Tutorial workflow

galaxy-interface-workflow-editor/main-workflow

Author(s)

Version
1
Last updated
Jul 17, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
galaxy-interface

Features
Tutorial
Creating, Editing and Importing Galaxy Workflows
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00080
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Collection\nInput dataset collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Reverse dataset"];
  0 -->|output| 1;
  2["Select first lines"];
  1 -->|outfile| 2;
  daf1abd9-a5c8-4b25-add1-5475e594f187["Output\nFirst lines"];
  2 --> daf1abd9-a5c8-4b25-add1-5475e594f187;
  style daf1abd9-a5c8-4b25-add1-5475e594f187 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset collection

Outputs

From Output Label
Input dataset collection
Show beginning1 Select first Select first lines

Tools

Tool Links
Show beginning1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
3 9ce50a5ba 2020-07-17 15:35:33 Could have sworn I added those tags already ...
2 b3873844e 2020-07-17 15:15:46 Add workflow with annotation
1 e745bce97 2020-07-16 14:17:09 WIP Tutorial on workflows

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-editor/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows