genome-nexus-vep

Spring boot minimal REST wrapper service for VEP. This allows us to deploy a web service containing VEP without any other components of Ensembl REST API. The Ensembl VEP docker image has been extended to include the java runtime environment and this jar.

Compile and run

# Point to VEP cache directory. If you don't have this cache, see section "Create VEP cache"
VEP_CACHE=<local_vep_cache_directory_path>

# Set VEP assembly, for example GRCh37 or GRCh38
VEP_ASSEMBLY=GRCh38

# Create docker image
docker build -t genome-nexus_vep .

# Run Genome-Nexus-VEP on port 8889 and point it to local cache
docker run -d --name genome-nexus_vep -p 8889:8080 -e vep.assembly=$VEP_ASSEMBLY -v $VEP_CACHE:/opt/vep/.vep/:ro genome-nexus_vep:latest

Genome Nexus VEP is now running at http://localhost:8889

Create VEP cache

If you don't have a prepared VEP cache directory, start the container with the folder mounted with ":rw" (read&write) and install the VEP cache using INSTALL.pl. Downloading and optimizing the cache will take several hours.

# Point this to your preferred directory
VEP_CACHE=<local_vep_cache_directory_path>

# Ideally this is added to ~/.bashrc or ~/.bash_profile:
# export VEP_CACHE=<local_vep_cache_directory_path>
# And reload this file with:
# 'source ~/.bashrc' or 'source ~/.bash_profile'

# Create docker image
docker build -t genome-nexus_vep .

# Run Genome-Nexus-VEP on port 8889 and mount cache directory with write access.
docker run -d --name genome-nexus_vep_cache -p 8890:8080 -v $VEP_CACHE:/opt/vep/.vep/:rw genome-nexus_vep:latest

# Go into the docker container
docker exec -it genome-nexus_vep_cache bash

# Run the VEP installer and follow the instructions
# Suggested installation settings can be found below this code block
./INSTALL.pl

# When done, exit and remove the container
exit
docker stop genome-nexus_vep_cache; docker rm genome-nexus_vep_cache;

Installation instructions:

• Do you want to continue installing the API (y/n)? -> n
• Do you want to install any cache files (y/n)? -> y, install GRCh37 or GRCh38 cache
• Do you want to install any FASTA files (y/n)? -> y, install GRCh37 or GRCh38 FASTA
• Do you want to install any plugins (y/n)? -> n