<div dir="ltr">Hi,<div><br></div><div>It seems we haven't made available on our FTP site the dumps for *_76_37.</div><div><br></div><div>The data is in fact identical to *_75_37 so you've a couple of solutions:</div><div><br></div><div>1) Point VEP to the 75 database (--db_version) and the 76 cache (--cache_version)</div><div><br></div><div>2) Create *_76_37 databases with the *_75_37 data and patch the schemas to 76 using ensembl/misc-scripts/<a href="http://schema_patcher.pl">schema_patcher.pl</a></div><div><br></div><div>Regards</div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 15 September 2014 14:26, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</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="#000066">
Hello Will,<br>
<br>
Indeed I run a local Ensembl installation. I've installed
homo_sapiens_*_76_38 that's why I'm getting the error. It was a
missunderstading from my part. I guess it's time to move to GRCh38.<br>
Anyways I was trying to find homo_sapiens_*_76_37 MySQL links for
download but I just find homo_sapiens_*_76_38 on FTP server.<br>
<br>
Could you give me a link to a mirror for homo_sapiens_*_76_37?<span class=""><br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
</span><div>El 15/09/14 a las #4, Will McLaren
escribió:<br>
</div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>Are you also running your own database server?</div>
<div><br>
</div>
<div>The GRCh37 v76 databases are hosted on a different port on
<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>
(3337); to get the VEP to use this you can add the flag --port
3337 to your command line. If you don't use the DB (most VEP
functionality does not use the DB at all, see <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#limitations" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#limitations</a>),
you can bypass this completely and use --offline. See <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#assembly" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#assembly</a>
for more details.</div>
<div><br>
</div>
<div>If you are using your own DB server then you will need to
make sure you have mirrored the correct human databases; you
should have homo_sapiens_*_76_37 (* being core, variation and
funcgen).</div>
<div><br>
</div>
<div>HTH</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 15 September 2014 09:04, Guillermo
Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</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="#000066"> I forgot to mention
than I've already tried to specify assembly with VEP
"--assembly" flag:<br>
<br>
ERROR: Assembly version specified by --assembly (GRCh37)
and assembly.default meta key (GRCh38) do not match<br>
<br>
<div>El 15/09/14 a las #4, Guillermo Marco Puche escribió:<br>
</div>
<blockquote type="cite">
<div>
<div> Hello,<br>
<br>
I installed Ensembl 76 on my local server. I'm not
ready yet to annotate variants vs GRCh38.<br>
I thought that ensembl 76 version supports both
GRCh37 and GRCh38. I downloaded 76 vep cache for
GRCh37:<br>
<br>
<a href="ftp://ftp.ensembl.org/pub/release-76/variation/VEP/homo_sapiens_merged_vep_76_GRCh37.tar.gz" target="_blank">ftp://ftp.ensembl.org/pub/release-76/variation/VEP/homo_sapiens_merged_vep_76_GRCh37.tar.gz</a><br>
<br>
I get the following error:<br>
<br>
<b>ERROR: Cache assembly version (GRCh37) and
database or selected assembly version (GRCh38) do
not match.</b><b><br>
</b><br>
I got a bit confused since I saw both cache for
GRCh37/38, I would like to know if in Ensembl 76 I
can stilll annotate with GRCh37 or I just have to
move asap to GRCh38 to use 76 version.<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
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