Metadata-Version: 2.4
Name: machado
Version: 0.8.0
Summary: This library provides users with a framework to store, search and visualize biological data.
Author: LMB
License-Expression: GPL-3.0-only
Project-URL: Homepage, https://github.com/lmb-embrapa/machado
Project-URL: Repository, https://github.com/lmb-embrapa/machado
Classifier: Environment :: Console
Classifier: Framework :: Django :: 5.2
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: django~=5.2
Requires-Dist: django-environ~=0.12.0
Requires-Dist: whitenoise~=6.9.0
Requires-Dist: psycopg2-binary~=2.9.12
Requires-Dist: networkx~=3.6
Requires-Dist: obonet~=1.1.1
Requires-Dist: biopython~=1.87
Requires-Dist: tqdm~=4.67.3
Requires-Dist: bibtexparser~=1.4.4
Requires-Dist: pysam~=0.24.0
Dynamic: license-file

[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
[![CI: Machado](https://github.com/lmb-embrapa/machado/actions/workflows/django.yml/badge.svg)](https://github.com/lmb-embrapa/machado/actions/workflows/django.yml)

# Machado

Machado is a Django application that contains tools to interact with a Chado database.
It provides users with a framework to store, search and visualize biological data.
Detailed documentation can be found in the [docs](docs/index.md) directory or in the [PDF manual](docs/machado-manual.pdf).


## Features
- There are data loaders for the major bioinformatics formats: fasta, gff, obo, bibtex, blast, interproscan, orthomcl
- The Machado API delivers data directly to the JBrowse genome browser
- Full-text search powered by PostgreSQL (no external search service needed)

## Installation
Please refer to the [installation guide](docs/01-installation.md).

## Docker

You can build your Machado instance using Docker: https://github.com/lmb-embrapa/machado-docker

## Demo

[https://www.machado.cnptia.embrapa.br](https://www.machado.cnptia.embrapa.br "machado demo")

## Contributing

Machado is run by volunteers and we are always looking for people interested in helping with code development, documentation writing, and bug report.

If you wish to contribute, please create an issue.

## License

Machado - A Django implementation of Chado's schema.
Copyright (C) 2018 Embrapa

Machado is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.

Additional permission under GNU GPL version 3 section 7

If you modify this Program, or any covered work, by linking or combining
it with Chado (or a modified version of that library), containing parts
covered by the terms of Artistic License 2.0, the licensors of this Program
grant you additional permission to convey the resulting work. {Corresponding
Source for a non-source form of such a combination shall include the source
code for the parts of Chado used as well as that of the covered work.}

See LICENSE.txt for complete gpl-3.0 license.

[build-status-image]: https://secure.travis-ci.org/lmb-embrapa/machado.svg?branch=master
[travis]: https://travis-ci.org/lmb-embrapa/machado
[cov-status-image]: https://img.shields.io/codecov/c/github/lmb-embrapa/machado/master.svg
[codecov]: https://codecov.io/gh/lmb-embrapa/machado

## Please cite

Machado: Open source genomics data integration framework.<br/>
[GigaScience, Volume 9, Issue 9, September 2020, giaa097](https://academic.oup.com/gigascience/article-abstract/doi/10.1093/gigascience/giaa097/5905760) <br/>
[![doi](http://img.shields.io/badge/doi-10.1093%2Fgigascience%2Fgiaa097-blue.svg?style=flat)](https://doi.org/10.1093/gigascience/giaa097) 
[![pubmed](http://img.shields.io/badge/pubmed-32930331-blue.svg?style=flat)](https://pubmed.ncbi.nlm.nih.gov/32930331)

