The bioBakery help forum

Which version of pweave needed?

Run the command:
biobakery_workflows wmgx_vis --input results -o results_vis --project-name vis
report an error:
Task 0 failed
Name: document
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/xmk/anaconda3/envs/biobakery_workflows/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/home/xmk/anaconda3/envs/biobakery_workflows/lib/python3.7/site-packages/anadama2/document.py”, line 204, in create
from pweave import PwebPandocFormatter, Pweb, PwebProcessor
ImportError: cannot import name ‘PwebProcessor’ from ‘pweave’ (/home/xmk/anaconda3/envs/biobakery_workflows/lib/python3.7/site-packages/pweave/init.py)

Hello, Sorry for the confusion and thank you for including the detailed traceback error. Anadama2 requires pweave v0.25. This was the last pweave version that was python2 and python3 compatible. If you roll back your pweave to the prior version it should resolve the error you are seeing.

Thank you,
Lauren

I have used the following comand to create a good env for the biobakery_workflow.

conda create -n biobakery python=3.6 biobakery_workflows networkx=1.11 pweave=0.25 leveldb=0.193 hclust2 megahit prokka seqtk trimmomatic

Thanks for your help.