Identified the cause of this unreliability. I had “checking for updates” disabled for the template in global configs. Enabling this check substantially increased the reliability of checking for flatpak updates (even though it makes no difference for the distribution repos).
Hello solemne ,
I regret to say that this method of enabling Flatpak to install programs in templates isn’t working for me as of October 2025. In the template, the GNOME Store gets stuck loading the menu information, and Flatpak apps cannot be installed, even with a .flatpakref file.
Tested on a Debian-12 XFCE template
Can you describe exactly what you did so I can try to reproduce the problem?
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Wow, that was fast! First, let me congratulate you on your passion for supporting the Qubes OS community. I’m XXXXXX from ******, operating under the pseudonym Invictus. I’m a new user on the forum, but I’ve been using Qubes OS as my main system for about a year. I’m familiar with the basic functions needed to create my own basic privacy template.
Scenario details.
Flatpak Installation ======> Debian 12 xfce
Source: -----> Synaptic Package Manager
Packages used:
- gnome-software (+ all prerequisite dependencies)
- gnome-software-common
- gnome-software-plugin-flatpak
- libflatpak0
The GNOME Store and Flatpak support were successfully installed, but to make it functional and install a single app, I had to connect the template directly to the Qube firewall in addition to the default Sys-Whonix connection.
The commands:
export all_proxy=http://127.0.0.1:8082/
flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
These worked for me, so I tried to replicate your idea, but when I try to install apps from the GNOME Store, it just gets stuck loading the menu.
The command:
flatpak upgrade -y --noninteractive
This updated Flatpak, which shows that it was installed and is functional. Creating an AppMV from the GNOME + Flatpak template works, but nothing persistent can be installed without the previously mentioned --user option.
Regards.
There is a bug in gnome software, and I figured a workaround, see Solene'% : Flatpak integration in Qubes OS templates
I cloned the template and added the command lines to the specified file before reporting the problem, but it was unsuccessful.
you need to add the following line to /rw/config/rc.local:
ip route add default via 127.0.0.2
Do you consider my method of installing Flatpak acceptable or unreliable?
As I mentioned, it works in Flatpak appVM, which leads me to believe that, given it doesn’t work in templateVM, there’s a connection issue blocking the sys-whonix proxy. This is because it seems to be the same issue with the Synaptic package update command; in templateVM, it only returns a “no connection to repository” error. The command:
export all_proxy=http://127.0.0.1:8082/
doesn’t seem to resolve these communication problems, at least not in the current version I’m using.
You should never connect a template to an appvm. This is not required.
1 Like
Hi, I read the recommendations and I understand why, but at that time it was the only useful option to make it work.
all_proxy don’t work with flatpak - use http_proxy instead
3 Likes
I followed your guide and I cannot get past trying to add the repo. I continually get a can’t resolve hostname error.
Did you export the proxy variable under the same shell session and user before running the flatpak command?
Hi, I had the same problem. If you haven’t solved it yet, I wrote this for everyone.
Yes, I followed your writeup to the letter. Oh, I’m also in Fedora-41-xfce
Ok, installing gnome-software worked. Thank you
good luck
I used Selene’s guide with both Debian 13 and Fedora 42 and it works.
I only encountered one problem on Fedora 42. It asks for the access key for root privileges even with Qubes Passord I solved with “sudo su”.
Thanks for the guide!
For who want to use FreeCAD AppImage with bwrap (bubblewrap) sandbox system.
Dont lose your time. You cannot easily replicate Flatpak sandbox system with bwrap (bubblewrap), you will face FUSE permission restrictions and, even if you extract the AppImage, the bundled libraries are not fully self-contained and conflict with or depend on a particular host environment that stricter sandbox disrupts.
I dont want to use Flatpak. 
It seems freecad is packaged in Debian.
But the version is too old 
You are an angel @solene. Im testing my setup in Debian 12, but in Debian 13 the version is ok. Oh, lost time debugging it…