Key Points
Understanding your file system |
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Logging onto the Cloud |
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Introducing the Shell |
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Glossary
- 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.
- accession
- a unique identifier assigned to each sequence or set of sequences
- argument
- 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
- A user interface based on typing commands, usually at a REPL. See also: graphical user interface.
- 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 (but confusing!) to name an MP3 sound filehomepage.html
. Since many applications use filename extensions to identify the MIME type of the file, misnaming files may cause those applications to fail. - flag
- 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
. - graphical user interface
- A user interface based on selecting items and actions from a graphical display, 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 their home directory.
- NGS
- common acronym for “Next Generation Sequencing” currently being replaced by “High Throughput Sequencing”
- operating system
- Software that manages interactions between users, hardware, and software processes. Common examples are Linux, OS X, and Windows.
- 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”). - path
- A description that specifies the location of a file or directory within a file system. See also: absolute path, relative path.
- pipe
- 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”.
- process
- 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.
- prompt
- A character or characters display by a REPL to show that it is waiting for its next command.
- 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.
- redirect
- 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.
- shell
- 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.
- sub-directory
- 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.
- variable
- A name in a program that is associated with a value or a collection of values.
- wildcard
- 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
.
External references
Opening a terminal
- How to Use Terminal on a Mac
- Git for Windows
- How to Install Bash shell command-line tool on Windows 10
- Install and Use the Linux Bash Shell on Windows 10
- Using the Windows 10 Bash Shell
- Using a UNIX/Linux emulator (Cygwin) or Secure Shell (SSH) client (Putty)
- Addressing the digital divide in contemporary biology: Lessons from teaching UNIX
- Unix cheat sheet
Manuals
FASTQ files
High-throughput sequencing
- Illumina Sequencing Technology YouTube video