The bioBakery help forum

Metaphlan install error with pip

I am trying to follow the biobakery workflow tutorial and am running into errors trying to install the workflows with pip. I successfully installed kneaddata and humann, but metaphlan is giving me trouble.
Specifically, I am stuck here:
$ metaphlan --install --nproc 2

This returns an error related to bowtie2:
FileNotFoundError: [Errno 2] No such file or directory: ‘bowtie2-build’: ‘bowtie2-build’

How can I fix this?


You could download bowtie2 directly from Bowtie - Browse /bowtie2/2.4.4 at

After decompress, add that path to the $PATH