anchor.diff:      rm -rf $(brew --cache) && \
       rm -rf /usr/local/.git && \
       rm -rf /.cpanm && \
  -    rm -rf /tmp/bcbio-nextgen-install
  -RUN wget --no-check-certificate -O createsetuser \
  -      https://raw.github.com/chapmanb/bcbio-nextgen-vm/master/scripts/createsetuser && \
  -    chmod a+x createsetuser && mv createsetuser /sbin
  +    rm -rf /tmp/bcbio-nextgen-install && \
   
   # Create directories and symlinks for data 
  -RUN mkdir -p /mnt/biodata && \
  +    mkdir -p /mnt/biodata && \
       mkdir -p /tmp/bcbio-nextgen && \
       mv /usr/local/share/bcbio-nextgen/galaxy/bcbio_system.yaml /usr/local/share/bcbio-nextgen/config && \
       rmdir /usr/local/share/bcbio-nextgen/galaxy && \
  
positive.code:     echo -en '#!/bin/bash\nexit 0\n' > DEBIAN/postinst && \
      dpkg-deb -b . /fuse.deb && \
      dpkg -i /fuse.deb && \
      rm -rf /tmp/fuse-hack
  
  # bcbio-nextgen installation
  RUN mkdir -p /tmp/bcbio-nextgen-install && cd /tmp/bcbio-nextgen-install && \
      wget --no-check-certificate \
        https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py && \
      python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen \
        --nodata -u development
  RUN git config --global url.https://github.com/.insteadOf git://github.com/ && \
      /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py upgrade --sudo --tooldir=/usr/local --tools
  RUN /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py upgrade --isolate -u development --tools --toolplus data
  ENV PATH /usr/local/bin:/usr/local/share/bcbio-nextgen/anaconda/bin:${PATH}
  ENV LD_LIBRARY_PATH /usr/local/lib:${LD_LIBRARY_PATH}
  ENV PERL5LIB /usr/local/lib/perl5:${PERL5LIB}
  RUN echo 'export PATH=/usr/local/bin:$PATH' >> /etc/profile.d/bcbio.sh && \
      echo 'export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH' >> /etc/profile.d/bcbio.sh && \
      echo 'export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB}' >> /etc/profile.d/bcbio.sh && \
      echo '/usr/local/lib' >> /etc/ld.so.conf.d/bcbio.conf && ldconfig && \
      apt-get clean && \
      rm -rf /var/lib/apt/lists/* /var/tmp/* && \
      /usr/local/share/bcbio-nextgen/anaconda/bin/conda remove --yes qt && \
  
negative.code: FROM stackbrew/ubuntu:14.04
  MAINTAINER Brad Chapman "https://github.com/chapmanb"
  
  # Release 0.9.5a -- https://github.com/chapmanb/bcbio-nextgen/commit/40fb5ba
  
  # Setup a base system 
  RUN apt-get update && apt-get install -y build-essential zlib1g-dev wget curl python-setuptools git && \
      apt-get install -y openjdk-7-jdk openjdk-7-jre ruby libncurses5-dev libcurl4-openssl-dev libbz2-dev \
      unzip pigz bsdmainutils && \
  
  # Fake a fuse install; openjdk pulls this in 
  # https://github.com/dotcloud/docker/issues/514
  # https://gist.github.com/henrik-muehe/6155333
      mkdir -p /tmp/fuse-hack && cd /tmp/fuse-hack && \
      apt-get install libfuse2 && \
      apt-get download fuse && \
      dpkg-deb -x fuse_* . && \
  