[ensembl-dev] Ensembl Genomes BLAST: Parsing failed ERROR

ek ek at ebi.ac.uk
Tue Mar 5 13:38:43 GMT 2013

On 2013-03-05 10:13, Rafael Hernández wrote:
> Hi,
> So if I want to use BLAST in my LOCAL Ensembl Genome, Should the
> machine be connected to internet to access to EBI Blast service?
> Then, I've got a big trouble because the machine won't be connected
> to internet... 
> But Why for Ensembl is it possible to use local NCBI Blast and for EG
> not? 
you can use local NCBI blast but then you would need to take the blast 
db configuration options from the EG ini files

> And, Which EBI BLAST tool is been used through those web services? I
> suppose that EG use wu-blast not ncbiblast, and this is the reason
> that make the parsing step crash (because a wu_blast output is
> expected).


> I could try to change the scripts to use a local version of wu_blast
> instead the web services however wu_blast sources (as far as I know)
> are not available for downloading since all rights were acquired by
> Advanced Biocomputing. There is any place where I can find a open
> version of wu-blast? 
> Another option could be use NCBI Blast without the BLAST plugin (as
> Ensembl does), but then EG Blastview fails and I've got again the
> problem of empty comboboxes..... 

you can try to remove 
eg-plugins/blast/modules/EnsEMBL/Web/BlastView/MetaDataBlast.pm and see 
if it works for you

or modify the file to use the sensitivity options of ncbi blast

you can see what has been changed for EG blast by

  diff modules/EnsEMBL/Web/BlastView/MetaDataBlast.pm 



> Please help me, I need to solve it ASAP, it should be working before
> next week.
> Thank you and regards,
> Rafa Hernández de Diego
>  SLU-Global Bioinformatics Center
> Swedish University for Agricultural Sciences (SLU)
>  Gerda Nilssons väg 2,  
>  Box 7023, 750 07 Uppsala, Sweden.

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