Practical Linux Examples: Exercises 1
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HEP Computing Part I Intro to UNIX/LINUX Adrian Bevan
HEP Computing Part I Intro to UNIX/LINUX Adrian Bevan Lectures 1,2,3 [email protected] 1 Lecture 1 • Files and directories. • Introduce a number of simple UNIX commands for manipulation of files and directories. • communicating with remote machines [email protected] 2 What is LINUX • LINUX is the operating system (OS) kernel. • Sitting on top of the LINUX OS are a lot of utilities that help you do stuff. • You get a ‘LINUX distribution’ installed on your desktop/laptop. This is a sloppy way of saying you get the OS bundled with lots of useful utilities/applications. • Use LINUX to mean anything from the OS to the distribution we are using. • UNIX is an operating system that is very similar to LINUX (same command names, sometimes slightly different functionalities of commands etc). – There are usually enough subtle differences between LINUX and UNIX versions to keep you on your toes (e.g. Solaris and LINUX) when running applications on multiple platforms …be mindful of this if you use other UNIX flavours. – Mac OS X is based on a UNIX distribution. [email protected] 3 Accessing a machine • You need a user account you should all have one by now • can then log in at the terminal (i.e. sit in front of a machine and type in your user name and password to log in to it). • you can also log in remotely to a machine somewhere else RAL SLAC CERN London FNAL in2p3 [email protected] 4 The command line • A user interfaces with Linux by typing commands into a shell. -
Modern Programming Languages CS508 Virtual University of Pakistan
Modern Programming Languages (CS508) VU Modern Programming Languages CS508 Virtual University of Pakistan Leaders in Education Technology 1 © Copyright Virtual University of Pakistan Modern Programming Languages (CS508) VU TABLE of CONTENTS Course Objectives...........................................................................................................................4 Introduction and Historical Background (Lecture 1-8)..............................................................5 Language Evaluation Criterion.....................................................................................................6 Language Evaluation Criterion...................................................................................................15 An Introduction to SNOBOL (Lecture 9-12).............................................................................32 Ada Programming Language: An Introduction (Lecture 13-17).............................................45 LISP Programming Language: An Introduction (Lecture 18-21)...........................................63 PROLOG - Programming in Logic (Lecture 22-26) .................................................................77 Java Programming Language (Lecture 27-30)..........................................................................92 C# Programming Language (Lecture 31-34) ...........................................................................111 PHP – Personal Home Page PHP: Hypertext Preprocessor (Lecture 35-37)........................129 Modern Programming Languages-JavaScript -
101 Useful Linux Commands - Haydenjames.Io
101 Useful Linux Commands - haydenjames.io Some of these commands require elevated permissions (sudo) to run. Enjoy! 1. Execute the previous command used: !! 2. Execute a previous command starting with a specific letter. Example: !s 3. Short way to copy or backup a file before you edit it. For example, copy nginx.conf cp nginx.conf{,.bak} 4. Toggle between current directory and last directory cd - 5. Move to parent (higher level) directory. Note the space! cd .. 6. Go to home directory cd ~ 7. Go to home directory cd $HOME 8. Go to home directory (when used alone) cd 9. Set permissions to 755. Corresponds to these permissions: (-rwx-r-x-r-x), arranged in this sequence: (owner-group-other) chmod 755 <filename> 10. Add execute permission to all users. chmod a+x <filename> 11. Changes ownership of a file or directory to . chown <username> 12. Make a backup copy of a file (named file.backup) cp <file> <file>.backup 13. Copy file1, use it to create file2 cp <file1> <file2> 14. Copy directory1 and all its contents (recursively) into directory2 cp -r <directory1> <directory2>/ 15. Display date date 16. Zero the sdb drive. You may want to use GParted to format the drive afterward. You need elevated permissions to run this (sudo). dd if=/dev/zero of=/dev/sdb 17. Display disk space usage df -h 18. Take detailed messages from OS and input to text file dmesg>dmesg.txt 19. Display a LOT of system information. I usually pipe output to less. You need elevated permissions to run this (sudo). -
Useful Tai Ls Dino
SCIENCE & NATURE Useful Tails Materials Pictures of a possum, horse, lizard, rattlesnake, peacock, fish, bird, and beaver What to do 1. Display the animal pictures so the children can see them. 2. Say the following sentences. Ask the children to guess the animal by the usefulness of its tail. I use my tail for hanging upside down. (possum) I use my tail as a fly swatter. (horse) When my tail breaks off, I grow a new one. (lizard) I shake my noisy tail when I am about to strike. (rattlesnake) My tail opens like a beautiful fan. (peacock) I use my tail as a propeller. I cannot swim without it. (fish) I can’t fly without my tail. (bird) I use my powerful tail for building. (beaver) More to do Ask the children if they can name other animals that have tails. Ask them how these animals’Downloaded tails might by [email protected] useful. from Games: Cut out the tailsProFilePlanner.com of each of the animals. Encourage the children to pin the tails on the pictures (like “Pin the Tail on the Donkey”). Dotti Enderle, Richmond, TX Dino Dig Materials Plastic or rubber dinosaurs or bones Sand Wide-tip, medium-sized paintbrushes Plastic sand shovels Small plastic buckets Clipboards Paper Pencil or pens 508 The GIANT Encyclopedia of Preschool Activities for Four-Year-Olds Downloaded by [email protected] from ProFilePlanner.com SCIENCE & NATURE What to do 1. Beforehand, hide plastic or rubber dinosaurs or bones in the sand. 2. Give each child a paintbrush, shovel, and bucket. 3. -
“Linux at the Command Line” Don Johnson of BU IS&T We’Ll Start with a Sign in Sheet
“Linux at the Command Line” Don Johnson of BU IS&T We’ll start with a sign in sheet. We’ll end with a class evaluation. We’ll cover as much as we can in the time allowed; if we don’t cover everything, you’ll pick it up as you continue working with Linux. This is a hands-on, lab class; ask questions at any time. Commands for you to type are in BOLD The Most Common O/S Used By BU Researchers When Working on a Server or Computer Cluster Linux is a Unix clone begun in 1991 and written from scratch by Linus Torvalds with assistance from a loosely-knit team of hackers across the Net. 64% of the world’s servers run some variant of Unix or Linux. The Android phone and the Kindle run Linux. a set of small Linux is an O/S core programs written by written by Linus Richard Stallman and Torvalds and others others. They are the AND GNU utilities. http://www.gnu.org/ Network: ssh, scp Shells: BASH, TCSH, clear, history, chsh, echo, set, setenv, xargs System Information: w, whoami, man, info, which, free, echo, date, cal, df, free Command Information: man, info Symbols: |, >, >>, <, ;, ~, ., .. Filters: grep, egrep, more, less, head, tail Hotkeys: <ctrl><c>, <ctrl><d> File System: ls, mkdir, cd, pwd, mv, touch, file, find, diff, cmp, du, chmod, find File Editors: gedit, nedit You need a “xterm” emulation – software that emulates an “X” terminal and that connects using the “SSH” Secure Shell protocol. ◦ Windows Use StarNet “X-Win32:” http://www.bu.edu/tech/support/desktop/ distribution/xwindows/xwin32/ ◦ Mac OS X “Terminal” is already installed Why? Darwin, the system on which Apple's Mac OS X is built, is a derivative of 4.4BSD-Lite2 and FreeBSD. -
Shell Variables
Shell Using the command line Orna Agmon ladypine at vipe.technion.ac.il Haifux Shell – p. 1/55 TOC Various shells Customizing the shell getting help and information Combining simple and useful commands output redirection lists of commands job control environment variables Remote shell textual editors textual clients references Shell – p. 2/55 What is the shell? The shell is the wrapper around the system: a communication means between the user and the system The shell is the manner in which the user can interact with the system through the terminal. The shell is also a script interpreter. The simplest script is a bunch of shell commands. Shell scripts are used in order to boot the system. The user can also write and execute shell scripts. Shell – p. 3/55 Shell - which shell? There are several kinds of shells. For example, bash (Bourne Again Shell), csh, tcsh, zsh, ksh (Korn Shell). The most important shell is bash, since it is available on almost every free Unix system. The Linux system scripts use bash. The default shell for the user is set in the /etc/passwd file. Here is a line out of this file for example: dana:x:500:500:Dana,,,:/home/dana:/bin/bash This line means that user dana uses bash (located on the system at /bin/bash) as her default shell. Shell – p. 4/55 Starting to work in another shell If Dana wishes to temporarily use another shell, she can simply call this shell from the command line: [dana@granada ˜]$ bash dana@granada:˜$ #In bash now dana@granada:˜$ exit [dana@granada ˜]$ bash dana@granada:˜$ #In bash now, going to hit ctrl D dana@granada:˜$ exit [dana@granada ˜]$ #In original shell now Shell – p. -
Exercise I: Basic Unix for Manipulating NGS Data
Exercise I: Basic Unix for manipulating NGS data C. Hahn, July 2014 The purpose of this exercise is to practice manipulating NGS (Next Generation Sequencing) data using simple but incredibly powerful Unix commands. Try to solve the below tasks using your Unix skills. Do not hesitate to consult Google for help!! Hints for every task can be found on page 3 below. Possible solutions are suggested on page 4. 1. Download the testdata from https://www.dropbox.com/s/wcanmej6z03yfmt/testdata_1.tar?dl=0. Create a directory (exercise_1) in your home directory and copy the archive testdata.tar from ~/Downloads/ to this directory. 2. Decompress the archive. 3. Examine the content of the data files. For basic information on fastq format please visit: http://en.wikipedia.org/wiki/FASTQ_format. With this information try to interpret the content of your data files. Do you Know what all the lines represent? a) Which quality encoding (which offset) do these files use? b) What is the header of the third read in the file? Is this a single-end (forward) or a paired-end (reverse) read? c) What is the header of the last read in the file? Is this a forward or reverse read? 4. How many lines does the file have? 5. How many reads does the file contain? 6. How many single-end (“se” also referred to as forward reads) reads and how many paired-end (“pe” also reverse reads) reads does the file contain? 7. Extract all se/pe reads and write them to separate files testdata_1.fastq and testdata_2.fastq. -
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 -
Official Standard of the Portuguese Water Dog General Appearance
Page 1 of 3 Official Standard of the Portuguese Water Dog General Appearance: Known for centuries along Portugal's coast, this seafaring breed was prized by fishermen for a spirited, yet obedient nature, and a robust, medium build that allowed for a full day's work in and out of the water. The Portuguese Water Dog is a swimmer and diver of exceptional ability and stamina, who aided his master at sea by retrieving broken nets, herding schools of fish, and carrying messages between boats and to shore. He is a loyal companion and alert guard. This highly intelligent utilitarian breed is distinguished by two coat types, either curly or wavy; an impressive head of considerable breadth and well proportioned mass; a ruggedly built, well-knit body; and a powerful, thickly based tail, carried gallantly or used purposefully as a rudder. The Portuguese Water Dog provides an indelible impression of strength, spirit, and soundness. Size, Proportion, Substance: Size - Height at the withers - Males, 20 to 23 inches. The ideal is 22 inches. Females, 17 to 21 inches. The ideal is 19 inches. Weight - For males, 42 to 60 pounds; for females, 35 to 50 pounds. Proportion - Off square; slightly longer than tall when measured from prosternum to rearmost point of the buttocks, and from withers to ground. Substance - Strong, substantial bone; well developed, neither refined nor coarse, and a solidly built, muscular body. Head: An essential characteristic; distinctively large, well proportioned and with exceptional breadth of topskull. Expression - Steady, penetrating, and attentive. Eyes - Medium in size; set well apart, and a bit obliquely. -
UNIX (Solaris/Linux) Quick Reference Card Logging in Directory Commands at the Login: Prompt, Enter Your Username
UNIX (Solaris/Linux) QUICK REFERENCE CARD Logging In Directory Commands At the Login: prompt, enter your username. At the Password: prompt, enter ls Lists files in current directory your system password. Linux is case-sensitive, so enter upper and lower case ls -l Long listing of files letters as required for your username, password and commands. ls -a List all files, including hidden files ls -lat Long listing of all files sorted by last Exiting or Logging Out modification time. ls wcp List all files matching the wildcard Enter logout and press <Enter> or type <Ctrl>-D. pattern Changing your Password ls dn List files in the directory dn tree List files in tree format Type passwd at the command prompt. Type in your old password, then your new cd dn Change current directory to dn password, then re-enter your new password for verification. If the new password cd pub Changes to subdirectory “pub” is verified, your password will be changed. Many systems age passwords; this cd .. Changes to next higher level directory forces users to change their passwords at predetermined intervals. (previous directory) cd / Changes to the root directory Changing your MS Network Password cd Changes to the users home directory cd /usr/xx Changes to the subdirectory “xx” in the Some servers maintain a second password exclusively for use with Microsoft windows directory “usr” networking, allowing you to mount your home directory as a Network Drive. mkdir dn Makes a new directory named dn Type smbpasswd at the command prompt. Type in your old SMB passwword, rmdir dn Removes the directory dn (the then your new password, then re-enter your new password for verification. -
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.