Bacterial Genome Annotation

genome-annotation-bacterial-genome-annotation/bacterial-genome-annotation

Author(s)
Bérénice Batut, Pierre Marin
Version
2
Last updated
Aug 1, 2024
License
AGPL-3.0-or-later
Tags
genome-annotation

Features
Tutorial
Bacterial Genome Annotation
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00090
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\ncontigs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ISEScan"];
  0 -->|output| 1;
  2bb672cb-4536-46b0-8a22-8590a0ca36c7["Output\nisescan_results"];
  1 --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;
  style 2bb672cb-4536-46b0-8a22-8590a0ca36c7 stroke:#2c3143,stroke-width:4px;
  2["PlasmidFinder"];
  0 -->|output| 2;
  614064e6-4b0f-4e38-b04e-e3f61ba41b46["Output\nplasmidfinder_results"];
  2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;
  style 614064e6-4b0f-4e38-b04e-e3f61ba41b46 stroke:#2c3143,stroke-width:4px;
  3["Integron Finder"];
  0 -->|output| 3;
  d26788cf-2441-4f29-ac39-b6be96f192eb["Output\nintegronfinder_summary"];
  3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;
  style d26788cf-2441-4f29-ac39-b6be96f192eb stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  d3a40a8b-1bd1-42b6-a91e-756379b86d94["Output\nbakta_summary"];
  4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;
  style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;
  5["Group"];
  1 -->|all_results| 5;
  6["Group"];
  1 -->|all_results| 6;
  7["Replace Text"];
  2 -->|result_file| 7;
  8["Select last"];
  7 -->|outfile| 8;
  9["Table to GFF3"];
  8 -->|outfile| 9;
  10["JBrowse"];
  0 -->|output| 10;
  4 -->|annotation_gff3| 10;
  9 -->|output| 10;
  1 -->|annotation| 10;

Inputs

Input Label
Input dataset contigs

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 ISEScan
toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1 PlasmidFinder
toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0 Integron Finder
toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 Bakta

Tools

Tool Links
Grouping1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2 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
2 87968f9a6 2024-08-01 11:02:23 Update tool versions
1 217f251aa 2024-01-29 11:16:24 Update worklow and add tests

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.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