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Genome Nexus

Genome Nexus, a comprehensive one-stop resource for fast, automated and high-throughput annotation and interpretation of genetic variants in cancer. Genome Nexus will integrate information from a variety of existing resources, including databases that convert DNA changes to protein changes, predict the functional effects of protein mutations, and contain information about mutation frequencies, gene function, variant effects, and clinical actionability.

Three goals:

1. Data collection from various annotation sources
2. Integration of heterogeneous information into a harmonized structure and programmatic interface
3. Dissemination of the diverse information in a hierarchical digestible way for interpreting variants and patients.

Run

Alternative 1 - run genome-nexus, mongoDB and genome-nexus-vep in docker containers

First, set environment variables for Ensembl Release, VEP Assembly and location of VEP Cache. If these are not, the default values from .env will be set.

The reference genome and Ensembl release must be consistent with a version in genome-nexus-importer/data/. For example grch37_ensembl92, grch38_ensembl92 or grch38_ensembl95:

export REF_ENSEMBL_VERSION=grch38_ensembl92

If you would like to do local VEP annotations instead of using the public Ensembl API, please uncomment # gn_vep.region.url=http://localhost:6060/vep/human/region/VARIANT in your application.properties. This will require you to download the VEP cache files for the preferred Ensembl Release and Reference genome, see our documentation on downloading the Genome Nexus VEP Cache. This will take several hours.

# Set local cache dir
export VEP_CACHE=<local_vep_cache>

# GRCh38 or GRCh37
export VEP_ASSEMBLY=GRCh38

Run docker-compose to create images and containers:

docker-compose up --build -d

Run without recreating images:

docker-compose up -d

Run without Genome Nexus VEP:

# Start both the Web and DB (dependency of Web) containers
docker-compose up -d web

Stop and remove containers:

docker-compose down

Alternative 2 - run genome-nexus locally, but mongoDB in docker container

# the genomenexus/gn-mongo images comes with all the required tables imported
# change latest to different version if necessary (only need to run this once)
docker run --name=gn-mongo --restart=always -p 27017:27017 -d genomenexus/gn-mongo:latest 
mvn  -DskipTests clean install
java -jar web/target/web-*.war

Alternative 3 - install mongoDB locally and run with local java

Install mongoDB manually. Then follow instructions in genome-nexus-importer to initialize the database.

After that run this:

mvn clean install
java -jar web/target/web-*.war

Update data

If you need to update the data files see genome-nexus-importer

Programmatic access through R/Python

See notebooks/