Marine Omics identifying biosynthetic gene clusters

ecology-marine_omics_bgc/main-workflow

Author(s)
Marie Jossé
Version
1
Last updated
Aug 19, 2024
License
CC-BY-4.0
Tags
earth-system
Ocean
Marineomics

Features
Tutorial
Marine Omics identifying biosynthetic gene clusters
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00282
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
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;

Inputs

Input Label
Input dataset Fasta nucelotide file

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0 Prodigal Gene Predictor Prodigal Gene Predictor
toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1 Sanntis biosynthetic gene clusters Sanntis: Build Genbank
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3 Regex Find And Replace Regex Find And Replace
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3 InterProScan InterProScan
toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1 Sanntis biosynthetic gene clusters Sanntis: identify biosynthetic gene clusters

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0 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 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
3 f2570ea6f 2024-08-12 09:16:53 add again workflow with test
2 25c640725 2024-08-12 09:16:26 Delete topics/ecology/tutorials/marine_omics_bgc/workflows/main_workflow.ga
1 ded4748a7 2024-08-12 08:45:41 add marine omics tuto

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/ecology/tutorials/marine_omics_bgc/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