anchor.diff:  USER root
   RUN pip install git+https://github.com/FRED-2/Fred2
   RUN pip install docopt numpy pyomo pysam matplotlib tables  pandas  future 
  +
  +# FROM https://hub.docker.com/r/ljishen/samtools/~/dockerfile/
  +ENV SAMTOOLS_VERSION 1.3.1
  +WORKDIR /root
  +RUN mkdir samtools \
  +    && curl -fsSL https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2 \
  +        | tar -jxC samtools --strip-components=1
  +
  +WORKDIR /root/samtools
  +RUN ./configure && make all all-htslib && make install install-htslib
   
   # FRED 2  
   RUN apt-get update && apt-get install -y vim software-properties-common \
  
positive.code: 
  USER root
  RUN apt-get update && apt-get install -y \
  curl g++ gawk git m4 make patch ruby tcl  libarchive-zip-perl  libdbd-mysql-perl  libjson-perl cmake
  
  RUN apt-get install -y build-essential default-jdk gfortran texinfo unzip samtools \
  	libbz2-dev libcurl4-openssl-dev libexpat-dev libncurses-dev zlib1g-dev libmysqlclient-dev
  
negative.code: 
  ENV PATH /home/linuxbrew/Cancer_Epitopes_CSHL/src:/usr/local/bin/OptiType/:$PATH
  
  # Clean Up
  RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
  
  #USER linuxbrew
  RUN cd /home/linuxbrew && git clone https://github.com/NCBI-Hackathons/Cancer_Epitopes_CSHL.git
  