From 76e7cd8233d0cfeeeefe020aafc1a4c6073e6940 Mon Sep 17 00:00:00 2001
From: James Baker <59581582+jtb324@users.noreply.github.com>
Date: Sat, 27 Sep 2025 15:00:44 -0500
Subject: [PATCH] Update Dockerfile

IBDReduce was left out of docker at some point. This change adds it back
---
 Dockerfile | 38 ++++++++++++++++++++++++++++++++++----
 1 file changed, 34 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ed03027..5f45643 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,5 @@
-FROM ubuntu:22.04 AS build-container
+# This build container image ends up about 3GB
+FROM ubuntu:22.04 AS ibdmap-build-container
 
 RUN rm /bin/sh && ln -s /bin/bash /bin/sh
 
@@ -31,10 +32,31 @@ RUN cmake -DCMAKE_BUILD_TYPE=Release ..
 # It'd be smart to detect system threads, but alas
 RUN make -j4
 
+# We need to install the necessary python dependencies
+FROM ubuntu:22.04 AS ibdreduce-build-container
+
+RUN rm /bin/sh && ln -s /bin/bash /bin/sh
+
+# We need to install curl
+RUN apt-get update && \
+    apt-get install -y curl python3.11 python3.11-venv git && \
+    rm -rf /var/lib/apt/lists/* 
+
+WORKDIR /app
+
+COPY IBDReduce/requirements.txt .
+
+RUN python3.11 -m venv ibdreduce_venv
+RUN . ibdreduce_venv/bin/activate
+
+ENV PATH="/app/ibdreduce_venv/bin:$PATH"
+RUN pip3 install --upgrade pip && pip3 install -r requirements.txt
+
 # Make a leaner run container without build dependencies
 # How much leaner is it? It's about 170MB
 FROM ubuntu:22.04 AS run-container
 
+RUN rm /bin/sh && ln -s /bin/bash /bin/sh
 # We seem to not need libboost-numpy at runtime?!
 RUN apt-get update &&  \
     apt-get -y dist-upgrade && \
@@ -43,10 +65,18 @@ RUN apt-get update &&  \
     libboost-numpy1.74.0 \
     libboost-python1.74.0 \
     liblapack3 \
-    libpython3.10
+    libpython3.10 \
+    python3.11 \
+    python3.11-venv
 
 WORKDIR /app
-COPY --from=build-container /app/build/ibdmap ibdmap
-COPY --from=build-container /app/build/*.so .
+COPY --from=ibdmap-build-container /app/build/ibdmap ibdmap
+COPY --from=ibdmap-build-container /app/build/*.so .
+COPY --from=ibdreduce-build-container /app/ibdreduce_venv ./ibdreduce_venv
+# need to copy the scripts required for ibdreduce
+COPY IBDReduce/geneticmap.py .
+COPY IBDReduce/ibdreduce_v3.py .
+
+ENV PATH="/app/ibdreduce_venv/bin:$PATH"
 
 ENV PATH="/app:$PATH"