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setting up a history research machine. Follow the instructions.
# By Ben Marwick, from: https://gist.github.com/benmarwick/11204658 with modifications by S. Graham
Short instructions to setup a Lubuntu Virtual Machine with
R & RStudio:
1. Download these:
http://lubuntu.net/ (Intel x86 desktop cd)
https://www.virtualbox.org/wiki/Downloads (Oracle VM VirtualBox)
2. Install Oracle VM VirtualBox, open it (if using windows,
run as administrator), click 'New' button, at
'Name' put Lubuntu, 'Type' choose Linux, 'Version' choose
Ubuntu (32-bit), then click 'Next' and change memory size
to 2048 MB (or more, but as a rule of thumb not more
than a quarter of your total RAM), Click 'Next', select
'create virtual drive now', click 'Next',
select 'VDI', click 'Next', select 'Fixed size',
click 'Next', set disk size to 8GB, click 'Create'. Feel
free to make those values larger if you like. If you can't
set it to 8GB, set it as large as you can.
3. At the main Oracle VM VirtualBox window, double-click on
'Lubuntu' the VM you just set up. You will then get a little
window that asks you to 'select start-up disk', click on the
little folder icon to the right of the drop-down field, then
find where you downloaded the lubuntu desktop cd. It should
be a file that ends in iso and is about 700 MB. Once you've
selected that file, click 'start' on the 'select start-up disk'
window. If you get an error, try turning off your antivirus
software, if that doesn't help, uninstall VirtualBox and
download and install a new copy of VirtualBox
from here: https://www.virtualbox.org/wiki/Testbuilds
4. You will then be taken to the Lubuntu install menu,
choose 'English' by pressing enter, then on the next
screen 'Install Lubuntu' (use the arrow keys to select,
then press enter). Look in the lower right corner of the
window to see what button you need to press to free the
mouse (for me it's the right control key). It will take
a few minutes to install, keep an eye on it, you will
need to click 'continue', then 'download updates while
installing', then 'continue' again, then 'erase disk
and install Lubuntu', then 'continue', then edit your location
then 'continue', then 'continue again (the keyboard
layout is usually fine), then type your name and password,
keep it easy and simple as this is a very low security
use (we're not using this for online banking!) and
you'll be typing the password often. Select 'log in
automatically' then click 'continue'. Then wait a few
minutes and watch the 'copying files' progress bar.
Once that's done, it will probably want to restart,
click to accept a restart (you may have to hit enter
a few times to move the process along), or if you
don't get the option, click on the
little circular shutdown icon in the lower right
corner of the window, and choose 'reboot', and wait
for it to restart (hitting enter a few times if
it looks like it's stopped doing things).
5. Now open a terminal emulator window, which you
can do by clicking on the blue button in the lower
left corner, then click on 'Accessories' then click
on 'LXTerminal'. Or you can press CTRL-ALT-t
6. At the terminal prompt, type these, one line
at a time, exactly as printed here, and press
enter after each line (you will be prompted to
type your password, note that you wont see
anything on screen when you type in
your password, no dots or asterixes - this is
normal). Once you've typed your password, press
enter. Here are the lines to type in:
sudo apt-get update
sudo apt-get install virtualbox-guest-x11 -y
Wait for things to scroll past in the console,
it will take a few minutes. When you get your
prompt back (ie stuff stops scrolling by and
the console is ready for a new command), restart
your VM by clicking on the little circular
shutdown icon in the lower right corner of
the window, and choosing 'reboot' or you can
type this at the terminal:
sudo reboot
Once you're going again, look to the main
Oracle VM VirtualBox menu bar, click on
'Devices', then 'Shared clipboard', and set
'Shared Clipboard' to bidirectional.
Now you can copy and paste text to and from
your VM.
Go back to the 'Devices' menu you were just at
and click on 'Shared folder settings...' then
click on 'Machine Folders', then click on the
little button that is a picture of a folder
with a plus sign, that will make a little box
appear. In this box, click on the little down
arrow at the right of the 'Folder Path' field,
then click on 'Other...' and choose a folder
on your computer that contains files you want
to work with in your VM. Check the boxes for
'auto-mount' and 'make permanent', then click
OK, and click OK again. In your VM, open a terminal
and type:
sudo usermod -aG vboxsf MYUSERNAME
Where MYUSERNAME is the username you set up for
yourself when you made the VM. Enter your password
when prompted, then reboot the VM again. This will
give you access to the folder on your computer
from the VM, so you can easily transfer files between
the two environments. The shared folder can be
found on the VM in a directory called 'media',
which you can access by typing /media in the
file manager address bar.
7. Open a terminal and run these three lines
(you can now copy and paste, so do that):
wget https://gist.githubusercontent.com/shawngraham/fadc16465d6e27e0f37c/raw/install_things.sh
chmod +x install_things.sh
./install_things.sh
then press enter and wait, watching things
scroll by. This step downloads a small script
from github and runs it. The script installs
R, RStudio, and a bunch of other things.
This will take 30+ mins, the exact time
depends on the speed of your internet
connection. Keep an eye on it, you'll
need to enter your password here and
there, and press enter once or twice. If
know what you're doing you can edit the script
to add or subtract items. But as it is will be
fine for most purposes.
8. Now you're ready to compute! If you've
never used linux or the terminal before,
do check out the video lessons at:
https://www.youtube.com/playlist?list=PLA86D04D6E0BFD2E0
and the text at:
http://software-carpentry.org/v5/novice/shell/index.html
Here are a few tips to get started:
sudo firefox # opens a web browser
sudo rstudio # opens rstudio
sudo gedit # opens a text editor
sudo abiword # opens a word processor
sudo gnumeric # opens a spreadsheet
#!/bin/bash
# Copied and modified from
# Marwick Lab Computational Environment Setup
# this script can be run from the terminal with the next line (minus the #)
# bash install_things.sh
# you will need to enter your password at a few points, so keep an eye on it while it runs.
# in case we need to step through:
# set -x
# trap read debug
## Need this for Debian but not Lubuntu
## Make self su: http://stackoverflow.com/a/15067345/1036500
# install sudo to ensure we get access to everything
# su -c "aptitude install sudo"
# su root
## Here we assume your username is ben ... do edit this line if you chose a different username!
# sudo adduser ben sudo
echo "install a few dependancies for our workflow"
sudo apt-get update -y
# sudo apt-get upgrade -y
sudo apt-get install -y
# sudo apt-get -f install -y
sudo apt-get install libcurl4-openssl-dev -y
sudo apt-get install libopenblas-base -y
sudo apt-get install libxml2-dev -y
sudo apt-get install make -y
sudo apt-get install gcc -y
sudo apt-get install git -y
sudo apt-get install pandoc -y
sudo apt-get install libjpeg62 -y
sudo apt-get install unzip -y
sudo apt-get install curl -y
sudo apt-get install littler -y
sudo apt-get install openjdk-7-* -y
sudo apt-get install gedit -y
sudo apt-get install jags -y
sudo apt-get install imagemagick -y
# sudo apt-get install mysql-server -y
# ocr etc
sudo apt-get imagej
sudo apt-get install pandoc
sudo apt-get install tre-agrep
sudo apt-get install pdftk
sudo apt-get install tesseract-ocr tesseract-ocr-eng
# for Texlive with Lubuntu (making PDFs)
# these are BIG, not recommended if you're short on disk space!
# sudo add-apt-repository ppa:texlive-backports/ppa
# sudo apt-get update
# sudo apt-get install texlive-latex-base -y
# sudo apt-get install texlive-fonts-recommended -y
# sudo apt-get install texlive-latex-extra -y
# a few handy FOSS items for drawing, graphics and maps
sudo apt-get install inkscape -y
sudo apt-get install gimp -y
sudo apt-add-repository ppa:ubuntugis/ppa
sudo apt-get update
sudo apt-get install qgis -y
# also a few things in case we use python
# from http://faculty.washington.edu/rjl/uwhpsc-coursera/vm.html
#sudo apt-get install liblzma-dev -y
sudo apt-get install ipython -y
sudo apt-get install ipython-notebook -y
sudo apt-get install python-pandas -y
sudo apt-get install python-numpy -y
sudo apt-get install python-scipy -y
sudo apt-get install python-matplotlib -y
#sudo apt-get install python-dev -y
#sudo apt-get install python-sphinx -y
#sudo apt-get install gfortran -y
#sudo apt-get install openmpi-bin -y
#sudo apt-get install liblapack-dev -y
#sudo apt-get install thunar -y
#sudo apt-get install gitk -y
#sudo apt-get install docdiff -y
#sudo apt-get install python-setuptools -y
#python from historycrawler
wget https://bootstrap.pypa.io/ez_setup.py -O - | sudo python
sudo easy_install pip
# sudo pip install -U numpy
sudo pip install -U pyyaml nltk
sudo apt-get install python-sympy python-nose
sudo apt-get install python-beautifulsoup
sudo pip install internetarchive
echo "edit the sources file to prepare to install R"
# see http://cran.r-project.org/bin/linux/ubuntu/README
sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list' # if Lubuntu
echo "get keys to install R"
# sudo apt-key adv --keyserver keys.gnupg.net --recv-key 381BA480 # if Debian
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 # if Lubuntu
echo "install R and some helpers"
sudo apt-get update
sudo apt-get install r-base -y
sudo apt-get install r-base-dev -y
sudo apt-get install r-cran-xml -y
sudo apt-get install r-cran-rjava -y
sudo R CMD javareconf # for rJava
echo "install RStudio from the web"
# use daily build to get rmarkdown & latest goodies
# http://stackoverflow.com/a/15046782/1036500
# check if 32 or 64 bit and install appropriate version...
# http://stackoverflow.com/a/106416/1036500
MACHINE_TYPE=`uname -m`
if [ ${MACHINE_TYPE} == 'x86_64' ]; then
# 64-bit stuff here
URL=$(wget -q -O - http://www.rstudio.org/download/daily/desktop/ubuntu64 | grep -o -m 1 "https[^\']*" )
FILE=`mktemp`; sudo wget "$URL" -qO $FILE && sudo dpkg -i $FILE; rm $FILE
else
# 32-bit stuff here
URL=$(wget -q -O - http://www.rstudio.org/download/daily/desktop/ubuntu32 | grep -o -m 1 "https[^\']*" )
FILE=`mktemp`; sudo wget "$URL" -qO $FILE && sudo dpkg -i $FILE; rm $FILE
fi
echo "start R and install commonly used packages"
# http://stackoverflow.com/q/4090169/1036500
# Make an R script file to use in a moment...
LOADSTUFF="options(repos=structure(c(CRAN='http://cran.rstudio.com/')))
update.packages(checkBuilt = TRUE, ask = FALSE)
packages <- c('codetools', 'Rcpp', 'devtools', 'knitr', 'ggplot2', 'data.table', 'plyr', 'dplyr', 'XML', 'RCurl', 'gdata', 'stargazer')
# just some of my most often used ones
install.packages(packages)
# and some from github
devtools::install_git(c('https://github.com/rstudio/rmarkdown.git', 'https://github.com/rstudio/packrat', 'https://github.com/hadley/reshape'))" # close the R script
# put that R code into an R script file
FILENAME1="loadstuff.r"
sudo echo "$LOADSTUFF" > /tmp/$FILENAME1
# Make a shell file that contains instructions in bash for running that R script file
# from the command line. There may be a simpler way, but nothing I tried worked.
NEWBASH='#!/usr/bin/env
sudo Rscript /tmp/loadstuff.r'
FILENAME2="loadstuff.sh"
# put that bash code into a shell script file
sudo echo "$NEWBASH" > /tmp/$FILENAME2
# run the bash file to exectute the R code and install the packages
sh /tmp/loadstuff.sh
# clean up by deleting the temp file
rm /tmp/loadstuff.sh
# done.
echo "all done"
echo "type 'sudo rstudio' in the terminal to start RStudio"
# by Ben Marwick
# set cran repo so the user doesn't have to
options(repos=structure(c(CRAN='http://cran.rstudio.com/')))
# update installed pacakges
update.packages(checkBuilt = TRUE, ask = FALSE)
# make a list of additional packages to install
packages <- c('codetools', 'Rcpp', 'devtools', 'knitr', 'ggplot2', 'data.table', 'plyr', 'dplyr', 'XML', 'RCurl', 'gdata', 'stargazer')
# install that list
install.packages(packages)
# and some from github
devtools::install_git(c('https://github.com/rstudio/rmarkdown.git', 'https://github.com/rstudio/packrat', 'https://github.com/hadley/reshape'))"
message("All done installing additional packages")
# end
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