The ``twelve'' most important Unix commands

Carl Mason

carlm@demog.berkeley.edu

rev 1.0 Fall 2008

Introduction

Although Unix has a point and click graphic user interface, called X11, which works just like those other operating systems, Unix is at heart a command line operating system. So while it is possible in many cases to do what you want via pointing and clicking, using the command line and other text based tools will make you happier much more efficient... eventually.

To operate with the command line, you will need to know the 12 most important Unix commands described in Section 4. To enjoy it you will also need to know a few tricks that are also covered in this document.

You don't need to know much about Unix in order to start doing Science, but it would not hurt to learn more. In your copious free time, check out some of the Unix primers on the web. Ask google something like ``Unix beginner'' to find more resources than you could possibly want.

Terminal windows

In order to use the command line, you must open a terminal window (also knows an xterm window). The first terminal window can be launched from: [Application] $\rightarrow$ [System Tools] $\rightarrow$ [Terminal].

It should look something like Figure 1. Notice that the window features a menu bar, unfortunately the menu bar it is both useless and misleading. Make the menu bar disappear by pressing the $\fbox{\textsc{right button}}$ and clearing the ``show Menubar'' check-box.

Now aside from the title bar at the top, the only words in the terminal window should be the Unix prompt. In Figure 1 the Unix prompt is [carlm@twins ~]$, indicating the user, carlm, the machine, twins and the current directory which is indicated by the ~. In this and other documents, the Unix prompt will look like this: @: .

If you are in no particular hurry to finish your dissertation, you can modify a large number of colors and beeps and other important features of the terminal window. $\fbox{\textsc{right button}}$ [Edit Current Profile] is the place to start wasting time.

If you have already wasted time on this sort of thing and are thus old enough to find the default font a bit small, a useful trick with terminal windows (and browser windows too) is the $\fbox{\textsc{CTRL}}$ + $\fbox{\textsc{SHIFT}}$ + $\fbox{\textsc{+}}$ to increase and $\fbox{\textsc{CTR}}$ + $\fbox{\textsc{-}}$ to decrease the size of the typeface.

**Figure 1:** terminal window
$\includegraphics[scale=.4]{gnome-terminal}$

The command interpreter

The command interpreter, or shell is the program that runs in each terminal window. It waits for you to type something at the Unix prompt, @: , and then does what it thinks you meant. The shell we use here is called tcsh (pronounced ``teesh''). Tcsh is one of several modified versions of the original csh (pronounced ``sea shell'').

The most important thing that the shell does for you is to let you give commands to the computer. These include the 12 most important Unix commands (Section 4) as well as commands to launch applications like R, Stata, word processors or spreadsheets¹. The shell does several other things for you some are essential, some enhance efficiency and others are just cool.

Essential stuff

Among the essential features of the shell is a mechanism to communicate with running programs that are not expecting user input or have run amok. This is not all that common, but when it happens you need to be able to get the program's attention and tell it - generally to drop dead. $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{c}}$ does this.

Below is a list of some handy/essential key combinations that the shell recognizes:

$\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{c}}$ : This sends a "kill" signal to the program running in the xterm window where the $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{c}}$ is executed. The "kill" signal generally stops your program - but not always.
$\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{z}}$ : This "suspends" your program for later restarting. This is a very handy thing to be able to do, but it is extremely confusing if you do it accidentally. the "fg" command brings your program back to foreground.
$\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{d}}$ : This is the End Of File character. Programs which read from the standard input expect a $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{d}}$ to tell them when you are done talking. Many Unix utilities need this explicitly. Sometimes, $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{d}}$ will have a similar function as $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{c}}$ - it is certainly something to type when you are desperate.
$\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{s}}$ :This is the Xoff character. It tells the terminal to stop accepting input. DOS/NT and Unix machines all understand this character, but new users frequently do not. If you type $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{s}}$ inadvertently, the screen or xterm will freeze until you hit $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{q}}$ . It is useful if you program is spewing lots and lots of stuff on the screen too quickly for you to read. But mostly it is just a little trap into which users fall. NOTE: $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{s}}$ has a completely different and much more useful function in emacs.
$\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{q}}$ his is the Xon character, it tells the terminal to accept input once again. Try it when the xterm window freezes -- just in case you have recently inadvertently hit a $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{s}}$ .

Efficient stuff

To make you more efficient, the shell offers three particularly nice features: ``history'', `` $\fbox{\textsc{tab}}$ completion'' and ``scripting''.

history

The history feature allows you to recall and edit any command that you have previously issued. To make the previous command appear at the @: hit $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{p}}$ ². To see even more previous stuff type $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{p}}$ more times. $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{n}}$ will make the next command appear - obviously, this makes no sense unless you have type $\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{p}}$ at least once.

You can operate on a recalled command using several standard emacs editing keys:

$\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{a}}$ To go to the beginning of the current line
$\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{e}}$ To go to the end of the current line
$\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{f}}$ To go forward one character
$\fbox{\textsc{ctrl}}$ + $\fbox{\textsc{b}}$ To go backward one character

The $\fbox{\textsc{delete}}$ and $\fbox{\textsc{backspace}}$ keys do what you would expect.

$\fbox{\textsc{TAB}}$ completion

If you hit the $\fbox{\textsc{tab}}$ key anytime while constructing a command, tcsh will do it's best to figure out what you are planning to type next. If you are typing a command it will try to find a command that starts out with what you have already typed. If you are typing the name of a file tcsh will try to complete if for you. If what you have typed does not uniquely determine a command or filename, tcsh will beep at you and provide a list of possible completions. You can then type a few more characters and hit $\fbox{\textsc{tab}}$ again.

scripting

Whenever you find yourself typing the same command several times, it's time to consider scripting. A shell script is just a file of commands that you could have entered at the keyboard, but typed into a file instead. You can then set the file's execute bit (Section 7) and execute that file - perhaps now, perhaps later. Using emacs to create that shell script can save you lots of time and hair loss - particularly if many of the commands you are typing are quite similar.

Scripts are also very useful for people who like the idea of being able to reproduce results.

cool stuff

The shell is also responsible for displaying the results of the ls command (See 1) in lots of colors.

the 12 most important Unix commands

Below is a list of the 12 most important Unix commands. They are simple enough to be easily memorized by anyone who can keep the names of all twelve months in his head.

For the most part, these commands are for logging on and off; for printing; and for moving files and directories around. Many of these commands functions can be done using a file manager or under emacs, but knowing how to do them from the command line, opens the possibility of automating tasks with shell scripts.

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ls -lgdaF regular expression The ``list file'' command, ls is used -not surprisingly- to list the names and pertinent information about some or all of the files in a particular directory. The most common and useful option is -l that a lower case L not a one. It reveals the most interesting properties of your files.
A regular expression is a set of special characters (or ``meta-characters'') that can be used to represent a list of files or more generally, the set of all character strings with certain characteristics. Regular expressions come up in a lot of places and can be very useful when working with datasets that are full text and/or errors. Regular expressions are used with ls to limit the number of files displayed. For example ls X*Y would list only the filenames that start with an X and end with a Y; ls [aeiou]* would show you all the files that begin with a lower case vowel (In the previous example the [ ] are part of the command)
cd directory-name The ``change directory'' command makes another directory your present working directory. With no argument, it "moves you" to your home directory. To move one directory "higher" use ".." (two dots) in place of the directory's name. The parent directory of the current directory is always addressable as "..".
cp -R source file/directory target file/directory The copy command, cp is used to copy files and directories. The -R flag is used to copy entire directories and the contents thereof.
mkdir <new-directory-name> The ``make directory'' command is used to create a new sub-directory of the current working directory.
rm file-name or regular expression The ``remove'' command is used to remove, or erase files. Here again, regular expressions can be very useful - and quite dangerous.
rm is aliased to rm -i so that it asks you to verify that you really want to remove a file. If you get tired of this safety feature, use \rm instead.
rmdir directory-name the ``remove directory'' command removes directories. In order to remove a directory, it must be empty or files and sub-directories.
chmod aogu +/- rwx filename-or-directory The ``change mode'' command is used to modify the permissions (or mode) of a file or directory. Permissions are the characteristic of a file or directory which determine who has what type of access to it. All files and all directories have permissions, only the owner of the file/ directory is permitted to change modes.
The first argument is a string of characters that grant (+) or revoke (-) permission to read(r) write(w) or execute (x) the file or directory. The letters aogu indicate who is to receive or lose the given permission. u=user, g=group, o=other, and a=all. Thus to revoke write permission to all users you would type:
chmod a-w filename
To grant permission to yourself and the group to write and execute a file you would type:
chmod ug+wx filename
ln -s real-file-name artificial-file-name The ``link'' command creates an alternative name for an existing file or directory. This is particularly useful when using data sets that you keep in /data/commons (as you should). Rather than typing /data/commons/userid/datafile to reference your data, a symlink would allow you to type something much shorter.
ln -s /data/commons/userid DATA
would create a link in your current directory called ``DATA''. But DATA is really just a secret back way to /data/commons/userid. typing ls DATA for example is the equivalent of typing ls /data/commons/userid.
It would be a good idea to create the above link right now. Use the mkdir to create a new directory in /data/commons called your userid. Then create a link in your home directory so that you can start storing and accessing huge data sets right away.
mv file-name new-file-name The ``move'' command changes the name or location within the filesystem of a file or a directory.
less file-name Variant of the more command - less is used to scroll through a file on the screen. While displaying a file, $\fbox{\textsc{enter}}$ scrolls one additional line; $\fbox{\textsc{space}}$ scrolls one additional screen full; $\fbox{\textsc{b}}$ scrolls backwards, $\fbox{\textsc{q}}$ quits, $\fbox{\textsc{/\texttt{word}}}$ searches forward for ``word'', $\fbox{\textsc{?\texttt{word}}}$ searches backward for ``word''.

lpr

-Pprinter-name

filename The ``line printer'' command prints a file to the named printer.

Demography Department Printers

Printer	Location	Type
age	Basement Lab	HP Laserjet 4015 postscript monochrom duplex 1200dpi
parity	Room 101b	HP 4050n postscript monochrom 600dpi
class	2224 2nd floor	HP 4100n postscript 600dpi
cohort	2232 2nd floor	HP 4200n postscript 600dpi
status	Library	HP 4200n postscript monochrom 600dpi
ses	Xerox Room	Ricoh postscript color duplex 1200dpi

Note that by default each of the above printers is configured to print in economy mode thus saving toner and by extension the world. If you need high quality printouts add ``HQ'' to the printer name e.g. lpr -PsesHQ filename.

pwd ``present working directory'' tells you where you are, that is, it tells you which directory the shell thinks is the current directory.
du directory The ``disk use'' command is designed to tell you how much disk space each directory is consuming. It's main use, however, is simply to display the directory structure.
man -k key-word | command-name The "manual" command is used to display manual pages on your screen. To say that man pages are not particularly easy to read is is an understatement of almost biblical magnitude. But they are very handy for refreshing your memory or searching for something very specialized.
The man program puts the contents of the man page in a ``less'' process, see item 10 for a description of how to navigate in less.
In this century a very good source of information on Unix is google. The web knows all about Unix and while there are lots of different distributions, command line tools in particular are nearly identical in all distributions including Solaris, Hpux, every flavor Linux, BSD, and even Apple's OS X (which by the way is Unix too).
exit or logout closes the current Unix window, and logs you off - if the current window is the console window.

Special and ``meta'' characters

In addition to the key combinations and commands discussed Unix also supports several characters with special meanings to the shell. Below is a list some of the more common ones:

*

The asterisk or ``star'' character is used in regular expressions (See item 1). When the shell sees a * by itself as in @: ls * it replaces * with a list of all the files and subdirectories in the current directory. @: ls * tells the shell to run the ls command on each and every file and subdirectory in the current directory. So where @: ls will show files and subdirectories @: ls * will list the files that live in subdirectories of the current directory as well.

&

The ampersand tells the shell to run the process in the ``background''. When a process is launched in the background, the xterm (See 2) immediately returns with a prompt. When you run a process in the foreground (the usual case) the prompt comes back only when the process exits.

NOTE it only makes sense to run programs in the background if the program spawns a new window. So emacs, stata, userfirefox, or oowriter are all fine running in the background. The 12 most important Unix commands are not. They all write their responses to the terminal window. If you put them in the background they cannot do this.

REALLY important: R should not be run in the background for the same reason: it runs in the window from which it was launched. This will all make sense after the first week or two of 213.

To bring a backgrounded program to the foreground, type

@: fg %n

where %n is the percent sign followed by a number indicating which backgrounded process you want to foreground. You only need to enter the %n if you have more than one process running in the background. Type

@: jobs

to get a list of backgrounded processes associated with the current xterm.

$\sim$

the tilde character is interpreted by the shell to mean ``home directory'' by itself, it means your home directory, if it is followed by a username as in $\sim$ carlm it refers to that user's home directory. The $\sim$ can be used in complicated pathnames such as carlm/public_html/213F97/welcome.html. For it to make sense, the $\sim$ must be the first character (and perhaps the only character) of a pathname.

$\vert$

The ``pipe'' is used to send the standard output of one process into the standard input of another. For example, if you wanted to know the number of lines in every data file in the current directory you might type: @: ls *.data | wc -l . The ls *.data produces a list of files in the current directory that end in ``.data'', the $\vert$ then feeds this list to the word count command ``wc''. The -l argument tells wc to only report the number of lines. This example assumes that you have named all of your data files somethingorother.data.

The right angle bracket (or greater than sign) is used to send the output of a process into a file. @: ls > file.list would produce a file called file.list containing (surprise) a list of files. Use double angle brackets to append a process's output to an existing file.

@: ls /public_html » file.list

would add the names of the file's in your public_html directory.

About this document ...

The ``twelve'' most important Unix commands

This document was generated using the LaTeX2HTML translator Version 2002-2-1 (1.71)

The command line arguments were:
latex2html -split 0 12important

The translation was initiated by Carl Mason -- Director Demography Lab on 2008-08-18

Footnotes

... spreadsheets ¹: It is of course possible to launch most applications via the menu system or by clicking on corresponding data files in the file manager, but the command line is often faster
... ²: the up arrow key will also work

Carl Mason --- Director Demography Lab 2008-08-18