anchor.diff:  RUN tar -xzf augustus-3.3.1.tar.gz
   RUN echo 'COMGENEPRED = true' >> augustus-3.3.1/common.mk
   RUN cd augustus-3.3.1 && make
  -#### Unsure pathing ####
  -# RUN PATH=$PATH:~/augustus/bin:~/augustus/scripts
  -# RUN export AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/
   RUN cd augustus-3.3.1/src && make clean all
  +RUN cd augustus-3.3.1/auxprogs/homGeneMapping/src && sed 's/# BOOST = true/BOOST = true/g' -i Makefile && sed 's/# SQLITE = true/SQLITE = true/g' -i Makefile
  +RUN cd augustus-3.3.1/auxprogs && make clean && make
   
   # HDF5
   RUN wget http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz
   RUN tar xzf hdf5-1.10.1.tar.gz
  -RUN cd hdf5-1.10.1 && ./configure --prefix=/usr
  +RUN cd hdf5-1.10.1 && ./configure --enable-cxx --prefix=/usr 
   RUN cd hdf5-1.10.1 && make && make install
   # sonLib
   RUN git clone git://github.com/benedictpaten/sonLib.git
  
positive.code: RUN git clone git://github.com/glennhickey/hal.git
  RUN /bin/bash -c "pushd sonLib && make && popd"
  RUN cd hal && make
  #### Unsure pathing ####
  # RUN export PATH=hal/bin:${PATH} 
  
  # LibBigWig
  RUN git clone https://github.com/dpryan79/libBigWig.git
  
negative.code: RUN apt-get install git -y
  
  # Kent
  RUN for i in wigToBigWig faToTwoBit gff3ToGenePred genePredToBed genePredToFakePsl bamToPsl transMapPslToGenePred pslPosTarget axtChain chainMergeSort pslMap pslRecalcMatch pslMapPostChain gtfToGenePred genePredToGtf bedtools blat pslCheck pslCDnaFilter clusterGenes pslToBigPsl bedSort bedToBigBed ; do wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/$i -O /bin/$i ; chmod +x /bin/$i ; done
  
  # bedtools
  RUN apt-get install bedtools -y
  