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Merge pull request #1539 from oesteban/tst/Docker
[TST] Add base and conda docker images #1536
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‎docker/test-image-base/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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#
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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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#
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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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FROM ubuntu:vivid
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MAINTAINER Stanford Center for Reproducible Neuroscience <[email protected]>
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# Preparations
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RUN ln -snf /bin/bash /bin/sh
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ARG DEBIAN_FRONTEND=noninteractive
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# Update packages and install the minimal set of tools
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RUN apt-get update && \
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apt-get install -y curl \
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git \
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xvfb \
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bzip2 \
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unzip \
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apt-utils \
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gfortran \
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fusefat \
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liblapack-dev \
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libblas-dev \
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libatlas-dev \
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libatlas-base-dev \
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libblas3 \
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libblas-common \
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libopenblas-dev \
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libxml2-dev \
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libxslt1-dev \
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libfreetype6-dev \
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libpng12-dev \
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libqhull-dev \
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libxft-dev \
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libjpeg-dev \
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libyaml-dev
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# Install ANTs
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RUN mkdir -p /opt/ants && \
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curl -sSL "https://2a353b13e8d2d9ac21ce543b7064482f771ce658.googledrive.com/host/0BxI12kyv2olZVFhUcGVpYWF3R3c/ANTs-Linux_Ubuntu14.04.tar.bz2" \
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| tar -xjC /opt/ants --strip-components 1
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ENV ANTSPATH /opt/ants
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ENV PATH $ANTSPATH:$PATH
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# Enable neurodebian
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RUN curl -sSL http://neuro.debian.net/lists/vivid.de-m.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && \
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curl -sSL http://neuro.debian.net/lists/vivid.us-tn.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
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apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9 && \
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apt-get update && \
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apt-get install -y fsl-core afni
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RUN echo '#!/bin/bash' > /etc/profile.d/nipype_deps.sh && \
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echo 'export ANTSPATH=/opt/ants' >> /etc/profile.d/nipype_deps.sh && \
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echo 'export PATH=$ANTSPATH:$PATH' >> /etc/profile.d/nipype_deps.sh && \
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echo 'source /etc/fsl/fsl.sh' >> /etc/profile.d/nipype_deps.sh && \
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echo 'source /etc/afni/afni.sh' >> /etc/profile.d/nipype_deps.sh
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# Clear apt cache to reduce image size
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RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# Install Matlab: from the good old install_spm_mcr.sh of @chrisfilo
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WORKDIR /root
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RUN echo "destinationFolder=/root/mcr" > mcr_options.txt && \
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echo "agreeToLicense=yes" >> mcr_options.txt && \
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echo "outputFile=/tmp/matlabinstall_log" >> mcr_options.txt && \
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echo "mode=silent" >> mcr_options.txt && \
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mkdir -p matlab_installer && \
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curl -sSL http://www.mathworks.com/supportfiles/downloads/R2015a/deployment_files/R2015a/installers/glnxa64/MCR_R2015a_glnxa64_installer.zip \
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-o matlab_installer/installer.zip && \
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unzip matlab_installer/installer.zip -d matlab_installer/ && \
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matlab_installer/install -inputFile mcr_options.txt && \
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rm -rf matlab_installer mcr_options.txt && \
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echo 'export LD_LIBRARY_PATH=/root/mcr/v85/runtime/glnxa64:/root/mcr/v85/bin/glnxa64:/root/mcr/v85/sys/os/glnxa64:$LD_LIBRARY_PATH' >> /etc/profile.d/nipype_deps.sh && \
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echo 'export SPMMCRCMD="/root/spm12/run_spm12.sh /root/mcr/v85/ script"' >> /etc/profile.d/nipype_deps.sh && \
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echo 'export FORCE_SPMMCR=1' >> /etc/profile.d/nipype_deps.sh
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ENV LD_LIBRARY_PATH "/root/mcr/v85/runtime/glnxa64:/root/mcr/v85/bin/glnxa64:/root/mcr/v85/sys/os/glnxa64:$LD_LIBRARY_PATH"
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ENV SPMMCRCMD "/root/spm12/run_spm12.sh /root/mcr/v85/ script"
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ENV FORCE_SPMMCR 1
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# Install SPM
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RUN curl -sSL http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_r6472_Linux_R2015a.zip -o spm12.zip && \
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unzip spm12.zip && \
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rm -rf spm12.zip
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RUN echo "source /etc/profile.d/nipype_deps.sh" >> /etc/bash.bashrc
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CMD ["/bin/bash"]
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‎docker/test-image-nipype/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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#
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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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#
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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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FROM nipype/testbase
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MAINTAINER Stanford Center for Reproducible Neuroscience <[email protected]>
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# Preparations
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RUN ln -snf /bin/bash /bin/sh
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WORKDIR /root
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# Install miniconda
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RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh && \
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/bin/bash Miniconda-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
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rm Miniconda-latest-Linux-x86_64.sh && \
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echo '#!/bin/bash' >> /etc/profile.d/nipype.sh && \
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echo 'export PATH=/usr/local/miniconda/bin:$PATH' >> /etc/profile.d/nipype.sh
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ENV PATH /usr/local/miniconda/bin:$PATH
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# http://bugs.python.org/issue19846
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# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
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ENV LANG C.UTF-8
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# Add conda-forge channel in conda
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RUN conda config --add channels conda-forge
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# Create conda environment
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RUN conda create -y -n nipypetests-2.7 lockfile nipype && \
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echo '#!/bin/bash' >> /etc/profile.d/nipype.sh && \
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echo '#!/bin/bash' >> /etc/bashrc && \
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echo 'source activate nipypetests-2.7' >> /etc/profile.d/nipype.sh && \
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echo 'source activate nipypetests-2.7' >> /etc/bashrc
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# Create conda environment
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RUN conda create -y -n nipypetests-3.4 lockfile nipype python=3.4
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# Create conda environment
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RUN conda create -y -n nipypetests-3.5 lockfile nipype python=3.5
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# Install pip
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# RUN source activate nipypetests-2.7 && \
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# pip install --upgrade pip && \
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RUN echo "source /etc/profile.d/nipype.sh" >> /etc/bash.bashrc
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CMD ["/bin/bash"]

‎docker/test-image/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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#
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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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#
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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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FROM nipype/testnipype
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MAINTAINER Stanford Center for Reproducible Neuroscience <[email protected]>
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# Preparations
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RUN ln -snf /bin/bash /bin/sh
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WORKDIR /root
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RUN mkdir -p ~/examples/ && ln -sf /usr/share/fsl-feeds/ ~/examples/feeds
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RUN curl -sSL "https://dl.dropbox.com/s/jzgq2nupxyz36bp/nipype-tutorial.tar.bz2" && \
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tar jxvf nipype-tutorial.tar.bz2 && \
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mv nipype-tutorial/* ~/examples/ && \
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curl -sSL "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" && \
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curl -sSL "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz" && \
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curl -sSL "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz" && \
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mkdir ~/examples/fsl_course_data && \
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tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data && \
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tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data && \
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tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data && \
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echo 'export FSL_COURSE_DATA=/root/examples/fsl_course_data' >> /etc/profile.d/crn_neuro.sh && \
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echo 'export FSL_COURSE_DATA=/root/examples/fsl_course_data' >> /etc/bash.bashrc
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ENV FSL_COURSE_DATA /root/examples/fsl_course_data
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CMD ["/bin/bash"]

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