Run an OMERO client in Docker

Overview

Teaching: 10 min
Exercises: 25 min

Questions

• How do I create a Docker image for a complex application?

Objectives

• Create a Dockerfile for a complex application

This builds on the previous lesson to create a fully working Docker image for the OMERO python client.

Installing OMERO.py’s dependencies

We install OMERO.py in a virtual environment. To install OMERO.py we need additional dependencies, most notably the Ice Python bindings. We install a pre-compiled version matching our Docker image i.e. rockylinux and the Python version installed i.e. 3.9.

FROM rockylinux:9
LABEL maintainer="OME"

RUN dnf install -y epel-release
RUN dnf install -y python-pip

RUN dnf install -y python3

RUN python3 -mvenv /opt/omero/web/venv3

# But this is a shortcut that installs a precompiled version to install Ice Python
RUN /opt/omero/web/venv3/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl
RUN /opt/omero/web/venv3/bin/pip install omero-py

RUN useradd omero
WORKDIR /home/omero
USER omero

docker build -t my-omeropy-image .
docker run -it my-omeropy-image

/opt/omero/web/venv3/bin/omero version

OMERO.py version:
5.20.0

Connect to workshop.openmicroscopy.org usingCLI commands, e.g.:

/opt/omero/web/venv3/bin/omero login -s workshop.openmicroscopy.org

Default commands

When you run my-omeropy-dockerfile the bash shell is automatically started. This is the default in the parent rockylinux:9 image.

Change the default command by adding CMD to the end of your Dockerfile:

CMD ["/opt/omero/web/venv3/bin/omero"]

Re-build, and run:

docker build -t my-omeropy-image .
docker run -it my-omeropy-image

OMERO Python Shell. Version 5.20
Type "help" for more information, "quit" or Ctrl-D to exit
omero>

This time you enter the OMERO shell directly.

Can you pass command-line arguments?

docker run -it my-omeropy-image version

docker: Error response from daemon: oci runtime error: container_linux.go:265: starting container process caused "exec: \"version\": executable file not found in $PATH".

If you pass a command line to docker run it overwrites the default, so you need to pass the whole command line including omero:

docker run -it my-omeropy-image /opt/omero/web/venv3/bin/omero version

OMERO.py version:
5.20.0

ENTRYPOINT vs CMD

You can make the Docker image behave as the omero command using an ENTRYPOINT, see the Docker documentation for details.

Best practice for writing Dockerfiles

Writing a Dockerfile is easy, but there are several guidelines you should follow when developing a Docker image for production. See this article in the Docker documentation for more details.

Key Points