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Dockerfile
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FROM ubuntu:xenial-20200114
# The popularity-contest is causing docker build to hang on apt install.
# cf. https://github.com/BRAINSia/BRAINSTools/issues/382
ARG DEBIAN_FRONTEND=noninteractive
# Install fmriprep dependances. - removed nodejs and bids validator, previously installed.
# cf. https://github.com/nipreps/fmriprep/blob/master/Dockerfile
# Prepare environment
RUN apt-get update && \
apt-get install -y --no-install-recommends \
curl \
bzip2 \
ca-certificates \
xvfb \
build-essential \
autoconf \
libtool \
pkg-config \
git && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# 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
# cf. https://docs.scipy.org/doc/scipy-1.1.0/reference/building/linux.html
# 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/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
# apt-key add /usr/local/etc/neurodebian.gpg && \
# (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
RUN apt-get update && \
apt-get install -y --no-install-recommends wget \
&& wget -O- http://neuro.debian.net/lists/xenial.de-fzj.full | tee /etc/apt/sources.list.d/neurodebian.sources.list \
&& apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
RUN apt-get update && \
apt-get install -y --no-install-recommends \
fsl-core=5.0.9-5~nd16.04+1 \
fsl-mni152-templates=5.0.7-2 \
afni=16.2.07~dfsg.1-5~nd16.04+1 \
convert3d \
connectome-workbench=1.3.2-2~nd16.04+1 \
git-annex-standalone && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# install nodejs (for bids-validator)
# cf. https://github.com/nodesource/distributions/blob/master/README.md#installation-instructions
RUN curl -sL https://deb.nodesource.com/setup_14.x | bash - \
&& apt-get install -y nodejs \
&& npm install npm@latest -g \
&& rm -rf apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# in/stall bids-validator.
RUN npm install -g [email protected]
ENV FSLDIR="/usr/share/fsl/5.0" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
POSSUMDIR="/usr/share/fsl/5.0" \
LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$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 2.3.4 (NeuroDocker build)
ENV ANTSPATH=/usr/lib/ants
RUN mkdir -p $ANTSPATH && \
curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
| tar -xzC $ANTSPATH --strip-components 1
ENV PATH=$ANTSPATH:$PATH
# Installing SVGO
RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -
RUN apt-get install -y nodejs
RUN npm install -g svgo
# Installing and setting up ICA_AROMA
RUN mkdir -p /opt/ICA-AROMA && \
curl -sSL "https://github.com/oesteban/ICA-AROMA/archive/v0.4.5.tar.gz" \
| tar -xzC /opt/ICA-AROMA --strip-components 1 && \
chmod +x /opt/ICA-AROMA/ICA_AROMA.py
ENV PATH="/opt/ICA-AROMA:$PATH" \
AROMA_VERSION="0.4.5"
# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users my_user
#USER my_user
WORKDIR /home/my_user
ENV HOME="/home/my_user"
# Installing precomputed python packages
# removed:
RUN conda install -y python=3.7.1 \
pip=19.1 \
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 - install templateflow
RUN python -m pip install --no-cache-dir templateflow>0.6
RUN python -c "from templateflow import api as tfapi; \
tfapi.get('MNI152NLin6Asym', resolution=(1, 2), suffix='T1w', desc=None); \
tfapi.get('MNI152NLin6Asym', resolution=(1, 2), desc='brain', suffix='mask'); \
tfapi.get('MNI152NLin2009cAsym', resolution=(1, 2), suffix='T1w', desc=None); \
tfapi.get('MNI152NLin2009cAsym', resolution=(1, 2), desc='brain', suffix='mask'); \
tfapi.get('MNI152NLin2009cAsym', resolution=1, desc='carpet', suffix='dseg'); \
tfapi.get('MNI152NLin2009cAsym', resolution=1, label='brain', suffix='probseg'); \
tfapi.get('MNI152NLin2009cAsym', resolution=2, desc='fMRIPrep', suffix='boldref'); \
tfapi.get('OASIS30ANTs'); \
tfapi.get('fsaverage', density='164k', desc='std', suffix='sphere'); \
tfapi.get('fsaverage', density='164k', desc='vaavg', suffix='midthickness'); \
tfapi.get('fsLR', density='32k'); \
tfapi.get('MNI152NLin6Asym', resolution=2, atlas='HCP', suffix='dseg'); \
tfapi.get('MNI152NLin6Asym'); \
tfapi.get('MNI152NLin2009cAsym'); \
tfapi.get('OASIS30ANTs'); \
tfapi.get('fsaverage'); \
tfapi.get('fsLR');"
RUN find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
# Install FMRIPREP
RUN python -m pip install fmriprep==20.2.0
ENV IS_DOCKER_8395080871=1
# Install SMRIPREP
# cf. https://pypi.org/project/smriprep/
RUN python -m pip install smriprep==0.7.0
# Install MRIQC
# cf. https://mriqc.readthedocs.io/en/latest/install.html +
# https://pypi.org/project/mriqc/#history
RUN python -m pip install mriqc==0.15.2
RUN find $HOME -type d -exec chmod go=u {} + && \
find $HOME -type f -exec chmod go=u {} + && \
rm -rf $HOME/.npm $HOME/.conda $HOME/.empty
RUN ldconfig
# RUN conda update conda # needed for conda activate
# Install our pipeline
COPY requirements.txt /preprocessing-src/requirements.txt
WORKDIR /preprocessing-src
RUN python -m pip install -r requirements.txt
COPY . /preprocessing-src
# Fix smriprep cf. https://github.com/nipreps/smriprep/issues/224
COPY smriprep-fasttrack-fix/ /usr/local/miniconda/lib/python3.7/site-packages/smriprep/smriprep/utils/
# RUN apt-get install -y openmpi-bin
ENTRYPOINT ["python", "main.py"]