UGENE needs a permission to write to the HOME directory

UGENE writes some inner files to the HOME directory. But, sometimes, this directory could be forbidden to write at. In this case, it should be possible to configure everything UGENE is trying to write with application arguments. Some of these arguments was configured during the issue UGENE-6624. Need to check, that it's possible to set any directory.
Also, there are 2 external tools - T-Coffee and SnpEff. They are writing to the HOME directory too, so it's necessary to fix these tools.