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 3.6 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 20.09, you may need to install libssl-dev before installing the CLI.

To install omero-py using conda (preferred):

conda create -n myenv -c conda-forge python=3.8 omero-py
conda activate myenv

Alternatively install omero-py using venv with Python 3.7 or higher:

python -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

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.

omero-py < 5.8.0

If you are using an older version of omero-py you must download the JARs manually and place them under the OMERODIR directory:

  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