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enh: generate dockerfiles with neurodocker + rename base dockerfile
Rename base.Dockerfile to Dockerfile.base to conform to moby style. For now, the master Neurodocker Docker image is used, but a versioned image will be used once a newer Neurodocker version is released.
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‎Dockerfile

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# Copyright (c) 2016, The developers of the Stanford CRN
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# All rights reserved.
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# Generated by Neurodocker v0.3.1-2-g4dfcf56.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are met:
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
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# pull request on our GitHub repository:
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# https://github.com/kaczmarj/neurodocker
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#
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# * Redistributions of source code must retain the above copyright notice, this
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# list of conditions and the following disclaimer.
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#
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# * Redistributions in binary form must reproduce the above copyright notice,
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# this list of conditions and the following disclaimer in the documentation
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# and/or other materials provided with the distribution.
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#
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# * Neither the name of crn_base nor the names of its
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# contributors may be used to endorse or promote products derived from
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# this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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# Timestamp: 2017-10-02 22:55:57
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FROM kaczmarj/nipype:base
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#
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# Based on https://github.com/poldracklab/fmriprep/blob/9c92a3de9112f8ef1655b876de060a2ad336ffb0/Dockerfile
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#
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FROM nipype/base:latest
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MAINTAINER The nipype developers https://github.com/nipy/nipype
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ARG PYTHON_VERSION_MAJOR=3
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# Installing and setting up miniconda
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RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda${PYTHON_VERSION_MAJOR}-4.2.12-Linux-x86_64.sh && \
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bash Miniconda${PYTHON_VERSION_MAJOR}-4.2.12-Linux-x86_64.sh -b -p /usr/local/miniconda && \
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rm Miniconda${PYTHON_VERSION_MAJOR}-4.2.12-Linux-x86_64.sh
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ENV PATH=/usr/local/miniconda/bin:$PATH \
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LANG=C.UTF-8 \
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LC_ALL=C.UTF-8 \
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ACCEPT_INTEL_PYTHON_EULA=yes \
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MKL_NUM_THREADS=1 \
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OMP_NUM_THREADS=1
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# MKL/OMP_NUM_THREADS: unless otherwise specified, each process should
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# only use one thread - nipype will handle parallelization
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# Installing precomputed python packages
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ARG PYTHON_VERSION_MINOR=6
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RUN conda config --add channels conda-forge; sync && \
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conda config --set always_yes yes --set changeps1 no; sync && \
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conda install -y python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} \
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mkl \
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numpy \
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scipy \
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scikit-learn \
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matplotlib \
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pandas \
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libxml2 \
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libxslt \
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traits=4.6.0 \
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psutil \
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icu=58.1 && \
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sync;
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# matplotlib cleanups: set default backend, precaching fonts
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RUN sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages/matplotlib/mpl-data/matplotlibrc && \
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python -c "from matplotlib import font_manager"
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# Install CI scripts
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COPY docker/files/run_* /usr/bin/
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RUN chmod +x /usr/bin/run_*
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# Replace imglob with a Python3 compatible version
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COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
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RUN rm -rf ${FSLDIR}/bin/imglob && \
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chmod +x /usr/bin/fsl_imglob.py && \
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ln -s /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
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# Installing dev requirements (packages that are not in pypi)
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WORKDIR /src/
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COPY requirements.txt requirements.txt
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RUN pip install -r requirements.txt && \
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rm -rf ~/.cache/pip
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RUN git clone https://github.com/INCF/pybids.git && \
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cd pybids && python setup.py develop
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# Installing nipype
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COPY . /src/nipype
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RUN cd /src/nipype && \
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pip install -e .[all] && \
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rm -rf ~/.cache/pip
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WORKDIR /work/
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ARG DEBIAN_FRONTEND=noninteractive
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#----------------------------------------------------------
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# Install common dependencies and create default entrypoint
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#----------------------------------------------------------
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ENV LANG="en_US.UTF-8" \
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LC_ALL="C.UTF-8" \
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ND_ENTRYPOINT="/neurodocker/startup.sh"
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RUN apt-get update -qq && apt-get install -yq --no-install-recommends \
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apt-utils bzip2 ca-certificates curl locales unzip \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& localedef --force --inputfile=en_US --charmap=UTF-8 C.UTF-8 \
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&& chmod 777 /opt && chmod a+s /opt \
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&& mkdir -p /neurodocker \
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&& if [ ! -f "$ND_ENTRYPOINT" ]; then \
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echo '#!/usr/bin/env bash' >> $ND_ENTRYPOINT \
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&& echo 'set +x' >> $ND_ENTRYPOINT \
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&& echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT; \
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fi \
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&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
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ENTRYPOINT ["/neurodocker/startup.sh"]
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LABEL maintainer="The nipype developers https://github.com/nipy/nipype"
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ENV MKL_NUM_THREADS="1" \
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OMP_NUM_THREADS="1"
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# Create new user: neuro
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RUN useradd --no-user-group --create-home --shell /bin/bash neuro
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USER neuro
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#------------------
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# Install Miniconda
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#------------------
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ENV CONDA_DIR=/opt/conda \
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PATH=/opt/conda/bin:$PATH
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RUN echo "Downloading Miniconda installer ..." \
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&& miniconda_installer=/tmp/miniconda.sh \
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&& curl -sSL -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
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&& /bin/bash $miniconda_installer -b -p $CONDA_DIR \
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&& rm -f $miniconda_installer \
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&& conda config --system --prepend channels conda-forge \
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&& conda config --system --set auto_update_conda false \
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&& conda config --system --set show_channel_urls true \
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&& conda update -y -q --all && sync \
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&& conda clean -tipsy && sync
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#-------------------------
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# Create conda environment
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#-------------------------
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RUN conda create -y -q --name neuro \
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&& sync && conda clean -tipsy && sync
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ENV PATH=/opt/conda/envs/neuro/bin:$PATH
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COPY ["docker/files/run_builddocs.sh", "docker/files/run_examples.sh", "docker/files/run_pytests.sh", "nipype/external/fsl_imglob.py", "/usr/bin/"]
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COPY [".", "/src/nipype"]
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USER root
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# User-defined instruction
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RUN chmod 777 -R /src/nipype
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USER neuro
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ARG PYTHON_VERSION_MAJOR="3"
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ARG PYTHON_VERSION_MINOR="6"
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ARG BUILD_DATE
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ARG VCS_REF
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ARG VERSION
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LABEL org.label-schema.build-date=$BUILD_DATE \
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#-------------------------
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# Update conda environment
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#-------------------------
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RUN conda install -y -q --name neuro python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} \
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icu=58.1 \
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libxml2 \
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libxslt \
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matplotlib \
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mkl \
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numpy \
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pandas \
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psutil \
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scikit-learn \
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scipy \
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traits=4.6.0 \
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&& sync && conda clean -tipsy && sync \
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&& /bin/bash -c "source activate neuro \
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&& pip install -q --no-cache-dir -e /src/nipype[all]" \
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&& sync
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LABEL org.label-schema.build-date="$BUILD_DATE" \
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org.label-schema.name="NIPYPE" \
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org.label-schema.description="NIPYPE - Neuroimaging in Python: Pipelines and Interfaces" \
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org.label-schema.url="http://nipype.readthedocs.io" \
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org.label-schema.vcs-ref=$VCS_REF \
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org.label-schema.vcs-ref="$VCS_REF" \
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org.label-schema.vcs-url="https://github.com/nipy/nipype" \
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org.label-schema.version=$VERSION \
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org.label-schema.version="$VERSION" \
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org.label-schema.schema-version="1.0"
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#--------------------------------------
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# Save container specifications to JSON
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#--------------------------------------
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RUN echo '{ \
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\n "pkg_manager": "apt", \
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\n "check_urls": false, \
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\n "instructions": [ \
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\n [ \
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\n "base", \
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\n "kaczmarj/nipype:base" \
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\n ], \
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\n [ \
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\n "label", \
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\n { \
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\n "maintainer": "The nipype developers https://github.com/nipy/nipype" \
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\n } \
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\n ], \
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\n [ \
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\n "env", \
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\n { \
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\n "MKL_NUM_THREADS": "1", \
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\n "OMP_NUM_THREADS": "1" \
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\n } \
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\n ], \
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\n [ \
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\n "user", \
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\n "neuro" \
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\n ], \
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\n [ \
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\n "miniconda", \
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\n { \
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\n "env_name": "neuro", \
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\n "add_to_path": true \
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\n } \
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\n ], \
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\n [ \
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\n "copy", \
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\n [ \
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\n "docker/files/run_builddocs.sh", \
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\n "docker/files/run_examples.sh", \
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\n "docker/files/run_pytests.sh", \
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\n "nipype/external/fsl_imglob.py", \
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\n "/usr/bin/" \
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\n ] \
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\n ], \
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\n [ \
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\n "copy", \
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\n [ \
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\n ".", \
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\n "/src/nipype" \
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\n ] \
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\n ], \
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\n [ \
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\n "user", \
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\n "root" \
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\n ], \
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\n [ \
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\n "run", \
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\n "chmod 777 -R /src/nipype" \
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\n ], \
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\n [ \
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\n "user", \
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\n "neuro" \
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\n ], \
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\n [ \
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\n "arg", \
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\n { \
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\n "PYTHON_VERSION_MAJOR": "3", \
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\n "PYTHON_VERSION_MINOR": "6", \
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\n "BUILD_DATE": "", \
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\n "VCS_REF": "", \
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\n "VERSION": "" \
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\n } \
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\n ], \
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\n [ \
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\n "miniconda", \
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\n { \
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\n "env_name": "neuro", \
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\n "conda_install": "python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} icu=58.1 libxml2 libxslt matplotlib mkl numpy pandas psutil scikit-learn scipy traits=4.6.0", \
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\n "pip_opts": "-e", \
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\n "pip_install": "/src/nipype[all]" \
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\n } \
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\n ], \
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\n [ \
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\n "label", \
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\n { \
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\n "org.label-schema.build-date": "$BUILD_DATE", \
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\n "org.label-schema.name": "NIPYPE", \
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\n "org.label-schema.description": "NIPYPE - Neuroimaging in Python: Pipelines and Interfaces", \
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\n "org.label-schema.url": "http://nipype.readthedocs.io", \
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\n "org.label-schema.vcs-ref": "$VCS_REF", \
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\n "org.label-schema.vcs-url": "https://github.com/nipy/nipype", \
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\n "org.label-schema.version": "$VERSION", \
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\n "org.label-schema.schema-version": "1.0" \
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\n } \
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\n ] \
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\n ], \
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\n "generation_timestamp": "2017-10-02 22:55:57", \
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\n "neurodocker_version": "0.3.1-2-g4dfcf56" \
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\n}' > /neurodocker/neurodocker_specs.json

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