Command and Keystroke Differences Between OpenVMS and UNIX

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Overview

Command-Line Differences

OpenVMS

UNIX

Control-Key Differences

Program Differences

Wisconsin Package Program Supported Only on OpenVMS VAX

Wisconsin Package Programs Supported Only on UNIX

Program Names Modified From Previous Wisconsin Package Versions

UNIX Metacharacter Descriptions

Summary of OpenVMS/UNIX Command-Line Differences

Overview

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This appendix is intended for users whose sites have switched from the OpenVMS version of the Wisconsin Package to the UNIX version (or vice versa). You will find the following information in this appendix:

Command-line differences.
Control-key differences.
Program differences.
UNIX metacharacter differences.
Table summarizing OpenVMS/UNIX command-line differences.

Command-Line Differences

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OpenVMS

Command-Line Syntax: $ Command /PARameter

Command lines are case insensitive. That is, you can type the command in lowercase, uppercase, or mixed case.
You can abbreviate OpenVMS commands and parameters. The fewest number of letters you must type for a command is indicated in bold. The fewest number of letters you must type for a parameter is indicated in bold, uppercase text.
Parameters, which modify the action of the command, are preceded with a slash (/). Some parameters require a value that modifies the parameter.
For long command lines that wrap onto a second line, type a dash (-) at the end of the first line, press <Return>, and continue typing the remainder of the command on the second line.

UNIX

Command-Line Syntax: % command -PARameter

Command lines are case sensitive. You must type all Wisconsin Package commands in lowercase.
You cannot abbreviate Wisconsin Package program names or UNIX commands.
Parameters, which modify the action of the command, are preceded with a space and a dash (-). Some parameters require a value that modifies the parameter.
You cannot type spaces between a parameter and its value.
You can abbreviate Wisconsin Package parameters. The fewest number of letters you must type is indicated in bold, uppercase text.
For long command lines that wrap onto a second line, type a backslash (\) at the end of the first line, press <Return>, and continue to type the remainder of the command on the second line.
For more information on UNIX command-line syntax, see "Fundamentals: Using UNIX" in Chapter 1, Getting Started.

Control-Key Differences

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The following table lists the control key combinations that are different between UNIX and OpenVMS.

OpenVMS	UNIX	Description
<Ctrl>C <Ctrl>Y	<Ctrl>c	Ends a program.
Not Available	<Ctrl>z	Suspends a program.
<Ctrl>Z	<Ctrl>d	End of file.

Program Differences

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Wisconsin Package Program Supported Only on OpenVMS VAX

PlotMetaFile

Plots a GKS metafile on any GKS supported device. (GKS is not supported on UNIX or OpenVMS AXP.)

Wisconsin Package Programs Supported Only on UNIX

Name	Displays and manipulates the Wisconsin Package logical names. For more information, see the Program Manual.
Symbol	Displays and manipulates the Wisconsin Package symbols. For more information, see the Program Manual.

(Logical names and symbols are an innate part of the OpenVMS operating system. However, GCG created the logical name and symbol service on UNIX.)

Program Names Modified From Previous Wisconsin Package Versions

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Because of conflicts between Wisconsin Package program names and UNIX operating system commands, some Wisconsin Package program names have been modified. The name changes have occurred since Version 7. The following program names are correct for both OpenVMS and UNIX in Version 10:

Previous Versions' Program Names	Current Program Names
Clear	ClearPlot
Echo	EchoKey
Extract	ExtractPeptide
Find	FindPatterns
Shift	ShiftOver
Strings	StringSearch
ToBLAST	GCGToBLAST
NewDiverge	Diverge

UNIX Metacharacter Descriptions

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The UNIX shell recognizes some characters as having special meaning (see % man csh for more information). Although these characters, called shell metacharacters, may have no particular meaning in a OpenVMS environment, they do have meaning 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 Wisconsin Package command to disable globbing. Therefore, you can freely use these characters on the command line when invoking Wisconsin Package programs.

Summary of OpenVMS/UNIX Command-Line Differences

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The following table compares the general rules for entering Wisconsin Package command-line information in OpenVMS and UNIX.

Topic	OpenVMS	UNIX
Abbreviations	You can abbreviate most commands. The documentation indicates the abbreviation in bold.	You cannot abbreviate commands.
	You can abbreviate most parameters. The documentation indicates the abbreviation in bold uppercase.	Same as OpenVMS.
Case Sensitivity	Commands are case insensitive.	Commands are always lowercase.
	Parameter qualifiers are case insensitive.	Same as OpenVMS.
	Parameter values are case insensitive.	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 insensitive.	Directory names are case sensitive.
	File names are case insensitive.	File names are case sensitive.
	Database names, logical names, and sequence entries are case insensitive.	Same as OpenVMS.
Naming Devices	The syntax for device names vary from that of directory or file names. For example `LTA13:` (printer) `DISK:[Dir]FileName.Txt` (file)	The syntax for device names is the same as for directory and filenames. For example `/dev/tty16` (printer) `/usr/dir/filename.txt` (file)
	You can name and refer to disks (`DISK:`).	You cannot name or refer to disks.
Parameters	A slash (/) indicates a command-line parameter. An equal sign (=) indicates a parameter that requires a value. Not all parameters require values. For example `/OUT=MyFile.Test /Default`	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 ignored between a command and its parameter(s).	Spaces are required (at least one) between a command and its parameters.
	Spaces are ignored between command-line parameters.	Spaces are required (at least one) between command-line parameters.
	Spaces are not allowed between a parameter and its value.	Same as OpenVMS.
Wildcards	The asterisk () wildcard serves as an ambiguous replacement for a character or group of characters; the means "anything or nothing." For example `gamma.` matches all files that begin with "gamma." `gam.map` matches all files that begin with "gam" and have an extension of "map."	Same as OpenVMS.
	The percent sign (`%`) 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."	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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