anchor.diff:  # Required basic stuff, make, gcc, wget etc
   RUN apt-get update
   RUN apt-get install -y gcc g++
  -RUN apt-get install -y python
  +RUN apt-get install -y python-dev
   RUN apt-get install -y make tabix
   RUN apt-get install -y git-core wget unzip
   RUN apt-get install -y zlib1g-dev libncurses5-dev
  
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: # 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 ngsgroup pipeman
  
  #------------------ INSTALL PIPELINE COMPONENTS --------------------------
  
  #---------------------- Sequence Aligners --------------------------------
  # 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 \
  