To all who want to install OMERO 5.6.1 on Ubuntu 16.04:
I noticed some problems related to Python 3.5 (the standard version on Ubuntu 16.04) and omero-web, omero-iviewer, and maybe other components:
- see Query for DatasetImageLink ID for an issue with moving objects between Datasets. @mtbc’s PR fixes the issue but that isn’t yet in the current release.
- in omero-iviewer, users cannot save any ROIs applied to the image - you get an error message.
- in omero-iviewer, users cannot save their rendering settings - this silently fails. But using the classical viewer and the preview, one CAN save rendering settings just fine.
To resolve problems 1 and 2, I found that you can install a Python 3.6 environment in Ubuntu 16.04 and modify the installation instructions for OMERO.web (see: https://docs.openmicroscopy.org/omero/5.6.1/sysadmins/unix/install-web/walkthrough/omeroweb-install-ubuntu1604-ice3.6.html) as follows:
- instead of the lines:
apt-get -y install python3 apt-get -y install python3-venv
add-apt-repository ppa:deadsnakes/ppa apt-get update apt-get install python3.6 python3.6-venv python3.6-dev
- instead of these lines:
python3 -mvenv /opt/omero/web/venv3 /opt/omero/web/venv3/bin/pip install --upgrade https://github.com/ome/zeroc-ice-py-ubuntu1604/releases/download/0.2.0/zeroc_ice-3.6.5-cp35-cp35m-linux_x86_64.whl
python3.6 -mvenv /opt/omero/web/venv3 /opt/omero/web/venv3/bin/pip install zeroc-ice==3.6.5
This will take a while to compile and install.
Now your omero-web and all plugins run under Python 3.6 which resolved some of the issues I noticed but issue #3 was resolved in some circumstances but not in others. I’ll keep investigating but maybe @will-moore has an idea? Might it have something to do with log messages such as:
2020-05-07 00:48:45,893 INFO [ omero.gateway] (proc.32371) getWindowMin():7646 getStatsInfo() is null. See #9695