Workflow 2: Community Profile

microbiome-metatranscriptomics-short/workflow2-community-profile

Author(s)
Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep
Version
1
Last updated
Jan 15, 2024
License
MIT
Tags

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 (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output_file
krona_output_file
out_file1
annotation
tree
output_tree
ℹ️ Input Dataset
QC controlled forward reads
ℹ️ Input Dataset
QC controlled reverse reads
Taxonomic assignation
Cut
Krona pie chart
Export to GraPhlAn
Generation, personalization and annotation of tree
Visualisation GraPhlAn
Output
MetaPhlAn on input dataset(s): SAM file
Output
MetaPhlAn on input dataset(s): Predicted taxon relative abundances
Output
MetaPhlAn on input dataset(s): Bowtie2 output
Output
MetaPhlAn on input dataset(s): BIOM file
Output
Export to GraPhlAn on input dataset(s): Annotation
Output
Export to GraPhlAn on input dataset(s): Tree
Output
Generation, personalization and annotation of tree on input dataset(s): Tree in PhyloXML
Output
GraPhlAn on input dataset(s): PNG

Inputs

Input Label
Input dataset QC controlled forward reads
Input dataset QC controlled reverse reads

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy0 MetaPhlAn Taxonomic assignation
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 Krona pie chart
toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 Export to GraPhlAn
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0 Generation, personalization and annotation of tree
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0 GraPhlAn Visualisation (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/1.0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy0 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
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