[EMBOSS] [Fwd: mEMBOSS: Jemboss and proxy servers]

E. Hack Ethan.Hack at ncl.ac.uk
Tue Jul 24 11:01:51 UTC 2007

Perfect!  Problem solved.  I think it would be worth adding this 
information somewhere conspicuous (for Windows, the README.win file 
would be good, as it has high visibility) - everything else in the 
installation is pretty much automatic.

Thanks very much.

Ethan Hack

On Tue, 24 Jul 2007, you wrote:

> Hi Ethan
> Try editing the jemboss.properties file in :
> mEMBOSS\jemboss\jar\resources\jemboss.properties
> And add EMBOSS_PROXY to the embossEnvironment entry, see the documentation
> for the jemboss.properties file at:
> http://emboss.sourceforge.net/Jemboss/install/properties.html
> So try adding a line like this:
> embossEnvironment=EMBOSS_PROXY=wwwcache.ncl.ac.uk:8080
> Then re-run Jemboss. If this works you should be able to access external
> databases.
> To get the jemboss browser working for the help files I think you can just
> edit the properties of the jemboss shortcut on your desktop and add "java
> -DproxyHost= wwwcache.ncl.ac.uk -DproxyPort=8080 -jar ..." to the start of
> the Target: field.
> Regards
> Tim
> On 24/7/07 10:25, "ajb at ebi.ac.uk" <ajb at ebi.ac.uk> wrote:
>> ---------------------------- Original Message ----------------------------
>> Subject: [EMBOSS] mEMBOSS: Jemboss and proxy servers
>> From:    "E. Hack" <Ethan.Hack at ncl.ac.uk>
>> Date:    Tue, July 24, 2007 9:28 am
>> To:      emboss at lists.open-bio.org
>> --------------------------------------------------------------------------
>> I have installed the new Windows mEMBOSS.  To use external databases, I
>> have to connect to the web via a proxy server.  When running EMBOSS
>> programs from a Windows command prompt, I can do this successfully using
>> the EMBOSS_PROXY environment variable.  With Jemboss, however, external
>> connections to databases give me a "socket connect failed" error
>> message, and I can't reach external help files either.
>> The default setting in my Java Control Panel is "Use browser settings".
>> I have tried changing this to "Use proxy server" and I have also tried
>> specifying the proxy server from inside Jemboss under Preferences -
>> Jemboss - Browser Proxies.  Neither of these methods seems to make any
>> difference.
>> I'd be grateful for any suggestions as to what the problem might be. I
>> hope the question is an appropriate use of this mailing list and
>> apologise if it isn't.  I suspect the solution may be helpful to others
>> too (even it should be obvious...) - I don't think there's anything
>> particularly unusual about the way my computer is set up.
>> Ethan Hack

Dr Ethan Hack                           | E-mail: Ethan.Hack at ncl.ac.uk
School of Biology and Psychology        | Phone:  +44 191 222 8576
Newcastle University                    | Fax:    +44 191 222 5228
Newcastle upon Tyne  NE1 7RU, UK

More information about the EMBOSS mailing list