Workflows

These workflows are associated with Evaluating and ranking a set of pathways based on multiple metrics

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.

Pathway Analysis

Last updated Sep 16, 2022

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Tests: ❌ Results: Not yet automated

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;
	

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