OMERO ubuntu/docker test

README.md

see https://www.openmicroscopy.org/community/viewtopic.php?t=8568&p=19886#p19886

docker-compose.yml

---
version: '3'

# http://www.openmicroscopy.org/explore/

services:
  db:
    image: postgres
    environment:
      - POSTGRES_PASSWORD=postgres
  omero:
    image: openmicroscopy/omero-server:5.4
    environment:
      - CONFIG_omero_db_user=postgres
      - CONFIG_omero_db_name=postgres
      - CONFIG_omero_db_pass=postgres
      - ROOTPASS=omero
  test:
    image: test
    tty: true
    stdin_open: true

Dockerfile

FROM ubuntu:16.04

RUN apt-get update && apt-get install -y locales && rm -rf /var/lib/apt/lists/* \
    && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8
ENV LANG en_US.utf8


env OMERO_OPT_DIR=/opt/omero
RUN apt-get update

# installed for convenience
RUN apt-get -y install unzip wget bc

# install Java
RUN apt-get -y install software-properties-common
RUN add-apt-repository -y ppa:openjdk-r/ppa
RUN apt-get update
RUN apt-get -y install openjdk-8-jre

# install dependencies
RUN apt-get update
RUN apt-get -y install \
	unzip \
	wget \
	python-pip python-tables python-virtualenv python-yaml python-jinja2

# Omero Core
RUN apt-get -y install zlib1g-dev
RUN apt-get -y install python-pillow python-numpy

# Install Ice
env DEBIAN_FRONTEND=noninteractive
RUN apt-get -y install db5.3-util
RUN apt-get -y install libssl-dev libbz2-dev libmcpp-dev libdb++-dev libdb-dev

RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 5E6DA83306132997
RUN apt-add-repository "deb http://zeroc.com/download/apt/ubuntu16.04 stable main"
RUN apt-get update
RUN apt-get -y install zeroc-ice-all-runtime zeroc-ice-all-dev

RUN pip install "zeroc-ice>3.5,<3.7"

# install Postgres
RUN apt-get -y install apt-transport-https
RUN add-apt-repository -y "deb https://apt.postgresql.org/pub/repos/apt/ xenial-pgdg main 9.6"
RUN wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -
RUN apt-get update
RUN apt-get -y install postgresql-9.6

# Create an omero user
RUN adduser -disabled-password -q  --gecos "" phenomic
RUN mkdir -p "$OMERO_OPT_DIR"

WORKDIR $OMERO_OPT_DIR
env SERVER=https://downloads.openmicroscopy.org/latest/omero5/server-ice36.zip
RUN wget $SERVER -O OMERO.server-ice36.zip
RUN unzip -q OMERO.server*

RUN ln -s OMERO.server-*/ OMERO.server

RUN chown -R phenomic $PWD

RUN echo "export PYTHON_PATH=/opt/omero/server/OMERO.server/lib/python:$PYTHON_PATH" >> /home/phenomic/.bashrc

RUN update-alternatives --config java
RUN java -version