Installation

Funannotate2 can be installed using pip or conda.

Requirements

Funannotate2 has the following dependencies:

  • Python 3.7 or later

  • Minimap2

  • Miniprot

  • SNAP

  • Augustus (==3.5.0)

  • GlimmerHMM

  • GeneMark-ES/ET [optional]

  • Diamond

  • tRNAscan-SE

  • table2asn

  • natsort

  • numpy

  • mappy

  • gfftk (>=24.10.29)

  • BUSCOlite (>=24.7.29)

  • gapmm2

  • pyhmmer (>=0.10.15)

  • pyfastx (>=2.0.0)

  • requests

  • gb-io (>=0.3.2)

  • json-repair

  • pytantan

Some tools like GeneMark-ES/ET must be installed manually due to licensing restrictions (see below).

Installing with conda

The recommended way to install Funannotate2 is using conda/mamba:

mamba create -n funannotate2 gfftk gapmm2 minimap2 miniprot snap "augustus==3.5.0" glimmerhmm diamond trnascan-se table2asn gb-io buscolite
conda activate funannotate2
python -m pip install git+https://github.com/nextgenusfs/funannotate2.git

Installation on apple silicon (M series) is a little bit more involved due to some dependency issues and non-native builds of some software. I’ve not been able to find or build a version of augustus that will run, so instead I’ve been running augustus and genemark locally with Docker. I’ve setup two repos with instructions on how to get this working (Need Docker Desktop installed) and then will need to put the bash wrapper files in your PATH to mimic the CLI interface.

https://github.com/nextgenusfs/dockerized-augustus

https://github.com/nextgenusfs/dockerized-genemark

Once that is working, you can then install most of the remaining dependencies with conda, although we need to leave out both buscolite and funannotate2 because they have augustus as a dependency, instead we will install those python packages with pip.

# first install most of the dependencies
mamba create -n funannotate2 --platform osx-64 "python>=3.7,<3.13" gfftk gapmm2 minimap2 miniprot snap glimmerhmm diamond trnascan-se gb-io pyhmmer pyfastx requests json-repair "mkl<2022" pytantan

# we can then add the required FUNANNOTATE2_DB env variable to the conda environment, note need to reactivate to use it
conda activate funannotate2
conda env config vars set FUNANNOTATE2_DB=/path/to/funannotate2-db
conda env config vars set AUGUSTUS_CONFIG_PATH=/path/to/augustus-3.5.0/config
conda deactivate

# now reactivate environment, and install the remaining python dependencies with pip
conda activate funannotate2
python -m pip install buscolite git+https://github.com/nextgenusfs/funannotate2.git

# now we can install the databases
funannotate2 install -d all

Installing with pip

To install the latest release version using pip:

pip install funannotate2

To install the development version directly from GitHub:

pip install git+https://github.com/nextgenusfs/funannotate2.git

Verifying Installation

To verify that Funannotate2 is installed correctly:

funannotate2 --version

This should display the version of Funannotate2.

Installing Databases

Funannotate2 requires several databases to be installed. Note: funannotate2 scripts expect the $FUNANNOTATE2_DB environment variable to be set. These can be installed using the following command:

funannotate2 install -d all

Installing GeneMark

GeneMark-ES/ET must be installed manually due to licensing restrictions:

  1. Register and download GeneMark-ES/ET from the GeneMark website

  2. Follow the installation instructions provided with the download

  3. Make sure the GeneMark executables are in your PATH

  4. You may also need to install GeneMark specific perl libraries, specifically perl-hash-merge and perl-mce have been mentioned by users adding to the existing conda environment.