[ensembl-dev] VEP: Plugin problems with gene adaptor

[Guillermo Marco Puche]

Hi Laurent,

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?
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.

Best regards,
Guillermo.


On 05/15/2017 12:17 PM, Laurent Gil wrote:
>
> Hi Guillermo,
>
> Unfortunately the VEP plugin is not compatible with the new 
> ensembl-vep repository.
> We need to document this plugin about this compatibility issue.
>
> However the new VEP (ensembl-vep) has a new option '-nearest gene' you 
> can use with the cache:
> http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#output
>
> Best regards,/
> /
>
> Laurent
> On 15/05/2017 08:44, Guillermo Marco Puche wrote:
>>
>> Dear devs,
>>
>> 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.
>>
>> /WARNING: Plugin 'NearestGene' went wrong: ERROR: Could not get gene 
>> adaptor; this plugin does not work in --offline mode/
>>
>> There's an issue with gene adaptor code,*$self->{ga} ||= 
>> $self->{config}->{ga}*. Trying to guess where did {ga} gone printing 
>> Dump of $self->{config} but I can't figure this out:
>>
>> $VAR1 = {
>>   'buffer_size' => 5000,
>>   'af_1kg' => 1,
>>   'species' => 'homo_sapiens',
>>   'stats_html' => 1,
>>   'host' => 'sake',
>>   'format' => 'vcf',
>>   'reg' => 'Bio::EnsEMBL::Registry',
>>   'chunk_size' => 50000,
>>   'check_existing' => 1,
>>   'freq_pop' => '1KG_ALL',
>>   'custom' => [],
>>   'cell_type' => [],
>>   'input_file' => 'test.vcf',
>>   'tmpdir' => '/tmp',
>>   'freq_filter' => 'exclude',
>>   'user' => 'bioinfo',
>>   'phastCons' => [],
>>   'terms' => 'SO',
>>   'delimiter' => '    ',
>>   'dir_cache' => '/home/gmarco/.vep',
>>   'polyphen_analysis' => 'humvar',
>>   'cache' => 1,
>>   'port' => '3306',
>>   'plugin' => [
>>     'Test'
>>   ],
>>   'freq_gt_lt' => 'gt',
>>   'output_format' => 'vcf',
>>   'phyloP' => [],
>>   'numbers' => 1,
>>   'af_exac' => 1,
>>   'output_file' => '/tmp/test_88.vcf',
>>   'database' => 0,
>>   'freq_freq' => '0.01',
>>   'dir_plugins' => '/home/gmarco/repositories/vep_ensembl/Plugins',
>>   'core_type' => 'core',
>>   'vcf' => 1,
>>   'assembly' => 'GRCh38',
>>   'af' => 1,
>>   'terminal_width' => 48,
>>   'vcf_info_field' => 'CSQ',
>>   'transcript_filter' => [],
>>   'af_esp' => 1,
>>   'pick_order' => [
>>     'canonical',
>>     'appris',
>>     'tsl',
>>     'biotype',
>>     'ccds',
>>     'rank',
>>     'length',
>>     'ensembl',
>>     'refseq'
>>   ],
>>   'biotype' => 1,
>>   'cache_region_size' => 1000000,
>>   'symbol' => 1,
>>   'ucsc_data_root' => 'http://hgdownload.cse.ucsc.edu/goldenpath/',
>>   'synonyms' => 
>> '/home/gmarco/.vep/homo_sapiens/88_GRCh38/chr_synonyms.txt',
>>   'dir' => '/home/gmarco/.vep',
>>   'password' => 'A29bcd1234#',
>>   'no_slice_cache' => 1,
>>   'failed' => 0,
>>   'force_overwrite' => 1,
>>   'fasta' => 
>> '/home/gmarco/.vep/homo_sapiens/88_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz'
>> };
>>
>> Regards,
>> Guillermo
>>
>>
>>
>>
>>
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