<div dir="ltr">Thanks for spotting that link - will get it updated.<div><br></div><div>Regarding the test failures, it looks like the tests are picking up an out-of-date version of the ensembl-variation API - do you have this installed somewhere else and added to your PERL5LIB? If so you may want to update it (and any other API modules) to release/89. VEP *should* use the modules downloaded by INSTALL.pl to the ensembl-vep directory, but it looks like the test run is not picking these up.</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 1 June 2017 at 15:47, Nicolas Thierry-Mieg <span dir="ltr"><<a href="mailto:Nicolas.Thierry-Mieg@univ-grenoble-alpes.fr" target="_blank">Nicolas.Thierry-Mieg@univ-grenoble-alpes.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">oups! I had missed that.<br>
<br>
You might want to update the "Download latest version" (under "Standalone perl script") on this page then:<br>
<a href="http://www.ensembl.org/info/docs/tools/vep/index.html" rel="noreferrer" target="_blank">http://www.ensembl.org/info/do<wbr>cs/tools/vep/index.html</a><br>
<br>
<br>
Unfortunately the latest version obtained with git clone fails to INSTALL for me. It ends with:<br>
Result: FAIL<br>
Failed 25/38 test programs. 26/800 subtests failed.<br>
<br>
<br>
Looking at the stderr output, it seems many of the failures are due to:<br>
<br>
# Error: "trim_sequences" is not exported by the Bio::EnsEMBL::Variation::Utils<wbr>::Sequence module<br>
<br>
<br>
Any ideas?<br>
Thanks<span class=""><br>
<br>
<br>
<br>
On 06/01/2017 04:16 PM, Will McLaren wrote:<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
Hi Nicolas,<br>
<br>
The version of VEP in ensembl-tools is no longer supported and will be<br>
phased out soon.<br>
<br>
Please switch to using the ensembl-vep repository instead.<br>
<br>
<a href="http://www.ensembl.org/info/docs/tools/vep/script/index.html" rel="noreferrer" target="_blank">http://www.ensembl.org/info/do<wbr>cs/tools/vep/script/index.html</a><br>
<br>
Regards<br>
<br>
Will McLaren<br>
Ensembl Variation<br>
<br>
On 1 June 2017 at 15:10, Nicolas Thierry-Mieg<br>
<<a href="mailto:Nicolas.Thierry-Mieg@univ-grenoble-alpes.fr" target="_blank">Nicolas.Thierry-Mieg@univ-gre<wbr>noble-alpes.fr</a><br></span><span class="">
<mailto:<a href="mailto:Nicolas.Thierry-Mieg@univ-grenoble-alpes.fr" target="_blank">Nicolas.Thierry-Mieg@u<wbr>niv-grenoble-alpes.fr</a>>> wrote:<br>
<br>
Hi,<br>
<br>
I just installed the latest VEP from ensembl-tools-release-89.zip ,<br>
perl INSTALL claims it "is configured to install v88 of the Ensembl<br>
API for use by the VEP" [NOTE: v88 not v89]. It then grabs a lot of<br>
stuff that has 88 in it's name or path, and when I install the human<br>
refseq cache it gets:<br>
- downloading<br>
<a href="ftp://ftp.ensembl.org/pub/release-88/variation/VEP/homo_sapiens_refseq_vep_88_GRCh37.tar.gz" rel="noreferrer" target="_blank">ftp://ftp.ensembl.org/pub/rele<wbr>ase-88/variation/VEP/homo_sapi<wbr>ens_refseq_vep_88_GRCh37.tar.<wbr>gz</a><br>
<<a href="ftp://ftp.ensembl.org/pub/release-88/variation/VEP/homo_sapiens_refseq_vep_88_GRCh37.tar.gz" rel="noreferrer" target="_blank">ftp://ftp.ensembl.org/pub/rel<wbr>ease-88/variation/VEP/homo_sap<wbr>iens_refseq_vep_88_GRCh37.tar.<wbr>gz</a>><br>
<br>
<br>
I guess someone forgot to increment something somewhere ;-)<br>
<br>
Regards,<br>
Nicolas<br>
<br>
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<br>
-- <br>
------------------------------<wbr>-----------------------------<br>
Nicolas Thierry-Mieg<br>
Laboratoire TIMC-IMAG/BCM, CNRS UMR 5525<br>
Pavillon Taillefer, Faculte de Medecine<br>
38700 La Tronche, France<br>
tel: <a href="tel:%28%2B33%29456.520.067" value="+33456520067" target="_blank">(+33)456.520.067</a>, fax: <a href="tel:%28%2B33%29456.520.055" value="+33456520055" target="_blank">(+33)456.520.055</a><br>
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