VEP with CONDA, installing annotation sources manually, what is the right directory to save the sources?

Question

[Manuel]

[Context]

I am working in a Window computer that is limited by IT company. I am being allow to install a Ubuntu virtual machine (with wsl --install -d Ubuntu). I have installed VEP with Conda without any problem. Doing some testing, I got this error

 -------------------- EXCEPTION --------------------
MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org' (11)
STACK Bio::EnsEMBL::Registry::load_registry_from_db /home/manuel/anaconda3/envs/VEP/share/ensembl-vep-105.0-0/Bio/EnsEMBL/Registry.pm:1771
STACK Bio::EnsEMBL::VEP::BaseVEP::registry /home/manuel/anaconda3/envs/VEP/share/ensembl-vep-105.0-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:252
STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /home/manuel/anaconda3/envs/VEP/share/ensembl-vep-105.0-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:120
STACK Bio::EnsEMBL::VEP::Runner::init /home/manuel/anaconda3/envs/VEP/share/ensembl-vep-105.0-0/modules/Bio/EnsEMBL/VEP/Runner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::run /home/manuel/anaconda3/envs/VEP/share/ensembl-vep-105.0-0/modules/Bio/EnsEMBL/VEP/Runner.pm:199
STACK toplevel /home/manuel/anaconda3/envs/VEP/bin/vep:232
Date (localtime)    = Tue Dec 20 16:07:53 2022
Ensembl API version = 105
---------------------------------------------------

And I think this is because some of the limitation from my lovely IT team. I believe this because people with the same problem (see last post https://github.com/Ensembl/ensembl-vep/issues/603).

After this, I would like to install the libraries, to avoid to connect with external sources. The easiest way is by using vep_install but again this is blocked

 vep_install -a cf -s plasmodium_relictum -y PRELSG -c ./
curl failed (000), trying to fetch using LWP::Simple
LWP::Simple failed (500), trying to fetch using HTTP::Tiny
 - getting list of available cache files
ERROR: Could not connect to FTP host ftp.ensembl.org
Connection refused

So I would like to do this manually.

My question is, where shall I leave the annotation resources to be picked up by VEP when running the annotation???

Answer 1

[barslmn]

VEP's default file structure looks like this. You can download vep cache over your browser and extract here. Fasta is also placed under the version_assembly directory.

Answer 2

[dariober]

If you have annotation in GFF format and genome in fasta format, you should be able to run vep like this and avoid depending on external connections:

vep --gff {input.gff} --fasta {input.fasta} -i ... -o ...

You may need to edit the GFF to be compatible with VEP (see https://github.com/Ensembl/ensembl-vep/issues/1217).