anchor.diff: -FROM    ubuntu:14.04
  +FROM  ubuntu:14.04
   
   MAINTAINER  keiranmraine@gmail.com
   
  -LABEL   uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \
  -        version="0.0.1" \
  -        description="The CGP somatic calling pipeline 'in-a-box'"
  -
  -USER    root
  +LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \
  +      version="0.0.1" \
  +      description="The CGP somatic calling pipeline 'in-a-box'"
  +
  +USER  root
   
   ENV OPT /opt/wtsi-cgp
   ENV PATH $OPT/bin:$PATH
   ENV PERL5LIB $OPT/lib/perl5
   
   
  -RUN     apt-get -yqq update && \
  -        apt-get -yqq install build-essential autoconf software-properties-common python-software-properties \
  -          wget curl zlib1g-dev libncurses5-dev libgd-dev \
  -          libgd2-xpm-dev libexpat1-dev python unzip libboost-dev libboost-iostreams-dev \
  -          libpstreams-dev libglib2.0-dev libreadline6-dev gfortran libcairo2-dev openjdk-7-jdk\
  -          cpanminus awscli && \
  -        apt-get clean
  +RUN apt-get -yqq update && \
  +    apt-get -yqq install build-essential autoconf software-properties-common python-software-properties \
  +      wget curl zlib1g-dev libncurses5-dev libgd-dev \
  +      libgd2-xpm-dev libexpat1-dev python unzip libboost-dev libboost-iostreams-dev \
  +      libpstreams-dev libglib2.0-dev libreadline6-dev gfortran libcairo2-dev openjdk-7-jdk\
  +      cpanminus bsdtar && \
  +    apt-get clean
   
   #libtest-warn-perl may still be needed
   
  
positive.code: ENV CGPVCF_UUID 5cc538ded838a4ba94feedff1b51ee3ebc4b65f4
  
  # build tabix using patch from cgpVcf release
  RUN curl -sSL -o tmp.zip --retry 10 https://github.com/samtools/tabix/archive/master.zip && \
      unzip tmp.zip && \
      cd /tmp/downloads/tabix-master && \
      make && \
      cp tabix $OPT/bin/. && \
  
negative.code:     rm tmp.R
  
  # Add ssearch36 BRASS dep
  RUN curl -sSL -o tmp.tar.gz --retry 10 https://github.com/wrpearson/fasta36/releases/download/v36.3.8/fasta-36.3.8-linux64.tar.gz && \
      mkdir  /tmp/downloads/fasta && \
      tar -C /tmp/downloads/fasta --strip-components 2 -zxf tmp.tar.gz && \
      cp /tmp/downloads/fasta/bin/ssearch36 $OPT/bin/. && \
      rm -rf /tmp/downloads/fasta
  
  RUN curl -sSL https://s3.amazonaws.com/aws-cli/awscli-bundle.zip | bsdtar -xvf - && \
      python awscli-bundle/install -i /usr/local/aws -b /usr/local/bin/aws && \
      rm -rf /tmp/downloads/awscli-bundle
  
  COPY scripts/runCgp.sh $OPT/bin/runCgp.sh
  COPY scripts/getRef.sh $OPT/bin/getRef.sh
  