How to use augustus in busco 5.5


I want to use the --augustus_parameters option in busco 5.5.0 but I get an error saying I need to set the environmental variable of AUGUSTUS_CONFIG_PATH, what path can I provide? or what can I do to be able to use this?

thank you in advance


Could you try to export this PATH before using busco:

export AUGUSTUS_CONFIG_PATH=/shared/software/miniconda/envs/busco-5.5.0/config/


Thanks for your reply. It didn't work though. I get this error now:
Cannot write to Augustus species folder, please make sure you have write permissions to /shared/software/miniconda/envs/busco-5.5.0/config/species

I'm trying to train Augustus after the first round of MAKER gene annotation, and this is what I'm trying to run:

busco -i all.maker.transcripts1000.fasta -l pleosporales_odb10 -o all.maker -m genome -c 8 --long --augustus_parameters='--progress=true' -f

Is there anything I can do to make it work?

Thank you in advance


Maybe you can just copy the config folder of Augustus from the repository

Or copy /shared/software/miniconda/envs/busco-5.5.0/config/ in your project directory.

And modify the path to use it. For example:

export AUGUSTUS_CONFIG_PATH=/shared/projects/<yourproject>/config_augustus/
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