From d366ac4f481b535d2cd07712f24f370a610229d9 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Tue, 7 Nov 2023 13:12:44 -0800
Subject: [PATCH] [wip] Remove pyfastx build/runtime dependencies

The next version of Augur (to be released) will support versions of
pyfastx that provide wheels for Python 3.10.

After the release, run CI on this commit and see if it works. Not sure
if the pyfastx wheel includes the runtime dependencies. Maybe separate
installation is still necessary?
---
 Dockerfile | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index cd19673..c8110fd 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -244,16 +244,13 @@ ARG TARGETARCH
 # curl, jq: used in builder-scripts/latest-augur-release-tag
 # git: for git pip installs
 # gcc: for building datrie (for Snakemake)
-# libsqlite3-dev, zlib1g-dev: for building pyfastx (for Augur)
 # make: for building isal (if necessary, for Augur)
 RUN apt-get update && apt-get install -y --no-install-recommends \
         curl \
         gcc \
         git \
         make \
-        jq \
-        libsqlite3-dev \
-        zlib1g-dev
+        jq
 
 
 # 1. Install programs via pip
@@ -368,11 +365,9 @@ SHELL ["/bin/bash", "-e", "-u", "-o", "pipefail", "-c"]
 # jq: may be used by workflows
 # less: for usability in an interactive prompt
 # libgomp1: for running FastTree
-# libsqlite3: for pyfastx (for Augur)
 # perl: for running VCFtools
 # ruby: may be used by workflows
 # wget: may be used by workflows
-# zlib1g: for pyfastx (for Augur)
 # nodejs: for running Auspice
 RUN apt-get update && apt-get install -y --no-install-recommends \
         bzip2 \
@@ -384,14 +379,12 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
         jq \
         less \
         libgomp1 \
-        libsqlite3-0 \
         perl \
         ruby \
         util-linux \
         wget \
         xz-utils \
         zip unzip \
-        zlib1g \
         zstd
 
 # Install a specific Node.js version