From c05f4d667e148be080ea7417980ecd661a9b2192 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 14 Oct 2022 17:15:07 +0000
Subject: [PATCH 1/3] Simplify builder-scripts/ COPY command

There's no need to list every script since all should be used in the
Dockerfile now, following 3d45a6160e1cbe32c83b286545fdfc63a6541ba3.
---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index efe513fe..a465e999 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -155,8 +155,8 @@ RUN curl -fsSL -o /final/bin/nextalign2 https://github.com/nextstrain/nextclade/
 RUN curl -fsSL -o /final/bin/nextclade2 https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-unknown-linux-gnu \
  && ln -sv nextclade2 /final/bin/nextclade
 
-# Add helpers for build
-COPY builder-scripts/download-repo builder-scripts/latest-augur-release-tag /builder-scripts/
+# Add helper scripts
+COPY builder-scripts/ /builder-scripts/
 
 # Fauna
 RUN /builder-scripts/download-repo https://github.com/nextstrain/fauna master /nextstrain/fauna

From c9d1bcaaed81766c281c0214ed0d5d94dbf2f250 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 14 Oct 2022 17:17:27 +0000
Subject: [PATCH 2/3] Move builder-scripts/ COPY command

Move the command before Nextclade downloads since it is a "setup" step.
This keeps download commands closer to each other, and allows Nextclade
download commands to use scripts if needed in the future.
---
 Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index a465e999..d31e934e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -142,6 +142,9 @@ RUN pip3 install git+https://github.com/cov-lineages/pango-designation.git@19d9a
 # docker build --build-arg CACHE_DATE="$(date)"
 ARG CACHE_DATE
 
+# Add helper scripts
+COPY builder-scripts/ /builder-scripts/
+
 # Nextclade/Nextalign v2 are downloaded directly but using the latest version,
 # so they belong after CACHE_DATE (unlike Nextclade/Nextalign v1).
 
@@ -155,9 +158,6 @@ RUN curl -fsSL -o /final/bin/nextalign2 https://github.com/nextstrain/nextclade/
 RUN curl -fsSL -o /final/bin/nextclade2 https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-unknown-linux-gnu \
  && ln -sv nextclade2 /final/bin/nextclade
 
-# Add helper scripts
-COPY builder-scripts/ /builder-scripts/
-
 # Fauna
 RUN /builder-scripts/download-repo https://github.com/nextstrain/fauna master /nextstrain/fauna
 

From 218e0453d3fef90652a8c8ebcec0ca8b4cb870cf Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Mon, 17 Oct 2022 17:51:31 +0000
Subject: [PATCH 3/3] 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.
---
 Dockerfile | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d31e934e..850b0fdc 100644
--- a/Dockerfile
+++ b/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
 
 # ———————————————————————————————————————————————————————————————————— #