Gene Cluster Product Similarity Search

genome-annotation-secondary-metabolite-discovery/main-workflow

Author(s)

version Version
1
last_modification Last updated
Feb 21, 2024
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
sempi3

Features

Tutorial
hands_on Secondary metabolite discovery

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00099
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
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

Input Label
Input parameter Query Genomes
Input dataset Jupyter Notebook Genbank2Features
Input dataset Target Molecules (Natural Compound Library)

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 NCBI Accession Download
toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1 Antismash
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 Collapse Collection Collapse clusters in one Genbank entry

Tools

Tool Links
Remove beginning1
interactive_tool_jupyter_notebook
toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remduplicates/openbabel_remDuplicates/3.1.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/simsearch/ctb_simsearch/0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 af81c1a8e 2024-02-13 08:21:40 init

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