Dockerfile

# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# ============================================================================
#
# THIS IS A GENERATED DOCKERFILE.
#
# This file was assembled from multiple pieces, whose use is documented
# below. Please refer to the the TensorFlow dockerfiles documentation for
# more information. Build args are documented as their default value.
#
# Ubuntu-based, Nvidia-GPU-enabled environment for developing changes for TensorFlow.
#
# Start from Nvidia's Ubuntu base image with CUDA and CuDNN, with TF development
# packages.
# --build-arg UBUNTU_VERSION=16.04
#    ( no description )
#
# Python is required for TensorFlow and other libraries.
# --build-arg USE_PYTHON_3_NOT_2=True
#    Install python 3 over Python 2
#
# Install the latest version of Bazel and Python development tools.
#
# Configure TensorFlow's shell prompt and login tools.

ARG UBUNTU_VERSION=16.04
FROM nvidia/cuda:9.0-base-ubuntu${UBUNTU_VERSION}

RUN apt-get update && apt-get install -y --no-install-recommends \
        build-essential \
        cuda-command-line-tools-9-0 \
        cuda-cublas-dev-9-0 \
        cuda-cudart-dev-9-0 \
        cuda-cufft-dev-9-0 \
        cuda-curand-dev-9-0 \
        cuda-cusolver-dev-9-0 \
        cuda-cusparse-dev-9-0 \
        curl \
        git \
        libcudnn7=7.2.1.38-1+cuda9.0 \
        libcudnn7-dev=7.2.1.38-1+cuda9.0 \
        libnccl2=2.2.13-1+cuda9.0 \
        libnccl-dev=2.2.13-1+cuda9.0 \
        libcurl3-dev \
        libbz2-dev \
        liblzma-dev \
        libfreetype6-dev \
        libhdf5-serial-dev \
        libpng12-dev \
        libzmq3-dev \
        libconfig-dev \
        pkg-config \
        rsync \
        software-properties-common \
        unzip \
        zip \
        zlib1g-dev \
        wget \
        python3-tk \
        tk-dev \
	bamtools \
        && \
    rm -rf /var/lib/apt/lists/* && \
    find /usr/local/cuda-9.0/lib64/ -type f -name 'lib*_static.a' -not -name 'libcudart_static.a' -delete && \
    rm /usr/lib/x86_64-linux-gnu/libcudnn_static_v7.a

RUN apt-get update && \
        apt-get install nvinfer-runtime-trt-repo-ubuntu1604-4.0.1-ga-cuda9.0 && \
        apt-get update && \
        apt-get install libnvinfer4=4.1.2-1+cuda9.0 && \
        apt-get install libnvinfer-dev=4.1.2-1+cuda9.0

RUN apt-get upgrade -y --no-install-recommends \
    python3-tk

# Link NCCL libray and header where the build script expects them.
RUN mkdir /usr/local/cuda-9.0/lib &&  \
    ln -s /usr/lib/x86_64-linux-gnu/libnccl.so.2 /usr/local/cuda/lib/libnccl.so.2 && \
    ln -s /usr/include/nccl.h /usr/local/cuda/include/nccl.h

ARG USE_PYTHON_3_NOT_2=True
ARG _PY_SUFFIX=${USE_PYTHON_3_NOT_2:+3}
ARG PYTHON=python${_PY_SUFFIX}
ARG PIP=pip${_PY_SUFFIX}

RUN apt-get update && apt-get install -y \
    ${PYTHON} \
    ${PYTHON}-pip

RUN ${PIP} install --upgrade \
    pip \
    setuptools

RUN apt-get update && apt-get install -y \
    build-essential \
    curl \
    git \
    openjdk-8-jdk \
    ${PYTHON}-dev \
    swig

# Install bazel
RUN echo "deb [arch=amd64] http://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list && \
    curl https://bazel.build/bazel-release.pub.gpg | apt-key add - && \
    apt-get update && \
    apt-get install -y bazel

# Install htslib
RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
RUN tar -xvf htslib-1.9.tar.bz2
RUN cd htslib-1.9 && ./configure && make && make install

RUN pip --no-cache-dir install \
        Pillow \
        h5py \
        setuptools \
        keras_applications==1.0.5 \
        keras_preprocessing==1.0.3 \
        matplotlib \
        numpy \
        pandas \
        pysam \
        scipy \
        sklearn \
		progressbar2\
        tensorflow-gpu==1.9.0\
        cython


RUN ln -s /usr/include/python3.5 python3
RUN ln -s /usr/include/python3.5 python

WORKDIR /CNNpeaks

RUN alias python='/usr/bin/python3'

RUN git clone http://github.com/odb9402/CNNPeaks 
RUN cd CNNPeaks/dependencies && ./install_samtools.sh
RUN cd CNNPeaks && ./build.sh

RUN ["/bin/bash"]