anchor.diff:  # sambamba
   RUN wget https://github.com/biod/sambamba/releases/download/v0.6.7/sambamba_v0.6.7_linux.tar.bz2
   RUN tar xvjf sambamba_v0.6.7_linux.tar.bz2
  +
  +RUN apt-get install python-pip -y
  +# toil
  +RUN pip install bd2k-python-lib 
  +
  +RUN pip install pyfasta 
  +
  +ENV PATH=$PATH:/augustus-3.3.1/bin:/augustus-3.3.1/scripts:/hal/bin:/WiggleTools/bin:/
  +ENV AUGUSTUS_CONFIG_PATH=/augustus-3.3.1/scripts
  +ENV LD_LIBRARY_PATH=/libBigWig:$LD_LIBRARY_PATH
  
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 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
  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 --enable-cxx --prefix=/usr 
  RUN cd hdf5-1.10.1 && make && make install
  # sonLib
  RUN git clone git://github.com/benedictpaten/sonLib.git
  