anchor.diff:  
   # + 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
  +# 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
   
  -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
  +# + 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 -----------------------------------
   
  
positive.code: 
  # Required basic stuff, make, gcc, wget etc
  RUN apt-get update
  RUN apt-get install -y make tabix
  RUN apt-get install -y gcc g++
  RUN apt-get install -y wget unzip
  RUN apt-get install zlib1g-dev
  
  # Mount a volume external to the container to store stuff that needs to persist
  VOLUME ["/media/ngsEasy/data/reference"] # reference indexed genomes
  
negative.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/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/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
  
  
  
  