anchor.diff:  # Results Folder by projetc and sample
   
   
  -# Create a pipeline user
  +
  +#------------------------------------------------------------------------
  +# USER SETUP
  +#------------------------------------------------------------------------
  +# Create a pipeline user:pipeman and group:ngsgroup
   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 --------------------------
  +
  +#------------------------------------------------------------------------
  +#***************** INSTALL PIPELINE COMPONENTS **************************
  +#------------------------------------------------------------------------
   
   #---------------------- Sequence Aligners --------------------------------
   # Aligner options: 1)*novoalign*  2)bowtie, 3)stampy, 4)bwa
  
positive.code: RUN apt-get install -y git-core wget unzip
  RUN apt-get install -y zlib1g-dev libncurses5-dev
  
  # Mount a volume external to the container to store stuff that needs to persist
  VOLUME ["/media/ngsEasy/data/reference"] # reference indexed genomes
  
  # Set up file structure
  # RUN mkdir /pipeln
  # FASTQ Staging Area
  #RUN bash mkdir /pipeln/staging/ ## !!! this should be in an external volume !!!!
  
negative.code: #########################################################################
  # -- Author: Amos Folarin                                               #
  # -- Author: Stephen J Newhouse                                         #
  # -- Organisation: KCL/SLaM                                             #
  # -- Email: amosfolarin@gmail.com                                       #
  #########################################################################
  