Chado with MySQL

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Chado with MySQL

sganesh02
Hello Scott and other members at GMOD,
 
I am looking at setting up a MySQL database for genomic data and to use the Chado schema. Our group would prefer to use MySQL , as some of our other data (bases) and systems use MySQL.
The GMOD pages do state that the community does not support MySQL actively, but some of the information/documentation seemed to be dated very old.
It would be very helpful if you could give us some current information on:
1)      How much change is required to the existing Chado code (DDL, loading scripts/tools etc) to make it work for MySQL (esp the newer release, since the GMOD pages refer to somewhat older versions of MySQL) ?  
2)      If there are tool problems while using them with MySQL, does the GMOD group provide any support for fixing the issues ?
3)      Any other potential problems we should take into account before we start towards adopting MySQL for Chado?
Thanks a lot
Ganesh

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Re: Chado with MySQL

Scott Cain
Hi Ganesh,

We continue to not support MySQL, but I'll try to answer your questions below.

Scott


On Mon, Feb 11, 2013 at 2:25 PM, Ganesh S Moorthy <[hidden email]> wrote:

> Hello Scott and other members at GMOD,
>
> I am looking at setting up a MySQL database for genomic data and to use the
> Chado schema. Our group would prefer to use MySQL , as some of our other
> data (bases) and systems use MySQL.
> The GMOD pages do state that the community does not support MySQL actively,
> but some of the information/documentation seemed to be dated very old.
> It would be very helpful if you could give us some current information on:
> 1)      How much change is required to the existing Chado code (DDL, loading
> scripts/tools etc) to make it work for MySQL (esp the newer release, since
> the GMOD pages refer to somewhat older versions of MySQL) ?

For the DDL, probably not too much.  SQL::Translator (perl module)
could probably do the trick.  Range/GIS functions that are used for
location indexing probably won't translate.  I have no idea what
similar sorts of things are available for MySQL; might have to revert
to B-tree indexes.

Tools could be interesting: command line tools probably would vary
considerably on how much would need to be done.  The GFF loading
script is written so that the primary class it uses could be
subclassed, allowing you to make a MySQL loading class, then you'd
have to track down and replace, at a minimum, the portions of the code
that have to do with loading the database, since those are RDMS
specific; it wouldn't surprise me if queries had to be changed too.
Of course Tripal is only written to support PostgreSQL, so if you
wanted to use that, it would require translating.  The GBrowse
adaptor, Bio::DB::Das::Chado (which is a god-awful mess and should be
rewritten anyway) assumes PostgreSQL as well.


> 2)      If there are tool problems while using them with MySQL, does the
> GMOD group provide any support for fixing the issues ?

I would certainly do as much as I could to help.  I think the huge
bulk of what would be needed would be grunt work, and perhaps only a
few items would really require help, but that is just a guess..

> 3)      Any other potential problems we should take into account before we
> start towards adopting MySQL for Chado?

Yes, that you might sink a lot of time into it for very little
payback.  I'd think about using PostgreSQL long and hard before
deciding not to use it.  The biggest problem I think you're likely to
face is what other GMOD software you want to use (like Tripal) and
what would be involved in porting those too.


> Thanks a lot
> Ganesh
>
> ------------------------------------------------------------------------------
> Free Next-Gen Firewall Hardware Offer
> Buy your Sophos next-gen firewall before the end March 2013
> and get the hardware for free! Learn more.
> http://p.sf.net/sfu/sophos-d2d-feb
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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