On 23 May 2006, at 15:24, Marc Logghe wrote:
Hi,
Hi Marc,
I am probably missing something obvious but I went trough all availabe
user docs for the versions 0.2,0.3 and 0.4 and could not find it :-(
yes, apologies. I don't think our docs have any specific sequence
example.
1) how can you configure a DataSet so that a user can choose between
different Attribute pages ? Guess, you need to define somewhere what is
the type of the attributes: 'attribute' or 'sequence'. In the perl
martview package it seems that the Basically I am trying to find out
how one must handle fasta sequence data: where should it be stored, how
can you configure, how can you dump it ?
You can define different attribute pages in the dataset configuration
xml
file for each individual dataset. These files live on the database
server in each mart schema in the
mart_conf__xml__dm table. The easiest way to inspect the file is to use
MartEditor and connect to ensembl mart on ensembldb (user anonymous,
host ensembldb.ensembl.org, mart ensembl_mart_38, schema
ensembl_mart_38, port 3306)
choose any dataset *_gene_ensembl
The actual dna sequence lives in a separate sequence_mart_38 on the
same database server
along with the appropriate dataset configuration files.
2) in order to have a look at the configuration of a real example, I
tried to import the DatasetConfig of some ensembl datasets but failed.
Connecting seems not to be the problem (got the settings from a
defaultMartRegistry.xml:
<RegistryDBPointer
databaseType = "mysql"
host = "martdb.ebi.ac.uk"
port = "3306"
database = "central_registry"
schema = "central_registry"
user = "anonymous"
password = ""
/>
But as soon as I try to import the configuration I get the message:
"No datasets available for import - is this a BioMart compatible schema
? Absent or empty meta_configuration table"
I tried both martj 0.3 and 0.4.
you need to use MartEditor and connect using Database connection
window from MartEditor with settings as indicated above (ensembldb,
ensembl_mart_38 etc).
The registry pointer in your example simply points you to where the
registry file lives so this not
what you want to use
please let us know if this is unclear,
a.
Regards,
Marc
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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