FROM ubuntu:14.04

MAINTAINER Fernando Andreotti <fernando.andreotti@eng.ox.ac.uk>

# Versions used for some packages

ARG CONDA_VERSION=4.3.1

ARG CONDA_ENV

ARG TENSORFLOW_VERSION=1.0*

ARG KERAS_VERSION=2.0.2

ARG PYTHON_VERSION=3.5

ENTRYPOINT ["/bin/bash", "-c" ]

USER root

# Install some dependencies

ENV DEBIAN_FRONTEND noninteractive

ENV CONDA_ENV_PATH /opt/miniconda

ENV MYCONDA_ENV "deeplearn"

ENV CONDA_ACTIVATE "source $CONDA_ENV_PATH/bin/activate $MYCONDA_ENV"

RUN apt-get update --fix-missing -qq \

     && apt-get install --no-install-recommends -y \

        autoconf \

        automake \  

        bc \

        build-essential \

        bzip2 \

        cmake \

        curl \

        g++ \

        gfortran \

        git \

        language-pack-en \

        libatlas-dev \

        libatlas3gf-base \

        libcurl4-openssl-dev \ 

        libffi-dev \

        libfreetype6-dev \

        libglib2.0-0 \   

        libhdf5-dev \

        liblcms2-dev \

        libopenblas-dev \       

        libssl-dev \

        libtiff5-dev \

        libtool \

        libwebp-dev \

        libzmq3-dev \

        make \

        nano \

        pkg-config \

        software-properties-common \

        unzip \

        wget \

        zlib1g-dev \

        qt5-default \

        libvtk6-dev \

        zlib1g-dev

# Install miniconda to /opt/miniconda

RUN curl -LO http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh

RUN /bin/bash Miniconda-latest-Linux-x86_64.sh -p $CONDA_ENV_PATH -b

RUN rm Miniconda-latest-Linux-x86_64.sh

ENV PATH=$CONDA_ENV_PATH/bin:${PATH}

RUN conda update --quiet --yes conda

ENV PATH ${CONDA_ENV_PATH}/bin:$PATH

# Creating Anaconda environment

RUN conda create -y --name $MYCONDA_ENV python=${PYTHON_VERSION}

# Install Python 3 packages

RUN conda install -c conda-forge -y -n $MYCONDA_ENV\

     'beautifulsoup4=4.5*' \

    'hdf5=1.8.17' \

    'h5py=2.7*' \

    'ipython=5.1*' \    

    'ipykernel=4.5*' \

    'ipywidgets=5.2*' \

    'jupyter=1.0*' \

    'lxml=3.8*' \

    'matplotlib=2.0*' \

    'notebook=4.3*' \

    'numpy=1.12*' \

    'pandas=0.20*' \

    'pillow=4.2*' \

    'pip=9.0*' \

    'python=3.5*' \

    'rpy2=2.8*'  \

    'scipy=0.19*' \

    'scikit-learn=0.19*' \

    'scikit-image=0.13*' \

    'setuptools=36.3*' \

    'six=1.10*' \

    'sphinx=1.5*' \

    'spyder=3.1*'  && \

    conda clean -tipsy

# Some R dependencies

RUN conda install -c conda-forge -n $MYCONDA_ENV r-r.utils r-lme4 r-nlme

# Install TensorFlow

RUN conda install -c conda-forge -n $MYCONDA_ENV tensorflow=${TENSORFLOW_VERSION}

# Install Keras

ENV KERAS_BACKEND=tensorflow

RUN conda install -c conda-forge -n $MYCONDA_ENV keras=${KERAS_VERSION}

RUN rm /bin/sh && ln -s /bin/bash /bin/sh

RUN conda info --envs

RUN sed -i 's/theano/tensorflow/g' ${CONDA_ENV_PATH}/envs/${MYCONDA_ENV}/etc/conda/activate.d/keras_activate.sh # make tensorflow default 

# Visualization tools

RUN conda install -c conda-forge -y -n $MYCONDA_ENV \

    graphviz=2.38.0 \

    pydotplus=2.0.2

RUN $CONDA_ACTIVATE && pip install --upgrade pip && \

    pip install git+git://github.com/stared/keras-sequential-ascii.git \

    pydot3

####################

## Running tests ###

####################

ENV HOME /sharedfolder

WORKDIR /sharedfolder

# Add a notebook profile.

RUN mkdir -p -m 700 /sharedfolder/.jupyter/ && \

    echo "c.NotebookApp.ip = '*'" >> /sharedfolder/.jupyter/jupyter_notebook_config.py \

    echo "c.NotebookApp.port = 8888" >> /sharedfolder/.jupyter/jupyter_notebook_config.py \

    echo "c.NotebookApp.open_browser = False" >> /sharedfolder/.jupyter/jupyter_notebook_config.py \

    echo "c.MultiKernelManager.default_kernel_name = 'python3'" >> /sharedfolder/.jupyter/jupyter_notebook_config.py \

    echo "c.NotebookApp.allow_root = True" >> /sharedfolder/.jupyter/jupyter_notebook_config.py \

    echo "c.NotebookApp.password_required = False" >> /sharedfolder/.jupyter/jupyter_notebook_config.py \

    echo "c.NotebookApp.token = ''" >> /sharedfolder/.jupyter/jupyter_notebook_config.py

# Expose Ports for TensorBoard (6006), Ipython (8888)

EXPOSE 6006 8888

CMD ["source activate deeplearn && /bin/bash"]