The transmission-daemon program is a daemon-based Transmission session that can be controlled via IPC commands by transmission-remote(1) . This program is used by default in FreeNAS, and maybe you want to use it on Linux box. It's very likely you distribution come with transmission by default. In that case, you need to install transmission-daemon only:
# apt-get install transmission-daemon
Configuration file is /var/lib/transmission-daemon/info/settings.json (it's quiet safe to add *.*.*.* to rpc-whitelist option). After editing (user, password, paths, etc), we need to reload the daemon itself:
# /etc/init.d/transmission-daemon reload
Using remote client was discussed before .
Note: transmission-daemon configuration is very well documented on this web site. You are recommended to read (at least to feel the power of FreeNAS's web interface).
1. man transmission-daemon
2. Cross-platform transmission-remote-gui