# Docker file for mmp-dyf-skat docker image found here: https://hub.docker.com/r/ttimbers/mmp-dyf-skat/
# Tiffany Timbers, April 5, 2016

# use ubuntu:14.04 as base image
FROM ubuntu:14.04

# install base R
RUN sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list'
RUN gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
RUN sudo apt-get update
RUN sudo apt-get -y --force-yes install r-base

# download & install R packages 
# !!! These commands only work in Docker interatively!!! So this Dockerfile doesn't work.
sudo su - -c "R -e \"install.packages('dplyr', repos = 'http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('fdrtool', repos = 'http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('plyr', repos = 'http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('SKAT', repos = 'http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('stringr', repos = 'http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('pwr', repos = 'http://cran.rstudio.com/')\""

# install git
RUN apt-get install -y wget
RUN apt-get install -y make git

# install plink
RUN wget https://www.cog-genomics.org/static/bin/plink160331/plink_linux_x86_64.zip
RUN mkdir /usr/bin/plink
RUN unzip plink_linux_x86_64.zip
RUN mv plink /usr/bin/plink

# modify .bash_rc to put plink in the path
# note - to be able to run plink in path you need to exit docker container and re-enter it
# before running code
RUN echo PATH="/usr/bin/plink:$PATH" >> ~/.bashrc