Question

how can I configure my proxy to get connected to biomart

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Bioinformatics ▴ 30

@bioinformatics-10931

Last seen 2.9 years ago

United States

I am having problem with connection to Biomart due to proxy

At first I tried to analysis get the Mart using the following command which led to error

hsapiens = useMart("ensembl",
+                    dataset="hsapiens_gene_ensembl")
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Error in if (!grepl(x = registry, pattern = "^\n*<MartRegistry>")) { : 
  argument is of length zero

Then I tried to set the proxy and I got this error

options(RCurlOptions = list(proxy="http://proxy.swmed.edu:3328", proxyuserpwd="user:pwd"))
> hsapiens = useMart("ensembl",
+                    dataset="hsapiens_gene_ensembl")
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
  Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt

biomart connection host • 1.5k views

ADD COMMENT • link 6.8 years ago Bioinformatics ▴ 30

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What do you see if you follow the instructions in those error messages and go to http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt in a browser?

ADD REPLY • link 6.8 years ago Mike Smith ★ 6.6k

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@Mike Smith it gives me this

<MartRegistry>
  <MartURLLocation database="ensembl_mart_91" default="1" displayName="Ensembl Genes 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_91" default="" displayName="Mouse strains 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_91" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_91" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_91" default="" displayName="Genomic features 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_91" default="" displayName="Ensembl Variation 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_91" default="" displayName="Ensembl Regulation 91" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>

ADD REPLY • link 6.8 years ago Bioinformatics ▴ 30

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Ok, so that's exactly what you're supposed to see, so at least your browser can connect to Ensembl BioMart fine. If your web browser is also using a proxy, I suggest you copy the setting being used there.

ADD REPLY • link 6.8 years ago Mike Smith ★ 6.6k

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@Mike Smith can you tell me how for example use those information to get through ? I have safari

ADD REPLY • link 6.8 years ago Bioinformatics ▴ 30