Dockerfile

FROM jupyter/datascience-notebook:7a3e968dd212

# Neurodebian:

USER root
# https://bugs.debian.org/830696 (apt uses gpgv by default in newer releases, rather than gpg)
RUN set -x \
	&& apt-get update \
	&& { \
		which gpg \
		|| apt-get install -y --no-install-recommends gnupg \
	; } \
# Ubuntu includes "gnupg" (not "gnupg2", but still 2.x), but not dirmngr, and gnupg 2.x requires dirmngr
# so, if we're not running gnupg 1.x, explicitly install dirmngr too
	&& { \
		gpg --version | grep -q '^gpg (GnuPG) 1\.' \
		|| apt-get install -y --no-install-recommends dirmngr \
	; } \
	&& rm -rf /var/lib/apt/lists/*

# apt-key is a bit finicky during "docker build" with gnupg 2.x, so install the repo key the same way debian-archive-keyring does (/etc/apt/trusted.gpg.d)
# this makes "apt-key list" output prettier too!
RUN set -x \
	&& export GNUPGHOME="$(mktemp -d)" \
	&& gpg --batch --keyserver ha.pool.sks-keyservers.net --recv-keys DD95CC430502E37EF840ACEEA5D32F012649A5A9 \
	&& gpg --batch --export DD95CC430502E37EF840ACEEA5D32F012649A5A9 > /etc/apt/trusted.gpg.d/neurodebian.gpg \
	&& rm -rf "$GNUPGHOME" \
	&& apt-key list | grep neurodebian

RUN { \
	echo 'deb http://neuro.debian.net/debian trusty main'; \
	echo 'deb http://neuro.debian.net/debian data main'; \
	echo '#deb-src http://neuro.debian.net/debian-devel trusty main'; \
} > /etc/apt/sources.list.d/neurodebian.sources.list

# Minimalistic package to assist with freezing the APT configuration
# which would be coming from neurodebian repo.
# Also install and enable eatmydata to be used for all apt-get calls
# to speed up docker builds.
RUN set -x \
	&& apt-get update \
	&& apt-get install -y --no-install-recommends neurodebian-freeze eatmydata \
	&& ln -s /usr/bin/eatmydata /usr/local/bin/apt-get \
	&& rm -rf /var/lib/apt/lists/*

# Neurodocker:
ARG DEBIAN_FRONTEND="noninteractive"

ENV LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8" \
    ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           apt-utils \
           bzip2 \
           ca-certificates \
           curl \
           locales \
           unzip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
    && dpkg-reconfigure --frontend=noninteractive locales \
    && update-locale LANG="en_US.UTF-8" \
    && chmod 777 /opt && chmod a+s /opt \
    && mkdir -p /neurodocker \
    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
    fi \
    && chmod -R 777 /neurodocker && chmod a+s /neurodocker

ENTRYPOINT ["/neurodocker/startup.sh"]

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           ants \
           gcc \
           g++ \
           graphviz \
           tree \
           git-annex-standalone \
           vim \
           emacs-nox \
           nano \
           less \
           ncdu \
           tig \
           git-annex-remote-rclone \
           octave \
           netbase \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

ENV FREESURFER_HOME="/opt/freesurfer-6.0.0-min" \
    PATH="/opt/freesurfer-6.0.0-min/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libgomp1 \
           libxmu6 \
           libxt6 \
           perl \
           tcsh \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FreeSurfer ..." \
    && mkdir -p /opt/freesurfer-6.0.0-min \
    && curl -fsSL --retry 5 https://dl.dropbox.com/s/nnzcfttc41qvt31/recon-all-freesurfer6-3.min.tgz \
    | tar -xz -C /opt/freesurfer-6.0.0-min --strip-components 1 \
    && sed -i '$isource "/opt/freesurfer-6.0.0-min/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"

### End neurodocker

RUN mkdir /data && chown jovyan /data && chmod 777 /data && mkdir /output && chown jovyan /output && chmod 777 /output && mkdir /repos && chown jovyan /repos && chmod 777 /repos

USER jovyan

RUN  pip install  --no-cache-dir \
             https://github.com/nipy/nipype/tarball/master \
             https://github.com/INCF/pybids/tarball/master \
             https://github.com/ipython-contrib/jupyter_contrib_nbextensions/tarball/master \
             https://github.com/nipype/pydra/tarball/master \
             https://github.com/noahbenson/popeye/tarball/master \
             https://github.com/rflamary/POT/tarball/master \
             https://github.com/hichamjanati/mtw/tarball/master \
             mne \
             s3fs \
             pytest \
             cookiecutter \
             flake8 \
             black \
             neuropythy \
             ipyvolume \
             nilearn \
             datalad[full] \
             nipy \
             duecredit \
             nbval \
             dipy \
             tensorflow \
             keras \
             cloudknot \
             nbgitpuller \
             psutil\
             memory_profiler \
             pybids \
             neurosynth\
             pythreejs \
             voila \
             jupyter_nbextensions_configurator

# This is for https://github.com/rkern/line_profiler/issues/132
RUN git clone https://github.com/rkern/line_profiler.git && find line_profiler -name '*.pyx' -exec cython {} \; && cd line_profiler && pip install . --user && cd && rm -rf line_profiler

RUN conda update -n base conda && conda install \
    python-graphviz

RUN conda install -c conda-forge altair vega_datasets ipyvolume

RUN conda install -c r rpy2 r-ggplot2

RUN cd /data && datalad install -r ///workshops/nih-2017/ds000114 \
        && cd ds000114 \
        && datalad update -r \
        && datalad get -r sub-01/ses-test/anat sub-01/ses-test/func/


RUN jupyter labextension install @jupyterlab/hub-extension
RUN jupyter labextension install ipyvolume
RUN jupyter labextension install jupyter-threejs
RUN jupyter labextension install @lckr/jupyterlab_variableinspector
RUN jupyter labextension install @jupyter-voila/jupyterlab-preview
RUN jupyter contrib nbextension install --user
RUN jupyter nbextension enable exercise2/main
RUN jupyter nbextensions_configurator enable --user


# Begin stuff for Noah's tutorial:
RUN mkdir -p /data/freesurfer_subjects \
 && curl -L -o /data/freesurfer_subjects/fsaverage.tar.gz https://github.com/noahbenson/neuropythy/wiki/files/fsaverage.tar.gz \
 && curl -L -o /data/freesurfer_subjects/fsaverage_sym.tar.gz https://github.com/noahbenson/neuropythy/wiki/files/fsaverage_sym.tar.gz \
 && cd /data/freesurfer_subjects && tar zxf fsaverage.tar.gz && tar zxf fsaverage_sym.tar.gz && rm ./fsaverage.tar.gz ./fsaverage_sym.tar.gz

# Get the npythyrc file:
RUN curl -L -o "$HOME/.npythyrc" https://raw.githubusercontent.com/noahbenson/neuropythy/master/docker/npythyrc
# Make a directory for the HCP data and neuropythy's cache
RUN mkdir -p /data/hcp/subjects /data/cache
# End of stuff for Noah's tutorial