def set_workdir(self, workdir, chroot=False):
        """
        Set the working directory. Cannot be set more than once unless chroot is True
        """
        if not chroot and hasattr(self, "workdir") and self.workdir != workdir:
            raise ValueError("self.workdir != workdir: %s, %s" % (self.workdir,  workdir))

        # Directories with (input|output|temporary) data.
        self.workdir = os.path.abspath(workdir)
        self.indir = Directory(os.path.join(self.workdir, "indata"))
        self.outdir = Directory(os.path.join(self.workdir, "outdata"))
        self.tmpdir = Directory(os.path.join(self.workdir, "tmpdata"))
        self.wdir = Directory(self.workdir)
Set the working directory. Cannot be set more than once unless chroot is True