Lecture for the "Programming for Evolutionary Biology" workshop in Leipzig 2012 (http://evop.bioinf.uni-leipzig.de/)

1. Programming for Evolutionary Biology
April 3rd- 19th 2013
Leipzig, Germany
Introduction to Unix-like systems
Part 1: What is Unix?
Giovanni Marco Dall'Olio
Universitat Pompeu Fabra
Barcelona (Spain)

2. Schedule
 9.30 – 11.00: “What is Unix?”
 11.30 – 12.30: Introducing the terminal
 14:30 – 16:30: Grep & Unix philosophy
 17:00 – 18:00: awk, make, and question time

3. Schedule
 9.30 – 11.00: “What is Unix?”
 11.30 – 12.30: Introducing the terminal
 14:30 – 16:30: Grep, cut and sort
 17:00 – 18:00: Unix philosophy, piping and free
discussion

4. What are Unix, GNU, Linux?
 Computer programmers like to use acronyms and
strange names for their software
 As a result, in this course you are going to learn a
lot of new difficult words :­)
 Let's clarify: Unix, GNU and Linux

5. What does “Unix” mean?
 Let's go back to the '70s, when computers were very
large like houses
 A big problem was that each computer carried a
different operating system: so, a software written
for one computer didn't work in any other

6. What is an operating
system?
 The set of all the programs needed to use a
computer properly
 A software to coordinate all the components of the
computer (kernel)
 A software to draw windows and folders (graphical
interface)
 Software to edit texts, browse Internet, install other
software, etc..

7. What does “Unix” mean?
 To solve the problem of
computer compatibility,
the Bell lab released an
operating system called
Unix

8. What does “Unix” mean?
 To solve the problem of
computer compatibility,
the Bell lab released an
operating system called
Unix
 Unix was rapidly adopted
worldwide, and became
the standard operating
system, specially in
universities

9. What does “Unix” mean?
 To solve the problem of
computer compatibility,
the Bell lab released an
operating system called
Unix
 Unix was rapidly adopted
worldwide, and became
the standard operating
system, specially in Ken Thompson and Dennis Ritchie, creators of Unix
universities

10. Innovations introduced by
Unix
 A novel approach to organizing files and scripts
 Good approach to data analysis
 Free License for universities and companies

11. Commercial versions of Unix
 Solaris → developed by Sun microsystems
 The computers in our room run Solaris
 Historically used in many multi­processor clusters
 BSD → developed by the University of Berkeley
 ….

12. What is GNU?
 In the '80s, commercial versions of Unix started
appearing
 As a reaction a group leaded by Richard Stallman at
MIT started developing a new operating system
called GNU

13. What is GNU?
 In the '80s, commercial versions of Unix started
appearing
 As a reaction a group leaded by Richard Stallman at
MIT started developing a new operating system
called GNU
Richard Stallman, creator of GNU and of the GNU GPL license

14. What is GNU?
 GNU is the name of an operating system, inspired
to Unix and distributed as free software
 It was never fully completed, but most of its tools
are still used

15. What is GNU?
 GNU is the name of an operating system, inspired
to Unix and distributed as free software
 It was never fully completed, but most of its tools
are still used
 Most of the commands we will see today are GNU

16. What is GNU/Linux?
 The original GNU project was never fully
completed
 In 1991, it was merged with another project called
Linux, which provided the last component that
missing in GNU

17. GNU/Linux: a free Unix-like
system
 When it appeared in 1991, GNU/Linux finally
provided a free Unix­like operating system
 Thanks to the adoption of GNU/Linux servers,
Internet grew considerably in 1991­1992,

18. Resume: Unix, GNU, and
Linux
 Unix is the name of an operating system developed
in the '70s
 GNU is the name of a operating system, inspired to
Unix but distributed for free, developed in the
'80s
 GNU/Linux is a modern operating system, merging
GNU with another project (Linux)

19. Which operating system are
we going to use in this
course?
 All the computers in front of you use the Solaris
operating system.
 However, we are going to connect to a central
server, where a GNU/Linux system (Fedora) is
installed.

20. What is the difference
between Solaris and
GNU/Linux?
 Most of the software will be compatible
 Solaris is a commercial system, bundled together
with a specific hardware

21. Raise-your-hands time!
 Have you ever used a Unix­based operating system
before today?

22. Hands on Solaris
 Let's turn on the computers!
● Username: evop<computer id>
– Example: if your computer is 30, the username is
evop30
● Password: Pro4EvBi (Programming 4 Evolutionary
Biology)

23. While the computer loads:
make yourself comfortable!
http://www.codinghorror.com/blog/2007/08/computer-workstation-ergonomics.html

24. This is how your desktop should
look like, after logging in:

25. The Solaris interface
 The Solaris interface is different from Windows and
MacOS, but it should not be difficult to use
● You have a “Launch” menu, from which you can
access all the applications installed
● The interface is similar to an early Windows system

26. Our course - computers
infrastructure

27. Connecting to evopserver
 During this course, we are going to do all the
exercises on a remote Fedora server
 Let's see how to connect to it

28. Connecting to evopserver
 The first thing to do is to launch a terminal emulator
● Go to Applications­>Utilities­>Terminal

29. How does a terminal looks
like?

30. Connect to the evopserver
 Use the following command to connect to the evopserver:
● “ssh ­X <your_username>@evopserver.bioinf.uni­leipzig.de”
 Password:
 “HafbbiL!” (as “Have again fun by bioinf in Leipzig !”)

31. Connect to the evopserver
 Use the following command to connect to the evopserver:
● “ssh ­X <your_username>@evopserver.bioinf.uni­leipzig.de”
 For example, if your username is giovanni, you should type:
● “ssh ­X giovanni@evopserver.bioinf.uni­leipzig.de”
 Don't forget the “­X” option!

32. Connecting to the
evopserver
 The evopserver will ask you to confirm if you want
to connect
 Type “yes” (not “y”), and press Enter

33. Connecting to the
evopserver
 Now you should be asked for a password. Enter it
and you should be able to access to the
evopserver

34. Are you here?
 If you have done everything right, you should see
something like the following:

35. Browsing files in the
evopserver
 We will see how to use the terminal later today
 For now, let's see which files are in the server
 Do to so, type “nautilus” in the terminal

36. Type “nautilus” in the
terminal

37. Did you get an error when
typing “nautilus” ?
 Did you get the following error: “Could not
parse arguments: Can not open display” ?
 It means that you forgot to provide the ­X
option when you connected
 Type “exit” to logout, then ssh ­X
giovanni@evopserver.bioinf.uni­leipzig.de

38. nautilus
 When you type “nautilus”, you should see a
windows showing all the files in the evopserver
computer

39. Nautilus - explanation
 “nautilus” is the name
of the software used
to visualize folders in
GNU/Linux
 When we type
“nautilus” in the
terminal, we execute
it from the
evopserver computer

40. The Unix file system
 All the files in a Unix system are organized in
directories
 Directories are organized as a “tree” of diretories
 The base directory is called “root” and indicated by
a “/”

41. Exercise: look at the file
system of a Unix system
 Click on “File System” on the left frame

42. Contents of the “root”
directory
 /bin, /usr, /local, /sys → these folders contain the
software installed
 /etc, /var, → system­wide configuration
 /home → contains users' private files
 Other folders → you can ignore them for now

43. The Home folder
 The /home folder contains all the users' folder
 If you open it, you will see a different folder for
each of you
● Only the administrator has the right of open other
people's folder
 There is a special folder called “evopadmin”, which
contains the materials of the course

44. The home folder

45. The course materials
 All the course materials are located in the
/home/evopadmin folder
 The slides of this module are in
/home/evopadmin/unix_intro

46. Exercise
 Copy all the materials of the course in your home
directory
 Just open two separate windows, one for your home
and one for /evopadmin, and drag­drop the
unix_course folder

47. What is in the unix_intro
directory?
 exercises: files needed for exercises today
 slides: all the slides of this module
 cheatsheets: some cards to help you remember the
commands we are going to use today

48. Launching a text editor
from evopserver
 gedit is a text editor software
 You will use it to write scripts in the next modules
of this course

49. Launching a text editor
from evopserver
 gedit is a text editor software
 You will use it to write scripts in the next modules
of this course
 To run it, execute gedit from the command line:

50. Launching a web browser
from evopserver
 Some modules of this course will require to use a
web browser
 Use the command google­chrome on evopserver:

51. Launching a web browser
from evopserver
 Some modules of this course will require to use a
web browser
 Use the command google­chrome on evopserver:

52. Restoring the prompt
after launching
google-chrome
 Note that after launching google­chrome, the
terminal will not accept commands anymore
 To restore it, use the key CTRL­z

53. Restoring the prompt
after launching
google-chrome
 To restore google­chrome, after CTRL­z, use the bg
command

54. How can I use a Unix system
at my home / lab?

55. The GNU/Linux distributions
 There is not a single official “GNU/Linux”
operating system
 Rather, there are many “Linux distributions”,
created by different groups of people for different
tasks

56. What is the difference
between linux distributions?
 The software included by default when you install the
system
● e.g. some may have a different default text editor
● Some linux distributions include only free software,
others are less strict
● However, all the software available for Linux is
installable in any other distribution

57. What is the difference
between linux distributions?
 The software included by default when you install the
system
● e.g.: one linux distribution can have “gedit” as the default
editor, while another has “emacs”
● Some linux distributions include only free software,
others are less strict
● However, all the software available for Linux is
installable in any other distribution
 Some technical details such as the libraries used to compile
the software
 The default configuration (desktop, windows...)

58. Examples of Linux
Distributions
(2012)
 Ubuntu is a popular Linux distribution targeted at
beginners
 BioLinux is a Linux distribution targeted at
bioinformaticians
 Fedora is a popular Linux distribution, used in
many academic institutions

59. Ubuntu
 One of the most
popular distributions
 Good for novices
(doesn't need much
extra configuration)

60. BioLinux
 Distribution designed
for bioinformaticians
 When installed, it
already contains a lot
of bioinformatics
tools
 Blast, bioperl, etc..

61. Biolinux DVDs
 You should have
received a DVD of
Bio­Linux along with
the materials of the
course
 To use it, insert it in
your computer and
reboot

62. Fedora
 Fedora is another
GNU/Linux
distribution
 Popular in many
universities

63. Is MacOS an Unix-based
operating system?
 Yes, the MacOS system is also inspired to Unix
 In principle, you can do bioinformatics and follow
this course on a MacOS system
 Installing bioinformatics­specific software may be a
bit more difficult

64. What if I don't want to
switch from Windows?
 Many alternatives:
 Cygwin → simulates a Linux environment and
command line from Windows
 Emulation → emulate a whole computer, which can
run Linux or other operating systems
 Connect to a cluster or a Cloud computing instance

65. Cygwin
 Cygwin can be installed as
a standard Windows
software
 It provides a command
line interface, and
allows to launch Linux
software
 Installing non­standard
software may be
difficult, because you'll
need to compile it

66. Emulating Linux from
Windows
 A popular emulation
software is
“virtualbox”
 https://www.virtualbox
.org/wiki/Downloads

67. Connecting to a cluster
 putty: allows to
connect to a remote
server (from
Windows)

68. Cloud computing
 Cloud computing is a
service where you
“rent” a remote
computer
 You pay depending on
the CPUs/RAM/time
used

69. Resume of the session
 Unix → Operating system that in the '70s,
introduced innovative approach
 Materials of the course → they are all in the
/home/evopadmin folder
 GNU/Linux, Fedora, Ubuntu → modern operating
systems inspired to Unix

70. Let's have a break!