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

[Nick James]

Hi Ankit,

I'm not sure what you are asking - if your blast was working OK then you 
must have registered the Blast search methods successfully? Or are you 
referring to configuring the parameters used by blast itself? Do you 
have any error messages that might help?

Anyway, as a quick recap, you should have:
In your DEFAULTS.ini :
  - the blast_methods section below
  - definitions of the blast program names eg. 
ENSEMBL_BLASTN_PROGRAM_NAME = blastn
- a blast datasources section

In your MULTI.ini, you have:
- for each blast method defined in DEFAULTS.ini there should be a 
datasource section, eg
  [BLASTN_DATASOURCES]
DATASOURCE_TYPE = dna
LATESTGP        = %_
LATESTGP_MASKED = %_

Hope that helps,

Thanks,

Nick

On 09/02/11 09:01, Ankit wrote:
>
> 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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