A Short Introduction to Unix
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UNIX Workshop Series: Quick-Start Objectives
Part I UNIX Workshop Series: Quick-Start Objectives Overview – Connecting with ssh Command Window Anatomy Command Structure Command Examples Getting Help Files and Directories Wildcards, Redirection and Pipe Create and edit files Overview Connecting with ssh Open a Terminal program Mac: Applications > Utilities > Terminal ssh –Y [email protected] Linux: In local shell ssh –Y [email protected] Windows: Start Xming and PuTTY Create a saved session for the remote host name centos.css.udel.edu using username Connecting with ssh First time you connect Unix Basics Multi-user Case-sensitive Bash shell, command-line Commands Command Window Anatomy Title bar Click in the title bar to bring the window to the front and make it active. Command Window Anatomy Login banner Appears as the first line of a login shell. Command Window Anatomy Prompts Appears at the beginning of a line and usually ends in $. Command Window Anatomy Command input Place to type commands, which may have options and/or arguments. Command Window Anatomy Command output Place for command response, which may be many lines long. Command Window Anatomy Input cursor Typed text will appear at the cursor location. Command Window Anatomy Scroll Bar Will appear as needed when there are more lines than fit in the window. Command Window Anatomy Resize Handle Use the mouse to change the window size from the default 80x24. Command Structure command [arguments] Commands are made up of the actual command and its arguments. command -options [arguments] The arguments are further broken down into the command options which are single letters prefixed by a “-” and other arguments that identify data for the command. -
State Notation Language and Sequencer Users' Guide
State Notation Language and Sequencer Users’ Guide Release 2.0.99 William Lupton ([email protected]) Benjamin Franksen ([email protected]) June 16, 2010 CONTENTS 1 Introduction 3 1.1 About.................................................3 1.2 Acknowledgements.........................................3 1.3 Copyright...............................................3 1.4 Note on Versions...........................................4 1.5 Notes on Release 2.1.........................................4 1.6 Notes on Releases 2.0.0 to 2.0.12..................................7 1.7 Notes on Release 2.0.........................................9 1.8 Notes on Release 1.9......................................... 12 2 Installation 13 2.1 Prerequisites............................................. 13 2.2 Download............................................... 13 2.3 Unpack................................................ 14 2.4 Configure and Build......................................... 14 2.5 Building the Manual......................................... 14 2.6 Test.................................................. 15 2.7 Use.................................................. 16 2.8 Report Bugs............................................. 16 2.9 Contribute.............................................. 16 3 Tutorial 19 3.1 The State Transition Diagram.................................... 19 3.2 Elements of the State Notation Language.............................. 19 3.3 A Complete State Program...................................... 20 3.4 Adding a -
CIS 90 - Lesson 2
CIS 90 - Lesson 2 Lesson Module Status • Slides - draft • Properties - done • Flash cards - NA • First minute quiz - done • Web calendar summary - done • Web book pages - gillay done • Commands - done • Lab tested – done • Print latest class roster - na • Opus accounts created for students submitting Lab 1 - • CCC Confer room whiteboard – done • Check that headset is charged - done • Backup headset charged - done • Backup slides, CCC info, handouts on flash drive - done 1 CIS 90 - Lesson 2 [ ] Has the phone bridge been added? [ ] Is recording on? [ ] Does the phone bridge have the mike? [ ] Share slides, putty, VB, eko and Chrome [ ] Disable spelling on PowerPoint 2 CIS 90 - Lesson 2 Instructor: Rich Simms Dial-in: 888-450-4821 Passcode: 761867 Emanuel Tanner Merrick Quinton Christopher Zachary Bobby Craig Jeff Yu-Chen Greg L Tommy Eric Dan M Geoffrey Marisol Jason P David Josh ? ? ? ? Leobardo Gabriel Jesse Tajvia Daniel W Jason W Terry? James? Glenn? Aroshani? ? ? ? ? ? ? = need to add (with add code) to enroll in Ken? Luis? Arturo? Greg M? Ian? this course Email me ([email protected]) a relatively current photo of your face for 3 points extra credit CIS 90 - Lesson 2 First Minute Quiz Please close your books, notes, lesson materials, forum and answer these questions in the order shown: 1. What command shows the other users logged in to the computer? 2. What is the lowest level, inner-most component of a UNIX/Linux Operating System called? 3. What part of UNIX/Linux is both a user interface and a programming language? email answers to: [email protected] 4 CIS 90 - Lesson 2 Commands Objectives Agenda • Understand how the UNIX login • Quiz operation works. -
A Rapid, Sensitive, Scalable Method for Precision Run-On Sequencing
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.18.102277; this version posted May 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 A rapid, sensitive, scalable method for 2 Precision Run-On sequencing (PRO-seq) 3 4 Julius Judd1*, Luke A. Wojenski2*, Lauren M. Wainman2*, Nathaniel D. Tippens1, Edward J. 5 Rice3, Alexis Dziubek1,2, Geno J. Villafano2, Erin M. Wissink1, Philip Versluis1, Lina Bagepalli1, 6 Sagar R. Shah1, Dig B. Mahat1#a, Jacob M. Tome1#b, Charles G. Danko3,4, John T. Lis1†, 7 Leighton J. Core2† 8 9 *Equal contribution 10 1Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA 11 2Department of Molecular and Cell Biology, Institute of Systems Genomics, University of 12 Connecticut, Storrs, CT 06269, USA 13 3Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, 14 NY 14853, USA 15 4Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, 16 Ithaca, NY 14853, USA 17 #aPresent address: Koch Institute for Integrative Cancer Research, Massachusetts Institute of 18 Technology, Cambridge, MA 02139, USA 19 #bPresent address: Department of Genome Sciences, University of Washington, Seattle, WA, 20 USA 21 †Correspondence to: [email protected] or [email protected] 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.18.102277; this version posted May 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Specification of the "Sequ" Command
1 Specification of the "sequ" command 2 Copyright © 2013 Bart Massey 3 Revision 0, 1 October 2013 4 This specification describes the "universal sequence" command sequ. The sequ command is a 5 backward-compatible set of extensions to the UNIX [seq] 6 (http://www.gnu.org/software/coreutils/manual/html_node/seq-invo 7 cation.html) command. There are many implementations of seq out there: this 8 specification is built on the seq supplied with GNU Coreutils version 8.21. 9 The seq command emits a monotonically increasing sequence of numbers. It is most commonly 10 used in shell scripting: 11 TOTAL=0 12 for i in `seq 1 10` 13 do 14 TOTAL=`expr $i + $TOTAL` 15 done 16 echo $TOTAL 17 prints 55 on standard output. The full sequ command does this basic counting operation, plus 18 much more. 19 This specification of sequ is in several stages, known as compliance levels. Each compliance 20 level adds required functionality to the sequ specification. Level 1 compliance is equivalent to 21 the Coreutils seq command. 22 The usual specification language applies to this document: MAY, SHOULD, MUST (and their 23 negations) are used in the standard fashion. 24 Wherever the specification indicates an error, a conforming sequ implementation MUST 25 immediately issue appropriate error message specific to the problem. The implementation then 26 MUST exit, with a status indicating failure to the invoking process or system. On UNIX systems, 27 the error MUST be indicated by exiting with status code 1. 28 When a conforming sequ implementation successfully completes its output, it MUST 29 immediately exit, with a status indicating success to the invoking process or systems. -
Unix: Beyond the Basics
Unix: Beyond the Basics BaRC Hot Topics – September, 2018 Bioinformatics and Research Computing Whitehead Institute http://barc.wi.mit.edu/hot_topics/ Logging in to our Unix server • Our main server is called tak4 • Request a tak4 account: http://iona.wi.mit.edu/bio/software/unix/bioinfoaccount.php • Logging in from Windows Ø PuTTY for ssh Ø Xming for graphical display [optional] • Logging in from Mac ØAccess the Terminal: Go è Utilities è Terminal ØXQuartz needed for X-windows for newer OS X. 2 Log in using secure shell ssh –Y user@tak4 PuTTY on Windows Terminal on Macs Command prompt user@tak4 ~$ 3 Hot Topics website: http://barc.wi.mit.edu/education/hot_topics/ • Create a directory for the exercises and use it as your working directory $ cd /nfs/BaRC_training $ mkdir john_doe $ cd john_doe • Copy all files into your working directory $ cp -r /nfs/BaRC_training/UnixII/* . • You should have the files below in your working directory: – foo.txt, sample1.txt, exercise.txt, datasets folder – You can check they’re there with the ‘ls’ command 4 Unix Review: Commands Ø command [arg1 arg2 … ] [input1 input2 … ] $ sort -k2,3nr foo.tab -n or -g: -n is recommended, except for scientific notation or start end a leading '+' -r: reverse order $ cut -f1,5 foo.tab $ cut -f1-5 foo.tab -f: select only these fields -f1,5: select 1st and 5th fields -f1-5: select 1st, 2nd, 3rd, 4th, and 5th fields $ wc -l foo.txt How many lines are in this file? 5 Unix Review: Common Mistakes • Case sensitive cd /nfs/Barc_Public vs cd /nfs/BaRC_Public -bash: cd: /nfs/Barc_Public: -
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 -
Introduction to Unix (PDF)
Introduction to… UNIX Bob Booth December 2004 AP-UNIX2 © University of Sheffield Contents 1. INTRODUCTION....................................................................................................................................... 3 1.1 THE SHELL ........................................................................................................................................... 3 1.2 FORMAT OF COMMANDS ...................................................................................................................... 4 1.3 ENTERING COMMANDS ......................................................................................................................... 4 2. ACCESSING UNIX MACHINES ............................................................................................................. 5 2.1 TERMINAL EMULATION SOFTWARE...................................................................................................... 5 2.2 LOGGING IN.......................................................................................................................................... 6 2.3 LOGGING OUT ...................................................................................................................................... 6 2.4 CHANGING YOUR PASSWORD............................................................................................................... 8 3. BASIC UNIX COMMANDS...................................................................................................................... 9 3.1 FILENAMES.......................................................................................................................................... -
UNIX Text Processing Tools—Programs for Sorting, Compar- Ing, and in Various Ways Examining the Contents of Text Files
UNIX® TEXT PROCESSING DALE DOUGHERTY AND TIM O’REILLY and the staffofO’Reilly & Associates, Inc. CONSULTING EDITORS: Stephen G. Kochan and PatrickH.Wood HAYDEN BOOKS ADivision of HowardW.Sams & Company 4300 West 62nd Street Indianapolis, Indiana 46268 USA Copyright © 1987 Dale Dougherty and Tim O’Reilly FIRST EDITION SECOND PRINTING — 1988 INTERNET "UTP Revival" RELEASE — 2004 The UTP RevivalRelease is distributed according to the terms of the Creative Commons Attribution License. A copyofthe license is available at http://creativecommons.org/licenses/by/1.0 International Standard Book Number: 0-672-46291-5 Library of Congress Catalog Card Number: 87-60537 Trademark Acknowledgements All terms mentioned in this book that are known to be trademarks or service marks are listed below. Nei- ther the authors nor the UTP Revivalmembers can attest to the accuracyofthis information. Use of a term in this book should not be regarded as affecting the validity of anytrademark or service mark. Apple is a registered trademark and Apple LaserWriter is a trademark of Apple Computer,Inc. devps is a trademark of Pipeline Associates, Inc. Merge/286 and Merge/386 are trademarks of Locus Computing Corp. DDL is a trademark of Imagen Corp. Helvetica and Times Roman are registered trademarks of Allied Corp. IBM is a registered trademark of International Business Machines Corp. Interpress is a trademark of Xerox Corp. LaserJet is a trademark of Hewlett-Packard Corp. Linotronic is a trademark of Allied Corp. Macintosh is a trademark licensed to Apple Computer,Inc. Microsoft is a registered trademark of Microsoft Corp. MKS Toolkit is a trademark of Mortice Kern Systems, Inc. -
Mandoc: Becoming the Main BSD Manual Toolbox
mandoc: becoming the main BSD manual toolbox BSDCan 2015, June 13, Ottawa Ingo Schwarze <[email protected]> Cynthia Livingston’sOTTB “Bedifferent” (c) 2013 C. Livingston (with permission) > Ingo Schwarze: mandoc page 2: INTROI BSDCan 2015, June 13, Ottawa Brief history of UNIX documentation • The key point: All documentation in one place and one format. Easy to find, uniform and easy to read and write. Be correct, complete, concise. • 1964: RUNOFF/roffmarkup syntax by Jerome H. Saltzer,MIT. Unobtrusive,diff(1)-friendly,easy to hand-edit, simple tools, high quality output. • 1971: Basic manual structure by Ken Thompson and Dennis Ritchie for the AT&T Version 1 UNIX manuals, Bell Labs. • 1979: man(7) physical markup language for AT&T Version 7 UNIX. • 1989: mdoc(7) semantic markup by Cynthia Livingston for 4.3BSD-Reno. Powerful, self-contained, portable. • 1989: GNU troffbyJames Clarke. • 2001: mdoc(7) rewrite by Werner Lemberg and Ruslan Ermilovfor groff-1.17. • 2008: mandoc(1) started by Kristaps Dzonsons. • 2010: mandoc(1) is the only documentation formatter in the OpenBSD base system. • 2014: mandoc(1) used by default in OpenBSD, FreeBSD, NetBSD, illumos. 16:19:30 What is the mandoc toolbox? → < > Ingo Schwarze: mandoc page 3: INTROIIBSDCan 2015, June 13, Ottawa What is the mandoc toolbox? User perspective:man(1), the manual viewer One comprehensive tool! Normal operation always proceeds in three steps: 1. Find one or more manuals in the file system or using a database by manual name — man(1) — or by search query — apropos(1) =man -k The result of this step can be printed out with man -w. -
Frequently Asked Questions Welcome Aboard! MV Is Excited to Have You
Frequently Asked Questions Welcome Aboard! MV is excited to have you join our team. As we move forward with the King County Access transition, MV is committed to providing you with up- to-date information to ensure you are informed of employee transition requirements, critical dates, and next steps. Following are answers to frequency asked questions. If at any time you have additional questions, please refer to www.mvtransit.com/KingCounty for the most current contacts. Applying How soon can I apply? MV began accepting applications on June 3rd, 2019. You are welcome to apply online at www.MVTransit.com/Careers. To retain your current pay and seniority, we must receive your application before August 31, 2019. After that date we will begin to process external candidates and we want to ensure we give current team members the first opportunity at open roles. What if I have applied online, but I have not heard back from MV? If you have already applied, please contact the MV HR Manager, Samantha Walsh at 425-231-7751. Where/how can I apply? We will process applications out of our temporary office located at 600 SW 39th Street, Suite 100 A, Renton, WA 98057. You can apply during your lunch break or after work. You can make an appointment if you are not be able to do it during those times and we will do our best to meet your schedule. Please call Samantha Walsh at 425-231-7751. Please bring your driver’s license, DOT card (for drivers) and most current pay stub. -
R for Beginners
R for Beginners Emmanuel Paradis Institut des Sciences de l'Evolution´ Universit´e Montpellier II F-34095 Montpellier c´edex 05 France E-mail: [email protected] I thank Julien Claude, Christophe Declercq, Elo´ die Gazave, Friedrich Leisch, Louis Luangkesron, Fran¸cois Pinard, and Mathieu Ros for their comments and suggestions on earlier versions of this document. I am also grateful to all the members of the R Development Core Team for their considerable efforts in developing R and animating the discussion list `rhelp'. Thanks also to the R users whose questions or comments helped me to write \R for Beginners". Special thanks to Jorge Ahumada for the Spanish translation. c 2002, 2005, Emmanuel Paradis (12th September 2005) Permission is granted to make and distribute copies, either in part or in full and in any language, of this document on any support provided the above copyright notice is included in all copies. Permission is granted to translate this document, either in part or in full, in any language provided the above copyright notice is included. Contents 1 Preamble 1 2 A few concepts before starting 3 2.1 How R works . 3 2.2 Creating, listing and deleting the objects in memory . 5 2.3 The on-line help . 7 3 Data with R 9 3.1 Objects . 9 3.2 Reading data in a file . 11 3.3 Saving data . 14 3.4 Generating data . 15 3.4.1 Regular sequences . 15 3.4.2 Random sequences . 17 3.5 Manipulating objects . 18 3.5.1 Creating objects .