Workflows

These workflows are associated with From peaks to genes

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.

Galaxy Introduction Peaks2Genes - Part 1

Last updated Oct 20, 2020

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Australia Galaxy Main Galaxy France Galaxy Europe Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nPeaks"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGenes"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Select last"];
  0 -->|output| 2;
  3["Replace Text"];
  0 -->|output| 3;
  4["Get flanks"];
  1 -->|output| 4;
  5["Replace Text"];
  3 -->|outfile| 5;
  6["Replace Text"];
  5 -->|outfile| 6;
  7["Convert Genomic Intervals To BED"];
  6 -->|outfile| 7;
  8["Intersect"];
  4 -->|out_file1| 8;
  7 -->|output1| 8;
  9["Group"];
  8 -->|output| 9;
  9402c4c7-9139-414e-86a5-d882cb9ce42f["Output\nchr_count"];
  9 --> 9402c4c7-9139-414e-86a5-d882cb9ce42f;
  style 9402c4c7-9139-414e-86a5-d882cb9ce42f 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 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