anchor.diff:  # 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 nasgroup pipeman
  +RUN usermod -G ngsgroup pipeman
   
   #------------------ INSTALL PIPELINE COMPONENTS --------------------------
   
   #---------------------- Sequence Aligners --------------------------------
  -# 1)*novoalign*  2)bowtie, 3)bwa, 4) stampy
  +# Aligner options: 1)*novoalign*  2)bowtie, 3)stampy, 4)bwa
  +
  +# + novoalign
  +ADD novocraftV3.02.06.Linux3.0.tar.gz /usr/local/pipeline/novocraftV3.02.06.Linux3.0
  +RUN sed  -i '$aPATH=${PATH}:/usr/local/pipeline/novocraftV3.02.06.Linux3.0/novocraft' /home/pipeman/.bashrc
   
   # + bowtie
   RUN wget -O /tmp/bowtie2-2.2.3-linux-x86_64.zip http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.3/bowtie2-2.2.3-linux-x86_64.zip/download \
  
positive.code: # + GATK (see licence, and registration) 
  # use ADD to copy the downloaded GATK binary from <buildcontext_path>/GenomeAnalysisTK-3.1-1.tar.bz2 to the /tmp dir in the container
  # NOTE: ADD automatically unpacks compressed files
  ADD GenomeAnalysisTK-3.1-1.tar.bz2 /usr/local/pipeline/GenomeAnalysisTK-3.1-1.tar.bz2 
  RUN chmod 755 /usr/local/pipeline/GenomeAnalysisTK-3.1-1.tar.bz2 \
      && chown -R pipeman:ngsgroup /usr/local/pipeline/GenomeAnalysisTK-3.1-1.tar.bz2 \
      && sed -i '$aCLASSPATH=.:${CLASSPATH}:/usr/local/pipeline/GenomeAnalysisTK-3.1-1.tar.bz2/GenomeAnalysisTK.jar' /home/pipeman/.bashrc
  
  # + BEDtools
  RUN cd /usr/local/pipeline \
  
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
  