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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Ahhh, that’s great, thank you. I had tried to find it in git as assumed that was the reason I was failing, but the git ensembl –list command gave the biomart-perl
repo as being…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">biomart-perl (<a href="https://github.com/Ensembl/biomart-perl.git">https://github.com/Ensembl/biomart-perl.git</a>)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">which of course still didn’t work.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Thanks for your help.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Yours,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Ellen.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">--
</span><span style="color:black"><br>
</span><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Ellen Schofield</span></b><span style="color:black">
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</span><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Bioinformatician</span></b><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Animal<i> Health</i> Trust</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">, Lanwades Park,
Kentford,</span><span lang="EN-US" style="color:black"> </span><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Newmarket, Suffolk, CB8 7UU</span><span style="color:black">
<br>
</span><span lang="EN-US" style="font-size:7.5pt;font-family:"Tahoma","sans-serif";color:black">Switchboard: 01638 751000 Ext: 1243</span><span style="color:black">
<br>
</span><span lang="EN-US" style="font-size:7.5pt;font-family:"Tahoma","sans-serif";color:black">Reg Charity No 209642</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Ben Moore<br>
<b>Sent:</b> 29 July 2016 14:33<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] BioMart Perl API installation via Sanger CVS<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Hi Ellen,</span><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"><span style="font-family:"Arial","sans-serif"">The public CVS Sanger server has been shutdown, so our documentation is now out of date. We will make sure to update for the next release of Ensembl.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">The code has been moved to GitHub so you can get the code by running the following command:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial","sans-serif";background:#EFEFEF">git clone —branch cvs/release-0_7 </span><span style="font-family:"Arial","sans-serif""><a href="https://github.com/biomart/biomart-perl">https://github.com/biomart/biomart-perl</a></span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Best wishes</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Ben</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Ensembl Outreach officer</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal">On 29 Jul 2016, at 14:27, Ellen Schofield <<a href="mailto:Ellen.Schofield@aht.org.uk">Ellen.Schofield@aht.org.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Hi All,</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">I have been trying to get the Ensembl BioMart api set up and running on my machine by following these instructions -<span class="apple-converted-space"> </span><a href="http://www.ensembl.org/info/data/biomart/biomart_perl_api.html"><span style="color:purple">http://www.ensembl.org/info/data/biomart/biomart_perl_api.html</span></a><span class="apple-converted-space"> </span>-
however, I am unable to connect to the sanger cvs server. Has this been turned off now or is it just not available today for some reason?</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Many thanks,</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Ellen.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">--<span class="apple-converted-space"> </span></span><br>
<b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Ellen Schofield</span></b><span class="apple-converted-space"> </span><br>
<b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Bioinformatician</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Animal<span class="apple-converted-space"><i> </i></span><i>Health</i><span class="apple-converted-space"> </span>Trust</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">,
Lanwades Park, Kentford,</span><span lang="EN-US"> </span><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Newmarket, Suffolk, CB8 7UU</span><span class="apple-converted-space"> </span><br>
<span lang="EN-US" style="font-size:7.5pt;font-family:"Tahoma","sans-serif"">Switchboard: 01638 751000 Ext: 1243</span><span class="apple-converted-space"> </span><br>
<span lang="EN-US" style="font-size:7.5pt;font-family:"Tahoma","sans-serif"">Reg Charity No 209642</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""><br>
<br>
<br>
The Animal Health Trust fights disease and injury in animals. Find out more about our work at<span class="apple-converted-space"> </span></span><a href="http://www.aht.org.uk/"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";color:purple">www.aht.org.uk</span></a><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">.<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="color:black">Ben Moore<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Ensembl Outreach Officer<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:black">European Bioinformatics Institute (EMBL-EBI)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">European Molecular Biology Laboratory<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Wellcome Trust Genome Campus<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Hinxton<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Cambridge<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">CB10 1SD<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">UK<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><a href="mailto:bmoore@ebi.ac.uk">bmoore@ebi.ac.uk</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">+44 (0)1223 494265<o:p></o:p></span></p>
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