Hi Syed,
Thanks for that - it wasn't the full solution (as it turns out), but it lead me
to it. :)
I was foolishly setting the 'severHost' directive (in settings.conf) to the
hostname!!! Added the proxy setting and the correct serverHost and it's
working happily now.
Thanks,
Daz
On 3 Jun 2010, at 15:43, Syed Haider wrote:
> Hi Darren,
>
> please scroll down to see the reply,
>
> On 01/06/2010 09:31, Darren Oakley 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:
>
> You need to set proxy="80" in the settings.conf, that should do the trick. I
> am assuming these marts in your registry file have martDBLocation type
> connections and point to a database locally.
>
> Best
> Syed
>
>
>>
>> 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?
>>
>> ---
>>
>> <?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>
>>
>>
>>
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