Primer design of a virus family (imported from uploaded file)

sequence-analysis-viral_primer_design/main-workflow

Author(s)
Wolfgang Maier
Version
1
Last updated
Mar 20, 2025
License
AGPL-3.0-or-later
Tags
name:Sequenceanalysis

Features
Tutorial
Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00322
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nInput virus gene sequences"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Multiple alignment"];
  0 -->|output| 1;
  759daedf-eac7-4200-a83e-5a4b005d068c["Output\noutputAlignment"];
  1 --> 759daedf-eac7-4200-a83e-5a4b005d068c;
  style 759daedf-eac7-4200-a83e-5a4b005d068c stroke:#2c3143,stroke-width:4px;
  2["Primer design"];
  1 -->|outputAlignment| 2;
  029f5ab6-1ded-4867-8bac-6c20e6b0de52["Output\nvarvamp_log"];
  2 --> 029f5ab6-1ded-4867-8bac-6c20e6b0de52;
  style 029f5ab6-1ded-4867-8bac-6c20e6b0de52 stroke:#2c3143,stroke-width:4px;
  97c5a307-ef91-4eab-a7b3-4ad497a82fcc["Output\nprimers_bed"];
  2 --> 97c5a307-ef91-4eab-a7b3-4ad497a82fcc;
  style 97c5a307-ef91-4eab-a7b3-4ad497a82fcc stroke:#2c3143,stroke-width:4px;
  032a54ac-d133-42a5-a7b8-943861051e4b["Output\nprimer_seqs"];
  2 --> 032a54ac-d133-42a5-a7b8-943861051e4b;
  style 032a54ac-d133-42a5-a7b8-943861051e4b stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Input virus gene sequences

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.526+galaxy1 MAFFT Multiple alignment
toolshed.g2.bx.psu.edu/repos/iuc/varvamp/varvamp/1.2.2+galaxy0 varVAMP Primer design

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/varvamp/varvamp/1.2.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.526+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
  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
2 b7b1dc7ab 2025-03-19 11:20:46 Add test for workflow and fix workfolw
1 524d821a8 2024-04-09 06:55:13 Clean up and fix things - part 1

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/viral_primer_design/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