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

[CHANDAN SINGH]

Just now i found that their are environment variables as
proxy_user=login
proxy_passwd=pass

try using them
Chandan


On 9/27/05, CHANDAN SINGH <chandan.kr.singh at gmail.com> wrote:
>
> 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 <http://www.duke.edu/%7Ejes12>
> >
> >
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> >
>
>