I am trying to install and use Humann 3.9, but I keep getting the errror message: The metaphlan executable can not be found.
I’ve previously installed MetaPhlAn 4.1.1 and run the metaphlan script on both demo and real data, and it’s worked fine. I used
conda create --name mpa -c bioconda python=3.7 metaphlan
and set up a new environment, which was automatically placed in my home directory.
When setting up humann, I’ve tried downloading from source, humann.tar.gz and creating a clone git clone https://github.com/biobakery/humann , both in my home directory and scratch (where packages are normally installed on our system), and keep getting the same error. I’ve tried as many variations of --metaphlan <METAPHLAN.PY LOCATION> as I can think of, but it just can’t find the executable. Is it because I’ve installed MetaPhlAn in its own environment? Or should I be pointing to something else?
If MetaPhlAn and HUMAnN aren’t in the same environment then HUMAnN won’t be able to find MetaPhlAn. I would recommend installing both in the same conda environment. If you create a fresh conda environment for HUMAnN, then when you conda install it it should also fetch and setup MetaPhlAn for you.
If you are having trouble getting MetaPhlAn to run within HUMAnN, always make sure that MetaPhlAn itself is directly callable from the environment (e.g. you should be able to call metaphlan.py -h and see a help message). If not, then something is wrong with MetaPhlAn setup (unrelated to HUMAnN).
Would you be able to give me step by step instructions please? I’ve tried several times but can’t seem to set up a working conda env for humann - I’m fairly new to python so I’m not sure what I’m doing wrong.
Karen
We have some more detailed conda installation instructions at the link below that might be helpful to you?