Sequin How to Download

The latest versions of Sequin for Macintosh, PC/MS Windows, and Unix Computers are available from the NCBI ftp site at ftp://ncbi.nlm.nih.gov/sequin and the EBI ftp site at ftp://ftp.ebi.ac.uk/pub/software/sequin. Instructions for how to retrieve and install the application follow.

• Macintosh
• Microsoft Windows
• Unix
• Multiple Unix users

You can download Sequin from NCBI (USA) or the EBI (UK). Convert the archive sequin.hqx to sequin.sea wit h BinHex. Double click on the sequin.sea archive once you have received it. This will self-extract into a folder called Sequin Folder containing the Sequin application, a README file, and the asnload, config, data, and errmsg folders. Some WWW browsers will do one or both of these steps automatically. We suggest that you properly configure Sequin before launching the application.

Downloading Sequin using an FTP program

Downloading can be performed using an FTP (File Transfer Protocol) program such as HyperFTP.

• Create a Sequin folder on your hard disk, if one does not already exist.
• Launch HyperFTP.
• Connect to ncbi.nlm.nih.gov (USA) or ftp.ebi.ac.uk(UK).
• Enter anonymous as the user name.
• Enter your Internet e-mail address as the password.
• Set the BinHex file Transfer Mode.
• Double click on the sequin directory (USA) or on the pub, then the software and then the sequin directory (UK).
• Receive the sequin.hqx file, saving as sequin.sea in the Sequin folder.
• Disconnect from the ftp file server.
• Quit HyperFTP.
• Double click on the sequin.sea application. This will self-extract into the Sequin application, a README file, and the asnload, config, data, and errmsg folders
• Configure Sequin before launching the application.

Configuring Sequin on the Macintosh

The instructions presented here describe how to move the Sequin configuration files into the System Folder where they will be recognised by Sequin. If you move the files, certain styles in Sequin will be automatically set when you launch the applicati on. Furthermore, you will be able to save personal modifications which you make to these styles. However, if you have installed a previous version of Sequin and have made style modifications which you do not wish to lose, you may not want to overwrite t he files which are already in the System Folder.

• Open the config folder located inside the Sequin Folder.
• Open the System Folder
• Copy the three files in the config folder to the Preferences folder in the System Folder
  • Select all three files
  • Hold down the option key as you drag them into the Preferences folder
• Launch the sequin application to start Sequin.

Downloading Sequin with your WWW browser

You will need to place the downloaded file sequinz.exe into the directory (e.g. c:\sequin) you wish to use to run the program. Create such a directory, if one does not already exist, and specify that directory as the target w hen you download the program.

Two versions of Microsoft Windows compatible Sequin clients are available for downloading, a Win16 version (UK download or USA download) (for Windows 3.1 or Win-OS/2) and a Win32 version (UK download or USA download) (Windows95, Windows NT and Windows 3.1 with Win32 support).

Continue with the Installation instructions, below.

Downloading Sequin using an FTP program

• Change directory (cd) into the proper directory, (e.g. c:\sequin) creating one if necessary. This directory may be created anywhere, not necessarily on the C: drive, and not necessarily at the disk root (\).
• Type ftp ncbi.nlm.nih.gov (USA download) or ftp ftp.ebi.ac.uk (UK download).
• Enter anonymous as the user name.
• Enter your Internet e-mail address as the password.
• Type bin to set the binary transfer mode.
• Type cd sequin (USA download) or cd /pub/software/sequin (UK download).
• Type cd win16 for the WinSock 1.1 Win16 version ,
  OR cd win32 for the Windows 32-bit version.
• Type get sequinz.exe
• Type bye
• Continue with the Installation instructions, below.

Installation

• Start an MS-DOS window and change directory (cd) into a directory for Sequin (e.g. c:\sequin).
• Verify that the file sequinz.exe is present using the dir command. If other files are present, remove them.
• To extract the file and the directories type the command sequinz.exe . This will extract the Sequin application, a README file, and the Config, Data, and Errmsg directories. In the Win16 version, the Asnload directory will also be extracted.
• Windows 3.1, Windows NT or Win-OS/2: use the Program Manager's "File | New" menu and create a new program group for Sequin - or use an existing group. From the Windows File Manager program, locate the sequin.exe progra m. Drag its icon from the File Manager to the desired program group in the Program Manager.
• Windows95: To see the icons, type start . from the MS-DOS prompt in the directory containing sequin.exe.
• Windows95: You can put the Sequin icon on the desktop using drag-and-drop. To add Sequin to the Start button's list, right click on the lower bar. From the pop-up menu select "Properties..." Select the folder tab "Start Menu Programs". From here you may browse your hard disk, select sequin.exe and add it to a folder on the Start menu.
• Additional instructions describe how to move the Sequin configuration files into the Windows directory where they will be recognised by Sequin. If you move the files, certain styles in Sequin will be automatically set when you launch the application. Furthermore, you will be able to save personal modifications which you make to these styles. However, if you have installed a previous version of Sequin and have made style modifications which you do not wish to lose, you may not want to overwrite the files which are already in the System Folder.
  • Open the config directory located inside the sequin directory.
  • Open the Windows directory
  • Copy the three files in the config directory to the Windows directory.
• Launch the sequin application to start Sequin.

Win32 users: If you have problems starting up the Win32 version of Sequin, install the Win16 version instead.

Downloading Sequin with your WWW browser

You may need to make a directory (mkdir) before downloading - or if you have an old directory, erase its contents first.

Versions of Sequin are available for:

• SunOS 4 (USA download or UK download),
• Solaris (USA download or UK download),
• SGI Irix5.3 and higher (USA download) or UK download),
• Linux (USA download or UK download),
• DEC Alpha OSF1/Digital Unix (USA download or UK download).

  Continue with the Installation instructions, below.

  Downloading Sequin using an FTP program

  • Make a directory for Sequin, e.g. mkdir sequin
  • Type cd sequin to change directory to your Sequin directory.
  • Remove any old files from your existing Sequin directory.
  • Type ftp ncbi.nlm.nih.gov (USA download) or ftp ftp.ebi.ac.uk (UK download)
  • Enter anonymous as the user name.
  • Enter your Internet e-mail address as the password.
  • Type bin to set the binary transfer mode.
  • Type cd sequin (USA download) or cd /pub/software/sequin
  • Type ls to get a list of tar archives. You will recognize a file named "*.tar.Z" where the * is either
    sun (SunOS 4),
    solaris (Solaris),
    sgi (Irix5.3 and higher),
    linux (Linux), or
    alphaOSF1 (DEC Alpha OSF1/Digital Unix).
  • Type get followed by name of the tar archive for your system, e.g. "get sun.tar.Z".
  • Type bye
  • Continue with the Installation instructions, below.
    
    

  Installation

  • From the directory into which the downloaded file was put, type uncompress *.tar.Z
  • Type tar -xvf *.tar This will extract the data, config, and errmsg directories as well as the sequin executable.
  • Additional instructions describe how to move the Sequin configuration files into your home directory where they will be recognised by Sequin. If you move the files, certain styles in Sequin will be automatically set when you launch the applicatio n. Furthermore, you will be able to save personal modifications which you make to these styles. However, if you have installed a previous version of Sequin and have made style modifications which you do not wish to lose, you may not want to overwrite th e files which are already in the home directory.
    • Type cd config to move to the config directory
    • Type
      cp ncbidtrc ~/.ncbidtrc
      cp nlmstmanrc ~/.nlmstmanrc
      cp sequinrc ~/.sequinrc
      to copy the configuration files, rename them in a standard Unix format, and move the new files into your home directory.
  • Run an X window manager. Note that your system must be configured for the appropriate version of the X Window System (X11R4 or X11R5).
  • Launch the sequin application to start Sequin.

Sun users: read this note regarding Sun keymaps.

Installing Sequin under Unix for multiple users

System administrators can install Sequin so that multiple users can work with it.

• Download Sequin into the system administrator's home directory
  • Make a directory for Sequin, if one does not already exist, e.g., mkdir sequin
  • Type cd sequin to change to the Sequin directory.
  • Remove any old files from the existing Sequin directory.
  • Type ftp ncbi.nlm.nih.gov (USA download) or ftp ftp.ebi.ac.uk (UK download)
  • Enter anonymous as the user name.
  • Enter your Internet e-mail address as the password.
  • Type bin to set the binary transfer mode.
  • Type cd sequin
  • Type ls to get a list of tar archives. You will recognise a file named "*.tar.Z" where the * is either
    sun (SunOS 4),
    solaris (Solaris),
    sgi (Irix5.3 and higher),
    linux (Linux), or
    alphaOSF1 (DEC Alpha OSF1/Digital Unix).
  • Type get followed by name of the tar archive for your system, e.g., "get sun.tar.Z".
  • Type bye
• Uncompress and extract the downloaded files
  • Uncompress the downloaded files by typing uncompress *.tar.Z
  • Type tar -xvf *.tar This will extract the data, config, and errmsg directories as well as the sequin executable.
• Set up the Sequin configuration files in the system administrator's home directory
  These instructions describe how to move the Sequin configuration files into the home directory where they will be recognised by Sequin. If you move the files, certain styles in Sequin will be automatically set when you launch the application. Furthermore, you will be able to save personal modifications which you make to these styles. However, if you have installed a previous version of Sequin and have made style modifications which you do not wish to lose, you may not want to overwrite the files which are already in the home directory.
  • Type cd config to move to the config directory
  • Type
    cp ncbidtrc ~/.ncbidtrc
    cp nlmstmanrc ~/.nlmstmanrc
    cp sequinrc ~/.sequinrc
    to copy the configuration files packaged with Sequin, rename them in a standard Unix format, and move the new files into your home directory.
• In order to continue the installation, the system administrator must run the Sequin program and set it up in its network-aware mode.
  • Run an X window manager. Note that the system must be configured for the appropriate version of the X Window System (X11R4 or X11R5).
  • Launch the sequin application to start Sequin.
  • Under the Misc menu on the startup screen, select Net Configure
  • Click on Yes to enable network usage
  • Click on Yes to run the configuration program
  • You will see a new page, entitled "Internet Setup Preferences" on which you must supply information for the network configuration program. In most cases, the default settings already filled out on this page are sufficient. If your computer must connect to the Internet through a firewall at your institution, you may need to check the box marked "Outgoing Connections Only." If you select this option, your client computer will make only outgoing connections to the NCBI. Next, fill out the page entitled "Dispatcher Internet Address." Again, in most cases, the default dispatcher 130.14.25.211 is sufficient. On the next page, "Entrez Service Selection," select the Entrez service to receive the broadest class of service. If, after clicking on Next Page, you receive a message that Entrez service is not availabe, you may need to go back one page and select a different dispatcher. Once your configuration is complete, click on Accept to save new new configuration. You must restart the program for the changes to go into effect. If you have problems setting up the network configuration, contact

  Sun users: read this note regarding Sun keymaps.

• Running the net configure program will create a new file in the system administrator's home directory called .ncbirc, and modify the existing file called .sequinrc.
• Set up a common area (directory) on the server for the Sequin files (for example, create a directory on the server called "Sequin")
• Copy the Sequin data and errmsg directories from the system administrator's sequin directory to this common area
• Move (not copy) the four Sequin configuration files from the system administrators home directory into the common area. These configuration files include the original .ncbidtrc and .nlmstmanrc, the modified .sequinrc, and the new .ncbirc .
• Copy the Sequin executable to a common area on the server where binaries are stored (for example, a bin directory)
• Since the .ncbirc file was created in the system administrator's home directory and moved to the common area, some paths which it points to are now incorrect. Edit the .ncbirc file, now in the common area, to point to the location of the data and errmsg directories, also in the common area. The .ncbirc file should contain the following lines:

  [NCBI]
  DATA=pathToDataDirectory

  [ErrorProcessing]
  MsgPath=pathToErrmsgDirectory
  EO_BEEP=No

  where pathToDataDirectory and pathToErrmsgDirectory are the actual paths to those common directories.

• Set the $NCBI environment variable on each user's machine to point to the common directory (the "Sequin" directory)

Note: Sequin will not write to any configuration files which are present in the common area. Thus, an individual user cannot overwrite either the Sequin program or any of its configuration files. Sequin looks for configuration files first in the current directory, then in the user's home directory, and finally in the area to which the $NCBI variable points. If an individual user makes changes to the configuration file, these changes will be saved in a file in the user's home directory.

Revised May 2, 1997

If you have problems downloading Sequin from the EBI ftp server, please contact http://www.ebi.ac.uk/support/

Other comments and questions to: info@ncbi.nlm.nih.gov