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
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
--
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Alexandre Gattiker Bioinformatics & Biostatistics Core Facility
EPFL School of Life Sciences / Faculté des Sciences de la vie FSV
http://people.epfl.ch/Alexandre.Gattiker
