anchor.diff:  #########################################################################
   # -- Author: Amos Folarin                                               #
  +# -- Author: Stephen J Newhouse                                         #
   # -- Organisation: KCL/SLaM                                             #
   # -- Email: amosfolarin@gmail.com                                       #
   #########################################################################
  
positive.code: 
  #------------------------------------------------------------------------
  # This dockerfile should build the enviroment required for the ngs 
  # pipeline. Of course you can just get the docker container pre-built
  # from our repository
  #------------------------------------------------------------------------
  
  #------------------------------------------------------------------------
  # BUILDING THE DOCKER IMAGE:
  # download this Dockerfile into a clean directory e.g. build_dir
  # Due to licencing, you should get your own versions of:
  # Download the compressed files into the build_dir, then edit the lines
  # of the Dockerfile to the correct versions of ANNOVAR and GATK
  #   * novoalign http://www.novocraft.com/
  #   * Stampy http://www.well.ox.ac.uk/project-stampy
  #   * GATK https://www.broadinstitute.org/gatk/
  #   * ANNOVAR http://www.openbioinformatics.org/annovar/
  #
  # $ cd build_dir
  # $ sudo docker build --tag <repo-name:tag> .
  #------------------------------------------------------------------------
  
  # Base image will be Trusty
  
negative.code: RUN apt-get install -y git-core wget unzip
  RUN apt-get install -y zlib1g-dev libncurses5-dev
  
  
  #------------------------------------------------------------------------
  # VOLUMES and VOLUME CONTAINERS
  # Mount a volume external to the container to store stuff that needs to persist
  #------------------------------------------------------------------------
  # VOLUME ["/media/ngsEasy/data/reference"]
  # VOLUME ["/media/ngsEasy/data/reference"]
  # Shared data should sit in a Volume Container, 
  
  # RUN mkdir /pipeln
  # FASTQ Staging Area
  #RUN bash mkdir /pipeln/staging/ ## !!! this should be in an external volume !!!!
  