Basic Omero Install

Hope this is helpful to someone else. I hobbled this together with a basic understanding and the docs online. Finally managed to get it working! I’m sure there are many changes to be made. My goal was to get this running locally.

Basic Install Notes for Omero Server and Web on CentOS 7

Install everything as root.
Run as root.

REQUIREMENTS

Install CENTOS - “Minimal Install”

NOTE !!: Set up all users and network in config screens

UPDATE CENTOS - How To Update CentOS 7.0/7.1/7.2/7.3/7.4/7.5 to CentOS 7.6

# yum check-update
# yum update
# reboot

INSTALL REPOSITORIES AND SOME PREREQUISITES and HELPFUL TOOLS

# yum install -y wget make epel-release nano mlocate
# updatedb

INSTALL PYTHON 3.7 - Install Python 3.7.0 on Centos 7 · GitHub

# yum install gcc openssl-devel bzip2-devel libffi-devel -y
# cd /usr/src
# wget https://www.python.org/ftp/python/3.7.0/Python-3.7.0.tgz
# tar xzf Python-3.7.0.tgz
# cd Python-3.7.0
# ./configure --enable-optimizations
# make altinstall
# rm /usr/src/Python-3.7.0.tgz
# python3.7 -V
# pip3.7 -V
# pip3.7 install --upgrade pip

INSTALL DOCKER - Install Docker Engine on CentOS | Docker Documentation

# yum install -y yum-utils
# yum-config-manager \
    --add-repo \
    https://download.docker.com/linux/centos/docker-ce.repo
# yum install -y docker-ce docker-ce-cli containerd.io

# systemctl enable docker
# systemctl start docker

INSTALL DOCKER - COMPOSE - GitHub - ome/docker-example-omero at 94a6a77d4efa98304ab8bcfb3e333343bd795603

# pip3.7 install docker-compose

ADD DOCKER COMPOSE FILE

Add file “docker-compose.yml” added to “homes” directory. Copy and paste below.

version: "3"

services:

  database:
    image: "postgres:11"
    environment:
      POSTGRES_USER: omero
      POSTGRES_DB: omero
      POSTGRES_PASSWORD: omero
    networks:
      - omero
    volumes:
      - "database:/var/lib/postgresql/data"

  omeroserver:
    image: "openmicroscopy/omero-server:5.6"
    environment:
      CONFIG_omero_db_host: database
      CONFIG_omero_db_user: omero
      CONFIG_omero_db_pass: omero
      CONFIG_omero_db_name: omero
      ROOTPASS: omero
    networks:
      - omero
    ports:
      - "4063:4063"
      - "4064:4064"
    volumes:
      - "omero:/OMERO"

  omeroweb:
    image: "openmicroscopy/omero-web-standalone:5.6"
    environment:
      OMEROHOST: omeroserver
    networks:
      - omero
    ports:
      - "4080:4080"

networks:
  omero:

volumes:
  database:
  omero:

RUN - GitHub - ome/docker-example-omero at 94a6a77d4efa98304ab8bcfb3e333343bd795603

docker-compose up -d
docker-compose logs -f

OMERO.server is listening on the standard OMERO ports 4063 and 4064.
OMERO.web is listening on port 4080 (http://localhost:4080/).

Log in as user root password omero.
The initial password can be changed in docker-compose.yml.

1 Like

Hi Adam,

thanks for sharing your complete workflow. One quick feedback while looking at your configuration: the image: "openmicroscopy/omero-web-standalone:5.6" image will pull an version of OMERO.web which does not include the latest security fixes relased in OMERO.web 5.9. Either

-   image: "openmicroscopy/omero-web-standalone:5.6"
+   image: "openmicroscopy/omero-web-standalone:5.9"

or

-   image: "openmicroscopy/omero-web-standalone:5.6"
+   image: "openmicroscopy/omero-web-standalone:latest"

will give you the latest available image. You might need to run docker-compose pull in the latter case.

We noticed that the issue comes directly from our example Docker compose YML files and I have opened Use latest OMERO versions for the default compose image by sbesson · Pull Request #10 · ome/docker-example-omero · GitHub to try and propose a sustainable solution.