Final - Unsupervised Analysis of Bone Marrow Cells

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\ntrain clinincal data"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ntest clinincal data"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\ntrain omics 1"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\ntest omics 1"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\ntrain omics 2"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\ntest omics 2"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["Flexynesis"];
  5 -->|output| 6;
  4 -->|output| 6;
  1 -->|output| 6;
  3 -->|output| 6;
  0 -->|output| 6;
  2 -->|output| 6;
  5791b446-d5ab-4647-a04f-d96daa9f615b["Output\nflexynesis output"];
  6 --> 5791b446-d5ab-4647-a04f-d96daa9f615b;
  style 5791b446-d5ab-4647-a04f-d96daa9f615b stroke:#2c3143,stroke-width:4px;
  7["Extract test embeddings"];
  6 -->|results| 7;
  8["Louvain clustering"];
  7 -->|output| 8;
  1 -->|output| 8;
  344ac387-2dfa-4629-8c03-3d5b336420da["Output\nlouvain clustering"];
  8 --> 344ac387-2dfa-4629-8c03-3d5b336420da;
  style 344ac387-2dfa-4629-8c03-3d5b336420da stroke:#2c3143,stroke-width:4px;
  9["Dimred true value"];
  7 -->|output| 9;
  1 -->|output| 9;
  9ba13d6c-2caf-4625-bde6-874da3516cf6["Output\numap - true_value"];
  9 --> 9ba13d6c-2caf-4625-bde6-874da3516cf6;
  style 9ba13d6c-2caf-4625-bde6-874da3516cf6 stroke:#2c3143,stroke-width:4px;
  10["Get optimal clusters"];
  7 -->|output| 10;
  8 -->|util_out| 10;
  e12faae2-19cd-478e-951d-541769ab0988["Output\nk-means clustering"];
  10 --> e12faae2-19cd-478e-951d-541769ab0988;
  style e12faae2-19cd-478e-951d-541769ab0988 stroke:#2c3143,stroke-width:4px;
  11["Label concordance true vs louvain"];
  10 -->|util_out| 11;
  1cd385d5-ed0b-4344-9a5c-ffebaae59349["Output\nconcordance plot"];
  11 --> 1cd385d5-ed0b-4344-9a5c-ffebaae59349;
  style 1cd385d5-ed0b-4344-9a5c-ffebaae59349 stroke:#2c3143,stroke-width:4px;
  12["compute ami_ari true vs lovain"];
  10 -->|util_out| 12;
  727d1cde-f4a5-4ddf-8e17-3aa117f61b68["Output\namir_ari true vs louvain"];
  12 --> 727d1cde-f4a5-4ddf-8e17-3aa117f61b68;
  style 727d1cde-f4a5-4ddf-8e17-3aa117f61b68 stroke:#2c3143,stroke-width:4px;
  13["compute ami_ari true vs optimal_cluster"];
  10 -->|util_out| 13;
  7b904d9a-e082-460e-bd2e-3f18b27dc3dc["Output\namir_ari true vs k-means"];
  13 --> 7b904d9a-e082-460e-bd2e-3f18b27dc3dc;
  style 7b904d9a-e082-460e-bd2e-3f18b27dc3dc stroke:#2c3143,stroke-width:4px;
  14["Dimred louvain"];
  7 -->|output| 14;
  10 -->|util_out| 14;
  6346a63f-fd06-44ad-93b3-42b41675d1a5["Output\numap - louvain"];
  14 --> 6346a63f-fd06-44ad-93b3-42b41675d1a5;
  style 6346a63f-fd06-44ad-93b3-42b41675d1a5 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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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/flexynesis_unsupervised/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