This is a bit involved, and has a bunch of stuff to be done on the terminal, in desktop mode. It's possible that playing later would be possible in deck ("big picture") mode as well, but I can't confirm it for reasons of not using a deck myself. I did get integrated mode working on linux though.
Make sure you've installed the game, verified it's integrity, and have launched it at least once after that. The following instructions uses non-flatpak Steam. I don't know where flatpak installations of Steam keep the user data, and modding involves quite a bit of manipulation of folders. You may be able to adapt this guide to flatpak with looking up where those paths are on the distribution of linux that you're using.
Use the browser to download the Oracle JDK version 25. You want the Windows version, use either of the installers (not the "compressed archive" one). Site will probably put you to Linux tab, be sure to use the Windows one. https://www.oracle.com/java/technologies/downloads/#jdk25-windows
Because Deck's desktop mode doesn't provide regular wine by default, and wants you to use Proton instead, we need to find it. Open steam and note down which version of Proton it uses (better yet, select one manually). Per-game settings are available after right-clicking the game -> Properties -> Compatibility. If you're using the default one, you can check which it is by going to Steam's Settings -> Compatibility.
In my case, the version is called "Proton-GE Latest".
Open the terminal.
Run (here and later in terminal "run" means: Input the following (press tab key for autocompletion) and press enter)
cd /home/deck/.local/share/Steam/compatibilitytools.d/
(on non-deck linux installations, this is likely to be different. At the very least deck part should be replaced by the username used on your system. If you get "this "No such file or directory", check to see if your distribution has steam files in a different folder)
The above command simply changes directory (cd) to the path provided.
Now run ls — this will list the files and directories in the current path.
You should see here one or several directories called "Proton ..."
cd to the one your Thumper is configured to use in the same way done before, i.e:
cd "Proton-GE Latest" <- quote marks are necessary if your path has spaces or other special symbols.
Now it's needed to enter "files/bin" folder. To do so, run cd files/bin
ls to make sure that you have "wine" file available. If not, try with a different Proton directory — cd .. will move you to the parent directory. wine is the binary we're going to be using to launch a few other commands inside the prefix with Windows compatibility mode.
Type this make sure you don't make typos there, the following as one long line:
export WINEPREFIX=/home/deck/.local/share/Steam/steamapps/compatdata/356400/pfx
And press enter.
This sets the location for where the "pretend windows installation" that wine creates and uses to store the non-game files is.
These locations are known as "prefixes" and they're kept separate from one game to the other for compatibility purposes.
356400 here is Thumper's Steam AppID (Outside of Steam on deck, this location is likely different. Look up the steamapps location on your distro or check in Steam's Settings -> Storage)
We're done with the terminal preparation. If you close the terminal before finishing the rest of step 2, you'll need to repeat this — terminal session is reset upon startup.
Run ./wine explorer
A bit of a wait and it should launch a windows-like file manager. Ignore the "fixme" messages in terminal, if any appear.
From Desktop, navigate to / -> home -> deck -> path/where/you/saved/jdk/installer, in my case
/home/deck/Downloads/
Double-click and proceed with the installation instructions, install into default location.
Note: This might become unnecessary if Java installation detection is changed, but is currently.
Close the file manager launched in 2.2 if it's still running, but keep the terminal open. Run wine regedit to open the registry editor.
Using the tree on the left side, navigate to HKEY_LOCAL_MACHINE -> Software -> JavaSoft -> JDK . Double-click JDK.
On the left side there should be "25.X.Y" where X and Y are numbers. If it isn't there, Java isn't installed correctly and you need to re-do at least step 2.2.
On the right side there should be the entry named (Default) with Data (value not set).
If there's also CurrentVersion with Data set to 25.X.Y, matching the one on the left side, you're good to proceed to the easier steps 3-5.
If not, right-click under (Default) and select New -> String Value. Set the name to CurrentVersion (notice, there is no space in the name and C/V are capitalized) and press enter. (right-click -> rename if you clicked away) Double-click CurrentVersion or right-click -> Modify. Enter the version you see under JDK on left side. 25.x.y i.e. 25.0.1. Again, no spaces or extra punctuation.
Press OK and close registry editor.
Now for the easy part.
You want the Aurora_vX.Y.Z.zip (X Y Z are numbers here) file, not the source code.
Do not skip this. Even for updates. This cleans up some changes mod makes to the game's files and makes for a clean environment for new version. Open game's properties in Steam -> Installed files, run Verify Integrity.
On deck this is normally in /home/deck/.local/share/Steam/steamapps/common/Thumper. This path is most likely different if following the guide not from the deck, you can see it in Steam's Settings -> Storage
If .local in your user's home is hidden, type it into the path bar at the top of the file manager, or run xdg-open $WINEPREFIX in terminal to open the file manager in the game's compatdata/pfx directory, and from there navigate to the parent directory 3 times to get to steamapps.
Open Steam properties for the game. Under General -> Launch Options, enter into the text field: WINEDLLOVERRIDES=steam_api64.dll=n,b %command%
This should be it, game should now launch it's own terminal window and then ask where your game installation is. Select My Computer, then Z "drive" and then navigate to home\deck\.local\share\Steam\steamapps\common\Thumper. Again, this path might be different depending on your Steam install location.
For mods, I'd suggest using a folder that is easily accessible from Desktop mode and pointing to it once via Aurora. For example, /home/deck/Music/Thumper-mods/ which would appear as Z:\home\deck\Music\Thumper-mods\ inside Aurora.
Mods need to be in TCLE V3 format or newer, see Thumper Discord for more info and new releases. Older ones can be downloaded from this google drive: https://drive.google.com/drive/folders/1mKfxEfkFWfHcSxqzJrySgo76QZ2z2X-B?usp=sharing
Do steps 3, 4.1, 4.2 and 4.4. The rest are not necessary. Do not remove steam_api64.dll.bak, it is absolutely necessary to launch the game. Verifying integrity is necessary.
If you removed steam_api64.dll.bak, do steps 4.1-4.4
Open the folder from 4.1. Remove steam_api64.dll. Rename steam_api64.dll.bak to steam_api64.dll. Java installation shouldn't impact the game when ran without mods, so there's no need in removing it.