anchor.diff:  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 \
  -                    last-align libboost-iostreams-dev libgsl0ldbl \
  -                    libcolamd2.8.0 libstdc++6 --yes --force-yes
  -RUN ln -fs /usr/bin/fasttree /usr/bin/FastTree && \
  -    cpanm --force SVG Carp Storable Bio::SearchIO List::Util \
  -                    Getopt::Long && \
  -    rm -rf /root/.cpanm/work/
  +                    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 (binaries)
  +# 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
  +    rm -rf augustus/docs && \
  +    cd augustus && \
  +    make -j2
   
   #
   # Install GenomeTools (most recent git master)
  
positive.code:     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
  
negative.code: #
  ADD ./ABACAS2 /opt/ABACAS2
  
  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/:$PERL5LIB
  ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/augustus/bin:/opt/augustus/scripts:/opt/ORTHOMCLV1.4:/opt/RATT:/opt/ABACAS2:$PATH
  