[Bioperl-l] bioperl-db and postgres8.3 - status query

Dan Kortschak dan.kortschak at adelaide.edu.au
Wed Aug 18 22:15:03 EDT 2010


Hi Everyone,

I'm wanting to set up a persistent data store for some of my work and am
in the process of choosing parts for my system. From my brief look
around I think I'd like to use BioSQL (next best choice being Chado -
but BioPerl bindings in bioperl-db for BioSQL being the decider here),
but have noticed comments some time back that bioperl-db and PostgreSQL
8.3 (my prefered engine - though MySQL is possible, but makes the whole
system messier) don't play well together.

What is the status of the casting expectation conflict between
bioperl-db and Pg8.3? The scripts are run with safe data, so
placeholders aren't strictly crucial (though speed may be an issue?) and
`$dbh->{pg_server_prepare} = 0;' seems like it could be an option.

Can anybody provide any advice on this issue?

thanks
Dan Kortschak



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