Turns out to be a simple fix. Just set host="bacteria.ensembl.org" within the
biomaRt functions:
> listMarts(host="bacteria.ensembl.org")
biomart version
1 bacteria_mart_13 Ensembl Bacteria Genes 13
Thanks for your help Dan :)
> -----Original Message-----
> From: Gareth Morgan
> Sent: Thursday, March 08, 2012 11:23 PM
> To: Dan Staines
> Cc: [email protected]
> Subject: Re: [BioMart Users] ensembl_bacteria_12 not accessible
>
> Cheers Dan, I'll see if I can figure out how to do that. I'm a bit of an R
> newbie
> (or to be honest a complete beginner at all things bioinformatic), but that
> should be possible in theory, I guess. I'll post a fix if I can make something
> work.
> Thanks,
> Gareth
>
>
> On 8 Mar 2012, at 23:03, Dan Staines wrote:
>
> > Hi Gareth,
> >
> > I suspect you're connecting directly through biomart central, and I
> > don't think they've repacked/restarted their servers yet, as Arek
> > mentioned a slight lag due to a reorganisation of their services. I
> > imagine you can point your biomaRt adaptor directly at the EBI mart
> > servers/dbs (e.g. bacteria.ensembl.org/biomart/martview or
> > [email protected]:4157), though I confess this is something I
> > don't know much about. Maybe someone else can suggest how to modify
> > things to use EBI directly?
> >
> > Best,
> >
> > Dan.
> >
> > On 03/08/2012 06:46 PM, Gareth Morgan wrote:
> >> Thanks Dan. I guessed that it might have something to do with the new
> >> Ensembl release.
> >> However, I can't see bacteria_mart_13 from within R:
> >>
> >>> listMarts()
> >> biomart
> >> version
> >> 1 ensembl
> >> ENSEMBL GENES 65 (SANGER UK)
> >> 2 snp ENSEMBL
> >> VARIATION 65 (SANGER UK)
> >> 3 functional_genomics ENSEMBL
> >> REGULATION 65
> (SANGER UK)
> >> 4 vega
> >> VEGA 45 (SANGER UK)
> >> 5 bacteria_mart_12
> >> ENSEMBL BACTERIA 12 (EBI
> UK)
> >>
> >>
> >>> mart=useMart("bacteria_mart_13")
> >> Error in useMart("bacteria_mart_13") :
> >> Incorrect BioMart name, use the listMarts function to see which
> >> BioMart databases are available
> >>
> >>
> >> Any idea how to get at it from R, or when it will be released?
> >> Cheers,
> >> Gareth
> >>
> >>
> >> On 03/08/2012 12:14 AM, Dan Staines wrote:
> >>> Hi Gareth,
> >>>
> >>> As mentioned in a mail I sent to the list yesterday, we've now
> >>> released Ensembl Genomes 13, so bacteria_mart_13 has been retired
> >>> and is no longer available through our mart interface. The db is
> >>> still there on our public server if you need to use it directly, but
> >>> there is no change in the data so I'd suggest you change to use v13
> instead.
> >>>
> >>> Best,
> >>>
> >>> Dan Staines.
> >>>
> >>
> >
> > --
> > Dan Staines, PhD Ensembl Genomes Technical Coordinator
> > EMBL-EBI Tel: +44-(0)1223-492507
> > Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
> > Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
_______________________________________________
Users mailing list
[email protected]
https://lists.biomart.org/mailman/listinfo/users
