[ensembl-dev] BioMart Ensembl version

[Thomas Maurel]

Dear Guillermo,

If you are using:
1) the biomart-perl/scripts/webExample.pl script and an xml file
You can change the path to the biomart website in the following line:
my $path="http://www.biomart.org/biomart/martservice?";
With the path to our Ensembl release 75 archive:
my $path="http://feb2014.archive.ensembl.org/biomart/martservice?";

2) A BioMart perl script
a) You first need to edit your configuration file in "biomart-perl/conf/martURLLocation.xml" and paste the content of the mart registry page for the Ensembl release 75 archive website: http://feb2014.archive.ensembl.org/biomart/martservice?type=registry
b) Then edit your script and make sure that "my $confFile" variable is looking at the martURLLocation.xml configuration file in biomart-perl/conf
c) Finally, make sure to update the following line in your script:

my $action='cached';

with:

my $action='clean';

The first run of your script on Ensembl 75 might be a bit slow as BioMart will cache some data from the BioMart website.
Once you have run your script with the action variable set to "clean", you can set the variable to "cached" again.

Hope this helps,
Best regards,
Thomas
On 19 Sep 2014, at 13:28, Guillermo Marco Puche <guillermo.marco at sistemasgenomicos.com> wrote:

> Dear developers,
> 
> I would like to know how to specify BioMart Perl code to query against older Ensembl version (ie:75) and not latest (I believe used by default).
> 
> Thank you.
> 
> Best regards,
> Guillermo.
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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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