Installing agtools

It is recommended to install agtools using either PyPI or Conda.

PyPI

Before installing agtools, you will need to have pycairo installed.

pip install pycairo

Then use the following command to install agtools globally.

pip install agtools

Conda

You can install agtools through Bioconda using conda or mamba.

mamba install -c bioconda agtools

If you prefer to install agtools in a dedicated environment, you can do so as follows.

mamba create -n agtools
mamba activate agtools
mamba install -c bioconda agtools

Alternatively:

mamba create -n agtools -c bioconda agtools
mamba activate agtools

Installing agtools from source

If you want to use the development version of agtools, you can install it using flit as follows. Please ensure that flit is installed beforehand.

# clone repository
git clone https://github.com/Vini2/agtools.git

# move to agtools directory
cd agtools

# create and activate conda env
conda env create -f environment.yml
conda activate agtools

# install using flit
flit install -s --python `which python`

# test installation
agtools --help

If you prefer not to create a dedicated environment and only want to install agtools, ensure the following dependencies are installed:

• Python - 3.10 or higher
• flit - for installation
• click - for CLI argument parsing
• loguru - for logging
• bidict - for bidirectional lookup
• python-igraph - for graph operations
• biopython - for sequence operations
• pandas - for dataframes
• pycairo - for plotting in igraph