You can try install AutoGK in Ubuntu through Wine. I found these informations, they're a bit old, but maybe they can help you with this:

1. Run "winecfg" and change:

Graphics tab: Emulate a virtual desktop, at least 800x600
Direct3D Vertex Shader Support none

Audio Tab: Hardware Acceleration: Emulation
Check driver emulation.

Applications tab: Windows Version Windows XP

Libraries (I think this is the important one) tab

Add the following overrides:
mfc42u, msvcrt, msvfw32, vorbis

1. Download and installed AutoGK on this machine.




2. Then, copy the DLL's "mfc42u, msvcrt, msvfw32" from a windows machine's system32 directory to the WINE system32 directory.




3. Rename msvcrt.dll MSVCRT.DLL. Probably not necessary, but I know linux is case sensitive (although WINE probably isn't) and the virtualdub error message had a capital msvcrt.

   
   
   
   
   

   1. Copy vorbis.dll from the autogkirtualdubmod directory to the windowssystem32 directory.

   
   

   2. Type "wine AutoGK.exe" in the AutoGK directory

   
   

Troubleshooting:
If the installer doens't come up (just a blue screen), make sure you have the graphics resolution at least 800x600 in the graphics tab of winecfg

If trying to encode a movie fails on the audio portion (Demuxing, decoding, normalizing, encoding happens in about a second, then fails) it is probably your virtualdub. I fixed this by copying a new msvcrt.dll over to wine, and the vorbis.dll. Try manually running "wine autogk/tools/virtualdubmod.exe" and see if virtualdub comes up. If it doesn't, fix whatever it complains about.

Source

More info on installing AutoGk through Wine

There's also some alternatives to AutoGk:

Handbrake

MediaCoder

MakeMKV

Lemon Rip

k9copy

acidrip