Steve, not sure how things are at EBI these days but back in the days, if you are connecting an external URL (ensembl.org via webservice), you need to set proxy="wwwcache.something.something.uk:8080"
set this attribute in MartURLLocation element and see if works for you ? It it fixes it, Matthew's problem will be solved too - i think. Best, Syed On 8 April 2013 12:28, Steven Rosanoff <[email protected]> wrote: > Hello, > > For several releases I have been getting an error when trying to link the > Ensembl Genes biomart to the UniProt Biomart. Like wise, InterPro are > experiencing the same issue when trying to link the UniProt biomart to > their own. > > We are both using Biomart v0.7. I contacted Ensembl and retrieve the most > recent information for the registry.xml > * > <MartURLLocation > host="www.ensembl.org" > database="ensembl_mart_70" > name="ENSEMBL_MART_ENSEMBL" > path="/biomart/martservice" > serverVirtualSchema="default" > displayName="ENSEMBL GENES 70(EBI UK)" > port="80" > visible="1" > default="1" > includeDatasets="" > martUser="" > /> > * > When I run the command, perl bin/configure.pl --clean -r > conf/uniprot_registry.xml, I receive the message below: > > Connection parameters of [UniProtKB Unimart (EBI UK)] [ OK ] > Connection parameters of [ENSEMBL GENES 70(EBI UK)] [ OK ] > Connection parameters of [INTERPRO (EBI UK)] [ OK ] > Connection parameters of [PRIDE (EBI UK)] [ OK ] > > Problems with the web server: 500 Can't connect to > www.ensembl.org:80(connect: timeout) > > Any help or tips for troubleshooting would be appreciated. > > Regards, > Steve > > -- > Steven Rosanoff > Software Engineer > EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus > Hinxton, Cambridge CB10 1SD, UK > Phone: +44 (0)1223 494565 > Email: [email protected] > > Learn more about EBI at: http://www.ebi.ac.uk > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > >
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