Clustering in Machine Learning

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\niris"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ncircles"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Numeric Clustering"];
  2 -->|output| 10;
  11["Numeric Clustering"];
  2 -->|output| 11;
  12["Numeric Clustering"];
  3 -->|tabular| 12;
  13["Numeric Clustering"];
  3 -->|tabular| 13;
  14["Numeric Clustering"];
  3 -->|tabular| 14;
  15["Scatterplot with ggplot2"];
  5 -->|outfile| 15;
  275528af-4af3-4dc6-a958-737f4d2f89bd["Output\nheirarchical_clustering_circles"];
  15 --> 275528af-4af3-4dc6-a958-737f4d2f89bd;
  style 275528af-4af3-4dc6-a958-737f4d2f89bd stroke:#2c3143,stroke-width:4px;
  16["Scatterplot with ggplot2"];
  6 -->|outfile| 16;
  870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9["Output\nkmeans_clustering_circles"];
  16 --> 870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9;
  style 870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9 stroke:#2c3143,stroke-width:4px;
  17["Scatterplot with ggplot2"];
  7 -->|outfile| 17;
  9664ba05-4664-4ceb-8f93-0974b20bf9e1["Output\ndbscan_clustering_circles"];
  17 --> 9664ba05-4664-4ceb-8f93-0974b20bf9e1;
  style 9664ba05-4664-4ceb-8f93-0974b20bf9e1 stroke:#2c3143,stroke-width:4px;
  18["Scatterplot with ggplot2"];
  9 -->|outfile| 18;
  d82a4483-7f38-4614-96b4-2a9b3316c808["Output\nheirarchical_clustering_moon"];
  18 --> d82a4483-7f38-4614-96b4-2a9b3316c808;
  style d82a4483-7f38-4614-96b4-2a9b3316c808 stroke:#2c3143,stroke-width:4px;
  19["Scatterplot with ggplot2"];
  10 -->|outfile| 19;
  00c0ca58-4ee5-4606-8c1b-c172431e5dbd["Output\ndbscan_clustering_moon"];
  19 --> 00c0ca58-4ee5-4606-8c1b-c172431e5dbd;
  style 00c0ca58-4ee5-4606-8c1b-c172431e5dbd stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nmoon"];
  style 2 stroke:#2c3143,stroke-width:4px;
  20["Scatterplot with ggplot2"];
  11 -->|outfile| 20;
  5717bf22-83e3-46a2-8f6d-12a1fa41439b["Output\nkmeans_clustering_moon"];
  20 --> 5717bf22-83e3-46a2-8f6d-12a1fa41439b;
  style 5717bf22-83e3-46a2-8f6d-12a1fa41439b stroke:#2c3143,stroke-width:4px;
  21["Scatterplot with ggplot2"];
  12 -->|outfile| 21;
  0ace8714-ff3a-4efd-a649-70924b1e6230["Output\nheirarchical_clustering_iris"];
  21 --> 0ace8714-ff3a-4efd-a649-70924b1e6230;
  style 0ace8714-ff3a-4efd-a649-70924b1e6230 stroke:#2c3143,stroke-width:4px;
  22["Scatterplot with ggplot2"];
  13 -->|outfile| 22;
  e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd["Output\nkmeans_clustering_iris"];
  22 --> e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd;
  style e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd stroke:#2c3143,stroke-width:4px;
  23["Scatterplot with ggplot2"];
  14 -->|outfile| 23;
  119d1cde-567a-47f0-99de-00d3557c38a2["Output\ndbscan_clustering_iris"];
  23 --> 119d1cde-567a-47f0-99de-00d3557c38a2;
  style 119d1cde-567a-47f0-99de-00d3557c38a2 stroke:#2c3143,stroke-width:4px;
  3["Convert CSV to tabular"];
  0 -->|output| 3;
  4["Scatterplot with ggplot2"];
  1 -->|output| 4;
  5["Numeric Clustering"];
  1 -->|output| 5;
  6["Numeric Clustering"];
  1 -->|output| 6;
  7["Numeric Clustering"];
  1 -->|output| 7;
  8["Scatterplot with ggplot2"];
  2 -->|output| 8;
  9["Numeric Clustering"];
  2 -->|output| 9;

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/statistics/tutorials/clustering_machinelearning/workflows/clustering.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