Hi @Jacob95, welcome to :qiime2:! Hopefully, we can get you running LEfSe.
Regarding the post:
If you read the dokdo documentation and the tutorials you'll see that dokdo uses the QIIME 2 API and is intended to be used with QIIME 2.
Again, everything you need to know is in the dokdo documentation. Here are the installation instructions. Though it is much easier to simply install like this:
conda activate qiime2-2022.8
pip install git+https://github.com/sbslee/dokdo
dokdo --help
Then run the prepare-lefse command as described here.