update docs

docs/source/installation.rst

@@ -166,41 +166,43 @@ If you already have a dataset on your machine, you can download and deploy the a
 
 .. code-block:: bash
 
-  $ docker run -e GA4GH_DATA_SOURCE=/data -v my/ga4gh_data/:/data:ro -itd -p 8000:80 --name ga4gh_server afirth/ga4gh_apache_server:prod
+  $ docker run -e GA4GH_DATA_SOURCE=/data -v /my/ga4gh_data/:/data:ro -itd -p 8000:80 --name ga4gh_server afirth/ga4gh_apache_server:prod
 
-If you do not have a dataset yet, you can deploy the a container which includes the demo data:
+Replace ``/my/ga4gh_data/`` with the path to your data.
+
+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
 
 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.
+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.
 From a terminal on the host to forward traffic from localhost:8000 to the VM 8000 on OSX:
 
 .. code-block:: bash
 
   $ VBoxManage controlvm boot2docker-vm natpf1 "ga4gh,tcp,127.0.0.1,8000,,8000"
 
-For more info see https://www.virtualbox.org/manual/ch06.html#natforward and https://github.com/CenturyLinkLabs/panamax-ui/wiki/How-To%3A-Port-Forwarding-on-VirtualBox
+For more info on port forwarding see https://www.virtualbox.org/manual/ch06.html#natforward and https://github.com/CenturyLinkLabs/panamax-ui/wiki/How-To%3A-Port-Forwarding-on-VirtualBox
 
 ++++++++
 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/)
-builds automatically on new commits, so this is only needed if you want to modify the Dockerfiles
+builds automatically on new commits, so this is only needed if you want to modify the Dockerfiles, or build from a different source.
 
-Build and run for production, serving a dataset on local host located at ``/my/dataset``
+Build the code at server/ and run for production, serving a dataset on local host located at ``/my/dataset``
 
 .. code-block:: bash
 
  $ cd server/
  $ docker build -t my-repo/my-image .
  $ docker run -e GA4GH_DATA_SOURCE=/dataset -v /my/dataset:/dataset:ro -itd -p 8000:80 --name ga4gh_server my-repo/my-image
 
-Build and run the production build, with the demo dataset in the container
+Build and run the production build from above, with the demo dataset in the container
 (you will need to modify the FROM line in ``/deploy/variants/demo/Dockerfile`` if you want to use your image from above as the base):
 
 .. code-block:: bash
@@ -209,7 +211,14 @@ Build and run the production build, with the demo dataset in the container
  $ docker build -t my-repo/my-demo-image .
  $ docker run -itd -p 8000:80 --name ga4gh_demo my-repo/my-demo-image
 
+##### Variants #####
+
 Other Dockerfile implementations are available in the variants folder which install manually.
+To build one of these images:
+
+ $ 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
 
 ++++++++++++++++++++++
 Troubleshooting Docker
@@ -225,7 +234,7 @@ From a terminal on the host:
 
   $ eval "$(boot2docker shellinit)"
   $ boot2docker ssh
-  $	sudo udhcpc
+  >	sudo udhcpc
   (password is tcuser)
 
 ##### DEBUG #####
@@ -237,3 +246,5 @@ To enable DEBUG on your docker server, call docker run with ``-e GA4GH_DEBUG=Tru
   $ docker run -itd -p 8000:80 --name ga4gh_demo -e GA4GH_DEBUG=True afirth/ga4gh_server_apache:demo
 
 This will set the environment variable which is read by config.py
+
+You can then get logs from the docker container by running ``docker logs (container)`` e.g. ``docker logs ga4gh_demo``