[ensembl-dev] e59 mart

[Kiran Mukhyala]

Thanks Rhoda, the scripts worked without a hitch.

I appreciate the fast response and reliable help provided by the Ensembl
teams!

-Kiran

On Wed, Apr 20, 2011 at 12:50 AM, Rhoda Kinsella <rhoda at ebi.ac.uk> wrote:

> Hi Kiran
> These columns are added as a post build patch as the martbuilder tool
> cannot calculate this data for us. Please find attached the scripts you
> need. This is what you need to do:
>
>                NB: Always make sure to do a cvs update on the ensembl
>                API before running the calculated data script.
>
>                Run the calculated data script like this:
>
>                ./calculated_data_patch.pl -h host [-P port] [-u user] [-p
> pass] [-r release]
>
>                The SQL patches for the species are created in the
>                calculated_data directory.
>
>                To run these patches, modify the run_sql_files.ksh
>                script and add the host server and version of the
>                ensembl_mart database that you want to patch.
>
>                Then to run this script:
>
>                  ./run_sql_files.ksh calculated_data/*.sql
>
> The other option is to just download the table from our ftp site (
> ftp://ftp.ensembl.org/pub/release-59/mysql/ensembl_mart_59/)
> I hope that helps
> Regards
> Rhoda
>
>
>
>
>
>
>
> On 19 Apr 2011, at 22:20, Kiran Mukhyala wrote:
>
>  Hello,
>>
>>    I am having some problems with my local e59 based mart.
>> The *exon_transcript__dm tables are missing some columns like
>> five_prime_utr_start,  cdna_coding_start, cds_start etc. I used mart builder
>> generated SQL to create my mart using the same schema transformation as
>> Ensembl. I would either need the right sql to create and load the
>> exon_transcript__dm table or the right mart builder XML file which would
>> generate these columns.
>>
>> Thank you in advance.
>>
>> -Kiran
>>
>>
>>
> Rhoda Kinsella Ph.D.
> Ensembl Bioinformatician,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton
> Cambridge CB10 1SD,
> UK.
>
>
>
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