Hi Alexandre,
On Thu, 2008-07-24 at 18:22 +0200, Alexandre Gattiker wrote:
> Hello,
>
> Kudos for this great piece of software. I managed to whip up a very
> functional biomart by mashing up some lab data with the Ensembl biomart,
> almost accidentally, as I didn't even expect that to be possible! It's
> rare enough that software works even better than advertised and in such
> a modular way.
:)
>
> I have a small issue, however. When I go to the Attributes -> Sequences
> page, the SEQUENCES section has:
>
> No visible attributes in collection seq_scope_type
> No visible attributes in collection upstream
> No visible attributes in collection downstream
thats because your registry does not contain sequence mart. try adding
this to your registry
<MartDBLocation
name = "ensembl"
displayName = "ENS 49"
databaseType = "mysql"
host = "martdb.ensembl.org"
port = "5316"
database = "ensembl_mart_49"
schema = "ensembl_mart_49"
user = "anonymous"
password = ""
visible = "1"
default = ""
includeDatasets = "mmusculus_gene_ensembl"
martUser = ""
/>
<MartDBLocation
name = "sequence"
displayName = "SEQ 49"
databaseType = "mysql"
host = "martdb.ensembl.org"
port = "5316"
database = "sequence_mart_49"
schema = "sequence_mart_49"
user = "anonymous"
password = ""
visible = ""
default = ""
includeDatasets = "mmusculus_genomic_sequence"
martUser = ""
/>
then rerun configure script. I am assuming, you are only interested in
ensembl mouse. Otherwise, set the includedatasets property to "" or a
list of dataset names you want.
> I assume that's linked to warnings I get running configure.pl:
>
> Setting possible links between datasets
> ....(scanning) 33% WARNING: Pointer attributes from
> mmusculus_genomic_sequence will not be available as
> mmusculus_genomic_sequence not in registry
> WARNING: Pointer attributes from mmusculus_genomic_sequence will
> not be available as mmusculus_genomic_sequence not in registry
> WARNING: Pointer attributes from mmusculus_genomic_sequence will
> not be available as mmusculus_genomic_sequence not in registry
>
> My config is as follows. I have biomart 0.7.
>
> <MartURLLocation
> name = "ensembl"
> displayName = "Ensembl Genes (release 49)"
> host = "www.biomart.org"
> port = "80"
> visible = "1"
> default = ""
> includeDatasets = "mmusculus_gene_ensembl"
> martUser = ""
> />
>
> I tried
> includeDatasets = "mmusculus_gene_ensembl,mmusculus_genomic_sequence"
> but that didn't solve the problem. I also tried to leave includeDatasets
> empty but I still get the warning (now for all species).
>
> Best,
> Alexandre
>
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
