Galaxy Introduction Peaks2Genes - Part 1

introduction-galaxy-intro-peaks2genes/galaxy-introduction-peaks2genes-part-1-workflow

Author(s)

Version
1
Last updated
Oct 20, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
introduction

Features
Tutorial
From peaks to genes
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00111
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 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;
  0a9bff82-5c5d-430e-9ae3-771bd580a243["Output\nchr_count"];
  9 --> 0a9bff82-5c5d-430e-9ae3-771bd580a243;
  style 0a9bff82-5c5d-430e-9ae3-771bd580a243 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Peaks Peaks
Genes Genes

Outputs

From Output Label
Grouping1 Group

Tools

Tool Links
CONVERTER_interval_to_bed_0
Grouping1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0 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
1 48c2e99e6 2020-10-19 19:31:03 Add workflow test yml.

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-peaks2genes/workflows/Galaxy-Introduction-Peaks2Genes-Part-1-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