Consolidate repo download with later usage

This mirrors the existing pattern of WORKDIR+RUN for each tool in the
"build from source" section. Also makes it easier to move things around
if needed.

Author: victorlin

Dockerfile

@@ -159,32 +159,31 @@ RUN curl -fsSL -o /final/bin/nextclade2 https://github.com/nextstrain/nextclade/
  && ln -sv nextclade2 /final/bin/nextclade
 
 # Fauna
-RUN /builder-scripts/download-repo https://github.com/nextstrain/fauna master /nextstrain/fauna
+WORKDIR /nextstrain/fauna
+RUN /builder-scripts/download-repo https://github.com/nextstrain/fauna master . \
+ && pip3 install --requirement=requirements.txt
 
 # Augur
-RUN /builder-scripts/download-repo https://github.com/nextstrain/augur "$(/builder-scripts/latest-augur-release-tag)" /nextstrain/augur
-
-# Auspice
-RUN /builder-scripts/download-repo https://github.com/nextstrain/auspice release /nextstrain/auspice
-
-# Install Fauna deps
-RUN pip3 install --requirement=/nextstrain/fauna/requirements.txt
-
 # Augur is an editable install so we can overlay the augur version in the image
 # with --volume=.../augur:/nextstrain/augur and still have it globally
 # accessible and importable.
-RUN pip3 install --editable "/nextstrain/augur"
+WORKDIR /nextstrain/augur
+RUN /builder-scripts/download-repo https://github.com/nextstrain/augur "$(/builder-scripts/latest-augur-release-tag)" . \
+ && pip3 install --editable .
 
 # pysam (for ncov/Pangolin)
 RUN pip3 install pysam
 
+# Auspice
 # Install Node deps, build Auspice, and link it into the global search path.  A
 # fresh install is only ~40 seconds, so we're not worrying about caching these
 # as we did the Python deps.  Building auspice means we can run it without
 # 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 update && npm install && npm run build && npm link
+WORKDIR /nextstrain/auspice
+RUN /builder-scripts/download-repo https://github.com/nextstrain/auspice release . \
+ && npm update && npm install && npm run build && npm link
 
 # ———————————————————————————————————————————————————————————————————— #