Installing mods on Atlas is a little different to other games such as ARK. It involves adding the ModIDs into the clustered.json file that is uploaded to a server when creating a grid.
How to install Mods on Atlas from the Steam Workshop?
If the mod is already available on the Steam Workshop you have to download the current cluster configuration .json file and change the “ModIDs”:"" field to a comma separated list of mods for example “ModIDs”:“1652044230,1648830674” and then reupload the .json file. Now you can restart the whole cluster and the mods will download and activate in the background.
To remove mods you can remove them from the ModIds list and restart the cluster again. The mods will be automatically removed.
How to add local mods that are currently not public? (DEV mods, private mods, etc)
It is the same procedure to which ARK uses. Copy the mod folder and the “.mod” file with an FTP client such as FileZilla to “atlasmain\ShooterGame\Content\Mods” with a unique id (for devs only: use an id, which is not connected to a workshop mod) and add the mod id you have chosen to the cluster .json config file.
Please note: The cluster has to be stopped before adding/removing any mods from both the steam workshop and locally.