anchor.diff:  ENV AUGUSTUS_CONFIG_PATH /opt/augustus/config
   ENV RATT_HOME /opt/RATT
   ENV GT_RETAINIDS yes
  -ENV PERL5LIB /opt/ORTHOMCLV1.4/:/opt/RATT:$PERL5LIB
  +ENV PERL5LIB /opt/ORTHOMCLV1.4/:/opt/RATT/:/opt/ABACAS2/:$PERL5LIB
   ENV PATH_TO_ORTHOMCL /opt/ORTHOMCLV1.4/
  -ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/augustus/bin:/opt/augustus/scripts:/opt/ORTHOMCLV1.4:/opt/RATT:/opt/ABACAS2
  +ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/augustus/bin:/opt/augustus/scripts:/opt/ORTHOMCLV1.4:/opt/RATT:/opt/ABACAS2:$PATH
  
positive.code:                     --yes --force-yes
  
  #
  # Install AUGUSTUS
  #
  ADD http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.0.3.tar.gz /opt/augustus-3.0.3.tar.gz
  RUN cd /opt && \
      tar -xzvf augustus* && \
      rm -rf *.tar.gz && \
      mv augustus* augustus && \
      cd augustus && \
      make
  
  #
  # Install GenomeTools (most recent git master)
  
negative.code:     rm -rf /opt/genometools-master*
  
  #
  # Add Perl deps (needed for OrthoMCL)
  #
  RUN cpanm --force Carp Bio::SearchIO List::Util Getopt::Long && \
      rm -rf /root/.cpanm/work/
  
  #
  