From a8fa8625d5e8a19628d441c6a974664150224cd5 Mon Sep 17 00:00:00 2001
From: Stephen Beckstrom-Sternberg <Stephen.Beckstrom-Sternberg@azdhs.gov>
Date: Fri, 10 Nov 2023 14:36:35 -0700
Subject: [PATCH] Update Dockerfile

Save copy of Dockerfile in /github/workflows
---
 .github/workflows/Dockerfile | 56 ++++++++++++++++++++++++++++++------
 1 file changed, 48 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/Dockerfile b/.github/workflows/Dockerfile
index 27b1434..4d58470 100644
--- a/.github/workflows/Dockerfile
+++ b/.github/workflows/Dockerfile
@@ -1,12 +1,52 @@
-FROM python:3.11.6-alpine
+ARG HEATCLUSTER_VER="0.4.12"
 
-COPY .github /app/
-COPY assets /app/
-COPY test /app/
-COPY HeatCluster.py LICENSE README.md /app/
+FROM ubuntu:jammy as app
+USER root
 
-WORKDIR /app
+# re-instantiating for the app build layer if using ARG as a global variable above
+ARG HEATCLUSTER_VER
 
-RUN HeatCluster.py
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="3"
+LABEL software="HeatCluster"
+LABEL software.version="${HEATCLUSTER_VER}"
+LABEL description="This software produces a heatmap for a SNP matrix"
+LABEL website="https://github.com/DrB-S/HeatCluster"
+LABEL license="https://github.com/DrB-S/HeatCluster/blob/master/LICENSE"
+LABEL name="heatcluster/${HEATCLUSTER_VER}"
+LABEL maintainer="Stephen Beckstrom-Sternberg"
+LABEL maintainer.email="stephen.beckstrom-sternberg@azdhs.gov"
 
-CMD 
+# Install Python and pip
+RUN apt-get update && apt-get install -y --no-install-recommends \
+apt-utils python3 python3-pip && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Install Python dependencies
+RUN pip3 install pandas numpy pathlib seaborn matplotlib scipy 
+
+# Set /data as working dir
+RUN mkdir /data
+WORKDIR /data
+
+RUN echo "installing heatcluster" && echo
+
+COPY . .
+
+RUN echo && echo && ls -latr /data && echo
+
+# 'ENV' instructions set environment variables that persist from the build into the resulting image
+# Use for e.g. $PATH and locale settings for compatibility with Singularity
+ENV PATH="/heatcluster-${HEATCLUSTER_VER}/bin:$PATH" \
+ LC_ALL=C
+
+FROM app as test
+
+# print help and version info
+# Mostly this ensures the tool of choice is in path and is executable
+RUN echo && echo "Show heatcluster help file and program version number:  " && echo && \
+python3 HeatCluster.py --help && \
+python3 HeatCluster.py --version
+ 
+ RUN echo && echo "Run a test matrix thru the program" && \
+python3 HeatCluster.py -i test/snp-dists.txt && echo