funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at http://funannotate.readthedocs.io

Quickstart:

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 funannotate

If you want to use GeneMark-ES/ET you will need to install that manually following developers instructions: http://topaz.gatech.edu/GeneMark/license_download.cgi

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 gmes_petap.pl 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:

pip install funannotate

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

python2 -m pip install git+https://github.com/nextgenusfs/funannotate.git