EAN-Network Configuration
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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. -
Expression Definition FS.COMMAND Qualifier. Operates on a File System Command
Expression Definition FS.COMMAND Qualifier. Operates on a file system command. The user can issue multiple commands on a file transfer portal. (For example, ls to list files or mkdir to create a directory). This expression returns the current action that the user is taking. Possible values: Neighbor, login, ls, get, put, rename, mkdir, rmdir, del, logout, any. Following is an example: Add authorization policy pol1 “fs.command eq login && (fs.user eq administrator || fs.serverip eq 10.102.88.221 –netmask 255.255.255.252)” allow FS.USER Returns the user who is logged on to the file system. FS.SERVER Returns the host name of the target server. In the following example, the string win2k3-88-22 is the server name: fs.server eq win2k3-88-221 FS.SERVERIP Returns the IP address of the target server. FS.SERVICE Returns a shared root directory on the file server. If a particular folder is exposed as shared, a user can directly log on to the specified first level folder. This first level folder is called a service. For example, in the path \\hostname\SERVICEX\ETC, SERVICEX is the service. As another example, if a user accesses the file \\hostname\service1\dir1\file1.doc, FS.SERVICE will return service1. Following is an example: fs.service notcontains New FS.DOMAIN Returns the domain name of the target server. FS.PATH Returns the complete path of the file being accessed. For example, if a user accesses the file \\hostname\service1\dir1\file1.doc, FS.PATHwill return \service\dir1\file1.doc. Following is an example: fs.path notcontains SSL Expression Definition FS.FILE Returns the name of the file being accessed. -
The Linux Command Line
The Linux Command Line Fifth Internet Edition William Shotts A LinuxCommand.org Book Copyright ©2008-2019, William E. Shotts, Jr. This work is licensed under the Creative Commons Attribution-Noncommercial-No De- rivative Works 3.0 United States License. To view a copy of this license, visit the link above or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042. A version of this book is also available in printed form, published by No Starch Press. Copies may be purchased wherever fine books are sold. No Starch Press also offers elec- tronic formats for popular e-readers. They can be reached at: https://www.nostarch.com. Linux® is the registered trademark of Linus Torvalds. All other trademarks belong to their respective owners. This book is part of the LinuxCommand.org project, a site for Linux education and advo- cacy devoted to helping users of legacy operating systems migrate into the future. You may contact the LinuxCommand.org project at http://linuxcommand.org. Release History Version Date Description 19.01A January 28, 2019 Fifth Internet Edition (Corrected TOC) 19.01 January 17, 2019 Fifth Internet Edition. 17.10 October 19, 2017 Fourth Internet Edition. 16.07 July 28, 2016 Third Internet Edition. 13.07 July 6, 2013 Second Internet Edition. 09.12 December 14, 2009 First Internet Edition. Table of Contents Introduction....................................................................................................xvi Why Use the Command Line?......................................................................................xvi -
Powerview Command Reference
PowerView Command Reference TRACE32 Online Help TRACE32 Directory TRACE32 Index TRACE32 Documents ...................................................................................................................... PowerView User Interface ............................................................................................................ PowerView Command Reference .............................................................................................1 History ...................................................................................................................................... 12 ABORT ...................................................................................................................................... 13 ABORT Abort driver program 13 AREA ........................................................................................................................................ 14 AREA Message windows 14 AREA.CLEAR Clear area 15 AREA.CLOSE Close output file 15 AREA.Create Create or modify message area 16 AREA.Delete Delete message area 17 AREA.List Display a detailed list off all message areas 18 AREA.OPEN Open output file 20 AREA.PIPE Redirect area to stdout 21 AREA.RESet Reset areas 21 AREA.SAVE Save AREA window contents to file 21 AREA.Select Select area 22 AREA.STDERR Redirect area to stderr 23 AREA.STDOUT Redirect area to stdout 23 AREA.view Display message area in AREA window 24 AutoSTOre .............................................................................................................................. -
Shell Variables
Shell Using the command line Orna Agmon ladypine at vipe.technion.ac.il Haifux Shell – p. 1/55 TOC Various shells Customizing the shell getting help and information Combining simple and useful commands output redirection lists of commands job control environment variables Remote shell textual editors textual clients references Shell – p. 2/55 What is the shell? The shell is the wrapper around the system: a communication means between the user and the system The shell is the manner in which the user can interact with the system through the terminal. The shell is also a script interpreter. The simplest script is a bunch of shell commands. Shell scripts are used in order to boot the system. The user can also write and execute shell scripts. Shell – p. 3/55 Shell - which shell? There are several kinds of shells. For example, bash (Bourne Again Shell), csh, tcsh, zsh, ksh (Korn Shell). The most important shell is bash, since it is available on almost every free Unix system. The Linux system scripts use bash. The default shell for the user is set in the /etc/passwd file. Here is a line out of this file for example: dana:x:500:500:Dana,,,:/home/dana:/bin/bash This line means that user dana uses bash (located on the system at /bin/bash) as her default shell. Shell – p. 4/55 Starting to work in another shell If Dana wishes to temporarily use another shell, she can simply call this shell from the command line: [dana@granada ˜]$ bash dana@granada:˜$ #In bash now dana@granada:˜$ exit [dana@granada ˜]$ bash dana@granada:˜$ #In bash now, going to hit ctrl D dana@granada:˜$ exit [dana@granada ˜]$ #In original shell now Shell – p. -
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 -
Sleep 2.1 Manual
Sleep 2.1 Manual "If you put a million monkeys at a million keyboards, one of them will eventually write a Java program. The rest of them will write Perl programs." -- Anonymous Raphael Mudge Sleep 2.1 Manual Revision: 06.02.08 Released under a Creative Commons Attribution-ShareAlike 3.0 License (see http://creativecommons.org/licenses/by-sa/3.0/us/) You are free: • to Share -- to copy, distribute, display, and perform the work • to Remix -- to make derivative works Under the following conditions: Attribution. You must attribute this work to Raphael Mudge with a link to http://sleep.dashnine.org/ Share Alike. If you alter, transform, or build upon this work, you may distribute the resulting work only under the same, similar or a compatible license. • For any reuse or distribution, you must make clear to others the license terms of this work. The best way to do this is with a link to the license. • Any of the above conditions can be waived if you get permission from the copyright holder. • Apart from the remix rights granted under this license, nothing in this license impairs or restricts the author's moral rights. Your fair use and other rights are in no way affected by the above. Table of Contents Introduction................................................................................................. 1 I. What is Sleep?...................................................................................................1 II. Manual Conventions......................................................................................2 III. -
Netstat Statistics Comparison with Perl by Noah Davids
Netstat Statistics Comparison with Perl By Noah Davids Comparing sets of numeric output can be tiresome. Using the output from the netstat command helps diagnose problems. Over time, the changes in the statistics reported can be very informative.This article explains how this network specialist and Perl novice decided to write a program to do the comparison for him. INTRODUCTION THE SCRIPT Comparing sets of numeric output can be tedious, especially when The script expects as input a file with the following format: the numbers are large and there are a lot of them. Unfortunately it is Some number of random lines something I have to do fairly often. As a network support specialist, I Line with unique string indicating start of data set 1 often use the output from the netstat command to help diagnose Some fixed number of lines with the format: problems. Changes in the statistics reported over time can be very enlightening. In addition, as part of the support process, I have to LABEL NUMBER LABEL NUMBER LABEL include those differences in my written analysis. Punching the long numbers into a calculator and copying the answer back out is a drag. Some number of random lines Using cut and paste helps only marginally. Line with the same unique string indicating start of data 2 To make my life simpler, I decided to write a program to do the Some fixed number of lines with the format: comparison for me. However, I support four different operating sys- tems, and while each has a netstat command, the format and content LABEL NUMBER LABEL NUMBER LABEL of the output varies with each OS. -
APPENDIX a Aegis and Unix Commands
APPENDIX A Aegis and Unix Commands FUNCTION AEGIS BSD4.2 SYSS ACCESS CONTROL AND SECURITY change file protection modes edacl chmod chmod change group edacl chgrp chgrp change owner edacl chown chown change password chpass passwd passwd print user + group ids pst, lusr groups id +names set file-creation mode mask edacl, umask umask umask show current permissions acl -all Is -I Is -I DIRECTORY CONTROL create a directory crd mkdir mkdir compare two directories cmt diff dircmp delete a directory (empty) dlt rmdir rmdir delete a directory (not empty) dlt rm -r rm -r list contents of a directory ld Is -I Is -I move up one directory wd \ cd .. cd .. or wd .. move up two directories wd \\ cd . ./ .. cd . ./ .. print working directory wd pwd pwd set to network root wd II cd II cd II set working directory wd cd cd set working directory home wd- cd cd show naming directory nd printenv echo $HOME $HOME FILE CONTROL change format of text file chpat newform compare two files emf cmp cmp concatenate a file catf cat cat copy a file cpf cp cp Using and Administering an Apollo Network 265 copy std input to std output tee tee tee + files create a (symbolic) link crl In -s In -s delete a file dlf rm rm maintain an archive a ref ar ar move a file mvf mv mv dump a file dmpf od od print checksum and block- salvol -a sum sum -count of file rename a file chn mv mv search a file for a pattern fpat grep grep search or reject lines cmsrf comm comm common to 2 sorted files translate characters tic tr tr SHELL SCRIPT TOOLS condition evaluation tools existf test test -
Introduction to Unix Shell
Introduction to Unix Shell François Serra, David Castillo, Marc A. Marti- Renom Genome Biology Group (CNAG) Structural Genomics Group (CRG) Run Store Programs Data Communicate Interact with each other with us The Unix Shell Introduction Interact with us Rewiring Telepathy Typewriter Speech WIMP The Unix Shell Introduction user logs in The Unix Shell Introduction user logs in user types command The Unix Shell Introduction user logs in user types command computer executes command and prints output The Unix Shell Introduction user logs in user types command computer executes command and prints output user types another command The Unix Shell Introduction user logs in user types command computer executes command and prints output user types another command computer executes command and prints output The Unix Shell Introduction user logs in user types command computer executes command and prints output user types another command computer executes command and prints output ⋮ user logs off The Unix Shell Introduction user logs in user types command computer executes command and prints output user types another command computer executes command and prints output ⋮ user logs off The Unix Shell Introduction user logs in user types command computer executes command and prints output user types another command computer executes command and prints output ⋮ user logs off shell The Unix Shell Introduction user logs in user types command computer executes command and prints output user types another command computer executes command and prints output -
Learning Objectives ECHO Commands. Command. 10. Explain
. SA Learning Objectives After completing this chapter you will be able to: 1. List commands used in batch files. 2. List and explain batch file rules. 3. Use a batch file with a shortcut. 3. Explore the function of the REM, 4. Use the SHIFT command to move param- ECHO commands. eters. 4. Explain the use of batch files with shortcuts. 5. Use the IF command with strings for condi- 5. Explain the purpose and function of the tional processing. GOTO command. 6. Test for null values in a batch file. 6. Explain the purpose and function of the 7. Use the IF EXIST /IF SHIFT command. test for the existence of a file or a 7. Explain the purpose and function of the IF subdirectory. command. 8. Use the SET command. 8. Explain the purpose and function of the IF 9. Use the environment and environmental EXIST /IF variables in batch files. 9. Explain the purpose and function of the IF 10. Use the IF ERRORLEVEL command ERRORLEVEL command. XCOpy to write a batch file for testing exit 10. Explain the purpose and function of writing codes. programs. 11. Use the FOR...IN...OO command for repeti- 11. Explain the purpose and function of the tive processing. environment and environmental variables. 12. Use the CALL command in a batch file. 12. Explain the use of the SET command. 13. Explain the purpose and function of the Chapter Overview FOR...IN...OO command. You learned in Chapter 10 how to write simple 14. Explain the purpose and function of the batch files and use replaceable parameters.