Mtb phylogeny

evolution-mtb_phylogeny/main-workflow

Author(s)

Version
1
Last updated
Mar 16, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
evolution

Features
Tutorial
Tree thinking for tuberculosis evolution and epidemiology
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00073
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nInput alignment"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["RStudio"];
  2["Estimate phylogeny with RAxML"];
  0 -->|output| 2;
  9f8ae577-c583-4a2d-b64d-14c25fb859d9["Output\nBest-scoring ML Tree"];
  2 --> 9f8ae577-c583-4a2d-b64d-14c25fb859d9;
  style 9f8ae577-c583-4a2d-b64d-14c25fb859d9 stroke:#2c3143,stroke-width:4px;
  bdb8cf2f-b553-4a96-8b55-38b4b499ab88["Output\nInfo"];
  2 --> bdb8cf2f-b553-4a96-8b55-38b4b499ab88;
  style bdb8cf2f-b553-4a96-8b55-38b4b499ab88 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Input alignment

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2 Phyogenetic reconstruction with RAxML Estimate phylogeny with RAxML

Tools

Tool Links
interactive_tool_rstudio
toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2 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
3 afdd9be4b 2022-03-16 09:29:14 add tag
2 946859f78 2022-03-16 09:28:52 prettyprint workflow
1 2e7ba7852 2022-03-16 09:24:13 tweak

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_phylogeny/workflows/main_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