Installation

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 3.9 or higher. You can ensure that your python executable is correct with the python --version command.

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.

Note

On Ubuntu 20.04, you may need to install libssl-dev before installing the CLI.

Before installing omero-py, we recommend to install the Zeroc IcePy 3.6 Python bindings.

Our commercial partner Glencoe Software has produced several Python wheels to install the Ice-Python bindings depending on the desired Python version and the operating system. Please visit the Ice binaries for omero page to find the full URLs to the wheels that are used in the examples below.

To install omero-py using pip in a conda environment with Python 3.11 on Ubuntu 22.04:

conda create -n myenv python=3.11
conda activate myenv
pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl
pip install omero-py

Alternatively install omero-py using venv with Python 3.9 or higher:

python -m venv myenv
. myenv/bin/activate
pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl
pip install omero-py

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

omero login

If you install omero-py>=5.8.0 the CLI provides all functionalities except the import functionality.

The import functionality requires a supported version of Java, and some JARs which are automatically downloaded the first time you do an import.

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