# Build the base image.  This is the starting point for both the build
# stage and the final stage.
# the "AS base" names the image within the Dockerfile
FROM debian:10-slim AS base
MAINTAINER Peter Amstutz <peter.amstutz@curii.com>

# Install libz, because the bwa binary will depend on it.
# As it happens, this already included in the base Debian distribution
# because lots of things use libz specifically, but it is good practice
# to explicitly declare that we need it.
RUN apt-get update -qy
RUN apt-get install -qy zlib1g


# This is the builder image.  It has the commands to install the
# prerequisites and then build the bwa binary.
FROM base as builder
RUN apt-get install -qy build-essential wget unzip zlib1g-dev

# Install BWA 07.7.17
RUN wget https://github.com/lh3/bwa/archive/v0.7.17.zip
RUN unzip v0.7.17
RUN cd bwa-0.7.17 && \
    make && \
    cp bwa /usr/bin


# Build the final image.  It starts from base (where we ensured that
# libz was installed) and then copies the bwa binary from the builder
# image.  The result is the final image only has the compiled bwa
# binary, but not the clutter from build-essentials or from compiling
# the program.
FROM base AS final

# This is the key command, we use the COPY command described earlier,
# but instead of copying from the host, the --from option copies from
# the builder image.
COPY --from=builder /usr/bin/bwa /usr/bin/bwa