From a47e358c8ce5a224cf794bddeb3c0ac85cedfc47 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 14 Oct 2022 17:45:26 +0000
Subject: [PATCH 1/3] Remove libpng-dev, add zlib1g-dev

Upon removing libpng-dev, the build error from VCFtools is:

    No package 'zlib' found

libpng-dev also installs zlib1g-dev as a dependency, which is why that
worked. The build succeeds if zlib1g-dev is installed directly, so do
that to avoid unnecessary installs.
---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index efe513fe..0668d8e5 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -20,8 +20,8 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
         git \
         jq \
         libgmp-dev \
-        libpng-dev \
-        pkg-config
+        pkg-config \
+        zlib1g-dev
 
 # Install a specific Node.js version
 # https://github.com/nodesource/distributions/blob/0d81da75/README.md#installation-instructions

From 1bcd494c2cacf6f4c04fab8627214d23d4daee53 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 14 Oct 2022 17:53:45 +0000
Subject: [PATCH 2/3] Remove unused libgmp-dev

The build succeeds without this installed. It was likely used at some
point since added in 3917c1b9aa0aa19e694f94f6bd3e56418f248269, but
building from that commit no longer works due to changes in upstream URL
availability. I did not dig deeper to find out exactly where it was used.
---
 Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 0668d8e5..6d727717 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -19,7 +19,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
         curl \
         git \
         jq \
-        libgmp-dev \
         pkg-config \
         zlib1g-dev
 

From 10ecb42656927aabecac019bb759dd90f182fd61 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Thu, 13 Oct 2022 10:54:29 -0700
Subject: [PATCH 3/3] Annotate package installs

Currently, the reasoning on why each package is used

1. can be deduced from direct references in the Dockerfile (e.g. curl), or
2. can be deduced from git blame (e.g. jq: c256a30eccf08ba5c245656a2b2bc3b1f2f713f9), or
3. is unclear.

To make this easier, document why each package is installed.
---
 Dockerfile | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 6d727717..e6d5b6cf 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,6 +11,15 @@ FROM python:3.7-slim-buster AS builder
 SHELL ["/bin/bash", "-c"]
 
 # Add system deps for building
+# autoconf, automake: for building VCFtools; may be used by package managers to build from source
+# build-essential: contains gcc, g++, make, etc. for building various tools; may be used by package managers to build from source
+# ca-certificates: for secure HTTPS connections
+# curl: for downloading source files
+# git: for git pip installs
+# jq: used in builder-scripts/latest-augur-release-tag
+# pkg-config: for building VCFtools; may be used by package managers to build from source
+# zlib1g-dev: for building VCFtools; may be used by package managers to build from source
+# nodejs: for installing Auspice
 RUN apt-get update && apt-get install -y --no-install-recommends \
         autoconf \
         automake \
@@ -191,6 +200,15 @@ RUN cd /nextstrain/auspice && npm update && npm install && npm run build && npm
 FROM python:3.7-slim-buster AS final
 
 # Add system runtime deps
+# bzip2, gzip, xz-utils, zip, unzip, zstd: install compression tools
+# ca-certificates: [Dockerfile] for secure HTTPS connections; may be used by workflows
+# curl: [Dockerfile] for downloading binaries directly; may be used by workflows
+# jq: may be used by workflows
+# less: for usability in an interactive prompt
+# perl: for running VCFtools
+# ruby: may be used by workflows
+# wget: may be used by workflows
+# nodejs: for running Auspice
 RUN apt-get update && apt-get install -y --no-install-recommends \
         bzip2 \
         ca-certificates \