Workflow Constructed From History 'Heinz Workflow Trial Sep 11'
transcriptomics-network-analysis-with-heinz/galaxy-workflow-heinz
Launch in Tutorial Mode
question
galaxy-download Download
galaxy-download Download
flowchart TD 0["ℹ️ Input Dataset\nEdge File"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Collection\nInput dataset collection"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Collection\nInput dataset collection"]; style 2 stroke:#2c3143,stroke-width:4px; 3["DESeq2"]; 1 -->|output| 3; 2 -->|output| 3; 4["Cut"]; 3 -->|deseq_out| 4; 5["Cut"]; 3 -->|deseq_out| 5; 6["Fit a BUM model"]; 4 -->|out_file1| 6; 7["Calculate a Heinz score"]; 5 -->|out_file1| 7; 6 -->|dist_params| 7; 8["Identify optimal scoring subnetwork"]; 7 -->|score| 8; 0 -->|output| 8; 9["Visualize"]; 8 -->|subnetwork| 9;
Inputs
Input | Label |
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Input dataset | Edge File |
Input dataset collection | |
Input dataset collection |
Outputs
From | Output | Label |
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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 |
---|---|---|---|
3 | 667ff3de9 | 2020-01-22 10:59:29 | annotation |
2 | eb4d724e0 | 2020-01-15 10:41:35 | Workflow renaming |
1 | 6a6b3b2cf | 2018-10-10 11:42:48 | Renamed the folder, rewrote the key points; added tags; added a paragraph in the end to correspond to the research question in this tutorial. |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/network-analysis-with-heinz/workflows/Galaxy-Workflow-Heinz.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