2012-12-01", "2013-01-08" and"2013-01-27"
  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/.

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/
A directory tree below the Users directory where "/Users" contains the directories "backup" and "thing"; "/Users/backup" contains "original","pnas_final" and "pnas_sub"; "/Users/thing" contains "backup"; and"/Users/thing/backup" contains "2012-12-01", "2013-01-08" and"2013-01-27"
  1. ls pwd
  2. ls -r -F
  3. ls -r -F /Users/backup
  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.

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:

BASH 

$ ls -F /
General syntax of a shell command

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:

BASH 

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

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.

BASH 

$ ls -S exercise-data

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:

BASH 

$ ls -F /

OUTPUT 

Applications/         System/
Library/              Users/
Network/              Volumes/

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.

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:

BASH 

$ ls north-pacific-gyre/

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:

BASH 

$ ls nor

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

BASH 

$ 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’.

BASH 

$ ls north-pacific-gyre/goo

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

BASH 

ls north-pacific-gyre/goo
goodiff.sh   goostats.sh

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’.

This chapter is from “Software Carpentry The Unix Shell”. It is licensed under the CC-BY-4.0.

Content from Working With Files and Directories

Last updated on 2024-01-29 | Edit this page

Overview

Questions

  • How can I create, copy, and delete files and directories?
  • How can I edit files?

Objectives

  • Create a directory hierarchy that matches a given diagram.
  • Create files in that hierarchy using an editor or by copying and renaming existing files.
  • Delete, copy and move specified files and/or directories.

Creating directories

We now know how to explore files and directories, but how do we create them in the first place?

In this episode we will learn about creating and moving files and directories, using the exercise-data/writing directory as an example.

Step one: see where we are and what we already have

We should still be in the shell-lesson-data directory on the Desktop, which we can check using:

BASH 

$ pwd

OUTPUT 

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

Next we’ll move to the exercise-data/writing directory and see what it contains:

BASH 

$ cd exercise-data/writing/
$ ls -F

OUTPUT 

haiku.txt  LittleWomen.txt

Create a directory

Let’s create a new directory called thesis using the command mkdir thesis (which has no output):

BASH 

$ mkdir thesis

As you might guess from its name, mkdir means ‘make directory’. Since thesis is a relative path (i.e., does not have a leading slash, like /what/ever/thesis), the new directory is created in the current working directory:

BASH 

$ ls -F

OUTPUT 

haiku.txt  LittleWomen.txt  thesis/

Since we’ve just created the thesis directory, there’s nothing in it yet:

BASH 

$ ls -F thesis

Note that mkdir is not limited to creating single directories one at a time. The -p option allows mkdir to create a directory with nested subdirectories in a single operation:

BASH 

$ mkdir -p ../project/data ../project/results

The -R option to the ls command will list all nested subdirectories within a directory. Let’s use ls -FR to recursively list the new directory hierarchy we just created in the project directory:

BASH 

$ ls -FR ../project

OUTPUT 

../project/:
data/  results/

../project/data:

../project/results:

Two ways of doing the same thing

Using the shell to create a directory is no different than using a file explorer. If you open the current directory using your operating system’s graphical file explorer, the thesis directory will appear there too. While the shell and the file explorer are two different ways of interacting with the files, the files and directories themselves are the same.

Good names for files and directories

Complicated names of files and directories can make your life painful when working on the command line. Here we provide a few useful tips for the names of your files and directories.

  1. Don’t use spaces.

Spaces can make a name more meaningful, but since spaces are used to separate arguments on the command line it is better to avoid them in names of files and directories. You can use - or _ instead (e.g. north-pacific-gyre/ rather than north pacific gyre/). To test this out, try typing mkdir north pacific gyre and see what directory (or directories!) are made when you check with ls -F.

  1. Don’t begin the name with - (dash).

Commands treat names starting with - as options.

  1. Stick with letters, numbers, . (period or ‘full stop’), - (dash) and _ (underscore).

Many other characters have special meanings on the command line. We will learn about some of these during this lesson. There are special characters that can cause your command to not work as expected and can even result in data loss.

If you need to refer to names of files or directories that have spaces or other special characters, you should surround the name in quotes ("").

Create a text file

Let’s change our working directory to thesis using cd, then run a text editor called Nano to create a file called draft.txt:

BASH 

$ cd thesis
$ nano draft.txt

Which Editor?

When we say, ‘nano is a text editor’ we really do mean ‘text’. It can only work with plain character data, not tables, images, or any other human-friendly media. We use it in examples because it is one of the least complex text editors. However, because of this trait, it may not be powerful enough or flexible enough for the work you need to do after this workshop. On Unix systems (such as Linux and macOS), many programmers use Emacs or Vim (both of which require more time to learn), or a graphical editor such as Gedit or VScode. On Windows, you may wish to use Notepad++. Windows also has a built-in editor called notepad that can be run from the command line in the same way as nano for the purposes of this lesson.

No matter what editor you use, you will need to know where it searches for and saves files. If you start it from the shell, it will (probably) use your current working directory as its default location. If you use your computer’s start menu, it may want to save files in your Desktop or Documents directory instead. You can change this by navigating to another directory the first time you ‘Save As…’

Let’s type in a few lines of text.

screenshot of nano text editor in action with the text It's not publish or perish any more, it's share and thrive

Once we’re happy with our text, we can press Ctrl+O (press the Ctrl or Control key and, while holding it down, press the O key) to write our data to disk. We will be asked to provide a name for the file that will contain our text. Press Return to accept the suggested default of draft.txt.

Once our file is saved, we can use Ctrl+X to quit the editor and return to the shell.

Control, Ctrl, or ^ Key

The Control key is also called the ‘Ctrl’ key. There are various ways in which using the Control key may be described. For example, you may see an instruction to press the Control key and, while holding it down, press the X key, described as any of:

  • Control-X
  • Control+X
  • Ctrl-X
  • Ctrl+X
  • ^X
  • C-x

In nano, along the bottom of the screen you’ll see ^G Get Help ^O WriteOut. This means that you can use Control-G to get help and Control-O to save your file.

nano doesn’t leave any output on the screen after it exits, but ls now shows that we have created a file called draft.txt:

BASH 

$ ls

OUTPUT 

draft.txt

Creating Files a Different Way

We have seen how to create text files using the nano editor. Now, try the following command:

BASH 

$ touch my_file.txt

  1. What did the touch command do? When you look at your current directory using the GUI file explorer, does the file show up?

  2. Use ls -l to inspect the files. How large is my_file.txt?

  3. When might you want to create a file this way?

  1. The touch command generates a new file called my_file.txt in your current directory. You can observe this newly generated file by typing ls at the command line prompt. my_file.txt can also be viewed in your GUI file explorer.

  2. When you inspect the file with ls -l, note that the size of my_file.txt is 0 bytes. In other words, it contains no data. If you open my_file.txt using your text editor it is blank.

  3. Some programs do not generate output files themselves, but instead require that empty files have already been generated. When the program is run, it searches for an existing file to populate with its output. The touch command allows you to efficiently generate a blank text file to be used by such programs.

Creating Files a Different Way (continued)

To avoid confusion later on, we suggest removing the file you’ve just created before proceeding with the rest of the episode, otherwise future outputs may vary from those given in the lesson. To do this, use the following command:

BASH 

$ rm my_file.txt

What’s In A Name?

You may have noticed that all of Nelle’s files are named ‘something dot something’, and in this part of the lesson, we always used the extension .txt. This is just a convention; we can call a file mythesis or almost anything else we want. However, most people use two-part names most of the time to help them (and their programs) tell different kinds of files apart. The second part of such a name is called the filename extension and indicates what type of data the file holds: .txt signals a plain text file, .pdf indicates a PDF document, .cfg is a configuration file full of parameters for some program or other, .png is a PNG image, and so on.

This is just a convention, albeit an important one. Files merely contain bytes; it’s up to us and our programs to interpret those bytes according to the rules for plain text files, PDF documents, configuration files, images, and so on.

Naming a PNG image of a whale as whale.mp3 doesn’t somehow magically turn it into a recording of whale song, though it might cause the operating system to associate the file with a music player program. In this case, if someone double-clicked whale.mp3 in a file explorer program,the music player will automatically (and erroneously) attempt to open the whale.mp3 file.

Moving files and directories

Returning to the shell-lesson-data/exercise-data/writing directory,

BASH 

$ cd ~/Desktop/shell-lesson-data/exercise-data/writing

In our thesis directory we have a file draft.txt which isn’t a particularly informative name, so let’s change the file’s name using mv, which is short for ‘move’:

BASH 

$ mv thesis/draft.txt thesis/quotes.txt

The first argument tells mv what we’re ‘moving’, while the second is where it’s to go. In this case, we’re moving thesis/draft.txt to thesis/quotes.txt, which has the same effect as renaming the file. Sure enough, ls shows us that thesis now contains one file called quotes.txt:

BASH 

$ ls thesis

OUTPUT 

quotes.txt

One must be careful when specifying the target file name, since mv will silently overwrite any existing file with the same name, which could lead to data loss. By default, mv will not ask for confirmation before overwriting files. However, an additional option, mv -i (or mv --interactive), will cause mv to request such confirmation.

Note that mv also works on directories.

Let’s move quotes.txt into the current working directory. We use mv once again, but this time we’ll use just the name of a directory as the second argument to tell mv that we want to keep the filename but put the file somewhere new. (This is why the command is called ‘move’.) In this case, the directory name we use is the special directory name . that we mentioned earlier.

BASH 

$ mv thesis/quotes.txt .

The effect is to move the file from the directory it was in to the current working directory. ls now shows us that thesis is empty:

BASH 

$ ls thesis

OUTPUT 

$

Alternatively, we can confirm the file quotes.txt is no longer present in the thesis directory by explicitly trying to list it:

BASH 

$ ls thesis/quotes.txt

ERROR 

ls: cannot access 'thesis/quotes.txt': No such file or directory

ls with a filename or directory as an argument only lists the requested file or directory. If the file given as the argument doesn’t exist, the shell returns an error as we saw above. We can use this to see that quotes.txt is now present in our current directory:

BASH 

$ ls quotes.txt

OUTPUT 

quotes.txt

Moving Files to a new folder

After running the following commands, Jamie realizes that she put the files sucrose.dat and maltose.dat into the wrong folder. The files should have been placed in the raw folder.

BASH 

$ ls -F
 analyzed/ raw/
$ ls -F analyzed
fructose.dat glucose.dat maltose.dat sucrose.dat
$ cd analyzed

Fill in the blanks to move these files to the raw/ folder (i.e. the one she forgot to put them in)

BASH 

$ mv sucrose.dat maltose.dat ____/____

BASH 

$ mv sucrose.dat maltose.dat ../raw

Recall that .. refers to the parent directory (i.e. one above the current directory) and that . refers to the current directory.

Copying files and directories

The cp command works very much like mv, except it copies a file instead of moving it. We can check that it did the right thing using ls with two paths as arguments — like most Unix commands, ls can be given multiple paths at once:

BASH 

$ cp quotes.txt thesis/quotations.txt
$ ls quotes.txt thesis/quotations.txt

OUTPUT 

quotes.txt   thesis/quotations.txt

We can also copy a directory and all its contents by using the recursive option -r, e.g. to back up a directory:

BASH 

$ cp -r thesis thesis_backup

We can check the result by listing the contents of both the thesis and thesis_backup directory:

BASH 

$ ls thesis thesis_backup

OUTPUT 

thesis:
quotations.txt

thesis_backup:
quotations.txt

It is important to include the -r flag. If you want to copy a directory and you omit this option you will see a message that the directory has been omitted because -r not specified.

BASH 

$ cp thesis thesis_backup
cp: -r not specified; omitting directory 'thesis'

Renaming Files

Suppose that you created a plain-text file in your current directory to contain a list of the statistical tests you will need to do to analyze your data, and named it statstics.txt

After creating and saving this file you realize you misspelled the filename! You want to correct the mistake, which of the following commands could you use to do so?

  1. cp statstics.txt statistics.txt
  2. mv statstics.txt statistics.txt
  3. mv statstics.txt .
  4. cp statstics.txt .
  1. No. While this would create a file with the correct name, the incorrectly named file still exists in the directory and would need to be deleted.
  2. Yes, this would work to rename the file.
  3. No, the period(.) indicates where to move the file, but does not provide a new file name; identical file names cannot be created.
  4. No, the period(.) indicates where to copy the file, but does not provide a new file name; identical file names cannot be created.

Moving and Copying

What is the output of the closing ls command in the sequence shown below?

BASH 

$ pwd

OUTPUT 

/Users/jamie/data

BASH 

$ ls

OUTPUT 

proteins.dat

BASH 

$ mkdir recombined
$ mv proteins.dat recombined/
$ cp recombined/proteins.dat ../proteins-saved.dat
$ ls
  1. proteins-saved.dat recombined
  2. recombined
  3. proteins.dat recombined
  4. proteins-saved.dat

We start in the /Users/jamie/data directory, and create a new folder called recombined. The second line moves (mv) the file proteins.dat to the new folder (recombined). The third line makes a copy of the file we just moved. The tricky part here is where the file was copied to. Recall that .. means ‘go up a level’, so the copied file is now in /Users/jamie. Notice that .. is interpreted with respect to the current working directory, not with respect to the location of the file being copied. So, the only thing that will show using ls (in /Users/jamie/data) is the recombined folder.

  1. No, see explanation above. proteins-saved.dat is located at /Users/jamie
  2. Yes
  3. No, see explanation above. proteins.dat is located at /Users/jamie/data/recombined
  4. No, see explanation above. proteins-saved.dat is located at /Users/jamie

Removing files and directories

Returning to the shell-lesson-data/exercise-data/writing directory, let’s tidy up this directory by removing the quotes.txt file we created. The Unix command we’ll use for this is rm (short for ‘remove’):

BASH 

$ rm quotes.txt

We can confirm the file has gone using ls:

BASH 

$ ls quotes.txt

ERROR 

ls: cannot access 'quotes.txt': No such file or directory

Deleting Is Forever

The Unix shell doesn’t have a trash bin that we can recover deleted files from (though most graphical interfaces to Unix do). Instead, when we delete files, they are unlinked from the file system so that their storage space on disk can be recycled. Tools for finding and recovering deleted files do exist, but there’s no guarantee they’ll work in any particular situation, since the computer may recycle the file’s disk space right away.

Using rm Safely

What happens when we execute rm -i thesis_backup/quotations.txt? Why would we want this protection when using rm?

OUTPUT 

rm: remove regular file 'thesis_backup/quotations.txt'? y

The -i option will prompt before (every) removal (use Y to confirm deletion or N to keep the file). The Unix shell doesn’t have a trash bin, so all the files removed will disappear forever. By using the -i option, we have the chance to check that we are deleting only the files that we want to remove.

If we try to remove the thesis directory using rm thesis, we get an error message:

BASH 

$ rm thesis

ERROR 

rm: cannot remove 'thesis': Is a directory

This happens because rm by default only works on files, not directories.

rm can remove a directory and all its contents if we use the recursive option -r, and it will do so without any confirmation prompts:

BASH 

$ rm -r thesis

Given that there is no way to retrieve files deleted using the shell, rm -r should be used with great caution (you might consider adding the interactive option rm -r -i).

Operations with multiple files and directories

Oftentimes one needs to copy or move several files at once. This can be done by providing a list of individual filenames, or specifying a naming pattern using wildcards. Wildcards are special characters that can be used to represent unknown characters or sets of characters when navigating the Unix file system.

Copy with Multiple Filenames

For this exercise, you can test the commands in the shell-lesson-data/exercise-data directory.

In the example below, what does cp do when given several filenames and a directory name?

BASH 

$ mkdir backup
$ cp creatures/minotaur.dat creatures/unicorn.dat backup/

In the example below, what does cp do when given three or more file names?

BASH 

$ cd creatures
$ ls -F

OUTPUT 

basilisk.dat  minotaur.dat  unicorn.dat

BASH 

$ cp minotaur.dat unicorn.dat basilisk.dat

If given more than one file name followed by a directory name (i.e. the destination directory must be the last argument), cp copies the files to the named directory.

If given three file names, cp throws an error such as the one below, because it is expecting a directory name as the last argument.

ERROR 

cp: target 'basilisk.dat' is not a directory

Using wildcards for accessing multiple files at once

Wildcards

* is a wildcard, which represents zero or more other characters. Let’s consider the shell-lesson-data/exercise-data/alkanes directory: *.pdb represents ethane.pdb, propane.pdb, and every file that ends with ‘.pdb’. On the other hand, p*.pdb only represents pentane.pdb and propane.pdb, because the ‘p’ at the front can only represent filenames that begin with the letter ‘p’.

? is also a wildcard, but it represents exactly one character. So ?ethane.pdb could represent methane.pdb whereas *ethane.pdb represents both ethane.pdb and methane.pdb.

Wildcards can be used in combination with each other. For example, ???ane.pdb indicates three characters followed by ane.pdb, giving cubane.pdb ethane.pdb octane.pdb.

When the shell sees a wildcard, it expands the wildcard to create a list of matching filenames before running the preceding command. As an exception, if a wildcard expression does not match any file, Bash will pass the expression as an argument to the command as it is. For example, typing ls *.pdf in the alkanes directory (which contains only files with names ending with .pdb) results in an error message that there is no file called *.pdf. However, generally commands like wc and ls see the lists of file names matching these expressions, but not the wildcards themselves. It is the shell, not the other programs, that expands the wildcards.

List filenames matching a pattern

When run in the alkanes directory, which ls command(s) will produce this output?

ethane.pdb methane.pdb

  1. ls *t*ane.pdb
  2. ls *t?ne.*
  3. ls *t??ne.pdb
  4. ls ethane.*

The solution is 3.

1. shows all files whose names contain zero or more characters (*) followed by the letter t, then zero or more characters (*) followed by ane.pdb. This gives ethane.pdb methane.pdb octane.pdb pentane.pdb.

2. shows all files whose names start with zero or more characters (*) followed by the letter t, then a single character (?), then ne. followed by zero or more characters (*). This will give us octane.pdb and pentane.pdb but doesn’t match anything which ends in thane.pdb.

3. fixes the problems of option 2 by matching two characters (??) between t and ne. This is the solution.

4. only shows files starting with ethane..

More on Wildcards

Sam has a directory containing calibration data, datasets, and descriptions of the datasets:

BASH 

.
├── 2015-10-23-calibration.txt
├── 2015-10-23-dataset1.txt
├── 2015-10-23-dataset2.txt
├── 2015-10-23-dataset_overview.txt
├── 2015-10-26-calibration.txt
├── 2015-10-26-dataset1.txt
├── 2015-10-26-dataset2.txt
├── 2015-10-26-dataset_overview.txt
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
├── 2015-11-23-dataset_overview.txt
├── backup
│   ├── calibration
│   └── datasets
└── send_to_bob
    ├── all_datasets_created_on_a_23rd
    └── all_november_files

Before heading off to another field trip, she wants to back up her data and send some datasets to her colleague Bob. Sam uses the following commands to get the job done:

BASH 

$ cp *dataset* backup/datasets
$ cp ____calibration____ backup/calibration
$ cp 2015-____-____ send_to_bob/all_november_files/
$ cp ____ send_to_bob/all_datasets_created_on_a_23rd/

Help Sam by filling in the blanks.

The resulting directory structure should look like this

BASH 

.
├── 2015-10-23-calibration.txt
├── 2015-10-23-dataset1.txt
├── 2015-10-23-dataset2.txt
├── 2015-10-23-dataset_overview.txt
├── 2015-10-26-calibration.txt
├── 2015-10-26-dataset1.txt
├── 2015-10-26-dataset2.txt
├── 2015-10-26-dataset_overview.txt
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
├── 2015-11-23-dataset_overview.txt
├── backup
│   ├── calibration
│   │   ├── 2015-10-23-calibration.txt
│   │   ├── 2015-10-26-calibration.txt
│   │   └── 2015-11-23-calibration.txt
│   └── datasets
│       ├── 2015-10-23-dataset1.txt
│       ├── 2015-10-23-dataset2.txt
│       ├── 2015-10-23-dataset_overview.txt
│       ├── 2015-10-26-dataset1.txt
│       ├── 2015-10-26-dataset2.txt
│       ├── 2015-10-26-dataset_overview.txt
│       ├── 2015-11-23-dataset1.txt
│       ├── 2015-11-23-dataset2.txt
│       └── 2015-11-23-dataset_overview.txt
└── send_to_bob
    ├── all_datasets_created_on_a_23rd
    │   ├── 2015-10-23-dataset1.txt
    │   ├── 2015-10-23-dataset2.txt
    │   ├── 2015-10-23-dataset_overview.txt
    │   ├── 2015-11-23-dataset1.txt
    │   ├── 2015-11-23-dataset2.txt
    │   └── 2015-11-23-dataset_overview.txt
    └── all_november_files
        ├── 2015-11-23-calibration.txt
        ├── 2015-11-23-dataset1.txt
        ├── 2015-11-23-dataset2.txt
        └── 2015-11-23-dataset_overview.txt

BASH 

$ cp *calibration.txt backup/calibration
$ cp 2015-11-* send_to_bob/all_november_files/
$ cp *-23-dataset* send_to_bob/all_datasets_created_on_a_23rd/

Organizing Directories and Files

Jamie is working on a project, and she sees that her files aren’t very well organized:

BASH 

$ ls -F

OUTPUT 

analyzed/  fructose.dat    raw/   sucrose.dat

The fructose.dat and sucrose.dat files contain output from her data analysis. What command(s) covered in this lesson does she need to run so that the commands below will produce the output shown?

BASH 

$ ls -F

OUTPUT 

analyzed/   raw/

BASH 

$ ls analyzed

OUTPUT 

fructose.dat    sucrose.dat

BASH 

mv *.dat analyzed

Jamie needs to move her files fructose.dat and sucrose.dat to the analyzed directory. The shell will expand *.dat to match all .dat files in the current directory. The mv command then moves the list of .dat files to the ‘analyzed’ directory.

Reproduce a folder structure

You’re starting a new experiment and would like to duplicate the directory structure from your previous experiment so you can add new data.

Assume that the previous experiment is in a folder called 2016-05-18, which contains a data folder that in turn contains folders named raw and processed that contain data files. The goal is to copy the folder structure of the 2016-05-18 folder into a folder called 2016-05-20 so that your final directory structure looks like this:

OUTPUT 

2016-05-20/
└── data
   ├── processed
   └── raw

Which of the following set of commands would achieve this objective? What would the other commands do?

BASH 

$ mkdir 2016-05-20
$ mkdir 2016-05-20/data
$ mkdir 2016-05-20/data/processed
$ mkdir 2016-05-20/data/raw

BASH 

$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ cd data
$ mkdir raw processed

BASH 

$ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20/data/processed

BASH 

$ mkdir -p 2016-05-20/data/raw
$ mkdir -p 2016-05-20/data/processed

BASH 

$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ mkdir raw processed

The first two sets of commands achieve this objective. The first set uses relative paths to create the top-level directory before the subdirectories.

The third set of commands will give an error because the default behavior of mkdir won’t create a subdirectory of a non-existent directory: the intermediate level folders must be created first.

The fourth set of commands achieve this objective. Remember, the -p option, followed by a path of one or more directories, will cause mkdir to create any intermediate subdirectories as required.

The final set of commands generates the ‘raw’ and ‘processed’ directories at the same level as the ‘data’ directory.

Key Points

  • cp [old] [new] copies a file.
  • mkdir [path] creates a new directory.
  • mv [old] [new] moves (renames) a file or directory.
  • rm [path] removes (deletes) a file.
  • * matches zero or more characters in a filename, so *.txt matches all files ending in .txt.
  • ? matches any single character in a filename, so ?.txt matches a.txt but not any.txt.
  • Use of the Control key may be described in many ways, including Ctrl-X, Control-X, and ^X.
  • The shell does not have a trash bin: once something is deleted, it’s really gone.
  • 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.
  • Depending on the type of work you do, you may need a more powerful text editor than Nano.

title: Navigating Files and Directories teaching: 30 exercises: 10

Overview

Questions

  • How can I create, copy, and delete files and directories?
  • How can I edit files?

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.

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.

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:

BASH 

$ pwd

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 file system is made up of a root directory that contains sub-directories titled bin, data, users, and tmp

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.

Like other directories, home directories are sub-directories underneath "/Users" like "/Users/imhotep", "/Users/larry" or"/Users/nelle"

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:

BASH 

$ 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.

BASH 

$ ls -F

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:

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

BASH 

$ ls --help
  1. We can read its manual with man (available on Linux and macOS):

BASH 

$ man ls

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.

BASH 

$ ls --help

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
...        ...        ...

Unsupported command-line options

If you try to use an option that is not supported, ls and other commands will usually print an error message similar to:

BASH 

$ ls -j

ERROR 

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

The man command

The other way to learn about ls is to type

BASH 

$ 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.

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:

BASH 

$ ls -F Desktop

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:

BASH 

$ ls -F Desktop/shell-lesson-data

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:

BASH 

$ cd Desktop
$ cd shell-lesson-data
$ cd exercise-data

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:

BASH 

$ pwd

OUTPUT 

/Users/nelle/Desktop/shell-lesson-data/exercise-data

BASH 

$ ls -F

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:

BASH 

$ cd shell-lesson-data

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:

BASH 

$ 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/shell-lesson-data:

BASH 

$ pwd

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:

BASH 

$ ls -F -a

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.

Other Hidden Files

In addition to the hidden directories .. and ., you may also see a file called .bash_profile. This file usually contains shell configuration settings. You may also see other files and directories beginning with .. 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 ls command is used.

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?

BASH 

$ cd

How can you check what happened? pwd gives us the answer!

BASH 

$ pwd

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:

BASH 

$ cd Desktop/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.

BASH 

$ pwd

OUTPUT 

/Users/nelle/Desktop/shell-lesson-data/exercise-data

BASH 

$ cd /Users/nelle/Desktop/shell-lesson-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).

BASH 

$ cd ~/Desktop/shell-lesson-data

Then cd into the exercise-data/creatures directory

BASH 

$ cd exercise-data/creatures

Now if you run

BASH 

$ cd -

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?

  1. cd .
  2. cd /
  3. cd /home/nelle
  4. cd ../..
  5. cd ~
  6. cd home
  7. cd ~/data/..
  8. cd
  9. cd ..
  1. No: . stands for the current directory.
  2. No: / stands for the root directory.
  3. No: Nelle’s home directory is /Users/nelle.
  4. No: this command goes up two levels, i.e. ends in /Users.
  5. Yes: ~ stands for the user’s home directory, in this case /Users/nelle.
  6. No: this command would navigate into a directory home in the current directory if it exists.
  7. Yes: unnecessarily complicated, but correct.
  8. Yes: shortcut to go back to the user’s home directory.
  9. Yes: goes up one level.

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/
A directory tree below the Users directory where "/Users" contains the directories "backup" and "thing"; "/Users/backup" contains "original","pnas_final" and "pnas_sub"; "/Users/thing" contains "backup"; and"/Users/thing/backup" contains "2012-12-01", "2013-01-08" and"2013-01-27"
  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/.

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/
A directory tree below the Users directory where "/Users" contains the directories "backup" and "thing"; "/Users/backup" contains "original","pnas_final" and "pnas_sub"; "/Users/thing" contains "backup"; and"/Users/thing/backup" contains "2012-12-01", "2013-01-08" and"2013-01-27"
  1. ls pwd
  2. ls -r -F
  3. ls -r -F /Users/backup
  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.

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:

BASH 

$ ls -F /
General syntax of a shell command

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:

BASH 

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

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.

BASH 

$ ls -S exercise-data

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:

BASH 

$ ls -F /

OUTPUT 

Applications/         System/
Library/              Users/
Network/              Volumes/

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.

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:

BASH 

$ ls north-pacific-gyre/

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:

BASH 

$ ls nor

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

BASH 

$ 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’.

BASH 

$ ls north-pacific-gyre/goo

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

BASH 

ls north-pacific-gyre/goo
goodiff.sh   goostats.sh

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’.

This chapter is from “Software Carpentry The Unix Shell”. It is licensed under the CC-BY-4.0.