InstallationΒΆ

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,

To provide an easier installation, funannotate can also be installed with conda. The recommended way of doing this is to create a conda environment, for example:

Download/install miniconda and configure the proper channels:

#If you do not have conda, install: miniconda3
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
/bin/bash ~/miniconda.sh -b -p /conda/installation/path

#setup bioconda repository
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

#then create environment
conda create -n funannotate python=2.7 funannotate

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/funannotate.sh
echo "unset FUNANNOTATE_DB" > /conda/installation/path/envs/funannotate/etc/conda/deactivate.d/funannotate.sh

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