dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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Not recognizing BUSCO? #236

Open incoreygible opened 2 years ago

incoreygible commented 2 years ago

I have BUSCOv5.2.2 installed via conda and the metazoa busco database included in the database folder I point to with --database-dir. When attempting to execute the annotate step, it looks like dammit is not recognizing busco:

Traceback (most recent call last):
  File "/data1/rennolds/miniconda3/bin/dammit", line 9, in <module>
    sys.exit(app.DammitApp(arg_src=sys.argv[1:]).run())
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/app.py", line 45, in run
    return self.args.func()
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/app.py", line 333, in handle_annotate
    build_default_pipeline(annotate_handler,
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/annotate.py", line 133, in build_default_pipeline
    register_busco_task(handler, config, databases)
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/annotate.py", line 245, in register_busco_task
    task = BuscoTask().task(input_fn,
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/utils.py", line 89, in d_to_t
    task_dict = task_dict_func(*args, **kwargs)
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/profile.py", line 163, in func
    task = task_func(*args, **kwargs)
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/tasks/busco.py", line 61, in task
    exc = self.deps()
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/tasks/busco.py", line 29, in deps
    raise InstallationError('BUSCO not found. NOTE: '\
dammit.tasks.utils.InstallationError: BUSCO not found. NOTE: dammit 1.0 requires BUSCO v2 or greater

I definitely have Busco v2 or greater. I am using the most recent version of dammit. Any idea how to fix this?