Introduction 2 linux
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What is Linux? Command-line Interface, Shell & BASH Popular commands File Permissions and Owners Installing programs Piping and Scripting Variables Common applications in bioinformatics Conclusion
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Introduction 2 linux
- 1. Introduction to Linux PRESENTED TO:- Mrs. SONYMOL KOSHY BY:- PAPU KUMAR SECTION:- B ROLL NO.:- 2061424(47) SEMESTEWR:- III BRANCH:- C.S.E.
- 2. Outline 1. What is Linux? 2. Command-line Interface, Shell & BASH 3. Popular commands 4. File Permissions and Owners 5. Installing programs 6. Piping and Scripting 7. Variables 8. Common applications in bioinformatics 9. Conclusion
- 3. 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
- 4. What is Linux? Operating system (OS): Set of programs that manage computer hardware resources and provide common services for application software. Kernel
- 5. 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
- 6. What is Linux? Linux Distributio n Supporting packages Linux kernel Free, open- source, proprietary software
- 7. What is Linux? There are over 600 Linux distributions, over 300 of which are in active development.
- 8. What is Linux? Linux distributions share core components but may look different and include different programs and files. For example:
- 9. 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
- 10. Shell, Command-line Interface & BASH Command-line interface (CLI) Graphical User Interface (GUI) The shell provides an interface for users of an operating system.
- 11. Shell, Command-line Interface & BASH Topic CLI GUI Ease 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.
- 12. 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)
- 13. Shell, Command-line Interface & BASH A Linux command typically consists of a program name, followed by options and arguments.
- 14. Shell, Command-line Interface & BASH Useful BASH shortcuts… Shortcut Meaning
- 15. Popular commands Directory structure Default working directory after user login Complete directory path: /home/user/Documents/LinuxClass
- 16. Popular commands Changing working directories Command: cd Default working directory after user login Move to parent directory Move to child directory Move using complete path: cd /home/user/Documents/LinuxClass
- 17. Popular Commands Navigating directories
- 18. Popular Commands Compressing and archiving files
- 19. Popular Commands Task Command Hard disk usage df -lh RAM memory usage free mem What 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
- 20. 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.
- 21. 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).
- 22. 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
- 23. Command-line help Getting help (offline) More information about a command can be found from manual pages COMMAND: man Example: man ls ARGUMENTS: -h or –help Example: blastall --help
- 24. Command-line help Getting help (online) Go to explainshell.com Write down a command-line to see the help text that matches each argument.
- 25. Command-line help Output from explainshell.com, for: grep '>' fasta | sed 's/>//' > id.txt
- 26. 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?
- 27. 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.
- 28. 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>
- 29. 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
- 30. 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/
- 31. Installing Programs 1. Using package managers 1.1 Graphical package manager, example Synaptic for Ubuntu 1.2 High-level command-line package manager, example apt for Debian 1.3 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
- 32. Installing Programs 1.1 Using graphical package manager (Synaptic on Ubuntu)
- 33. Installing Programs Search and install programs using Synaptic on Ubuntu
- 34. Installing Programs Install program dependencies (Synaptic on Ubuntu) to
- 35. 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:
- 36. Piping and Scripting Another popular combination is redirect the stdout (output) to a file using '>' (write or overwrite if it exists) or '>>' (append). Example:
- 37. 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 ‘>’ $1 To run this script: 1. Give script execute permission: chmod u+x fasta_seq_count.sh 2. bash fasta_seq_count.sh <fasta_file>
- 38. Variables A variable is a name assigned to a location or set of locations in computer memory, holding an item of data. Variables in BASH can be put into two categories: 1. System variables: Variables defined by system, such as PATH and HOME 2. User-defined variables: Variables defined by a user during shell session. Example:
- 40. Variables Commands to interact with variables Example: Add a program executable directory to your PATH. export PATH=/home/user/shscripts:$PATH
- 41. 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.
- 42. Common applications in bioinformatics Fasta file manipulation
- 43. 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
- 44. Common applications in bioinformatics BLAST output manipulation
- 45. 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.
- 46. 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.
Hinweis der Redaktion
- 1
- In computing, the kernel is a computer program that manages input/output requests from software and translates them into data processing instructions for the central processing unit and other electronic components of a computer. The kernel is a fundamental part of a modern computer's operating system.[1]
- Quite often people new to another operating system than Microsoft Windows are confronted with the terms CLI (Command Line Interface) and GUI (Graphical User Interface). Pretty soon they get a notion about what those two are but at this stage they are still far away from being able to tell what is the "better" one. Well, there is no better -- it depends on the tasks that need be done, how experienced a user is and his personal likings.
- This interaction between a computer operating system or application software and user is facilitated by the Shell. The shell includes both command-line and graphical elements for interacting with OS and apps. Graphical user interfaces (GUIs) are helpful for many tasks, but they are not good for all tasks.
- There may be several Options, or none at all.
- The easiest way to check from the Unix command line whether the internet connection works, is to send a request to a known server (e.g. www.google.com) using the ping <web address> command. The command reports, how long a message takes back and forth to the given server. It sends an ECHO_REQUEST datagram to elicit an ICMP ECHO_RESPONSE from a host or gateway.
- Pipes - curl is more in the traditional unix-style, it sends more stuff to stdout, and reads more from stdin in a "everything is a pipe" manner. Curl vs wget: http://daniel.haxx.se/docs/curl-vs-wget.html Recursive! Wget's major strong side compared to curl is its ability to download recursively, or even just download everything that is referred to from a remote resource, be it a HTML page or a FTP directory listing.
- Ssh encrypts all data that travels across its connection including your username and password (which you’ll use to login to the remote machine). When the node’s server arrives user’s will be able to login remotely to run jobs on the server. This is common for bioinformatics facilities, and enables users to use the existing (greater) resources such as storage, processing capacity of the server. Other commands such as sftp and scp allow users to securely copy a file to/ from remote hosts.
- Some commands have additional arguments
- To extract id lines from a fasta file, remove the id and # redirect the output to a id.txt file
- Linux has inherited from UNIX the concept of ownerships and permissions for files. This is basically because it was conceived as a networked system where different people would be using a variety of programs, files, etc. Linux is also multi-tasking, meaning one user can use the same computer to do multiple jobs. UNIX everything is a file.
- The Unix operating system (and likewise, Linux) differs from other computing environments in that it is not only a multitasking system but it is also a multi-user system as well. Each file has assigned 9 different permissions, 3 for the file user-owner (u), 3 for the group-owner (g) and 3 for everyone else (o). Ls -alshows something like this for each file/dir: drwxrwxrwx
- The chmod (change mode) command protects files and directories from unauthorized users on the same system, by setting access permissions.
- Does Linux need antivirus software? All computer systems can suffer from malware and viruses, including Linux. Thankfully, very few viruses exist for Linux, so users typically do not install antivirus software. It is still recommended that Linux users have antivirus software installed. Some users may argue that antivirus software uses up too much resources. Thankfully, low-footprint software exists for Linux.
- Path contains directories separated by colons, and tells the shell where to look for programs. $PATH is a colon-separated list of directories in which the shell looks for commands.
- Standard users, by default, cannot install applications on a Linux machine. In order to successfully install an application on a Linux machine you have to have super user privileges. So, to change a command so that you can successfully run an installation you have to prefix it with “sudo”, for example: sudo dpkg -i software.deb. To add a user to list of sudoers: # adduser foo sudo.
- PHYLIP : Phylogeny Inference Package, computer programs for inferring phylogenies
- A compiler is a computer program (or set of programs) that transforms source code written in a programming language (the source language) into another computer language (the target language, often having a binary form known as object code).[1] The most common reason for wanting to transform source code is to create an executable program. Check from program author’s website for detailed instructions on how to build program from source.
- The standard output of command is connected via a pipe to the standard input of command2. This connection is performed before any redirections specified by the command (see REDIRECTION below). If |& is used, the standard error of command is connected to command2's standard input through the pipe; it is shorthand for 2>&1 |. This implicit redirection of the standard error is performed after any redirections specified by the command.
- A pipeline is a sequence of one or more commands separated by one of the control operators: | or |&.
- A shell program, called a script, is an easy-to-use tool for building applications by "gluing together" system calls, tools, utilities, and compiled binaries. scripts, programs written for a special run-time environment that can interpret (rather than compile) and automate the execution of tasks which could alternatively be executed one-by-one by a human operator. More than just the insulating layer between the operating system kernel and the user, it's also a fairly powerful programming language. Bash has become a de facto standard for shell scripting on most flavors of UNIX. Bourne shell compliant scripts are created with a .sh extension.
- A variable is nothing more than a label, a name assigned to a location or set of locations in computer memory holding an item of data. PATH – Your shell search path: directories separated by colons HOME – Your home directory, such as /home/Smith
- BASH variable is the full path name used to invoke the current instance of BASH
- You can use env or printenv <variable_name> to print shell variable.The scope of a variable (i.e., which programs know about it) is by default, the shell in which it is defined. To make a variable and its value available to other programs your shell invokes (i.e., subshells), use the export command. This variable then becomes an environment variable since it’s available to other programs in your shell’s “environment”. The configuration of your bash shell is found in the hidden file .bashrc Usually the SYNTAX for setting an environment variable in your .bashrc (which is found in your home directory) is the following: export VARIABLE=value 1.2 NOTE: There shouldn't be any space between the variable and the equals sign ("=") and the value. If your value has spaces then the whole value should be put in quotes For the case of the environement variable PATH it is a good practice to prepend additional paths to it using colons ":" since it is a system defined environment variable. For example: export PATH=$HOME/bin/perl:$PATH 1.3 NOTE: That environment variables are accessed by prepending the dollar sign ("$"), but when defined the dollar sign is ommitted PATH is a variable that contains the directories from which your shell (BASH) looks for commands. These directories are separated by colons.
- Pattern matching and data extraction of Linux command line tools like grep, sort, cut, etc. Enable handling of large text files which would otherwise consume large chunks of memory on other platforms such as Windows (or Linux) GUI for example.
- The BLAST programs are widely used tools for searching DNA and protein databases for sequence similarity to identify homologs to a query sequence. The BLAST command line interface offers additional features such as querying a custom database eg. Chromosome of your organism of interest. More advanced usage generally involves taking the output of BLAST as a first step in some kind of script. For example, Torsten's "prokka" tool uses BLAST (amongst other things) to automatically annotate a sequence. Which can best be achieved from the command-line.
- A number of cutting edge programs (Bowtie, Velvet, Trinity, Stampy, etc.) do not come with an web interface, because the developers neither have time nor computing resources to provide web services for everyone. As a rule of thumb, easier an website is to use, more difficult it is to develop. Furthermore, it costs a lot of money to maintain data-intensive web services.
- Freedoms of the OS fosters/ encourages the development of more software to add to the already large existing ,command line, bioinformatics tools. Therefore, it will become common for primarily, wet lab, biomedical researchers to have some command-line knowledge and skill. While learning to use these tools may be challenging, at first, the rewards of UNIX/ Linux command-line proficiency is worth the effort. Therefore, in the tutorial to follow later today we are going to guide you through using some commands and we hope that you have fun doing it.