[ensembl-dev] mfetch / pfetch executables

Javier Herrero jherrero at ebi.ac.uk
Fri Feb 11 21:09:21 GMT 2011


Hi Paolo

In short, mfetch is a local (Sanger) implementation of a sequence retrieval 
system, a home-made SRS if you wish. Unfortunately, the system is not 
available for external users.

Javier

On Friday 11 Feb 2011 08:45:15 Paolo Cozzi wrote:
> Thank you for your reply, William.
> 
> But what is mfetch? is a tool for downloading uniprot data?
> 
> best regards
> 
> Paolo.
> 
> Il 10/02/2011 15:05, William Spooner ha scritto:
> > Hi Paolo,
> > 
> > You will be unable to run the LoadUniProt analysis without replacing
> > mfetch with some other way of accessing the UniProt sequences. However,
> > the UniProt analysis is related to the ensembl family (tribe-mcl) data,
> > which is not required for the GeneTree. Just comment the UniProt stuff
> > out of your compara config file or delete the analysis/jobs from the
> > database.
> > 
> > Will
> > 
> > On 10 Feb 2011, at 08:36, Paolo Cozzi wrote:
> >> Dear all
> >> 
> >> I'm trying to do the genetree tutorial of the ensembl-compara pipeline.
> >> During the execution of the LoadUniProt analysis, the worker dies with
> >> this message:
> >> 
> >> mfetch returned nothing, mole server probably down at
> >> /home/pcozzi/ensembl-libraries/ensembl-compara/modules/Bio/EnsEMBL/Compa
> >> ra/RunnableDB/LoadUniProt.pm line 195
> >> 
> >> By looking into LoadUniProt.pm module, I see that this module dies if
> >> the "mfetch" execution returns no lines. In my local installation, I
> >> don't have this executable.
> >> 
> >> Where I can get "mfetch" code or binary file?
> >> 
> >> Thanks for your attention
> >> 
> >> Best regards,
> >> 
> >> Paolo.
> >> 
> >> 
> >> 
> >> Dott. Paolo Cozzi
> >> National Research Council, Institute for Biomedical Technologies
> >> Via Fratelli Cervi 93, 20090 Segrate (MI) Italy
> >> Office: +39 02 264 22600
> >> Mobile: +39 338 5451244
> >> Fax: +39 02 264 22660
> >> Mail: paolo.cozzi at itb.cnr.it
> >> skype: paolo.cozzi81
> >> 
> >> 
> >> 
> >> _______________________________________________
> >> Dev mailing list
> >> Dev at ensembl.org
> >> http://lists.ensembl.org/mailman/listinfo/dev
> > 
> > --
> > William Spooner
> > whs at eaglegenomics.com
> > http://www.eaglegenomics.com

-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK




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