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<title>Software Carpentry: The Unix Shell</title>
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<h1 class="title">The Unix Shell</h1>
<h2 class="subtitle">Reference</h2>
<h2 id="introducing-the-shell"><a href="00-intro.html">Introducing the Shell</a></h2>
<ul>
<li>A shell is a program whose primary purpose is to read commands and run other programs.</li>
<li>The shell’s main advantages are its high action-to-keystroke ratio, its support for automating repetitive tasks, and that it can be used to access networked machines.</li>
<li>The shell’s main disadvantages are its primarily textual nature and how cryptic its commands and operation can be.</li>
</ul>
<h2 id="files-and-directories"><a href="01-filedir.html">Files and Directories</a></h2>
<ul>
<li>The file system is responsible for managing information on the disk.</li>
<li>Information is stored in files, which are stored in directories (folders).</li>
<li>Directories can also store other directories, which forms a directory tree.</li>
<li><code>cd path</code> changes the current working directory.</li>
<li><code>ls path</code> prints a listing of a specific file or directory; <code>ls</code> on its own lists the current working directory.</li>
<li><code>pwd</code> prints the user’s current working directory.</li>
<li><code>whoami</code> shows the user’s current identity.</li>
<li><code>/</code> on its own is the root directory of the whole file system.</li>
<li>A relative path specifies a location starting from the current location.</li>
<li>An absolute path specifies a location from the root of the file system.</li>
<li>Directory names in a path are separated with ‘/’ on Unix, but ‘\’ on Windows.</li>
<li>‘..’ means “the directory above the current one”; ‘.’ on its own means “the current directory”.</li>
<li>Most files’ names are <code>something.extension</code>. The extension isn’t required, and doesn’t guarantee anything, but is normally used to indicate the type of data in the file.</li>
<li>Most commands take options (flags) which begin with a ‘-’.</li>
</ul>
<h2 id="creating-things"><a href="02-create.html">Creating Things</a></h2>
<ul>
<li><code>cp old new</code> copies a file.</li>
<li><code>mkdir path</code> creates a new directory.</li>
<li><code>mv old new</code> moves (renames) a file or directory.</li>
<li><code>rm path</code> removes (deletes) a file.</li>
<li><code>rmdir path</code> removes (deletes) an empty directory.</li>
<li>Unix documentation uses ‘^A’ to mean “control-A”.</li>
<li>The shell does not have a trash bin: once something is deleted, it’s really gone.</li>
<li>Nano is a very simple text editor — please use something else for real work.</li>
</ul>
<h2 id="pipes-and-filters"><a href="03-pipefilter.html">Pipes and Filters</a></h2>
<ul>
<li><code>cat</code> displays the contents of its inputs.</li>
<li><code>head</code> displays the first few lines of its input.</li>
<li><code>tail</code> displays the last few lines of its input.</li>
<li><code>sort</code> sorts its inputs.</li>
<li><code>wc</code> counts lines, words, and characters in its inputs.</li>
<li><code>command > file</code> redirects a command’s output to a file.</li>
<li><code>first | second</code> is a pipeline: the output of the first command is used as the input to the second.</li>
<li>The best way to use the shell is to use pipes to combine simple single-purpose programs (filters).</li>
</ul>
<h2 id="loops"><a href="04-loop.html">Loops</a></h2>
<ul>
<li>A <code>for</code> loop repeats commands once for every thing in a list.</li>
<li>Every <code>for</code> loop needs a variable to refer to the current “thing”.</li>
<li>Use <code>$name</code> to expand a variable (i.e., get its value).</li>
<li>Do not use spaces, quotes, or wildcard characters such as ’*‘or’?’ in filenames, as it complicates variable expansion.</li>
<li>Give files consistent names that are easy to match with wildcard patterns to make it easy to select them for looping.</li>
<li>Use the up-arrow key to scroll up through previous commands to edit and repeat them.</li>
<li>Use <code>history</code> to display recent commands, and <code>!number</code> to repeat a command by number.</li>
</ul>
<h2 id="shell-scripts"><a href="05-script.html">Shell Scripts</a></h2>
<ul>
<li>Save commands in files (usually called shell scripts) for re-use.</li>
<li><code>bash filename</code> runs the commands saved in a file.</li>
<li><code>$*</code> refers to all of a shell script’s command-line parameters.</li>
<li><code>$1</code>, <code>$2</code>, etc., refer to specified command-line parameters.</li>
<li>Place variables in quotes if the values might have spaces in them.</li>
<li>Letting users decide what files to process is more flexible and more consistent with built-in Unix commands.</li>
</ul>
<h2 id="finding-things"><a href="06-find.html">Finding Things</a></h2>
<ul>
<li><code>find</code> finds files with specific properties that match patterns.</li>
<li><code>grep</code> selects lines in files that match patterns.</li>
<li><code>man command</code> displays the manual page for a given command.</li>
<li><code>*</code> matches zero or more characters in a filename, so <code>*.txt</code> matches all files ending in <code>.txt</code>.</li>
<li><code>?</code> matches any single character in a filename, so <code>?.txt</code> matches <code>a.txt</code> but not <code>any.txt</code>.</li>
<li><code>$(command)</code> inserts a command’s output in place.</li>
<li><code>man command</code> displays the manual page for a given command.</li>
</ul>
<h2 id="glossary">Glossary</h2>
<dl>
<dt><span id="absolute-path">absolute path</span></dt>
<dd>A <a href="#path">path</a> that refers to a particular location in a file system. Absolute paths are usually written with respect to the file system’s <a href="#root-directory">root directory</a>, and begin with either “/” (on Unix) or “\” (on Microsoft Windows). See also: <a href="#relative-path">relative path</a>.
</dd>
<dt><span id="argument">argument</span></dt>
<dd>A value given to a function or program when it runs. The term is often used interchangeably (and inconsistently) with <a href="#parameter">parameter</a>.
</dd>
<dt><span id="command-shell">command shell</span></dt>
<dd>See <a href="#shell">shell</a>
</dd>
<dt><span id="command-line-interface">command-line interface</span></dt>
<dd>An interface based on typing commands, usually at a <a href="#read-evaluate-print-loop">REPL</a>. See also: <a href="#graphical-user-interface">graphical user interface</a>.
</dd>
<dt><span id="comment">comment</span></dt>
<dd>A remark in a program that is intended to help human readers understand what is going on, but is ignored by the computer. Comments in Python, R, and the Unix shell start with a <code>#</code> character and run to the end of the line; comments in SQL start with <code>--</code>, and other languages have other conventions.
</dd>
<dt><span id="current-working-directory">current working directory</span></dt>
<dd>The directory that <a href="#relative-path">relative paths</a> are calculated from; equivalently, the place where files referenced by name only are searched for. Every <a href="#process">process</a> has a current working directory. The current working directory is usually referred to using the shorthand notation <code>.</code> (pronounced “dot”).
</dd>
<dt><span id="file-system">file system</span></dt>
<dd>A set of files, directories, and I/O devices (such as keyboards and screens). A file system may be spread across many physical devices, or many file systems may be stored on a single physical device; the <a href="#operating-system">operating system</a> manages access.
</dd>
<dt><span id="filename-extension">filename extension</span></dt>
<dd>The portion of a file’s name that comes after the final “.” character. By convention this identifies the file’s type: <code>.txt</code> means “text file”, <code>.png</code> means “Portable Network Graphics file”, and so on. These conventions are not enforced by most operating systems: it is perfectly possible to name an MP3 sound file <code>homepage.html</code>. Since many applications use filename extensions to identify the <a href="#mime-type">MIME type</a> of the file, misnaming files may cause those applications to fail.
</dd>
<dt><span id="filter">filter</span></dt>
<dd>A program that transforms a stream of data. Many Unix command-line tools are written as filters: they read data from <a href="#standard-input">standard input</a>, process it, and write the result to <a href="#standard-output">standard output</a>.
</dd>
<dt><span id="flag">flag</span></dt>
<dd>A terse way to specify an option or setting to a command-line program. By convention Unix applications use a dash followed by a single letter, such as <code>-v</code>, or two dashes followed by a word, such as <code>--verbose</code>, while DOS applications use a slash, such as <code>/V</code>. Depending on the application, a flag may be followed by a single argument, as in <code>-o /tmp/output.txt</code>.
</dd>
<dt><span id="for-loop">for loop</span></dt>
<dd>A loop that is executed once for each value in some kind of set, list, or range. See also: <a href="#while-loop">while loop</a>.
</dd>
<dt><span id="graphical-user-interface">graphical user interface</span></dt>
<dd>A graphical user interface, usually controlled by using a mouse. See also: <a href="#command-line-interface">command-line interface</a>.
</dd>
<dt><span id="home-directory">home directory</span></dt>
<dd>The default directory associated with an account on a computer system. By convention, all of a user’s files are stored in or below her home directory.
</dd>
<dt><span id="loop">loop</span></dt>
<dd>A set of instructions to be executed multiple times. Consists of a <a href="#loop-body">loop body</a> and (usually) a condition for exiting the loop. See also <a href="#for-loop">for loop</a> and <a href="#while-loop">while loop</a>.
</dd>
<dt><span id="loop-body">loop body</span></dt>
<dd>The set of statements or commands that are repeated inside a <a href="#for-loop">for loop</a> or <a href="#while-loop">while loop</a>.
</dd>
<dt><span id="mime-type">MIME type</span></dt>
<dd>MIME (Multi-Purpose Internet Mail Extensions) types describe different file types for exchange on the Internet, for example images, audio, and documents.
</dd>
<dt><span id="operating-system">operating system</span></dt>
<dd>Software that manages interactions between users, hardware, and software <a href="#process">processes</a>. Common examples are Linux, OS X, and Windows.
</dd>
<dt><span id="orthogonal">orthogonal</span></dt>
<dd>To have meanings or behaviors that are independent of each other. If a set of concepts or tools are orthogonal, they can be combined in any way.
</dd>
<dt><span id="parameter">parameter</span></dt>
<dd>A variable named in the function’s declaration that is used to hold a value passed into the call. The term is often used interchangeably (and inconsistently) with <a href="#argument">argument</a>.
</dd>
<dt><span id="parent-directory">parent directory</span></dt>
<dd>The directory that “contains” the one in question. Every directory in a file system except the <a href="#root-directory">root directory</a> has a parent. A directory’s parent is usually referred to using the shorthand notation <code>..</code> (pronounced “dot dot”).
</dd>
<dt><span id="path">path</span></dt>
<dd>A description that specifies the location of a file or directory within a <a href="#file-system">file system</a>. See also: <a href="#absolute-path">absolute path</a>, <a href="#relative-path">relative path</a>.
</dd>
<dt><span id="pipe">pipe</span></dt>
<dd>A connection from the output of one program to the input of another. When two or more programs are connected in this way, they are called a “pipeline”.
</dd>
<dt><span id="process">process</span></dt>
<dd>A running instance of a program, containing code, variable values, open files and network connections, and so on. Processes are the “actors” that the <a href="#operating-system">operating system</a> manages; it typically runs each process for a few milliseconds at a time to give the impression that they are executing simultaneously.
</dd>
<dt><span id="prompt">prompt</span></dt>
<dd>A character or characters display by a <a href="#read-evaluate-print-loop">REPL</a> to show that it is waiting for its next command.
</dd>
<dt><span id="quoting">quoting</span></dt>
<dd>(in the shell): Using quotation marks of various kinds to prevent the shell from interpreting special characters. For example, to pass the string <code>*.txt</code> to a program, it is usually necessary to write it as <code>'*.txt'</code> (with single quotes) so that the shell will not try to expand the <code>*</code> wildcard.
</dd>
<dt><span id="read-evaluate-print-loop">read-evaluate-print loop</span></dt>
<dd>(REPL): A <a href="#command-line-interface">command-line interface</a> that reads a command from the user, executes it, prints the result, and waits for another command.
</dd>
<dt><span id="redirect">redirect</span></dt>
<dd>To send a command’s output to a file rather than to the screen or another command, or equivalently to read a command’s input from a file.
</dd>
<dt><span id="regular-expression">regular expression</span></dt>
<dd>A pattern that specifies a set of character strings. REs are most often used to find sequences of characters in strings.
</dd>
<dt><span id="relative-path">relative path</span></dt>
<dd>A <a href="#path">path</a> that specifies the location of a file or directory with respect to the <a href="#current-working-directory">current working directory</a>. Any path that does not begin with a separator character (“/” or “\”) is a relative path. See also: <a href="#absolute-path">absolute path</a>.
</dd>
<dt><span id="root-directory">root directory</span></dt>
<dd>The top-most directory in a <a href="#file-system">file system</a>. Its name is “/” on Unix (including Linux and Mac OS X) and “\” on Microsoft Windows.
</dd>
<dt><span id="shell">shell</span></dt>
<dd>A <a href="#cli">command-line interface</a> such as Bash (the Bourne-Again Shell) or the Microsoft Windows DOS shell that allows a user to interact with the <a href="#operating-system">operating system</a>.
</dd>
<dt><span id="shell-script">shell script</span></dt>
<dd>A set of <a href="#shell">shell</a> commands stored in a file for re-use. A shell script is a program executed by the shell; the name “script” is used for historical reasons.
</dd>
<dt><span id="standard-input">standard input</span></dt>
<dd>A process’s default input stream. In interactive command-line applications, it is typically connected to the keyboard; in a <a href="#pipe">pipe</a>, it receives data from the <a href="#standard-output">standard output</a> of the preceding process.
</dd>
<dt><span id="standard-output">standard output</span></dt>
<dd>A process’s default output stream. In interactive command-line applications, data sent to standard output is displayed on the screen; in a <a href="#pipe">pipe</a>, it is passed to the <a href="#standard-input">standard input</a> of the next process.
</dd>
<dt><span id="sub-directory">sub-directory</span></dt>
<dd>A directory contained within another directory.
</dd>
<dt><span id="tab-completion">tab completion</span></dt>
<dd>A feature provided by many interactive systems in which pressing the Tab key triggers automatic completion of the current word or command.
</dd>
<dt><span id="variable">variable</span></dt>
<dd>A name in a program that is associated with a value or a collection of values.
</dd>
<dt><span id="while-loop">while loop</span></dt>
<dd>A loop that keeps executing as long as some condition is true. See also: <a href="#for-loop">for loop</a>.
</dd>
<dt><span id="wildcard">wildcard</span></dt>
<dd>A character used in pattern matching. In the Unix shell, the wildcard <code>*</code> matches zero or more characters, so that <code>*.txt</code> matches all files whose names end in <code>.txt</code>.
</dd>
</dl>
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