CTB Workflow

Run Workflow in Galaxy

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

flowchart TD
  11["Compound Search"];
  5 -->|outfile| 11;
  13["Remove duplicated molecules"];
  5 -->|outfile| 13;
  19["Remove counterions and fragments"];
  13 -->|outfile| 19;
  2["Online data"];
  29["Filter"];
  19 -->|outfile| 29;
  30["Compound Convert"];
  19 -->|outfile| 30;
  31["Molecules to Fingerprints"];
  19 -->|outfile| 31;
  39["Natural Product"];
  29 -->|outfile| 39;
  40["Molecules to Fingerprints"];
  29 -->|outfile| 40;
  44["NxN Clustering"];
  40 -->|outfile| 44;
  5["Change Title"];
  2 -->|output| 5;

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/cheminformatics/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