[Bioperl-l] RemoteBlast by Bio::Perl Through proxy

[CHANDAN SINGH]

Hi Sachin

if u have found the solution to ur prob , u can escape reading henceforth.
It seems setting the env variable containig login and password does not
work with LWP , still u can try setting it as
http://login:pass@server:port <http://login:pass@server/>
but i dont think it will work .

I am going to ask u to try something similar to what i had done for the
proxy
earlier . I know messing up with the modules is not a good idea and even
Jason
had expressed his dislike to my previous solution because of it but i dont
think
using Bio::Perl leaves another option . If u can use
Remoteblast.pm<http://remoteblast.pm/>directly ,
u can use objects to meet ur need .Anyway , if in the LWP::UserAgent module
u add the line

$request->proxy_authorization _basic("login" , "passwd" ) ;

in the
sub request {
after its first line , it might work .

I could not check it , as my proxy does not require authentication .
I hope it works , though i did not try it .
Do respond .
Cheers
Chandan


On 9/25/05, Jason Stajich <jason.stajich at duke.edu> wrote:
>
> If you look at the code for setting the proxy in the module you see
> that we are just delegating to the LWP::UserAgent object, so read the
> documentation for LWP::UserAgent as that is where the proxy stuff is
> handled. There should be a way to do all of this via environment
> variables as well - this is outlined in the LWP document, you may
> have to add $blast->ua->env_proxy call to your code, I'm not sure.
>
>
> sub proxy {
> my ($self,$protocol,$proxy) = @_;
> return undef if ( !defined $self->ua || !defined $protocol
> || !defined $proxy );
> return $self->ua->proxy($protocol,$proxy);
> }
>
>
> On Sep 21, 2005, at 9:40 AM, Sachin Pundhir wrote:
>
> > Hi
> > I have a problem regarding performing remote blast through
> > RemoteBlast.pmmodule if Bioperl. I am getting the error
> > 500 Can't connect to www.ncbi.nlm.nih.gov:80<http://www.ncbi.nlm.nih.gov:80>
> > <http://www.ncbi.nlm.nih.gov/>(Bad hostname '
> > www.ncbi.nlm.nih.gov <http://www.ncbi.nlm.nih.gov> <
> http://www.ncbi.nlm.nih.gov>')
> > I am not able to set the proxy setting, which i have done
> > successfully to
> > retrieve a sequence from the genbank.
> > It will be great help from your side.
> > waiting for ur timely help.
> > Sachin
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>
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