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
   
   #------------------ INSTALL PIPELINE COMPONENTS --------------------------
   
  
positive.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 \
      && sed -i '$aCLASSPATH=.:${CLASSPATH}:/usr/local/pipeline/GenomeAnalysisTK-3.1-1.tar.bz2/GenomeAnalysisTK.jar' /home/pipeman/.bashrc
  
  # + BEDtools
  
negative.code: 
  # + Picard
  RUN wget -O /tmp/picard-tools-1.115.zip http://sourceforge.net/projects/picard/files/picard-tools/1.115/picard-tools-1.115.zip/download \
      && mkdir /usr/local/pipeline/picardtools \
      && unzip /tmp/picard-tools-1.115.zip -d /usr/local/pipeline/picardtools/ \
      && chown -R pipeman:ngsgroup /usr/local/pipeline/picardtools \
      && sed -i '$aCLASSPATH=.:${CLASSPATH}:/usr/local/pipeline/picardtools/picard-tools-1.115' /home/pipeman/.bashrc
  