docker-compose.yml

version: '3.3'
services:

  jupyter:
    image: dbmi/r-datascience-notebook:nhanes-pic-sure-notebook-development-only-August-20-2018
    restart: always
    networks:
      - public
    expose:
      - 8888
    ports:
      - 80:8888
    volumes:
      - ./jupyter-notebooks:/home/jovyan/work

  pic-sure-hpds-1kgenome:
    image: dbmi/pic-sure-hpds:master_d1da0b6
    restart: always
    networks:
      - public
    expose:
      - 8080
      - 8000
    ports:
      - 8080:8080
      - 8000:8000
    entrypoint: java  -Xdebug -Xrunjdwp:transport=dt_socket,address=0.0.0.0:8000,server=y,suspend=n -XX:+UseParallelGC -XX:SurvivorRatio=250 -Xmx1024m -server -jar hpds.jar -httpPort 8080 -DCACHE_SIZE=10000 -DSMALL_TASK_THREADS=1 -DLARGE_TASK_THREADS=1 -DSMALL_JOB_LIMIT=100 -DID_BATCH_SIZE=2000 "-DALL_IDS_CONCEPT=NONE"  "-DID_CUBE_NAME=NONE"
#    entrypoint: java  -XX:+UseParallelGC -XX:SurvivorRatio=250 -Xmx1024m -server -jar hpds.jar -httpPort 8080 -DCACHE_SIZE=10000 -DSMALL_TASK_THREADS=1 -DLARGE_TASK_THREADS=1 -DSMALL_JOB_LIMIT=100 -DID_BATCH_SIZE=2000 "-DALL_IDS_CONCEPT=NONE"  "-DID_CUBE_NAME=NONE"
    volumes:
      - ./hpds:/opt/local/hpds
      - ./hpds/all:/opt/local/hpds/vcfOutput
networks:
  public: