Pathway Analysis

synthetic-biology-pathway_analysis/main-workflow

Author(s)

Version
1
Last updated
Sep 26, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
synthetic-biology

Features
Tutorial
Evaluating and ranking a set of pathways based on multiple metrics
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00232
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 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

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1 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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on 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