Workflow Methylation Seq

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy Main
• Galaxy France
• Galaxy Europe
• 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["FastQC"];
  0 -->|output| 9;
  10["FastQC"];
  1 -->|output| 10;
  11["bwameth"];
  0 -->|output| 11;
  1 -->|output| 11;
  12["Replace column"];
  3 -->|output| 12;
  4 -->|output| 12;
  13["metilene"];
  2 -->|output| 13;
  5 -->|output| 13;
  3 -->|output| 13;
  8 -->|output| 13;
  7 -->|output| 13;
  6 -->|output| 13;
  14["MethylDackel"];
  11 -->|output| 14;
  15["MethylDackel"];
  11 -->|output| 15;
  16["Select last"];
  12 -->|outfile_replace| 16;
  17["Select last"];
  15 -->|outFileExtractCpGFraction| 17;
  18["computeMatrix"];
  16 -->|outfile| 18;
  2 -->|output| 18;
  19["Text reformatting"];
  17 -->|outfile| 19;
  20["computeMatrix"];
  19 -->|outfile| 20;
  2 -->|output| 20;
  21["plotProfile"];
  20 -->|outFileName| 21;
  9ea1396b-ec1a-4721-8f65-3f67f1d90ab7["Output\nplot_profile_tabular"];
  21 --> 9ea1396b-ec1a-4721-8f65-3f67f1d90ab7;
  style 9ea1396b-ec1a-4721-8f65-3f67f1d90ab7 stroke:#2c3143,stroke-width:4px;

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/epigenetics/tutorials/methylation-seq/workflows/methylation-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