anchor.diff:  ADD ./RATT /opt/RATT
   
   #
  -# clean up dev stuff
  +# clean up dev stuff (not strictly necessary)
   #
   RUN apt-get purge build-essential --yes --force-yes
  -RUN apt-get remove liblua5.1-0-dev \
  -                   lua-md5-dev lua-filesystem-dev lua-lpeg-dev libcairo2-dev \
  -                   zlib1g-dev libbz2-dev libexpat1-dev libncurses5-dev \
  -                   libsqlite3-dev libbam-dev libpango1.0-dev libtre-dev \
  -                   --yes --force-yes
  +RUN apt-get remove liblua5.1-0-dev lua-md5-dev lua-filesystem-dev lua-lpeg-dev \
  +                   libcairo2-dev zlib1g-dev libbz2-dev libexpat1-dev \
  +                   libncurses5-dev libsqlite3-dev libbam-dev libpango1.0-dev \
  +                   libtre-dev --yes --force-yes
   
   # TODO: add ABACAS
   
  -# TODO: add ref species
  +
  +# TODO: add ref species models etc.
   # ADD fgram_base /opt/augustus/config/species/
   
   ENV AUGUSTUS_CONFIG_PATH /opt/augustus/config
  
positive.code: #
  # Install OrthoMCL
  #
  RUN apt-get install bioperl libstorable-perl --yes --force-yes
  ADD http://www.orthomcl.org/common/downloads/software/unsupported/v1.4/ORTHOMCL_V1.4_mcl-02-063.tar /opt/omcl.tar
  RUN cd /opt && \
      tar -xvf omcl.tar && \
  
negative.code:     mv augustus* augustus && \
      cd augustus && \
      make
  
  #
  # Install GenomeTools (most recent git master)
  