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The Wisconsin Package - GCG FAQs | Print |
These are the GCG FAQs. They are the key to using the GCG software properly.
  1. I would like to use GCG -- how do I get started?
  2. How do I print to my laboratory printer from GCG and Seqlab?
  3. My print-out does not fit on one page, is there a way to control the printing formats?
  4. How do I cut and paste sequences?
  5. How do I search for information on GCG?
  6. What is the preferred program for telnet for PC and Macintosh?
  7. What is SSH and where can I get it?
  8. How do I query network databases with BLAST?
  9. How do I upload sequences? Download sequences?
  10. How do I format graphics and sequences from GCG for publishing?
  11. What 3rd party software is currently available?
  12. I'm moving my sequences from another application, how can I convert all my sequence files to another format?
  13. I have a compressed file, what do I have to do to expand and use it?
  14. I can't login to Amadeus, what's wrong?
  15. I can't get to my BioDesk session, it tells me "VNC authentication failed"
  16. Who do I call for help?

 

  1. I would like to use GCG -- how do I get started?

    Version 10.3 of GCG is currently available.

    First thing is to request a BioDesk account to run the GCG package. There is a form available online. You will then be sent a login, password, and links to instructions on how to establish a BioDesk session on the BCF server.

    The programs of the GCG package can be run in two ways, either from the command line, or through Seqlab with an X-windows emulator.

    • Command-line GCG consists of initializing the GCG package and then typing the commands. It can be run through any telnet session, on or off-campus
      (To initialize version 10.3 type: gcg).


    • The Seqlab graphical interface for GCG consists of starting a BioDesk session from telnet, then using a small viewer program to display the applications on your local machine.

    Documentation available online includes the Tutorials used for our introductory workshops, Introductions to the basic GCG system and a full Software listing.

    Full documentation of GCG commands is available in the GCG Manual.

    For help with GCG usage, there is a search engine at the top of the page that can be used to search through the GCG documentation on our site, as well as email support at: This e-mail address is being protected from spam bots, you need JavaScript enabled to view it

     

  2. How do I print to my laboratory printer from GCG and Seqlab?

    A print queue must be established to direct output from GCG to your local printer. Send email to This e-mail address is being protected from spam bots, you need JavaScript enabled to view it , including the following information:

    1. Name of Laboratory/PI
    2. Printer information:
      1. Printer brand and model#
      2. IP# (Internet Address) of the machine attached to the printer.
      3. The Operating System (e.g. MacOSx/Win9x/NT).
      4. The Printer Name (for PCs this is defined under 'Sharing...' in Start:Settings:Printers, right-click on icon and select 'Properties' -- the printer must be shared)
      5. If the printer is networked directly, the IP# of the printer.
    3. Building & Room where printer is located.
    4. Full name, email, and phone of contact person.

    We may have to install additional software on your local machine to enable local printing.

     

  3. My print-out does not fit on one page, is there a way to control the printing formats?

    GNU enscript 1.5 is installed for formatting all text print jobs.

    To use enscript, replace the 'lpr' command under print [in SeqLab and command line GCG ] with:

    'enscript -v -G2r -f Courier9 -Pmyprinter'

    • The '-v' is for verbose mode: it will indicate how many pages its printing.
    • The '-G2r' is for '2' columns per page in landscape mode [the 'r' is for landscape].
    • The '-Pmyprinter' is for selecting the print queue, where '-P' is the queue name selector and 'myprinter' is the queue, replace myprinter with the name of your printer [if you already have a queue setup - see the previous question].

    This command can also be abbreviated with the following aliases:

      glpr Verbose mode, 2 columns landscape, Courier 9 point.
      glpr4 Verbose mode, 2 columns landscape, Courier 4 point.
      glpr5 Verbose mode, 2 columns landscape, Courier 5 point.
      glpr6 Verbose mode, 2 columns landscape, Courier 6 point.
      glpr7 Verbose mode, 2 columns landscape, Courier 7 point.
      glpr8 Verbose mode, 2 columns landscape, Courier 8 point.
      glpr Verbose mode, 2 columns landscape, default Courier 9 point.
      glpr10 Verbose mode, 2 columns landscape, Courier 10 point.
      glpr11 Verbose mode, 2 columns landscape, Courier 11 point.
      glpr12 Verbose mode, 2 columns landscape, Courier 12 point


    enscript provides the filename, date, time and page number as a header on each page, while correctly wrapping lines to make the printout more readable.

    Type 'man enscript' at the command prompt for full documentation.

     

  4. How do I cut and paste sequences?

    Cutting and pasting can be difficult.

    For instructions on how to Cut/Copy from BioDesk and paste into Windows/Mac applications, please go to the BioDesk pages on Copying & Pasting

     

  5. How do I search for information on GCG?

    A search engine has been established at this site to search local documentation and help pages. The documentation pages at the GCG site can also be searched directly.
    A good resource for Internet-wide searching is Google.

     

  6. What is the preferred program for telnet for PC and Macintosh?

    For Windows9x/NT/2K/XP, the shareware emulator QVT Terminal is available, free for educational use.

    For Mac users, NCSA Telnet is freely available from NSCA.

    For both platforms, SSH is the new preferred method to connect to Amadeus for command line interaction and file transfer.

     

  7. What is SSH and where can I get it?

    SSH is "Secure Shell"; telnet is also a "shell" program, but it transmits your password in clear text and and cares nothing for how secure the destination host is. SSH encrypts your password and requires an authentication key to be generated and set between host and client (this prevents your session from being rerouted to another machine). SSH is freely available to U of A Students, Faculty and Staff through the campus site license web site.

  8. How do I query network databases with BLAST?

    When GCG 9.0 was first released, the BLAST command allowed direct queries to database resources at the NIH. This function is now covered with NETBLAST under GCG 10.3.

     

  9. How do I upload sequences? Download sequences? Convert Sequences?

    Available options for transferring files may depend on what platform you are using.

    For PC users, please see our How-To Page page for instructions on how to transfer files via sftp to your BioDesk folder.


    For Mac users connected to the internet, the best option is Fetch or Fugu.

  10. How do I format graphics and sequences from GCG for publishing?

    This isn't an easy question to answer quickly.
    In fact, we've designed an entire workshop to cover this topic:

    'Preparing Data for Publication' is available as a pdf file from our Workshops & Tutorials page.

     

  11. What 3rd party software is currently available?

    GCG and Seqlab allows the addition of 3rd party software to function as 'extensions', expanding the normal GCG functionality. A list of current software is available.
    For additional processing software, send inquiries to This e-mail address is being protected from spam bots, you need JavaScript enabled to view it .

     

  12. I'm moving my sequences from another application, how can I convert all my sequence files to another format?

    We recommend an available freeware program by GeneStudio called SeqVerter. This is a multifunction PC based (Win95/98/NT) program that allows a variety of sequence conversions and manipulations. Including batch conversions, sequence merging, splitting, and trimming.

     

  13. I have a compressed file, what do I have to do to expand and use it?

    Programs for expanding compressed archives are available from:

    Aladdin Systems - UnStuffit Lite for Mac users.
    Nico Mak Computing - WinZip for PC (Win9x/NT) users.

     

  14. I can't login to Amadeus, what's wrong?

    If you're unsure why your connection is being refused, please check the Session Manager page for information about the condition of Amadeus.

    Telnet and SSH connections from off campus may be refused depending on your internet service provider. If you have a great need to work from home and/or are still unsure of why you are being refused access, please This e-mail address is being protected from spam bots, you need JavaScript enabled to view it us for assistance.

     

  15. I can't get to my BioDesk session, it tells me "VNC authentication failed"

    This usually means that your BioDesk session has been killed for some reason.
    Go to the Session Manager page to see if there are/were any problems with the server.
    If that checks out OK, telnet or SSH to Amadeus and check to see if your account is over quota:

    amadeus% quota -v

    If so you may need to delete or compress some files before attempting to start a new session.

    If you still cannot connect, please This e-mail address is being protected from spam bots, you need JavaScript enabled to view it us for assistance.

     

  16. Who do I call for help?

    GCG is owned by Accelrys, and support is available here:
    http://www.accelrys.com/support/bio/genhelp/
    For general questions contact:
    This e-mail address is being protected from spam bots, you need JavaScript enabled to view it