Understanding the Command-Line Interface
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At—At, Batch—Execute Commands at a Later Time
at—at, batch—execute commands at a later time at [–csm] [–f script] [–qqueue] time [date] [+ increment] at –l [ job...] at –r job... batch at and batch read commands from standard input to be executed at a later time. at allows you to specify when the commands should be executed, while jobs queued with batch will execute when system load level permits. Executes commands read from stdin or a file at some later time. Unless redirected, the output is mailed to the user. Example A.1 1 at 6:30am Dec 12 < program 2 at noon tomorrow < program 3 at 1945 pm August 9 < program 4 at now + 3 hours < program 5 at 8:30am Jan 4 < program 6 at -r 83883555320.a EXPLANATION 1. At 6:30 in the morning on December 12th, start the job. 2. At noon tomorrow start the job. 3. At 7:45 in the evening on August 9th, start the job. 4. In three hours start the job. 5. At 8:30 in the morning of January 4th, start the job. 6. Removes previously scheduled job 83883555320.a. awk—pattern scanning and processing language awk [ –fprogram–file ] [ –Fc ] [ prog ] [ parameters ] [ filename...] awk scans each input filename for lines that match any of a set of patterns specified in prog. Example A.2 1 awk '{print $1, $2}' file 2 awk '/John/{print $3, $4}' file 3 awk -F: '{print $3}' /etc/passwd 4 date | awk '{print $6}' EXPLANATION 1. Prints the first two fields of file where fields are separated by whitespace. 2. Prints fields 3 and 4 if the pattern John is found. -
1 A) Login to the System B) Use the Appropriate Command to Determine Your Login Shell C) Use the /Etc/Passwd File to Verify the Result of Step B
CSE ([email protected] II-Sem) EXP-3 1 a) Login to the system b) Use the appropriate command to determine your login shell c) Use the /etc/passwd file to verify the result of step b. d) Use the ‘who’ command and redirect the result to a file called myfile1. Use the more command to see the contents of myfile1. e) Use the date and who commands in sequence (in one line) such that the output of date will display on the screen and the output of who will be redirected to a file called myfile2. Use the more command to check the contents of myfile2. 2 a) Write a “sed” command that deletes the first character in each line in a file. b) Write a “sed” command that deletes the character before the last character in each line in a file. c) Write a “sed” command that swaps the first and second words in each line in a file. a. Log into the system When we return on the system one screen will appear. In this we have to type 100.0.0.9 then we enter into editor. It asks our details such as Login : krishnasai password: Then we get log into the commands. bphanikrishna.wordpress.com FOSS-LAB Page 1 of 10 CSE ([email protected] II-Sem) EXP-3 b. use the appropriate command to determine your login shell Syntax: $ echo $SHELL Output: $ echo $SHELL /bin/bash Description:- What is "the shell"? Shell is a program that takes your commands from the keyboard and gives them to the operating system to perform. -
Modern Programming Languages CS508 Virtual University of Pakistan
Modern Programming Languages (CS508) VU Modern Programming Languages CS508 Virtual University of Pakistan Leaders in Education Technology 1 © Copyright Virtual University of Pakistan Modern Programming Languages (CS508) VU TABLE of CONTENTS Course Objectives...........................................................................................................................4 Introduction and Historical Background (Lecture 1-8)..............................................................5 Language Evaluation Criterion.....................................................................................................6 Language Evaluation Criterion...................................................................................................15 An Introduction to SNOBOL (Lecture 9-12).............................................................................32 Ada Programming Language: An Introduction (Lecture 13-17).............................................45 LISP Programming Language: An Introduction (Lecture 18-21)...........................................63 PROLOG - Programming in Logic (Lecture 22-26) .................................................................77 Java Programming Language (Lecture 27-30)..........................................................................92 C# Programming Language (Lecture 31-34) ...........................................................................111 PHP – Personal Home Page PHP: Hypertext Preprocessor (Lecture 35-37)........................129 Modern Programming Languages-JavaScript -
Getting to Grips with Unix and the Linux Family
Getting to grips with Unix and the Linux family David Chiappini, Giulio Pasqualetti, Tommaso Redaelli Torino, International Conference of Physics Students August 10, 2017 According to the booklet At this end of this session, you can expect: • To have an overview of the history of computer science • To understand the general functioning and similarities of Unix-like systems • To be able to distinguish the features of different Linux distributions • To be able to use basic Linux commands • To know how to build your own operating system • To hack the NSA • To produce the worst software bug EVER According to the booklet update At this end of this session, you can expect: • To have an overview of the history of computer science • To understand the general functioning and similarities of Unix-like systems • To be able to distinguish the features of different Linux distributions • To be able to use basic Linux commands • To know how to build your own operating system • To hack the NSA • To produce the worst software bug EVER A first data analysis with the shell, sed & awk an interactive workshop 1 at the beginning, there was UNIX... 2 ...then there was GNU 3 getting hands dirty common commands wait till you see piping 4 regular expressions 5 sed 6 awk 7 challenge time What's UNIX • Bell Labs was a really cool place to be in the 60s-70s • UNIX was a OS developed by Bell labs • they used C, which was also developed there • UNIX became the de facto standard on how to make an OS UNIX Philosophy • Write programs that do one thing and do it well. -
101 Useful Linux Commands - Haydenjames.Io
101 Useful Linux Commands - haydenjames.io Some of these commands require elevated permissions (sudo) to run. Enjoy! 1. Execute the previous command used: !! 2. Execute a previous command starting with a specific letter. Example: !s 3. Short way to copy or backup a file before you edit it. For example, copy nginx.conf cp nginx.conf{,.bak} 4. Toggle between current directory and last directory cd - 5. Move to parent (higher level) directory. Note the space! cd .. 6. Go to home directory cd ~ 7. Go to home directory cd $HOME 8. Go to home directory (when used alone) cd 9. Set permissions to 755. Corresponds to these permissions: (-rwx-r-x-r-x), arranged in this sequence: (owner-group-other) chmod 755 <filename> 10. Add execute permission to all users. chmod a+x <filename> 11. Changes ownership of a file or directory to . chown <username> 12. Make a backup copy of a file (named file.backup) cp <file> <file>.backup 13. Copy file1, use it to create file2 cp <file1> <file2> 14. Copy directory1 and all its contents (recursively) into directory2 cp -r <directory1> <directory2>/ 15. Display date date 16. Zero the sdb drive. You may want to use GParted to format the drive afterward. You need elevated permissions to run this (sudo). dd if=/dev/zero of=/dev/sdb 17. Display disk space usage df -h 18. Take detailed messages from OS and input to text file dmesg>dmesg.txt 19. Display a LOT of system information. I usually pipe output to less. You need elevated permissions to run this (sudo). -
A First Course to Openfoam
Basic Shell Scripting Slides from Wei Feinstein HPC User Services LSU HPC & LON [email protected] September 2018 Outline • Introduction to Linux Shell • Shell Scripting Basics • Variables/Special Characters • Arithmetic Operations • Arrays • Beyond Basic Shell Scripting – Flow Control – Functions • Advanced Text Processing Commands (grep, sed, awk) Basic Shell Scripting 2 Linux System Architecture Basic Shell Scripting 3 Linux Shell What is a Shell ▪ An application running on top of the kernel and provides a command line interface to the system ▪ Process user’s commands, gather input from user and execute programs ▪ Types of shell with varied features o sh o csh o ksh o bash o tcsh Basic Shell Scripting 4 Shell Comparison Software sh csh ksh bash tcsh Programming language y y y y y Shell variables y y y y y Command alias n y y y y Command history n y y y y Filename autocompletion n y* y* y y Command line editing n n y* y y Job control n y y y y *: not by default http://www.cis.rit.edu/class/simg211/unixintro/Shell.html Basic Shell Scripting 5 What can you do with a shell? ▪ Check the current shell ▪ echo $SHELL ▪ List available shells on the system ▪ cat /etc/shells ▪ Change to another shell ▪ csh ▪ Date ▪ date ▪ wget: get online files ▪ wget https://ftp.gnu.org/gnu/gcc/gcc-7.1.0/gcc-7.1.0.tar.gz ▪ Compile and run applications ▪ gcc hello.c –o hello ▪ ./hello ▪ What we need to learn today? o Automation of an entire script of commands! o Use the shell script to run jobs – Write job scripts Basic Shell Scripting 6 Shell Scripting ▪ Script: a program written for a software environment to automate execution of tasks ▪ A series of shell commands put together in a file ▪ When the script is executed, those commands will be executed one line at a time automatically ▪ Shell script is interpreted, not compiled. -
“Linux at the Command Line” Don Johnson of BU IS&T We’Ll Start with a Sign in Sheet
“Linux at the Command Line” Don Johnson of BU IS&T We’ll start with a sign in sheet. We’ll end with a class evaluation. We’ll cover as much as we can in the time allowed; if we don’t cover everything, you’ll pick it up as you continue working with Linux. This is a hands-on, lab class; ask questions at any time. Commands for you to type are in BOLD The Most Common O/S Used By BU Researchers When Working on a Server or Computer Cluster Linux is a Unix clone begun in 1991 and written from scratch by Linus Torvalds with assistance from a loosely-knit team of hackers across the Net. 64% of the world’s servers run some variant of Unix or Linux. The Android phone and the Kindle run Linux. a set of small Linux is an O/S core programs written by written by Linus Richard Stallman and Torvalds and others others. They are the AND GNU utilities. http://www.gnu.org/ Network: ssh, scp Shells: BASH, TCSH, clear, history, chsh, echo, set, setenv, xargs System Information: w, whoami, man, info, which, free, echo, date, cal, df, free Command Information: man, info Symbols: |, >, >>, <, ;, ~, ., .. Filters: grep, egrep, more, less, head, tail Hotkeys: <ctrl><c>, <ctrl><d> File System: ls, mkdir, cd, pwd, mv, touch, file, find, diff, cmp, du, chmod, find File Editors: gedit, nedit You need a “xterm” emulation – software that emulates an “X” terminal and that connects using the “SSH” Secure Shell protocol. ◦ Windows Use StarNet “X-Win32:” http://www.bu.edu/tech/support/desktop/ distribution/xwindows/xwin32/ ◦ Mac OS X “Terminal” is already installed Why? Darwin, the system on which Apple's Mac OS X is built, is a derivative of 4.4BSD-Lite2 and FreeBSD. -
Bash Crash Course + Bc + Sed + Awk∗
Bash Crash course + bc + sed + awk∗ Andrey Lukyanenko, CSE, Aalto University Fall, 2011 There are many Unix shell programs: bash, sh, csh, tcsh, ksh, etc. The comparison of those can be found on-line 1. We will primary focus on the capabilities of bash v.4 shell2. 1. Each bash script can be considered as a text file which starts with #!/bin/bash. It informs the editor or interpretor which tries to open the file, what to do with the file and how should it be treated. The special character set in the beginning #! is a magic number; check man magic and /usr/share/file/magic on existing magic numbers if interested. 2. Each script (assume you created “scriptname.sh file) can be invoked by command <dir>/scriptname.sh in console, where <dir> is absolute or relative path to the script directory, e.g., ./scriptname.sh for current directory. If it has #! as the first line it will be invoked by this command, otherwise it can be called by command bash <dir>/scriptname.sh. Notice: to call script as ./scriptname.sh it has to be executable, i.e., call command chmod 555 scriptname.sh before- hand. 3. Variable in bash can be treated as integers or strings, depending on their value. There are set of operations and rules available for them. For example: #!/bin/bash var1=123 # Assigns value 123 to var1 echo var1 # Prints ’var1’ to output echo $var1 # Prints ’123’ to output var2 =321 # Error (var2: command not found) var2= 321 # Error (321: command not found) var2=321 # Correct var3=$var2 # Assigns value 321 from var2 to var3 echo $var3 # Prints ’321’ to output -
Exercise I: Basic Unix for Manipulating NGS Data
Exercise I: Basic Unix for manipulating NGS data C. Hahn, July 2014 The purpose of this exercise is to practice manipulating NGS (Next Generation Sequencing) data using simple but incredibly powerful Unix commands. Try to solve the below tasks using your Unix skills. Do not hesitate to consult Google for help!! Hints for every task can be found on page 3 below. Possible solutions are suggested on page 4. 1. Download the testdata from https://www.dropbox.com/s/wcanmej6z03yfmt/testdata_1.tar?dl=0. Create a directory (exercise_1) in your home directory and copy the archive testdata.tar from ~/Downloads/ to this directory. 2. Decompress the archive. 3. Examine the content of the data files. For basic information on fastq format please visit: http://en.wikipedia.org/wiki/FASTQ_format. With this information try to interpret the content of your data files. Do you Know what all the lines represent? a) Which quality encoding (which offset) do these files use? b) What is the header of the third read in the file? Is this a single-end (forward) or a paired-end (reverse) read? c) What is the header of the last read in the file? Is this a forward or reverse read? 4. How many lines does the file have? 5. How many reads does the file contain? 6. How many single-end (“se” also referred to as forward reads) reads and how many paired-end (“pe” also reverse reads) reads does the file contain? 7. Extract all se/pe reads and write them to separate files testdata_1.fastq and testdata_2.fastq. -
Useful Commands in Linux and Other Tools for Quality Control
Useful commands in Linux and other tools for quality control Ignacio Aguilar INIA Uruguay 05-2018 Unix Basic Commands pwd show working directory ls list files in working directory ll as before but with more information mkdir d make a directory d cd d change to directory d Copy and moving commands To copy file cp /home/user/is . To copy file directory cp –r /home/folder . to move file aa into bb in folder test mv aa ./test/bb To delete rm yy delete the file yy rm –r xx delete the folder xx Redirections & pipe Redirection useful to read/write from file !! aa < bb program aa reads from file bb blupf90 < in aa > bb program aa write in file bb blupf90 < in > log Redirections & pipe “|” similar to redirection but instead to write to a file, passes content as input to other command tee copy standard input to standard output and save in a file echo copy stream to standard output Example: program blupf90 reads name of parameter file and writes output in terminal and in file log echo par.b90 | blupf90 | tee blup.log Other popular commands head file print first 10 lines list file page-by-page tail file print last 10 lines less file list file line-by-line or page-by-page wc –l file count lines grep text file find lines that contains text cat file1 fiel2 concatenate files sort sort file cut cuts specific columns join join lines of two files on specific columns paste paste lines of two file expand replace TAB with spaces uniq retain unique lines on a sorted file head / tail $ head pedigree.txt 1 0 0 2 0 0 3 0 0 4 0 0 5 0 0 6 0 0 7 0 0 8 0 0 9 0 0 10 -
Install and Run External Command Line Softwares
job monitor and control top: similar to windows task manager (space to refresh, q to exit) w: who is there ps: all running processes, PID, status, type ps -ef | grep yyin bg: move current process to background fg: move current process to foreground jobs: list running and suspended processes kill: kill processes kill pid (could find out using top or ps) 1 sort, cut, uniq, join, paste, sed, grep, awk, wc, diff, comm, cat All types of bioinformatics sequence analyses are essentially text processing. Unix Shell has the above commands that are very useful for processing texts and also allows the output from one command to be passed to another command as input using pipe (“|”). less cosmicRaw.txt | cut -f2,3,4,5,8,13 | awk '$5==22' | cut -f1 | sort -u | wc This makes the processing of files using Shell very convenient and very powerful: you do not need to write output to intermediate files or load all data into the memory. For example, combining different Unix commands for text processing is like passing an item through a manufacturing pipeline when you only care about the final product 2 Hands on example 1: cosmic mutation data - Go to UCSC genome browser website: http://genome.ucsc.edu/ - On the left, find the Downloads link - Click on Human - Click on Annotation database - Ctrl+f and then search “cosmic” - On “cosmic.txt.gz” right-click -> copy link address - Go to the terminal and wget the above link (middle click or Shift+Insert to paste what you copied) - Similarly, download the “cosmicRaw.txt.gz” file - Under your home, create a folder -
The AWK Programming Language
The Programming ~" ·. Language PolyAWK- The Toolbox Language· Auru:o V. AHo BRIAN W.I<ERNIGHAN PETER J. WEINBERGER TheAWK4 Programming~ Language TheAWI(. Programming~ Language ALFRED V. AHo BRIAN w. KERNIGHAN PETER J. WEINBERGER AT& T Bell Laboratories Murray Hill, New Jersey A ADDISON-WESLEY•• PUBLISHING COMPANY Reading, Massachusetts • Menlo Park, California • New York Don Mills, Ontario • Wokingham, England • Amsterdam • Bonn Sydney • Singapore • Tokyo • Madrid • Bogota Santiago • San Juan This book is in the Addison-Wesley Series in Computer Science Michael A. Harrison Consulting Editor Library of Congress Cataloging-in-Publication Data Aho, Alfred V. The AWK programming language. Includes index. I. AWK (Computer program language) I. Kernighan, Brian W. II. Weinberger, Peter J. III. Title. QA76.73.A95A35 1988 005.13'3 87-17566 ISBN 0-201-07981-X This book was typeset in Times Roman and Courier by the authors, using an Autologic APS-5 phototypesetter and a DEC VAX 8550 running the 9th Edition of the UNIX~ operating system. -~- ATs.T Copyright c 1988 by Bell Telephone Laboratories, Incorporated. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopy ing, recording, or otherwise, without the prior written permission of the publisher. Printed in the United States of America. Published simultaneously in Canada. UNIX is a registered trademark of AT&T. DEFGHIJ-AL-898 PREFACE Computer users spend a lot of time doing simple, mechanical data manipula tion - changing the format of data, checking its validity, finding items with some property, adding up numbers, printing reports, and the like.