[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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