anchor.diff:  RUN \
       git clone https://github.com/RNAcentral/auto-traveler.git $AUTO_TRAVELER_PY && \
       cd $AUTO_TRAVELER_PY && \
  -    git checkout python3-update
  +    git checkout single-entry-point && \
  +    git pull origin single-entry-point && \
  +    /usr/local/bin/pip3 install -r requirements.txt
   
   WORKDIR $AUTO_TRAVELER_PY
  -ARG CACHE_DATE=not_a_date
  -RUN \
  -    /usr/local/bin/pip install -r requirements.txt && \
  -    python3 ./auto-traveler.py rrna setup && \
  -    python3 utils/generate_model_info.py --cm-library data/cms
  +RUN python3 ./auto-traveler.py setup
   
   ENV PATH="$AUTO_TRAVELER_PY:$PATH"
   
  
positive.code: # Setup environmental variables
  ENV PERL5LIB="$RIBODIR:$EPNOPTDIR:$EPNOFILEDIR:$EPNTESTDIR:/usr/bin/env:$PERL5LIB"
  
  ENV RIBOINFERNALDIR="$RNA/infernal-1.1.2/bin" RIBOEASELDIR="$RNA/infernal-1.1.2/bin"
  ENV DATAPATH="$RNA_STRUCTURE/data_tables/"
  
  
negative.code: # Copy everything that auto-traveler needs into place. This mimicks the same
  # directory structure as the auto-traveler Dockerfile.
  WORKDIR /
  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"
  
  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 /
  