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<p>Hi Kevin,</p>
<p>Using VEP via remote databases can be slow, so we would recommend
downloading cache files of annotation and fasta files of genomic
sequence for more efficient local use. There is information on how
to do this here:<br>
</p>
<p><a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html</a></p>
<p>Best wishes,</p>
<p>Sarah<br>
</p>
<br>
<div class="moz-cite-prefix">On 08/02/2018 19:48, Steve Trevanion
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:c1a3dad1-5b2a-66a4-86ac-21f5fbbf44b7@ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<p>Hi Kevin,</p>
<p>ensembldb.ensembl.org is hosted at EMBL-EBI and the IP is
stable.</p>
<p>So you need to use port 5306 for all applications. I guess you
could set it as an environment variable and then use that in
your scripts (<a class="moz-txt-link-freetext"
href="http://www.ensembl.org/info/docs/api/registry.html"
moz-do-not-send="true">http://www.ensembl.org/info/docs/api/registry.html</a>)
but that's not very elegant. Can anyone from Ensembl @core or
@variation comment ?</p>
<p>Cheers,<br>
</p>
<p>Steve<br>
</p>
<p> <br>
</p>
<br>
<div class="moz-cite-prefix">On 08/02/2018 03:48, Ernst, Kevin
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:8778b57f-8ca8-0e5f-d196-a2610fc501a4@cchmc.org">
<meta http-equiv="Content-Type" content="text/html;
charset=utf-8">
<div class="moz-cite-prefix">Hi Steve, thanks for your reply.
I'll share that information with our research IT people and
see what they say.<br>
<br>
What about <tt>ensembldb.ensembl.org</tt> (<tt>ensembldb.ebi.ac.uk</tt>)?
That does not appear to be hosted with AWS. Is that IP (or
that of the load balancer, if there is one) likely to change
on a whim, or have they been fairly stable? Perhaps that's our
only option.<br>
<br>
I have an additional question about the MySQL port number as
well. I was unable to convince our organizational network
security team to make exceptions for the "standard" port 3306
(which is, sadly, opposite the motivation described in <a
moz-do-not-send="true"
href="http://www.ensembl.info/2013/05/02/database-port-changes/">
this Ensembl blog post</a>).<br>
<br>
So... will Ensembl tools like VEP generally try one port and
then the other, or is there a way we could globally configure
anything using the Perl API to prefer the non-standard port
number—for all users of our cluster? Perhaps with a <tt>Makefile.PL</tt>
flag, or an environment variable?<br>
<br>
(I see that creating an <tt>/etc/skel/.vep/vep.in</tt><tt>i</tt>
for new users is one potential option for VEP, for example,
but there are hundreds of existing users, so setting an
environment variable in our Environment Modules modulefile for
VEP would work much better.)<br>
<br>
Thanks very much.<br>
<br>
Cheers,<br>
Kevin Ernst<br>
<br>
<br>
On 07.02.18 19:07, Steve Trevanion wrote:<br>
</div>
<blockquote type="cite"
cite="mid:a1f29c8e-c8e8-f34e-b157-6314e486d1a0@ebi.ac.uk"> Can
you speak again with your IT colleagues ? I am not a
specialist in this area so I will talk next week with members
of the EMBL-EBI network team to see if they can suggest any
ways around this.<br>
</blockquote>
<br>
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