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Introduction to Linux for bioinformatics

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This 1st presentation in the training "Introduction to linux for bioinformatics" gives an introduction to Linux, and the concepts by which Linux operates.

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Introduction to Linux li for bioinformatics Joachim Jacob 8 and 15 November 2013
Mixing exercises and theory This training will introduce you to Linux in a broad range of concepts. Exercises ● Graphical ● Terminology ● >>> command line
Linux ... Can somebody tell me what they think about when hearing 'Linux' ?
A bunch of hardware: a computer!
Linux drives the computer hardware Get me that file! OK The linux kernel
Linux drives the computer hardware Get me that file! OK The linux kernel
Linux drives the computer hardware Get me that file! OK Here you are: The linux kernel Thank you
Who's asking? GNU! Get me that file! The operating system OK GNU Here you are: The linux kernel Thank you Provides the low level commands to communicate with the hardware through Linux
There a lot of chatter What's in that directory? ('ls' in GNU language) The operating system 3 files: reads.fastq, pe_aln.sam, README GNU Show me the content of that file reads.fastq (e.g. 'head') The linux kernel I read: >HS:0012541 ATCGAATATACGATG ...
GNU/Linux goes along very well The operating system GNU The linux kernel While the linux kernel takes care of managing the computer resources (CPU, disks, file system, RAM, networkcards, …), GNU provides the means of communication with the linux kernel through the well-known commands and programs (bash, ls, mkdir,...). GNU is usually the first layer of user interaction. http://www.gnu.org/software/
But who cares? The operating system GNU/Linux GNU The goal of linux is to be as invisible as possible, doing the heavy lifting on the background. This GNU/Linux operating system is a solid core for a lot of computers and devices. The linux kernel https://www.dlitz.net/go/sticker/linuxstk800.jpg http://coe.uncc.edu/mosaic/mosaic-linux/linux-basics/linux-kernel.html Other OSes: Windows, Mac OS x, Solaris, ….
Why Linux? Open source: the kernel code is viewable by anyone. ● Open development: anybody can propose enhancements /change it to their needs. ● Free-to-use: anybody can use the kernel to drive their own computer or device (always interesting in ● academics: a lot of development here) Stable: it is one of the most stable OS you can find. ● * since so many people use the linux kernel for their projects, and because of the many eyes watching it, debugging happens at an astonishing rate. ** all this is protected (to remain open) by powerful licenses such as GPL, Apache license, creative commons,...
But, the teacher's computer runs not 'linux'
This is the Ubuntu flavour of Linux Ubuntu's applications and graphical interface The rock solid Linux kernel Many different organisations use the Linux kernel. Some, such as Canonical, to create the Ubuntu Linux distribution, adding their graphical sauce to it.
So – who of you is using Linux already? http://www.linuxfoundation.org/ http://www.youtube.com/watch?v=yVpbFMhOAwE Graphics: http://thenakedhero.com
So – who of you is using Linux already?
Start! Pick a Linux distribution Different distributions to run on your computer exist:. They use OS kernel (Linux) ● They add their graphical user interface (desktop environment) ● They add tools and applications (backup, texteditor,...) ● They provide a software package manager ● initialization & configuration scripts ● commercial support There are many distributions (600+), but perhaps only a few that really matter... ● http://www.distrowatch.com http://www.linuxtoday.com/
How do I choose? http://fedoraproject.org http://linuxmint.com/ http://www.ubuntu.com http://pinguyos.com/
Guide to choosing your distribution ● Server ● Commercial support (company driven) – ● Free and community driven – ● SUSE Linux ES, Red Hat EL, Ubuntu Server Debian, CentOS, Scientific Linux Computer ● Old hardware, slow: – ● Puppy Linux, Crunchbang, Lubuntu, ... New hardware, fast: – For home use: Linux Mint, Ubuntu ... – For work use: Crunchbang, OpenSuse, Ubuntu,... http://distrowatch.com/dwres.php?resource=major http://www.linux.org/threads/selecting-a-linux-distribution.4087/
Guide to choosing your distribution Perhaps it's easier to define the opposite ● Want stability? Don't choose Fedora. ● Want the latest and hottest? Don't choose CentOS ● Want a lightweight distro? Don't choose Ubuntu ● Want classic look? Don't choose Elementary OS ● ● Want to do bioinformatics? Don't choose CentOS, go for the latest actively developed. ... (guess I can keep going) Thread: Distro best for bioinformatics: http://www.biostars.org/p/16778/
Email client Browser File manager System settings Linux in different disguises ... Desktop environment Linux kernel The philosophy is to have the choice of several exchangeable components to customize your experience
They differ in 'desktop environment' KDE Unity Gnome Cinnamon http://en.wikipedia.org/wiki/Desktop_environmen
They differ in file managers Dolphin Nautilus Krusader Thunar http://en.wikipedia.org/wiki/File_manager
Very easy ways to try them out exist Live modus! 1. Grab a USB key or CD 2. Download an ISO file: pick the 64-bit version 3. Put the ISO image to the USB key or CD, e.g. with Unetbootin 4. Boot your computer from the USB key or CD (press F2 during boot) http://unetbootin.sourceforge.net/
Notes about installing Linux : level of difficulty Straight forward Give your complete hard disk to Linux. The current installers are very user friendly. If you want access to other OSes on your computer (Windows,...): 2 options VIRTUALISATION DUAL BOOT Linux Windows Choose during boot which OS you want to launch. http://www.virtualbox.org http://www.gnu.org/software/grub/
Exercise: let's play! To complete the exercises, you will find .iso images of different distributions in the Downloads folder. Pick one of those 2 exercises (click on the link): A: Create a bootable live USB or B: Install Linux as a virtual machine
Keywords operating system linux GNU open source distribution desktop environment live CD virtual machine dual boot Write in your own words what the terms mean
Break

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Introduction to Linux for bioinformatics

  • 1. Introduction to Linux li for bioinformatics Joachim Jacob 8 and 15 November 2013
  • 2. Mixing exercises and theory This training will introduce you to Linux in a broad range of concepts. Exercises ● Graphical ● Terminology ● >>> command line
  • 3. Linux ... Can somebody tell me what they think about when hearing 'Linux' ?
  • 4. A bunch of hardware: a computer!
  • 5. Linux drives the computer hardware Get me that file! OK The linux kernel
  • 6. Linux drives the computer hardware Get me that file! OK The linux kernel
  • 7. Linux drives the computer hardware Get me that file! OK Here you are: The linux kernel Thank you
  • 8. Who's asking? GNU! Get me that file! The operating system OK GNU Here you are: The linux kernel Thank you Provides the low level commands to communicate with the hardware through Linux
  • 9. There a lot of chatter What's in that directory? ('ls' in GNU language) The operating system 3 files: reads.fastq, pe_aln.sam, README GNU Show me the content of that file reads.fastq (e.g. 'head') The linux kernel I read: >HS:0012541 ATCGAATATACGATG ...
  • 10. GNU/Linux goes along very well The operating system GNU The linux kernel While the linux kernel takes care of managing the computer resources (CPU, disks, file system, RAM, networkcards, …), GNU provides the means of communication with the linux kernel through the well-known commands and programs (bash, ls, mkdir,...). GNU is usually the first layer of user interaction. http://www.gnu.org/software/
  • 11. But who cares? The operating system GNU/Linux GNU The goal of linux is to be as invisible as possible, doing the heavy lifting on the background. This GNU/Linux operating system is a solid core for a lot of computers and devices. The linux kernel https://www.dlitz.net/go/sticker/linuxstk800.jpg http://coe.uncc.edu/mosaic/mosaic-linux/linux-basics/linux-kernel.html Other OSes: Windows, Mac OS x, Solaris, ….
  • 12. Why Linux? Open source: the kernel code is viewable by anyone. ● Open development: anybody can propose enhancements /change it to their needs. ● Free-to-use: anybody can use the kernel to drive their own computer or device (always interesting in ● academics: a lot of development here) Stable: it is one of the most stable OS you can find. ● * since so many people use the linux kernel for their projects, and because of the many eyes watching it, debugging happens at an astonishing rate. ** all this is protected (to remain open) by powerful licenses such as GPL, Apache license, creative commons,...
  • 13. But, the teacher's computer runs not 'linux'
  • 14. This is the Ubuntu flavour of Linux Ubuntu's applications and graphical interface The rock solid Linux kernel Many different organisations use the Linux kernel. Some, such as Canonical, to create the Ubuntu Linux distribution, adding their graphical sauce to it.
  • 15. So – who of you is using Linux already? http://www.linuxfoundation.org/ http://www.youtube.com/watch?v=yVpbFMhOAwE Graphics: http://thenakedhero.com
  • 16. So – who of you is using Linux already?
  • 17. Start! Pick a Linux distribution Different distributions to run on your computer exist:. They use OS kernel (Linux) ● They add their graphical user interface (desktop environment) ● They add tools and applications (backup, texteditor,...) ● They provide a software package manager ● initialization & configuration scripts ● commercial support There are many distributions (600+), but perhaps only a few that really matter... ● http://www.distrowatch.com http://www.linuxtoday.com/
  • 18. How do I choose? http://fedoraproject.org http://linuxmint.com/ http://www.ubuntu.com http://pinguyos.com/
  • 19. Guide to choosing your distribution ● Server ● Commercial support (company driven) – ● Free and community driven – ● SUSE Linux ES, Red Hat EL, Ubuntu Server Debian, CentOS, Scientific Linux Computer ● Old hardware, slow: – ● Puppy Linux, Crunchbang, Lubuntu, ... New hardware, fast: – For home use: Linux Mint, Ubuntu ... – For work use: Crunchbang, OpenSuse, Ubuntu,... http://distrowatch.com/dwres.php?resource=major http://www.linux.org/threads/selecting-a-linux-distribution.4087/
  • 20. Guide to choosing your distribution Perhaps it's easier to define the opposite ● Want stability? Don't choose Fedora. ● Want the latest and hottest? Don't choose CentOS ● Want a lightweight distro? Don't choose Ubuntu ● Want classic look? Don't choose Elementary OS ● ● Want to do bioinformatics? Don't choose CentOS, go for the latest actively developed. ... (guess I can keep going) Thread: Distro best for bioinformatics: http://www.biostars.org/p/16778/
  • 21. Email client Browser File manager System settings Linux in different disguises ... Desktop environment Linux kernel The philosophy is to have the choice of several exchangeable components to customize your experience
  • 22. They differ in 'desktop environment' KDE Unity Gnome Cinnamon http://en.wikipedia.org/wiki/Desktop_environmen
  • 23. They differ in file managers Dolphin Nautilus Krusader Thunar http://en.wikipedia.org/wiki/File_manager
  • 24. Very easy ways to try them out exist Live modus! 1. Grab a USB key or CD 2. Download an ISO file: pick the 64-bit version 3. Put the ISO image to the USB key or CD, e.g. with Unetbootin 4. Boot your computer from the USB key or CD (press F2 during boot) http://unetbootin.sourceforge.net/
  • 25. Notes about installing Linux : level of difficulty Straight forward Give your complete hard disk to Linux. The current installers are very user friendly. If you want access to other OSes on your computer (Windows,...): 2 options VIRTUALISATION DUAL BOOT Linux Windows Choose during boot which OS you want to launch. http://www.virtualbox.org http://www.gnu.org/software/grub/
  • 26. Exercise: let's play! To complete the exercises, you will find .iso images of different distributions in the Downloads folder. Pick one of those 2 exercises (click on the link): A: Create a bootable live USB or B: Install Linux as a virtual machine
  • 27.
  • 28. Keywords operating system linux GNU open source distribution desktop environment live CD virtual machine dual boot Write in your own words what the terms mean
  • 29. Break