[ensembl-dev] Ensembl BLAST: database files names

[ek]

Hi Rafael

the pattern for the blast db names is set in
eg-plugins/common/modules/EnsEMBL/Web/ConfigPacker.pm

an EG site expects the files to be in the following format
          my $file = sprintf( '%s.%s.%s', $species, $assembly, $type 
).".fa";
e.g
    Albugo_laibachii.ENA1.dna.toplevel.fa

you can rename your files by removing the version number , or you can 
modify the file mentioned above ..
regards

Eugene

On 2013-02-26 15:52, Rafael Hernández wrote:
> Hi,
>
> I've got a problem with the Ensembl BLAST databases and probably it's
> something misconfigured.
> Eg. For Ensembl protists I downloaded all the fasta files in
> /usr/local/blastdb/ensembl_protists and added the following line in
> the SiteDefs.pm file:
>
> $SiteDefs::ENSEMBL_BLAST_DATA_PATH =
> '/usr/local/blastdb/ensembl_protists';
>
> After that, I rebuilt the protists site and in the Blastview page all
> the databases are listed. However when I chose one and run Blast, it
> crashes and show the error below:
>
> [blastall 2.2.26] WARNING: Unable to open
> Albugo_laibachii.ENA1.dna.toplevel.fa.nin
> [blastall 2.2.26] WARNING: Unable to open
> Albugo_laibachii.ENA1.dna.toplevel.fa.nin
> BLASTN 2.2.26 [Sep-21-2011]
>
>  ....
>
> However this database exits, but with the name
> Albugo_laibachii.ENA1.70.dna.toplevel.fa.nin.
>
> What should I do? I found a previous thread talking about this 
> problem
> but nobdy answered it.  
>
> http://lists.ensembl.org/ensembl-dev/msg05579.html
>
> Thank you and best 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.