Conda python-omero Package for Windows

Hi,

I have developed a set of Python scripts that upload data to OMERO server 5.4.10. My dev environment is linux, so it was easy to install the required python-omero dependency with Conda. I am expecting to have to deploy the scripts on Windows machines though, and I note that there doesn’t seem to be a Windows package listed at https://anaconda.org/bioconda/python-omero.

Could you advise please if there is a Windows package for python-omero that can be installed with Conda? Is there a recommended alternative method for running such scripts in a Windows environment, e.g. with a Docker container or with Windows Subsystem for Linux? Many thanks.

Kind regards,

Johnny Hay

Hi @jhay,

bioconda doesn’t support Windows: https://bioconda.github.io/contributor/guidelines.html#bat-files

We are investigating moving to conda-forge which should lift this restriction.

There is no native code in python-omero so there are a number of options. For example, if you upgrade to OMERO 5.5, you might be interested in testing the currently dev release of https://pypi.python.org/pypi/omero-py

Alternatively, you need only have the Python files on your PYTHONPATH, so you can equally download the appropriate file (e.g. https://downloads.openmicroscopy.org/omero/5.4.10/artifacts/OMERO.py-5.4.10-ice36-b105.zip) and unpack it.

Docker will definitely work. A good starting point is likely https://hub.docker.com/r/openmicroscopy/omero-server

All the best,
~Josh

Hi @joshmoore,

Thanks very much, that’s very helpful. It sounds like building a Docker image on top of the base OMERO server image is probably the best way to go for now, so I will use that approach - thanks!

All the best,

Johnny

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