InstallationΒΆ

Note

The CLI is currently untested on Windows but may be supported in the future.

Since OMERO 5.6, only Python 3 is supported. We assume that you have already installed Python 3.6.

We recommend installing client library omero-py and the CLI plugins in a Python virtual environment. You can create one using either venv or conda (preferred). If you opt for Conda, you will need to install it first, see miniconda for more details.

To install omero-py using conda (preferred):

conda create -n myenv -c ome python=3.6 zeroc-ice36-python omero-py
conda activate myenv

Alternatively install omero-py using venv:

python3.6 -m venv myenv
. myenv/bin/activate
pip install omero-py

The omero command is now available in the terminal where the environment has been activated:

omero login

The CLI installed in this way provides all functionalities except the import functionality.

The import functionality requires to have a supported version of Java e.g. Java 11 and Ice 3.6.5 installed. It also requires JARs in the OMERO.server package to be available under the OMERODIR directory.

To install Java and Ice, go to OMERO.server installation and select the walkthrough corresponding to your OS.

To make the JARs available, you need to:

  1. download the OMERO.server zip from the Downloads page

  2. unzip the zip file

  3. set $OMERODIR to the unzipped directory:

    export OMERODIR=/path/to/OMERO.server-x.x.x-ice36-bxx

The import functionality is now available:

omero import /path/to/image.tiff