Introduction to Linux

PRESENTED TO:- Mrs. SONYMOL KOSHYBY:- PAPU KUMARSECTION:- BROLL NO.:- 2061424(47)SEMESTEWR:- IIIBRANCH:- C.S.E.

Outline1. What is Linux?2. Command-line Interface, Shell & BASH3. Popular commands4. File Permissions and Owners5. Installing programs6. Piping and Scripting7. Variables8. Common applications in bioinformatics9. Conclusion

What is Linux?

Linux is a Unix-like computer operating system assembled under the model of free and open source software development

and distribution.

UNIX is a multitasking, multi-user computer OS originally developed in 1969.

Linus Torvalds – Former Chief architect of Linux Kernel and current project Coordinator

What is Linux? Operating

system (OS): Set of programs that manage computer hardware resources and provide common services for application software.

Kernel

What is Linux?

Linux kernel (v 0.01) was 1st released in 1991. Current stable version is 3.13 released in January 2014.

The underlying source code of Linux kernel may be used, modified, and distributed — commercially or non-commercially — by anyone under licenses such as the GNU General Public License. 

Therefore, different varieties of Linux have arisen to serve different needs and tastes. These are called Linux distributions (or distros).

All Linux distros have the Linux kernel in common

What is Linux?

Linux Distribut

ion

Supporting

packages

Linux kernel

Free, open-source,

proprietary software

What is Linux? There are over 600 Linux distributions, over 300 of

which are in active development.

What is Linux?

Linux distributions share core components but may look different and include different programs and files.

For example:

What is Linux?

Commercially-backed distros Fedora (Red Hat) OpenSUSE (Novell) Ubuntu (Canonical Ltd.) Mandriva Linux

(Mandriva)

Ubuntu is the most popular desktop Linux distribution with 20 million daily users worldwide, according to ubuntu.com.

Community-driven distros Debian Gentoo Slackware Arch Linux

Shell, Command-line Interface & BASH

Command-line interface (CLI)

Graphical User Interface (GUI)

The shell provides an interface for users of an operating system.

Shell, Command-line Interface & BASH

Topic CLI GUIEase of use

Generally more difficult to successfully navigate and operate a CLI.

Much easier when compared to a CLI.

Control Greater control of file system and operating system in a CLI.

More advanced tasks may still need a CLI.

Resources Uses less resources. Requires more resources to load icons etc.

Scripting Easily script a sequence of commands to perform a task or execute a program.

Limited ability to create and execute tasks, compared to CLI.

Shell, Command-line Interface & BASH

• A command is a directive to a computer program, acting as an interpreter of some kind, to perform a specific task.

• BASH is the primary shell for GNU/Linux and Mac OS X.

Shell→ CLI→ BASH (Bourne-Again SHell)

Shell, Command-line Interface & BASH A Linux command typically consists of a

program name, followed by options and arguments.

Shell, Command-line Interface & BASHUseful BASH shortcuts…Shortcut Meaning

Popular commands

Directory structureDefault working directory after user login

Complete directory path: /home/user/Documents/LinuxClass

Popular commands

Changing working directoriesCommand: cd

Default working directory after user login

Move to parent directory

Move to child directory

Move using complete path: cd /home/user/Documents/LinuxClass

Popular Commands

Navigating directories

Popular Commands Compressing and archiving files

Popular Commands

Task CommandHard disk usage df -lhRAM memory usage free memWhat processes are running in real-time?

top

Snapshot of current processes

ps aux

Stop a process running in the terminal

CTRL + C

Stop a process that is running outside the terminal

kill <PID>

• Monitoring & managing resources

Popular Commands

Monitoring Network Connections Do I have an internet connection? ping <web address>

The ping command reports, how long a message takes back and forth to the given server.

Popular Commands Downloading files

wget <url of file> curl <url of file>

wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols.

curl is a tool to transfer data from or to a server, using one of several supported protocols (DICT, FILE, FTP, FTPS, GOPHER, HTTP, HTTPS, IMAP, etc).

Popular Commands Remote Connections

How can I get access to a remote computer? ssh user@hostname

The ssh (secure shell) command securely logs you into a remote computer where you already have an account.

X11 connections are possible using -X option.

Example: ssh -X user1@cbsuwrkst1.tc.cornell.edu

scp, sftp commands allow users to securely copy files to or from remote computers

Command-line help

Getting help (offline)

More information about a command can be found from manual pages

COMMAND: manExample: man ls

ARGUMENTS: -h or –helpExample: blastall --help

Command-line helpGetting help (online)

Go to explainshell.com Write down a command-line to see

the help text that matches each argument.

Command-line help

Output from explainshell.com, for: grep '>' fasta | sed 's/>//' > id.txt

File Permissions and Owners Linux is a multi-user OS. Therefore, different

users can create modify or delete the same files.

To control access and modification of user files, Linux has a file permission and ownership system.

This system consists of two parts: Who is the owner of the file or directory? What type of access does each user have?

File Permissions and Owners Each file and directory has three user based permission groups:

1. Owner (u) - The Owner permissions apply only the owner of the file or directory.

2. Group (g)- The Group permissions apply only to the group that has been assigned to the file or directory.

3. All Users (‘o’ or ‘a’) - The All Users permissions apply to all other users on the system.

Each file or directory has three basic permission types:

1. Read (r) - The Read permission refers to a user's capability to read the contents of the file.

2. Write (w) - The Write permissions refer to a user's capability to write or modify a file or directory.

3. Execute(x) - The Execute permission affects a user's capability to execute a file or view the contents of a directory.

File Permissions and Owners[me@linuxbox me]$ ls -l some_file

-rw-rw-r-- 1 me me 1097374 Sep 26 18:48 some_file

Information about a file permissions: ls -l <file_name>

File Permissions and Owners The chmod command is used to modify files

and directory permissions. Typical permissions are read (r), write (w), execute (x).

syntax: chmod [options] permissions files

File Permissions and Owners sudo

is a command for Unix-like computer operating systems that allows users to run programs with the security privileges of another user (normally the superuser, or root). Its name is a concatenation of the su command (which grants the user a shell for the superuser) and "do", or take action.

Example: sudo cp ./myscript.pl /usr/local/bin/

Installing Programs

1. Using package managers1.1 Graphical package manager, example Synaptic for Ubuntu1.2 High-level command-line package manager, example apt for Debian1.3 Low-level command-line package manager, example dpkg for Debian

2. Copy executable file of program to PATH* 2.1 Pre-compiled

2.2 Build from source

* - PATH can be a directory, such as /usr/local/bin where BASH looks for commands

Installing Programs

1.1 Using graphical package manager (Synaptic on Ubuntu)

Installing Programs

Search and install programs using Synaptic on Ubuntu

Installing Programs

Install program dependencies (Synaptic on Ubuntu)

to

Piping and Scripting

Piping: Run different programs sequentially where the output of one program becomes the input for the next one.

Bash uses the “|” sign (pipe) to pipe the output of one program as the input of another program.

For example:

Piping and Scripting

Another popular combination is redirect the stdout (output) to a file using '>' (write or overwrite if it exists) or '>>' (append).

Example:

Piping and Scripting A shell program, called a script, is a tool for building

applications by "gluing together" system calls, tools, utilities, and compiled binaries.

For example: fasta_seq_count.sh

#! /bin/bash# Count sequences in fasta file (1st argument)grep –c ‘>’ $1

To run this script:1. Give script execute permission: chmod u+x fasta_seq_count.sh2. bash fasta_seq_count.sh <fasta_file>

Variables

A variable is a name assigned to a location or set of locations in computer memory, holding an item of data.

Variables in BASH can be put into two categories:1. System variables: Variables defined by system,

such as PATH and HOME2. User-defined variables: Variables defined by a

user during shell session.Example:

Variables

System variables

Variables

Commands to interact with variables

Example: Add a program executable directory to your PATH.

export PATH=/home/user/shscripts:$PATH

Common applications in bioinformatics

Fasta file manipulation

Fasta file is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes.

Common applications in bioinformatics Fasta file manipulation

Common applications in bioinformatics BLAST output manipulation

The BLAST tabular format is one of the most common and useful formats for presenting BLAST output. It has 12 columns: query_id, subject_id, %identity, align_length, mismatches, gaps_openings, q_start, q_end, s_start, s_end, e_value, bit_score

Common applications in bioinformatics

BLAST output manipulation

Common applications in bioinformatics

High throughput sequencing software

Create a report on the quality of a read set: fastqc

Assemble reads into contigs: velvet, SPAdes, etc.

Align reads to a known reference sequence: SHRiMP, Bowtie2, BWA etc.

Many other tools: samtools, picard, GATK, etc.

Conclusion

Linux is a free and open source OS with powerful and flexible command-line tools to advance your bioinformatics research projects.

While learning to use these tools may be challenging, at first, the rewards of UNIX/ Linux command-line proficiency is worth the effort.

References

EdX.org

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