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.
Run with docker (assumes mvn installed locally):
mvn -DskipTests clean install docker-compose up --build
The mongo image
genomenexus/gn-mongo comes with all the required tables
# 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
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
If you need to update the data files see genome-nexus-importer