What is UNIX (The history)?

1
(No Transcript)
2
What is UNIX (The history)?

• Originated as a research project at ATT Bell
  Labs in 1969 by Ken Thompson and Dennis Ritchie.
• Developed in several different versions for
  various hardware platforms (Sun Sparc, Power PC,
  Motorola, HP RISC Processors).
• In 1991, Linus Torvalds created a UNIX-like
  system to run on the Intel 386 processor. Intel
  had already started dominating the PC market, but
  UNIX was nearly absent from the initial Intel
  market.
• In January 2000, Apple announced MAC OS X, a
  UNIX/Mach hybrid that provides UNIX command line
  features.

3
Is LINUX really UNIX?

• Well, yes and no
• Yes, because it has essentially the same look and
  feel like any UNIX operating System.
• Yes, because it offers the ability to run nearly
  any program that runs on UNIX systems (through
  API conventions such as POSIX, etc..).
• No because the heart of the system (kernel) has a
  lot of new features that go beyond the classical
  design philosophy of UNIX kernels.

4
Why should you choose UNIX/LINUX?

• Noted for its reliability, multi-tasking
  performance and network application capabilities.
  
• Because it has started life in academia, where
  most of the scientific analysis programs are
  developed, you will find a lot of good scientific
  software that runs on UNIX/LINUX. Windows has
  certainly scored to a smaller extent on this
  area.
• Unix/LINUX is rich in commands and software
  development capabilities. Every UNIX/LINUX OS
  comes with a built set of compilers/debug tools
  that have are used widely by the world scientific
  community. This is not true for Windows.

5
What is GNU?

• GNU stands for GNU's Not Unix. The three letter
  abbreviation is not a joke. It emphasizes a major
  project of the Free Software Foundation (FSF)
  that really created the LINUX operating system
  with many of its popular tools.
• Richard Stallman created FSF, in order to
  encourage the development and use of freely
  redistributable code.
• Freely means the freedom of redistributing your
  code under certain conditions. It does NOT mean
  zero financial cost!
• The Gnu Public License (GPL) defines the terms
  and conditions of redistributing the LINUX kernel
  and other tools that make it usable, forming a
  LINUX distribution.

6
What is a LINUX distribution?

• The GPL framework allowed LINUX distributions
  (RedHat, SuSE, Mandrake) to be formed. These are
  organised bindings of the LINUX kernel together
  with a set of programs (text editors, compilers,
  office and scientific suites) to make a system
  suitable for a particular task.
• The MCC distribution made by Manchester Computer
  Centre at the University of Manchester in England
  together with 'SoftLanding Systems' (now called
  'Slackware') were the first official LINUX
  distributions.
• RedHat, SuSE , Ubuntu and others followed being
  more successfull today, simply because they are
  more user friendly.

7
The case for LINUX

• LINUX is certainly a cheaper alternative to other
  proprietary UNIX systems such as Sun Solaris or
  HP-UX because
• It runs on a wider range of hardware than them.
• You could either download it for free (no
  support) or purchase it a set of installation
  media (CD/DVDs) with support from a commercial
  LINUX vendor (see references) at a cost which is
  a small fraction of the TCO of a UNIX system.
• Today LINUX can also give you an integrated
  desktop environment with Word Processing,
  Spreadsheet and development tools at a
  substantially lower cost than purchasing a
  Microsoft Windows system.

8
The UNIX 'shell'

• Provides a powerful interface to the UNIX
  Operating System, so you can manipulate data and
  execute several applications under certain
  conditions.
• Also known as the 'command-line' interface, a bit
  like the old Command Prompt in Windows/DOS
  systems, but it is not the same.
• Comes under different flavours, but all of them
  do the same thing in slightly different ways.
• Knowing the shell well is the ONLY WAY to make
  the most out of a UNIX system. It can be a bit
  difficult at the beginning, but since you get
  used to it, you have made a good friend that will
  help you address every computational problem!

9
Logging in to the shell

• In order to be able to use the UNIX shell, you
  will have to authenticate yourself (tell the
  system who you are). This process is commonly
  called the 'login' process, and it involves two
  steps.
• - Know your username and a password.
• - Have a means of communicating with the UNIX
  shell, so you can provide this kind of
  information.
• The first step is quite easy. You contact your
  system administrator or relevant authority and
  you obtain a login name and a password for the
  system. The second step requires a little bit
  more attention.

10
Connecting to a UNIX system (1)

• Back in the old UNIX days, users had dedicated
  machines called terminals that used to display
  text only information.
• Today, most people connect to a UNIX system by
  means of faster TCP/IP network connections from
  another UNIX-like workstation or a Microsoft
  Windows machine.
• The safest and most widespread way to connect is
  the Secure Shell (SSH) protocol. This allows for
  secure point-to-point communication between your
  system and the UNIX machine you are trying to
  login to.

11
Using SSH from a UNIX workstation

• UNIX/LINUX and MAC OS X workstations make the SSH
  UNIX login process very easy. You will need the
  IP address or the DNS name of the UNIX
  workstation. If, for example, you username is
  georgios and you want to login to the UNIX
  server frigg.uio.no ,I would type
• ssh georgios_at_frigg.uio.no press enter
• The server would then ask me the password for
  username georgios. If I type the password
  correctly (note you won't see the password as you
  type it), then I will be greeted by the shell
  prompt.

12
Using SSH from a Windows Workstation

• Windows will almost certainly require the
  installation of additional SSH terminal client
  software for this purpose. Programs such as
  'F-Secure SSH 'or 'PuTTY' give a basic terminal
  window for interacting with the Shell.
• If you need to display graphics generated on the
  UNIX machine, you will need an X-Windows client
  for Windows such as Exceed or X-Win32. Additional
  configuration steps need to be made, in order to
  make X-Windows communication possible.
• Ask the help of your local system administrator
  to set up these programs.

13
Basic Shell Principles (1)

• There is a basic syntax for all commands
  executed at the shell
• command argument1 argument2 argument3...
• command is the name of the actual shell command
  you wish to
• execute. Every command may take a certain number
  of
• arguments (or operands). For example
• cd /mn/proteas/data
• cd is the actual command and it takes one
  argument
• /mn/proteas/data.
• Always make sure that you have a space between a
  shell command and its argument(s).

14
Basic Shell Principles (2)

• All UNIX shells are case sensitive with regards
  to both the commands and their arguments, in
  contrast to versions of Windows/DOS systems. This
  means that typing
• cd /mydirectory/programs
• is not the same as typing
• CD /MYDIRECTORY/PROGRAMS
• or even
• Cd /MyDirectory/Programs
• Usually, shell commands are lower case, unless
  otherwise stated.

15
The Shell Prompt

• When you login into a UNIX system, you will
  encounter the shell prompt. The shell prompt is
  an indication that the system is ready to execute
  your commands, but it also contains useful
  information. A typical shell prompt looks like
  the one below
• georgios_at_frigg /usr/bin/virexp
• saying that I am currently logged in as user
  georgios at a server called frigg and I am
  currently in a directory called virexp that
  resides under a directory with name /usr/bin/.
  The sign says 'you can type now' and it should
  have a (sometimes blinking) cursor after it.

16
The Shell Execution Path

• Every shell session has a collection of variables
  collectively known as the shell environment.
  They control a number of issues like the
  appearance of the Shell prompt, what program
  might be your default text editor and many other
  issues.
• Perhaps the most important of these variables
  that can affect your actions is the execution
  path. This is a list of directories that the
  shell remembers all the time, in order to
  automatically reference certain applications
  (without you remembering where they are). Type
  echo PATH at the shell prompt to see this list
  of directories.

17
Filesystem basics (1)

• A Filesystem is a special part of the Operating
  System that is responsible for organising the
  storage of your data inside a computer.
• Again, like the shell, there are several
  different types of filesystems, but they all
  perform essentially the same functions
  (transparent and efficient data storage).
• However, for large server systems, the choice of
  filesystem usually makes or breaks issues such as
  performance, reliability and storage efficiency.
• Network-aware filesystems deserve a special
  mention, since they allow for efficient and
  transparent data access via computer networks.
  Examples CIFS(Windows and UNIX) and NFS(Unix).

18
Filesystem basics (2) UNIX files

• UNIX files are named locations on the computer's
  storage device. Each filename points to a special
  filesystem record that contains information
  about
• The type of file (plain data, executable program,
  special device)
• The user who created the file
• Access permissions for the file
• The beginning and end of the file record in the
  filesystem area, as well as its exact position in
  the filesystem.

19
Filesystem Basics (3) Directories and file
'paths'

• Directories (or folders) are containers in which
  files can be grouped.
• In a UNIX system, they are arranged in
  hierarchical mode, starting from the top-level
  root directory ( / ). The root directory
  branches into several files and root
  subdirectories.
• The consequence of this hierarchy is that each
  file can be uniquely identified by a 'path'. A
  'path' begins with a / (hintroot directory) and
  continues through a list of subdirectories, all
  the way down to the filename
• For example /home/gm/mydata/bac1.seq
• Remember not to confuse the term 'path' with the
  shell's execution path, as described in
  earlier slides.

20
Directory Hierarchy Diagram
lt- toplevel
lt-1st level down
lt-2nd level down
lt-3rd level down
/home/gm/mydata/
Back1.seq
21
Navigating the filesystem

• Use pwd to Print your Working Directory. For
  example, if I login to the host 'biotin' and I
  type pwd, I get the following
• georgios_at_frigg pwd
• /mn/proteas/u1/georgios
• georgios_at_frigg
• This means that I am currently in a directory
  georgios, which is under a directory called u1.
  This directory itself is under the proteas
  directory, which lives under the mn directory.
  Finally the mn directory is under the root
  (toplevel) directory.

22
Navigating the Filesystem (2)

• In the previous slide, /mn/proteas/u1/georgios
  is your home directory (note the symbol after
  the hostname frigg). This means that whenever you
  login as an ordinary user, you always have an
  entry point position in the filesystem.
• Your supervisor is now saying Under your home
  directory, you will find a directory called
  mysequences. Could you go to that directory and
  tell me what kind of files exist under it?
• Certainly you reply. I can use the cd command
  to get there
• georgios_at_frigg cd mysequences
• ./mysequences
• georgios_at_frigg /mysequences

23
Navigating the Filesystem (3)

• The cd command (Change Directory) can be used
  for moving around the filesystem. It takes a path
  as its argument.
• The path can be absolute. For exampleFrom your
  home directory, you can go to the /usr/bin
  directory by typing
• georgios_at_frigg cd /usr/bin
• georgios_at_frigg /usr/bin
• The path can also be relative. For example If
  you are already under the /usr directory, you
  could just type
• georgios_at_biotin /usr cd bin
• ./bin
• georgios_at_biotin /usr/bin

24
Navigating the Filesystem (4)

• The command cd .. will get you one level up.
  For example, if we go back to your supervisors
  request and we assume that you are under the
  mysequences directory, if you want to go back to
  the toplevel of your home directory, you type
• georgios_at_frigg /mysequences cd ..
• georgios_at_frigg
• .. is a shorthand notation for the previous
  directory level and it can really save you from
  typing long directory names that you cannot
  remember. It always works in a relative path
  context.
• The alternative would be to give an absolute
  path to the cd command
• georgios_at_frigg /mysequences cd
  /mn/proteas/u1/georgios
• georgios_at_frigg

25
Listing Files (1)

• You are back at the mysequences directory under
  your home directory. Your supervisor asked you to
  list the files in the directory
• georgios_at_frigg /mysequences ls
• seqdocs v2.3_admin.pdf xlrhodop.fasta
• georgios_at_frigg /mysequences
• The ls command lists all the directory contents
  and is the equivalent of the dir command in
  DOS/Windows.

26
Listing Files (2)

• Your supervisor says That's not good enough. I
  want details (file size, permissions, etc). Why
  don't you use the -la options of the ls command?
• georgios_at_frigg /mysequences ls -la
• total 340
• drwx------ 3 georgios biotek 62 Mar 26
  1631 .
• drwx--x--x 63 georgios biotek 8192 Mar 28
  0845 ..
• drwx------ 2 georgios biotek 6 Mar 26
  1631 seqdocs
• -rw------- 1 georgios biotek 325479 Mar 26
  1522 v2.3_admin.pdf
• -rwxrw---- 1 georgios biotek 1777 Mar 26
  1522 xlrhodop.fasta

27
Listing Files (3)

• georgios_at_frigg /mysequences ls -la
• total 340
• drwx------ 3 georgios biotek 62 Mar 26
  1631 .
• drwx--x--x 63 georgios biotek 8192 Mar 28
  0845 ..
• drwx------ 2 georgios biotek 6 Mar 26
  1631 seqdocs
• -rw------- 1 georgios biotek 325479 Mar 26
  1522 v2.3_admin.pdf
• -rwxrw---- 1 georgios biotek 1777 Mar 26
  1522 xlrhodop.fasta
• The third column from the left states the user
  owner of the listed files (georgios). The biotek
  indication of the fourth column indicates the
  file group (concept introduced later). The fifth
  column indicates the size of the file in bytes.

28
Locating files in the directory tree

• The supervisor says Help! I have placed a file
  called xlrhodop.fast or xlrhodop.fasta (I can't
  remember the name) and now I can't find it. Can
  you help me locate it?
• In order to save the day, you can employ the find
  command. Its generic syntax is
• find starting point -name filename -print
• starting point indicates the directory tree
  position that we wish to start searching.
  Filename could be an approximation of the file
  name (it doesn't have to be exact).

29
Locating filenames in the directory tree (2)

• georgios_at_frigg find / -name xlrhodop.fas
• /mn/proteas/u1/georgios/xlrhodop.fasta
• /mn/proteas/u1/georgios/mysequences/xlrhodop.fasta
  
• Note that the wildcard character () towards the
  end of the filename we are trying to search for.
  This says that we know that the name contains the
  string xlrhodop.fas. This would match all
  relevant filenames (reporting their exact
  location in the directory tree)
• /mn/biotroll/u1/georgios/xlrhodop.fasta
• /mn/biotroll/u1/georgios/mysequences/xlrhodop.fast
  a

30
File Permissions (1)

• You ask the supervisor What are these strange
  characters in the left most column of the ls -la
  output mean (-rw------- )??.
• Every file in UNIX has a set of permission flags
  that define in a strict way, who is allowed to
  read, write (modify) or execute that file.
• For example, let's take one of the listed files
  of the ls -la output command
• -rwx------ 1 georgios biotek 325479 Mar 26
  1522 v2.3_admin.pdf
• Starting from the left, this says The file
  xlrhodop.fasta can be read (r)read,
  (w)modified,(x)executed by its owner (georgios).
  Ignore the rest of the flags for now.

31
File Permissions (2)

• Directories (remember they are UNIX special
  files) are no exception to this rule and they
  also have permission flags. For example
• drwx------ 2 georgios biotek 6 Mar 26
  1631 seqdocs
• Note the leftmost flag (d). This indicates that
  seqdocs is a directory and user georgios has full
  permissions (read, write and execute) for that
  directory. Hence, what we say about file
  permissions is true for directory permissions
  with a few exceptions (see special file
  permission consideration slides).

32
Changing File Permissions (1)

• The supervisor says The file v2.3_admin.pdf is
  quite important and should not be modified. Can
  we have it as read only please? Use the chmod
  (change mode) command.
• The generic syntax for the chmod command is
• chmod ugo (-) (r,w,x) filename
• DON'T PANIC! We will explain this cryptic syntax
  with some examples!

33
Changing File Permissions (2)

• In order to satisfy your supervisors request,
  the file permissions were
• -rw------- 1 georgios biotek 325479 Mar 26
  1522 v2.3_admin.pdf
• Thus, in order to make the file read only we need
  to remove the (w) flag. We type at the prompt
• georgios_at_frigg /mysequences chmod u-w
  v2.3_admin.pdf
• The above says remove (-) the write permission
  (w) for the user (u) who is the owner of the
  file. This is the meaning of the u-w flag. After
  this action, ls -la should now indicate
• -r-------- 1 georgios biotek 325479 Mar 26
  1522 v2.3_admin.pdf
• This is now a read-only (ro) file.

34
Changing File Permissions (3)

• If we wanted to add back the write permission
  flag, we would type
• georgios_at_frigg /mysequences chmod uw
  v2.3_admin.pdf
• The sign says add write permissions (w) for the
  user (u) that owns the file.
• You can also add/remove more than one flag at a
  time
• georgios_at_frigg /mysequences chmod u-wx
  v2.3_admin.pdf
• This would remove write (w) and execute
  permissions (x).

35
Special File Permission Considerations (1)

• The execute permission is important when you are
  dealing with programs that you wish to run.
  Whether these programs are binary files or
  collections of shell commands (scripts) it
  doesn't matter. In order to run those programs,
  you will always have to set the (x) permission
  flag.
• When changing permissions for directories, keep
  in mind that under some special cases, you will
  need to enable the x flag, in order to allow
  access to the directory. Read permission might
  not be enough to allow access to the directory.
  This varies amongst different UNIX flavours.

36
Special File Permission Considerations (2)

• If a chmod command fails to execute by giving you
  an error message of the type, when typing
• chmod changing permissions of testfile.fasta'
  Operation not permitted
• make sure you check who owns the file with the ls
  -la command. If you try and change the
  permissions of a file you do not own, the
  operation will fail. In fact, insufficient
  permissions can affect the behaviour of all UNIX
  shell commands, not only chmode.

37
Deleting files

• Given the right permissions, you can remove a
  file using the rm command. If, for example, you
  have a file named testfile.fasta and you want to
  remove it, you type
• georgios_at_frigg /mysequences rm testfile.fasta
• CAUTION Take great care when you use the rm
  command. Whatever you delete, you WILL NOT BE
  ABLE TO UNDELETE. There is no Recycle Bin in
  command line UNIX. Always check where you are
  with the pwd command

38
Viewing the file contents

• The supervisor says How do I view the contents
  of a file? I want a simple shell command that
  will show the file contents.
• The cat command is probably one of the most
  frequently used commands. It displays the
  contents of the file. For example
• cat xlrhodop.fasta
• will display the contents of the file
  xlrhodop.fasta on the screen, despite the fact
  that this command is used for concatenatig files.
• An alternative way of viewing the file contents
  is to use a text editor. We are going to cover
  the basics of text-editors in the tutorial later
  in the course.

39
Viewing file contents (2)

• Be carefull NOT to attempt to view the contents
  of an executable (binary) file with cat. Your
  terminal will be filled with garbage characters
  and you might loose your connection. Here is a
  sample output of viewing a binary file with cat
• 000731 (Red H Li 7.2 2.96-10701.001.001.001.0
  01.001.001.001.001.001.001.001.001.001.01.syb.s
  rb.shsrb.ierp.oe.ABI-.hsh.dysy.dy
  sr..-ersio..-ersio_r.re.dy.re.p.ii
  .e.ii.rod.d.eh_re.dyic.cors.dor
  s.o.bss.coe.oe??? 1(?(X7????
• If you are uncertain about whether a file is a
  text file or a binary one, you can use the
  strings command. This will give you all the valid
  alphanumeric characters of the file and will
  certainly prevent you from loosing your terminal
  connection
• strings xlrhodop.fasta

40
Viewing file contents (3)

• The supervisor says Ohh! I tried to use cat to
  view a file but the output is too long for my
  terminal screen. The text keeps scrolling and I
  loose the first lines of the text. Can I stop
  this somehow?
• The less command can actually allow you to view a
  file, but it will stop the scrolling of the
  output, when your terminal window is filled. You
  can then press enter to gradually scroll down to
  the rest of the file content output
• less xlrhodop.fasta
• The more command would do exactly the same thing.

41
Viewing File Contents (4)

• Alternatively, if you suspect that the
  information you want to retrieve is towards the
  beginning or the end of the file, you can use
  head
• head xlrhodop.fasta
• This displays the beginning of the file. On the
  other hand, tail can display the end of the file.
  
• tail xlrhodop.fasta
• Both of these commands can be tailored to display
  a certain number of lines from the beginning
  (head) or the end (tail of the file)
• head -3 xlrhodop.fasta -gt displays the first 3
  lines of the file
• tail -3 xlrhodop.fasta -gt displays the last 3
  lines of the file
• OR
• head n 3 xlrhodop.fasta -gt newer systems use n
  instead of -
• tail n 3 xlrhodop.fasta -gt newer systems use
  n instad of -

42
Creating Directories

• The supervisor says We need a new directory to
  store all the pdf documents. Could you create a
  new directory called pdfdoc under the mysequences
  directory?
• georgios_at_frigg /mysequences mkdir pdfdoc
• georgios_at_frigg /mysequences ls -la
• total 340
• drwx------ 4 georgios biotek 75 Mar 28
  1515 .
• drwx--x--x 63 georgios biotek 8192 Mar 28
  1453 ..
• drwx------ 2 georgios biotek 6 Mar 28
  1515 pdfdoc
• drwx------ 2 georgios biotek 6 Mar 26
  1631 seqdocs
• -r-------- 1 georgios biotek 325479 Mar 26
  1522 v2.3_admin.pdf
• -r-------- 1 georgios biotek 1777 Mar 26
  1522 xlrhodop.fasta

43
Removing Directories (1)

• What about the seqdocs directory?, you ask.
  Delete it using the rmdir command, the
  supervisor replies.
• georgios_at_frigg /mysequences rmdir seqdocs
• So your directory structure should now look like
  this.
• total 340
• drwx------ 3 georgios biotek 61 Mar 28
  1525 .
• drwx--x--x 63 georgios biotek 8192 Mar 28
  1453 ..
• drwx------ 2 georgios biotek 6 Mar 28
  1515 pdfdoc
• -r-------- 1 georgios biotek 325479 Mar 26
  1522 v2.3_admin.pdf
• -r-------- 1 georgios biotek 1777 Mar 26
  1522 xlrhodop.fasta

44
Removing Directories (2)

• The rmdir command will promptly remove a
  directory if and only if it is empty. If the
  directory you are trying to remove
  (examplepfddoc) contains files, rmdir will fail
  with the following error message
• rmdir pdfdoc' File exists
• You then have to delete all the files under the
  directory pdfdoc and then issue the rmdir
  command.
• The alternative would be to use the rm command.
  Remember, directories are 'special' files, so you
  could remove them with rm. The next slide shows
  you how.

45
Removing Directories (3)

• rm -r -f directory name
• The -r option says delete directories
  recursively. The -f option forces the command to
  go ahead, despite the fact that the target is a
  directory and has files under it. Both options
  are required. For example, in order to delete a
  directory pdfdoc under the /mysequences
  directory, you would type
• rm -r -f pdfdoc/
• CAUTION The usage of rm in this way is even more
  dangerous, because it will delete EVERYTHING at a
  selected directory tree point, all the way down
  to the leaf nodes. Always check where you are
  with pwd first. If you delete the files, they
  will be gone forever!

46
Copying Files (1)

• The supervisor saysUnder the /mysequences
  directory there is a file called v2.3_admin.pdf .
  Could you make another copy of that file with the
  name 23adminbeta.pdf ?
• You can now use the cp command. The command's
  general syntax is
• cp sourcefilepath destfilepath
• sourcefilepathabsolute or relative path of the
  file we want to copy.
• destfilepathabsolute or relative path of the new
  file. This might include a new filename. If you
  specify a different directory for the new
  destination file and NOT a filename, the source
  file's name is used by default.
• Some examples to illustrate these points follow.

47
Copying Files (2)

• copy the v2.3_admin.pdf file as 23adminbeta.pdf
  under the same directory (/mysequences),we type
  the following
• georgios_at_frigg /mysequences cp v2.3_admin.pdf
  23adminbeta.pdf
• As a result, we should now have two files with
  exactly identical contents. Note that the size
  and the permission contents indicate that the
  files are identical.
• -r-------- 1 georgios biotek 325479 Mar 28
  1701 23adminbeta.pdf
• -r-------- 1 georgios biotek 325479 Mar 26
  1522 v2.3_admin.pdf
• Also note that cp was executed this time with
  relative paths for the source and destination
  files.

48
Copying Files (3)

• If the supervisor had saidCould you make a copy
  of the v2.3_admin.pdf file into the pdfdoc
  directory with the name 23adminbeta.pdf, you
  could then type
• cp v2.3_admin.pdf perldoc/23adminbeta.pdf
• By default, the copy command preserves the
  permissions and ownership rights of files. If in
  doubt, use the -p flag. This situation can occur
  when performing a copy of the file from computer
  to computer using specialist filesystems such as
  NFS..

49
Copying Directories

• You could copy entire directories recursively
  (including any files and their entire
  subdirectories) by using the cp command. If the
  sourcefilepath is a directory and the command is
  called with the -p and -r flags. For example, to
  make an exact copy of the pdfdoc directory under
  the /mysequences directory, type
• georgios_at_frigg /mysequences cp -p -r pdfdoc/
  pdfcopy/
• The -p flag preserves the permission and
  ownership properties and the -r instructs copy to
  copy all subdirectories under pdfdoc (recursive
  copy).

50
Moving Files

• cp copies a file (or directory) under a different
  name or new location, but it leaves the source
  file in its old place. However, sometimes we wish
  to move the file, in that we wish to copy the
  file to a new location without preserving the old
  one. This is when we can use the mv command, with
  the following syntax
• mv sourcefilepath destfilepath
• sourcefilepathabsolute or relative path of the
  file we want to copy.
• destfilepathabsolute or relative path of the new
  file. This might include a new filename. If you
  specify a different directory for the new
  destination file and NOT a filename, the source
  file's name is used by default.

51
Moving (or renaming) Files (2)

• In order to move the file xlrhodop.fasta to
  myxlr.fasta we type
• georgios_at_frigg /mysequences mv xlrhodop.fasta
  myxlr.fasta
• This removes the xlrhodop.fasta file and
  re-generates it with the name myxlr.fasta, under
  the same directory.
• -r-------- 1 georgios biotek 1777 Mar 26
  1522 myxlr.fasta
• mv does not only preserve file permissions and
  ownership rights but it does also preserve
  timestamps, so it is an effective way to rename a
  file. The UNIX shell has a rename command, but mv
  could be used effectively to rename a file. All
  the points we have made about mv for files are
  also true for directories.

52
Redirecting command output

• The gt symbol is the output redirection operator
  and can be used to re-direct the output of any
  UNIX command that prints something on the screen.
• Lets suppose that you want to merge two fasta
  sequences into a single file. We have seen
  earlier that the cat command can be used to
  concatenate (ie join) the contents of a file. So,
  if you type something like
• cat myseq1.fasta myseq2.fasta
• it would print the contents of boh files
  one-after the other on the screen (stdout). But
  what you really want is to place this output to a
  file. You can then type
• cat myseq1.fasta myseq2.fasta gt mergedseq.fasta
• to place the output in the file mergedseq.fasta .

53
Redirecting command input

• Suppose that you have finished an extensive blast
  search, and you want to mail the results to your
  lecturer or colleague. Mail is a UNIX-level
  program that performs the function of sending
  simple e-mails. Normally, you would type mail and
  then type the message on the keyboard. However,
  if you just want to mail the results, you could
  type
• mail myfriend_at_myfriend-email.com lt blast_report
• So here, you utilise the input redirector (lt) to
  say to the mail program, don't expect input from
  the keyboard, but mail all the file contents
  instead as input.

54
Chaining command outputs and inputs using 'pipes'

• Quite often in UNIX, we need to direct the
  standard output of one command to the standard
  input of another. The most commonly used operator
  to do that is the pipe oparator .
• Suppose for example that we need to count the
  number of lines of a text file to see how long it
  is. The command wc -l can perform this action.
  However, this command expects its standard input
  from the keyboard. So, what if we redirect all
  the file contents to this command by doing
  something like
• cat mytext.txt wc -l
• The cat command will print all the lines of the
  file. However, instead of doing that on the
  screen, it gives all the output to the wc -l
  command. The result is an integer representing
  the number of lines of the mytext.txt file.

55
Powerful Pipes

• Just to demonstrate the power of the UNIX shell,
  this line extracts all the DNA triplets from the
  output of a compseq command and places them on a
  single file. All in one shell command line (watch
  the demonstration). Remember, your ability to
  extract pattern from files is a key tool for
  those of you who are going to follow the
  bioinformatics path!
• cat l02870.timer grep ATCG grep -iv tot
  cut -c1-3

56
References

• UNIX has a wealth of on-line and hard-copy
  references available. This tutorial is by no
  means exhaustive and you should consult a variety
  of sources to further enhance your knowledge.
• UNIX has a built-in reference manual. The man
  command should be you best friend, whenever you
  need help for a particular command. For example,
  type man cat at your shell prompt. Every UNIX
  system should have this facility.
• However, man is good when you roughly know the
  basics of the command you are having a problem
  with. What if you don't know which command to
  use. Then you use the apropos command. Let's say
  for example that I am looking for pattern
  matching commands. I would type apropos pattern
  at the shell prompt, and this would give me a
  list of relevant commands.

57
References (2)

• EMBnet UNIX Quick Quide Useful summary of basic
  UNIX commands
• http//www.no.embnet.org/EMBNET/quickguides/UNIX03
  .pdf
• University of Surrey Unix Tutorial for Beginners
  on the World Wide Web http//www.ee.surrey.ac.uk/
  Teaching/Unix/
• The LINUX tutorialhttp//www.tldp.org/LDP/gs/node
  1.html
• Developing Bioinformatics Computer Skills,
  O'REILLY PRESS, ISBN 1-56592-664-1, useful for
  Biologists and Bioinformaticians, especially for
  beginners.