Biobakery Workflows: Errors with downloading database, "unpicking error", “topological_sort()" error, and "Unable to find Trimmomatic" error

Infrastructure and utilities bioBakery workflows
4

Hi, I’m so sorry for making another post.

Problem 6:

I was able to run a wmgx workflow test with one full-sized paired-end metagenomic sample. However, when I tried wmgx_vis, I got the following error:

ImportError: cannot import name 'PwebProcessor'

I found over here that other people have also had this problem, and that they solved this by changing the Pweave version to 0.25. My version was 0.30.2. So I decided to do the same thing, and re-created my environment like this:

conda create -c biobakery -n biobakery python=3.6 biobakery_workflows tbb=2020.2 networkx=1.11 pweave=0.25 python-leveldb

I again tried to run wmgx_vis with the following command:

biobakery_workflows wmgx_vis --input /home/bsingh/output_data/ --project-name JSA10 --output output_vis_flow --format pdf

And I got this error in the log file:

  File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.6/site-packages/anadama2/runners.py", line 201, in _run_task_locally
    action_func(task)
  File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.6/site-packages/anadama2/document.py", line 286, in create
    doc.weave(shell=PwebProcessorSpaces)
  File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.6/site-packages/pweave/pweb.py", line 198, in weave
    self.run(shell)
  File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.6/site-packages/pweave/pweb.py", line 149, in run
    runner.run()
  File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.6/site-packages/pweave/processors.py", line 65, in run
    self.executed = list(map(self._runcode, self.parsed))
  File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.6/site-packages/pweave/processors.py", line 131, in _runcode
    chunk['content'] = self.loadinline(chunk['content'])
  File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.6/site-packages/anadama2/document.py", line 234, in loadinline
    result = self.loadstring(code_str).lstrip().replace("\n","",1)
  File "/home/bsingh/miniconda3/envs/biobakerywf/lib/python3.6/site-packages/pweave/processors.py", line 296, in loadstring
    exec(compiled, scope)
  File "chunk", line 1, in <module>
NameError: name 'caption' is not defined

The problem seems to be with Pweave again. I’m not sure which version I should be using?