The metaboverse-cli-r from kkami1115

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Metaboverse command line utility for modeling user data on the global reaction network

License: MIT License

Shell 0.76% Python 90.09% R 9.15%

metaboverse-cli-r's Introduction

Using Metaboverse

To use the Metaboverse app, please click here

What does Metaboverse do?

A current draft of the manuscript describing Metaboverse can be found here

Requirements

Python 3.6 or greater
An internet connection for network curation
The Metaboverse app

Other Notes

This product includes color specifications and designs developed by Cynthia Brewer (http://colorbrewer.org/).

Build `metaboverse-cli` for the first time

conda create -n pyinstaller
conda activate pyinstaller

conda install python=3.8
pip install pyinstaller 
pip install pandas numpy scipy scikit-learn networkx requests

pyinstaller metaboverse-cli.spec

Re-use `metaboverse-cli` build environment

conda activate pyinstaller

conda install python=3.8
pip install pyinstaller --upgrade
pip install pandas numpy scipy scikit-learn networkx requests --upgrade

pyinstaller metaboverse-cli.spec

Utilizing a custom Metaboverse network

Custom networks are archived at https://github.com/Metaboverse/Custom-Networks/curated_organisms. Once a network is curated, input it into the Metaboverse GUI .....

Example for building organism network

metaboverse-cli-windows.exe curate --output . --organism_id M_leprae --database_source custom --force_new_curation --organism_curation_file E:\projects\Custom-Networks\curated_organisms\m_leprae\m_leprae.json

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