Optimize layers, remove commented lines, and include Ruby

Addresses Tom's comments about how to optimize the Dockerfile. This commit will
be squashed into the original commit on rebase.

Dockerfile

@@ -11,8 +11,7 @@ FROM python:3.7-slim-buster AS builder
 SHELL ["/bin/bash", "-c"]
 
 # Add system deps for building
-RUN apt-get update
-RUN apt-get install -y --no-install-recommends \
+RUN apt-get update && apt-get install -y --no-install-recommends \
         autoconf \
         automake \
         build-essential \
@@ -23,7 +22,6 @@ RUN apt-get install -y --no-install-recommends \
         libpng-dev \
         nodejs \
         npm \
-        perl \
         pkg-config
 
 # Downloading dependencies, these should be pinned to specific versions
@@ -74,9 +72,6 @@ ARG CACHE_DATE
 # Add download helper
 COPY devel/download-repo /devel/
 
-# # sacra
-# RUN /devel/download-repo https://github.com/nextstrain/sacra master /nextstrain/sacra
-
 # fauna
 RUN /devel/download-repo https://github.com/nextstrain/fauna master /nextstrain/fauna
 
@@ -86,9 +81,6 @@ RUN /devel/download-repo https://github.com/nextstrain/augur release /nextstrain
 # auspice
 RUN /devel/download-repo https://github.com/nextstrain/auspice release /nextstrain/auspice
 
-# # Install Python 2 deps
-# RUN pip2 install --requirement=/nextstrain/sacra/requirements.txt
-
 # Install Python 3 deps
 RUN pip3 install --requirement=/nextstrain/fauna/requirements.txt
 
@@ -110,27 +102,23 @@ RUN pip3 install seaborn==0.9.0
 # hot-reloading, which is time-consuming and generally unnecessary in the
 # container image.  Linking is equivalent to an editable Python install and
 # used for the same reasons described above.
-RUN cd /nextstrain/auspice && npm install && npm run build && npm link
-
-RUN apt-get clean
+RUN cd /nextstrain/auspice && npm update && npm install && npm run build && npm link
 
 # ———————————————————————————————————————————————————————————————————— #
 
 # Now build the final image.
 FROM python:3.7-slim-buster
 
 # Add system runtime deps
-RUN apt-get update
-RUN apt-get install -y \
+RUN apt-get update && apt-get install -y --no-install-recommends \
         ca-certificates \
         curl \
         gzip \
         nodejs \
+        ruby \
         wget \
         zip unzip
 
-RUN apt-get clean
-
 # Configure the prompt for interactive usage
 COPY prompt.sh /etc/profile.d/
 
@@ -151,7 +139,6 @@ COPY --from=builder /build/vcftools/built/share/  /usr/local/share/
 RUN chmod a+rX /usr/local/bin/* /usr/local/libexec/*
 
 # Add installed Python libs
-# COPY --from=builder /usr/lib/python2.7/site-packages/ /usr/lib/python2.7/site-packages/
 COPY --from=builder /usr/local/lib/python3.7/site-packages/ /usr/local/lib/python3.7/site-packages/
 
 # Add installed Python scripts that we need.