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>
