Clean up and vet Docker page

And move it into /learn, since it's an ImageJ usage topic.

The docs are Fiji-specific right now, unfortunately, but the plan
is to generalize the Docker image(s) to be ImageJ2, not only Fiji.

Author: ctrueden

_pages/plugins/docker.md renamed to _pages/learn/docker.md

@@ -1,7 +1,5 @@
 ---
-mediawiki: Docker
 title: Docker
-categories: [Uncategorized]
 ---
 
 [Docker](https://www.docker.com/whatisdocker/) provides a platform for distribution of application state. This facilitates the highest level of scientific [reproducibility](/develop/architecture#reproducible-builds) - as a Docker image can bundle operating system, Java version, update site and plugin state, and even sample data. These images can then be reused by remote users and scientists worldwide, with no dependency concerns (beyond Docker itself).
@@ -13,30 +11,36 @@ You will need to [install Docker](https://docs.docker.com/installation/#installa
 # How to use the Fiji Docker images
 
 The base Fiji images are provided on [Docker Hub](https://registry.hub.docker.com/u/fiji/fiji/). These images call the Fiji executable by default. For example:
-
-` docker run -it --rm fiji/fiji`
+```shell
+docker run -it --rm fiji/fiji
+```
 
 will call the default Fiji image, attempting to open the ImageJ UI with Java 7.
 
 Several [tags](https://registry.hub.docker.com/u/fiji/fiji/tags/manage/) are provided to run Fiji with different Java versions. For example, if you wanted to run with Oracle's Java 6, you would use:
-
-` docker run -it --rm fiji/fiji:fiji-oracle-jdk6`
-
-**Important** - without some extra setup, there is no display used by Docker. So if you just tried one of the above commands, you likely got an error:
-
-` No GUI detected.  Falling back to headless mode.`
-
+```shell
+docker run -it --rm fiji/fiji:fiji-oracle-jdk6
+```
+
+{% include notice icon='warning' content="
+Without some extra setup, there is no display used by Docker. So if you just tried one of the above commands, you likely got an error:
+```
+No GUI detected.  Falling back to headless mode.
+```
 The following sections cover [headless](#running-headless) and [graphical](#running-the-ui) uses.
+" %}
 
 # Running headless
 
 Running ImageJ headlessly in Docker is not much different than normal headless operation - see the [headless guide](/learn/headless) for general information. To start a headless ImageJ invocation from Docker, use:
-
-` docker run -it --rm fiji/fiji fiji-linux64 --headless`
+```shell
+docker run -it --rm fiji/fiji fiji-linux64 --headless
+```
 
 If you want to manually explore the Fiji Docker image, e.g. to install additional plugins or utility software, you can start the command prompt via:
-
-` docker run -it --rm fiji/fiji bash`
+```shell
+docker run -it --rm fiji/fiji bash
+```
 
 Just be sure to [commit any changes](https://docs.docker.com/userguide/dockerimages/#updating-and-committing-an-image)!
 
@@ -52,30 +56,35 @@ We can adapt [this blog post](http://fabiorehm.com/blog/2014/09/11/running-gui-a
 
 Use this Dockerfile as a starting point:
 
-` # Modify this tag if a different java version is desired`  
-` FROM fiji/fiji:fiji-openjdk-7`  
-` # Replace 1000 with your user / group id`  
-` RUN export uid=1000 gid=1000 && \`  
-`     mkdir -p /home/developer && \`  
-`     echo "developer:x:${uid}:${gid}:Developer,,,:/home/developer:/bin/bash" >> /etc/passwd && \`  
-`     echo "developer:x:${uid}:" >> /etc/group && \`  
-`     echo "developer ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/developer && \`  
-`     chmod 0440 /etc/sudoers.d/developer && \`  
-`     chown ${uid}:${gid} -R /home/developer`  
-` USER developer`  
-` ENV HOME /home/developer`  
-` CMD fiji-linux64`
+```docker
+# Modify this tag if a different java version is desired
+FROM fiji/fiji:fiji-openjdk-7
+# Replace 1000 with your user / group id
+RUN export uid=1000 gid=1000 && \
+    mkdir -p /home/developer && \
+    echo "developer:x:${uid}:${gid}:Developer,,,:/home/developer:/bin/bash" >> /etc/passwd && \
+    echo "developer:x:${uid}:" >> /etc/group && \
+    echo "developer ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/developer && \
+    chmod 0440 /etc/sudoers.d/developer && \
+    chown ${uid}:${gid} -R /home/developer
+USER developer
+ENV HOME /home/developer
+CMD fiji-linux64
+```
 
 Install the Dockerfile with:
-
-` docker build -t fiji .`
+```shell
+docker build -t fiji .
+```
 
 Run Fiji with:
 
-` docker run -ti --rm \`  
-`      -e DISPLAY=$DISPLAY \`  
-`      -v /tmp/.X11-unix:/tmp/.X11-unix \`  
-`      fiji/fiji`
+```shell
+docker run -ti --rm \
+     -e DISPLAY=$DISPLAY \
+     -v /tmp/.X11-unix:/tmp/.X11-unix \
+     fiji/fiji
+```
 
 Which should pop up a window with Fiji running.
 
@@ -91,46 +100,51 @@ First, you will need to install the following:
 2.  [Homebrew-cask](https://github.com/caskroom/homebrew-cask)
 
 Then, from a terminal, use Homebrew to install [socat](http://www.cyberciti.biz/faq/linux-unix-tcp-port-forwarding/) and [XQuartz](http://xquartz.macosforge.org/landing/) via:
-
-` brew install socat`
-
-` brew cask install xquartz`
+```shell
+brew install socat
+brew cask install xquartz
+```
 
 Now open a new terminal window and type
-
-` echo $DISPLAY`
-
+```shell
+echo $DISPLAY
+```
 and ensure it is not empty (it should print something like `/private/tmp/com.apple.launchd.GYg5TvcMIf/org.macosforge.xquartz:0`).
 
 Then run:
-
-` ifconfig`
-
+```shell
+ifconfig
+```
 which will print output that should end with something like:
-
-` vboxnet0: flags=0000<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST>`  
-` ether 00:00:00:00:00:00`  
-` inet 192.168.15.2 netmask 0xffffffff broadcast 192.168.0.0`
+```
+vboxnet0: flags=0000<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST>
+ether 00:00:00:00:00:00
+inet 192.168.15.2 netmask 0xffffffff broadcast 192.168.0.0
+```
 
 And take note of the ip address on the last line (`192.168.15.2` in this case).
 
 Since you are using macOS it is assumed you are using [boot2docker](http://boot2docker.io/). Now, in the same terminal you started boot2docker, you should have set up the environment variables e.g. with
-
-` $(boot2docker shellinit)`
+```shell
+$(boot2docker shellinit)
+```
 
 From this same terminal, open XQuartz with:
-
-` open -a XQuartz`
+```shell
+open -a XQuartz
+```
 
 This will start up a new X11 session. You will want two X11 terminals open here (`Application > Terminal` to open a new X11 terminal).
 
 In one X11 terminal, run:
-
-` socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\"`
+```shell
+socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\"
+```
 
 to start listening for X11 forwarding. In the second terminal, you can now use Docker to launch a Fiji GUI. For example:
-
-` docker run -e DISPLAY=192.168.15.2:0 fiji/fiji`
+```shell
+docker run -e DISPLAY=192.168.15.2:0 fiji/fiji
+```
 
 Where the IP address was what we found earlier with `ifconfig`.
 
@@ -147,8 +161,9 @@ Once you have Fiji up and running, you will probably want to open some images.
 The best way to share data with Docker is to use volumes, as described in [this blog post](http://haven.nightlyart.com/fiji-is-now-available-on-docker-hub/).
 
 For example, if your data is in `/Users/foo/data`, launching the Fiji image with:
-
-` docker run -v /Users/foo/data:/fiji/data -e DISPLAY=192.168.15.2:0 fiji/fiji`
+```shell
+docker run -v /Users/foo/data:/fiji/data -e DISPLAY=192.168.15.2:0 fiji/fiji
+```
 
 will create a `data` subdirectory in the Fiji installation, which you can then open images from as normal.