[ensembl-dev] e59 mart

[Rhoda Kinsella]

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

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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.