[ensembl-dev] Help on Blast view set-up.

[Ankit]

Hi Nick,

 

My Blast was working fine with the settings you mentioned.

However, I need to configure all the methods. The documentation on the site
for Registering Blast search methods is incomplete.

Can you please help me in any possible way with the blast methods
registration in the conf files.

 

From: nick [mailto:nick at eaglegenomics.com] 
Sent: Thursday, November 18, 2010 4:37 PM
To: Ankit Agrawal
Cc: dev at ensembl.org
Subject: Re: [ensembl-dev] Urgent help on Blast view set-up.

 

Hi Ankit, 

Do you have an ENSEMBL_BLAST_METHODS section in you DEFAULTS.ini? The format
of it has changed fairly recently, so it should now look something like the
example below: 

[ENSEMBL_BLAST_METHODS]
BLASTN = [ blast dna dna ncbiblastn ] 
BLASTX = [ blast dna peptide ncbiblastx ]
BLASTP = [ blast peptide peptide ncbiblastp ]
TBLASTN = [ blast peptide dna ncbitblastn ]
TBLASTX = [ blast dna dna ncbitblastx ]

The 4th element of the array above corresponds to the
Bio::Tools::Run::Search wrapper class, so you will need to change that
depending on which blast type you are using and whether it is local or not. 

Thanks,

Nick

On 18/11/10 09:13, Ankit Agrawal wrote: 

Hi,

I am setting up Ensembl - Blastview (ver 59).
The setup for ensembl is complete and is running perfectly without any error
logs.
Now, when i am trying to set-up BLAST view on that, I am getting the
following error.

------------- 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
-----------------------------------------------------------

I know, I have made some config errors. However, I am unable to interpret
it.
It would be grateful if someone who has done this recently can help me on
this.
I just want the basic Blast view running.
If anybody can provide me with the working Default.ini and any one
species.ini or just the basic mandatory configurations, it will be VERY VERY
helpful.
I am in critical phase of the project and this needs to be done urgently.
Please help me in any way you can!



Thanks and Regards,
ANKIT AGRAWAL



 
 
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