mrsa AMR gene detection

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\ncontigs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nforward_reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nreverse_reads"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["staramr"];
  0 -->|output| 3;
  8320025f-8a15-4c6d-a2ba-bb6c340124e2["Output\nstararm_detailed_summary"];
  3 --> 8320025f-8a15-4c6d-a2ba-bb6c340124e2;
  style 8320025f-8a15-4c6d-a2ba-bb6c340124e2 stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  e45c0a06-f902-409e-abb8-a1e40a81ece0["Output\nbakta_annotation_summary"];
  4 --> e45c0a06-f902-409e-abb8-a1e40a81ece0;
  style e45c0a06-f902-409e-abb8-a1e40a81ece0 stroke:#2c3143,stroke-width:4px;
  5["Bowtie2"];
  1 -->|output| 5;
  2 -->|output| 5;
  0 -->|output| 5;
  877e061b-c2f6-4d0f-9825-8e7521e66820["Output\nbowtie_mapping_stats"];
  5 --> 877e061b-c2f6-4d0f-9825-8e7521e66820;
  style 877e061b-c2f6-4d0f-9825-8e7521e66820 stroke:#2c3143,stroke-width:4px;
  6["Select"];
  3 -->|detailed_summary| 6;
  7["Table to GFF3"];
  6 -->|out_file1| 7;
  8["JBrowse"];
  4 -->|annotation_gff3| 8;
  7 -->|output| 8;
  5 -->|output| 8;
  d974005b-229d-420f-8891-e9eac4cffa71["Output\njbrowse_output"];
  8 --> d974005b-229d-420f-8891-e9eac4cffa71;
  style d974005b-229d-420f-8891-e9eac4cffa71 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/genome-annotation/tutorials/amr-gene-detection/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