Finding the Muon Stopping Site: pymuon-suite in Galaxy

materials-science-muon-stopping-sites-muairss-uep/muairss-uep

Author(s)
Muon Spectroscopy Computational Project
Version
1
Last updated
Jan 22, 2024
License
MIT
Tags

Features
Tutorial
Finding the muon stopping site with pymuon-suite in Galaxy
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00116
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\nCopper-out.cell"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nCopper.den_fmt"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nCopper.castep"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["PyMuonSuite AIRSS UEP Optimise"];
  2 -->|output| 3;
  1 -->|output| 3;
  0 -->|output| 3;
  f3be7cd2-3974-49f2-aa0e-96c79b4ab34c["Output\nAll muons in host material"];
  3 --> f3be7cd2-3974-49f2-aa0e-96c79b4ab34c;
  style f3be7cd2-3974-49f2-aa0e-96c79b4ab34c stroke:#2c3143,stroke-width:4px;
  4["PyMuonSuite AIRSS Cluster"];
  3 -->|uep_results| 4;

Inputs

Input Label
Input dataset Copper-out.cell
Input dataset Copper.den_fmt
Input dataset Copper.castep

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1 PyMuonSuite AIRSS UEP Optimise PyMuonSuite AIRSS UEP Optimise

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_muairss_read/pm_muairss_read/0.3.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+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
  • 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 cd4b1f827 2023-12-08 15:57:03 Changes for linting and remove MuSpinSim content #1
2 5b3763af3 2023-12-05 08:24:09 Updated tutorial for finding the muon stopping site with Galaxy
1 593f4002b 2023-01-16 15:23:24 Address various review comments

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/workflows/muairss-uep.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