cli_setup

Installing OMERO CLI for 5.4.1

1 Create a virtual env for python 2.7:

conda create -n OMERO_CLI python=2.7 anaconda

Down the package from:

Get the "OMERO python" package download

• https://www.openmicroscopy.org/omero/downloads/

or directly from this link.

install the ICE library

pip install zeroc-ice==3.6.4

Add the path to the library. Instructions from conda webpage

cd /Users/evenhuis/anaconda3/envs/OMERO_5.4_CLI
mkdir -p ./etc/conda/activate.d
mkdir -p ./etc/conda/deactivate.d
touch ./etc/conda/activate.d/env_vars.sh
touch ./etc/conda/deactivate.d/env_vars.sh

Add the following to the activate.d/env_vars.sh:

#!/bin/sh
export ORIGPATH=$PATH
export ORIGPYTHONPATH=$PYTHONPATH
export OMERO_PREFIX=~/Dropbox/MIF/OMERO/downloads_5.4.1/OMERO.py-5.4.1-ice36-b75
export PATH=$PATH:$PYTHONPATH:$OMERO_PREFIX/bin
export PYTHONPATH=$PYTHONPATH:$OMERO_PREFIX/lib/python

This appends the OMERO library to the search path. And the following in deactivate.d/env_vars.sh restores the path variabeles

export PATH=$ORIGPATH
export PYTHONPATH=$ORIGPYTHONPATH

unset ORIGPATH
unset ORIGPYTHONPATH