Gene Cluster Product Similarity Search

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Parameter\nQuery Genomes"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Dataset\nJupyter Notebook Genbank2Features"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nTarget Molecules Natural Compound Library"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["NCBI Accession Download"];
  0 -->|output| 3;
  faecdec3-711d-43ba-bb91-38a4b4b3932d["Output\nNCBI Accession Download on input dataset(s): Log"];
  3 --> faecdec3-711d-43ba-bb91-38a4b4b3932d;
  style faecdec3-711d-43ba-bb91-38a4b4b3932d stroke:#2c3143,stroke-width:4px;
  c8857c6f-ec99-4d29-8c98-be7a63a9f029["Output\nNCBI Accession Download on input dataset(s): Downloaded Files"];
  3 --> c8857c6f-ec99-4d29-8c98-be7a63a9f029;
  style c8857c6f-ec99-4d29-8c98-be7a63a9f029 stroke:#2c3143,stroke-width:4px;
  4["Molecule to fingerprint"];
  2 -->|output| 4;
  5["Antismash"];
  3 -->|output| 5;
  cc813ad7-f423-4cb8-ba79-8201abab206a["Output\nAntismash on input dataset(s): HTML report"];
  5 --> cc813ad7-f423-4cb8-ba79-8201abab206a;
  style cc813ad7-f423-4cb8-ba79-8201abab206a stroke:#2c3143,stroke-width:4px;
  6["Collapse clusters in one Genbank entry"];
  5 -->|genbank| 6;
  7["Extract SMILES qualifiers"];
  1 -->|output| 7;
  6 -->|output| 7;
  8["Convert table to smi format"];
  7 -->|output_collection| 8;
  9["Remove beginning"];
  8 -->|outfile| 9;
  10["Remove duplicated molecules"];
  9 -->|out_file1| 10;
  11["Molecule to fingerprint"];
  10 -->|outfile| 11;
  12["Natural Product"];
  10 -->|outfile| 12;
  13["Drug-likeness"];
  10 -->|outfile| 13;
  14["Similarity Search"];
  11 -->|outfile| 14;
  4 -->|outfile| 14;

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/genome-annotation/tutorials/secondary-metabolite-discovery/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