reportcreatormahcine.Vagrantfile

#Define the list of machines
machines = {
    :reportcreatormahcine => {
        :hostname => "reportcreatormahcine",
        :ipaddress => "10.10.10.99" #gretzky
    },
}

#--------------------------------------
# General provisioning inline script
#--------------------------------------
$script = <<SCRIPT

# Start by making yum faster
sudo yum install yum-plugin-fastestmirror
sudo yum upgrade

wget --no-clobber -P /tmp  http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
cd /tmp
sudo rpm -ivh epel-release-6-8.noarch.rpm

sudo yum install -y java-1.7.0-openjdk-devel openssl-devel libxml2-devel
sudo yum install -y git nano
sudo yum -y install libcurl libcurl-devel
sudo yum -y groupinstall "Development tools"

sudo yum install -y perl-devel perl rsync dos2unix perl-CPAN gcc zlib-devel.x86_64 zlib.x86_64 expat-devel
curl -L http://cpanmin.us | perl - --sudo App::cpanminus

#Install the perl modules!
sudo /usr/local/bin/cpanm Archive::Zip
sudo /usr/local/bin/cpanm PerlIO::gzip
sudo /usr/local/bin/cpanm XML::Simple
sudo /usr/local/bin/cpanm MD5
sudo /usr/local/bin/cpanm ExtUtils::MakeMaker
# sudo /usr/local/bin/cpanm --force Module::Compile
# sudo /usr/local/bin/cpanm XML::LibXSLT
# sudo /usr/local/bin/cpanm PDL

sudo yum install -y R

cat | Rscript /dev/stdin <<EOF

update.packages(repos="http://ftp.sunet.se/pub/lang/CRAN/", ask=FALSE)
# "httr" "RCurl" devtools "glmnet"
packages <- c("getopt", "plyr", "reshape", "devtools",
  "data.table", "ggplot2", "knitr", "xtable", "uuid", "pamr" )
biocpackages <- c("CNAnorm", "QDNAseq", "DESeq")
githubrepos <- c("dakl/clinseqr")

for( package in packages ){ # package <- packages[1]
  if( !require(package = package, character.only = TRUE) ){
    install.packages(package, repos="http://ftp.sunet.se/pub/lang/CRAN/")
  }
}
library(devtools)
for( repo in githubrepos ){ # repo <- githubrepos[1]
  package <- unlist(strsplit(x = repo, split = "/"))[2]
  if( !require(package = package, character.only = TRUE) ){
    install_github(repo)
  }
}

source("http://bioconductor.org/biocLite.R")
for( package in biocpackages ){ # package <- biocpackages[1]
  if( !require(package = package, character.only = TRUE) ){
    biocLite(package)
  }
}

EOF


SCRIPT

#--------------------------------------
# Fire up the machine
#--------------------------------------
Vagrant.configure("2") do |global_config|
    machines.each_pair do |name, options|
        global_config.vm.define name do |config|
            #VM configurations
            config.vm.box = "bento/centos-6.7"
            config.vm.hostname = "#{name}"
            config.vm.network :private_network, ip: options[:ipaddress]

            config.vm.synced_folder "~/projects/clinseq-reporting", "/home/vagrant/projects/clinseq-reporting"
            config.vm.synced_folder "/proj", "/proj"

            #VM specifications
            config.vm.provider :virtualbox do |v|
                v.customize ["modifyvm", :id, "--memory", "4096", "--cpus", 2]
            end

            #VM provisioning
            config.vm.provision :shell,
                :inline => $script

        end
    end
end