Hi all and thank you for your immediate responses.
In the end what I was looking for was not the "midi through port" but a virtual midi port.
To do that I had to add in /etc/modules-load.d/audio.conf
snd-virmidi midi_devs=1 index=5

then I could see
$ amidi -l
Dir Device    Name
..... (other devices) .....
IO  hw:5,0    Virtual Raw MIDI (16 subdevices)

and at the same time it would show up in jack's "midi" tab
then I could simply use it as

amidi -phw:5,0 -S <hexbytes>

and the midi msg was surely enough sent correctly to the HW controller.

Thank you for your help!
I hope this helps others as well

On Sun, Oct 8, 2017 at 2:50 AM, Jeanette C. <julien@mail.upb.de> wrote:
Oct 8 2017, Athanasios Silis has written:
...
amidi -p"14:0" -S <3x bytes depicting the midi CC command>
...
Hi Athanasios,
amidi uses ALSA hardware ports, not ALSA SEQuencer ports. On my system
MIDI thru doesn't show up under those. You can list them with:
amidi -l
or look at:
/proc/asound/cards

Since you're sending MIDI CCs and no SysEx you can use a tool that
supports ALSA SEQ ports.

If your CCs and values are always the same - or just a few setups - you
could put them inside a MIDI file and then use aplaymidi. Otherwise
there is midish a commandline tool, that supports its own bash-like
scripting. It wouldn't be too hard to set something like this up.
http://www.midish.org

If Python or other scripting languages are an option, there are some
packages for these languages which support ALSASEQ I/O. If midish looks
promising, but too much work for a start, I could help.

HTH.

Best wishes,

Jeanette

--------
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