[Bioperl-l] bioperl-db and postgres

[Anthony Underwood]

Hi all,

I am trying to set up a postgres database and enter sequences using the 
load_seqdatabase.pl. Being fairly new to databases I am a bit confused 
by the options. I understand that I need to create a database named 
biosql with the postgres schema. However I also have read in the HOWTO: 
(in the bioperl-db docs) that it is important to specify a dataset 
identifier. In this way it says that many 'biodatabases' can be stored 
in a single biosql instance.
Having looked at the load_seqdatabase.pl script I am not sure how this 
can be specified and am confused by what the difference is between 
database (which is set to biosql and can not be changed by command line 
options) and dbname  (which is set by default to biosql but can be 
changed in the options).

Please can anybody clarify this terminology (specifically dataset 
identifier, database and dbname). The namespace option is a bit 
mystifying to me also. Should that be left as bioperl?

On an aside, what is the best way to apply the postgres patch that was 
posted a few days ago on this mailing list? Should I download the 
bioperl-db tarball and put that in the appropriate place in the perl 
directory and then some how apply the patch?


Sorry to be so clueless on these items but I am a biologist with only 
self-taught knowledge of perl etc.

Many thanks in advance,


Anthony Underwood