Using Linux as a Virtual Machine

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "Using Linux as a Virtual Machine"

Transcription

1 Intro to UNIX

2 Using Linux as a Virtual Machine We will use the VMware Player to run a Virtual Machine which is a way of having more than one Operating System (OS) running at once. Your Virtual OS (Linux) will run within your primary OS (Windows). There will be shared resources between your primary OS and your Virtual Machine such as memory and CPUs. We will use the Linux distribution Ubuntu as our Virtual OS. Start VMware and load your Virtual Machine from the USB drive. User Name Password genomics genomics7620

3 Finding your way around the UNIX directory structure / root tmp etc home sarah genomics scripts genomics_lab var log www / /root /tmp /etc /home /home/sarah /home/genomics /home/genomics/scripts /home/genomics/genomics_lab /var /var/log /var/www

4 Unix Commands pwd ls # show the name of your present working directory # list files and directories in the present working directory mkdir scripts # make a directory called scripts File and Directory Names are Case Sensitive. suggestions: Use underscore instead of spaces in file names and directories. Use lower case characters for file names and directories

5 Gedit text editor From the UNIX terminal command line enter this command to start gedit gedit my_favorite_food.txt & the & will detach gedit from the terminal so you can continue to use the terminal Naming files: use all lower case characters separate words with an underscore make the file name very descriptive of what is in the file even if its rather long common file extensions:.pl a Perl script.fa FASTA formatted sequences.fastq genome sequencing data files.gz a file that has been compressed (zipped) to reduce file size (.zip).txt a generic text file.tsv values are separated by a tab (tab separated values).csv comma separated values.bed genomic data file format for genome browsers

6 Types of File Paths pwd cd scripts mkdir ws{1..15} cd../genomics_lab # show the present working directory # change pwd to the scripts directory # make 15 directories, one for each workshop # type: cd../gen then hit the tab key Relative path cd../downloads/ # relative paths do not begin with / cd /home/genomics/downloads # absolute path begin with / /ho<tab>gen<tab>down<tab> Absolute path cd /home/genomics cd ~/ cd All of these will take you to your home directory

7 Unix Commands have Arguments Arguments are like options not verbal conflicts. Search for arguments in the ls manual page man ls /all n N q # browse the manual page for ls # search for the text all # next found text # previous found text # quit double dash means there is a single argument which is usually a descriptive word ls all ls al # has one argument; show hidden files hidden files begin with.. current directory.. back one directory # has two arguments; show hidden files and show details single dash means each character is an argument

8 Search the man page of the ls command ls lh ls lt # list file details as human readable # list file details and sort by modification time Getting around in the man page: /human n up-arrow key down-arrow key page-up key page-down key q # search for the term 'human' # next found search term # move up in the man page # move down in the man page # move up one page # move down one page # quit

9 wget ftp://ftp.ncbi.nih.gov/genomes/h_sapiens/protein/protein.fa.gz wget ftp://ftp.ncbi.nih.gov/genomes/h_sapiens/rna/rna.fa.gz mkdir genomes/human man mkdir # search how to make parent directories as necessary mkdir p genomes/human mv protein.fa.gz genomes/human/ # move file to a different directory cd genomes/human/ ls../.. cp../../rna.fa.gz. rm../../rna.fa.gz # list files two directories back # copy file to current directory # remove a file using relative path

10 What is the size of the file protein.fa.gz? Preview a zipped file without opening entire file into memory: zmore protein.fa.gz <spacebar> = next screen full q = quit gunzip protein.fa.gz more protein.fa # unzip a zipped file # preview a non-zipped file less protein.fa gzip protein.fa # searchable file preview <spacebar> = next screen full u = up one screen full / = search n = find next N = find previous q = quit # zip 'compress' a file

11 Make a directory in your home directory called states and go to the states directory Move the states.csv from your Downloads directory to your states directory.csv means all lines in the file have comma separated values wc states.csv wc l states.csv cat states.csv # show number of lines,characters and bytes # for non zipped files only # show just the number of lines in a file # output the entire file to screen clear head states.csv head 25 states.csv tail states.csv # clear the terminal screen: Ctrl+l # show first 10 lines of file # show first 25 lines of file # show last 10 lines of file

12 The grep command print lines matching a pattern grep New states.csv grep c New states.csv # show all lines matching the text 'New' # count the number of lines matching New > # save output to a file; overwrite if it already exists >> # append output to an existing file; create file if it doesn't exist grep New states.csv > new_states.csv # pipe used to process output again # create a new file that has all New states grep New states.csv grep Pine # show all lines that match the text 'New', then take the results and show all lines that match the text 'Pine'

13 Deleting (removing) files rm../my_favorite_food.txt rm states.csv new_states.csv cd.. rmdir states # remove 'delete' a file # hint: type: rm../my<tab> # always double check what you are deleting # remove multiple files at once # go back one directory # remove an empty directory

14 View your commands history list Your commands are saved even when you exit your terminal session history # show all your past commands used history grep wget # show all commands where you used wget

15 exit # exit the terminal session; Ctrl+d

16 Tape Archive Files (.tar) Consists of a single file which contains of a group of files and/or directories ncbi blast x64 linux.tar 346 Mb ncbi-blast / ncbi-blast /changelog ncbi-blast /license ncbi-blast /ncbi_package_info ncbi-blast /readme ncbi-blast /doc/ ncbi-blast /doc/readme.txt ncbi-blast /bin/....tgz files (.tar.gz) Consists of a tar file that has been zipped (compressed) to make it smaller ncbi blast x64 linux.tar.gz 110 Mb

17 Download Blast (command line version) 1. Go to the Downloads directory in your home directory 2. Use Firefox to Search the web for a download Linux version of Blast and use wget to download file from the command line. Right click the link and select: Copy Link Location then paste in your terminal at the command line wget ftp://ftp /ncbi blast x64 linux.tar.gz 3. Decompress and open the tar file tar xzvf ncbi<tab> ls cd ncbi<tab> ls # look for files: INSTALL or README and read 4. View the README file gedit README & 5. View the user manual pdf xpdf doc/user_manual.pdf # q=quit

18 Review for next week Make sure you understand the following UNIX commands: pwd ls cd grep head tail wget cp mv rm mkdir rmdir cat more less man and the following directories:... ~/ and the following UNIX redirection operators: > >> This is the main list of UNIX commands that you will most likely use.

Linux Essentials Objectives Topics:

Linux Essentials Objectives Topics: Linux Essentials Linux Essentials is a professional development certificate program that covers basic knowledge for those working and studying Open Source and various distributions of Linux. Exam Objectives

More information

Linux command line basics II: downloading data and controlling files. Yanbin Yin

Linux command line basics II: downloading data and controlling files. Yanbin Yin Linux command line basics II: downloading data and controlling files Yanbin Yin 1 Things you should know about programming Learning programming has to go through the hands-on practice, a lot of practice

More information

Introduction to Unix: Fundamental Commands

Introduction to Unix: Fundamental Commands Introduction to Unix: Fundamental Commands Ricky Patterson UVA Library Based on slides from Turgut Yilmaz Istanbul Teknik University 1 What We Will Learn The fundamental commands of the Unix operating

More information

Introduction to Unix and Linux. Workshop 1: Directories and Files

Introduction to Unix and Linux. Workshop 1: Directories and Files Introduction to Unix and Linux Workshop 1: Directories and Files Genomics Core Lab TEXAS A&M UNIVERSITY CORPUS CHRISTI Anvesh Paidipala, Evan Krell, Kelly Pennoyer, Chris Bird Genomics Core Lab Informatics

More information

Read the relevant material in Sobell! If you want to follow along with the examples that follow, and you do, open a Linux terminal.

Read the relevant material in Sobell! If you want to follow along with the examples that follow, and you do, open a Linux terminal. Warnings 1 First of all, these notes will cover only a small subset of the available commands and utilities, and will cover most of those in a shallow fashion. Read the relevant material in Sobell! If

More information

The Unix Shell. Pipes and Filters

The Unix Shell. Pipes and Filters The Unix Shell Copyright Software Carpentry 2010 This work is licensed under the Creative Commons Attribution License See http://software-carpentry.org/license.html for more information. shell shell pwd

More information

Unix/Linux Operating System. Introduction to Computational Statistics STAT 598G, Fall 2011

Unix/Linux Operating System. Introduction to Computational Statistics STAT 598G, Fall 2011 Unix/Linux Operating System Introduction to Computational Statistics STAT 598G, Fall 2011 Sergey Kirshner Department of Statistics, Purdue University September 7, 2011 Sergey Kirshner (Purdue University)

More information

Lab Working with Linux Command Line

Lab Working with Linux Command Line Introduction In this lab, you will use the Linux command line to manage files and folders and perform some basic administrative tasks. Recommended Equipment A computer with a Linux OS, either installed

More information

EECS Software Tools. Lab 2 Tutorial: Introduction to UNIX/Linux. Tilemachos Pechlivanoglou

EECS Software Tools. Lab 2 Tutorial: Introduction to UNIX/Linux. Tilemachos Pechlivanoglou EECS 2031 - Software Tools Lab 2 Tutorial: Introduction to UNIX/Linux Tilemachos Pechlivanoglou (tipech@eecs.yorku.ca) Sep 22 & 25, 2017 Material marked with will be in your exams Sep 22 & 25, 2017 Introduction

More information

Linux for Beginners Part 1

Linux for Beginners Part 1 Linux for Beginners Part 1 3CPG Workshop Robert Bukowski Computational Biology Service Unit http://cbsu.tc.cornell.edu/lab/doc/linux_workshop_part1.pdf Compute clusters BioHPC infrastructure at CBSU BioHPC

More information

Useful Unix Commands Cheat Sheet

Useful Unix Commands Cheat Sheet Useful Unix Commands Cheat Sheet The Chinese University of Hong Kong SIGSC Training (Fall 2016) FILE AND DIRECTORY pwd Return path to current directory. ls List directories and files here. ls dir List

More information

A Brief Introduction to the Linux Shell for Data Science

A Brief Introduction to the Linux Shell for Data Science A Brief Introduction to the Linux Shell for Data Science Aris Anagnostopoulos 1 Introduction Here we will see a brief introduction of the Linux command line or shell as it is called. Linux is a Unix-like

More information

BIOINFORMATICS POST-DIPLOMA PROGRAM SUBJECT OUTLINE Subject Title: OPERATING SYSTEMS AND PROJECT MANAGEMENT Subject Code: BIF713 Subject Description:

BIOINFORMATICS POST-DIPLOMA PROGRAM SUBJECT OUTLINE Subject Title: OPERATING SYSTEMS AND PROJECT MANAGEMENT Subject Code: BIF713 Subject Description: BIOINFORMATICS POST-DIPLOMA PROGRAM SUBJECT OUTLINE Subject Title: OPERATING SYSTEMS AND PROJECT MANAGEMENT Subject Code: BIF713 Subject Description: This course provides Bioinformatics students with the

More information

VERY SHORT INTRODUCTION TO UNIX

VERY SHORT INTRODUCTION TO UNIX VERY SHORT INTRODUCTION TO UNIX Tore Samuelsson, Nov 2009. An operating system (OS) is an interface between hardware and user which is responsible for the management and coordination of activities and

More information

Introduction to Linux Part 1. Anita Orendt and Wim Cardoen Center for High Performance Computing 24 May 2017

Introduction to Linux Part 1. Anita Orendt and Wim Cardoen Center for High Performance Computing 24 May 2017 Introduction to Linux Part 1 Anita Orendt and Wim Cardoen Center for High Performance Computing 24 May 2017 ssh Login or Interactive Node kingspeak.chpc.utah.edu Batch queue system kp001 kp002. kpxxx FastX

More information

CSE Linux VM. For Microsoft Windows. Based on opensuse Leap 42.2

CSE Linux VM. For Microsoft Windows. Based on opensuse Leap 42.2 CSE Linux VM For Microsoft Windows Based on opensuse Leap 42.2 Dr. K. M. Flurchick February 2, 2017 Contents 1 Introduction 1 2 Requirements 1 3 Procedure 1 4 Usage 3 4.1 Start/Stop.................................................

More information

Unix tutorial. Thanks to Michael Wood-Vasey (UPitt) and Beth Willman (Haverford) for providing Unix tutorials on which this is based.

Unix tutorial. Thanks to Michael Wood-Vasey (UPitt) and Beth Willman (Haverford) for providing Unix tutorials on which this is based. Unix tutorial Thanks to Michael Wood-Vasey (UPitt) and Beth Willman (Haverford) for providing Unix tutorials on which this is based. Terminal windows You will use terminal windows to enter and execute

More information

Introduction to Linux Basics

Introduction to Linux Basics Introduction to Linux Basics Part-I Georgia Advanced Computing Resource Center University of Georgia Zhuofei Hou, HPC Trainer zhuofei@uga.edu Outline What is GACRC? What is Linux? Linux Command, Shell

More information

Welcome to getting started with Ubuntu Server. This System Administrator Manual. guide to be simple to follow, with step by step instructions

Welcome to getting started with Ubuntu Server. This System Administrator Manual. guide to be simple to follow, with step by step instructions Welcome to getting started with Ubuntu 12.04 Server. This System Administrator Manual guide to be simple to follow, with step by step instructions with screenshots INDEX 1.Installation of Ubuntu 12.04

More information

Linux Command Line Primer. By: Scott Marshall

Linux Command Line Primer. By: Scott Marshall Linux Command Line Primer By: Scott Marshall Draft: 10/21/2007 Table of Contents Topic Page(s) Preface 1 General Filesystem Background Information 2 General Filesystem Commands 2 Working with Files and

More information

Std: XI CHAPTER-3 LINUX

Std: XI CHAPTER-3 LINUX Commands: General format: Command Option Argument Command: ls - Lists the contents of a file. Option: Begins with minus sign (-) ls a Lists including the hidden files. Argument refers to the name of a

More information

Advanced Linux Commands & Shell Scripting

Advanced Linux Commands & Shell Scripting Advanced Linux Commands & Shell Scripting Advanced Genomics & Bioinformatics Workshop James Oguya Nairobi, Kenya August, 2016 Man pages Most Linux commands are shipped with their reference manuals To view

More information

Lab 1 Introduction to UNIX and C

Lab 1 Introduction to UNIX and C Name: Lab 1 Introduction to UNIX and C This first lab is meant to be an introduction to computer environments we will be using this term. You must have a Pitt username to complete this lab. NOTE: Text

More information

In this exercise you will practice working with HDFS, the Hadoop. You will use the HDFS command line tool and the Hue File Browser

In this exercise you will practice working with HDFS, the Hadoop. You will use the HDFS command line tool and the Hue File Browser Access HDFS with Command Line and Hue Data Files (local): ~/labs/data/kb/* ~/labs/data/base_stations.tsv In this exercise you will practice working with HDFS, the Hadoop Distributed File System. You will

More information

Handling Ordinary Files

Handling Ordinary Files Handling Ordinary Files Unit 2 Sahaj Computer Solutions visit : projectsatsahaj.com 1 cat: Displaying and Creating Files cat is one of the most frequently used commands on Unix-like operating systems.

More information

Basic Linux Command Line Interface Guide

Basic Linux Command Line Interface Guide This basic Linux Command-Line Interface (CLI) Guide provides a general explanation of commonly used Bash shell commands for the Barracuda NG Firewall. You can access the command-line interface by connecting

More information

Introduction to Unix The Windows User perspective. Wes Frisby Kyle Horne Todd Johansen

Introduction to Unix The Windows User perspective. Wes Frisby Kyle Horne Todd Johansen Introduction to Unix The Windows User perspective Wes Frisby Kyle Horne Todd Johansen What is Unix? Portable, multi-tasking, and multi-user operating system Software development environment Hardware independent

More information

Shell Programming Overview

Shell Programming Overview Overview Shell programming is a way of taking several command line instructions that you would use in a Unix command prompt and incorporating them into one program. There are many versions of Unix. Some

More information

Open Source Computational Fluid Dynamics

Open Source Computational Fluid Dynamics Open Source Computational Fluid Dynamics An MSc course to gain extended knowledge in Computational Fluid Dynamics (CFD) using open source software. Teachers: Miklós Balogh and Zoltán Hernádi Department

More information

Introduction to Bio-Linux. February 4, 2009

Introduction to Bio-Linux. February 4, 2009 Introduction to Bio-Linux February 4, 2009 1 Table of Contents INTRODUCTION TO BIO-LINUX...1 PART ONE: INTRODUCTION TO THE BIO-LINUX SYSTEM...4 Logging in and exploring the Bio-Linux desktop...4 Finding

More information

Hands-on Keyboard: Cyber Experiments for Strategists and Policy Makers

Hands-on Keyboard: Cyber Experiments for Strategists and Policy Makers Hands-on Keyboard: Cyber Experiments for Strategists and Policy Makers Review of the Linux File System and Linux Commands 1. Introduction Becoming adept at using the Linux OS requires gaining familiarity

More information

Command Line Interface The basics

Command Line Interface The basics Command Line Interface The basics Marco Berghoff, SCC, KIT Steinbuch Centre for Computing (SCC) Funding: www.bwhpc-c5.de Motivation In the Beginning was the Command Line by Neal Stephenson In contrast

More information

CHEM5302 Fall 2015: Introduction to Maestro and the command line

CHEM5302 Fall 2015: Introduction to Maestro and the command line CHEM5302 Fall 2015: Introduction to Maestro and the command line Ronald Levy October 29, 2015 1 Introduction As this course has evolved through the years, the landscape of computational hardware and software

More information

Basic Linux (Bash) Commands

Basic Linux (Bash) Commands Basic Linux (Bash) Commands Hint: Run commands in the emacs shell (emacs -nw, then M-x shell) instead of the terminal. It eases searching for and revising commands and navigating and copying-and-pasting

More information

Introduction to UNIX Command Line

Introduction to UNIX Command Line Introduction to UNIX Command Line Files and directories Some useful commands (echo, cat, grep, find, diff, tar) Redirection Pipes Variables Background processes Remote connections (e.g. ssh, curl) Scripts

More information

Exercise 1: Basic Tools

Exercise 1: Basic Tools Exercise 1: Basic Tools This exercise is created so everybody can learn the basic tools we will use during this course. It is really more like a tutorial than an exercise and, you are not required to submit

More information

COMS 6100 Class Notes 3

COMS 6100 Class Notes 3 COMS 6100 Class Notes 3 Daniel Solus September 1, 2016 1 General Remarks The class was split into two main sections. We finished our introduction to Linux commands by reviewing Linux commands I and II

More information

Unix Guide. Meher Krishna Patel. Created on : Octorber, 2017 Last updated : December, More documents are freely available at PythonDSP

Unix Guide. Meher Krishna Patel. Created on : Octorber, 2017 Last updated : December, More documents are freely available at PythonDSP Unix Guide Meher Krishna Patel Created on : Octorber, 2017 Last updated : December, 2017 More documents are freely available at PythonDSP Table of contents Table of contents i 1 Unix commands 1 1.1 Unix

More information

Common File System Commands

Common File System Commands Common File System Commands ls! List names of all files in current directory ls filenames! List only the named files ls -t! List in time order, most recent first ls -l! Long listing, more information.

More information

Unix L555. Dept. of Linguistics, Indiana University Fall Unix. Unix. Directories. Files. Useful Commands. Permissions. tar.

Unix L555. Dept. of Linguistics, Indiana University Fall Unix. Unix. Directories. Files. Useful Commands. Permissions. tar. L555 Dept. of Linguistics, Indiana University Fall 2010 1 / 21 What is? is an operating system, like DOS or Windows developed in 1969 by Bell Labs works well for single computers as well as for servers

More information

Lab #8: Introduction to UNIX and GMT

Lab #8: Introduction to UNIX and GMT Geol 335.3 1 Lab #8: Introduction to UNIX and GMT In this lab, you ll familiarize yourself with some of the leading components of scientific computing: UNIX operating system, and a free, open-source, GIS/plotting

More information

Linux Refresher (1) 310/ Fourth Workshop on Distributed Laboratory Instrumentation Systems (30 October - 24 November 2006)

Linux Refresher (1) 310/ Fourth Workshop on Distributed Laboratory Instrumentation Systems (30 October - 24 November 2006) 310/1779-4 Fourth Workshop on Distributed Laboratory Instrumentation Systems (30 October - 24 November 2006) Linux Refresher (1) Razaq Babalola IJADUOLA These lecture notes are intended only for distribution

More information

UNIX Basics. UNIX Basics CIS 218 Oakton Community College

UNIX Basics. UNIX Basics CIS 218 Oakton Community College UNIX Basics UNIX Basics CIS 218 Oakton Community College History UNIX was invented in 1969 at AT&T Bell Labs Ken Thompson and Dennis Ritchie are credited as the original architects and developers of C.

More information

An Introduction to Linux and Bowtie

An Introduction to Linux and Bowtie An Introduction to Linux and Bowtie Cavan Reilly November 10, 2017 Table of contents Introduction to UNIX-like operating systems Installing programs Bowtie SAMtools Introduction to Linux In order to use

More information

Introduction Into Linux Lecture 1 Johannes Werner WS 2017

Introduction Into Linux Lecture 1 Johannes Werner WS 2017 Introduction Into Linux Lecture 1 Johannes Werner WS 2017 Table of contents Introduction Operating systems Command line Programming Take home messages Introduction Lecturers Johannes Werner (j.werner@dkfz-heidelberg.de)

More information

Helpful Tips for Labs. CS140, Spring 2015

Helpful Tips for Labs. CS140, Spring 2015 Helpful Tips for Labs CS140, Spring 2015 Linux/Unix Commands Creating, Entering, Changing Directories to Create a Directory (a Folder) on the command line type mkdir folder_name to Enter that Folder cd

More information

Chapter 6. Linux File System

Chapter 6. Linux File System Chapter 6 Linux File System 1 File System File System management how to store informations on storage devices The Hierarchical Structure Types of file Common File system Tasks 2 The Hierarchical Structure

More information

SIEMENS UserAdmin Workshop TELEPERM XP Version 4 Chapter 1

SIEMENS UserAdmin Workshop TELEPERM XP Version 4 Chapter 1 1 UNIX... 1-2 1.1 USER-ENVIRONMENT... 1-2 1.1.1 User-environment... 1-3 1.1.2 Basic commands... 1-3 1.1.3 SCO Unix specific commands... 1-4 1.1.4 HP Unix specific commands... 1-4 1.2 FILE SYSTEM... 1-5

More information

Introduction to Linux Workshop 1

Introduction to Linux Workshop 1 Introduction to Linux Workshop 1 The George Washington University SEAS Computing Facility Created by Jason Hurlburt, Hadi Mohammadi, Marco Suarez hurlburj@gwu.edu Logging In The lab computers will authenticate

More information

Research. We make it happen. Unix Basics. User Support Group help-line: personal:

Research. We make it happen. Unix Basics. User Support Group help-line: personal: Research. We make it happen. Unix Basics Presented by: Patton Fast User Support Group help-line: help@msi.umn.edu 612-626-0802 personal: pfast@msi.umn.edu 612-625-6573 Outline I. Warnings! II. III. IV.

More information

Practical Sessions Metagenomics course

Practical Sessions Metagenomics course Practical Sessions Metagenomics course Aitor Gonzaga, Ana-Belen Martin- Cuadrado, Carolina Mizuno, Inmaculada Garcia-Heredia, Mario López-Pérez, Nikole Kimes, Rohit Ghai Program 9-12 th December Session

More information

Introduction to the Linux Command Line. Ken Weiss HITS Computational Research Consulting Division

Introduction to the Linux Command Line. Ken Weiss HITS Computational Research Consulting Division Introduction to the Linux Command Line Ken Weiss HITS Computational Research Consulting Division A word from our sponsor This class is brought to you courtesy of: Advanced Research Computing Technical

More information

Linux Command Line Interface. December 27, 2017

Linux Command Line Interface. December 27, 2017 Linux Command Line Interface December 27, 2017 Foreword It is supposed to be a refresher (?!) If you are familiar with UNIX/Linux/MacOS X CLI, this is going to be boring... I will not talk about editors

More information

Linux & Shell Programming 2014

Linux & Shell Programming 2014 Unit -1: Introduction to UNIX/LINUX Operating System Practical Practice Questions: Find errors (if any) otherwise write output or interpretation of following commands. (Consider default shell is bash shell.)

More information

EECS2301. Lab 1 Winter 2016

EECS2301. Lab 1 Winter 2016 EECS2301 Lab 1 Winter 2016 Lab Objectives In this lab, you will be introduced to the Linux operating system. The basic commands will be presented in this lab. By the end of you alb, you will be asked to

More information

USING THE OOSIML/JAVA. With a Terminal Window

USING THE OOSIML/JAVA. With a Terminal Window USING THE OOSIML/JAVA With a Terminal Window On Linux Operating System José M. Garrido Department of Computer Science December 2017 College of Computing and Software Engineering Kennesaw State University

More information

Practical 4. Linux Commands: Working with Directories

Practical 4. Linux Commands: Working with Directories Practical 4 Linux Commands: Working with Directories 1. pwd: pwd stands for Print Working Directory. As the name states, command pwd prints the current working directory or simply the directory user is,

More information

Network Monitoring & Management. A few Linux basics

Network Monitoring & Management. A few Linux basics Network Monitoring & Management A few Linux basics Our chosen platform Ubuntu Linux 14.04.3 LTS 64-bit LTS = Long Term Support no GUI, we administer using ssh Ubuntu is Debian underneath There are other

More information

CSc33200: Operating Systems, CS-CCNY, Fall 2003 Jinzhong Niu September 26, Nachos Overview

CSc33200: Operating Systems, CS-CCNY, Fall 2003 Jinzhong Niu September 26, Nachos Overview CSc33200: Operating Systems, CS-CCNY, Fall 2003 Jinzhong Niu September 26, 2003 Nachos Overview Operating Systems is one of the fundamental courses for a student who majors in computer software. A good

More information

commands exercises Linux System Administration and IP Services AfNOG 2015 Linux Commands # Notes

commands exercises Linux System Administration and IP Services AfNOG 2015 Linux Commands # Notes Linux System Administration and IP Services AfNOG 2015 Linux Commands # Notes * Commands preceded with "$" imply that you should execute the command as a general user not as root. * Commands preceded with

More information

Linux/Unix Filesystems

Linux/Unix Filesystems Linux/Unix Filesystems Objectives: The lab exercise is designed to introduce you to the linux operating system and environment employed in the Geography Department's Lab. This exercise covers: - How to

More information

GNU/Linux Course Lesson 1. Puria Nafisi

GNU/Linux Course Lesson 1. Puria Nafisi GNU/Linux Course Lesson 1 Puria Nafisi Azizi @pna http://netstudent.polito.it Netstudent is an students volunteer association within the Politecnico di Torino. Is build of different people and students

More information

Oxford University Computing Services. Getting Started with Unix

Oxford University Computing Services. Getting Started with Unix Oxford University Computing Services Getting Started with Unix Unix c3.1/2 Typographical Conventions Listed below are the typographical conventions used in this guide. Names of keys on the keyboard are

More information

Basics. proper programmers write commands

Basics. proper programmers write commands Scripting Languages Basics proper programmers write commands E.g. mkdir john1 rather than clicking on icons If you write a (set of) command more that once you can put them in a file and you do not need

More information

LAB 0: LINUX COMMAND LINE AND SVN

LAB 0: LINUX COMMAND LINE AND SVN CSE427S LAB 0: LINUX COMMAND LINE AND SVN M. Neumann Due: TUE 23 JAN 2018 1PM No group work. The submission for this lab needs to be done via SVN repository commit. The completion of this tutorial counts

More information

mkdir Phys338 s2017 Draw the tree of the directories and files for this step and all the following cd Phys338 s2017

mkdir Phys338 s2017 Draw the tree of the directories and files for this step and all the following cd Phys338 s2017 Linux Exercise The following steps will guide you through the most common Linux commands. If you are using windows (Library and any Windows lab on campus), then start with step 1. If you are using a linux

More information

Essentials for Scientific Computing: Bash Shell Scripting Day 3

Essentials for Scientific Computing: Bash Shell Scripting Day 3 Essentials for Scientific Computing: Bash Shell Scripting Day 3 Ershaad Ahamed TUE-CMS, JNCASR May 2012 1 Introduction In the previous sessions, you have been using basic commands in the shell. The bash

More information

Exercise sheet 1 To be corrected in tutorials in the week from 23/10/2017 to 27/10/2017

Exercise sheet 1 To be corrected in tutorials in the week from 23/10/2017 to 27/10/2017 Einführung in die Programmierung für Physiker WS 207/208 Marc Wagner Francesca Cuteri: cuteri@th.physik.uni-frankfurt.de Alessandro Sciarra: sciarra@th.physik.uni-frankfurt.de Exercise sheet To be corrected

More information

Joint High Performance Computing Exchange (JHPCE) Cluster Orientation.

Joint High Performance Computing Exchange (JHPCE) Cluster Orientation. Joint High Performance Computing Exchange (JHPCE) Cluster Orientation http://www.jhpce.jhu.edu/ Schedule - Introductions who are we, who are you? - Terminology - Logging in and account setup - Basics of

More information

Linux File System and Basic Commands

Linux File System and Basic Commands Linux File System and Basic Commands 0.1 Files, directories, and pwd The GNU/Linux operating system is much different from your typical Microsoft Windows PC, and probably looks different from Apple OS

More information

Unix Introduction to UNIX

Unix Introduction to UNIX Unix Introduction to UNIX Get Started Introduction The UNIX operating system Set of programs that act as a link between the computer and the user. Developed in 1969 by a group of AT&T employees Various

More information

The Unix Family. Linux 101. GNU/Linux distributions. Even more. MULTICS MIT/GE/Bell Labs. UNIX AT&T (Bell Labs) Mach, Carnegie Mellon

The Unix Family. Linux 101. GNU/Linux distributions. Even more. MULTICS MIT/GE/Bell Labs. UNIX AT&T (Bell Labs) Mach, Carnegie Mellon The Unix Family MULTICS MIT/GE/Bell Labs Linux 101 Johan Montelius KTH 2017 Mach, Carnegie Mellon GNU/Hurd OS X, Apple UNIX AT&T (Bell Labs) BSD Berkeley SysV AT&T Minix, Tanenbaum FreeBSD NetBSD GNU/Linux,

More information

Install and run external command line softwares. Yanbin Yin

Install and run external command line softwares. Yanbin Yin Install and run external command line softwares Yanbin Yin 1 Create a folder under your home called hw8 Change directory to hw8 Homework #8 Download Escherichia_coli_K_12_substr MG1655_uid57779 faa file

More information

PROGRAMMAZIONE I A.A. 2015/2016

PROGRAMMAZIONE I A.A. 2015/2016 PROGRAMMAZIONE I A.A. 2015/2016 SHELL SHELL SHELL A program that interprets commands Allows a user to execute commands by typing them manually at a terminal, or automatically in programs called shell scripts.

More information

C++ Programming on Linux

C++ Programming on Linux C++ Programming on Linux What is Linux? CS 2308 Spring 2017 Jill Seaman Slides 14-end are for your information only, you will not be tested over that material. 1 l an operating system l Unix-like l Open

More information

Oregon State University School of Electrical Engineering and Computer Science. CS 261 Recitation 1. Spring 2011

Oregon State University School of Electrical Engineering and Computer Science. CS 261 Recitation 1. Spring 2011 Oregon State University School of Electrical Engineering and Computer Science CS 261 Recitation 1 Spring 2011 Outline Using Secure Shell Clients GCC Some Examples Intro to C * * Windows File transfer client:

More information

ALICE Grid/Analysis Tutorial Exercise-Solutions

ALICE Grid/Analysis Tutorial Exercise-Solutions WLCG Asia Workshop, 2.12.2006 ALICE Grid/Analysis Tutorial Exercise-Solutions Andreas-Joachim Peters CERN www.eu-egee.org cern.ch/lcg http://cern.ch/arda EGEE is a project funded by the European Union

More information

Unix Workshop Aug 2014

Unix Workshop Aug 2014 Unix Workshop 2014 5 Aug 2014 What is Unix Multitasking, multiuser operating system Often the OS of choice for large servers, large clusters Unix Around You You re probably familiar with these: Linux Solaris

More information

02. At the command prompt, type usermod -l bozo bozo2 and press Enter to change the login name for the user bozo2 back to bozo. => steps 03.

02. At the command prompt, type usermod -l bozo bozo2 and press Enter to change the login name for the user bozo2 back to bozo. => steps 03. Laboratory Exercises: ===================== Complete the following laboratory exercises. All steps are numbered but not every step includes a question. You only need to record answers for those steps that

More information

Helsinki 19 Jan Practical course in genome bioinformatics DAY 0

Helsinki 19 Jan Practical course in genome bioinformatics DAY 0 Helsinki 19 Jan 2017 529028 Practical course in genome bioinformatics DAY 0 This document can be downloaded at: http://ekhidna.biocenter.helsinki.fi/downloads/teaching/spring2017/exercises_day0.pdf The

More information

Unix Basics. Benjamin S. Skrainka University College London. July 17, 2010

Unix Basics. Benjamin S. Skrainka University College London. July 17, 2010 Unix Basics Benjamin S. Skrainka University College London July 17, 2010 Overview We cover basic Unix survival skills: Why you need some Unix in your life How to get some Unix in your life Basic commands

More information

The UNIX Operating System. HORT Lecture 2 Instructor: Kranthi Varala

The UNIX Operating System. HORT Lecture 2 Instructor: Kranthi Varala The UNIX Operating System HORT 59000 Lecture 2 Instructor: Kranthi Varala Operating Systems Image By Golftheman - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=4558519 Operating

More information

Introduction to Linux

Introduction to Linux p. 1/40 Introduction to Linux Xiaoxu Guan High Performance Computing, LSU January 31, 2018 p. 2/40 Outline What is an OS or Linux OS? Basic commands for files/directories Basic commands for text processing

More information

Unix Basics. Systems Programming Concepts

Unix Basics. Systems Programming Concepts Concepts Unix directories Important Unix file commands man, pwd, ls, mkdir, cd, cp, mv File and directory access rights through permission settings Using chmod to change permissions Other important Unix

More information

CS101 Linux Shell Handout

CS101 Linux Shell Handout CS101 Linux Shell Handout Introduction This handout is meant to be used as a quick reference to get a beginner level hands on experience to using Linux based systems. We prepared this handout assuming

More information

Filesystem Hierarchy Operating systems I800 Edmund Laugasson

Filesystem Hierarchy Operating systems I800 Edmund Laugasson Filesystem Hierarchy Operating systems I800 Edmund Laugasson edmund.laugasson@itcollege.ee There has been used materials from Margus Ernits, Katrin Loodus when creating current slides. Current document

More information

Operating Systems Linux 1-2 Measurements Background material

Operating Systems Linux 1-2 Measurements Background material Operating Systems Linux 1-2 Measurements Background material Introduction The Linux measurements were designed to allow you to have an impression about the administration of Linux severs along with providing

More information

UNIX. Basic UNIX Command

UNIX. Basic UNIX Command UNIX Basic UNIX Command Command List ls mkdir mv chmod groupadd hostname kill head top compress/ uncompress pwd Cat find chown useradd id ioscan pdf sar cd more grep chgrp passwd mount dmesg netstat tar

More information

Introduction in Unix. Linus Torvalds Ken Thompson & Dennis Ritchie

Introduction in Unix. Linus Torvalds Ken Thompson & Dennis Ritchie Introduction in Unix Linus Torvalds Ken Thompson & Dennis Ritchie My name: John Donners John.Donners@surfsara.nl Consultant at SURFsara And Cedric Nugteren Cedric.Nugteren@surfsara.nl Consultant at SURFsara

More information

CSC 2500: Unix Lab Fall 2016

CSC 2500: Unix Lab Fall 2016 CSC 2500: Unix Lab Fall 2016 IO Redirection Mohammad Ashiqur Rahman Department of Computer Science College of Engineering Tennessee Tech University Agenda Standard IO IO Redirection Pipe Various File Processing

More information

Linux hep.wisc.edu

Linux hep.wisc.edu Linux Environment @ hep.wisc.edu 1 Your Account : Login Name and usage You are given a unique login name (e.g. john) A temporary password is given to you Use this to login name and password to enter the

More information

*nix Crash Course. Presented by: Virginia Tech Linux / Unix Users Group VTLUUG

*nix Crash Course. Presented by: Virginia Tech Linux / Unix Users Group VTLUUG *nix Crash Course Presented by: Virginia Tech Linux / Unix Users Group VTLUUG Ubuntu LiveCD No information on your hard-drive will be modified. Gives you a working Linux system without having to install

More information

Presented by Bill Genske Gary Jackson

Presented by Bill Genske Gary Jackson Quintessential School Systems Session C Linux Presented by Bill Genske Gary Jackson Copyright Quintessential School Systems, 2009 All Rights Reserved 867 American Street --- Second Floor --- San Carlos,

More information

The Command Line. Matthew Bender. September 10, CMSC Command Line Workshop. Matthew Bender (2015) The Command Line September 10, / 25

The Command Line. Matthew Bender. September 10, CMSC Command Line Workshop. Matthew Bender (2015) The Command Line September 10, / 25 The Command Line Matthew Bender CMSC Command Line Workshop September 10, 2015 Matthew Bender (2015) The Command Line September 10, 2015 1 / 25 Introduction Section 1 Introduction Matthew Bender (2015)

More information

ECE 2400 Computer Systems Programming, Fall 2017 Tutorial 1: Linux Development Environment

ECE 2400 Computer Systems Programming, Fall 2017 Tutorial 1: Linux Development Environment School of Electrical and Computer Engineering Cornell University revision: 2017-09-16-13-20 1 Introduction 3 2 ECE Computing Resources 3 2.1 The ecelinux Workstations in 314 Phillips Hall.......................

More information

Lab01: Part I. Introduction to Linux. Professional Training Academy Linux Series

Lab01: Part I. Introduction to Linux. Professional Training Academy Linux Series Lab01: Part I Introduction to Linux Professional Training Academy Linux Series What is Linux? Linux is an operating system. Specifically, Linux is the kernel or the core of the system Originally developed

More information

Analytical Processing of Data of statistical genetics research in UNIX like Systems

Analytical Processing of Data of statistical genetics research in UNIX like Systems Survival Skills for Analytical Processing of Data of statistical genetics research in UNIX like Systems robert yu :: March 2011 anote UNIX like? Traditional/classical UNIX, e.g. System V (Solaris), BSD

More information

CHEM 5412 Spring 2017: Introduction to Maestro and Linux Command Line

CHEM 5412 Spring 2017: Introduction to Maestro and Linux Command Line CHEM 5412 Spring 2017: Introduction to Maestro and Linux Command Line March 28, 2017 1 Introduction Molecular modeling, as with other computational sciences, has rapidly grown and taken advantage of the

More information

Practical Linux examples: Exercises

Practical Linux examples: Exercises Practical Linux examples: Exercises 1. Login (ssh) to the machine that you are assigned for this workshop (assigned machines: https://cbsu.tc.cornell.edu/ww/machines.aspx?i=87 ). Prepare working directory,

More information

bash, part 3 Chris GauthierDickey

bash, part 3 Chris GauthierDickey bash, part 3 Chris GauthierDickey More redirection As you know, by default we have 3 standard streams: input, output, error How do we redirect more than one stream? This requires an introduction to file

More information