Debian Stretch

installDebianStretch

#!/usr/bin/env bash
# I ran the lines below in super user mode (*i.e.* using su; as you can see I install sudo below)
# libappindicator1 was required to use google-chrome
# **Few notes regarding R packages**: I first used the debian package (i.e. r-cran-XXXX) but with 3.4.1 
# and higher there was an issue with r-api-x that leads me to install packages from R (this may be changed).
# Dependencies are required:
# - libfreetype6-dev for showtext
# - libpoppler-cpp-dev for pdftools 
# - libudunits2-dev for some leaflet dependencies 
# - libssl-dev for devtools
# - libmagick++-dev for magick package (one of kableExtra dependency).
# - openjdk-8-jdk to run R CMD javareconf seamlessly

##-- synchro
apt-get update && apt-get upgrade

##--- to get the wifi working and other devices 
apt-get install iwlwifi firmware-misc-nonfree 
##--- Note that I keep repeating `apt-get` for the sack of readibility
apt-get install sudo gconf2 gconf-service gtk2.0 gtk3.0 openjdk-8-jdk dirmngr conky-all zsh curl tree valgrind clang
apt-get install libfreetype6-dev libssl-dev libgdal-dev libgeos-dev libproj-dev libpoppler-cpp-dev libudunits2-dev 
apt-get install libmagick++-dev libcanberra-gtk-module libappindicator1
apt-get install postgresql postgis gnuplot openssh-server docker ffmpeg
apt-get install nmap nethogs lftp ncftp pass vim rsync backup-manager xdotool lshw inxi unrar  
apt-get install fortune-mod gnumeric scrot gpick  okular festival thunderbird lyx
apt-get install mopidy mopidy-podcast  jekyll mkdocs youtube-dl own-cloud-client pidgin 
apt-get install vlc imagemagick graphicsmagick calibre xournal
apt-get install texlive-full font-manager fonts-font-awesome fonts-roboto ttf-mscorefonts-installer 
apt-get install libreoffice-l10n-fr mythes-fr zotero-standalone xul-ext-zotero libreoffice-zotero-integration 
apt-get install python-pip julia r-base r-recommended r-base-dev sagemath 

##-- Pandoc & pandoc-citeproc (more recent versions)
wget https://github.com/jgm/pandoc/releases/download/2.0.1.1/pandoc-2.0.1.1-1-amd64.deb -O /tmp/pandoc.deb && sudo dpkg -i /tmp/pandoc.deb

##-- Setting R up 
git clone https://gist.github.com/aaa83151e9d12cc07fbe379e2c32a385.git /tmp/pkgsR
sudo R CMD javareconf 
sudo Rscript /tmp/pkgsR/myPackages.R

##-- Setup Julia
echo 'println("Greetings KevCaz")' > ~/.juliarc.jl

##-- Python packages 
pip install numpy scipy matplotlib psycopg2 pyparsing future
pip install pandoc-fignos pandoc-tablenos pandoc-eqnos
pip install zotero-cli plotly

##-- Node.js 9 https://nodejs.org/en/download/package-manager/#debian-and-ubuntu-based-linux-distributions
curl -sL https://deb.nodesource.com/setup_9.x | sudo -E bash -
sudo apt-get install -y nodejs

##-- npm packages
npm install -g decktape jquerry bootstrap 

##-- Atom 
## download atom first (use wget)
wget https://github.com/atom/atom/releases/download/v1.23.3/atom-amd64.deb -O /tmp/atom.deb && sudo dpkg -i /tmp/atom.deb
## themes
apm install atom-material-syntax atom-material-syntax-dark atom-material-ui dash-ui
## packages 
apm install language-knitr language-latex language-r language-matlab language-docker language-julia \
    autocomplete-bibtex autocomplete-R autocomplete-emojis autocomplete-font-awesome greek-snippets wordcount \
    minimap pdf-view pigments color-picker dictionary gist-it file-icons ascii-unicode-escape data-atom tablr \
    intentions busy-signal ink julia-client sourcerer linter linter-lintr atom-beautify git-time-machine \
    platformio-ide-terminal teletype 

##-- Hugo (more recent verison)
wget https://github.com/gohugoio/hugo/releases/download/v0.35/hugo_0.35_Linux-64bit.deb -O /tmp/hugo.deb && sudo dpkg -i /tmp/hugo.deb

##-- Jobber 
wget https://github.com/dshearer/jobber/releases/download/v1.2/jobber_1.2-1_amd64.deb -O /tmp/jobber.deb && sudo dpkg -i /tmp/jobber.deb

##-- Skype see https://wiki.debian.org/skype
## wget https://www.skype.com/fr/download-skype/skype-for-linux/downloading/?type=weblinux-deb -0
## sudo dpkg -i skypeforlinux-64.deb 

##-- Dropbox (see https://wiki.debian.org/dropbox)
cd ~ && wget -O - "https://www.dropbox.com/download?plat=lnx.x86_64" | tar xzf -

##-- Setting git up 
git config --global color.diff auto
git config --global color.status auto
git config --global color.branch auto
git config --global user.name "Kevin Cazelles"
git config --global user.email "kcazelle@uoguelph.ca"
git config --global github.user KevCaz
git config --global core.editor "nano"
git config --global credential.helper 'cache --timeout 7200'

##-- Github repositories (the repo I used the most). Note that it should be possible to use the API to retrieve them all
mkdir -p ~/Github/Websites ~/Github/Rpackages 
wget https://gist.githubusercontent.com/KevCaz/ac3e3a0566707ff4a12bc72286ffab1c/raw/e68d15aef8c247c62a2a799c82f556b6049c95e8/package2date.R  -O ~/Github/Rpackages/pkg2date.R
cd ~/Github/Website
git clone https://github.com/KevCaz/kevcazHugoWebsite.git
git clone https://github.com/inSileco/inSileco.github.io.git
cd ~/Github/Rpackages
git clone https://github.com/TheoreticalEcosystemEcology/alien.git
git clone https://github.com/inSileco/graphicsutils.git
git clone https://github.com/inSileco/letiRmisc.git

##-- powerline font 
git clone https://github.com/powerline/fonts.git
# install
cd fonts
./install.sh
# clean-up a bit
cd ..
rm -rf fonts
##-- prezto
zsh
git clone --recursive https://github.com/sorin-ionescu/prezto.git "${ZDOTDIR:-$HOME}/.zprezto"
setopt EXTENDED_GLOB
  for rcfile in "${ZDOTDIR:-$HOME}"/.zprezto/runcoms/^README.md(.N); do
    ln -s "$rcfile" "${ZDOTDIR:-$HOME}/.${rcfile:t}"
  done
# change shell 
chsh -s /bin/zsh