funannotate: eukaryotic genome annotation pipeline
Project description
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
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