[ensembl-dev] BioMart Ensembl version
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue Sep 23 14:10:34 BST 2014
Dear Thomas,
Ok I didn't understand correctly, now I do.
As you say biomart website registry is still showing ensembl 75.
Thank you.
Best regards,
Guillermo.
On 23/09/14 14:01, Thomas Maurel wrote:
> Dear Guillermo,
>
> The biomart.org <http://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
> <http://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 <http://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
> <mailto: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
>>> <mailto: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 <mailto:Dev at ensembl.org>
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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
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing listDev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog:http://www.ensembl.info/
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
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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
>
>
>
> _______________________________________________
> 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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