A man page is a form of software documentation usually found on a Unix or Unix-like operating system. Topics covered include computer programs, formal standards and conventions, and even abstract concepts. A user may invoke a man page by issuing the man command.
A filename extension, file name extension or file extension is a suffix to the name of a computer file. The extension indicates a characteristic of the file contents or its intended use. A filename extension is typically delimited from the rest of the filename with a full stop (period), but in some systems it is separated with spaces.
In computing, tar is a computer software utility for collecting many files into one archive file, often referred to as a tarball, for distribution or backup purposes. The name is derived from "tape archive", as it was originally developed to write data to sequential I/O devices with no file system of their own, such as devices that use magnetic tape. The archive data sets created by tar contain various file system parameters, such as name, timestamps, ownership, file-access permissions, and directory organization. POSIX abandoned tar in favor of pax, yet tar sees continued widespread use.
In computing, ls is a command to list computer files and directories in Unix and Unix-like operating systems. It is specified by POSIX and the Single UNIX Specification.
In computing, a command is a directive to a computer program to perform a specific task. It may be issued via a command-line interface or as input to a network service as part of a network protocol, or as an event triggered in a graphical user interface.
fortune is a program that displays a pseudorandom message from a database of quotations. Early versions of the program appeared in Version 7 Unix in 1979. The most common version on modern systems is the BSD fortune, originally written by Ken Arnold. Distributions of fortune are usually bundled with a collection of themed files, containing sayings like those found on fortune cookies, quotations from famous people, jokes, or poetry.
In computing, redirection is a form of interprocess communication, and is a function common to most command-line interpreters, including the various Unix shells that can redirect standard streams to user-specified locations. The concept of redirection is quite old, dating back to the earliest operating systems (OS). A discussion of the design goals for redirection can be found already in the 1971 description of the input-output subsystem of the Multics OS. However, prior to the introduction of UNIX OS with its "pipes", redirection in operating systems was hard or even impossible to do.
In Unix-like computer operating systems, a pipeline is a mechanism for inter-process communication using message passing. A pipeline is a set of processes chained together by their standard streams, so that the output text of each process (stdout) is passed directly as input (stdin) to the next one. The second process is started as the first process is still executing, and they are executed concurrently. The concept of pipelines was championed by Douglas McIlroy at Unix's ancestral home of Bell Labs, during the development of Unix, shaping its toolbox philosophy. It is named by analogy to a physical pipeline. A key feature of these pipelines is their "hiding of internals". This in turn allows for more clarity and simplicity in the system.
In software engineering, a pipeline consists of a chain of processing elements, arranged so that the output of each element is the input of the next. The concept is analogous to a physical pipeline. Usually some amount of buffering is provided between consecutive elements. The information that flows in these pipelines is often a stream of records, bytes, or bits, and the elements of a pipeline may be called filters. This is also called the pipe(s) and filters design pattern which is monolithic. Its advantages are simplicity and low cost while its disadvantages are lack of elasticity, fault tolerance and scalability. Connecting elements into a pipeline is analogous to function composition.
x11vnc is a Virtual Network Computing (VNC) server program. It allows remote access from a remote client to a computer hosting an X Window session and the x11vnc software, continuously polling the X server's frame buffer for changes. This allows the user to control their X11 desktop from a remote computer either on the user's own network, or from over the Internet as if the user were sitting in front of it. x11vnc can also poll non-X11 frame buffer devices, such as webcams or TV tuner cards, iPAQ, Neuros OSD, the Linux console, and the Mac OS X graphics display. x11vnc is part of the LibVNCServer project and is free software available under the GNU General Public License. x11vnc was written by Karl Runge.
The file command is a standard program of Unix and Unix-like operating systems for recognizing the type of data contained in a computer file.
In Unix-like operating systems, find is a command-line utility that locates files based on some user-specified criteria and either prints the pathname of each matched object or, if another action is requested, performs that action on each matched object.
In computing, more is a command to view the contents of a text file one screen at a time. It is available on Unix and Unix-like systems, DOS, Digital Research FlexOS, IBM/Toshiba 4690 OS, IBM OS/2, Microsoft Windows and ReactOS. Programs of this sort are called pagers. more is a very basic pager, originally allowing only forward navigation through a file, though newer implementations do allow for limited backward movement.
tail is a program available on Unix, Unix-like systems, FreeDOS and MSX-DOS used to display the tail end of a text file or piped data.
In computing, tee is a command in command-line interpreters (shells) using standard streams which reads standard input and writes it to both standard output and one or more files, effectively duplicating its input. It is primarily used in conjunction with pipes and filters. The command is named after the T-splitter used in plumbing.
yes is a command on Unix and Unix-like operating systems, which outputs an affirmative response, or a user-defined string of text, continuously until killed.
A command-line interface (CLI) is a means of interacting with a computer program by inputting lines of text called command-lines. Command-line interfaces emerged in the mid-1960s, on computer terminals, as an interactive and more user-friendly alternative to the non-interactive interface available with punched cards.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. Both simple and advanced tools are provided, supporting complex tasks like variant calling and alignment viewing as well as sorting, indexing, data extraction and format conversion. SAM files can be very large, so compression is used to save space. SAM files are human-readable text files, and BAM files are simply their binary equivalent, whilst CRAM files are a restructured column-oriented binary container format. BAM files are typically compressed and more efficient for software to work with than SAM. SAMtools makes it possible to work directly with a compressed BAM file, without having to uncompress the whole file. Additionally, since the format for a SAM/BAM file is somewhat complex - containing reads, references, alignments, quality information, and user-specified annotations - SAMtools reduces the effort needed to use SAM/BAM files by hiding low-level details.
cat is a standard Unix utility that reads files sequentially, writing them to standard output. The name is derived from its function to (con)catenate files . It has been ported to a number of operating systems.
