anchor.diff:  # Install R packages
   RUN R -e "install.packages(c('devtools', 'gplots', 'httr', 'igraph', 'knitr', 'methods', 'plyr', 'RColorBrewer', 'rJava', 'rjson', 'R.methodsS3', 'R.oo', 'sqldf', 'stringr', 'testthat', 'XML', 'DT', 'htmlwidgets'), repos='http://cran.rstudio.com/')"
   
  -RUN R -e 'setRepositories(ind=1:6); \
  -  options(repos="http://cran.rstudio.com/"); \
  -  if(!require(devtools)) { install.packages("devtools") }; \
  -  library(devtools); \
  -  install_github("ramnathv/rCharts"); \
  -  install.packages("cgdsr")'
  -
   # Install Bioconductor
   RUN R -e "source('http://bioconductor.org/biocLite.R'); biocLite(c('Biobase', 'BiocCheck', 'BiocGenerics', 'BiocStyle', 'S4Vectors', 'IRanges', 'AnnotationDbi'))"
  -
  -# Install rcellminer/paxtoolsr
  -RUN R -e "source('http://bioconductor.org/biocLite.R'); biocLite('rcellminer')"
  -#RUN R -e "source('http://bioconductor.org/biocLite.R'); biocLite('rcellminerData')"
  -RUN R -e "source('http://bioconductor.org/biocLite.R'); biocLite('paxtoolsr')"
   
   ##### INSTALL IPYRMD
   
  
positive.code: VOLUME /workspace
  WORKDIR /workspace
  
  COPY examples/using_paxtoolsr.ipynb /workspace/using_paxtoolsr.ipynb
  COPY examples/using_rcellminer.ipynb /workspace/using_rcellminer.ipynb
  COPY examples/cgdsr.ipynb /workspace/cgdsr.ipynb
  
  # https://github.com/ipython/ipython/issues/7062
  CMD sh -c "ipython notebook --ip=*"
  
negative.code: # RUN apt-get update && apt-get install -y texlive-latex-extra   # required for adjustbox.sty, probably is an easier way
  
  # Install basic commands
  RUN apt-get -y install links nano wget git htop
  
  # Install new version of R
  RUN sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
  