Cloud Computing and Unix: an Introduction
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At—At, Batch—Execute Commands at a Later Time
at—at, batch—execute commands at a later time at [–csm] [–f script] [–qqueue] time [date] [+ increment] at –l [ job...] at –r job... batch at and batch read commands from standard input to be executed at a later time. at allows you to specify when the commands should be executed, while jobs queued with batch will execute when system load level permits. Executes commands read from stdin or a file at some later time. Unless redirected, the output is mailed to the user. Example A.1 1 at 6:30am Dec 12 < program 2 at noon tomorrow < program 3 at 1945 pm August 9 < program 4 at now + 3 hours < program 5 at 8:30am Jan 4 < program 6 at -r 83883555320.a EXPLANATION 1. At 6:30 in the morning on December 12th, start the job. 2. At noon tomorrow start the job. 3. At 7:45 in the evening on August 9th, start the job. 4. In three hours start the job. 5. At 8:30 in the morning of January 4th, start the job. 6. Removes previously scheduled job 83883555320.a. awk—pattern scanning and processing language awk [ –fprogram–file ] [ –Fc ] [ prog ] [ parameters ] [ filename...] awk scans each input filename for lines that match any of a set of patterns specified in prog. Example A.2 1 awk '{print $1, $2}' file 2 awk '/John/{print $3, $4}' file 3 awk -F: '{print $3}' /etc/passwd 4 date | awk '{print $6}' EXPLANATION 1. Prints the first two fields of file where fields are separated by whitespace. 2. Prints fields 3 and 4 if the pattern John is found. -
A Brief Introduction to Unix-2019-AMS
Brief Intro to Linux/Unix Brief Intro to Unix (contd) A Brief Introduction to o Brief History of Unix o Compilers, Email, Text processing o Basics of a Unix session o Image Processing Linux/Unix – AMS 2019 o The Unix File System Pete Pokrandt o Working with Files and Directories o The vi editor UW-Madison AOS Systems Administrator o Your Environment [email protected] o Common Commands Twitter @PTH1 History of Unix History of Unix History of Unix o Created in 1969 by Kenneth Thompson and Dennis o Today – two main variants, but blended o It’s been around for a long time Ritchie at AT&T o Revised in-house until first public release 1977 o System V (Sun Solaris, SGI, Dec OSF1, AIX, o It was written by computer programmers for o 1977 – UC-Berkeley – Berkeley Software Distribution (BSD) linux) computer programmers o 1983 – Sun Workstations produced a Unix Workstation o BSD (Old SunOS, linux, Mac OSX/MacOS) o Case sensitive, mostly lowercase o AT&T unix -> System V abbreviations 1 Basics of a Unix Login Session Basics of a Unix Login Session Basics of a Unix Login Session o The Shell – the command line interface, o Features provided by the shell o Logging in to a unix session where you enter commands, etc n Create an environment that meets your needs n login: username n Some common shells n Write shell scripts (batch files) n password: tImpAw$ n Define command aliases (this Is my password At work $) Bourne Shell (sh) OR n Manipulate command history IHateHaving2changeMypasswordevery3weeks!!! C Shell (csh) n Automatically complete the command -
Unix Essentials (Pdf)
Unix Essentials Bingbing Yuan Next Hot Topics: Unix – Beyond Basics (Mon Oct 20th at 1pm) 1 Objectives • Unix Overview • Whitehead Resources • Unix Commands • BaRC Resources • LSF 2 Objectives: Hands-on • Parsing Human Body Index (HBI) array data Goal: Process a large data file to get important information such as genes of interest, sorting expression values, and subset the data for further investigation. 3 Advantages of Unix • Processing files with thousands, or millions, of lines How many reads are in my fastq file? Sort by gene name or expression values • Many programs run on Unix only Command-line tools • Automate repetitive tasks or commands Scripting • Other software, such as Excel, are not able to handle large files efficiently • Open Source 4 Scientific computing resources 5 Shared packages/programs https://tak.wi.mit.edu Request new packages/programs Installed packages/programs 6 Login • Requesting a tak account http://iona.wi.mit.edu/bio/software/unix/bioinfoaccount.php • Windows PuTTY or Cygwin Xming: setup X-windows for graphical display • Macs Access through Terminal 7 Connecting to tak for Windows Command Prompt user@tak ~$ 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 -
ECOGEO Workshop 2: Introduction to Env 'Omics
ECOGEO Workshop 2: Introduction to Env ‘Omics Unix and Bioinformatics Ben Tully (USC); Ken Youens-Clark (UA) Unix Commands pwd rm grep tail install ls ‘>’ sed cut cd cat nano top mkdir ‘<’ history screen touch ‘|’ $PATH ssh cp sort less df mv uniq head rsync/scp Unix Command Line 1. Open Terminal window Unix Command Line 2. Open Chrome and navigate to Unix tutorial at Protocols.io 3. Group: ECOGEO 4. Protocol: ECOGEO Workshop 2: Unix Module ! This will allow you to copy, paste Unix scripts into terminal window ! ECOGEO Protocols.io for making copy, paste easier Unix Command Line $ ls ls - lists items in the current directory Many commands have additional options that can be set by a ‘-’ $ ls -a Unix Command Line $ ls -a lists all files/directories, including hidden files ‘.’ $ ls -l lists the long format File Permissions | # Link | User | Group | Size | Last modified $ ls -lt lists the long format, but ordered by date last modified Unix Command Line Unix Command Line $ cd ecogeo/ cd - change directory List the contents of the current directory Move into the directory called unix List contents $ pwd pwd - present working directory Unix Command Line /home/c-debi/ecogeo/unix When were we in the directory home? Or c-debi? Or ecogeo? $ cd / Navigates to root directory List contents of root directory This where everything is stored in the computer All the commands we are running live in /bin Unix Command Line / root bin sys home mnt usr c-debi BioinfPrograms cdebi Desktop Downloads ecogeo unix assembly annotation etc Typical Unix Layout Unix Command Line Change directory to home Change directory to c-debi Change directory to ecogeo Change directory to unix List contents Change directory to data Change directory to root Unix Command Line Change directory to unix/data in one step $ cd /home/c-debi/ecogeo/unix/data Tab can be used to auto complete names $ cd . -
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 -
Student Number: Surname: Given Name
Computer Science 2211a Midterm Examination Sample Solutions 9 November 20XX 1 hour 40 minutes Student Number: Surname: Given name: Instructions/Notes: The examination has 35 questions on 9 pages, and a total of 110 marks. Put all answers on the question paper. This is a closed book exam. NO ELECTRONIC DEVICES OF ANY KIND ARE ALLOWED. 1. [4 marks] Which of the following Unix commands/utilities are filters? Correct answers are in blue. mkdir cd nl passwd grep cat chmod scriptfix mv 2. [1 mark] The Unix command echo HOME will print the contents of the environment variable whose name is HOME. True False 3. [1 mark] In C, the null character is another name for the null pointer. True False 4. [3 marks] The protection code for the file abc.dat is currently –rwxr--r-- . The command chmod a=x abc.dat is equivalent to the command: a. chmod 755 abc.dat b. chmod 711 abc.dat c. chmod 155 abc.dat d. chmod 111 abc.dat e. none of the above 5. [3 marks] The protection code for the file abc.dat is currently –rwxr--r-- . The command chmod ug+w abc.dat is equivalent to the command: a. chmod 766 abc.dat b. chmod 764 abc.dat c. chmod 754 abc.dat d. chmod 222 abc.dat e. none of the above 2 6. [3 marks] The protection code for def.dat is currently dr-xr--r-- , and the protection code for def.dat/ghi.dat is currently -r-xr--r-- . Give one or more chmod commands that will set the protections properly so that the owner of the two files will be able to delete ghi.dat using the command rm def.dat/ghi.dat chmod u+w def.dat or chmod –r u+w def.dat 7. -
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 -
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 -
Manipulating Files and Directories
MANIPULATING FILES AND DIRECTORIES At this point, we are ready for some real work! This chapter will introduce the following commands: z cp—Copy files and directories. z mv—Move/rename files and directories. z mkdir—Create directories. z rm—Remove files and directories. z ln—Create hard and symbolic links. These five commands are among the most frequently used Linux com- mands. They are used for manipulating both files and directories. Now, to be frank, some of the tasks performed by these commands are more easily done with a graphical file manager. With a file manager, we can drag and drop a file from one directory to another, cut and paste files, delete files, and so on. So why use these old command-line programs? www.it-ebooks.info The answer is power and flexibility. While it is easy to perform simple file manipulations with a graphical file manager, complicated tasks can be easier with the command-line programs. For example, how could we copy all the HTML files from one directory to another—but only those that do not exist in the destination directory or are newer than the versions in the destination directory? Pretty hard with a file manager. Pretty easy with the command line: cp -u *.html destination Wildcards Before we begin using our commands, we need to talk about the shell fea- ture that makes these commands so powerful. Because the shell uses file- names so much, it provides special characters to help you rapidly specify groups of filenames. These special characters are called wildcards. -
A Crash Course on UNIX
AA CCrraasshh CCoouurrssee oonn UUNNIIXX UNIX is an "operating system". Interface between user and data stored on computer. A Windows-style interface is not required. Many flavors of UNIX (and windows interfaces). Solaris, Mandrake, RedHat (fvwm, Gnome, KDE), ... Most UNIX users use "shells" (or "xterms"). UNIX windows systems do provide some Microsoft Windows functionality. TThhee SShheellll A shell is a command-line interface to UNIX. Also many flavors, e.g. sh, bash, csh, tcsh. The shell provides commands and functionality beyond the basic UNIX tools. E.g., wildcards, shell variables, loop control, etc. For this tutorial, examples use tcsh in RedHat Linux running Gnome. Differences are minor for the most part... BBaassiicc CCoommmmaannddss You need these to survive: ls, cd, cp, mkdir, mv. Typically these are UNIX (not shell) commands. They are actually programs that someone has written. Most commands such as these accept (or require) "arguments". E.g. ls -a [show all files, incl. "dot files"] mkdir ASTR688 [create a directory] cp myfile backup [copy a file] See the handout for a list of more commands. AA WWoorrdd AAbboouutt DDiirreeccttoorriieess Use cd to change directories. By default you start in your home directory. E.g. /home/dcr Handy abbreviations: Home directory: ~ Someone else's home directory: ~user Current directory: . Parent directory: .. SShhoorrttccuuttss To return to your home directory: cd To return to the previous directory: cd - In tcsh, with filename completion (on by default): Press TAB to complete filenames as you type. Press Ctrl-D to print a list of filenames matching what you have typed so far. Completion works with commands and variables too! Use ↑, ↓, Ctrl-A, & Ctrl-E to edit previous lines. -
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.