GTN Training: Galaxy 101 For Everyone

Run Workflow in Galaxy

• Galaxy Main
• Galaxy France
• Galaxy Europe
• Galaxy Australia
• Import to another server (≥23.0+ only!)

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;
  d4def008-5894-4e31-9199-8c1774b07d86["Output\ndatamash_output"];
  2 --> d4def008-5894-4e31-9199-8c1774b07d86;
  style d4def008-5894-4e31-9199-8c1774b07d86 stroke:#2c3143,stroke-width:4px;
  3["Remove beginning"];
  1 -->|tabular| 3;
  4["Cut"];
  3 -->|out_file1| 4;
  5["Group"];
  3 -->|out_file1| 5;
  e99bda54-3046-4a16-bff8-e3ebfc0a8953["Output\ngroup1"];
  5 --> e99bda54-3046-4a16-bff8-e3ebfc0a8953;
  style e99bda54-3046-4a16-bff8-e3ebfc0a8953 stroke:#2c3143,stroke-width:4px;
  6["Group"];
  3 -->|out_file1| 6;
  4dd2734c-4da2-4793-bab5-02c15522e5c5["Output\ngroup2"];
  6 --> 4dd2734c-4da2-4793-bab5-02c15522e5c5;
  style 4dd2734c-4da2-4793-bab5-02c15522e5c5 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;

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

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:

Version History

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