[ensembl-dev] BioMart Ensembl version

Thomas Maurel maurel at ebi.ac.uk
Tue Sep 23 13:01:40 BST 2014


Dear Guillermo,

The biomart.org website seems to be very slow at the moment and I am afraid the website is still displaying our release 75 marts on hg19 (GRCh37). According to the biomart.org mart registry page: http://www.biomart.org/biomart/martservice?type=registry, port '80' is still valid.
If you want to use hg38 (GRCh38), the best way would be to point your mart XML config to the ensembl.org website in order to access our release 76 mart databases on hg38 (GRCh38).
You can follow the previous instruction but just change the mart registry URL page to get the mart release 76 registry informations:

>> 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 website on release 76 (hg38): http://www.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.


I am afraid $action=clean is quite resource consuming but you will only need to run your script with this setting when you change the registry information.

Hope this helps,
Best regards,
Thomas
On 23 Sep 2014, at 12:43, Guillermo Marco Puche <guillermo.marco at sistemasgenomicos.com> wrote:

> Dear Thomas,
> 
> My BioMart perl script is using the following mart XML config file:
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
>     <MartURLLocation
>         name         = "ensembl"
>         displayName  = "ensembl"
>         host         = "www.biomart.org"
>         port         = "80"
>         visible      = "1"
>         default      = ""
>         includeDatasets = "hsapiens_gene_ensembl"
>         martUser     = ""
>     />
> </MartRegistry>
> 
> However, I'm getting BioMart queries from hg19 and not hg38. Does the default port '80' still working on hg19? how can I specify I would like to use hg38 biomart service.
> 
> On the other hand, it's always useful to know how to query older Ensembl versions with Biomart. However using $action=clean with conf file of ensembl 75 archive it's leading me to massive amounts of RAM consumption in my Perl script.
> 
> Thanks.
> 
> Best regards,
> Guillermo.
> On 19/09/14 15:48, Thomas Maurel wrote:
>> 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.
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>> 
>> --
>> 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
>> 
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
> _______________________________________________
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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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