Updated README w/lego brick directions. Added option to use docker.

.dockerignore

@@ -0,0 +1,5 @@
+/instance/sequencer.sqlite
+/instance/cache
+/logs
+/.venv
+/.git

Dockerfile

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+FROM python:3.5-alpine
+
+RUN pip install pipenv
+
+WORKDIR /app
+COPY Pipfile* /app/
+RUN pipenv install
+
+COPY . /app/
+
+EXPOSE 5000
+CMD ./run_alpine_site.sh

README.md

@@ -4,24 +4,70 @@
 
 To run this project, you'll need the following:
 
-- Python 3.5.3 + pipenv
+- Python 3.x + pipenv
 - A LEGO Mindstorms ev3 unit with Minipython installed
 
 Follow these instructions to set up your device with rpyc
 - https://www.ev3dev.org/docs/tutorials/
 - https://ev3dev-lang.readthedocs.io/projects/python-ev3dev/en/stable/rpyc.html
 
+Check out the source code to a directory of your choosing, e.g.:
+
+```
+# creates a folder called lego_sequencer under the current directory.
+git clone https://github.com/ETH-NEXUS/lego_sequencer.git
+```
+
+We'll refer to this folder, `lego_sequencer`, as the source directory below.
 
 ## Usage
 
-You should already have the ev3 connected and running the rpyc daemon. First, install the Python requirements like so:
+The LEGO Sequencer consists of two components:
+- the Mindstorms unit, which handles moving the tray and scanning bricks, and
+- the webserver, which communicates with the Mindstorms unit to get the bricks that were scanned, convert them
+  to a sequence, then send the sequence to NCBI's BLAST API for determining the species to which it might belong.
+
+## LEGO Mindstorms Setup
+
+Ensure that the device is plugged in both to power and to a USB port on your computer.
+
+To turn the unit on, press the dark gray center button on the unit's face. You'll see some text scroll by on the display
+as the brick boots up Linux. This can take up to a minute, so be patient. (In the unlikely case that it freezes, you can
+hold down the left, center, and right buttons, then press the back button to reboot the unit.)
+
+Eventually, you'll see a menu appear with a number of options. The option "File Browser" should be selected; press
+the center button to activate it, at which point you'll see a list of files. The first file, `rpyc_server.sh`, should
+also already be selected. To run it, press the center button again. At this point the screen will go blank, but the 
+unit is ready to accept commands from the webserver which you'll soon launch on your computer.
+
+When you're done with your demo, press the back button (the top-left button on the unit's face, separate from the other
+buttons). You'll again see the file browser. Hold down the back button until a popup menu appears with power options
+(i.e., "Power Off", "Reboot", and "Cancel"); press the center button again to turn the unit off.
+
+## Webserver Setup
+
+Inside the source directory, run the following to install the required Python libraries for the project:
 
 ```pipenv install```
 
-Run the following to start the webserver:
+Finally, run the following script to start the webserver:
 
 `./run_site.sh`
 
 If you're using Windows, you'll probably want to run the webserver via [Waitress](https://docs.pylonsproject.org/projects/waitress/en/stable/), like so:
 
 `run_site.bat`
+
+The site should be accessible at [http://localhost:5000](http://localhost:5000).
+
+### Alternate Docker Setup
+
+If you prefer to use Docker, inside the source directory you can build the project as an image like so:
+
+```docker build -t lego-sequencer .```
+
+Then, you can launch the image as a container:
+
+```docker run --rm -d -p 5000:50000 lego-sequencer```
+
+As before, you should be able to access the site at [http://localhost:5000](http://localhost:5000).

run_alpine_site.sh

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+#!/bin/sh
+
+export FLASK_APP=sequencer
+export FLASK_ENV=development
+pipenv run python waitress_server.py