anchor.diff:  # 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
   FROM ubuntu:trusty
  
positive.code: # Required basic stuff, make, gcc, wget etc
  RUN apt-get update
  RUN apt-get install -y gcc g++
  RUN apt-get install -y python
  RUN apt-get install -y make tabix
  RUN apt-get install -y git-core wget unzip
  RUN apt-get install -y zlib1g-dev libncurses5-dev
  
negative.code:     && chown -R pipeman:ngsgroup /usr/local/pipeline/bowtie2-2.2.3 \
      && sed  -i '$aPATH=${PATH}:/usr/local/pipeline/bowtie2-2.2.3' /home/pipeman/.bashrc 
  
  # + stampy (registration required, get compressed file and put in context dir for the build)
  ADD Stampy-latest.tgz /usr/local/pipeline/
  # (below) require to replace the -Wl flags for building in ubuntu, see stampy README file
  RUN sed -i 's/-Wl//' /usr/local/pipeline/stampy-1.0.23/makefile \
      && chmod -R 755 /usr/local/pipeline/stampy-1.0.23 \
      && cd /usr/local/pipeline/stampy-1.0.23 && make \
      && chown -R pipeman:ngsgroup /usr/local/pipeline/stampy-1.0.23 \
      && sed -i '$aPATH=${PATH}:/usr/local/pipeline/stampy-1.0.23' /home/pipeman/.bashrc
  
  # stampy install alternative if registration already completed -- seems to have a static download page.
  #RUN wget Stampy-latest.tgz -O http://www.well.ox.ac.uk/bioinformatics/Software/Stampy-latest.tgz
  #    && tar xzvf Stampy-latest.tgz -C /usr/local/pipeline/
  #    && sed -i "$aPATH=${PATH}:"$(readlink -f stampy-*) /home/pipeman/.bashrc
  
  #---------------------- SAM/BAM Processing -------------------------------
  # + VCFtools: http://vcftools.sourceforge.net/index.html
  