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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks –It is working now<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"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Will McLaren<br>
<b>Sent:</b> Wednesday, June 20, 2012 10:34 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Condel Plugin<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Sunita,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This Condel.pm file is not the plugin - it is part of the API. It will be removed in the next release of Ensembl as it has been deprecated.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The Condel.pm you should be using is the one from the GitHub repository:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a href="https://github.com/ensembl-variation/VEP_plugins">https://github.com/ensembl-variation/VEP_plugins</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">There you will see the Condel.pm file and the config/ directory. If you clone the whole plugins repository you should get the files you need.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Will McLaren<o:p></o:p></p>
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<p class="MsoNormal">Ensembl Variation<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 20 June 2012 15:46, Koul, Sunita <<a href="mailto:sunita@pathology.wustl.edu" target="_blank">sunita@pathology.wustl.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks Michael for the response.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Please bear with me as I am little confused about the config directory</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Condel.pm is under
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">\Bio\ensembl-variation\modules\Bio\EnsEMBL\Variation\Utils directory.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I see a Config.pm file under that besides
<a href="http://condel.pm" target="_blank">condel.pm</a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">There is no config directory as such.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Sunita</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Michael Yourshaw [mailto:<a href="mailto:myourshaw@ucla.edu" target="_blank">myourshaw@ucla.edu</a>]
<br>
<b>Sent:</b> Friday, June 15, 2012 5:38 PM<br>
<b>To:</b> Koul, Sunita<br>
<b>Cc:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Condel Plugin</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">You need to specify some parameters for the Condel plugin<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">--plugin Condel,/path/to/VEP_plugins/config/Condel/config,b,2<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br>
<span style="font-size:13.5pt;font-family:Mangal">ॐ</span><o:p></o:p></p>
<p style="margin-bottom:4.5pt"><span style="font-size:7.5pt;font-family:"Lucida Grande","serif"">Michael Yourshaw</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:7.5pt;font-family:"Lucida Grande","serif"">UCLA Geffen School of Medicine</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:7.5pt;font-family:"Lucida Grande","serif"">Department of Human Genetics, Nelson Lab</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:7.5pt;font-family:"Lucida Grande","serif"">695 Charles E Young Drive S</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:7.5pt;font-family:"Lucida Grande","serif"">Gonda 5554</span><o:p></o:p></p>
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<p style="margin-bottom:2.25pt"><span style="font-size:7.5pt;font-family:"Lucida Grande","serif"">Los Angeles CA 90095-8348 USA</span><o:p></o:p></p>
<p style="margin-bottom:2.25pt"><u><span style="font-size:7.5pt;font-family:"Lucida Grande","serif";color:#000099"><a href="mailto:myourshaw@ucla.edu" target="_blank">myourshaw@ucla.edu</a></span></u><o:p></o:p></p>
<p style="margin-bottom:4.5pt"><span style="font-size:7.5pt;font-family:"Lucida Grande","serif""><a href="tel:970.691.8299" target="_blank">970.691.8299</a></span><o:p></o:p></p>
<p style="margin-bottom:4.5pt"><span style="font-size:7.0pt;font-family:"Lucida Grande","serif"">This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT.
 If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately.
 Thank you.</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""> </span><o:p></o:p></p>
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<br>
</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Jun 15, 2012, at 15:04, Koul, Sunita wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Hi</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I am trying to run Condel using the variant effect predictor using the following command</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Courier New"">perl
<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i input.vcf --plugin Condel</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Courier New"">I get the error</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Courier New"">Can't locate loadable object for module Win32 in @INC (@INC contains: E:\Perl\variant_effect_predictor\Bio\bioperl-1.2.3
 E:\Perl\variant_effect_predictor\Bio\ensembl\modules E:\Perl\variant_effect_predictor\Bio\ensembl-compara\modules</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Courier New"">E:\Perl\variant_effect_predictor\Bio\ensembl-variation\modules E:\Perl\variant_effect_predictor\Bio\ensembl-functgenomics\modules
 E:\Perl\variant_effect_predictor\Bio\ensembl-variation\modules\Bio\EnsEMBL\Variation\Utils ---</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Courier New"">Any idea why this is happening(I am using Windows to run this tool)</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Courier New"">Sunita</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:13.5pt"><span style="font-size:13.5pt;font-family:"Lucida Grande","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:13.5pt;font-family:"Lucida Grande","serif"">_______________________________________________<br>
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Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a></span><o:p></o:p></p>
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_______________________________________________<br>
Dev mailing list    <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">
http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p>
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