Improve --registry and --db_version

[nuno-agostinho]

Changelog

• Improvements to --registry
  • Allow using a relative filename for --registry
  • Throw error when the registry file is not found
• Warn when selected --db_version is not found in any database names
  • Instead of simply returning the warning MSG: human is not a valid species name (check DB and API version), also return a VEP warning stating:

WARNING: No database names in ensembldb.ensembl.org:3306 contain version 112

-------------------- WARNING ----------------------
MSG: human 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)    = Fri Jan 19 12:28:53 2024
Ensembl API version = 112
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: Can not find internal name for species 'human'
STACK Bio::EnsEMBL::Registry::get_adaptor /hps/software/users/ensembl/repositories/nuno/ensembl/modules/Bio/EnsEMBL/Registry.pm:1111
STACK Bio::EnsEMBL::VEP::BaseVEP::get_adaptor /hps/software/users/ensembl/repositories/nuno/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:351
STACK Bio::EnsEMBL::VEP::BaseVEP::get_database_assembly /hps/software/users/ensembl/repositories/nuno/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:462
STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /hps/software/users/ensembl/repositories/nuno/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::init /hps/software/users/ensembl/repositories/nuno/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::run /hps/software/users/ensembl/repositories/nuno/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:200
STACK toplevel /hps/software/users/ensembl/repositories/nuno/ensembl-vep/vep:46
Date (localtime)    = Fri Jan 19 12:28:53 2024
Ensembl API version = 112
---------------------------------------------------

Testing

• Run VEP with a registry file
  • Use a relative filename in --registry: VEP should use the registry file from relative file path
  • Use an incorrect filename in --registry: VEP should throw an error stating the registry file does not exist
• Run VEP with --db_version
  • Use a current --db_version like 109: VEP should run without any warnings
  • Use a future --db_version like 112: VEP should warn that the --db_version was not found in any database names before erroring out

[dglemos]

Merged into release/112 and main