[ensembl-dev] Urgent help on Blast view set-up.

nick nick at eaglegenomics.com
Thu Nov 18 11:06:33 GMT 2010


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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