Metadata-Version: 2.1
Name: bgcflow_wrapper
Version: 0.3.2
Summary: A snakemake wrapper and utility tools command line interface for BGCFlow.
Home-page: https://github.com/NBChub/bgcflow_wrapper
License: MIT
Author: Matin Nuhamunada
Author-email: matinnu@biosustain.dtu.dk
Requires-Python: >=3.8,<4.0
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Provides-Extra: dev
Provides-Extra: doc
Provides-Extra: test
Requires-Dist: black (>=22.3.0,<23.0.0) ; extra == "test"
Requires-Dist: click (>=8.1.3,<9.0.0)
Requires-Dist: dbt-metabase (>=0.9.15,<0.10.0)
Requires-Dist: flake8 (==4.0.1) ; extra == "test"
Requires-Dist: flake8-docstrings (>=1.6.0,<2.0.0) ; extra == "test"
Requires-Dist: gitpython (>=3.1.35,<4.0.0)
Requires-Dist: isort (==5.10.1) ; extra == "test"
Requires-Dist: livereload (>=2.6.3,<3.0.0)
Requires-Dist: mike (>=1.1.2,<2.0.0) ; extra == "doc"
Requires-Dist: mkdocs (>=1.2.3,<2.0.0) ; extra == "doc"
Requires-Dist: mkdocs-autorefs (>=0.3.1,<0.4.0) ; extra == "doc"
Requires-Dist: mkdocs-include-markdown-plugin (>=3.2.3,<4.0.0) ; extra == "doc"
Requires-Dist: mkdocs-jupyter (>=0.24.2,<0.25.0)
Requires-Dist: mkdocs-macros-plugin (>=1.0.4,<2.0.0)
Requires-Dist: mkdocs-material (>=9.2.0b3,<10.0.0) ; extra == "doc"
Requires-Dist: mkdocs-material-extensions (>=1.0.3,<2.0.0)
Requires-Dist: mkdocstrings (>=0.18.0,<0.19.0) ; extra == "doc"
Requires-Dist: numpy (>=1.22.0)
Requires-Dist: pandas (<2.1.0)
Requires-Dist: panoptes-ui (>=0.2.0,<0.3.0)
Requires-Dist: peppy (>=0.35.4,<0.36.0)
Requires-Dist: pip (>=22.0.3,<23.0.0) ; extra == "dev"
Requires-Dist: pre-commit (>=2.17.0,<3.0.0) ; extra == "dev"
Requires-Dist: pyreadline (>=2.1,<3.0)
Requires-Dist: pytest (>=7.2.0) ; extra == "test"
Requires-Dist: pytest-cov (>=3.0.0,<4.0.0) ; extra == "test"
Requires-Dist: setuptools (>=65.5.1,<66.0.0) ; extra == "doc"
Requires-Dist: snakedeploy (>=0.8.2,<0.9.0)
Requires-Dist: snakemake (>=7.18.2,<8.0.0)
Requires-Dist: sqlalchemy (==1.4.46)
Requires-Dist: toml (>=0.10.2,<0.11.0) ; extra == "dev"
Requires-Dist: tox (>=4.6.4,<5.0.0) ; extra == "dev"
Requires-Dist: twine (>=3.8.0,<4.0.0) ; extra == "dev"
Requires-Dist: virtualenv (>=20.13.1,<21.0.0) ; extra == "dev"
Project-URL: Documentation, https://nbchub.github.io/bgcflow_wrapper
Project-URL: Repository, https://github.com/NBChub/bgcflow_wrapper
Description-Content-Type: text/markdown

# BGCFlow Wrapper


<p align="left">
<a href="https://pypi.python.org/pypi/bgcflow_wrapper">
    <img src="https://img.shields.io/pypi/v/bgcflow_wrapper.svg"
        alt = "Release Status">
</a>

<a href="https://github.com/NBChub/bgcflow_wrapper/actions">
    <img src="https://github.com/NBChub/bgcflow_wrapper/actions/workflows/dev.yml/badge.svg?" alt="CI Status">
</a>

<a href="https://NBChub.github.io/bgcflow_wrapper/">
    <img src="https://img.shields.io/website/https/NBChub.github.io/bgcflow_wrapper/index.html.svg?label=docs&down_message=unavailable&up_message=available" alt="Documentation Status">
</a>

</p>


A snakemake wrapper and utility tools for [BGCFlow](https://github.com/NBChub/bgcflow), a systematic workflow for the analysis of biosynthetic gene clusters across large genomic datasets.

For more details, see [documentation](https://NBChub.github.io/bgcflow_wrapper/).

## Publication
> Matin Nuhamunada, Omkar S. Mohite, Patrick V. Phaneuf, Bernhard O. Palsson, and Tilmann Weber. (2023). BGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. bioRxiv 2023.06.14.545018; doi: [https://doi.org/10.1101/2023.06.14.545018](https://doi.org/10.1101/2023.06.14.545018)

## Setup
--------
### Setup via Conda
To install `bgcflow_wrapper` with conda, run this command in your
terminal:

```bash
# create and activate new conda environment
conda create -n bgcflow pip -y
conda activate bgcflow

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

## Features
![function](https://raw.githubusercontent.com/NBChub/bgcflow_wrapper/main/docs/assets/Figure_01.png)
--------
```bash

$ 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](https://zillionare.github.io/python-project-wizard) tool. For more information, please visit the [project page](https://zillionare.github.io/python-project-wizard/).

