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==The Linux Command Line==
===Software Carpentry's Unix Shell Lesson===
The Linux command line provides a way to type commands in a text terminal to perform actions on the system you are connected to, either locally or remotely. Linux supports multiple "shells" which are command interpreters. While each shell has its own special features, they tend to have a lot of overlap so it is fairly easy to become acclimated with a new shell.  The ELSA HPC cluster uses the '''bash''' shell [[Wikipedia:Bash_(Unix_shell)|(<u>B</u>ourne <u>A</u>gain <u>Sh</u>ell)]] with is currently the very command and popular shell. Other shells include the original [[Wikipedia:Bourne_shell|Bourne Shell]], [[Wikipedia:Tcsh|Tcsh]], [[Wikipedia:KornShell|KornShell]] and [[Wikipedia:Z_shell|Z Shell]].
[https://software-carpentry.org/ Software Carpentry] focuses on teaching researchers the computing skills they need to get more done in less time and with less pain. Their lesson on the Unix Shell is excellent and will be linked here. Note that while they refer to it as Unix, it applies to its younger cousin Linux as well.


===Command Structure===
::[http://swcarpentry.github.io/shell-novice/ The Unix Shell Lesson]


The basic format of the is <code>command options arguments</code> where <code>options</code> and <code>arguments</code> may either be optional or required depending on the command being run. Command <code>options</code> begin with a <code>-</code> or <code>--</code> to indicate they are options, not arguments.
::[http://swcarpentry.github.io/shell-novice/reference/The Unix Shell Summary of Basic Commands Reference]


Let's look at some real-life examples:
===Ryan's Tutorials===
[https://ryanstutorials.net/ Ryan's Tutorials] is also has some excellent tutorials. Two relevant tutorials are linked below.


* <p><code>ls -l</code>
::[https://ryanstutorials.net/linuxtutorial/ Linux Tutorial]
: This command <code>ls</code> lists files while the optional <code>-l</code> (that's a small "L") argument tells the command to do a long listing. A long listing includes the file permissions, owners, group and other info.</p>
::[https://ryanstutorials.net/bash-scripting-tutorial/ Bash Scripting Tutorial]
<br>
 
* <p><code>ls myfile</code>
: This <code>ls</code> doesn't include any options but does include an argument <code>myfile</code>.  This will list the file <code>myfile</code> to the terminal if it exists in the current directory. If not, you'll get a message such as <code>ls: cannot access myfile: No such file or directory</code> instead.</p>
<br>
 
* <p><code>ls -l myfile</code>
: In this next example, we combine command, options and arguments. This will list the file to the terminal with the file permissions, owners, etc. if it exists in the current directory.</p>
<br>
 
* <p><code>ls -lh myfile yourfile</code>
: In this final example, multiple options and arguments are specified. Not all commands have multiple options or allow multiple arguments, but the <code>ls</code> command does. The <code>-lh</code> combined options tell the <code>ls</code> command to not only show all the additional information about the files but convert any the output (e.g. the file size) to "human readable" format. If multiple arguments are permitted, the command applies to all that are specified.  This command could also have been specified with the options listed separately as <code>ls -l -h myfile yourfile</code>.</p>
<br>


===On-line Manual Pages===
===On-line Manual Pages===

Revision as of 13:07, 16 May 2019

Software Carpentry's Unix Shell Lesson

Software Carpentry focuses on teaching researchers the computing skills they need to get more done in less time and with less pain. Their lesson on the Unix Shell is excellent and will be linked here. Note that while they refer to it as Unix, it applies to its younger cousin Linux as well.

The Unix Shell Lesson
Unix Shell Summary of Basic Commands Reference

Ryan's Tutorials

Ryan's Tutorials is also has some excellent tutorials. Two relevant tutorials are linked below.

Linux Tutorial
Bash Scripting Tutorial

On-line Manual Pages

Linux consists of thousands of commands. While the syntax is common among most of them as command options arguments, it may be daunting to remember the various options for each command. Options don't necessary represent the same thing between commands. For example, the -i option means different things in the ls command and the grep command. To eliminate the need to keep a thick Linux command "bible" next to you at all times, the system provides "manual pages" on-line that can be called up as needed. These are called man pages in Linux lingo. You use the man command to bring the manual pages for a command you provide as an argument, e.g. man ls.

$ man cat 

CAT(1)                                                            User Commands                                                           CAT(1)



NAME
       cat - concatenate files and print on the standard output

SYNOPSIS
       cat [OPTION]... [FILE]...

DESCRIPTION
       Concatenate FILE(s), or standard input, to standard output.

       -A, --show-all
              equivalent to -vET

       -b, --number-nonblank
              number nonempty output lines, overrides -n

       -e     equivalent to -vE

       -E, --show-ends
              display $ at end of each line

       -n, --number
              number all output lines

       -s, --squeeze-blank
              suppress repeated empty output lines

       -t     equivalent to -vT

       -T, --show-tabs
              display TAB characters as ^I

       -u     (ignored)

       -v, --show-nonprinting
              use ^ and M- notation, except for LFD and TAB

       --help display this help and exit

       --version
              output version information and exit

       With no FILE, or when FILE is -, read standard input.

EXAMPLES
       cat f - g
              Output f's contents, then standard input, then g's contents.

       cat    Copy standard input to standard output.

       GNU coreutils online help: <http://www.gnu.org/software/coreutils/> Report cat translation bugs to <http://translationproject.org/team/>

AUTHOR
       Written by Torbjorn Granlund and Richard M. Stallman.

COPYRIGHT
       Copyright © 2013 Free Software Foundation, Inc.  License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to the extent permitted by law.

SEE ALSO
       tac(1)

       The  full documentation for cat is maintained as a Texinfo manual.  If the info and cat programs are properly installed at your site, the
       command

              info coreutils 'cat invocation'

       should give you access to the complete manual.



GNU coreutils 8.22                                                November 2015                                                           CAT(1)

Orthogonality

Manipulating Files

Additional Resources

Below are additional resources for learning the Linux command-line. The Lynda.com resource below may require you to provide your TCNJ login information to access.

  • Lynda.com course titled Learning Linux Command Line. In the "What do you already know?" section, only watch the "A very quick intro to Linux" lesson before skipping down to section 2 "What is the command line?" Watch all the videos in sections 2, 3 and 4.
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