Taxonomic Profiling and Visualization of Metagenomic Data

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nraw-reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nmetadata"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Unzip collection"];
  0 -->|output| 2;
  3["Kraken2"];
  0 -->|output| 3;
  23edf15b-3629-49d4-ac00-e631237e245f["Output\nkraken_report"];
  3 --> 23edf15b-3629-49d4-ac00-e631237e245f;
  style 23edf15b-3629-49d4-ac00-e631237e245f stroke:#2c3143,stroke-width:4px;
  4["MetaPhlAn"];
  2 -->|forward| 4;
  2 -->|reverse| 4;
  11c16c72-e8bc-4d86-aa24-c37f23cf4db1["Output\nmetaphlan_output"];
  4 --> 11c16c72-e8bc-4d86-aa24-c37f23cf4db1;
  style 11c16c72-e8bc-4d86-aa24-c37f23cf4db1 stroke:#2c3143,stroke-width:4px;
  5["Krakentools: Convert kraken report file"];
  3 -->|report_output| 5;
  d36f8369-d61e-41d9-a9af-1277da522ded["Output\nkrakentool_report"];
  5 --> d36f8369-d61e-41d9-a9af-1277da522ded;
  style d36f8369-d61e-41d9-a9af-1277da522ded stroke:#2c3143,stroke-width:4px;
  6["Kraken-biom"];
  3 -->|report_output| 6;
  1 -->|output| 6;
  7["Pavian"];
  3 -->|report_output| 7;
  8["Estimate Abundance at Taxonomic Level"];
  3 -->|report_output| 8;
  9["Krona pie chart"];
  4 -->|krona_output_file| 9;
  10["Krona pie chart"];
  5 -->|output| 10;
  11["Phinch Visualisation"];
  6 -->|biomOutput| 11;

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/microbiome/tutorials/taxonomic-profiling/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