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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Code fix: wrong path for evidence_modeler.pl in funannotate-runEVM.py #972

Closed Bio-finder closed 8 months ago

Bio-finder commented 8 months ago

Hello, Just a short message for a quick fix in your script: funannotate-runEVM.py

cmd = [os.path.join(EVM, 'evidence_modeler.pl'),
should be cmd = [os.path.join(EVM, 'EvmUtils', 'evidence_modeler.pl'),

I hope this helps. Best,

hyphaltip commented 8 months ago

what version of funannotate are you working from? this code has worked for many releases so it may depend on what you set the EVMHOME variable to. we could probably detect if either path is installed that way. Can you describe how EVM was installed - via conda or manually?

nextgenusfs commented 8 months ago

They changed the location of the script in version 2. Currently funannotate only supports EVM v1.1.1.

Bio-finder commented 8 months ago

Ok my bad then, I thought that funannotate was supporting the newest version of EVM. Sorry for the time lost. Just for your knowledge, after this fix, EVM 2.1 runs as it should.

nextgenusfs commented 8 months ago

Yeah I will try to find time to add the EVM version check and modify the command accordingly than it should support all versions.