Simple Analysis

computational-chemistry-analysis-md-simulations/main-workflow

Author(s)

Version
5
Last updated
Oct 3, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
computational-chemistry

Features
Tutorial
Analysis of molecular dynamics simulations
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00030
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\nprotein_mdsimulation_dcd"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nprotein_pdb"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["RMSD Analysis"];
  0 -->|output| 2;
  1 -->|output| 2;
  6de2beaf-f80e-4788-8598-229a1c582757["Output\nrmsd_tabular_output"];
  2 --> 6de2beaf-f80e-4788-8598-229a1c582757;
  style 6de2beaf-f80e-4788-8598-229a1c582757 stroke:#2c3143,stroke-width:4px;
  3["RMSF Analysis"];
  0 -->|output| 3;
  1 -->|output| 3;
  1f2d715d-230a-4ec5-a509-e8ae501e7634["Output\nrmsf_tabular_output"];
  3 --> 1f2d715d-230a-4ec5-a509-e8ae501e7634;
  style 1f2d715d-230a-4ec5-a509-e8ae501e7634 stroke:#2c3143,stroke-width:4px;
  4["PCA"];
  0 -->|output| 4;
  1 -->|output| 4;
  92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5["Output\npca_tabular_output"];
  4 --> 92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5;
  style 92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset protein_mdsimulation_dcd
Input dataset protein_pdb

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3 RMSD Analysis
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3 RMSF Analysis
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3 PCA

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3 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
5 6614b58c1 2020-10-03 01:32:28 md-simulations
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 faf6d298a 2019-12-12 13:02:33 unflatten workflows
1 be6fece7f 2019-05-04 09:37:46 Simonbray compchem (#6)

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/analysis-md-simulations/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