# 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

# 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;