<div dir="ltr">Hi Guillermo,<div><br></div><div>Another user contributed a pull request which should fix this issue for you:</div><div><br></div><div><a href="https://github.com/Ensembl/VEP_plugins/commit/7c865b4898540bff2d9acfb68f4e9ac513c9e74a">https://github.com/Ensembl/VEP_plugins/commit/7c865b4898540bff2d9acfb68f4e9ac513c9e74a</a><br></div><div><br></div><div>Cheers</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 15 May 2017 at 15:51, Laurent Gil <span dir="ltr"><<a href="mailto:lgil@ebi.ac.uk" target="_blank">lgil@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 bgcolor="#FFFFFF" text="#000000">
<p>Hi Guillermo,</p>
<p>We need look into it to highlight/fix the compatibility issues of
the VEP plugins with the new VEP.<br>
</p>
<p>In the meantime, you can define your own Gene adaptor in your
self coded plugins, by inserting this code in each plugin (sorry):</p>
<span class="m_8868361657833624851sh_keyword">use</span> Bio<span class="m_8868361657833624851sh_symbol">::</span>EnsEMBL<span class="m_8868361657833624851sh_symbol">::</span>Registry<span class="m_8868361657833624851sh_symbol">;</span>
<span class="m_8868361657833624851sh_keyword"><br>
<br>
my</span> <span class="m_8868361657833624851sh_variable">$registry</span> <span class="m_8868361657833624851sh_symbol">=</span> <span class="m_8868361657833624851sh_string">'Bio::EnsEMBL::Registry'</span><span class="m_8868361657833624851sh_symbol">;</span><br>
<span class="m_8868361657833624851sh_variable">$registry</span><span class="m_8868361657833624851sh_symbol">-></span><span class="m_8868361657833624851sh_function">load_registry_from_<wbr>db</span><span class="m_8868361657833624851sh_symbol">(</span><br>
<span class="m_8868361657833624851sh_symbol">-</span>host <span class="m_8868361657833624851sh_symbol">=></span>
<span class="m_8868361657833624851sh_string">'<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>'</span><span class="m_8868361657833624851sh_symbol">,</span> <span class="m_8868361657833624851sh_comment">#
alternatively '<a href="http://useastdb.ensembl.org" target="_blank">useastdb.ensembl.org</a>'<br>
</span> <span class="m_8868361657833624851sh_symbol">-</span>user <span class="m_8868361657833624851sh_symbol">=></span> <span class="m_8868361657833624851sh_string">'anonymous'</span><span class="m_8868361657833624851sh_symbol"><br>
);</span><br>
my $gene_adaptor = <span class="m_8868361657833624851sh_variable">$registry</span><span class="m_8868361657833624851sh_symbol">-></span><span class="m_8868361657833624851sh_function">get_adaptor</span><span class="m_8868361657833624851sh_symbol">(</span> <span class="m_8868361657833624851sh_string">'Human'</span><span class="m_8868361657833624851sh_symbol">,</span> <span class="m_8868361657833624851sh_string">'Core'</span><span class="m_8868361657833624851sh_symbol">,</span> <span class="m_8868361657833624851sh_string">'Gene'</span>
<span class="m_8868361657833624851sh_symbol">); # e.g. if you work on human data<br>
<br>
</span><span class="m_8868361657833624851pl-smi">$self</span><span class="m_8868361657833624851pl-k">-></span>{<span class="m_8868361657833624851pl-c1">ga</span>} = $gene_adaptor; # If you want to keep
using the variable <span class="m_8868361657833624851pl-smi">$self</span><span class="m_8868361657833624851pl-k">-></span>{<span class="m_8868361657833624851pl-c1">ga</span>}.<br>
<span class="m_8868361657833624851pl-smi"></span><span class="m_8868361657833624851pl-k"></span><span class="m_8868361657833624851pl-c1"></span><br>
You can have further explanations about this code in the Ensembl API
tutorial:
<a class="m_8868361657833624851moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/core/core_tutorial.html" target="_blank">http://www.ensembl.org/info/<wbr>docs/api/core/core_tutorial.<wbr>html</a><br>
<br>
I hope this will solve your issue.<br>
Best regards,<br>
<pre class="m_8868361657833624851moz-signature" cols="72">Laurent
Ensembl Variation
</pre><div><div class="h5">
<div class="m_8868361657833624851moz-cite-prefix">On 15/05/2017 12:06, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote type="cite">
<p>Hi Laurent,</p>
<p>Thank you for your quick answer. I'm using gene adaptor in some
self coded plugins too. Do you have any quick-fix in mind or
workaround?<br>
I'm really looking forward for this document. Will it be
announced in mailing list or blog? I was really scared with this
big VEP update for the plugin compatibility. <br>
</p>
<p>Best regards,<br>
Guillermo.<br>
</p>
<br>
<div class="m_8868361657833624851moz-cite-prefix">On 05/15/2017 12:17 PM, Laurent Gil
wrote:<br>
</div>
<blockquote type="cite">
<p>Hi Guillermo,</p>
<p>Unfortunately the VEP plugin is not compatible with the new
ensembl-vep repository.<br>
We need to document this plugin about this compatibility
issue.<br>
</p>
However the new VEP (ensembl-vep) has a new option '-nearest
gene' you can use with the cache:<br>
<a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#output" target="_blank">http://www.ensembl.org/info/<wbr>docs/tools/vep/script/vep_<wbr>options.html#output</a><br>
<p>Best regards,<i><br>
</i></p>
<pre class="m_8868361657833624851moz-signature" cols="72">Laurent</pre>
<div class="m_8868361657833624851moz-cite-prefix">On 15/05/2017 08:44, Guillermo
Marco Puche wrote:<br>
</div>
<blockquote type="cite">
<p>Dear devs,</p>
<p>I've recently updated to Ensembl VEP 88 and I'm facing some
problems with some plugins. Trying to run NearestGene.pm
plugin and I can't make it run.</p>
<p><i>WARNING: Plugin 'NearestGene' went wrong: ERROR: Could
not get gene adaptor; this plugin does not work in
--offline mode</i></p>
<p>There's an issue with gene adaptor code,<b> $self->{ga}
||= $self->{config}->{ga}</b>. Trying to guess where
did {ga} gone printing Dump of $self->{config} but I
can't figure this out:</p>
<p>$VAR1 = {<br>
'buffer_size' => 5000,<br>
'af_1kg' => 1,<br>
'species' => 'homo_sapiens',<br>
'stats_html' => 1,<br>
'host' => 'sake',<br>
'format' => 'vcf',<br>
'reg' => 'Bio::EnsEMBL::Registry',<br>
'chunk_size' => 50000,<br>
'check_existing' => 1,<br>
'freq_pop' => '1KG_ALL',<br>
'custom' => [],<br>
'cell_type' => [],<br>
'input_file' => 'test.vcf',<br>
'tmpdir' => '/tmp',<br>
'freq_filter' => 'exclude',<br>
'user' => 'bioinfo',<br>
'phastCons' => [],<br>
'terms' => 'SO',<br>
'delimiter' => ' ',<br>
'dir_cache' => '/home/gmarco/.vep',<br>
'polyphen_analysis' => 'humvar',<br>
'cache' => 1,<br>
'port' => '3306',<br>
'plugin' => [<br>
'Test'<br>
],<br>
'freq_gt_lt' => 'gt',<br>
'output_format' => 'vcf',<br>
'phyloP' => [],<br>
'numbers' => 1,<br>
'af_exac' => 1,<br>
'output_file' => '/tmp/test_88.vcf',<br>
'database' => 0,<br>
'freq_freq' => '0.01',<br>
'dir_plugins' =>
'/home/gmarco/repositories/<wbr>vep_ensembl/Plugins',<br>
'core_type' => 'core',<br>
'vcf' => 1,<br>
'assembly' => 'GRCh38',<br>
'af' => 1,<br>
'terminal_width' => 48,<br>
'vcf_info_field' => 'CSQ',<br>
'transcript_filter' => [],<br>
'af_esp' => 1,<br>
'pick_order' => [<br>
'canonical',<br>
'appris',<br>
'tsl',<br>
'biotype',<br>
'ccds',<br>
'rank',<br>
'length',<br>
'ensembl',<br>
'refseq'<br>
],<br>
'biotype' => 1,<br>
'cache_region_size' => 1000000,<br>
'symbol' => 1,<br>
'ucsc_data_root' => '<a class="m_8868361657833624851moz-txt-link-freetext" href="http://hgdownload.cse.ucsc.edu/goldenpath/" target="_blank">http://hgdownload.cse.ucsc.<wbr>edu/goldenpath/</a>',<br>
'synonyms' =>
'/home/gmarco/.vep/homo_<wbr>sapiens/88_GRCh38/chr_<wbr>synonyms.txt',<br>
'dir' => '/home/gmarco/.vep',<br>
'password' => 'A29bcd1234#',<br>
'no_slice_cache' => 1,<br>
'failed' => 0,<br>
'force_overwrite' => 1,<br>
'fasta' =>
'/home/gmarco/.vep/homo_<wbr>sapiens/88_GRCh38/Homo_<wbr>sapiens.GRCh38.dna.primary_<wbr>assembly.fa.gz'<br>
};</p>
<p>Regards,<br>
Guillermo<br>
</p>
<p><br>
<br>
</p>
<br>
<fieldset class="m_8868361657833624851mimeAttachmentHeader"></fieldset>
<br>
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</blockquote>
</blockquote>
</blockquote>
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