anchor.diff:  # Use baseimage-docker's init system.
   CMD ["/sbin/my_init"]
   
  -MAINTAINER Simon Frost <sdwfrost@gmail.com>
  +MAINTAINER Simon Frost <sdwfrost@gmail.com> and Mukarram Hossain <mukarram819@gmail.com>
   
   ## Set a default user. Available via runtime flag `--user docker`
   RUN useradd docker \
  
positive.code: 	make install && \
  	rm /home/docker/programs/hmmer-3.1b2.tar.gz && \
  	rm -rf /home/docker/programs/hmmer-3.1b2
  
  # Install Pipelign
  RUN cd /home/docker/programs && \
  	git clone http://github.com/asmmhossain/pipelign.git && \
  	cd pipelign && \
  	chmod +x ./Pipelign.py && \
  	cp ./Pipelign.py /usr/local/bin && \
  	rm -rf /home/docker/programs/pipelign
  
  # Clean up APT when done.
  RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
  
  VOLUME ["/home/docker"]
  
negative.code: 	mkdir build && \
  	cd build && \
  	cmake -DIQTREE_FLAGS=omp .. && \
  	make && \
  	cp iqtree-omp /usr/local/bin && \
  	rm -rf /home/docker/programs/IQ-TREE
  
  # Install MAFFT
  RUN cd /home/docker/programs && \
  	wget http://mafft.cbrc.jp/alignment/software/mafft-7.294-without-extensions-src.tgz && \
  	tar zxvf mafft-7.294-without-extensions-src.tgz && \
  	cd mafft-7.294-without-extensions/core && \
  	make clean && \
  	make && \
  	make install && \
  	rm /home/docker/programs/mafft-7.294-without-extensions-src.tgz && \
  	rm -rf /home/docker/programs/mafft-7.294-without-extensions
  
  # Install HMMER3
  RUN cd /home/docker/programs && \
  