Genetic Map Rad Seq Workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nInput dataset"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nInput dataset"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nInput dataset"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nInput dataset"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nInput dataset"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nInput dataset"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nInput dataset"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["ℹ️ Input Dataset\nInput dataset"];
  style 9 stroke:#2c3143,stroke-width:4px;
  10["ℹ️ Input Dataset\nInput dataset"];
  style 10 stroke:#2c3143,stroke-width:4px;
  11["ℹ️ Input Dataset\nInput dataset"];
  style 11 stroke:#2c3143,stroke-width:4px;
  12["ℹ️ Input Dataset\nInput dataset"];
  style 12 stroke:#2c3143,stroke-width:4px;
  13["ℹ️ Input Dataset\nInput dataset"];
  style 13 stroke:#2c3143,stroke-width:4px;
  14["ℹ️ Input Dataset\nInput dataset"];
  style 14 stroke:#2c3143,stroke-width:4px;
  15["ℹ️ Input Dataset\nInput dataset"];
  style 15 stroke:#2c3143,stroke-width:4px;
  16["ℹ️ Input Dataset\nInput dataset"];
  style 16 stroke:#2c3143,stroke-width:4px;
  17["ℹ️ Input Dataset\nInput dataset"];
  style 17 stroke:#2c3143,stroke-width:4px;
  18["ℹ️ Input Dataset\nInput dataset"];
  style 18 stroke:#2c3143,stroke-width:4px;
  19["ℹ️ Input Dataset\nInput dataset"];
  style 19 stroke:#2c3143,stroke-width:4px;
  20["ℹ️ Input Dataset\nInput dataset"];
  style 20 stroke:#2c3143,stroke-width:4px;
  21["ℹ️ Input Dataset\nInput dataset"];
  style 21 stroke:#2c3143,stroke-width:4px;
  22["Stacks: de novo map"];
  1 -->|output| 22;
  0 -->|output| 22;
  15 -->|output| 22;
  14 -->|output| 22;
  13 -->|output| 22;
  12 -->|output| 22;
  11 -->|output| 22;
  10 -->|output| 22;
  9 -->|output| 22;
  8 -->|output| 22;
  7 -->|output| 22;
  6 -->|output| 22;
  5 -->|output| 22;
  4 -->|output| 22;
  3 -->|output| 22;
  2 -->|output| 22;
  17 -->|output| 22;
  18 -->|output| 22;
  19 -->|output| 22;
  20 -->|output| 22;
  21 -->|output| 22;
  16 -->|output| 22;
  23["Stacks: genotypes"];
  22 -->|all_output| 23;

Inputs

Outputs

Tools

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/ecology/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.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