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

[CHANDAN SINGH]

I know there are ways to do it but if u remember my program was nothing but 
the second example in bptutorial on net and no such one liner can help it .
You seem to be referring to your script which might be a different one .
That example is disheartening enough for a newbie . It seems there are options 
to include proxy if we directly use the RemoteBlast.pm . 

chandan 

On 7/12/05, Jason Stajich <jason.stajich at duke.edu> wrote:
> Sorry I meant just do this.
> $remoteblast->ua->env_proxy;
> 
> The ua function is not currently written to accept storing a new ua object
> but of course you can just do:
>  $remoteblast->{'_ua'} = LWP::UserAgent->new(env_proxy => 1).
> 
> -jason
> 
> 
> 
> On Jul 11, 2005, at 2:32 PM, Jason Stajich wrote:
> 
> 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 .
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
>  
> 
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l 
> 
>  
> 
> -- 
> 
> Jason Stajich 
> 
> jason.stajich at duke.edu 
> 
> http://www.duke.edu/~jes12/ 
>  
>