Funannotation installation

The funannotate pipeline is written in python. It’s easy to use conda for installation due to funannotate has a lot of dependencies.

Installation

test

Bioconda install:

add appropriate channels:

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

install with new environment:

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

mamba install:

If conda is taking forever to solve the environment, mamba is the way to speed up the process

install mamba into base environment:

conda install -n base mamba

use mamba as drop in replacement:

mamba create -n funannotate funannotate

GeneMark-ES/ET install:

GeneMark-ES/ET needs to be installed manually due to it required academic license agreement

Fill the academic license agreement and download from: http://topaz.gatech.edu/GeneMark/license_download.cgi

1. Download the software and key

cd ~/opt   
wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_lqacT/gm_key_64.gz
wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_lqacT/gm_et_linux_64.tar.gz
tar xzvf gm_et_linux_64.tar.gz
gunzip gm_key_64.gz
cp gm_key_64 ~/.gm_key

1. Change all of the GeneMark script headers to conda perl path

   cd ~/opt/gm_et_linux_64 which perl perl ./change_path_in_perl_scripts.pl

2. Add GeneMark to .profile

   export PATH=$PATH:/your_home_folder/opt/gm_et_linux_64

Setup database for funannotation:

1. start up conda ENV

   conda activate funannotate

2. check that all modules are installed

   funannotate check –show-versions

3. download/setup databases to a writable/readable location

   funannotate setup -d ~/Data/funannotate_db

4. set ENV variable for $FUNANNOTATE_DB and GENEMARK_PATH

   echo “export FUNANNOTATE_DB=~/Data/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

   echo “export GENEMARK_PATH=~/opt/gmes_linux_64” » /conda/installation/path/envs/funannotate/etc/conda/activate.d/funannotate.sh echo “unset GENEMARK_PATH” » /conda/installation/path/envs/funannotate/etc/conda/deactivate.d/funannotate.sh

If the bio-perl is not detect after you install it with conda, please do

export PERL5LIB=/your_conda_path/envs/virsorter/lib/perl5/site_perl/5.22.0/ 

run tests for funannotation

funannotate test -t all --cpus X