Bacterial Genome Annotation

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\ncontigs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ISEScan"];
  0 -->|output| 1;
  2bb672cb-4536-46b0-8a22-8590a0ca36c7["Output\nisescan_results"];
  1 --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;
  style 2bb672cb-4536-46b0-8a22-8590a0ca36c7 stroke:#2c3143,stroke-width:4px;
  2["PlasmidFinder"];
  0 -->|output| 2;
  614064e6-4b0f-4e38-b04e-e3f61ba41b46["Output\nplasmidfinder_results"];
  2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;
  style 614064e6-4b0f-4e38-b04e-e3f61ba41b46 stroke:#2c3143,stroke-width:4px;
  3["Integron Finder"];
  0 -->|output| 3;
  d26788cf-2441-4f29-ac39-b6be96f192eb["Output\nintegronfinder_summary"];
  3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;
  style d26788cf-2441-4f29-ac39-b6be96f192eb stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  d3a40a8b-1bd1-42b6-a91e-756379b86d94["Output\nbakta_summary"];
  4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;
  style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;
  5["Group"];
  1 -->|all_results| 5;
  6["Group"];
  1 -->|all_results| 6;
  7["Replace Text"];
  2 -->|result_file| 7;
  8["Select last"];
  7 -->|outfile| 8;
  9["Table to GFF3"];
  8 -->|outfile| 9;
  10["JBrowse"];
  0 -->|output| 10;
  4 -->|annotation_gff3| 10;
  9 -->|output| 10;
  1 -->|annotation| 10;

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/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.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