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Dockerfile
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Dockerfile
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# Generated by Neurodocker version 0.4.3-6-g12a2b6f
# Timestamp: 2019-02-28 22:10:25 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@sha256:5fbbad8c68525b588a459092254094436aae9dc1f3920f8d871a03053b10377c
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/* /tmp/* /var/tmp/* \
&& 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 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
LABEL maintainer="Christopher J. Markiewicz"
ENV MKL_NUM_THREADS="1" \
OMP_NUM_THREADS="1"
RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro
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 "$conda_installer" \
&& conda update -yq -nbase conda \
&& conda config --system --prepend channels conda-forge \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
&& sync && conda clean -tipsy && sync \
&& conda create -y -q --name neuro \
&& conda install -y -q --name neuro \
'python=3.6' \
'icu=58.1' \
'mkl=2018.0.1' \
'mkl-service' \
'git=2.9.3' \
&& sync && conda clean -tipsy && sync
RUN conda install -y -q --name neuro \
'numpy=1.15' \
'scipy=1.2.0' \
'scikit-learn=0.19.1' \
'matplotlib=3.0.2' \
'seaborn=0.9.0' \
'pytables=3.4.4' \
'pandas=0.24.1' \
'patsy' \
'traits' \
&& sync && conda clean -tipsy && sync
COPY [".", "/src/fitlins"]
USER root
ARG VERSION
RUN echo "$VERSION" > /src/fitlins/fitlins/VERSION
RUN mkdir /work && chown -R neuro /src /work && chmod a+w /work
USER neuro
RUN bash -c "source activate neuro \
&& pip install --no-cache-dir -r \
'/src/fitlins/requirements.txt'" \
&& rm -rf ~/.cache/pip/* \
&& sync
RUN bash -c "source activate neuro \
&& pip install --no-cache-dir -e \
'/src/fitlins[all]'" \
&& rm -rf ~/.cache/pip/* \
&& sync \
&& sed -i '$isource activate neuro' $ND_ENTRYPOINT
WORKDIR /work
ENTRYPOINT ["/neurodocker/startup.sh", "fitlins"]
ARG BUILD_DATE
ARG VCS_REF
LABEL org.label-schema.build-date="$BUILD_DATE" \
org.label-schema.name="FitLins" \
org.label-schema.description="FitLins - Fit Linear Models to BIDS datasets" \
org.label-schema.url="http://github.com/poldracklab/fitlins" \
org.label-schema.vcs-ref="$VCS_REF" \
org.label-schema.vcs-url="https://github.com/poldracklab/fitlins" \
org.label-schema.version="$VERSION" \
org.label-schema.schema-version="1.0"
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "neurodebian@sha256:5fbbad8c68525b588a459092254094436aae9dc1f3920f8d871a03053b10377c" \
\n ], \
\n [ \
\n "label", \
\n { \
\n "maintainer": "Christopher J. Markiewicz" \
\n } \
\n ], \
\n [ \
\n "env", \
\n { \
\n "MKL_NUM_THREADS": "1", \
\n "OMP_NUM_THREADS": "1" \
\n } \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "create_env": "neuro", \
\n "conda_install": [ \
\n "python=3.6", \
\n "icu=58.1", \
\n "mkl=2018.0.1", \
\n "mkl-service", \
\n "git=2.9.3" \
\n ] \
\n } \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "use_env": "neuro", \
\n "conda_install": [ \
\n "numpy=1.15", \
\n "scipy=1.2.0", \
\n "scikit-learn=0.19.1", \
\n "matplotlib=3.0.2", \
\n "seaborn=0.9.0", \
\n "pytables=3.4.4", \
\n "pandas=0.24.1", \
\n "patsy", \
\n "traits" \
\n ] \
\n } \
\n ], \
\n [ \
\n "copy", \
\n [ \
\n ".", \
\n "/src/fitlins" \
\n ] \
\n ], \
\n [ \
\n "user", \
\n "root" \
\n ], \
\n [ \
\n "arg", \
\n { \
\n "VERSION": "" \
\n } \
\n ], \
\n [ \
\n "run", \
\n "echo \"$VERSION\" > /src/fitlins/fitlins/VERSION" \
\n ], \
\n [ \
\n "run", \
\n "mkdir /work && chown -R neuro /src /work && chmod a+w /work" \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "use_env": "neuro", \
\n "pip_opts": "-r", \
\n "pip_install": [ \
\n "/src/fitlins/requirements.txt" \
\n ] \
\n } \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "use_env": "neuro", \
\n "pip_opts": "-e", \
\n "pip_install": [ \
\n "/src/fitlins[all]" \
\n ], \
\n "activate": true \
\n } \
\n ], \
\n [ \
\n "workdir", \
\n "/work" \
\n ], \
\n [ \
\n "entrypoint", \
\n "/neurodocker/startup.sh fitlins" \
\n ], \
\n [ \
\n "arg", \
\n { \
\n "BUILD_DATE": "", \
\n "VCS_REF": "" \
\n } \
\n ], \
\n [ \
\n "label", \
\n { \
\n "org.label-schema.build-date": "$BUILD_DATE", \
\n "org.label-schema.name": "FitLins", \
\n "org.label-schema.description": "FitLins - Fit Linear Models to BIDS datasets", \
\n "org.label-schema.url": "http://github.com/poldracklab/fitlins", \
\n "org.label-schema.vcs-ref": "$VCS_REF", \
\n "org.label-schema.vcs-url": "https://github.com/poldracklab/fitlins", \
\n "org.label-schema.version": "$VERSION", \
\n "org.label-schema.schema-version": "1.0" \
\n } \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json