Pathway Analysis
synthetic-biology-pathway_analysis/main-workflow
Launch in Tutorial Mode
question
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flowchart TD 0["ℹ️ Input Collection\nHeterologous pathways"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nChassis where to produce target from"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Parameter\nCell compartment ID"]; style 2 fill:#ded,stroke:#393,stroke-width:4px; 3["ℹ️ Input Parameter\nBiomass reaction ID"]; style 3 fill:#ded,stroke:#393,stroke-width:4px; 4["Flux balance analysis"]; 3 -->|output| 4; 2 -->|output| 4; 1 -->|output| 4; 0 -->|output| 4; 5["Thermo"]; 4 -->|pathway_with_fba| 5; 6["Score Pathway"]; 5 -->|pathway_with_thermo| 6; 7["Rank Pathways"]; 6 -->|scored_pathway| 7; 8111f525-5845-4ac2-a1d6-c4bfd218cf3f["Output\nRanked Pathways"]; 7 --> 8111f525-5845-4ac2-a1d6-c4bfd218cf3f; style 8111f525-5845-4ac2-a1d6-c4bfd218cf3f stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset collection | Heterologous pathways |
Input dataset | Chassis where to produce target from |
Input parameter | Cell compartment ID |
Input parameter | Biomass reaction ID |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1 | Flux balance analysis | |
toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1 | Thermo | |
toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1 | Score Pathway | |
toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1 | Rank Pathways |
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 |
---|---|---|---|
2 | 25d6ed2bc | 2022-09-16 08:13:35 | fix(main_workflow.ga): add tag and annotation |
1 | 47a55fc0c | 2022-08-09 14:04:58 | feat(pathway_analysis): add pathway analysis tutorial |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/pathway_analysis/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