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![alt tag](https://raw.githubusercontent.com/tripal/tripal/7.x-3.x/tripal/theme/images/tripal_logo.png)

Tripal is a toolkit for constructing online biological (genetics, genomics, breeding, etc.) community databases, and Tripal is a member of the [GMOD](http://www.gmod.org) family of tools. **Tripal v3** provides integration with the [GMOD Chado database](http://gmod.org/wiki/Chado_-_Getting_Started) by default.

Genetics, genomics, breeding, and other biological data are increasingly complicated and time-consuming to publish online for others to search, browse and make discoveries with. Tripal provides a framework to reduce the complexity of creating such a site, and provides access to a community of similar groups that share community-standards. The users of Tripal are encouraged to interact to address questions and learn the best practices for sharing, storing, and visualizing complex biological data.

The primary goals of Tripal are to:
1. Provide a framework for creating sites that allow display, search, and visualization of biological data, including genetics, genomics, and breeding data;
2. Use community-derived standards and ontologies to facilitate continuity between sites and foster collaboration and sharing;
3. Provide an out-of-the-box setup for a genomics site to put new genome assemblies and annotations online; and
4. Provide Application Programming Interfaces (APIs) to support customized displays, look-and-feel, and new functionality.


# Features
The following major features
are available in Tripal v3.

* Tripal v3's design is centered around controlled vocabularies and ontologies.
This allows for greater integration with the semantic web and will help
support data exchange between Tripal sites.
* RESTful web services. Tripal v3 introduces RESTful web services for Tripal.
The resources provided by these web services uses JSON-LD and WC3 Hydra
vocabulary to deliver content.
* Tripal v3 introduces new content pages. In older versions of Tripal all
content was provided via Drupal "nodes". Now content is delivered using
new content types (e.g. gene, genetic_marker, organism, germplasm, etc.)
and the site admin controls which content types are available on the site.
* Chado support:
* Tripal v3 represents a major redesign from previous versions. Previously,
Chado was the only storage backend supported. Tripal v3 provides by default
support for Chado, but also sports a new design that affords integration of
other storage backends (including noSQL options).
* A Chado v1.2 or v1.3 installer
* Data loaders for ontologies (controlled vocabularies), GFF files, and
FASTA files, publications (from PubMed and AGIRCOLA).
* Generic Bulk Data Loader Modules allows for creation of custom loaders
without programming (requires an understanding of Chado).
* Supports creation of materialized views for faster data queries.
Welcome to the home of Tripal Development! If you are thinking to yourself "What is Tripal?", head over to [our website, Tripal.info](http://tripal.info/).

# Current Status

- Recommended Version: ![GitHub release (latest by date)](https://img.shields.io/github/v/release/tripal/tripal?color=brightgreen)
- Development:
- [![Tripal 3](https://img.shields.io/badge/dev-7.x--3.x-yellow)](https://github.com/tripal/tripal): Focus is on bug fixes
- [![Tripal 4](https://img.shields.io/badge/dev-7.x--4.x-yellow)](https://github.com/tripal/t4d8): Full upgrade to Drupal 8/9 (development in [T4D8 Repository](https://github.com/tripal/t4d8)).
- Tripal ![Tripal 1.x](https://img.shields.io/badge/unsupported-7.x--1.x-red) and ![Tripal 2.x](https://img.shields.io/badge/unsupported-7.x--2.x-red) are no longer supported by the Project Management Committee, although we will accept community submitted fixes for Tripal 2.x.

# Resources

- For information on **how to use Tripal** through the Administrative Interface: [Tripal Users Guide](https://tripal.readthedocs.io/en/latest/user_guide.html)
- For help **extending Tripal** or understanding how it works: [Tripal Developers Guide](https://tripal.readthedocs.io/en/latest/dev_guide.html)
- To check if another group already developed the functionality you need: [Listing of **Available Extension Modules**](https://tripal.readthedocs.io/en/latest/extensions.html)
- Tripal is developed by a world-wide community! See the [description of our **Governance Structure**](https://tripal.readthedocs.io/en/latest/contributing/governance.html)
- If you are the head of a research group looking to fund Tripal Development: [Guide to **Funding Proposal** Development](https://tripal.readthedocs.io/en/latest/contributing/funding.html)
- For how to **install Tripal**, follow the instructions in the online Tripal User's Guide for [Tripal v2](https://tripal.info/tutorials/v2.x/installation) or [Tripal v3](https://tripal.readthedocs.io/en/latest/user_guide.html).
- For how to **upgrade from Tripal 2 to Tripal 3**, follow the [Upgrade Instructions](https://tripal.readthedocs.io/en/latest/user_guide/install_tripal/upgrade_from_tripal2.html) in the Tripal v3 User's Guide.

# Contribution

Looking to contribute? That's Amazing -Welcome!!! Here's a quick run-down to get you started:

- We welcome all contributions!
- This github issue queue is open to: bug reports, usability concerns, performance issues, site administration or development questions, data storage discussions, etc.
- We ask that questions/concerns/bugs with **extension modules** be addressed in their respective repositories (including those under the Tripal organization).
- For **feature request**, please open an issue with detailed use cases and description. We would love to help you design a generic solution for the community whether it belongs in Tripal Core or an Extension module! Please wait to submit a PR until the Project Management Committee (PMC) indicates it is generally applicable and should be included in Core.
- For **potential bugs or concerns**, please open an issue being as descriptive as possible. Screenshots and steps to reproduce will help us, help you! If you know how to fix the issue, feel free to submit a pull request (PR) linked to the issue!
- For **documentation** contributions, click the "Edit on Github" link at the top of the page you want to improve! [Instructions for our flavour of ReadtheDocs can be found on ReadtheDocs](https://tripal.readthedocs.io/en/latest/contributing/documentation.html).
- See our quickstart if you need help on how to submit a PR: [ReadtheDocs, how to create a PR](https://tripal.readthedocs.io/en/latest/contributing/pull_requests.html#how-to-create-a-pr).
- Click on issues > New Issue for helpful issue templates.
- For Tripal 4 (Drupal 8/9), see the [T4D8 repository](https://github.com/tripal/t4d8).

For more detailed guidelines see our [full Contribution Documentation](https://tripal.readthedocs.io/en/latest/contributing/pull_requests.html)!


# Github Communication Tips

- Don’t be afraid to mention people (@username) who are knowledgeable on the topic or invested. We are academics and overcommitted, it’s too easy for issues to go unanswered: don’t give up on us!
- Likewise, don’t be shy about bumping an issue if no one responds after a few days. Balancing responsibilities is hard.
- Want to get more involved? Issues marked with “Good beginner issue” are a good place to start if you want to try your hand at submitting a PR.
- Everyone is encouraged/welcome to comment on the issue queue! Tell us if you
- are experiencing the same problem
- have tried a suggested fix
- know of a potential solution or work-around
- have an opinion, idea or feedback of any kind!
- Be kind when interacting with others on Github! (see Code of Conduct below for further guidelines). We want to foster a welcoming, inclusive community!
- Constructive criticism is welcome and encouraged but should be worded such that it is helpful :-) Direct criticism towards the idea or solution rather than the person and focus on alternatives or improvements.

# Code of Conduct

Be nice! If that’s insufficient, Tripal community defers to https://www.contributor-covenant.org/

# Required Dependencies
* Drupal:
* Drupal:
* Drupal 7.x
* Drupal core modules: Search, Path and PHP modules.
* Drupal contributed modules:
* Drupal contributed modules:
* [Views](http://drupal.org/project/views)
* [Entity API](http://drupal.org/project/entity)
* PostgreSQL 9.3 or higher (9.5 required for Chado 1.2 to 1.3 upgrade)
* PHP 5.5+
* UNIX/Linux


# Installation
Please follow the instructions in the online Tripal User's Guide for [Tripal v2](https://tripal.info/tutorials/v2.x/installation) or [Tripal v3](https://tripal.readthedocs.io/en/latest/user_guide.html).


# Upgrade from Tripal v2.x to v3.x
Please follow the [Upgrade Instructions](https://tripal.readthedocs.io/en/latest/user_guide/install_tripal/upgrade_from_tripal2.html) in the Tripal v3 User's Guide


# Customization
Tripal can be used “as is” but also allows for complete customization.
PHP-based template files are provided for all data types to allow for
precise customizations as required by the community. A well-developed
Tripal API provides a uniform set of variables and functions for
accessing any and all data within the Chado database. See the Tripal 3.x
Developer's Handbook for additional details.


# Development Testing

To run PHP unit tests on your local system, run `composer install` to install developer-specific requirements. Next, create a `.env` file in your `/Tests/` directory that defines the `DRUPAL_ROOT` variable, for example
To run PHP unit tests on your local system, run `composer install` to install developer-specific requirements. Next, create a `.env` file in your `/Tests/` directory that defines the `DRUPAL_ROOT` variable, for example

```
DRUPAL_ROOT=/var/www/html
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PHPUnit tests will also be run in the Travis CI build.

Read our [testing guidelines](tests/README.md)
Read our [testing guidelines](https://tripal.readthedocs.io/en/latest/contributing/tests.html).

## Contributors

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<!-- prettier-ignore-end -->
<!-- ALL-CONTRIBUTORS-LIST:END -->

This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

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