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
   
   #------------------ INSTALL PIPELINE COMPONENTS --------------------------
   
  
positive.code: 
  # + 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 \
      && unzip /tmp/bowtie2-2.2.3-linux-x86_64.zip -d /usr/lib/ \
      && sed  -i '$aPATH=${PATH}:/usr/lib/bowtie2-2.2.3' /home/pipeman/.bashrc 
  
  
  #---------------------- SAM/BAM Processing -------------------------------
  # + VCFtools: http://vcftools.sourceforge.net/index.html
  RUN wget -O /tmp/vcftools_0.1.12a.tar.gz http://sourceforge.net/projects/vcftools/files/vcftools_0.1.12a.tar.gz/download \
      && tar xzvf /tmp/vcftools_0.1.12a.tar.gz -C /usr/lib/  \
      && cd /usr/lib/vcftools_0.1.12a/ && make \
      && sed  -i '$aPATH=${PATH}:/usr/lib/vcftools_0.1.12a/bin' /home/pipeman/.bashrc
  
  
  
  
negative.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 \
      && sed -i '$aCLASSPATH=.:${CLASSPATH}:/usr/local/pipeline/GenomeAnalysisTK-3.1-1.tar.bz2/GenomeAnalysisTK.jar' /home/pipeman/.bashrc
  
  # + BEDtools
  RUN cd /usr/local/pipeline \
      && git clone https://github.com/arq5x/bedtools2.git \
      && cd bedtools2 && make clean && make all \
      && chown -R pipeman:ngsgroup /usr/local/pipeline/bedtools2 \
      && sed -i '$aPATH=${PATH}:/usr/local/pipeline/bedtools2/bin' /home/pipeman/.bashrc
  
  # + 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
  
  # + SAMtools
  RUN wget -O /tmp/samtools-0.1.19.tar.bz2 http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download \
      && tar xjvf /tmp/samtools-0.1.19.tar.bz2 -C /usr/local/pipeline/ \
      && cd /usr/local/pipeline/samtools-0.1.19 && make \
      && chown -R pipeman:ngsgroup /usr/local/pipeline/samtools-0.1.19 \
      && sed -i '$aPATH=${PATH}:/usr/local/pipeline/samtools-0.1.19/bin' /home/pipeman/.bashrc
  
  
  
  #---------------------- Visualisations -----------------------------------
  
  