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: 
  # + 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
  
negative.code: 
  
  # Cleanup the temp dir
  # RUN rm -rf /tmp/*
  
  
  
  