Flexynesis - get data from Cbioportal

Run Workflow in Galaxy

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

flowchart TD
  0["Flexynesis cBioPortal import"];
  1["extract expression data"];
  0 -->|data| 1;
  2["extract mutation data 2"];
  0 -->|data| 2;
  3["extract clinical data"];
  0 -->|data| 3;
  4["remove duplicate genes from expression data"];
  1 -->|output| 4;
  5["remove comment lines from mutation data"];
  2 -->|output| 5;
  6["remove comment lines from clinical data"];
  3 -->|output| 6;
  7["remove ENTREZ gene ids from expression data"];
  4 -->|outfile| 7;
  8["remove index column from mutation data"];
  5 -->|table| 8;
  9["remove index column from clinical data"];
  6 -->|table| 9;
  10["Binarize mutation data"];
  8 -->|output| 10;
  11["Flexynesis utils"];
  9 -->|output| 11;
  7 -->|output| 11;
  10 -->|util_out| 11;
  a34a9c32-55d0-4ea7-b52c-c7446ba56439["Output\ntest data"];
  11 --> a34a9c32-55d0-4ea7-b52c-c7446ba56439;
  style a34a9c32-55d0-4ea7-b52c-c7446ba56439 stroke:#2c3143,stroke-width:4px;
  6a451d6f-6920-40da-b77f-e1926514a498["Output\ntrain data"];
  11 --> 6a451d6f-6920-40da-b77f-e1926514a498;
  style 6a451d6f-6920-40da-b77f-e1926514a498 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_cbio_import/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