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Name: Tripal

Type: Organization

Bio: An open-source toolkit for construction of genomic, genetic, breeding and biological databases.

Tripal 4 (Drupal 10)

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Compatibility

Tested on +

Drupal	10.2.x	10.3.x
PHP 8.1
PHP 8.2
PHP 8.3

Code Coverage

This project uses Code Climate to determine the quality of our codebase and the coverage of our test suite. Compatibility above is based on passing of this test suite.

Current Timeline

Required for Tripal 4.alpha3 Release

Display suite / page work
Importers: Publications
Search (ElasticSearch + Views)

How to get involved!

This upgrade to Drupal 10 is a community effort. As such, we NEED YOUR HELP!

To get involved, please join our Tripal Slack and comment in the #core-dev channel.
- Alternatively, feel free to contact Lacey-Anne Sanderson through Slack direct message.
- We can use help both with programming, documentation, outreach and welcome all individuals from all backgrounds!
We prefer automated testing for all Pull Requests (PRs) and are happy to guide you through the process!
- Just comment on the issue if you need help designing tests
- If you need help implementing tests see our documentation
If more documentation would be helpful, please create an issue here and we'll add it.

Documentation

Documentation for Tripal 4 has begun on ReadtheDocs.

Tripal Docker

Tripal Docker is currently focused on Development and Automated Testing. There will be a production focused Tripal Docker soon and if you're interested in helping or providing tips -please join us on our Slack channel!

For more information about how to use our fully functional development docker, see our documentation on ReadtheDocs!

Tripal's Projects

brapi

Breeding API client-server implementation (v1 & v2) for Tripal

chado_linker_fields

Tripal fields to display content linked to a different content type through linker tables

chado_search

Mainlab Chado Search: enabling advanced search function for a Tripal/Chado database

docker-tripal-centos

Docker container for Tripal 2 and Tripal 3

fields_generator

A composer tool for easily generating Tripal Fields

mainlab_chado_loader

Mainlab Chado Loader

mainlab_tripal

Mainlab Tripal Data Display: extending the display of a Tripal database

private_biodata

Make individual pages private while others of the same Tripal Content Type remain public!

setup-tripal-action

Provides a GitHub Action to setup a basic Tripal site in your GitHub Action Workflows.

t4d8

This is a temporary repository for Drupal 9 upgrade for Tripal v4. It is meant to house issues related to the upgrade.

test-tripal-action

Provides a Github Action to make automated testing workflows for Tripal Extension modules easy!

tripal

The Tripal package is a suite of Drupal modules for creating biological (genomic, genetic, breeding) websites. Visit the Tripal homepage at http://tripal.info for documentation, support, and other information. The Drupal project page is at http://drupal.org/project/tripal.

tripal4_services_proof-of-concept

Experimental code for a services-driven approach to Tripal 4

tripal_analysis_blast

This module extends the Tripal Analysis Module and provides a method for loading XML results from the NCBI blast program. Blast results appear on each feature page.

tripal_analysis_expression

Extension module for the Tripal toolset to show differential expression data. This module was made for Drupal 7, Tripal 3, and Chado 1.3.

tripal_analysis_go

This module is responsible for displaying reports from Gene Ontology (GO) analyses. This module contains a Gene Ontology Annotation Format (GAF) file loader to import GO terms assigned to features. Otherwise, GO assignments must already be loaded into the Tripal database using other data loaders (e.g. using the Tripal InterPro Analysis module or a GFF file)

tripal_analysis_interpro

This module extends the Tripal Analysis Module and provides a method for loading XML results from the InterProScan program. The module can load InterProScan XML v4 or InterProScan XML v5 generated from the command-line or web-based versions of InterProScan. Additionally, GO terms mapped by InterProScan can optionally be assigned to features.

tripal_analysis_kegg

This module extends the Tripal Analysis Module and provides a method for loading of KEGG ortholog assignments derived from the KEGG Automated Annotation Server (KAAS). The module reads the compressed .heir file or alternatively an expanded heir directory. KEGG assignments appear on each feature page, and a full KEGG report is available for browsing results once uploaded.

tripal_analysis_unigene

DEPRECATED. This module is no longer needed for Tripal v3. Only major bug fixes will be considered for Tripal v2 sites that still use it. But, in summary, This module extends the Tripal v2 Analysis Module and provides visualization of Unigenes derived from ESTs.