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