Mtb phylogeny

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 alignment"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["RStudio"];
  2["Estimate phylogeny with RAxML"];
  0 -->|output| 2;
  9f8ae577-c583-4a2d-b64d-14c25fb859d9["Output\nBest-scoring ML Tree"];
  2 --> 9f8ae577-c583-4a2d-b64d-14c25fb859d9;
  style 9f8ae577-c583-4a2d-b64d-14c25fb859d9 stroke:#2c3143,stroke-width:4px;
  bdb8cf2f-b553-4a96-8b55-38b4b499ab88["Output\nInfo"];
  2 --> bdb8cf2f-b553-4a96-8b55-38b4b499ab88;
  style bdb8cf2f-b553-4a96-8b55-38b4b499ab88 stroke:#2c3143,stroke-width:4px;

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/evolution/tutorials/mtb_phylogeny/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