The Living Thing / Notebooks :

Comfy Ubuntu

Various bits of setup to use the hippest science software with minimum friction

Ah, Ubuntu! The linux distro that realises that whilst your might be lured to Linux by its promise of a fast light secure OS, if you really want to get grumpy developers to come to your platform and bring their users you had better deliver something as bloated and messy as Windows.

Ubuntu is a kind of lowest-common-denominator system for HOWTO guides to target for linux users because, AFAICT, there is a gigantic amount of crap already pre-installed so odds are your software of choice is already installed, or at least the dependencies. It always feels like using a circular saw with integrated wiffle bat to crack a nut, though, and I have a vague inking that it’s probably not as secure as I hope.

I am interested in more minimalist approaches than the mainline Ubuntu rolling mess, such as Elementary or possibly even a super sleek hardened OS.


Why would I not use at least a perfunctory firewall?

sudo ufw enable


See DNS servers.

Non-packaged apps

homebrew is the goods:

sh -c "$(curl -fsSL \"
test -d ~/.linuxbrew && \
    eval $(~/.linuxbrew/bin/brew shellenv)
test -d /home/linuxbrew/.linuxbrew && \
    eval $(/home/linuxbrew/.linuxbrew/bin/brew shellenv)
test -r ~/.bash_profile && \
    echo "eval \$($(brew --prefix)/bin/brew shellenv)" >>~/.bash_profile
echo "eval \$($(brew --prefix)/bin/brew shellenv)" >>~/.profile

This is obviously slightly horrifying since it involves running scripts straight of the internet; one should inspect the script does what is expected first.

Alternatively, one could check out manually

git clone ~/.linuxbrew/Homebrew
mkdir ~/.linuxbrew/bin
ln -s ../Homebrew/bin/brew ~/.linuxbrew/bin
eval $(~/.linuxbrew/bin/brew shellenv)

This still ultimately runs wacky foreign code of course; that’s the whole point.

Linuxbrew is how you would install shiny things such as fish, which would otherwise be hopelessly outdated in a more elderly distro e.g. Ubuntu 16.04. It claims to support julia, but AFAICT that doesn’t work. node.js does, though.

Probably I want all the libraries which are too patent-encumbered to be bundled with my holier-than-me distribution. This means codecs and other content-related shit.

brew install libsamplerate libsndfile ffmpeg node

Packaged apps

See packaged apps.

Running apps that don’t come through the intimate Debian packaging, but rather as sandboxed binary thingies including all their own dependencies. Obviously there are several philosophically different approaches to this idea and I would not mind this if they didn’t waste so much hard disk space.

Probably that means flatpak support as well as the native snap.


As of Ubuntu 19.04 there is a medium-fresh (1.0) version of syncthing in the repository, so one can simply

sudo apt-get install syncthing

If I want a fresher version than your ubuntu release supports (and I do) I can choose, for example or bonus apt PPAs, or the packaged snap. All seem AFAICT equivalent.

# Add the release PGP keys:
curl -s | sudo apt-key add -

# Add the "stable" channel to your APT sources:
echo "deb syncthing stable" | \
    sudo tee /etc/apt/sources.list.d/syncthing.list

# Update and install syncthing:
sudo apt-get update
sudo apt-get install syncthing

Now choose my autostart method. I probably want to do this as a user, not as a system service, because root access is from a different devops era.

But wait! Does it report my disk is full when I try to use filesystem monitors? I need to allocate more resources to that.

$ cat /proc/sys/fs/inotify/max_user_watches
$ sudo sh -c 'echo 204800 > /proc/sys/fs/inotify/max_user_watches'
$ echo "fs.inotify.max_user_watches=204800" | sudo tee -a /etc/sysctl.conf
$ cat /proc/sys/fs/inotify/max_user_watches

Google Chrome

A nice browser is necessary, no?

If I want profile sync or some other features not in plain chromium, askubuntu says:

sudo bash
wget -q -O - | \
    apt-key add -
echo "deb [arch=amd64] stable main" >> \
apt-get update
apt-get install google-chrome-stable

Standard disclaimer: the other features that are not in plain chromium may include Google spyware.


My current favourite numerical software! I download julia as a plain installer package; It’s too rapidly evolving for anything else.


I give in, and just run anaconda. It is easy for science stuff.

Bonus: then I get pytorch and and other such tricky-GPU-dependency packages without messing about.

conda install pytorch torchvision cuda91 -c pytorch


Not all the good editors are packaged up. In fact the hippest ones are installed separately.

Also, a passable CLI editor, neovim

sudo add-apt-repository ppa:neovim-ppa/stable
sudo apt-get update
sudo apt-get install neovim
sudo update-alternatives --install /usr/bin/vi vi /usr/bin/nvim 60
sudo update-alternatives --config vi
sudo update-alternatives --install /usr/bin/vim vim /usr/bin/nvim 60
sudo update-alternatives --config vim
sudo update-alternatives --install /usr/bin/editor editor /usr/bin/nvim 60
sudo update-alternatives --config editor

Password manager

Obviously password managers are essential. How painful is passwordstore? Because it looks like the best one in terms of supporting everything, albeit clunkily.

sudo apt-get install pass

Clipboard manager

CopyQ (every desktop) seem most popular and works well.

sudo add-apt-repository ppa:hluk/copyq
sudo apt update
sudo apt install copyq copyq-plugins

Useful: CopyQ Keyboard shortcuts.

Alternatively, Zazu offers a clipboard manager.

These raise security questions, i.e. in CopyQ there is no way of marking passwords on the clipboard as secret unless they come from certain password apps, and that is quite tedious, and presumes you aren’t using a command-line password manager, or a browser plugin.

See also clipboard managers for some in-depth and cross-platform comparison.


How bes to emulate 1970s hardware on Ubuntu? Hmmm. They are all a bit shit.

If you are worried that your current terminal doesn’t use enough RAM, you can use hyper which is a javascript app version of terminal. It’s not too bad for one of these web technology desktop apps It has lots of sexy features and graphics, and UX detailwork, to compensate for the hefty RAM usage.

Terminator seems to be an acceptable default option for a pure native app without many frills, or much resource usage, although one would really like a couple of wind chimes and a duck call after all it’s the 21st century!

There are many more half-arsed options available.

Switching applications, why can’t it be smooth like on a Mac did Apple patent intuitiveness?

One could use a custom [launcher]{filename}, e.g. Zazu or do. But the built-in launcher on Gnome is pretty good, so I do not bother.


Also trackpad buttons. For my Razerblade there were extra things to do. There are also some tips there about making settings persist.

Kai Koenig reveals that I can have the button assignments different between mouse and keyboard. This is useful for me, since I mouse left-handed and trackpad right-handed, for reasons of avoiding RSI.

This needs the xinput trick

xinput -list

to find the name of my mouse, then

xinput set-button-map "2.4G Mouse" 3 2 1 &&

Making it work generically for all peripherals requires fancier footwork.

Desktop could be nicer

Ubuntu 17.0 or later: GNOME

Oh wait Unity desktop is over now I need to convert all the classic tweaking to GNOME. See comfy GNOME shell.

Ubuntu before 17.10: Unity

Here are the keyboard shortcuts needed to have a civilised desktop experience.

The default OS switcher is configurable

sudo apt-get install compizconfig-settings-manager compiz-plugins

I simply don’t like the default Unity alt-tab application switcher. It may work for a lot of people, but it just slows me down. For me it’s faster to have a single application switcher that cycles through all open windows, possibly within one desktop, but I’m not sure about that. I am really not compatible with the default unity switcher that groups windows, for example terminals, together so when hitting alt-tab you can’t (in an effective way) switch between terminals. Having a different key combo for that slows my brain down. […] Open compizconfig-settings-manager with alt-F2, type ccsm.

Scroll down to “Ubuntu Unity Plugin”. Choose the tab “Switcher”. Disable the alt-tab and shift-alt-tab key bindings. (“Key to start the switcher” and “Key to switch to the previous window in the Switcher”. Click the “Back” button.

Scroll down to the “Window management” section. Here you can select another switcher. I enable the “Static Application Switcher”, resolve any potential conflicts by setting the setting for “Static Application Switcher”. Now you can tweak the switcher by clicking on it. I have changed alt-tab and shift-alt-tab to “Next window (All windows)” and “Prev window (All windows)”.

Unity tweak tool does unity-specific tweaks of this kind of nonsense.

sudo add-apt-repository ppa:freyja-dev/unity-tweak-tool-daily
sudo apt-get install unity-tweak-tool

See also the nifty run-or-raise hack.

Encryption and verification infrastructure

Encrypting, signing, certifying, swapping keys etc. For when one is worried about the state apparatus interfering with your life:

sudo apt-get install debian-keyring  ## keys of extra-paranoid nerds
sudo add-apt-repository ppa:tails-team/tails-installer
sudo apt-get install tails-installer  ## for installing the paranois tails OS
sudo apt-get-install pius signing-party  ## citizen identity verification

Encrypted folders/disks

My latest roadbump. 🚧 definitive fix. NB: all of these are a world of pain and stupid edge-cases.

Before 18.04 ecryptfs did home folder encryption. From 18.04 along the system totally changed. The previous one, ecryptfs turned out to be a bag of trouble. It’s not clear to me which of fscrypt, encfs, gocryptfs, luks or veracrypt are better. See encrypting file systems for a run-down. From 19.04 LUKS whole disk encryption is the default option. fscrypt seems not too much trouble. It works OK on the desktop. Downside: you need to type 2 passwords to log in, the hard drive decrypt key, plus the user key.

fscrypt doesn’t have this problem; I can log in and use my keychain to decrypt specail user data. Encrypting the whole disk is probably better in the sense that it makes it harder to tamper with my computer, but then, if you are tampering with my computer unattended you can probably still mess with me by going for hardware or firmware without substantially greater effort, so this trade-off is not clear-cut.

I probably want to go with LUKS because there is less for me to mess up in that the automatic installer configures it for me, and just live with the horrible double-password situation.

NB the ubuntu encrypted FS docs are outdated on this issue.

Don’t confuse Windows time/date when dual booting

Windows updates the time not the time zone to stay compatible with MS-DOS. Who knew.

Linux has to bear the compatibility burden on this bit of arse-backwardsery, but the command in that link seems to work more or less. I also needed to kick the hardware clock for consistency.

timedatectl set-local-rtc 1 --adjust-system-clock
hwclock -w --localtime

To revert to sanity:

timedatectl set-local-rtc 0 --adjust-system-clock
hwclock -w --utc

Or, my life hack: tell Windows OS that the timezone is in UTC and deal with Windows thinking it is 4am when I am at work. Since I only use Windows for an hour here and there each month it’s much easier. (Not recommended: tell Windows to use UTC via advanced registry settings but still set a non-trivial time-zone.)

Fish shell

If Ubuntu 16.04, I either use linuxbrew for an updated shell or use an updated PPA. In 18.04 such is no longer needed.

The former: Add /home/linuxbrew/.linuxbrew/bin/fish to /etc/shells. Then run

chsh -s /home/linuxbrew/.linuxbrew/bin/fish

The latter:

sudo apt-add-repository ppa:fish-shell/release-2
sudo apt-get update
sudo apt-get install fish
chsh -s /usr/bin/fish

Offline documentation

Zeal is not bad.

sudo add-apt-repository ppa:zeal-developers/ppa


RStudio can be downloaded from its site R is already in the repository. ONe might want a fresher version but nothing has made that worth the bother for me yet.


See comfy razer.

Oh arse I have to do design stuff

Install Scribus

sudo add-apt-repository ppa:scribus/ppa
sudo apt-get update
sudo apt-get install scribus-ng

Typing non-ASCII characters from a US keyboard how does that work again?

See applied typography.

Virtual machines

I want to run virtual machines?? Be aware Ubuntu may have special needs wrt config.

virtualbox is passable. These days I prefer libvirt, unless there is some particular machine image that I need that only runs on virtualbox for some reason. ATM there are none.


Easyish! Fastish! Open! BAdly documented!

sudo apt install virt-manager libvirt-bin qemu-kvm


Semi-open! Confusing! Circuitous! Opaque! Hard to remove! Well-documented!

wget -q -O- | sudo apt-key add -
wget -q -O- | sudo apt-key add -
sudo add-apt-repository ' contrib'
sudo apt-get install virtualbox virtualbox-ext-pack

macOS-style quicklook previews

Gnome Sushi does that very well.

sudo apt-get install gnome-sushi

If only I could temporarily disable lock screen


Mounting that Windows partition on login

By default the various disks that I plug in to my machine are visible in the sidebar, but util I click on them they are not actually mounted so I can’t use the files. “Clicking on stuff” is not a satisfactory workflow, especially if you have other scripts which depend on data on my external drive. So fix that.

GUI automount

The official option:

sudo apt install dconf-editor

Now in set automount to True.

Apparently this is equivalent to:

gsettings set automount true


dconf write /org/gnome/desktop/media-handling/automount true

GUIless automount

e.g. for the server. Install usbmount. I didn’t try this.


Userspace mounting is not hard but the command is not at all obvious. The virtue of this method is that it works also without root privileges, in principle. However, it also requires logging out and in again to test and frequently fails for me and I don’t know where the error logs go.

udisksctl mount --block-device /dev/disk/by-uuid/[uuid]

Or perhaps it is the slightly easier

/usr/bin/udisks --mount /dev/[sdc1 or something]

except that this one mounts it in the wrong place because otherwise it would be too useful.

But what is the UUID? Find it using blkid

sudo blkid

or if you are not root

ls /dev/disk/by-uuid

and apply some deduction.

NB: this could be slightly easier for external disks which have a label. Then it’s something like

udisksctl mount --block-device /dev/disk/by-label/[label]

This works on some of my Ubuntu machines but not others; can’t work out why.

Playing music

Playing music: as not-quite-good as ever.

The built-in Rhythmbox is OK. For those who wish to do fancy metadata management, perhaps quod libet?

sudo add-apt-repository ppa:lazka/dumpingplace
sudo apt isntall quodlibet

Also available through flatpak.


Fiddly on Linux. See VPN

Signal desktop

Note, be careful about installing this; The more instances of Signal you have, the bigger your attack surface, and Signal Desktop is not secure to be run on a non-encrypted FS.

curl -s | sudo apt-key add -
echo "deb [arch=amd64] xenial main" \
 | sudo tee -a /etc/apt/sources.list.d/signal-xenial.list
sudo apt update && sudo apt install signal-desktop

Mounting android devices

I found that some newer/rarer MTPFS devices aren’t supported by 18.04 as filesystems. Should I try another MTPFS entirely, such as go-mtpfs?

Research ongoing for this one.

sudo apt-get install golang-go
sudo apt-get install libusb1-devel
mkdir /tmp/go
export GOPATH=/tmp/go
go get
mkdir xoom
go-mtpfs xoom &
cp -a ~/Music/Some-Album xoom/Music/
fusermount -u xoom

Additional config


Ubuntu journald can get very big because there is no limit per default /etc/systemd/journald.conf:


Manual cleanup right now:

sudo journalctl --rotate
sudo journalctl --vacuum-time=2d

Booting and kernels

grub customizer customizes the GRUB2 boot menus without typos, if ones trust this developer to manage the boot setup.

sudo add-apt-repository ppa:danielrichter2007/grub-customizer
sudo apt-get update
sudo apt-get install grub-customizer

There is a version manager specifically for linux kernels (HT Abishek Prakash.) It is called UKUU.

sudo add-apt-repository ppa:teejee2008/ppa
sudo apt-get update
sudo apt-get install ukuu