Dockerfile

FROM ubuntu:18.04

ARG TENSORFLOW_VERSION=2.1.0
ARG TENSORFLOW_ARCH=cpu
ARG KERAS_VERSION=2.3.1
ENV TZ=America/New_York
ARG DEBIAN_FRONTEND=noninteractive

# Install some dependencies
RUN apt-get update && apt-get install -y \
        tzdata \
		bc \
		build-essential \
		cmake \
		curl \
		g++ \
		gfortran \
		git \
		libffi-dev \
		libfreetype6-dev \
		libhdf5-dev \
		libjpeg-dev \
		liblcms2-dev \
		libopenblas-dev \
		liblapack-dev \
		# libopenjpeg2 \
		# libpng12-dev \
		libssl-dev \
		libtiff5-dev \
		libwebp-dev \
		libzmq3-dev \
		nano \
		pkg-config \
		python-dev \
		software-properties-common \
		unzip \
		vim \
		wget \
		zlib1g-dev \
		qt5-default \
		libvtk6-dev \
		zlib1g-dev \
		libjpeg-dev \
		libwebp-dev \
		libpng-dev \
		libtiff5-dev \
		# libjasper-dev \
		libopenexr-dev \
		libgdal-dev \
		libdc1394-22-dev \
		libavcodec-dev \
		libavformat-dev \
		libswscale-dev \
		libtheora-dev \
		libvorbis-dev \
		libxvidcore-dev \
		libx264-dev \
		yasm \
		libopencore-amrnb-dev \
		libopencore-amrwb-dev \
		libv4l-dev \
		libxine2-dev \
		libtbb-dev \
		libeigen3-dev \
		python-dev \
		python-tk \
		python-numpy \
		python3-dev \
		python3-tk \
		python3-numpy \
		ant \
		default-jdk \
		doxygen \
		&& \
	apt-get clean && \
	apt-get autoremove && \
	rm -rf /var/lib/apt/lists/*  
# Link BLAS library to use OpenBLAS using the alternatives mechanism (https://www.scipy.org/scipylib/building/linux.html#debian-ubuntu)
	# update-alternatives --set libblas.so.3 /usr/lib/openblas-base/libblas.so.3


# Install OpenJDK-8
RUN apt-get update && \
    apt-get install -y openjdk-8-jdk && \
    apt-get install -y ant && \
    apt-get clean;

# Fix certificate issues
RUN apt-get update && \
    apt-get install ca-certificates-java && \
    apt-get clean && \
    update-ca-certificates -f;

# Setup JAVA_HOME -- useful for docker commandline
ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64/
RUN export JAVA_HOME

# Install pip3
RUN curl -O https://bootstrap.pypa.io/get-pip.py && \
	python3 get-pip.py && \
	rm get-pip.py

# Add SNI support to Python
RUN pip3 --no-cache-dir install \
		pyopenssl \
		ndg-httpsclient \
		pyasn1

# Install useful Python packages using apt-get to avoid version incompatibilities with Tensorflow binary
# especially numpy, scipy, skimage and sklearn (see https://github.com/tensorflow/tensorflow/issues/2034)
RUN apt-get update && apt-get install -y \
		python-numpy \
		python-scipy \
		python-nose \
		python-h5py \
		python-skimage \
		python-matplotlib \
		python-pandas \
		python-sklearn \
		python-sympy \
		&& \
	apt-get clean && \
	apt-get autoremove && \
	rm -rf /var/lib/apt/lists/*

# Install other useful Python packages using pip3
RUN pip3 --no-cache-dir install --upgrade ipython && \
	pip3 --no-cache-dir install \
		Cython \
		#ipykernel \
		jupyter \
		path.py \
		Pillow \
		pygments \
		six \
		sphinx \
		wheel \
		zmq 
		# \
	#	&& \
	#python -m ipykernel.kernelspec

# PYQT dependencies
# RUN sudo apt-get install --reinstall libxcb-xinerama0 libqt5x11extras5

# Additional packages
RUN pip3 install --upgrade numpy pandas sklearn scipy matplotlib XlsxWriter h5py progressbar2 PyQt5 PySide2

# Install BedTools
RUN apt-get update && apt-get install bedtools --upgrade -y

# Install Bio tools
RUN pip3 install cython pybedtools scikit-bio==0.5.5 biopython


# Install TensorFlow
RUN pip3 --no-cache-dir install tensorflow==${TENSORFLOW_VERSION}


# Install Keras
RUN pip3 --no-cache-dir install git+git://github.com/fchollet/keras.git@${KERAS_VERSION}


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

WORKDIR "/root"
CMD ["/bin/bash"]