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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
# Installing Neurodebian packages (FSL, AFNI, git)
RUN apt-get update && \
apt-get install -y --no-install-recommends curl && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
curl -sSL "http://neuro.debian.net/lists/xenial.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)
# Prepare environment
RUN apt-get update && \
apt-get install -y --no-install-recommends \
autoconf \
build-essential \
bzip2 \
ca-certificates \
curl \
cython3 \
ed \
git \
git-annex-standalone \
graphviz=2.38.0-12ubuntu2 \
gsl-bin \
libglib2.0-0 \
libglu1-mesa-dev \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libtool \
libxm4 \
netpbm \
pkg-config \
tcsh \
xfonts-base \
xvfb \
fsl-core=5.0.9-5~nd16.04+1 \
fsl-mni152-templates && \
curl -sSL https://deb.nodesource.com/setup_10.x | bash - && \
apt-get install -y --no-install-recommends \
nodejs && \
echo "Install libxp (not in all ubuntu/debian repositories)" && \
apt-get install -yq --no-install-recommends libxp6 \
|| /bin/bash -c " \
curl --retry 5 -o /tmp/libxp6.deb -sSL http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& dpkg -i /tmp/libxp6.deb && rm -f /tmp/libxp6.deb" && \
echo "Install libpng12 (not in all ubuntu/debian repositories" && \
apt-get install -yq --no-install-recommends libpng12-0 \
|| /bin/bash -c " \
curl -o /tmp/libpng12.deb -sSL http://mirrors.kernel.org/debian/pool/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
&& dpkg -i /tmp/libpng12.deb && rm -f /tmp/libpng12.deb" && \
ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.19 /usr/lib/x86_64-linux-gnu/libgsl.so.0 && \
ldconfig && \
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:$LD_LIBRARY_PATH" \
FSLTCLSH="/usr/bin/tclsh" \
FSLWISH="/usr/bin/wish"
ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$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:$PATH
# Installing AFNI (version 17_3_03 archived on OSF)
RUN mkdir -p /opt/afni && \
curl -o afni.tar.gz -sSLO "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5a0dd9a7b83f69027512a12b" && \
tar zxv -C /opt/afni --strip-components=1 -f afni.tar.gz && \
rm -rf afni.tar.gz
ENV PATH=/opt/afni:$PATH \
AFNI_MODELPATH="/opt/afni/models" \
AFNI_IMSAVE_WARNINGS="NO" \
AFNI_TTATLAS_DATASET="/opt/afni/atlases" \
AFNI_PLUGINPATH="/opt/afni/plugins"
# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users bidsapp
WORKDIR /home/bidsapp
ENV HOME="/home/bidsapp"
# Installing SVGO
RUN npm install -g svgo
# Installing and setting up miniconda
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
rm Miniconda3-4.5.11-Linux-x86_64.sh
# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
ENV PATH="/usr/local/miniconda/bin:$PATH" \
CPATH="/usr/local/miniconda/include/:$CPATH" \
LANG="C.UTF-8" \
LC_ALL="C.UTF-8" \
PYTHONNOUSERSITE=1
# Consider PYTHONWARNINGS="ignore,default:::mriqc,default:::nipype"
# Installing precomputed python packages
RUN conda install -y python=3.7.1 \
graphviz=2.40.1 \
libxml2=2.9.8 \
libxslt=1.1.32 \
matplotlib=2.2.2 \
mkl-service \
mkl=2018.0.3 \
numpy=1.15.4 \
pandas=0.23.4 \
scikit-learn=0.19.1 \
scipy=1.1.0 \
setuptools>=40.0.0 \
traits=4.6.0 \
pip=19.1 \
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' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
# Installing dev requirements (packages that are not in pypi)
WORKDIR /src/
COPY requirements.txt requirements.txt
RUN pip install --no-cache-dir -r requirements.txt
# Precaching atlases
RUN python -c "from templateflow import api as tfapi; \
tfapi.get('MNI152NLin2009cAsym', resolution=[1, 2], suffix='T1w', desc=None); \
tfapi.get('MNI152NLin2009cAsym', resolution=[1, 2], suffix='mask',\
desc=['brain', 'head']); \
tfapi.get('MNI152NLin2009cAsym', resolution=1, suffix='dseg', desc='carpet'); \
tfapi.get('MNI152NLin2009cAsym', resolution=1, suffix='probseg',\
label=['CSF', 'GM', 'WM']);\
tfapi.get('MNI152NLin2009cAsym', resolution=[1, 2], suffix='boldref')"
# Installing MRIQC
COPY . /src/mriqc
ARG VERSION
# Force static versioning within container
RUN echo "${VERSION}" > /src/mriqc/mriqc/VERSION && \
echo "include mriqc/VERSION" >> /src/mriqc/MANIFEST.in && \
cd /src/mriqc && \
pip install --no-cache-dir .[all]
RUN find $HOME -type d -exec chmod go=u {} + && \
find $HOME -type f -exec chmod go=u {} +
# Best practices
RUN ldconfig
WORKDIR /tmp/
# Run mriqc by default
ENTRYPOINT ["/usr/local/miniconda/bin/mriqc"]
ARG BUILD_DATE
ARG VCS_REF
LABEL org.label-schema.build-date=$BUILD_DATE \
org.label-schema.name="MRIQC" \
org.label-schema.description="MRIQC - Automated Quality Control and visual reports for Quality Assesment of structural (T1w, T2w) and functional MRI of the brain" \
org.label-schema.url="http://mriqc.readthedocs.io" \
org.label-schema.vcs-ref=$VCS_REF \
org.label-schema.vcs-url="https://github.com/poldracklab/mriqc" \
org.label-schema.version=$VERSION \
org.label-schema.schema-version="1.0"