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Dockerfile
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Dockerfile
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# Use Ubuntu 16.04 LTS
FROM ubuntu:xenial-20161213
# Pre-cache neurodebian key
COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
# Prepare environment
RUN apt-get update && \
apt-get install -y --no-install-recommends \
curl \
bzip2 \
ca-certificates \
xvfb \
cython3 \
build-essential \
autoconf \
libtool \
pkg-config \
git && \
curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
apt-get install -y --no-install-recommends \
nodejs && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# Install latest pandoc
RUN curl -o pandoc-2.2.2.1-1-amd64.deb -sSL "https://github.com/jgm/pandoc/releases/download/2.2.2.1/pandoc-2.2.2.1-1-amd64.deb" && \
dpkg -i pandoc-2.2.2.1-1-amd64.deb && \
rm pandoc-2.2.2.1-1-amd64.deb
# Installing freesurfer
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
--exclude='freesurfer/diffusion' \
--exclude='freesurfer/docs' \
--exclude='freesurfer/fsfast' \
--exclude='freesurfer/lib/cuda' \
--exclude='freesurfer/lib/qt' \
--exclude='freesurfer/matlab' \
--exclude='freesurfer/mni/share/man' \
--exclude='freesurfer/subjects/fsaverage_sym' \
--exclude='freesurfer/subjects/fsaverage3' \
--exclude='freesurfer/subjects/fsaverage4' \
--exclude='freesurfer/subjects/cvs_avg35' \
--exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
--exclude='freesurfer/subjects/bert' \
--exclude='freesurfer/subjects/lh.EC_average' \
--exclude='freesurfer/subjects/rh.EC_average' \
--exclude='freesurfer/subjects/sample-*.mgz' \
--exclude='freesurfer/subjects/V1_average' \
--exclude='freesurfer/trctrain'
ENV FSL_DIR="/usr/share/fsl/5.0" \
OS="Linux" \
FS_OVERRIDE=0 \
FIX_VERTEX_AREA="" \
FSF_OUTPUT_FORMAT="nii.gz" \
FREESURFER_HOME="/opt/freesurfer"
ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
MNI_DIR="$FREESURFER_HOME/mni" \
LOCAL_DIR="$FREESURFER_HOME/local" \
MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
MNI_DATAPATH="$FREESURFER_HOME/mni/data"
ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
# Installing Neurodebian packages (FSL, AFNI, git)
RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
apt-key add /usr/local/etc/neurodebian.gpg && \
(apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
RUN apt-get update && \
apt-get install -y --no-install-recommends \
fsl-core=5.0.9-5~nd16.04+1 \
afni=16.2.07~dfsg.1-5~nd16.04+1 \
convert3d \
git-annex-standalone && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
ENV FSLDIR="/usr/share/fsl/5.0" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
POSSUMDIR="/usr/share/fsl/5.0" \
LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" \
FSLTCLSH="/usr/bin/tclsh" \
FSLWISH="/usr/bin/wish" \
AFNI_MODELPATH="/usr/lib/afni/models" \
AFNI_IMSAVE_WARNINGS="NO" \
AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \
AFNI_PLUGINPATH="/usr/lib/afni/plugins"
ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
# Installing ANTs 2.2.0 (NeuroDocker build)
ENV ANTSPATH=/usr/lib/ants
RUN mkdir -p $ANTSPATH && \
curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz" \
| tar -xzC $ANTSPATH --strip-components 1
ENV PATH=$ANTSPATH:$PATH
# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users fmriprep
WORKDIR /home/fmriprep
ENV HOME="/home/fmriprep"
# Installing SVGO
RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -
RUN apt-get install -y nodejs
RUN npm install -g svgo
# Installing bids-validator
RUN npm install -g bids-validator@1.1.3
# Installing and setting up ICA_AROMA
RUN mkdir -p /opt/ICA-AROMA && \
curl -sSL "https://github.com/maartenmennes/ICA-AROMA/archive/v0.4.4-beta.tar.gz" \
| tar -xzC /opt/ICA-AROMA --strip-components 1 && \
chmod +x /opt/ICA-AROMA/ICA_AROMA.py
ENV PATH=/opt/ICA-AROMA:$PATH
# Installing and setting up miniconda
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
rm Miniconda3-4.5.11-Linux-x86_64.sh
# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
ENV PATH="/usr/local/miniconda/bin:$PATH" \
CPATH="/usr/local/miniconda/include/:$CPATH" \
LANG="C.UTF-8" \
LC_ALL="C.UTF-8" \
PYTHONNOUSERSITE=1
# Installing precomputed python packages
RUN conda install -y python=3.7.1 \
mkl=2018.0.3 \
mkl-service \
numpy=1.15.4 \
scipy=1.1.0 \
scikit-learn=0.19.1 \
matplotlib=2.2.2 \
pandas=0.23.4 \
libxml2=2.9.8 \
libxslt=1.1.32 \
graphviz=2.40.1 \
traits=4.6.0 \
zlib; sync && \
chmod -R a+rX /usr/local/miniconda; sync && \
chmod +x /usr/local/miniconda/bin/*; sync && \
conda build purge-all; sync && \
conda clean -tipsy && sync
# Unless otherwise specified each process should only use one thread - nipype
# will handle parallelization
ENV MKL_NUM_THREADS=1 \
OMP_NUM_THREADS=1
# Precaching fonts, set 'Agg' as default backend for matplotlib
RUN python -c "from matplotlib import font_manager" && \
sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
# Precaching atlases
ENV TEMPLATEFLOW_HOME="/opt/templateflow"
RUN mkdir -p $TEMPLATEFLOW_HOME
RUN pip install --no-cache-dir "templateflow>=0.1.0,<0.2.0a0" && \
python -c "from templateflow import api as tfapi; \
tfapi.get('MNI152Lin'); \
tfapi.get('MNI152NLin2009cAsym'); \
tfapi.get('OASIS30ANTs'); \
tfapi.get('NKI');"
# Installing dev requirements (packages that are not in pypi)
WORKDIR /src/
COPY requirements.txt requirements.txt
RUN pip install --no-cache-dir -r requirements.txt
# Installing FMRIPREP
COPY . /src/fmriprep
ARG VERSION
# Force static versioning within container
RUN echo "${VERSION}" > /src/fmriprep/fmriprep/VERSION && \
echo "include fmriprep/VERSION" >> /src/fmriprep/MANIFEST.in && \
cd /src/fmriprep && \
pip install --no-cache-dir .[all]
RUN install -m 0755 \
/src/fmriprep/scripts/generate_reference_mask.py \
/usr/local/bin/generate_reference_mask
RUN find $HOME -type d -exec chmod go=u {} + && \
find $HOME -type f -exec chmod go=u {} +
ENV IS_DOCKER_8395080871=1
RUN ldconfig
WORKDIR /tmp/
ENTRYPOINT ["/usr/local/miniconda/bin/fmriprep"]
ARG BUILD_DATE
ARG VCS_REF
ARG VERSION
LABEL org.label-schema.build-date=$BUILD_DATE \
org.label-schema.name="fMRIPrep" \
org.label-schema.description="fMRIPrep - robust fMRI preprocessing tool" \
org.label-schema.url="http://fmriprep.org" \
org.label-schema.vcs-ref=$VCS_REF \
org.label-schema.vcs-url="https://github.com/poldracklab/fmriprep" \
org.label-schema.version=$VERSION \
org.label-schema.schema-version="1.0"