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Hello Mingyi,<br>
<br>
No, I said the VM could be used to point at your own local mirror
once installed. An Ensembl mirror really is no more than a MySQL
database populated with one of our release dumps for one or more
species. The magic sauce is in the API which simply needs to be
pointed at whichever public or private Ensembl database mirror you
wish.<br>
<br>
The Ensembl Web Code is a bit more of an advanced topic, there are
instructions for installing the Ensembl web code at
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/webcode/index.html">http://www.ensembl.org/info/docs/webcode/index.html</a> <br>
<br>
<div class="moz-cite-prefix">On 08/06/16 21:34, Liu, Mingyi wrote:<br>
</div>
<blockquote
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<p class="MsoNormal"><span style="color:#1F497D">Hi, Matthew,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks for your
reply! So as you said, VM is not for local mirror, which I
understood. You also said that VM could be used for local
mirror once registry is pointed to the local MySQL instance.
This part I’m confused about.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">A local mirror
for Ensembl should also contain a website that serves up the
Ensembl genome browser/search results etc., and allow a
local DAS server as needed. How is that done with the VM? I
couldn't find any apache webserver included, or where the
usual Ensembl webcode config scripts are located.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Or by a local
mirror, you meant the mirror for the Ensembl data (in
MySQL), not the mirror for the Ensembl website? The latter
is what I want to use VM for but I think it’s not possible
(would’ve been nice though!).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks again!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Mingyi<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:.5in"><b><span
style="color:windowtext">From:</span></b><span
style="color:windowtext"> <a class="moz-txt-link-abbreviated" href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>
[<a class="moz-txt-link-freetext" href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Matthew Laird<br>
<b>Sent:</b> Wednesday, June 08, 2016 4:22 PM<br>
<b>To:</b> Ensembl developers list
<a class="moz-txt-link-rfc2396E" href="mailto:dev@ensembl.org"><dev@ensembl.org></a><br>
<b>Subject:</b> Re: [ensembl-dev] Ensembl VM possible to
use for house Ensembl installation?<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">Hello
Mingyi,<br>
<br>
Indeed the VM is intended to assist users in rapidly using the
API, users who might be running Windows or not want to install
the API locally, the VM lets them prototype or rapidly start
using the API with minimal effort. As you've discovered it's
not intended to be a local Ensembl mirror, it's a client side
installation.<br>
<br>
Installing a mirror is actually even easier than setting up
the API, dumps of all the Ensembl databases are available on
our ftp site at
<a moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/current_mysql/">ftp://ftp.ensembl.org/pub/current_mysql/</a>
And instructions for loading them in to a local MySQL instance
are available at
<a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/webcode/mirror/install/ensembl-data.html">http://www.ensembl.org/info/docs/webcode/mirror/install/ensembl-data.html</a>
Once that's done, all you need to do is point the Registry at
your local instance rather than one of the public mirrors, and
voila, you have your own mirror of an Ensembl release.<br>
<br>
If you have any other questions don't hesitate to drop us
another message.<span style="font-size:12.0pt"><o:p></o:p></span></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">On 16-06-08
08:33 PM, Liu, Mingyi wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="margin-left:.5in"><span
style="color:#1F497D">Hi, can anyone confirm my question
below? Are the Ensembl VMs only for Ensembl API +
Ensembl’s own MySQL access, or the VM has everything
needed for in-house Ensembl installation (one just need to
change some parameters to point to in-house MySQL etc)? If
the latter that’d be fantastic, but so far it doesn’t look
like the case.</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><span
style="color:#1F497D">Thanks!</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><span
style="color:#1F497D">Mingyi</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:1.0in"><b><span
style="color:windowtext">From:</span></b><span
style="color:windowtext"> Liu, Mingyi
<br>
<b>Sent:</b> Tuesday, June 07, 2016 1:48 PM<br>
<b>To:</b> Ensembl developers list <a
moz-do-not-send="true" href="mailto:dev@ensembl.org"><a class="moz-txt-link-rfc2396E" href="mailto:dev@ensembl.org"><dev@ensembl.org></a></a><br>
<b>Subject:</b> Ensembl VM possible to use for house
Ensembl installation?</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal" style="margin-left:1.0in"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-left:1.0in"><span
style="color:#1F497D">Hi,</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:1.0in"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:1.0in"><span
style="color:#1F497D">I downloaded Ensembl VMs in the hope
that this is an easy way to set up Ensembl in-house (once
MySQL data are all downloaded/imported). However it seems
that the VM doesn’t have webserver and is only meant to be
used for running scripts that utilize Ensembl API? Is
that correct? I’m a bit confused as I thought one doesn’t
need a VM to run scripts using Ensembl API, just need to
download Ensembl/Bioperl and install dependency. So the VM
is mostly for saving efforts installing dependency?</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:1.0in"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:1.0in"><span
style="color:#1F497D">Thanks!
</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:1.0in"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:1.0in"><span
style="color:#1F497D">Mingyi</span><o:p></o:p></p>
<div class="MsoNormal"
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Roman",serif">
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<br>
<br>
<o:p></o:p></span></p>
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<br>
<pre class="moz-signature" cols="72">--
Matthew Laird - Ensembl Core Developer
The European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD, United Kingdom
Tel: +44-(0)1223-494274
Fax: +44-(0)1223-494468
<a class="moz-txt-link-freetext" href="http://www.ebi.ac.uk/">http://www.ebi.ac.uk/</a>
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