fix links for docs

docs/source/installation.rst

@@ -159,8 +159,10 @@ Deployment on Docker
 --------------------
 It is also possible to deploy the server using Docker.
 
-First, you need an environment running the docker daemon. For non-production use, we recommend [boot2docker](http://boot2docker.io/). For production use you should install docker on a stable linux distro.
-[Platform specific Docker installation instructions](https://docs.docker.com/installation/) (OS X and Windows are instructions for boot2docker)
+First, you need an environment running the docker daemon. For non-production use, we recommend `boot2docker <http://boot2docker.io/>`_. For production use you should install docker on a stable linux distro.
+`Platform specific Docker installation instructions <https://docs.docker.com/installation/) (OS X and Windows are instructions for boot2docker>`_
+
+**Local Dataset Mounted as Volume**
 
 If you already have a dataset on your machine, you can download and deploy the apache server in one command: 
 
@@ -170,12 +172,16 @@ If you already have a dataset on your machine, you can download and deploy the a
 
 Replace ``/my/ga4gh_data/`` with the path to your data.
 
+**Demo Dataset Inside Container**
+
 If you do not have a dataset yet, you can deploy a container which includes the demo data:
 
 .. code-block:: bash
 
   $ docker run -itd -p 8000:80 --name ga4gh_demo afirth/ga4gh_server_apache:demo
 
+**Ports**
+
 This will run the docker container in the background, and translate calls from your host environment
 port 8000 to the docker container port 80. At that point you should be able to access it like a normal website, albeit on port 8000.
 Running in boot2docker, you will need to forward the port from the boot2docker vm to the host.
@@ -191,7 +197,7 @@ For more info on port forwarding see https://www.virtualbox.org/manual/ch06.html
 Advanced
 ++++++++
 
-If you want to build the images yourself, that is possible. The [afirth/ga4gh_server_apache repo](https://registry.hub.docker.com/u/afirth/ga4gh_server_apache/)
+If you want to build the images yourself, that is possible. The `afirth/ga4gh_server_apache repo <https://registry.hub.docker.com/u/afirth/ga4gh_server_apache/>`_
 builds automatically on new commits, so this is only needed if you want to modify the Dockerfiles, or build from a different source.
 
 Build the code at server/ and run for production, serving a dataset on local host located at ``/my/dataset``
@@ -211,11 +217,13 @@ Build and run the production build from above, with the demo dataset in the cont
  $ docker build -t my-repo/my-demo-image .
  $ docker run -itd -p 8000:80 --name ga4gh_demo my-repo/my-demo-image
 
-##### Variants #####
+**Variants**
 
 Other Dockerfile implementations are available in the variants folder which install manually.
 To build one of these images:
 
+.. code-block:: bash
+
  $ cd server/deploy/variants/xxxx
  $ docker build -t my-repo/my-image .
  $ docker run -itd -p 8000:80 --name my_container my-repo/my-image
@@ -224,7 +232,7 @@ To build one of these images:
 Troubleshooting Docker
 ++++++++++++++++++++++
 
-##### DNS #####
+**DNS**
 
 The docker daemon's DNS may be corrupted if you switch networks, especially if run in a VM.
 For boot2docker, running udhcpc on the VM usually fixes it. 
@@ -237,7 +245,7 @@ From a terminal on the host:
   >	sudo udhcpc
   (password is tcuser)
 
-##### DEBUG #####
+**DEBUG**
 
 To enable DEBUG on your docker server, call docker run with ``-e GA4GH_DEBUG=True``