add install docs

ippisite/docs/source/index.rst

@@ -9,7 +9,8 @@ Welcome to iPPI-DB's documentation!
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
- 
+
+   install
    modules
 
 

ippisite/docs/source/install.rst

+Installation
+============
+
+Basic installation and run
+--------------------------
+
+You need **python3** to install and use ippidb-web. 
+
+.. code-block:: shell
+
+    git clone https://gitlab.pasteur.fr/hub/ippidb-web.git
+    virtualenv -p python3 venv
+    . venv/bin/activate
+    cd ippisite
+    pip install -r requirements.txt
+
+Important note: for now official openbabel distributions are bugged, especially for Tanimoto functionalities. The best solution for local deployments is to clone openbabel, compile it and copy the generated python modules to the virtualenv you have created.
+
+.. code-block:: shell
+
+    sudo apt install cmake
+    git clone https://github.com/openbabel/openbabel.git
+    cd openbabel
+    mkdir build
+    cd build
+    cmake
+    cmake .. -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
+    make
+    sudo make install
+    # then in the virtualenv we copy the python library installed by make install
+    (venv) user@linux:~/ippidb-web/openbabel/build$ cp /usr/local/lib/python3.6/site-packages/_openbabel.so /home/user/ippidb-web/venv/lib/python3.6/site-packages/
+    (venv) user@linux:~/ippidb-web/openbabel/build$ cp /usr/local/lib/python3.6/site-packages/openbabel.py /home/user/ippidb-web/venv/lib/python3.6/site-packages/
+    (venv) user@linux:~/ippidb-web/openbabel/build$ cp /usr/local/lib/python3.6/site-packages/pybel.py /home/user/ippidb-web/venv/lib/python3.6/site-packages/
+
+
+Public server deployment
+------------------------
+
+Ansible playbooks are available in the `ansible folder of the source repository <https://gitlab.pasteur.fr/hub/ippidb-web/tree/master/ansible>`_. These playbooks automate the initial configuration of the system (for a server using CentOS), and the initial installation or the update of the code from the repository.