mrsa AMR gene detection

genome-annotation-amr-gene-detection/main-workflow

Author(s)
Bazante Sanders, Bérénice Batut, Tristan Reynolds
Version
2
Last updated
Dec 18, 2025
License
MIT
Tags
genome-annotation
microgalaxy

Features
Tutorial
Identification of AMR genes in an assembled bacterial genome
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00085
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\ncontigs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nInput Paired End Reads Collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["staramr"];
  0 -->|output| 2;
  a84f1c10-0c72-423c-a85c-643c39e44dac["Output\nstararm_detailed_summary"];
  2 --> a84f1c10-0c72-423c-a85c-643c39e44dac;
  style a84f1c10-0c72-423c-a85c-643c39e44dac stroke:#2c3143,stroke-width:4px;
  3["Bakta"];
  0 -->|output| 3;
  b9beba76-7b6e-42ae-a085-819f4b577100["Output\nbakta_annotation_summary"];
  3 --> b9beba76-7b6e-42ae-a085-819f4b577100;
  style b9beba76-7b6e-42ae-a085-819f4b577100 stroke:#2c3143,stroke-width:4px;
  4["Bowtie2"];
  1 -->|output| 4;
  0 -->|output| 4;
  b85fac67-e102-475e-95d9-35e0adecb0c9["Output\nmapping_stats"];
  4 --> b85fac67-e102-475e-95d9-35e0adecb0c9;
  style b85fac67-e102-475e-95d9-35e0adecb0c9 stroke:#2c3143,stroke-width:4px;
  5["Select"];
  2 -->|detailed_summary| 5;
  6["Table to GFF3"];
  5 -->|out_file1| 6;
  7["JBrowse"];
  0 -->|output| 7;
  3 -->|annotation_gff3| 7;
  6 -->|output| 7;
  4 -->|output| 7;
  c4e08c51-4520-483a-b48a-99adc9a5d09f["Output\njbrowse_output"];
  7 --> c4e08c51-4520-483a-b48a-99adc9a5d09f;
  style c4e08c51-4520-483a-b48a-99adc9a5d09f stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset contigs
Input dataset collection Input Paired End Reads Collection

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1 staramr
toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0 Bakta
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 Bowtie2
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 JBrowse

Tools

Tool Links
Grep1
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1 View in ToolShed

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

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on 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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
6 f52ead1fa 2025-12-11 23:55:30 Correct creator names
5 8f5019e24 2025-12-10 00:31:50 Updated workflow and workflow tests
4 597f8ce95 2024-01-23 13:57:43 Add Bazante's ORCID
3 03e429090 2024-01-23 10:04:17 Fix workflows
2 c88bcbb6f 2024-01-19 15:28:57 Add license and creator to workflows
1 6d6129376 2024-01-15 16:01:34 Expand the AMR detection tutorial

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