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

[Fields, Christopher J]

Sorry, this got delayed a bit but I just pushed out a new Bio::DB::SeqFeature release, v 1.7.5.  Let me know if you have any issues with it!

chris

From: Schlachter, Kai <kai.schlachter at dkfz-heidelberg.de>
Date: Wednesday, September 18, 2024 at 8:01 AM
To: Fields, Christopher J <cjfields at illinois.edu>
Cc: bioperl-l at bioperl.org <bioperl-l at bioperl.org>
Subject: AW: [Bioperl-l] [Extern] - Re: Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::

Hi Chris,



This is great news und will facilitate our container building process.



I also hope this enables many projects to use the most recent tech stack on debian based distributions (many projects I got involved were using CentOS and now found themselves in a bad position as the support ended in June this year).



Greetings,



Kai

________________________________
Von: Fields, Christopher J <cjfields at illinois.edu>
Gesendet: Mittwoch, 18. September 2024 14:51:11
An: Schlachter, Kai
Cc: bioperl-l at bioperl.org
Betreff: Re: [Bioperl-l] [Extern] - Re: Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::

Thanks Kai. I merged that request and will work on a new point release for CPAN

Chris


On Sep 5, 2024, at 6:35 AM, Schlachter, Kai <kai.schlachter at dkfz-heidelberg.de> wrote:

Hi,

just to give you an update:
For the purpose I needed it, I was able to change the files to use MariaDB.
See the following pull request:
https://github.com/bioperl/Bio-DB-SeqFeature/pull/4<https://urldefense.com/v3/__https:/github.com/bioperl/Bio-DB-SeqFeature/pull/4__;!!DZ3fjg!-QX_z6zzyv4Wfl0sG0ILBNkvGSm0XUsW1FwDZtQGbo18vGmLvLHiaY8DSClaWt0ttUvPazvFJM6IIp84XoVjwj8TbAEBSQmWT7-Shxc$>

Greetings,
Kai Schlachter

Von: Bioperl-l <bioperl-l-bounces at bioperl.org> im Auftrag von "Schlachter, Kai" <kai.schlachter at dkfz-heidelberg.de>
Datum: Mittwoch, 4. September 2024 um 14:44
An: "bioperl-l at bioperl.org" <bioperl-l at bioperl.org>
Betreff: Re: [Bioperl-l] [Extern] - Re: Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::

Hi,

So I did my first steps towards creating a perl module although I am not a perl expert.
I also created a pull request to add MariaDB-Support to the project.
I did not find any test specifications, so I left those out of scope for the moment.

I will also try to see what happens if I add the module manually to our containers as long as it is not included in CPAN.

Greetings,

Kai Schlachter

Von: Bioperl-l <bioperl-l-bounces at bioperl.org> im Auftrag von "Fields, Christopher J" <cjfields at illinois.edu>
Datum: Mittwoch, 4. September 2024 um 00:02
An: Timothy Parnell <timothy.parnell at hci.utah.edu>, "bioperl-l at bioperl.org" <bioperl-l at bioperl.org>
Betreff: [Extern] - Re: [Bioperl-l] Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::

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

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