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Hi Ankit, <br>
<br>
No problem. If your blast link isn't appearing then you might need
to add: <br>
<br>
$SiteDefs::ENSEMBL_BLAST_ENABLED = 1;<br>
<br>
to your SiteDefs.pm file. <br>
<br>
Thanks,<br>
<br>
Nick<br>
<br>
<br>
On 18/11/10 17:56, Ankit Agrawal wrote:
<blockquote
cite="mid:AANLkTi=P17jOjiqtTDhSwq6gZP=HLc51SO6gBcu6XiFK@mail.gmail.com"
type="cite">HI Nick,<br>
<br>
Thanks for your quick response.<br>
This worked and the error was removed, however i am not able to
see the link for blast view on top of the page.<br>
Any suggestions as to what went wrong??<br>
<br>
Thanks & Regards,<br>
Ankit<br>
<br>
<div class="gmail_quote">On Thu, Nov 18, 2010 at 4:36 PM, nick <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:nick@eaglegenomics.com">nick@eaglegenomics.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"> 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
<div>
<div class="h5"><br>
<br>
On 18/11/10 09:13, Ankit Agrawal wrote: </div>
</div>
<blockquote type="cite">
<div>
<div class="h5">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>
<font size="1"><span style="font-family: courier
new,monospace;">------------- EXCEPTION:
Bio::Root::Exception -------------</span><br
style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">MSG:
Need a method arg</span><br style="font-family:
courier new,monospace;">
<span style="font-family: courier new,monospace;">STACK:
Error::throw</span><br style="font-family: courier
new,monospace;">
<span style="font-family: courier new,monospace;">STACK:
Bio::Root::Root::throw
/media/Data/cvs.ensembl59/bioperl-live/Bio/Root/Root.pm:342</span><br
style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">STACK:
Bio::Tools::Run::Search::new
/media/Data/cvs.ensembl59/modules/Bio/Tools/Run/Search.pm:126</span><br
style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">STACK:
/media/Data/cvs.ensembl59/modules/EnsEMBL/Web/BlastView/MetaDataBlast.pm:409</span><br
style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">-----------------------------------------------------------</span></font><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>
</div>
</div>
<pre><fieldset></fieldset>
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</div></pre>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
ANKIT AGRAWAL<br>
</blockquote>
<br>
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