Yvert Lab - Virtual Machine with vagrant

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##### Documented script to create a virtual machine with vagrant ##### 
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Created on 2017.05.18

# This script contains commands and annotations
# that will allow you to create a virtual machine (VM) using vagrant, 
# get into it and out, and install in it R libraries and rotines.

# The interest of doing this is to then give this VM to someone else
# so that he/she can use your tools that you developed in R.
# In principle, you can build this vm on any machine.

# In the example below, the vm is then equipped with Ubuntu 14.04 LTS.
# 

##################################
##### Create Virtual Machine #####
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# Create a directory called VirtualMachine

# Open a terminal and cd into this directory.

# Create a virtual machine by running in the terminal:
vagrant init ubuntu/trusty64 
# This will load ubuntu 14.04 LTS box. 
# This will generate a Vagrantfile (txt file). 
# Open it and increase memory by modifying the following lines:
  config.vm.provider "virtualbox" do |vb|
     vb.memory = "8192"
  end

# Increase virtual hard disk size (https://tuhrig.de/resizing-vagrant-box-disk-space/).
# Go in the directory where the "box-disk1.vmdk" was created and save it as a .vdi disk.
VBoxManage clonehd "box-disk1.vmdk" "cloned.vdi" --format vdi
VBoxManage modifyhd "cloned.vdi" --resize 51200 # 50Gb

# Then open virtual box interface > Configuration > Storage > click on "+" to add an hard disk > Existing > "cloned.vdi".
Eventually "remove box-disk1.vmdk" within virtual box interface.


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##### Start Virtual Machine and connect to it #####
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# Switch the virtual machine ON by running in the terminal:
vagrant up
# note that it is essential to turn on the machine before trying to connect to it.

# Connect to the virtual machine by running in the terminal:
vagrant ssh

# You are now in the virtual machine, under vagrant user name.

# To disconnect from the virtual machine, type:
exit

# To turn OFF the virtual machine, type in the terminal:
vagrant halt


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##### Install R libraries and tools on the virtual machine #####
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##### (Needed the first time you connect)                  #####
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# Switch ON the virtual machine and connect to it as explained above.
# Once you are into it, do the following to install the libraries.
# You only need to do this the first time you connect: the libraries will 
# then be stored on the vm (in the .vdi) and be available at later sessions.

# Add R repository in your source list /etc/apt/sources.list by typing:
sudo add-apt-repository "deb https://cran.rstudio.com/bin/linux/ubuntu trusty/" 
# Add external R repository maintained by CRAN 
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 

sudo apt-get update

# Install R
sudo apt-get install r-base 

# Install other R packages required for the R librairies needed (not mandatory for a basic installation)
sudo apt-get install r-cran-rgl
sudo apt-get install r-cran-XML
sudo apt-get install libxml2-dev
sudo apt-get install libhdf5-serial-dev

# Run R in sudo mode
sudo R

# Within R, install the following R packages:
packages <- c("quantmod", "ggplot2", "hexbin", "RColorBrewer", "gridExtra", "latticeExtra")
install.packages(packages)

# Install the following bioconductor packages
source("https://bioconductor.org/biocLite.R")
biocLite() # Say "y" to update packages but say "n" if it suggests to update rgl only
packages_biocond <- c("ncdfFlow", "flowStats", "ggcyto")
biocLite(packages_biocond)


#####################################################
#####              Install Latex                #####
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##### (Needed the first time you connect)       #####
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# On your VM, install Latex by typing:
sudo apt-get install texinfo
sudo apt-get install texlive texlive-xetex texlive-latex-extra


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####      Enjoy your virtual machine     #####
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# Connect to your virtual machine (see above)
# Once connected, you can access files of your local computer by following the /vagrant/ path directory.
# the R libraries installed above now allow you to analyse data contained on your local computer,
# by accessing it using this path.
# 
# Enjoy!