Eggsplorer functional profile of a bacterial genome

genome-annotation-eggsplorer/main-workflow

Author(s)
Vesselin Baev
Version
1
Last updated
Nov 2, 2026
License
CC-BY-4.0
Tags
genome-annotation
prokaryote
eggsplorer

Features
Tutorial
Functional profiling of a bacterial genome with Eggsplorer
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Parameter\nAssembly accession"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["Download proteome"];
  0 -->|output| 1;
  12a1d70f-d0fb-402b-8388-1025747e2103["Output\ngenome_data_report"];
  1 --> 12a1d70f-d0fb-402b-8388-1025747e2103;
  style 12a1d70f-d0fb-402b-8388-1025747e2103 stroke:#2c3143,stroke-width:4px;
  2["eggNOG-mapper"];
  1 -->|protein_fasta| 2;
  b1d71667-38de-4949-90f0-883c9a215d21["Output\nemapper_annotations"];
  2 --> b1d71667-38de-4949-90f0-883c9a215d21;
  style b1d71667-38de-4949-90f0-883c9a215d21 stroke:#2c3143,stroke-width:4px;
  3["Eggsplorer"];
  2 -->|annotations| 3;
  0510d76e-3988-4401-954c-54df6b8ba8dd["Output\neggsplorer_report"];
  3 --> 0510d76e-3988-4401-954c-54df6b8ba8dd;
  style 0510d76e-3988-4401-954c-54df6b8ba8dd stroke:#2c3143,stroke-width:4px;
  3eecf8d3-7e88-4e01-8d8c-3da85e2e008c["Output\neggsplorer_tables"];
  3 --> 3eecf8d3-7e88-4e01-8d8c-3da85e2e008c;
  style 3eecf8d3-7e88-4e01-8d8c-3da85e2e008c stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input parameter Assembly accession

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets/datasets_download_genome/18.39.0+galaxy0 NCBI Datasets Genomes Download proteome
toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.13+galaxy0 eggNOG Mapper eggNOG-mapper
toolshed.g2.bx.psu.edu/repos/galaxyp/eggsplorer/eggsplorer/1.1.0+galaxy0 Eggsplorer Eggsplorer

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.13+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/eggsplorer/eggsplorer/1.1.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets/datasets_download_genome/18.39.0+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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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 b7d469543 2026-10-26 09:22:05 Add Eggsplorer tutorial: functional profile of a bacterial genome

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/eggsplorer/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