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Overview
Fundamentals: Using OpenVMS
Getting Help for OpenVMS
Logging On
Recalling and Editing Command Lines
Working with Directories
Displaying Directory Contents
Creating Directories
Changing Directories
Defining and Using Logical Names for Directories
Working with Files
Creating and Editing Files
Specifying Files
Deleting Files
Displaying and Changing File Protections
Using Wildcards
Viewing Files
Logging Off
Quick Reference
DCL Commands
Controlling Screen Output
Getting Started with the Wisconsin Package
Initializing the Wisconsin Package
For Advanced Users
Customizing Your Login
Initializing the Wisconsin Package
Automating Program Commands
Defining Logical Names
Defining Your Graphics Configuration
This chapter helps prepare you to use the Wisconsin Package. Written with the novice user in mind, it provides you with the fundamentals of working with the OpenVMS operating system. While the commands and procedures in later chapters and in the Program Manual often assume that you have a working knowledge of OpenVMS commands, this chapter assumes you have little or no experience working with the computer, and it provides you with that basic groundwork.
You can find the details on working with files and directories, logging on and off the system, and customizing your login environment in this chapter. It also explains how to start running the Package.
The Wisconsin Package you use is installed on a minicomputer using the OpenVMS operating system. You are connecting to that computer in one of two ways: 1) you are directly connected to the computer, or 2) you connect to the computer over the network. The device you are using could be a dumb terminal, a console, an X Windows terminal, or a PC or Macintosh running terminal emulation software. Regardless of what device you are using to access the Package, you must become familiar with OpenVMS commands to use the Wisconsin Package programs and manipulate the output.
Note: In this documentation, "OpenVMS" refers to both OpenVMS VAX and OpenVMS AXP.
Also, if you are more familiar with UNIX commands than OpenVMS commands, see Appendix D, Command and Keystroke Differences between OpenVMS and UNIX.
Your system manager has just set up a OpenVMS account for you to use the Wisconsin Package. But what if you've never used OpenVMS before and you're not sure where to start? This chapter will walk you through the basics of using the OpenVMS operating system. If you take a little time now to learn the basics of OpenVMS, you will increase the efficiency with which you can later work with the Wisconsin Package.
This section teaches you how to
OpenVMS (Open Virtual Memory System) is an operating system designed for Digital Equipment Corporation computers such as the VAX and AXP models. An operating system is the software that controls and manages the computer. You communicate with the operating system through DCL (Digital Command Language) commands. You use DCL commands to tell the computer to display the contents of a directory or file or to move you to a different location, among other things.
Keep the following points in mind as you work with DCL commands and the tasks in this chapter and manual.
Note: This documentation uses the convention that when commands are provided, the entire command is included but the unique abbreviation is bold, for example Directory.
Wisconsin Package program commands follow similar guidelines as DCL commands. However, Wisconsin Package commands work only if you initialize the Package first (see "Getting Started with the Wisconsin Package" in this chapter for more information).
You use DCL commands to manipulate files and directories. Think of a directory as being similar to a file cabinet. Within the file cabinet you can find drawers (subdirectories) and files. Subdirectories, like file cabinet drawers, help you organize your files into loosely related groups. Files are where you store information in the computer--for example, sequence information or the output of a program. Most Wisconsin Package programs require a file as input and produce an output file of results.
Each directory and file in the OpenVMS system is under DCL file protection. This protects you and others from writing in directories or reading or executing files for which you do not have the privilege. For example, you can set a file's protection so that only you can read it.
In your work with the OpenVMS files, there are times when you must use a text editor to complete a task. The default text editors in OpenVMS are EDT (or $ Edit) and EVE (or $ Edit /TPU). However, you can use other text editors, if available.
It is beyond the scope of this manual to provide detailed instructions in the use of text editors. However, we do provide the basics to get started using EDT in Appendix B, Text Editor Basics. For more information about the default text editors EDT and EVE, see the VAX General User Guide or OpenVMS User's Manual. For other text editors, see the appropriate program documentation.
Type $ Help. The system displays directions on how to use Help.
For access to paper OpenVMS documentation, see the VAX General User Guide, OpenVMS User's Manual, or ask your system manager for help.
To use the Wisconsin Package, you will be in one of two possible situations: 1) you are directly connected to the computer, or 2) you connect to the computer over the network. The device you are using could be a dumb terminal, a console, an X Windows terminal, or a PC or Macintosh running terminal emulation software.
Note: You must have an approved account, also called a login, from the system manager to use any OpenVMS computer. The system manager usually sets up a user name, which is typically your first or last name, and lets you specify a password for security. No one can access the system through your account without your password. Keep your password secret.
When you are connected, you should see the prompt "Username:" on the screen. If you don't, press <Return> until you do.
Note: If you make a mistake in typing your user name or password, press <Delete> to delete the error or press <Return> and try again.
When you see the operating system prompt ($) in the left margin of your screen, the computer is ready for your commands. Note that the $ prompt is a convention used in this guide. Your site may have set up a different prompt.
Command lines are what you type after the operating system prompt to communicate with the computer. You type command lines to do tasks like run programs and manage your files. They always include a command and also may optionally include input files, output files, and parameters. Sometimes the command lines you type may be lengthy; to extend long commands onto a second line, type a dash (-) at the end of the preceding line. The OpenVMS operating system makes it easy for you to recall previously typed command lines to edit them, to avoid retyping them, or, if you're running a program repeatedly with the same parameters, to ensure consistency.
Press the <Up Arrow> key repeatedly to move backward through your last 20 commands; press the <Down Arrow> key repeatedly to move forward through the list.
Choose from the following.
For more information about editing command lines, type $ Help Line_Editing.
You can think of a directory as being similar to a file cabinet. Within the file cabinet you can find drawers (or subdirectories) and files. Subdirectories, like file cabinet drawers, help you organize your files into loosely related groups.
When you log in, you will be in your top directory, also known as your home directory. Your current (or default) directory refers to whatever directory you are presently working in.
For more information on working with directories and DCL commands, see the VAX General User Guide, OpenVMS User's Guide, or your system manager.
Type $ Directory.
Type $ Show Default.
To see your new subdirectory, type $ Directory *.Dir. The screen displays a list of all subdirectories in your current directory, including the new subdirectory Project. Notice that your new subdirectory has the extension ".Dir". OpenVMS gives all directories the .Dir extension, making them easy to distinguish from files.
You've learned how to create directories, and now you want to know how to move between them. Consider the following example of a directory tree as you read through the tasks below.
Type $ Set Default [Directory.Subdirectory], for example
$ Set Default [Smith] or $ Set Default [Smith.Project].
GCG has defined simple commands to aid you in easily changing directories. These commands are especially helpful when you have many subdirectories to work with. Choose from the following.
Note: The above commands are simplified versions of the DCL command
Set Default. They are provided by GCG and are available only when the Wisconsin Package has been initialized (see "Logging On" in this chapter for more information). They are not DCL commands.
If you move to a directory other than your home directory often, you can assign it a logical name. A logical name is a shorthand name you can give a filename or directory. Logical names often reduce typing and are easier to remember than full specifications.
For example, let's say you assigned [Smith.Project] the logical name Proj. Regardless of the directory you are located in, you can move to [Smith.Project] with the command $ Set Default Proj instead of typing the entire directory specification.
Note that before you define a logical name, you first should check to make sure you will not overwrite an existing logical name. To do so, type $ Show Logical Logical_Name.
Type $ Assign [Directory.Subdirectory] Logical_Name, where Directory.Subdirectory is the specification of the directory you want to assign a logical name to, and Logical_Name is the logical name you want to assign. For example, $ Assign [Smith.Project] Proj defines "Proj" as the logical name for the directory [Smith.Project].
Note: Each time you log out of the system, your logical names are lost unless you save them in your GCGMyInit.Com file. For more information on the GCGMyInit.Com file, see "Customizing Your Login" in the "For Advanced Users" section of this chapter.
Type the logical name followed by a colon and a filename, for example Proj:Gamma.Seq. You must use a colon (:) between a directory logical name and the filename that follows it.
If you forget what a logical name is defined as, type $ Show Logical Logical_Name. For example $ Show Logical Proj.
Files are where you store information in the computer--for example, sequence information or the output of a program. Most Wisconsin Package programs require one or more files as input and produce an output file of results.
Filenames have a particular format: Filename.Extension;Version, for example Gamma.Seq;1.
Filename (Gamma) names the file and can be up to 39 characters in length. Filenames can include the letters A to Z (uppercase or lowercase), numbers 0 to 9, and an underscore(_), hyphen (-), or dollar sign ($).
Extension (.Seq) identifies the kind of file and can be up to 39 characters in length. If you create a file but do not specify an extension, some Wisconsin Package programs supply an extension for you.
Version (;1) displays the version number of the file. The operating system automatically assigns version numbers to each file. Every file has a version number which differentiates it from another version of the same file. That is, when you create a file, the system assigns it a version number of 1. Each time you edit the file and save a new copy, the version number is incremented by one. Thus, you may have several versions of a file in a directory. When a program tries to read a file for which more than one version exists, it always reads the most recent (highest numbered) version unless you specify the version.
For more information on working with files and the DCL commands described below, see the VAX General User Guide, OpenVMS User's Manual, or your system manager.
Most Wisconsin Package programs create output files, some of which you can use as input to other programs. To create files in a directory, you must have privileges to write in that directory (see "Displaying and Changing File Protections" in this chapter). If you don't, change the directory protections (if possible) or move to another directory in which you do have the necessary privileges.
We recommend that you learn to use a text editor to create and edit files. Files written by most Wisconsin Package programs are easily edited using text editors.
Choose one of the following.
Note: If you create a file and do not add an extension to the filename, the operating system will add a period (.) to the end of the name. That is, if you name a file "Gamma", the computer will create a file named "Gamma.;1".
You can use other text editors as well. For more information about EDT and EVE, see the VAX General User Guide, OpenVMS User's Manual, or your system manager.
OpenVMS and Wisconsin Package commands often require one or more filename(s) to do their job. A simple example of a OpenVMS command is when you type $ Delete, the computer expects you to supply it with the name of the file to remove. As an example of a Wisconsin Package command, when you run the Map program, it asks you "MAP of what sequence?" In such instances you need to specify a filename.
Choose one of the following.
Note: For more information about directories, see "Working with Directories" in this chapter.
You will find it necessary to clean up your directories at times and to delete unnecessary files. You can do this with two commands: Delete and Purge.
Choose from the following.
File protection is a means of security by which four categories of users are assigned privileges to each file: system, owner, group, and world. Each category has certain privileges of access and use:
(R) Read - Users can read the contents of the file or directory.
(W) Write - Users can write in and edit the file or directory.
(E) Execute - Users can execute the file in the directory.
(D) Delete - Users can delete a file or directory.
Type $ Directory /Protection.
The system displays the name of each file followed by the protections (RWED) grouped by system, owner, group, and world. For example
As you can see in this example, directories as well as files have protections assigned to them.
Type $ Set File /Protections=O:RWED Filename, where O: defines the category of user, in this case "owner," and RWED defines the number of protections you want to set (read, write, execute, delete).
Use wildcards to specify multiple files. An asterisk (*) wildcard serves as an ambiguous replacement for one or more characters; the * means "anything or nothing." You can also use a percent sign (%) wildcard as an ambiguous replacement for a single character. Consider the following examples:
Most DCL commands and some Wisconsin Package programs accept wildcards in file specifications.
Enter $ Type Filename, for example $ Type Gamma.Seq to display the file on your screen. By default, the computer selects the most recent (highest numbered) version of the file. If you want to use a different version, include the semicolon and version number, for example $ Type Gamma.Seq;3.
TIP - To view a file one screen at a time, add the /Page parameter, for example $ Type /Page Gamma.Seq. To advance from screen to screen, press <Return>.
Type $ Logout.
You should become familiar with the following OpenVMS operating system DCL commands to use the computer and Wisconsin Package programs effectively and efficiently. For more information on DCL commands, see the OpenVMS User's Manual and OpenVMS DCL Dictionary.
The following list is provided only as a starting point for your work with OpenVMS.
| Command | Example | Description |
| $ Append Filename1 Filename2 | $ Append Temp.Txt Gamma.Txt | Appends the file Temp.Txt to the end of the file Gamma.Txt. |
| $ Assign [Directory] Logical_Name | $ Assign [Smith.Project] Proj | Assigns the logical name "Proj" to the directory [Smith.Project]. |
| $ Copy Filename1 Filename2 | $ Copy Gamma.Seq Temp.Seq | Makes a new copy of the file Gamma.Seq and names it Temp.Seq. |
| $ Create/Directory [.Directory] | $ Create/Directory [.Project] | Creates a subdirectory called Project under your current directory. |
| $ Delete Filename | $ Delete Gamma.Seq;* | Deletes all versions of the file Gamma.Seq. |
| $ Directory $ Directory *.Extension |
$ Directory $ Directory *.Seq |
Displays a list of all the files or those that match the wildcard specification in your current directory. |
| $ Edit /EDT Filename | $ Edit /EDT Gamma.Seq | Starts an editing session with the EDT editor. |
| $ Edit/TPU Filename | $ Edit/TPU Gamma.Seq | Starts an editing session with the EVE editor. |
| $ Help | -- | Displays online documentation for OpenVMS commands. |
| $ Logout | -- | Ends your session with the computer. |
| $ Purge Filename | $ Purge $ Purge *.Seq $ Purge Gamma.Seq |
Deletes all but the most recent, or highest, version of the specified file(s) in your current directory. $ Purge removes all but the latest version of all files in your directory. |
| $ Rename Filename1 Filename2 | $ Rename Gamma.Seq Temp.Txt | Changes the name of the file Gamma.Seq to Temp.Txt. |
| $ Search Filename Pattern | $ Search Gamma.Seq Smithies | Searches the file Gamma.Seq for the character pattern "Smithies". |
| $ Set Default [Directory] | $ Set Default [Smith] | Changes your current directory to the directory [Smith]. |
| $ Set File /Protections Filename | $ Set File /Protections=o:rwed Temp.txt | Changes the protections on a file. |
| $ Type Filename | $ Type Gamma.Seq $ Type /Page Gamma.Seq |
Displays the contents of the file Gamma.Seq on your terminal screen. Use the /Page parameter to display one page at a time. |
The following is a partial list of key combinations you will find helpful in controlling screen output. For more information on terminal keyboard combinations, see the OpenVMS User's Manual and OpenVMS DCL Dictionary.
| Control Key | Description |
| <Ctrl>C | Cancels a program or an executing DCL command. |
| <Ctrl>Y | Interrupts a program or an executing DCL command. Type $ Continue to start the program or DCL command where it left off. |
| <Ctrl>S | Stops screen output from scrolling off the screen. |
| <Ctrl>Q | Starts screen output that has been stopped by <Ctrl>S. |
| <Ctrl>H | Moves the cursor to the left margin, or front of a line. |
| <Ctrl>E | Moves the cursor to the end of a line. |
| <Ctrl>U | Deletes text from the cursor to the beginning of a line. |
| <Ctrl>R | Refreshes the screen while editing. |
Note: Chapters 2-5 in this guide provide general instructions for all programs in the Wisconsin Package. For detailed instructions about a specific program, see the Program Manual.
To use the Wisconsin Package, you must first initialize your environment. Initializing your environment gives you access to the Wisconsin Package programs, the databases, data files the programs need, logical names, and other information required for the Package to run smoothly.
Type $ GCG. The system takes a few seconds to initialize the Package and displays a banner similar to the following:
The banner displays the version of the Package you are running, as well as the reference you can cite if you use the Wisconsin Package in your publishable research. (Because the banner changes with each update to the available databases, your banner may look slightly different than the one above.)
When you see the operating system prompt ($), the Wisconsin Package is ready for use.
Note: The $ prompt is a convention used in this guide. Your site may have set up a different prompt. Also, if the command $ GCG does not initialize the Wisconsin Package on your system, see your system manager.
TIP - If your primary reason for using the computer is to use the Wisconsin Package, you may want to customize your login to automatically initialize it for you each time you log in. To do so, you need to create or edit your Login.Com file. For more information on working with Login.Com files, see "Customizing Your Login" in the "For Advanced Users" section of this chapter.
For help working with the Wisconsin Package, check the documentation, look in the GenManual or GenHelp online help, or contact technical support. For more information, see "Getting Help" in the preface "Before You Begin."
The information in this section is intended for users who are familiar with the operating system. This section teaches you how to
You or your system manager can customize your login to ensure that certain commands execute or are available every time you log in. For example, you may want to customize your login to automatically initialize the Wisconsin Package. Or, you can assign logical names for filenames and directories so that each time you log in, they will be defined automatically. To do these things and more, you can create a Login.Com and GCGMyInit.Com file in your home directory.
Each time you log in, OpenVMS checks for a Login.Com file and, if it finds one, executes the commands within it. The Login.Com file is a command procedure which you can use to execute the same commands each time you log in. The Login.Com file must be located in your home directory for it to run.
GCGMyInit.Com is a command procedure which automatically executes commands for you when you run the Wisconsin Package. The GCGMyInit.Com file must be located in your home directory for it to run.
We recommend placing the commands for initializing the Wisconsin Package in your Login.Com file, and commands for automating programs and defining logical names in your GCGMyInit.Com file.
(For more information about command procedures, see "Working with Command Procedures" in the "For Advanced Users" section of Chapter 3, Using Programs.)
Use a text editor of your choice, for example EDT or EVE. Create the file in your top level directory. The following tasks describe commands you may want to include in your Login.Com or GCGMyInit.Com file.
Note: To test your Login.Com or GCGMyInit.Com file after you've edited and saved it, type an at sign (@) followed by the name of the file (for example $ @Login.Com). The system reruns your login.
If your primary reason for using the computer is to use the Wisconsin Package, you may want to customize your login to automatically initialize the Package each time you log in. A file, such as your Login.Com file, which automatically runs commands for you is called a command procedure.
Note: For more information, see "Working with Command Procedures" in the "For Advanced Users" section of Chapter 3, Using Programs.
You may find that you frequently run a Wisconsin Package program using the same parameters each time. You can define a foreign command, also called a symbol, to create a shortcut command for the program and its parameters.
Before you create a symbol, you should check to make sure the symbol is not already defined. To do so, type $ Show Symbol symbol_name. Then (if the symbol is not defined, or if you want to redefine a symbol) use the following syntax to define one:
$ Symbol_name :== Command_line
If you define a symbol at the operating system prompt, it will be in effect until you log out. To save your symbol from one session to the next, add it to your GCGMyInit.Com file.
$ MC :== 'MapPlot' /CIRcular
You must include the dollar sign ($) and the single quotation marks (') around the program name.
Note: The Wisconsin Package must previously be initialized (for example, in your Login.Com file) for the computer to interpret the Wisconsin Package commands you include in your GCGMyInit.Com file.
Note: If you forget what a foreign command is defined as, type $ Show Symbol Foreign_command. The system displays the symbol definition. For example
$ Show Symbol MC
$ MC == "$GENUTIL:MAPPLOT /CIRCULAR"
For more information, see "Using Foreign Commands" in the "For Advanced Users" section of Chapter 3, Using Programs.
You can assign logical names to files you use frequently or directories that you move to frequently. When you define logical names in your GCGMyInit.Com file, they are available every time you initialize the Wisconsin Package.
Note that before you define a logical name, you first should check to make sure the logical name is not already defined. To do so, type $ Show Logical Logical_Name.
For more information on defining logical names, see the topic "Defining and Using Logical Names for Directories" earlier in this chapter.
Before you run a Wisconsin Package program that produces graphic output, you must define your graphics configuration. Defining your graphics configuration means telling the computer what graphics language you want to use and on what device you want to display. For more information, see "Initializing Your Graphics Configuration" in Chapter 5, Using Graphics.
Graphics_language is the name of the graphics language you want to use. For more information about what graphics languages are available, see "Configuring Graphics Languages and Devices" in Appendix C, Graphics.
Graphics_device is the device you want to send output to, for example a graphics terminal screen, printer, or plotter. Supported devices also are listed in "Configuring Graphics Languages and Devices" in Appendix C, Graphics.
Port_or_queue is where the graphics device is attached, for example Term: or LTA15:.
For example, to set up a graphics configuration for a LaserWriter, you might type $ PostScript LaserWriter LTA15:.
Note: Some graphics configuration commands have fewer prompts, such as XWindows, and some have more, such as HPGL. Make sure you answer all the prompts when you set up your graphics configuration in your GCGMyInit.Com file.
TIP - "Initializing Your Graphics Configuration" in Chapter 5, Using Graphics describes using the SetPlot command to define your graphics configuration from the command line. You also can use the SetPlot command in your GCGMyInit.Com file to define your graphics configuration for you when you log in. To do so, follow these steps:
- Open your GCGMyInit.Com file in the text editor of your choice, for example EDT or EVE.
- Move to the point in your GCGMyInit.Com file where you want to define the configuration commands.
- Type $ SetPlot Graphics_Device where Graphics_Device is the name of one of the menu items when you run SetPlot.
- Save the file and exit from the text editor. The next time you log in, your graphics configuration will automatically be initialized.
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Copyright (c) 1982, 1983, 1985, 1986, 1987, 1989, 1991, 1994, 1995, 1996, 1997, 1998 Genetics Computer Group Inc., a wholly owned subsidiary of Oxford Molecular Group, Inc. All rights reserved.
Licenses and Trademarks Wisconsin Package is a trademark of Genetics Computer Group, Inc. GCG and the GCG logo are registered trademarks of Genetics Computer Group, Inc.
All other product names mentioned in this documentation may be trademarks, and if so, are trademarks or registered trademarks of their respective holders and are used in this documentation for identification purposes only.