Data management in Medicinal Chemistry workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nBenzenesulfonyl chloride"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nEthylamine"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Compound conversion"];
  0 -->|output| 2;
  aff8fa4f-c254-4f05-9560-52bad6c7e04a["Output\nBenzenesulfonyl chloride SDF"];
  2 --> aff8fa4f-c254-4f05-9560-52bad6c7e04a;
  style aff8fa4f-c254-4f05-9560-52bad6c7e04a stroke:#2c3143,stroke-width:4px;
  3["Search ChEMBL database"];
  0 -->|output| 3;
  044d2c08-92ed-45c9-9868-ee802998d92c["Output\nSubstructures from ChEMBL database"];
  3 --> 044d2c08-92ed-45c9-9868-ee802998d92c;
  style 044d2c08-92ed-45c9-9868-ee802998d92c stroke:#2c3143,stroke-width:4px;
  4["Search ChEMBL database"];
  0 -->|output| 4;
  99274b60-732d-4276-969f-ccc3673a872a["Output\nLipinski substructures from ChEMBL database"];
  4 --> 99274b60-732d-4276-969f-ccc3673a872a;
  style 99274b60-732d-4276-969f-ccc3673a872a stroke:#2c3143,stroke-width:4px;
  5["Compound conversion"];
  1 -->|output| 5;
  77ad7b99-5761-46a3-b9a6-1dd3d8e2baac["Output\nEthylamine SDF"];
  5 --> 77ad7b99-5761-46a3-b9a6-1dd3d8e2baac;
  style 77ad7b99-5761-46a3-b9a6-1dd3d8e2baac stroke:#2c3143,stroke-width:4px;
  6["Reaction maker"];
  2 -->|outfile| 6;
  5 -->|outfile| 6;
  f9d1d7fd-e854-469b-a464-6811998e058e["Output\nReaction product"];
  6 --> f9d1d7fd-e854-469b-a464-6811998e058e;
  style f9d1d7fd-e854-469b-a464-6811998e058e stroke:#2c3143,stroke-width:4px;
  b0bd7ed2-a80b-44ce-994b-999e1d472281["Output\nReaction maker logfile"];
  6 --> b0bd7ed2-a80b-44ce-994b-999e1d472281;
  style b0bd7ed2-a80b-44ce-994b-999e1d472281 stroke:#2c3143,stroke-width:4px;
  7["Visualisation"];
  6 -->|outfile| 7;
  fc618f3f-6aa5-4970-841d-56f4eabf47b7["Output\nVisualisation of reaction product"];
  7 --> fc618f3f-6aa5-4970-841d-56f4eabf47b7;
  style fc618f3f-6aa5-4970-841d-56f4eabf47b7 stroke:#2c3143,stroke-width:4px;
  8["Drug-likeness"];
  6 -->|outfile| 8;
  7ad8c184-e10d-4fce-a402-3e79da6e09ac["Output\nDrug-likeness of product molecule"];
  8 --> 7ad8c184-e10d-4fce-a402-3e79da6e09ac;
  style 7ad8c184-e10d-4fce-a402-3e79da6e09ac stroke:#2c3143,stroke-width:4px;

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/med-chem-data/workflows/Data-management-in-Medicinal-Chemistry-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