<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">Thanks Ian</span><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">
<br></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">You are right the api says 63.</div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">
<br></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">But I am pretty sure I downloaded it from your current api page. It that version still v63? This is very confusing.</div>
<div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); "><br></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">
I can checkout the CVS for release 64 ... but I think you should make it clear for people that the version here:</div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">
<a href="http://www.ensembl.org/info/docs/api/api_installation.html" target="_blank" style="color: rgb(17, 85, 204); ">http://www.ensembl.org/info/docs/api/api_installation.html</a></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">
<br></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">is really v63.</div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">
<br></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">Best regards</div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">
<br></div><font color="#888888" style="font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); "><div>Duarte</div><div><br></div></font>=========================<br> Duarte Miguel Paulo Molha<br>
Tel: +447772111304<br> Email: <a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a><br>=========================<br>
<br><br><div class="gmail_quote">On 19 October 2011 10:32, ian Longden <span dir="ltr"><<a href="mailto:ianl@ebi.ac.uk">ianl@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Check<br>
/ensembl/v64/ensembl-api/ensembl/modules/Bio/EnsEMBL/ApiVersion.pm<br>
<br>
and make sure that this has:<br>
my $API_VERSION = 64;<br>
<br>
<br>
The script seems to think it is release 63. You may need to checkout<br>
from cvs release 64 again.<br>
<br>
-Ian.<br>
<div><div></div><div class="h5"><br>
<br>
On Wed, Oct 19, 2011 at 10:25 AM, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br>
> I am having issues using a local version of ensembl database.<br>
> I have already installed both the v62 version and the v64 version of the<br>
> ensembl database and respective APIs.<br>
> If I use v62 api I can query the database with no issues, using V64 api the<br>
> registry does not seem to read the mySQL database.<br>
> As a test I used the local v64 api to query the remote database and pull out<br>
> the tables it finds. Here are the ones I retrieve for Human:<br>
> species/group homo_sapiens/core<br>
> database homo_sapiens_core_63_37<br>
> host:port <a href="http://ensembldb.ensembl.org:5306" target="_blank">ensembldb.ensembl.org:5306</a><br>
> species/group homo_sapiens/cdna<br>
> database homo_sapiens_cdna_63_37<br>
> host:port <a href="http://ensembldb.ensembl.org:5306" target="_blank">ensembldb.ensembl.org:5306</a><br>
> species/group homo_sapiens/vega<br>
> database homo_sapiens_vega_63_37<br>
> host:port <a href="http://ensembldb.ensembl.org:5306" target="_blank">ensembldb.ensembl.org:5306</a><br>
> species/group homo_sapiens/otherfeatures<br>
> database homo_sapiens_otherfeatures_63_37<br>
> host:port <a href="http://ensembldb.ensembl.org:5306" target="_blank">ensembldb.ensembl.org:5306</a><br>
> species/group homo_sapiens/variation<br>
> database homo_sapiens_variation_63_37<br>
> host:port <a href="http://ensembldb.ensembl.org:5306" target="_blank">ensembldb.ensembl.org:5306</a><br>
> species/group homo_sapiens/funcgen<br>
> database homo_sapiens_funcgen_63_37<br>
> host:port <a href="http://ensembldb.ensembl.org:5306" target="_blank">ensembldb.ensembl.org:5306</a><br>
><br>
> Why is this query pulling out V63 tables? Should it not be querying the V64<br>
> tables instead? Is the current api on the server really v63 instead?<br>
> I got the API from<br>
> : <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><br>
> Your help is most appreciated.<br>
> Best regards,<br>
> Duarte<br>
> PS: This is the script I used to query<br>
> #!/usr/bin/perl -w<br>
> #<br>
> use strict;<br>
> #Import Libs<br>
> use lib '/ensembl/v64/ensembl-api/ensembl/modules'; # points to HG19 ensembl<br>
> API<br>
> #Use ENSEMBL modules<br>
> use Bio::EnsEMBL::Registry;<br>
> my $registry = 'Bio::EnsEMBL::Registry';<br>
><br>
> #Create Registry for connecting to database<br>
> $registry->load_registry_from_db( -host => '<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>',<br>
> -user => 'anonymous');<br>
> my @db_adaptors = @{ $registry->get_all_DBAdaptors() };<br>
> foreach my $db_adaptor (@db_adaptors) {<br>
> my $db_connection = $db_adaptor->dbc();<br>
> printf(<br>
> "species/group\t%s/%s\ndatabase\t%s\nhost:port\t%s:%s\n\n",<br>
> $db_adaptor->species(), $db_adaptor->group(),<br>
> $db_connection->dbname(), $db_connection->host(),<br>
> $db_connection->port()<br>
> );<br>
> }<br>
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><br>
><br>
</blockquote></div><br>