anchor.diff:      kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json && \
       pip uninstall kernda -y
   
  -
  -
  -USER $NB_USER
  -
  +RUN echo "===> add webupd8 repository..."  && \
  +    echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" | tee /etc/apt/sources.list.d/webupd8team-java.list  && \
  +    echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" | tee -a /etc/apt/sources.list.d/webupd8team-java.list  && \
  +    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys EEA14886  && \
  +    apt-get update
  +
  +
  +RUN echo "===> install Java"  && \
  +    echo debconf shared/accepted-oracle-license-v1-1 select true | debconf-set-selections  && \
  +    echo debconf shared/accepted-oracle-license-v1-1 seen true | debconf-set-selections  && \
  +    DEBIAN_FRONTEND=noninteractive  apt-get install -y --force-yes oracle-java8-installer oracle-java8-set-default
  +
  +
  +RUN echo "===> clean up..."  && \
  +    rm -rf /var/cache/oracle-jdk8-installer  && \
  +    apt-get clean  && \
  +    rm -rf /var/lib/apt/lists/*
  +
  +
  +# define default command
  +#CMD ["java"]
  +
  +ENV MZMINE_VERSIONS /home/$NB_USER/repos/mzmine_components/versions
  +RUN mkdir -p $MZMINE_VERSIONS && \
  +    cd $MZMINE_VERSIONS && \
  +    wget $(curl -s https://api.github.com/repos/mzmine/mzmine2/releases/latest | grep 'browser_' | cut -d\" -f4) -O mzmine_latest.zip && \
  +    unzip mzmine_latest.zip
  +    #cp ../MZmine-2.23/startMZmine_NERSC_* .
  +
  +
  +USER $NB_USER
  +#TODO: fix the bouncing around between USERs
  +#Currently 231023 files
  +#docker run -it benbowen/metatlas /bin/bash
  +#find / -type f -print | wc -l
  +
  
positive.code: # Configure environment
  ENV CONDA_DIR /opt/conda
  ENV PATH $CONDA_DIR/bin:$PATH
  ENV PYTHONPATH $PYTHONPATH:/home/jovyan/work/BASTet
  ENV PYTHONPATH $PYTHONPATH:/home/jovyan/work/pactolus
  ENV SHELL /bin/bash
  ENV NB_USER jovyan
  ENV NB_UID 1000
  ENV HOME /home/$NB_USER
  ENV LC_ALL en_US.UTF-8
  ENV LANG en_US.UTF-8
  ENV LANGUAGE en_US.UTF-8
  
  # Create jovyan user with UID=1000 and in the 'users' group
  RUN useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
      mkdir -p $CONDA_DIR && \
      chown $NB_USER $CONDA_DIR
  
  USER $NB_USER
  
  # Setup jovyan home directory
  RUN mkdir /home/$NB_USER/work && \
      mkdir /home/$NB_USER/.jupyter && \
      echo "cacert=/etc/ssl/certs/ca-certificates.crt" > /home/$NB_USER/.curlrc
  
  # Install conda as jovyan
  RUN cd /tmp && \
      mkdir -p $CONDA_DIR && \
      wget --quiet https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh && \
  
negative.code: 
  #install rdkit for both python3 and python2
  # consider pinning rdkit with version: rdkit=2016.09.4
  # RUN /opt/conda/bin/conda install -c https://conda.anaconda.org/rdkit rdkit -y --quiet
  RUN /opt/conda/bin/conda install -n python2 -c rdkit rdkit -y --quiet
  
  # Add shortcuts to distinguish pip for python2 and python3 envs
  RUN ln -s $CONDA_DIR/envs/python2/bin/pip $CONDA_DIR/bin/pip2 && \
      ln -s $CONDA_DIR/bin/pip $CONDA_DIR/bin/pip3
  
  
  RUN cd /home/metatlas/repos/ && \
      git clone https://github.com/biorack/metatlas.git && \
      cd /home/metatlas/repos/metatlas/ && \
      # pip3 install . --ignore-installed && \
      pip2 install . --ignore-installed
  
  RUN cd /home/metatlas/repos/ && \
      git clone https://github.com/quantopian/qgrid && \
      cd /home/metatlas/repos/qgrid/ && \
      pip2 install . --ignore-installed --quiet && \
      # pip3 install . --ignore-installed && \
      pip2 install pyteomics --ignore-installed --quiet && \
      # pip3 install pyteomics --ignore-installed --quiet && \
      pip2 install pyimzml --ignore-installed --quiet && \
      # pip3 install pyimzml --ignore-installed --quiet && \
      pip2 install lxml --ignore-installed --quiet
      # pip3 install lxml --ignore-installed --quiet
  
  RUN cd /home/metatlas/repos/ && \
      git clone https://github.com/biorack/BASTet.git
      
  RUN cd /home/metatlas/repos/ && \
      git clone https://github.com/biorack/pactolus.git
  
      
  
  # Import matplotlib the first time to build the font cache.
  ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
  # RUN MPLBACKEND=Agg $CONDA_DIR/envs/python2/bin/python -c "import matplotlib.pyplot"
  
  # Configure ipython kernel to use matplotlib inline backend by default
  # RUN mkdir -p $HOME/.ipython/profile_default/startup
  