Dockerfile and update documentation accordingly

Dockerfile

@@ -0,0 +1,5 @@
+FROM gcr.io/distroless/java:11
+COPY target/bluegenes.jar /
+WORKDIR /
+EXPOSE 5000
+CMD ["bluegenes.jar"]

docs/building.md

@@ -116,10 +116,26 @@ There is also a shortcut that in addition cleans and compiles CSS.
 
 ## Deploying your build
 
-One of the easiest ways to deploy the prod minified version is to set up [Dokku](http://dokku.viewdocs.io/dokku/) on your intended server. You can also use BlueGenes with [heroku](https://www.heroku.com/).
+### docker
 
+BlueGenes has a Dockerfile which you can build with a fresh uberjar.
 
-### Minified deployment using dokku
+    lein uberjar
+    docker build -t bluegenes .
+
+Run it and the web server should default to port 5000.
+
+    docker run -p 5000:5000 -it --rm bluegenes
+
+You can specify environment variables by using the `-e` or `--env-file` arguments when calling docker. See [Configuring](/docs/configuring.md) for a list of all available environment variables.
+
+There is also a prebuilt docker image available on Docker Hub.
+
+    docker pull intermine/bluegenes:latest
+
+### Dokku
+
+[Dokku](http://dokku.viewdocs.io/dokku/) allows you to push a Git branch and have it automatically build and serve it using the appropriate docker container. (You can also use BlueGenes with [heroku](https://www.heroku.com/).)
 
 Once dokku is configured on your remote host, you'll need to add your public key, create a remote for your host and push to it:
 
@@ -139,7 +155,7 @@ To compile and package BlueGenes into an executable jar, run the following comma
 
     lein uberjar
 
-Then, to start the application, execute the jar and pass in a [`config.edn` file](../config/dev/README.md):
+Then, to start the application, execute the jar and pass in a [`config.edn` file](/docs/configuring.md):
 
     java -jar -Dconfig="config/prod/config.edn" target/bluegenes.jar
 

docs/configuring.md

@@ -1,22 +1,25 @@
-# Configuration
+# Configuring BlueGenes
 
-This applies primarily to standalone BlueGenes.
+## Environment variables
 
+| Envvar | Description | Default |
+| ------ | ----------- | ------- |
+| SERVER_PORT | Port used by web server | 5000 |
+| LOGGING_LEVEL | Minimum level for logging | :info |
+| GOOGLE_ANALYTICS | Google Analytics tracking ID | nil |
+| JWT_SECRET | Secret for signing JSON Web Tokens | nil |
+| BLUEGENES_DEFAULT_SERVICE_ROOT | InterMine service that is default | https://alpha.flymine.org/alpha/ |
+| BLUEGENES_DEFAULT_MINE_NAME | Optional default mine name to display until it gets fetched | FlyMine |
+| BLUEGENES_TOOL_PATH | Server directory where BlueGenes tools are installed | ./tools |
 
-## Note: Ways to Configure
+## How to configure
 
-The preferred way to configure BlueGenes is via `.edn` configuration files, and it is the one being explained here. All keys can be overridden with environment variables. Please refer to  [Yogthos's config docs](https://github.com/yogthos/config#yogthosconfig) for more details regarding this method.
+BlueGenes supports the many methods of specifying configuration keys provided by [Yogthos' config](https://github.com/yogthos/config#yogthosconfig). The configuration keys listed above can be specified in uppercase or lowercase, and with dashes, underscores or periods as separators.
 
-
-## Configuration via `.edn` files
+### Configuration via `config.edn` files
 
 Copy and paste the code from the `.template` files in `config/dev/` and `config/prod/`, tweak it to match your preferences, and save it as `config.edn` in the same folder.
 
-
 ### Analytics (optional)
 
-For now, the only supported statistics service is [Google analytics](https://analytics.google.com/). If you wish to use this service, configure your domain and then add your Google Analytics ID.
-
-```clojure
-  {:google-analytics "UA-12345678-9"}
-```
+For now, the only supported statistics service is [Google analytics](https://analytics.google.com/). If you wish to use this service, configure your domain and then add your Google Analytics ID using the `GOOGLE_ANALYTICS` key listed above.