Basic Guide to the Command Line
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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 $6}' EXPLANATION 1. Prints the first two fields of file where fields are separated by whitespace. 2. Prints fields 3 and 4 if the pattern John is found. -
Unix Essentials (Pdf)
Unix Essentials Bingbing Yuan Next Hot Topics: Unix – Beyond Basics (Mon Oct 20th at 1pm) 1 Objectives • Unix Overview • Whitehead Resources • Unix Commands • BaRC Resources • LSF 2 Objectives: Hands-on • Parsing Human Body Index (HBI) array data Goal: Process a large data file to get important information such as genes of interest, sorting expression values, and subset the data for further investigation. 3 Advantages of Unix • Processing files with thousands, or millions, of lines How many reads are in my fastq file? Sort by gene name or expression values • Many programs run on Unix only Command-line tools • Automate repetitive tasks or commands Scripting • Other software, such as Excel, are not able to handle large files efficiently • Open Source 4 Scientific computing resources 5 Shared packages/programs https://tak.wi.mit.edu Request new packages/programs Installed packages/programs 6 Login • Requesting a tak account http://iona.wi.mit.edu/bio/software/unix/bioinfoaccount.php • Windows PuTTY or Cygwin Xming: setup X-windows for graphical display • Macs Access through Terminal 7 Connecting to tak for Windows Command Prompt user@tak ~$ 8 Log in to tak for Mac ssh –Y [email protected] 9 Unix Commands • General syntax Command Options or switches (zero or more) Arguments (zero or more) Example: uniq –c myFile.txt command options arguments Options can be combined ls –l –a or ls –la • Manual (man) page man uniq • One line description whatis ls 10 Unix Directory Structure root / home dev bin nfs lab . jdoe BaRC_Public solexa_public -
ECOGEO Workshop 2: Introduction to Env 'Omics
ECOGEO Workshop 2: Introduction to Env ‘Omics Unix and Bioinformatics Ben Tully (USC); Ken Youens-Clark (UA) Unix Commands pwd rm grep tail install ls ‘>’ sed cut cd cat nano top mkdir ‘<’ history screen touch ‘|’ $PATH ssh cp sort less df mv uniq head rsync/scp Unix Command Line 1. Open Terminal window Unix Command Line 2. Open Chrome and navigate to Unix tutorial at Protocols.io 3. Group: ECOGEO 4. Protocol: ECOGEO Workshop 2: Unix Module ! This will allow you to copy, paste Unix scripts into terminal window ! ECOGEO Protocols.io for making copy, paste easier Unix Command Line $ ls ls - lists items in the current directory Many commands have additional options that can be set by a ‘-’ $ ls -a Unix Command Line $ ls -a lists all files/directories, including hidden files ‘.’ $ ls -l lists the long format File Permissions | # Link | User | Group | Size | Last modified $ ls -lt lists the long format, but ordered by date last modified Unix Command Line Unix Command Line $ cd ecogeo/ cd - change directory List the contents of the current directory Move into the directory called unix List contents $ pwd pwd - present working directory Unix Command Line /home/c-debi/ecogeo/unix When were we in the directory home? Or c-debi? Or ecogeo? $ cd / Navigates to root directory List contents of root directory This where everything is stored in the computer All the commands we are running live in /bin Unix Command Line / root bin sys home mnt usr c-debi BioinfPrograms cdebi Desktop Downloads ecogeo unix assembly annotation etc Typical Unix Layout Unix Command Line Change directory to home Change directory to c-debi Change directory to ecogeo Change directory to unix List contents Change directory to data Change directory to root Unix Command Line Change directory to unix/data in one step $ cd /home/c-debi/ecogeo/unix/data Tab can be used to auto complete names $ cd . -
Introduction to Unix
Introduction to Unix Rob Funk <[email protected]> University Technology Services Workstation Support http://wks.uts.ohio-state.edu/ University Technology Services Course Objectives • basic background in Unix structure • knowledge of getting started • directory navigation and control • file maintenance and display commands • shells • Unix features • text processing University Technology Services Course Objectives Useful commands • working with files • system resources • printing • vi editor University Technology Services In the Introduction to UNIX document 3 • shell programming • Unix command summary tables • short Unix bibliography (also see web site) We will not, however, be covering these topics in the lecture. Numbers on slides indicate page number in book. University Technology Services History of Unix 7–8 1960s multics project (MIT, GE, AT&T) 1970s AT&T Bell Labs 1970s/80s UC Berkeley 1980s DOS imitated many Unix ideas Commercial Unix fragmentation GNU Project 1990s Linux now Unix is widespread and available from many sources, both free and commercial University Technology Services Unix Systems 7–8 SunOS/Solaris Sun Microsystems Digital Unix (Tru64) Digital/Compaq HP-UX Hewlett Packard Irix SGI UNICOS Cray NetBSD, FreeBSD UC Berkeley / the Net Linux Linus Torvalds / the Net University Technology Services Unix Philosophy • Multiuser / Multitasking • Toolbox approach • Flexibility / Freedom • Conciseness • Everything is a file • File system has places, processes have life • Designed by programmers for programmers University Technology Services -
VMS CRA Y Station Now Available It Is Now Possible to Submit Jobs Functions Closely
VMS CRA Y Station Now Available It is now possible to submit jobs Functions closely. It is implemented as a to the CRAY-1 from UCC's VAX/VMS The VMS station provides these series of commands entered in system. functions: response to the system's $ A CRAY-1 running the cos oper prompt. The commands look like ating system requires another -It submits jobs to the CRAY-1, VMS commands: they have pa computer to act as a "front-end" and returns output as a file un rameters and /qualifiers; they fol system. You prepare jobs and der the user's VMS directory. low much the same syntax and data on the front-end system, us -It transfers files between the interpretation rules (for example, ing whatever tools that system machines using the cos AC wild cards are handled correctly); provides, then submit the files as QUIRE and DISPOSE commands. and they prompt for required a batch job to the CRAY for proc The source of an ACQUIREd file parameters not present on the essing. Output is returned to the can be disk or tape; the desti command line. You can always front-end system for viewing. nation of a DISPOSEd file can recognize a station command, The software that runs on the be disk, tape, printer, or the though, because it always begins front-end machine to provide this VMS batch input queue. with the letter C. For example, communication is called a -At your option, it sends bulle the station command to submit a "station." tins to the terminal chronicling job to the CRAY is CSUBMIT. -
Metadefender Core V4.12.2
MetaDefender Core v4.12.2 © 2018 OPSWAT, Inc. All rights reserved. OPSWAT®, MetadefenderTM and the OPSWAT logo are trademarks of OPSWAT, Inc. All other trademarks, trade names, service marks, service names, and images mentioned and/or used herein belong to their respective owners. Table of Contents About This Guide 13 Key Features of Metadefender Core 14 1. Quick Start with Metadefender Core 15 1.1. Installation 15 Operating system invariant initial steps 15 Basic setup 16 1.1.1. Configuration wizard 16 1.2. License Activation 21 1.3. Scan Files with Metadefender Core 21 2. Installing or Upgrading Metadefender Core 22 2.1. Recommended System Requirements 22 System Requirements For Server 22 Browser Requirements for the Metadefender Core Management Console 24 2.2. Installing Metadefender 25 Installation 25 Installation notes 25 2.2.1. Installing Metadefender Core using command line 26 2.2.2. Installing Metadefender Core using the Install Wizard 27 2.3. Upgrading MetaDefender Core 27 Upgrading from MetaDefender Core 3.x 27 Upgrading from MetaDefender Core 4.x 28 2.4. Metadefender Core Licensing 28 2.4.1. Activating Metadefender Licenses 28 2.4.2. Checking Your Metadefender Core License 35 2.5. Performance and Load Estimation 36 What to know before reading the results: Some factors that affect performance 36 How test results are calculated 37 Test Reports 37 Performance Report - Multi-Scanning On Linux 37 Performance Report - Multi-Scanning On Windows 41 2.6. Special installation options 46 Use RAMDISK for the tempdirectory 46 3. Configuring Metadefender Core 50 3.1. Management Console 50 3.2. -
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 -
Ascii, Baudot, and the Radio Amateur
ASCII, BAUDOT AND THE RADIO AMATEUR George W. Henry, Jr. K9GWT Copyright © 1980by Hal Communications Corp., Urbana, Illinois HAL COMMUNICATIONS CORP. BOX365 ASCII, BAUDOT, AND THE RADIO AMATEUR The 1970's have brought a revolution to amateur radio RTTY equipment separate wire to and from the terminal device. Such codes are found in com and techniques, the latest being the addition of the ASCII computer code. mon use with computer and line printer devices. Radio amateurs in the Effective March 17, 1980, radio amateurs in the United States have been United States are currently authorized to use either the Baudot or ASCII authorized by the FCC to use the American Standard Code for Information serial asynchronous TTY codes. Interchange(ASCII) as well as the older "Baudot" code for RTTY com munications. This paper discusses the differences between the two codes, The Baudot TTY Code provides some definitions for RTTY terms, and examines the various inter facing standards used with ASCII and Baudot terminals. One of the first data codes used with mechanical printing machines uses a total of five data pulses to represent the alphabet, numerals, and symbols. Constructio11 of RTTY Codes This code is commonly called the Baudot or Murray telegraph code after the work done by these two pioneers. Although commonly called the Baudot Mark Ull s,.ce: code in the United States, a similar code is usually called the Murray code in other parts of the world and is formally defined as the International Newcomers to amateur radio RTTY soon discover a whole new set of terms, Telegraphic Alphabet No. -
Unix and Linux System Administration and Shell Programming
Unix and Linux System Administration and Shell Programming Unix and Linux System Administration and Shell Programming version 56 of August 12, 2014 Copyright © 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2009, 2010, 2011, 2012, 2013, 2014 Milo This book includes material from the http://www.osdata.com/ website and the text book on computer programming. Distributed on the honor system. Print and read free for personal, non-profit, and/or educational purposes. If you like the book, you are encouraged to send a donation (U.S dollars) to Milo, PO Box 5237, Balboa Island, California, USA 92662. This is a work in progress. For the most up to date version, visit the website http://www.osdata.com/ and http://www.osdata.com/programming/shell/unixbook.pdf — Please add links from your website or Facebook page. Professors and Teachers: Feel free to take a copy of this PDF and make it available to your class (possibly through your academic website). This way everyone in your class will have the same copy (with the same page numbers) despite my continual updates. Please try to avoid posting it to the public internet (to avoid old copies confusing things) and take it down when the class ends. You can post the same or a newer version for each succeeding class. Please remove old copies after the class ends to prevent confusing the search engines. You can contact me with a specific version number and class end date and I will put it on my website. version 56 page 1 Unix and Linux System Administration and Shell Programming Unix and Linux Administration and Shell Programming chapter 0 This book looks at Unix (and Linux) shell programming and system administration. -
Redalyc.A Lossy Method for Compressing Raw CCD Images
Revista Mexicana de Astronomía y Astrofísica ISSN: 0185-1101 [email protected] Instituto de Astronomía México Watson, Alan M. A Lossy Method for Compressing Raw CCD Images Revista Mexicana de Astronomía y Astrofísica, vol. 38, núm. 2, octubre, 2002, pp. 233-249 Instituto de Astronomía Distrito Federal, México Available in: http://www.redalyc.org/articulo.oa?id=57138212 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative Revista Mexicana de Astronom´ıa y Astrof´ısica, 38, 233{249 (2002) A LOSSY METHOD FOR COMPRESSING RAW CCD IMAGES Alan M. Watson Instituto de Astronom´ıa Universidad Nacional Aut´onoma de M´exico, Campus Morelia, M´exico Received 2002 June 3; accepted 2002 August 7 RESUMEN Se presenta un m´etodo para comprimir las im´agenes en bruto de disposi- tivos como los CCD. El m´etodo es muy sencillo: cuantizaci´on con p´erdida y luego compresi´on sin p´erdida con herramientas de uso general como gzip o bzip2. Se convierten los archivos comprimidos a archivos de FITS descomprimi´endolos con gunzip o bunzip2, lo cual es una ventaja importante en la distribuci´on de datos com- primidos. El grado de cuantizaci´on se elige para eliminar los bits de bajo orden, los cuales sobre-muestrean el ruido, no proporcionan informaci´on, y son dif´ıciles o imposibles de comprimir. El m´etodo es con p´erdida, pero proporciona ciertas garant´ıas sobre la diferencia absoluta m´axima, la diferencia RMS y la diferencia promedio entre la imagen comprimida y la imagen original; tales garant´ıas implican que el m´etodo es adecuado para comprimir im´agenes en bruto. -
MTS on Wikipedia Snapshot Taken 9 January 2011
MTS on Wikipedia Snapshot taken 9 January 2011 PDF generated using the open source mwlib toolkit. See http://code.pediapress.com/ for more information. PDF generated at: Sun, 09 Jan 2011 13:08:01 UTC Contents Articles Michigan Terminal System 1 MTS system architecture 17 IBM System/360 Model 67 40 MAD programming language 46 UBC PLUS 55 Micro DBMS 57 Bruce Arden 58 Bernard Galler 59 TSS/360 60 References Article Sources and Contributors 64 Image Sources, Licenses and Contributors 65 Article Licenses License 66 Michigan Terminal System 1 Michigan Terminal System The MTS welcome screen as seen through a 3270 terminal emulator. Company / developer University of Michigan and 7 other universities in the U.S., Canada, and the UK Programmed in various languages, mostly 360/370 Assembler Working state Historic Initial release 1967 Latest stable release 6.0 / 1988 (final) Available language(s) English Available programming Assembler, FORTRAN, PL/I, PLUS, ALGOL W, Pascal, C, LISP, SNOBOL4, COBOL, PL360, languages(s) MAD/I, GOM (Good Old Mad), APL, and many more Supported platforms IBM S/360-67, IBM S/370 and successors History of IBM mainframe operating systems On early mainframe computers: • GM OS & GM-NAA I/O 1955 • BESYS 1957 • UMES 1958 • SOS 1959 • IBSYS 1960 • CTSS 1961 On S/360 and successors: • BOS/360 1965 • TOS/360 1965 • TSS/360 1967 • MTS 1967 • ORVYL 1967 • MUSIC 1972 • MUSIC/SP 1985 • DOS/360 and successors 1966 • DOS/VS 1972 • DOS/VSE 1980s • VSE/SP late 1980s • VSE/ESA 1991 • z/VSE 2005 Michigan Terminal System 2 • OS/360 and successors -
Computer Terminal Placement and Workflow in an Emergency Department: an Agent-Based Model Mollie R
Computer terminal placement and workflow in an emergency department: An agent-based model Mollie R. Poynton, University of Utah, Salt Lake City, Utah, USA Vikas M. Shah, Department of Internal Medicine, Banner Good Samaritan Medical Center, Phoenix, AZ, USA Rhonda BeLue, The Pennsylvania State University, University Park, PA, USA Ben Mazzotta, Tufts University, Medford, MA, USA Heather Beil, University of North Carolina, Chapel Hill, NC, USA Saleha Habibullah, Kinnaird College for Women, Lahore, Pakistan I. INTRODUCTION Adequate analysis and consideration of workflow in relation to new systems/ technology implementation is essential in health care settings. Certainly, adequate analysis of workflow and exploration of potential unintended consequences seems essential prior to implementation of any new system or technology. However, typical analysis is limited to observation of pre- implementation workflow. Specialized settings such as emergency departments are of particular concern, because systems and technologies chosen for broad implementation in tertiary care facilities may not be appropriate. Severe unintended consequences, including increased mortality, were observed in one emergency department upon implementation of a computerized provider order entry (CPOE) system. 1 Agent-based modeling enables exploration of system behavior over a broad range of parameters, and so agent-based modeling may provide crucial pre-implementation insight into the impact of a new system/technology on workflow and/or outcomes. We developed a prototype agent-based model designed to simulate patient flow and provider workflow in an emergency department setting, relative to the number and placement of computer terminals, and explored the behavior of the system in response to various configurations. II. BACKGROUND AND SIGNIFICANCE A 2005 study by Han and colleagues found increased mortality after implementation of a CPOE system in the Pittsburgh Children’s Hospital emergency department (ED) and PICU (pediatric intensive care unit).