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Dear Thomas,<br>
<br>
Ok I didn't understand correctly, now I do.<br>
As you say biomart website registry is still showing ensembl 75.<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 23/09/14 14:01, Thomas Maurel wrote:<br>
</div>
<blockquote
cite="mid:F1A87ED1-E57D-4289-8CCD-2965E6FAAC28@ebi.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Dear Guillermo,
<div><br>
</div>
<div>The <a moz-do-not-send="true" href="http://biomart.org">biomart.org</a>
website seems to be very slow at the moment and I am afraid the
website is still displaying our release 75 marts on hg19
(GRCh37). According to the <a moz-do-not-send="true"
href="http://biomart.org">biomart.org</a> mart registry page: <a
moz-do-not-send="true"
href="http://www.biomart.org/biomart/martservice?type=registry">http://www.biomart.org/biomart/martservice?type=registry</a>, port
'80' is still valid.</div>
<div>If you want to use hg38 (GRCh38), the best way would be to
point your mart XML config to the <a moz-do-not-send="true"
href="http://ensembl.org">ensembl.org</a> website in order to
access our release 76 mart databases on hg38 (GRCh38).</div>
<div>You can follow the previous instruction but just change the
mart registry URL page to get the mart release 76 registry
informations:</div>
<div><br>
</div>
<div>
<blockquote type="cite">
<div text="#000066" bgcolor="#FFFFFF">
<blockquote
cite="mid:4B2EFDEF-33F9-4F59-8B37-30795F2DA7CA@ebi.ac.uk"
type="cite">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 </div>
</blockquote>
</div>
</blockquote>
<div text="#000066" bgcolor="#FFFFFF">
<div>Ensembl website on release 76 (hg38): <a
moz-do-not-send="true"
href="http://www.ensembl.org/biomart/martservice?type=registry">http://www.ensembl.org/biomart/martservice?type=registry</a></div>
</div>
<blockquote type="cite">
<div text="#000066" bgcolor="#FFFFFF">
<blockquote
cite="mid:4B2EFDEF-33F9-4F59-8B37-30795F2DA7CA@ebi.ac.uk"
type="cite">
<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><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>
</div>
</blockquote>
</div>
</blockquote>
</div>
<div><br>
</div>
<div>I am afraid $action=clean is quite resource consuming but you
will only need to run your script with this setting when you
change the registry information.</div>
<div><br>
</div>
<div>Hope this helps,</div>
<div>Best regards,</div>
<div>Thomas</div>
<div>
<div>
<div>On 23 Sep 2014, at 12:43, Guillermo Marco Puche <<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
<div text="#000066" bgcolor="#FFFFFF"> Dear Thomas,<br>
<br>
My BioMart perl script is using the following mart XML
config file:<br>
<br>
<pre><?xml version="1.0" encoding="UTF-8"?>
</pre>
<pre><!DOCTYPE MartRegistry>
</pre>
<pre><MartRegistry>
</pre>
<pre> <MartURLLocation
</pre>
<pre> name = "ensembl"
</pre>
<pre> displayName = "ensembl"
</pre>
<pre> host = "<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="http://www.biomart.org/">www.biomart.org</a>"
</pre>
<pre> port = "80"
</pre>
<pre> visible = "1"
</pre>
<pre> default = ""
</pre>
<pre> includeDatasets = "hsapiens_gene_ensembl"
</pre>
<pre> martUser = ""
</pre>
<pre> />
</pre>
<pre></MartRegistry>
</pre>
However, I'm getting BioMart queries from hg19 and not
hg38. Does the default port '80' still working on hg19?
how can I specify I would like to use hg38 biomart
service.<br>
<br>
On the other hand, it's always useful to know how to query
older Ensembl versions with Biomart. However using
$action=clean with conf file of ensembl 75 archive it's
leading me to massive amounts of RAM consumption in my
Perl script.<br>
<br>
Thanks.<br>
<br>
Best regards,<br>
Guillermo.<br>
<div class="moz-cite-prefix">On 19/09/14 15:48, Thomas
Maurel wrote:<br>
</div>
<blockquote
cite="mid:4B2EFDEF-33F9-4F59-8B37-30795F2DA7CA@ebi.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<meta http-equiv="content-type"
content="text/html; charset=windows-1252">
<div bgcolor="#FFFFFF" text="#000066"> 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>
</div>
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<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>
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-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>
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