<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Dear Guillermo,<div><br></div><div>If you are using:</div><div>1) the biomart-perl/scripts/webExample.pl script and an xml file</div><div>You can change the path to the biomart website in the following line:</div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>my $path="<a href="http://www.biomart.org/biomart/martservice?">http://www.biomart.org/biomart/martservice?</a>";</div></blockquote><div>With the path to our Ensembl release 75 archive:</div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>my $path="<a href="http://feb2014.archive.ensembl.org/biomart/martservice?">http://feb2014.archive.ensembl.org/biomart/martservice?</a>";</div></blockquote><div><br></div>2) A BioMart perl script<div>a) You first need to edit your configuration file in "biomart-perl/conf/martURLLocation.xml" and paste the content of the mart registry page for the Ensembl release 75 archive website: <a href="http://feb2014.archive.ensembl.org/biomart/martservice?type=registry">http://feb2014.archive.ensembl.org/biomart/martservice?type=registry</a></div><div>b) Then edit your script and make sure that "my $confFile" variable is looking at the martURLLocation.xml configuration file in biomart-perl/conf</div><div>c) Finally, make sure to update the following line in your script:</div><div><br></div><div>my $action='cached';</div><div><div><br></div><div>with:</div><div><br></div><div>my $action='clean';</div><div><div><div><br></div><div>The first run of your script on Ensembl 75 might be a bit slow as BioMart will cache some data from the BioMart website.</div><div>Once you have run your script with the action variable set to "clean", you can set the variable to "cached" again.</div><div><br></div><div>Hope this helps,</div><div>Best regards,</div><div>Thomas</div><div>On 19 Sep 2014, at 13:28, Guillermo Marco Puche <<a href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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Dear developers,<br>
<br>
I would like to know how to specify BioMart Perl code to query
against older Ensembl version (ie:75) and not latest (I believe used
by default).<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
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<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>--</div><div>Thomas Maurel<br>Bioinformatician - Ensembl Production Team<br>European Bioinformatics Institute (EMBL-EBI)<br>European Molecular Biology Laboratory<br>Wellcome Trust Genome Campus<br>Hinxton<br>Cambridge CB10 1SD<br>United Kingdom</div></div></span></div></span></div></span></div></span>
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