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: 
  # 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 make tabix
  RUN apt-get install -y git-core wget unzip
  RUN apt-get install -y zlib1g-dev libncurses5-dev
  
  # Mount a volume external to the container to store stuff that needs to persist
  VOLUME ["/media/ngsEasy/data/reference"] # reference indexed genomes
  