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

In the previous image we installed omego. To install OMERO.py we need additional dependencies, most notably Ice. The “proper” way to do this is to pip install zeroc-ice, but since this takes a long time and requires installing a full compiler toolchain we can cheat and install a pre-compiled version.

FROM centos:7
MAINTAINER spli@dundee.ac.uk

RUN yum install -y epel-release
RUN yum install -y python-pip
RUN pip install omego

# This is the proper way to install Ice Python:
#RUN pip install zeroc-ice
# But this is a shortcut that installs a precompiled version
RUN pip install https://github.com/openmicroscopy/zeroc-ice-py-centos7/releases/download/0.0.3/zeroc_ice-3.6.4-cp27-cp27mu-linux_x86_64.whl

RUN useradd omero
WORKDIR /home/omero
USER omero
RUN omego download python --ice 3.6 --sym OMERO.py

If you are feeling lazy you can download the Dockerfile.

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

/home/omero/OMERO.py/bin/omero version

ERROR:omero.gateway:No Pillow installed, line plots and split channel will fail!
5.4.0-ice36-b74

Fix the error/warning

ERROR:omero.gateway:No Pillow installed indicates there is a missing dependency. Can you modify the Dockerfile to remove this error?

Solution

Add this line:

RUN pip install pillow

after the existing RUN pip install lines.

It’s a bit annoying that you have to type the full path to /home/omero/OMERO.py/bin/omero, so add it to the PATH in the image using the Dockerfile ENV command:

ENV PATH="/home/omero/OMERO.py/bin:${PATH}"

Rebuild the image. You should now have a fully working OMERO.py client. Try connecting to nightshade.openmicroscopy.org and running some CLI commands, e.g.:

omero login -s nightshade.openmicroscopy.org
omero user list

Default commands

When you run my-omeropy-dockerfile the bash shell is automatically started. This is the default in the parent centos:7 image.

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

CMD ["/home/omero/OMERO.py/bin/omero"]

Re-build, and run:

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

OMERO Python Shell. Version 5.4.0-ice36-b74
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 omero version

5.4.0-ice36-b74

ENTRYPOINT vs CMD

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

Advanced: Compile and install Ice

The current image uses a pre-compiled version of Ice. Modify the image to install ice using the recommended Zeroc method (pip install zeroc-ice). You will need to install a compiler and all development libraries required to compile Ice.

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