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NPLinker is a python framework for data mining microbial natural products by integrating genomics and metabolomics data.

For a deep understanding of NPLinker, please refer to the original paper.

Installation

Requirements

NPLinker is a python package that has both pypi packages and non-pypi packages as dependencies. It requires ~4.5GB of disk space to install all the dependencies.

Install nplinker package as following:

Install nplinker package
# Create a new virtual environment and activate it
conda create -n npl-3.11 python=3.11  # (1)!
conda activate npl-3.11 

# install nplinker package (requiring ~300MB of disk space)
pip install nplinker

# install nplinker non-pypi dependencies and databases (~4GB)
install-nplinker-deps # (2)!
  1. A virtual environment is required to install the non-pypi dependencies. It's recommended to use conda to manage python virtual environments. Check conda documentation for installation instructions.
  2. Use which install-nplinker-deps command to check if the command install-nplinker-deps is in the activated python virtual environment. If not, make sure you have activated the virtual environment and/or reinstall the nplinker package.

Install from source code

You can also install NPLinker from source code:

Install from latest source code
pip install git+https://github.com/nplinker/nplinker@dev  # (1)!
install-nplinker-deps
  1. The @dev is the branch name. You can replace it with the branch name, commit or tag.