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Debian Testing (Stretch) install

This is a complete tutorial to install Debian Stretch. Most of the instructions are general enough to be applied on any computer. Keep in mind, however, that:

  • Hardware configuration (including keyboard layout) is tuned for a laptop DELL XPS 13 (9350);
  • Keyboard layout is based on QWERTY, and adds extra key combinations to enable French characters and accents, as well as most Greek letters.
  • The installation is geared towards an academic work, primarily based on the use of Emacs, R and PostGIS (see Office and R, QGIS and PostGIS sections).
  • Internet admin mostly deals with remote access of resources offered by the University of Florida (and is thus only relevant for UF members).

Table of contents

Installing Debian with the base Gnome desktop

Download the installer

The Debian way

Start by downloading an image of the Debian Installer for Debian Testing (Stretch), according to the platform of the computer. A good choice is the Network install (netinst), which will fetch all system packages directly on-line when installing. In this case, the file to download is the netinst weekly snapshot for amd64 (debian-testing-amd64-netinst.iso). Then check MD5 sums to guarantee the integrity of the file:

md5sum debian-testing-amd64-netinst.iso 
0ae2ef8a422522eca17d38bade946ec0  debian-testing-amd64-netinst.iso

The next step is to copy the ISO on a USB flash drive. First check on which device the flash drive is mounted:

df -h
Filesystem      Size  Used Avail Use% Mounted on
/dev/sda1        28G   15G   12G  55% /
...
/dev/sda3       204G  195G  2.8G  99% /home
tmpfs           789M   40K  789M   1% /run/user/1000
/dev/sdb1       7.5G  184K  7.5G   1% /media/<user>/<FLASH>

In this case, this shows that the flash drive is associated to sdb1. We can then use it to overwrite the flash drive with the ISO (WARNING #1: This formats the entire stick! WARNING #2: Change the value of sdb1 accordingly!):

sudo dd if=debian-testing-amd64-netinst.iso of=/dev/sdb1
587776+0 records in
587776+0 records out
300941312 bytes (301 MB) copied, 104.177 s, 2.9 MB/s

Now unmount the flash drive, and from now on, all other steps will be on the ‘target’ computer.

sudo umount /dev/sdb1

The easy way

NOTE: For a reason, the standard procedure above failed for me this time, with the system being unable to boot on the flash drive… A workaround is simply to use Unetbootin GUI to create the USB bootable image (using the Netinstall 64 bits for Debian testing), check that the boot flag is set on the drive (with GParted), and move directly to the next step.

Install Debian

You can now boot the computer on the USB flash drive (on a modern DELL laptop, that requires to turn off UEFI Security Boot, in favor of Legacy boot) and follow the instructions. General guidelines:

  • Root: Leave the password empty — that way, root permissions are given to the first user using sudo.
  • Partitions: Use Guided - use entire disk and set up encrypted LVM, with separate /home partition. When required to do so, enter a good passphrase (it will be required on every boot, but not when resuming from sleep). The partitioner will allocate 30 GB for the system (which is plenty) and 8 GB for the swap (equal to RAM amount). Two good modifications are to keep only 3 % of reserved blocks for root (maintenance) on /home, as well as increasing /boot to 512MB.
  • It’s a good idea to participate in the package usage survey (results are encrypted).
  • Chose GNOME for the desktop, and leave print server and standard system utilities.
  • Finally, install the GRUB boot loader to the master boot record on the first hard drive (pick the hard drive, not the USB flash drive!).
  • Time to restart!

Terminal setup

  • Bash configuration: 
    nano ~/.bashrc
    • Autocompletion: check that following lines are uncommented:
    if ! shopt -oq posix; then
  if [ -f /usr/share/bash-completion/bash_completion ]; then
    . /usr/share/bash-completion/bash_completion
  elif [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
  fi
fi
    • Other: add the following at the end of the file:
    # Ctrl-N keeps current directory
export PS1='\[$(__vte_ps1)\]'$PS1

# Manpages with colors
export MANPAGER="/usr/bin/most -s"

# Alias ls to have colors and directories before files 
alias ls='ls --color=auto --group-directories-first'

# Alias upgrade & upgrade-full
alias upgrade='sudo apt update && sudo apt upgrade'
alias upgrade-full='sudo apt update && sudo apt full-upgrade && sudo apt clean && sudo apt autoclean && sudo apt autoremove'

    :

    # Alias to restart Emacs daemon
alias emacs-restart="systemctl --user restart emacs"

# For Tilix and Powerline
# https://gnunn1.github.io/tilix-web/manual/vteconfig/
if [ $TILIX_ID ] || [ $VTE_VERSION ]; then
        source /etc/profile.d/vte.sh
fi
if [ -f `which powerline-daemon` ]; then
        powerline-daemon -q
        POWERLINE_BASH_CONTINUATION=1
        POWERLINE_BASH_SELECT=1
        . /usr/share/powerline/bindings/bash/powerline.sh
fi
  • Install Tilix, powerline and most (man needs most): 
    sudo apt install -t unstable libvted-3-0 libgtkd-3-0
sudo apt install tilix python-powerline most
    • Tilix configuration (in Window menu > Preferences):
      • Global: Uncheck Warn when attempting unsafe paste, check Automatically copy text to clipboard when selecting
      • Appearance: Terminal title style: none, Theme variant: dark
      • Quake: Hide the titlebar of the window
      • Shortcuts: Ctrl+Shift+D for Add terminal down; Ctrl+Shift+R for Add terminal right
      • Profile: Edit Default
        • General: Terminal bell: Icon
        • Color: Color scheme: Linux, and add some transparency
    • ‘Open Tilix here…’ in Nautilus comes with python-nautilus and libnautilus-extension1a, which should be there already.
    • Shortcuts: in Gnome preferences > Keyboard, add two Custom shortcuts (at the bottom of the list):
      • Tilix / tilix / Super+T
      • Tilix (Quake mode) / tilix --quake / ~
  • Get insulted on errors for password: 
    sudo visudo

    Add this line at the beginning of the file:

    Defaults        insults

System settings

  • Remove the system beep: in Settings > Sound > Sound Effects, turn off the Alert volume.
  • Optimize SSD:
    • /tmp in RAM:
    sudo cp /usr/share/systemd/tmp.mount /etc/systemd/system/
sudo systemctl enable tmp.mount
  • Use only SWAP when 99% of RAM is used: 
    sudo nano /etc/sysctl.conf

    Add at the end of the file:

    # SWAP after 99% RAM used 
vm.swappiness = 1
  • Date in the top bar with time, and calendar displaying the week number: 
    gsettings set org.gnome.desktop.interface clock-show-date true
gsettings set org.gnome.desktop.calendar show-weekdate true
  • Week starting on Monday, not Sunday: [DOESN’T WORK!] First check locales: 
    locale$ locale
    
    […]
LC_TIME=en_US.UTF-8

    Then edit the corresponding locale (should be en_US):

    sudo nano /usr/share/i18n/locales/en_US

    And add

    % Next two lines to have weeks start on Monday:
first_weekday   2
first_workday   2

    After:

    week 7;19971130;1

    (requires to log off from the session)

  • Keyboard shortcuts:
    • Home folder: Super+H
    • Hide all normal windows: Super+D
    • Save a screenshot of a window to Pictures: Shift+Ctrl+Super+P
    • Save a screenshot of an area to Pictures: Shift+Ctrl+Shift+P
    • Save a screenshot to Pictures: Shift+Ctrl+P
    • Lock screen: Ctrl+Echap
    • Toggle maximization state: Super+Return
    • Custom shortcut: Terminator: Super+T
  • Right-Alt used to access key 3rd level: in gnome-tweak-tool, Typing > Key to choose 3rd level: Right Alt (add key 'lv3:ralt_switch' in org.gnome.desktop.input-sources).
  • Keep numpad activated between sessions: 
    gsettings set org.gnome.settings-daemon.peripherals.keyboard remember-numlock-state true
  • Disable the sleep button (mapped to Fn+Insert) [doesn’t work?]: 
    gsettings set org.gnome.settings-daemon.plugins.power power-button-action "nothing"
  • Nautilus: Preferences > Views: Sort folders before files

APT and upgrade

  • Copy sources.list and preferences in /etc/apt/: 
    sudo rsync -rt sources.list_Stretch-testing/ /etc/apt/
sudo cp preferences_Stretch-testing/preferences /etc/apt/preferences
  • Avoid downloading translation indexes: 
    sudo nano /etc/apt/apt.conf.d/apt.conf

    And add:

    Acquire::Languages "none";
  • Enable the installation of i386 packages: 
    sudo dpkg --add-architecture i386
  • Update the indexes and keys: 
    sudo apt update
sudo apt install deb-multimedia-keyring pkg-mozilla-archive-keyring
wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
wget --quiet -O - http://qgis.org/downloads/qgis-2016.gpg.key | sudo apt-key add -
wget --quiet -O - http://repos.fds-team.de/Release.key | sudo apt-key add -
sudo apt-key adv --keyserver hkp://pgp.mit.edu:80 --recv-keys 379CE192D401AB61
curl https://repo.skype.com/data/SKYPE-GPG-KEY | sudo apt-key add -
sudo apt install apt-listbugst
  • Check the preferences (no repository should be left at 500): 
    sudo apt-cache policy
  • First upgrade 
    sudo apt upgrade
sudo apt full-upgrade
upgrade-full

Hardware

  • Laptop stuff (battery, wifi, non-free firmware): 
    sudo apt install firmware-linux-free firmware-linux-nonfree firmware-iwlwifi firmware-brcm80211 tlp tlp-rdw 
sudo modprobe -r brcmsmac ; sudo modprobe brcmsmac

    Note: TLP seems like a better alternative to laptop-mode-tools. Now for other non-free firmware (missing firmware for module i915):

    wget https://01.org/sites/default/files/downloads/intelr-graphics-linux/sklgucver61.tar.bz2 && \
tar xvjf sklgucver61.tar.bz2 && cd skl_guc_ver6_1/ && sudo ./install.sh
cd
wget https://01.org/sites/default/files/downloads/intelr-graphics-linux/kbldmcver101.tar.bz2 && \
tar xjvf kbldmcver101.tar.bz2 && cd kbl_dmc_ver1_01/ && sudo ./install.sh 
cd
rm -r skl_guc_ver6_1 && rm sklgucver61.tar.bz2 && rm -r kbl_dmc_ver1_01 && rm kbldmcver101.tar.bz2
sudo update-initramfs -u -k all
  • Bios update: As of 2017-05-23, the latest BIOS available is 1.4.17 (available here), with signatures: 
    md5sum XPS_9350_1.4.17.exe
f0bbf7c2bf7945923a70b61d7498acd2  XPS_9350_1.4.17.exe
sha1sum XPS_9350_1.4.17.exe
 a37feb837ac3e9619a729105a868a2d4a4d71eff  XPS_9350_1.4.17.exe
sha256sum XPS_9350_1.4.17.exe 
4f8d14538576778225ad627e59ef2b700a005898b5e4856e3d75fe54b9059475  XPS_9350_1.4.17.exe

    Download and store on a USB flash drive, reboot, hit F12, check “BIOS Flash update”, and follow instructions. To check current version of BIOS:

    sudo dmidecode | less
  • Firmware updates with fwupd (Dell provides firmware updates via Linux Vendor Firmware Service (LVFS)): 
    sudo apt install fwupd
sudo fwupdmgr get-devices
sudo fwupdmgr refresh
sudo fwupdmgr get-updates
sudo fwupdmgr update
  • Information on CPU frequency: 
    sudo apt install linux-cpupower
cpupower frequency-info
  • Keyboard set as PC 105 keys: :sudo nano /etc/default/keyboard and add as first line: 
    XKBMODEL="pc105"

    And apply the changes:

    sudo update-initramfs -u
  • Graphical boot: use Plymouth. 
    sudo apt install plymouth plymouth-themes

    Then edit /etc/initramfs-tools/modules:

    sudo nano /etc/initramfs-tools/modules

    and add the following lines:

    # KMS
intel_agp
drm
i915 modeset=1

    Then edit /etc/default/grub:

    sudo nano /etc/default/grub

    and add this line (note that preferred resolution is 3200x1800 by default, which is painfully slow; reducing even further to 800x600 or 640x480 can make it slighlty more responsive):

    GRUB_GFXMODE=1024x768

    And edit the GRUB_CMDLINE_LINUX_DEFAULT line to read:

    GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"

    Update Grub to pick up the changes:

    sudo update-grub2

    Set the default theme to lines:

    sudo /usr/sbin/plymouth-set-default-theme lines

    And finally apply the changes:

    sudo update-initramfs -u

Internationalization

  • Add French in the list of languages: 
    sudo dpkg-reconfigure locales

    Select en-CA.UTF-8, en-GB.UTF-8, en-US.UTF-8 (default), fr-CA.UTF-8, fr-FR.UTF-8.

  • Remove unnecessary locales: 
    sudo apt install localepurge
sudo localepurge
  • Keyboard layout:
    • The list of characters and functions can be found here: /usr/include/X11/keysymdef.h.
    • Custom keyboard adjusted to Dell XPS 13, including Home/End on PrtScr/Insert, special characters (←→²³€°–©☆§, etc.), math operators (±×÷≠≤≥), French and Spanish letters, accents and quotes (ÆæÀàÉéÈèÑñŒœÙù «» “” ¡¿, etc.), and most Greek letters (αβγδσΔΦΨΣ, etc.):
    sudo mv /usr/share/X11/xkb/symbols/us /usr/share/X11/xkb/symbols/us.bkp
sudo cp keyboard-DELL-XPS-13-9350_us /usr/share/X11/xkb/symbols/us

    Then restart Gnome Shell (Alt + F2 r) and choose “English (US, international with dead keys)” as Input Source in Settings > Region & Language (for French, add “French (alternative, Latin-9 only)”; for Greek alphabet, add “Greek (extended)”). Note that the Menu button doesn’t seem to work in Nautilus.

Installing a full system

Miscellaneous

sudo apt install autoconf build-essential cmake cmake-curses-gui cowsay debian-goodies detox disper dos2unix elinks espeak etcher-electron fortune git gnome-common gparted gtick hibernate libcanberra-gtk3-0:i386 mlocate ntp privoxy subversion transmission tree unetbootin units unrar virtualbox wakeonlan
sudo apt install -t unstable git-flow

Git to list files in subfolders:

git config --global status.showUntrackedFiles all

Gnome extensions

To be able to install Gnome extensions from Firefox ≥v.52, a Debian package and a Firefox extension are required:

sudo apt install chrome-gnome-shell gnome-shell-extension-redshift

List of extensions (o Installed; x Installed but not activated):

  • ✓ Alt-Alt+Tab
  • x AlternateTab
  • x Applications Menu
  • ✓ Auto Move Windows
  • ✓ BackSlide
  • ✓ Disconnect Wifi
  • ✓ Focus my window
  • x Gnote/Tomboy Integration (outdated)
  • ✓ gTile
  • ✓ Hibernate Status Button
  • x Launch new instance
  • ✓ Media player indicator (reinstall from source after media install) Outdated on official GNOME respository, but available on GitHub: 
    git clone https://github.com/eonpatapon/gnome-shell-extensions-mediaplayer.git
cd gnome-shell-extensions-mediaplayer/
./autogen.sh
make install-zip

    Then restart GNOME Shell (Alt-F2 + r)

  • ✓ Modern Calc
  • x Native Window Placement
  • ✓ Nothing to say Change shortcut to Super+F1: 
    dconf write /org/gnome/shell/extensions/nothing-to-say/keybinding-toggle-mute '["<Super>F1"]'
  • ✓ OpenWeather
  • x Places Status Indicator
  • ✓ Refresh Wifi Connections
  • x Removable Drive Menu
  • ✓ Remove Dropdown Arrows
  • x Return to Monitor (outdated)
  • x Screenshot Window Sizer
  • ✓ SincroDirs
  • ✓ Skype Integration
  • ✓ Sound Input & Output Device Chooser
  • ✓ Super+Tab Launcher
  • ✓ Suspend Button
  • ✓ TopIcons Plus
  • x User Themes
  • x Window List
  • ✓ Window Corner Preview
  • ✓ windowNavigator
  • x Workspace Indicator
  • x workspaceAltTab (outdated)

Web

sudo apt install firefox thunderbird lightning enigmail privoxy torbrowser-launcher chromium epiphany-browser iridium-browser mozplugger pipelight-multi

Firefox

To get a “clean” Firefox profile: Simply connect to Sync with your Firefox account to synchronize Tabs, Bookmarks, Passwords, History, Add-ons and Preferences from old Firefox. Leave Firefox open for some time… After all add-ons are installed, a little bit of tweaking is necessary after:

  • Enable GNOME theme (in Appearance).
  • Add-ons: Some add-ons were not synced and installed: HTTPS Everywhere, Privacy Badger; some options need to be reset (e.g. notifications for Self-Destructing Cookies).
  • Plugins: Need to activate OpenH264 Video Codec provided by Cisco.
  • Open tabs: Open tabs (including permanent tabs) are not synced: Close both old and new Firefox. Check the sessionstore.js file created in old Firefox’s profile when Firefox closes. Copy it in the new profile.
  • Search engines: Copy the search.json.mozlz4 file from old to new profile.
  • Add-on data is not synced: Copy necessary folders in tne new profile (e.g. Scrapbook).
  • Restart new Firefox and customize interface (buttons in the top bar and menu).

Here is the full list of add-ons that I normally install:

And the list of search engines that I keep:

The next step is to install additional plugins. Unfortunately, Flash may still be necessary for some websites, and Silverlight is necessary for NetFlix. The Pipelight project conveniently provides Windows-only plugins directly inside the browsers. First update the pipelight plugin:

sudo pipelight-plugin --update

Just to be safe, close Firefox, then enable Flash and Silverlight:

sudo pipelight-plugin --enable flash
sudo pipelight-plugin --enable silverlight
sudo pipelight-plugin --create-mozilla-plugins
sudo pipelight-plugin --list-enabled

After restarting Firefox, plugins can be check in the Plugins section of the Add-ons panel (then select “Ask to activate” for both). Flash in particular can be checked at: http://isflashinstalled.com/

If BetterPrivacy is installed too, use ~/.wine-pipelight as the Flash-Data directory.

Update January 2017: Pipelight is not maintained anymore. The good news is that now Adobe ships the latest Flash version for Linux too! Disable Flash from Pipelight (if it was installed/enabled), and simply install the flashplugin-nonfree from Debian repositories, or flashplayer-mozilla and flashplayer-chromium from Debian Multimedia repositories (the later allowing for Flash updates through general system update):

pipelight-plugin --disable flash
pipelight-plugin --list-enabled
sudo apt install flashplayer-mozilla flashplayer-chromium

Thunderbird

  • From a previous installation, simply copy the content of the former profile into the default profile folder in ~/.thunderbird.
  • Enigmail (needs version >= 2.07): Then change Gnome settings for the passphrase: 
    gsettings list-recursively org.gnome.crypto.cache

    Lists relevant settings: the method can be ‘session’ (never expires during the session), ‘idle’ (timer is reset each time there’s activity on the computer) or ‘timeout’ (simple timer since entering the passphrase). We set it to ‘idle’ with 5 minutes of delay:

    gsettings set org.gnome.crypto.cache gpg-cache-method "timeout"
gsettings set org.gnome.crypto.cache gpg-cache-ttl 300

    If it comes from a former installation, copy the .gnupg/ folder in ~/, and ensure permissions are correct:

    chmod -R go-rwx ~/.gnupg

    Check that GnuPG is installed with a version >2:

    gpg --version

    And finally migrate from old version:

    gpg -K

    Note that there is a bug with Enigmail 1.9.6-1 (which doesn’t recognize gpg); fixed in 1.9.6-2:

Here is the full list of add-ons that I normally install:

  • Essential add-ons:
    • CardBook
    • Enigmail
    • HTitle
    • Lightning
    • Show InOut
    • Virtual Identity
  • Appearance:
    • Allow HTML Temp
    • Calendar Tweaks
    • CompactHeader
    • Display Mail User Agent
    • GNOME-Thunderbird (theme Adwaita)
    • GNotifier
    • Manually sort folders
    • QuickFolders
    • Toolbar Buttons
  • Email content and display:
    • LookOut (fix version)
    • Image Zoom
    • Quote Colors
  • Email editing:
    • NestedQuote Remover
    • Send Later
  • Utilies:
    • Copy Folder
    • DKIM Verifier
    • Signature Switch
    • ownCloud for FileLink
    • Provider for Google Calendar
    • Remove Duplicate Messages (Alternate)

NextCloud integration

In Settings > Online accounts, add a new ownCloud account (works for NextCloud). Simply fill in the server address (where NextCloud is installed, not one of the scripts for CalDav/CardDav), username and password, and keep it for Calendar, Contacts, Documents and Files. Now events should appear in the calendar in the top bar, contacts should be synchronized with the Contacts application, and Files (Nautilus) should provide a shortcut to the NextCloud root folder.

Others

Internet admin

sudo apt install cifs-utils dnsutils gftp gvncviewer network-manager-openconnect-gnome network-manager-vpnc-gnome revelation rsync screen unison

VPN

In Settings > Network, add a ‘Cisco AnyConnect Compatible VPN (openconnect)’. Simply enter the ‘Gateway’: vpn.ufl.edu and leave all other empty. To turn the VPN on, click VPN in the top-right corner menu:

  • Username: GatorLink account (with @ufl.edu)
  • Password: GatorLink password (check ‘Save passwords’)

SSH

Copy the entire folder .ssh in /home. It contains key configuration for basille.net, Gargantua, MabLab server, as well as the keys for GitHub.

Gftp

Simply copy the bookmarks file from the .gftp folder in /home/ (it contains all bookmarks and passwords).

Clients for NextCloud and Dropbox

sudo aptitude install nautilus-owncloud nautilus-dropbox

For NextCloud, install the client:

cd Downloads
wget https://download.nextcloud.com/desktop/releases/Linux/Nextcloud-2.3.2-x86_64.AppImage
sudo mkdir /usr/local/lib/nextcloud/
sudo mv Nextcloud-2.3.2-x86_64.AppImage /usr/local/lib/nextcloud/
sudo ln -s /usr/local/lib/nextcloud/Nextcloud-2.3.2-x86_64.AppImage /usr/local/bin/nextcloud

Then run nextcloud, fill in the proper credentials, choose what to sync and where (in Public seems like a natural choice); in General, “Use Monochrome Icons”. To launch it at startup:

echo -e '[Desktop Entry]\nName=Nextcloud\nGenericName=File Synchronizer\nExec=/usr/local/bin/nextcloud\nTerminal=false\nIcon=nextcloud\nCategories=Network\nType=Application\nStartupNotify=false\nX-GNOME-Autostart-enabled=true\nName[en_US]=nextcloud.desktop' | tee ~/.config/autostart/nextcloud.desktop

For DropBox, install the proprietary deamon:

dropbox start -i

And follow the instructions (UF has a single sign-in process that works by just adding the UF address without password, with a passcode generated on the web).

Windows share

First create a credential file:

nano .smb

With the following information:

username=<GatorLink account>
password=<GatorLink password>

And reduce permissions on it:

chmod 600 .smb

Revelation

  • Create a new password file in ~/.revelation or copy an existing one in this folder.
  • Change preferences:
    • “Open file on startup:” and pick the file mentioned above;
    • Check “Automatically save data when changed”
    • “Length of generated passwords”: 12

Multimedia

  • Pictures 
    sudo aptitude install gimp-gmic gimp-plugin-registry gimp-resynthesizer gthumb hugin imagemagick darktable rawtherapee phatch qtpfsgui
  • Audio/video 
    sudo apt install audacity cuetools easytag flac gstreamer1.0-ffmpeg gstreamer1.0-fluendo-mp3 gstreamer1.0-plugins-bad gstreamer1.0-plugins-ugly monkeys-audio shntool soundconverter devede gnome-mpv mkvtoolnix oggconvert pitivi frei0r-plugins gnome-video-effects-frei0r openshot rhythmbox-plugins rhythmbox-plugin-alternative-toolbar sound-juicer sox subtitleeditor vlc vorbis-tools vorbisgain qarte
    • Plugins Rhythmbox: A repository for Ubuntu provides updated plugins for Rhythmbox. Instructions can be found here, and deb files can be found here. In summary, download the file corresponding to the most recent version of Ubuntu (Xenial at the time of writing), and install them using dpkg. If all deb files are in a dedicated folder: 
      sudo dpkg -i *.deb

      And if necessary:

      sudo apt -f install

      Currently, the following packages work:

      • Art Display
      • Equalizer (not up-to-date but works)
      • Fullscreen Plugin
      • lLyrics
      • Open containing folder
      • Playlist Import Export
      • Random Album Player
      • Remember-the-Rhythm

      One very interesting package is not up to date and does not work:

      • lastfm-queue

      Finally, rhythmbox-plugins also provides Cover Art/Search, Internet Radios, Replay Gain and other potentially interesting plugins, and rhythmbox-plugin-alternative-toolbar gives a simplified and enhanced user interface.

  • Leisure 
    sudo apt install chromium-bsu dosbox marble stellarium sweethome3d

Office

sudo apt install abiword aspell aspell-fr aspell-en gnote homebank hunspell hunspell-en-ca hunspell-en-us hunspell-fr inkscape jabref libreoffice-gnome libreoffice-gtk libreoffice-pdfimport libreoffice-style-breeze libreoffice-style-oxygen libreoffice-style-sifr myspell-en-gb pandoc pandoc-citeproc tesseract-ocr tesseract-ocr-eng tesseract-ocr-fra
  • Need to remove all links to French dictionaries: 
    sudo rm /usr/share/hunspell/fr_*
sudo rm /usr/share/myspell/dicts/fr_*

    In case of trouble, just reinstal hunspell-fr.

  • Change Icon style of LibreOffice (Tools > Options > LibreOffice > View) to Breeze, and possibly Show Icons in menus.
  • Preferences for HomeBank are stored in ~/.config/homebank. It’s probably safe to simply copy this folder.

Hugo

Debian does not provide up-to-date Hugo. Check the latest release here, then:

cd Downloads/
wget https://github.com/gohugoio/hugo/releases/download/v0.30.2/hugo_0.30.2_Linux-32bit.deb
sudo dpkg -i hugo_0.27.1_Linux-64bit.deb
hugo version

Fonts

sudo apt install fonts-arphic-ukai fonts-arphic-uming fonts-arphic-gkai00mp fonts-arphic-gbsn00lp fonts-arphic-bkai00mp fonts-arphic-bsmi00lp fonts-bebas-neue fonts-crosextra-carlito fonts-crosextra-caladea fonts-hack-ttf ttf-mscorefonts-installer ttf-kochi-gothic ttf-kochi-mincho ttf-baekmuk unifont
  • Use gnome-tweak-tool to change Monospace font to Hack Regular 11.
  • Alternatives for Calibri/Cambria (MS fonts) : Carlito and Caladea. Once installed, in LibreOffice: Options > Fonts, check ‘Apply replacement table’, and add a replacement rule for each (Calibri -> Carlito, Cambria -> Caladea). Leave everything unchecked (Always and screen only).

LaTeX and PDF

sudo aptitude install gedit-latex-plugin gummi ispell texlive-full bibtex2html rubber latex2rtf xpdf pdftk pdfjam poppler-utils libtext-pdf-perl pdf2svg impressive pdfchain pdfshuffler calibre mupdf pdf2djvu scribus xournal ditaa

Note that biblatex lives in texlive-bibtex-extra, which comes with texlive-full; pdfmanipulate comes with calibre.

  • Adobe Reader (in dmo) 
    sudo aptitude install acroread:i386
  • Link folder of main BibTeX file to the Tex install. First check with: 
    kpsewhich -show-path=.bib

    It should include /home/<user>/.texlive2016/texmf-var/bibtex/bib//. The trick is then to create this path as a link to the main bibliographic directory. For instance:

    mkdir -p ~/.texlive2016/texmf-var/bibtex/bib
ln -s ~/Work/Biblio/ ~/.texlive2016/texmf-var/bibtex/bib
  • Install a package (e.g. moderncv) 
    sudo nano /etc/texmf/texmf.d/03local.cnf
    
    TEXMFHOME = ~/.texlive2016/texmf
      
    sudo update-texmf

    Check with:

    kpsewhich --var-value TEXMFHOME

    Copy packages in ~/.texlive2016/texmf/tex/latex/ and complete install when necessary, e.g.:

    latex moderntimeline.ins
latex moderntimeline.dtx
  • Install a font: copy the font in ~/.texlive2016.d/texmf/fonts/truetype/, then update the TeX index: 
    sudo texhash

Emacs

sudo aptitude install emacs25 libpoppler-glib-dev

Configuration via Git:

git clone [email protected]:basille/.emacs.d ~/.emacs.d/

And load Emacs, potentially several times until all packages are installed.

JabRef configuration

Debian recently integrated the 3.x series in the official repositories, with JabRef 3.8 now available for Stretch (July 2017).

In Options > Preferences:

  • Import preferences (jabref-preferences.xml). Should be enough, but just in case, check the following:
  • In General: check owner name and English as language;
  • In File: check the main file directory (currently /home/mathieu/Work/biblio/PDF/);
  • In Appearance: “Use other look and feel”, and set up the Class name to: com.sun.java.swing.plaf.gtk.GTKLookAndFeel for GTK look & feel;
  • In BibTeX key generator: check the different key patterns;
  • In Advanced: activate “Listen for remote operation on port:” 6050 (for use with JabFox).

Finally, install Zotero and JabFox add-ons for Firefox, and then adjust JabFox preferences:

  • Adjust the path to JabRef launcher, usually /usr/bin/jabref (‘[email protected]’ preference of Firefox);
  • Export format to BibTeX.

Gnote configuration

  • Synchronization using WebDav seems really complicated to set up; one solution is to use ownCloud client to sync a =Gnote= folder localy, and then configure it in Gnote Preferences > Synchronization using Local folder as a service (and check the Automatic sync every 10 minutes).
    • Synchronization seems to cause many crashes of Gnote… Hence simply copying the note folder (~/.local/share/gnote) should be enough.
  • Other preferences:
    • General: Always open notes in new window
    • Plugins: Enable ‘Export to HTML’ and ‘Table of contents’.
  • Using gnome-tweak-tool, add Gnote to the list of Startup Applications.

R, QGIS and PostGIS

GDAL, GEOS and PROJ.4

sudo apt install gdal-bin libgdal-dev libgeos-dev proj-bin libproj-dev

R

sudo apt install r-base-core r-base-dev r-recommended r-cran-rodbc r-cran-rjava r-cran-tkrplot littler jags libcairo2-dev libglu1-mesa-dev libssl-dev libxt-dev libudunits2-dev

Configuration via Git:

git clone [email protected]:basille/R ~/.R-site/
mkdir ~/.R-site/site-library
ln -s ~/.R-site/.Renviron ~/.Renviron

Then in R:

gdal <- TRUE; options(repos = c(CRAN = "http://cran.r-project.org/")); source("~/.R-site/install.selected.R")

And finally link to the R profile:

ln -s ~/.R-site/.Rprofile ~/.Rprofile

RStudio is unfortunately not in the Debian repositories (yet). So the recommanded way to install it is to download the latest installer, which is, on Dec 2 2016, for version 1.0.44 (check here first):

wget https://download1.rstudio.org/rstudio-1.0.44-amd64.deb
sudo dpkg -i rstudio-1.0.44-amd64.deb 
rm rstudio-1.0.44-amd64.deb

(RStudio has a tendancy to mess a bit with file associations, so it might be necessary to clean that after if RStudio is not supposed to be the default R editor; as a matter of fact, if it is the case, it is the easiest way to associate .R or .Rmd files to any editor, while keeping the association to Gedit for plain text documents)

RStudio is provided with its own version of Pandoc, but it seems to come with potential problems. The easiest way to overcome this is simply to rename the Pandoc executable provided by RStudio (requests will then fallback on the system Pandoc):

sudo mv /usr/lib/rstudio/bin/pandoc/pandoc /usr/lib/rstudio/bin/pandoc/pandoc.bkp

Note that RStudio is not adapted to very high resolution (for instance Retina) and may look very tiny in this case.

QGIS and PostGIS

sudo apt install qgis python-qgis

Or if it fails due to a missing package (gdal-abi-2), then prefer the install from Debian repositories:

sudo apt install -t o=Debian,n=stretch qgis python-qgis

Then, from inside QGIS, install the Time manager plugin.

Other

Google Stuff

Google Earth

The Debian way:

sudo apt install googleearth-package
make-googleearth-package
sudo dpkg -i googleearth*.deb
sudo apt -f install

But dependencies impossible to reconcile (libcurl3:i386)… Solution: get official .deb from Google, then:

sudo dpkg -i google-earth-stable_current_amd64.deb
sudo apt -f install

Google Chrome

Add Google Chrome repository (sources.list + preferences), then:

sudo apt install google-chrome-stable

Skype

At last, Microsoft now provides a decent version of Skype for Linux (based on their new web version), currently in its alpha stage. The application seems to work fine, and can be concurrently installed with the ‘legacy’ version (it’s called “Skype for Linux” and the binary is skypeforlinux):

wget https://repo.skype.com/latest/skypeforlinux-64-alpha.deb
sudo dpkg -i skypeforlinux-64-alpha.deb 
sudo apt -f install
rm skypeforlinux-64-alpha.deb

Note that alternatives exist, such as Ghetto Skype (which does not currently provide video calls).

Rockbox utility

  • Download Rockbox utility
  • Unzip file, and copy RockboxUtility in /usr/local/bin/: 
    tar xvjf RockboxUtility-v1.4.0-64bit.tar.bz2
sudo mv RockboxUtility-v1.4.0-64bit/RockboxUtility /usr/local/bin/rockbox
sudo chmod 755 /usr/local/bin/rockbox 
rm -R RockboxUtility-v1.4.0-64bit
  • Launch rockbox
  • Install Ambiance theme (activate icons).

Final stage

  • Check default applications (Settings > Details > Default Applications).
  • Check applications on startup with gnome-tweak-tool (Startup Applications: icedove, firefox, nautilus, gnote).
  • Final cleaning: 
    upgrade-full

Admin operations

Backup

The easiest way is to use CRON on a daily basis to backup the entire /home, as well as the databases. To do this, prepare a file home-backup (or any other name), with something like the following:

#!/bin/sh

### Mount operations (needs credentials in ~/.smb)
mount.cifs //XX.YYY.ZZZ/<USER> /mnt/<USER>/ -o credentials=/home/<USER>/.smb,uid=<USER>,gid=<USER>

### Save PostgreSQL databases (full dump):
pg_dumpall | gzip > /mnt/<USER>/home/postgresql/full_`date -I`.sql.gz

### Save file ACLs (permission, ownership)
cd ~
getfacl -R . > /mnt/<USER>/home/<USER>.file-acl
### Restore file ACLs (in the file-acl directory)
# setfacl --restore=<USER>.file-acl

### Entire /home except: 
### Downloads, caches/thumbnails, .extraswap, emacs.d/elpa/,
### .R-site/site-library/, Torbrowser, Trash
###  --modify-window=1 to consider rounded timestamp 
rsync -avz --progress --delete-during --modify-window=1 --exclude=Downloads --exclude=.local/share/torbrowser --exclude=.cache --exclude=.gftp/cache --exclude=.googleearth/Cache/ --exclude=.thumbnails --exclude=.emacs.d/elpa --exclude=.R-site/site-library/ --exclude=.local/share/Trash /home/<USER>/ /mnt/<USER>/home/<USER>/

### Unmount operations
umount /mnt/<USER>/

Then make the file executable and copy it to /etc/cron.daily:

chmod +x home-backup
sudo cp home-backup /etc/cron.daily/

CRON will run daily at the time setup in /etc/crontab:

grep run-parts /etc/crontab

In this case, every day at 6:25AM. If the computer is not turned on at this time, CRON looks for /etc/anacrontab

less /etc/anacrontab

In this case, every day after a period of 5 minutes since wake-up.

This results in a directory home with

  • The home backup in home/<USER>/
  • The databases backup as a full compressed dump in home/postgresql
  • The file permissions in home/<USER>.file-acl

Recovery

There is currently an important bug with the absence of a root user (due to the use of sudo): recovery mode (from GRUBS) fails to load, arguing that root is locked (it is actually absent). So there is currently no way to load recovery mode directly from the system.

One alternative is to use a Live USB to load a working system, mount the computer file system, and do the necessary modifications from there. A very good candidate is the Tails live OS, which is security and privacy oriented (a good distribution to always have on a flash drive).

To install Tails on a flash drive, follow the Debian way:

sudo apt install tails-installer

Download the Tails ISO image, start the Tails Installer Launcher, and follow the instructions. When the flash drive is ready to use, plug it into the laptop and boot on it. Don’t forget to give a root password on login (check the options).

The key here is to be able to mount an encrypted partition in Tails. It can be all achieved in command line, so first open a terminal. The first step is to identify existing partitions:

sudo lsblk

The interesting part looks like the following:

nvme0n1     … 238.5G … disk
├─nvme0n1p1 …   243M … part	
├─nvme0n1p2 …     1K … part
└─nvme0n1p5 … 238.2G … part

Let’s now access the encrypted volume, that we will call crypt from now on:

sudo modprobe dm-crypt
sudo cryptsetup luksOpen /dev/nvme0n1p5 crypt

This requires to enter the passphrase AND the root password from Tails.

sudo lsblk
  
nvme0n1     … 238.5G … disk
├─nvme0n1p1 …   243M … part	
├─nvme0n1p2 …     1K … part
└─nvme0n1p5 … 238.2G … part
  └─crypt   … 238.2G … crypt

The encrypted volume is now visible. Let’s see what’s inside, and activate the proper volume:

sudo modprobe dm-mod
sudo vgscan
  
Found volume group "mablap2-vg" using metadata type lvm2
    
sudo vgchange -a y mablap2-vg
  
3 logical volume(s) in volume group "mablap2-vg" now active

The last step is to look at the partitions inside, and mount what is necessary (here the /root partition):

sudo lvscan
  
ACTIVE  '/dev/mablap2-vg/root' [27.94 GiB] inherit
ACTIVE  '/dev/mablap2-vg/swap' [7.61 GiB] inherit
ACTIVE  '/dev/mablap2-vg/home' [202.68 GiB] inherit
    
sudo mkdir /media/root
sudo mount /dev/mablap-vg/root /media/root
cd /media/root
ls
  
bin boot etc …

The system is now ready for any modifications. When it’s done, it’s time to close everything:

sudo umount /media/root
sudo vgchange -a n mablap2-vg 
sudo cryptsetup luksClose crypt

Removing old kernels

Kernels tend to accumulate, and eat space in the /boot partition. If /boot is full, it becomes necessary to remove old kernels. First check the current kernel:

uname -r

and the list of installed kernels:

dpkg --list | egrep -i --color 'linux-image|linux-headers'

then remove unnecessary kernels (it is a good idea to keep current kernel and one older):

sudo apt purge linux-image-XXX-amd64

where XXX stands for the actual version number, and update GRUB:

sudo update-grub2

Useful resources