Shell Lessons for Librarians: Reference

Key Points

What is the shell?
  • the shell is powerful

  • the shell can be used to copy, move, and combine multiple files

  • use the command pwd to find out where you are in on your computer

  • use the command ls to list directory contents

  • use flags -l and -lh to guide the output of the ls command

  • use the command cd to move around your computer

  • use the man command to check the manual page

  • use the command mv to rename and move files.

  • use the command cp to create a file from an existing file.

  • use the command cat to combine more than one file of the same file type.

  • use the wildcards * and ? as place holders that delimit which files are to be manipulated by a given an action.

  • use the command echo to output text to the screen.

  • use the rm command to delete unwanted files, with caution.

Counting and mining with the shell
  • wc is a command that counts

  • use the wc command with the flags -w and -l to count the words and lines in a file or a series of files

  • use the redirector and structure > subdirectory/filename to save results into a subdirectory

  • use the grep command to search for instances of a string inside files

  • use grep with the -c flag to count instances of a string, the -i flag to return a case insensitive search for a string, the -v flag to exclude a string from the results, and -w to return a whole word only search

  • use --file=list.txt to use the file list.txt as the source of strings used in a query

  • combine these commands and flags to build complex queries in a way that suggests the potential for using the Unix shell to count and mine your research data and research projects

Working with free text
  • shell tools can be combined to powerful effect

Summary of Basic Commands

Action Files Folders
Inspect ls ls
View content cat ls
Navigate to   cd
Move mv mv
Copy cp cp -r
Create nano mkdir
Delete rm rmdir, rm -r


absolute path
A path that refers to a particular location in a file system. Absolute paths are usually written with respect to the file system’s root directory, and begin with either “/” (on Unix) or “\” (on Microsoft Windows). See also: relative path.
A value given to a function or program when it runs. The term is often used interchangeably (and inconsistently) with parameter.
command shell
See shell
command-line interface
An interface based on typing commands, usually at a REPL. See also: graphical user interface.
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 # character and run to the end of the line; comments in SQL start with --, and other languages have other conventions.
current working directory
The directory that relative paths are calculated from; equivalently, the place where files referenced by name only are searched for. Every process has a current working directory. The current working directory is usually referred to using the shorthand notation . (pronounced “dot”).
file system
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 operating system manages access.
filename extension
The portion of a file’s name that comes after the final “.” character. By convention this identifies the file’s type: .txt means “text file”, .png 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 homepage.html. Since many applications use filename extensions to identify the MIME type of the file, misnaming files may cause those applications to fail.
A program that transforms a stream of data. Many Unix command-line tools are written as filters: they read data from standard input, process it, and write the result to standard output.
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 -v, or two dashes followed by a word, such as --verbose, while DOS applications use a slash, such as /V. Depending on the application, a flag may be followed by a single argument, as in -o /tmp/output.txt.
for loop
A loop that is executed once for each value in some kind of set, list, or range. See also: while loop.
graphical user interface
A graphical user interface, usually controlled by using a mouse. See also: command-line interface.
home directory
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.
A set of instructions to be executed multiple times. Consists of a loop body and (usually) a condition for exiting the loop. See also for loop and while loop.
loop body
The set of statements or commands that are repeated inside a for loop or while loop.
MIME type
MIME (Multi-Purpose Internet Mail Extensions) types describe different file types for exchange on the Internet, for example images, audio, and documents.
operating system
Software that manages interactions between users, hardware, and software processes. Common examples are Linux, OS X, and Windows.
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.
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 argument.
parent directory
The directory that “contains” the one in question. Every directory in a file system except the root directory has a parent. A directory’s parent is usually referred to using the shorthand notation .. (pronounced “dot dot”).
A description that specifies the location of a file or directory within a file system. See also: absolute path, relative path.
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”.
A running instance of a program, containing code, variable values, open files and network connections, and so on. Processes are the “actors” that the operating system manages; it typically runs each process for a few milliseconds at a time to give the impression that they are executing simultaneously.
A character or characters display by a REPL to show that it is waiting for its next command.
(in the shell): Using quotation marks of various kinds to prevent the shell from interpreting special characters. For example, to pass the string *.txt to a program, it is usually necessary to write it as '*.txt' (with single quotes) so that the shell will not try to expand the * wildcard.
read-evaluate-print loop
(REPL): A command-line interface that reads a command from the user, executes it, prints the result, and waits for another command.
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.
regular expression
A pattern that specifies a set of character strings. REs are most often used to find sequences of characters in strings.
relative path
A path that specifies the location of a file or directory with respect to the current working directory. Any path that does not begin with a separator character (“/” or “\”) is a relative path. See also: absolute path.
root directory
The top-most directory in a file system. Its name is “/” on Unix (including Linux and Mac OS X) and “\” on Microsoft Windows.
A command-line interface such as Bash (the Bourne-Again Shell) or the Microsoft Windows DOS shell that allows a user to interact with the operating system.
shell script
A set of shell 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.
standard input
A process’s default input stream. In interactive command-line applications, it is typically connected to the keyboard; in a pipe, it receives data from the standard output of the preceding process.
standard output
A process’s default output stream. In interactive command-line applications, data sent to standard output is displayed on the screen; in a pipe, it is passed to the standard input of the next process.
A directory contained within another directory.
tab completion
A feature provided by many interactive systems in which pressing the Tab key triggers automatic completion of the current word or command.
A name in a program that is associated with a value or a collection of values.
while loop
A loop that keeps executing as long as some condition is true. See also: for loop.
A character used in pattern matching. In the Unix shell, the wildcard * matches zero or more characters, so that *.txt matches all files whose names end in .txt.