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Dockerfile
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Dockerfile
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# Your version: 0.6.0 Latest version: 0.8.0
# Generated by Neurodocker version 0.6.0
# Timestamp: 2022-04-05 13:16:21 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#
# https://github.com/kaczmarj/neurodocker
FROM neurodebian:stretch-non-free
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' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
git \
num-utils \
gcc \
g++ \
curl \
build-essential \
nano \
graphviz \
tree \
git-annex-standalone \
nano \
less \
ncdu \
git-annex-remote-rclone \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN test "$(getent passwd neuroscout)" || useradd --no-user-group --create-home --shell /bin/bash neuroscout
USER neuroscout
ENV CONDA_DIR="/opt/miniconda-latest" \
PATH="/opt/miniconda-latest/bin:$PATH"
RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
&& echo "Downloading Miniconda installer ..." \
&& conda_installer="/tmp/miniconda.sh" \
&& curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& bash "$conda_installer" -b -p /opt/miniconda-latest \
&& rm -f "$conda_installer" \
&& conda update -yq -nbase conda \
&& conda config --system --prepend channels conda-forge \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
&& sync && conda clean --all && sync \
&& conda create -y -q --name neuroscout_paper \
&& conda install -y -q --name neuroscout_paper \
"python=3.8" \
"nb_conda" \
"nb_conda_kernels" \
"nbconvert==6.4.5" \
"nbformat" \
"jupyter" \
&& sync && conda clean --all && sync \
&& bash -c "source activate neuroscout_paper \
&& pip install --no-cache-dir \
"seaborn" \
"pyns==0.4.10" \
"nilearn==0.8.0" \
"altair" \
"nimare==0.0.11" \
"pymare==0.0.2" \
"jupytext==1.11.5" \
"ghp-import" \
"jupyter-book==0.12.2" \
"myst-nb==0.13.2" \
"sympy==1.2" \
"sphinx-book-theme" \
"jupyter_contrib_nbextensions" \
"nbval" \
"duecredit"" \
&& rm -rf ~/.cache/pip/* \
&& sync \
&& sed -i '$isource activate neuroscout_paper' $ND_ENTRYPOINT
COPY [".", "/home/neuroscout/info"]
USER root
RUN chown -R neuroscout /home/neuroscout/info
RUN rm -rf /opt/conda/pkgs/*
USER neuroscout
RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
WORKDIR /home/neuroscout/info/paper
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "neurodebian:stretch-non-free" \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "git", \
\n "num-utils", \
\n "gcc", \
\n "g++", \
\n "curl", \
\n "build-essential", \
\n "nano", \
\n "graphviz", \
\n "tree", \
\n "git-annex-standalone", \
\n "nano", \
\n "less", \
\n "ncdu", \
\n "git-annex-remote-rclone" \
\n ] \
\n ], \
\n [ \
\n "user", \
\n "neuroscout" \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "conda_install": [ \
\n "python=3.8", \
\n "nb_conda", \
\n "nb_conda_kernels", \
\n "nbconvert==6.4.5", \
\n "nbformat", \
\n "jupyter" \
\n ], \
\n "pip_install": [ \
\n "seaborn", \
\n "pyns==0.4.10", \
\n "nilearn==0.8.0", \
\n "altair", \
\n "nimare==0.0.11", \
\n "pymare==0.0.2", \
\n "jupytext==1.11.5", \
\n "ghp-import", \
\n "jupyter-book==0.12.2", \
\n "myst-nb==0.13.2", \
\n "sympy==1.2", \
\n "sphinx-book-theme", \
\n "jupyter_contrib_nbextensions", \
\n "nbval", \
\n "duecredit" \
\n ], \
\n "create_env": "neuroscout_paper", \
\n "activate": true \
\n } \
\n ], \
\n [ \
\n "copy", \
\n [ \
\n ".", \
\n "/home/neuroscout/info" \
\n ] \
\n ], \
\n [ \
\n "user", \
\n "root" \
\n ], \
\n [ \
\n "run", \
\n "chown -R neuroscout /home/neuroscout/info" \
\n ], \
\n [ \
\n "run", \
\n "rm -rf /opt/conda/pkgs/*" \
\n ], \
\n [ \
\n "user", \
\n "neuroscout" \
\n ], \
\n [ \
\n "run", \
\n "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py" \
\n ], \
\n [ \
\n "workdir", \
\n "/home/neuroscout/info/paper" \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json