VEP with CONDA, installing annotation sources manually, what is the right directory to save the sources?
Entering edit mode
5 months ago
Manuel ▴ 40


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; check your settings & DBI error message: Can't connect to MySQL server on '' (11)
STACK Bio::EnsEMBL::Registry::load_registry_from_db /home/manuel/anaconda3/envs/VEP/share/ensembl-vep-105.0-0/Bio/EnsEMBL/
STACK Bio::EnsEMBL::VEP::BaseVEP::registry /home/manuel/anaconda3/envs/VEP/share/ensembl-vep-105.0-0/modules/Bio/EnsEMBL/VEP/
STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /home/manuel/anaconda3/envs/VEP/share/ensembl-vep-105.0-0/modules/Bio/EnsEMBL/VEP/
STACK Bio::EnsEMBL::VEP::Runner::init /home/manuel/anaconda3/envs/VEP/share/ensembl-vep-105.0-0/modules/Bio/EnsEMBL/VEP/
STACK Bio::EnsEMBL::VEP::Runner::run /home/manuel/anaconda3/envs/VEP/share/ensembl-vep-105.0-0/modules/Bio/EnsEMBL/VEP/
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

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
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???

CONDA VEP • 968 views
Entering edit mode
5 months ago
barslmn ★ 1.6k

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.

enter image description here

Entering edit mode
5 months ago

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


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