Shellscripts Using Bash Shell
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Shell Scripting with Bash
Introduction to Shell Scripting with Bash Charles Jahnke Research Computing Services Information Services & Technology Topics for Today ● Introductions ● Basic Terminology ● How to get help ● Command-line vs. Scripting ● Variables ● Handling Arguments ● Standard I/O, Pipes, and Redirection ● Control Structures (loops and If statements) ● SCC Job Submission Example Research Computing Services Research Computing Services (RCS) A group within Information Services & Technology at Boston University provides computing, storage, and visualization resources and services to support research that has specialized or highly intensive computation, storage, bandwidth, or graphics requirements. Three Primary Services: ● Research Computation ● Research Visualization ● Research Consulting and Training Breadth of Research on the Shared Computing Cluster (SCC) Me ● Research Facilitator and Administrator ● Background in biomedical engineering, bioinformatics, and IT systems ● Offices on both CRC and BUMC ○ Most of our staff on the Charles River Campus, some dedicated to BUMC ● Contact: [email protected] You ● Who has experience programming? ● Using Linux? ● Using the Shared Computing Cluster (SCC)? Basic Terminology The Command-line The line on which commands are typed and passed to the shell. Username Hostname Current Directory [username@scc1 ~]$ Prompt Command Line (input) The Shell ● The interface between the user and the operating system ● Program that interprets and executes input ● Provides: ○ Built-in commands ○ Programming control structures ○ Environment -
Windows Command Prompt Cheatsheet
Windows Command Prompt Cheatsheet - Command line interface (as opposed to a GUI - graphical user interface) - Used to execute programs - Commands are small programs that do something useful - There are many commands already included with Windows, but we will use a few. - A filepath is where you are in the filesystem • C: is the C drive • C:\user\Documents is the Documents folder • C:\user\Documents\hello.c is a file in the Documents folder Command What it Does Usage dir Displays a list of a folder’s files dir (shows current folder) and subfolders dir myfolder cd Displays the name of the current cd filepath chdir directory or changes the current chdir filepath folder. cd .. (goes one directory up) md Creates a folder (directory) md folder-name mkdir mkdir folder-name rm Deletes a folder (directory) rm folder-name rmdir rmdir folder-name rm /s folder-name rmdir /s folder-name Note: if the folder isn’t empty, you must add the /s. copy Copies a file from one location to copy filepath-from filepath-to another move Moves file from one folder to move folder1\file.txt folder2\ another ren Changes the name of a file ren file1 file2 rename del Deletes one or more files del filename exit Exits batch script or current exit command control echo Used to display a message or to echo message turn off/on messages in batch scripts type Displays contents of a text file type myfile.txt fc Compares two files and displays fc file1 file2 the difference between them cls Clears the screen cls help Provides more details about help (lists all commands) DOS/Command Prompt help command commands Source: https://technet.microsoft.com/en-us/library/cc754340.aspx. -
Name Synopsis Description
Perl version 5.10.0 documentation - vmsish NAME vmsish - Perl pragma to control VMS-specific language features SYNOPSIS use vmsish; use vmsish 'status';# or '$?' use vmsish 'exit'; use vmsish 'time'; use vmsish 'hushed'; no vmsish 'hushed'; vmsish::hushed($hush); use vmsish; no vmsish 'time'; DESCRIPTION If no import list is supplied, all possible VMS-specific features areassumed. Currently, there are four VMS-specific features available:'status' (a.k.a '$?'), 'exit', 'time' and 'hushed'. If you're not running VMS, this module does nothing. vmsish status This makes $? and system return the native VMS exit statusinstead of emulating the POSIX exit status. vmsish exit This makes exit 1 produce a successful exit (with status SS$_NORMAL),instead of emulating UNIX exit(), which considers exit 1 to indicatean error. As with the CRTL's exit() function, exit 0 is also mappedto an exit status of SS$_NORMAL, and any other argument to exit() isused directly as Perl's exit status. vmsish time This makes all times relative to the local time zone, instead of thedefault of Universal Time (a.k.a Greenwich Mean Time, or GMT). vmsish hushed This suppresses printing of VMS status messages to SYS$OUTPUT andSYS$ERROR if Perl terminates with an error status. and allowsprograms that are expecting "unix-style" Perl to avoid having to parseVMS error messages. It does not suppress any messages from Perlitself, just the messages generated by DCL after Perl exits. The DCLsymbol $STATUS will still have the termination status, but with ahigh-order bit set: EXAMPLE:$ perl -e"exit 44;" Non-hushed error exit%SYSTEM-F-ABORT, abort DCL message$ show sym $STATUS$STATUS == "%X0000002C" $ perl -e"use vmsish qw(hushed); exit 44;" Hushed error exit $ show sym $STATUS $STATUS == "%X1000002C" The 'hushed' flag has a global scope during compilation: the exit() ordie() commands that are compiled after 'vmsish hushed' will be hushedwhen they are executed. -
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 -
Beginning Portable Shell Scripting from Novice to Professional
Beginning Portable Shell Scripting From Novice to Professional Peter Seebach 10436fmfinal 1 10/23/08 10:40:24 PM Beginning Portable Shell Scripting: From Novice to Professional Copyright © 2008 by Peter Seebach All rights reserved. No part of this work may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or by any information storage or retrieval system, without the prior written permission of the copyright owner and the publisher. ISBN-13 (pbk): 978-1-4302-1043-6 ISBN-10 (pbk): 1-4302-1043-5 ISBN-13 (electronic): 978-1-4302-1044-3 ISBN-10 (electronic): 1-4302-1044-3 Printed and bound in the United States of America 9 8 7 6 5 4 3 2 1 Trademarked names may appear in this book. Rather than use a trademark symbol with every occurrence of a trademarked name, we use the names only in an editorial fashion and to the benefit of the trademark owner, with no intention of infringement of the trademark. Lead Editor: Frank Pohlmann Technical Reviewer: Gary V. Vaughan Editorial Board: Clay Andres, Steve Anglin, Ewan Buckingham, Tony Campbell, Gary Cornell, Jonathan Gennick, Michelle Lowman, Matthew Moodie, Jeffrey Pepper, Frank Pohlmann, Ben Renow-Clarke, Dominic Shakeshaft, Matt Wade, Tom Welsh Project Manager: Richard Dal Porto Copy Editor: Kim Benbow Associate Production Director: Kari Brooks-Copony Production Editor: Katie Stence Compositor: Linda Weidemann, Wolf Creek Press Proofreader: Dan Shaw Indexer: Broccoli Information Management Cover Designer: Kurt Krames Manufacturing Director: Tom Debolski Distributed to the book trade worldwide by Springer-Verlag New York, Inc., 233 Spring Street, 6th Floor, New York, NY 10013. -
Bash Shell Scripts
Bash Shell Scripts Writing Bash shell scripts Bash shell scripts are text files Text files most efficiently built with programming editors (emacs or vi) File must be executable and in search path chmod 700 my_script PATH environment variable may not include .! An example shell script: #!/bin/bash #My first script echo "Hello World!" Bash Shell Scripts Writing Bash shell scripts Compile a Verilog file with vlog #!/bin/bash if [ ! d work ] ; then echo work does not exist, making it vlib work fi if [ ! s adder.v ] ; then vlog adder.v fi work directory must exist before compilation Get scripts via wget, eg: wget http://web.engr.oregonstate.edu/~traylor/ece474/script --- Bash Shell Scripts Writing Bash shell scripts File attribute checking #!/bin/bash if [ ! s junk_dir ] ; then mkdir junk_dir fi Spaces around brackets are needed! File attribute checking d exists and is a directory e, a file exists f exists and is a regular file s file exists and is not empty --- Bash Shell Scripts Writing Bash shell scripts Compile Verilog then run a simultion #!/bin/bash if [ ! -d "work" ] ; then vlib work fi if [ -s "adder.v" ] ; then vlog adder.v #runs simulation with a do file and no GUI vsim adder -do do.do quiet c else echo verilog file missing fi --- Bash Shell Scripts Writing Bash shell scripts vsim command and arguments vsim entity_name do dofile.do quiet -c -quiet (do not report loading file messages) -c (console mode, no GUI) -do (run vsim from a TCL do file) +nowarnTFMPC (don’t warn about mismatched ports, scary) +nowarnTSCALE (don’t warn about timing mismatches) Try vsim help for command line arguements --- Bash Shell Scripts Writing Bash Shell Scripts (TCL Script) In another text file, we create a TCL script with commands for the simulator. -
Tcl/Tk for Xspecta Michael Flynn Tcl: Tcl (Ie Tool Command Language)
Tcl/Tk for XSPECTa Michael Flynn Tcl: Tcl (i.e. Tool Command Language) is an open source scripting language similar to other modern script languages such as Perl or Python. It is substantially more powerful than UNIX/LINUX/POSIX shell script languages such as the Bourne Shell (sh), the C Shell (csh), or the Korn Shell (https://en.wikipedia.org/wiki/Shell_script). Tcl and its associated graphical user interface toolkit, Tk, were developed by John Ousterhout of the University of California. Ousterhout's group subsequently continued development of Tcl/Tk while at Sun Microsystems and later at Scriptics. Continued development is now done by an open source project team. The language has been popular for developing graphic applications and is available as public domain software for almost all computer systems (Linux, Windows and MacOS). Installation: Tcl/Tk software can be found at: http://www.activestate.com/activeTcl Binary Windows installers are available from this site for both 32 and 64 bit systems as a Free Community Edition. The lab modules were last validated with Version 8.6.4.1 but more recent versions should not be problematic. Unless Tcl has already been installed on the system being used, download and install the software from ActiveState. The installer should be run with administrative privileges. On Windows7, you should right click and 'run as administrator'. Installing with elevated privilege will allow the registry changes that map Tcl extensions and will configure the un-installer database, making later removal of ActiveTcl easier. The ActiveState default installation directory is C:/Tcl. During the installation, the installer will ask if you want this changed. -
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 -
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. -
Shell Script & Advance Features of Shell Programming
Kirti Kaushik et al, International Journal of Computer Science and Mobile Computing, Vol.4 Issue.4, April- 2015, pg. 458-462 Available Online at www.ijcsmc.com International Journal of Computer Science and Mobile Computing A Monthly Journal of Computer Science and Information Technology ISSN 2320–088X IJCSMC, Vol. 4, Issue. 4, April 2015, pg.458 – 462 RESEARCH ARTICLE Shell Script & Advance Features of Shell Programming Kirti Kaushik* Roll No.15903, CS, Department of Computer science, Dronacharya College of Engineering, Gurgaon-123506, India Email: [email protected] Jyoti Yadav Roll No. 15040, CS, Department of Applied Computer science, Dronacharya College of Engineering, Gurgaon-123506, India Email: [email protected] Kriti Bhatia Roll No. 15048, CS, Department of Applied Computer science, Dronacharya College of Engineering, Gurgaon-123506, India Email: [email protected] Abstract-- In this research paper, the idea of shell scripting and writing computer programs is examined and different parts of shell programming are likewise contemplated. A shell script is a PC system intended to be controlled by the UNIX shell which is a charge line translator. The different tongues of shell scripts are thought to be scripting dialects. Regular operations performed by shell scripts incorporate document control, program execution, and printing content. A shell script can give an advantageous variety ofa framework order where unique environment settings, charge alternatives, or post-transforming apply naturally, yet in a manner that permits the new script to still go about as a completely typical UNIX summon. The real ideas like Programming in the Borne and C-shell, in which it would be clarified that how shell programming could be possible in Borne and C-shell. -
“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. -
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.