GTN Training: Workflow Reports - Galaxy 101 For Everyone

galaxy-interface-workflow-reports/galaxy-101-everyone

Author(s)

Version
2
Last updated
Jul 6, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
galaxy-interface

Features
Tutorial
Workflow Reports
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00083
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nIris Dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Convert CSV to tabular"];
  0 -->|output| 1;
  2["Datamash"];
  1 -->|tabular| 2;
  5fc8c705-b9e2-4008-aa85-e84504b8395f["Output\ndatamash_output"];
  2 --> 5fc8c705-b9e2-4008-aa85-e84504b8395f;
  style 5fc8c705-b9e2-4008-aa85-e84504b8395f stroke:#2c3143,stroke-width:4px;
  3["Remove beginning"];
  1 -->|tabular| 3;
  4["Cut"];
  3 -->|out_file1| 4;
  5["Group"];
  3 -->|out_file1| 5;
  7e07839c-e8ca-4692-8b8e-6eb3607066de["Output\ngroup1"];
  5 --> 7e07839c-e8ca-4692-8b8e-6eb3607066de;
  style 7e07839c-e8ca-4692-8b8e-6eb3607066de stroke:#2c3143,stroke-width:4px;
  6["Group"];
  3 -->|out_file1| 6;
  9cb98227-aa5b-4b77-933c-ffba1e98566e["Output\ngroup2"];
  6 --> 9cb98227-aa5b-4b77-933c-ffba1e98566e;
  style 9cb98227-aa5b-4b77-933c-ffba1e98566e stroke:#2c3143,stroke-width:4px;
  7["Scatterplot with ggplot2"];
  3 -->|out_file1| 7;
  8["Scatterplot with ggplot2"];
  3 -->|out_file1| 8;
  9["Unique"];
  4 -->|out_file1| 9;
  fc73409c-7878-4391-bc91-f99a5be0ba06["Output\nunique_output"];
  9 --> fc73409c-7878-4391-bc91-f99a5be0ba06;
  style fc73409c-7878-4391-bc91-f99a5be0ba06 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Iris Dataset

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 Datamash
Grouping1 Group
Grouping1 Group
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0 Scatterplot with ggplot2
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0 Scatterplot with ggplot2
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 Unique

Tools

Tool Links
Cut1
Grouping1
Remove beginning1
csv_to_tabular
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0 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 bffad5337 2022-07-06 13:19:10 update worfklow to not hide png output
2 56ef1bde9 2022-06-01 13:20:32 update topic tag on workflow
1 b200300b4 2022-06-01 09:02:04 start workflow reports tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/galaxy-101-everyone.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