Try   HackMD

Galaxy Team

The objective of this is to document the work, progress and efforts of the team during the Codefest. Members of the team should be able to check in to this document to find project details, instructions, design descriptions, etc. as needed fo the Codefest activities.

Team Lead

Name Organization Contact Time Zone
Stephen Ficklin Washington State Univ. stephen.ficklin@wsu.edu US Pacific

Members

Name Organization Contact Time Zone
Irene Cobo Univ. of Connecticut irenecobo88@gmail.com US Eastern
Jill Wegrzyn Univ. of Connecticut jill.wegrzyn@uconn.edu US Eastern
Carolyn Caron Univ. of Saskatchewan carolyn.caron@usask.ca Regina, Canada
Sean Buehler Univ. of Connecticut US Eastern

Schedule

Team leaders should reach out prior to Jan 11-15th to schedule team meetings when members can meet to discuss project objectives and divide work.

Date Time Where
Jan 11 11:00 am PST GatherTown Tripal Galaxy Room
Jan 13 1pm EST/10am PST Gaterthtown Tripal Galaxy Room

Background

  • TreeGenes/Hardwoods sharing the same Galaxy instance.

Workflows

Available Workflows near ready

  • RNA-seq workflow for hardwoods
  • WGCNA is also available

Challenges

  • Conda dependencies can cause problems for.
  • Result files that live on the Galaxy server.

Module

Issues to address

Plans

Action items

  1. File Management
    • Autmatically load files in the global Galaxy library that are listed as site-wide on the Tripal site – Stephen
    • Create a tool in Galaxy that will provide genomes for selection and share out all appropriate files for that genome for downstream tools in the workflow –
  2. Authentication
    • Explore options for how to have unified logins with Drupal and Galaxy.
  3. UI Bugs/Requests

Resources

TreeGenes Galaxy Server
Hardwood Tripal Galaxy notes
Galaxy Local Files

Accomplishments

Once the Codefest week is over, here is where the team documents the accomplishments that were made during the week!

Last changed by 
 
Tripal Codefest
0
316

Read more

Tripal 4 Upgrade Notes

This document is indended to quickly save upgrade information. During the process of upgrading Tripal Core we're going to place useful information here until it can be more formally written up into docs. tripal_set_message() and tripal_report_error() These functions have been upgraded and thus can be used as is. However, the new way is use a logger service as shown below. $logger = \Drupal::service('tripal.logger'); $logger->notice('Hello world'); $logger->info('Hello world'); $logger->warning('Hello world'); $logger->error('Hello world');

Jun 14, 2021
Wrap up Meeting Agenda

Thank You Survey Stats & Accomplishments 19 registered attendees Accomplishments Pull requests: Tripal v3 (3 PRs)

Feb 2, 2021
Tripal v4 Development Team

The objective of this is to document the work, progress and efforts of the team during the Codefest. Members of the team should be able to check in to this document to find project details, instructions, design descriptions, etc. as needed for the Codefest activities. Schedule Preparation for Codefest Useful Commands for TripalDocker The Plan Core Objectives

Jan 15, 2021
Implementation

The so__transcript field is only ever attached to a gene. The entity that is passed into the field is the gene entity (feature_id belongs to the gene). Dynamic Gene Pages Work on branch named 100-tv3-gene_pages Let's use the orange data that comes with the Tripal Tutorial so__transcript.inc file: (Stephen) Add the following in the $default_instance_settings

Jan 15, 2021
Read more from Tripal Codefest
Published on HackMD