[ensembl-dev] Blast View set-up

Ankit Agrawal mailme.ankit at gmail.com
Tue Nov 16 04:48:18 GMT 2010


Hi,

I have been trying to set-up a basic Blast view on Ensembl v59.

I need to set-up basic Blast view to work with Homo Sapiens.

I have added the following entries based on the description in
documentation.



Defaults.ini

[databases]
 ENSEMBL_BLAST = ensembl_blast

[ENSEMBL_BLAST]
 HOST =localhost
 PORT = 3306
 USER = scott
 PASS = tiger


[BLAST_DATASOURCES]

 The path the all the Fasta Files

[ENSEMBL_BLAST_METHODS]
BLASTN  = ensembl_wublastn;



<species.ini>

[ENSEMBL_BLAST_METHODS]

# Register of BlastView sequence databases.

Accept defaults



[BLAST_DATASOURCES]

# Register of BlastView sequence databases.

Accept defaults

[BLASTN_DATASOURCES] DATASOURCE_TYPE = dna
LATESTGP      =Homo_sapiens.NCBI36.40.dna.seqlevel.fa
CDNA_ALL      =Homo_sapiens.NCBI36.40.cdna.all.fa
CDNA_ABINITIO =Homo_sapiens.NCBI36.40.cdna.abinitio.fa




Path to Binaries<Defaults.ini>:

These have been set appropraitely as mentioned in the documentation.

However,
After doing the settings, I am not able to get the Balst View on the
Ensembl setup.


Its giving Error as follows:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Need a method arg
STACK: Error::throw
STACK: Bio::Root::Root::throw
/media/Data/cvs.ensembl59/bioperl-live/Bio/Root/Root.pm:342

STACK: Bio::Tools::Run::Search::new
/media/Data/cvs.ensembl59/modules/Bio/Tools/Run/Search.pm:126
STACK: /media/Data/cvs.ensembl59/modules/EnsEMBL/Web/BlastView/MetaDataBlast.pm:409
-----------------------------------------------------------



-- 
ANKIT AGRAWAL
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