Problems with Conda environment and biobakery_workflows in cluster

Infrastructure and utilities bioBakery workflows
1

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.

2

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

1 Like
3

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.

4

Were you able to resolve the above error? If yes, I would appreciate if you could help me resolving the same error.