Dockerfile

FROM python:latest
MAINTAINER vsochat@stanford.edu

RUN apt-get update 
RUN apt-get -y install build-essential
RUN apt-get -y install apt-utils
RUN apt-get -y install cmake
RUN apt-get -y install wget
RUN apt-get -y install unzip
RUN apt-get -y install python-tk
RUN apt-get -y install python-dev 
RUN apt-get -y install pkg-config
RUN apt-get -y install libffi-dev 
RUN apt-get -y install libssl-dev
RUN apt-get -y install qt-sdk
RUN apt-get -y install libtool \
                       autotools-dev \
                       automake \
                       autoconf \
                       git


# Software dependencies. 
# This is equivalent of requirements.txt, run on image build
RUN pip install --upgrade pip
RUN pip install cycler==0.10.0
RUN pip install h5py==2.6.0
RUN pip install matplotlib==1.5.3
RUN pip install nose==1.3.7
RUN pip install numpy==1.11.0
RUN pip install pandas==0.18.1
RUN pip install Pillow==3.2.0
RUN pip install pydicom==0.9.9
RUN pip install pyparsing==2.1.10
RUN pip install python-dateutil==2.5.3
RUN pip install pytz==2016.4
RUN pip install runcython==0.2.5
RUN pip install scipy==0.18.1
RUN pip install six==1.10.0
RUN pip install simplejson

# Dependencies for simple web app demo
RUN pip install Flask==0.10.1
RUN pip install Flask-SQLAlchemy==2.0
RUN pip install Jinja2==2.7.3
RUN pip install MarkupSafe==0.23
RUN pip install SQLAlchemy==0.9.9
RUN pip install Werkzeug==0.10.4
RUN pip install gunicorn==19.3.0
RUN pip install itsdangerous==0.24
RUN pip install flask-restful
RUN pip install singularity
RUN pip install butterfly

RUN butterfly.server.py --generate-certs --host="localhost" 
RUN butterfly.server.py --generate-user-pkcs=$USER

# Install Singularity

WORKDIR /tmp
RUN git clone http://www.github.com/singularityware/singularity
WORKDIR /tmp/singularity
RUN git checkout -b development
RUN git pull origin development
RUN ./autogen.sh
RUN ./configure --prefix=/usr/local 
RUN make 
RUN make install


# Make directories for code and data
RUN mkdir /code
RUN mkdir /data

# Add the code
ADD . /code
RUN ./code/data/bases/generate_bases.sh

# Clean up
RUN apt-get autoremove -y
RUN apt-get clean
RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

EXPOSE 8000

WORKDIR /code