anchor.diff:  FROM ubuntu:14.04
  -MAINTAINER Shigeru Kitazaki <skitazaki@gmail.com>
  +MAINTAINER Itoshi NIKAIDO "dritoshi@gmail.com"
  +
  +RUN locale-gen en_US.UTF-8
  +RUN update-locale LANG=en_US.UTF-8
  +ENV LC_ALL C
  +ENV LC_ALL en_US.UTF-8
  +
  +# apt-get
  +ENV DEBIAN_FRONTEND noninteractive
  +RUN echo "deb http://jp.archive.ubuntu.com/ubuntu/ trusty main restricted\n\
  +deb-src http://jp.archive.ubuntu.com/ubuntu/ trusty main restricted\n\
  +deb http://jp.archive.ubuntu.com/ubuntu/ trusty-updates main restricted\n\
  +deb-src http://jp.archive.ubuntu.com/ubuntu/ trusty-updates main restricted\n\
  +deb http://jp.archive.ubuntu.com/ubuntu/ trusty universe\n\
  +deb-src http://jp.archive.ubuntu.com/ubuntu/ trusty universe\n\
  +deb http://jp.archive.ubuntu.com/ubuntu/ trusty-updates universe\n\
  +deb-src http://jp.archive.ubuntu.com/ubuntu/ trusty-updates universe\n\
  +deb http://jp.archive.ubuntu.com/ubuntu/ trusty multiverse\n\
  +deb-src http://jp.archive.ubuntu.com/ubuntu/ trusty multiverse\n\
  +deb http://jp.archive.ubuntu.com/ubuntu/ trusty-updates multiverse\n\
  +deb-src http://jp.archive.ubuntu.com/ubuntu/ trusty-updates multiverse\n\
  +deb http://jp.archive.ubuntu.com/ubuntu/ trusty-backports main restricted universe multiverse\n\
  +deb-src http://jp.archive.ubuntu.com/ubuntu/ trusty-backports main restricted universe multiverse\n\
  +deb http://security.ubuntu.com/ubuntu trusty-security main restricted\n\
  +deb-src http://security.ubuntu.com/ubuntu trusty-security main restricted\n\
  +deb http://security.ubuntu.com/ubuntu trusty-security universe\n\
  +deb-src http://security.ubuntu.com/ubuntu trusty-security universe\n\
  +deb http://security.ubuntu.com/ubuntu trusty-security multiverse\n\
  +deb-src http://security.ubuntu.com/ubuntu trusty-security multiverse\n"> /etc/apt/sources.list
  +
  +# CRAN
  +RUN echo "deb http://cran.ism.ac.jp/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list
  +RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
   
   RUN apt-get update
   RUN apt-get upgrade -y
  
positive.code: RUN pip3 install Sphinx
  RUN pip3 install ipython[notebook]
  
  # For IPython Notebook to share resources with host.
  EXPOSE 8888
  VOLUME ["/notebook"]
  
negative.code: 
  CMD ["ipython-notebook-startup.sh" , "/notebook"]
  
  # bioconductor
  RUN R -q -e 'source("http://bioconductor.org/biocLite.R"); biocLite("edgeR");'
  RUN wget --no-check-certificate http://cran.r-project.org/src/contrib/Archive/multicore/multicore_0.2.tar.gz
  RUN echo '.First <- function() { options(repos = c(CRAN = "http://cran.ism.ac.jp/")) }' > ~/.Rprofile
  RUN R CMD INSTALL multicore_0.2.tar.gz
  RUN R -q -e 'install.packages(c("Rcpp", "RcppArmadillo", "flexmix"))'
  RUN R -q -e 'install.packages(c("caTools", "RColorBrewer"))'
  
  # SCDE
  RUN apt-get install -y libxtst-dev libxt-dev
  RUN apt-get install -y libcairo2-dev r-cran-cairodevice
  RUN R -q -e 'install.packages(c("Cairo"))'
  RUN wget --no-check-certificate http://pklab.med.harvard.edu/scde/scde_1.1.tar.gz
  RUN R CMD INSTALL scde_1.1.tar.gz
  
  # RStudio
  # EXPOSE 8787
  # RUN apt-get install -y gdebi-core
  # RUN apt-get install -y libapparmor1 # Required only for Ubuntu, not Debian
  # RUN apt-get install -y wget
  # RUN wget --no-check-certificate http://download2.rstudio.org/rstudio-server-0.98.1073-amd64.deb
  # RUN gdebi -n rstudio-server-0.98.1073-amd64.deb
  
  RUN apt-get clean
  