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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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#
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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/testnipypedata
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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 .nipype && \
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echo '[logging]' > .nipype/nipype.cfg && \
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echo 'workflow_level = DEBUG' >> .nipype/nipype.cfg && \
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echo 'interface_level = DEBUG' >> .nipype/nipype.cfg && \
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echo 'filemanip_level = DEBUG' >> .nipype/nipype.cfg
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WORKDIR /root/src
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ADD . nipype/
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# Install the checked out version of nipype, check that requirements are
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# installed and install it for each of the three environments.
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RUN cd nipype/ && \
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source activate nipypetests-2.7 && \
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pip install -r requirements.txt && \
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pip install -e .
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RUN cd nipype/ && \
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source activate nipypetests-3.4 && \
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pip install -r requirements.txt && \
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pip install -e .
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RUN cd nipype/ && \
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source activate nipypetests-3.5 && \
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pip install -r requirements.txt && \
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pip install -e .
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WORKDIR /root/
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ADD docker/circleci/run_* /usr/bin/
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RUN chmod +x /usr/bin/run_*
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WORKDIR /scratch
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# RUN echo 'source /etc/profile.d/nipype_tests.sh' >> /etc/bash.bashrc
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ENTRYPOINT ["/usr/bin/run_examples.sh"]
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CMD ["--help"]
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‎circle.yml

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machine:
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services:
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- docker
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dependencies:
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cache_directories:
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- "~/.apt-cache"
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- "~/examples/data"
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- "~/examples/fsdata"
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- "~/mcr"
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- "~/spm12"
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- "~/examples/fsl_course_data"
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- "~/scratch"
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- "~/docker"
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pre:
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# Let CircleCI cache the apt archive
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- sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives && mkdir -p ~/.apt-cache/partial
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- bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
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- pip install coverage
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override:
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# Install apt packages
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- sudo apt-get install -y fsl-core fsl-atlases fsl-mni152-templates fsl-feeds afni swig python-vtk xvfb fusefat
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- echo 'source /etc/fsl/fsl.sh' >> $HOME/.profile
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- echo 'source /etc/afni/afni.sh' >> $HOME/.profile
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- mkdir -p ~/examples/ && ln -sf /usr/share/fsl-feeds/ ~/examples/feeds
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# Enable system-wide vtk
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- ln -sf /usr/lib/pymodules/python2.7/vtk ~/virtualenvs/venv-system/lib/python2.7/site-packages/
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# Set up python environment
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- pip install --upgrade pip
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- pip install -e .
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- pip install matplotlib sphinx ipython boto coverage dipy
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# Add tvtk
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- pip install http://effbot.org/downloads/Imaging-1.1.7.tar.gz
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- pip install -e git+https://github.com/enthought/etsdevtools.git#egg=etsdevtools
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- pip install -e git+https://github.com/enthought/blockcanvas.git#egg=blockcanvas
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- pip install -e git+https://github.com/enthought/etsproxy.git#egg=etsproxy
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- pip install -e git+https://github.com/enthought/ets.git#egg=ets
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- pip install https://github.com/rtfd/readthedocs-sphinx-ext/archive/master.zip
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- gem install fakes3
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- if [[ ! -d ~/examples/data ]]; then wget "https://dl.dropbox.com/s/jzgq2nupxyz36bp/nipype-tutorial.tar.bz2" && tar jxvf nipype-tutorial.tar.bz2 && mv nipype-tutorial/* ~/examples/; fi
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- if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" && wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz" && wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz" && mkdir ~/examples/fsl_course_data && tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data && tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data && tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
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- bash ~/nipype/tools/install_spm_mcr.sh
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- mkdir -p ~/.nipype && echo '[logging]' > ~/.nipype/nipype.cfg && echo 'workflow_level = DEBUG' >> ~/.nipype/nipype.cfg && echo 'interface_level = DEBUG' >> ~/.nipype/nipype.cfg && echo 'filemanip_level = DEBUG' >> ~/.nipype/nipype.cfg
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machine:
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environment:
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FSLOUTPUTTYPE: NIFTI_GZ
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- if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
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- docker info
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- docker pull nipype/testnipypedata
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- mkdir -p ~/docker; docker save nipype/testnipypedata > ~/docker/image.tar
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- docker build -t nipype/testbench .
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test:
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override:
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- mkdir -p ${CIRCLE_TEST_REPORTS}/nose
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- source $HOME/.profile; nosetests --with-doctest --xunit-file="${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml" -c ./.noserc --logging-level=DEBUG --verbosity=3:
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environment:
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SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
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FORCE_SPMMCR: 1
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FSL_COURSE_DATA: "$HOME/examples/fsl_course_data"
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timeout: 2600
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- set -o pipefail && cd doc && make html 2>&1 | tee ~/log.txt
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- cat ~/log.txt && if grep -q "ERROR" ~/log.txt; then false; else true; fi
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- source $HOME/.profile; python ~/nipype/tools/run_examples.py test_spm Linear workflow3d workflow4d:
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pwd: ../examples
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environment:
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SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
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FORCE_SPMMCR: 1
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timeout: 1600
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- source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_fsl_feeds Linear l1pipeline:
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pwd: ../examples
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- source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_spm_dartel Linear level1 l2pipeline:
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pwd: ../examples
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environment:
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SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
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FORCE_SPMMCR: 1
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timeout: 1600
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- source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_fsl_reuse Linear level1_workflow:
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pwd: ../examples
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- source $HOME/.profile; python ~/nipype/tools/run_examples.py fmri_spm_nested Linear level1 l2pipeline:
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pwd: ../examples
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environment:
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SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
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FORCE_SPMMCR: 1
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general:
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artifacts:

‎docker/circleci/run_examples.sh

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#!/bin/bash
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for i in /etc/profile.d/*.sh; do
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source $i
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done
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source activate nipypetests-2.7
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cd /root/examples
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python /root/src/nipype/tools/run_examples.py $@

‎docker/test-image-base/Dockerfile

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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:$LD_LIBRARY_PATH' >> /etc/profile.d/nipype_deps.sh && \
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# echo 'export LD_LIBRARY_PATH=/root/mcr/v85/runtime/glnxa64:/root/mcr/v85/bin/glnxa64:/root/mcr/v85/sys/os/glnxa64:$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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‎docker/test-image/Dockerfile renamed to ‎docker/test-image-data/Dockerfile

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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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RUN curl -sSL "https://dl.dropbox.com/s/jzgq2nupxyz36bp/nipype-tutorial.tar.bz2" -o nipype-tutorial.tar.bz2 && \
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tar jxf nipype-tutorial.tar.bz2 -C /root/examples && \
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curl -sSL "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" -o fdt1.tar.gz && \
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curl -sSL "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz" -o fdt2.tar.gz && \
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curl -sSL "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz" -o 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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echo 'Untarring fsl course data...' && \
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tar zxf fdt1.tar.gz -C ~/examples/fsl_course_data && \
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tar zxf fdt2.tar.gz -C ~/examples/fsl_course_data && \
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tar zxf 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/nipype_data.sh
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt-get update && \
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apt-get install -y fsl-feeds && \
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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ENV FSL_COURSE_DATA /root/examples/fsl_course_data
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RUN echo 'source /etc/profile.d/nipype_data.sh' >> /etc/bash.bashrc
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CMD ["/bin/bash"]

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