BGCFlow Wrapper

A snakemake wrapper and utility tools for BGCFlow.

For more details, see documentation.

Setup

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To install bgcflow_wrapper, run this command in your terminal:

# create a new virtual environment
python -m venv env
source env/bin/activate

# install BGCFlow wrapper
pip install git+https://github.com/matinnuhamunada/bgcflow_wrapper.git

Features

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$ bgcflow

Usage: bgcflow [OPTIONS] COMMAND [ARGS]...

  A snakemake wrapper and utility tools for BGCFlow
  (https://github.com/NBChub/bgcflow)

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  build       Use DBT to build DuckDB database from BGCFlow results.
  clone       Use git to clone BGCFlow to local directory.
  deploy      [EXPERIMENTAL] Deploy BGCFlow locally using snakedeploy.
  get-result  View a tree of a project results or get a copy using Rsync.
  init        Create projects or initiate BGCFlow config.
  rules       Get description of available rules from BGCFlow.
  run         A snakemake CLI wrapper to run BGCFlow.
  serve       Generate static HTML report for BGCFlow run(s)

Credits

This package was created with the ppw tool. For more information, please visit the project page.