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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. -
Cygwin User's Guide
Cygwin User’s Guide Cygwin User’s Guide ii Copyright © Cygwin authors Permission is granted to make and distribute verbatim copies of this documentation provided the copyright notice and this per- mission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this documentation under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this documentation into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the Free Software Foundation. Cygwin User’s Guide iii Contents 1 Cygwin Overview 1 1.1 What is it? . .1 1.2 Quick Start Guide for those more experienced with Windows . .1 1.3 Quick Start Guide for those more experienced with UNIX . .1 1.4 Are the Cygwin tools free software? . .2 1.5 A brief history of the Cygwin project . .2 1.6 Highlights of Cygwin Functionality . .3 1.6.1 Introduction . .3 1.6.2 Permissions and Security . .3 1.6.3 File Access . .3 1.6.4 Text Mode vs. Binary Mode . .4 1.6.5 ANSI C Library . .4 1.6.6 Process Creation . .5 1.6.6.1 Problems with process creation . .5 1.6.7 Signals . .6 1.6.8 Sockets . .6 1.6.9 Select . .7 1.7 What’s new and what changed in Cygwin . .7 1.7.1 What’s new and what changed in 3.2 . -
GNU Emacs Manual
GNU Emacs Manual GNU Emacs Manual Sixteenth Edition, Updated for Emacs Version 22.1. Richard Stallman This is the Sixteenth edition of the GNU Emacs Manual, updated for Emacs version 22.1. Copyright c 1985, 1986, 1987, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007 Free Software Foundation, Inc. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with the Invariant Sections being \The GNU Manifesto," \Distribution" and \GNU GENERAL PUBLIC LICENSE," with the Front-Cover texts being \A GNU Manual," and with the Back-Cover Texts as in (a) below. A copy of the license is included in the section entitled \GNU Free Documentation License." (a) The FSF's Back-Cover Text is: \You have freedom to copy and modify this GNU Manual, like GNU software. Copies published by the Free Software Foundation raise funds for GNU development." Published by the Free Software Foundation 51 Franklin Street, Fifth Floor Boston, MA 02110-1301 USA ISBN 1-882114-86-8 Cover art by Etienne Suvasa. i Short Contents Preface ::::::::::::::::::::::::::::::::::::::::::::::::: 1 Distribution ::::::::::::::::::::::::::::::::::::::::::::: 2 Introduction ::::::::::::::::::::::::::::::::::::::::::::: 5 1 The Organization of the Screen :::::::::::::::::::::::::: 6 2 Characters, Keys and Commands ::::::::::::::::::::::: 11 3 Entering and Exiting Emacs ::::::::::::::::::::::::::: 15 4 Basic Editing -
A Brief Introduction to the Use of Shell Variables
A Brief Introduction to the Use of Shell Variables Norman Matloff July 25, 2001 Contents 1 Two Popular Shells: tcsh and bash 1.1 Overview There are many different shells available for Unix systems. Here we focus on two of the most popular ones, tcsh and bash. Other shells tend to be very similar to one or both of these. Your Unix account has a preset login shell for you, typically tcsh in academic settings and bash in Linux. When you log in, a shell of the given type is automatically started for you. (This can be seen in the file /etc/passwd.) If you wish to temporarily run a different shell, just type its name. If you wish to change your login shell, run the chsh command. 1.2 Command Commonality Among Shells Most of what people tend to think of as “basic Unix commands” are actually shell commands which are common to almost all of the shells. So for example you could type cd /abc/def to change to the directory /abc/def in either tcsh or bash.1 2 Shell Variables 2.1 Introduction to Shell Variable Syntax The tcsh shell uses “set” and = for the assignment operation. For example, 1Technically speaking, the “change directory” command for Unix itself is chdir(), a function which must be called from a program. A shell is a program, and when for example you issue the cd command to a shell, that program in turn calls chdir(). 1 set x = 3 would assign the value 3 to the shell variable x. -
Your Performance Task Summary Explanation
Lab Report: 11.2.5 Manage Files Your Performance Your Score: 0 of 3 (0%) Pass Status: Not Passed Elapsed Time: 6 seconds Required Score: 100% Task Summary Actions you were required to perform: In Compress the D:\Graphics folderHide Details Set the Compressed attribute Apply the changes to all folders and files In Hide the D:\Finances folder In Set Read-only on filesHide Details Set read-only on 2017report.xlsx Set read-only on 2018report.xlsx Do not set read-only for the 2019report.xlsx file Explanation In this lab, your task is to complete the following: Compress the D:\Graphics folder and all of its contents. Hide the D:\Finances folder. Make the following files Read-only: D:\Finances\2017report.xlsx D:\Finances\2018report.xlsx Complete this lab as follows: 1. Compress a folder as follows: a. From the taskbar, open File Explorer. b. Maximize the window for easier viewing. c. In the left pane, expand This PC. d. Select Data (D:). e. Right-click Graphics and select Properties. f. On the General tab, select Advanced. g. Select Compress contents to save disk space. h. Click OK. i. Click OK. j. Make sure Apply changes to this folder, subfolders and files is selected. k. Click OK. 2. Hide a folder as follows: a. Right-click Finances and select Properties. b. Select Hidden. c. Click OK. 3. Set files to Read-only as follows: a. Double-click Finances to view its contents. b. Right-click 2017report.xlsx and select Properties. c. Select Read-only. d. Click OK. e. -
Downloads." the Open Information Security Foundation
Performance Testing Suricata The Effect of Configuration Variables On Offline Suricata Performance A Project Completed for CS 6266 Under Jonathon T. Giffin, Assistant Professor, Georgia Institute of Technology by Winston H Messer Project Advisor: Matt Jonkman, President, Open Information Security Foundation December 2011 Messer ii Abstract The Suricata IDS/IPS engine, a viable alternative to Snort, has a multitude of potential configurations. A simplified automated testing system was devised for the purpose of performance testing Suricata in an offline environment. Of the available configuration variables, seventeen were analyzed independently by testing in fifty-six configurations. Of these, three variables were found to have a statistically significant effect on performance: Detect Engine Profile, Multi Pattern Algorithm, and CPU affinity. Acknowledgements In writing the final report on this endeavor, I would like to start by thanking four people who made this project possible: Matt Jonkman, President, Open Information Security Foundation: For allowing me the opportunity to carry out this project under his supervision. Victor Julien, Lead Programmer, Open Information Security Foundation and Anne-Fleur Koolstra, Documentation Specialist, Open Information Security Foundation: For their willingness to share their wisdom and experience of Suricata via email for the past four months. John M. Weathersby, Jr., Executive Director, Open Source Software Institute: For allowing me the use of Institute equipment for the creation of a suitable testing -
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. -
Text Editing in UNIX: an Introduction to Vi and Editing
Text Editing in UNIX A short introduction to vi, pico, and gedit Copyright 20062009 Stewart Weiss About UNIX editors There are two types of text editors in UNIX: those that run in terminal windows, called text mode editors, and those that are graphical, with menus and mouse pointers. The latter require a windowing system, usually X Windows, to run. If you are remotely logged into UNIX, say through SSH, then you should use a text mode editor. It is possible to use a graphical editor, but it will be much slower to use. I will explain more about that later. 2 CSci 132 Practical UNIX with Perl Text mode editors The three text mode editors of choice in UNIX are vi, emacs, and pico (really nano, to be explained later.) vi is the original editor; it is very fast, easy to use, and available on virtually every UNIX system. The vi commands are the same as those of the sed filter as well as several other common UNIX tools. emacs is a very powerful editor, but it takes more effort to learn how to use it. pico is the easiest editor to learn, and the least powerful. pico was part of the Pine email client; nano is a clone of pico. 3 CSci 132 Practical UNIX with Perl What these slides contain These slides concentrate on vi because it is very fast and always available. Although the set of commands is very cryptic, by learning a small subset of the commands, you can edit text very quickly. What follows is an outline of the basic concepts that define vi. -
Shells and Shell Scripting
Shells and Shell scripting What is a Shell? • A shell is a command line interpreter that is the interface between the user and the OS. • A “program launcher” of sorts. • The shell: o analyzes each command o determines what actions are to be performed o performs the actions • Example: wc –l file1 > file2 Which shell? • sh – Bourne shell o Most common, other shells are a superset o Good for programming • csh or tcsh – default for command line on CDF o C-like syntax o Best for interactive use. Not good for programming. • bash – default on Linux (Bourne again shell) o Based on sh, with some csh features. • korn – written by David Korn o Based on sh – Some claim best for programming. o Commercial product. Common shell facilities Shell startup When a shell is invoked, it does the following: 1. Read a special startup file (usually in home directory) 2. display prompt and wait for command 3. Ctrl-D on its own line terminates shell, otherwise, goto step 2. Shell startup files used to set shell options, set up environment variables, alias sh – executes .profile if it’s there. ksh – executes .profile if in interactive mode. Executes $ENV (usually $HOME/.kshrc) csh – executes .cshrc if it exists. If a login shell, executes .login bash – executes .bashrc, if a login shell, executes .bash_profile instead Executables vs. built-in commands Most commands you run are other compiled programs. Found in /bin Example: ls – shell locates ls binary in /bin directory and launches it Some are not compiled programs, but built into the shell: cd, echo Input-output redirection prog < infile > outfile ls > outfile 2>&1 # sh stdout and stderr Pipelining commands send the output from one command to the input of the next: ls -l | wc ps –aux | grep reid | sort Before a program is executed, the shell recognizes the special characters such as <, >, |, and rewires the standard input, output, or error file descriptors of the program about to be executed to point to the right files (or the standard input of another program). -
UNIX X Command Tips and Tricks David B
SESUG Paper 122-2019 UNIX X Command Tips and Tricks David B. Horvath, MS, CCP ABSTRACT SAS® provides the ability to execute operating system level commands from within your SAS code – generically known as the “X Command”. This session explores the various commands, the advantages and disadvantages of each, and their alternatives. The focus is on UNIX/Linux but much of the same applies to Windows as well. Under SAS EG, any issued commands execute on the SAS engine, not necessarily on the PC. X %sysexec Call system Systask command Filename pipe &SYSRC Waitfor Alternatives will also be addressed – how to handle when NOXCMD is the default for your installation, saving results, and error checking. INTRODUCTION In this paper I will be covering some of the basics of the functionality within SAS that allows you to execute operating system commands from within your program. There are multiple ways you can do so – external to data steps, within data steps, and within macros. All of these, along with error checking, will be covered. RELEVANT OPTIONS Execution of any of the SAS System command execution commands depends on one option's setting: XCMD Enables the X command in SAS. Which can only be set at startup: options xcmd; ____ 30 WARNING 30-12: SAS option XCMD is valid only at startup of the SAS System. The SAS option is ignored. Unfortunately, ff NOXCMD is set at startup time, you're out of luck. Sorry! You might want to have a conversation with your system administrators to determine why and if you can get it changed. -
UNIX Essentials (Hands-On)
UNIX essentials (hands-on) • the directory tree • running programs • the shell (using the T-shell) → command line processing → special characters → command types → shell variables → environment variables → wildcards → shell scripts → shell commands → pipes and redirection • OS commands • special files 1 • The Directory Tree → directories contain files and/or directories → / : means either the root directory, or a directory separator • consider /home/afniuser/AFNI_data3 afniuser/suma_demo → an "absolute" pathname begins with '/', a "relative" pathname does not • a relative pathname depends on where you start from • in the directories above, note which is a relative pathname → every directory has a parent directory • the relative pathname for the parent directory is '..' • the relative pathname for the current directory is '.' • consider './run_this_script' and '/bin/ls ../../suma_demo' → many commands can be used to return to the home directory (of "afniuser") • cd, cd ~, cd ~afniuser, cd $HOME, cd /home/afniuser • note the 2 special characters, '~' and '$' → while you work, keep your location within the directory tree in mind 2 → class work: • open a terminal window • commands: cd, pwd, ls, ls -al • use the "cd" command to go to the given directories e.g. for directory /usr/bin, use the command: cd /usr/bin once there, use the commands "pwd", "ls", and "ls -al" note that you can always return to the home directory via: cd / home/afniuser AFNI_data3 .. AFNI_data3/afni /usr/bin ~/abin ../../afniuser/../afniuser • first example (starting with the '/'directory), use the commands: cd / pwd ls ls -al 3 • Running Programs → a program is something that gets "executed", or "run" → the first element of a command line is generally a program (followed by a space) → most shells are case sensitive when processing a command → command examples: /bin/ls $HOME ~/AFNI_data3 count -digits 2 1 10 → script: an interpreted program (interpreted by another program) • e.g.