mrsa AMR gene detection
genome-annotation-amr-gene-detection/main-workflow
Launch in Tutorial Mode
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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; 9c248903-c3b5-48f4-a89a-46b70d855646["Output\nstararm_detailed_summary"]; 3 --> 9c248903-c3b5-48f4-a89a-46b70d855646; style 9c248903-c3b5-48f4-a89a-46b70d855646 stroke:#2c3143,stroke-width:4px; 4["Bakta"]; 0 -->|output| 4; b39db603-5081-4f0b-b051-16df9550795e["Output\nbakta_annotation_summary"]; 4 --> b39db603-5081-4f0b-b051-16df9550795e; style b39db603-5081-4f0b-b051-16df9550795e stroke:#2c3143,stroke-width:4px; 5["Bowtie2"]; 1 -->|output| 5; 2 -->|output| 5; 0 -->|output| 5; 45f0db56-827f-4d9a-a889-bafb26f8b671["Output\nbowtie_mapping_stats"]; 5 --> 45f0db56-827f-4d9a-a889-bafb26f8b671; style 45f0db56-827f-4d9a-a889-bafb26f8b671 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; 6769525c-2758-4ec8-8d4c-2b6f2c6f54d9["Output\njbrowse_output"]; 8 --> 6769525c-2758-4ec8-8d4c-2b6f2c6f54d9; style 6769525c-2758-4ec8-8d4c-2b6f2c6f54d9 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 galaxy-workflows-activity 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
- 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