[EMBOSS] Negotiating a proxy server

[Pierre Scotney]

Hello,

I have installed EMBOSS-2.8.0 and using the CLI (while I try to get Jemboss 
to work).  I am trying to configure the emboss.defaults file so that I can 
access the EMBL and UNIPROT SRS databases at the www.ebi.ac.uk site.  I have 
read the Administrators guide and I am unsure if I should use SRSWWW or URL 
methods for access.  I have set the entry in emboss.default to:

DB embl [ type: N method: srswww format: embl release: EBI
   dbalias: embl
   url: "http://srs.ebi.ac.uk/cgi-bin/wgetz"
   comment: "EMBL from EBI"
   ]

DB uniprot [ type: P method: srswww format: swiss release: EBI
   dbalias: uniprot
   url: "http://srs.ebi.ac.uk/cgi-bin/wgetz"
   comment: "UNIPROT from EBI"
   ]

but then I try

$ seqret -sequence embl:AL627275 -outseq embl_AL627275
Reads and writes (returns) sequences
Error: Unable to read sequence 'embl:AL627275'
Died: seqret terminated: Bad value for '-sequence' and no prompt

This problem is compounded by the fact that I have to access the internet 
via a proxy server which I have SET emboss_proxy "myproxyserver:8080" in the 
emboss.default file.  The problem is the proxy server normally requires a 
username and password (which works for the Galeon browser).  Who can I get 
EMBOSS to issue a username and password to the proxy server for 
authentification?

I apologise for so many questions.

Regards

--
Dr Pierre Scotney
Melbourne
Australia

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