UNIX Command Line Description

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Table of Contents

Overview

Control-Keys

UNIX Metacharacter Descriptions

 

Overview

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This appendix is intended for users who are new to using UNIX commands required for running the Accelrys GCG (GCG) programs. You will find the following information in this appendix:

Control-keys

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The following table lists the control key combinations that are used in UNIX.

UNIX

Description

<Ctrl>c

Ends a program.

<Ctrl>z

Suspends a program.

UNIX Metacharacter descriptions

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The UNIX shell recognizes some characters as having special meaning (see % man csh for more information). These characters are called shell metacharacters, having specific meanings in a UNIX environment.

The following table lists common UNIX shell metacharacters and their descriptions.

Character

Example

Description

$
(dollar sign)

% cd $GCGCOREROOT

Specifies that the non-blank characters following the $ are the name of a shell or environment variable.

&
(ampersand)

% fasta in:drogpdh -def &

Specifies that the part of the command line preceding the & should be run in the background.

>
(greater than)

% fasta in:drogpdh -def > fasta.log &

Specifies that the output from the part of the command line preceding the > should be redirected into a file with the name of the word following it.

<
(less than)

% cat < fasta.log

Specifies that the command input be taken from a file following the <.

|
(pipe)

% typedata in:drogpdh | more

Specifies that the output from the command should be piped into the command following the |.

!
(exclamation point)

% !!
% !21

Specifies a history substitution, that is, use of a previously entered command line. % !! recalls your previous command. % !n recalls command n on your list of previously entered commands.

\
(backslash)

% stringsearch gb_pr:* drb3\$ -Default

Specifies that the character following the \ should be prevented from shell interpretation.

( )
(parentheses)

% (cd adhdir ; fetch in:droadh*)

Specifies that the command line enclosed in ( ) should be executed in a subshell.

;
(semicolon)

% cd adhdir ; fetch in:droadh*

Specifies that the command line is two commands (one on both sides of the semicolon).

`
(backquote)

% cd `name -f GenDocData`

Specifies that the text enclosed between a pair of backquotes should be run as a command first, before submitting its output to the rest of the command line.

'
(single quotation marks)

% stringsearch gb_pr:* 'drd3$' -Default

Specifies that the shell should not interpret the characters enclosed within the single quotation marks. You can include spaces, * or ? wildcards, or the $ within the single quotes.

"
(double quotation marks)

% stringsearch in:* "light chain" -Default

Specifies that the shell should not interpret the characters enclosed in double quotes, including spaces and * or ? wildcards. Note that the $ shell variable will be interpreted.

*
(asterisk)

% ls gam*

Used as a wildcard in a filename specification, it specifies zero or more of any character.

?
(question mark)

% fetch ?gamma.seq

Used as a wildcard in a filename specification specifies one of any character.

~
(tilde)

% more ~/fasta.log

Used as a wildcard in a filename specification expands to the home directory of the user.

Note: Because the asterisk (*) and question mark (?) are frequently used characters for specifying ambiguous database entries, GCG provides an alias for each GCG command to disable globbing. Therefore, you can freely use these characters on the command line when invoking GCG programs.

Summary of UNIX command-line usage

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The following table elucidates the general rules for entering GCG command-line information in UNIX.

Topic

UNIX

Abbreviations

You cannot abbreviate commands.

Case Sensitivity

Commands are always lowercase.

 

The case sensitivity for parameter values varies depending on the parameter. For example, if you provide a filename as a parameter value, it is case sensitive.

 

Directory names are case sensitive.

 

File names are case sensitive.

Naming Devices

The syntax for device names is the same as for directory and filenames. For example

/dev/tty16 (printer)
/usr/dir/filename.txt (file)

 

You cannot name or refer to disks.

Parameters

A dash (-) indicates a command-line parameter. An equal sign (=) indicates a parameter that requires a value. Not all parameters require a value. For example

-OUT=myfile.test -Default

Spaces

Spaces are required (at least one) between a command and its parameters.

 

Spaces are required (at least one) between command-line parameters.

Wildcards

The question mark (?) wildcard serves as an ambiguous replacement for one character. You can use multiple ? to specify a defined number of ambiguous characters.

For example gamma.s?? matches all files that begin with "gamma" and have a three-letter extension starting with "s."

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