aiida-docker-base/Dockerfile at develop · adegomme/aiida-docker-base · GitHub

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# See https://github.com/phusion/baseimage-docker/blob/master/Changelog.md
# Based on Ubuntu 18.04 since v0.11
FROM phusion/baseimage:0.11
#FROM continuumio/miniconda3:latest
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ENV PATH /opt/conda/bin:$PATH

RUN apt-get update --fix-missing && \
    apt-get install -y wget bzip2 ca-certificates curl git && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh && \
    /opt/conda/bin/conda clean -tipsy && \
    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
    echo "conda activate base" >> ~/.bashrc

# This file is automatically generated from tpl.Dockerfile
# FROM intelpython3_core
USER root
ENV ACCEPT_INTEL_PYTHON_EULA=yes

RUN conda config --add channels intel\
    && conda install  -y -q intelpython3_core python=3 \
    && conda clean --all \
    && apt-get update -qqq \
    && apt-get install -y -q g++ \
    && apt-get autoremove


# Add switch mirror to fix the issue
# https://github.com/aiidalab/aiidalab-docker-stack/issues/9
RUN echo "deb http://mirror.switch.ch/ftp/mirror/ubuntu/ bionic main \ndeb-src http://mirror.switch.ch/ftp/mirror/ubuntu/ bionic main \n" >> /etc/apt/sources.list

# install debian packages
# Note: prefix all 'apt-get install' lines with 'apt-get update' to prevent failures in partial rebuilds
RUN apt-get clean && rm -rf /var/lib/apt/lists/*
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
    tzdata

RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends   \
    build-essential       \
    graphviz              \
    libpq-dev             \
    libgirepository1.0-dev\
    libcairo2-dev         \
    pkg-config            \
    gir1.2-gtk-3.0        \
    ssh                   &&\
   rm -rf /var/lib/apt/lists/* \
  && apt-get clean all


# update build-tools
RUN pip install -U pip

RUN pip install cython setuptools wheel tk psycopg2 PyGobject pycairo cython

# launch start-singleuser
COPY opt/start-singleuser.sh /opt/start-singleuser-base.sh
COPY my_init.d/start-singleuser.sh /etc/my_init.d/30_start-singleuser.sh


# Install AiiDA and BigDFT plugin
# aiida from gh, as we have numpy 1.17 in intelpython. Replace by pip one after 1.0.2 release.
RUN git clone https://github.com/aiidateam/aiida-core.git
RUN pip install -e aiida-core['rest','atomic_tools','notebook']
EXPOSE 8888

# Add aiida user (no password)
RUN mkdir /home/aiida                                             && \
    useradd --home /home/aiida --uid 1234 --shell /bin/bash aiida && \
    chown -R aiida:aiida /home/aiida

# Add .bashrc file to the aiida user
RUN cp -v /etc/skel/.bashrc /etc/skel/.bash_logout /etc/skel/.profile /home/aiida/
RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/aiida/.bashrc
RUN echo "conda activate base" >> /home/aiida/.bashrc
RUN echo 'eval "$(verdi completioncommand)"' >> /home/aiida/.bashrc
RUN echo 'export PYTHONPATH="/home/aiida"' >> /home/aiida/.bashrc
RUN echo 'export PATH=$PATH:"/home/aiida/.local/bin"' >> /home/aiida/.bashrc
RUN chown -R aiida:aiida /home/aiida

# Install rest of the packages as normal user
USER aiida

# Populate reentry cache for aiida user https://pypi.python.org/pypi/reentry/
RUN reentry scan

# Set $HOME, create git directory
ENV HOME /home/aiida
ENV PATH /opt/conda/bin:$PATH

# Make ssh dir and create host entry for bitbucket.org
RUN mkdir --mode=0700 $HOME/.ssh/ && \
    touch $HOME/.ssh/known_hosts


RUN mkdir -p $HOME/.ipython/profile_default/startup && cp aiida-core/aiida/tools/ipython/aiida_magic_register.py /home/aiida/.ipython/profile_default/startup/aiida_magic_register.py
# Important to end as user root!
USER root

# Specify landing folder when login to the docker container
WORKDIR $HOME

# Use baseimage-docker's init system.
CMD ["/sbin/my_init"]

#EOF