funannotate2: eukaryotic genome annotation pipeline

This is work in progress. Do not expect it to work until a release is tagged.

Setting up a conda environment with these packages is necessary, then it can be installed with pip.

mamba create -n funannotate2 "python<=3.10" biopython "evidencemodeler>=2" minimap2 miniprot snap "augustus==3.5.0" glimmerhmm diamond trnascan-se table2asn
conda activate funannotate2
python -m pip install git+https://github.com/nextgenusfs/funannotate2.git

Additional tools like genemarkHMM must be installed manually due to licensing.

To install release versions use the pip package manager, like so:

python -m pip install funannotate2

To install the most up to date code from this repo, you can run:

python -m pip install git+https://github.com/nextgenusfs/funannotate2.git --upgrade --force --no-deps