Tripal User's Meeting 2017/04/07

• Tripal 2.1 was released on April 1

  • Includes major bug fixes, support for Chado v1.3 and a number of community contributions!

  • Upgrade from Tripal v2.0 to v2.1:  http://tripal.info/tutorials/v2.x/upgrade_2.0_to_2.1

  • Upgrade from Tripal v1.1 to v2.1:  http://tripal.info/tutorials/v2.x/upgrade_6.11_to_2.1

• Tripal Issue Queue has moved to GitHub

  • All pre-existing issues have been moved over and checked to be sure they still exist

  • Please add any problems you encounter with either Tripal 2 or 3 and label/tag them appropriately

  • This issue queue is friendly to help requests as well as the typical bugs or feature requests :-)

• We have added a “Powered by Tripal” block in Tripal 2.1

  • Please consider adding this block to the footer section of your site

  • There are also a number of “Powered by Tripal” images if you would rather include it in an About page or some other appropriate place :-)

  • http://tripal.info/logos

• A Big Thank you to everyone who has contributed bug fixes and features! For anyone else who wants to contribute to core Tripal development, we welcome pull requests and would Love to hear from you :-)

• Training meeting on Friday April 14th at 8am Pacific Daylight Time.   

  • Expect 3 hours.

  • Training will be on using the bulk loader to load custom file formats.

  • We will try to provide a Docker container that you can use to follow along with the training.  

  • Watch for an email early in the week.

Reminders

• You can add your modules into the Tripal GitHub organization.  This allows all of our Tripal extension modules to be in one place but you still maintain control of your repository.  

  • If you want to move your extension module let us know so we can coordinate it.

  • Or consider just creating new repositories right there in the Tripal organization.

• Remember to update the status of your modules on the Tripal.info site.  

  • All modules that were 2.0 compatible have been automatically marked as 2.1 compatible as well.  

• If you have a new site or major updates to your existing site let us now and we can publish those on the Tripal news feed and twitter accounts.

Agenda:

• Views in Tripal 3.x

  • Do you currently have views containing chado content not shown on your node pages?

  • Do you use the Tripal Views integration configuration to change field/filter/sort handlers and/or add relationships?

• Module Releases/Updates

  • Please update your repository to use GitHub “topics”. This allows your modules to be more easily found even if they are not under the Tripal Organization.

    • You can add “Topic:tripal” in the search box to bring up all Tripal modules tagged on Github:

    • https://github.com/search?utf8=%E2%9C%93&q=topic%3Atripal&type=Repositories

  • With the release of Tripal 2.1 there was also a new release of many Tripal Analysis Extension modules

    • These changes are mostly user contributions --Thanks!

    • Includes Tripal Analysis: Interpro, KEGG, Blast, GO

  • ND Genotypes (Lacey)

    • https://github.com/UofS-Pulse-Binfo/nd_genotypes

    • First beta version just released.

    • Has already had extensive use in a production setting.

  • VCF Filter (Lacey)

    • https://github.com/UofS-Pulse-Binfo/vcf_filter

    • Provides a simple interface to users to filter VCF files and export them in a variety of formats using VCFtools.

    • Users only have access to a set of admin supplied VCF files to keep down server load from unrelated users.

    • Think of it as a more helpful way to distribute bulk genotype sets.

    • Release will be available early next week (just adding 2 more format options).

  • CViT Embed (Lacey)

    • Embeds CViTjs diagrams (LegumeFederation) in Tripal sites to provide whole genome diagrams.

    • https://github.com/UofS-Pulse-Binfo/cvitembed

    • Beta version just released.

  • CV Browser (VG)
    
    A CV browser like the GO Browser ( http://banana-genome-hub.southgreen.fr/ontology_browser )  has been developped and will be released soon (already fully functionnal). Git: https://github.com/SouthGreenPlatform/tripal_cvb This browser allows to browse any (hierarchical) CV (or sub-CV from a root CV term) and associate actions to terms like, for instance, displaying the number of features tagged by a gene ontology term, or displaying a detailed page (next to the browser) regarding a CV term. This module will be moved to drupal.org (my sandbox) soon and will be announced on the Tripal mailing list once a tutorial has been done. (VG)

  • Updates on other modules?