===========
Setup tools
===========

Install Neo4j
=============

Cell Interactome is built on a graph databse Neo4j. Users first need to download/install Neo4j and make initial settings as follows. 


Linux
-----

.. code-block:: bash
  
  # download executabules 
  wget https://neo4j.com/artifact.php?name=neo4j-community-5.5.0-unix.tar.gz -O neo4j-community-5.5.0-unix.tar.gz
  tar zxvf neo4j-community-5.5.0-unix.tar.gz
  
  # change password
  neo4j-admin dbms set-initial-password ${YOUR_PASSWORD}
  
  # execute neo4j
  neo4j start


Mac/Windows
-----------

1. Install Neo4j with as instructed in the `official document <https://neo4j.com/docs/operations-manual/current/installation/windows/>`__. 
2. Change password by opening the installed Neo4j Desktop (you will be asked when opening first time)


Install Cell Interactome
========================

You can create environment with conda and install the Cell Interactome tools as follows.

.. code-block:: bash
  
  # clone files
  git clone https://github.com/gagliani-lab/Cell-Interactome.git
  cd cell-interactome
  
  # setup environment
  python -m venv /path/to/your/venv/cell_interactome
  source /path/to/your/venv/cell_interactome/bin/activate
  
  # install Cell Interactome
  python setup.py install


Install CellInteractomeR
========================

`CellInteractomeR` is an R package to play with Neo4j-based Cell Interactome graph. 

.. code-block:: R
  
  # install following dependencies through devtools::install_github
  devtools::install_github("ColinFay/glouton")
  devtools::install_github("dreamRs/particlesjs")

  # install CellInteractomeR
  devtools::install_gitlab("gagliani-lab/Cell-InteractomeR")