OSError: fatal error running BowTie2

Issue #12 new
Jason Danley
created an issue

I am trying to run MetaPhlAn on galaxy through my university using the recommended practice dataset (http://huttenhower.sph.harvard.edu/sites/default/files/LC1.fna) but receive the following error message:

"OSError: fatal error running BowTie2. Is BowTie2 in the system path?"

BowTie2 is installed as I have used it before. Any idea how I can resolve this issue?

Comments (2)

  1. Nicola Segata repo owner

    Hi Jason, thanks for getting in touch. I'm forwarding this to the MetaPhlAn user group and to George, the Galaxy expert who implemented the MetaPhlAn Galaxy tool which I'm sure can be more helpful than me. A couple of questions that may be relevant here: - are you able to run MetaPhlAn with BowTie2 on the server where your galaxy instance? - did you import the MetaPhlAn Galaxy module from the Galaxy Tool Shed (built by George) or you implemented in on your own?

    many thanks Nicola

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