Introduction

The purpose of this introductory guide is to provide a gentle explanation of concepts fundamental to using the Unix command-line, in a manner that will hopefully be accessible to beginners. It relies heavily on small examples to illustrate these ideas with hopefully relevant situations. It does not provide a comprehensive description of everything that can be done with the Unix command-line, and does not even mention most of the many useful commands available on any Unix system. The hope is that by explaining the concepts behind how things actually work, readers will quickly be able to figure out the rest by themselves, and find out anything else they might need from the enormous amount of excellent documentation available online. It’s only a Google search away – but hopefully this document will help you to figure out what to ask in the first place.

What is the command-line?

The command line is simply a way of passing instructions to the computer. It is a text-only interface, and commands are supplied to the shell by typing them in and pressing the return key. Any output produced by these commands is printed out on the same text interface. Although daunting at first, the command line provides a very rich interface to the available functionality, and it is worth learning how to use it.

The command line interface will print out a prompt, after which commands can be typed. After the command has completed, the prompt will be printed out again, indicating that the shell is ready to accept new commands.

An important point to note is that Unix is case-sensitive: a file called Data is not the same as a file called data.

The command line prompt can vary from system to system, but usually consists of some text followed by the $ character. In many systems, it might look like this:

username@machine:path $

where username corresponds to your own username, machine corresponds to the name of the system you are currently logged onto, and path indicates your current working directory. Note that this can be configured differently, do not be surprised or alarmed if it looks different on your system.

Warning

If the prompt ends with a #, this most likely means that you are logged in as root (the super-user or Administrator). If this is the case, please log out before doing anything irreversible - unless you know what you are doing.

Note

A session will typically involve two separate programs:

• the shell: the program that actually interprets the commands that are typed in, and takes the appropriate action. There are a number of different shells available, each with their own syntax rules. The default shell in most Linux distributions is the Bourne Again Shell (bash). This is also the default on macOS and MSYS2 (used in Windows installations), and for this reason is the default assumed in this guide.
• the terminal: the program responsible for displaying the output of the shell, and what the user types in. There are a number of different terminals available, each with different levels of sophistication.

This leads to a bewildering array of combinations between the different shells and terminal programs available. Nonetheless, the general principles are fairly universal.

How to access the command line

There are many ways to start a command line session, depending on your OS and desktop environment.

• GNU/Linux

  Different Linux distributions include different desktop environments. For instance Ubuntu installations will typically be running Unity, Red Hat and derivatives will typically be running GNOME, while SuSE would typically come with KDE.

  Given the many different possible configurations, it is impossible to give specific instructions for each case. Nonetheless, in general you ought to be able to identify an application called ‘Terminal’ or similar in the desktop’s main menu.

• macOS

  You will find the ‘Terminal’ application within the Utilities folder in the Applications folder in the Finder.

• Windows (MSYS2)

  You will need to use the MSYS2 MinGW-w64 Win64 shell, either by double-clicking on the shortcut (on the Desktop or in the Start menu), or by searching for it (hit the Windows key and start typing ‘MSYS2’ – it should show up in the list of applications displayed).

Basic Structure of a command

In the simplest form, a command consists of a line of text, which is first broken up by splitting it using spaces as boundaries. The first ‘word’ must be the command name, corresponding to a real program to be executed. All other ‘words’ will eventually be passed to the program as arguments that should provide it with enough information to perform what is intended.

Command line arguments

To perform whatever action is required, the program that is being run may need some additional information. This information can be supplied to the program via the arguments that follow it in the command. Essentially, arguments are a series of ‘words’ specified in the right order so that the program can understand what is required of it.

For example, you need to supply two arguments to copy a file: the original file name, and the name of the file to be created. The program to do this, cp, expects the first argument to be the name of the file to be copied, and the second argument to be the name of the duplicate file to be created. If it does not find two arguments, it will produce an error message.

Note that some programs may accept a number of arguments, but use default values if they are omitted (example of these are cd and ls). Other programs may accept variable numbers of arguments, and process each argument in turn.

Command line options

There is a special type of argument that you might encounter, often referred to as a command line option or switch. The purpose of these optional arguments is to modify the behaviour of the program in some way. Command line options always start with a minus symbol to distinguish them from normal arguments. For example, passing the appropriate option (-l) to the ls command when listing the files in the current folder will produce a longer listing, including information such as file size and modification time as well as the file names normally output.

Command line options can also require additional arguments. In this case, these additional arguments should be entered immediately after the option itself – see the examples below.

Examples

Below are some typical command examples. (the $ symbol indicates the prompt):

• To list the contents of the current working directory:

  $ ls
  

• To list the contents of the current working directory, along with the file permissions, owner, size and modification date:

  $ ls -l
  

• To copy the file source, creating the file dest:

  $ cp source dest
  

• To convert image source.mif (MRtrix format) into image dest.nii (NIfTI format):

  $ mrconvert source.mif dest.nii
  

• To convert image source.mif into image dest.nii, changing the voxel size to 1.25 x 1 x 1 mm and changing the datatype to 32-bit floating-point:

  $ mrconvert source.mif -vox 1.25,1,1 -datatype float32 dest.nii
  

Dealing with spaces in arguments

As previously mentioned, the command actually typed in will first be split up into tokens using spaces as delimiters. In certain cases, it may be necessary to provide arguments that contain spaces within them. A common example of this is when file names contain spaces (note that this should be avoided, especially since other programs and scripts often have issues dealing with these). This is obviously a problem, since an argument with a space in it will be interpreted as two separate arguments. To supply an argument with a space in it, use the following syntax.

As an example, if we need to supply the argument “argument with spaces” to some command, we can use any of the following:

• argument\ with\ spaces
• 'argument with spaces'
• "argument with spaces"

In the first example, the backslash character tells the shell to ignore the subsequent space character and treat it as a normal character.

Escaping special characters

We have already seen that spaces are treated differently from other characters and need to be encapsulated by quotes ', " or escaped by a preceding \, to prevent them being interpreted by the shell as token delimiters. You will most likely also encounter other special characters such as !#$^&*?[](){}<>~;| in more advanced usages; these come in handy for instance for processing multiple files using wildcard characters.

One can influence the way the shell interprets these special characters by quoting and escaping the input. For instance, the string 'argument with spaces' uses single-quotes (strong quoting): this means that everything between the two ' symbols is treated as literal characters without special meaning. In the command below the series of special characters are treated as a simple string and printed to the terminal via the command echo.

$ echo look how ordinary these characters are: '!#$^&*?[](){}<>~;|\'

Unless encapsulated in single quotes, individual special characters can also be marked to lose their special meaning using the backslash. For instance, \'argument with spaces\' would expand to three arguments 'argument, with, and spaces'. The only exception to this rule is the newline character, which allows commands to span across multiple lines:

$ echo look how ordinary these characters are: '!#$^&*?[](){}<>~;|\' \
and \'

Double quotes " are used for weak quoting, which escapes all characters expect for \, $ and itself. This disables some of the shell’s interpretations (spaces, single-quotes, pattern matching, pathname expansions) while others remain active (such as parameter expansion $).

$ ls -l "$HOME/folder with spaces"

Note that special characters’ meaning can be shell- and context-dependent. For example, in the Bourne Again Shell (bash), the string filename[].mif is not interpreted but in the Z shell (zsh, the default shell for new user accounts since macOS version 10.15), the opening [ needs to be quoted "filename[].mif" or escaped using a backslash filename\[].mif.

For more information, consult your shell’s man page or this overview post,