docker-compose.yml

version: "3"

services:
  # oncokb requires that a MySQL server is started and has the the oncokb data imported into the database.
  # Reach out to contact@oncokb.org to get access to the data dump
  oncokb:
    image: oncokb/oncokb:3.11.0
    ports:
      - "8080:8080"
    environment:
      # Update jdbc.url
      JAVA_OPTS: >
        -Djdbc.driverClassName=com.mysql.jdbc.Driver
        -Djdbc.url=jdbc:mysql://[hostname]:3306/[database name]?useUnicode=yes&characterEncoding=UTF-8&useSSL=false
        -Djdbc.username=root
        -Djdbc.password=root
        -Doncokb_transcript.url=http://oncokb-transcript:9090
        -Doncokb_transcript.token=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkwIiwibmFtZSI6IkpvaG4gRG9lIiwiYXV0aCI6IlJPTEVfQURNSU4iLCJpYXQiOjE1MTYyMzkwMjJ9.XHIcA76cAnkgEIeJhyK9hyOrTsQhP3B5aUkVa4fkO6s
        -Dgenome_nexus.grch37.url=http://gn-spring-boot:8888
        -Dgenome_nexus.grch38.url=http://gn-spring-boot-grch38:8888
    depends_on:
      - "oncokb-transcript"
  
  # oncokb-transcript requires a MySQL server and oncokb-transcript data imported into the database.
  # Reach out to contact@oncokb.org to get access to the data dump
  oncokb-transcript:
    image: oncokb/oncokb-transcript:0.8.0
    ports:
      - "9090:9090"
    environment:
      - SPRING_PROFILES_ACTIVE=prod,api-docs,no-liquibase
      - APPLICATION_REDIS_ENABLED=false
      - SPRING_DATASOURCE_URL=jdbc:mysql://[hostname]:3306/[database name]
      - SPRING_DATASOURCE_USERNAME=root
      - SPRING_DATASOURCE_PASSWORD=root

  # Genome Nexus GRCh37
  gn-spring-boot:
    profiles: ["genome-nexus"]
    image: genomenexus/gn-spring-boot:v1.2.2
    ports:
      - "8888:8888"
    environment:
      - SERVER_PORT=8888
    command: java -Dgn_vep.region.url=http://gn-vep:8080/vep/human/region/VARIANT -Dspring.data.mongodb.uri=mongodb://gn-mongo:27017/annotator -jar /app.war
    links:
      - gn-mongo
    depends_on:
      - gn-mongo

  gn-mongo:
    profiles: ["genome-nexus"]
    image: genomenexus/gn-mongo:0.24
    restart: always

  gn-vep:
    profiles: ["genome-nexus"]
    image: genomenexus/genome-nexus-vep:v0.0.1
    environment:
      - VEP_ASSEMBLY=GRCh37
    restart: always
    ports:
      - "6060:8080"
    volumes:
      - ${VEP_CACHE}:/opt/vep/.vep/
  

  # Genome Nexus GRCh38
  gn-spring-boot-grch38:
    profiles: ["genome-nexus"]
    image: genomenexus/gn-spring-boot:v1.2.2
    ports:
      - "8889:8888"
    environment:
      - SERVER_PORT=8888
    command: >
      java 
      -Dspring.data.mongodb.uri=mongodb://gn-mongo-grch38:27017/annotator
      -Dgn_vep.region.url=http://gn-vep-grch38:8080/vep/human/region/VARIANT
      -jar 
      /app.war
    links:
      - gn-mongo-grch38
    depends_on:
      - gn-mongo-grch38

  gn-mongo-grch38:
    profiles: ["genome-nexus"]
    image: genomenexus/gn-mongo:v0.24_grch38_ensembl95
    restart: always

  gn-vep-grch38:
    profiles: ["genome-nexus"]
    image: genomenexus/genome-nexus-vep:v0.0.1
    environment:
      - VEP_ASSEMBLY=GRCh38
      - VEP_FASTAFILERELATIVEPATH=homo_sapiens/98_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
    restart: always
    ports:
      - "6061:8080"
    volumes:
      - ${VEP_GRCH38_CACHE}:/opt/vep/.vep/