[Bioperl-l] DEBUGGED Remoteblast from Bio::Perl through proxy..cont

[Jason Stajich]

Thanks - I think you can just reset the LWP object directly if you  
like in your script code w/o modifying the module:
  $remoteblast->ua(LWP::UserAgent->new(env_proxy =>1));

We can certainly update the module to add this default initialization  
though.

You should submit it as feature request at http://bugzilla.open- 
bio.org/  so we can track whether or not someone has done it.

On Jul 8, 2005, at 4:00 PM, CHANDAN SINGH wrote:

> sorry for the reduplication of the mail but i had forgot to mention
> the  more  bugging bug which is How come ,others dont get this  
> problem or
> have i misunderstood something .
> do reply
>
> Hi eveybody
> Those of u ,having problem in blasting sequences from Bio::Perl  
> module through
> proxy  and getting
>                              "time  out "  or  " no route to host "  
> errors
> do  need to set the  environment proxy variable ( hello smarty we  
> all know it )
> and just give the following argument
>                                                     ( env_proxy => 1 )
> to
>                  $self->{'_ua'} = new LWP::UserAgent(  );
> as
>              $self->{'_ua'} = new LWP::UserAgent( env_proxy => 1 );
>
> in  the following sub in Bio::Tools::Run::RemoteBlast.pm
> sub ua {
>    my ($self, $value) = @_;
>    if( ! defined $self->{'_ua'} ) {
>        $self->{'_ua'} = new LWP::UserAgent(  );
>        my $nm = ref($self);
>        $nm =~ s/::/_/g;
>        $self->{'_ua'}->agent("bioperl-$nm/$MODVERSION");
>    }
>    return $self->{'_ua'};
> }
> I saw this bug in the stable version and also in the one downloaded
> from CVS yesterday .
>
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>

--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/