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

[Laurent Gil]

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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