anchor.diff:  #########################################################################
   # -- Author: Amos Folarin                                               #
  +# -- Author: Stephen J Newhouse                                         #
   # -- Organisation: KCL/SLaM                                             #
   # -- Email: amosfolarin@gmail.com                                       #
   #########################################################################
  
positive.code: # Results Folder by projetc and sample
  
  
  # Create a pipeline user
  RUN useradd -m -s /bin/bash pipeman && cd /home/pipeman && echo "#bash config file for user pipeman" >> /home/pipeman/.bashrc
  RUN groupadd ngsgroup
  RUN usermod -G ngsgroup pipeman
  
  #------------------ INSTALL PIPELINE COMPONENTS --------------------------
  
  #---------------------- Sequence Aligners --------------------------------
  # Aligner options: 1)*novoalign*  2)bowtie, 3)stampy, 4)bwa
  
negative.code: 
  #------------------------------------------------------------------------
  # This dockerfile should build the enviroment required for the ngs 
  # pipeline. Alternatively you can just get the docker container pre-built
  # from our repository
  #------------------------------------------------------------------------
  
  #------------------------------------------------------------------------
  # BUILDING THE DOCKER IMAGE FROM THIS Dockerfile:
  # download this Dockerfile into a clean directory e.g. build_dir
  # Due to licencing, you should get your own versions of:
  # 
  # 1) 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/
  #
  # 2) $ cd build_dir
  # 3) $ sudo docker build --tag <repo-name:tag> .
  #------------------------------------------------------------------------
  
  # Base image will be Trusty
  