######################################################## 
# Set up RStudio and JAGS on an Amazon EC2 instance
# Using Ubuntu 64-bit
# Christopher Gandrud
# 16 December 2014
# Partially from http://blog.yhathq.com/posts/r-in-the-cloud-part-1.html 
# See yhat for EC2 instance set up
######################################################## 

# In your terminal navigate to key pair
# ssh -i YOUR_KEYPAIR.pem ubuntu@PUBLIC_DNS
 
# Get all programs up to date
sudo apt-get update

# Install latest g++ and clang
sudo apt-get install gcc
sudo apt-get install clang

# Install prerequisites for RCurl
sudo apt-get install libcurl4-openssl-dev

# Check that you have the latest R installed
## see also: http://askubuntu.com/a/352438
sudo apt-get update
apt-cache showpkg r-base
 
# If R is not the latest version add latest PACKAGE_VERSION returned 
# from the pervious line to:
sudo apt-get install -f r-base=PACKAGE_VERSION

# Install rJava
apt-get install r-cran-rjava
 
# Install Stan and rstan
# First find the number of cores
lscpu

# Load r, set cores, and install
R
Sys.setenv(MAKEFLAGS = "-j4") 
source('http://mc-stan.org/rstan/install.R', echo = TRUE, 
        max.deparse.length = 2000)
install_rstan()

# Install other packages I often use
## Dependencies include reshape2, dplyr
pkgs <- c('repmis', 'DataCombine', 'devtools')
install.packages(pkgs)

q()

######## Running Scripts and Downloading Results onto Local ####
# Run a script so that it runs even if the terminal hands up 
# sudo nohup Rscript R_SCRIPT_PATH

# Download a file from Amazon EC2 to your local machine 
# (current working directory)
# scp -i YOUR_KEYPAIR.pem ubuntu@PUBLIC_DNS:EC2_FILE_PATH .