Dockerfile

FROM nvidia/cuda:9.0-devel-ubuntu16.04

LABEL com.nvidia.volumes.needed="nvidia_driver"

# Installing dependencies

RUN apt-get update && \
    apt-get install -y software-properties-common && \
    add-apt-repository -y ppa:webupd8team/java && \
    apt-get update

RUN apt-get update && \
    apt-get install -y \
    ocl-icd-libopencl1 \
    clinfo \
    python-software-properties \
    wget \
    git \
    python3-pip \
    python3 \
    xvfb \
    libxtst6 \
    openjdk-9-jre \
    cmake \
    libboost*

RUN pip3 install snakemake pyyaml drmaa

# Just in case installing OpenCL support

RUN mkdir -p /etc/OpenCL/vendors && \
    echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd && \
    echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf && \
    echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf

# Defining ENV variables

ENV PATH /usr/local/nvidia/bin:${PATH}
ENV LD_LIBRARY_PATH /usr/local/cuda-9.0/lib64:/usr/lib/x86_64-linux-gnu:/usr/local/nvidia/lib:/usr/local/nvidia/lib64:${LD_LIBRARY_PATH}
ENV NUM_JOBS 1

# Downloading FIJI and scripts
WORKDIR /opt/multiview
RUN mkdir /data && \
    git clone https://github.com/mpicbg-scicomp/snakemake-workflows.git && \
    wget http://tomancak-srv1.mpi-cbg.de/~schmied/workflow/2015-06-30_Fiji.app.tar.gz && \
    tar zxvf 2015-06-30_Fiji.app.tar.gz
RUN git clone https://github.com/obmarg/libsysconfcpus.git
RUN cd libsysconfcpus && \
    CFLAGS=-ansi ./configure && \
    make && \
    make install

# Adding CUDA Fourier Library (not building inside the container as this is not working, if someone finds a fix for this please make pull request !!!)
ADD CUDA /opt/multiview/CUDA
ADD FourierConvolutionCUDALib /opt/multiview/FourierConvolutionCUDALib

# Going to the snakemake directory
WORKDIR /opt/multiview/snakemake-workflows/spim_registration/timelapse/

# SnakeMake command to launch the processing
CMD snakemake -j $NUM_JOBS -d /data --verbose --cluster-config /opt/multiview/snakemake-workflows/spim_registration/timelapse/cluster.json --cluster ""