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first revision of general Dockerfile
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‎Dockerfile

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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:latest
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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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#
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# Based on https://github.com/poldracklab/fmriprep/blob/9c92a3de9112f8ef1655b876de060a2ad336ffb0/Dockerfile
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#
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FROM ubuntu:xenial-20161213
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# Prepare environment
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RUN apt-get update && \
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apt-get install -y --no-install-recommends curl bzip2 ca-certificates xvfb && \
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curl -sSL http://neuro.debian.net/lists/xenial.us-ca.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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# Installing freesurfer
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RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
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--exclude='freesurfer/trctrain' \
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--exclude='freesurfer/subjects/fsaverage_sym' \
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--exclude='freesurfer/subjects/fsaverage3' \
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--exclude='freesurfer/subjects/fsaverage4' \
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--exclude='freesurfer/subjects/fsaverage5' \
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--exclude='freesurfer/subjects/fsaverage6' \
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--exclude='freesurfer/subjects/cvs_avg35' \
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--exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
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--exclude='freesurfer/subjects/bert' \
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--exclude='freesurfer/subjects/V1_average' \
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--exclude='freesurfer/average/mult-comp-cor' \
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--exclude='freesurfer/lib/cuda' \
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--exclude='freesurfer/lib/qt'
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ENV FSL_DIR=/usr/share/fsl/5.0 \
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OS=Linux \
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FS_OVERRIDE=0 \
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FIX_VERTEX_AREA= \
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FSF_OUTPUT_FORMAT=nii.gz \
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FREESURFER_HOME=/opt/freesurfer
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ENV SUBJECTS_DIR=$FREESURFER_HOME/subjects \
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FUNCTIONALS_DIR=$FREESURFER_HOME/sessions \
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MNI_DIR=$FREESURFER_HOME/mni \
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LOCAL_DIR=$FREESURFER_HOME/local \
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FSFAST_HOME=$FREESURFER_HOME/fsfast \
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MINC_BIN_DIR=$FREESURFER_HOME/mni/bin \
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MINC_LIB_DIR=$FREESURFER_HOME/mni/lib \
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MNI_DATAPATH=$FREESURFER_HOME/mni/data \
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FMRI_ANALYSIS_DIR=$FREESURFER_HOME/fsfast
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ENV PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
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MNI_PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
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PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH
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RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
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# Installing Neurodebian packages (FSL, AFNI, git)
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RUN apt-get install -y --no-install-recommends \
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fsl-core=5.0.9-1~nd+1+nd16.04+1 \
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afni=16.2.07~dfsg.1-2~nd16.04+1
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ENV FSLDIR=/usr/share/fsl/5.0 \
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FSLOUTPUTTYPE=NIFTI_GZ \
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FSLMULTIFILEQUIT=TRUE \
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POSSUMDIR=/usr/share/fsl/5.0 \
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LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
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FSLTCLSH=/usr/bin/tclsh \
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FSLWISH=/usr/bin/wish \
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AFNI_MODELPATH=/usr/lib/afni/models \
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AFNI_IMSAVE_WARNINGS=NO \
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AFNI_TTATLAS_DATASET=/usr/share/afni/atlases \
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AFNI_PLUGINPATH=/usr/lib/afni/plugins \
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PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH
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# Installing and setting up ANTs
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RUN mkdir -p /opt/ants && \
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curl -sSL "https://github.com/stnava/ANTs/releases/download/v2.1.0/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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PATH=$ANTSPATH:$PATH
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# Installing and setting up c3d
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RUN mkdir -p /opt/c3d && \
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curl -sSL "http://downloads.sourceforge.net/project/c3d/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz" \
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| tar -xzC /opt/c3d --strip-components 1
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ENV C3DPATH=/opt/c3d/ \
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PATH=$C3DPATH/bin:$PATH
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# Install some other required tools
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ENV apt-get install -y --no-install-recommends \
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unzip \
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apt-utils \
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fusefat \
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graphviz \
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make \
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ruby && \
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# Install fake-S3
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ENV GEM_HOME /usr/local/bundle
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ENV BUNDLE_PATH="$GEM_HOME" \
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BUNDLE_BIN="$GEM_HOME/bin" \
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BUNDLE_SILENCE_ROOT_WARNING=1 \
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BUNDLE_APP_CONFIG="$GEM_HOME"
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ENV PATH $BUNDLE_BIN:$PATH
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RUN mkdir -p "$GEM_HOME" "$BUNDLE_BIN" && \
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chmod 777 "$GEM_HOME" "$BUNDLE_BIN"
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RUN gem install fakes3
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# Install Matlab MCR: from the good old install_spm_mcr.sh of @chrisfilo
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WORKDIR /opt
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RUN echo "destinationFolder=/opt/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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# 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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ENV MATLABCMD="/opt/mcr/v85/toolbox/matlab" \
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SPMMCRCMD="/opt/spm12/run_spm12.sh /opt/mcr/v85/ script" \
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FORCE_SPMMCR=1
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# Install this branch's code
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WORKDIR /root/src
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# Installing and setting up miniconda
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RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh && \
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bash Miniconda3-4.2.12-Linux-x86_64.sh -b -p /usr/local/miniconda && \
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rm Miniconda3-4.2.12-Linux-x86_64.sh
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# Install matplotlib, sphinx and coverage to build documentation
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# and run tests with coverage
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RUN source activate nipypetests-2.7 && \
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pip install matplotlib sphinx coverage && \
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source activate nipypetests-3.4 && \
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pip install matplotlib sphinx coverage && \
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source activate nipypetests-3.5 && \
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pip install matplotlib sphinx coverage
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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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ADD . nipype/
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# Installing precomputed python packages
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RUN conda config --add channels intel && \
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conda config --set always_yes yes --set changeps1 no && \
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conda update -q conda && \
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conda install -y mkl=2017.0.1 \
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numpy=1.11.2 \
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scipy=0.18.1 \
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scikit-learn=0.17.1 \
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matplotlib=1.5.3 \
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pandas=0.19.0 \
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libxml2=2.9.4 \
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libxslt=1.1.29 \
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traits=4.6.0 \
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icu && \
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chmod +x /usr/local/miniconda/bin/* && \
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conda clean --all -y
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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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# Precaching fonts
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RUN python -c "from matplotlib import font_manager"
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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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# Installing Ubuntu packages and cleaning up
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RUN apt-get install -y --no-install-recommends \
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git=1:2.7.4-0ubuntu1 \
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graphviz=2.38.0-12ubuntu2 && \
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apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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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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# Unless otherwise specified each process should only use one thread - nipype
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# will handle parallelization
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ENV MKL_NUM_THREADS=1 \
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OMP_NUM_THREADS=1
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WORKDIR /scratch
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# Installing dev requirements (packages that are not in pypi)
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WORKDIR /root/
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ADD 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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# Install entrypoints
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ADD docker/circleci/run_* /usr/bin/
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RUN chmod +x /usr/bin/run_*
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# Installing nipype
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COPY . /root/src/nipype
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RUN cd /root/src/nipype && \
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pip install -e .[all] && \
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rm -rf ~/.cache/pip
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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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WORKDIR /root/
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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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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=$VCS_REF \
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org.label-schema.vcs-url="https://github.com/nipy/nipype" \
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org.label-schema.version=$VERSION \
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org.label-schema.schema-version="1.0"

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