Re: Question about Biomart

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Re: Question about Biomart

Syed Haider
Hi Dzu,

have you tried setting the variable:

my $confFile

to point to your local registry file under biomart-perl/conf/  ?

and does your registry file contains MartDB or MartURL parameters to the
specified mart ? see example registry xml files under conf/.

Hope this helps, and please let us know in detail what exactly you are
trying to do ?

thanks
Syed

On 07/10/2010 21:35, [hidden email] wrote:

> Hello,
>
> I was trying to use Perl script (the one given by the biomart site) to obtain
> SNPs and genes, and I come up with this error:
>
> Couldn't open /home/d/biomart-perl/registry_DOM_XML:
> No such file or directory at /home/d/biomart-perl/lib/BioMart/Initializer.pm
> line 661
>
> I may have installed Biomart incorrectly, I'm just trying to query the server
> instead of creating a local server myself, please help.
>
> Dzu Nguyen,
> [hidden email]
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Getting Perl script to work for Biomart

vilente
Hi, I am having problems connecting to the Biomart databases using the example
perl script given off of the site, I tried writing my own registry file and had
some suggestions on how to get it working but all I get are errors so far, here
is my registry file:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>

<MartDBLocation
                                databaseType="mysql"
                                host="martdb.ensembl.org"
                                database="ensembl_mart_49"
                                name="ensembl"
                                displayName="ENSEMBL 59 GENE (SANGER UK)"
                                port="5316"
                                schema="snp_mart_59"
                                user="anonymous"
                                password=""
                                visible="1"
                                default="1"
                                martUser=""
                                includeDatasets="" />
</MartRegistry>

And I recieve this error when running Perl:

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

 COULD NOT CONNECT TO DATABASE ensembl_mart_49.CHECK YOUR SETTINGS

 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!




 Problems with the retrieval of dataset configuration
               Please check:
               that your mart Registry files contains correct connection params,
               that you are using the correct version on XML::Simple,
               that BioMart  databases contain a populated meta_conf tables and
               that you have set martUser correctly if you are running in
restricted data
               access mode (populated meta_conf__user__dm)

Is there a syntax error in my registry file or am I doing something else wrong?
Thank you.

Dzu
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Re: Getting Perl script to work for Biomart

Anthony Cros
Hi Dzu,

the value of "schema" must match that of "database".
Hope this helps!

Regards,

Anthony


On 10/19/2010 04:24 PM, [hidden email] wrote:

> Hi, I am having problems connecting to the Biomart databases using the example
> perl script given off of the site, I tried writing my own registry file and had
> some suggestions on how to get it working but all I get are errors so far, here
> is my registry file:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
>
> <MartDBLocation
>                                  databaseType="mysql"
>                                  host="martdb.ensembl.org"
>                                  database="ensembl_mart_49"
>                                  name="ensembl"
>                                  displayName="ENSEMBL 59 GENE (SANGER UK)"
>                                  port="5316"
>                                  schema="snp_mart_59"
>                                  user="anonymous"
>                                  password=""
>                                  visible="1"
>                                  default="1"
>                                  martUser=""
>                                  includeDatasets="" />
> </MartRegistry>
>
> And I recieve this error when running Perl:
>
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
>   COULD NOT CONNECT TO DATABASE ensembl_mart_49.CHECK YOUR SETTINGS
>
>   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
>
>
>
>   Problems with the retrieval of dataset configuration
>                 Please check:
>                 that your mart Registry files contains correct connection params,
>                 that you are using the correct version on XML::Simple,
>                 that BioMart  databases contain a populated meta_conf tables and
>                 that you have set martUser correctly if you are running in
> restricted data
>                 access mode (populated meta_conf__user__dm)
>
> Is there a syntax error in my registry file or am I doing something else wrong?
> Thank you.
>
> Dzu
>