[Bioperl-l] Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::

[Fields, Christopher J]

I agree, this should be a simple way to get it going, and though it would likely result in code duplication it could eventually require settings specific to MariaDB (though as Tim mentioned it’s essentially a drop in replacement).

Kai, if you want to make a fork and then submit a pull request, I’m more than happy to test and add this to a new release.  One thing that would be beneficial is if you can get some basic tests running for it; IIRC this is a bit hacked in for the various DBI plugin modules.

chris

From: Bioperl-l <bioperl-l-bounces at bioperl.org> on behalf of Timothy Parnell <timothy.parnell at hci.utah.edu>
Date: Tuesday, September 3, 2024 at 12:19 PM
To: bioperl-l at bioperl.org <bioperl-l at bioperl.org>
Subject: Re: [Bioperl-l] Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::
Regarding support for DBD::MariaDB, here is one (naive), hack solution: Simply copy the Bio/DB/SeqFeature/DBI/mysql.pm file as mariadb.pm, and search and replace “MySQL” with “MariaDB” as appropriate (watch capitalization, etc). Since MariaDB is (more or less) a drop-in replacement for MySQL, in theory this should work just fine. If I remember correctly, the SQL commands and structures are not terribly complicated and fairly standard, so I wouldn’t expect much more modification. If it does work, it might be worth a pull request.

Tim

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