Analysis using MDAnalysis

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Australia
• Galaxy France
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nDCD input"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nPDB input"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["RDF Analysis"];
  0 -->|output| 2;
  1 -->|output| 2;
  ab90456f-d7ae-4fb1-ba2f-978a59791acc["Output\nRDF Analysis plot"];
  2 --> ab90456f-d7ae-4fb1-ba2f-978a59791acc;
  style ab90456f-d7ae-4fb1-ba2f-978a59791acc stroke:#2c3143,stroke-width:4px;
  1ee2fe4a-0e50-4a4f-828e-3b60d75120e7["Output\nRDF Analysis raw data"];
  2 --> 1ee2fe4a-0e50-4a4f-828e-3b60d75120e7;
  style 1ee2fe4a-0e50-4a4f-828e-3b60d75120e7 stroke:#2c3143,stroke-width:4px;
  3["Cosine Content"];
  0 -->|output| 3;
  1 -->|output| 3;
  5ca6c423-961b-4a55-a821-794a0d311e41["Output\nCosine Content raw data"];
  3 --> 5ca6c423-961b-4a55-a821-794a0d311e41;
  style 5ca6c423-961b-4a55-a821-794a0d311e41 stroke:#2c3143,stroke-width:4px;
  7854cbf9-187f-4117-b494-73a5a404d06f["Output\nCosine Content plot"];
  3 --> 7854cbf9-187f-4117-b494-73a5a404d06f;
  style 7854cbf9-187f-4117-b494-73a5a404d06f stroke:#2c3143,stroke-width:4px;
  4["Ramachandran Plots"];
  0 -->|output| 4;
  1 -->|output| 4;
  aa7afa97-8be6-4e6b-ad2c-5715f3c10362["Output\nRamachandran Plot"];
  4 --> aa7afa97-8be6-4e6b-ad2c-5715f3c10362;
  style aa7afa97-8be6-4e6b-ad2c-5715f3c10362 stroke:#2c3143,stroke-width:4px;
  178f112a-eb0b-4299-aff5-69efd9ffb52b["Output\nRamachandran Plot raw data"];
  4 --> 178f112a-eb0b-4299-aff5-69efd9ffb52b;
  style 178f112a-eb0b-4299-aff5-69efd9ffb52b stroke:#2c3143,stroke-width:4px;
  5["Distance Analysis"];
  0 -->|output| 5;
  1 -->|output| 5;
  eac670fb-f01e-49cd-a103-828a15149f48["Output\nDistance Analysis raw data"];
  5 --> eac670fb-f01e-49cd-a103-828a15149f48;
  style eac670fb-f01e-49cd-a103-828a15149f48 stroke:#2c3143,stroke-width:4px;
  6605884d-7bfa-4f43-bbc6-2352256d2bc7["Output\nDistance Analysis plot"];
  5 --> 6605884d-7bfa-4f43-bbc6-2352256d2bc7;
  style 6605884d-7bfa-4f43-bbc6-2352256d2bc7 stroke:#2c3143,stroke-width:4px;
  6["Dihedral Analysis"];
  0 -->|output| 6;
  1 -->|output| 6;
  755dbb99-3e3e-425b-a4b2-e375df6e39b4["Output\nDihedral Analysis plot"];
  6 --> 755dbb99-3e3e-425b-a4b2-e375df6e39b4;
  style 755dbb99-3e3e-425b-a4b2-e375df6e39b4 stroke:#2c3143,stroke-width:4px;
  e0234472-cc44-483e-997b-8b0e0719c8d7["Output\nDihedral Analysis raw data"];
  6 --> e0234472-cc44-483e-997b-8b0e0719c8d7;
  style e0234472-cc44-483e-997b-8b0e0719c8d7 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

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

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 galaxy-upload 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:

Version History

For Admins

Installing the workflow tools

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