[ensembl-dev] request for adding Sz pombe to VEP downloading list

[Yutze Li]

I found the pre-built genome cache of fission yeast schizosaccharomyces
pombe was on the ftp but not on the list when running the INSTALL.pl of VEP.
Also, adding the cache downloaded and uncompressed from the ftp to
my ~/.vep/ did not work.
My command and the error message goes like:

$ vep --cache --species schizosaccharomyces_pombe --cache_version 40 \

>     --appris --biotype --pick --symbol --tsl --distance 100 \

>     -i $BASE.filter.vcf -o $BASE.ann.vcf


-------------------- WARNING ----------------------

MSG: schizosaccharomyces_pombe is not a valid species name (check DB and
API version)

FILE: Bio/EnsEMBL/Registry.pm LINE: 1334

CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 1109

Date (localtime)    = Thu Sep 20 18:16:26 2018

Ensembl API version = 93

---------------------------------------------------


-------------------- EXCEPTION --------------------

MSG: Can not find internal name for species 'schizosaccharomyces_pombe'

STACK Bio::EnsEMBL::Registry::get_adaptor
/Users/lytzeseikiri/biotools/ensembl-vep/Bio/EnsEMBL/Registry.pm:1111

STACK Bio::EnsEMBL::VEP::BaseVEP::get_adaptor
/Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:308

STACK Bio::EnsEMBL::VEP::BaseVEP::get_database_assembly
/Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:419

STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection
/Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:123

STACK Bio::EnsEMBL::VEP::Runner::init
/Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:118

STACK Bio::EnsEMBL::VEP::Runner::run
/Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194

STACK toplevel /Users/lytzeseikiri/biotools/ensembl-vep/vep:224

Date (localtime)    = Thu Sep 20 18:16:26 2018

Ensembl API version = 93

---------------------------------------------------


Thanks.
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