1. I can't login to Amadeus - what's wrong?

Be sure that the Caps Lock key has not been pressed while you are typing your password! 

Also, if you have pasted the session info into the VNC connection box (e.g. amadeus.biosci.arizona.edu:15), be sure that there are NO BLANK SPACES at the beginning of this phrase (e.g. before 'amadeus')

If you're unsure why your connection is being refused, please check the ARL Support Site page for information about the status 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.

2. 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 (gzip) 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.

3. 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.

4. How can I see my disk space quota and usage?

Use the command

    quota  -v

to see your disk quota and usage.  The units are 1kb. To see how much space is used by each of your subdirectories, use the command:

    du  -k 

To see which directories are taking up the most space, use this command:

    du  -k  |  sort  -n

5. I have a compressed file or 'tar ball', what do I have to do to expand and use it?

If the file has a .gz extension, use the 'gunzip' command:

    gunzip  file.gz

If the file has a .Z extension, use 'uncompress':

    uncompress file.Z

If the file is a 'tar ball', it will usually have a .tar extension.  To see the contents of a tar file (without extracting), use the command:

    tar  tvf  file.tar

Notice whether the tar file contents are contained in a directory, and if not, make a directory and move the tar file into it before extracing the files:

    mkdir  newdir

    mv  file.tar  newdir

    cd  newdir

    tar  xvf  file.tar

If you have a gzipped tar file (extension .tar.gz), you can combine the commands:

    gunzip  -c  file.tar.gz  |  tar tvf -

6. How do I print to my laboratory printer from Biodesk?

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:

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

7. 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, type the following command:

8. How do I copy and paste sequences?

Copying and pasting can be tricky.  To assist in transfer of sequence data, a tool for moving sequences has been developed.

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

9. My job is taking too long on amadeus - how can I speed things up?

Many applications are available for the Condor grid and/or the campus supercomputer.  Examples are BLAST, FASTA, Paup, and the PAML suite.  See the Condor Grid and High Performance Computing FAQs.

10. How do I change my amadeus password?

It is important to choose  a secure password and not use a name or a word that is in the dictionary!  For hints on creating a secure password, see the UA Information Security and Privacy FAQs .  To change your amadeus password, open an Xterminal window and use the passwd command.  You will be prompted to enter your old password, then you will enter your new password and confirm it.

11. How do I change my BioDesk password?

Remember that your BioDesk password is independent of your amadeus password.  If you would like to have the ability to get help from the BCF staff by having a staff member access your BioDesk session, you will need to share your BioDesk password with us.  The BioDesk password can be changed at any time by clicking on 'To modify your BioDesk settings, click here' at the BioDesk Session Manager page.

12. How do I change my mySQL password?

At the mysql prompt, type:

SET PASSWORD = PASSWORD('newpasswd');

where newpasswd is your new password.

13. How can I change the size of the BioDesk screen?

 You can set an environment variable to do this.  From your home directory, use the following command to determine whether you have a .cshrc file:

    ls -la .cshrc 

If you do not have this file, you may copy it from the /etc directory using the command:

    cp  /etc/.cshrc  .cshrc 

Use the BioDesk editor (nedit) to open the .cshrc file and add a line specifying the desired dimensions of your BioDesk window, e.g.:

   setenv geometry "1680x1050";

After saving the .cshrc file, this setting will take effect the next time you start a new BioDesk session.