Sorry. I have read your reply now again and realize, that it will probably not solve my problem. The repo I am using has the script, that is being run, but it has a lot of python modules, that are being used as well, but not in relative way, but using PYTHONPATH. So this is the reason, why I need to set the pythonpath env variable to place (plus one subfolder) where the repo is clonned on agent start.
ADD: Yep, it did not work. So is there any way, how the ENV variable can be set as in docker run (or using env file) on trains-agent startup? (I can create special docker image for my runner with this variable, but I do not want to build another image just because of env variable)