GTN Training: Galaxy 101 For Everyone

introduction-galaxy-reproduce/main-workflow

Author(s)

version Version
1
last_modification Last updated
Aug 25, 2021
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
introduction

Features

Tutorial
hands_on How to reproduce published Galaxy analyses

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00115
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\niris"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Convert CSV to tabular"];
  0 -->|output| 1;
  2["Datamash"];
  1 -->|tabular| 2;
  d74b3ccf-3cfe-4b3d-a560-70c654798134["Output\ndatamash_output"];
  2 --> d74b3ccf-3cfe-4b3d-a560-70c654798134;
  style d74b3ccf-3cfe-4b3d-a560-70c654798134 stroke:#2c3143,stroke-width:4px;
  3["Remove beginning"];
  1 -->|tabular| 3;
  4["Cut"];
  3 -->|out_file1| 4;
  5["Group"];
  3 -->|out_file1| 5;
  0af99871-09eb-4b61-98e9-b4e308383cbf["Output\ngroup1"];
  5 --> 0af99871-09eb-4b61-98e9-b4e308383cbf;
  style 0af99871-09eb-4b61-98e9-b4e308383cbf stroke:#2c3143,stroke-width:4px;
  6["Group"];
  3 -->|out_file1| 6;
  e4a63107-f1a6-409d-bb2b-4ab82696f72c["Output\ngroup2"];
  6 --> e4a63107-f1a6-409d-bb2b-4ab82696f72c;
  style e4a63107-f1a6-409d-bb2b-4ab82696f72c stroke:#2c3143,stroke-width:4px;
  7["Scatterplot w ggplot2"];
  3 -->|out_file1| 7;
  8["Scatterplot w ggplot2"];
  3 -->|out_file1| 8;
  9["Unique"];
  4 -->|out_file1| 9;
  ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6["Output\nunique_output"];
  9 --> ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6;
  style ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
iris iris

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/2.2.1+galaxy1 Scatterplot w ggplot2
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1 Scatterplot w 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/2.2.1+galaxy1 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 galaxy-upload 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
1 03bdb9f97 2021-07-10 16:43:54 Adding new GTN how to reproduce Galaxy analyses

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-reproduce/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