Workflows

These workflows are associated with Marine Omics identifying biosynthetic gene clusters

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.

Marine Omics identifying biosynthetic gene clusters
Marie Jossé

Last updated Aug 19, 2024

Launch in Tutorial Mode
License: CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy France Galaxy Main Galaxy Europe Galaxy Australia Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nFasta nucelotide file"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Prodigal Gene Predictor "];
  0 -->|output| 1;
  351cf550-c05d-4bad-9394-fe9b45ef6298["Output\nProtein fasta file"];
  1 --> 351cf550-c05d-4bad-9394-fe9b45ef6298;
  style 351cf550-c05d-4bad-9394-fe9b45ef6298 stroke:#2c3143,stroke-width:4px;
  2["Sanntis: Build Genbank "];
  0 -->|output| 2;
  1 -->|output_faa| 2;
  1b9f0275-191a-4e90-b4b4-7b10475f4602["Output\nGenbank file"];
  2 --> 1b9f0275-191a-4e90-b4b4-7b10475f4602;
  style 1b9f0275-191a-4e90-b4b4-7b10475f4602 stroke:#2c3143,stroke-width:4px;
  3["Regex Find And Replace"];
  1 -->|output_faa| 3;
  e41e8fb9-c5f6-425f-a351-f8fa92f7821d["Output\nClean protein fasta file"];
  3 --> e41e8fb9-c5f6-425f-a351-f8fa92f7821d;
  style e41e8fb9-c5f6-425f-a351-f8fa92f7821d stroke:#2c3143,stroke-width:4px;
  4[" InterProScan"];
  3 -->|out_file1| 4;
  522b49db-7650-41e7-b888-01bb3cb1b451["Output\nTabular file (.tsv)"];
  4 --> 522b49db-7650-41e7-b888-01bb3cb1b451;
  style 522b49db-7650-41e7-b888-01bb3cb1b451 stroke:#2c3143,stroke-width:4px;
  5["Sanntis: identify biosynthetic gene clusters"];
  2 -->|output_sanntis_gb| 5;
  4 -->|outfile_tsv| 5;
  c96c8c7e-0a50-4506-a144-9d941f50eb5e["Output\n SMBGC Annotation"];
  5 --> c96c8c7e-0a50-4506-a144-9d941f50eb5e;
  style c96c8c7e-0a50-4506-a144-9d941f50eb5e stroke:#2c3143,stroke-width:4px;

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 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