anchor.diff:  # Copy everything that auto-traveler needs into place. This mimicks the same
   # directory structure as the auto-traveler Dockerfile.
   WORKDIR /
  -ENV RIBODIR="$RNA/ribotyper-v1"
  +ENV RIBODIR="$RNA/ribovore"
   ENV EPNOPTDIR="$RNA/epn-options"
   ENV EPNOFILEDIR="$RNA/epn-ofile"
   ENV EPNTESTDIR="$RNA/epn-test"
   ENV JIFFY_SCRIPTS="$RNA/jiffy-infernal-hmmer-scripts"
   ENV TRAVELER="$RNA/traveler"
   ENV RNA_STRUCTURE="$RNA/RNAstructure"
  -ENV RSCAPE="$RNA/rscape_v1.2.3"
  +ENV RSCAPE="$RNA/rscape"
   
  -COPY --from=rnacentral/auto-traveler:single-entry-point $EPNOFILEDIR $EPNOFILEDIR
  -COPY --from=rnacentral/auto-traveler:single-entry-point $EPNOPTDIR $EPNOPTDIR
  -COPY --from=rnacentral/auto-traveler:single-entry-point $EPNTESTDIR $EPNTESTDIR
  -COPY --from=rnacentral/auto-traveler:single-entry-point $RIBODIR $RIBODIR
  -COPY --from=rnacentral/auto-traveler:single-entry-point $JIFFY_SCRIPTS $JIFFY_SCRIPTS
  -COPY --from=rnacentral/auto-traveler:single-entry-point $TRAVELER $TRAVELER
  -COPY --from=rnacentral/auto-traveler:single-entry-point $RNA_STRUCTURE $RNA_STRUCTURE
  -COPY --from=rnacentral/auto-traveler:single-entry-point $RSCAPE $RSCAPE
  +COPY --from=rnacentral/auto-traveler:dev $EPNOFILEDIR $EPNOFILEDIR
  +COPY --from=rnacentral/auto-traveler:dev $EPNOPTDIR $EPNOPTDIR
  +COPY --from=rnacentral/auto-traveler:dev $EPNTESTDIR $EPNTESTDIR
  +COPY --from=rnacentral/auto-traveler:dev $RIBODIR $RIBODIR
  +COPY --from=rnacentral/auto-traveler:dev $JIFFY_SCRIPTS $JIFFY_SCRIPTS
  +COPY --from=rnacentral/auto-traveler:dev $TRAVELER $TRAVELER
  +COPY --from=rnacentral/auto-traveler:dev $RNA_STRUCTURE $RNA_STRUCTURE
  +COPY --from=rnacentral/auto-traveler:dev $RSCAPE $RSCAPE
   
   ENV PATH="$JIFFY_SCRIPTS:$PATH"
   ENV PATH="$AUTO_TRAVELER_PY:$PATH"
   ENV PATH="$RSCAPE/bin:$PATH"
   ENV PATH="$RIBODIR:$PATH"
   ENV PATH="$RNA_STRUCTURE/exe:$PATH"
  +ENV PATH="$RNA/infernal-1.1.2/bin:$PATH"
   
   # Install auto-traveler and related data
   WORKDIR /
  
positive.code:     rsync \
      sbcl \
      tar \
      unzip \
      wget
  
  
negative.code: RUN \
      git clone https://github.com/RNAcentral/auto-traveler.git $AUTO_TRAVELER_PY && \
      cd $AUTO_TRAVELER_PY && \
      git checkout single-entry-point && \
      git pull origin single-entry-point && \
      /usr/local/bin/pip3 install -r requirements.txt
  
  WORKDIR $AUTO_TRAVELER_PY
  RUN python3 ./auto-traveler.py setup
  
  ENV PATH="$AUTO_TRAVELER_PY:$PATH"
  
  