anchor.diff:  
   
   # Cleanup the temp dir
  -RUN rm -rf /tmp/*
  +# RUN rm -rf /tmp/*
   
   
   
  
positive.code: # 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
  
  #------------------ INSTALL PIPELINE COMPONENTS --------------------------
  
  
negative.code: # 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
  