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

[Peter Cock]

Hello Kai,

Interesting question (although I'm viewing it from a Python and Biopython
perspective).

https://mariadb.com/kb/en/upgrading-from-mysql-to-mariadb/ suggests this
should
just work, with existing MySQL bindings treating MariaDB as a newer version.

It sounds like your set is breaking in the Perl module DBD::mysql?
https://metacpan.org/dist/DBD-mysql

Looking at the change log there are entries from this year, and multiple
mentions
of MariaDB - so I would expect this to work:
https://metacpan.org/release/DVEEDEN/DBD-mysql-5.008/source/Changes

Can you take a look at their issue tracker
https://github.com/perl5-dbi/DBD-mysql
and see if you've hit a known issue?

Also can you double check the version of DBD::mysql you have installed?

Peter



On Fri, Aug 30, 2024 at 12:15 PM Schlachter, Kai <
kai.schlachter at dkfz-heidelberg.de> wrote:

> Hi there,
>
>
>
> I took over an older project to modernize the underlaying hardware /
> software.
>
> This also involves the use of gbrowse, which in turn relies quite a lot on
> BioPerl.
>
>
>
> As our freshly provided servers are all Debian based and we are highly
> encouraged to use a most recent version of Debian inside of our containers
> (docker), I ran into the following issue:
>
> Debian no longer supports MySQL but has switched to MariaDB, which leads
> me to the following:
>
>
>
> I tried to install gbrowse, resolving all the dependencies and stuff that
> came along. I also was able to compile the DBD::MariaDB as this is the
> required module for MariaDB-Connections.
>
> However I was not able to find a Module in Bio::DB:SeqFeature:Store::DBI
> called MariaDB, there is only Mysql :(
>
> Although both adaptors should share at least some basic functionality, it
> is not possible to install the Mysql-Version on a recent Debian because
> DBD::MySQL will refuse to work with mariadb because of a version mismatch
> (expected 8.x but reported 10.y).
>
>
>
> Are there any plans / ideas to add mariadb support to the modules?
>
> I am not an original perl programmer so I don’t think it’s a good idea to
> start implementing / contributing with such a complex thing.
>
>
>
> Greetings,
>
>
>
> Kai
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> Bioperl-l at bioperl.org
> https://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
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