[Bioperl-l] internet proxy

[Torsten Seemann]

Dr. Christoph Gille wrote:
> Please apologize my stupid question:
> How do I tell BioPerl that I have a http proxy ?
> I try  Bio/Tools/Analysis/Protein/Sopma.pm
> which computes second struct predictions using a HTTP server.
> Since I do not have direct Internet I've  set the variables http_proxy and
> HTTP_PROXY to the proxy server.
> But Sopma is not able to connect to the Internet.
> At home with direct Internet it worked fine.
> All other Internet programs can cope with the proxy without problem.
> For example wget http://www.google.de fetches the data.

Sopma.pm ISA Bio::WebAgent ISA LWP::UserAgent.
LWP::UserAgent does the actual HTTP work.
Try:

  my $sopma = Bio::Tools::Analysis::Protein::Sopma->new( ... );
  $sopma->env_proxy;  # tell LWP::UserAgent to use proxy env. vars.
  $sopma->run;

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/