From 75fcb0793ab3169c6f57b244f452ecac777a530d Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Thu, 22 Aug 2024 14:43:54 -0700
Subject: [PATCH] =?UTF-8?q?=F0=9F=9A=A7=20Remove=20pangolin/pangoLEARN?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Somehow the build for pangoLEARN failed: https://github.com/nextstrain/docker-base/actions/runs/10515575983/job/29135933031?pr=231

Didn't want to dig too deep so removing it now to unblock build.
---
 Dockerfile | 26 --------------------------
 1 file changed, 26 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index fb49b93..fc82b3f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -158,20 +158,6 @@ RUN curl -L https://github.com/shenwei356/csvtk/releases/download/v0.30.0/csvtk_
 # Download seqkit
 RUN curl -L https://github.com/shenwei356/seqkit/releases/download/v2.2.0/seqkit_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin
 
-# Download gofasta (for ncov/Pangolin)
-# NOTE: Running this program requires support for emulation on the Docker host
-# if the processor architecture is not amd64.
-# TODO: Build from source to avoid emulation. Instructions: https://github.com/virus-evolution/gofasta/tree/v0.0.6#installation
-RUN curl -fsSL https://github.com/virus-evolution/gofasta/releases/download/v0.0.6/gofasta-linux-amd64 \
-  -o /final/bin/gofasta
-
-# Download minimap2 (for ncov/Pangolin)
-# NOTE: Running this program requires support for emulation on the Docker host
-# if the processor architecture is not amd64.
-# TODO: Build from source to avoid emulation. Instructions: https://github.com/lh3/minimap2/tree/v2.24#install
-RUN curl -fsSL https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 \
-  | tar xjvpf - --no-same-owner --strip-components=1 -C /final/bin minimap2-2.24_x64-linux/minimap2
-
 
 # 3. Add unpinned programs
 
@@ -269,15 +255,6 @@ RUN pip3 install google-cloud-storage==2.7.0
 # Install epiweeks (for ncov)
 RUN pip3 install epiweeks==2.1.2
 
-# Install Pangolin and PangoLEARN + deps (for ncov)
-# The cov-lineages projects aren't available on PyPI, so install via git URLs.
-RUN pip3 install git+https://github.com/cov-lineages/pangolin.git@v3.1.17
-RUN pip3 install git+https://github.com/cov-lineages/pangoLEARN.git@2021-12-06
-RUN pip3 install git+https://github.com/cov-lineages/scorpio.git@v0.3.16
-RUN pip3 install git+https://github.com/cov-lineages/constellations.git@v0.1.1
-RUN pip3 install git+https://github.com/cov-lineages/pango-designation.git@19d9a537b9
-RUN pip3 install pysam==0.19.1
-
 # Install pango_aliasor (for forecasts-ncov)
 RUN pip3 install pango_aliasor==0.3.0
 
@@ -446,12 +423,9 @@ COPY --from=builder-target-platform \
     /usr/local/bin/aws \
     /usr/local/bin/envdir \
     /usr/local/bin/nextstrain \
-    /usr/local/bin/pangolin \
-    /usr/local/bin/pangolearn.smk \
     /usr/local/bin/pathogen-distance \
     /usr/local/bin/pathogen-embed \
     /usr/local/bin/pathogen-cluster \
-    /usr/local/bin/scorpio \
     /usr/local/bin/snakemake \
     /usr/local/bin/treetime \
     /usr/local/bin/