anchor.diff:  
   ENV DEBIAN_FRONTEND=noninteractive
   
  -RUN apt-get update && apt-get install -y gcc g++ perl python3 automake make \
  -                                       wget git curl libdb-dev \
  -                                       zlib1g-dev bzip2 libncurses5-dev \
  -				       texlive-latex-base \
  -                                       default-jre \
  -				       python3-pip python3-dev python3-setuptools python3-distutils \
  -				       gfortran \
  -				       build-essential libghc-zlib-dev libncurses-dev libbz2-dev liblzma-dev libpcre3-dev libxml2-dev \
  -				       libblas-dev gfortran git unzip ftp libzmq3-dev nano ftp fort77 libreadline-dev \
  -				       libcurl4-openssl-dev libx11-dev libxt-dev \
  -				       x11-common libcairo2-dev libpng-dev libreadline-dev libjpeg-dev pkg-config libtbb-dev \
  -					   cmake rsync libssl-dev tzdata \
  -	&& apt-get clean
  -
  -
  +RUN apt-get -qq update && apt-get -qq -y install \
  +    automake \
  +    build-essential \
  +    bzip2 \
  +    cmake \
  +    curl \
  +    default-jre \
  +    fort77 \
  +    ftp \
  +    g++ \
  +    gcc \
  +    gfortran \
  +    git \
  +    libblas-dev \
  +    libbz2-dev \
  +    libcairo2-dev \
  +    libcurl4-openssl-dev \
  +    libdb-dev \
  +    libghc-zlib-dev \
  +    libjpeg-dev \
  +    liblzma-dev \
  +    libncurses-dev \
  +    libncurses5-dev \
  +    libpcre3-dev \
  +    libpng-dev \
  +    libreadline-dev \
  +    libreadline-dev \
  +    libssl-dev \
  +    libtbb-dev \
  +    libx11-dev \
  +    libxml2-dev \
  +    libxt-dev \
  +    libzmq3-dev \
  +    make \
  +    nano \
  +    perl \
  +    pkg-config \
  +    python3 \
  +    python3-dev \
  +    python3-distutils \
  +    python3-pip \
  +    python3-setuptools \
  +    rsync \
  +    texlive-latex-base \
  +    tzdata \
  +    unzip \
  +    wget \
  +    x11-common \
  +    zlib1g-dev
   
   
   ## Perl stuff
  
positive.code: RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat -P $BIN && \
      chmod a+x $BIN/blat
  
  
  ####
  ## Picard tools
  
  WORKDIR $SRC
  RUN wget https://github.com/broadinstitute/picard/releases/download/2.23.3/picard.jar
  ENV PICARD_HOME $SRC
  
  ####
  ## GATK4 installation
  
  WORKDIR $SRC
  
  ENV GATK_VERSION=4.1.8.0
  RUN wget https://github.com/broadinstitute/gatk/releases/download/${GATK_VERSION}/gatk-${GATK_VERSION}.zip && \
      unzip gatk-${GATK_VERSION}.zip
  
negative.code: ENV PATH=${TRINITY_HOME}:${PATH}
  
  
  # some cleanup
  WORKDIR $SRC
  RUN rm -r ${R_VERSION} *.tar.gz *.zip *.bz2
  
  RUN apt-get -qq -y remove git && \
      apt-get -qq -y autoremove && \
      apt-get clean && \
      rm -rf /var/lib/apt/lists/* /var/log/dpkg.log
  
  ################################################
  ## be sure this is last!
  COPY Dockerfile $SRC/Dockerfile.$TRINITY_VERSION
  
  