The below walkthrough is for those who are running Skyrim SE via Steam Proton, and want to be able to manage mods via Vortex Mod Manager in Linux. You should be able to apply the same walkthrough to Oldrim or Fallout 4 as well. Note that with this guide you'll get an older version of Vortex (1.1.15), but IMHO it is still a better choice than Mod Manager 2. Also, you'll start Skyrim through Steam as usual, not through Vortex.
- If you have previously added mods through the Skyrim game menu, I recommend removing them all since all mods will be managed through Vortex. Mods => Load Order => Delete All. Also, consider taking a backup up your (vanilla) Skyrim game directory.
# archive vanilla game (update path to suit your needs)
cd /mnt/gameData/archive
cp -a /mnt/gameData/SteamLibrary/steamapps/common/Skyrim\ Special\ Edition/. skyrim-se
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Install Lutris (in my case via the Pop!_Shop, since I'm running Pop_OS)
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Install Vortex Mod Manager. The Lutris Mod Manager page targets version 1.4.15 of the app, and the one-click install seems to be broken. Instead, you will need to do an install through the CLI using rockerbacon's vortex.yml config file. This file, which targets an earlier version of Vortex (1.1.15), can be dowloaded from here.
lutris -i "$HOME/Downloads/vortex.yml"
Most likely, you will need to install Vortex in the same partition as your Steam library folder(s). In my case, I chose "/mnt/gameData/Vortex". When prompted by the Lutris installer, disable your internet connection. Start Vortex Mod Manager and go to Settings => Vortex and set Update to "No automatic update". Shut down Vortex, and enable your internet connection again.
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Add your Steam game folder(s). Start up Vortex, and go to Settings => Games => Add Search Directory. Select the Steam folder that contains your games, in my case "Z:\mnt\gameData\SteamLibrary". Click Dashboard => Scan for Missing Games. Alternatively, click Games => Scan => Scan:Full. Select the game(s) you would like to manage (Skyrim SE).
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Add mods. When adding mods from nexusmods.com, do not use the "Vortex" button... Instead, do a manual download of the zipped archive. Then, drag and drop the file from your File Manager to the games' mods area in Vortex, and install/enable the mod from there.
Another way is to right click the "Vortex" button and copy the link, click on the "Drop File(s)" area and paste in the copied nxm link into the dialog box. Thanks @Skulldugg3ry for this tip.
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Set the load order, and apply output fix. The mod load order is calculated in the Vortex plugins area... Select Plugins => Sort Now. Note that Vortex outputs the load order in a file location that is not expected by Skyrim. To fix this, first rename the Vortex output file "plugins.txt" to "Plugins.txt" and move it to the folder Skyrim expects it to be. Then, create a symbolic link from the Vortex file location to the Skyrim file location. Note that Vortex plays nice with symbolic links, but Skyrim does not, so you do need to place the symlink in the Vortex directory and not the other way around. Thanks @Ateya9 for pointing that out.
// Update paths and <username> to suit your system
cd "/mnt/gameData/Vortex/drive_c/users/<username>/Local Settings/Application Data/Skyrim Special Edition"
mv plugins.txt "/mnt/gameData/SteamLibrary/steamapps/compatdata/489830/pfx/drive_c/users/steamuser/Local Settings/Application Data/Skyrim Special Edition/Plugins.txt"
ln -s "/mnt/gameData/SteamLibrary/steamapps/compatdata/489830/pfx/drive_c/users/steamuser/Local Settings/Application Data/Skyrim Special Edition/Plugins.txt" plugins.txt
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Skyrim Script Extender. Many mods require SKSE64 to work. Download the latest version of SKSE for your version of Skyrim (SE/AE) from http://skse.silverlock.org/. Extract and copy all SKSE files and folders to the Skyrim SE game folder; in my case "/mnt/gameData/SteamLibrary/steamapps/common/Skyrim Special Edition".
Rename SkyrimSELauncher.exe => SkyrimSELauncher.orig.exe
Rename skse64_loader.exe => SkyrimSELauncher.exe.
Make sure Skyrim starts when clicking on it in your Steam library. Note that a window displaying the SKSE runtime log will show. This is normal. You should see the SKSE version under the in-game System tab.
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Sky_UI mod. If you're wanting to use the popular SkyUI mod, chances are you'll need to use a recent version of Glorious Eggroll, not the standard proton release. I'm currently using version GE-Proton7-30.
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Happy modding!
The version linked from the Lutris site under Vortex Mod Manager seems to work fine now. An easy workaround to the Add to Vortex button not working is to right click the button in the browser and copy the link, then click on Downloads in Vortex and click the area at the bottom where you drop files - it will pop up a box that you can paste the copied nxm link into, and it will start the download.