genome-nexus

by genome-nexus

GitHub Readme.md

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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 and mongoDB in docker containers

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 initialized.

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/