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steve-liang/sci_ubuntu_setup.sh

Forked from anhqle/sci_ubuntu_setup.sh
Created December 9, 2018 22:36
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A shell script to install common scientific / programming tools on Ubuntu
Raw
sci_ubuntu_setup.sh
#!/bin/bash
# Marwick Lab Computational Environment Setup (Anh's version)
# 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 libgstreamer0.10-0 -y
sudo apt-get install libgstreamer-plugins-base0.10-dev -y
sudo apt-get install libcurl4-openssl-dev -y
sudo apt-get install libssl-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 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 docker-engine -y
# sudo apt-get install mysql-server -y
echo "set up git"
sudo apt-get install git meld -y
git config --global user.name "Anh Le"
git config --global user.email anhle@example.com
git config --global merge.tool meld
# for Emacs / Spacemacs
echo "install Emacs"
sudo add-apt-repository ppa:kelleyk/emacs
sudo apt-get update
sudo apt-get install emacs25 -y
echo "install Spacemacs"
git clone https://github.com/syl20bnr/spacemacs.git ~/.emacs.d
git clone https://github.com/LaDilettante/.spacemacs.d.git ~/.spacemacs.d
# 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 texlive-fonts-recommended texlive-latex-extra -y
# Or with Ubuntu 16.04
# sudo apt-get install texlive-full texstudio -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
echo "edit the sources file to prepare to install R"
# see http://cran.r-project.org/bin/linux/ubuntu/README
# ubuntu xenial is 16.04
sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" >> /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 $FILE
fi
echo "start R and install commonly used packages"
# Create a folder for R libraries, http://zvfak.blogspot.com/2012/06/updating-r-but-keeping-your-installed.html
mkdir -p ~/Rlibs
echo "R_LIBS=~/Rlibs" > ~/.Renviron
# http://stackoverflow.com/q/4090169/1036500
# Make an R script file to use in a moment...
LOADSTUFF="options(repos=structure(c(CRAN='http://cran.rstudio.com/')))
update.packages(checkBuilt = TRUE, ask = FALSE)
packages <- c('Rcpp', 'devtools', 'knitr', 'tidyverse', 'gridExtra', 'scales',
'XML', 'RCurl', 'readxl', 'mice', 'gbm', 'xgboost', 'microbenchmark')
# just some of my most often used ones
install.packages(packages)"
# close the R script
# put that R code into an R script file
FILENAME1="loadstuff.r"
sudo echo "$LOADSTUFF" > /tmp/$FILENAME1
# Make a shell file that contains instructions in bash for running that R script file
# from the command line. There may be a simpler way, but nothing I tried worked.
NEWBASH='#!/usr/bin/env
Rscript /tmp/loadstuff.r'
FILENAME2="loadstuff.sh"
# put that bash code into a shell script file
sudo echo "$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
# install Oracle Java 8 (you'll have to run the GUI installer later)
sudo apt-add-repository ppa:webupd8team/java -y
sudo apt-get install oracle-java8-installer -y
##### This part needs user input #####
# If want to install Anaconda Python, replace Miniconda with Anaconda in download link
echo "install Miniconda Python. Need user input"
MACHINE_TYPE=`uname -m`
if [ ${MACHINE_TYPE} == 'x86_64' ]; then
# 64-bit stuff here
FILE=`mktemp`; sudo wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -qO $FILE && bash $FILE; rm $FILE
else
# 32-bit stuff here
FILE=`mktemp`; sudo wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86.sh -qO $FILE && bash $FILE; rm $FILE
fi
echo "## Add Miniconda path" >> ~/.bashrc
echo "export PATH=/home/anh/miniconda3/bin:$PATH" >> ~/.bashrc
source ~/.bashrc
conda install -y numpy scipy pandas scikit-learn jupyter
echo "gen ssh keys"
ssh-keygen -t rsa -C "aql3@duke.edu"
# done.
echo "all done"
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