anchor.diff:      python setup.py install && \
       cd / && \
       rm -rf /opt/genometools-master*
  -
  -#
  -# Install ARAGORN
  -# (this is done from source instead of Debian b/c Debian-built version hangs)
  -#
  -ADD http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.36.tgz /opt/aragorn.tgz
  -RUN cd /opt && \
  -    tar -xvf aragorn.tgz && \
  -    mv aragorn1* aragorn && \
  -    cd aragorn && \
  -    gcc -o aragorn aragorn*.c
   
   #
   # Install and configure OrthoMCL
  
positive.code: #
  ADD ./ABACAS2 /opt/ABACAS2
  
  #
  # install gff3 to EMBL converter
  #
  ADD https://github.com/sanger-pathogens/gff3toembl/archive/master.zip /opt/gff3toembl-master.zip
  RUN cd /opt && \
      unzip gff3toembl-master.zip && \
      cd /opt/gff3toembl-master && \
      python setup.py install
  
  ENV AUGUSTUS_CONFIG_PATH /opt/augustus/config
  ENV RATT_HOME /opt/RATT
  ENV GT_RETAINIDS yes
  ENV PERL5LIB /opt/ORTHOMCLV1.4/:/opt/RATT/:/opt/ABACAS2/:$PERL5LIB
  ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/augustus/bin:/opt/augustus/scripts:/opt/ORTHOMCLV1.4:/opt/RATT:/opt/ABACAS2:/opt/aragorn:$PATH
  
negative.code: RUN apt-get install build-essential hmmer lua5.1 ncbi-blast+ blast2 snap \
                      unzip cpanminus mummer infernal exonerate mafft fasttree \
                      circos libsvg-perl libgd-svg-perl python-setuptools \
                      libc6-i386 lib32stdc++6 lib32gcc1 netcat genometools \
                      last-align libboost-iostreams-dev libgsl0ldbl libgsl0-dev \
                      libcolamd2.9.1 liblpsolve55-dev libstdc++6 aragorn tantan \
                      libstorable-perl libbio-perl-perl libsqlite3-dev \
                       --yes --force-yes
  RUN ln -fs /usr/bin/fasttree /usr/bin/FastTree
  
  #
  # Install AUGUSTUS
  #
  ADD http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.tar.gz /opt/augustus-3.2.tar.gz
  RUN cd /opt && \
      tar -xzvf augustus* && \
      rm -rf *.tar.gz && \
      mv augustus* augustus && \
      rm -rf augustus/docs && \
      cd augustus && \
      make -j2
  
  #
  # Install GenomeTools (most recent git master)
  