reduce docker image size by almost half

docker/Dockerfile

@@ -1,30 +1,38 @@
-FROM debian:stable
+ARG DEBIAN_FRONTEND=noninteractive
+FROM python:3.6 as builder
 
 LABEL maintainer "Manuel Muñoz <manuel.munoz@crg.eu>" \
       version "1.0" \
       description "Docker image for PyHIST"
 
 # Install necessary tools
-RUN export DEBIAN_FRONTEND=noninteractive && \
-	apt-get update --fix-missing -qq && \
+RUN apt-get update -qq && \
 	apt-get install -y -q \
-	build-essential \
 	libgl1-mesa-glx \
-	python3.6 \
-	python3-pip \
-	openslide-tools \
-	python3-openslide && \
-	pip3 install pandas opencv-python
+	openslide-tools
 
 # Copy PyHIST to container
-WORKDIR /pyhist
-COPY pyhist* /pyhist/
-ADD src /pyhist/src
+WORKDIR /opt/pyhist
+RUN python -m venv venv \
+	&& ./venv/bin/python -m pip install --no-cache-dir -U pip setuptools wheel \
+	&& ./venv/bin/python -m pip install --no-cache-dir pandas opencv-python openslide-python
+ENV PATH="/opt/pyhist/venv/bin:$PATH"
+COPY pyhist* .
+COPY src src
 
 # Compile segmentation algorithm
 RUN cd src/graph_segmentation/ && \
 	make && \
 	chmod 755 segment
 
-# Entrypoing
+# Build final, slim image.
+FROM python:3.6-slim
+RUN apt-get update -qq \
+	&& apt-get install -y -q \
+		libgl1-mesa-glx \
+		libopenslide0 \
+	&& rm -rf /var/lib/apt/lists/*
+WORKDIR /opt/pyhist
+COPY --from=builder /opt/pyhist .
+ENV PATH="/opt/pyhist/venv/bin:$PATH"
 ENTRYPOINT ["python3", "pyhist.py"]