Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run'

microbiome-lotus2-identifying-fungi/lotus2-fungi-workflow

Author(s)
Society for the Protection of Underground Networks, Sujai Kumar, Bethan Manley
Version
1
Last updated
Sep 30, 2024
License
MIT
Tags
lotus2
fungi
ecology
metagenomics

Features
Tutorial
Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nMapping tsv"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nsdm Options txt"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nInput Dataset Collection"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["LotuS2"];
  2 -->|output| 3;
  0 -->|output| 3;
  1 -->|output| 3;
  7ff13687-fb95-4b54-8b5c-4c916500dfed["Output\nOTU Table"];
  3 --> 7ff13687-fb95-4b54-8b5c-4c916500dfed;
  style 7ff13687-fb95-4b54-8b5c-4c916500dfed stroke:#2c3143,stroke-width:4px;
  b3413904-3319-4fa0-8c17-2c4757af5b8c["Output\nOTU fasta"];
  3 --> b3413904-3319-4fa0-8c17-2c4757af5b8c;
  style b3413904-3319-4fa0-8c17-2c4757af5b8c stroke:#2c3143,stroke-width:4px;
  11ad8056-9572-428a-a3b2-5ceec0fa186e["Output\nComplete Output Zip"];
  3 --> 11ad8056-9572-428a-a3b2-5ceec0fa186e;
  style 11ad8056-9572-428a-a3b2-5ceec0fa186e stroke:#2c3143,stroke-width:4px;
  21d55970-8b95-4dca-9b46-e7c65340ce84["Output\nOTU Phylogenetic Tree"];
  3 --> 21d55970-8b95-4dca-9b46-e7c65340ce84;
  style 21d55970-8b95-4dca-9b46-e7c65340ce84 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Mapping tsv
Input dataset sdm Options txt
Input dataset collection Input Dataset Collection

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/2.32+galaxy0 LotuS2 LotuS2

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/2.32+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
  • 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 0cf85de6b 2024-09-27 13:56:59 Move tutorial to

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/lotus2-identifying-fungi/workflows/lotus2-fungi-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