anchor.diff:  #
   # 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 && \
  
positive.code:     mv augustus* augustus && \
      cd augustus && \
      make
  
  #
  # Install Git
  #
  RUN apt-get install unzip --yes --force-yes
  
  #
  # Install GenomeTools (most recent git master)
  
negative.code: ADD ./RATT /opt/RATT
  
  #
  # 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
  
  # TODO: add ABACAS
  
  
  # TODO: add ref species models etc.
  # ADD fgram_base /opt/augustus/config/species/
  
  ENV AUGUSTUS_CONFIG_PATH /opt/augustus/config
  