Funannotate has a lot of dependencies and therefore installation is the most difficult part of executing the pipeline. The funannotate pipeline is written in python and can be installed with pip, i.e. pip install funannotate. You can see a list of Dependencies,

### Quickest start Docker:

You can use docker to run funannotate. Caveats are that GeneMark is not included in the docker image (see licensing below and you can complain to the developers for making it difficult to distribute/use). I’ve also written a bash script that can run the docker image and auto-detect/include the proper user/volume bindings. This docker image is built off of the latest code in master, so it will be ahead of the tagged releases. The image includes the required databases as well, if you want just funannotate without the databases then that is located on docker hub as well nextgenusfs/funannotate-slim. So this route can be achieved with:

# download/pull the image from docker hub
$ docker pull nextgenusfs/funannotate

# download bash wrapper script (optional)
$ wget -O funannotate-docker

# might need to make this executable on your system
$ chmod +x /path/to/funannotate-docker

# assuming it is in your PATH, now you can run this script as if it were the funannotate executable script
$ funannotate-docker test -t predict --cpus 12

#### Quickstart Bioconda install:

The pipeline can be installed with conda (via [bioconda](

#add appropriate channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

#then create environment
conda create -n funannotate "python>=3.6,<3.9" funannotate

If conda is taking forever to solve the environment, I would recommend giving [mamba]( a try:

#install mamba into base environment
conda install -n base mamba

#then use mamba as drop in replacmeent
mamba create -n funannotate funannotate

If you want to use GeneMark-ES/ET you will need to install that manually following developers instructions:

Note that you will need to change the shebang line for all perl scripts in GeneMark to use /usr/bin/env perl. You will then also need to add to the $PATH or set the environmental variable $GENEMARK_PATH to the gmes_petap directory.

To install just the python funannotate package, you can do this with pip:

python -m pip install funannotate

To install the most updated code in master you can run:

python -m pip install git+

Please setup database and test your installation locally using the following:

#start up conda ENV
conda activate funannotate

#check that all modules are installed
funannotate check --show-versions

#download/setup databases to a writable/readable location
funannotate setup -d $HOME/funannotate_db

#set ENV variable for $FUNANNOTATE_DB
echo "export FUNANNOTATE_DB=$HOME/funannotate_db" > /conda/installation/path/envs/funannotate/etc/conda/activate.d/
echo "unset FUNANNOTATE_DB" > /conda/installation/path/envs/funannotate/etc/conda/deactivate.d/

#run tests -- requires internet connection to download data
funannotate test -t all --cpus X