Practical Linux

Introduction

Department of Human Genetics

Course Outline

• Introduction.

• Connecting to other machines.

• Practical session.

• Core 1: CLI intro and filesystem navigation.

• Practical session.

• Break

• Core 2: files inspection and manipulation.

• Practical session.

• Break

• User Environment.

• Practical session.

>_

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Operating Systems

Hardware

Operating System

Applications

User

An operating system is a software layer be-tween the hardware and the applications.

Applications can be the same on differentoperating systems (Skype, Firefox, Worldof Warcraft, ...).

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Operating Systems

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Operating Systems

There is more than Windows and macOS

Currently, there are two main classes:

• Microsoft Windows.• Unix-like operating systems.

• Linux.• BSD.

• macOS.

• HP-UX.• Solaris.

Note that:

• You can run Windows or Linux on an Apple computer.

• You can run macOS on an HP, Dell, etc. computer.

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Operating Systems

Operating systems family share - personal computers

%

mac

windows

na/mixed

unix

linux

0

10

20

30

40

50

60

70

80

90

1002010

2015

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Operating Systems

Operating systems family share - supercomputers

%

mac

bsd

windows

na/mixed

unix

linux

0

10

20

30

40

50

60

70

80

90

100

1995

2000

2005

2010

2015

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Linux

History

• In 1991 Linus Torvalds started developing the Linux kernel.

• He also put together other essential ingredients required toconstruct an entire operating system around his kernel.

Linux Kernel

Operating System

Other Essential Ingredients

Linux Kernel

Operating System

Other Essential Ingredients

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Linux

History

• Linux distributions were created by combining the Linuxkernel with other system components.

Scientific Linux

• Driving force in the open source software movement.• Provided the basis for fully free computing.• In 1998 IBM and Oracle began sustaining development efforts.

• The Android system is built on top of Linux.

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Linux

Distributions

Linux Kernel

Generic Proprietary Applications

Adobe Flash Player, Acrobat,device drivers, etc.

Generic FreeApplications

bash, Libre Office, X WindowSystem, GNOME, etc.

Distribution-specificApplications

Package Management,configuration utilities, etc.

ManualsFor applications, commands, configuration, etc.

Support ServicesPersonell, forum, wiki, email, etc.

Operating System

Scientific Linux

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Linux

Distributions Popularity

• Large commercial organizations:• Commercially supported Red Hat, SUSE, and Ubuntu.• CentOS is a popular free alternative.

• Educational realm:• Ubuntu and Fedora.

• Scientific research community:• Ubuntu and Scientific Linux.

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Linux

Why do people use it?

• Powerful command line tools.

• A fully multitasking multiuser operating system.

• Designed for networking.

• An open source computer operating system.

• Free.

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Other Courses

• Introduction to the Shark Clusterhttps://git.lumc.nl/shark/SHARK/wikis/home

• Code and Data Management with Githttps://git.lumc.nl/courses/gitcourse

• Scripting for Life Science Researchershttps://git.lumc.nl/courses/scriptingcourse

• Python Programminghttps://git.lumc.nl/courses/programming-course

• GitLab as a Collaborative Working Environmenthttps://git.lumc.nl/courses/gitlab-intro-course

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Course Material

https://git.lumc.nl/courses/practical-linux-course

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