Dockerfile

#
# A Docker image for running PyPe9 examples
#
# Steps to run the examples using Docker:
# 
#  1. Install Docker (see https://docs.docker.com/engine/installation/)
#
#  2. Pull the Pype9 "Docker image"
#
#        docker pull tclose/pype9
#
#  3. Create a "Docker container" from the downloaded image 
#
#        docker run -v `pwd`/<your-local-output-dir>:/home/docker/output -t -i tclose/pype9 /bin/bash
#
#    This will create a folder called <your-local-output-dir> in the
#    directory you are running the docker container, which you can access
#    from your host computer (i.e. outside of the container) and view the
#    output figures from.
#
#  4. From inside the running container, you will be able to run pype9, e.g.
#
#        pype9 simulate \
#	 	     ~/catalog/neuron/HodgkinHuxley#PyNNHodgkinHuxleyProperties \
#	 	     nest 500.0 0.001 \
#	 	     --init_value v 65 mV \
#	 	     --init_value m 0.0 unitless \
#	 	     --init_value h 1.0 unitless \
#	 	     --init_value n 0.0 unitless \
#	 	     --record v ~/output/hh-v.neo.pkl
#
#         pype9 plot ~/output/hh-v.neo.pkl --save ~/output/hh-v.png
#
#    Supply the '--help' option to see a full list of options for each example.
#
#  5. Edit the xml descriptions in the ~/catalog directory to alter the
#     simulated models as desired.
#

FROM ubuntu:16.04
MAINTAINER tom.g.close@gmail.com

ENV DEBIAN_FRONTEND noninteractive
ENV LANG=C.UTF-8

RUN apt-get update; apt-get install -y build-essential autoconf automake libtool libreadline6-dev \
    libncurses5-dev libgsl0-dev python-dev python3-dev openmpi-bin libopenmpi-dev inkscape \
    libhdf5-serial-dev libyaml-dev python3-pip python3-tk python-pip wget zip unzip flex bison vim nano emacs git

# Update python packages
RUN pip3 install --upgrade pip
RUN pip3 install --upgrade virtualenvwrapper

# Add non-root user
RUN useradd -ms /bin/bash docker
ENV HOME=/home/docker

# Copy pype9 repo to docker container
RUN mkdir -p $HOME/packages
ADD . $HOME/packages/pype9
RUN chown -R docker:docker $HOME/packages

# Switch to non-root user
USER docker

# Set up virtualenv
ENV VIRTUALENVWRAPPER_PYTHON /usr/bin/python3
RUN /bin/bash -c "source /usr/local/bin/virtualenvwrapper.sh; mkvirtualenv pype9"
ENV VENV /home/docker/.virtualenvs/pype9
ENV VENV_PIP $VENV/bin/pip

# Install some useful Python packages into the virtualenv
RUN $VENV_PIP install ipython nose

# Install Neuron and NEST
RUN /bin/bash -c "source /usr/local/bin/virtualenvwrapper.sh; workon pype9; $HOME/packages/pype9/install/nest.sh 2.14.0"
RUN /bin/bash -c "source /usr/local/bin/virtualenvwrapper.sh; workon pype9; $HOME/packages/pype9/install/neuron.sh tag-1665alpha"

# Install 9ML catalog as local git repo for easy editing
RUN git clone https://github.com/INCF/nineml-catalog.git $HOME/packages/nineml-catalog
RUN $VENV_PIP install -e $HOME/packages/nineml-catalog
RUN ln -s $HOME/packages/nineml-catalog/ninemlcatalog/catalog $HOME/catalog

# Install Pype9 package
RUN $VENV_PIP install -e $HOME/packages/pype9[plot]

# Manually ensure that NMODL files have been compiled in PyNN installation
WORKDIR $VENV/lib/python3.5/site-packages/pyNN/neuron/nmodl
RUN $VENV/bin/nrnivmodl
WORKDIR $HOME

# Set up matplotlib environemnt
RUN mkdir -p .config/matplotlib
RUN echo "backend: Agg" >> .config/matplotlib/matplotlibrc

# Set up bashrc vimrc and add welcome message
RUN sed 's/#force_color_prompt/force_color_prompt/' $HOME/.bashrc > $HOME/tmp; mv $HOME/tmp $HOME/.bashrc;
RUN echo "export VIRTUALENVWRAPPER_PYTHON=/usr/bin/python3"
RUN echo "source /usr/local/bin/virtualenvwrapper.sh" >> $HOME/.bashrc
RUN echo "workon pype9" >> $HOME/.bashrc
RUN echo "echo \"Type 'pype9 help' for instructions on how to run pype9\"" >> $HOME/.bashrc
RUN echo "echo \"See $HOME/catalog for example 9ML models\"" >> $HOME/.bashrc
RUN echo "set background=dark" >> $HOME/.vimrc
RUN echo "syntax on" >> $HOME/.vimrc
RUN echo "set number" >> $HOME/.vimrc
RUN echo "set autoindent" >> $HOME/.vimrc