Re: Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::

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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=E2=80=AFPM Schlachter, Kai <
[email protected]> 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 o=
n
> 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 container=
s
> (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=E2=80=99t think it=E2=80=99=
s a good idea to
> start implementing / contributing with such a complex thing.
>
>
>
> Greetings,
>
>
>
> Kai
> _______________________________________________
> Bioperl-l mailing list
> [email protected]
> https://mailman.open-bio.org/mailman/listinfo/bioperl-l
>

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<div dir=3D"ltr"><div>Hello Kai,<br><br>Interesting question (although I&#3=
9;m viewing it from a Python and Biopython perspective).</div><div><br></di=
v><div><a href=3D"https://mariadb.com/kb/en/upgrading-from-mysql-to-mariadb=
/">https://mariadb.com/kb/en/upgrading-from-mysql-to-mariadb/</a> suggests =
this should</div><div>just work, with existing MySQL bindings treating Mari=
aDB as a newer version.</div><div><br></div><div>It sounds like your set is=
 breaking in the Perl module DBD::mysql?<br></div><div><a href=3D"https://m=
etacpan.org/dist/DBD-mysql">https://metacpan.org/dist/DBD-mysql</a></div><d=
iv><br></div><div>Looking at the change log there are entries from this yea=
r, and multiple mentions</div><div>of MariaDB - so I would expect this to w=
ork:</div><div><a href=3D"https://metacpan.org/release/DVEEDEN/DBD-mysql-5.=
008/source/Changes">https://metacpan.org/release/DVEEDEN/DBD-mysql-5.008/so=
urce/Changes</a></div><div><br></div><div>Can you take a look at their issu=
e tracker <a href=3D"https://github.com/perl5-dbi/DBD-mysql">https://github=
.com/perl5-dbi/DBD-mysql</a></div><div>and see if you&#39;ve hit a known is=
sue?</div><div><br></div><div>Also can you double check the version of DBD:=
:mysql you have installed?</div><div><br></div><div>Peter<br></div><div><br=
></div><div><br></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr"=
 class=3D"gmail_attr">On Fri, Aug 30, 2024 at 12:15=E2=80=AFPM Schlachter, =
Kai &lt;<a href=3D"mailto:[email protected]">kai.schlachter=
@dkfz-heidelberg.de</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quot=
e" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204)=
;padding-left:1ex"><div class=3D"msg-8182923572737763296">





<div lang=3D"DE" style=3D"overflow-wrap: break-word;">
<div class=3D"m_-8182923572737763296WordSection1">
<p class=3D"MsoNormal">Hi there,<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">I took over an older project to=
 modernize the underlaying hardware / software.<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">This also involves the use of g=
browse, which in turn relies quite a lot on BioPerl.<u></u><u></u></span></=
p>
<p class=3D"MsoNormal"><span lang=3D"EN-US"><u></u>=C2=A0<u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">As our freshly provided servers=
 are all Debian based and we are highly encouraged to use a most recent ver=
sion of Debian inside of our containers (docker), I ran into the following =
issue:<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">Debian no longer supports MySQL=
 but has switched to MariaDB, which leads me to the following:<u></u><u></u=
></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US"><u></u>=C2=A0<u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">I tried to install gbrowse, res=
olving all the dependencies and stuff that came along. I also was able to c=
ompile the DBD::MariaDB as this is the required module for MariaDB-Connecti=
ons.<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">However I was not able to find =
a Module in Bio::DB:SeqFeature:Store::DBI called MariaDB, there is only Mys=
ql :(<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">Although both adaptors should s=
hare at least some basic functionality, it is not possible to install the M=
ysql-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).<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US"><u></u>=C2=A0<u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">Are there any plans / ideas to =
add mariadb support to the modules?<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">I am not an original perl progr=
ammer so I don=E2=80=99t think it=E2=80=99s a good idea to start implementi=
ng / contributing with such a complex thing.<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US"><u></u>=C2=A0<u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">Greetings,<u></u><u></u></span>=
</p>
<p class=3D"MsoNormal"><span lang=3D"EN-US"><u></u>=C2=A0<u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US">Kai<u></u><u></u></span></p>
</div>
</div>

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l.org</a><br>
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noreferrer" target=3D"_blank">https://mailman.open-bio.org/mailman/listinfo=
/bioperl-l</a><br>
</div></blockquote></div>

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