[ensembl-dev] biomaRt ListEnsemblArchives

[Rajneesh N Shetty]

what kind of hardware chipset did ARMANT Olivier use? Debian version# would be helpful here?

ABN:39740-48-24-36 (Rajneesh N. Shetty)
Please direct hand-written communications to GPO Box 1418, East Victoria Park-6981, Australia.
All electronic communications will be considered on it's merit by the above, and the stakeholder at, "Rajneesh N. Shetty", at the afore mentioned Australian Business Registeration number, will attempt to consider facts presented.


> Sent: Monday, December 16, 2019 at 2:24 PM
> From: "Steffen Möller" <steffen_moeller at gmx.de>
> To: "Ensembl developers list" <dev at ensembl.org>, "ARMANT Olivier" <olivier.armant at irsn.fr>
> Subject: Re: [ensembl-dev] biomaRt ListEnsemblArchives
>
> Hello,
> 
> 
> On 16.12.19 14:55, ARMANT Olivier wrote:
> >
> > Dear Ensembl dev list,
> >
> > First thanx for you great job !
> >
> > I use the R package biomaRt R version 3.6.1 (2019-07-05) -- "Action of
> > the Toes"
> >
> > to query ensembl on a debian system Ubuntu 18.04.3 LTS
> >
> > I can sucessfully connect to the current version of the assembly :
> >
> > > listMarts()
> >
> > biomart               version
> >
> > 1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 98
> >
> > 2 ENSEMBL_MART_MOUSE      Mouse strains 98
> >
> > 3 ENSEMBL_MART_SNP  Ensembl Variation 98
> >
> > 4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 98
> >
> > But this fail when I try to connect to archives :
> >
> > > listEnsemblArchives()
> >
> > Error: failed to load HTTP resource
> >
> > Your help and suggestion would be very much appreciated
> >
> I tried it on two Debian systems with that package where this works just
> fine. But I can confirm that error for a system with a very strict
> firewall - and a self-compiled biomaRt installation. My hunch is that
> the HTTP proxy settings are not forwarded to/used by curl. The way I
> help myself is that I execute what I want to execute with biomaRt with
> very lose filters on another machine and then read that file in the HPC
> environment where I apply the filters within R. This may not be
> applicable for your problem, though.
> 
> 
> Cheers,
> 
> Steffen
> 
> 
> 
> >
> > _______________________________________________
> > Dev mailing list    Dev at ensembl.org
> > Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> > Ensembl Blog: http://www.ensembl.info/
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
>