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Dockerfile
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# This Dockerfile constructs a docker image that contains an installation
# of the cortex-annotate project for annotating cortical surfaces.
#
# Example build:
# docker build --no-cache --tag cortex-annotate `pwd`
#
# (but really, use `docker-compose up` instead).
#
# Configuration ################################################################
# Start with the python 3.10 Jupyter scipy-notebook docker-image.
FROM jupyter/scipy-notebook:x86_64-python-3.10
# Note the Maintainer.
MAINTAINER Noah C. Benson <nben@uw.edu>
# The Root Operations ##########################################################
# The initial root operations are fast (making directories mostly), so we run
# them first; they are unlikely to fail or take any real time. Any COPY
# operations should come later on in the dockerfile after long-running layers
# have had an opportunity to fail (so that updates to the files don't force
# unrelated libraries to be reinstalled when building).
USER root
# Make some directories
RUN mkdir /cache \
&& mkdir /save \
&& mkdir /src \
&& mkdir /git \
&& mkdir /build \
&& mkdir /config \
&& mkdir /data \
&& mkdir -p /data/freesurfer/subjects \
&& mkdir -p /data/required_subjects \
&& mkdir -p /data/hcp/subjects \
&& mkdir -p /data/hcp/lines \
&& mkdir -p /data/hcp/meta \
&& chown -R $NB_USER /cache /save /src /git /config /data \
&& chmod -R 755 /cache /save /src /git /config /data
# Fix the ownership of the .ipython and .local directory if needed.
RUN [ -d /home/$NB_USER/.ipython/jupyter ] \
|| mkdir -p /home/$NB_USER/.ipython/jupyter
RUN [ -d /home/$NB_USER/.ipython/profile_default ] \
|| mkdir -p /home/$NB_USER/.ipython/profile_default
RUN chown -R $NB_USER /home/$NB_USER/.ipython \
&& chmod 700 /home/$NB_USER/.ipython
RUN [ -d /home/$NB_USER/.local ] \
|| mkdir /home/$NB_USER/.local
RUN chown -R $NB_USER /home/$NB_USER/.local
# Next, we want to make sure that we have an fsaverage and an fsaverage_sym
# subject for neuropythy to use if needed.
# Download the required FreeSurfer subjects.
RUN apt-get update \
&& apt-get install --yes --no-install-recommends curl
RUN curl -L -o /data/required_subjects/fsaverage.tar.gz \
https://github.com/noahbenson/neuropythy/wiki/files/fsaverage.tar.gz \
&& cd /data/required_subjects \
&& tar zxf fsaverage.tar.gz \
&& chown -R root.root ./fsaverage \
&& chmod -R 775 ./fsaverage \
&& rm fsaverage.tar.gz
RUN curl -L -o /data/required_subjects/fsaverage_sym.tar.gz \
https://github.com/noahbenson/neuropythy/wiki/files/fsaverage_sym.tar.gz \
&& cd /data/required_subjects \
&& tar zxf fsaverage_sym.tar.gz \
&& chown -R root.root ./fsaverage_sym \
&& chmod -R 775 ./fsaverage_sym \
&& rm ./fsaverage_sym.tar.gz
# The User Operations ##########################################################
# First, do the stuff that takes a long time but doesn't depend on anything from
# the filesystem outside this Dockerfile. That way if we tweak the files, we
# won't usually have to rebuild these dependencies.
USER $NB_USER
# Install some stuff we are likely to need, including neuropythy.
RUN mamba update -y -n base mamba
RUN mamba update --all -y
#RUN mamba install -y -cconda-forge nibabel s3fs
RUN mamba install -y -cconda-forge \
ipywidgets pip traitlets webcolors jsonschema-with-format-nongpl
RUN pip install --upgrade setuptools
RUN pip install ipycanvas pyyaml neuropythy nibabel s3fs
RUN pip install diplib
# Install collapsible cell extensions...
#RUN mamba install -cconda-forge jupyter_contrib_nbextensions \
# && jupyter contrib nbextension install --user \
# && jupyter nbextension enable collapsible_headings/main \
# && jupyter nbextension enable select_keymap/main
RUN mkdir -p /home/$NB_USER/.jupyter/custom
# Copy the config directory's requirements over and install them.
COPY config/requirements.txt /build/
RUN pip install -r /build/requirements.txt
# For some reason, tornado is causing major problems, so we downgrade to 6.1 here:
RUN pip install \
'tornado == 6.1' \
'jupyter-client == 7.3.2' \
'jupyter-server < 2.0.0'
# Copy User Files ##############################################################
user $NB_USER
# Now, do things that depend on the local files. COPY statements should go in
# this section rather than earlier when possible.
COPY docker/jupyter_notebook_config.py /home/$NB_USER/.jupyter/
COPY docker/custom.css /home/$NB_USER/.jupyter/custom/
COPY docker/custom.js /home/$NB_USER/.jupyter/custom/
COPY docker/ipython_kernel_config.py /home/$NB_USER/.ipython/profile_default/
COPY docker/npythy.json /home/$NB_USER/.npythyrc
COPY docker/ipython-startup.py /home/$NB_USER/.ipython/profile_default/startup/
COPY notebooks/annotate.ipynb /home/$NB_USER/work/AnnotationTool.ipynb
# We want to trust the notebook (this also fixed id-less cells).
RUN jupyter trust /home/$NB_USER/work/AnnotationTool.ipynb
# Finaly, copy over the annotate library and any other code.
COPY src/ /src/
# Custom Build Scripts #########################################################
# The last thing we do is run any custom build scripts. The root scripts get run
# first, then the user script.
USER root
COPY config/build_root.sh /build/
RUN chmod 755 /build/build_root.sh
# Run the root script.
RUN /bin/bash /build/build_root.sh
# Then the user script.
COPY config/build_user.sh /build/
RUN chmod 755 /build/build_user.sh
USER $NB_USER
RUN /bin/bash /build/build_user.sh
# Permission Cleanup ###########################################################
# We need to fix the permissions for anything created in the meantime.
USER root
RUN fix-permissions /home/$NB_USER/.ipython
# Entrypoint ###################################################################
USER $NB_USER
ENTRYPOINT ["tini", "-g", "--", "/usr/local/bin/start-notebook.sh"]