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

[Nick James]

Hi Ankit,

No problem. If your blast link isn't appearing then you might need to add:

  $SiteDefs::ENSEMBL_BLAST_ENABLED  = 1;

to your SiteDefs.pm file.

Thanks,

Nick


On 18/11/10 17:56, Ankit Agrawal wrote:
> HI Nick,
>
> Thanks for your quick response.
> This worked and the error was removed, however i am not able to see 
> the link for blast view on top of the page.
> Any suggestions as to what went wrong??
>
> Thanks & Regards,
> Ankit
>
> On Thu, Nov 18, 2010 at 4:36 PM, nick <nick at eaglegenomics.com 
> <mailto:nick at eaglegenomics.com>> wrote:
>
>     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
>>
>>
>>     _______________________________________________
>>     Dev mailing list
>>     Dev at ensembl.org <mailto:Dev at ensembl.org>
>>     http://lists.ensembl.org/mailman/listinfo/dev
>
>
>
>
> -- 
> ANKIT AGRAWAL

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