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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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KeyError: 'AUGUSTUS_CONFIG_PATH' in funannotate setup #1004

Closed joana-morais closed 4 months ago

joana-morais commented 4 months ago

Describe the bug I believe there is a problem with augustus pathway. However, I installed via conda and I dont know how to change the directory => KeyError: 'AUGUSTUS_CONFIG_PATH'

What command did you issue? funannotate setup -i all --busco_db tetrapoda --update --database /Users/Beta/funannotate_db

Logfiles

Traceback (most recent call last): File "/Volumes/HD_BioInfo/00_Analysis/oldpython_env/bin/funannotate", line 8, in sys.exit(main()) ^^^^^^ File "/Volumes/HD_BioInfo/00_Analysis/oldpython_env/lib/python3.11/site-packages/funannotate/funannotate.py", line 705, in main mod.main(arguments) File "/Volumes/HD_BioInfo/00_Analysis/oldpython_env/lib/python3.11/site-packages/funannotate/setupDB.py", line 688, in main training_species(args.force) File "/Volumes/HD_BioInfo/00_Analysis/oldpython_env/lib/python3.11/site-packages/funannotate/setupDB.py", line 526, in training_species for i in os.listdir(os.path.join(os.environ["AUGUSTUS_CONFIG_PATH"], 'species')):


  File "<frozen os>", line 679, in __getitem__
KeyError: 'AUGUSTUS_CONFIG_PATH'
**OS/Install Information**
 -  output of `funannotate check --show-versions`