The current "BowTie2" version we provide it the External Tools package can not work with spaces in paths at all. But, the last avaliable on the BowTie2 website version can do it. So, it's necessary to update BowTie2.
- blocks
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UGENE-6307 MetaPhlAn2 can't work with BowTie2 if the aligner is in the folder with spaces
- Closed