MetaPhlAn2 can't work with BowTie2 if the aligner is in the folder with spaces

If BowTie2 is in the folder which contains spaces in its path, then MetaPhlAn2 can't work with it properly.
Currently, the folder where BowTie2 aligner binary is passed to MetaPhlAn2 via environment variable. In this case MetaPhlAn2 launches script "bowtie" which is supposed to be in the folder. But this script can't work with spaces in paths properly.
To workaround the issue pass the BowTie2 aligner as argument to MetaPhlAn2 process (--bowtie2_exe).

Note that the database also can be in the folder with spaced path. Check it and add quotes to the appropriate argument if needed.