[BioSQL-l] Passwords on biosql databases

[Peter]

On Tue, Nov 25, 2008 at 11:09 AM, David Martin
<d.m.a.martin at dundee.ac.uk> wrote:
>
> I have set up a biosql database on Postgres. The Bio::DB::BioDB module
> croaks complaining that it needs the password. I have tried the obvious
> things (-password -passwd and reading what docs I could find) but to no avail.
>
> Any clues?

Your email only just reached me - maybe there was a delay somewhere.
However, in case you are still stuck, and assuming no one else has
answered in the mean time I'll try and help.

As an aside, I would say this is really a question for the BioPerl
mailing list, as it is about the BioPerl bindings to BioSQL.

>From a quick look at the BioPerl code for load_seqdatabase.pl, my
guess is you need to use "pass" as the argument name, e.g.

my $db = Bio::DB::BioDB->new(-database   => "biosql",
                             -printerror => $printerror,
                             -host       => $host,
                             -port       => $port,
                             -dbname     => $dbname,
                             -driver     => $driver,
                             -user       => $dbuser,
                             -pass       => $dbpass,
                             -dsn        => $dsn,
                             -schema     => $schema,
                             -initrc     => $initrc,
                             );


Peter