<div dir="ltr"><div>Hi Will</div><div><br></div>Thanks very much for your suggestion! It works!<div><br></div><div>However, it seems hard to load VEP_summary.html completely into a web browser (I use Safari). I can only see VEP Run Stats and General Stats on the web page, and no links can be clicked. Is this a browser issue? but I will try another one (e.g. IE) when I have a chance. BTW, the HTML file is ~63 MB and should not be a problem.</div><div><br></div><div>Cheers</div><div>Fred Peng</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 19 November 2014 02:04, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@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 dir="ltr">Hello,<div><br></div><div>By default when using --cache the VEP checks in with the DB server at <a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a> at the beginning of its run; barley is located on a different server, which you can have the VEP connect to using --genomes (see <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_genomes" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_genomes</a>)</div><div><br></div><div>You can also bypass this connection completely by using --offline (with limitations, 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>), though note in this case you must use the latin name for the species e.g. --species hordeum_vulgare<br><br>In both the above cases you will also need to specify the e!Genomes cache version using --cache_version 24, since the e!Genomes version numbers differ from the main Ensembl version numbers (see <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_cache_version" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_cache_version</a>)<br></div><div><br></div><div>So, in summary, you can use either:</div><div><br></div><div>perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --cache --cache_version 24 --species barley --genomes</div><div><br></div><div>or</div><div><br></div><div>perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --offline --cache_version 24 --species hordeum_vulgare<br></div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On 18 November 2014 21:37, Fred Peng <span dir="ltr"><<a href="mailto:fredyfpeng@ualberta.ca" target="_blank">fredyfpeng@ualberta.ca</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Dear Developer,<br><div class="gmail_quote"><div dir="ltr"><div><br></div><div>I am running VEP on barley (Hordeum vulgare L.) but could not make it work, with a message like: Hordeum_vulgare is not a valid species name (check DB and API version). I downloaded the cache file for barley <span style="font-family:Menlo;font-size:11px;background-color:rgb(235,254,243)">hordeum_vulgare_vep_24_082214v1.tar.gz</span> and unpacked it into ~/.vep directory. I run VEP with --cache option and specified --species Hordeum_vulgare. </div><div><br></div><div>Any help (especially regarding cache file prep, how to specify a species -- common name or Latin name?) is appreciated.</div><div><br></div><div>Cheers,</div><div>Fred Peng</div></div>
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