Unix/Linux basics for Biolinux
Table of Contents
1.What is Linux .................................................2
1.1 A brief history of Linux..................................................................................... 2
1.2 Free Software pre-Linux ................................................................................... 2
1.3 The kernel .......................................................................................................... 2
1.4 1991, a fateful year ............................................................................................ 2
1.5 Linux is introduced ............................................................................................ 3
1.6 Linux, at first, not for everybody ...................................................................... 3
1.7 Linux Today ...................................................................................................... 3
2. SSH (Logging in/out) ....................................5
2.1 The "Bash" shell ................................................................................................ 5
2.2 Typing Tricks .................................................................................................... 6
Moving around / Basic commands ....................7
3.1 Command syntax ............................................................................................... 7
3.2 Figuring out where you are ............................................................................... 7
3.3 Changing to another directory ........................................................................... 7
3.4 Seeing what's there ............................................................................................ 8
4. Files and Directories ......................................10
4.1 Unix File Names ................................................................................................ 10
4.2 Creating Files..................................................................................................... 10
4.3 Copying Files..................................................................................................... 10
4.4 Moving (Renaming) Files ................................................................................. 10
4.5 Viewing Files..................................................................................................... 11
4.6 Searching for something in a File ..................................................................... 11
4.7 Deleting Files..................................................................................................... 11
4.8 Creating Directories .......................................................................................... 12
4.9 Deleting Directories .......................................................................................... 12
5. Introduction to File Ownership/Permissions .13
5.1 File Ownership .................................................................................................. 13
5.2 File Permissions ................................................................................................ 13
5.3 Representing File Permissions .......................................................................... 13
Unix/Linux basics for Biolinux
5.3a Symbolic Representation ................................................................................. 13
5.3b Numeric Representation .................................................................................. 14
6. Obtaining Help ..............................................15
6.1 The "man" command ......................................................................................... 15
6.2 The "info" command ......................................................................................... 15
6.3 The "--help" option ............................................................................................ 15
6.4 Using “apropos” to find commands .................................................................. 15
6.5 Biolinux applications documenation ................................................................. 16
7. Using Pipes ....................................................17
7.1 General Approach.............................................................................................. 16
7.2 Some Examples ................................................................................................. 16
8. TAR and GZIP ..............................................18
8.1 TAR ................................................................................................................... 18
8.2 GZIP .................................................................................................................. 18
8.3 Using TAR and GZIP together.......................................................................... 19
9. Linux Filesystem ...........................................20
10. A UNIX Command Summary .....................21
Unix/Linux basics for biolinux
1. What is Linux?
Linux is an operating system that evolved from a kernel created by Linus Torvalds when he was a
student at the University of Helsinki. Generally, it is obvious to most people what Linux is,
however, both for political and practical reasons, it needs to be explained further. To say that Linux
is an operating system means that it's meant to be used as an alternative to other operating systems
like MS-DOS, the various versions of MS Windows, Mac OS, Solaris and others. Linux is not a
program like a word processor and is not a set of programs like an office suite.
1.1 A brief history of Linux
When Linus Torvalds was studying at the University of Helsinki, he was using a version of the
UNIX operating system called 'Minix'. Linus and other users sent requests for modifications and
improvements to Minix's creator, Andrew Tanenbaum, but he felt that they weren't necessary.
That's when Linus decided to create his own operating system that would take into account users'
comments and suggestions for improvements.
1.2 Free Software pre-Linux
This philosophy of asking for users comments and suggestions and using them to improve computer
programs was not new. Richard Stallman, who worked at the Massachusetts Institute of
Technology, had been advocating just such an approach to computer programming and use since
the early 1970's. He was a pioneer in the concept of 'free software', always pointing out that 'free'
means 'freedom', not zero cost. Finding it difficult to continue working under conditions that he felt
went against his concept of 'free software' he left MIT in 1984 and founded GNU. The goal of GNU
was to produce software that was free to use, distribute and modify. Linus Torvalds' goal 6 years
later was basically the same: to produce an operating system that took into account user feedback.
1.3 The kernel
We should point out here that the focal point of any operating system is its 'kernel'. Without going
into great detail, the kernel is what tells the big chip that controls your computer to do what you
want the program that you're using to do. To use a metaphor, if you go to your favorite Italian
restaurant and order 'Spaghetti alla Bolognese', this dish is like your operating system. There are a
lot of things that go into making that dish like pasta, tomato sauce, meatballs and cheese. Well, the
kernel is like the pasta. Without pasta, that dish doesn't exist. You might as well find some bread
and make a sandwich. A plate of just pasta is fairly unappetizing. Without a kernel, an operating
system doesn't exist. Without programs, a kernel is useless.
1.4 1991, a fateful year
In 1991, ideal conditions existed that would create Linux. In essence, Linus Torvalds had a kernel
but no programs of his own, Richard Stallman and GNU had programs but no working kernel. Read
the two men's own words about this:
Linus: "Sadly, a kernel by itself gets you nowhere. To get a working system you need a
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shell, compilers, a library etc."
RMS: The GNU Hurd is not ready for production use. Fortunately, another kernel is
available. [It is called] Linux.
So combining the necessary programs provided by GNU in Cambridge, Massachusetts and a kernel,
developed by Linus Torvalds in Helsinki, Finland, Linux was born. Due to the physical distances
involved, the means used to get Linus' kernel together with the GNU programs was the Internet,
then in its infancy. We can say then that Linux is an operating system that came to life on the
Internet. The Internet would also be crucial in Linux's subsequent development as the means of
coordinating the work of all the developers that have made Linux into what is is today.
1.5 Linux is introduced
Late in 1991, Linus Torvalds had his kernel and a few GNU programs wrapped around it so it
would work well enough to show other people what he had done. And that's what he did. The first
people to see Linux knew that Linus was on to something. At this point, though, he needed more
people to help him. Here's what Linus had to say back in 1991.
"Are you without a nice project and dying to cut your teeth on an OS you can try to
modify for your needs?... This post might just be for you."
People all over the world decided to take him up on it. At first, only people with extensive computer
programming knowledge would be able to do anything with that early public version of Linux.
These people started to offer their help. The version numbers of Linux were getting higher and
higher. People began writing programs specifically to be run under Linux. Developers began
writing drivers so different video cards, sound cards and other gadgets inside and outside your
computer could use Linux. Nevertheless, throughout most of first part of the 1990's Linux did not
get out of the 'GURU' stage. GURU is a term that has evolved to mean anyone who has special
expertise in a particular subject. That is, you had to have special expertise in how computers worked
to be able to install Linux in those days.
1.6 Linux, at first, not for everybody
Other popular software companies sold you a CD or a set of floppies and a brief instruction booklet
and in probably less than a half an hour, you could install a fully working operating system on your
PC. The only ability you needed was knowing how to read. Those companies had that intention
when they actually sat down and developed their operating systems. Linus Torvalds didn't have that
in mind when he developed Linux. It was just a hobby for him. Later on, companies like Red Hat
made it their goal to bring Linux to the point where it could be installed just like any other operating
system; by anyone who can follow a set of simple instructions, and they have succeeded. For some
reason, though, Linux hasn't shaken off completely that 'Gurus only' image that it took on at the
beginning. That is mostly the result of articles in the popular, quasi-technical press whose
experience with Linux has been quite limited.
1.7 Linux Today
Today, Linux is enjoying a favorable press for the most part. This comes from the fact that Linux
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Unix/Linux basics for biolinux
has proven to be a tremendously stable and versatile operating system, particularly as a network
server. When Linux is deployed as a web server or in corporate networks, its down-time is almost
negligible. There have been cases when Linux servers have been running for more than a year
without re-booting and then only taken down for a brief period for routine maintainance. Its cost
effectiveness has sold it more than anything else. Linux can be installed on a home PC as well as a
network server for a fraction of the cost of other companies' software packages. More reliability and
less cost - it's ideal.
If you're reading this, you're obviously here to learn how to use Linux. Any learning experience
means opening up to new ideas and new ways of doing things. As mentioned before, Linux is in the
UNIX family of operating systems. UNIX is primarily designed to be used by professionals. You
will have to learn some UNIX concepts in this lesson, but that doesn't mean that Linux is a
professionals-only operating system. Quite the contrary. Most major versions of Linux are designed
to be as user-friendly and as easy to install as any other operating system on the market today.
Now that you know what Linux is and how good it is, there's one more thing we have to do - install
Linux!
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Unix/Linux basics for biolinux
2. SSH (Logging in/out)
Providing you have a biolinux account, a safe and secure connection can be made to a biolinux
server using a protocol called SSH. This stands for Secure SHell. However, in order to run
graphical Linux applications remotely you also need to run something called Xwindows. If you are
logging into a Biolinux server for the first time, then you will need to configure Xwindows on your
PC so that it is tunneled through your SSH connection. This will enable you to securely run
graphical applications available on the Biolinux server. Instructions for doing this can be found at:
http://watson-bios.grid.cf.ac.uk/pdf/ssh_tunnelling_X-Win32.pdf
2.1 The "Bash" shell
When you first connect to a Biolinux server your current working directory will be your home
directory and you will see something like the following:
************* Welcome to your local Bio-Linux system *************
http://envgen.nox.ac.uk
The following software is available:
ACT APE ARB ARTEMIS ATV BIOCONDUCTOR BLAST BLIXEM CLUSTAL(X|W)
DOTTER EMBOSS
FASTA FASTDNAML FORESTER GDE GENESPRING HAPPY HMMER JALVIEW MAXD
MAXDLOAD MCL
MRBAYES MSPCRUNCH MVIEW NETBLAST NJPLOT PAML PARTIGENE PEDRO
PHYLIP PRIMER3
QTLCARTOGRAPHER R/BQTL R/QTL R/QTLSIM RASMOL READSEQ SEAVIEW
SPLITSTREE
STADEN STARS T-COFFEE TRACE2DBEST TREE-PUZZLE TRIBE-MCL WISE2
XMGRACE
The following languages are available:
C, C++, Perl/BioPerl, Python/BioPython, Ruby/BioRuby,
Java/BioJava, R
[manager@bioremediation manager]$
The SSH connection gives you access to something known as a “shell” or “terminal” and the “$”
sign at the bottom of the screen is known as the command prompt. A "shell" is a program which
interprets commands, either typed in directly by the user, or contained in a file called a "shell
script", which is a simple interpreted program. The equivalents in WindowsTM would be "command
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Unix/Linux basics for biolinux
processor" for shell, "COMMAND.COM" or "CMD.EXE" instead of bash, and ".BAT files"
instead of shell scripts.
The Shell in Unix/Linux is much more powerful than the DOS terminal in Windows. Linux has a
variety of different shells which all vary slightly, but the most popular is "bash". This is your
current shell on biolinux.
To run any bioloinux application simply type the executable name followed by an ampersand:
artemis &
The ampersand is important as it tells the shell to run the application in the background thus
enabling you to keep control of the shell so that you are able to carry out other tasks.
To exit your shell and SSH connection:
1. Close all Biolinux graphical applications you may have running
3. Type “exit” at the command prompt and press Enter.
2.2 Typing Tricks
When you're in the bash prompt, you can use the up- and down-arrow keys to recall previously
typed commands. You can also press “Ctrl-R” and start typing part of another command to find
the last command that contains the letters you are typing. Thus if you want to find the last changedirectory, type "[Ctrl-R]cd", and the command line will display the last "cd" command you
typed.
If you start typing a filename or directory name, you can press “[Tab]” and bash will complete the
file or directory name for you, assuming that such a file exists and is the only one that starts with
the typed-in part. For example, if you type "ls br[Tab]", bash will complete the filename to
"brushtopbm", if this file exists and is the only file starting with "br". If you make a mistake at the
command line and wish to interrupt just type “Ctrl-C” to cancel.
To copy and paste in the shell simply highlight the text you wish to copy, and then having
positioned the cursor, press both mouse keys at the same time to paste. This also works for
graphical applications. Also, if you have a wheel mouse you can press the wheel to paste instead.
Basically a mouse for a Unix machine traditionally has three keys instead of two. However,
biolinux machines should be configured by default to allow Windows users to be able to emulate
the missing third key by using one of the above methods.
Also see:
man history
man scp
man ssh
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3. Moving around / Basic commands
3.1 Command syntax
UNIX commands begin with a command name, often an abbreviation of the command's action
(such as cp for ``copy'' or mv for ``move''). Most commands include ``flags'' and ``arguments''. A
flag identifies some optional capability and begins with a hyphen. An argument is usually the name
of a file, such as one to be read. For example, the command line
cat -n stuff
calls the cat program (to ``concatenate'' files). In this case, cat reads the file named ``stuff'' and
displays it. The -n flag tells cat to number the lines in the display.
The hyphen that precedes a flag is a special character used to distinguish flags from filenames. In
the example above, the hyphen prevents cat from trying to display a file named ``n''. Commands
can contain other special characters as well. The shell interprets such characters, and sometimes
replaces them with other values, before it passes the command with its flags and arguments to the
program that actually executes the command.
Remember that uppercase and lowercase letters are not interchangeable. Thus if you tried to give
the cat command by typing CAT, it would fail; there is no program named (uppercase) CAT.
3.2 Figuring out where you are
As previously stated, when you first connect to a biolinux machine your current working directory
will always be your home directory.
pwd
Prints the current (working) directory, like so:
$ pwd
/home/user1
3.3 Changing to another directory
cd [directory]
Changes the current working directory.
To back up a directory, you'd do:
cd ..
To back up two directory levels, you'd do:
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cd ../..
To change to a subdirectory in your current directory, you can just type the name of that
subdirectory (remember to use tab to save typing the entire directory name):
cd public_html
To change to some other directory on the system, you must type the full path name:
cd /tmp
For a short cut to your home directory just type:
cd
3.4 Seeing what's there
ls [-options] [name]
List the current directory's contents. By itself, ls just prints a columnar list of files in your directory:
$ ls
News
admin
bin
biz
bkup
html-helper-mode.el
letters
lynx_bookmarks.html
mail
moo
perl-mode.el
perlmods
public_html
scripts
tempo.el
tiny.world
tmp
Here are a few other options that can format the listing or display additional information about the
files:
-a
list all files, including those starting with a "."
-d
list directories like other files, rather than displaying their contents
-k
list file sizes in kilobytes
-l
long (verbose) format — show permissions, ownership, size, and
modification date
-t
sort the listing according to modification time (most recently modified
files first)
-X
sort the files according to file extension
-1
display the listing in 1 column
Options can be combined; in this example, we show a verbose listing of files by last modification
date:
$ ls -lt
total 94
drwx-----drwx-----drwx-----drwxr-xr-x
drwx-----drwx------rw------drwx-----drwx-----drwx-----drwx------
6
2
13
2
7
2
1
2
2
2
2
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
1024
1024
1024
1024
1024
1024
29
1024
1024
1024
1024
8
Feb
Feb
Feb
Feb
Feb
Feb
Feb
Feb
Feb
Feb
Feb
28
28
28
28
28
26
21
20
14
12
1
19:42
19:41
19:39
19:38
19:00
18:45
16:29
09:25
01:29
13:40
17:19
admin
scripts
perlmods
public_html
moo
mail
tiny.world
bin
tmp
letters
biz
Unix/Linux basics for biolinux
drwx--x--x
drwx------rw-r--r--rw-rw-r--rw-rw-r--rw-rw-r--
2
2
1
1
1
1
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
kira
1024
1024
592
23815
25802
27491
Jan
Nov
Nov
Oct
Oct
Oct
9
13
8
25
25
25
20:59
09:02
18:12
07:35
07:35
07:35
News
bkup
lynx_bookmarks.html
tempo.el
perl-mode.el
html-helper-mode.el
Also, you can specify a filename or directory to list:
$ ls -l public_html/
total 1
-rwxr-xr-x
1 kira
kira
436 Feb 28 19:52 index.html
The verbose listing shows the file permissions of a given file:
-rwxr-xr-x
Directories have a "d" in the first column; regular files have a "-". The remaining 9 characters
indicate the owner, group, and world permissions of the file. An "r" indicates it's readable; "w" is
writable, and "x" is executable. A dash in the column instead of a letter means that particular
permission is turned off. So, "-rwxr-xr-x" is a plain file that is read-write-execute by the owner, and
read-execute by group and world. "drwx------" is a directory that is read-write-execute by owner,
and group and world have no permissions at all. This is explained in more detail later on in Section
5 'Introduction to ownership/permissions'.
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4. Files and Directories
4.1 Unix File Names
Unix filenames can't have spaces, slashes, or weird characters in them. (Or, sometimes they can, but
this will make your life miserable, because referring to strange characters requires a backlash in the
filename.) Also, file names are case sensitive, so if you create a script and upload it as
"SCRIPT.TXT", and then attempt to run it as “script.txt”, it won't work, because Unix can't find
"script.txt" in your directory.
4.2 Creating Files
You can create files by editing them with an editor, or ftp'ing them into your directory. Biolinux
includes gedit, a very simple text editor. To use it, just type
gedit newfile.txt &
There's also a way you can create an empty file without editing it: the touch command.
touch filename
The main use of touch is to update the timestamp on a file; if you touch an existing file, it changes
the last modification date of that file to now. However if the file doesn't exist, touch creates an
empty file. This may be useful for creating counter data files or output logs:
touch outlog
chmod 666 outlog
4.3 Copying Files
cp [options] source dest
Copies the source file to the destination. The source file remains after this. Options:
-b
backup files that are about to be overwritten or removed
-i
interactive mode; if dest exists, you'll be asked whether to overwrite
the file
-p
preserves the original file's ownership, group, permissions, and
timestamp
4.4 Moving (Renaming) Files
mv [options] source destination
Moves the source file to the destination. The source file ceases to exist after this. Options:
-b
backup files that are about to be overwritten or removed
-i
interactive mode; if dest exists, you'll be asked whether to overwrite
the file
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4.5 Viewing Files
more filename
less filename
These two commands allow you to page through a file. less is often preferred because it allows you
to back up in a file. Both commands scroll through the file, starting at the first line, and displaying
one page at a time. Press the space bar to continue to the next page. In less, pressing "b" instead of
the spacebar will backup to the previous page. Alternatively just use the up and down arrows on the
keyboard. A variety of other scrolling and searching options exist; consult the man pages for a
detailed listing.
head [options] filename
tail [options] filename
head displays lines from the beginning of a file. If no options are given, the default is 10 lines. An
optional argument of --lines can be used to specify the number of lines to display. For example, to
list the first 5 lines of a file, you'd do:
head -5 filename
tail is similar, except it shows lines from the end of a file. Again, with no arguments, it shows the
last 10 lines. Try:
tail filename
4.6 Searching for something in a File
grep [options] pattern filenames
fgrep [options] string filenames
grep and fgrep search a file or files for a given pattern. fgrep (or "fast grep") only searches for
strings; grep is a full-blown regular-expression matcher. Some of the valid options are:
-i
-n
-v
-w
case-insensitive search
show the line# along with the matched line
invert match, e.g. find all lines that do NOT match
match entire words, rather than substrings
An example: if you wanted to find all instances of the word "Fred" in a file, case-insensitive but
whole words (e.g. don't match "Frederick"), and display the line numbers:
$ grep -inw "Fred" fnord
3:Fred
9:Fred
There are a great many other options to grep. Check the man page for more information.
4.7 Deleting Files
rm [options] filenames
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Deletes the named file(s). Options:
-f
-i
-R
force, delete files without prompting
interactive — prompts whether you want to delete the file
recursively delete all files in directories
4.8 Creating Directories
mkdir dirname
Creates the named directory. If a full path is not given, the directory is created as a subdirectory of
your current working directory. You must have write permissions on the current directory to create
a new directory.
4.9 Deleting Directories
rmdir dirname
Deletes the named directory. If the directory is not empty, this will fail. To remove all files from the
directory, first do "rm -rf dirname" but BE CAREFUL!
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5. Introduction to File Ownership/Permissions
One of the key things that makes Unix different from Windows are file ownership and permissions.
5.1 File Ownership
All files are on a Unix system are owned by a user and a group. Users own files they create, and
root can change the ownership of files through the "chown" utility. A file's group is set to the
primary group of the user that creates it initially. Since users can belong to more than one group
(and often do), a user can change the group of any file they own with the "chgrp" utility to any
group they belong to. You can use the "groups" utility to list what groups you (and others) belong
to.
Commands:
chmod [permissions][file]
chgrp [group] [file]
groups [user]
5.2 File Permissions
File permissions control who can do what to a file. They're divided into four sections. Firstly, there
are “Extended Permissions” which are for the more advanced user and thus beyond the requirement
of this section. Secondly, “User Permissions” control what the user who owns a file can do to it.
Thirdly, “Group Permissions” control what members of a group that owns a file can do to it. And
fourthly, “World or Other Permissions” control what everyone else can do to the file.
Each section is represented internally as three bits, which gives three on/off fields for each. For
user, group, and other, the fields are:
read - The user/group can read the contents of the file. For directories, this means the user/group
can list its contents.
write - The user/group can write to the file, changing the data in it however they want. For
directories, it gives permission to create/remove files, so you can't actually DELETE a file unless
you've got write perms to the directory it’s in.
execute - The program can be run by the user/group. For directories, it means you can cd into the
directory.
5.3 Representing File Permissions
There are two ways to represent file permissions: symbolic and numeric
5.3a Symbolic Representation:
File modes are represented using letters and symbols familiar to humans. These are fairly easy to
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Unix/Linux basics for biolinux
understand:
chmod u+rwx,go+rx index.html
u is the owner's ("user's") permissions; g is the group permissions, and o is "other" or world
permissions. The + sign turns the stated permissions on; a — sign turns them off. So, if you want to
change a file so that it's group writable, but not readable or executable, you'd do:
chmod g+w,g-rx filename
5.3b Numeric Representation
This is a bit more confusing, so I'll go into more detail here.
As each field of the file's permissions is three bits, it can be represented as a series of octal (base 8)
numbers. The maximum base-10 value three bits can have is seven, which is the maximum value
for a single digit in base 8. Read perms (bit 3) are represented by a 4. Write perms (bit 2) are
represented by a 2. Execute perms (bit 1) are represented by a 1. To specify multiple permissions,
just add their values together. For example, to specify read and write perms, you'd use a 6. To
specify all of read, write, and execute, you'd use a 7. To specify none, use a 0.
Now, to actually specify these, you use four digits. The first specifies extended file perms (this is
optional), and is almost always 0. The second specifies user permissions, the third group
permissions, and the fourth world permissions.
So to specify user read, write and execute, group read and execute, and world read, you'd use:
0754 or simply 754
References:
info chmod
info groups
info chgrp
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6. Obtaining help
6.1
The "man" command
All commands on the Linux system are described online in a collection of files called "man pages",
because they were originally pages from the UNIX Programmer's Manual.
Try it now - type in "man ls". The resulting page will describe the command, then describe every
option, then give further details about the program, the author, and so on. This information is shown
using the "less" command. For now, it is sufficient to know that you can use the up and down
arrow, “PgUp” and “PgDn” keys to move around, and the “Q” key to quit.
6.2 The "info" command
Another source of online help is the "info" command. Some Linux commands may supply both
"man" and "info" documentation. As a general rule, "info" documentation is more verbose and
descriptive, like a user guide, while "man" documentation is more like a reference manual, giving
lists of options and parameters, and the meaning of each.
Try typing "info ls" now. The method for moving around in "info" is quite similar to "man" you can also use the arrows and “PgUp/PgDn” to move, and “Q” to quit. The main difference is that
info pages can contain "menus" of links which lead to other pages. To follow a link, move the text
cursor to it with the arrow keys, and press Enter.
6.3 The "--help" option
Most (but not all) programs have a “--help” option which displays a very short description of its
main options and parameters. Try typing "ls --help" to see. This will produce more than one
screenful of information, so you'll have to use the terminal's scrollbar to see what was displayed.
The "--help" information rarely says anything that isn't also found in the "man" documentation, so
it's rarely needed, except in a tiny number of programs which do not supply any other form of
documentation.
6.4 Using “apropos” to find commands
If you know the name of a command, you can view its man page at your terminal. If you don't
know its name, you can use the “apropos” command, which searches through the header lines of
the man pages for whatever keyword you supply and shows you a list of the man pages it finds. To
use it, type
apropos topic
where topic is a word describing what you want to know. The “apropos” command does not
require an exact case match and will also find partial words.
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6.5 Biolinux applications documentation
All documentation for biolinux software applications can be found under the following path:
/usr/software/documentation
In order to view a documentation file you'll need to first know what type of file it is. This is usually
obvious by its extension. Below are the different file viewers you'll need for different file types.
For a text editor type:
gedit documentation.txt &
For a pdf viewer type:
xpdf documentation.pdf &
For a simple Web browser type:
mozilla documentation.html &
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7. Using Pipes
One of the features that makes UNIX so flexible is the ability to combine two or more utilities
together to perform a more complex function. Pipes are the mechanisms that allow you to combine
several utilities together. Pipes let you take the standard output of one command and use it for the
standard input for another command. The vertical bar (|) is used to designate a pipe and is placed
between the two commands.
7.1 General Approach
1. To use pipes, you must have at least two commands: one that sends its output to standard
output for the first, and one that reads its input from standard input for the second. You can
connect more than two commands with a pipe. Usually the middle components of the pipe
are filters.
2. Type the commands in the order you want them executed, separating each command from
the next with the vertical bar, |.
3. Press the return key, and your commands will be executed.
7.2 Some Examples
Copy the file 'namesfile.txt' from the '/tmp/workshop' directory into your home directory.
Now, try the following command.
cat namesfile.txt | wc -l
Here we are using a pipe to combine the “cat” and “wc” utilities. (See man wc ).
Now try the following and see if you can work out what the command should do before executing
it. Use the man pages to look up the commands being used before hand.
ls | wc -l
who | sort
cat namesfile.txt | sort
grep -i e namesfile.txt | less
ls -l /home | grep users | wc -l
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8. TAR and GZIP
8.1 TAR
tar stands for “Tape ARchive”. It was originally designed for tape backups, but it is used to create a
tar file anywhere on the filesystem. tar creates one "tar file" (also known as a "tarball") out of
several files and directories. A tar file isn't compressed, it's just a heap of files assembled together in
"one container". So, the tar file will take up the same amount of space as all the individual files
combined, plus a little extra. A tar file can be compressed by using gzip. Here are some examples:
tar -xvf example.tar
Extract the contents of example.tar and display the files as they are extracted.
tar -cf backup.tar /home/ftp/pub
Create a tar file named backup.tar from the contents of the directory /home/ftp/pub
tar -tvf example.tar list contents of example.tar to the screen
Now, an example:
1. Log in to the linux box and make sure you are in the home directory.
2. Do an “ls -al” to see what is in the home directory. We should have a directory called
"Desktop". “cd Desktop” into that directory and look around. Type "cd" to bring yourself
back to the home directory. Again, confirm that you are in the home directory.
3. Type in the following command: "tar -cvf desktop.tar Desktop" (please pay attention
to CaSe)
4. Do an “ls -al” again to see what is in the directory now. You should see a file called
“desktop.tar”
5. Now type in "mv Desktop Desktop.old" to rename the Desktop directory. Do an “ls -l”
to confirm that the directory name has been changed and there no longer is a directory
named Desktop in the home directory.
6. “cd” into the Desktop.old directory and confirm that the files are the same as what you saw
in #2.
7. “cd” back to your home directory (to move up (back) one directory, you can type in "cd
.."
8. Now type in the command "tar -xvf desktop.tar" to extract the contents of the archive.
9. Do an “ls -al” again. You should see the original Desktop directory. “cd” into it and
make sure the files are in it.
10.
Remove the tar file and the Desktop.old directories if everything worked properly.
("rm desktop.tar", "rm -rf Desktop.old")
8.2 GZIP
gzip is the original UNIX ZIP format. It's common to first "tar" files and then compress them
afterwards using gzip. These files are normally given the extentions .tar.gz to show that they are tar
archives zipped up with gzip. You may also see the extension, .tgz. An archive that is compressed
with gzip is compatible with WinZip and PkZip. So, a file zipped up on a UNIX box can be
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unzipped with a Windows box.
Here are some examples:
To compress a file using gzip, execute the following command:
gzip filename.tar
(where filename.tar is the name of the file you wish to compress). The result of this operation is a
file called “filename.tar.gz”. Note: by default, gzip will delete the filename.tar file.
To decompress a file using gzip, execute the following command:
gzip -d filename.tar.gz
The result of this operation is a file called “filename.tar”. Note: by default, gzip will delete the
filename.tar.gz file.
You can also decompress the file using the command:
gunzip filename.tar.gz
This is the same as using the “gzip -d” command. There are many options that you can use with
gzip. Do a man on the utility to learn more.
8.3 Using TAR and GZIP together
Rather than typing two commands most Linux users will use gzip within tar like so:
tar -zcvf folder.tar.gz folder
creates a compressed archive called “folder.tar.gz” from a directory called “folder” including
all its subdirectories, and:
tar -zxvf folder.tar.gz
will decompress and extract the compressed archive “folder.tar.gz”
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9. Linux Filesystem
UNIX/Linux filesystems are very different from Windows. UNIX/Linux is organized in a
hierarchy, starting with "slash." Slash is this: / The rest of the directories and subdirectories
continue down from slash. For example, the directory, /etc/httpd/ , is a subdirectory in the the /etc
(pronounced "etsie") directory. /etc/ is a directory in slash. Unlike Windows that represents drives
as letters (e.g., a:,c:, e:), all devices, including hard drives, cdroms, and other storage media in
Linux all fit into the normal directory structure. Devices are mounted onto the file system tree and,
as a user, you might not be able to tell if a directory is actually located on your own hard drive or on
a hard drive of another computer.
Linux, allows for the great level of flexibility in terms of its file systems. You can literally put in
four drives and "mount" them to various directories in your tree. Here are some common mounts
you should know about:
/
swap
/boot
/usr*
/dev
/etc
/var
/bin
/home*
(Called root), this is equivalent to C:\ in the DOS/Windows world. You cannot run a
Linux system without the root partition. All other partitions are a subset of the root
partition.
Unless you have massive amounts of memory, you are going to need some swap
space. In Windows, you have Win386.swp; here, it's a separate drive partition.
This contains the necessary stuff to start the machine, including the base kernel. This
partition is optional, but usually present. You will not need to mess around in here if
you have a running system.
This is the directory where global executables are stored. It can be read-only, if you
want. Generally speaking, most software is installed here by default. All Biolinux
applications are installed here within a subdirectory called ‘software’. Documentation
and examples for these applications can be found within a subdirectory of software.
i.e. /usr/software/documentation
This is the directory where all of your devices are. There are a few useful examples
for you to know. /dev/hda is the first ide hard drive. /dev/hdb is the second. /dev/sda
would be the first SCSI drive, and /dev/sg0 is your robotic arm.
This is where most configuration files are stored. You will spend a lot of time in here
if you are an administrator. Most files require "root" access to change.
Many of the system log files are here, as well as spools (mail, printer...)
This directory is the home of binary executables. These include the common
commands we have already learned like ls, cat, gzip and tar.
This is where all users home directories are located
* = Important to biolinux users
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10. A Unix Command Summary
The following commands are grouped alphabetically by function. Each has a man page describing it
in full.
Access Control
exit - terminate a shell (see "man sh")
passwd - change login password
Communications
talk - talk to another logged-in user (full screen)
write - write to another logged-in user
Programming Tools
awk - pattern scanning and processing language
/bin/time - time a command
kill - kill a process
perl - Popular script interpreter
sh - Bourne shell command interpreter
Documentation
apropos - locate commands by keyword lookup
info - start the InfoExplorer program (ADS only)
man - find manual information about commands
whatis - describe what a command is
whereis - locate source, binary, or man page for a program
Editors
gedit – easy to use text editor
emacs - screen-oriented text editor
pico - simple, screen-oriented text editor (easiest for new users)
sed - stream-oriented text editor able to perform basic text transformations
vi - full-screen text editor
vim - full-screen text editor ("vi-improved")
File and Directory Management
cd - change working directory
chmod - change the protection of a file or directory
cmp - compare two files
comm - select/reject lines common to two sorted files
compress - compress a file
cp - copy files
crypt - encrypt/decrypt files (CCWF only)
diff - compare the contents of two ASCII files
file - determine file type
grep - search a file for a pattern
gzip – compress or expand files
ln - make a link to a file
ls - list the contents of a directory
mkdir - create a directory
mv - move or rename files and directories
pwd - show the full pathname of your working directory
rm - delete (remove) files
rmdir - delete (remove) directories
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Unix/Linux basics for biolinux
sort - sort or merge files
tar – create or extract archives
uncompress - restore compressed file
uniq - report (or delete) repeated lines in a file
wc - count lines, words, and characters in a file
File Display and Printing
cat - show the contents of a file; catenate files
fold - fold long lines to fit output device
head - show first few lines of a file
more - display a file, one screen at a time
less - display a file, one screen at a time with scroll option
page - like "more", but prints screens top to bottom
tail - show the last part of a file
zcat - display a compressed file
File Transfer
ftp - transfer files between network hosts
scp – secure transfer of files between networked UNIX hosts
Miscellaneous
alias - define synonym commands
chsh - change default login shell
clear - clear terminal screen
echo - echo arguments
stty - set terminal options
News/Networks
netstat - show network status (on UTS, /usr/sbin/netstat)
ssh - secure-shell version of rsh
telnet - run Telnet to log in to remote host
Process Control
bg - put suspended process into background
fg - bring process into foreground
jobs - list processes
Status Information
date - show date and time
df - summarize free disk space
du - summarize disk space used
env - display environment
finger - look up user information
history - list previously issued commands (C shell, bash, and ksh only)
last - indicate last login of users
manpath - show search path for man pages
printenv - print out environment
ps - show process status
pwd - print full pathname of working directory
set - set shell variables (C shell, bash, and ksh only)
stty - set terminal options
uptime - show system load, how long system has been up
w - show who is on system, what command each job is executing
who - show who is logged onto the system
whois - Internet user name directory service
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