ubuntu-laptop_for_data-science.md

Things to do After Installing Ubuntu 18.04

Code have to be entered using Terminal (CTRL+ALT+T to open it)

• add the following line to let the system configure wi-fi adapter (only for Lenovo 530S and similar)

  sudo tee /etc/modprobe.d/blacklist-ideapad.conf <<< "blacklist ideapad_laptop"

  then reboot.

• decrease swap usage:

  sudo nano /etc/sysctl.conf

  then add the following lines at the end:

  # Decrease swap usage to a reasonable level 
  vm.swappiness=15 
  # Improve cache management 
  vm.vfs_cache_pressure=50

• install some utilities prerequisites, just in case:

  sudo apt-get install -y apt-transport-https software-properties-common nano dos2unix man-db gdebi git-core libgit2-dev libauthen-oath-perl openssh-server build-essential net-tools

• install TLP (power manager, raise battery life, prevent CPU overheating):

  sudo apt install -y tlp tlp-rdw
  sudo tlp start

• install TLP GUI:

  sudo add-apt-repository ppa:linuxuprising/apps
  sudo apt-get install -y tlpui

• install Phoronix (test and benchmark suite) (see here for the link to the latest deb file)

  mkdir ~/software
  cd ~/software
  wget -O phoronix http://phoronix-test-suite.com/releases/repo/pts.debian/files/phoronix-test-suite_8.8.1_all.deb
  sudo gdebi phoronix

• Personalize GNOME GUI:

  • add to Launcher: Terminal, Chrome
  • move Laucher along the bottom, and hide it
  • change touchpad behaviour (not natural)
  • enable Night Light

• Some keyboard shortcut:

  • Switch to overview: Super key
  • List all applications: Super key + A
  • Switch workspaces: Ctrl + Alt + Up/Down

• Install GNOME Tweak Tool and Shell Extensions:

  sudo apt install -y gnome-tweak-tool gnome-shell-extensions

  See this blog posts: 1, 2, 3

  • Enable ‘Minimize on Click’ for the Ubuntu Dock

    gsettings set org.gnome.shell.extensions.dash-to-dock click-action 'minimize'

  • Install the material theme with the papirus icon set:

    sudo apt-get install -y materia-gtk-theme
    sudo apt-get install -y papirus-icon-theme

  • Some extension to install: Extensions, todo.txt, dropdown terminal, Applications Overview Tooltip, Clipboard Indicator, OpenWeather, Coverflow Alt-Tab, Appfolders Management, Apt Update Indicator, Auto Move Windows, Hide Activities Button, Panel OSD, Places Status Indicator, Steal My Focus, Workspaces to Dock, **

• Enable Firewall (ufw) and install a GUI to manage it

  sudo ufw enable
  sudo apt install -y gufw

• install Conky and Stacer (system monitoring tools) (see here for the link to the last version of the deb file):

  sudo apt-get install -y conky-all
  cd ~/software
  wget -O stacer https://netcologne.dl.sourceforge.net/project/stacer/v1.1.0/stacer_1.1.0_amd64.deb
  sudo gdebi stacer

• Install full multimedia support:

  sudo apt-get install -y mencoder flac faac faad sox ffmpeg2theora libmpeg2-4 uudeview mpeg3-utils mpegdemux liba52-dev mpeg2dec vorbis-tools id3v2 mpg321 mpg123 icedax lame libmad0 libjpeg-progs libdvdcss2 libdvdread4 libdvdnav4 ubuntu-restricted-extras

• Install most archiving capabilities (extract and compress files in various formats):

  sudo apt-get install -y unace unrar zip unzip p7zip-full p7zip-rar sharutils rar uudeview mpack arj cabextract file-roller

• install Double Commander (file manager):

  sudo add-apt-repository ppa:alexx2000/doublecmd
  sudo apt-get install -y doublecmd-gtk

• install keepass (password manager):

  sudo apt-add-repository ppa:jtaylor/keepass
  sudo apt-get install -y keepass2

• install KVM (Virtual Machine) and its graphhical manager (need reboot):

  sudo apt install -y qemu-kvm libvirt-clients libvirt-daemon-system bridge-utils virt-manager

• install last version (11) of the Java Runtime Environment (JRE) and the Java Developer Kit (JDK):

  sudo apt install install -y default-jdk

• install Chrome (browser)

  cd ~/software
  wget -O chrome https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
  sudo gdebi chrome

• install: FileZilla (FTP), shutter (screenshot), Clementine (audio music player), VLC (multi-media player), synaptic (package manager), GIMP (Photo Editor), Calibre (eBook manager), Pinta (Paint alternative), Kazam (screen recorder)

  sudo apt-get install -y filezilla shutter clementine vlc synaptic gimp calibre pinta kazam

• install Foxit PDF Reader (see here for the link to the latest deb file)

  cd ~/software
  wget -O foxitpdf http://cdn01.foxitsoftware.com/pub/foxit/reader/desktop/linux/2.x/2.4/en_us/FoxitReader.enu.setup.2.4.4.0911.x64.run.tar.gz
  tar xf foxitpdf
  sudo su
  ./'FoxitReader.enu.setup.2.4.4.0911(r057d814).x64.run'
  exit

• install insync (GDrive+OneDrive Manager) (see here for the link to the latest deb file)

  sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys ACCAF35C
  nano /etc/apt/sources.list.d/insync.list 
  deb http://apt.insync.io/ubuntu bionic non-free contrib
  sudo apt-get update
  sudo apt-get install insync

• install simplenote (Cloud Markdown Editor) (see here for the link to the latest deb file)

  cd ~/software
  wget -O simplenote https://github.com/Automattic/simplenote-electron/releases/download/v1.6.0/Simplenote-linux-1.6.0-amd64.deb
  sudo gdebi simplenote

• install atom (Text editor) (see here for the link to the latest deb file)

  cd ~/software
  wget -O atom https://atom-installer.github.com/v1.38.2/atom-amd64.deb
  sudo gdebi atom

• install Sublime Text (Text editor) (see [here]() for the link to the latest deb file)

  cd ~/software
  wget -O 
  sudo gdebi 

• install skype (video calling)

  cd ~/software
  wget -O skype https://repo.skype.com/latest/skypeforlinux-64.deb
  sudo gdebi skype

Install the Data Science Stack:

• R

  echo -e "\n# CRAN REPOSITORY\ndeb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/\n" | sudo tee -a /etc/apt/sources.list
  sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
  sudo apt-get update
  sudo apt-get install -y r-base r-base-dev

• add to R environment:

  sudo nano $(R RHOME)/etc/Renviron

  then at the end:

  PUB_PATH = '/usr/local/share/public'
  R_LIBS_USER = '/usr/local/share/public/R_library'
  R_MAX_NUM_DLLS = 1000

• RStudio Desktop (see here for the link to latest version)

  cd ~/software
  wget -O rstudio https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.2.1335-amd64.deb
  sudo gdebi rstudio

• Shiny Server (see here for the link to latest version)
  install first shiny and rmarkdown from inside RStudio:

  install.packages(c('rmarkdown', 'shiny'))

  then you're ready for Shiny Server:

  cd ~/software
  wget -O shiny https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.9.923-amd64.deb
  sudo gdebi shiny

  check it's working pointing the browser to http://localhost:3838/

• install Ubuntu dependencies for R packages

• install R packages)

• Python with the ScyPy and AI/DeepLearning stacks

• MySQL

• Docker

• LaTeX

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