Galaxy Workflow Galaxy Hi C

Run Workflow in Galaxy

• Galaxy Main
• Galaxy France
• Galaxy Australia
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nR1.fastq"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nR2.fastq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nH3K27me3.bw"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nH3K36me3.bw"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nH4K16ac.bw"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\ndm3_genes.bed"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["Map with BWA-MEM"];
  0 -->|output| 6;
  7["Map with BWA-MEM"];
  1 -->|output| 7;
  8["hicBuildMatrix"];
  7 -->|output| 8;
  6 -->|output| 8;
  9["hicMergeMatrixBins"];
  8 -->|outFileName| 9;
  10["hicCorrectMatrix"];
  8 -->|outFileName| 10;
  11["hicCorrectMatrix"];
  8 -->|outFileName| 11;
  12["hicPlotMatrix"];
  9 -->|outFileName| 12;
  13["hicPlotMatrix"];
  11 -->|outFileName| 13;
  14["hicFindTADs"];
  11 -->|outFileName| 14;
  15["hicPCA"];
  14 -->|matrix_output| 15;
  16["hicPlotTADs"];
  14 -->|domains| 16;
  11 -->|outFileName| 16;
  14 -->|tad_score| 16;
  15 -->|pca1| 16;
  15 -->|pca2| 16;
  3 -->|output| 16;
  2 -->|output| 16;
  4 -->|output| 16;
  5 -->|output| 16;

Inputs

Outputs

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

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/hicexplorer/workflows/Galaxy-Workflow-Galaxy_Hi-C.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