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ARG MIRACL_VERSION=latest
FROM mgoubran/miracl:revised-base-$MIRACL_VERSION
ADD . /code
# delete ruamel pkg
RUN rm -rf $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/ruamel* && \
pip install markupsafe==2.0.1 && \
# Install setuptools v65.6.0 as latest version (v67.0.0)
# breaks parsing. Temporary fix only. In the long run,
# scripts should be refactored to work with current version!
pip install setuptools==65.6.0 && \
pip install -e /code/ "botocore >= 1.20.110"
ENV MIRACL_HOME=/code/miracl
ENV ATLASES_HOME=/code/atlases
COPY ./utility_scripts /usr/bin
RUN chmod o+x /usr/bin/download_sample_data
# Point to g++-5 for NiftyReg compilation
RUN update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 50 --slave /usr/bin/g++ g++ /usr/bin/g++-5
#--- Install NiftyReg ---
ARG NR_INSTALL_DIR=/opt/niftyreg
RUN mkdir -p /tmp/niftyreg_source && \
git clone https://github.com/SuperElastix/niftyreg.git /tmp/niftyreg_source && \
mkdir -p /tmp/niftyreg && \
mkdir -p $NR_INSTALL_DIR
WORKDIR /tmp/niftyreg
RUN cmake \
-D BUILD_ALL_DEP=ON \
-D BUILD_SHARED_LIBS=OFF \
-D BUILD_TESTING=OFF \
-D CMAKE_BUILD_TYPE=Release \
-D CMAKE_INSTALL_PREFIX=$NR_INSTALL_DIR \
-D M_LIBRARY=/opt/miniconda/include \
-D PNG_INCLUDE_DIR=/opt/miniconda/lib/libpng.so \
-D USE_CUDA=OFF \
-D USE_OPENCL=OFF \
-D USE_OPENMP=ON \
-D USE_SSE=ON \
/tmp/niftyreg_source && \
make && \
make install && \
rm -r /tmp/niftyreg && \
rm -r /tmp/niftyreg_source
ENV PATH=$NR_INSTALL_DIR/bin:$PATH
ENV LD_LIBRARY_PATH=$NR_INSTALL_DIR/lib:$LD_LIBRARY_PATH
# Point back to latest GNU compiler (g++-9)
RUN update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 90 --slave /usr/bin/g++ g++ /usr/bin/g++-9
###############################################################################
#--- Allen atlas alias ----
WORKDIR /tmp
RUN mkdir -p /code/atlases/ara && \
wget -P /code/atlases https://www.dropbox.com/sh/j31vurlp6h4lvod/AAAIKpYJQizkAte3Ju5DZYj8a --content-disposition && \
unzip /code/atlases/ara.zip -x / -d /code/atlases/ara
# RUN conda install -y --no-update-deps pyqt=5
ENV aradir "/code/atlases/ara"
# Templates (atlas images)
ENV allen10 "/code/atlases/ara/template/average_template_10um.nii.gz"
ENV allen25 "/code/atlases/ara/template/average_template_25um.nii.gz"
ENV allen50 "/code/atlases/ara/template/average_template_50um.nii.gz"
# Annotations (labels)
ENV lbls10 "/code/atlases/ara/annotation/annotation_hemi_combined_10um.nii.gz"
ENV lbls25 "/code/atlases/ara/annotation/annotation_hemi_combined_25um.nii.gz"
ENV lbls50 "/code/atlases/ara/annotation/annotation_hemi_combined_50um.nii.gz"
# Grand-parents labels
ENV gplbls25="/code/atlases/ara/annotation/annotation_hemi_combined_25um_parent-level_3.nii.gz"
ENV gplbls50="/code/atlases/ara/annotation/annotation_hemi_combined_50um_parent-level_3.nii.gz"
# ITK-snap LUT
ENV snaplut "/code/atlases/ara/ara_snaplabels_lut.txt"
# Freeview LUT
ENV freelut "/code/atlases/ara/ara_freeviewlabels_lut.txt"
# ANTs commands
RUN ln -sf "/code/depends/ants/antsRegistrationMIRACL.sh" /usr/bin/ants_miracl_clar && \
chmod +x /usr/bin/ants_miracl_clar
RUN ln -sf "/code/depends/ants/antsRegistrationMIRACL_MRI.sh" /usr/bin/ants_miracl_mr && \
chmod +x /usr/bin/ants_miracl_mr
ENV ANTSPATH "${ANTSPATH}:/code/depends/ants"
ENV IN_DOCKER_CONTAINER Yes
#STARTUNCOMMENT#
#STOPUNCOMMENT#
################################################################################
# Temporarily uncommented to allow interactive shell access to Docker container
#ENTRYPOINT ["/opt/miniconda/bin/miracl"]