anchor.diff:  
   # + 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 
  +    && unzip /tmp/bowtie2-2.2.3-linux-x86_64.zip -d /usr/local/pipeline/ \
  +    && chown -R pipeman:ngsgroup /usr/local/pipeline/bowtie2-2.2.3 \
  +    && sed  -i '$aPATH=${PATH}:/usr/local/pipeline/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
  +    && tar xzvf /tmp/vcftools_0.1.12a.tar.gz -C /usr/local/pipeline/  \
  +    && cd /usr/local/pipeline/vcftools_0.1.12a/ && make \
  +    && chown -R pipeman:ngsgroup /usr/local/pipeline/vcftools_0.1.12a \
  +    && sed  -i '$aPATH=${PATH}:/usr/local/pipeline/vcftools_0.1.12a/bin' /home/pipeman/.bashrc
   
   
   
  
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
  ADD ./GenomeAnalysisTK-3.1-1.tar.bz2 /tmp/GenomeAnalysisTK-3.1-1.tar.bz2
  
  RUN mkdir /usr/lib/GenomeAnalysisTK-3.1-1 \
      && tar xjvf /tmp/GenomeAnalysisTK-3.1-1.tar.bz2 -C /usr/lib/GenomeAnalysisTK-3.1-1 \
      && sed -i '$aPATH=${PATH}:/usr/lib/GenomeAnalysisTK-3.1-1' /home/pipeman/.bashrc
  
  #---------------------- Visualisations -----------------------------------
  
  
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
  
  #------------------ INSTALL PIPELINE COMPONENTS --------------------------
  
  