On 2010-06-01, at 4:55, "Darren Oakley" <[email protected]> wrote:
> Hi All,
>
> I've just had an email from a user who is having problems accessing
> one of our marts via an R package (biomaRt). I tried to use the
> same package but it looks like we've got a slight mis-configuration
> on our server - in the registry, all of our 'host' directives are
> set the the hostname of the machine the mart is running on
> ('hpgen-1-14') - not what is configured in the registry file:
>
> http://www.i-dcc.org/biomart/martservice?type=registry
>
> compared to the attached XML at the base of this email...
>
> Any idea how I can fix this one?
>
> Thanks,
>
> Daz
>
> P.S. On a side note - is there any chance we can get the IKMC mart
> added to the biomart central portal too for easier access to our
> data too?
We will be very happy to do that Darren
a.
>
> ---
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
>
> <MartDBLocation
> name = "ikmc"
> displayName = "IKMC Genes and Products"
> databaseType = "mysql"
> host = "web-mii-shap.internal.sanger.ac.uk"
> port = "3303"
> database = "ikmc_mart_alt"
> schema = "ikmc_mart_alt"
> user = "ikmc"
> password = "ikmc"
> visible = "1"
> default = ""
> includeDatasets = ""
> martUser = ""
> />
>
> <MartURLLocation
> name = "biomart"
> database = "biomart"
> default = ""
> displayName = "MGI (Jackson Laboratory US)"
> host = "www.biomart.org"
> proxy = "http://wwwcache.sanger.ac.uk:3128";
> includeDatasets = "markers"
> martUser = ""
> path = "/biomart/martservice"
> port = "80"
> serverVirtualSchema = "default"
> visible = "1"
> />
> <MartURLLocation
> name = "htgt"
> database = "htgt_mart"
> default = ""
> displayName = "WTSI Mouse Genetics Programme (Sanger UK)"
> host = "www.sanger.ac.uk"
> proxy = "http://wwwcache.sanger.ac.uk:3128";
> includeDatasets = "htgt_targ"
> martUser = ""
> path = "/htgt/biomart/martservice"
> port = "80"
> serverVirtualSchema = "default"
> visible = "1"
> />
> <MartURLLocation
> name = "emma_biomart"
> database = "emma_biomart"
> default = ""
> displayName = "The European Mouse Mutant Archive (EMMA)"
> host = "www.emmanet.org"
> proxy = "http://wwwcache.sanger.ac.uk:3128";
> includeDatasets = ""
> martUser = ""
> path = "/biomart/martservice"
> port = "80"
> serverVirtualSchema = "default"
> visible = "1"
> />
> <MartURLLocation
> name = "Eurexpress Biomart"
> database = "ee_biomart_test5"
> default = ""
> displayName = "Eurexpress"
> host = "biomart.eurexpress.org"
> proxy = "http://wwwcache.sanger.ac.uk:3128";
> includeDatasets = "template"
> martUser = ""
> path = "/biomart/martservice"
> port = "80"
> serverVirtualSchema = "default"
> visible = "1"
> />
> <MartURLLocation
> name = "europhenomeannotations"
> database = "europhenome_annotation_1_3_3_20100414"
> default = ""
> displayName = "Europhenome"
> host = "www.europhenome.org"
> proxy = "http://wwwcache.sanger.ac.uk:3128";
> includeDatasets = "europhenome"
> martUser = ""
> path = "/biomart/martservice"
> port = "80"
> serverVirtualSchema = "default"
> visible = "1"
> />
> <MartURLLocation
> name = "ensembl"
> default = ""
> displayName = "Ensembl Gene (Sanger UK)"
> host = "www.biomart.org"
> proxy = "http://wwwcache.sanger.ac.uk:3128";
> includeDatasets = "mmusculus_gene_ensembl"
> martUser = ""
> path = "/biomart/martservice"
> port = "80"
> serverVirtualSchema = "default"
> visible = "1"
> />
> <MartURLLocation
> name = "sequence"
> default = ""
> displayName = "Ensembl Sequence (Sanger UK)"
> host = "www.biomart.org"
> proxy = "http://wwwcache.sanger.ac.uk:3128";
> includeDatasets = "mmusculus_genomic_sequence"
> martUser = ""
> path = "/biomart/martservice"
> port = "80"
> serverVirtualSchema = "default"
> visible = ""
> />
> <MartURLLocation
> name = "ontology"
> default = ""
> displayName = "Ensembl Ontology (Sanger UK)"
> host = "www.biomart.org"
> proxy = "http://wwwcache.sanger.ac.uk:3128";
> includeDatasets =
> "closure_biological_process,
> closure_cellular_component,closure_molecular_function"
> martUser = ""
> path = "/biomart/martservice"
> port = "80"
> serverVirtualSchema = "default"
> visible = ""
> />
> <MartURLLocation
> name = "genomic_features"
> default = ""
> displayName = "Ensembl Genomic Features (Sanger UK)"
> host = "www.biomart.org"
> proxy = "http://wwwcache.sanger.ac.uk:3128";
> includeDatasets =
> "mmus_karyotype_start,
> mmus_karyotype_end,mmus_marker_start,mmus_marker_end"
> martUser = ""
> path = "/biomart/martservice"
> port = "80"
> serverVirtualSchema = "default"
> visible = ""
> />
> <MartURLLocation
> name = "vega"
> default = ""
> displayName = "Vega (Sanger UK)"
> host = "www.biomart.org"
> proxy = "http://wwwcache.sanger.ac.uk:3128";
> includeDatasets = "mmusculus_gene_vega"
> martUser = ""
> path = "/biomart/martservice"
> port = "80"
> serverVirtualSchema = "default"
> visible = "1"
> />
> </MartRegistry>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
