Getting Started
===============

The BEELINE pipeline interfaces with the implementations of various
algorithms through Docker containers.  Please follow this tutorial on
how to `install docker
<https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-on-ubuntu-18-04>`_
on Ubuntu 18.04.



.. tip:: Setup docker to run without sudo using the following shell command

   .. code:: sh

                   sudo usermod -aG docker $USER

   See more details `here <https://askubuntu.com/questions/477551/how-can-i-use-docker-without-sudo>`_.

Once docker has been set up correctly, the next step is to create the
docker containers for each of the algorithms.  The script
``utils/initialize.sh`` pulls or builds these containers. Run the following in the
terminal

.. code:: bash

          . utils/initialize.sh

.. note:: This step may take a while!

We recommend using `Anaconda <https://www.anaconda.com>`_ for Python. Run the following command to automatically create an Anaconda virtual environment named BEELINE and install necessary libraries

.. code:: bash

    . utils/setupAnacondaVENV.sh


To compute proposed reconstructions using the 14 GRN algorithms on the example dataset, run

.. code:: python

          python BLRunner.py --config config-files/config.yaml

To compute areas under the ROC and PR curves for the proposed reconstructions, run

.. code:: bash

          python BLEvaluator.py --config config-files/config.yaml --auc

To display the complete list of evaluation options, run

.. code:: bash

          python BLEvaluator.py --help

Project Outline
---------------

This tutorial will first explain the structure of the BEELINE repository,
with a walkthrough of the different components that the user can customize.


.. code:: text

          BEELINE
          |-- inputs/
          |-- config-files/
          |   `-- config.yaml
          |-- BLRun/
          |   |-- runner.py
          |   |-- sinceritiesRunner.py
          |   `-- ...
          |-- BLPlot/
          |   |-- plotter.py
          |   |-- PlotAUPRC.py
          |   |-- PlotAUROC.py
          |   |-- PlotEPR.py
          |   `-- ...
          |-- BLEval/
          |   |-- evaluator.py
          |   |-- BLTime.py
          |   `-- ...
          |-- Algorithms/
          |     |-- SINCERITIES/
          |     `-- ...
          |-- utils/
          |   |-- initialize.sh
          |   `-- setupAnacondaVENV.sh
          |-- LICENSE
          |-- BLRunner.py
          |-- BLEvaluator.py
          `-- README.md