Transmission

I am running Transmission in Fedora and Ubuntu.
Is is possible to configure the system so only the torrents go through an openvpn server, leaving the rest of the system on clearnet?

I suppose I could run a vm and vpn the network within it but I was hoping to avoid a VM.

maybe through a container ?

You use HideMyAss VPN, I think it has the split tunneling feature through which you can divide your online traffic into two different ways. So, I usually use it for downloading torrents or doing online shopping.

You can achieve this using iptables and a routing table to redirect traffic for the transmission user to the vpn interface.

Use this to get you started: https://github.com/bendikro/deluge-vpn

You have to mark the packets coming from user under which is running transmission and send them in a separate routing table with interface openvpn as default gateway. I have exactly what is configured tranmission using openvpn on Debian. If you need detailed instructions let me know.