Tripal Developer's Meeting 2015-04-14

Meeting Date

Tue, 04/14/2015 - 12:00

Attendees

Stephen Ficklin, Chun-huai Cheng, Sook Jung, Taein Lee, Connor Wytko (WSU)

Meg Staton, Nate Henry (Univ Tenn)

Chris Childers, Vijaya Tsavatapalli (USDA-ARS-NAL)

Lacey-anne Sanderson (University of Saskatchewan)

Andrew Farmer, Iliana Toneva, Pooja Umale (NCGR)

Jun Chang(Noble)

Jacqueline Campbell, Ethy Cannon, Steven Cannon (ISU/Ames)

Status of Tripal stable release v2.0 -- May 31st.
Changes to tripal.info site.
Future Updates for Tripal
- Entities for Drupal 8.
- Installation profiles.
  - Make links for these notes online tripal.info.
  - Lacey has a generic installation profile. It’s close to be usable already. Lacey will reinvigorate efforts on this. She’ll explore including this in stable release.
- Changes to default pages.
- Addition of a Tripal module repository resource on tripal.info to make finding extensions easier.
  - Add a list of modules being worked on to help reduce duplication of effort.
  - Folks should also list new modules on listserv
  - Should add a document for how to share modules on tripal.info.
- Integration of Andrew Farmer’s (NCGR) Phylonode module.
- Unit Testing (to speed testing for release).
  - Steve Cannon may provide a student to help with development of unit testing.
  - Stephen Ficklin will add a section to the Developers Handbook for how to implement unit testing.
- Documentation Updates
  - Add instructions for setting permissions on page level
  - Add instructions for integrating non-Drupal Search
  - Is the documentation useful? How to improve?
Tripal default page interface
- Ethy, Meg: don’t like the collapsible sidebar.
- Ethy suggested wrapping panels under the sidebar if space is available.
- Ethy likes the breadcrumb trail. But how can we design this.
- Steve mentioned the circular pages to gene/mRNA pages.
  - On gene pages give this information for the primary transcript by default.
  - Chris: i5K folks will be willing to share styles and templates.
  - Need to add a place to share templates on tripal.info an extension theme.
- Need a way to more easily enhance templates on a “type” basis (for features, stocks, etc...)
- Need to add a missing templates for pub linker (and other linker).
Any new work? Questions?
Status of Extension Modules
- QTL (U. Iowa, WSU, U. Sask)
  - Sook and Ethy are trying to get it started up again. Nice to have more involvement. Need someone to implement it as there isn’t a much time perhaps in the summer. Goal is to have a working draft by PAG 2016.
  - Perhaps expand into genetic module to include markers and maps.
  - Meg expressed interest in being involved.
  - Lacey expressed interest in keeping genetic markers separate from QTLs.
- BLAST (U. Iowa, U. Sask)
  - http://peanutbase.org/blast & http://legumeinfo.org/blast
  - Code: https://www.drupal.org/project/tripal_blast
  - New feature: hit visualization, but in need of a quick repair to image of ‘target’ sequence.
  - Ames development effort has a github instance which makes pull requests to a master development github instance. Stable versions of the code is pushed to the Drupal repository.
- Networks (WSU, Clemson)
  - https://www.drupal.org/sandbox/spficklin/1796198
- Web Services (WSU + community)
  - Part of Tripal 7.x-2.x on branch 7.x-2.x-toc
- Phylotree (NCGR, U. Iowa)
  - https://github.com/ncgr/tripal_phylogeny
  - http://legumeinfo.org/search/phylotree
- Pedigrees/d3 support (U Sask)
  - https://www.drupal.org/project/tripald3
  - There is a current production release at the URL above
  - Future plans include moving pedigrees out to a separate module (perhaps in the same download) and further developing a Tripal D3 API for developers allowing for consistent themeing, pop-ups, etc. between modules.
- KEGG module issues (WSU)
  - https://www.drupal.org/project/tripal_analysis_kegg
- Chado Controller (Bioversity International)
  - https://www.drupal.org/sandbox/guignonv/2428743
- Multi-Chado (Bioversity International)
  - https://www.drupal.org/sandbox/guignonv/2429515
- Ecommerce style shopping cart (NCGR) for collecting data. Currently gene oriented has some sequence download functionality.
- File module (associating images too). (WSU)
  - https://www.drupal.org/sandbox/spficklin/2458713
- Daemon API/Drush Daemon API / Tripal Daemon (USask)
  - https://www.drupal.org/project/drushd
  - https://www.drupal.org/project/tripal_daemon
  - Current releases available at the above URLs
  - Development is on hold pending suggestions from users on functionality they would like to see
- Others?
Next Meeting May 5th, an informal agenda.

Meeting Type

Users