Keine Beschreibung

Stephen Ficklin 144a3b49bc Fix to prevent GFF loader from importing malformed dbxrefs		vor 4 Jahren
.github	6fe860038b buxxxxxxx	vor 5 Jahren
docs	8f86ac135d Update administrative.rst	vor 4 Jahren
legacy	dd88e9fa9b Merge pull request #871 from tripal/310_mass_style_update	vor 5 Jahren
tests	e755ce05d5 Merge pull request #1023 from reynoldtan/patch-3	vor 4 Jahren
tripal	387b275147 Fixed issue pointed out by bcondon	vor 4 Jahren
tripal_bulk_loader	dd88e9fa9b Merge pull request #871 from tripal/310_mass_style_update	vor 5 Jahren
tripal_chado	144a3b49bc Fix to prevent GFF loader from importing malformed dbxrefs	vor 4 Jahren
tripal_chado_views	aeb71070d8 Merge branch '7.x-3.x' into patch-1	vor 5 Jahren
tripal_daemon	5a8103068a run phpstorm base style formatter	vor 5 Jahren
tripal_ds	dd88e9fa9b Merge pull request #871 from tripal/310_mass_style_update	vor 5 Jahren
tripal_ws	f626f6406c Merge pull request #1032 from risharde/risharde-patch-1	vor 4 Jahren
.all-contributorsrc	7451abd90e Merge branch '7.x-3.x' into all-contributors/add-srobb1	vor 4 Jahren
.gitignore	69bd91bbae Added documentation to describe creation offromatters and pagers to address issue #165	vor 6 Jahren
.travis.yml	e2c915a72e fix travis build	vor 5 Jahren
CONTRIBUTING.md	77a390944a fix link in contributing. fix JSON to json for RST documentation	vor 5 Jahren
LICENSE.txt	ad615a7bd5 Create LICENSE.txt	vor 7 Jahren
README.md	7451abd90e Merge branch '7.x-3.x' into all-contributors/add-srobb1	vor 4 Jahren
composer.json	f73dd89a62 Remove dataProvider tags and call the function directly in tests, also auto load the fields helper	vor 5 Jahren
composer.lock	1ece264d4b Added bundle lookup :-)	vor 5 Jahren
phpunit.xml	ecdc6dddd8 structure tests into suites	vor 6 Jahren

Tripal is a toolkit for constructing online biological (genetics, genomics, breeding, etc.) community databases, and Tripal is a member of the GMOD family of tools. Tripal v3 provides integration with the GMOD Chado database 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:

Provide a framework for creating sites that allow display, search, and visualization of biological data, including genetics, genomics, and breeding data;
Use community-derived standards and ontologies to facilitate continuity between sites and foster collaboration and sharing;
Provide an out-of-the-box setup for a genomics site to put new genome assemblies and annotations online; and
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.

Required Dependencies

Drupal:
- Drupal 7.x
- Drupal core modules: Search, Path and PHP modules.
- Drupal contributed modules:
- Views
- Entity API
PostgreSQL
PHP 5.5+
UNIX/Linux

Installation

Please follow the instructions in the online Tripal User's Guide for Tripal v2 or Tripal v3.

Upgrade from Tripal v2.x to v3.x

Please follow the Upgrade Instructions 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

DRUPAL_ROOT=/var/www/html

Then run PHPUnit from your root Tripal directory.

PHPUnit tests will also be run in the Travis CI build.

Read our testing guidelines

Contributors

Thanks goes to these wonderful people (emoji key):

_{Stephen Ficklin} 💻 📋 📖 📆 👀	_{Bradford Condon} 💻 📖 📆 📋 👀	_{Lacey-Anne Sanderson} 💻 📖 📆 📋 👀	_{chunhuaicheng} 💻	_Shawna 💻 🖋 📖 👀	_mboudet 🐛	_{Valentin Guignon} 🐛
_{Meg Staton} 🔍 📋	_{Anthony Bretaudeau} 💻	_colthom 📖	_{Abdullah Almsaeed} 💻 👀	_btski 💬	_ekcannon 🤔 📋	_jlwegrzyn 🔍
_{Douglas Senalik} 💻	_par12005 💻	_{Sofia Robb} 💻	_{katherynbuble} 💻	_risharde 💻