Flatpak#

Flatpak is an app packaging solution for Linux that solves the issue of differences between distributions and allows a single app to run on all Linux desktops. This means not just different distros but also both older and newer distros, so if you were stuck using an old version of Avogadro until now, give the flatpak a try.

The Avogadro team is aiming for flatpak to become the primary method of distribution of Avogadro 2 on Linux. (Though distribution via other routes will of course continue.)

As well as the usual benefits of flatpaks such as stability and the possibility for sandboxing, by using the Avogadro flatpak you can easily keep it up-to-date with the latest versions via updates.

If you’ve never used flatpak before, the first step is to make sure you have the flatpak package, but you likely already do – it is installed by default on most modern distros.

Avogadro is distributed through Flathub on two branches: a stable branch, which contains the most recent release, and a beta branch, which is similar to the “nightly” versions on other platforms and has the latest features and bug fixes.

Stable#

In many cases, flatpak is set up with Flathub out-of-the-box. If not, and you haven’t set it up yourself manually before, you can follow the instructions here.

Once flatpak is set up, you can easily install Avogadro from Flathub in one of two ways:

Through your distro’s “app store” (e.g. KDE Discover or GNOME Software) – just search for Avogadro, or click on install on the Flathub page
On the command line using:

flatpak install org.openchemistry.Avogadro2

After installation, Avogadro should show up in your applications menu/drawer like any other app. If not, you can always run a flatpak using:

flatpak run org.openchemistry.Avogadro2

Tip

By default, flatpak works on the system installation (see the flatpak usage guide), just like apt, dnf and friends. This means that to add repos and install Avogadro using the commands above, or using your distro’s software manager, you may need sudo privileges.

On the whole it is recommended to do things this way, but it might not always be possible. To do things just for your user without sudo privileges, use the flatpak command with the --user flag, e.g.

flatpak --user install org.openchemistry.Avogadro2
flatpak --user run org.openchemistry.Avogadro2

Beta#

Though our nightly builds are generally pretty robust, it is not allowed to distribute nightly, potentially unstable builds over Flathub, so instead we are providing an “almost-nightly” beta branch to fulfil the same purpose. It will receive the latest updates at regular intervals.

Warning

While it is possible, it is strongly recommended that you do not have both the stable and beta version of Avogadro installed at the same time, to avoid complications.

To get the beta branch, you will first have to add the flathub-beta repository, which is located at https://flathub.org/beta-repo/flathub-beta.flatpakrepo.

On the command line this is done using:

flatpak remote-add --if-not-exists flathub-beta https://flathub.org/beta-repo/flathub-beta.flatpakrepo

If using a GUI software manager to manage your flatpaks, they often also provide a way to add a repository.

Once the repo has been added, you can install the Avogadro beta flatpak in the usual way, done on the command line using:

flatpak install org.openchemistry.Avogadro2//beta

The flatpak can then be run in the usual way.