GTN tutorial: mapping

sequence-analysis-mapping/mapping

Author(s)
Saskia Hiltemann
Version
6
Last updated
Aug 19, 2026
License
MIT
Tags
sequence-analysis

Features
Tutorial
Mapping
Workflow Testing
Tests: ✅
Results:
FAIRness PURL
https://gxy.io/GTN:W00182
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\npairs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Bowtie2"];
  0 -->|output| 1;
  2["Samtools stats"];
  1 -->|output| 2;
  3["JBrowse"];
  1 -->|output| 3;

Inputs

Input Label
Input dataset collection pairs

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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
8 b44876270 2026-08-19 14:35:38 update workflow to match tutorial
7 b653b660d 2025-12-11 23:52:42 Update mapping.ga
6 eb177b74c 2025-12-09 21:56:25 Add creator and license to workflow
5 f223f09bb 2025-12-09 21:47:05 Updated workflow and workflow tests
4 505f7550f 2021-04-20 17:22:17 update-workflows
3 667ff3de9 2020-01-22 10:59:29 annotation
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 c06c5b151 2018-09-14 15:01:17 Expand mapping tutorial and add workflow + tests

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping.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