In that case when you create the Tasks for the step,do not specify any packages/requirements, then the agent will just use the "requirements.txt" from the repository.
If you need you can also specify them when you create the Task itself see https://github.com/allegroai/clearml/blob/912f6f5ba2328b26de042de03f02de5802df360f/clearml/task.py#L608
https://github.com/allegroai/clearml/blob/912f6f5ba2328b26de042de03f02de5802df360f/clearml/task.py#L609