GNU Linux Introduction

Diapositiva 1

Introduction to GNU/Linux

Xavier de Pedro Puente, Ph.D.

Xavier de Pedro Puente, Ph.D.

[email protected]

Academics:Degree in Biology

(University of Barcelona - UB)Ph.D. in Biology

(University of Barcelona - UB)Postgraduate in Bioinformatics

(Open University of Catalonia UOC)

Current Work:Bioinformatics technician (UEB, VHIR)

Systems administrator (UEB, VHIR)

Professor of Sustainability (IES Abroad Barcelona)

GNU/Linux OS (a.k.a. Linux)

- GNU/Linux Distributions- Your USBDISKs (et al.)Basic Differences between:

- GNU/Linux and Windows- GNU/Linux and MacOSXCommand line runs

Introduction to GNU/Linux (for VHIR Master students)

By: Xavier de Pedro

GNU/Linux OS (a.k.a. Linux)

End User Applications:

Operating System:

Computer: (Harware)

"Windows" "Mac" "Linux

Operating System (OS): GNU progs. + Linux kernel

GNU/Linux "Distribution

GNU/Linux "Distribution

Your USBDISKs (et al.): Option A

USBDISK BioLinux8 on local VirtualBox (VT-x in BIOS)

BioLinux: Dawn Field et al. (2006) "Open software for biologists: from famine to feast". Nature Biotechnology 24, 801 - 803 (2006). doi:10.1038/nbt0706-801

Your USBDISKs (et al.): Option B

USBDISK Lubuntu on VirtualBox (no VT-x, BIOS?)

Lubuntu: Lightweidht Desktop on a Ubuntu GNU/Linux Distribution. http://lubuntu.net

Your USBDISKs (et al.: "X2Go"): Option C

Connection to remote VBox (on ueb.vhir.org port 2201-5)

X2Go: Program to connect to a remote computer through GUI (Graphical User Interface)

Your USBDISKs (et al.: "X2Go"): Option C

Connection to remote VBox (on ueb.vhir.org port xxx1-5)

X2Go: http://wiki.x2go.org

Your USBDISKs (et al.): Option D

LiveUSB (Lubuntu-based; BIOS to boot from USB)

LXLE: A Lubuntu-based GNU/Distribution with improved desktop http://www.lxle.net

Basic Differences between: GNU/Linux & Windows

Technical differences User: root vs. administrator

Case sensitive vs. Case insensitive "MyFile != myfile" vs. "MyFile = myfile"

"Symbolic or Hard Links" vs. "Shortcuts"

Paths: Slash ("/") vs. Backslash ("\")

Main harddrive/partition: "/" vs. "C:\"

Partition formats: ext2, ext3, ext4, ... vs. fat16/fat32/ntfs

User default folder: /home/username vs. "C:\Documents and Settings\" or "c:\Users\username\MyDocuments"

USBdisk default folder: "/media/username/usbdiskname" vs. "X:\usbdiskname"

Secure (Viruses???) vs. Insecure (viruses, bots, worms, trojans, backdoors, ...)

It can extend computer useful life vs. Planned & perceived obsolescence

Performance, with same hardware: Faster vs. Slower (Antivirus, antispyware,...)

normal user: "sudo program" in console vs. "Run program as administrator"

Basic Differences between: GNU/Linux & Windows

Phylosophical differencesFreedom: "Free/Libre Open Source Software (FLOSS)" vs. "Closed Source/Propietary software"Software Sustainability: High vs. Low

Usually: product given for free (at no Cost) vs. product for (excessive?) profit

Money comes through: customizations and training vs. Selling Software

FLOSS Fosters local economies as well as big companies vs. Big & remote Corporations growth.

Basic Differences between: GNU/Linux & MacOSX

Technical differencesUsers:

Case:

Links:

Paths:

Main harddrive/partition

Partition formats: ext2, ext3, ext4, ... vs. HFS+

User default folder: /home/username vs. "/Users/Username"

USBdisk default folder:

Secure (Viruses???) vs. Secure (Viruses?)

It can extend computer useful life vs. Planned & perceived obsolescence

Performance, with same hardware: Faster??? vs. Extremely Fast

normal user:

Basic Differences between: GNU/Linux & MacOSX

Phylosophical differencesFreedom: "Free/Libre Open Source Software (FLOSS)" vs. "Closed Source/Propietary software"Software Sustainability: High vs. Low

Usually: product given for free (at no Cost) vs. product for (excessive?) profit

Money comes through: customizations and training vs. Selling Software & Hardware

FLOSS Fosters local economies as well as big companies vs. Big & remote Corporations growth.

Command line runs (i)

Serial vs. Parallel tasks

Shell = Terminal = Console ("Black" text screen to run commands)sSecure Shell = ssh = a safe way to connect to remote computers or servers (encrypted)

ftp: File Transfer Protocolto transfer files between computers or servers

you can NOT run commands (other than listings)

sftp: like FTP but "secure" (best: using ssh libraries)

Command line runs (ii)

Example of simple local commands: ps -e

ls -l

df -h

top

Example of bioinformatics shell programs: fastqc

fastx

blast*

Command line runs (iii)

Example of network commands: ping google.com

ifconfig

ftp [email protected]

sftp [email protected]

sftp -p 2200 [email protected]

ssh [email protected]

ssh -p 2200 [email protected]

Example of shell-based programs: nano (simple editor: press "Ctrl + X" to eXit)

htop (type "q" to quit/exit)

mc (Midnight Commander). Click on F10 (with mouse or trackpad) to quit

R ( Type "q()" to quit)

More information

Ubuntu GNU/Linux:http://www.ubuntu.com

Linkat (Ubuntu):Manual Installation with custom partitions (advanced, or for servers): http://linkat.xtec.cat/portal_linkat/wikilinkat/index.php/Wiki_Linkat_edu_14.04

Desktop installation (easy): http://linkat.xtec.cat/portal_linkat/wikilinkat/index.php/Linkat_edu_14.04_Autnom

Forums for help and support:VHIR:http://forums.vhir.org

Ubuntu (Catalan LoCo Team):http://ubuntuforums.org/forumdisplay.php?f=206

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Introduction to GNU/Linux

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