Merge pull request #97 from mutalyzer/docs

Documentation updates

CHANGES.rst

@@ -96,7 +96,7 @@ Released on March 27th 2015.
 
 - Return fault code and description on RPC service errors (`#31
   <https://github.com/LUMC/mutalyzer/pull/31>`_).
-- Use esummary 2.0 response format (`#31
+- Use esummary 2.0 response format (`#32
   <https://github.com/LUMC/mutalyzer/pull/32>`_).
 
 

README.rst

@@ -15,6 +15,11 @@ submit bug reports and feature requests.
 Developer documentation is `hosted at Read The Docs
 <http://mutalyzer.readthedocs.org>`_.
 
+If you're interested in running your own Mutalyzer installation, please have a
+look at our `Mutalyzer Ansible role
+<https://github.com/mutalyzer/ansible-role-mutalyzer>`_ for a completely
+automated deployment.
+
 
 Contributing
 ------------

doc/config.rst

@@ -174,6 +174,8 @@ LOG_TIME_FORMAT
 Website settings
 ^^^^^^^^^^^^^^^^
 
+.. _config-reverse-proxied:
+
 REVERSE_PROXIED
   If set to `True`, the WSGI application runs behind a reverse proxy (e.g.,
   nginx using ``proxy_pass``). This needs to be set if the application is

doc/deploy.rst

@@ -18,17 +18,21 @@ containers such as `Gunicorn`_.
 Below we briefly describe our recommended setup for a production environment
 using Gunicorn, nginx and Supervisor.
 
+See :ref:`deploy_ansible` for a solution to completely automate this.
+
 
 Configuration settings
 ----------------------
 
-It is recommended to at least set the following configuration settings:
+At a minimum, it is recommended to have a look at the following configuration
+settings:
 
 - :ref:`EMAIL <config-email>`
 - :ref:`DEBUG <config-debug>`
 - :ref:`CACHE_DIR <config-cache-dir>`
 - :ref:`SOAP_WSDL_URL <config-soap-wsdl-url>`
 - :ref:`JSON_ROOT_URL <config-json-root-url>`
+- :ref:`REVERSE_PROXIED <config-reverse-proxied>`
 
 
 WSGI application server: Gunicorn
@@ -150,6 +154,8 @@ website:
     environment=MUTALYZER_SETTINGS="/opt/mutalyzer/conf/settings.py"
 
 
+.. _deploy_ansible:
+
 Automated deployment with Ansible
 ---------------------------------
 

doc/index.rst

@@ -4,6 +4,9 @@ Mutalyzer developer documentation
 Mutalyzer is an HGVS variant nomenclature checker. The canonical Mutalyzer
 installation can be found at `mutalyzer.nl <https://mutalyzer.nl>`_.
 
+.. note:: If you're looking into running your own Mutalyzer installation, you
+   might be interested in :ref:`deploy_ansible`.
+
 This is the developer documentation for Mutalyzer. User documentation can be
 found on the `wiki <https://humgenprojects.lumc.nl/trac/mutalyzer>`_.
 

doc/install.rst

@@ -5,6 +5,10 @@
 Installation
 ============
 
+.. note:: If you're looking into deploying Mutayzer in a production
+   environment (as opposed to a local development installation), please see
+   :ref:`deploy`.
+
 Mutalyzer depends on a database server, `Python`_ 2.7, and several Python
 packages. `Redis`_ is a soft dependency. This section walks you through
 installing Mutalyzer with Redis and using `PostgreSQL`_ as database server,

doc/testing.rst

@@ -16,7 +16,7 @@ the Mutalyzer source directory.
           tests.
 
 By default, the tests use an in-memory SQLite database. This can be customized
-with the ``--database-uri` command line argument and a valid `SQLAlchemy
+with the ``--database-uri`` command line argument and a valid `SQLAlchemy
 connection URI
 <http://docs.sqlalchemy.org/en/rel_1_0/core/engines.html#database-urls>`_
 (obviously, the contents of this database will be lost). For example, to use

mutalyzer/website/templates/about.html

@@ -70,6 +70,13 @@ Development of Mutalyzer happens on
 GitHub: <a href="https://github.com/mutalyzer/mutalyzer">github.com/mutalyzer/mutalyzer</a>
 </p>
 
+<p>
+If you're interested in running your own Mutalyzer installation, please have a
+look at
+our <a href="https://github.com/mutalyzer/ansible-role-mutalyzer">Mutalyzer
+Ansible role</a> for a completely automated deployment.
+</p>
+
 <h2>Sponsors</h2>
 
 <p>