Error when running Gbrowse with mySQL database

[vttran]

Dear Colleagues,

I follow the section "Creating Databases From Scratch" to configurate
the Gbrowse with Mysql database:
- creating the GFF3 file from Genbank
- creating a database (cyp450) in my MySQL database
- loading the file_name.gb.gff into cyp450
- and using a file .conf with a modification:

db_adaptor= Bio::DB::GFF
db_args     = -adaptor dbi::mysql
                    - dbi:mysql:database:cyp450;host=localhost
                    -user name of user
                    - pass pasword

initial lanhmark=*reference sequence*:1..10000

The gbrowse can connect with  mySQl database cyp450 without any error
and displays all things but *it does not display the image*. Plus, when
i use an target in Examples, it displays "*The lanhmark named
'/reference sequence/' is not recognized*"

Thank you in advance!
Trang



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[Scott Cain-4]

Hi Trang,

Questions:

Is there anything in the Apache error_log?

How did you load the database, what script did you use?

Are the incorrect spellings in your conf file sample ("lanhmark") just
from your mistyping, or are the present in the config file?

What does the first few lines of the GFF file look like, specifically
the one with the chromosome in it?

Scott


On Wed, Oct 7, 2009 at 3:35 AM,  <vttran@...> wrote:

> Dear Colleagues,
>
> I follow the section "Creating Databases From Scratch" to configurate
> the Gbrowse with Mysql database:
> - creating the GFF3 file from Genbank
> - creating a database (cyp450) in my MySQL database
> - loading the file_name.gb.gff into cyp450
> - and using a file .conf with a modification:
>
> db_adaptor= Bio::DB::GFF
> db_args     = -adaptor dbi::mysql
>                    - dbi:mysql:database:cyp450;host=localhost
>                    -user name of user
>                    - pass pasword
>
> initial lanhmark=*reference sequence*:1..10000
>
> The gbrowse can connect with  mySQl database cyp450 without any error
> and displays all things but *it does not display the image*. Plus, when
> i use an target in Examples, it displays "*The lanhmark named
> '/reference sequence/' is not recognized*"
>
> Thank you in advance!
> Trang
>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--
------------------------------------------------------------------------
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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