omero docker compose

README.md

OMERO-NB-Index

source env.sh
docke-compose up

need to create public user

create read-only public group

add a "public user" into public group

Program

• omero2cnb

Docker

• omero-cnb in Docker Hub
• Dockerfile in GitHub

docker-compose.yml

version: "3.1"
services:
  db:
    image: postgres
    environment:
      POSTGRES_USER: ${DBUSER}
      POSTGRES_PASSWORD: ${DBPASSWD}
    networks:
      - omero-net
    volumes:
      - "db:/var/lib/postgresql/data"
    ports:
      - "5432:5432"
  omero-server:
    image: openmicroscopy/omero-server:5.5
    depends_on:
      - db
    environment:
      CONFIG_omero_db_user: ${DBUSER}
      CONFIG_omero_db_pass: ${DBPASSWD}
      CONFIG_omero_db_name: ${DBNAME}
      ROOTPASS: ${ROOTPASSWD}
    networks:
      - omero-net
    volumes:
      - "data:/OMERO"
    ports:
      - "4063:4063"
      - "4064:4064"
  omero-web:
    image: openmicroscopy/omero-web-standalone:5.5
    depends_on:
      - omero-server
    environment:
      CONFIG_omero_web_server__list: '[["${OMERO_SERVER}",4064,"omero"]]'
      CONFIG_omero_web_debug: 'true'
      CONFIG_omero_web_public_enabled: 'True'
      CONFIG_omero_web_public_user: ${OMERO_PUB_USER}
      CONFIG_omero_web_public_password: ${OMERO_PUB_PASSWD}
      CONFIG_omero_web_public_url__filter: '^/(webadmin/myphoto/|webclient/(?!(script_ui|ome_tiff|figure_script))|webgateway/(?!(archived_files|download_as)))'
      CONFIG_omero_web_public_server__id: 1
    ports:
      - "8090:4080"
  omero-cnb:
    image: nimezhu/cnb-index-omero:latest
    environment:
      CONFIG_omero_db_name: ${DBNAME}
      CONFIG_omero_db_pass: ${DBPASSWD}
      CONFIG_omero_db_user: ${DBUSER}
      CONFIG_omero_web_server: "http://${OMERO_SERVER}:8090"
    depends_on:
      - omero-web
    networks:
      - omero-net
networks:
  omero-net:
volumes:
  data:
  db:

env.sh

DBNAME="postgres"
DBUSER="postgres"
DBPASSWD="dbpassword"
ROOTPASSWD="rootpassword"
OMERO_SERVER="website" 
OMERO_PUB_USER="publicuser"
OMERO_PUB_PASSWD="publicpassword"
export DBNAME DBUSER DBPASSWD ROOTPASSWD OMERO_SERVER OMERO_PUB_USER OMERO_PUB_PASSWD