Genome Annotation with Prokka

genome-annotation-annotation-with-prokka/galaxy-workflow-workflow-constructed-from-history--prokka-workflow-

Author(s)
Anna Syme, Torsten Seemann, Simon Gladman
Version
6
Last updated
May 7, 2024
License
GPL-3.0-or-later
Tags
genome-annotation
GTN

Features
Tutorial
Genome annotation with Prokka
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00088
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.fasta"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Prokka"];
  0 -->|output| 1;
  a336c364-e69e-47eb-ace6-a7fe46d285fe["Output\ngff_output"];
  1 --> a336c364-e69e-47eb-ace6-a7fe46d285fe;
  style a336c364-e69e-47eb-ace6-a7fe46d285fe stroke:#2c3143,stroke-width:4px;
  2["JBrowse"];
  1 -->|out_fna| 2;
  1 -->|out_gff| 2;

Inputs

Input Label
Input dataset contigs.fasta

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 Prokka

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 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
10 70a555355 2024-05-07 09:29:23 Update topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga
9 466b451a0 2024-05-06 10:11:58 Add creators and license to workflow
8 499e257de 2024-04-30 06:02:44 update prokka workflow
7 56413bab7 2020-10-21 20:09:03 Add workflow test.
6 a3829a123 2020-02-04 16:04:52 Update Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga
5 bab7ab72c 2020-01-31 01:22:28 prokka@1.14.5 jbrowse@1.16.5+galaxy7
4 c69f09dd0 2020-01-23 16:24:32 Adding tag
3 920732bc2 2020-01-21 19:28:08 Updated prokka workflow to newest tool versions
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 b9a607296 2018-06-13 14:09:47 move tutorials to new topic

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-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