chore: fix bad venv setup

[rokroskar]

The line

COPY --from builder ${HOME}/.renku/venv ${HOME}/.renku/venv

does not replace the contents but simply adds to it, leading to a bad state of the packages in the virtualenv. This PR fixes this by brute force - removing the directory beforehand. A symptom of this was the renku CLI complaining about a bad version of the cwltool, e.g.

You are using cwltool version 3.1.20211107152837, which might not be compatible with version 3.1.20220628170238 used by Toil. You should consider running 'pip install cwltool==3.1.20220628170238' to match Toil's cwltool version.

In a project created with this template, no such warning/error is generated:

[m-alisafaee]

LGTM. Any specific reason for not using a separate RUN command?

[rokroskar]

Generally it's considered good practice to combine them unless they have to be separated.