Essentials of the Linux Command Line
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Windows Command Prompt Cheatsheet
Windows Command Prompt Cheatsheet - Command line interface (as opposed to a GUI - graphical user interface) - Used to execute programs - Commands are small programs that do something useful - There are many commands already included with Windows, but we will use a few. - A filepath is where you are in the filesystem • C: is the C drive • C:\user\Documents is the Documents folder • C:\user\Documents\hello.c is a file in the Documents folder Command What it Does Usage dir Displays a list of a folder’s files dir (shows current folder) and subfolders dir myfolder cd Displays the name of the current cd filepath chdir directory or changes the current chdir filepath folder. cd .. (goes one directory up) md Creates a folder (directory) md folder-name mkdir mkdir folder-name rm Deletes a folder (directory) rm folder-name rmdir rmdir folder-name rm /s folder-name rmdir /s folder-name Note: if the folder isn’t empty, you must add the /s. copy Copies a file from one location to copy filepath-from filepath-to another move Moves file from one folder to move folder1\file.txt folder2\ another ren Changes the name of a file ren file1 file2 rename del Deletes one or more files del filename exit Exits batch script or current exit command control echo Used to display a message or to echo message turn off/on messages in batch scripts type Displays contents of a text file type myfile.txt fc Compares two files and displays fc file1 file2 the difference between them cls Clears the screen cls help Provides more details about help (lists all commands) DOS/Command Prompt help command commands Source: https://technet.microsoft.com/en-us/library/cc754340.aspx. -
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 -
Mac Keyboard Shortcuts Cut, Copy, Paste, and Other Common Shortcuts
Mac keyboard shortcuts By pressing a combination of keys, you can do things that normally need a mouse, trackpad, or other input device. To use a keyboard shortcut, hold down one or more modifier keys while pressing the last key of the shortcut. For example, to use the shortcut Command-C (copy), hold down Command, press C, then release both keys. Mac menus and keyboards often use symbols for certain keys, including the modifier keys: Command ⌘ Option ⌥ Caps Lock ⇪ Shift ⇧ Control ⌃ Fn If you're using a keyboard made for Windows PCs, use the Alt key instead of Option, and the Windows logo key instead of Command. Some Mac keyboards and shortcuts use special keys in the top row, which include icons for volume, display brightness, and other functions. Press the icon key to perform that function, or combine it with the Fn key to use it as an F1, F2, F3, or other standard function key. To learn more shortcuts, check the menus of the app you're using. Every app can have its own shortcuts, and shortcuts that work in one app may not work in another. Cut, copy, paste, and other common shortcuts Shortcut Description Command-X Cut: Remove the selected item and copy it to the Clipboard. Command-C Copy the selected item to the Clipboard. This also works for files in the Finder. Command-V Paste the contents of the Clipboard into the current document or app. This also works for files in the Finder. Command-Z Undo the previous command. You can then press Command-Shift-Z to Redo, reversing the undo command. -
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). -
This Document Explains How to Copy Ondemand5 Data to Your Hard Drive
Copying Your Repair DVD Data To Your Hard Drive Introduction This document explains how to copy OnDemand5 Repair data to your hard drive, and how to configure your OnDemand software appropriately. The document is intended for your network professional as a practical guide for implementing Mitchell1’s quarterly updates. The document provides two methods; one using the Xcopy command in a DOS window, and the other using standard Windows Copy and Paste functionality. Preparing your System You will need 8 Gigabytes of free space per DVD to be copied onto a hard drive. Be sure you have the necessary space before beginning this procedure. Turn off screen savers, power down options or any other program that may interfere with this process. IMPORTANT NOTICE – USE AT YOUR OWN RISK: This information is provided as a courtesy to assist those who desire to copy their DVD disks to their hard drive. Minimal technical assistance is available for this procedure. It is not recommended due to the high probability of failure due to DVD drive/disk read problems, over heating, hard drive write errors and memory overrun issues. This procedure is very detailed and should only be performed by users who are very familiar with Windows and/or DOS commands. Novice computers users should not attempt this procedure. Copying Repair data from a DVD is a time-consuming process. Depending on the speed of your processor and/or network, could easily require two or more hours per disk. For this reason, we recommend that you perform the actual copying of data during non-business evening or weekend hours. -
“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. -
Dell EMC Powerstore CLI Guide
Dell EMC PowerStore CLI Guide May 2020 Rev. A01 Notes, cautions, and warnings NOTE: A NOTE indicates important information that helps you make better use of your product. CAUTION: A CAUTION indicates either potential damage to hardware or loss of data and tells you how to avoid the problem. WARNING: A WARNING indicates a potential for property damage, personal injury, or death. © 2020 Dell Inc. or its subsidiaries. All rights reserved. Dell, EMC, and other trademarks are trademarks of Dell Inc. or its subsidiaries. Other trademarks may be trademarks of their respective owners. Contents Additional Resources.......................................................................................................................4 Chapter 1: Introduction................................................................................................................... 5 Overview.................................................................................................................................................................................5 Use PowerStore CLI in scripts.......................................................................................................................................5 Set up the PowerStore CLI client........................................................................................................................................5 Install the PowerStore CLI client.................................................................................................................................. -
Powerview Command Reference
PowerView Command Reference TRACE32 Online Help TRACE32 Directory TRACE32 Index TRACE32 Documents ...................................................................................................................... PowerView User Interface ............................................................................................................ PowerView Command Reference .............................................................................................1 History ...................................................................................................................................... 12 ABORT ...................................................................................................................................... 13 ABORT Abort driver program 13 AREA ........................................................................................................................................ 14 AREA Message windows 14 AREA.CLEAR Clear area 15 AREA.CLOSE Close output file 15 AREA.Create Create or modify message area 16 AREA.Delete Delete message area 17 AREA.List Display a detailed list off all message areas 18 AREA.OPEN Open output file 20 AREA.PIPE Redirect area to stdout 21 AREA.RESet Reset areas 21 AREA.SAVE Save AREA window contents to file 21 AREA.Select Select area 22 AREA.STDERR Redirect area to stderr 23 AREA.STDOUT Redirect area to stdout 23 AREA.view Display message area in AREA window 24 AutoSTOre .............................................................................................................................. -
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. -
NETSTAT Command
NETSTAT Command | NETSTAT Command | Use the NETSTAT command to display network status of the local host. | | ┌┐────────────── | 55──NETSTAT─────6─┤ Option ├─┴──┬────────────────────────────────── ┬ ─ ─ ─ ────────────────────────────────────────5% | │┌┐───────────────────── │ | └─(──SELect───6─┤ Select_String ├─┴ ─ ┘ | Option: | ┌┐─COnn────── (1, 2) ──────────────── | ├──┼─────────────────────────── ┼ ─ ──────────────────────────────────────────────────────────────────────────────┤ | ├─ALL───(2)──────────────────── ┤ | ├─ALLConn─────(1, 2) ────────────── ┤ | ├─ARp ipaddress───────────── ┤ | ├─CLients─────────────────── ┤ | ├─DEvlinks────────────────── ┤ | ├─Gate───(3)─────────────────── ┤ | ├─┬─Help─ ┬─ ───────────────── ┤ | │└┘─?──── │ | ├─HOme────────────────────── ┤ | │┌┐─2ð────── │ | ├─Interval─────(1, 2) ─┼───────── ┼─ ┤ | │└┘─seconds─ │ | ├─LEVel───────────────────── ┤ | ├─POOLsize────────────────── ┤ | ├─SOCKets─────────────────── ┤ | ├─TCp serverid───(1) ─────────── ┤ | ├─TELnet───(4)───────────────── ┤ | ├─Up──────────────────────── ┤ | └┘─┤ Command ├───(5)──────────── | Command: | ├──┬─CP cp_command───(6) ─ ┬ ────────────────────────────────────────────────────────────────────────────────────────┤ | ├─DELarp ipaddress─ ┤ | ├─DRop conn_num──── ┤ | └─RESETPool──────── ┘ | Select_String: | ├─ ─┬─ipaddress────(3) ┬ ─ ───────────────────────────────────────────────────────────────────────────────────────────┤ | ├─ldev_num─────(4) ┤ | └─userid────(2) ─── ┘ | Notes: | 1 Only ALLCON, CONN and TCP are valid with INTERVAL. | 2 The userid -
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