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Hi Duarte,<br>
<br>
The VEP --assembly flag uses the solution I suggested initially,
which is to have the two databases on two separate servers.<br>
By specifying --assembly GRCh37, the default 3306 port is replaced
by the 3337 port, which is where the GRCh37 databases are hosted.<br>
It is worth noting as well that only the human databases on port
3337 are updated, all the other databases are identical to the ones
from release 75.<br>
<br>
The current implementation of the registry does not support two core
databases for a single species on the same server.<br>
<br>
The solutions are:<br>
- use two separate servers<br>
In the case of our live servers, we have ensembldb.ensembl.org:3306
for GRCh38 and ensembl.ensembl.org:3337 for GRCh37<br>
- bypass the registry and specify each required database
individually<br>
This will only work if connecting to one database at a time<br>
<br>
Our system is currently in transition between two models.<br>
Historically, one species has one assembly at one given time.<br>
With the migration from GRCh37 to GRCh38 and the future of genomics,
we see the need to support multiple assemblies for a single species.<br>
We are currently working on better solutions for this.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 28/04/2015 09:51, Duarte Molha
wrote:<br>
</div>
<blockquote
cite="mid:CAGqkoELxsZj_PPevbFQhAS9TZuivSu2x0b0Jc8djffVuaVwEjw@mail.gmail.com"
type="cite">
<div dir="ltr">Ok ... thanks Magali.
<div><br>
</div>
<div>I believe the latest VEP now supports an --assembly flag to
allow it to annotate against a specific assembly.</div>
<div>Can we not have the same flag on the registry ? </div>
<div>How does VEP do it?</div>
<div>This would be incredibly useful because I would not have to
create new scripts to support a different assembly.<br>
</div>
<div><br>
</div>
<div>I could just download all the tables and just tell the
registry which one to use.</div>
<div><br>
</div>
<div>Please correct me if I am wrong but your proposed solution
would mean I would have to bypass the registry completely and
I would need to create each each adaptor from scratch and thus
I would need to alter a lot of my scripts to support both
assemblies.</div>
<div><br>
</div>
<div>"--assembly GRCh37" would be a much more preferable route.</div>
<div><br>
</div>
<div>Best regards,<br>
</div>
<div><br>
</div>
<div> Duarte</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="gmail_signature"><font
style="background-color:rgb(255,255,255)" color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br>
</font>
<div><font style="background-color:rgb(255,255,255)"
color="#999999"> <a moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
</div>
<br>
<div class="gmail_quote">On 27 April 2015 at 17:48, mag <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@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">
<div bgcolor="#FFFFFF" text="#000000"> Hi Duarte,<br>
<br>
The mysql dumps for GRCh37 are available on the ftp site
as well<br>
<a moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/"
target="_blank">ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/</a><br>
<br>
I would recommend having only one copy of human for
release 79.<br>
So if you are interested in the GRCh37 data, you can
download the database from <a moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/"
target="_blank">ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/</a>
rather than <a moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/release-79/mysql/"
target="_blank">ftp://ftp.ensembl.org/pub/release-79/mysql/</a><br>
<br>
If you need both databases on the same server, you can
access a given database directly rather than using the
registry.<br>
my $human_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(<br>
-HOST => 'localhost',<br>
-PORT => 3306,<br>
-USER => 'user',<br>
-DBNAME => 'homo_sapiens_core_79_37',<br>
-SPECIES => 'homo_sapiens',<br>
-GROUP => 'core'<br>
);<br>
<br>
<br>
Hope that helps,<br>
Magali<span class=""><br>
<br>
<div>On 27/04/2015 17:11, Duarte Molha wrote:<br>
</div>
</span>
<blockquote type="cite">
<div dir="ltr"><span class="">Thanks Magali
<div><br>
</div>
<div>But I think you have not understtod my
question.</div>
<div><br>
</div>
<div>Assume I want to download the databases to my
local computer and use the perl API 79 to query
the latest 79_37 database instead of the default
79_38<font size="3">. </font></div>
<div><font size="3">Previously, I just had to
download the mysql tables corresponding to the
api I was using to fetch the data correctly,
however, now you have broken that link
API->Underlying_assembly</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3">So how do I tell my scripts what
database to query?</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3">My local sql will all be under
the same port.</font></div>
<div><font size="3"><br>
</font></div>
</span>
<div><font size="3">Best regards</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3">Duarte</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3"><br>
</font></div>
</div>
<div class="gmail_extra"><span class=""><br clear="all">
<div>
<div><font
style="background-color:rgb(255,255,255)"
color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br>
</font>
<div><font
style="background-color:rgb(255,255,255)"
color="#999999"> <a
moz-do-not-send="true"
href="http://about.me/duarte"
target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
</div>
<br>
</span>
<div class="gmail_quote"><span class="">On 27 April
2015 at 17:01, mag <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
wrote:<br>
</span>
<div>
<div class="h5">
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi
Duarte,<br>
<br>
The archive 75 website is still based on the
release 75 API.<br>
<br>
For the dedicated GRCh37 website though, we
have used a data freeze from release 75 and
have since been updating the website and
underlying databases along with the main
release.<br>
The GRCh37 databases are available on our
main MySQL server on port 3337 (instead of
the default 3306 which will give you access
to GRCh38 databases)<br>
<br>
<br>
Hope that helps,<br>
Magali
<div>
<div><br>
<br>
<div>On 27/04/2015 16:56, Duarte Molha
wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div dir="ltr">
<div>Dear developers</div>
<div><br>
</div>
<div>On your GRCh37 archive site you
say this:</div>
<div><br>
</div>
<div>===========================</div>
<div><br>
</div>
<h2>About this archive</h2>
<p>This archive is based on Ensembl
Release 75 data, and gives
continuing access to human
assembly GRCh37, as well as all
our other release 75 species (data
freeze March 2014) for comparative
purposes. Human variation and
regulation data has since been
updated in March 2015.</p>
<p>The API and website will be
updated in tandem with the release
of the main Ensembl website (<b>currently
version 79</b>), and we will
also periodically update this site
with new data human, which will be
announced in this panel.</p>
<div><span>MySQL dumps of human
databases on the most recent
schema version are available on
our</span><span> </span><a
moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/grch37/"
target="_blank">FTP site</a><span>.</span></div>
<div><br>
</div>
<div>=========================</div>
<div><br>
</div>
<div>It was my understanding that an
API version was directly linked to
a specific assembly. So I thought
that if I wanted to query the
latest GRCh37 assembly I would
need to use the api v75 and if I
wanted to use a local database, I
would download the corresponding
sql tables for that version.</div>
<div><br>
</div>
<div>However, according to this
announcement, I can now use the
V79 api and query the old
assembly... How is this
accomplished ?</div>
<div>What you I have to do on my
scripts to make sure I am querying
the 37 version even though I am
using the latest API?</div>
<div><br>
</div>
<div>Sorry, I hope this is not a
stupid question but I am a bit
confused.</div>
<div><br>
</div>
<div>Best regards</div>
<div><br>
</div>
<div>Duarte</div>
<div><br>
</div>
<div><br>
</div>
<br clear="all">
<div>
<div><font
style="background-color:rgb(255,255,255)"
color="#999999">=========================<br>
Duarte Miguel Paulo Molha
<br>
</font>
<div><font
style="background-color:rgb(255,255,255)"
color="#999999"> <a
moz-do-not-send="true"
href="http://about.me/duarte"
target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
</div>
</div>
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