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</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Nick,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>My Blast was working fine with the settings you mentioned.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'> nick [mailto:nick@eaglegenomics.com] <br><b>Sent:</b> Thursday, November 18, 2010 4:37 PM<br><b>To:</b> Ankit Agrawal<br><b>Cc:</b> dev@ensembl.org<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 href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><o:p></o:p></pre><pre><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><o:p></o:p></pre><p class=MsoNormal><o:p> </o:p></p></div></body></html>