What is the shell?

Overview

Teaching: 60 min
Exercises: 30 min

Questions

• What is the shell?

• What is the command line?

• Why should I use it?

Objectives

• Explain the basics of the Unix shell

• Explain why and how to use the command line

• Use shell commands to work with directories and files

• Use shell commands to find and manipulate data

Introduction

In this session we will introduce task automation by looking at how data can be manipulated, counted, and mined using the Unix shell, a command line interface to your computer and the files to which it has access.

The shell is a program that allows you to interact with your computer using commands. It is the interface used on Linux and UNIX-based systems, such as Mac OS, and can be used on Windows, if installed.

For Windows users, popular shells such as Cygwin or Git Bash provide a Unix-like interface. In Windows 10, the Power Shell provides that functionality.

This session will cover a small number of basic commands using Git Bash for Windows users, Terminal for Mac OS, and the shell for Linux users. These commands constitute building blocks upon which more complex commands can be constructed to fit your data or project. Even if you do not do your own programming or your work currently does not involve the command line, knowing some basics about the shell can be useful.

The shell is one of the most productive programming environments ever created. Once mastered, you can use it to experiment with different commands interactively, then use what you have learned to automate your work. Graphical user interfaces may be better at the first, but the shell is still unbeaten at the second.

Note to Lesson Instructor: consider providing an example here of how you’ve used the Unix shell to solve a problem in the last week or month

What you can quickly learn is how to query lots of data for the information you want very quickly. Using Bash or any other shell sometimes feels more like programming than like using a mouse. Commands are terse (often only a couple of characters long), their names are frequently cryptic, and their output is lines of text rather than something visual like a graph. On the other hand, with only a few keystrokes, the shell allows you to combine existing tools into powerful pipelines and to handle large volumes of data automatically. This automation not only makes you more productive, but also improves the reproducibility of your workflows by allowing you to save and then repeat them with a few simple commands. Understanding the basics of the shell provides a useful foundation for learning to program, since some of the tasks you learn here such as loops, and the language - values, variables - will translate to programming.

Navigating the shell

We will begin with the basics of navigating the Unix shell.

Let’s start by opening the shell. This likely results in seeing a black window with a cursor flashing next to a dollar sign. This is our command line, and the $ is the command prompt to show that the system is ready for our input. The appearance of the prompt will vary from system to system, depending on how the set up has been configured, but it usually ends with a $.

When working in the shell, you are always somewhere in the computer’s file system, in some folder (directory). We will therefore start by finding out where we are by using the pwd command, which you can use whenever you are unsure about where you are. It stands for “print working directory” and the result of the command is printed to your standard output, which is the screen.

Let’s type pwd and hit enter to execute the command: (The $ sign is used to indicate a command to be typed on the command prompt, but we never type the $ sign itself, just what follows after it.)

$ pwd

/Users/riley

The output will be a path to your home directory. Let’s check if we recognise it by listing the contents of the directory. To do that, we use the ls command:

$ ls

Applications Documents    Library      Music        Public
Desktop      Downloads    Movies       Pictures

We may want more information than just a list of files and directories. We can get this by specifying various flags (also known as options, parameters, or, most frequently, arguments) to go with our basic commands. Arguments modify the workings of the command by telling the computer what sort of output or manipulation we want.

If we type ls -l and hit enter, the computer returns a list of files that contains information similar to what we would find in our Finder (Mac) or Explorer (Windows): the size of the files in bytes, the date it was created or last modified, and the file name.

$ ls -l

total 0
drwx------+  6 riley  staff   204 Jul 16 11:50 Desktop
drwx------+  3 riley  staff   102 Jul 16 11:30 Documents
drwx------+  3 riley  staff   102 Jul 16 11:30 Downloads
drwx------@ 46 riley  staff  1564 Jul 16 11:38 Library
drwx------+  3 riley  staff   102 Jul 16 11:30 Movies
drwx------+  3 riley  staff   102 Jul 16 11:30 Music
drwx------+  3 riley  staff   102 Jul 16 11:30 Pictures
drwxr-xr-x+  5 riley  staff   170 Jul 16 11:30 Public

In everyday usage we are more used to units of measurement like kilobytes, megabytes, and gigabytes. Luckily, there’s another flag -h that when used with the -l option, use unit suffixes: Byte, Kilobyte, Megabyte, Gigabyte, Terabyte and Petabyte in order to reduce the number of digits to three or less using base 2 for sizes.

Now ls -h won’t work on its own. When we want to combine two flags, we can just run them together. So, by typing ls -lh and hitting enter we receive an output in a human-readable format (note: the order here doesn’t matter).

$ ls -lh

total 0
drwx------+  6 riley  staff   204B Jul 16 11:50 Desktop
drwx------+  3 riley  staff   102B Jul 16 11:30 Documents
drwx------+  3 riley  staff   102B Jul 16 11:30 Downloads
drwx------@ 46 riley  staff   1.5K Jul 16 11:38 Library
drwx------+  3 riley  staff   102B Jul 16 11:30 Movies
drwx------+  3 riley  staff   102B Jul 16 11:30 Music
drwx------+  3 riley  staff   102B Jul 16 11:30 Pictures
drwxr-xr-x+  5 riley  staff   170B Jul 16 11:30 Public

We’ve now spent a great deal of time in our home directory. Let’s go somewhere else. We can do that through the cd or Change Directory command: (Note: On Windows and Mac, by default, the case of the file/directory doesn’t matter On Linux it does.)

$ cd Desktop

Notice that the command didn’t output anything. This means that it was carried out successfully. Let’s check by using pwd:

$ pwd

/Users/riley/Desktop

If something had gone wrong, however, the command would have told you. Let’s test that by trying to move into a non-existentdirectory:

$ cd "Evil plan to destroy the world"

bash: cd: Evil plan to destroy the world: No such file or directory

Notice that we surrounded the name by quotation marks. The arguments given to any shell command are separated by spaces, so a way to let them know that we mean ‘one single thing called “Evil plan to destroy the world”’, not ‘six different things’, is to use (single or double) quotation marks.

We’ve now seen how we can go ‘down’ through our directory structure (as in into more nested directories). If we want to go back, we can type cd ... This moves us ‘up’ one directory, putting us back where we started. If we ever get completely lost, the command cd without any arguments will bring us right back to the home directory, the place where we started.

Previous Directory

To switch back and forth between two directories use cd -.

Try exploring

Move around the computer, get used to moving in and out of directories, see how different file types appear in the Unix shell. Be sure to use the pwd and cd commands, and the different flags for the ls command you learned so far.

If you run Windows, also try typing explorer . to open Explorer for the current directory (the single dot means “current directory”). If you’re on Mac or Linux, try open . instead.

Being able to navigate the file system is very important for using the Unix shell effectively. As we become more comfortable, we can get very quickly to the directory that we want.

Getting help

Use the man command to invoke the manual page (documentation) for a shell command. For example, man ls displays all the arguments available to you - which saves you remembering them all! Try this for each command you’ve learned so far. Use the spacebar to navigate the manual pages. Use q at any time to quit.

Note: this command is for Mac and Linux users only. It does not work directly for Windows users. If you use windows, you can search for the Shell command on http://man.he.net/, and view the associated manual page.

Answer

$ man ls

LS(1)                     BSD General Commands Manual                    LS(1)

NAME
    ls -- list directory contents

SYNOPSIS
    ls [-ABCFGHLOPRSTUW@abcdefghiklmnopqrstuwx1] [file ...]

DESCRIPTION
    For each operand that names a file of a type other than directory, ls
    displays its name as well as any requested, associated information.  For
    each operand that names a file of type directory, ls displays the names
    of files contained within that directory, as well as any requested, asso-
    ciated information.

    If no operands are given, the contents of the current directory are dis-
    played.  If more than one operand is given, non-directory operands are
    displayed first; directory and non-directory operands are sorted sepa-
    rately and in lexicographical order.

    The following options are available:

    -@      Display extended attribute keys and sizes in long (-l) output.

    -1      (The numeric digit ``one''.)  Force output to be one entry per
            line.  This is the default when output is not to a terminal.

    -A      List all entries except for . and ...  Always set for the super-
            user.

...several more pages...

BUGS
    To maintain backward compatibility, the relationships between the many
    options are quite complex.

BSD                              May 19, 2002                              BSD

Find out about advanced ls commands

Find out, using the manual page, how to list the files in a directory ordered by their filesize. Try it out in different directories. Can you combine it with the -l argument you learned before?

Afterwards, find out how you can order a list of files based on their last modification date. Try ordering files in different directories.

Answer

To order files in a directory by their filesize, in combination with the -l argument:

ls -lS

Note that the S is case-sensitive!

To order files in a directory by their last modification date, in combination with the -l argument:

ls -lt

Working with files and folders

As well as navigating directories, we can interact with files on the command line: we can read them, open them, run them, and even edit them. In fact, there’s really no limit to what we can do in the shell, but even experienced shell users still switch to graphical user interfaces (GUIs) for many tasks, such as editing formatted text documents (Word or OpenOffice), browsing the web, editing images, etc. But if we wanted to make the same crop on hundreds of images, say, the pages of a scanned book, then we could automate that cropping work by using shell commands.

We will try a few basic ways to interact with files. Let’s first move into the shell-lesson directory on your desktop.

$ cd
$ cd Desktop/shell-lesson
$ pwd

/Users/riley/Desktop/shell-lesson

Here, we will create a new directory and move into it:

$ mkdir firstdir
$ cd firstdir

Here we used the mkdir command (meaning ‘make directories’) to create a directory named ‘firstdir’. Then we moved into that directory using the cd command.

But wait! There’s a trick to make things a bit quicker. Let’s go up one directory.

$ cd ..

Instead of typing cd firstdir, let’s try to type cd f and then hit the Tab key. We notice that the shell completes the line to cd firstdir/.

Tab for Auto-complete

Hitting tab at any time within the shell will prompt it to attempt to auto-complete the line based on the files or sub-directories in the current directory. Where two or more files have the same characters, the auto-complete will only fill up to the first point of difference, after which we can add more characters, and try using tab again. We would encourage using this method throughout today to see how it behaves (as it saves loads of time and effort!).

Reading files

If you are in firstdir, use cd .. to get back to the shell-lesson directory.

Here there are copies of two public domain books downloaded from Project Gutenberg along with other files we will cover later.

$ ls -lh

total 139M
-rw-rw-r--  1 jb677  1322   383K 17 Oct 15:45 000003160_01_text.json
-rw-rw-r--  1 jb677  1322   582K 17 Oct 15:45 33504-0.txt
-rw-rw-r--  1 jb677  1322   598K 17 Oct 15:45 829-0.txt
-rw-r--r--@ 1 jb677  1322   920K 20 Oct 16:55 TNA-download-FO-881-file-level-only-csv.tsv
-rw-r--r--@ 1 jb677  1322   1.2M 20 Oct 16:56 TNA-download-HO-396-tagged-in-Excel-xlsx.tsv
-rw-r--r--@ 1 jb677  1322   1.0M 20 Oct 16:57 TNA-download-WO-97-multilevel-xlsx.tsv
-rw-rw-r--  1 jb677  1322    16K 17 Oct 15:45 callnumbers.txt
-rw-rw-r--  1 jb677  1322    18K 17 Oct 15:45 diary.html
-rw-rw-r--  1 jb677  1322    16K 17 Oct 15:45 pdflist.txt

The files 829-0.txt and 33504-0.txt holds the content of book #829 and #33504 on Project Gutenberg. But we’ve forgot which books, so we try the cat command to read the text of the first file:

$ cat 829-0.txt

The terminal window erupts and the whole book cascades by (it is printed to your terminal). Great, but we can’t really make any sense of that amount of text.

Canceling Commands

To cancel this print of 829-0.txt, or indeed any ongoing processes in the Unix shell, hit Ctrl+C

Often we just want a quick glimpse of the first or the last part of a file to get an idea about what the file is about. To let us do that, the Unix shell provides us with the commands head and tail.

$ head 829-0.txt

The Project Gutenberg eBook, Gulliver's Travels, by Jonathan Swift


This eBook is for the use of anyone anywhere at no cost and with
almost no restrictions whatsoever.  You may copy it, give it away or
re-use it under the terms of the Project Gutenberg License included
with this eBook or online at www.gutenberg.org

This provides a view of the first ten lines, whereas tail 829-0.txt provides a perspective on the last ten lines:

$ tail 829-0.txt

Most people start at our Web site which has the main PG search facility:

    http://www.gutenberg.org

This Web site includes information about Project Gutenberg-tm,
including how to make donations to the Project Gutenberg Literary
Archive Foundation, how to help produce our new eBooks, and how to
subscribe to our email newsletter to hear about new eBooks.

If ten lines is not enough (or too much), we would check man head to see if there exists an option to specify the number of lines to get (there is: head -n 20 will print 20 lines).

Another way to navigate files is to view the contents one screen at a time. Type less 829-0.txt to see the first screen, spacebar to see the next screen and so on, then q to quit (return to the command prompt).

$ less 829-0.txt

Like many other shell commands, the commands cat, head, tail and less can take any number of arguments (they can work with any number of files). We will see how we can get the first lines of several files at once. To save some typing, we introduce a very useful trick first.

Re-using commands

On a blank command prompt, hit the up arrow key and notice that the previous command you typed appears before your cursor. We can continue pressing the up arrow to cycle through your previous commands. The down arrow cycles back toward your most recent command. This is another important labour-saving function and something we’ll use a lot.

Hit the up arrow until you get to the head 829-0.txt command. Add a space and then 33504-0.txt (Remember your friend Tab? Type 3 followed by Tab to get 33504-0.txt), to produce the following command:

$ head 829-0.txt 33504-0.txt

==> 829-0.txt <==
The Project Gutenberg eBook, Gulliver's Travels, by Jonathan Swift


This eBook is for the use of anyone anywhere at no cost and with
almost no restrictions whatsoever.  You may copy it, give it away or
re-use it under the terms of the Project Gutenberg License included
with this eBook or online at www.gutenberg.org




==> 33504-0.txt <==
The Project Gutenberg EBook of Opticks, by Isaac Newton

This eBook is for the use of anyone anywhere at no cost and with
almost no restrictions whatsoever.  You may copy it, give it away or
re-use it under the terms of the Project Gutenberg License included
with this eBook or online at www.gutenberg.org


Title: Opticks
       or, a Treatise of the Reflections, Refractions, Inflections,

All good so far, but if we had lots of books, it would be tedious to enter all the filenames. Luckily the shell supports wildcards! The ? (matches exactly one character) and * (matches zero or more characters) are probably familiar from archival search systems. We can use the * wildcard to write the above head command in a more compact way:

$ head *.txt

More on wildcards

Wildcards are a feature of the shell and will therefore work with any command. The shell will expand wildcards to a list of files and/or directories before the command is executed, and the command will never see the wildcards. As an exception, if a wildcard expression does not match any file, Bash will pass the expression as a parameter to the command as it is. For example typing ls *.pdf results in an error message that there is no file called *.pdf.

Moving, copying and deleting files

We may also want to change the file name to something more descriptive. We can move it to a new name by using the mv or move command, giving it the old name as the first argument and the new name as the second argument:

$ mv 829-0.txt gulliver.txt

This is equivalent to the ‘rename file’ function.

Afterwards, when we perform a ls command, we will see that it is now called gulliver.txt:

$ ls

000003160_01_text.json   33504-0.txt   gulliver.txt
TNA-download-FO-881-file-level-only-csv.tsv   TNA-download-HO-396-tagged-in-Excel-xlsx.tsv
TNA-download-WO-97-multilevel-xlsx.tsv   callnumbers.txt
diary.html   pdflist.txt

Copying a file

Instead of moving a file, you might want to copy a file (make a duplicate), for instance to make a backup before modifying a file. Just like the mv command, the cp command takes two arguments: the old name and the new name. How would you make a copy of the file gulliver.txt called gulliver-backup.txt? Try it!

Answer

cp gulliver.txt gulliver-backup.txt

Renaming a directory

Renaming a directory works in the same way as renaming a file. Try using the mv command to rename the firstdir directory to backup.

Answer

mv firstdir backup

Moving a file into a directory

If the last argument you give to the mv command is a directory, not a file, the file given in the first argument will be moved to that directory. Try using the mv command to move the file gulliver-backup.txt into the backup folder.

Answer

mv gulliver-backup.txt backup

This would also work:

mv gulliver-backup.txt backup/gulliver-backup.txt

The wildcards and regular expressions

The ? wildcard matches one character. The * wildcard matches zero or more characters. If you attended the lesson on regular expressions, do you remember how you would express that as regular expressions?

(Regular expressions are not a feature of the shell, but some commands support them. We’ll get back to that.)

Answer

• The ? wildcard matches the regular expression . (a dot)
• The * wildcard matches the regular expression .*

Using history

Use the history command to see a list of all the commands you’ve entered during the current session. You can also use Ctrl + r to do a reverse lookup. Hit Ctrl + r, then start typing any part of the command you’re looking for. The past command will autocomplete. Hit enter to run the command again, or press the arrow keys to start editing the command. If you can’t find what you’re looking for in the reverse lookup, use Ctrl + c to return to the prompt. If you want to save your history, maybe to extract some commands from which to build a script later on, you can do that with history > history.txt. This will output all history to a text file called history.txt that you can later edit. To recall a command from history, enter history. Note the command number, e.g. 2045. Recall the command by entering !2045. This will execute the command.

Using the echo command

The echo command simply prints out a text you specify. Try it out: echo "Library Carpentry is awesome!". Interesting, isn’t it?

You can also specify a variable, for instance NAME= followed by your name. Then type echo "$NAME is a fantastic library carpentry student". What happens?

You can combine both text and normal shell commands using echo, for example the pwd command you have learned earlier today. You do this by enclosing a shell command in $( and ), for instance $(pwd). Now, try out the following: echo "Finally, it is nice and sunny on" $(date). Note that the output of the date command is printed together with the text you specified. You can try the same with some of the other commands you have learned so far.

Why do you think the echo command is actually quite important in the shell environment?

Answer

You may think there is not much value in such a basic command like echo. However, from the moment you start writing automated shell scripts, it becomes very useful. For instance, you often need to output text to the screen, such as the current status of a script.

Moreover, you just used a shell variable for the first time, which can be used to temporarily store information, that you can reuse later on. It will give many opportunities from the moment you start writing automated scripts.

Finally, onto deleting. We won’t use it now, but if you do want to delete a file, for whatever reason, the command is rm, or remove.

Using wildcards, we can even delete lots of files. And adding the -r flag we can delete folders with all their content.

Unlike deleting from within our graphical user interface, there is no warning, no recycling bin from which you can get the files back and no other undo options! For that reason, please be very careful with rm and extremely careful with rm -r.

Writing a Loop

Loops are key to productivity improvements through automation as they allow us to execute commands repetitively. Similar to wildcards and tab completion, using loops also reduces the amount of typing (and typing mistakes). Suppose we have several hundred document files named project_1825.doc, project_1863.doc, XML_project.docand so on. We would like to change these files, but also save a version of the original files, naming the copies backup_project_1825.doc and so on.

We can use a loop to do that. Here’s a simple example that creates a backup copy of four text files in turn.

Let’s first create those files:

$ touch a.txt b.txt c.txt d.txt

This will create four empty files with those names. It is easy to use the shell to create a batch of files in one go.

Now we will use a loop to create a backup version of those files. Accordingly, we enter:

$ for filename in *.txt
> do
>    echo $filename
>    cp $filename backup_$filename
> done

a.txt
b.txt
c.txt
d.txt

When the shell sees the keyword for, it knows to repeat a command (or group of commands) once for each thing in a list. For each iteration, the name of each thing is sequentially assigned to the variable and the commands inside the loop are executed before moving on to the next thing in the list. Inside the loop, we call for the variable’s value by putting $ in front of it. The $ tells the shell interpreter to treat the variable as a variable name and substitute its value in its place, rather than treat it as text or an external command.

In this example, the list is four filenames: ‘a.txt’, ‘b.txt’, ‘c.txt’, and ‘d.txt’ Each time the loop iterates, it will assign a file name to the variable filename and run the cp command. The first time through the loop, $filename is a.txt. The interpreter runs the command cp on a.txt, and then prints the filename to the screen (because we asked it to echo each filename as it works its way through the loop). For the second iteration, $filename becomes b.txt. This time, the shell runs cp on b.txt and then prints the filename to the screen. The loop performs the same operations for c.txt and then for d.txt and then, since the list only included these four items, the shell exits the for loop at that point.

Follow the Prompt

The shell prompt changes from $ to > and back again as we were typing in our loop. The second prompt, >, is different to remind us that we haven’t finished typing a complete command yet. A semicolon, ;, can be used to separate two commands written on a single line.

Same Symbols, Different Meanings

Here we see > being used a shell prompt, whereas > is also used to redirect output. Similarly, $ is used as a shell prompt, but, as we saw earlier, it is also used to ask the shell to get the value of a variable.

If the shell prints > or $ then it expects you to type something, and the symbol is a prompt.

If you type > or $ yourself, it is an instruction from you that the shell to redirect output or get the value of a variable.

We have called the variable in this loop filename in order to make its purpose clearer to human readers. The shell itself doesn’t care what the variable is called.

This is our first look at loops. We will run another loop in the Counting and Mining with the Shell segment.

Key Points

• The shell is powerful

• Knowing where you are in your directory structure is key to working with the shell

• The shell can be used to copy, move, and combine multiple files