extensions

The following changes exist with this version:

• Supports Chado v1.3.
• The addition of a phylogeny module that provides a newick file loader, a basic tree visualization, and an NCBI Taxonomy importer for organisms present in the database.
• Supports new drush options for automating job launching (--max_jobs and --single)
• Fixes to the GFF loader
• Fixes to the Jobs API. Users can now run quick jobs from the GUI.
• An updated patch for Views (#30)
• Improved logging such that information messages aren't logged to the Apache error logs.
• Added a "Powered by Tripal" block for positioning on a site.
• Lots of bug fixes.

This is the last 2.1 beta release. The next will be the full v2.1 release.  This version should be the most stable yet for v2.1 and provides all of the functionality that v2.1 will offer including:

1) A Chado v1.2 to v1.3 upgrade.
2) A new phylogeny module that includes a newick file importer for phylogenetic trees and  an NCBI taxonomy importer for taxonomic trees.  Much thanks to Andrew Farmer and the LegumeInfo group for their assistance and collaboration in development and inclusion of this new module!
3) Improved support for multiple Chado installations
4)  Many bug fixes.

For a more details listing please see the release page:

https://www.drupal.org/project/tripal/releases/7.x-2.1-beta3

For upgrade instructions please see these links at the Tripal User's Guide:

Upgrading from a Tripal v1.1 site:
http://tripal.info/tutorials/v2.x/upgrade_6.11_to_2.1

Upgrading from a Tripal v2.0 site:
http://tripal.info/tutorials/v2.x/upgrade_2.0_to_2.1

To upgrade, follow the typical instructions for upgrading any Drupal module.  Note: Always be sure to backup your site before performing any update!

For a quick Drush update use the following commands inside your Drupal's installation path:

drush pm-download tripal
drush updatedb

That's it!  

To Upgrade from an Existing pre-release 3.x version:

Simply use Drupal or Drush to retrieve the most recent version of Tripal v3 and update the database.  For example, to update using Drush:

drush updatedb

To Upgrade from Tripal v2

Please see the Upgrade Instructions in the User's Guide:

Release Notes

The following improvements have been made:

• Tripal v3.0 represents a major overhaul from Tripal v2.0. Specifically, all content is now organized via controlled vocabularies
• Content types are more tightly integrated with Drupal Entities and Fields.
• Tripal v3.0 requires no editing of PHP templates to alter the placement and order of content on the page
• More of Chado is supported than in previous versions.
• RESTful web services are provided to allow for programmatic access to data on the site,
• New data collections are available to allow site visitors to place content found via searching into collections for download or use by other tools.

In addition, several more changes have been made leading up to this release:

• The User's Guide and Developer's Handbook have been converted to restructuredText and is now part of the Tripal source code allowing for more easy updates by anyone. Both Guides have been moved to ReadTheDocs.
• Tripal now includes unit testing to help speed new releases and to maintain quality.

We have worked to test as much as possible and therefore make this a "release candidate".  This is the step just before stable 7.x-3.0 release.  There will be no major changes to infrastructure or design in later releases as this release represents a completed design.  The only exception is some additional updates to come for web services.   We are currently in the process of upgrading several Tripal sites to use Tripal v3 for production so we will have multiple Tv3 sites online soon!

We have improved the User's Guide and you can find it on the Tripal.info site here:  http://tripal.info/tutorials/v3.x.  We will be adding more content within the next several weeks as well.

Please provide bug reports to our GitHub Issue Queue at https://github.com/tripal/tripal/issues

1) Tripal v3 is backwards compatible with Tripal v2.  We have switched content types from Drupal "nodes" to Drupal "entities" but you can continue to use your current Tv2 "nodes" and templates as these are still supported.  You can migrate your content to the new entities as time allows and at your own pace.

2)  All data is categorized using controlled vocabularies.  Once web services are completed this will allow for improved data exchange between Tripal sites and collation of data from different sites.

3)  Tripal is no longer dependent on Chado for organization, although Chado is still the primary data storage back-end.

4) Because data are now organized via controlled vocabularies, the organization is more intuitive.  For example, you can create a "germplasm" content type rather than a Chado-centric "stock" content type, and data from your site will be shared via Web Services as germplasm data and not "stock" data.

5)  Content is uniform:  what you see on a gene page (or any other content type) is the same data that appears in web services and is available in Drupal Views.  If you hide a field (i.e. piece of data) it is hidden everywhere else.

6)  Tripal v3 fully adopts Drupal's Entities and Fields.  This means you no longer need to edit PHP template files just to move or hide data on your pages.

7)  You can customize your page layouts if you do not like the defaults that Tripal provides without any programming.  No more PHP templates.  Using Drupal extension modules such as Display Suite or Panels you can lay out your pages how you desire.

8)  For developers, Tripal is now more object oriented!  If you need custom content we have expanded our API to more easily support integration of new fields.  This includes fields to support brand new content, or new "formatters" to change the way a field looks.

9) We have added a middle-layer separating the data storage back-end (e.g. Chado) from the data presentation layer.  This means we can more easily support other storage methods such as no-SQL options, direct access to files (e.g. indexed BAM/VCF), etc.

This release represents a variety of important bug fixes, improved performance and new features.  In addition we have updated Tutorials and the Tripal v3 API is now online via the API link at the top of this site.   We expect to release a final stable release of v3.0 within the next few months as there is no new functionality, just some last remaining issues that are available on our GitHub issue queue.

Changes in this release:

• Addition of new autocomplete API functions for analyses, assays, biomaterials, featuremaps, projects, studies and contacts
• Better support for infraspecific naming and linking for organisms including updates to:
  • Fixes to the Newick phylogenetic tree loader
  • Fixes to the Taxonomy Importer
  • Fixes to the FASTA Importer
  • Fixes to the GFF3 Importer
  • Fixes to the phylogenetic tree API
  • Updates to Chado API functions
• Tooltips on the phylogenetic tree viewer
• Bug fix in the Tripal OBO importer related to specifying local files
• Bug fix in the Tripal GFF importer related to finding landmarks
• Bug fix in progress report when publishing
• PHP 8 warnings/errors fixes
• Documentation updates
• Fixes/updates to functional/unit testing
• Bug fix to the relationship field widget
• Bug fix to the publication field widget
• Bug fix to the contact field widget and formatter
• Bug fix to the location on map field
• Bug fix to the location on seqeunce record field
• Bug fix for Tripal Job tracking
• Bug fix in the analysis data source field related to text lenght limits
• Minor update to Bulk Loader sorting

We have just released Tripal v3.2 which contains a variety of important bug fixes.  There is also a new registration page that allows site owners/developers to register their site. This is optional and the information collected will help the Tripal advisory and project management committee stay better engaged with the Tripal community and help provide usage statistics for anyone seeking funding for Tripal-related projects.

Users can upgrade by using  the command:

 drush pm-update tripal

As an open-source tool, Tripal is successful via involvement by users and stakeholders.  We request that everyone contribute by submitting bug reports, responding to issues to help others, sharing extension modules or sharing your ideas!   Contribute and get noticed with your name on our contributor listing! https://github.com/tripal/tripal#contributors

Also, we have recently added new updates to the Tripal.info site!  These include

• A formal listing of known extension modules, organized by category: https://tripal.readthedocs.io/en/latest/extensions.html
• Information about the new Tripal Advisory Committee and Project Management Committee: http://www.tripal.info/community
• Detailed documentation about new governance policies: https://tripal.readthedocs.io/en/latest/contributing.html
• Guidelines for contribution to the Tripal core software: https://tripal.readthedocs.io/en/latest/contributing/pull_requests.html

Thanks to everyone who has contributed!