Tripal User's Meeting 2019/09/10

Agenda

1. October's meeting is for the advisory committee.

   • everyone is invited.

2. Updates from the PMC

   • Tripal v4 progress

     1. Straight port to Drupal 8 (no new features)

     2. Jump on Github to contribute!

        1. https://github.com/tripal/t4d8

        2. Note this is a temporary repo to keep things organized, will be merged back in to normal core repo later

     3. Backwards compatible unless Drupal forces us not to be.

   • Questions about core development?

3. Updates from the TAC (Meg Staton, Chair)

   • Organizing Grant efforts

     1. Who is writing grants, will it impact core, can it help fund core development?

     2. Perhaps explore some Microsoft Research funding.

     3. Meg perhaps lead a CSSI

     4. USDA FACT possibility for US folks.

   • Next month:  what do we see is the impetus for our community to grow:  "big ideas". Where should we go? Where should it be in 5 years.

     1. use cases

     2. portable version:  give individual labs the ability to use Tripal more easily and connect to established community databases & reproducible workflows.

     3. Jill can start a brainstorming document.

4. PAG. 

   • Organizing committee:  Lacey & Jill

   • Please reach out to the committee about the Hackathon if you have ideas on how to improve.

     1. How can folks join remotely? 

        1. We will be working on making this more seamless

5. Training Galaxy Module (Stephen Ficklin, WSU)

   • Documentation: https://tripal-galaxy.readthedocs.io/en/latest/index.html 

   • Github: https://github.com/tripal/tripal_galaxy

   • The purpose of this module is to integrate Tripal and Galaxy

   • Previously the community would create a module which would write the glue for a specific workflow but with more complex workflows and since Galaxy is a moving target this resulted in a lot of developer time

   • The Tripal Galaxy module takes care of a lot of the overhead to reduce developer input

   • When using the Tripal Galaxy module make sure to use a compatible version of Galaxy

   • Supports both automatic webform creation and custom applications submitting to and receiving from Galaxy

   • Uses blend4php which maps the galaxy API over to PHP: github.com/galaxyproject/blend4php

   • See the documentation for how to setup: https://tripal-galaxy.readthedocs.io/en/latest/?badge=latest

     1. You also need to make sure the Tripal: upload files permission is set for users using the workflows

   • Automatic webform creation will create a Tripal/Drupal form on your Tripal site which hides Galaxy behind it

     1. The keeps a consistent user experience

     2. It also allows you to provide custom help to your specific community for an already set workflow

   • A nice thing about using Galaxy is that we can use existing tools and save a lot of time over creating our own workflow management system. It is also a great tool with a large dedicated developer community

   • Allows you to upload site-wide files which any user can utilize in their workflows

   • If you don’t have a dedicated galaxy instance you can configure the module to use https://usegalaxy.org

     1. Create a specific user for your Tripal site rather then using a personal account

   • Even with automatic webform generation you can still tweak a variety of settings including the workflow title, instructions to the user, “About this step” field for each step, and information for each tool.

     1. The user is able to control specific options of the galaxy workflow as they step through the Tripal Galaxy webform. Everything that they can set in the galaxy workflow will be displayed in the webform! Some options will be preset and not changable to make submission easier for the user (e.g. files from previous steps)

     2. Once you submit the last step you are given a full summary of all options picked. This is great for users to keep track of what was done for a publication

   • Tripal > User file management (provided by core Tripal) allows administrators to set site-wide and per user file quotas which apply to files uploaded as part of Tripal Galaxy.

     1. Workflow forms will tell the user where they are in their specific quota and prevent them from uploading files over their quota

   • Files are removed automatically after 60 days (configurable).

   • Any workflows submitted through the automatic form will be submitted as Tripal Jobs and if you use the Tripal Daemon the job will be launched automatically.

     1. The Tripal Daemon also has settings to allow parallel execution of jobs and you can control how many threads are used.

   • Tripal Galaxy provides an API for checking for workflow status

     1. Users are emailed when their job is submitted and when it completes. These email messages can be configured on a per-workflow basis.

     2. There is also an “Analyses” tab on the user page which allows users to check their submission details, retrieve their results and look at any error messages if the analyses did not complete successfully

   • Meg: we have trouble scaling to if someone submits a very large file that will take 3mo. To run

     1. Jill/Sean: Galaxy does configure with your job management system which will allow to configure allocations for cores and memory

        1. You can configure this at the workflow or tool level through Galaxy

     2. Stephen: Tripal Galaxy only provides regulation of storage size, everything else is on the galaxy side

   • Power Applications (option 2 for using Tripal Galaxy)

     1. This is used for Cartogratree

     2. Tripal Galaxy provides an API which allows a more powerful application which then submits to galaxy behind the scenes

     3. This is well documented on the Tripal Galaxy RTD documentation: https://tripal-galaxy.readthedocs.io/en/latest/API/api.html