The Linux Commands Handbook Follows the 80/20 Rule: Learn in 20% of the Time the 80% of a Topic
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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 Introduction
Unix introduction Mikhail Dozmorov Summer 2018 Mikhail Dozmorov Unix introduction Summer 2018 1 / 37 What is Unix Unix is a family of operating systems and environments that exploits the power of linguistic abstractions to perform tasks Unix is not an acronym; it is a pun on “Multics”. Multics was a large multi-user operating system that was being developed at Bell Labs shortly before Unix was created in the early ’70s. Brian Kernighan is credited with the name. All computational genomics is done in Unix http://www.read.seas.harvard.edu/~kohler/class/aosref/ritchie84evolution.pdfMikhail Dozmorov Unix introduction Summer 2018 2 / 37 History of Unix Initial file system, command interpreter (shell), and process management started by Ken Thompson File system and further development from Dennis Ritchie, as well as Doug McIlroy and Joe Ossanna Vast array of simple, dependable tools that each do one simple task Ken Thompson (sitting) and Dennis Ritchie working together at a PDP-11 Mikhail Dozmorov Unix introduction Summer 2018 3 / 37 Philosophy of Unix Vast array of simple, dependable tools Each do one simple task, and do it really well By combining these tools, one can conduct rather sophisticated analyses The Linux help philosophy: “RTFM” (Read the Fine Manual) Mikhail Dozmorov Unix introduction Summer 2018 4 / 37 Know your Unix Unix users spend a lot of time at the command line In Unix, a word is worth a thousand mouse clicks Mikhail Dozmorov Unix introduction Summer 2018 5 / 37 Unix systems Three common types of laptop/desktop operating systems: Windows, Mac, Linux. Mac and Linux are both Unix-like! What that means for us: Unix-like operating systems are equipped with “shells”" that provide a command line user interface. -
Program #6: Word Count
CSc 227 — Program Design and Development Spring 2014 (McCann) http://www.cs.arizona.edu/classes/cs227/spring14/ Program #6: Word Count Due Date: March 11 th, 2014, at 9:00 p.m. MST Overview: The UNIX operating system (and its variants, of which Linux is one) includes quite a few useful utility programs. One of those is wc, which is short for Word Count. The purpose of wc is to give users an easy way to determine the size of a text file in terms of the number of lines, words, and bytes it contains. (It can do a bit more, but that’s all of the functionality that we are concerned with for this assignment.) Counting lines is done by looking for “end of line” characters (\n (ASCII 10) for UNIX text files, or the pair \r\n (ASCII 13 and 10) for Windows/DOS text files). Counting words is also straight–forward: Any sequence of characters not interrupted by “whitespace” (spaces, tabs, end–of–line characters) is a word. Of course, whitespace characters are characters, and need to be counted as such. A problem with wc is that it generates a very minimal output format. Here’s an example of what wc produces on a Linux system when asked to count the content of a pair of files; we can do better! $ wc prog6a.dat prog6b.dat 2 6 38 prog6a.dat 32 321 1883 prog6b.dat 34 327 1921 total Assignment: Write a Java program (completely documented according to the class documentation guidelines, of course) that counts lines, words, and bytes (characters) of text files. -
Contrasting the Performance of Compression Algorithms on Genomic Data
Contrasting the Performance of Compression Algorithms on Genomic Data Cornel Constantinescu, IBM Research Almaden Outline of the Talk: • Introduction / Motivation • Data used in experiments • General purpose compressors comparison • Simple Improvements • Special purpose compression • Transparent compression – working on compressed data (prototype) • Parallelism / Multithreading • Conclusion Introduction / Motivation • Despite the large number of research papers and compression algorithms proposed for compressing genomic data generated by sequencing machines, by far the most commonly used compression algorithm in the industry for FASTQ data is gzip. • The main drawbacks of the proposed alternative special-purpose compression algorithms are: • slow speed of either compression or decompression or both, and also their • brittleness by making various limiting assumptions about the input FASTQ format (for example, the structure of the headers or fixed lengths of the records [1]) in order to further improve their specialized compression. 1. Ibrahim Numanagic, James K Bonfield, Faraz Hach, Jan Voges, Jorn Ostermann, Claudio Alberti, Marco Mattavelli, and S Cenk Sahinalp. Comparison of high-throughput sequencing data compression tools. Nature Methods, 13(12):1005–1008, October 2016. Fast and Efficient Compression of Next Generation Sequencing Data 2 2 General Purpose Compression of Genomic Data As stated earlier, gzip/zlib compression is the method of choice by the industry for FASTQ genomic data. FASTQ genomic data is a text-based format (ASCII readable text) for storing a biological sequence and the corresponding quality scores. Each sequence letter and quality score is encoded with a single ASCII character. FASTQ data is structured in four fields per record (a “read”). The first field is the SEQUENCE ID or the header of the read. -
DC Console Using DC Console Application Design Software
DC Console Using DC Console Application Design Software DC Console is easy-to-use, application design software developed specifically to work in conjunction with AML’s DC Suite. Create. Distribute. Collect. Every LDX10 handheld computer comes with DC Suite, which includes seven (7) pre-developed applications for common data collection tasks. Now LDX10 users can use DC Console to modify these applications, or create their own from scratch. AML 800.648.4452 Made in USA www.amltd.com Introduction This document briefly covers how to use DC Console and the features and settings. Be sure to read this document in its entirety before attempting to use AML’s DC Console with a DC Suite compatible device. What is the difference between an “App” and a “Suite”? “Apps” are single applications running on the device used to collect and store data. In most cases, multiple apps would be utilized to handle various operations. For example, the ‘Item_Quantity’ app is one of the most widely used apps and the most direct means to take a basic inventory count, it produces a data file showing what items are in stock, the relative quantities, and requires minimal input from the mobile worker(s). Other operations will require additional input, for example, if you also need to know the specific location for each item in inventory, the ‘Item_Lot_Quantity’ app would be a better fit. Apps can be used in a variety of ways and provide the LDX10 the flexibility to handle virtually any data collection operation. “Suite” files are simply collections of individual apps. Suite files allow you to easily manage and edit multiple apps from within a single ‘store-house’ file and provide an effortless means for device deployment. -
Linux Commands Cheat Sheet
LINUX COMMANDS CHEAT SHEET System File Permission uname => Displays Linux system information chmod octal filename => Change file permissions of the file to octal uname -r => Displays kernel release information Example uptime => Displays how long the system has been running including chmod 777 /data/test.c => Set rwx permissions to owner, group and everyone (every- load average one else who has access to the server) hostname => Shows the system hostname chmod 755 /data/test.c => Set rwx to the owner and r_x to group and everyone hostname -i => Displays the IP address of the system chmod 766 /data/test.c => Sets rwx for owner, rw for group and everyone last reboot => Shows system reboot history chown owner user-file => Change ownership of the file date => Displays current system date and time chown owner-user: owner-group => Change owner and group owner of the file timedatectl => Query and change the System clock file_name chown owner-user:owner-group- => Change owner and group owner of the directory cal => Displays the current calendar month and day directory w => Displays currently logged in users in the system whoami => Displays who you are logged in as Network finger username => Displays information about the user ip addr show => Displays IP addresses and all the network interfaces Hardware ip address add => Assigns IP address 192.168.0.1 to interface eth0 192.168.0.1/24 dev eth0 dmesg => Displays bootup messages ifconfig => Displays IP addresses of all network interfaces cat /proc/cpuinfo => Displays more information about CPU e.g model, model name, cores, vendor id ping host => ping command sends an ICMP echo request to establish a connection to server / PC cat /proc/meminfo => Displays more information about hardware memory e.g. -
A Brief Introduction to Unix-2019-AMS
Brief Intro to Linux/Unix Brief Intro to Unix (contd) A Brief Introduction to o Brief History of Unix o Compilers, Email, Text processing o Basics of a Unix session o Image Processing Linux/Unix – AMS 2019 o The Unix File System Pete Pokrandt o Working with Files and Directories o The vi editor UW-Madison AOS Systems Administrator o Your Environment [email protected] o Common Commands Twitter @PTH1 History of Unix History of Unix History of Unix o Created in 1969 by Kenneth Thompson and Dennis o Today – two main variants, but blended o It’s been around for a long time Ritchie at AT&T o Revised in-house until first public release 1977 o System V (Sun Solaris, SGI, Dec OSF1, AIX, o It was written by computer programmers for o 1977 – UC-Berkeley – Berkeley Software Distribution (BSD) linux) computer programmers o 1983 – Sun Workstations produced a Unix Workstation o BSD (Old SunOS, linux, Mac OSX/MacOS) o Case sensitive, mostly lowercase o AT&T unix -> System V abbreviations 1 Basics of a Unix Login Session Basics of a Unix Login Session Basics of a Unix Login Session o The Shell – the command line interface, o Features provided by the shell o Logging in to a unix session where you enter commands, etc n Create an environment that meets your needs n login: username n Some common shells n Write shell scripts (batch files) n password: tImpAw$ n Define command aliases (this Is my password At work $) Bourne Shell (sh) OR n Manipulate command history IHateHaving2changeMypasswordevery3weeks!!! C Shell (csh) n Automatically complete the command -
Unix/Linux Command Reference
Unix/Linux Command Reference .com File Commands System Info ls – directory listing date – show the current date and time ls -al – formatted listing with hidden files cal – show this month's calendar cd dir - change directory to dir uptime – show current uptime cd – change to home w – display who is online pwd – show current directory whoami – who you are logged in as mkdir dir – create a directory dir finger user – display information about user rm file – delete file uname -a – show kernel information rm -r dir – delete directory dir cat /proc/cpuinfo – cpu information rm -f file – force remove file cat /proc/meminfo – memory information rm -rf dir – force remove directory dir * man command – show the manual for command cp file1 file2 – copy file1 to file2 df – show disk usage cp -r dir1 dir2 – copy dir1 to dir2; create dir2 if it du – show directory space usage doesn't exist free – show memory and swap usage mv file1 file2 – rename or move file1 to file2 whereis app – show possible locations of app if file2 is an existing directory, moves file1 into which app – show which app will be run by default directory file2 ln -s file link – create symbolic link link to file Compression touch file – create or update file tar cf file.tar files – create a tar named cat > file – places standard input into file file.tar containing files more file – output the contents of file tar xf file.tar – extract the files from file.tar head file – output the first 10 lines of file tar czf file.tar.gz files – create a tar with tail file – output the last 10 lines -
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 . -
Chapter 19 RECOVERING DIGITAL EVIDENCE from LINUX SYSTEMS
Chapter 19 RECOVERING DIGITAL EVIDENCE FROM LINUX SYSTEMS Philip Craiger Abstract As Linux-kernel-based operating systems proliferate there will be an in evitable increase in Linux systems that law enforcement agents must process in criminal investigations. The skills and expertise required to recover evidence from Microsoft-Windows-based systems do not neces sarily translate to Linux systems. This paper discusses digital forensic procedures for recovering evidence from Linux systems. In particular, it presents methods for identifying and recovering deleted files from disk and volatile memory, identifying notable and Trojan files, finding hidden files, and finding files with renamed extensions. All the procedures are accomplished using Linux command line utilities and require no special or commercial tools. Keywords: Digital evidence, Linux system forensics !• Introduction Linux systems will be increasingly encountered at crime scenes as Linux increases in popularity, particularly as the OS of choice for servers. The skills and expertise required to recover evidence from a Microsoft- Windows-based system, however, do not necessarily translate to the same tasks on a Linux system. For instance, the Microsoft NTFS, FAT, and Linux EXT2/3 file systems work differently enough that under standing one tells httle about how the other functions. In this paper we demonstrate digital forensics procedures for Linux systems using Linux command line utilities. The ability to gather evidence from a running system is particularly important as evidence in RAM may be lost if a forensics first responder does not prioritize the collection of live evidence. The forensic procedures discussed include methods for identifying and recovering deleted files from RAM and magnetic media, identifying no- 234 ADVANCES IN DIGITAL FORENSICS tables files and Trojans, and finding hidden files and renamed files (files with renamed extensions. -
The /Proc File System
09 0430 CH07 5/22/01 10:30 AM Page 147 7 The /proc File System TRY INVOKING THE mount COMMAND WITHOUT ARGUMENTS—this displays the file systems currently mounted on your GNU/Linux computer.You’ll see one line that looks like this: none on /proc type proc (rw) This is the special /proc file system. Notice that the first field, none, indicates that this file system isn’t associated with a hardware device such as a disk drive. Instead, /proc is a window into the running Linux kernel. Files in the /proc file system don’t corre- spond to actual files on a physical device. Instead, they are magic objects that behave like files but provide access to parameters, data structures, and statistics in the kernel. The “contents” of these files are not always fixed blocks of data, as ordinary file con- tents are. Instead, they are generated on the fly by the Linux kernel when you read from the file.You can also change the configuration of the running kernel by writing to certain files in the /proc file system. Let’s look at an example: % ls -l /proc/version -r--r--r-- 1 root root 0 Jan 17 18:09 /proc/version Note that the file size is zero; because the file’s contents are generated by the kernel, the concept of file size is not applicable.Also, if you try this command yourself, you’ll notice that the modification time on the file is the current time. 09 0430 CH07 5/22/01 10:30 AM Page 148 148 Chapter 7 The /proc File System What’s in this file? The contents of /proc/version consist of a string describing the Linux kernel version number. -
Spirent Testcenter Automation Validating the Environment and Configuring the System Variables – an Overview
Spirent TestCenter Automation Validating the environment and configuring the system variables – an overview August 10 2016 SRE Chicago Vijay Muthucumarasamy Principle Field Service Engineer Spirent Communications PROPRIETARY AND CONFIDENTIAL 1 Agenda Spirent Automation and Supported Platforms Operating System and Validation Environment Set up and Verification • TCL • Python • Perl Lab Server HLTAPI Command Sequencer Q & A Spirent Communications PROPRIETARY AND CONFIDENTIAL 2 Supported OS and API 1. Multi-threaded 2. If you are using Avalanche on Spirent TestCenter, Windows 2008 server is not officially supported at this time. 3. Running as a 32-bit application 4. Requires LabServer 5. Requires openssh-client package **** PLEASE Check the release notes for updated information Spirent Communications PROPRIETARY AND CONFIDENTIAL 3 Spirent API Packages for Linux Environment Spirent Communications PROPRIETARY AND CONFIDENTIAL 4 Verify and Validate the OS & API Before install the STC installation packages • Verify the Operating System - Kernel - CPU - Memory - Validate the requirement : Check the Spirent TestCenter releases and verify Spirent requirements • Verify the API (TCL/Python/Perl) - Release version - Whether 32/64 bit platform - Whether need a Spirent Lab Server - Validate the requirement : Check the Spirent TestCenter releases and verify Spirent requirements Spirent Communications PROPRIETARY AND CONFIDENTIAL 5 Operating System and Validation Verify Kernel version • CentOS/RedHat/Ubuntu - cat /etc/issue - cat /etc/redhat-release