[Bioperl-l] Bioperl install tests behind firewall

[Jason Stajich]

I don't think the tests are picking up the proxy information
but you set the proxy with
my $db = new Bio::DB::GenBank;
$db->proxy(...)

See
% perldoc Bio::DB::WebDBSeqI

There are proxy and authentication methods.

The modules which use LWP should p/u the proxy info from ENV variables
while others use Lincoln's HTTPget module which I'm not sure is picking up
the env vars.  Need those behind proxies to put it through the paces I
guess to find where that info is not getting loaded.

-jason

On Wed, 30 Jul 2003, simon andrews (BI) wrote:

> Dear All,
>
> I'm just setting up Bioperl on a new server and have been bitten by something which I've come across before but never bothered to sort out.  Our servers sit behind a firewall and network access generally has to happen through a proxy.  I've set the http_proxy environment variable so programs like wget can still work properly.
>
> The problem is that the test suite in Bioperl doesn't seem to pick this up, so make test takes forever to complete (and seems to hang indefinitely in t/Perl.t).  Any module which needs to do network access just sits for ages, presumably waiting for something to time out.
>
> Is there some way to specify proxy information to Bioperl which I've missed in my reading of the docs, or if not is there an easy way to get make test to skip any tests requiring network access?
>
> Cheers
>
> Simon.
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu