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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I will look into this option. I was able to get the VEP code running after setting the Lib path to point to the Bio modules.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I am currently looking for ways on how to get the Condel scores as an output just like the SIFT and Polyphen for a given VCF file.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Any help in that direction will be helpful.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks again<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Sunita<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>Fiona Cunningham<br>
<b>Sent:</b> Friday, June 01, 2012 10:02 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Vraint Effect Predictor<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dear 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">We have also just released code for an Ensembl Virtual Machine which has all the code for the API and VEP already installed. Maybe this will be easier for you. For instructions see here:<o:p></o:p></p>
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<p class="MsoNormal"><a href="http://www.ensembl.org/info/data/virtual_machine.html">http://www.ensembl.org/info/data/virtual_machine.html</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">and announcement here:<o:p></o:p></p>
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<p class="MsoNormal"><a href="http://www.ensembl.info/blog/2012/05/10/ensembl-67-has-been-released/">http://www.ensembl.info/blog/2012/05/10/ensembl-67-has-been-released/</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">Best wishes,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Fiona<br>
<br>
-----------------------------------------------------------------------------------<br>
Fiona Cunningham<br>
Ensembl Coordinator, Ensembl Variation Project Leader.<br>
EMBL-EBI, Genome Campus, Hinxton, UK<br>
<a href="http://www.ensembl.org" target="_blank">www.ensembl.org</a> || <a href="http://www.lrg-sequence.org" target="_blank">
www.lrg-sequence.org</a><br>
<a href="mailto:fiona@ebi.ac.uk" target="_blank">fiona@ebi.ac.uk</a> || t: +44 1223 494612<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On 1 June 2012 09:32, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal">Hello Sunita,<o:p></o:p></p>
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<p class="MsoNormal">It looks like you are using a Windows machine; the VEP is not well tested on Windows and I'm not sure if the installer script will work.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You may still be able to get the VEP running by installing the Ensembl API manually; see here for details:<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="http://www.ensembl.org/info/docs/api/api_installation.html" target="_blank">http://www.ensembl.org/info/docs/api/api_installation.html</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">You will need the ensembl, ensembl-variation and ensembl-functgenomics modules installed.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hope this helps!<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" style="margin-bottom:12.0pt">Will<o:p></o:p></p>
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<p class="MsoNormal">On 31 May 2012 17:17, 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">Hi,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am trying to install the perl API for Variant Effect Predictor.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">When I run the INSTALL.pl (as per instructions in
<a href="http://useast.ensembl.org/info/docs/variation/vep/vep_script.html#run_install" target="_blank">
http://useast.ensembl.org/info/docs/variation/vep/vep_script.html#run_install</a>)<o:p></o:p></p>
<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">I am getting the following error
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Testing VEP script<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">ERROR: Testing VEP script failed with the following error<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Can't locate Bio/EnsEMBL/Variation/Utils/Sequence.pm in @INC (@INC contains: E:/<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Perl/variant_effect_predictor C:/Perl/site/lib C:/Perl/lib .) at variant_effect_<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="http://predictor.pl" target="_blank">predictor.pl</a> line 40.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">BEGIN failed--compilation aborted at
<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> line 40.<o:p></o:p></p>
<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"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Any idea why I am getting this error<o:p></o:p></p>
<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"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Sunita<o:p></o:p></p>
<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"><b><i><span style="font-size:8.5pt;font-family:"Arial","sans-serif"">The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure,
copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.<o:p></o:p></span></i></b></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
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