Helsinki 19 Jan Practical course in genome bioinformatics DAY 0
|
|
- Corey Jackson
- 6 years ago
- Views:
Transcription
1 Helsinki 19 Jan Practical course in genome bioinformatics DAY 0 This document can be downloaded at: The upcoming course homepage will be located at: 1. Connecting to CSC-server Taito (taito-shell.csc.fi) using PuTTY PuTTY is a secure shell (ssh) client application can be found in the Start menu (button with the Windows icon on the bottom left side of the screen). Go to All Programs > PuTTY > PuTTY. In the opening window, type the following information: Host Name (or IP address): taito-shell.csc.fi Then click Open. When connecting for the first time a PuTTY Security Alert is shown. This is a completely normal notification when connecting to a new host. Click Yes. The server will now ask your login credentials. Those are the ones on the piece of paper that was given to you. If you already have your own CSC credentials, you can use those. Otherwise, enter the following information: login as: (your username from the paper) Press Enter. lhbioxx@taito-shell.csc.fi's password: (your password from the paper) Press Enter. Typos are quite frequent when entering credentials. If login fails, just re-open PuTTY and repeat the previous steps. With successful login, a welcoming message from the server is shown on the PuTTY screen and finally, a command line with the characteristic green cursor: [lhbioxx@c3xx ~]$ The X:s in the above example are numbers and they do differ between users. This is due to the unique user names and various login nodes in use. Please always log in with the same exact username that was given to you on the paper! 2. Connecting to CSC-server taito using WinSCP
2 WinSCP will provide a graphical user interface into the taito.csc.fi file system. This is the most convenient way in Windows of managing files between your local computer and the server. WinSCP can be found in the start menu (button with the Windows icon on the bottom left side of the screen). Go to All Programs > WinSCP In the opening window, fill in the following information: Host name: taito-shell.csc.fi User name: (your username from the paper) Password: (your password from the paper) Then click the Login button on the bottom of the window. Again, a Warning is shown when connecting for the first time. This is a completely normal notification when connecting to a new host. Click Yes. 3. Learning UNIX basics Go back to PuTTY. If the connection is not open already, connect to taito-shell.csc.fi using PuTTY as in chapter 1 of these exercises. Now you should see a command line with something like this: [lhbioxx@c30x ~]$ UNIX is a family of operating systems and Linux is called a Unix-like operating system because of the command line resembling original UNIX and mainly following the same commands and protocols. The commands we use in these exercises apply to all UNIX and Unix-like operating systems. 3.1 Where are we? Type the following command and press Enter: pwd pwd is short for present working directory and this is just what this command will display. The default login directory is called a home directory.
3 It is also useful to see what is inside a directory. You can do this by typing: ls -all 3.2 Hello world! It is customary to greet the world somehow in a new computing environment. On UNIX command line you can do this by typing the following: echo Hello world! The echo command will print out useful information in the command line. Next, please type: echo $WRKDIR This will show you the location of your CSC working directory that has much more space than the home directory. This location info is useful when you navigate into the working directory using WinSCP. Change now into the working directory by typing command: You can then confirm this change by typing: pwd 3.3 Using a text editor for files Change into the working directory if you are not there already by typing command: Open a new text file called test.txt by typing: nano test.txt This opens a new editable area for text in a popular UNIX editor called nano. Write something
4 e.g. Hello world! to the area. To save the file, press Ctrl and O-key simultaneously (Ctrl-O). Then press Enter. Finally, press Ctrl and X-key simultaneously (Ctrl-X) to exit the editor. If you now type ls -all you will see your file listed in the directory. You can quickly view the contents of the file by typing: cat test.txt 3.4 Creating a new directory and copying files Change into the working directory if you are not there already by typing command: Create a new directory by typing: mkdir preview If you now type ls -all you will see your new directory listed in the directory. Change into the new directory by typing: cd preview If you now type ls -all you will see that the directory is empty. You can change back to the working directory ( parent directory ) by typing: cd.. Now copy the test.txt file into the preview directory by typing: cp test.txt preview By changing into the preview directory (cd preview) and typing ls -all you can now see a copy of test.txt listed in the directory. To confirm that the copy is proper, check the contents of the file by typing: cat test.txt 4. Loading the biokit module for analysis If the connection is not open already, connect to taito-shell.csc.fi using PuTTY as in
5 chapter 1 of these exercises. Navigate to your working directory if not there already (cd $WRKDIR) CSC serves all national scientific computing for multiple fields of sciece. They have bundled the field-specific applications into suitable modules in their Linux environment. The bioinformatics module is called biokit. You can load the module by typing: module load biokit This will quickly load and list all programs and their versions in the module. With these steps complete, you are ready to all practical work on the course. 5. Running a bioinformatics program Load the biokit module if you haven't already: module load biokit Navigate into your working directory (). Then create 2 new directories: mkdir bioinfo2017 mkdir bioinfo2017/day0 The day0 directory was hereby created within the bioinfo2017 directory. Then navigate into the day0 directory: cd bioinfo2017/day0 Next, get some material, namely a test FASTQ file for some bioinformatics analysis: rsync /wrk/lhbio1/bioinfo2016/day0/anabaenasyke758a_paired_r1.fastq./ The dot and slash at the end of the line are very important to include. You will see that a file called AnabaenaSYKE758A_paired_R1.fastq has appeared in your day0 directory. View the contents of the file by typing: less AnabaenaSYKE758A_paired_R1.fastq TIP: Tapping the TAB-key while inputing a filename will automatically fill the correct filename for you. Same goes for directory paths when using other commands. You can scroll around the file with the up and down arrow keys. The less command is exited by pressing the q key. Next, we will check quality of the reads in the FASTQ file: fastqc AnabaenaSYKE758A_paired_R1.fastq
6 Running the program creates an HTML file (a web page) and a.zip file. Copy the HTML file into your local computer (using WinSCP) and open it with an internet browser (Internet Explorer or Firefox). You have just completed a quality control for a sequencing reads FASTQ file, congratulations! 6. Running programs with a graphical user interface in Taito Tomorrow we will run a software called Mauve that we will use to view multiple sequence alignments. We will now test that everybody can get Mauve working. As the PuTTY program by default provides only a command-line access to taito-shell.csc.fi, we will need to make a change to the connection settings in order to be able to run GUI programs there. This is called X11-windowing. For this step, you will need to shut down your existing PuTTY connection to taito-shell.csc.fi. A controlled exit is possible with the exit command: exit On the the other hand the X in the top right corner will terminate the connection but will also terminate the whole PuTTY program on the same. Both ways work, but the first approach will leave PuTTY configuration open for another connection. Start the X-window server in Windows. This can be located from Start menu > All programs > Xming (OR Cygwin-X) > Xming (OR Cygwin-X). The service is started successfully when the characteristic graphical X will appear in the Windows tray on the bottom right side of the desktop. NOTE: If the X-window server is not started, the following steps will ultimately fail to launch Mauve successfully. After shut down, restart PuTTY if needed. Then, on the left side of the PuTTY configuration window, navigate to SSH by clicking the small + next to it. Then, navigate into X11 (that has just appeared under the SSH settings) by clicking the mouse on the text. Click active the Enable X11 forwarding checkbox. Navigate back into the Session settings (the top most text in the left side menu). Then connect normally to taito-shell.csc.fi using your credentials from the piece of paper. Upon login to taito-shell.csc.fi, navigate into your working directory:
7 Load the biokit module (module load biokit) and then run the Mauve program: Mauve & Note that the first M of the command is a capital letter. The & ensures you can still use the command-line despite a graphical user interface launches. After checking that the program launches properly, exit the program from the File menu on the top left and clicking Quit. Then exit taito-shell.csc.fi and shut down both PuTTY and WinSCP. Please send all feedback and questions to pashupati.mishra@helsinki.fi You can also post into the Padlet wall at:
CS CS Tutorial 2 2 Winter 2018
CS CS 230 - Tutorial 2 2 Winter 2018 Sections 1. Unix Basics and connecting to CS environment 2. MIPS Introduction & CS230 Interface 3. Connecting Remotely If you haven t set up a CS environment password,
More informationCENG 334 Computer Networks. Laboratory I Linux Tutorial
CENG 334 Computer Networks Laboratory I Linux Tutorial Contents 1. Logging In and Starting Session 2. Using Commands 1. Basic Commands 2. Working With Files and Directories 3. Permission Bits 3. Introduction
More informationOur data for today is a small subset of Saimaa ringed seal RNA sequencing data (RNA_seq_reads.fasta). Let s first see how many reads are there:
Practical Course in Genome Bioinformatics 19.2.2016 (CORRECTED 22.2.2016) Exercises - Day 5 http://ekhidna.biocenter.helsinki.fi/downloads/teaching/spring2016/ Answer the 5 questions (Q1-Q5) according
More informationYou can use the WinSCP program to load or copy (FTP) files from your computer onto the Codd server.
CODD SERVER ACCESS INSTRUCTIONS OVERVIEW Codd (codd.franklin.edu) is a server that is used for many Computer Science (COMP) courses. To access the Franklin University Linux Server called Codd, an SSH connection
More informationLinux 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 informationUoW HPC Quick Start. Information Technology Services University of Wollongong. ( Last updated on October 10, 2011)
UoW HPC Quick Start Information Technology Services University of Wollongong ( Last updated on October 10, 2011) 1 Contents 1 Logging into the HPC Cluster 3 1.1 From within the UoW campus.......................
More informationGetting Started With UNIX Lab Exercises
Getting Started With UNIX Lab Exercises This is the lab exercise handout for the Getting Started with UNIX tutorial. The exercises provide hands-on experience with the topics discussed in the tutorial.
More informationTutorial 1: Unix Basics
Tutorial 1: Unix Basics To log in to your ece account, enter your ece username and password in the space provided in the login screen. Note that when you type your password, nothing will show up in the
More informationLocate your Advanced Tools and Applications
WordPress is an easy-to-use weblog system, providing numerous features like categories, ratings, as well as plugins installation. This installer application will easily install the WordPress tool to a
More informationFirewalls can prevent access to the Unix Servers. Please make sure any firewall software or hardware allows access through Port 22.
EINSTEIN OVERVIEW Einstein (Einstein.franklin.edu) and Codd (codd.franklin.edu) are two servers that are used for many Computer Science (COMP) courses. Students will be directed to use either Einstein
More informationInstalling VPN client by Jupiter Networks:
Installing VPN client by Jupiter Networks: 1. Open Firefox. The icon is likely on your desktop. If you are using internet explorer, much of the steps will be the same, but the way that Internet Explorer
More informationSession 1: Accessing MUGrid and Command Line Basics
Session 1: Accessing MUGrid and Command Line Basics Craig A. Struble, Ph.D. July 14, 2010 1 Introduction The Marquette University Grid (MUGrid) is a collection of dedicated and opportunistic resources
More informationPractical Course in Genome Bioinformatics
Practical Course in Genome Bioinformatics 20/01/2017 Exercises - Day 1 http://ekhidna.biocenter.helsinki.fi/downloads/teaching/spring2017/ Answer questions Q1-Q3 below and include requested Figures 1-5
More informationPart I. Introduction to Linux
Part I Introduction to Linux 7 Chapter 1 Linux operating system Goal-of-the-Day Familiarisation with basic Linux commands and creation of data plots. 1.1 What is Linux? All astronomical data processing
More informationIntermediate Programming, Spring Misha Kazhdan
600.120 Intermediate Programming, Spring 2017 Misha Kazhdan Outline Unix/Linux command line Basics of the Emacs editor Compiling and running a simple C program Cloning a repository Connecting to ugrad
More informationIntroduction to Linux for BlueBEAR. January
Introduction to Linux for BlueBEAR January 2019 http://intranet.birmingham.ac.uk/bear Overview Understanding of the BlueBEAR workflow Logging in to BlueBEAR Introduction to basic Linux commands Basic file
More informationLinux for Biologists Part 2
Linux for Biologists Part 2 Robert Bukowski Institute of Biotechnology Bioinformatics Facility (aka Computational Biology Service Unit - CBSU) http://cbsu.tc.cornell.edu/lab/doc/linux_workshop_part2.pdf
More informationLab 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 informationJoomla Installer User Guide. Version 1.0
Joomla Installer User Guide Version 1.0 Contents 0. Document History... 3 1. Introduction... 4 1.1. Navigation... 5 2. Install... 6 3. Uninstall... 8 4. Go to... 9 5. Manage... 10 6. Application Changes...
More informationCSC BioWeek 2018: Using Taito cluster for high throughput data analysis
CSC BioWeek 2018: Using Taito cluster for high throughput data analysis 7. 2. 2018 Running Jobs in CSC Servers Exercise 1: Running a simple batch job in Taito We will run a small alignment using BWA: https://research.csc.fi/-/bwa
More informationOperating System Interaction via bash
Operating System Interaction via bash bash, or the Bourne-Again Shell, is a popular operating system shell that is used by many platforms bash uses the command line interaction style generally accepted
More informationPart I. UNIX Workshop Series: Quick-Start
Part I UNIX Workshop Series: Quick-Start Objectives Overview Connecting with ssh Command Window Anatomy Command Structure Command Examples Getting Help Files and Directories Wildcards, Redirection and
More informationUser Guide Version 2.0
User Guide Version 2.0 Page 2 of 8 Summary Contents 1 INTRODUCTION... 3 2 SECURESHELL (SSH)... 4 2.1 ENABLING SSH... 4 2.2 DISABLING SSH... 4 2.2.1 Change Password... 4 2.2.2 Secure Shell Connection Information...
More informationLinux Operating System Environment Computadors Grau en Ciència i Enginyeria de Dades Q2
Linux Operating System Environment Computadors Grau en Ciència i Enginyeria de Dades 2017-2018 Q2 Facultat d Informàtica de Barcelona This first lab session is focused on getting experience in working
More informationLinux Exercise. pwd answer: We call this directory (into which you get when you log in) your home directory.
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 informationParallel Programming Pre-Assignment. Setting up the Software Environment
Parallel Programming Pre-Assignment Setting up the Software Environment Authors: B. Wilkinson and C. Ferner. Modification date: Aug 21, 2014 (Minor correction Aug 27, 2014.) Software The purpose of this
More informationIntroduction to the UNIX command line
Introduction to the UNIX command line Steven Abreu Introduction to Computer Science (ICS) Tutorial Jacobs University s.abreu@jacobs-university.de September 19, 2017 Overview What is UNIX? UNIX Shell Commands
More informationIntroduction 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 informationCommand 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 informationIntroduction: What is Unix?
Introduction Introduction: What is Unix? An operating system Developed at AT&T Bell Labs in the 1960 s Command Line Interpreter GUIs (Window systems) are now available Introduction: Unix vs. Linux Unix
More informationSTA 303 / 1002 Using SAS on CQUEST
STA 303 / 1002 Using SAS on CQUEST A review of the nuts and bolts A.L. Gibbs January 2012 Some Basics of CQUEST If you don t already have a CQUEST account, go to www.cquest.utoronto.ca and request one.
More informationWorking With Unix. Scott A. Handley* September 15, *Adapted from UNIX introduction material created by Dr. Julian Catchen
Working With Unix Scott A. Handley* September 15, 2014 *Adapted from UNIX introduction material created by Dr. Julian Catchen What is UNIX? An operating system (OS) Designed to be multiuser and multitasking
More informationC++ 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 informationRoss Whetten, North Carolina State University
Your First EC2 Cloud Computing Session Jan 2013 Ross Whetten, North Carolina State University BIT815 notes 1. After you set up your AWS account, and you receive the confirmation email from Amazon Web Services
More informationCENG393 Computer Networks Labwork 1
CENG393 Computer Networks Labwork 1 Linux is the common name given to a large family of operating systems. All Linux-based operating systems are essentially a large set of computer software that are bound
More informationCpSc 1111 Lab 1 Introduction to Unix Systems, Editors, and C
CpSc 1111 Lab 1 Introduction to Unix Systems, Editors, and C Welcome! Welcome to your CpSc 111 lab! For each lab this semester, you will be provided a document like this to guide you. This material, as
More informationNew User Tutorial. OSU High Performance Computing Center
New User Tutorial OSU High Performance Computing Center TABLE OF CONTENTS Logging In... 3-5 Windows... 3-4 Linux... 4 Mac... 4-5 Changing Password... 5 Using Linux Commands... 6 File Systems... 7 File
More informationIntroduction to the Linux Command Line
Introduction to the Linux Command Line May, 2015 How to Connect (securely) ssh sftp scp Basic Unix or Linux Commands Files & directories Environment variables Not necessarily in this order.? Getting Connected
More informationHPC Introductory Course - Exercises
HPC Introductory Course - Exercises The exercises in the following sections will guide you understand and become more familiar with how to use the Balena HPC service. Lines which start with $ are commands
More informationUsing WestGrid from the desktop Oct on Access Grid
Using WestGrid from the desktop Oct 11 2007 on Access Grid Introduction Simon Sharpe, UCIT Client Services The best way to contact WestGrid support is to email support@westgrid.ca This seminar gives you
More informationDatathon 2018 Connecting to MicroStrategy on AWS Cloud
Datathon 2018 Connecting to MicroStrategy on AWS Cloud Introduction This document describes how to connect to MicroStrategy on AWS cloud. The first part will show screenshots and introduction to the MicroStrategy
More information15-122: Principles of Imperative Computation
15-122: Principles of Imperative Computation Lab 0 Navigating your account in Linux Tom Cortina, Rob Simmons Unlike typical graphical interfaces for operating systems, here you are entering commands directly
More informationIn 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 informationHistory. Terminology. Opening a Terminal. Introduction to the Unix command line GNOME
Introduction to the Unix command line History Many contemporary computer operating systems, like Microsoft Windows and Mac OS X, offer primarily (but not exclusively) graphical user interfaces. The user
More informationOperating Systems and Using Linux. Topics What is an Operating System? Linux Overview Frequently Used Linux Commands
Operating Systems and Using Linux Topics What is an Operating System? Linux Overview Frequently Used Linux Commands 1 What is an Operating System? A computer program that: Controls how the CPU, memory
More informationGetting Started with UNIX
Getting Started with UNIX What is UNIX? Boston University Information Services & Technology Course Number: 4000 Course Instructor: Kenny Burns Operating System Interface between a user and the computer
More informationConnecting to Grace and using Stata from an Xinteractive perspective
Connecting to Grace and using Stata from an Xinteractive perspective Prior to using Grace you will need to register for an account. This can be done from the link below. We aim to setup all new accounts
More informationNo Food or Drink in this room. Logon to Windows machine
While you are waiting No Food or Drink in this room Logon to Windows machine Username/password on right-hand monitor Not the username/password I gave you earlier We will walk through connecting to the
More informationThe Command Shell. Fundamentals of Computer Science
The Command Shell Fundamentals of Computer Science Outline Starting the Command Shell Locally Remote Host Directory Structure Moving around the directories Displaying File Contents Compiling and Running
More informationWinSCP. Author A.Kishore/Sachin
WinSCP WinSCP is a freeware windows client for the SCP (secure copy protocol), a way to transfer files across the network using the ssh (secure shell) encrypted protocol. It replaces other FTP programs
More informationLocate your Advanced Tools and Applications
. phpmyadmin is a web-based application used to manage a MySQL database. It is free and open-source software. We have modified phpmyadmin so that it functions without errors on a shared hosting platform.
More informationCS 215 Fundamentals of Programming II Spring 2019 Very Basic UNIX
CS 215 Fundamentals of Programming II Spring 2019 Very Basic UNIX This handout very briefly describes how to use Unix and how to use the Linux server and client machines in the EECS labs that dual boot
More informationAPP-J: WHAT IS APPLICATION JUKEBOX?
APP-J: WHAT IS APPLICATION JUKEBOX? Use Application Jukebox (App-J) to run University software on any Windows PC or laptop. Launch apps from the Application Jukebox web page Install the Application Jukebox
More informationDigital Humanities. Tutorial Regular Expressions. March 10, 2014
Digital Humanities Tutorial Regular Expressions March 10, 2014 1 Introduction In this tutorial we will look at a powerful technique, called regular expressions, to search for specific patterns in corpora.
More informationAuthor A.Kishore/Sachin WinSCP
WinSCP WinSCP is a freeware windows client for the SCP (secure copy protocol), a way to transfer files across the network using the ssh (secure shell) encrypted protocol. It replaces other FTP programs
More informationmkdir 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 informationCSCI 161: Introduction to Programming I Lab 1b: Hello, World (Eclipse, Java)
Goals - to learn how to compile and execute a Java program - to modify a program to enhance it Overview This activity will introduce you to the Java programming language. You will type in the Java program
More informationIntroduction 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 informationIntroduction 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 informationWhen talking about how to launch commands and other things that is to be typed into the terminal, the following syntax is used:
Linux Tutorial How to read the examples When talking about how to launch commands and other things that is to be typed into the terminal, the following syntax is used: $ application file.txt
More informationBioinformatics? Reads, assembly, annotation, comparative genomics and a bit of phylogeny.
Bioinformatics? Reads, assembly, annotation, comparative genomics and a bit of phylogeny stefano.gaiarsa@unimi.it Linux and the command line PART 1 Survival kit for the bash environment Purpose of the
More informationIntroduction to UNIX. Logging in. Basic System Architecture 10/7/10. most systems have graphical login on Linux machines
Introduction to UNIX Logging in Basic system architecture Getting help Intro to shell (tcsh) Basic UNIX File Maintenance Intro to emacs I/O Redirection Shell scripts Logging in most systems have graphical
More informationFirst-Time Login Procedure on XWin32
First-Time Login Procedure on XWin32 Configuring XWin32 The first time you log into X-Win32, you ll need to do a bit of profile setup; this is a one-time thing, and once done you shouldn t ever need to
More informationLAB #5 Intro to Linux and Python on ENGR
LAB #5 Intro to Linux and Python on ENGR 1. Pre-Lab: In this lab, we are going to download some useful tools needed throughout your CS career. First, you need to download a secure shell (ssh) client for
More informationCMSC 104 Lecture 2 by S Lupoli adapted by C Grasso
CMSC 104 Lecture 2 by S Lupoli adapted by C Grasso A layer of software that runs between the hardware and the user. Controls how the CPU, memory and I/O devices work together to execute programs Keeps
More informationCS 246 Winter Tutorial 1
CS 246 Winter 2015 - Tutorial 1 January 11, 2016 1 Summary General Administration Stuff CS Undergraduate Environment Useful Software Basic Commands.profile Text Editors 2 General Administration Stuff Course
More informationCarnegie Mellon. Linux Boot Camp. Jack, Matthew, Nishad, Stanley 6 Sep 2016
Linux Boot Camp Jack, Matthew, Nishad, Stanley 6 Sep 2016 1 Connecting SSH Windows users: MobaXterm, PuTTY, SSH Tectia Mac & Linux users: Terminal (Just type ssh) andrewid@shark.ics.cs.cmu.edu 2 Let s
More informationSan Jacinto College. Secure SSL VPN Instruction Manual. Contents
1 San Jacinto College Secure SSL VPN Instruction Manual The new Secure SSL VPN provides a more secure and convenient method of accessing San Jacinto College resources remotely. This document provides an
More informationEnable SSH Access on the Tenable Virtual Appliance (4.4.x-4.7.x) Last Revised: February 27, 2018
Enable SSH Access on the Tenable Virtual Appliance (4.4.x-4.7.x) Last Revised: February 27, 2018 Table of Contents Introduction 3 Requirements 4 Terminology 5 Generate the Key File 6 Generate a Key for
More informationSun VirtualBox Installation Tutorial
Sun VirtualBox Installation Tutorial Installing Linux Mint 5 LTS Guest OS By Dennis Berry Welcome to the world of virtualization and Linux. This tutorial is intended to help users who are new to the world
More informationRobert Bukowski Jaroslaw Pillardy 6/27/2011
COMPUTATIONAL BIOLOGY SERVICE UNIT, 3CPG RNA Seq CBSU Computational Resources for the Workshop Robert Bukowski (bukowski@cornell.edu); Jaroslaw Pillardy (jp86@cornell.edu) 6/27/2011 In this edition of
More informationMOZILLA FIREFOX (Version 52) EXTENDED SUPPORT RELEASE (ESR) Guidance for Windows PC Patient Portal End Users
MOZILLA FIREFOX (Version 52) EXTENDED SUPPORT RELEASE (ESR) Guidance for Windows PC Patient Portal End Users 1 Downloading/ Installing Firefox Extended Support Release (ESR) Version 52 As of version 52,
More informationSoftware Installation - Accessing Linux and Checking your Environmental Variables
Accessing Linux and Checking your Environmental Although you may be fortunate enough to have a powerful multi-processor desktop running Linux, most of our sponsors do not. Most of our sponsors will have
More informationFaxFinder Fax Servers
FaxFinder Fax Servers Models: FF130 FF230 FF430 FF830 Client User Guide FaxFinder Client User Guide Fax Client Software for FaxFinder Series PN S000460B, Version B Copyright This publication may not be
More informationLinux + Galaxy Server Tutorial
Linux + Galaxy Server Tutorial Pei-Chen Peng Linux+Galaxy Pei-Chen Peng 2017 1 Introduction Exercise 1. Download lab data to flash drive. 2. Run a simple bioinformatics program on linux.. 3. Learn Galaxy
More informationLinux Kung Fu. Ross Ventresca UBNetDef, Fall 2017
Linux Kung Fu Ross Ventresca UBNetDef, Fall 2017 GOTO: https://apps.ubnetdef.org/ What is Linux? Linux generally refers to a group of Unix-like free and open source operating system distributions built
More informationEKT332 COMPUTER NETWORK
EKT332 COMPUTER NETWORK LAB 1 INTRODUCTION TO GNU/LINUX OS Lab #1 : Introduction to GNU/Linux OS Objectives 1. Introduction to Linux File System (Red Hat Distribution). 2. Introduction to various packages
More informationMills HPC Tutorial Series. Linux Basics I
Mills HPC Tutorial Series Linux Basics I Objectives Command Line Window Anatomy Command Structure Command Examples Help Files and Directories Permissions Wildcards and Home (~) Redirection and Pipe Create
More informationAMS 200: Working on Linux/Unix Machines
AMS 200, Oct 20, 2014 AMS 200: Working on Linux/Unix Machines Profs. Nic Brummell (brummell@soe.ucsc.edu) & Dongwook Lee (dlee79@ucsc.edu) Department of Applied Mathematics and Statistics University of
More informationWindows Subsystem for Linux Guide Documentation
Windows Subsystem for Linux Guide Documentation Release Kenneth Reitz Aug 30, 2017 Contents: 1 Background on WSL (Windows Subsystem for Linux) 3 1.1 What is WSL?..............................................
More informationBeginner Workshop Activity Guide 2012 User Conference
Beginner Workshop Activity Guide 2012 User Conference TUESDAY, MARCH 6 2:00PM 5:00 PM Beginner Training Workshop Attendees will learn the end user functions of OU Campus TM. They will learn how to log
More informationIntroduction. SSH Secure Shell Client 1
SSH Secure Shell Client 1 Introduction An SSH Secure Shell Client is a piece of software that allows a user to do a number of functions. Some of these functions are: file transferring, setting permissions,
More informationCS 261 Recitation 1 Compiling C on UNIX
Oregon State University School of Electrical Engineering and Computer Science CS 261 Recitation 1 Compiling C on UNIX Winter 2017 Outline Secure Shell Basic UNIX commands Editing text The GNU Compiler
More informationOregon 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 informationThis lab exercise is to be submitted at the end of the lab session! passwd [That is the command to change your current password to a new one]
Data and Computer Security (CMPD414) Lab II Topics: secure login, moving into HOME-directory, navigation on Unix, basic commands for vi, Message Digest This lab exercise is to be submitted at the end of
More informationCMSC 201 Spring 2017 Lab 01 Hello World
CMSC 201 Spring 2017 Lab 01 Hello World Assignment: Lab 01 Hello World Due Date: Sunday, February 5th by 8:59:59 PM Value: 10 points At UMBC, our General Lab (GL) system is designed to grant students the
More informationIntroduction to Unix - Lab Exercise 0
Introduction to Unix - Lab Exercise 0 Along with this document you should also receive a printout entitled First Year Survival Guide which is a (very) basic introduction to Unix and your life in the CSE
More informationUsing.htaccess to Restrict Access to OU Directories
Using.htaccess to Restrict Access to OU Directories Last Updated: 7/8/15/ by lucero@uark.edu Webmasters can place.htaccess files in any directory in OU or on Cavern to restrict access. The two examples
More informationCS 2400 Laboratory Assignment #1: Exercises in Compilation and the UNIX Programming Environment (100 pts.)
1 Introduction 1 CS 2400 Laboratory Assignment #1: Exercises in Compilation and the UNIX Programming Environment (100 pts.) This laboratory is intended to give you some brief experience using the editing/compiling/file
More informationLinux/Cygwin Practice Computer Architecture
Linux/Cygwin Practice 2010 Computer Architecture Linux Login Use ssh client applications to connect (Port : 22) SSH Clients zterm ( http://www.brainz.co.kr/products/products4_2.php ) Putty ( http://kldp.net/frs/download.php/3411/hangulputty-0.58.h2.exe
More informationKB How to upload large files to a JTAC Case
KB23337 - How to upload large files to a JTAC Case SUMMARY: This article explains how to attach/upload files larger than 10GB to a JTAC case. It also and describes what files can be attached/uploaded to
More informationIntroduction to UNIX command-line II
Introduction to UNIX command-line II Boyce Thompson Institute 2017 Prashant Hosmani Class Content Terminal file system navigation Wildcards, shortcuts and special characters File permissions Compression
More informationIntroduction to Linux Environment. Yun-Wen Chen
Introduction to Linux Environment Yun-Wen Chen 1 The Text (Command) Mode in Linux Environment 2 The Main Operating Systems We May Meet 1. Windows 2. Mac 3. Linux (Unix) 3 Windows Command Mode and DOS Type
More informationWindows 8.1 User Guide for ANU Staff
Windows 8.1 User Guide for ANU Staff This guide has been created to assist with basic tasks and navigating Windows 8.1. Further tips for using Windows 8.1 can be found on the IT Services website, or by
More informationIntroduction to remote command line Linux. Research Computing Team University of Birmingham
Introduction to remote command line Linux Research Computing Team University of Birmingham Linux/UNIX/BSD/OSX/what? v All different v UNIX is the oldest, mostly now commercial only in large environments
More informationUNIT 9 Introduction to Linux and Ubuntu
AIR FORCE ASSOCIATION S CYBERPATRIOT NATIONAL YOUTH CYBER EDUCATION PROGRAM UNIT 9 Introduction to Linux and Ubuntu Learning Objectives Participants will understand the basics of Linux, including the nature,
More informationContents. Note: pay attention to where you are. Note: Plaintext version. Note: pay attention to where you are... 1 Note: Plaintext version...
Contents Note: pay attention to where you are........................................... 1 Note: Plaintext version................................................... 1 Hello World of the Bash shell 2 Accessing
More informationHow to use Zinio. April 2017
How to use Zinio April 2017 Zinio gives you free access to over 70 popular magazines on a wide range of topics including art, computers, crafts, current affairs, families & parenting, health & fitness,
More informationWelcome to your Lacerte products! We appreciate your business.
Welcome to your Lacerte products! We appreciate your business. Please follow steps 1 through 4 in this guide: Step 1: Install the Final 2014 Program Step 2: Install the 2015 Program Step 3: Transfer Your
More informationEssential Linux Shell Commands
Essential Linux Shell Commands Special Characters Quoting and Escaping Change Directory Show Current Directory List Directory Contents Working with Files Working with Directories Special Characters There
More information