JALview connection.

Hello Michael.

I have had a problem submitting jobs for sequence alignments in JALVIEW.
I wanted to ask you where I might start to track down the problem.

What is the problem - do you get a 'Server error' .. or is nothing happening at all ?

To start with, you need to check if any error messages are being output by Jalview. I assume you're using the latest version of Jalview. Try opening the Jalview java console (Desktop -> Tools -> Java console), and once the window is open, try to submit the job again. Hopefully, some error messages will be output in the console - if there are, simply cut and paste the whole lot into an email and sent it to me! Otherwise, you'll need to follow the bug report instructions in the FAQ ( http://www.jalview.org/faq.html#reportbug )

the alignment server appears to be running fine, so its most likely a problem at your end. There are two likely issues - one is a firewall on your machine blocking Java, the other is that you need to configure your proxy correctly. Either way, an easy test for network connectivity is to open the DAS source tab in the feature settings dialog box. If there are no sources listed, then Jalview couldn't contact the registry.

If you need a proxy, and you can't see any sources, then check and edit the proxy settings in the Preferences dialog box (the connections tab), hit ok, then quit and restart Jalview. If that doesn't fix the problem, or you don't need a proxy, then its possible that a firewall on your machine is the issue. On windows, you'll need to enable javaw.exe to access the internet.

That should be enough to get you started - let me know how you get on!


On 07/06/2010 12:15, michael wilson (BI) wrote:

J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
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