ECOGEO Workshop 2: Introduction to Env 'Omics
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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 $6}' EXPLANATION 1. Prints the first two fields of file where fields are separated by whitespace. 2. Prints fields 3 and 4 if the pattern John is found. -
Unix Essentials (Pdf)
Unix Essentials Bingbing Yuan Next Hot Topics: Unix – Beyond Basics (Mon Oct 20th at 1pm) 1 Objectives • Unix Overview • Whitehead Resources • Unix Commands • BaRC Resources • LSF 2 Objectives: Hands-on • Parsing Human Body Index (HBI) array data Goal: Process a large data file to get important information such as genes of interest, sorting expression values, and subset the data for further investigation. 3 Advantages of Unix • Processing files with thousands, or millions, of lines How many reads are in my fastq file? Sort by gene name or expression values • Many programs run on Unix only Command-line tools • Automate repetitive tasks or commands Scripting • Other software, such as Excel, are not able to handle large files efficiently • Open Source 4 Scientific computing resources 5 Shared packages/programs https://tak.wi.mit.edu Request new packages/programs Installed packages/programs 6 Login • Requesting a tak account http://iona.wi.mit.edu/bio/software/unix/bioinfoaccount.php • Windows PuTTY or Cygwin Xming: setup X-windows for graphical display • Macs Access through Terminal 7 Connecting to tak for Windows Command Prompt user@tak ~$ 8 Log in to tak for Mac ssh –Y [email protected] 9 Unix Commands • General syntax Command Options or switches (zero or more) Arguments (zero or more) Example: uniq –c myFile.txt command options arguments Options can be combined ls –l –a or ls –la • Manual (man) page man uniq • One line description whatis ls 10 Unix Directory Structure root / home dev bin nfs lab . jdoe BaRC_Public solexa_public -
Introduction to Unix
Introduction to Unix Rob Funk <[email protected]> University Technology Services Workstation Support http://wks.uts.ohio-state.edu/ University Technology Services Course Objectives • basic background in Unix structure • knowledge of getting started • directory navigation and control • file maintenance and display commands • shells • Unix features • text processing University Technology Services Course Objectives Useful commands • working with files • system resources • printing • vi editor University Technology Services In the Introduction to UNIX document 3 • shell programming • Unix command summary tables • short Unix bibliography (also see web site) We will not, however, be covering these topics in the lecture. Numbers on slides indicate page number in book. University Technology Services History of Unix 7–8 1960s multics project (MIT, GE, AT&T) 1970s AT&T Bell Labs 1970s/80s UC Berkeley 1980s DOS imitated many Unix ideas Commercial Unix fragmentation GNU Project 1990s Linux now Unix is widespread and available from many sources, both free and commercial University Technology Services Unix Systems 7–8 SunOS/Solaris Sun Microsystems Digital Unix (Tru64) Digital/Compaq HP-UX Hewlett Packard Irix SGI UNICOS Cray NetBSD, FreeBSD UC Berkeley / the Net Linux Linus Torvalds / the Net University Technology Services Unix Philosophy • Multiuser / Multitasking • Toolbox approach • Flexibility / Freedom • Conciseness • Everything is a file • File system has places, processes have life • Designed by programmers for programmers University Technology Services -
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 -
Pingdirectory Administration Guide Version
Release 7.3.0.3 Server Administration Guide PingDirectory | Contents | ii Contents PingDirectory™ Product Documentation................................................ 20 Overview of the Server............................................................................. 20 Server Features.................................................................................................................................20 Administration Framework.................................................................................................................21 Server Tools Location....................................................................................................................... 22 Preparing Your Environment....................................................................22 Before You Begin.............................................................................................................................. 22 System requirements..............................................................................................................22 Installing Java......................................................................................................................... 23 Preparing the Operating System (Linux).......................................................................................... 24 Configuring the File Descriptor Limits.................................................................................... 24 File System Tuning.................................................................................................................25 -
Environment Variable and Set-UID Program Lab 1
SEED Labs – Environment Variable and Set-UID Program Lab 1 Environment Variable and Set-UID Program Lab Copyright © 2006 - 2016 Wenliang Du, All rights reserved. Free to use for non-commercial educational purposes. Commercial uses of the materials are prohibited. The SEED project was funded by multiple grants from the US National Science Foundation. 1 Overview The learning objective of this lab is for students to understand how environment variables affect program and system behaviors. Environment variables are a set of dynamic named values that can affect the way running processes will behave on a computer. They are used by most operating systems, since they were introduced to Unix in 1979. Although environment variables affect program behaviors, how they achieve that is not well understood by many programmers. As a result, if a program uses environment variables, but the programmer does not know that they are used, the program may have vulnerabilities. In this lab, students will understand how environment variables work, how they are propagated from parent process to child, and how they affect system/program behaviors. We are particularly interested in how environment variables affect the behavior of Set-UID programs, which are usually privileged programs. This lab covers the following topics: • Environment variables • Set-UID programs • Securely invoke external programs • Capability leaking • Dynamic loader/linker Readings and videos. Detailed coverage of the Set-UID mechanism, environment variables, and their related security problems can be found in the following: • Chapters 1 and 2 of the SEED Book, Computer & Internet Security: A Hands-on Approach, 2nd Edition, by Wenliang Du. -
Useful Commands in Linux and Other Tools for Quality Control
Useful commands in Linux and other tools for quality control Ignacio Aguilar INIA Uruguay 05-2018 Unix Basic Commands pwd show working directory ls list files in working directory ll as before but with more information mkdir d make a directory d cd d change to directory d Copy and moving commands To copy file cp /home/user/is . To copy file directory cp –r /home/folder . to move file aa into bb in folder test mv aa ./test/bb To delete rm yy delete the file yy rm –r xx delete the folder xx Redirections & pipe Redirection useful to read/write from file !! aa < bb program aa reads from file bb blupf90 < in aa > bb program aa write in file bb blupf90 < in > log Redirections & pipe “|” similar to redirection but instead to write to a file, passes content as input to other command tee copy standard input to standard output and save in a file echo copy stream to standard output Example: program blupf90 reads name of parameter file and writes output in terminal and in file log echo par.b90 | blupf90 | tee blup.log Other popular commands head file print first 10 lines list file page-by-page tail file print last 10 lines less file list file line-by-line or page-by-page wc –l file count lines grep text file find lines that contains text cat file1 fiel2 concatenate files sort sort file cut cuts specific columns join join lines of two files on specific columns paste paste lines of two file expand replace TAB with spaces uniq retain unique lines on a sorted file head / tail $ head pedigree.txt 1 0 0 2 0 0 3 0 0 4 0 0 5 0 0 6 0 0 7 0 0 8 0 0 9 0 0 10 -
Install and Run External Command Line Softwares
job monitor and control top: similar to windows task manager (space to refresh, q to exit) w: who is there ps: all running processes, PID, status, type ps -ef | grep yyin bg: move current process to background fg: move current process to foreground jobs: list running and suspended processes kill: kill processes kill pid (could find out using top or ps) 1 sort, cut, uniq, join, paste, sed, grep, awk, wc, diff, comm, cat All types of bioinformatics sequence analyses are essentially text processing. Unix Shell has the above commands that are very useful for processing texts and also allows the output from one command to be passed to another command as input using pipe (“|”). less cosmicRaw.txt | cut -f2,3,4,5,8,13 | awk '$5==22' | cut -f1 | sort -u | wc This makes the processing of files using Shell very convenient and very powerful: you do not need to write output to intermediate files or load all data into the memory. For example, combining different Unix commands for text processing is like passing an item through a manufacturing pipeline when you only care about the final product 2 Hands on example 1: cosmic mutation data - Go to UCSC genome browser website: http://genome.ucsc.edu/ - On the left, find the Downloads link - Click on Human - Click on Annotation database - Ctrl+f and then search “cosmic” - On “cosmic.txt.gz” right-click -> copy link address - Go to the terminal and wget the above link (middle click or Shift+Insert to paste what you copied) - Similarly, download the “cosmicRaw.txt.gz” file - Under your home, create a folder -
CS2043 - Unix Tools & Scripting Cornell University, Spring 20141
CS2043 - Unix Tools & Scripting Cornell University, Spring 20141 Instructor: Bruno Abrahao January 31, 2014 1 Slides evolved from previous versions by Hussam Abu-Libdeh and David Slater Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting Vim: Tip of the day! Line numbers Displays line number in Vim: :set nu Hides line number in Vim: :set nonu Goes to line number: :line number Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting Counting wc How many lines of code are in my new awesome program? How many words are in this document? Good for bragging rights Word, Character, Line, and Byte count with wc wc -l : count the number of lines wc -w : count the number of words wc -m : count the number of characters wc -c : count the number of bytes Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting Sorting sort Sorts the lines of a text file alphabetically. sort -ru file sorts the file in reverse order and deletes duplicate lines. sort -n -k 2 -t : file sorts the file numerically by using the second column, separated by a colon Example Consider a file (numbers.txt) with the numbers 1, 5, 8, 11, 62 each on a separate line, then: $ sort numbers.txt $ sort numbers.txt -n 1 1 11 5 5 8 62 11 8 62 Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting uniq uniq uniq file - Discards all but one of successive identical lines uniq -c file - Prints the number of successive identical lines next to each line Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting Character manipulation! The Translate Command tr [options] <char_list1> [char_list2] Translate or delete characters char lists are strings of characters By default, searches for characters in char list1 and replaces them with the ones that occupy the same position in char list2 Example: tr 'AEIOU' 'aeiou' - changes all capital vowels to lower case vowels Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting Pipes and redirection tr only receives input from standard input (stdin) i.e. -
IBM Education Assistance for Z/OS V2R1
IBM Education Assistance for z/OS V2R1 Item: ASCII Unicode Option Element/Component: UNIX Shells and Utilities (S&U) Material is current as of June 2013 © 2013 IBM Corporation Filename: zOS V2R1 USS S&U ASCII Unicode Option Agenda ■ Trademarks ■ Presentation Objectives ■ Overview ■ Usage & Invocation ■ Migration & Coexistence Considerations ■ Presentation Summary ■ Appendix Page 2 of 19 © 2013 IBM Corporation Filename: zOS V2R1 USS S&U ASCII Unicode Option IBM Presentation Template Full Version Trademarks ■ See url http://www.ibm.com/legal/copytrade.shtml for a list of trademarks. Page 3 of 19 © 2013 IBM Corporation Filename: zOS V2R1 USS S&U ASCII Unicode Option IBM Presentation Template Full Presentation Objectives ■ Introduce the features and benefits of the new z/OS UNIX Shells and Utilities (S&U) support for working with ASCII/Unicode files. Page 4 of 19 © 2013 IBM Corporation Filename: zOS V2R1 USS S&U ASCII Unicode Option IBM Presentation Template Full Version Overview ■ Problem Statement –As a z/OS UNIX Shells & Utilities user, I want the ability to control the text conversion of input files used by the S&U commands. –As a z/OS UNIX Shells & Utilities user, I want the ability to run tagged shell scripts (tcsh scripts and SBCS sh scripts) under different SBCS locales. ■ Solution –Add –W filecodeset=codeset,pgmcodeset=codeset option on several S&U commands to enable text conversion – consistent with support added to vi and ex in V1R13. –Add –B option on several S&U commands to disable automatic text conversion – consistent with other commands that already have this override support. –Add new _TEXT_CONV environment variable to enable or disable text conversion. -
User's Manual
USER’S MANUAL USER’S > UniQTM UniQTM User’s Manual Ed.: 821003146 rev.H © 2016 Datalogic S.p.A. and its Group companies • All rights reserved. • Protected to the fullest extent under U.S. and international laws. • Copying or altering of this document is prohibited without express written consent from Datalogic S.p.A. • Datalogic and the Datalogic logo are registered trademarks of Datalogic S.p.A. in many countries, including the U.S. and the E.U. All other brand and product names mentioned herein are for identification purposes only and may be trademarks or registered trademarks of their respective owners. Datalogic shall not be liable for technical or editorial errors or omissions contained herein, nor for incidental or consequential damages resulting from the use of this material. Printed in Donnas (AO), Italy. ii SYMBOLS Symbols used in this manual along with their meaning are shown below. Symbols and signs are repeated within the chapters and/or sections and have the following meaning: Generic Warning: This symbol indicates the need to read the manual carefully or the necessity of an important maneuver or maintenance operation. Electricity Warning: This symbol indicates dangerous voltage associated with the laser product, or powerful enough to constitute an electrical risk. This symbol may also appear on the marking system at the risk area. Laser Warning: This symbol indicates the danger of exposure to visible or invisible laser radiation. This symbol may also appear on the marking system at the risk area. Fire Warning: This symbol indicates the danger of a fire when processing flammable materials. -
Ubuntu Server Guide Basic Installation Preparing to Install
Ubuntu Server Guide Welcome to the Ubuntu Server Guide! This site includes information on using Ubuntu Server for the latest LTS release, Ubuntu 20.04 LTS (Focal Fossa). For an offline version as well as versions for previous releases see below. Improving the Documentation If you find any errors or have suggestions for improvements to pages, please use the link at thebottomof each topic titled: “Help improve this document in the forum.” This link will take you to the Server Discourse forum for the specific page you are viewing. There you can share your comments or let us know aboutbugs with any page. PDFs and Previous Releases Below are links to the previous Ubuntu Server release server guides as well as an offline copy of the current version of this site: Ubuntu 20.04 LTS (Focal Fossa): PDF Ubuntu 18.04 LTS (Bionic Beaver): Web and PDF Ubuntu 16.04 LTS (Xenial Xerus): Web and PDF Support There are a couple of different ways that the Ubuntu Server edition is supported: commercial support and community support. The main commercial support (and development funding) is available from Canonical, Ltd. They supply reasonably- priced support contracts on a per desktop or per-server basis. For more information see the Ubuntu Advantage page. Community support is also provided by dedicated individuals and companies that wish to make Ubuntu the best distribution possible. Support is provided through multiple mailing lists, IRC channels, forums, blogs, wikis, etc. The large amount of information available can be overwhelming, but a good search engine query can usually provide an answer to your questions.