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BGCFlow Wrapper

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A snakemake wrapper and utility tools for BGCFlow, a systematic workflow for the analysis of biosynthetic gene clusters across large genomic datasets.

For more details, see documentation.

Please refer to the BGCFlow WIKI for detailed examples and use cases:

wiki

Publication

Matin Nuhamunada, Omkar S Mohite, Patrick V Phaneuf, Bernhard O Palsson, Tilmann Weber, BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets, Nucleic Acids Research, 2024;, gkae314, https://doi.org/10.1093/nar/gkae314

Setup

Setup via Conda

To install bgcflow_wrapper with conda/mamba, run this command in your terminal:

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# create and activate new conda environment
mamba create -n bgcflow -c conda-forge python=3.11 pip openjdk -y
conda activate bgcflow

# install BGCFlow wrapper
pip install bgcflow_wrapper

Features

function

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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       Build Markdown report or use dbt to build DuckDB database.
  clone       Get a clone of 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 from template.
  pipelines   Get description of available pipelines from BGCFlow.
  run         A snakemake CLI wrapper to run BGCFlow.
  serve       Serve static HTML report or other utilities (Metabase, etc.).
  sync        Upload and sync DuckDB database to Metabase.

Credits

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