MySQL backend problem

[Ramiro Costa]

Hi,

I'm trying to set up a MySQL database for use with GBrowse. To do so, I loaded GFF format file into a MySQL database named "test_db" using the bulk_load_gff.pl Perl script provided with the GBrowse package. Then I linked the MySQL database from the GBrowse configuration file (which I named test_db.conf) and opened the corresponding URL in my browser. When I did so a few database errors showed up in the browser, basically telling that the data necessary to render the plots was not found on the database; Apparently the Perl script that loaded the data into MySQL named all tables and fields with a starting "f" letter, not sure why, so I stripped out the f from the meta table and the errors disappeared but the data still doesn't show up.

Bellow I pasted the [GENERAL] section from my GBrowse configuration file:

[GENERAL]
description   = Sample Test by test_db
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn     test_db
                -user    nobody
 
I couldn't find in the GBrowse documentation how to set up a MySQL database for using with GBrowse, I did found the bulk_load_gff.pl script to load the data into the DB from a GFF source file, but when I did so I got the errors I mentioned before.

Please let me know what am I doing wrong or if you know how to solve this problem.

Thanks,

Ramiro

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[Scott Cain-3]

Hi Ramiro,

This is not your fault, and will be easy to fix: when you loaded with
the bp_bulk_load_gff.pl script, it loaded the data into a Bio::DB::GFF
database, but your configuration file is trying to use
Bio::DB::SeqFeature::Store.  The quickest fix is to change the adaptor
to use Bio:DB::GFF and the -adaptor line to dbi::mysql (with the
lowercase dbi) and add the 'f' back to fmeta.

The other alternative if you are using GFF3 is use the
SeqFeature::Store loader, bp_seqfeature_load.pl which works pretty
much the same way as the gff loader.

On a side note, it seems that perhaps we should add notes at the end
of the loads for both the gff and seqfeature::store loaders what
adaptor to use with GBrowse--it might cut down on the confusion.

Scott


On Thu, Sep 25, 2008 at 12:56 PM, Ramiro Costa
<costar@...> wrote:

> Hi,
>
> I'm trying to set up a MySQL database for use with GBrowse. To do so, I loaded GFF format file into a MySQL database named "test_db" using the bulk_load_gff.pl Perl script provided with the GBrowse package. Then I linked the MySQL database from the GBrowse configuration file (which I named test_db.conf) and opened the corresponding URL in my browser. When I did so a few database errors showed up in the browser, basically telling that the data necessary to render the plots was not found on the database; Apparently the Perl script that loaded the data into MySQL named all tables and fields with a starting "f" letter, not sure why, so I stripped out the f from the meta table and the errors disappeared but the data still doesn't show up.
>
> Bellow I pasted the [GENERAL] section from my GBrowse configuration file:
>
> [GENERAL]
> description   = Sample Test by test_db
> db_adaptor    = Bio::DB::SeqFeature::Store
> db_args       = -adaptor DBI::mysql
>                -dsn     test_db
>                -user    nobody
>
> I couldn't find in the GBrowse documentation how to set up a MySQL database for using with GBrowse, I did found the bulk_load_gff.pl script to load the data into the DB from a GFF source file, but when I did so I got the errors I mentioned before.
>
> Please let me know what am I doing wrong or if you know how to solve this problem.
>
> Thanks,
>
> Ramiro
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl@...
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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