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Hi Ankit, <br>
<br>
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? <br>
<br>
Anyway, as a quick recap, you should have: <br>
In your DEFAULTS.ini : <br>
- the blast_methods section below <br>
- definitions of the blast program names eg.
ENSEMBL_BLASTN_PROGRAM_NAME = blastn<br>
- a blast datasources section <br>
<br>
In your MULTI.ini, you have: <br>
- for each blast method defined in DEFAULTS.ini there should be a
datasource section, eg<br>
[BLASTN_DATASOURCES]<br>
DATASOURCE_TYPE = dna<br>
LATESTGP = %_<br>
LATESTGP_MASKED = %_<br>
<br>
Hope that helps, <br>
<br>
Thanks,<br>
<br>
Nick<br>
<br>
On 09/02/11 09:01, Ankit wrote:
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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">Hi Nick,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">My Blast was working fine with the settings you
mentioned.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">However, I need to configure all the methods. The
documentation on the site for Registering Blast search
methods is incomplete.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">Can you please help me in any possible way with
the blast methods registration in the conf files.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);"><o:p> </o:p></span></p>
<div>
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<p class="MsoNormal"><b><span style="font-size: 10pt;
font-family:
"Tahoma","sans-serif"; color:
windowtext;">From:</span></b><span style="font-size:
10pt; font-family:
"Tahoma","sans-serif"; color:
windowtext;"> nick [<a class="moz-txt-link-freetext" href="mailto:nick@eaglegenomics.com">mailto:nick@eaglegenomics.com</a>] <br>
<b>Sent:</b> Thursday, November 18, 2010 4:37 PM<br>
<b>To:</b> Ankit Agrawal<br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
<b>Subject:</b> Re: [ensembl-dev] Urgent help on Blast
view set-up.<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Ankit, <br>
<br>
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: <br>
<br>
[ENSEMBL_BLAST_METHODS]<br>
BLASTN = [ blast dna dna ncbiblastn ] <br>
BLASTX = [ blast dna peptide ncbiblastx ]<br>
BLASTP = [ blast peptide peptide ncbiblastp ]<br>
TBLASTN = [ blast peptide dna ncbitblastn ]<br>
TBLASTX = [ blast dna dna ncbitblastx ]<br>
<br>
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. <br>
<br>
Thanks,<br>
<br>
Nick<br>
<br>
On 18/11/10 09:13, Ankit Agrawal wrote: <o:p></o:p></p>
<p class="MsoNormal">Hi,<br>
<br>
I am setting up Ensembl - Blastview (ver 59).<br>
The setup for ensembl is complete and is running perfectly
without any error logs.<br>
Now, when i am trying to set-up BLAST view on that, I am
getting the following error.<br>
<br>
<span style="font-size: 7.5pt; font-family: "Courier
New";">------------- EXCEPTION: Bio::Root::Exception
-------------<br>
MSG: Need a method arg<br>
STACK: Error::throw<br>
STACK: Bio::Root::Root::throw
/media/Data/cvs.ensembl59/bioperl-live/Bio/Root/Root.pm:342<br>
STACK: Bio::Tools::Run::Search::new
/media/Data/cvs.ensembl59/modules/Bio/Tools/Run/Search.pm:126<br>
STACK:
/media/Data/cvs.ensembl59/modules/EnsEMBL/Web/BlastView/MetaDataBlast.pm:409<br>
-----------------------------------------------------------</span><br>
<br>
I know, I have made some config errors. However, I am unable
to interpret it.<br>
It would be grateful if someone who has done this recently can
help me on this.<br>
I just want the basic Blast view running.<br>
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.<br>
I am in critical phase of the project and this needs to be
done urgently.<br>
Please help me in any way you can!<br>
<br>
<br clear="all">
<br>
Thanks and Regards,<br>
ANKIT AGRAWAL<br>
<br>
<o:p></o:p></p>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Dev mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><o:p></o:p></pre>
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