anchor.diff:  WORKDIR /tmp/downloads
   
   RUN cpanm --mirror http://cpan.metacpan.org -l $OPT File::ShareDir File::ShareDir::Install LWP::UserAgent Bio::Root::Version Const::Fast Graph && \
  -     rm -rf ~/.cpanm
  +    rm -rf ~/.cpanm
   
   RUN export SOURCE_JKENT_BIN=https://github.com/ENCODE-DCC/kentUtils/raw/master/bin/linux.x86_64 && \
       curl -sSL -o $OPT/bin/wigToBigWig -C - --retry 10 ${SOURCE_JKENT_BIN}/wigToBigWig && chmod +x $OPT/bin/wigToBigWig && \
  
positive.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
  
  COPY scripts/runCgp.sh $OPT/bin/runCgp.sh
  COPY scripts/getRef.sh $OPT/bin/getRef.sh
  
negative.code: 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
  
  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 bsdtar && \
      apt-get clean
  
  #libtest-warn-perl may still be needed
  
  