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The Cytomine-Python-client and  Cytomine-Python-DataMining packages are already installed together with other Cytomine components using our regular Docker installation. These algorithms can be executed from the Cytomine-WebUi (see user guide). Indeed, following the standard installation procedure, algorithms are installed locally in the software_router docker container and we use RabbitMQ to send messages from Cytomine-WebUi/Cytomine-Core to the corresponding docker container. You can have access to algorithm code and logs here:

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Code Block
languagebash
linenumberstrue
./Miniconda2-latest-Linux-x86_64.sh -b -p $HOME/miniconda2
export PATH="$HOME/miniconda2/bin:$PATH"
conda create -n cytomine python=2.7 shapely opencv scikit-learn pillow joblib
cython
source activate cytomine

In order to avoid having to update you path everytime you come back on you machine, you might want to append the export command (line 2) at the end of the ~/.bashrc file and then run:

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2.3 Install pyxit (located in cytomine-datamining/algorithms/pyxit/)

Cythonize, compile and install Install pyxit:

Code Block
languagebash
linenumberstrue
cd $HOME/Cytomine/Cytomine-python-datamining/cytomine-datamining/algorithms/pyxit/
cython _estimator.pyx
python setup.py build
python setup.py install

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