[ensembl-dev] e67 mart builder files

Thomas Maurel maurel at ebi.ac.uk
Mon Jul 9 16:49:07 BST 2012


Hi Kiran,

I am sorry, I forgot to mention that we are now using these MTMP tables to help us build the ensembl, snp and functional genomics marts.
You will have to create them before updating the mart schema.

1) MTMP_probestuff_helper tables for the Ensembl mart: 
This table need to be built for all the funcgen databases.
You can use the iterate_tables.ksh script to iterate over multiple species databases and use the probestuff_helper.sql file to create this table in each database.
2) Variation views for snp mart and Ensembl mart :
You will need to run the variation_views.sql and the structural_variation.sql files for all the variation databases using the iterate_tables.ksh script.
3) eFG views for Functional genomics mart:
The functional genomics views and tables are created for all the funcgen databases using the iterate_tables.ksh script.

Please find the sql files and the iterate_tables.ksh script at the following location:  http://www.ebi.ac.uk/~maurel/mart_prebuild_patches/

Hope this helps,
Regards,
Thomas
On 9 Jul 2012, at 06:40, Kiran Mukhyala wrote:

> Thanks Thomas for the mart builder files.
> 
> It looks like the Ensembl Mart building process has introduced usage of new tables like MTMP_transcript_variation and MTMP_probestuff_helper, etc.
> Would you please explain how to generate these tables? If its documented anywhere, please do point me to it.
> 
> Thanks,
> -Kiran
> 
> On Sat, Jun 30, 2012 at 1:59 AM, Thomas Maurel <maurel at ebi.ac.uk> wrote:
> Hi Kiran,
> 
> Please find the martbuilder xmls for release 67 at the following location : 
> http://www.ebi.ac.uk/~maurel/v67_xml/
> 
> Regards,
> Thomas
> 
> On 29 Jun 2012, at 18:28, Kiran Mukhyala wrote:
> 
>> Hi Rhoda,
>> 
>> Could you please provide the e67 core, funcgen and variation martbuilder files?
>> 
>> Thanks,
>> -Kiran
>> 
>> On Wed, Jan 11, 2012 at 3:16 AM, Rhoda Kinsella <rhoda at ebi.ac.uk> wrote:
>> Hi Kiran
>> I have provided the files you requested for release 64 and release 65 at the following location:
>> 
>> http://www.ebi.ac.uk/~rhoda/v64_v65_xml/
>> 
>> Regards
>> Rhoda
>> 
>> 
>> On 9 Jan 2012, at 19:46, Kiran Mukhyala wrote:
>> 
>>> Hello Ensembl BioMart Team,
>>> 
>>> Could you please provide the e64 core, funcgen and variation martbuilder files?
>>> 
>>> Thanks,
>>> -Kiran
>>> 
>>> On Mon, May 9, 2011 at 5:38 AM, Rhoda Kinsella <rhoda at ebi.ac.uk> wrote:
>>> Hi Kiran
>>> You can find the files you need at:
>>> 
>>> http://www.ebi.ac.uk/~rhoda/v62_xml/
>>> 
>>> Regards
>>> Rhoda
>>> 
>>> 
>>> On 7 May 2011, at 04:08, Kiran Mukhyala wrote:
>>> 
>>> Hello,
>>> 
>>> I'd like to upgrade my mart to e62, could you please provide the e62 core, funcgen and variation mart builder files?
>>> 
>>> Thanks,
>>> -Kiran
>>> 
>>> Rhoda Kinsella Ph.D.
>>> Ensembl Bioinformatician,
>>> European Bioinformatics Institute (EMBL-EBI),
>>> Wellcome Trust Genome Campus,
>>> Hinxton
>>> Cambridge CB10 1SD,
>>> UK.
>>> 
>>> 
>> 
>> Rhoda Kinsella Ph.D.
>> Ensembl Production Project Leader,
>> European Bioinformatics Institute (EMBL-EBI),
>> Wellcome Trust Genome Campus, 
>> Hinxton
>> Cambridge CB10 1SD,
>> UK.
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
> 
> 
> 
> --
> Thomas Maurel
> Bioinformatician - Ensembl Production Team
> European Bioinformatics Institute (EMBL-EBI)
> 
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
> 
> 

--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK



--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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