Problems with Conda environment and biobakery_workflows in cluster

Hi you all, we have installed in a cluster with Conda, biobakery_workflows together with all the dependencies it needs for whole genome sequencing, MetaPhlAn, kneaddata, humann, but I am getting this error when running
biobakery_workflows_databases --install wmgx ERROR: Unable to find tool required for database install: strainphlan.py. Please install StrainPhlAn.

StrainPhlan is installed and the file is also present. We are working in a Conda environment, could it be a problem related to this?

Many thanks for your help.

Hello, Thank you for your detailed post. It looks like your install of StrainPhlAn might be newer then your workflows install. If you update to the latest workflows version I think it should be able to find your StrainPhlAn install (as the executables changed from “strainphlan.py” to “strainphlan”).

Thank you,
Lauren

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Hi,

I also have the same issue and cannot seem to resolve it.

Python- version 3.9.7
Metaphlan- version 3.0.14
Strainphlan- version 3

I can see both metahphlan and strainphlan there, but the workflow can’t seem to find it?

Thank you.