[ensembl-dev] VEP registry with local database

[Patrice Dehais]

Hi,

I try to set up a full local install of VEP for 
Escherichia_coli_str_k_12_substr_mg1655.
No problem for the API part or for the 
bacteria_22_collection_core_20_73_1 database local installtions.

The problem is how to configure the registry file to point precisely to 
escherichia_coli_str_k_12_substr_mg1655.
With single species core database, the registry would have been like that:

Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(
   '-species' => "Escherichia_coli_str_k_12_substr_mg1655",
   '-group'   => "core",
   '-port'    => 3306,
   '-host'    => 'my.local.server',
   '-user'    => 'xxxxx',
   '-pass'    => 'xxxxx',
   '-dbname'  => 'bacteria_22_collection_core_20_73_1'
);

Bio::EnsEMBL::Registry->add_alias("Escherichia_coli_str_k_12_substr_mg1655","e_coli_k12");

... but with mutispecies database ???

My input test file works fine on the EnemblGenomes Web VEP (retrieves 
transcripts)
Chromosome    2849032    2849031    -/C    +
Chromosome    2848938    2848938    T/C    +
Chromosome    2848938    2848938    T/A    +
Chromosome    2848654    2848654    G/C    +
Chromosome    2848575    2848575    C/T    +

The local VEP installation works fine this single species (like cow), 
but when I try:
variant_effect_predictor.pl  --species 
Escherichia_coli_str_k_12_substr_mg1655 --database -i test.txt 
--force_overwrite --registry my_registry_file
or
variant_effect_predictor.pl  --species 
Escherichia_coli_str_k_12_substr_mg1655 --database -i test.txt 
--force_overwrite --registry my_registry_file --genomes

NO transcript has been found

please help

Patrice


-- 
Patrice Dehais : INRA - LCG - SIGENAE,
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