Dockerfile

FROM ubuntu:14.04
 
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update

#Runit
RUN apt-get install -y runit 
CMD /usr/sbin/runsvdir-start

#SSHD
RUN apt-get install -y openssh-server && \
    mkdir -p /var/run/sshd && \
    echo 'root:root' |chpasswd
RUN sed -i "s/session.*required.*pam_loginuid.so/#session    required     pam_loginuid.so/" /etc/pam.d/sshd
RUN sed -i "s/PermitRootLogin without-password/#PermitRootLogin without-password/" /etc/ssh/sshd_config

#Utilities
RUN apt-get install -y vim less net-tools inetutils-ping curl git telnet nmap socat dnsutils netcat tree htop unzip sudo software-properties-common

#Required by Python packages
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential python-dev python-pip liblapack-dev libatlas-dev gfortran libfreetype6 libfreetype6-dev libpng12-dev python-lxml libyaml-dev g++ libffi-dev

#0MQ
RUN cd /tmp && \
    wget http://download.zeromq.org/zeromq-4.0.3.tar.gz && \
    tar xvfz zeromq-4.0.3.tar.gz && \
    cd zeromq-4.0.3 && \
    ./configure && \
    make install && \
    ldconfig

#Upgrade pip
RUN pip install -U setuptools
RUN pip install -U pip

#matplotlib needs latest distribute
RUN pip install -U distribute

#IPython
RUN pip install ipython
ENV IPYTHONDIR /ipython
RUN mkdir /ipython && \
    ipython profile create nbserver

#NumPy v1.7.1 is required for Numba
RUN pip install numpy==1.7.1

#Pandas
RUN pip install pandas

#Optional
RUN pip install cython
RUN pip install jinja2 pyzmq tornado
RUN pip install numexpr bottleneck scipy pygments 
RUN apt-get install pkg-config
RUN pip install matplotlib
RUN pip install sympy pymc
RUN pip install patsy
RUN pip install statsmodels
RUN pip install beautifulsoup4 html5lib

#Pattern
RUN pip install --allow-external pattern

#NLTK
RUN pip install pyyaml nltk

#Networkx
RUN pip install networkx

#LLVM and Numba
RUN cd /tmp && \
    wget http://llvm.org/releases/3.2/llvm-3.2.src.tar.gz && \
    tar zxvf llvm-3.2.src.tar.gz && \
    cd llvm-3.2.src && \
    ./configure --enable-optimized && \
    REQUIRES_RTTI=1 make install && \
    pip install llvmpy && \
    pip install llvmmath && \
    pip install numba

#Biopython
RUN pip install biopython

#Bokeh
#RUN pip install requests bokeh

#Install R 3+
RUN echo 'deb http://cran.rstudio.com/bin/linux/ubuntu trusty/' > /etc/apt/sources.list.d/r.list
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
RUN apt-get update
RUN apt-get install -y r-base
#Rmagic
RUN pip install rpy2

#Vincent
RUN pip install vincent

#Add runit services
ADD sv /etc/service