[Bioperl-l] bioperl - must it have mysql to work?

[Jason Stajich]

On Thu, 7 Mar 2002 Sciencelife@aol.com wrote:

>
>
> it sounds like I want to use bioperl "core" then.  Which download is
> that?  I want for Solaris sparc & for windows.
>
Well you need both if you want to use our database implementation.
The core provides implementation of sequences and other
bioinformatics objects.  The db package is a specific implementation for
persistence of sequences and their related objects (annotations and
features). This is an area of active development so we don't have a
release package for the latest biosql db implementation.

You can get the core by going to bioperl.org and clicking on the link that
says "download latest stable release" on the front page.  Note that a 1.0
release will be out in a few weeks.  You can read all about this process
in the archives of this mailing list by following the link found at the
bottom of this message.

> I want to use with oracle if possible or if
> not then on its own merit with no particular
> database (if not with Oracle).
>
> I want to use bioperl without using mysql or
> postgres ( if possible) unless you can tell me
> why is should use mysql (given that I'd rather
> not manage 2 databases since we use oracle).
>
It's open source.  It's fast.  It's easy to setup and maintain.  You're
welcome to implement the bioperl db layer for Oracle if you are stuck on
not using the solutions we've implemented.  The whitehead and cshl folks
may be looking into doing this anyways in a while so you can either join
their effort when they get started or wait until it is completed.

-jason
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu