mrsa AMR gene detection
genome-annotation-amr-gene-detection/main-workflow
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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; bf50d64d-39d0-4e20-855f-25b7d401ce79["Output\nstararm_detailed_summary"]; 3 --> bf50d64d-39d0-4e20-855f-25b7d401ce79; style bf50d64d-39d0-4e20-855f-25b7d401ce79 stroke:#2c3143,stroke-width:4px; 4["Bakta"]; 0 -->|output| 4; 5e6918a9-f46a-4687-a859-f5055e35d2cb["Output\nbakta_annotation_summary"]; 4 --> 5e6918a9-f46a-4687-a859-f5055e35d2cb; style 5e6918a9-f46a-4687-a859-f5055e35d2cb stroke:#2c3143,stroke-width:4px; 5["Bowtie2"]; 1 -->|output| 5; 2 -->|output| 5; 0 -->|output| 5; 3bed079d-ce71-4147-b14e-3c864b23b27b["Output\nbowtie_mapping_stats"]; 5 --> 3bed079d-ce71-4147-b14e-3c864b23b27b; style 3bed079d-ce71-4147-b14e-3c864b23b27b 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; b86baa67-861d-4c51-a027-d8121c7a031a["Output\njbrowse_output"]; 8 --> b86baa67-861d-4c51-a027-d8121c7a031a; style b86baa67-861d-4c51-a027-d8121c7a031a stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
contigs | contigs |
forward_reads | forward_reads |
reverse_reads | reverse_reads |
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/bowtie2/2.5.0+galaxy0 | Bowtie2 | |
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 | JBrowse |
Tools
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
- 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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
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