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: 
  #------------------------------------------------------------------------
  # 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: 
  
  
  # Cleanup the temp dir
  RUN rm -rf /tmp/*
  
  
  
  