Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 2: Community profile

microbiome-metatranscriptomics-short/workflow2-community-profile

Author(s)
Bérénice Batut, Pratik Jagtap, Subina Mehta, Saskia Hiltemann, Paul Zierep
Version
2
Last updated
Jun 16, 2025
License
MIT
Tags
microbiome

Features
Tutorial
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00129
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\nForward reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReverse reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["MetaPhlAn"];
  0 -->|output| 2;
  1 -->|output| 2;
  b13521db-f5e7-4bf3-b7fa-673d13fc2911["Output\nmetaphlan_predicted_taxons"];
  2 --> b13521db-f5e7-4bf3-b7fa-673d13fc2911;
  style b13521db-f5e7-4bf3-b7fa-673d13fc2911 stroke:#2c3143,stroke-width:4px;
  3["Cut"];
  2 -->|output_file| 3;
  4["Krona pie chart"];
  2 -->|krona_output_file| 4;
  5["Export to GraPhlAn"];
  3 -->|out_file1| 5;
  6["Generation, personalization and annotation of tree"];
  5 -->|annotation| 6;
  5 -->|tree| 6;
  7["GraPhlAn"];
  6 -->|output_tree| 7;
  21fca66f-dce0-496f-994f-dc8e855e0c8f["Output\ngraphlan_output_image"];
  7 --> 21fca66f-dce0-496f-994f-dc8e855e0c8f;
  style 21fca66f-dce0-496f-994f-dc8e855e0c8f stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Forward reads
Input dataset Reverse reads

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 MetaPhlAn
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 GraPhlAn

Tools

Tool Links
Cut1
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 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
2 604d1261b 2025-06-16 13:56:44 Update metatranscriptomics tutorials:
1 0e0a2f2cc 2024-01-10 15:47:09 Rename metagenomics topic to microbiome

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow2_community_profile.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