de novo Rad Seq

ecology-de-novo-rad-seq/galaxy-workflow-de-novo-rad-seq

Author(s)

Version
3
Last updated
Jan 23, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
ecology

Features
Tutorial
RAD-Seq de-novo data analysis
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00047
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\nPopulation_map.txt"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nBarcodes_SRR034310.tabular"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nSRR034310.fastq"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nref_genome_chromFa.tar"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Stacks: process radtags"];
  1 -->|output| 4;
  2 -->|output| 4;
  5["Stacks: process radtags"];
  1 -->|output| 5;
  2 -->|output| 5;
  6["Stacks: process radtags"];
  1 -->|output| 6;
  2 -->|output| 6;
  7["FastQC"];
  2 -->|output| 7;
  8["Stacks: de novo map"];
  4 -->|demultiplexed| 8;
  0 -->|output| 8;
  9["Stacks: populations"];
  8 -->|all_output| 9;
  0 -->|output| 9;

Inputs

Input Label
Input dataset Population_map.txt
Input dataset Barcodes_SRR034310.tabular
Input dataset SRR034310.fastq
Input dataset ref_genome_chromFa.tar

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0 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
5 00cfc1f08 2020-01-22 13:19:46 out_fastpĥase
4 667ff3de9 2020-01-22 10:59:29 annotation
3 ea197f141 2020-01-15 12:30:09 small changes
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 bfc1c8c3f 2019-09-12 09:03:30 Move RAD-Seq tutorials to ecology topic

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/ecology/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.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