Installation¶

BUSCOlite can be installed using pip or conda.

Requirements¶

BUSCOlite has the following dependencies:

Python 3.6 or later
pyhmmer (>=0.12.0)
pyfastx
natsort
augustus (for genome mode)
miniprot (for genome mode)

Installing with pip¶

To install the latest release version using pip:

pip install buscolite

To install the development version directly from GitHub:

pip install git+https://github.com/nextgenusfs/buscolite.git

Installing with conda¶

BUSCOlite is available on the bioconda channel:

conda install -c bioconda buscolite

Installing External Dependencies¶

For genome mode, you need to install Augustus and miniprot:

Augustus¶

Augustus can be installed using conda:

conda install -c bioconda augustus

Augustus PPX Mode

Many versions of Augustus on conda have non-functional PPX/--proteinprofile mode. If you encounter issues, you may need to compile Augustus from source.

To compile Augustus from source:

git clone https://github.com/Gaius-Augustus/Augustus.git
cd Augustus
make
make install

Miniprot¶

Miniprot can be installed using conda:

conda install -c bioconda miniprot

Or compiled from source:

git clone https://github.com/lh3/miniprot.git
cd miniprot
make
make install

BUSCO Lineages¶

BUSCOlite requires BUSCO lineage data, which can be downloaded from the BUSCO website:

Download the appropriate lineage for your organism:

# Example: Download the fungi lineage
wget https://busco-data.ezlab.org/v5/data/lineages/fungi_odb10.2020-09-10.tar.gz
tar -xzf fungi_odb10.2020-09-10.tar.gz

Verifying Installation¶

To verify that BUSCOlite is installed correctly:

buscolite --version

This should display the version of BUSCOlite.