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Dockerfile_v0.3
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Dockerfile_v0.3
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# This Dockerfile is written with the help of the output of Neurodocker
FROM debian:buster-slim
ARG DEBIAN_FRONTEND=noninteractive
LABEL maintainer="Tamas Spisak <[email protected]>"
ARG NB_USER="pumi"
ARG NB_UID="1000"
ARG NB_GID="100"
USER root
# [ROOT] SET UP CONDA:
ENV CONDA_DIR="/opt/miniconda-latest" \
PATH="/opt/miniconda-latest/bin:$PATH"
RUN apt-get update --yes && apt-get upgrade --yes && apt-get install --yes --no-install-recommends \
git \
bzip2 \
ca-certificates \
curl \
&& rm -rf /var/lib/apt/lists/* \
&& export PATH="/opt/miniconda-latest/bin:$PATH" \
&& echo "Downloading Miniconda installer ..." \
&& conda_installer="/tmp/miniconda.sh" \
&& curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& bash "$conda_installer" -b -p /opt/miniconda-latest \
&& rm -f "$conda_installer" \
&& conda update -yq -nbase conda \
&& conda config --system --prepend channels conda-forge \
&& conda config --set channel_priority strict \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
# Enable `conda activate`
&& conda init bash \
&& conda install -y --name base \
"python=3.9" \
# Clean up
&& sync && conda clean --all --yes && sync \
&& rm -rf ~/.cache/pip/*
# **********************************************************************************************************************
# [ROOT] CREATE USER:
# The following part for the user-creation is adapted from Jupyter Docker Stacks
# https://github.com/jupyter/docker-stacks/blob/main/docker-stacks-foundation/Dockerfile
ENV HOME="/home/${NB_USER}"
RUN apt-get update --yes && apt-get upgrade --yes && apt-get install --yes --no-install-recommends \
bzip2 \
ca-certificates \
sudo && \
apt-get clean && rm -rf /var/lib/apt/lists/*
RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && \
mkdir -p "${CONDA_DIR}" && \
chown "${NB_USER}:${NB_GID}" "${CONDA_DIR}" && \
chmod g+w /etc/passwd
# fix permissions
RUN chgrp -R "${NB_GID}" "${HOME}" && chmod -R g+rwX "${HOME}" && find "${HOME}" -type d -exec chmod +6000 {} +
RUN chgrp -R "${NB_GID}" "${CONDA_DIR}" && chmod -R g+rwX "${CONDA_DIR}" && find "${CONDA_DIR}" -type d -exec chmod +6000 {} +
# **********************************************************************************************************************
# [ROOT] INSTALL AFNI:
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
git \
&& rm -rf /var/lib/apt/lists/*
ENV PATH="/opt/afni-latest:$PATH" \
AFNI_PLUGINPATH="/opt/afni-latest"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ca-certificates \
curl \
ed \
gsl-bin \
libgl1-mesa-dri \
libglib2.0-0 \
libglu1-mesa-dev \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libxm4 \
multiarch-support \
netpbm \
tcsh \
xfonts-base \
xvfb \
&& rm -rf /var/lib/apt/lists/* \
&& _reproenv_tmppath="$(mktemp -t tmp.XXXXXXXXXX.deb)" \
&& curl -fsSL --retry 5 -o "${_reproenv_tmppath}" http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& apt-get install --yes -q "${_reproenv_tmppath}" \
&& rm "${_reproenv_tmppath}" \
&& _reproenv_tmppath="$(mktemp -t tmp.XXXXXXXXXX.deb)" \
&& curl -fsSL --retry 5 -o "${_reproenv_tmppath}" http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
&& apt-get install --yes -q "${_reproenv_tmppath}" \
&& rm "${_reproenv_tmppath}" \
&& apt-get update -qq \
&& apt-get install --yes --quiet --fix-missing \
&& rm -rf /var/lib/apt/lists/* \
&& gsl_path="$(find / -name 'libgsl.so.??' || printf '')" \
&& if [ -n "$gsl_path" ]; then \
ln -sfv "$gsl_path" "$(dirname $gsl_path)/libgsl.so.0"; \
fi \
&& ldconfig \
&& mkdir -p /opt/afni-latest \
&& echo "Downloading AFNI ..." \
&& curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
| tar -xz -C /opt/afni-latest --strip-components 1
# **********************************************************************************************************************
# [ROOT] INSTALL ANTS:
ENV ANTSPATH="/opt/ants-2.3.4/" \
PATH="/opt/ants-2.3.4:$PATH"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ca-certificates \
curl \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading ANTs ..." \
&& mkdir -p /opt/ants-2.3.4 \
&& curl -fsSL https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz \
| tar -xz -C /opt/ants-2.3.4 --strip-components 1
# **********************************************************************************************************************
# [ROOT] INSTALL Convert3D:
ENV C3DPATH="/opt/convert3d-1.0.0" \
PATH="/opt/convert3d-1.0.0/bin:$PATH"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ca-certificates \
curl \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading Convert3D ..." \
&& mkdir -p /opt/convert3d-1.0.0 \
&& curl -fsSL https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
| tar -xz -C /opt/convert3d-1.0.0 --strip-components 1
# **********************************************************************************************************************
# [ROOT] INSTALL FSL:
ENV FSLDIR="/opt/fsl-6.0.1" \
PATH="/opt/fsl-6.0.1/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl-6.0.1/bin/fsltclsh" \
FSLWISH="/opt/fsl-6.0.1/bin/fslwish" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
ca-certificates \
curl \
dc \
file \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libgl1-mesa-dri \
libglu1-mesa-dev \
libgomp1 \
libice6 \
libopenblas-base \
libxcursor1 \
libxft2 \
libxinerama1 \
libxrandr2 \
libxrender1 \
libxt6 \
nano \
sudo \
wget \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading FSL ..." \
&& mkdir -p /opt/fsl-6.0.1 \
&& curl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.1-centos7_64.tar.gz \
| tar -xz -C /opt/fsl-6.0.1 --strip-components 1 \
&& echo "Installing FSL conda environment ..." \
&& bash /opt/fsl-6.0.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.1
# **********************************************************************************************************************
USER ${NB_UID}
# [USER] INSTALL REQUIRED PUMI PACKAGES:
RUN conda install -y --name base \
"python=3.8" \
"networkx<3" \
"jupyter" \
"jupyterlab" \
"jupyter_contrib_nbextensions" \
"traits" \
"pandas" \
"matplotlib" \
"scikit-learn==1.1.2" \
"scikit-image" \
"seaborn" \
"nbformat" \
"nb_conda" \
"numpy" \
"scipy" \
"numpydoc" \
"nbsphinx" \
"pytest" \
"nipype" \
"graphviz" \
"nilearn" \
"seaborn" \
"graphviz" \
"nbsphinx" \
"pybids" \
"poetry" \
"poetry-dynamic-versioning" \
"dot2tex" \
"click"
RUN pip install --no-cache-dir \
"pydeface" \
"neurodocker==0.8.0" \
"templateflow" \
"nipy" \
"duecredit" \
"nbval" \
"datalad[full]" \
"git+https://github.com/MIC-DKFZ/HD-BET"
# **********************************************************************************************************************
# [USER] SET WORKDIR & CREATE PUMI OUTPUT DIRECTORY:
WORKDIR "${HOME}"
RUN mkdir -p "${HOME}"/PUMI/data_out
# **********************************************************************************************************************
USER root
# [ROOT] FIX PERMISSIONS:
RUN chgrp -R "${NB_GID}" "${HOME}" && chmod -R g+rwX "${HOME}" && find "${HOME}" -type d -exec chmod +6000 {} +
# **********************************************************************************************************************
USER ${NB_UID}