anchor.diff:  ############################################################################################
   FROM base AS run
   
  -COPY --from=build /vg/bin/vg /vg/bin/vg
  -COPY --from=build /vg/scripts /vg/scripts
  +RUN echo run > /stage.txt
  +
  +RUN ls -lah /vg || echo "No vg directory exists yet"
  +
  +COPY --from=build /vg/bin/vg /vg/bin/
  +COPY --from=build /vg/scripts /vg/
  +
  +RUN ls -lah /vg || echo "No vg directory exists yet"
   
   # Install packages which toil-vg needs to be available inside the image, for pipes
   # TODO: which of these can be removed?
   # Make sure to clean so we don't ship old apt package indexes in our Docker.
  -RUN apt-get -qq -y update && \
  +RUN ls -lah /vg && \
  +    apt-get -qq -y update && \
       apt-get -qq -y upgrade && \
       apt-get -qq -y install \
       curl \
  
positive.code:     fontconfig-config \
      && apt-get -qq -y clean
  
  WORKDIR /vg
  ENV PATH /vg/bin:$PATH
  
  
  
negative.code: # Since we build and run protoc, we need ivybridge or later to actually build the container.
  # But we then don't depend on the build host's architecture
  RUN sed -i s/march=native/march=ivybridge/ deps/sdsl-lite/CMakeLists.txt
  RUN make get-deps && . ./source_me.sh && env && CXXFLAGS=" -march=ivybridge " make -j$(nproc) && make static && strip bin/vg
  
  ENV PATH /vg/bin:$PATH
  
  ############################################################################################
  FROM build AS test
  
  RUN echo test > /stage.txt
  
  # The test need BWA
  COPY --from=quay.io/ucsc_cgl/bwa:0.7.15--a17c6544342330f6ea7a23a37d23273ab1c52d21 /usr/local/bin/bwa /usr/local/bin/bwa
  